From 6993519605bef2abfcf42b681d89ecc92636a86b Mon Sep 17 00:00:00 2001 From: George Dan Miron <44091914+gdmiron@users.noreply.github.com> Date: Thu, 9 Apr 2020 12:34:09 +0200 Subject: [PATCH] Units defined in the database files are now used (properties and parameters are converted to default units upon reading the data) (#20) * parsing and converting units provided in loaded data * std T and P default values, bugfix * extended with derived units for powers of K^ and bar^ * converting read units to default upon parsing of data, added ThermoParameters to python api, extended tests for units conversion * added test for cp of reaction at high T and P * fix for units conversion, extended tests with landau, BM, AD models * fix for HKF units * extended aggregateState options compatible with Cox, J. D. (1982) * Overloaded thermoProperties functions * tests for reactions, now calculate properties functions can be called with a substance or a reaction object * removed schemas folder, used only by ThermoFunGui * changed enum indexes * removed tests on macos --- CMakeLists.txt | 2 +- README.md | 2 +- Resources/data/README.md | 2 - Resources/data/schemas/aragraphdb.schema.json | 4028 -- .../data/schemas/chemeqspeciation.schema.json | 242 - .../data/schemas/chemeqsysdef.schema.json | 376 - .../data/schemas/chemeqsysrecipe.schema.json | 427 - .../data/schemas/composition.schema.json | 339 - Resources/data/schemas/compound.schema.json | 178 - .../data/schemas/constituent.schema.json | 219 - Resources/data/schemas/datasource.schema.json | 395 - Resources/data/schemas/docpages.schema.json | 102 - Resources/data/schemas/element.schema.json | 588 - Resources/data/schemas/impex.schema.json | 971 - Resources/data/schemas/ingredient.schema.json | 238 - .../data/schemas/interaction.schema.json | 589 - .../data/schemas/kineticmodel.schema.json | 446 - .../data/schemas/kineticrate.schema.json | 491 - .../data/schemas/mixingmodel.schema.json | 421 - .../data/schemas/newdb/araimpex.schema.json | 947 - .../data/schemas/newdb/graphdb.schema.json | 3005 -- Resources/data/schemas/phase.schema.json | 534 - Resources/data/schemas/prop.schema.json | 1163 - Resources/data/schemas/query.schema.json | 180 - Resources/data/schemas/reaction.schema.json | 803 - .../data/schemas/reactionset.schema.json | 432 - Resources/data/schemas/substance.schema.json | 1068 - .../data/schemas/thermodataset.schema.json | 396 - ThermoFun/Common/ParseJsonToData.cpp | 240 +- ThermoFun/Common/Units.cpp | 19 +- ThermoFun/Database.h | 6 +- ThermoFun/GlobalVariables.h | 42 +- ThermoFun/Reaction.cpp | 20 +- ThermoFun/Reaction.h | 5 +- ThermoFun/Reactions/DolejsManning2010.cpp | 4 +- ThermoFun/Reactions/FrantzMarshall.cpp | 4 +- ThermoFun/Reactions/LogK_function_of_T.cpp | 6 +- ThermoFun/Reactions/RyzhenkoBryzgalyn.cpp | 4 +- ThermoFun/Reactions/Volume_function_of_T.cpp | 10 +- ThermoFun/Substances/Solids/SolidHPLandau.cpp | 5 +- .../Substances/Solids/SolidMurnaghanHP98.cpp | 2 +- ThermoFun/ThermoEngine.cpp | 393 +- ThermoFun/ThermoEngine.h | 54 +- ThermoFun/ThermoParameters.h | 3 + ci/travis/install.sh | 2 +- pytests/test-aq17-gem-lma-thermofun.json | 38796 ++++++++++++++++ pytests/test-database-thermofun.json | 160 +- pytests/test-thermoengine-thermofun.json | 841 +- pytests/test_database.py | 13 +- pytests/test_thermoengine.py | 23 + python/pyThermoFun/PyThermoFun.cpp | 3 + python/pyThermoFun/PyThermoFun.hpp | 3 + python/pyThermoFun/pyReaction.cpp | 10 +- python/pyThermoFun/pyThermoEngine.cpp | 29 +- python/pyThermoFun/pyThermoParameters.cpp | 66 + 55 files changed, 40400 insertions(+), 18947 deletions(-) delete mode 100644 Resources/data/README.md delete mode 100644 Resources/data/schemas/aragraphdb.schema.json delete mode 100644 Resources/data/schemas/chemeqspeciation.schema.json delete mode 100644 Resources/data/schemas/chemeqsysdef.schema.json delete mode 100644 Resources/data/schemas/chemeqsysrecipe.schema.json delete mode 100644 Resources/data/schemas/composition.schema.json delete mode 100644 Resources/data/schemas/compound.schema.json delete mode 100644 Resources/data/schemas/constituent.schema.json delete mode 100644 Resources/data/schemas/datasource.schema.json delete mode 100644 Resources/data/schemas/docpages.schema.json delete mode 100644 Resources/data/schemas/element.schema.json delete mode 100644 Resources/data/schemas/impex.schema.json delete mode 100644 Resources/data/schemas/ingredient.schema.json delete mode 100644 Resources/data/schemas/interaction.schema.json delete mode 100644 Resources/data/schemas/kineticmodel.schema.json delete mode 100644 Resources/data/schemas/kineticrate.schema.json delete mode 100644 Resources/data/schemas/mixingmodel.schema.json delete mode 100644 Resources/data/schemas/newdb/araimpex.schema.json delete mode 100644 Resources/data/schemas/newdb/graphdb.schema.json delete mode 100644 Resources/data/schemas/phase.schema.json delete mode 100644 Resources/data/schemas/prop.schema.json delete mode 100644 Resources/data/schemas/query.schema.json delete mode 100644 Resources/data/schemas/reaction.schema.json delete mode 100644 Resources/data/schemas/reactionset.schema.json delete mode 100644 Resources/data/schemas/substance.schema.json delete mode 100644 Resources/data/schemas/thermodataset.schema.json create mode 100644 pytests/test-aq17-gem-lma-thermofun.json create mode 100644 python/pyThermoFun/pyThermoParameters.cpp diff --git a/CMakeLists.txt b/CMakeLists.txt index 7af58f3b..f540ad69 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.0) # Set the name of the project -project(ThermoFun VERSION 0.3.0 LANGUAGES CXX) +project(ThermoFun VERSION 0.3.3 LANGUAGES CXX) # Set the cmake module path of the project set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake/modules") diff --git a/README.md b/README.md index 18ceba32..153220fb 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # ThermoFun [![Build Status](https://travis-ci.com/thermohub/thermofun.svg?branch=master)](https://travis-ci.com/thermohub/thermofun) -[![Build status](https://ci.appveyor.com/api/projects/status/13098q3j713uo06v/branch/master?svg=true)](https://ci.appveyor.com/project/gdmiron/thermofun-44e8m/branch/master) +[![Build status](https://ci.appveyor.com/api/projects/status/j4ex4bwl8u8crg3q/branch/master?svg=true)](https://ci.appveyor.com/project/gdmiron/thermofun-bus2d/branch/master) A code for calculating the standard state thermodynamic properties at a given temperature and pressure. diff --git a/Resources/data/README.md b/Resources/data/README.md deleted file mode 100644 index 4c5d1283..00000000 --- a/Resources/data/README.md +++ /dev/null @@ -1,2 +0,0 @@ -This folder contains data schcemas and local databases used by the BSONUI/BSONIO application. - diff --git a/Resources/data/schemas/aragraphdb.schema.json b/Resources/data/schemas/aragraphdb.schema.json deleted file mode 100644 index 0cbcefc0..00000000 --- a/Resources/data/schemas/aragraphdb.schema.json +++ /dev/null @@ -1,4028 +0,0 @@ -{ - "name": "aragraphdb", - "doc": "Apache Thrift IDL definition for AQL and ArangoDB graph database interface\n", - "namespaces": { - "*": "graph" - }, - "includes": [ -"prop", -"datasource", -"element", -"substance", -"reaction", -"reactionset", -"thermodataset", -"interaction", -"mixingmodel", -"kineticrate", -"kineticmodel", -"phase", -"compound", -"constituent", -"ingredient", -"chemeqsysdef", -"chemeqsysrecipe", -"chemeqspeciation" - ], - "enums": [ - ], - "typedefs": [ - ], - "structs": [ - { - "name": "VertexDataSource", - "doc": "Datasource vertex document\n", - "isException": false, - "isUnion": false, - "to_select": [ "5", "6.1", "6.3.0", "6.2" ], - "to_key": [ "6.1" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\" in MongoDB (may be absent in ArangoDB)\n", - "required": "required", - "default": "vertex" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label is \"datasource\" for all datasources: goes to the name of collection in ArangoDB\n", - "required": "required", - "default": "datasource" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "datasource.DataSource" - }, - "doc": "properties of datasource as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexElement", - "doc": "Element vertex document\n", - "isException": false, - "isUnion": false, - "to_select": [ "6.1", "6.3","6.13", "6.14"], - "to_key": [ "6.1", "6.5", "6.14" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\" in MongoDB (may be absent in ArangoDB)\n", - "required": "required", - "default": "vertex" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label is \"element\" for all elements: goes into the name of collection in ArangoDB\n", - "required": "required", - "default": "element" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "element.Element" - }, - "doc": "properties of element as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexSubstance", - "doc": "Substance vertex document\n", - "isException": false, - "isUnion": false, - "to_select": [ "6.1", "6.3", "6.6", "6.2", "6.5" ], - "to_key": [ "properties.symbol", "properties.class_", "properties.sourcetdb" ], - "to_unique": [ "properties.symbol", "properties.sourcetdb" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all substances\n", - "required": "required", - "default": "substance" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "substance.Substance" - }, - "doc": "properties of substance as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexReaction", - "doc": "Reaction vertex document\n", - "isException": false, - "isUnion": false, - "to_select": [ "6.1", "6.4", "6.6", "6.2", "6.3" ], - "to_key": [ "properties.symbol", "properties.sourcetdb", "properties.level" ], - "to_unique": [ "properties.symbol", "properties.sourcetdb" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all reactions\n", - "required": "required", - "default": "reaction" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "reaction.Reaction" - }, - "doc": "properties of reaction as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexReactionSet", - "doc": "Reactionset vertex document\n", - "isException": false, - "isUnion": false, - "to_select": [ "6.1", "6.4", "6.2", "6.8", "6.3" ], - "to_key": [ "properties.symbol", "properties.stype", "properties.level" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all reactionsets\n", - "required": "required", - "default": "reactionset" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "reactionset.ReactionSet" - }, - "doc": "properties of reactionset as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexThermoDataSet", - "doc": "Thermodataset vertex document\n", - "isException": false, - "isUnion": false, - "to_select": [ "6.1", "6.4", "6.2", "6.8" ], - "to_key": [ "properties.symbol", "properties.stype", "properties.level" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all reactionsets\n", - "required": "required", - "default": "thermodataset" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "thermodataset.ThermoDataSet" - }, - "doc": "properties of thermodataset as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexInteraction", - "doc": "Interaction vertex document\n", - "isException": false, - "isUnion": false, - "to_select": [ "5", "6.1", "6.2", "6.3", "6.4", "6.5", "6.6" ], - "to_key": [ "properties.symbol", "properties.sourcetdb", "properties.level" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all interactions\n", - "required": "required", - "default": "interaction" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "interaction.Interaction" - }, - "doc": "properties of interaction as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexMixingModel", - "doc": "MixingModel vertex document\n", - "isException": false, - "isUnion": false, - "to_select": [ "5", "6.1", "6.2", "6.3", "6.6" ], - "to_key": [ "properties.symbol", "properties.sourcetdb" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all mixingmodels\n", - "required": "required", - "default": "mixingmodel" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "mixingmodel.MixingModel" - }, - "doc": "properties of mixingmodel as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexKineticRate", - "doc": "KineticRate vertex document\n", - "isException": false, - "isUnion": false, - "to_select": [ "5", "6.1", "6.2", "6.3", "6.4", "6.5", "6.6" ], - "to_key": [ "properties.symbol", "properties.sourcetdb", "properties.level" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all kinetic rates\n", - "required": "required", - "default": "kineticrate" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "kineticrate.KineticRate" - }, - "doc": "properties of interaction as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexKineticModel", - "doc": "KineticModel vertex document\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all mixingmodels\n", - "required": "required", - "default": "kineticmodel" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "kineticmodel.KineticModel" - }, - "doc": "properties of kineticmodel as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexPhase", - "doc": "Phase vertex document\n", - "isException": false, - "isUnion": false, - "to_select": [ "5", "6.1", "6.2", "6.4", "6.5", "6.6", "6.7" ], - "to_key": [ "properties.symbol", "properties.aggregate_state", "properties.sourcetdb" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all phases\n", - "required": "required", - "default": "phase" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "phase.Phase" - }, - "doc": "properties of phase as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexCompound", - "doc": "Composition compound entity vertex document\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all composition compound entities\n", - "required": "required", - "default": "compound" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "compound.Compound" - }, - "doc": "properties of composition compound as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexConstituent", - "doc": "Composition constituent entity vertex document\n", - "isException": false, - "isUnion": false, - "to_select": [ "5", "6.1", "6.2", "6.6", "6.7" ], - "to_key": [ "properties.symbol" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all composition entities\n", - "required": "required", - "default": "constituent" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "constituent.Constituent" - }, - "doc": "properties of composition constituent as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexIngredient", - "doc": "Composition ingredient entity vertex document\n", - "isException": false, - "isUnion": false, - "to_select": [ "5", "6.1", "6.2", "6.6", "6.7" ], - "to_key": [ "properties.symbol" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all composition entities\n", - "required": "required", - "default": "ingredient" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "ingredient.Ingredient" - }, - "doc": "properties of composition ingredient as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexChemEqSysDef", - "doc": "Chemical system definition (chemsysdef) vertex document\n", - "isException": false, - "isUnion": false, - "to_select": [ "5", "6.1", "6.2", "6.3", "6.5" ], - "to_key": [ "properties.symbol", "properties.cesdtyp", "properties.thermodataset" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all chemical system definitions\n", - "required": "required", - "default": "chemeqsysdef" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "chemeqsysdef.ChemEqSysDef" - }, - "doc": "properties of chemsystdef as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexChemEqSysRecipe", - "doc": "Chemical system instance recipe vertex document\n", - "isException": false, - "isUnion": false, - "to_select": [ "5", "6.1", "6.2", "6.3", "6.4" ], - "to_key": [ "properties.symbol", "properties.chemeqsysdef" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all chemical system recipes\n", - "required": "required", - "default": "chemeqsysrecipe" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "chemeqsysrecipe.ChemEqSysRecipe" - }, - "doc": "properties of recipe as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexChemEqSpeciation", - "doc": "Chemical system instance recipe vertex document\n", - "isException": false, - "isUnion": false, - "to_select": [ "5", "6.1", "6.2", "6.3", "6.4", "6.5" ], - "to_key": [ "properties.symbol", "properties.chemeqsysrecipe" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all chemical system recipes\n", - "required": "required", - "default": "chemeqspeciation" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "chemeqspeciation.ChemEqSpeciation" - }, - "doc": "properties of recipe as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "Citing", - "doc": "Edge: citing (properties for citing edges)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "for_field", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "Data field path connected to DS e.g. { \"for_field\": \"properties.entropy.values.0\" }\n", - "required": "req_out", - "default": [ - "properties" - ] - } - ] - }, - { - "name": "EdgeCiting", - "doc": "Edge of type \"citing\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "7", "8.1.0", "4", "5" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_from", - "typeId": "string", - "doc": "full id of outgoing vertex of any type (formerly outV)\n", - "required": "required" - }, - { - "key": 5, - "name": "_to", - "typeId": "string", - "doc": "full id of incoming datasource vertex (formerly inV)\n", - "required": "required" - }, - { - "key": 6, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\" (the name of ArangoDB collection is \"edges\")\n", - "required": "required", - "default": "edge" - }, - { - "key": 7, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"citing\"\n", - "required": "required", - "default": "citing" - }, - { - "key": 8, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Citing" - }, - "doc": "Properties of citing edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Inherits", - "doc": "Edge inherits (properties for inherits edges)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "for_property", - "typeId": "string", - "doc": "Fieldpath or short name for property, e.g. \"for_property\" \"sG0\"\n", - "required": "req_out" - }, - { - "key": 2, - "name": "asop", - "typeId": "string", - "doc": "This string identifies the relation: { \"asop\": \"equal\" } | ...\n", - "required": "req_out" - } - ] - }, - { - "name": "EdgeInherits", - "doc": "Edge of type \"inherits\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "7", "8.1", "8.2", "4", "5" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_from", - "typeId": "string", - "doc": "full id of outgoing vertex of any type (formerly outV)\n", - "required": "required" - }, - { - "key": 5, - "name": "_to", - "typeId": "string", - "doc": "full id of incoming datasource vertex (formerly inV)\n", - "required": "required" - }, - { - "key": 6, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\" (type of ArangoDB collection is \"edges\")\n", - "required": "required", - "default": "edge" - }, - { - "key": 7, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"inherits\"\n", - "required": "required", - "default": "inherits" - }, - { - "key": 8, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Inherits" - }, - "doc": "Properties of inherits edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Sstate", - "doc": "Edge sstate: connecting a substance representing a standard state of an element to the corresponding element\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "stoi_coeff", - "typeId": "double", - "doc": "Stoichiometry coefficient of element in substance, e.g. 1 for C; 2 for O2\n", - "required": "req_out" - } - ] - }, - { - "name": "EdgeSstate", - "doc": "Edge of type \"sstate\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "7", "8.1", "4", "5" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_from", - "typeId": "string", - "doc": "full id of outgoing vertex of any type (formerly outV)\n", - "required": "required" - }, - { - "key": 5, - "name": "_to", - "typeId": "string", - "doc": "full id of incoming datasource vertex (formerly inV)\n", - "required": "required" - }, - { - "key": 6, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\" (type of ArangoDB collection is \"edges\")\n", - "required": "required", - "default": "edge" - }, - { - "key": 7, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"sstate\"\n", - "required": "required", - "default": "sstate" - }, - { - "key": 8, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Sstate" - }, - "doc": "Properties of sstate edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Takes", - "doc": "Edge: takes (properties for \"takes\" edges)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "stoi_coeff", - "typeId": "double", - "doc": "Stoichiometry coefficient: negative for reactants, positive for products { \"SC\": -0.5 }\n", - "required": "req_out" - }, - { - "key": 2, - "name": "rct", - "typeId": "i32", - "doc": "Reaction component type: enum validated with class ReactionComponentType\n", - "class": "ReactionComponentType", - "required": "req_out" - } - ] - }, - { - "name": "EdgeTakes", - "doc": "Edge of type \"takes\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "7", "8.1", "8.2", "4", "5" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_from", - "typeId": "string", - "doc": "full id of outgoing vertex of any type (formerly outV)\n", - "required": "required" - }, - { - "key": 5, - "name": "_to", - "typeId": "string", - "doc": "full id of incoming datasource vertex (formerly inV)\n", - "required": "required" - }, - { - "key": 6, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\" (type of ArangoDB collection is \"edges\")\n", - "required": "required", - "default": "edge" - }, - { - "key": 7, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"takes\"\n", - "required": "required", - "default": "takes" - }, - { - "key": 8, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Takes" - }, - "doc": "Properties of takes edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Defines", - "doc": "Edge defines (properties for defines edges) for product substance defined via reaction\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "for_prop", - "typeId": "string", - "doc": "This string contains one of the keywords for substance properties, e.g. \"for_prop\" \"whole\"\n", - "required": "req_out" - }, - { - "key": 2, - "name": "asop", - "typeId": "string", - "doc": "This string identifies the relation: { \"asop\": \"retrieved\" } | ...\n", - "required": "req_out" - }, - { - "key": 3, - "name": "level", - "typeId": "i32", - "doc": "Level (color) of this reaction 0 | 1 | 2 | 3 | 4 | ...\n", - "required": "req_out" - } - ] - }, - { - "name": "EdgeDefines", - "doc": "Edge of type \"defines\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "7", "8.1", "8.2", "4", "5" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_from", - "typeId": "string", - "doc": "full id of outgoing vertex of any type (formerly outV)\n", - "required": "required" - }, - { - "key": 5, - "name": "_to", - "typeId": "string", - "doc": "full id of incoming datasource vertex (formerly inV)\n", - "required": "required" - }, - { - "key": 6, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\" (type of ArangoDB collection is \"edges\")\n", - "required": "required", - "default": "edge" - }, - { - "key": 7, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"defines\"\n", - "required": "required", - "default": "defines" - }, - { - "key": 8, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Defines" - }, - "doc": "Properties of defines edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Master", - "doc": "Edge master (properties for master edges) for master species in reactionset\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "ms_type", - "typeId": "i32", - "doc": "Type of master species - validated by enum class SpeciesTypeRS\n", - "class": "SpeciesTypeRS", - "required": "req_out" - } - ] - }, - { - "name": "EdgeMaster", - "doc": "Edge of type \"defines\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "7", "8.1", "4", "5" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_from", - "typeId": "string", - "doc": "full id of outgoing vertex of any type (formerly outV)\n", - "required": "required" - }, - { - "key": 5, - "name": "_to", - "typeId": "string", - "doc": "full id of incoming datasource vertex (formerly inV)\n", - "required": "required" - }, - { - "key": 6, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\" (type of ArangoDB collection is \"edges\")\n", - "required": "required", - "default": "edge" - }, - { - "key": 7, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"master\"\n", - "required": "required", - "default": "master" - }, - { - "key": 8, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Master" - }, - "doc": "Properties of master edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Product", - "doc": "Edge product (properties for product edges) for product species in reactionset\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "ps_type", - "typeId": "i32", - "doc": "Type of master species - validated by enum class SpeciesTypeRS\n", - "class": "SpeciesTypeRS", - "required": "req_out" - } - ] - }, - { - "name": "EdgeProduct", - "doc": "Edge of type \"defines\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "7", "8.1", "4", "5" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_from", - "typeId": "string", - "doc": "full id of outgoing vertex of any type (formerly outV)\n", - "required": "required" - }, - { - "key": 5, - "name": "_to", - "typeId": "string", - "doc": "full id of incoming datasource vertex (formerly inV)\n", - "required": "required" - }, - { - "key": 6, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\" (type of ArangoDB collection is \"edges\")\n", - "required": "required", - "default": "edge" - }, - { - "key": 7, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"product\"\n", - "required": "required", - "default": "product" - }, - { - "key": 8, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Product" - }, - "doc": "Properties of product edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Prodreac", - "doc": "Edge: Prodreac (properties for \"prodreac\" edges) defining reactions for product species in reactionset\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "for_ps", - "typeId": "string", - "doc": "This string contains sybmol of substance - one of the product species\n", - "required": "req_out" - }, - { - "key": 2, - "name": "level", - "typeId": "i32", - "doc": "Level (of alternative or generated reaction)\n", - "required": "req_out" - } - ] - }, - { - "name": "EdgeProdreac", - "doc": "Edge of type \"prodreac\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "7", "8.1", "8.2", "4", "5" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_from", - "typeId": "string", - "doc": "full id of outgoing vertex of any type (formerly outV)\n", - "required": "required" - }, - { - "key": 5, - "name": "_to", - "typeId": "string", - "doc": "full id of incoming datasource vertex (formerly inV)\n", - "required": "required" - }, - { - "key": 6, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\" (type of ArangoDB collection is \"edges\")\n", - "required": "required", - "default": "edge" - }, - { - "key": 7, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"prodreac\"\n", - "required": "required", - "default": "prodreac" - }, - { - "key": 8, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Prodreac" - }, - "doc": "Properties of prodreac edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Combined", - "doc": "Edge: Combined (properties for \"combined\" edges) defining reactions combined in an isocoulombic reaction\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "coeff", - "typeId": "double", - "doc": "coefficient of the combined reaction\n", - "required": "req_out" - }, - { - "key": 2, - "name": "rc_type", - "typeId": "i32", - "doc": "Type of combined reaction, INVESTIGATED or MODEL\n", - "required": "req_out" - }, - { - "key": 3, - "name": "level", - "typeId": "i32", - "doc": "Level (of alternative or generated reaction)\n", - "required": "req_out" - } - ] - }, - { - "name": "EdgeCombined", - "doc": "Edge of type \"prodreac\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "7", "8.1", "8.2","8.3", "4", "5" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_from", - "typeId": "string", - "doc": "full id of outgoing vertex of any type (formerly outV)\n", - "required": "required" - }, - { - "key": 5, - "name": "_to", - "typeId": "string", - "doc": "full id of incoming datasource vertex (formerly inV)\n", - "required": "required" - }, - { - "key": 6, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\" (type of ArangoDB collection is \"edges\")\n", - "required": "required", - "default": "edge" - }, - { - "key": 7, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"combined\"\n", - "required": "required", - "default": "combined" - }, - { - "key": 8, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Combined" - }, - "doc": "Properties of combined edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Basis", - "doc": "Edge: Basis (linking to elements or ligands or other basis species)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "b_type", - "typeId": "string", - "doc": "Type of basis component\n", - "required": "req_out" - } - ] - }, - { - "name": "EdgeBasis", - "doc": "Edge of type \"basis\" definition\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_from", - "typeId": "string", - "doc": "full id of outgoing vertex of any type (formerly outV)\n", - "required": "required" - }, - { - "key": 5, - "name": "_to", - "typeId": "string", - "doc": "full id of incoming datasource vertex (formerly inV)\n", - "required": "required" - }, - { - "key": 6, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\" (type of ArangoDB collection is \"edges\")\n", - "required": "required", - "default": "edge" - }, - { - "key": 7, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"basis\"\n", - "required": "required", - "default": "basis" - }, - { - "key": 8, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Basis" - }, - "doc": "Properties of basis edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Pulls", - "doc": "Edge: Pulls (linking to substances or master species)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "level_of_data", - "typeId": "string", - "required": "req_out" - } - ] - }, - { - "name": "EdgePulls", - "doc": "Edge of type \"pulls\" definition\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_from", - "typeId": "string", - "doc": "full id of outgoing vertex of any type (formerly outV)\n", - "required": "required" - }, - { - "key": 5, - "name": "_to", - "typeId": "string", - "doc": "full id of incoming datasource vertex (formerly inV)\n", - "required": "required" - }, - { - "key": 6, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\" (type of ArangoDB collection is \"edges\")\n", - "required": "required", - "default": "edge" - }, - { - "key": 7, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"pulls\"\n", - "required": "required", - "default": "pulls" - }, - { - "key": 8, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Pulls" - }, - "doc": "Properties of pulls edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Involves", - "doc": "Edge: Involves (linking to Reactionset instance for LMA_TDS)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "level_of_data", - "typeId": "string", - "required": "req_out" - } - ] - }, - { - "name": "EdgeInvolves", - "doc": "Edge of type \"involves\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "7", "8.1", "4", "5" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_from", - "typeId": "string", - "doc": "full id of outgoing vertex of any type (formerly outV)\n", - "required": "required" - }, - { - "key": 5, - "name": "_to", - "typeId": "string", - "doc": "full id of incoming datasource vertex (formerly inV)\n", - "required": "required" - }, - { - "key": 6, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\" (type of ArangoDB collection is \"edges\")\n", - "required": "required", - "default": "edge" - }, - { - "key": 7, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"involves\"\n", - "required": "required", - "default": "involves" - }, - { - "key": 8, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Involves" - }, - "doc": "Properties of involves edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Interacts", - "doc": "Edge: interacts (properties for \"interacts\" edges)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "weight", - "typeId": "double", - "doc": "{ \"weight\": 1 } set to 1.0 for now\n", - "required": "req_out" - }, - { - "key": 2, - "name": "level", - "typeId": "i32", - "doc": "Level (of alternative or generated interaction)\n", - "required": "req_out" - } - ] - }, - { - "name": "EdgeInteracts", - "doc": "Edge of type \"interacts\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "7", "4", "5" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_from", - "typeId": "string", - "doc": "full id of outgoing vertex of any type (formerly outV)\n", - "required": "required" - }, - { - "key": 5, - "name": "_to", - "typeId": "string", - "doc": "full id of incoming datasource vertex (formerly inV)\n", - "required": "required" - }, - { - "key": 6, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\" (type of ArangoDB collection is \"edges\")\n", - "required": "required", - "default": "edge" - }, - { - "key": 7, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"interacts\"\n", - "required": "required", - "default": "interacts" - }, - { - "key": 8, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Interacts" - }, - "doc": "Properties of interacts edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Specific", - "doc": "Edge: specific (properties for \"specific\" edges connecting interactions with mixingmodel\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "weight", - "typeId": "double", - "doc": "{ \"weight\": 1 } set to 1.0 for now\n", - "required": "req_out" - }, - { - "key": 2, - "name": "level", - "typeId": "i32", - "doc": "Level (of alternative or generated interaction)\n", - "required": "req_out" - } - ] - }, - { - "name": "EdgeSpecific", - "doc": "Edge of type \"specific\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "7", "4", "5" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_from", - "typeId": "string", - "doc": "full id of outgoing vertex of any type (formerly outV)\n", - "required": "required" - }, - { - "key": 5, - "name": "_to", - "typeId": "string", - "doc": "full id of incoming datasource vertex (formerly inV)\n", - "required": "required" - }, - { - "key": 6, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\" (type of ArangoDB collection is \"edges\")\n", - "required": "required", - "default": "edge" - }, - { - "key": 7, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"specific\"\n", - "required": "required", - "default": "specific" - }, - { - "key": 8, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Specific" - }, - "doc": "Properties of specific edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Mechanism", - "doc": "Edge: kinetics (properties for \"mechanism\" edges)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "weight", - "typeId": "double", - "doc": "{ \"weight\": 1 } set to 1.0 for now\n", - "required": "req_out" - }, - { - "key": 2, - "name": "level", - "typeId": "i32", - "doc": "Level (of alternative or generated mechanism)\n", - "required": "req_out" - }, - { - "key": 3, - "name": "order", - "typeId": "double", - "doc": "Generic order of kinetics for this mechanism in the phase\n", - "required": "req_out" - } - ] - }, - { - "name": "EdgeMechanism", - "doc": "Edge of type \"mechanism\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "7", "8.1", "8.2","8.3", "4", "5" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_from", - "typeId": "string", - "doc": "full id of outgoing vertex of any type (formerly outV)\n", - "required": "required" - }, - { - "key": 5, - "name": "_to", - "typeId": "string", - "doc": "full id of incoming datasource vertex (formerly inV)\n", - "required": "required" - }, - { - "key": 6, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\" (type of ArangoDB collection is \"edges\")\n", - "required": "required", - "default": "edge" - }, - { - "key": 7, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"mechahism\"\n", - "required": "required", - "default": "mechanism" - }, - { - "key": 8, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Mechanism" - }, - "doc": "Properties of kinetics edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Mixing", - "doc": "Edge: kinetic link to species used in activity terms (properties for \"kinspecies\" edges)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "weight", - "typeId": "double", - "doc": "{ \"weight\": 1 } set to 1.0 for now\n", - "required": "req_out" - }, - { - "key": 2, - "name": "level", - "typeId": "i32", - "doc": "Level (of alternative or generated interaction)\n", - "required": "req_out" - }, - { - "key": 3, - "name": "order", - "typeId": "double", - "doc": "Order (power at activity) for this mechanism relative to the species (substance or moiety)\n", - "required": "req_out" - } - ] - }, - { - "name": "EdgeMixing", - "doc": "Edge of type \"kinspecies\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "7", "4", "5" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_from", - "typeId": "string", - "doc": "full id of outgoing vertex of any type (formerly outV)\n", - "required": "required" - }, - { - "key": 5, - "name": "_to", - "typeId": "string", - "doc": "full id of incoming datasource vertex (formerly inV)\n", - "required": "required" - }, - { - "key": 6, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\" (type of ArangoDB collection is \"edges\")\n", - "required": "required", - "default": "edge" - }, - { - "key": 7, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"mixing\"\n", - "required": "required", - "default": "mixing" - }, - { - "key": 8, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Mixing" - }, - "doc": "Properties of kinspecies edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Kinetics", - "doc": "Edge: kinetics (properties for \"mechanism\" edges)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "weight", - "typeId": "double", - "doc": "{ \"weight\": 1 } set to 1.0 for now\n", - "required": "req_out" - }, - { - "key": 2, - "name": "level", - "typeId": "i32", - "doc": "Level (of alternative or generated mechanism)\n", - "required": "req_out" - }, - { - "key": 3, - "name": "order", - "typeId": "double", - "doc": "Generic order of kinetics for this mechanism in the phase\n", - "required": "req_out" - } - ] - }, - { - "name": "EdgeKinetics", - "doc": "Edge of type \"mechanism\" definition\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_from", - "typeId": "string", - "doc": "full id of outgoing vertex of any type (formerly outV)\n", - "required": "required" - }, - { - "key": 5, - "name": "_to", - "typeId": "string", - "doc": "full id of incoming datasource vertex (formerly inV)\n", - "required": "required" - }, - { - "key": 6, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\" (type of ArangoDB collection is \"edges\")\n", - "required": "required", - "default": "edge" - }, - { - "key": 7, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"mechahism\"\n", - "required": "required", - "default": "kinetics" - }, - { - "key": 8, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Kinetics" - }, - "doc": "Properties of kinetics edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Component", - "doc": "Edge component (properties for phase end member) for components in phase\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "pc_type", - "class": "SubstanceClass", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Type of phase component - validated by enum class SubstanceClass in prop\n", - "required": "req_out", - "default": { - "0": "SC_COMPONENT" - } - }, - { - "key": 2, - "name": "pc_conscale", - "class": "ConcentrationScale", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Concentration scale used in this phase model of mixing\n", - "required": "req_out", - "default": { - "0": "C_UNITY" - } - }, - { - "key": 3, - "name": "pc_props", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Optional properties of this component in the phase e.g. Kielland ion radius\n", - "required": "req_out" - }, - { - "key": 4, - "name": "pc_uptake", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Optional parameters for the uptake kinetics model (UUCM)\n", - "required": "req_out" - } - ] - }, - { - "name": "EdgeComponent", - "doc": "Edge of type \"component\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "7", "4", "5", "8.1" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_from", - "typeId": "string", - "doc": "full id of outgoing vertex of any type (formerly outV)\n", - "required": "required" - }, - { - "key": 5, - "name": "_to", - "typeId": "string", - "doc": "full id of incoming datasource vertex (formerly inV)\n", - "required": "required" - }, - { - "key": 6, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\" (type of ArangoDB collection is \"edges\")\n", - "required": "required", - "default": "edge" - }, - { - "key": 7, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"component\"\n", - "required": "required", - "default": "component" - }, - { - "key": 8, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Component" - }, - "doc": "Properties of component edge\n", - "required": "req_out" - } - ] - }, - { - "name": "SiteMoiety", - "doc": "Edge sitemoiety (properties for moiety) for phase with sublattice model of mixing\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "sm_type", - "class": "SpeciesTypeRS", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Type of edge - validated by enum class SpeciesTypeRS\n", - "required": "req_out", - "default": { - "5": "SC_SITEMOIETY" - } - }, - { - "key": 2, - "name": "mo_pc_conscale", - "class": "ConcentrationScale", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Concentration scale used in this phase model of mixing for this moiety\n", - "required": "req_out", - "default": { - "8": "C_SITEFRACTION" - } - }, - { - "key": 3, - "name": "site_index", - "typeId": "i16", - "doc": "Index of site (sublattice) to which this moiety is assigned\n", - "required": "req_out", - "default": 0 - }, - { - "key": 4, - "name": "mo_pc_props", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Optional properties of this site moiety\n", - "required": "req_out" - } - ] - }, - { - "name": "EdgeSiteMoiety", - "doc": "Edge of type \"component\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "7", "8.1", "8.3","8.4", "4", "5" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_from", - "typeId": "string", - "doc": "full id of outgoing vertex of any type (formerly outV)\n", - "required": "required" - }, - { - "key": 5, - "name": "_to", - "typeId": "string", - "doc": "full id of incoming datasource vertex (formerly inV)\n", - "required": "required" - }, - { - "key": 6, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\" (type of ArangoDB collection is \"edges\")\n", - "required": "required", - "default": "edge" - }, - { - "key": 7, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"sitemoiety\"\n", - "required": "required", - "default": "sitemoiety" - }, - { - "key": 8, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Component" - }, - "doc": "Properties of sitemoiety edge\n", - "required": "req_out" - } - ] - }, - { - "name": "AddsTo", - "doc": "Edge: AddsTo (linking to substance, constituent or ingredient formula)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "amount", - "typeId": "double", - "doc": "amount added\n", - "required": "req_out" - }, - { - "key": 2, - "name": "unit_a", - "typeId": "string", - "doc": "units of measurement for this quantity\n", - "required": "req_out" - }, - { - "key": 3, - "name": "mass", - "typeId": "double", - "doc": "mass added\n", - "required": "req_out" - }, - { - "key": 4, - "name": "unit_m", - "typeId": "string", - "doc": "units of measurement for mass\n", - "required": "req_out" - }, - { - "key": 5, - "name": "extent", - "typeId": "double", - "doc": "reaction extent for linked object\n", - "required": "req_out" - }, - { - "key": 6, - "name": "mode", - "typeId": "bool", - "doc": "mode of addition: false: replacing \"composition\" field in the To vertex; true: adding to it\n", - "required": "req_out" - } - ] - }, - { - "name": "EdgeAddsTo", - "doc": "Edge of type \"addsto\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "7", "4", "5" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_from", - "typeId": "string", - "doc": "full id of outgoing vertex of any type (formerly outV)\n", - "required": "required" - }, - { - "key": 5, - "name": "_to", - "typeId": "string", - "doc": "full id of incoming datasource vertex (formerly inV)\n", - "required": "required" - }, - { - "key": 6, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\" (type of ArangoDB collection is \"edges\")\n", - "required": "required", - "default": "edge" - }, - { - "key": 7, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"adds\"\n", - "required": "required", - "default": "addsto" - }, - { - "key": 8, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "AddsTo" - }, - "doc": "Properties of adds edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Collect", - "doc": "Edge: Colllect (linking to phases)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "rank", - "typeId": "i32", - "required": "req_out" - } - ] - }, - { - "name": "EdgeCollect", - "doc": "Edge of type \"collects\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "7", "8.1", "4", "5" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_from", - "typeId": "string", - "doc": "full id of outgoing vertex of any type (formerly outV)\n", - "required": "required" - }, - { - "key": 5, - "name": "_to", - "typeId": "string", - "doc": "full id of incoming datasource vertex (formerly inV)\n", - "required": "required" - }, - { - "key": 6, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\" (type of ArangoDB collection is \"edges\")\n", - "required": "required", - "default": "edge" - }, - { - "key": 7, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"collects\"\n", - "required": "required", - "default": "collect_" - }, - { - "key": 8, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Collect" - }, - "doc": "Properties of collects edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Uses", - "doc": "Edge: Uses (linking to thermodataset)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "mode", - "typeId": "string", - "required": "req_out" - } - ] - }, - { - "name": "EdgeUses", - "doc": "Edge of type \"uses\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "7", "8.1", "4", "5" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_from", - "typeId": "string", - "doc": "full id of outgoing vertex of any type (formerly outV)\n", - "required": "required" - }, - { - "key": 5, - "name": "_to", - "typeId": "string", - "doc": "full id of incoming datasource vertex (formerly inV)\n", - "required": "required" - }, - { - "key": 6, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\" (type of ArangoDB collection is \"edges\")\n", - "required": "required", - "default": "edge" - }, - { - "key": 7, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"uses\"\n", - "required": "required", - "default": "uses" - }, - { - "key": 8, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Uses" - }, - "doc": "Properties of uses edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Belongs", - "doc": "Edge: Belongs (linking to thermodataset)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "mode", - "typeId": "string", - "required": "req_out" - } - ] - }, - { - "name": "EdgeBelongs", - "doc": "Edge of type \"uses\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "7", "8.1", "4", "5" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_from", - "typeId": "string", - "doc": "full id of outgoing vertex of any type (formerly outV)\n", - "required": "required" - }, - { - "key": 5, - "name": "_to", - "typeId": "string", - "doc": "full id of incoming datasource vertex (formerly inV)\n", - "required": "required" - }, - { - "key": 6, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\" (type of ArangoDB collection is \"edges\")\n", - "required": "required", - "default": "edge" - }, - { - "key": 7, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"belongs\"\n", - "required": "required", - "default": "belongs" - }, - { - "key": 8, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Belongs" - }, - "doc": "Properties of belongs edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Yields", - "doc": "Edge: Yields (linking from recipe to speciation)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "Iniguess", - "typeId": "string", - "required": "req_out" - }, - { - "key": 2, - "name": "Time", - "typeId": "string", - "required": "req_out" - } - ] - }, - { - "name": "EdgeYields", - "doc": "Edge of type \"uses\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "7", "8.1", "8.2", "4", "5" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_from", - "typeId": "string", - "doc": "full id of outgoing vertex of any type (formerly outV)\n", - "required": "required" - }, - { - "key": 5, - "name": "_to", - "typeId": "string", - "doc": "full id of incoming datasource vertex (formerly inV)\n", - "required": "required" - }, - { - "key": 6, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\" (type of ArangoDB collection is \"edges\")\n", - "required": "required", - "default": "edge" - }, - { - "key": 7, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"yields\"\n", - "required": "required", - "default": "yields" - }, - { - "key": 8, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Yields" - }, - "doc": "Properties of yields edge\n", - "required": "req_out" - } - ] - }, - { - "name": "EqState", - "doc": "Edge: EqState (linking to thermodataset)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "T", - "typeId": "double", - "required": "req_out" - }, - { - "key": 2, - "name": "P", - "typeId": "double", - "required": "req_out" - }, - { - "key": 3, - "name": "V", - "typeId": "double", - "required": "req_out" - }, - { - "key": 4, - "name": "H", - "typeId": "double", - "required": "req_out" - }, - { - "key": 5, - "name": "U", - "typeId": "double", - "required": "req_out" - }, - { - "key": 6, - "name": "S", - "typeId": "double", - "required": "req_out" - } - ] - }, - { - "name": "EdgeEqState", - "doc": "Edge of type \"uses\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "7", "8.1", "8.2","8.3", "4", "5" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_from", - "typeId": "string", - "doc": "full id of outgoing vertex of any type (formerly outV)\n", - "required": "required" - }, - { - "key": 5, - "name": "_to", - "typeId": "string", - "doc": "full id of incoming datasource vertex (formerly inV)\n", - "required": "required" - }, - { - "key": 6, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\" (type of ArangoDB collection is \"edges\")\n", - "required": "required", - "default": "edge" - }, - { - "key": 7, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"EqState\"\n", - "required": "required", - "default": "eqstate" - }, - { - "key": 8, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EqState" - }, - "doc": "Properties of eqstate edge\n", - "required": "req_out" - } - ] - }, - { - "name": "MadeOf", - "doc": "Edge: MadeOf (linking recipe to recipe, constituent to constituent, etc.)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "composition", - "typeId": "double", - "required": "req_out" - }, - { - "key": 2, - "name": "unit", - "typeId": "string", - "doc": "units of measurement for this quantity\n", - "required": "req_out" - }, - { - "key": 3, - "name": "mode", - "typeId": "bool", - "required": "req_out" - } - ] - }, - { - "name": "EdgeMadeOf", - "doc": "Edge of type \"MadeOf\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "7", "8.1", "4", "5" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Full database ID (0 if not known); =_label+_key in ArangoDB; =_key in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of database record (_key inside ArangoDB collection)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Revision #: native in ArangoDB, needs to be maintained in MongoDB or EJDB\n", - "required": "required" - }, - { - "key": 4, - "name": "_from", - "typeId": "string", - "doc": "full id of outgoing vertex of any type (formerly outV)\n", - "required": "required" - }, - { - "key": 5, - "name": "_to", - "typeId": "string", - "doc": "full id of incoming datasource vertex (formerly inV)\n", - "required": "required" - }, - { - "key": 6, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\" (type of ArangoDB collection is \"edges\")\n", - "required": "required", - "default": "edge" - }, - { - "key": 7, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"madeof\"\n", - "required": "required", - "default": "madeof" - }, - { - "key": 8, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "MadeOf" - }, - "doc": "Properties of belongs edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Vertex", - "doc": "Generalized vertex\n", - "isException": false, - "isUnion": true, - "fields": [ - { - "key": 1, - "name": "v_datasource", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexDataSource" - }, - "required": "optional" - }, - { - "key": 2, - "name": "v_element", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexElement" - }, - "required": "optional" - }, - { - "key": 3, - "name": "v_substance", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexSubstance" - }, - "required": "optional" - }, - { - "key": 4, - "name": "v_reaction", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexReaction" - }, - "required": "optional" - }, - { - "key": 5, - "name": "v_reactionset", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexReactionSet" - }, - "required": "optional" - }, - { - "key": 6, - "name": "v_thermodataset", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexThermoDataSet" - }, - "required": "optional" - }, - { - "key": 7, - "name": "v_interaction", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexInteraction" - }, - "required": "optional" - }, - { - "key": 8, - "name": "v_mixingmodel", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexMixingModel" - }, - "required": "optional" - }, - { - "key": 9, - "name": "v_kineticrate", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexKineticRate" - }, - "required": "optional" - }, - { - "key": 10, - "name": "v_kineticmodel", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexKineticModel" - }, - "required": "optional" - }, - { - "key": 11, - "name": "v_phase", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexPhase" - }, - "required": "optional" - }, - { - "key": 12, - "name": "v_chemeqsysdef", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexChemEqSysDef" - }, - "required": "optional" - }, - { - "key": 13, - "name": "v_compound", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexCompound" - }, - "required": "optional" - }, - { - "key": 14, - "name": "v_constituent", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexConstituent" - }, - "required": "optional" - }, - { - "key": 15, - "name": "v_ingredient", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexIngredient" - }, - "required": "optional" - }, - { - "key": 16, - "name": "v_chemeqsysrecipe", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexChemEqSysRecipe" - }, - "required": "optional" - }, - { - "key": 17, - "name": "v_chemeqspeciation", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexChemEqSpeciation" - }, - "required": "optional" - } - ] - }, - { - "name": "Edge", - "doc": "Generalized edge\n", - "isException": false, - "isUnion": true, - "fields": [ - { - "key": 1, - "name": "e_citing", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeCiting" - }, - "required": "optional" - }, - { - "key": 2, - "name": "e_inherits", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeInherits" - }, - "required": "optional" - }, - { - "key": 3, - "name": "e_sstate", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeSstate" - }, - "required": "optional" - }, - { - "key": 4, - "name": "e_takes", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeTakes" - }, - "required": "optional" - }, - { - "key": 5, - "name": "e_defines", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeDefines" - }, - "required": "optional" - }, - { - "key": 6, - "name": "e_master", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeMaster" - }, - "required": "optional" - }, - { - "key": 7, - "name": "e_product", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeProduct" - }, - "required": "optional" - }, - { - "key": 8, - "name": "e_prodreac", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeProdreac" - }, - "required": "optional" - }, - { - "key": 9, - "name": "e_combined", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeCombined" - }, - "required": "optional" - }, - { - "key": 10, - "name": "e_basis", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeBasis" - }, - "required": "optional" - }, - { - "key": 11, - "name": "e_pulls", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgePulls" - }, - "required": "optional" - }, - { - "key": 12, - "name": "e_involves", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeInvolves" - }, - "required": "optional" - }, - { - "key": 13, - "name": "e_interacts", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeInteracts" - }, - "required": "optional" - }, - { - "key": 14, - "name": "e_specific", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeSpecific" - }, - "required": "optional" - }, - { - "key": 15, - "name": "e_mechanism", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeMechanism" - }, - "required": "optional" - }, - { - "key": 16, - "name": "e_mixing", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeMixing" - }, - "required": "optional" - }, - { - "key": 17, - "name": "e_kinetics", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeKinetics" - }, - "required": "optional" - }, - { - "key": 18, - "name": "e_component", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeComponent" - }, - "required": "optional" - }, - { - "key": 19, - "name": "e_sitemoiety", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeSiteMoiety" - }, - "required": "optional" - }, - { - "key": 20, - "name": "e_addsto", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeAddsTo" - }, - "required": "optional" - }, - { - "key": 21, - "name": "e_collect", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeCollect" - }, - "required": "optional" - }, - { - "key": 22, - "name": "e_uses", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeUses" - }, - "required": "optional" - }, - { - "key": 23, - "name": "e_belongs", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeBelongs" - }, - "required": "optional" - }, - { - "key": 24, - "name": "e_yields", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeYields" - }, - "required": "optional" - }, - { - "key": 25, - "name": "e_eqstate", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeEqState" - }, - "required": "optional" - }, - { - "key": 26, - "name": "e_madeof", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeMadeOf" - }, - "required": "optional" - } - ] - }, - { - "name": "GraphData", - "doc": "Generalized graph data (file)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "mode", - "typeId": "string", - "doc": "Mode of rendering NORMAL [ | EXTENDED | COMPACT ]\n", - "required": "req_out", - "default": "NORMAL" - }, - { - "key": 2, - "name": "vertices", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "union", - "elemType": { - "typeId": "union", - "class": "Vertex" - } - }, - "doc": "List of vertices (documents), can be empty (followed by only graph edges)\n", - "required": "req_out" - }, - { - "key": 3, - "name": "edges", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "union", - "elemType": { - "typeId": "union", - "class": "Edge" - } - }, - "doc": "list of edges (graph links), can be empty for a non-graph data (with only documents)\n", - "required": "req_out" - } - ] - } - ], - "constants": [ - ], - "services": [ - ] -} diff --git a/Resources/data/schemas/chemeqspeciation.schema.json b/Resources/data/schemas/chemeqspeciation.schema.json deleted file mode 100644 index 15f9619a..00000000 --- a/Resources/data/schemas/chemeqspeciation.schema.json +++ /dev/null @@ -1,242 +0,0 @@ -{ - "name": "chemeqspeciation", - "doc": "Apache Thrift IDL definition for the chemical system (partial) equilibrium speciation\n", - "namespaces": { - "*": "chemeqspeciation" - }, - "includes": [ -"prop", -"chemeqsysdef", -"chemeqsysrecipe" - ], - "enums": [ - { - "name": "ChemEqSpeciationType", - "members": [ - { - "name": "EQS_COMPLETE", - "value": 0, - "doc": "Complete equilibrium state - no kinetic controls\n" - }, - { - "name": "EQS_PARTIAL", - "value": 1, - "doc": "Partial equilibrium state - some species and phases under kinetic control\n" - }, - { - "name": "EQS_LOCAL", - "value": 2, - "doc": "Local partial equilibrium state from reactive transport simulation\n" - }, - { - "name": "EQS_OTHER", - "value": 101, - "doc": "Other types of equilibrium state\n" - } - ] - } - ], - "typedefs": [ - ], - "structs": [ - { - "name": "ChemEqSpeciation", - "doc": "and to its parent ChemEqSysDef record via the edge \"Belongs\"\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "symbol", - "typeId": "string", - "doc": "Unique name\/ID of this speciation e.g. \"eqs_in_pw+bentonite\"\n", - "required": "required" - }, - { - "key": 2, - "name": "comment", - "typeId": "string", - "doc": "Name comment of the recipe (e.g. \"equilibrium speciation for bentonite+porewater\")\n", - "required": "req_out" - }, - { - "key": 3, - "name": "csdtype", - "class": "csdType", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Type of this chemical equilibrium calculation\n", - "required": "req_out", - "default": { - "0": "CSD_GEM" - } - }, - { - "key": 4, - "name": "cestype", - "class": "ChemEqSpeciationType", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Type of this chemical equilibrium speciation\n", - "required": "req_out", - "default": { - "0": "EQS_COMPLETE" - } - }, - { - "key": 5, - "name": "chemeqsysdef", - "typeId": "string", - "doc": "Symbol of chemeqsysdef to which this speciation belongs - via \"belongs\" link\n", - "required": "req_out" - }, - { - "key": 6, - "name": "chemeqsysrecipe", - "typeId": "string", - "doc": "Symbol of chemeqsysrecipe that yileds this speciation via \"yields\" link\n", - "required": "req_out" - }, - { - "key": 7, - "name": "initialGuess", - "class": "InitialGuessType", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Type of the initial guess used\n", - "required": "req_out" - }, - { - "key": 8, - "name": "Temperature", - "typeId": "double", - "doc": "Temperature, degK\n", - "required": "req_out" - }, - { - "key": 9, - "name": "Pressure", - "typeId": "double", - "doc": "Pressure, Pa\n", - "required": "req_out" - }, - { - "key": 10, - "name": "Volume", - "typeId": "double", - "doc": "Volume (constraining the system), m^3\n", - "required": "req_out" - }, - { - "key": 11, - "name": "system", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.TDSProperties" - }, - "doc": "Properties of the whole system\n", - "required": "req_out" - }, - { - "key": 12, - "name": "phases", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "prop.TDSProperties" - } - }, - "doc": "Properties of phases-solutions\n", - "required": "req_out" - }, - { - "key": 21, - "name": "masters", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "List of symbols of master species (from chemsysdef)\n", - "required": "req_out" - }, - { - "key": 22, - "name": "nmsp", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "double" - }, - "doc": "Bulk composition in moles of master species\n", - "required": "req_out" - }, - { - "key": 25, - "name": "dataSources", - "typeId": "set", - "type": { - "typeId": "set", - "elemTypeId": "string" - }, - "doc": "labels of datasource DB objects\n", - "required": "optional" - }, - { - "key": 26, - "name": "timeStamp", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.TimeStamp" - }, - "doc": "timestamp\n", - "required": "optional" - } - ] - }, - { - "name": "ChemEqSpeciations", - "doc": "Definition of an array of calculated speciations\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 2, - "name": "speciations", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "ChemEqSpeciation" - } - }, - "doc": "List of CemGEMS chemical system speciations\n", - "required": "req_out" - } - ] - } - ], - "constants": [ - ], - "services": [ - ] -} diff --git a/Resources/data/schemas/chemeqsysdef.schema.json b/Resources/data/schemas/chemeqsysdef.schema.json deleted file mode 100644 index e6769303..00000000 --- a/Resources/data/schemas/chemeqsysdef.schema.json +++ /dev/null @@ -1,376 +0,0 @@ -{ - "name": "chemeqsysdef", - "doc": "Apache Thrift IDL definition for the chemsystem service interface\n", - "namespaces": { - "*": "chemeqsysdef" - }, - "includes": [ -"prop", -"element", -"substance", -"reactionset", -"thermodataset", -"phase" - ], - "enums": [ - { - "name": "csdType", - "doc": "classes (types) of chemsysdefs\n", - "members": [ - { - "name": "CSD_GEM", - "value": 0, - "doc": "GEM-type chemical system\n" - }, - { - "name": "CSD_LMA", - "value": 1, - "doc": "LMA-type chemical system definition\n" - }, - { - "name": "CSD_UNI", - "value": 2, - "doc": "Universal system definition (for exporting both )\n" - }, - { - "name": "CSD_REF", - "value": 3, - "doc": "Reference system definition\n" - }, - { - "name": "CSD_OTHER", - "value": 101, - "doc": "other type\n" - } - ] - } - ], - "typedefs": [ - { - "name": "dcrow", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "double" - }, - "doc": "row of stoichiometry matrix for DC (substance)\n" - } - ], - "structs": [ - { - "name": "ChemEqSysDef", - "doc": "description of chemical system definition\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "symbol", - "typeId": "string", - "doc": "unique name\/ID of this chemsysdef set\n", - "required": "required" - }, - { - "key": 2, - "name": "csdtyp", - "class": "csdType", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "type of chemsysdef - validate with class csdType\n", - "required": "required", - "default": { - "0": "CSD_GEM" - } - }, - { - "key": 3, - "name": "thermodataset", - "typeId": "string", - "doc": "Used thermodataset symbol (also csdinvolves link)\n", - "required": "required" - }, - { - "key": 5, - "name": "comment", - "typeId": "string", - "doc": "Full name comment of the chemsysdef (not compulsory)\n", - "required": "req_out" - }, - { - "key": 6, - "name": "elements", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "element.ElementInfo" - } - }, - "doc": "List of element symbols and infos, a subset of the thermodataset list\n", - "required": "req_out" - }, - { - "key": 8, - "name": "phases", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "phase.PhaseInfo" - } - }, - "doc": "can be constructed automatically using \"Collect\" edges to phases\n", - "required": "req_out" - }, - { - "key": 10, - "name": "nspiph", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "i32" - }, - "doc": "numbers of species (DCs) in phases\n", - "required": "req_out" - }, - { - "key": 11, - "name": "nphsol", - "typeId": "i32", - "doc": "number of phases - solutions\n", - "required": "req_out" - }, - { - "key": 12, - "name": "substances", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "substance.SubstanceInfo" - } - }, - "doc": "list of chemical species symbols (arranged by phases) - a subset of that in thermodataset\n", - "required": "req_out" - }, - { - "key": 14, - "name": "speciesMap", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "string", - "valueTypeId": "i32" - }, - "doc": "Map of species symbols and types (class SpeciesTypeRS) - a re-sorted subset, for LMA-type\n", - "required": "req_out" - }, - { - "key": 17, - "name": "limitsTP", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.LimitsTP" - }, - "doc": "lower and upper T, P limits fof applicability\n", - "required": "req_out", - "default": { - "range": 0, - "lowerT": 273.15, - "upperT": 298.15, - "lowerP": 0.1, - "upperP": 1000000 - } - }, - { - "key": 18, - "name": "datasources", - "typeId": "set", - "type": { - "typeId": "set", - "elemTypeId": "string" - }, - "doc": "labels of datasource DB objects\n", - "required": "optional" - }, - { - "key": 19, - "name": "time_stamp", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.TimeStamp" - }, - "doc": "timestamp\n", - "required": "optional" - } - ] - }, - { - "name": "ChemEqSysDefs", - "doc": "Definition of an array of recipes and data for chemical system definitions\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 2, - "name": "systems", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "ChemEqSysDef" - } - }, - "doc": "List of chemical system definitions\n", - "required": "req_out" - } - ] - }, - { - "name": "chemsysdefdata", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "Nelements", - "typeId": "i32", - "required": "req_out" - }, - { - "key": 2, - "name": "elements", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "element.ElementInfo" - } - }, - "required": "req_out" - }, - { - "key": 3, - "name": "bic", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "double" - }, - "required": "req_out" - }, - { - "key": 5, - "name": "Nspecies", - "typeId": "i32", - "required": "req_out" - }, - { - "key": 6, - "name": "species", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "substance.SubstanceInfo" - } - }, - "required": "req_out" - }, - { - "key": 7, - "name": "ndc", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "double" - }, - "required": "req_out" - }, - { - "key": 8, - "name": "A", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "list", - "elemType": { - "typeId": "list", - "elemTypeId": "double" - } - }, - "required": "req_out" - }, - { - "key": 13, - "name": "Nphases", - "typeId": "i32", - "required": "req_out" - }, - { - "key": 14, - "name": "phases", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "phase.PhaseInfo" - } - }, - "required": "req_out" - }, - { - "key": 15, - "name": "nph", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "double" - }, - "required": "req_out" - }, - { - "key": 16, - "name": "ndcinph", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "i32" - }, - "required": "req_out" - }, - { - "key": 19, - "name": "processedCSD", - "typeId": "bool", - "required": "req_out", - "default": 0 - } - ] - } - ], - "constants": [ - ], - "services": [ - ] -} diff --git a/Resources/data/schemas/chemeqsysrecipe.schema.json b/Resources/data/schemas/chemeqsysrecipe.schema.json deleted file mode 100644 index cd4e0505..00000000 --- a/Resources/data/schemas/chemeqsysrecipe.schema.json +++ /dev/null @@ -1,427 +0,0 @@ -{ - "name": "chemeqsysrecipe", - "doc": "Apache Thrift IDL definition for the chemical system recipe\n", - "namespaces": { - "*": "chemeqsysrecipe" - }, - "includes": [ -"prop", -"element", -"phase", -"chemeqsysdef", -"ingredient", -"compound" - ], - "enums": [ - { - "name": "SysRecipeType", - "members": [ - { - "name": "RCP_FORWARD", - "value": 0, - "doc": "Forward equilibrium modeling recipe - speciation from bulk composition, T and P\n" - }, - { - "name": "RCP_INVERSE", - "value": 1, - "doc": "Inverce modeling recipe - some activities, concentrations, ... known; bc, T, P to be determined\n" - }, - { - "name": "RCP_OTHER", - "value": 101, - "doc": "Other types of recipe\n" - } - ] - }, - { - "name": "InitialGuessType", - "members": [ - { - "name": "START_COLD", - "value": 0, - "doc": "Cold start\n" - }, - { - "name": "START_WARM", - "value": 1, - "doc": "Warm start\n" - }, - { - "name": "START_OTHER", - "value": 101, - "doc": "other\n" - } - ] - } - ], - "typedefs": [ - ], - "structs": [ - { - "name": "ChemEqSysRecipe", - "doc": "should be connected to its parent ChemEqSysDef record via the edge \"Belongs\"\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "symbol", - "typeId": "string", - "doc": "Unique name\/ID of this recipe e.g. \"pw+bentonite\"\n", - "required": "required" - }, - { - "key": 2, - "name": "comment", - "typeId": "string", - "doc": "Name comment of the recipe (e.g. \"bentonite+porewater\")\n", - "required": "req_out" - }, - { - "key": 3, - "name": "formula", - "typeId": "string", - "doc": "Optional shortcut formula of 1 mole of this constituent e.g. Fe | Fe2O3 | Fe+2\n", - "required": "req_out" - }, - { - "key": 4, - "name": "recipeType", - "class": "SysRecipeType", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Type of this recipe - validate with class SysRecipeType\n", - "required": "req_out", - "default": { - "0": "RCP_FORWARD" - } - }, - { - "key": 5, - "name": "chemeqSysdef", - "typeId": "string", - "doc": "should be connected to this parent ChemEqSysDef record via the edge \"Belongs\"\n", - "required": "req_out", - "default": "CSD#1" - }, - { - "key": 6, - "name": "initialGuessType", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Type of initial guess for GEMS3K to use, validate with class InitialGuessType\n", - "required": "req_out", - "default": { - "0": "START_COLD" - } - }, - { - "key": 7, - "name": "reactionExtent", - "typeId": "double", - "doc": "Extent of reaction, i.e. mass fraction of constituent composition to equilibrate\n", - "required": "req_out", - "default": 1 - }, - { - "key": 11, - "name": "quantity", - "typeId": "double", - "doc": "Amount\/mass of the recipe material (to normalize the contributions from ingredients and formulae\n", - "required": "req_out", - "default": 1 - }, - { - "key": 12, - "name": "unit_q", - "typeId": "string", - "doc": "Units\n", - "required": "req_out", - "default": "kg" - }, - { - "key": 13, - "name": "density", - "typeId": "double", - "doc": "Initial volume or density of the recipe\n", - "required": "req_out", - "default": 0 - }, - { - "key": 14, - "name": "unit_d", - "typeId": "string", - "doc": "Units\n", - "required": "req_out", - "default": "kg\/m^3" - }, - { - "key": 15, - "name": "ss_area", - "typeId": "double", - "doc": "Specific surface area\n", - "required": "req_out", - "default": 0 - }, - { - "key": 16, - "name": "unit_a", - "typeId": "string", - "doc": "Units for area\n", - "required": "req_out", - "default": "m^2\/kg" - }, - { - "key": 17, - "name": "enthalpy", - "typeId": "double", - "doc": "Enthalpy content\n", - "required": "req_out" - }, - { - "key": 18, - "name": "unit_h", - "typeId": "string", - "doc": "Units of measurement for enthalpy\n", - "required": "req_out", - "default": "kJ\/kg" - }, - { - "key": 19, - "name": "heat_capacity", - "typeId": "double", - "doc": "Heat capacity of this consituent in J\/K\/kg\n", - "required": "req_out" - }, - { - "key": 20, - "name": "unit_cp", - "typeId": "string", - "required": "req_out", - "default": "J\/K\/kg" - }, - { - "key": 21, - "name": "pressure", - "typeId": "double", - "doc": "Total pressure P\n", - "required": "req_out", - "default": 0.1 - }, - { - "key": 22, - "name": "unit_p", - "typeId": "string", - "doc": "Units of pressure\n", - "required": "req_out", - "default": "MPa" - }, - { - "key": 23, - "name": "temperature", - "typeId": "double", - "doc": "Total temperature P\n", - "required": "req_out", - "default": 25 - }, - { - "key": 24, - "name": "unit_t", - "typeId": "string", - "doc": "Units of temperature\n", - "required": "req_out", - "default": "degC" - }, - { - "key": 27, - "name": "ingredients", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "ingredient.Ingredient" - } - }, - "doc": "can be constructed automatically using \"AddTo\" edges from ingredients\n", - "required": "req_out" - }, - { - "key": 29, - "name": "scalvals", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.ScalingValues" - }, - "doc": "Scaling values at the whole recipe level\n", - "required": "req_out" - }, - { - "key": 31, - "name": "bcObjectComputed", - "typeId": "bool", - "doc": "Indicator of calculation consistency\n", - "required": "req_out", - "default": 0 - }, - { - "key": 32, - "name": "bcObject", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "compound.bcObjectItem" - } - }, - "doc": "List of elements and their amounts for this recipe [ {\"Al\": 0.35}, {\"Ca\": 0.9} ...\n", - "required": "req_out", - "default": [ - { - "el": "O", - "am": 0, - "ma": 0 - } - ] - }, - { - "key": 33, - "name": "bcMass", - "typeId": "double", - "doc": "Mass of this rbcObject \"Mass\" in kg\/mol (calculated using the elements list)\n", - "required": "req_out", - "default": 0 - }, - { - "key": 35, - "name": "eqStateComputed", - "typeId": "bool", - "doc": "Indicator of equilibrium calculation consistency\n", - "required": "req_out", - "default": 0 - }, - { - "key": 41, - "name": "initialSpeciation", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "string", - "valueTypeId": "double" - }, - "doc": "for example \"Al+3\":1e-6, \"Al(OH)+2\": 4e-9, \"Al(OH)2+\": 3e-8, ...\n", - "required": "req_out" - }, - { - "key": 43, - "name": "sKinUpper", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "string", - "valueTypeId": "double" - }, - "doc": "Additional kinetic restrictions for species (name,value) - upper (from above)\n", - "required": "req_out" - }, - { - "key": 44, - "name": "sKinLower", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "string", - "valueTypeId": "double" - }, - "doc": "Additional kinetic restrictions for species - lower (from above)\n", - "required": "req_out" - }, - { - "key": 45, - "name": "pKinUpper", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "string", - "valueTypeId": "double" - }, - "doc": "Additional kinetic restrictions for phases - upper (from above)\n", - "required": "req_out" - }, - { - "key": 46, - "name": "pKinLower", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "string", - "valueTypeId": "double" - }, - "doc": "Additional kinetic restrictions for phases - lower (from above)\n", - "required": "req_out" - }, - { - "key": 49, - "name": "timeStamp", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.TimeStamp" - }, - "doc": "Timestamp of the last modification\n", - "required": "req_out" - }, - { - "key": 50, - "name": "datasources", - "typeId": "set", - "type": { - "typeId": "set", - "elemTypeId": "string" - }, - "doc": "Labels of datasource DB objects\n", - "required": "optional" - } - ] - }, - { - "name": "ChemEqSysRecipes", - "doc": "Definition of an array of chemical system recipes\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 2, - "name": "recipes", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "ChemEqSysRecipe" - } - }, - "doc": "List of CemGEMS chemical system recipes\n", - "required": "req_out" - } - ] - } - ], - "constants": [ - ], - "services": [ - ] -} diff --git a/Resources/data/schemas/composition.schema.json b/Resources/data/schemas/composition.schema.json deleted file mode 100644 index 7296de47..00000000 --- a/Resources/data/schemas/composition.schema.json +++ /dev/null @@ -1,339 +0,0 @@ -{ - "name": "composition", - "doc": "Apache Thrift IDL definition for the composition service interface\n", - "namespaces": { - "*": "composition" - }, - "includes": [ -"prop", -"element", -"substance" - ], - "enums": [ - ], - "typedefs": [ - { - "name": "Compositions", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "Composition" - } - }, - "doc": "Definition of compositions (composition array) type\n" - } - ], - "structs": [ - { - "name": "Composition", - "doc": "Description of composition (chemical species, chemical component)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "symbol", - "typeId": "string", - "doc": "Unique name\/ID of this composition e.g. \"pw-bentonite\"\n", - "required": "required" - }, - { - "key": 2, - "name": "name", - "typeId": "string", - "doc": "Name of the composition (e.g. \"bentonite porewater\")\n", - "required": "req_out" - }, - { - "key": 3, - "name": "elements", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "element.ElementInfo" - } - }, - "doc": "List of elements and their masses as basis of this composition\n", - "required": "req_out" - }, - { - "key": 5, - "name": "pco", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "string", - "valueTypeId": "double" - }, - "doc": "Composition in moles of elements (after calculation or from cformula if entered) as [ {\"Al\": 0.35}, {\"Ca\": 0.9} ... ]\n", - "required": "req_out" - }, - { - "key": 6, - "name": "cmMass", - "typeId": "double", - "doc": "Mass per 1 mole of this pco \"mM\" in kg\/mol (calculated using the elements list)\n", - "required": "req_out" - }, - { - "key": 7, - "name": "cformula", - "typeId": "string", - "doc": "Optionally: contents of pco generated as a single formula string\n", - "required": "req_out" - }, - { - "key": 11, - "name": "Moles", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "double", - "valueTypeId": "i32" - }, - "doc": "Input scaling values for various concentration scales, unit of measurement\n", - "required": "optional", - "default": { - "0": 0 - } - }, - { - "key": 12, - "name": "Ptotal", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "double", - "valueTypeId": "i32" - }, - "required": "optional", - "default": { - "100000": 2 - } - }, - { - "key": 13, - "name": "Mwater", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "double", - "valueTypeId": "i32" - }, - "required": "optional", - "default": { - "1": 5 - } - }, - { - "key": 14, - "name": "Vaqtotal", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "double", - "valueTypeId": "i32" - }, - "required": "optional", - "default": { - "0.001": 9 - } - }, - { - "key": 15, - "name": "Mass", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "double", - "valueTypeId": "i32" - }, - "required": "optional", - "default": { - "1": 5 - } - }, - { - "key": 16, - "name": "SurfMoles", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "double", - "valueTypeId": "i32" - }, - "required": "optional", - "default": { - "0.001": 0 - } - }, - { - "key": 17, - "name": "SurfMolal", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "double", - "valueTypeId": "i32" - }, - "required": "optional", - "default": { - "0.001": 3 - } - }, - { - "key": 18, - "name": "SurfArea", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "double", - "valueTypeId": "i32" - }, - "required": "optional", - "default": { - "1": 8 - } - }, - { - "key": 21, - "name": "qformulae", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.CompositionFormulaAmountArray" - }, - "doc": "Optionally: Input quantities of user-defined formulae to add, can also be formulae of substances\n", - "required": "optional" - }, - { - "key": 22, - "name": "qelements", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Optionally: Input amounts of elements to add, values in the same order as in the elements list\n", - "required": "optional", - "default": { - "name": "qe" - } - }, - { - "key": 24, - "name": "comment", - "typeId": "string", - "doc": "Comment e.g. who entered\/modified, ...\n", - "required": "optional", - "default": "comment (element)" - }, - { - "key": 25, - "name": "datasources", - "typeId": "set", - "type": { - "typeId": "set", - "elemTypeId": "string" - }, - "doc": "Labels of datasource DB objects\n", - "required": "optional" - }, - { - "key": 26, - "name": "time_stamp", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.TimeStamp" - }, - "doc": "Timestamp\n", - "required": "optional" - } - ] - }, - { - "name": "composdata", - "doc": "Work structure keeping the data to check\/calculate composition\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "Nelems", - "typeId": "i16", - "required": "req_out" - }, - { - "key": 2, - "name": "elems", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "required": "req_out" - }, - { - "key": 4, - "name": "Ncel", - "typeId": "i16", - "required": "req_out" - }, - { - "key": 5, - "name": "elams", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "double" - }, - "required": "req_out" - }, - { - "key": 7, - "name": "Nfus", - "typeId": "i16", - "required": "req_out" - }, - { - "key": 8, - "name": "fuams", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "double" - }, - "required": "req_out" - }, - { - "key": 10, - "name": "compos", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "double" - }, - "required": "req_out" - }, - { - "key": 11, - "name": "computed", - "typeId": "bool", - "required": "req_out", - "default": 0 - } - ] - } - ], - "constants": [ - ], - "services": [ - ] -} diff --git a/Resources/data/schemas/compound.schema.json b/Resources/data/schemas/compound.schema.json deleted file mode 100644 index 9f85ea63..00000000 --- a/Resources/data/schemas/compound.schema.json +++ /dev/null @@ -1,178 +0,0 @@ -{ - "name": "compound", - "doc": "Apache Thrift IDL definition of a formula compound for the recipe service interface\n", - "namespaces": { - "*": "compound" - }, - "includes": [ -"prop", -"element", -"substance" - ], - "enums": [ - ], - "typedefs": [ - ], - "structs": [ - { - "name": "bcObjectItem", - "doc": "Element of bcObject (bulk composition object)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "el", - "typeId": "string", - "doc": "Symbol of (chemical) element\n", - "required": "req_out" - }, - { - "key": 2, - "name": "am", - "typeId": "double", - "doc": "Amount (moles)\n", - "required": "req_out" - }, - { - "key": 3, - "name": "ma", - "typeId": "double", - "doc": "Mass (kg)\n", - "required": "req_out" - } - ] - }, - { - "name": "Compound", - "doc": "Description of a composition constituent\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "symbol", - "typeId": "string", - "doc": "Unique name\/ID of this compound e.g. \"SiO2\"\n", - "required": "required" - }, - { - "key": 2, - "name": "comment", - "typeId": "string", - "doc": "Full name of the compound (e.g. \"silicon dioxide compound\")\n", - "required": "req_out" - }, - { - "key": 3, - "name": "formula", - "typeId": "string", - "doc": "Formula of 1 mole of this compound e.g. Fe | Fe2O3 | Fe+2\n", - "required": "required" - }, - { - "key": 5, - "name": "reactionExtent", - "typeId": "double", - "doc": "Extent of reaction, i.e. mass fraction of constituent composition to equilibrate\n", - "required": "req_out", - "default": 1 - }, - { - "key": 7, - "name": "bcObjectComputed", - "typeId": "bool", - "doc": "Indicator of formula parsing and calculation consistency\n", - "required": "req_out", - "default": 0 - }, - { - "key": 8, - "name": "bcObject", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "bcObjectItem" - } - }, - "doc": "List of elements and their amounts as a basis of 1 mole of this compound composition\n", - "required": "req_out", - "default": [ - { - "el": "H", - "am": 1, - "ma": 1 - } - ] - }, - { - "key": 9, - "name": "bcMass", - "typeId": "double", - "doc": "Mass of 1 mole this bcObject \"Mass\" in kg\/mol (calculated from the formula)\n", - "required": "req_out", - "default": 0 - }, - { - "key": 10, - "name": "substance", - "typeId": "string", - "doc": "Optional _id of substance where the formula was taken\n", - "required": "optional" - }, - { - "key": 11, - "name": "timeStamp", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.TimeStamp" - }, - "doc": "Timestamp\n", - "required": "optional" - }, - { - "key": 12, - "name": "datasources", - "typeId": "set", - "type": { - "typeId": "set", - "elemTypeId": "string" - }, - "doc": "Labels of datasource DB objects\n", - "required": "optional" - } - ] - }, - { - "name": "Compounds", - "doc": "Definition of an array of compounds\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 2, - "name": "compounds", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "Compound" - } - }, - "doc": "List of chemical composition constituents\n", - "required": "req_out" - } - ] - } - ], - "constants": [ - ], - "services": [ - ] -} diff --git a/Resources/data/schemas/constituent.schema.json b/Resources/data/schemas/constituent.schema.json deleted file mode 100644 index 0b0aa8fa..00000000 --- a/Resources/data/schemas/constituent.schema.json +++ /dev/null @@ -1,219 +0,0 @@ -{ - "name": "constituent", - "doc": "Apache Thrift IDL definition of a constituent for the recipe service interface\n", - "namespaces": { - "*": "constituent" - }, - "includes": [ -"prop", -"element", -"substance", -"compound" - ], - "enums": [ - ], - "typedefs": [ - ], - "structs": [ - { - "name": "Constituent", - "doc": "Description of a composition constituent\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "symbol", - "typeId": "string", - "doc": "Unique name\/ID of this constituent e.g. \"pw-bentonite\"\n", - "required": "required" - }, - { - "key": 2, - "name": "comment", - "typeId": "string", - "doc": "Full name of the constituent (e.g. \"bentonite porewater\")\n", - "required": "req_out" - }, - { - "key": 3, - "name": "formula", - "typeId": "string", - "doc": "Optional shortcut formula of 1 mole of this constituent e.g. Fe | Fe2O3 | Fe+2\n", - "required": "req_out" - }, - { - "key": 5, - "name": "density", - "typeId": "double", - "doc": "Volume or density\n", - "required": "req_out", - "default": 0 - }, - { - "key": 6, - "name": "unit_d", - "typeId": "string", - "doc": "Units of density\n", - "required": "req_out", - "default": "kg\/m^3" - }, - { - "key": 7, - "name": "ss_area", - "typeId": "double", - "doc": "Specific surface area\n", - "required": "req_out", - "default": 0 - }, - { - "key": 8, - "name": "unit_a", - "typeId": "string", - "doc": "Units for area\n", - "required": "req_out", - "default": "m^2\/kg" - }, - { - "key": 9, - "name": "enthalpy", - "typeId": "double", - "doc": "Enthalpy content\n", - "required": "req_out" - }, - { - "key": 10, - "name": "unit_h", - "typeId": "string", - "doc": "Units of measurement for enthalpy\n", - "required": "req_out", - "default": "kJ\/kg" - }, - { - "key": 11, - "name": "heat_capacity", - "typeId": "double", - "doc": "Heat capacity of this consituent in J\/K\/kg\n", - "required": "req_out" - }, - { - "key": 12, - "name": "unit_cp", - "typeId": "string", - "required": "req_out", - "default": "J\/K\/kg" - }, - { - "key": 13, - "name": "reactionExtent", - "typeId": "double", - "doc": "Extent of reaction, i.e. mass fraction of constituent composition to equilibrate\n", - "required": "req_out", - "default": 1 - }, - { - "key": 15, - "name": "compounds", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "compound.Compound" - } - }, - "doc": "can be extended using \"AddTo\" edges from compounds or substances\n", - "required": "req_out" - }, - { - "key": 17, - "name": "bcComputed", - "typeId": "bool", - "doc": "Indicator of calculation consistency\n", - "required": "req_out", - "default": 0 - }, - { - "key": 18, - "name": "bcObject", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "compound.bcObjectItem" - } - }, - "doc": "List of elements and their masses as a basis of this constituent composition\n", - "required": "req_out", - "default": [ - { - "el": "O", - "am": 0, - "ma": 0 - } - ] - }, - { - "key": 19, - "name": "bcMass", - "typeId": "double", - "doc": "Mass of this cbcObject \"Mass\" in kg\/mol (calculated using the elements list)\n", - "required": "req_out", - "default": 0 - }, - { - "key": 21, - "name": "timeStamp", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.TimeStamp" - }, - "doc": "Timestamp\n", - "required": "optional" - }, - { - "key": 22, - "name": "datasources", - "typeId": "set", - "type": { - "typeId": "set", - "elemTypeId": "string" - }, - "doc": "Labels of datasource DB objects\n", - "required": "optional" - } - ] - }, - { - "name": "Constituents", - "doc": "Definition of an array of constituents\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 2, - "name": "constituents", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "Constituent" - } - }, - "doc": "List of chemical composition constituents\n", - "required": "req_out" - } - ] - } - ], - "constants": [ - ], - "services": [ - ] -} diff --git a/Resources/data/schemas/datasource.schema.json b/Resources/data/schemas/datasource.schema.json deleted file mode 100644 index ade3e42a..00000000 --- a/Resources/data/schemas/datasource.schema.json +++ /dev/null @@ -1,395 +0,0 @@ -{ - "name": "datasource", - "doc": "Apache Thrift IDL definition for the datasource service interface\n", - "namespaces": { - "*": "datasource" - }, - "includes": [ - ], - "enums": [ - { - "name": "BibType", - "doc": "Type of publication\/datasource according to bibtex documentation\n", - "members": [ - { - "name": "ARTICLE", - "value": 0, - "doc": "An article from a journal or magazine\n" - }, - { - "name": "BOOK", - "value": 1, - "doc": "A book with an explicit publisher\n" - }, - { - "name": "BOOKLET", - "value": 2, - "doc": "A work that is printed and bound, but without a named publisher or sponsoring institution\n" - }, - { - "name": "CONFERENCE", - "value": 3, - "doc": "The same as INPROCEEDINGS, included for Scribe compatibility\n" - }, - { - "name": "INBOOK", - "value": 4, - "doc": "A part of a book, which may be a chapter (or section or whatever) and\/or a range of pages\n" - }, - { - "name": "INCOLLECTION", - "value": 5, - "doc": "A part of a book having its own title\n" - }, - { - "name": "INPROCEEDINGS", - "value": 6, - "doc": "An article in a conference proceedings\n" - }, - { - "name": "MANUAL", - "value": 7, - "doc": "Technical documentation\n" - }, - { - "name": "MASTERTHESIS", - "value": 8, - "doc": "A Master thesis. Required fields: author, booktitle, school, year\n" - }, - { - "name": "MISC", - "value": 9, - "doc": "Use this type when nothing else fits. Required fields: none\n" - }, - { - "name": "PHDTHESIS", - "value": 10, - "doc": "A PhD thesis. Required fields: author, booktitle, school, year\n" - }, - { - "name": "PROCEEDINGS", - "value": 11, - "doc": "The proceedings of a conference. Required fields: title, year\n" - }, - { - "name": "TECHREPORT", - "value": 12, - "doc": "A report published by a school or other institution, usually numbered within a series\n" - }, - { - "name": "UNPUBLISHED", - "value": 13, - "doc": "A document having an author and booktitle, but not formally published\n" - }, - { - "name": "RESEARCHNOTE", - "value": 14, - "doc": "Preliminary research note. Required fields: none\n" - }, - { - "name": "PREPRINT", - "value": 15, - "doc": "Preliminary publication. Required fields: none\n" - } - ] - } - ], - "typedefs": [ - ], - "structs": [ - { - "name": "DataSource", - "doc": "Description of data source following the OKFN bibjson schema, with bibtex schema extensions\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "shortname", - "typeId": "string", - "doc": "Short name that is unique within all datasource records, e.g. 2012a_ALA_BOR\n", - "required": "required" - }, - { - "key": 2, - "name": "year", - "typeId": "string", - "doc": "Year of publication\n", - "required": "required" - }, - { - "key": 3, - "name": "author", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "List of author name strings\n", - "required": "req_out", - "default": [ - "Author1, B.C." - ] - }, - { - "key": 5, - "name": "bibliographic_type", - "class": "BibType", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Bibliographic type, as found in bibtex: validate with class BibType\n", - "required": "req_out", - "default": { - "0": "ARTICLE" - } - }, - { - "key": 6, - "name": "title", - "typeId": "string", - "doc": "Title (of a journal paper)\n", - "required": "req_out", - "default": "title" - }, - { - "key": 7, - "name": "journal", - "typeId": "string", - "doc": "Journal title\n", - "required": "req_out", - "default": "journal" - }, - { - "key": 8, - "name": "volume", - "typeId": "string", - "doc": "Journal or book volume\n", - "required": "req_out", - "default": "volume" - }, - { - "key": 9, - "name": "number", - "typeId": "string", - "doc": "Number of a journal issue\n", - "required": "req_out" - }, - { - "key": 10, - "name": "month", - "typeId": "string", - "doc": "Month of a journal issue\n", - "required": "req_out" - }, - { - "key": 11, - "name": "pages", - "typeId": "string", - "doc": "Pages\n", - "required": "req_out", - "default": "pages" - }, - { - "key": 13, - "name": "booktitle", - "typeId": "string", - "doc": "Book title\n", - "required": "req_out" - }, - { - "key": 14, - "name": "chapter", - "typeId": "string", - "doc": "Chapter number\n", - "required": "optional" - }, - { - "key": 15, - "name": "edition", - "typeId": "string", - "doc": "Book edition\n", - "required": "optional" - }, - { - "key": 16, - "name": "series", - "typeId": "string", - "doc": "Book series\n", - "required": "optional" - }, - { - "key": 17, - "name": "editor", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "Book editors\n", - "required": "optional" - }, - { - "key": 18, - "name": "publisher", - "typeId": "string", - "doc": "Book publisher\n", - "required": "optional" - }, - { - "key": 19, - "name": "how_published", - "typeId": "string", - "doc": "Some info on how a strange publication has been published\n", - "required": "optional" - }, - { - "key": 20, - "name": "university", - "typeId": "string", - "doc": "University for thesis\n", - "required": "optional" - }, - { - "key": 21, - "name": "institution", - "typeId": "string", - "doc": "Institution for reports, preprints\n", - "required": "optional" - }, - { - "key": 22, - "name": "organization", - "typeId": "string", - "doc": "Organization\n", - "required": "optional" - }, - { - "key": 23, - "name": "identifiers", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "string", - "valueTypeId": "string" - }, - "doc": "Bibliographic identifiers e.g. :, :, :> ...\n", - "required": "optional" - }, - { - "key": 24, - "name": "links", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "string", - "valueTypeId": "string" - }, - "doc": "Map of link objects relevant to this record\n", - "required": "optional" - }, - { - "key": 25, - "name": "uuid", - "typeId": "string", - "doc": "Universally unique identification key, created with this record\n", - "required": "optional" - }, - { - "key": 26, - "name": "collection", - "typeId": "set", - "type": { - "typeId": "set", - "elemTypeId": "string" - }, - "doc": "Collection of books this record belongs to\n", - "required": "optional" - }, - { - "key": 27, - "name": "annotation", - "typeId": "string", - "doc": "Annotation, not in OKFN but in bibtex schema\n", - "required": "optional" - }, - { - "key": 28, - "name": "note", - "typeId": "string", - "doc": "Note, in bibtex schema\n", - "required": "optional" - }, - { - "key": 29, - "name": "address", - "typeId": "string", - "doc": "Address, in bibtex schema\n", - "required": "optional" - }, - { - "key": 30, - "name": "crossref", - "typeId": "string", - "doc": "Crossreference, in bibtex schema\n", - "required": "optional" - }, - { - "key": 31, - "name": "key", - "typeId": "string", - "doc": "Key, in bibtex schema\n", - "required": "optional" - }, - { - "key": 32, - "name": "abstracttext", - "typeId": "string", - "doc": "Abstract in bibtex schema, thrift does not allow the use of abstract\n", - "required": "optional" - }, - { - "key": 33, - "name": "keywords", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "List of reference keywords\n", - "required": "optional" - } - ] - }, - { - "name": "DataSources", - "doc": "Definition of a list of data sources\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 2, - "name": "datasources", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "DataSource" - } - }, - "doc": "List of data sources and bibliographic references\n", - "required": "req_out" - } - ] - } - ], - "constants": [ - ], - "services": [ - ] -} diff --git a/Resources/data/schemas/docpages.schema.json b/Resources/data/schemas/docpages.schema.json deleted file mode 100644 index 4f7b2bf3..00000000 --- a/Resources/data/schemas/docpages.schema.json +++ /dev/null @@ -1,102 +0,0 @@ -{ - "name": "docpages", - "doc": "Apache Thrift IDL definition for the query service interface\n", - "namespaces": { - "*": "docpages" - }, - "includes": [ - ], - "enums": [ - { - "name": "DocFileTypes", - "doc": "Types of Help files\n", - "members": [ - { - "name": "Markdown", - "value": 0, - "doc": "Markdown text file\n" - }, - { - "name": "Image", - "value": 1, - "doc": "Image binary file\n" - } - ] - } - ], - "typedefs": [ - ], - "structs": [ - { - "name": "DocPages", - "doc": "description of Help record ( Markdown or image file )\n", - "isException": false, - "isUnion": false, - "to_select": [ "4", "5", "6", "1" ], - "to_key": [ "4", "5" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this help record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of this record within the impex collection (part of _id)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Code of revision (changed by the system at every update)\n", - "required": "required" - }, - { - "key": 4, - "name": "name", - "typeId": "string", - "doc": "name of file (used as key field)\n", - "required": "required" - }, - { - "key": 5, - "name": "ext", - "typeId": "string", - "doc": "extension of file (used as key field)\n", - "required": "required" - }, - { - "key": 6, - "name": "type", - "typeId": "i32", - "doc": "type of content (used as key field)\n", - "class": "DocFileTypes", - "required": "required" - }, - { - "key": 7, - "name": "markdown", - "typeId": "string", - "doc": "markdown content\n", - "required": "req_out" - }, - { - "key": 8, - "name": "image", - "typeId": "string", - "doc": "image content\n", - "required": "req_out" - } - ] - } - ], - "constants": [ - ], - "services": [ - ] -} diff --git a/Resources/data/schemas/element.schema.json b/Resources/data/schemas/element.schema.json deleted file mode 100644 index 0f1625ff..00000000 --- a/Resources/data/schemas/element.schema.json +++ /dev/null @@ -1,588 +0,0 @@ -{ - "name": "element", - "doc": "Apache Thrift IDL definition for the element service interface\n", - "namespaces": { - "*": "element" - }, - "includes": [ -"prop" - ], - "enums": [ - { - "name": "ElementClass", - "doc": "Classes (types) of elements (independent components)\n", - "members": [ - { - "name": "ELEMENT", - "value": 0, - "doc": "Chemical element\n" - }, - { - "name": "ISOTOPE", - "value": 1, - "doc": "Isotope of chemical element\n" - }, - { - "name": "LIGAND", - "value": 2, - "doc": "Ligand such as Oxa (oxalate)\n" - }, - { - "name": "SURFSITE", - "value": 3, - "doc": "Surface site in adsorption models\n" - }, - { - "name": "CHARGE", - "value": 4, - "doc": "Electrical charge\n" - }, - { - "name": "OTHER_EC", - "value": 5, - "doc": "Other type of independent component\n" - } - ] - }, - { - "name": "DecayType", - "doc": "Types of radioactive decay\n", - "members": [ - { - "name": "STABLE", - "value": 0, - "doc": "Stable isotope (no decay)\n" - }, - { - "name": "ALPHA", - "value": 1, - "doc": "Alpha decay\n" - }, - { - "name": "BETA", - "value": 2, - "doc": "Beta decay\n" - }, - { - "name": "GAMMA", - "value": 3, - "doc": "Gamma decay\n" - }, - { - "name": "POSITRON", - "value": 4, - "doc": "Positron decay\n" - }, - { - "name": "NEUTRON", - "value": 5, - "doc": "Neutron decay\n" - }, - { - "name": "PROTON", - "value": 6, - "doc": "Proton decay\n" - }, - { - "name": "OTHER_DT", - "value": 7, - "doc": "Other type of decay\n" - }, - { - "name": "FISSION", - "value": 8, - "doc": "Fission\n" - }, - { - "name": "TRANSMUTATION", - "value": 9, - "doc": "Transmutation\n" - } - ] - }, - { - "name": "SourceTDB", - "doc": "Codes of source thermodynamic data bases for substances and reactions\n", - "members": [ - { - "name": "CODATA", - "value": 0, - "doc": "CODATA 1989\n" - }, - { - "name": "NIST", - "value": 1, - "doc": "NIST Wagman et al. 1989\n" - }, - { - "name": "SUPCRT", - "value": 2, - "doc": "SUPCRT slop98.dat\n" - }, - { - "name": "HOLLAND_POWELL", - "value": 3, - "doc": "Holland and Powell 2001\n" - }, - { - "name": "BERMAN_BROWN", - "value": 4, - "doc": "Berman and Brown 1998\n" - }, - { - "name": "ROBIE_HEMINGWAY", - "value": 5, - "doc": "Robie and Hemingway 1995\n" - }, - { - "name": "GOTTSCHALK", - "value": 6, - "doc": "Gottschalk 1999\n" - }, - { - "name": "BABUSHKIN", - "value": 7, - "doc": "Babushkin et al. 1986\n" - }, - { - "name": "KUBASCHEWSKI", - "value": 8, - "doc": "Kubaschewski er al. 1993\n" - }, - { - "name": "KONINGS", - "value": 9, - "doc": "Konings et al. 1998\n" - }, - { - "name": "REID_GL", - "value": 10, - "doc": "Reid et al. 1987 (gases and liquids)\n" - }, - { - "name": "NEA", - "value": 11, - "doc": "NEA TDB Project\n" - }, - { - "name": "THEREDA", - "value": 12, - "doc": "THEREDA Project\n" - }, - { - "name": "THERMODDEM", - "value": 13, - "doc": "THERMODDEM Project\n" - }, - { - "name": "SMITH_MARTELL", - "value": 14, - "doc": "Smith and Martell 1978\n" - }, - { - "name": "PSI_NAGRA", - "value": 15, - "doc": "PSI-Nagra TDB 12\/07\n" - }, - { - "name": "MOIETY", - "value": 16, - "doc": "Moiety in multi-site phase models (no TDB source)\n" - }, - { - "name": "HKF_DEW", - "value": 17, - "doc": "Sverjensky et al. 2014\n" - }, - { - "name": "MINES", - "value": 18, - "doc": "Mines16 TDB Gysi, 2016\n" - }, - { - "name": "AQ17", - "value": 19, - "doc": "Aq17 TDB Miron et al., 2017\n" - }, - { - "name": "CEMDATA18", - "value": 20, - "doc": "CEMDATA 18 Lothenbach et al., 2018\n" - }, - { - "name": "SUPCRT07", - "value": 21, - "doc": "SUPCRT 2007 slop07.dat\n" - }, - { - "name": "HERACLES", - "value": 22, - "doc": "Heracles\n" - }, - { - "name": "WORK1", - "value": 1001, - "doc": "SourceTDB code for data under work\/development\n" - }, - { - "name": "WORK2", - "value": 1002, - "doc": "SourceTDB code for data under work\/development\n" - }, - { - "name": "WORK3", - "value": 1003, - "doc": "SourceTDB code for data under work\/development\n" - }, - { - "name": "WORK4", - "value": 1004, - "doc": "SourceTDB code for data under work\/development\n" - }, - { - "name": "OTHER", - "value": 1111, - "doc": "Other data sources\n" - } - ] - } - ], - "typedefs": [ - ], - "structs": [ - { - "name": "Radioactivity", - "doc": "Radioactivity properties of an isotope\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "decay_type", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Decay type: enum validated with class DecayType\n", - "class": "DecayType", - "required": "req_out" - }, - { - "key": 2, - "name": "half_life_lambda", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Time of decay of half amount in s; 0 if unknown\n", - "required": "req_out" - }, - { - "key": 4, - "name": "daughters", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "Symbols of daugther (product) isotopes\n", - "required": "req_out" - }, - { - "key": 5, - "name": "isotope_masses", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "i32" - }, - "doc": "Mass of daughter isotopes (at. units)\n", - "required": "req_out" - } - ] - }, - { - "name": "Element", - "doc": "description of element (independent component)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "symbol", - "typeId": "string", - "doc": "Element symbol max 6 characters, 1st uppercase, other lowercase letters\n", - "required": "required" - }, - { - "key": 2, - "name": "isotope_mass", - "typeId": "i32", - "doc": "Isotope mass or 0 if natural mixture of isotopes\n", - "required": "required" - }, - { - "key": 3, - "name": "name", - "typeId": "string", - "doc": "Element name e.g. Oxygen\n", - "required": "required" - }, - { - "key": 4, - "name": "atomic_mass", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Atomic mass of this element, relative to mass of 1\/12 mol of 12C isotope\n", - "required": "req_out" - }, - { - "key": 5, - "name": "class_", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Class of element: enum validated with class ElementClass\n", - "class": "ElementClass", - "required": "req_out", - "default": { - "5": "OTHER_EC" - } - }, - { - "key": 6, - "name": "aggregate_state", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "(Standard) state of this element: enum validated with class AggregateState\n", - "class": "AggregateState", - "required": "req_out" - }, - { - "key": 8, - "name": "isotope_abundance", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Isotope abundance fraction, default 1.0\n", - "required": "req_out" - }, - { - "key": 9, - "name": "entropy", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Standard absolute entropy J\/K\/mol per atom per mole\n", - "required": "req_out" - }, - { - "key": 10, - "name": "volume", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Standard volume cm3 per atom per mole\n", - "required": "req_out" - }, - { - "key": 11, - "name": "heat_capacity", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Standard heat capacity J\/K\/mol\n", - "required": "req_out" - }, - { - "key": 12, - "name": "valences", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Possible valences for this element - at least one value\n", - "required": "optional" - }, - { - "key": 13, - "name": "number", - "typeId": "i16", - "doc": "Number in periodic table; 0 if not a true chemical element\n", - "required": "optional" - }, - { - "key": 14, - "name": "sourcetdb", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Source TDB: enum validated with class SourceTDB\n", - "class": "SourceTDB", - "required": "optional" - }, - { - "key": 15, - "name": "formula", - "typeId": "string", - "doc": "Standard state substance formula, in elements only e.g. Fe for iron; H2 for hydrogen\n", - "required": "optional" - }, - { - "key": 16, - "name": "substance", - "typeId": "string", - "doc": "Symbol of pure substance which is standard state for this element (in substances database)\n", - "required": "optional" - }, - { - "key": 17, - "name": "comment", - "typeId": "string", - "doc": "E.g. who entered\/modified, ...\n", - "required": "optional" - }, - { - "key": 18, - "name": "datasources", - "typeId": "set", - "type": { - "typeId": "set", - "elemTypeId": "string" - }, - "doc": "Short names of datasource database objects\n", - "required": "optional" - }, - { - "key": 19, - "name": "radioactivity", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Radioactivity" - }, - "doc": "Radioactivity properties\n", - "required": "optional" - }, - { - "key": 20, - "name": "time_stamp", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.TimeStamp" - }, - "doc": "Time stamp when the record was created or modified\n", - "required": "optional" - }, - { - "key": 2001, - "name": "temp_import", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "Field for storing temporary values needed during import script\n", - "required": "optional" - } - ] - }, - { - "name": "ElementInfo", - "doc": "Short description of element (independent component)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "symbol", - "typeId": "string", - "doc": "Element symbol max 6 characters, 1st uppercase, other lowercase letters\n", - "required": "req_out" - }, - { - "key": 2, - "name": "isotope_mass", - "typeId": "i32", - "doc": "Isotope mass or 0 if natural mixture of isotopes\n", - "required": "req_out" - }, - { - "key": 3, - "name": "class_", - "typeId": "i32", - "doc": "Class of element: enum validated with class ElementClass\n", - "class": "ElementClass", - "required": "req_out" - }, - { - "key": 4, - "name": "atomic_mass", - "typeId": "double", - "doc": "Mass (in kg) per mole of this element - to compute molar masses\n", - "required": "req_out" - }, - { - "key": 5, - "name": "atomic_charge", - "typeId": "double", - "doc": "Default valence charge of this element - to compute formula charge\n", - "required": "req_out" - } - ] - }, - { - "name": "Elements", - "doc": "Definition of an array of elements\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 2, - "name": "elements", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "Element" - } - }, - "doc": "List of chemical elements\n", - "required": "req_out" - } - ] - } - ], - "constants": [ - ], - "services": [ - ] -} diff --git a/Resources/data/schemas/impex.schema.json b/Resources/data/schemas/impex.schema.json deleted file mode 100644 index f99aff8e..00000000 --- a/Resources/data/schemas/impex.schema.json +++ /dev/null @@ -1,971 +0,0 @@ -{ - "name": "impex", - "doc": "Apache Thrift IDL definition for text import-export interfaces\n", - "namespaces": { - "*": "impex" - }, - "includes": [ - ], - "enums": [ - { - "name": "DirectionType", - "doc": "Classes of direction types\n", - "members": [ - { - "name": "IMPORT", - "value": 0, - "doc": "import\n" - }, - { - "name": "EXPORT", - "value": 1, - "doc": "export\n" - } - ] - } - ], - "typedefs": [ - ], - "structs": [ - { - "name": "FormatValue", - "doc": "Definition of the data value format in imported\/exported file\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "format", - "typeId": "string", - "doc": "Format scanf\/printf (to string first): \"%s\" | \"in\" | \"out\" | \"endl\" | \"txel\" | \"txkw\"; \"in\" | \"out\" | \"endl\" for stream input\n", - "required": "req_out" - }, - { - "key": 2, - "name": "factor", - "typeId": "double", - "doc": "Factor != 0, default 1; Each num.value is multiplied (import) or divided (export) by factor\n", - "required": "optional" - }, - { - "key": 3, - "name": "increment", - "typeId": "double", - "doc": "Increment, default 0; added to each numerical value (import) or subtracted from (export)\n", - "required": "optional" - } - ] - }, - { - "name": "FormatKeyword", - "doc": "Format to read\/print keywords in key-value pair file\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "format", - "typeId": "string", - "doc": "scanf\/printf format for keyword\n", - "required": "req_out" - }, - { - "key": 2, - "name": "delim_begin", - "typeId": "string", - "doc": "delimiter for keyword begin e.g. \"\\\"\" | \"<\" | \"\"\n", - "required": "optional" - }, - { - "key": 3, - "name": "delim_end", - "typeId": "string", - "doc": "delimiter for keyword end e.g. \"\\\"\" | \">\" | \"\"\n", - "required": "optional" - } - ] - }, - { - "name": "DataType", - "doc": "Type of object from the imported or exported file (for use in keyword lookup list or map)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "datatype", - "typeId": "string", - "doc": "Basis type \"string\" | \"float\" | \"double\" | \"i16\" | \"i32\" | \"bool\" | ...\n", - "required": "req_out" - }, - { - "key": 2, - "name": "organization", - "typeId": "string", - "doc": "Organization: \"\" | \"list\" | \"set\" | \"map\" | \"group\" | \"embedded\" | ...\n", - "required": "req_out" - } - ] - }, - { - "name": "DataObject", - "doc": "Thrift key of data object \"8\" or \"3.8\" or \"2.3.8\" or \"\" to ignore (import); any string not starting from a digit as comment (export)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "field", - "typeId": "string", - "doc": "Either Thrift key or name of the data field in recursive form (s e.g. \"4.3.1\" or name1.name2 )\n", - "required": "req_out" - }, - { - "key": 2, - "name": "ignore", - "typeId": "bool", - "doc": "Set to true if the corresponding value in file has to be ignored (default: false)\n", - "required": "optional" - }, - { - "key": 3, - "name": "script", - "typeId": "string", - "doc": "Default \"\" or contains lua script for operation on data values in block\n", - "required": "optional" - }, - { - "key": 4, - "name": "convert", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "string", - "valueTypeId": "string" - }, - "doc": "Default empty or contains pair(s) read_value : saved_value e.g. \"e\": \"4\" (usually for setting enum values)\n", - "required": "optional" - } - ] - }, - { - "name": "Separators", - "doc": "Definition of value, line, row, block, comment, end-of-data separators\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "v_sep", - "typeId": "string", - "doc": "Value separator (for arrays) \" \" | \",\" | \"\\t\" | \"integer\" (=fixed field width)\n", - "required": "req_out" - }, - { - "key": 2, - "name": "l_sep", - "typeId": "string", - "doc": "Line separator \"\\n\" ...\n", - "required": "req_out" - }, - { - "key": 3, - "name": "r_sep", - "typeId": "string", - "doc": "Row separator (table), \"\\n\" ...\n", - "required": "optional" - }, - { - "key": 4, - "name": "c_head", - "typeId": "string", - "doc": "Head comment separator e.g. \"#\" or '%'\n", - "required": "optional" - }, - { - "key": 5, - "name": "c_end", - "typeId": "string", - "doc": "End comment separator e.g. \"\\n\"\n", - "required": "optional" - }, - { - "key": 6, - "name": "eod", - "typeId": "string", - "doc": "string indicating end of data (as list of blocks) in file or \"\" as default ']' (end of file)\n", - "required": "optional" - }, - { - "key": 7, - "name": "encoding", - "typeId": "string", - "doc": "encoding (\"\" for standard system encoding)\n", - "required": "optional" - }, - { - "key": 8, - "name": "str_delim", - "typeId": "string", - "doc": "Delimiter for strings - default \"\\\"\"\n", - "required": "optional" - }, - { - "key": 9, - "name": "bod", - "typeId": "string", - "doc": "string indicating begin of data (as list of blocks) in file or \"\" as default '['\n", - "required": "optional" - } - ] - }, - { - "name": "FormatBlock", - "doc": "Text block format in file corresponding to one database document (record)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "defaults", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "string", - "valueTypeId": "string" - }, - "doc": "Default Key, Value pairs to DOM (import) or to output (export)\n", - "required": "req_out" - }, - { - "key": 2, - "name": "pairs", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "string", - "valueTypeId": "struct", - "valueType": { - "typeId": "struct", - "class": "DataType" - } - }, - "doc": "Lookup map of keyword-value pair format\n", - "required": "req_out" - }, - { - "key": 3, - "name": "matches", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "string", - "valueTypeId": "struct", - "valueType": { - "typeId": "struct", - "class": "DataObject" - } - }, - "doc": ">=1 keywd, DataObject pairs connecting the block of data in file with DOM.\n", - "required": "required" - }, - { - "key": 4, - "name": "script", - "typeId": "string", - "doc": "Default \"\" or contains lua script for operation on data values in full DOM\n", - "required": "optional" - } - ] - }, - { - "name": "FormatTextFile", - "doc": "Definition of text data file format\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "block", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "FormatBlock" - }, - "doc": "Format definition for one or more blocks for data records - default 1 block\n", - "required": "required" - }, - { - "key": 2, - "name": "lines", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "Will be format lines list\n", - "required": "required" - }, - { - "key": 3, - "name": "label", - "typeId": "string", - "doc": "Label of data type (vertex type), e.g. \"datasource\", \"element\" ...\n", - "required": "required" - }, - { - "key": 4, - "name": "separs", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Separators" - }, - "doc": "Definition of value, line, row, block, comment, end-of-data separators\n", - "required": "req_out" - }, - { - "key": 5, - "name": "comment", - "typeId": "string", - "doc": "Export: the whole comment text; Import: the comment begin markup string (to skip until endl)\n", - "required": "optional" - }, - { - "key": 6, - "name": "file_name", - "typeId": "string", - "doc": "File name or \"console\" for export\n", - "required": "optional" - }, - { - "key": 7, - "name": "Nblocks", - "typeId": "i32", - "doc": "number of data block in file >=1, 0 if unknown\n", - "required": "optional" - }, - { - "key": 8, - "name": "Nlines", - "typeId": "i32", - "doc": "number of text lines in file (>=1), 0 if unknown\n", - "required": "optional" - }, - { - "key": 9, - "name": "Nchars", - "typeId": "i32", - "doc": "total number of characters in file, 0 if unknown\n", - "required": "optional" - }, - { - "key": 10, - "name": "direction", - "typeId": "i32", - "doc": "direction\n", - "class": "DirectionType", - "required": "req_out" - } - ] - }, - { - "name": "FormatKeyValue", - "doc": "Definition of key-value import\/export format\nWe use Regular Expression in case of import and Print Format in case of export.\nUse names \"head0\", ..., \"headN\", \"end0\", ..., \"endN\" to import\/export data from\/to head and end part\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "head_regexp", - "typeId": "string", - "doc": "Head of Block: \"\\\\s*([^\\\\s]+)\\\\s*;\\\\s*(([\\\\w\\\\t \\\\+\\\\-\\\\(\\\\):\\\\.]+)\\\\s*=\\\\s*([^;]+))\" (import)\nor \"\\n%head0\\n\\t%head1\\n\" (export)\n", - "required": "required" - }, - { - "key": 2, - "name": "end_regexp", - "typeId": "string", - "doc": "End of Block: \"([^\\n]+)\" (import) or \"%end0\\n\" (export)\n", - "required": "required" - }, - { - "key": 3, - "name": "key_regexp", - "typeId": "string", - "doc": "Keyword: \"\\\\s*;\\\\s*\\\\-{0,1}([a-zA-Z]\\\\w*)\\\\s*\" (import) or \"\\t-%key\\t\" (export)\n", - "required": "required" - }, - { - "key": 4, - "name": "value_regexp", - "typeId": "string", - "doc": "Data Value(s): \"\\\\s*([^#\\\\n;]*)\" (import) or \"%value\" (export)\n", - "required": "req_out" - }, - { - "key": 5, - "name": "value_next", - "typeId": "string", - "doc": "Key-Value pair end delimiter (used if empty value_regexp or export mode )\n", - "required": "req_out", - "default": "\n" - }, - { - "key": 6, - "name": "value_token_regexp", - "typeId": "string", - "doc": "Regular Expression to iterate over matches (used to convert value to string list or if export mode )\n", - "required": "optional", - "default": " " - }, - { - "key": 7, - "name": "comment_regexp", - "typeId": "string", - "doc": "Regular Expression for skip comments\n", - "required": "optional" - }, - { - "key": 8, - "name": "Ndata", - "typeId": "i32", - "doc": "number of data items per block (0 if not set)\n", - "required": "optional" - }, - { - "key": 9, - "name": "strvalue_exp", - "typeId": "string", - "doc": "Data String Value(s): only for export \"\\'%value\\'\"\n", - "required": "req_out" - }, - { - "key": 10, - "name": "key_order", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "Keyword order list: only for export\n", - "required": "optional" - } - ] - }, - { - "name": "FormatKeyValueFile", - "doc": "Definition of text file with key-value pair data\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "block", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "FormatBlock" - }, - "doc": "Format for one or more blocks for data records\n", - "required": "required" - }, - { - "key": 2, - "name": "format", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "FormatKeyValue" - }, - "doc": "Definition of key-value block in file\n", - "required": "required" - }, - { - "key": 3, - "name": "renderer", - "typeId": "string", - "doc": "Rendering syntax for the foreign key-value file \"GEMS3K\" | \"BIB\" | \"RIS\" | ...\n", - "required": "required" - }, - { - "key": 4, - "name": "label", - "typeId": "string", - "doc": "Label of data type (vertex type), e.g. \"datasource\", \"element\" ...\n", - "required": "required" - }, - { - "key": 5, - "name": "separators", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Separators" - }, - "doc": "Definition of value, line, row, block, comment, end-of-data separators\n", - "required": "req_out" - }, - { - "key": 6, - "name": "comment", - "typeId": "string", - "doc": "Export: the whole comment text; Import: the comment begin markup string (to skip until endl)\n", - "required": "optional" - }, - { - "key": 7, - "name": "fname", - "typeId": "string", - "doc": "File name or \"console\" for export\n", - "required": "optional" - }, - { - "key": 8, - "name": "Nblocks", - "typeId": "i32", - "doc": "number of data blocks (records) >=1, 0 if unknown\n", - "required": "optional" - }, - { - "key": 9, - "name": "Nlines", - "typeId": "i32", - "doc": "total number of text lines in the file, 0 if unknown\n", - "required": "optional" - }, - { - "key": 10, - "name": "direction", - "typeId": "i32", - "doc": "direction\n", - "class": "DirectionType", - "required": "req_out" - } - ] - }, - { - "name": "FormatTable", - "doc": "Definition of of the table input format\nif defined colsizes, split by sizes\nif defined value_regexp, split used regexpr\notherwise split by columns delimiter\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "Nhcols", - "typeId": "i32", - "doc": "Number of header columns\n", - "required": "req_out" - }, - { - "key": 2, - "name": "Nhrows", - "typeId": "i32", - "doc": "Number of header rows (start porting from row )\n", - "required": "req_out" - }, - { - "key": 3, - "name": "headers", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "Names of header columns\n", - "required": "req_out" - }, - { - "key": 4, - "name": "rowend", - "typeId": "string", - "doc": "Row delimiter\n", - "required": "req_out", - "default": "\n" - }, - { - "key": 5, - "name": "rows_one_block", - "typeId": "i32", - "doc": "Number of lines in one block (could be more than one)\n", - "required": "req_out", - "default": 1 - }, - { - "key": 6, - "name": "row_header_regexp", - "typeId": "string", - "doc": "Regular expression: next block head in case the number of lines in one block is not fixed\n", - "required": "req_out", - "default": "" - }, - { - "key": 7, - "name": "colends", - "typeId": "string", - "doc": "Columns delimiters\n", - "required": "req_out", - "default": "\t " - }, - { - "key": 8, - "name": "usequotes", - "typeId": "bool", - "doc": "Quoted field as text\n", - "required": "req_out", - "default": 1 - }, - { - "key": 9, - "name": "usemore", - "typeId": "bool", - "doc": "Can be more than one delimiter between columns\n", - "required": "req_out", - "default": 0 - }, - { - "key": 10, - "name": "comment_regexp", - "typeId": "string", - "doc": "Regular Expression for skip comments\n", - "required": "optional" - }, - { - "key": 11, - "name": "row_size", - "typeId": "i32", - "doc": "Row size in case of using fixed colsizes\n", - "required": "optional", - "default": 0 - }, - { - "key": 12, - "name": "colsizes", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "i32" - }, - "doc": "Fixed size of columns for importing ( apply to all if one item )\n", - "required": "optional" - }, - { - "key": 13, - "name": "value_regexp", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "Regular Expression for column value(s) ( apply to all if one item )\n", - "required": "optional" - } - ] - }, - { - "name": "FormatTableFile", - "doc": "Definition of table text file format\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "block", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "FormatBlock" - }, - "doc": "Format for one or more blocks for data records\n", - "required": "required" - }, - { - "key": 2, - "name": "format", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "FormatTable" - }, - "doc": "Definition of key-value block in file\n", - "required": "required" - }, - { - "key": 3, - "name": "renderer", - "typeId": "string", - "doc": "Rendering syntax for the foreign key-value file \"GEMS3K\" | \"BIB\" | \"RIS\" | ...\n", - "required": "required" - }, - { - "key": 4, - "name": "label", - "typeId": "string", - "doc": "Label of data type (vertex type), e.g. \"datasource\", \"element\" ...\n", - "required": "required" - }, - { - "key": 5, - "name": "separators", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Separators" - }, - "doc": "Definition of value, line, row, block, comment, end-of-data separators\n", - "required": "req_out" - }, - { - "key": 6, - "name": "comment", - "typeId": "string", - "doc": "Export: the whole comment text; Import: the comment begin markup string (to skip until endl)\n", - "required": "optional" - }, - { - "key": 7, - "name": "fname", - "typeId": "string", - "doc": "File name or \"console\" for export\n", - "required": "optional" - }, - { - "key": 8, - "name": "Nblocks", - "typeId": "i32", - "doc": "number of data blocks (records) >=1, 0 if unknown\n", - "required": "optional" - }, - { - "key": 9, - "name": "Nlines", - "typeId": "i32", - "doc": "total number of text lines in the file, 0 if unknown\n", - "required": "optional" - }, - { - "key": 10, - "name": "direction", - "typeId": "i32", - "doc": "direction\n", - "class": "DirectionType", - "required": "req_out" - } - ] - }, - { - "name": "FormatStructDataFile", - "doc": "Definition of foreign structured data JSON\/YAML\/XML text file\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "block", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "FormatBlock" - }, - "doc": "Format for one or more blocks for data records\n", - "required": "required" - }, - { - "key": 2, - "name": "renderer", - "typeId": "string", - "doc": "Rendering syntax for the foreign file \"JSON\" | \"YAML\" | \"XML\" | ...\n", - "required": "required", - "default": "JSON" - }, - { - "key": 3, - "name": "label", - "typeId": "string", - "doc": "Label of data type (vertex type), e.g. \"datasource\", \"element\" ...\n", - "required": "required" - }, - { - "key": 4, - "name": "comment", - "typeId": "string", - "doc": "Definition of value, line, row, block, comment, end-of-data separators\n", - "required": "optional" - }, - { - "key": 5, - "name": "fname", - "typeId": "string", - "doc": "File name or \"console\" for export\n", - "required": "optional" - }, - { - "key": 6, - "name": "Nblocks", - "typeId": "i32", - "doc": "number of data blocks (records) >=1, 0 if unknown\n", - "required": "optional" - }, - { - "key": 7, - "name": "Nlines", - "typeId": "i32", - "doc": "total number of text lines in the file, 0 if unknown\n", - "required": "optional" - }, - { - "key": 10, - "name": "direction", - "typeId": "i32", - "doc": "direction\n", - "class": "DirectionType", - "required": "req_out" - } - ] - }, - { - "name": "FormatImportExportFile", - "doc": "Generalized import-export data file format\n", - "isException": false, - "isUnion": true, - "fields": [ - { - "key": 1, - "name": "ff_text", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "FormatTextFile" - }, - "doc": "Definition of text data file format\n", - "required": "optional" - }, - { - "key": 2, - "name": "ff_table", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "FormatTableFile" - }, - "doc": "Definition of data table file format\n", - "required": "optional" - }, - { - "key": 3, - "name": "ff_keyvalue", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "FormatKeyValueFile" - }, - "doc": "Definition of file format with key-value pair data\n", - "required": "optional" - }, - { - "key": 4, - "name": "ff_stdata", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "FormatStructDataFile" - }, - "doc": "Definition of foreign structured data JSON\/YAML\/XML file format\n", - "required": "optional" - } - ] - }, - { - "name": "ImpexFormat", - "doc": "description of import\/export format record\n", - "isException": false, - "to_select": [ "4", "5", "6", "7" ], - "to_key": [ "4" ], - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Handle (id) of this record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of this record within the impex collection (part of _id)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Code of revision (changed by the system at every update)\n", - "required": "required" - }, - { - "key": 4, - "name": "name", - "typeId": "string", - "doc": "short description\/keywd (used as key field)\n", - "required": "required" - }, - { - "key": 5, - "name": "impexschema", - "typeId": "string", - "doc": "impex schema\n", - "required": "required" - }, - { - "key": 6, - "name": "schema", - "typeId": "string", - "doc": "record schema\n", - "required": "req_out" - }, - { - "key": 7, - "name": "comment", - "typeId": "string", - "doc": "description of record\n", - "required": "req_out" - }, - { - "key": 8, - "name": "direction", - "typeId": "i32", - "doc": "direction\n", - "class": "DirectionType", - "required": "req_out" - }, - { - "key": 9, - "name": "impex", - "typeId": "string", - "doc": "format structure\n", - "required": "required" - }, - { - "key": 10, - "name": "format", - "typeId": "string", - "doc": "Id\/description of foreign file format\n", - "required": "optional" - }, - { - "key": 11, - "name": "extension", - "typeId": "string", - "doc": "file extension\n", - "required": "optional" - } - ] - } - ], - "constants": [ - ], - "services": [ - ] -} diff --git a/Resources/data/schemas/ingredient.schema.json b/Resources/data/schemas/ingredient.schema.json deleted file mode 100644 index 5bfd2e19..00000000 --- a/Resources/data/schemas/ingredient.schema.json +++ /dev/null @@ -1,238 +0,0 @@ -{ - "name": "ingredient", - "doc": "Apache Thrift IDL definition for the ingredient service interface\n", - "namespaces": { - "*": "ingredient" - }, - "includes": [ -"prop", -"element", -"substance", -"compound", -"constituent" - ], - "enums": [ - ], - "typedefs": [ - ], - "structs": [ - { - "name": "Ingredient", - "doc": "Description of ingredient = aggregated compositions (e.g. rocks from real minerals)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "symbol", - "typeId": "string", - "doc": "Ingredient symbol e.g. \"Solid\" or \"Aqueous\"\n", - "required": "required" - }, - { - "key": 2, - "name": "comment", - "typeId": "string", - "doc": "Name comment of the ingredient (e.g. \"Portland cement clinker powder\")\n", - "required": "req_out" - }, - { - "key": 3, - "name": "formula", - "typeId": "string", - "doc": "Optional shortcut formula of 1 mole of this constituent e.g. Fe | Fe2O3 | Fe+2\n", - "required": "req_out" - }, - { - "key": 4, - "name": "aggr_state", - "typeId": "i32", - "doc": "Assumed aggregate state of ingredient (class prop.AggregateState)\n", - "required": "req_out" - }, - { - "key": 5, - "name": "density", - "typeId": "double", - "doc": "Volume or density\n", - "required": "req_out", - "default": 0 - }, - { - "key": 6, - "name": "unit_d", - "typeId": "string", - "doc": "Units of density\n", - "required": "req_out", - "default": "kg\/m^3" - }, - { - "key": 7, - "name": "ss_area", - "typeId": "double", - "doc": "Specific surface area\n", - "required": "req_out", - "default": 0 - }, - { - "key": 8, - "name": "unit_a", - "typeId": "string", - "doc": "Units for area\n", - "required": "req_out", - "default": "m^2\/kg" - }, - { - "key": 9, - "name": "enthalpy", - "typeId": "double", - "doc": "Enthalpy content\n", - "required": "req_out" - }, - { - "key": 10, - "name": "unit_h", - "typeId": "string", - "doc": "Units of measurement for enthalpy\n", - "required": "req_out", - "default": "kJ\/kg" - }, - { - "key": 11, - "name": "heat_capacity", - "typeId": "double", - "doc": "Heat capacity of this consituent in J\/K\/kg\n", - "required": "req_out" - }, - { - "key": 12, - "name": "unit_cp", - "typeId": "string", - "required": "req_out", - "default": "J\/K\/kg" - }, - { - "key": 13, - "name": "reactionExtent", - "typeId": "double", - "doc": "Extent of reaction, i.e. mass fraction of constituent composition to equilibrate\n", - "required": "req_out", - "default": 1 - }, - { - "key": 15, - "name": "constituents", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "constituent.Constituent" - } - }, - "doc": "List of constituents (solid, gaseous, aqueous)\n", - "required": "req_out" - }, - { - "key": 16, - "name": "scalval", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.ScalingValues" - }, - "doc": "Scaling values at the whole ingredient level\n", - "required": "req_out" - }, - { - "key": 17, - "name": "bcObjectComputed", - "typeId": "bool", - "doc": "Indicator of calculation consistency\n", - "required": "req_out", - "default": 0 - }, - { - "key": 18, - "name": "bcObject", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "compound.bcObjectItem" - } - }, - "doc": "List of elements and their masses for this ingredient\n", - "required": "req_out", - "default": [ - { - "el": "O", - "am": 0, - "ma": 0 - } - ] - }, - { - "key": 19, - "name": "bcMass", - "typeId": "double", - "doc": "Mass of this ibcObject in kg\/mol (calculated using the elements list)\n", - "required": "req_out", - "default": 0 - }, - { - "key": 21, - "name": "timeStamp", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.TimeStamp" - }, - "doc": "Timestamp\n", - "required": "optional" - }, - { - "key": 22, - "name": "datasources", - "typeId": "set", - "type": { - "typeId": "set", - "elemTypeId": "string" - }, - "doc": "Labels of datasource DB objects\n", - "required": "optional" - } - ] - }, - { - "name": "Ingredients", - "doc": "Definition of an array of ingredients\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 2, - "name": "ingredients", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "Ingredient" - } - }, - "doc": "List of chemical composition ingredients\n", - "required": "req_out" - } - ] - } - ], - "constants": [ - ], - "services": [ - ] -} diff --git a/Resources/data/schemas/interaction.schema.json b/Resources/data/schemas/interaction.schema.json deleted file mode 100644 index 403f464b..00000000 --- a/Resources/data/schemas/interaction.schema.json +++ /dev/null @@ -1,589 +0,0 @@ -{ - "name": "interaction", - "doc": "Apache Thrift IDL definition for the interaction service interface\n", - "namespaces": { - "*": "interaction" - }, - "includes": [ -"prop", -"element", -"substance" - ], - "enums": [ - { - "name": "MixModel", - "doc": "Selection of models of mixing and non-ideal interactions\n", - "members": [ - { - "name": "M_PURE", - "value": 0, - "doc": "No mixing - this is a pure condensed phase\n" - }, - { - "name": "M_IDEAL", - "value": 1, - "doc": "Ideal mixing (also in sublattice solutions or in ion exchange)\n" - }, - { - "name": "M_REGULAR", - "value": 2, - "doc": "Regular (multicomponent) mixing\n" - }, - { - "name": "M_MARGULES2", - "value": 3, - "doc": "Margules (binary) subregular\n" - }, - { - "name": "M_MARGULES3", - "value": 4, - "doc": "Margules (ternary) subregular\n" - }, - { - "name": "M_REDKIST2", - "value": 5, - "doc": "Redlich-Kister (binary) model\n" - }, - { - "name": "M_GUGGENHEIM", - "value": 6, - "doc": "Guggenheim (0 to 3rd order) also Redlich-Kister\n" - }, - { - "name": "M_VANLAAR", - "value": 7, - "doc": "Van Laar mix model (melt, solid solution)\n" - }, - { - "name": "M_BERMAN", - "value": 8, - "doc": "Sublattice mixing after Berman\n" - }, - { - "name": "M_CEF", - "value": 9, - "doc": "Sublattice mixing after Hillert (Compound Energy Formalism)\n" - }, - { - "name": "M_WILSON", - "value": 10, - "doc": "Wilson model of mixing in liquids\n" - }, - { - "name": "M_VANDERVAALS", - "value": 11, - "doc": "Van der Vaals model of mixing\n" - }, - { - "name": "M_UNIQUAC", - "value": 12, - "doc": "UNIQUAC non-electrolyte mixing in liquids\n" - }, - { - "name": "M_NRTL", - "value": 13, - "doc": "NRTL non-electrolyte mixing in liquids\n" - }, - { - "name": "M_DONNAN", - "value": 14, - "doc": "Donnan volume polyelectrolyte model\n" - }, - { - "name": "M_NEM", - "value": 15, - "doc": "NEM - non-electrostatic SCM (competitive Langmuir)\n" - }, - { - "name": "M_CCM", - "value": 16, - "doc": "CCM - constant-capacitance SCM\n" - }, - { - "name": "M_DLM", - "value": 17, - "doc": "DLM - Diffuse double layer SCM\n" - }, - { - "name": "M_BSM", - "value": 18, - "doc": "BSM - Basic Stern model SCM\n" - }, - { - "name": "M_TLM", - "value": 19, - "doc": "TLM - Triple layer model SCM\n" - }, - { - "name": "M_CD3LM", - "value": 20, - "doc": "CD3LM - CD-MUSIC 3-layer SCM\n" - }, - { - "name": "M_BET", - "value": 21, - "doc": "BET - Brunauer-Emmet-Teller adsorption isotherm model\n" - }, - { - "name": "M_CGFLUID", - "value": 22, - "doc": "Churakov-Gottschalk\n" - }, - { - "name": "M_PRFLUID", - "value": 23, - "doc": "Peng-Robinson-Stryjek-Vera\n" - }, - { - "name": "M_PCSFLUID", - "value": 24, - "doc": "PCSAFT\n" - }, - { - "name": "M_STPFLUID", - "value": 25, - "doc": "Sterner-Pitzer\n" - }, - { - "name": "M_PR78FLUID", - "value": 26, - "doc": "Peng-Robinson 1978\n" - }, - { - "name": "M_CORKFLUID", - "value": 27, - "doc": "Compensated Redlich-Kwong\n" - }, - { - "name": "M_REFLUID", - "value": 28, - "doc": "Reference EOS fluid model (TBD)\n" - }, - { - "name": "M_SRFLUID", - "value": 29, - "doc": "Soave-Redlich-Kwong\n" - }, - { - "name": "M_AQSIT", - "value": 30, - "doc": "Aqueous electrolyte - SIT model\n" - }, - { - "name": "M_AQPITZER", - "value": 31, - "doc": "Aqueous electrolyte - Pitzer model\n" - }, - { - "name": "M_AQPITZERHMW", - "value": 32, - "doc": "Aqueous electrolyte - Pitzer HMW model\n" - }, - { - "name": "M_AQMSE", - "value": 33, - "doc": "Mixed-solvent electrolyte model (TBD)\n" - }, - { - "name": "M_AQEXUQ", - "value": 34, - "doc": "Extended UNIQUAC (Thomsen)\n" - }, - { - "name": "M_AQREXUQ", - "value": 35, - "doc": "Revised extended UNIQUAC (Hingerl et al.)\n" - }, - { - "name": "M_AQDAVIES", - "value": 36, - "doc": "Davies (0.3) model, truncated after I = 0.4 m\n" - }, - { - "name": "M_AQDH1", - "value": 37, - "doc": "Debye-Hueckel limiting law\n" - }, - { - "name": "M_AQDH2", - "value": 38, - "doc": "Debye-Hueckel 2-term\n" - }, - { - "name": "M_AQDH3", - "value": 39, - "doc": "Debye-Hueckel 3-term\n" - }, - { - "name": "M_AQDHH", - "value": 40, - "doc": "Debye-Hueckel 3-term (HKF)\n" - }, - { - "name": "M_AQDHS", - "value": 41, - "doc": "Debye-Hueckel 3-term (Shvarov)\n" - }, - { - "name": "M_OTHER", - "value": 101, - "doc": "Other type of specific-interaction model of mixing\n" - } - ] - }, - { - "name": "InteractionType", - "doc": "Interaction (parameter) type for some specific interaction models\n", - "members": [ - { - "name": "TYPICAL", - "value": 0, - "doc": "Typical format of interaction parameter for the respective model\n" - }, - { - "name": "PITZ_BETA", - "value": 1, - "doc": "Pitzer type beta parameter more will be added here\n" - }, - { - "name": "PITZ_THETA", - "value": 2, - "doc": " " - }, - { - "name": "PITZ_LAMBDA", - "value": 3, - "doc": " " - }, - { - "name": "PITZ_PSI", - "value": 4, - "doc": " " - }, - { - "name": "SIT", - "value": 5, - "doc": " " - } - ] - }, - { - "name": "ipMethod", - "doc": "Code of method of pressure, temperature, and ionic strength correction of the interaction parameters\n", - "members": [ - { - "name": "IP_CONSTANT", - "value": 100, - "doc": "Constant on P\n" - }, - { - "name": "IP_LINEAR", - "value": 101, - "doc": "Linear on P\n" - }, - { - "name": "IP_CUBIC", - "value": 102, - "doc": "Cubic on P\n" - }, - { - "name": "IP_OTHER", - "value": 199, - "doc": "Other on P\n" - }, - { - "name": "IT_CONSTANT", - "value": 200, - "doc": "Constant on T\n" - }, - { - "name": "IT_LINEAR", - "value": 201, - "doc": "Linear on T\n" - }, - { - "name": "IT_CUBIC", - "value": 202, - "doc": "Cubic on T\n" - }, - { - "name": "IT_POLYNOM", - "value": 204, - "doc": "Polynomial with ln on P\n" - }, - { - "name": "IT_PITZER", - "value": 205, - "doc": "f(T)=A+B*(1/T-1/298.15)+C*ln(T/298.15)+D*(T-298.15)+E*(T^2-298.15^2)\n" - }, - { - "name": "IT_OTHER", - "value": 299, - "doc": "Other on T\n" - }, - { - "name": "IS_CONSTANT", - "value": 300, - "doc": "Constant on IS\n" - }, - { - "name": "IS_LINEAR", - "value": 301, - "doc": "Linear on IS\n" - }, - { - "name": "IS_OTHER", - "value": 399, - "doc": "Other on IS\n" - } - ] - } - ], - "typedefs": [ - ], - "structs": [ - { - "name": "InteractionMethodData", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "method", - "class": "ipMethod", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "required": "req_out" - }, - { - "key": 2, - "name": "limitsTP", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.LimitsTP" - }, - "doc": "Overall T,P limits for all methods involved\n", - "required": "req_out" - }, - { - "key": 3, - "name": "intparcoeff", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Interaction parameter coefficients - interpreted by model and method codes below\n", - "required": "req_out" - }, - { - "key": 4, - "name": "comment", - "typeId": "string", - "doc": "Comment: e.g. who entered\/modified, ...\n", - "required": "optional" - }, - { - "key": 5, - "name": "datasources", - "typeId": "set", - "type": { - "typeId": "set", - "elemTypeId": "string" - }, - "doc": "Labels of datasource DB objects\n", - "required": "optional" - } - ] - }, - { - "name": "Interaction", - "doc": "Description of interaction between substances or moieties\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "symbol", - "typeId": "string", - "doc": "Unique name\/ID of this interaction\n", - "required": "required" - }, - { - "key": 2, - "name": "sourcetdb", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Source TDB: enum validated with class SourceTDB\n", - "class": "SourceTDB", - "required": "required" - }, - { - "key": 3, - "name": "level", - "typeId": "i32", - "doc": "Level of the interaction (for superimposed IC or LMA reaction sets)\n", - "required": "required", - "default": 0 - }, - { - "key": 4, - "name": "name", - "typeId": "string", - "doc": "Name of the interaction (not compulsory)\n", - "required": "req_out" - }, - { - "key": 5, - "name": "mixmod", - "class": "MixModel", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Code of model of mixing - validate with class MixModel\n", - "required": "req_out", - "default": { - "1": "M_IDEAL" - } - }, - { - "key": 6, - "name": "intpart", - "class": "InteractionType", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Code of interaction parameter type - validate with class InteractionType\n", - "required": "req_out", - "default": { - "0": "TYPICAL" - } - }, - { - "key": 7, - "name": "Tst", - "typeId": "double", - "doc": "Reference temperature (usually 298.15 K)\n", - "required": "req_out", - "default": 298.15 - }, - { - "key": 8, - "name": "Pst", - "typeId": "double", - "doc": "Reference pressure (usually 1 bar !0^5 Pa, sometimes 1.013 bar = 1 atm\n", - "required": "req_out", - "default": 100000 - }, - { - "key": 11, - "name": "intpar", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Interaction parameter coefficients - interpreted by model and method codes below\n", - "required": "req_out" - }, - { - "key": 14, - "name": "TPIMethods", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "InteractionMethodData" - } - }, - "doc": "List of Methods temperature T, pressure P, and ionic strength I correction of the interaction parameters\n", - "required": "req_out" - }, - { - "key": 22, - "name": "limitsTP", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.LimitsTP" - }, - "doc": "Overall T,P limits for all methods involved\n", - "required": "req_out" - }, - { - "key": 18, - "name": "comment", - "typeId": "string", - "doc": "Comment: e.g. who entered\/modified, ...\n", - "required": "optional" - }, - { - "key": 19, - "name": "datasources", - "typeId": "set", - "type": { - "typeId": "set", - "elemTypeId": "string" - }, - "doc": "Labels of datasource DB objects\n", - "required": "optional" - }, - { - "key": 20, - "name": "time_stamp", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.TimeStamp" - }, - "doc": "Timestamp\n", - "required": "optional" - } - ] - }, - { - "name": "Interactions", - "doc": "Definition of an array of interactions\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 2, - "name": "interactions", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "Interaction" - } - }, - "doc": "List of interactions in activity models\n", - "required": "req_out" - } - ] - } - ], - "constants": [ - ], - "services": [ - ] -} diff --git a/Resources/data/schemas/kineticmodel.schema.json b/Resources/data/schemas/kineticmodel.schema.json deleted file mode 100644 index a7f16974..00000000 --- a/Resources/data/schemas/kineticmodel.schema.json +++ /dev/null @@ -1,446 +0,0 @@ -{ - "name": "kineticmodel", - "doc": "Apache Thrift IDL definition for the phase service interface\n", - "namespaces": { - "*": "kineticmodel" - }, - "includes": [ -"prop", -"element", -"substance", -"kineticrate" - ], - "enums": [ - ], - "typedefs": [ - ], - "structs": [ - { - "name": "KineticModel", - "doc": "Description of (thermodynamic) phase\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "symbol", - "typeId": "string", - "doc": "unique name\/ID of this phase (e.g. \"bentpw\")\n", - "required": "required" - }, - { - "key": 2, - "name": "sourcetdb", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Source TDB: enum validated with class SourceTDB - do we need it or thermodataset is enough?\n", - "required": "required" - }, - { - "key": 3, - "name": "thermodataset", - "typeId": "string", - "doc": "Used thermodataset symbol (also phaseinvolves link)\n", - "required": "required" - }, - { - "key": 4, - "name": "name", - "typeId": "string", - "doc": "Extended name comment of the phase (e.g. \"aqueous electrolyte Davies model\")\n", - "required": "req_out" - }, - { - "key": 5, - "name": "aggregate_state", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Aggregate state of this phase: enum validated with class AggregateState\n", - "required": "req_out" - }, - { - "key": 7, - "name": "kinratemod", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Kinetic rate model - validate using class RateModel in kineticrate\n", - "required": "req_out", - "default": { - "0": "KIN_INSTANT" - } - }, - { - "key": 8, - "name": "associatedProperties", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "prop.Item" - } - }, - "doc": "list of possile asociated indirect properties which are calculated using an expression\n", - "required": "req_out" - }, - { - "key": 9, - "name": "associatedPropertiesExpressions", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "expression, lua script for calculating property values (e.g. molar ratio of element in phase, mChainL, Rd); same order as in associatedProperties\n", - "required": "req_out" - }, - { - "key": 10, - "name": "SpecSurfaceArea", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Specific surface area of (carrier) phase\n", - "required": "req_out" - }, - { - "key": 11, - "name": "SpecInterfaceEnergy", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "SigmaA surface energy of solid-aqueous interface and other interfaces\n", - "required": "req_out" - }, - { - "key": 13, - "name": "SpecPoreVolume", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "new: Specific pore volume of (carrier) phase, m3\/g (default: 0)\n", - "required": "req_out" - }, - { - "key": 14, - "name": "SurfaceAreaFraction", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "new: fraction of surface area of the sorbent (ref. in lPh) occupied by this surface tile (def. 1)\n", - "required": "req_out" - }, - { - "key": 15, - "name": "PoreVolumeFraction", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "new: fraction of phase pore volume occupied by this Donnan electrolyte (default 1)\n", - "required": "req_out" - }, - { - "key": 17, - "name": "PermSurfChargeDensity", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "new: permanent surface charge density (eq\/m2), default: 0\n", - "required": "req_out" - }, - { - "key": 18, - "name": "PermVolumeChargeDensity", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "new: permanent Donnan volume charge density (eq\/m3), default: 0\n", - "required": "req_out" - }, - { - "key": 19, - "name": "IonExchangeCapacity", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "new: ion exchange capacity (eg\/g), default: 0\n", - "required": "req_out" - }, - { - "key": 21, - "name": "elements", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "element.ElementInfo" - } - }, - "doc": "Set of elements (IComps) represented in all components in kinmod\n", - "required": "req_out" - }, - { - "key": 23, - "name": "components", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "substance.SubstanceInfo" - } - }, - "doc": "Set of substances (components, end members) in kinmod\n", - "required": "req_out" - }, - { - "key": 25, - "name": "kineticrates", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "kineticrate.KineticRate" - } - }, - "doc": "Full Set of kinetic rate laws covered by this kinetic model\n", - "required": "req_out" - }, - { - "key": 27, - "name": "KinRateComponentProps", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "prop.Item" - } - }, - "doc": "optional array: properties of phase components used in the model of mixing\n", - "required": "req_out" - }, - { - "key": 31, - "name": "limitsTP", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.LimitsTP" - }, - "doc": "Overall lower and upper T, P limits for T,P corrections\n", - "required": "req_out", - "default": { - "range": 0, - "lowerT": 273.15, - "upperT": 298.15, - "lowerP": 0.1, - "upperP": 1000000 - } - }, - { - "key": 32, - "name": "comment", - "typeId": "string", - "doc": "Comment - e.g. who entered\/modified, ...\n", - "required": "optional" - }, - { - "key": 33, - "name": "datasources", - "typeId": "set", - "type": { - "typeId": "set", - "elemTypeId": "string" - }, - "doc": "Labels of datasource DB objects\n", - "required": "optional" - }, - { - "key": 34, - "name": "time_stamp", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.TimeStamp" - }, - "doc": "Timestamp when the record was created or modified\n", - "required": "optional" - } - ] - }, - { - "name": "kmpcdata", - "doc": "Data extracted from a substance connected to the phase via components edges\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "SC", - "typeId": "double", - "required": "req_out" - }, - { - "key": 2, - "name": "units", - "typeId": "string", - "required": "req_out" - }, - { - "key": 3, - "name": "subsid", - "typeId": "i32", - "required": "optional" - }, - { - "key": 4, - "name": "symbol", - "typeId": "string", - "required": "optional" - }, - { - "key": 5, - "name": "formula", - "typeId": "string", - "required": "optional" - }, - { - "key": 6, - "name": "subsx", - "typeId": "i32", - "required": "optional" - } - ] - }, - { - "name": "kmpsmdata", - "doc": "Data extracted from a substance\/moiety connected to the phase via sitemoieties edges\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "siteid", - "typeId": "string", - "required": "req_out" - }, - { - "key": 3, - "name": "subsid", - "typeId": "i32", - "required": "optional" - }, - { - "key": 4, - "name": "symbol", - "typeId": "string", - "required": "optional" - }, - { - "key": 5, - "name": "moix", - "typeId": "i32", - "required": "optional" - } - ] - }, - { - "name": "kmkrdata", - "doc": "Data extracted from a kineticrate connected to kinmodel via kinmodips edges\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "krtype", - "typeId": "string", - "required": "req_out" - }, - { - "key": 3, - "name": "interid", - "typeId": "i32", - "required": "optional" - }, - { - "key": 4, - "name": "symbol", - "typeId": "string", - "required": "optional" - }, - { - "key": 5, - "name": "order", - "typeId": "i32", - "required": "optional" - }, - { - "key": 6, - "name": "Nkrc", - "typeId": "i32", - "required": "optional" - }, - { - "key": 8, - "name": "krindx", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "i32" - }, - "required": "optional" - }, - { - "key": 9, - "name": "krpc", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "double" - }, - "required": "optional" - } - ] - } - ], - "constants": [ - ], - "services": [ - ] -} diff --git a/Resources/data/schemas/kineticrate.schema.json b/Resources/data/schemas/kineticrate.schema.json deleted file mode 100644 index af828d44..00000000 --- a/Resources/data/schemas/kineticrate.schema.json +++ /dev/null @@ -1,491 +0,0 @@ -{ - "name": "kineticrate", - "doc": "Apache Thrift IDL definition for the kineticrate service interface\n", - "namespaces": { - "*": "kineticrate" - }, - "includes": [ -"prop", -"element", -"substance" - ], - "enums": [ - { - "name": "KineticModel", - "doc": "Selection of kinetic models\n", - "members": [ - { - "name": "KIN_INSTANT", - "value": 0, - "doc": "No kinetics - instant reactions, equilibrium\n" - }, - { - "name": "KIN_TST", - "value": 1, - "doc": "Generic TST dissolution\/precipitation model following (Shott ea 2012)\n" - }, - { - "name": "KIN_PARALLEL", - "value": 2, - "doc": "Parallel dissolution (precipitation) reactions after Palandri 2004\n" - }, - { - "name": "KIN_STEPS", - "value": 3, - "doc": "Kinetics of growth (dissolution) derived from step propagation\n" - }, - { - "name": "KIN_RDIST", - "value": 4, - "doc": "Rate distribution dissolution kinetics (Fischer, Luettge)\n" - }, - { - "name": "KIN_CNT", - "value": 5, - "doc": "Classical nucleation theory model: nucleation kinetics\n" - }, - { - "name": "KIN_CNTS", - "value": 6, - "doc": "Simplified CNT kinetics (Hellevang)\n" - }, - { - "name": "KIN_OTHER", - "value": 101, - "doc": "Other kinetic models\n" - } - ] - }, - { - "name": "KineticType", - "doc": "Kinetic type (for reactions)\n", - "members": [ - { - "name": "KT_NOT_KNOWN", - "value": 0, - "doc": "Not known whether hetero- or homoheneous\n" - }, - { - "name": "KT_HETE_MIN_AQ", - "value": 1, - "doc": "Heterogeneous reaction kinetics mineral-water\n" - }, - { - "name": "KT_HETE_MIN_MELT", - "value": 2, - "doc": "Heterogeneous reaction kinetics mineral-melt\n" - }, - { - "name": "KT_HETE_MIN_GAS", - "value": 3, - "doc": "Heterogeneous reaction kinetics mineral-gas\n" - }, - { - "name": "KT_HETE_MELT_GAS", - "value": 4, - "doc": "Heterogeneous reaction kinetics melt-gas\n" - }, - { - "name": "KT_HETE_AQ_GAS", - "value": 5, - "doc": "Heterogeneous reaction kinetics water-gas\n" - }, - { - "name": "KT_HETE_AQ_MELT", - "value": 6, - "doc": "Heterogeneous reaction kinetics water-melt\n" - }, - { - "name": "KT_HETE_SURF_AQ", - "value": 7, - "doc": "Heterogeneous reaction kinetics surface-water\n" - }, - { - "name": "KT_HETE_SURF_GAS", - "value": 8, - "doc": "Heterogeneous reaction kinetics surface-gas\n" - }, - { - "name": "KT_HOMO_AQ", - "value": 9, - "doc": "Homogeneous in aqueous solution\n" - }, - { - "name": "KT_HOMO_GAS", - "value": 10, - "doc": "Homogeneous in gas phase or plasma\n" - }, - { - "name": "KT_HOMO_MELT", - "value": 11, - "doc": "Homogeneous in non-electrolyte liquid (melt)\n" - }, - { - "name": "KT_HOMO_MIN", - "value": 12, - "doc": "Homogeneous in solid (transformation)\n" - }, - { - "name": "KT_OTHER", - "value": 101, - "doc": "Other\n" - } - ] - }, - { - "name": "KineticMethodT", - "doc": "Code of method of temperature correction of kinetic rate constant\n", - "members": [ - { - "name": "KMT_CONSTANT_T", - "value": 0, - "doc": "Constant on T\n" - }, - { - "name": "KMT_ARRHENIUS_ABS", - "value": 1, - "doc": "Arrhenius equation evaluated at absolute temperature\n" - }, - { - "name": "KMT_ARRHENIUS_DIF", - "value": 2, - "doc": "Arrhenius equation evaluated at temperature relative to Tref\n" - }, - { - "name": "KMT_OTHER", - "value": 101, - "doc": "Other methods of rate constant correction on T\n" - } - ] - }, - { - "name": "KineticMethodA", - "doc": "Code of selection of the affinity term type\n", - "members": [ - { - "name": "KMA_NONE", - "value": 0, - "doc": "No term for affinity\n" - }, - { - "name": "KMA_TST_CLASSIC", - "value": 1, - "doc": "Classic TST affinity term\n" - }, - { - "name": "KMA_TST_REVERSE", - "value": 2, - "doc": "Classic TST affinity term, reversed\n" - }, - { - "name": "KMA_SCHOTT", - "value": 3, - "doc": "Affinity term from Schott et al. (2012), Fig. 1e\n" - }, - { - "name": "KMA_HELLMANN", - "value": 4, - "doc": "Affinity term from Hellmann & Tisserand (2006), eq 9\n" - }, - { - "name": "KMA_TENG_A", - "value": 5, - "doc": "Affinity term from Teng et al. (2000), eq.13\n" - }, - { - "name": "KMA_TENG_B", - "value": 6, - "doc": "Affinity term from Teng et al. (2000), Fig.6\n" - }, - { - "name": "KMA_FRITZ", - "value": 7, - "doc": "Nucleation affinity term from Fritz et al. (2009), eq 6\n" - }, - { - "name": "KMA_OTHER", - "value": 101 - } - ] - }, - { - "name": "KineticMethodSSA", - "doc": "Code of selection of the method of (specific) surface area correction\n", - "members": [ - { - "name": "SSA_CONSTANT", - "value": 0, - "doc": "Constant specific surface area\n" - }, - { - "name": "SSA_CUBICROOT", - "value": 1, - "doc": "Cubic root SSA correction\n" - }, - { - "name": "SSA_SPHERICITY_SI", - "value": 2, - "doc": "Sphericity factor SSA correction upon saturation index\n" - }, - { - "name": "SSA_OTHER", - "value": 101 - } - ] - } - ], - "typedefs": [ - ], - "structs": [ - { - "name": "KineticRate", - "doc": "Description of kinetic rate law (partial mechanism)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "symbol", - "typeId": "string", - "doc": "Unique name\/ID of this kinetic rate law\n", - "required": "required" - }, - { - "key": 2, - "name": "sourcekdb", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Source KDB: enum validated with class SourceTDB\n", - "class": "SourceTDB", - "required": "required" - }, - { - "key": 3, - "name": "level", - "typeId": "i32", - "doc": "Level of the kinetic rate (for superimposed rates)\n", - "required": "required", - "default": 0 - }, - { - "key": 4, - "name": "name", - "typeId": "string", - "doc": "Name of the kinetic rate (not compulsory)\n", - "required": "req_out" - }, - { - "key": 5, - "name": "kinmod", - "class": "KineticModel", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Code of kinetic rate model; validate with class KineticModel\n", - "required": "req_out", - "default": { - "1": "KIN_TST" - } - }, - { - "key": 6, - "name": "kintype", - "class": "KineticType", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Code of kinetics type - validate with class KineticType\n", - "required": "req_out", - "default": { - "1": "KT_HETE_MIN_AQ" - } - }, - { - "key": 7, - "name": "methodT", - "class": "KineticMethodT", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Method of temperature correction of rate constant\n", - "required": "req_out", - "default": { - "0": "KMT_CONSTANT_T" - } - }, - { - "key": 8, - "name": "methodA", - "class": "KineticMethodA", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Method of calculation of the affinity term\n", - "required": "req_out", - "default": { - "0": "KMA_NONE" - } - }, - { - "key": 9, - "name": "methodS", - "class": "KineticMethodSSA", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Method of the specific surface area correction\n", - "required": "req_out", - "default": { - "0": "SSA_CONSTANT" - } - }, - { - "key": 11, - "name": "rate_param_temp", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "4 kinetic rate law parameter coefficients for the arrrhenius part cf. KineticMethodT\n", - "required": "req_out" - }, - { - "key": 12, - "name": "rate_param_activ", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "5 kinetic rate law parameter coefficients for the activity term\n", - "required": "req_out" - }, - { - "key": 13, - "name": "rate_param_affin", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "5 kinetic rate law parameter coefficients for the affinity term cf KineticMethodA\n", - "required": "req_out" - }, - { - "key": 14, - "name": "rate_param_ssa", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "4 kinetic rate law parameter coefficients for specific surface area correction cf KineticMethodS\n", - "required": "req_out" - }, - { - "key": 16, - "name": "Tst", - "typeId": "double", - "doc": "Reference temperature (usually 298.15 K)\n", - "required": "req_out", - "default": 298.15 - }, - { - "key": 17, - "name": "Pst", - "typeId": "double", - "doc": "Reference pressure (usually 1 bar !0^5 Pa, sometimes 1.013 bar = 1 atm\n", - "required": "req_out", - "default": 100000 - }, - { - "key": 10, - "name": "limitsTP", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.LimitsTP" - }, - "doc": "Overall lower and upper T, P limits for T,P corrections\n", - "required": "req_out" - }, - { - "key": 20, - "name": "comment", - "typeId": "string", - "doc": "Comment: e.g. who entered\/modified, ...\n", - "required": "optional" - }, - { - "key": 21, - "name": "datasources", - "typeId": "set", - "type": { - "typeId": "set", - "elemTypeId": "string" - }, - "doc": "Labels of datasource DB objects\n", - "required": "optional" - }, - { - "key": 22, - "name": "time_stamp", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.TimeStamp" - }, - "doc": "Timestamp\n", - "required": "optional" - } - ] - }, - { - "name": "KineticRates", - "doc": "Definition of an array of kinetic rates\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 2, - "name": "kineticrates", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "KineticRate" - } - }, - "doc": "List of chemical kinetic ratess\n", - "required": "req_out" - } - ] - } - ], - "constants": [ - ], - "services": [ - ] -} diff --git a/Resources/data/schemas/mixingmodel.schema.json b/Resources/data/schemas/mixingmodel.schema.json deleted file mode 100644 index 763186c5..00000000 --- a/Resources/data/schemas/mixingmodel.schema.json +++ /dev/null @@ -1,421 +0,0 @@ -{ - "name": "mixingmodel", - "doc": "Apache Thrift IDL definition for the phase service interface\n", - "namespaces": { - "*": "mixingmodel" - }, - "includes": [ -"prop", -"element", -"substance", -"interaction" - ], - "enums": [ - ], - "typedefs": [ - ], - "structs": [ - { - "name": "MixingModel", - "doc": "Description of (thermodynamic activity) model of mixing\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "symbol", - "typeId": "string", - "doc": "unique name\/ID of this phase (e.g. \"bentpw\")\n", - "required": "required" - }, - { - "key": 2, - "name": "sourcetdb", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Source TDB: enum validated with class SourceTDB - do we need it or thermodataset is enough?\n", - "required": "required" - }, - { - "key": 3, - "name": "thermodataset", - "typeId": "string", - "doc": "Used thermodataset symbol (also phaseinvolves link)\n", - "required": "required" - }, - { - "key": 4, - "name": "name", - "typeId": "string", - "doc": "Extended name comment of the phase (e.g. \"aqueous electrolyte Davies model\")\n", - "required": "req_out" - }, - { - "key": 5, - "name": "aggregate_state", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Aggregate state for this mixing model: enum validated with class AggregateState\n", - "required": "req_out" - }, - { - "key": 6, - "name": "mixmod", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Type of mixing model - validate using class MixModel in interaction\n", - "required": "req_out", - "default": { - "0": "M_PURE" - } - }, - { - "key": 8, - "name": "associatedProperties", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "prop.Item" - } - }, - "doc": "list of possile asociated indirect properties which are calculated using an expression\n", - "required": "req_out" - }, - { - "key": 9, - "name": "associatedPropertiesExpressions", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "expression, lua script for calculating property values (same order as in associatedProperties)\n", - "required": "req_out" - }, - { - "key": 11, - "name": "elements", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "element.ElementInfo" - } - }, - "doc": "Full Set of elements (IComps) covered by this mixing model\n", - "required": "req_out" - }, - { - "key": 12, - "name": "components", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "substance.SubstanceInfo" - } - }, - "doc": "Full Set of substances (components, end members, moieties) covered by this mixing model\n", - "required": "req_out" - }, - { - "key": 13, - "name": "interactions", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "interaction.Interaction" - } - }, - "doc": "Full Set of interactions (between components, end members, moieties) covered by this mixing model\n", - "required": "req_out" - }, - { - "key": 15, - "name": "Nsites", - "typeId": "i32", - "doc": "Number of sublattice sites: 1 to 5; 0 for aq, gas\n", - "required": "req_out", - "default": 1 - }, - { - "key": 16, - "name": "sitemults", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "i32" - }, - "doc": "Multiplicity numbers of sublattice sites\n", - "required": "req_out" - }, - { - "key": 17, - "name": "moieties", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "list of symbols of site moieties involved\n", - "required": "req_out" - }, - { - "key": 19, - "name": "limitsTP", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.LimitsTP" - }, - "doc": "Overall lower and upper T, P limits for T,P corrections\n", - "required": "req_out", - "default": { - "range": 0, - "lowerT": 273.15, - "upperT": 298.15, - "lowerP": 0.1, - "upperP": 1000000 - } - }, - { - "key": 21, - "name": "MixModComponentProps", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "prop.Item" - } - }, - "doc": "optional array: properties of phase components used in the model of mixing\n", - "required": "req_out" - }, - { - "key": 22, - "name": "SizeParams", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Size parameters of components\n", - "required": "optional" - }, - { - "key": 23, - "name": "DarkenParams", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Darken parameters of components\n", - "required": "optional" - }, - { - "key": 24, - "name": "OrderingParams", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Ordering parameters of the phase or components\n", - "required": "optional" - }, - { - "key": 31, - "name": "comment", - "typeId": "string", - "doc": "Comment - e.g. who entered\/modified, ...\n", - "required": "optional" - }, - { - "key": 32, - "name": "datasources", - "typeId": "set", - "type": { - "typeId": "set", - "elemTypeId": "string" - }, - "doc": "Labels of datasource DB objects\n", - "required": "optional" - }, - { - "key": 33, - "name": "time_stamp", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.TimeStamp" - }, - "doc": "Timestamp when the record was created or modified\n", - "required": "optional" - } - ] - }, - { - "name": "mmpcdata", - "doc": "Data extracted from a substance connected to the mixing model via components edges\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "SC", - "typeId": "double", - "required": "req_out" - }, - { - "key": 2, - "name": "units", - "typeId": "string", - "required": "req_out" - }, - { - "key": 3, - "name": "subsid", - "typeId": "i32", - "required": "optional" - }, - { - "key": 4, - "name": "symbol", - "typeId": "string", - "required": "optional" - }, - { - "key": 5, - "name": "formula", - "typeId": "string", - "required": "optional" - }, - { - "key": 6, - "name": "subsx", - "typeId": "i32", - "required": "optional" - } - ] - }, - { - "name": "mmpsmdata", - "doc": "Data extracted from a substance\/moiety connected to mixmod via sitemoieties edges\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "siteid", - "typeId": "string", - "required": "req_out" - }, - { - "key": 3, - "name": "subsid", - "typeId": "i32", - "required": "optional" - }, - { - "key": 4, - "name": "symbol", - "typeId": "string", - "required": "optional" - }, - { - "key": 5, - "name": "moix", - "typeId": "i32", - "required": "optional" - } - ] - }, - { - "name": "mmipdata", - "doc": "Data extracted from an interaction connected to the mixmodel via mixmodips edges\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "iptype", - "typeId": "string", - "required": "req_out" - }, - { - "key": 3, - "name": "interid", - "typeId": "i32", - "required": "optional" - }, - { - "key": 4, - "name": "symbol", - "typeId": "string", - "required": "optional" - }, - { - "key": 5, - "name": "order", - "typeId": "i32", - "required": "optional" - }, - { - "key": 6, - "name": "Nipc", - "typeId": "i32", - "required": "optional" - }, - { - "key": 8, - "name": "mindx", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "i32" - }, - "required": "optional" - }, - { - "key": 9, - "name": "ipc", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "double" - }, - "required": "optional" - } - ] - } - ], - "constants": [ - ], - "services": [ - ] -} diff --git a/Resources/data/schemas/newdb/araimpex.schema.json b/Resources/data/schemas/newdb/araimpex.schema.json deleted file mode 100644 index 366baaef..00000000 --- a/Resources/data/schemas/newdb/araimpex.schema.json +++ /dev/null @@ -1,947 +0,0 @@ -{ - "name": "araimpex", - "doc": "Apache Thrift IDL definition for text import-export interfaces\n", - "namespaces": { - "*": "impex" - }, - "includes": [ - ], - "enums": [ - { - "name": "DirectionType", - "doc": "Classes of direction types\n", - "members": [ - { - "name": "IMPORT", - "value": 0, - "doc": "import\n" - }, - { - "name": "EXPORT", - "value": 1, - "doc": "export\n" - } - ] - } - ], - "typedefs": [ - ], - "structs": [ - { - "name": "FormatValue", - "doc": "Definition of the data value format in imported\/exported file\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "format", - "typeId": "string", - "doc": "Format scanf\/printf (to string first): \"%s\" | \"in\" | \"out\" | \"endl\" | \"txel\" | \"txkw\"; \"in\" | \"out\" | \"endl\" for stream input\n", - "required": "req_out" - }, - { - "key": 2, - "name": "factor", - "typeId": "double", - "doc": "Factor != 0, default 1; Each num.value is multiplied (import) or divided (export) by factor\n", - "required": "optional" - }, - { - "key": 3, - "name": "increment", - "typeId": "double", - "doc": "Increment, default 0; added to each numerical value (import) or subtracted from (export)\n", - "required": "optional" - } - ] - }, - { - "name": "FormatKeyword", - "doc": "Format to read\/print keywords in key-value pair file\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "format", - "typeId": "string", - "doc": "scanf\/printf format for keyword\n", - "required": "req_out" - }, - { - "key": 2, - "name": "delim_begin", - "typeId": "string", - "doc": "delimiter for keyword begin e.g. \"\\\"\" | \"<\" | \"\"\n", - "required": "optional" - }, - { - "key": 3, - "name": "delim_end", - "typeId": "string", - "doc": "delimiter for keyword end e.g. \"\\\"\" | \">\" | \"\"\n", - "required": "optional" - } - ] - }, - { - "name": "DataType", - "doc": "Type of object from the imported or exported file (for use in keyword lookup list or map)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "datatype", - "typeId": "string", - "doc": "Basis type \"string\" | \"float\" | \"double\" | \"i16\" | \"i32\" | \"bool\" | ...\n", - "required": "req_out" - }, - { - "key": 2, - "name": "organization", - "typeId": "string", - "doc": "Organization: \"\" | \"list\" | \"set\" | \"map\" | \"group\" | \"embedded\" | ...\n", - "required": "req_out" - } - ] - }, - { - "name": "DataObject", - "doc": "Thrift key of data object \"8\" or \"3.8\" or \"2.3.8\" or \"\" to ignore (import); any string not starting from a digit as comment (export)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "field", - "typeId": "string", - "doc": "Either Thrift key or name of the data field in recursive form (s e.g. \"4.3.1\" or name1.name2 )\n", - "required": "req_out" - }, - { - "key": 2, - "name": "ignore", - "typeId": "bool", - "doc": "Set to true if the corresponding value in file has to be ignored (default: false)\n", - "required": "optional" - }, - { - "key": 3, - "name": "script", - "typeId": "string", - "doc": "Default \"\" or contains lua script for operation on data values in block\n", - "required": "optional" - }, - { - "key": 4, - "name": "convert", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "string", - "valueTypeId": "string" - }, - "doc": "Default empty or contains pair(s) read_value : saved_value e.g. \"e\": \"4\" (usually for setting enum values)\n", - "required": "optional" - } - ] - }, - { - "name": "Separators", - "doc": "Definition of value, line, row, block, comment, end-of-data separators\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "v_sep", - "typeId": "string", - "doc": "Value separator (for arrays) \" \" | \",\" | \"\\t\" | \"integer\" (=fixed field width)\n", - "required": "req_out" - }, - { - "key": 2, - "name": "l_sep", - "typeId": "string", - "doc": "Line separator \"\\n\" ...\n", - "required": "req_out" - }, - { - "key": 3, - "name": "r_sep", - "typeId": "string", - "doc": "Row separator (table), \"\\n\" ...\n", - "required": "optional" - }, - { - "key": 4, - "name": "c_head", - "typeId": "string", - "doc": "Head comment separator e.g. \"#\" or '%'\n", - "required": "optional" - }, - { - "key": 5, - "name": "c_end", - "typeId": "string", - "doc": "End comment separator e.g. \"\\n\"\n", - "required": "optional" - }, - { - "key": 6, - "name": "eod", - "typeId": "string", - "doc": "string indicating end of data (as list of blocks) in file or \"\" as default ']' (end of file)\n", - "required": "optional" - }, - { - "key": 7, - "name": "encoding", - "typeId": "string", - "doc": "encoding (\"\" for standard system encoding)\n", - "required": "optional" - }, - { - "key": 8, - "name": "str_delim", - "typeId": "string", - "doc": "Delimiter for strings - default \"\\\"\"\n", - "required": "optional" - }, - { - "key": 9, - "name": "bod", - "typeId": "string", - "doc": "string indicating begin of data (as list of blocks) in file or \"\" as default '['\n", - "required": "optional" - } - ] - }, - { - "name": "FormatBlock", - "doc": "Text block format in file corresponding to one database document (record)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "defaults", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "string", - "valueTypeId": "string" - }, - "doc": "Default Key, Value pairs to DOM (import) or to output (export)\n", - "required": "req_out" - }, - { - "key": 2, - "name": "pairs", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "string", - "valueTypeId": "struct", - "valueType": { - "typeId": "struct", - "class": "DataType" - } - }, - "doc": "Lookup map of keyword-value pair format\n", - "required": "req_out" - }, - { - "key": 3, - "name": "matches", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "string", - "valueTypeId": "struct", - "valueType": { - "typeId": "struct", - "class": "DataObject" - } - }, - "doc": ">=1 keywd, DataObject pairs connecting the block of data in file with DOM.\n", - "required": "required" - }, - { - "key": 4, - "name": "script", - "typeId": "string", - "doc": "Default \"\" or contains lua script for operation on data values in full DOM\n", - "required": "optional" - } - ] - }, - { - "name": "FormatTextFile", - "doc": "Definition of text data file format\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "block", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "FormatBlock" - }, - "doc": "Format definition for one or more blocks for data records - default 1 block\n", - "required": "required" - }, - { - "key": 2, - "name": "lines", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "Will be format lines list\n", - "required": "required" - }, - { - "key": 3, - "name": "label", - "typeId": "string", - "doc": "Label of data type (vertex type), e.g. \"datasource\", \"element\" ...\n", - "required": "required" - }, - { - "key": 4, - "name": "separs", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Separators" - }, - "doc": "Definition of value, line, row, block, comment, end-of-data separators\n", - "required": "req_out" - }, - { - "key": 5, - "name": "comment", - "typeId": "string", - "doc": "Export: the whole comment text; Import: the comment begin markup string (to skip until endl)\n", - "required": "optional" - }, - { - "key": 6, - "name": "file_name", - "typeId": "string", - "doc": "File name or \"console\" for export\n", - "required": "optional" - }, - { - "key": 7, - "name": "Nblocks", - "typeId": "i32", - "doc": "number of data block in file >=1, 0 if unknown\n", - "required": "optional" - }, - { - "key": 8, - "name": "Nlines", - "typeId": "i32", - "doc": "number of text lines in file (>=1), 0 if unknown\n", - "required": "optional" - }, - { - "key": 9, - "name": "Nchars", - "typeId": "i32", - "doc": "total number of characters in file, 0 if unknown\n", - "required": "optional" - }, - { - "key": 10, - "name": "direction", - "typeId": "i32", - "doc": "direction\n", - "class": "DirectionType", - "required": "req_out" - } - ] - }, - { - "name": "FormatKeyValue", - "doc": "Definition of key-value import\/export format\nWe use Regular Expression in case of import and Print Format in case of export.\nUse names \"head0\", ..., \"headN\", \"end0\", ..., \"endN\" to import\/export data from\/to head and end part\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "head_regexp", - "typeId": "string", - "doc": "Head of Block: \"\\\\s*([^\\\\s]+)\\\\s*;\\\\s*(([\\\\w\\\\t \\\\+\\\\-\\\\(\\\\):\\\\.]+)\\\\s*=\\\\s*([^;]+))\" (import)\nor \"\\n%head0\\n\\t%head1\\n\" (export)\n", - "required": "required" - }, - { - "key": 2, - "name": "end_regexp", - "typeId": "string", - "doc": "End of Block: \"([^\\n]+)\" (import) or \"%end0\\n\" (export)\n", - "required": "required" - }, - { - "key": 3, - "name": "key_regexp", - "typeId": "string", - "doc": "Keyword: \"\\\\s*;\\\\s*\\\\-{0,1}([a-zA-Z]\\\\w*)\\\\s*\" (import) or \"\\t-%key\\t\" (export)\n", - "required": "required" - }, - { - "key": 4, - "name": "value_regexp", - "typeId": "string", - "doc": "Data Value(s): \"\\\\s*([^#\\\\n;]*)\" (import) or \"%value\" (export)\n", - "required": "req_out" - }, - { - "key": 5, - "name": "value_next", - "typeId": "string", - "doc": "Key-Value pair end delimiter (used if empty value_regexp or export mode )\n", - "required": "req_out", - "default": "\n" - }, - { - "key": 6, - "name": "value_token_regexp", - "typeId": "string", - "doc": "Regular Expression to iterate over matches (used to convert value to string list or if export mode )\n", - "required": "optional", - "default": " " - }, - { - "key": 7, - "name": "comment_regexp", - "typeId": "string", - "doc": "Regular Expression for skip comments\n", - "required": "optional" - }, - { - "key": 8, - "name": "Ndata", - "typeId": "i32", - "doc": "number of data items per block (0 if not set)\n", - "required": "optional" - }, - { - "key": 9, - "name": "strvalue_exp", - "typeId": "string", - "doc": "Data String Value(s): only for export \"\\'%value\\'\"\n", - "required": "req_out" - }, - { - "key": 10, - "name": "key_order", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "Keyword order list: only for export\n", - "required": "optional" - } - ] - }, - { - "name": "FormatKeyValueFile", - "doc": "Definition of text file with key-value pair data\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "block", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "FormatBlock" - }, - "doc": "Format for one or more blocks for data records\n", - "required": "required" - }, - { - "key": 2, - "name": "format", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "FormatKeyValue" - }, - "doc": "Definition of key-value block in file\n", - "required": "required" - }, - { - "key": 3, - "name": "renderer", - "typeId": "string", - "doc": "Rendering syntax for the foreign key-value file \"GEMS3K\" | \"BIB\" | \"RIS\" | ...\n", - "required": "required" - }, - { - "key": 4, - "name": "label", - "typeId": "string", - "doc": "Label of data type (vertex type), e.g. \"datasource\", \"element\" ...\n", - "required": "required" - }, - { - "key": 5, - "name": "separators", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Separators" - }, - "doc": "Definition of value, line, row, block, comment, end-of-data separators\n", - "required": "req_out" - }, - { - "key": 6, - "name": "comment", - "typeId": "string", - "doc": "Export: the whole comment text; Import: the comment begin markup string (to skip until endl)\n", - "required": "optional" - }, - { - "key": 7, - "name": "fname", - "typeId": "string", - "doc": "File name or \"console\" for export\n", - "required": "optional" - }, - { - "key": 8, - "name": "Nblocks", - "typeId": "i32", - "doc": "number of data blocks (records) >=1, 0 if unknown\n", - "required": "optional" - }, - { - "key": 9, - "name": "Nlines", - "typeId": "i32", - "doc": "total number of text lines in the file, 0 if unknown\n", - "required": "optional" - }, - { - "key": 10, - "name": "direction", - "typeId": "i32", - "doc": "direction\n", - "class": "DirectionType", - "required": "req_out" - } - ] - }, - { - "name": "FormatTable", - "doc": "Definition of of the table input format\nif defined colsizes, split by sizes\nif defined value_regexp, split used regexpr\notherwise split by columns delimiter\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "Nhcols", - "typeId": "i32", - "doc": "Number of header columns\n", - "required": "req_out" - }, - { - "key": 2, - "name": "Nhrows", - "typeId": "i32", - "doc": "Number of header rows (start porting from row )\n", - "required": "req_out" - }, - { - "key": 3, - "name": "headers", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "Names of header columns\n", - "required": "req_out" - }, - { - "key": 4, - "name": "rowend", - "typeId": "string", - "doc": "Row delimiter\n", - "required": "req_out", - "default": "\n" - }, - { - "key": 5, - "name": "colends", - "typeId": "string", - "doc": "Columns delimiters\n", - "required": "req_out", - "default": "\t " - }, - { - "key": 6, - "name": "usequotes", - "typeId": "bool", - "doc": "Quoted field as text\n", - "required": "req_out", - "default": 1 - }, - { - "key": 7, - "name": "usemore", - "typeId": "bool", - "doc": "Can be more than one delimiter between columns\n", - "required": "req_out", - "default": 0 - }, - { - "key": 8, - "name": "comment_regexp", - "typeId": "string", - "doc": "Regular Expression for skip comments\n", - "required": "optional" - }, - { - "key": 9, - "name": "colsizes", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "i32" - }, - "doc": "Fixed size of columns for importing ( apply to all if one item )\n", - "required": "optional" - }, - { - "key": 10, - "name": "value_regexp", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "Regular Expression for column value(s) ( apply to all if one item )\n", - "required": "optional" - } - ] - }, - { - "name": "FormatTableFile", - "doc": "Definition of table text file format\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "block", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "FormatBlock" - }, - "doc": "Format for one or more blocks for data records\n", - "required": "required" - }, - { - "key": 2, - "name": "format", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "FormatTable" - }, - "doc": "Definition of key-value block in file\n", - "required": "required" - }, - { - "key": 3, - "name": "renderer", - "typeId": "string", - "doc": "Rendering syntax for the foreign key-value file \"GEMS3K\" | \"BIB\" | \"RIS\" | ...\n", - "required": "required" - }, - { - "key": 4, - "name": "label", - "typeId": "string", - "doc": "Label of data type (vertex type), e.g. \"datasource\", \"element\" ...\n", - "required": "required" - }, - { - "key": 5, - "name": "separators", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Separators" - }, - "doc": "Definition of value, line, row, block, comment, end-of-data separators\n", - "required": "req_out" - }, - { - "key": 6, - "name": "comment", - "typeId": "string", - "doc": "Export: the whole comment text; Import: the comment begin markup string (to skip until endl)\n", - "required": "optional" - }, - { - "key": 7, - "name": "fname", - "typeId": "string", - "doc": "File name or \"console\" for export\n", - "required": "optional" - }, - { - "key": 8, - "name": "Nblocks", - "typeId": "i32", - "doc": "number of data blocks (records) >=1, 0 if unknown\n", - "required": "optional" - }, - { - "key": 9, - "name": "Nlines", - "typeId": "i32", - "doc": "total number of text lines in the file, 0 if unknown\n", - "required": "optional" - }, - { - "key": 10, - "name": "direction", - "typeId": "i32", - "doc": "direction\n", - "class": "DirectionType", - "required": "req_out" - } - ] - }, - { - "name": "FormatStructDataFile", - "doc": "Definition of foreign structured data JSON\/YAML\/XML text file\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "block", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "FormatBlock" - }, - "doc": "Format for one or more blocks for data records\n", - "required": "required" - }, - { - "key": 2, - "name": "renderer", - "typeId": "string", - "doc": "Rendering syntax for the foreign file \"JSON\" | \"YAML\" | \"XML\" | ...\n", - "required": "required", - "default": "JSON" - }, - { - "key": 3, - "name": "label", - "typeId": "string", - "doc": "Label of data type (vertex type), e.g. \"datasource\", \"element\" ...\n", - "required": "required" - }, - { - "key": 4, - "name": "comment", - "typeId": "string", - "doc": "Definition of value, line, row, block, comment, end-of-data separators\n", - "required": "optional" - }, - { - "key": 5, - "name": "fname", - "typeId": "string", - "doc": "File name or \"console\" for export\n", - "required": "optional" - }, - { - "key": 6, - "name": "Nblocks", - "typeId": "i32", - "doc": "number of data blocks (records) >=1, 0 if unknown\n", - "required": "optional" - }, - { - "key": 7, - "name": "Nlines", - "typeId": "i32", - "doc": "total number of text lines in the file, 0 if unknown\n", - "required": "optional" - }, - { - "key": 10, - "name": "direction", - "typeId": "i32", - "doc": "direction\n", - "class": "DirectionType", - "required": "req_out" - } - ] - }, - { - "name": "FormatImportExportFile", - "doc": "Generalized import-export data file format\n", - "isException": false, - "isUnion": true, - "fields": [ - { - "key": 1, - "name": "ff_text", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "FormatTextFile" - }, - "doc": "Definition of text data file format\n", - "required": "optional" - }, - { - "key": 2, - "name": "ff_table", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "FormatTableFile" - }, - "doc": "Definition of data table file format\n", - "required": "optional" - }, - { - "key": 3, - "name": "ff_keyvalue", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "FormatKeyValueFile" - }, - "doc": "Definition of file format with key-value pair data\n", - "required": "optional" - }, - { - "key": 4, - "name": "ff_stdata", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "FormatStructDataFile" - }, - "doc": "Definition of foreign structured data JSON\/YAML\/XML file format\n", - "required": "optional" - } - ] - }, - { - "name": "ImpexFormat", - "doc": "description of import\/export format record\n", - "isException": false, - "to_select": [ "4", "5", "6", "7" ], - "to_key": [ "4" ], - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Handle (id) of this record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of this record within the impex collection (part of _id)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Code of revision (changed by the system at every update)\n", - "required": "required" - }, - { - "key": 4, - "name": "name", - "typeId": "string", - "doc": "short description\/keywd (used as key field)\n", - "required": "required" - }, - { - "key": 5, - "name": "impexschema", - "typeId": "string", - "doc": "impex schema\n", - "required": "required" - }, - { - "key": 6, - "name": "schema", - "typeId": "string", - "doc": "record schema\n", - "required": "req_out" - }, - { - "key": 7, - "name": "comment", - "typeId": "string", - "doc": "description of record\n", - "required": "req_out" - }, - { - "key": 8, - "name": "direction", - "typeId": "i32", - "doc": "direction\n", - "class": "DirectionType", - "required": "req_out" - }, - { - "key": 9, - "name": "impex", - "typeId": "string", - "doc": "format structure\n", - "required": "required" - }, - { - "key": 10, - "name": "format", - "typeId": "string", - "doc": "Id\/description of foreign file format\n", - "required": "optional" - }, - { - "key": 11, - "name": "extension", - "typeId": "string", - "doc": "file extension\n", - "required": "optional" - } - ] - } - ], - "constants": [ - ], - "services": [ - ] -} diff --git a/Resources/data/schemas/newdb/graphdb.schema.json b/Resources/data/schemas/newdb/graphdb.schema.json deleted file mode 100644 index 7280ca5e..00000000 --- a/Resources/data/schemas/newdb/graphdb.schema.json +++ /dev/null @@ -1,3005 +0,0 @@ -{ - "name": "graphdb", - "doc": "Apache Thrift IDL definition for GraphSON and TitanDB graph database interface\n", - "namespaces": { - "*": "graph" - }, - "includes": [ -"prop", -"datasource", -"element", -"substance", -"reaction", -"reactionset", -"thermodataset", -"interaction", -"kineticrate", -"phase", -"composition", -"chemeqsysdef", -"chemeqsysrecipe", -"chemeqspeciation" - ], - "enums": [ - ], - "typedefs": [ - ], - "structs": [ - { - "name": "VertexDataSource", - "doc": "Datasource vertex document\n", - "isException": false, - "isUnion": false, - "to_select": [ "3", "4.1", "4.3.0", "4.2" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Database ID (0 if not known)\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 3, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all datasources\n", - "required": "required", - "default": "datasource" - }, - { - "key": 4, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "datasource.DataSource" - }, - "doc": "properties of datasource as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexElement", - "doc": "Element vertex document\n", - "isException": false, - "isUnion": false, - "to_select": [ "3", "4.1", "4.2", "4.3" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Database ID (0 if not known)\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 3, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all elements\n", - "required": "required", - "default": "element" - }, - { - "key": 4, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "element.Element" - }, - "doc": "properties of element as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexSubstance", - "doc": "Substance vertex document\n", - "isException": false, - "isUnion": false, - "to_select": [ "3", "4.1", "4.2", "4.5", "4.3" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Database ID (0 if not known)\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 3, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all substances\n", - "required": "required", - "default": "substance" - }, - { - "key": 4, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "substance.Substance" - }, - "doc": "properties of substance as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexReaction", - "doc": "Reaction vertex document\n", - "isException": false, - "isUnion": false, - "to_select": [ "3", "4.1", "4.2", "4.4", "4.3", "4.11.3.0" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Database ID (0 if not known)\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 3, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all reactions\n", - "required": "required", - "default": "reaction" - }, - { - "key": 4, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "reaction.Reaction" - }, - "doc": "properties of reaction as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexReactionSet", - "doc": "Reactionset vertex document\n", - "isException": false, - "isUnion": false, - "to_select": [ "3", "4.1", "4.2", "4.3", "4.4", "4.8" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Database ID (0 if not known)\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 3, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all reactionsets\n", - "required": "required", - "default": "reactionset" - }, - { - "key": 4, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "reactionset.ReactionSet" - }, - "doc": "properties of reactionset as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexThermoDataSet", - "doc": "Thermodataset vertex document\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Database ID (0 if not known)\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 3, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all reactionsets\n", - "required": "required", - "default": "thermodataset" - }, - { - "key": 4, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "thermodataset.ThermoDataSet" - }, - "doc": "properties of thermodataset as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexInteraction", - "doc": "Interaction vertex document\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Database ID (0 if not known)\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 3, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all interactions\n", - "required": "required", - "default": "interaction" - }, - { - "key": 4, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "interaction.Interaction" - }, - "doc": "properties of interaction as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexKineticRate", - "doc": "KineticRate vertex document\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Database ID (0 if not known)\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 3, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all kinetic rates\n", - "required": "required", - "default": "kineticrate" - }, - { - "key": 4, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "kineticrate.KineticRate" - }, - "doc": "properties of interaction as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexPhase", - "doc": "Phase vertex document\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Database ID (0 if not known)\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 3, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all phases\n", - "required": "required", - "default": "phase" - }, - { - "key": 4, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "phase.Phase" - }, - "doc": "properties of phase as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexComposition", - "doc": "Composition entity vertex document\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Database ID (0 if not known)\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 3, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all composition entities\n", - "required": "required", - "default": "composition" - }, - { - "key": 4, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "composition.Composition" - }, - "doc": "properties of composition as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexChemEqSysDef", - "doc": "Chemical system definition (chemsysdef) vertex document\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Database ID (0 if not known)\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 3, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all chemical system definitions\n", - "required": "required", - "default": "chemeqsysdef" - }, - { - "key": 4, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "chemeqsysdef.ChemEqSysDef" - }, - "doc": "properties of chemsystdef as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexChemEqSysRecipe", - "doc": "Chemical system instance recipe vertex document\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Database ID (0 if not known)\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 3, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all chemical system recipes\n", - "required": "required", - "default": "chemeqsysrecipe" - }, - { - "key": 4, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "chemeqsysrecipe.ChemEqSysRecipe" - }, - "doc": "properties of recipe as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "VertexChemEqSpeciation", - "doc": "Chemical system instance recipe vertex document\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "Database ID (0 if not known)\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "This field must contain \"vertex\"\n", - "required": "required", - "default": "vertex" - }, - { - "key": 3, - "name": "_label", - "typeId": "string", - "doc": "This label should be the same for all chemical system recipes\n", - "required": "required", - "default": "chemeqspeciation" - }, - { - "key": 4, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "chemeqspeciation.ChemEqSpeciation" - }, - "doc": "properties of recipe as embedded object\n", - "required": "req_out" - } - ] - }, - { - "name": "Citing", - "doc": "Edge: citing (properties for citing edges)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "for_field", - "typeId": "string", - "doc": "Data field path connected to DS e.g. { \"for_field\": \"properties.entropy.values.0\" }\n", - "required": "req_out" - } - ] - }, - { - "name": "EdgeCiting", - "doc": "Edge of type \"citing\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "2", "5", "6.1", "3", "4" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this edge record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\"\n", - "required": "required", - "default": "edge" - }, - { - "key": 3, - "name": "_outV", - "typeId": "string", - "doc": "id of outgoing vertex of any type\n", - "required": "required" - }, - { - "key": 4, - "name": "_inV", - "typeId": "string", - "doc": "id of incoming datasource vertex\n", - "required": "required" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"citing\"\n", - "required": "required", - "default": "citing" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Citing" - }, - "doc": "Properties of citing edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Inherits", - "doc": "Edge inherits (properties for inherits edges)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "for_property", - "typeId": "string", - "doc": "Fieldpath or short name for property, e.g. \"for_property\" \"sG0\"\n", - "required": "req_out" - }, - { - "key": 2, - "name": "asop", - "typeId": "string", - "doc": "This string identifies the relation: { \"asop\": \"equal\" } | ...\n", - "required": "req_out" - } - ] - }, - { - "name": "EdgeInherits", - "doc": "Edge of type \"inherits\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "2", "5", "6.1", "6.2", "3", "4" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this edge record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\"\n", - "required": "required", - "default": "edge" - }, - { - "key": 3, - "name": "_outV", - "typeId": "string", - "doc": "id of outgoing vertex from which the property is inherited\n", - "required": "required" - }, - { - "key": 4, - "name": "_inV", - "typeId": "string", - "doc": "id of incoming vertex which inherits the property\n", - "required": "required" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"inherits\"\n", - "required": "required", - "default": "inherits" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Inherits" - }, - "doc": "Properties of inherits edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Sstate", - "doc": "Edge sstate: connecting a substance representing a standard state of an element to the corresponding element\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "stoi_coeff", - "typeId": "double", - "doc": "Stoichiometry coefficient of element in substance, e.g. 1 for C; 2 for O2\n", - "required": "req_out" - } - ] - }, - { - "name": "EdgeSstate", - "doc": "Edge of type \"sstate\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "2", "5", "6.1", "3", "4" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this edge record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\"\n", - "required": "required", - "default": "edge" - }, - { - "key": 3, - "name": "_outV", - "typeId": "string", - "doc": "id of outgoing element vertex\n", - "required": "required" - }, - { - "key": 4, - "name": "_inV", - "typeId": "string", - "doc": "id of incoming substance vertex\n", - "required": "required" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"sstate\"\n", - "required": "required", - "default": "sstate" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Sstate" - }, - "doc": "Properties of sstate edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Takes", - "doc": "Edge: takes (properties for \"takes\" edges)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "stoi_coeff", - "typeId": "double", - "doc": "Stoichiometry coefficient: negative for reactants, positive for products { \"SC\": -0.5 }\n", - "required": "req_out" - }, - { - "key": 2, - "name": "rct", - "typeId": "i32", - "doc": "Reaction component type: enum validated with class ReactionComponentType\n", - "class": "ReactionComponentType", - "required": "req_out" - } - ] - }, - { - "name": "EdgeTakes", - "doc": "Edge of type \"takes\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "2", "5", "6.1", "6.2", "3", "4" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this edge record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\"\n", - "required": "required", - "default": "edge" - }, - { - "key": 3, - "name": "_outV", - "typeId": "string", - "doc": "id of outgoing reaction vertex\n", - "required": "required" - }, - { - "key": 4, - "name": "_inV", - "typeId": "string", - "doc": "id of incoming substance vertex\n", - "required": "required" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"takes\"\n", - "required": "required", - "default": "takes" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Takes" - }, - "doc": "Properties of takes edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Defines", - "doc": "Edge defines (properties for defines edges) for product substance defined via reaction\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "for_prop", - "typeId": "string", - "doc": "This string contains one of the keywords for substance properties, e.g. \"for_prop\" \"whole\"\n", - "required": "req_out" - }, - { - "key": 2, - "name": "asop", - "typeId": "string", - "doc": "This string identifies the relation: { \"asop\": \"retrieved\" } | ...\n", - "required": "req_out" - }, - { - "key": 3, - "name": "level", - "typeId": "i32", - "doc": "Level (color) of this reaction 0 | 1 | 2 | 3 | 4 | ...\n", - "required": "req_out" - } - ] - }, - { - "name": "EdgeDefines", - "doc": "Edge of type \"defines\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "2", "5", "6.1", "6.2", "3", "4" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this edge record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\"\n", - "required": "required", - "default": "edge" - }, - { - "key": 3, - "name": "_outV", - "typeId": "string", - "doc": "id of outgoing reaction vertex\n", - "required": "required" - }, - { - "key": 4, - "name": "_inV", - "typeId": "string", - "doc": "id of incoming species vertex\n", - "required": "required" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"defines\"\n", - "required": "required", - "default": "defines" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Defines" - }, - "doc": "Properties of defines edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Master", - "doc": "Edge master (properties for master edges) for master species in reactionset\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "ms_type", - "typeId": "i32", - "doc": "Type of master species - validated by enum class SpeciesTypeRS\n", - "class": "SpeciesTypeRS", - "required": "req_out" - } - ] - }, - { - "name": "EdgeMaster", - "doc": "Edge of type \"defines\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "2", "5", "6.1", "3", "4" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this edge record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\"\n", - "required": "required", - "default": "edge" - }, - { - "key": 3, - "name": "_outV", - "typeId": "string", - "doc": "id of outgoing reactionset vertex\n", - "required": "required" - }, - { - "key": 4, - "name": "_inV", - "typeId": "string", - "doc": "id of incoming species vertex\n", - "required": "required" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"master\"\n", - "required": "required", - "default": "master" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Master" - }, - "doc": "Properties of master edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Product", - "doc": "Edge product (properties for product edges) for product species in reactionset\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "ps_type", - "typeId": "i32", - "doc": "Type of master species - validated by enum class SpeciesTypeRS\n", - "class": "SpeciesTypeRS", - "required": "req_out" - } - ] - }, - { - "name": "EdgeProduct", - "doc": "Edge of type \"defines\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "2", "5", "6.1", "3", "4" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this edge record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\"\n", - "required": "required", - "default": "edge" - }, - { - "key": 3, - "name": "_outV", - "typeId": "string", - "doc": "id of outgoing reactionset vertex\n", - "required": "required" - }, - { - "key": 4, - "name": "_inV", - "typeId": "string", - "doc": "id of incoming species vertex\n", - "required": "required" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"product\"\n", - "required": "required", - "default": "product" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Product" - }, - "doc": "Properties of product edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Prodreac", - "doc": "Edge: Prodreac (properties for \"prodreac\" edges) defining reactions for product species in reactionset\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "for_ps", - "typeId": "string", - "doc": "This string contains sybmol of substance - one of the product species\n", - "required": "req_out" - }, - { - "key": 2, - "name": "level", - "typeId": "i32", - "doc": "Level (of alternative or generated reaction)\n", - "required": "req_out" - } - ] - }, - { - "name": "EdgeProdreac", - "doc": "Edge of type \"prodreac\" definition\n", - "isException": false, - "isUnion": false, - "to_select": [ "1", "2", "5", "6.1", "6.2", "3", "4" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this edge record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\"\n", - "required": "required", - "default": "edge" - }, - { - "key": 3, - "name": "_outV", - "typeId": "string", - "doc": "id of outgoing reactionset vertex\n", - "required": "required" - }, - { - "key": 4, - "name": "_inV", - "typeId": "string", - "doc": "id of incoming reaction vertex\n", - "required": "required" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"prodreac\"\n", - "required": "required", - "default": "prodreac" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Prodreac" - }, - "doc": "Properties of prodreac edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Combined", - "doc": "Edge: Combined (properties for \"combined\" edges) defining reactions combined in an isocoulombic reaction\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "coeff", - "typeId": "double", - "doc": "coefficient of the combined reaction\n", - "required": "req_out" - }, - { - "key": 2, - "name": "rc_type", - "typeId": "i32", - "doc": "Type of combined reaction, INVESTIGATED or MODEL\n", - "required": "req_out" - }, - { - "key": 3, - "name": "level", - "typeId": "i32", - "doc": "Level (of alternative or generated reaction)\n", - "required": "req_out" - } - ] - }, - { - "name": "EdgeCombined", - "doc": "Edge of type \"prodreac\" definition\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this edge record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\"\n", - "required": "required", - "default": "edge" - }, - { - "key": 3, - "name": "_outV", - "typeId": "string", - "doc": "id of outgoing reaction vertex\n", - "required": "required" - }, - { - "key": 4, - "name": "_inV", - "typeId": "string", - "doc": "id of incoming isocoulombic reaction vertex\n", - "required": "required" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"combined\"\n", - "required": "required", - "default": "combined" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Combined" - }, - "doc": "Properties of combined edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Basis", - "doc": "Edge: Basis (linking to elements or ligands or other basis species)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "b_type", - "typeId": "string", - "doc": "Type of basis component\n", - "required": "req_out" - } - ] - }, - { - "name": "EdgeBasis", - "doc": "Edge of type \"basis\" definition\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this edge record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\"\n", - "required": "required", - "default": "edge" - }, - { - "key": 3, - "name": "_outV", - "typeId": "string", - "doc": "id of outgoing element vertex\n", - "required": "required" - }, - { - "key": 4, - "name": "_inV", - "typeId": "string", - "doc": "id of incoming thermodataset vertex\n", - "required": "required" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"basis\"\n", - "required": "required", - "default": "basis" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Basis" - }, - "doc": "Properties of basis edge\n", - "required": "optional" - } - ] - }, - { - "name": "Pulls", - "doc": "Edge: Pulls (linking to substances or master species)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "level_of_data", - "typeId": "string", - "required": "req_out" - } - ] - }, - { - "name": "EdgePulls", - "doc": "Edge of type \"pulls\" definition\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this edge record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\"\n", - "required": "required", - "default": "edge" - }, - { - "key": 3, - "name": "_outV", - "typeId": "string", - "doc": "id of outgoing substance vertex\n", - "required": "required" - }, - { - "key": 4, - "name": "_inV", - "typeId": "string", - "doc": "id of incoming thermodataset vertex\n", - "required": "required" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"pulls\"\n", - "required": "required", - "default": "pulls" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Pulls" - }, - "doc": "Properties of pulls edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Involves", - "doc": "Edge: Involves (linking to Reactionset instance for LMA_TDS)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "level_of_data", - "typeId": "string", - "required": "optional" - } - ] - }, - { - "name": "EdgeInvolves", - "doc": "Edge of type \"involves\" definition\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this edge record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\"\n", - "required": "required", - "default": "edge" - }, - { - "key": 3, - "name": "_outV", - "typeId": "string", - "doc": "id of outgoing reactionset vertex\n", - "required": "required" - }, - { - "key": 4, - "name": "_inV", - "typeId": "string", - "doc": "id of incoming thermodataset vertex\n", - "required": "required" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"involves\"\n", - "required": "required", - "default": "involves" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Involves" - }, - "doc": "Properties of involves edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Interacts", - "doc": "Edge: interacts (properties for \"interacts\" edges)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "weight", - "typeId": "double", - "doc": "{ \"weight\": 1 } set to 1.0 for now\n", - "required": "req_out" - }, - { - "key": 2, - "name": "level", - "typeId": "i32", - "doc": "Level (of alternative or generated interaction)\n", - "required": "req_out" - } - ] - }, - { - "name": "EdgeInteracts", - "doc": "Edge of type \"interacts\" definition\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this edge record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\"\n", - "required": "required", - "default": "edge" - }, - { - "key": 3, - "name": "_outV", - "typeId": "string", - "doc": "id of outgoing substance vertex\n", - "required": "required" - }, - { - "key": 4, - "name": "_inV", - "typeId": "string", - "doc": "id of incoming interaction vertex\n", - "required": "required" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"interacts\"\n", - "required": "required", - "default": "interacts" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Interacts" - }, - "doc": "Properties of interacts edge\n", - "required": "optional" - } - ] - }, - { - "name": "Specific", - "doc": "Edge: specific (properties for \"specific\" edges connecting interactions with the phase\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "weight", - "typeId": "double", - "doc": "{ \"weight\": 1 } set to 1.0 for now\n", - "required": "req_out" - }, - { - "key": 2, - "name": "level", - "typeId": "i32", - "doc": "Level (of alternative or generated interaction)\n", - "required": "req_out" - } - ] - }, - { - "name": "EdgeSpecific", - "doc": "Edge of type \"specific\" definition\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this edge record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\"\n", - "required": "required", - "default": "edge" - }, - { - "key": 3, - "name": "_outV", - "typeId": "string", - "doc": "id of outgoing interaction vertex\n", - "required": "required" - }, - { - "key": 4, - "name": "_inV", - "typeId": "string", - "doc": "id of incoming phase vertex\n", - "required": "required" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"specific\"\n", - "required": "required", - "default": "specific" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Specific" - }, - "doc": "Properties of specific edge\n", - "required": "optional" - } - ] - }, - { - "name": "Kinetics", - "doc": "Edge: kinetics (properties for \"kinetics\" edges)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "weight", - "typeId": "double", - "doc": "{ \"weight\": 1 } set to 1.0 for now\n", - "required": "req_out" - }, - { - "key": 2, - "name": "level", - "typeId": "i32", - "doc": "Level (of alternative or generated interaction)\n", - "required": "req_out" - }, - { - "key": 3, - "name": "order", - "typeId": "double", - "doc": "Generic order of kinetics for this mechanism in the phase\n", - "required": "optional" - } - ] - }, - { - "name": "EdgeKinetics", - "doc": "Edge of type \"interacts\" definition\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this edge record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\"\n", - "required": "required", - "default": "edge" - }, - { - "key": 3, - "name": "_outV", - "typeId": "string", - "doc": "id of outgoing kineticrate vertex\n", - "required": "required" - }, - { - "key": 4, - "name": "_inV", - "typeId": "string", - "doc": "id of incoming phase vertex\n", - "required": "required" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"kinetics\"\n", - "required": "required", - "default": "kinetics" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Kinetics" - }, - "doc": "Properties of kinetics edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Kinspecies", - "doc": "Edge: kinetic link to species used in activity terms (properties for \"kinspecies\" edges)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "weight", - "typeId": "double", - "doc": "{ \"weight\": 1 } set to 1.0 for now\n", - "required": "req_out" - }, - { - "key": 2, - "name": "level", - "typeId": "i32", - "doc": "Level (of alternative or generated interaction)\n", - "required": "req_out" - }, - { - "key": 3, - "name": "order", - "typeId": "double", - "doc": "Order (power at activity) for this mechanism relative to the species (substance or moiety)\n", - "required": "req_out" - } - ] - }, - { - "name": "EdgeKinspecies", - "doc": "Edge of type \"kinspecies\" definition\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this edge record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\"\n", - "required": "required", - "default": "edge" - }, - { - "key": 3, - "name": "_outV", - "typeId": "string", - "doc": "id of outgoing kineticrate vertex\n", - "required": "required" - }, - { - "key": 4, - "name": "_inV", - "typeId": "string", - "doc": "id of incoming substance vertex\n", - "required": "required" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"kinspecies\"\n", - "required": "required", - "default": "kinspecies" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Kinspecies" - }, - "doc": "Properties of kinspecies edge\n", - "required": "optional" - } - ] - }, - { - "name": "Component", - "doc": "Edge component (properties for phase end member) for components in phase\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "pc_type", - "typeId": "i32", - "doc": "Type of phase component - validated by enum class SubstanceClass in prop\n", - "required": "req_out", - "default": 0 - }, - { - "key": 2, - "name": "pc_conscale", - "typeId": "i32", - "doc": "Concentration scale used in this phase model of mixing\n", - "required": "req_out", - "default": 0 - }, - { - "key": 3, - "name": "pc_props", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Optional properties of this component in the phase e.g. Kielland ion radius\n", - "required": "optional", - "default": { - "name": "PCP" - } - }, - { - "key": 4, - "name": "pc_uptake", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Optional parameters for the uptake kinetics model (UUCM)\n", - "required": "req_out", - "default": { - "name": "UUCMP" - } - } - ] - }, - { - "name": "EdgeComponent", - "doc": "Edge of type \"component\" definition\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this edge record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\"\n", - "required": "required", - "default": "edge" - }, - { - "key": 3, - "name": "_outV", - "typeId": "string", - "doc": "id of outgoing reactionset vertex\n", - "required": "required" - }, - { - "key": 4, - "name": "_inV", - "typeId": "string", - "doc": "id of incoming species vertex\n", - "required": "required" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"component\"\n", - "required": "required", - "default": "component" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Component" - }, - "doc": "Properties of component edge\n", - "required": "optional" - } - ] - }, - { - "name": "SiteMoiety", - "doc": "Edge sitemoiety (properties for moiety) for phase with sublattice model of mixing\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "sm_type", - "typeId": "i32", - "doc": "Type of edge - validated by enum class SpeciesTypeRS\n", - "required": "req_out", - "default": 5 - }, - { - "key": 2, - "name": "pc_props", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Optional properties of this site moiety\n", - "required": "req_out", - "default": { - "name": "SMP" - } - }, - { - "key": 3, - "name": "pc_conscale", - "typeId": "i32", - "doc": "Concentration scale used in this phase model of mixing for this moiety\n", - "required": "req_out", - "default": 8 - }, - { - "key": 4, - "name": "site_index", - "typeId": "i16", - "doc": "Index of site (sublattice) to which this moiety is assigned\n", - "required": "optional", - "default": 0 - } - ] - }, - { - "name": "EdgeSiteMoiety", - "doc": "Edge of type \"component\" definition\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this edge record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\"\n", - "required": "required", - "default": "edge" - }, - { - "key": 3, - "name": "_outV", - "typeId": "string", - "doc": "id of outgoing reactionset vertex\n", - "required": "required" - }, - { - "key": 4, - "name": "_inV", - "typeId": "string", - "doc": "id of incoming species vertex\n", - "required": "required" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"sitemoiety\"\n", - "required": "required", - "default": "sitemoiety" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Component" - }, - "doc": "Properties of sitemoiety edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Adds", - "doc": "Edge: Adds (linking to substance or composition formula)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "q", - "typeId": "double", - "required": "req_out" - }, - { - "key": 2, - "name": "unit", - "typeId": "string", - "doc": "units of measurement for this quantity\n", - "required": "req_out" - } - ] - }, - { - "name": "EdgeAdds", - "doc": "Edge of type \"adds\" definition\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this edge record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\"\n", - "required": "required", - "default": "edge" - }, - { - "key": 3, - "name": "_outV", - "typeId": "string", - "doc": "id of outgoing Composition or Chemsystem (recipe) vertex\n", - "required": "required" - }, - { - "key": 4, - "name": "_inV", - "typeId": "string", - "doc": "id of incoming substance or composition vertex\n", - "required": "required" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"adds\"\n", - "required": "required", - "default": "adds" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Adds" - }, - "doc": "Properties of adds edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Collects", - "doc": "Edge: Colllects (linking to phases)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "rank", - "typeId": "i32", - "required": "req_out" - } - ] - }, - { - "name": "EdgeCollects", - "doc": "Edge of type \"collects\" definition\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this edge record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\"\n", - "required": "required", - "default": "edge" - }, - { - "key": 3, - "name": "_outV", - "typeId": "string", - "doc": "id of outgoing ChemSysDef vertex\n", - "required": "required" - }, - { - "key": 4, - "name": "_inV", - "typeId": "string", - "doc": "id of incoming Phase vertex\n", - "required": "required" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"collects\"\n", - "required": "required", - "default": "collects" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Collects" - }, - "doc": "Properties of collects edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Uses", - "doc": "Edge: Uses (linking to thermodataset)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "mode", - "typeId": "string", - "required": "req_out" - } - ] - }, - { - "name": "EdgeUses", - "doc": "Edge of type \"uses\" definition\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this edge record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\"\n", - "required": "required", - "default": "edge" - }, - { - "key": 3, - "name": "_outV", - "typeId": "string", - "doc": "id of outgoing ChemSysDef vertex\n", - "required": "required" - }, - { - "key": 4, - "name": "_inV", - "typeId": "string", - "doc": "id of incoming thermodataset vertex\n", - "required": "required" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"uses\"\n", - "required": "required", - "default": "uses" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Uses" - }, - "doc": "Properties of uses edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Belongs", - "doc": "Edge: Belongs (linking to thermodataset)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "mode", - "typeId": "string", - "required": "req_out" - } - ] - }, - { - "name": "EdgeBelongs", - "doc": "Edge of type \"uses\" definition\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this edge record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\"\n", - "required": "required", - "default": "edge" - }, - { - "key": 3, - "name": "_outV", - "typeId": "string", - "doc": "id of outgoing ChemSysDef vertex\n", - "required": "required" - }, - { - "key": 4, - "name": "_inV", - "typeId": "string", - "doc": "id of incoming thermodataset vertex\n", - "required": "required" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"belongs\"\n", - "required": "required", - "default": "belongs" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Belongs" - }, - "doc": "Properties of belongs edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Yields", - "doc": "Edge: Yields (linking from recipe to speciation)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "Iniguess", - "typeId": "string", - "required": "req_out" - }, - { - "key": 2, - "name": "Time", - "typeId": "string", - "required": "req_out" - } - ] - }, - { - "name": "EdgeYields", - "doc": "Edge of type \"uses\" definition\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this edge record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\"\n", - "required": "required", - "default": "edge" - }, - { - "key": 3, - "name": "_outV", - "typeId": "string", - "doc": "id of outgoing ChemSysDef vertex\n", - "required": "required" - }, - { - "key": 4, - "name": "_inV", - "typeId": "string", - "doc": "id of incoming thermodataset vertex\n", - "required": "required" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"yields\"\n", - "required": "required", - "default": "yields" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "Yields" - }, - "doc": "Properties of yields edge\n", - "required": "req_out" - } - ] - }, - { - "name": "EqState", - "doc": "Edge: EqState (linking to thermodataset)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "T", - "typeId": "double", - "required": "req_out" - }, - { - "key": 2, - "name": "P", - "typeId": "double", - "required": "req_out" - }, - { - "key": 3, - "name": "V", - "typeId": "double", - "required": "req_out" - }, - { - "key": 4, - "name": "H", - "typeId": "double", - "required": "req_out" - }, - { - "key": 5, - "name": "U", - "typeId": "double", - "required": "req_out" - }, - { - "key": 6, - "name": "S", - "typeId": "double", - "required": "req_out" - } - ] - }, - { - "name": "EdgeEqState", - "doc": "Edge of type \"uses\" definition\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this edge record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\"\n", - "required": "required", - "default": "edge" - }, - { - "key": 3, - "name": "_outV", - "typeId": "string", - "doc": "id of outgoing ChemSysDef vertex\n", - "required": "required" - }, - { - "key": 4, - "name": "_inV", - "typeId": "string", - "doc": "id of incoming thermodataset vertex\n", - "required": "required" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"EqState\"\n", - "required": "required", - "default": "eqstate" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EqState" - }, - "doc": "Properties of eqstate edge\n", - "required": "req_out" - } - ] - }, - { - "name": "MadeOf", - "doc": "Edge: MadeOf (linking recipe to recipe)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "mode", - "typeId": "string", - "required": "req_out" - } - ] - }, - { - "name": "EdgeMadeOf", - "doc": "Edge of type \"uses\" definition\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this edge record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_type", - "typeId": "string", - "doc": "this must be always \"edge\"\n", - "required": "required", - "default": "edge" - }, - { - "key": 3, - "name": "_outV", - "typeId": "string", - "doc": "id of outgoing ChemSysDef vertex\n", - "required": "required" - }, - { - "key": 4, - "name": "_inV", - "typeId": "string", - "doc": "id of incoming thermodataset vertex\n", - "required": "required" - }, - { - "key": 5, - "name": "_label", - "typeId": "string", - "doc": "This label must be \"madeof\"\n", - "required": "required", - "default": "madeof" - }, - { - "key": 6, - "name": "properties", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "MadeOf" - }, - "doc": "Properties of belongs edge\n", - "required": "req_out" - } - ] - }, - { - "name": "Vertex", - "doc": "Generalized vertex\n", - "isException": false, - "isUnion": true, - "fields": [ - { - "key": 1, - "name": "v_datasource", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexDataSource" - }, - "required": "optional" - }, - { - "key": 2, - "name": "v_element", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexElement" - }, - "required": "optional" - }, - { - "key": 3, - "name": "v_substance", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexSubstance" - }, - "required": "optional" - }, - { - "key": 4, - "name": "v_reaction", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexReaction" - }, - "required": "optional" - }, - { - "key": 5, - "name": "v_reactionset", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexReactionSet" - }, - "required": "optional" - }, - { - "key": 6, - "name": "v_thermodataset", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexThermoDataSet" - }, - "required": "optional" - }, - { - "key": 7, - "name": "v_interaction", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexInteraction" - }, - "required": "optional" - }, - { - "key": 8, - "name": "v_kineticrate", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexKineticRate" - }, - "required": "optional" - }, - { - "key": 9, - "name": "v_phase", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexPhase" - }, - "required": "optional" - }, - { - "key": 10, - "name": "v_composition", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexComposition" - }, - "required": "optional" - }, - { - "key": 11, - "name": "v_chemeqsysdef", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexChemEqSysDef" - }, - "required": "optional" - }, - { - "key": 12, - "name": "v_chemeqsysrecipe", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexChemEqSysRecipe" - }, - "required": "optional" - }, - { - "key": 13, - "name": "v_chemeqspeciation", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "VertexChemEqSpeciation" - }, - "required": "optional" - } - ] - }, - { - "name": "Edge", - "doc": "Generalized edge\n", - "isException": false, - "isUnion": true, - "fields": [ - { - "key": 1, - "name": "e_citing", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeCiting" - }, - "required": "optional" - }, - { - "key": 2, - "name": "e_inherits", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeInherits" - }, - "required": "optional" - }, - { - "key": 3, - "name": "e_sstate", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeSstate" - }, - "required": "optional" - }, - { - "key": 4, - "name": "e_takes", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeTakes" - }, - "required": "optional" - }, - { - "key": 5, - "name": "e_defines", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeDefines" - }, - "required": "optional" - }, - { - "key": 6, - "name": "e_master", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeMaster" - }, - "required": "optional" - }, - { - "key": 7, - "name": "e_product", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeProduct" - }, - "required": "optional" - }, - { - "key": 8, - "name": "e_prodreac", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeProdreac" - }, - "required": "optional" - }, - { - "key": 9, - "name": "e_combined", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeCombined" - }, - "required": "optional" - }, - { - "key": 10, - "name": "e_basis", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeBasis" - }, - "required": "optional" - }, - { - "key": 11, - "name": "e_pulls", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgePulls" - }, - "required": "optional" - }, - { - "key": 12, - "name": "e_involves", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeInvolves" - }, - "required": "optional" - }, - { - "key": 13, - "name": "e_specific", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeSpecific" - }, - "required": "optional" - }, - { - "key": 14, - "name": "e_interacts", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeInteracts" - }, - "required": "optional" - }, - { - "key": 15, - "name": "e_kinetics", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeKinetics" - }, - "required": "optional" - }, - { - "key": 16, - "name": "e_kinspecies", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeKinspecies" - }, - "required": "optional" - }, - { - "key": 17, - "name": "e_component", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeComponent" - }, - "required": "optional" - }, - { - "key": 18, - "name": "e_sitemoiety", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeSiteMoiety" - }, - "required": "optional" - }, - { - "key": 19, - "name": "e_adds", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeAdds" - }, - "required": "optional" - }, - { - "key": 20, - "name": "e_collects", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeCollects" - }, - "required": "optional" - }, - { - "key": 21, - "name": "e_uses", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeUses" - }, - "required": "optional" - }, - { - "key": 22, - "name": "e_belongs", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeBelongs" - }, - "required": "optional" - }, - { - "key": 23, - "name": "e_yields", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeYields" - }, - "required": "optional" - }, - { - "key": 24, - "name": "e_eqstate", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeEqState" - }, - "required": "optional" - }, - { - "key": 25, - "name": "e_madeof", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "EdgeMadeOf" - }, - "required": "optional" - } - ] - }, - { - "name": "GraphData", - "doc": "Generalized graph data (file)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "mode", - "typeId": "string", - "doc": "Mode of rendering NORMAL [ | EXTENDED | COMPACT ]\n", - "required": "req_out", - "default": "NORMAL" - }, - { - "key": 2, - "name": "vertices", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "union", - "elemType": { - "typeId": "union", - "class": "Vertex" - } - }, - "doc": "List of vertices (documents), can be empty (followed by only graph edges)\n", - "required": "req_out" - }, - { - "key": 3, - "name": "edges", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "union", - "elemType": { - "typeId": "union", - "class": "Edge" - } - }, - "doc": "list of edges (graph links), can be empty for a non-graph data (with only documents)\n", - "required": "req_out" - } - ] - } - ], - "constants": [ - ], - "services": [ - ] -} diff --git a/Resources/data/schemas/phase.schema.json b/Resources/data/schemas/phase.schema.json deleted file mode 100644 index 8dd51017..00000000 --- a/Resources/data/schemas/phase.schema.json +++ /dev/null @@ -1,534 +0,0 @@ -{ - "name": "phase", - "doc": "Apache Thrift IDL definition for the phase service interface\n", - "namespaces": { - "*": "phase" - }, - "includes": [ -"prop", -"element", -"substance", -"interaction", -"mixingmodel", -"kineticrate", -"kineticmodel" - ], - "enums": [ - ], - "typedefs": [ - ], - "structs": [ - { - "name": "Phase", - "doc": "Description of (thermodynamic) phase\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "symbol", - "typeId": "string", - "doc": "unique name\/ID of this phase (e.g. \"bentpw\")\n", - "required": "required" - }, - { - "key": 2, - "name": "sourcetdb", - "class": "SourceTDB", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Source TDB: enum validated with class SourceTDB - do we need it or thermodataset is enough?\n", - "required": "required" - }, - { - "key": 3, - "name": "thermodataset", - "typeId": "string", - "doc": "Used thermodataset symbol (also phaseinvolves link)\n", - "required": "required" - }, - { - "key": 4, - "name": "name", - "typeId": "string", - "doc": "Extended name comment of the phase (e.g. \"aqueous electrolyte Davies model\")\n", - "required": "req_out" - }, - { - "key": 5, - "name": "aggregate_state", - "class": "AggregateState", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Aggregate state of this phase: enum validated with class AggregateState\n", - "required": "req_out" - }, - { - "key": 6, - "name": "mixmod", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Model of mixing - validate using class MixModel in interaction\n", - "class": "MixModel", - "required": "req_out", - "default": { - "0": "M_PURE" - } - }, - { - "key": 7, - "name": "kinratemod", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Kinetic rate model - validate using class RateModel in kineticrate\n", - "class": "RateModel", - "required": "req_out", - "default": { - "0": "KIN_INSTANT" - } - }, - { - "key": 11, - "name": "associatedProperties", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "prop.Item" - } - }, - "doc": "list of possile asociated indirect properties which are calculated using an expression\n", - "required": "req_out" - }, - { - "key": 13, - "name": "associatedPropertiesExpressions", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "expression, lua script for calculating property values (e.g. molar ratio of element in phase, mChainL, Rd); same order as in associatedProperties\n", - "required": "req_out" - }, - { - "key": 15, - "name": "SpecSurfaceArea", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Specific surface area of (carrier) phase\n", - "required": "req_out" - }, - { - "key": 16, - "name": "SpecPoreVolume", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "new: Specific pore volume of (carrier) phase, m3\/g (default: 0)\n", - "required": "req_out" - }, - { - "key": 17, - "name": "PermSurfChargeDensity", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "new: permanent surface charge density (eq\/m2), default: 0\n", - "required": "req_out" - }, - { - "key": 18, - "name": "PermVolumeChargeDensity", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "new: permanent Donnan volume charge density (eq\/m3), default: 0\n", - "required": "req_out" - }, - { - "key": 19, - "name": "IonExchangeCapacity", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "new: ion exchange capacity (eg\/g), default: 0\n", - "required": "req_out" - }, - { - "key": 22, - "name": "elements", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "Set of elements (IComps) represented in all components of the phase\n", - "required": "req_out" - }, - { - "key": 24, - "name": "substances", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "Set of substances (components, end members) of the phase\n", - "required": "req_out" - }, - { - "key": 25, - "name": "Ncomps", - "typeId": "i32", - "doc": "Number of phase components incl solvents\n", - "required": "req_out", - "default": 1 - }, - { - "key": 27, - "name": "limitsTP", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.LimitsTP" - }, - "doc": "Overall lower and upper T, P limits for T,P corrections\n", - "required": "req_out", - "default": { - "range": 0, - "lowerT": 273.15, - "upperT": 298.15, - "lowerP": 0.1, - "upperP": 1000000 - } - }, - { - "key": 28, - "name": "comment", - "typeId": "string", - "doc": "Comment - e.g. who entered\/modified, ...\n", - "required": "optional" - }, - { - "key": 29, - "name": "datasources", - "typeId": "set", - "type": { - "typeId": "set", - "elemTypeId": "string" - }, - "doc": "Labels of datasource DB objects\n", - "required": "optional" - }, - { - "key": 30, - "name": "time_stamp", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.TimeStamp" - }, - "doc": "Timestamp when the record was created or modified\n", - "required": "optional" - }, - { - "key": 2001, - "name": "temp_import", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "Field for storing temporary values needed during import script\n", - "required": "optional" - } - ] - }, - { - "name": "Phases", - "doc": "Definition of an array of phases\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 2, - "name": "phases", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "Phase" - } - }, - "doc": "List of chemical thermodynamic phases\n", - "required": "req_out" - } - ] - }, - { - "name": "PhaseInfo", - "doc": "Short description of phase (for using in ChemSysDef etc.)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "symbol", - "typeId": "string", - "doc": "unique name\/ID of this phase (e.g. \"bentpw\")\n", - "required": "required" - }, - { - "key": 2, - "name": "aggregate_state", - "typeId": "i32", - "doc": "Aggregate state of this phase: enum validated with class AggregateState\n", - "class": "AggregateState", - "required": "req_out" - }, - { - "key": 3, - "name": "mixmod", - "typeId": "i32", - "doc": "Model of mixing - validate using class MixModel in interaction\n", - "class": "MixModel", - "required": "req_out" - }, - { - "key": 4, - "name": "kinratemod", - "typeId": "i32", - "doc": "Kinetic rate model - validate using class RateModel in kineticrate\n", - "class": "RateModel", - "required": "req_out" - }, - { - "key": 5, - "name": "Ncomps", - "typeId": "i32", - "doc": "Number of phase components incl solvents\n", - "required": "req_out" - } - ] - }, - { - "name": "pcdata", - "doc": "Data extracted from a substance connected to the phase via components edges\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "SC", - "typeId": "double", - "required": "req_out" - }, - { - "key": 2, - "name": "units", - "typeId": "string", - "required": "req_out" - }, - { - "key": 3, - "name": "subsid", - "typeId": "i32", - "required": "optional" - }, - { - "key": 4, - "name": "symbol", - "typeId": "string", - "required": "optional" - }, - { - "key": 5, - "name": "formula", - "typeId": "string", - "required": "optional" - }, - { - "key": 6, - "name": "subsx", - "typeId": "i32", - "required": "optional" - } - ] - }, - { - "name": "psmdata", - "doc": "Data extracted from a substance\/moiety connected to the phase via sitemoieties edges\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "siteid", - "typeId": "string", - "required": "req_out" - }, - { - "key": 3, - "name": "subsid", - "typeId": "i32", - "required": "optional" - }, - { - "key": 4, - "name": "symbol", - "typeId": "string", - "required": "optional" - }, - { - "key": 5, - "name": "moix", - "typeId": "i32", - "required": "optional" - } - ] - }, - { - "name": "phasedata", - "doc": "Work structure keeping the data to assemble\/check\/calculate the phase\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "Nelems", - "typeId": "i16", - "required": "req_out" - }, - { - "key": 2, - "name": "elems", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "required": "req_out" - }, - { - "key": 3, - "name": "Ncomps", - "typeId": "i16", - "required": "req_out" - }, - { - "key": 4, - "name": "ctype", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "required": "req_out" - }, - { - "key": 5, - "name": "comps", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "pcdata" - } - }, - "required": "req_out" - }, - { - "key": 6, - "name": "Nsites", - "typeId": "i16", - "required": "req_out" - }, - { - "key": 7, - "name": "sites", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "required": "req_out" - }, - { - "key": 8, - "name": "smult", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "double" - }, - "required": "req_out" - }, - { - "key": 9, - "name": "Nsmois", - "typeId": "i16", - "required": "req_out" - }, - { - "key": 10, - "name": "smois", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "psmdata" - } - }, - "required": "req_out" - }, - { - "key": 21, - "name": "computed", - "typeId": "bool", - "required": "req_out", - "default": 0 - } - ] - } - ], - "constants": [ - ], - "services": [ - ] -} diff --git a/Resources/data/schemas/prop.schema.json b/Resources/data/schemas/prop.schema.json deleted file mode 100644 index 0ba21668..00000000 --- a/Resources/data/schemas/prop.schema.json +++ /dev/null @@ -1,1163 +0,0 @@ -{ - "name": "prop", - "doc": "Apache Thrift IDL definition for the properties service interface\n", - "namespaces": { - "*": "prop" - }, - "includes": [ - ], - "enums": [ - { - "name": "ValueStatus", - "doc": "Current status of value(s)\n", - "members": [ - { - "name": "EMPTY", - "value": 0, - "doc": "No value provided\n" - }, - { - "name": "ENTERED", - "value": 1, - "doc": "Value entered\n" - }, - { - "name": "TOCALCULATE", - "value": 2, - "doc": "Value to be calculated\n" - }, - { - "name": "CALCULATED", - "value": 3, - "doc": "Value calculated\n" - }, - { - "name": "IMPORTED", - "value": 4, - "doc": "Value imported from external sources\n" - } - ] - }, - { - "name": "ErrorDistribution", - "doc": "Type of statistical distribution of errors\n", - "members": [ - { - "name": "NORMAL", - "value": 0, - "doc": "Normal error distribution\n" - }, - { - "name": "LOGNORMAL", - "value": 1, - "doc": "Lognormal error distribution\n" - }, - { - "name": "PARETO", - "value": 2, - "doc": "Pareto error distribution\n" - }, - { - "name": "UNIFORM", - "value": 3, - "doc": "Uniform error distribution\n" - }, - { - "name": "OTHER", - "value": 101, - "doc": "Other error distribution\n" - } - ] - }, - { - "name": "MeasurementUnits", - "doc": "Amount or concentration units for parts of compositions (SI units) - not used so far\n", - "members": [ - { - "name": "U_MOLAMOUNT", - "value": 0, - "doc": "Amount in moles\n" - }, - { - "name": "U_MOLFRACTION", - "value": 1, - "doc": "Mole fraction - needs total amount of moles Moles\n" - }, - { - "name": "U_PARTIALPRESSURE", - "value": 2, - "doc": "Partial pressure in Pa - needs total pressure Ptotal and total moles Moles\n" - }, - { - "name": "U_MOLALITY", - "value": 3, - "doc": "Molality in mol per kg - needs mass of water-solvent Mwater\n" - }, - { - "name": "U_MOLARITY", - "value": 4, - "doc": "Molarity in mol per dm3 - needs total volume of aqueous phase Vaqtotal\n" - }, - { - "name": "U_MASS", - "value": 5, - "doc": "Mass in kg\n" - }, - { - "name": "U_MASSFRACTION", - "value": 6, - "doc": "Mass fraction - needs total mass Mass\n" - }, - { - "name": "U_LENGTH", - "value": 7, - "doc": "Length in m\n" - }, - { - "name": "U_AREA", - "value": 8, - "doc": "Area in m2\n" - }, - { - "name": "U_VOLUME", - "value": 9, - "doc": "Volume in m3\n" - }, - { - "name": "U_SURFACEDENSITY", - "value": 10, - "doc": "Surface density in mol per m2 - needs total surface area SurfArea\n" - }, - { - "name": "U_SURFACEFRACTION", - "value": 11, - "doc": "Surface fraction - needs total amount of surface (site) species SurfMoles or SurfMolal\n" - }, - { - "name": "U_SPECIFICSURFACEAREA_MASS", - "value": 12, - "doc": "specific surface area per unit mass in m2 per kg - needs total mass Mass\n" - }, - { - "name": "U_SPECIFICSURFACEAREA_VOLUME", - "value": 13, - "doc": "specific surface area per unit volume in m2 per dm3 - needs total volume Volume\n" - }, - { - "name": "U_OTHER", - "value": 101, - "doc": "Other type of measurement unit\n" - } - ] - }, - { - "name": "ConcentrationScale", - "doc": "Concentration scales for substances (dependent components)\n", - "members": [ - { - "name": "CS_UNITY", - "value": 0, - "doc": "Unity mole fraction concentration in pure phase\n" - }, - { - "name": "CS_MOLFRACTION", - "value": 1, - "doc": "Mole fraction concentration\n" - }, - { - "name": "CS_PARTIALPRESSURE", - "value": 2, - "doc": "Partial pressure\n" - }, - { - "name": "CS_MOLALITY", - "value": 3, - "doc": "Molality - moles per 1 kg of (water) solvent\n" - }, - { - "name": "CS_MOLARITY", - "value": 4, - "doc": "Molarity - moles per 1 dm3 of aqueous electrolyte\n" - }, - { - "name": "CS_MASSFRACTION", - "value": 5, - "doc": "Mass fraction\n" - }, - { - "name": "CS_SURFACEFRACTION", - "value": 6, - "doc": "Surface (mole) fraction concentration\n" - }, - { - "name": "CS_SURFACEDENSITY", - "value": 7, - "doc": "Surface density in moles per m2\n" - }, - { - "name": "CS_SITEFRACTION", - "value": 8, - "doc": "Moiety site fraction concentration\n" - }, - { - "name": "CS_OTHER", - "value": 101, - "doc": "Other concentration scales\n" - } - ] - }, - { - "name": "SubstanceClass", - "doc": "Classes (types) of substances (dependent components)\n", - "members": [ - { - "name": "SC_COMPONENT", - "value": 0, - "doc": "Component of a condensed phase\n" - }, - { - "name": "SC_GASFLUID", - "value": 1, - "doc": "Component of gaseous fluid\n" - }, - { - "name": "SC_AQSOLUTE", - "value": 2, - "doc": "Aqueous solute (species in aqueous electrolyte phase)\n" - }, - { - "name": "SC_AQSOLVENT", - "value": 3, - "doc": "Solvent in aqueous electrolyte phase\n" - }, - { - "name": "SC_SURFSPECIES", - "value": 4, - "doc": "Surface (adsorption) species\n" - }, - { - "name": "SC_SITEMOIETY", - "value": 5, - "doc": "Site moiety in a sublattice (solid) solution\n" - }, - { - "name": "SC_PURE", - "value": 6, - "doc": "Component of pure condenced phase phase (pure substance)\n" - }, - { - "name": "SC_OTHER", - "value": 101, - "doc": "Other type of component\n" - } - ] - }, - { - "name": "AggregateState", - "doc": "Standard phase aggregate state (for elements, substances, phases)\n", - "members": [ - { - "name": "AS_GAS", - "value": 0, - "doc": "Gaseous aggregate state\n" - }, - { - "name": "AS_LIQUID", - "value": 1, - "doc": "Condensed liquid aggregate state\n" - }, - { - "name": "AS_GLASS", - "value": 2, - "doc": "Glass state\n" - }, - { - "name": "AS_CRYSTAL", - "value": 3, - "doc": "Crystalline solid aggregate state\n" - }, - { - "name": "AS_AQUEOUS", - "value": 4, - "doc": "Aqueous electrolyte\n" - }, - { - "name": "AS_SURFACE", - "value": 5, - "doc": "Surface layer\n" - }, - { - "name": "AS_IONEX", - "value": 6, - "doc": "Ion exchange (Donnan etc.)\n" - }, - { - "name": "AS_OTHER", - "value": 7, - "doc": "Other states\n" - } - ] - } - ], - "typedefs": [ - ], - "structs": [ - { - "name": "Item", - "doc": "Definition of (numerical) property item and array data for thermodynamic database\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "values", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "double" - }, - "doc": "Data values - must always be set (to 0 if status = EMPTY)\n", - "required": "req_out" - }, - { - "key": 2, - "name": "status", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "map", - "elemType": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - } - }, - "doc": "Status of values (ENTERED if edited etc.): enum validate with class ValueStatus\n", - "class": "ValueStatus", - "required": "optional" - }, - { - "key": 3, - "name": "errors", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "double" - }, - "doc": "Errors (statistical confidence intervals)\n", - "required": "optional" - }, - { - "key": 4, - "name": "errortypes", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "map", - "elemType": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - } - }, - "doc": "Type of statistical distribution of errors: enum validate with class ErrorDistribution\n", - "class": "ErrorDistribution", - "required": "optional" - }, - { - "key": 5, - "name": "units", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "Units of measurement, default - unscaled SI units; to be parsed using Units class code\n", - "class": "MeasurementUnits", - "required": "optional" - }, - { - "key": 6, - "name": "names", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "Short name for each coefficient in values\n", - "required": "optional" - }, - { - "key": 7, - "name": "list_size", - "typeId": "i32", - "doc": "Number of coefficients in values\n", - "required": "optional" - }, - { - "key": 8, - "name": "name", - "typeId": "string", - "doc": "Unique short name for the whole list such as IP\n", - "required": "optional" - }, - { - "key": 9, - "name": "datasources", - "typeId": "set", - "type": { - "typeId": "set", - "elemTypeId": "string" - }, - "doc": "Shortnames of datasource database objects\n", - "required": "optional" - }, - { - "key": 10, - "name": "comment", - "typeId": "string", - "doc": "Explanatory comment e.g. confidence interval level\n", - "required": "optional" - } - ] - }, - { - "name": "TimeStamp", - "doc": "Timestamp\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "year", - "typeId": "i16", - "doc": "Year\n", - "required": "req_out" - }, - { - "key": 2, - "name": "month", - "typeId": "i16", - "doc": "Month\n", - "required": "req_out" - }, - { - "key": 3, - "name": "day", - "typeId": "i16", - "doc": "Day\n", - "required": "req_out" - }, - { - "key": 4, - "name": "hour", - "typeId": "i16", - "doc": "Hour\n", - "required": "req_out" - }, - { - "key": 5, - "name": "minute", - "typeId": "i16", - "doc": "Minute\n", - "required": "req_out" - }, - { - "key": 6, - "name": "second", - "typeId": "i16", - "doc": "Second\n", - "required": "req_out" - } - ] - }, - { - "name": "LimitsTP", - "doc": "Limits for pressure and temeprature intervals (of data or method applicability)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "range", - "typeId": "bool", - "doc": "Range applicability: false means soft\/extrapolatable; true means hard\/not extrapolatable\n", - "required": "req_out", - "default": 0 - }, - { - "key": 2, - "name": "lowerP", - "typeId": "double", - "doc": "Lower pressure limit - default 0.1 Pa\n", - "required": "req_out", - "default": 0.1 - }, - { - "key": 3, - "name": "lowerT", - "typeId": "double", - "doc": "Lower temperature limit - default 273.15 K\n", - "required": "req_out", - "default": 273.15 - }, - { - "key": 4, - "name": "upperP", - "typeId": "double", - "doc": "Upper pressure limit - default 1 GPa\n", - "required": "req_out", - "default": 1000000000 - }, - { - "key": 5, - "name": "upperT", - "typeId": "double", - "doc": "Upper temperature limit - default 1273.15 K\n", - "required": "req_out", - "default": 1273.15 - } - ] - }, - { - "name": "PropertiesPT", - "doc": "Values of properties for a P,T pair\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "P", - "typeId": "double", - "doc": "Current pressure P\n", - "required": "req_out" - }, - { - "key": 2, - "name": "T", - "typeId": "double", - "doc": "Current temperature T\n", - "required": "req_out" - }, - { - "key": 3, - "name": "values", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "double" - }, - "doc": "One or more property values\n", - "required": "req_out" - } - ] - }, - { - "name": "PropertiesPTArray", - "doc": "Array of property data for several P,T pairs\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "pptv", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "PropertiesPT" - } - }, - "doc": "property P,T values (data array)\n", - "required": "req_out" - }, - { - "key": 2, - "name": "status", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "i32" - }, - "doc": "P,T pair property data status (ENTERED if edited etc.): enum validated with class ValueStatus\n", - "class": "ValueStatus", - "required": "optional" - }, - { - "key": 3, - "name": "errors", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "double" - }, - "doc": "Errors (statistical confidence intervals)\n", - "required": "optional" - }, - { - "key": 4, - "name": "errortypes", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "map", - "elemType": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - } - }, - "doc": "Type of statistical distribution of errors: enum validated with class ErrorDistribution\n", - "class": "ErrorDistribution", - "required": "optional" - }, - { - "key": 5, - "name": "units", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "Units of measurement: to be parsed using Units class code from ThermoFun\n", - "required": "optional" - }, - { - "key": 6, - "name": "names", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "Short names for each property in PropertiesPT values\n", - "required": "optional" - }, - { - "key": 7, - "name": "sizePT", - "typeId": "i32", - "doc": "Number of properties per P,T pair\n", - "required": "optional" - }, - { - "key": 8, - "name": "list_size", - "typeId": "i32", - "doc": "Number of values in a P,T pair data\n", - "required": "optional" - }, - { - "key": 9, - "name": "name", - "typeId": "string", - "doc": "Unique short name for the whole list such as G0PT\n", - "required": "optional" - }, - { - "key": 10, - "name": "datasources", - "typeId": "set", - "type": { - "typeId": "set", - "elemTypeId": "string" - }, - "doc": "Symbols of datasource database objects\n", - "required": "optional" - }, - { - "key": 11, - "name": "comment", - "typeId": "string", - "doc": "Explanatory comment\n", - "required": "optional" - }, - { - "key": 12, - "name": "limits", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "LimitsTP" - }, - "doc": "TP limits of applicability\n", - "required": "req_out" - } - ] - }, - { - "name": "ScalingValues", - "doc": "Input scaling values for various concentration scales, with units of measurement\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "MolesTotal", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "double", - "valueTypeId": "string" - }, - "doc": "Total moles for scaling of mole fractions etc.\n", - "required": "req_out", - "default": { - "1": "mol" - } - }, - { - "key": 2, - "name": "PTotal", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "double", - "valueTypeId": "string" - }, - "doc": "Total pressure for scaling partial pressures\n", - "required": "req_out", - "default": { - "0.1": "MPa" - } - }, - { - "key": 3, - "name": "MWater", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "double", - "valueTypeId": "string" - }, - "doc": "Total mass of water for scaling of molalities\n", - "required": "req_out", - "default": { - "1": "kg" - } - }, - { - "key": 4, - "name": "VaqTotal", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "double", - "valueTypeId": "string" - }, - "doc": "Total volume of aqueous solution for scaling of molarities\n", - "required": "req_out", - "default": { - "0.001": "m^3" - } - }, - { - "key": 5, - "name": "Mass", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "double", - "valueTypeId": "string" - }, - "doc": "Total mass for scaling of mass%, wt%, mass fractions\n", - "required": "req_out", - "default": { - "1": "kg" - } - }, - { - "key": 6, - "name": "SurfMoles", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "double", - "valueTypeId": "string" - }, - "doc": "Total amount of surface sites for scaling of surface site fractions\n", - "required": "req_out", - "default": { - "0.001": "mol" - } - }, - { - "key": 7, - "name": "SurfMolal", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "double", - "valueTypeId": "string" - }, - "doc": "Total molality of surface sites for scaling surface fractions\n", - "required": "req_out", - "default": { - "0.001": "molal" - } - }, - { - "key": 8, - "name": "SurfArea", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "double", - "valueTypeId": "string" - }, - "doc": "Total surface area for scaling surface area fractions\n", - "required": "req_out", - "default": { - "1": "m^2" - } - } - ] - }, - { - "name": "TDSProperties", - "doc": "Thermodynamic properties at equilibrium state of phase (false) or whole system (true)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "TDPtype", - "typeId": "bool", - "doc": "Type of data: phase (false) or whole system (true)\n", - "required": "req_out", - "default": 0 - }, - { - "key": 2, - "name": "aggrState", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "required": "req_out", - "default": { - "7": "AS_OTHER" - } - }, - { - "key": 3, - "name": "conScale", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Concentration scale (for phase species), C_UNITY for the whole system\n", - "required": "req_out", - "default": { - "0": "CS_UNITY" - } - }, - { - "key": 11, - "name": "elements", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "List of symbols of elements (from chemsysdef)\n", - "required": "req_out" - }, - { - "key": 12, - "name": "nel", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "double" - }, - "doc": "List of bulk elemental composition in moles of elements\n", - "required": "req_out" - }, - { - "key": 13, - "name": "mbrel", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "double" - }, - "doc": "Mass balance residuals for elements\n", - "required": "req_out" - }, - { - "key": 14, - "name": "uel", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "double" - }, - "doc": "Chemical potentials of elements\n", - "required": "req_out" - }, - { - "key": 21, - "name": "species", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "List of symbols of components (species)\n", - "required": "req_out" - }, - { - "key": 22, - "name": "nsp", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "double" - }, - "doc": "List of amounts of species in moles\n", - "required": "req_out" - }, - { - "key": 23, - "name": "asp", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "double" - }, - "doc": "List of activities of chemical species\n", - "required": "req_out" - }, - { - "key": 24, - "name": "csp", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "double" - }, - "doc": "List of concentrations of chemical species\n", - "required": "req_out" - }, - { - "key": 25, - "name": "gsp", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "double" - }, - "doc": "List of activity coefficients of chemical species\n", - "required": "req_out" - }, - { - "key": 31, - "name": "Amount", - "typeId": "double", - "doc": "Total amount in mol\n", - "required": "req_out" - }, - { - "key": 32, - "name": "Mass", - "typeId": "double", - "doc": "Mass in kg\n", - "required": "req_out" - }, - { - "key": 33, - "name": "Volume", - "typeId": "double", - "doc": "Volume, m^3\n", - "required": "req_out" - }, - { - "key": 34, - "name": "GibbsEnergy", - "typeId": "double", - "doc": "Total Gibbs energy, J\n", - "required": "req_out" - }, - { - "key": 35, - "name": "HelmholtzEnergy", - "typeId": "double", - "doc": "Total Gibbs energy, J\n", - "required": "req_out" - }, - { - "key": 36, - "name": "InternalEnergy", - "typeId": "double", - "doc": "Internal energy, J\n", - "required": "req_out" - }, - { - "key": 37, - "name": "Enthalpy", - "typeId": "double", - "doc": "Enthalpy, J\n", - "required": "req_out" - }, - { - "key": 38, - "name": "Entropy", - "typeId": "double", - "doc": "Entropy, J\/K\n", - "required": "req_out" - }, - { - "key": 39, - "name": "HeatCapacity", - "typeId": "double", - "doc": "Heat capacity J\/K\n", - "required": "req_out" - }, - { - "key": 40, - "name": "SI", - "typeId": "double", - "doc": "Stability index (phase) or GEM convergence criterion (system)\n", - "required": "req_out" - }, - { - "key": 41, - "name": "Charge", - "typeId": "double", - "doc": "Total charge\n", - "required": "req_out" - }, - { - "key": 43, - "name": "VolumeEx", - "typeId": "double", - "doc": "Excess volume of mixing, m3\/mol\n", - "required": "req_out" - }, - { - "key": 44, - "name": "GibbsEnergyEx", - "typeId": "double", - "doc": "Excess Gibbs energy of mixing, J\/mol\n", - "required": "req_out" - }, - { - "key": 47, - "name": "EnthalpyEx", - "typeId": "double", - "doc": "Enthalpy, J\/mol\n", - "required": "req_out" - }, - { - "key": 48, - "name": "EntropyEx", - "typeId": "double", - "doc": "Entropy, J\/K\/mol\n", - "required": "req_out" - }, - { - "key": 53, - "name": "VolumeId", - "typeId": "double", - "doc": "Volume of ideal mixing, m^3\/mol\n", - "required": "req_out" - }, - { - "key": 54, - "name": "GibbsEnergyId", - "typeId": "double", - "doc": "Gibbs energy of ideal mixing, J\/mol\n", - "required": "req_out" - }, - { - "key": 57, - "name": "EnthalpyId", - "typeId": "double", - "doc": "Enthalpy of ideal mixing, J\/mol\n", - "required": "req_out" - }, - { - "key": 58, - "name": "EntropyId", - "typeId": "double", - "doc": "Entropy of ideal mixing, J\/K\/mol\n", - "required": "req_out" - }, - { - "key": 63, - "name": "VolumeMix", - "typeId": "double", - "doc": "Volume of mixing, m^3\/mol\n", - "required": "req_out" - }, - { - "key": 64, - "name": "GibbsEnergyMix", - "typeId": "double", - "doc": "Gibbs energy of mixing, J\/mol\n", - "required": "req_out" - }, - { - "key": 67, - "name": "EnthalpyMix", - "typeId": "double", - "doc": "Enthalpy of mixing, J\/mol\n", - "required": "req_out" - }, - { - "key": 68, - "name": "EntropyMix", - "typeId": "double", - "doc": "Entropy of mixing, J\/K\/mol\n", - "required": "req_out" - }, - { - "key": 73, - "name": "VolumeRef", - "typeId": "double", - "doc": "Reference volume of mixing, m^3\/mol\n", - "required": "req_out" - }, - { - "key": 74, - "name": "GibbsEnergyRef", - "typeId": "double", - "doc": "Reference Gibbs energy of mixing, J\/mol\n", - "required": "req_out" - }, - { - "key": 77, - "name": "EnthalpyRef", - "typeId": "double", - "doc": "Reference enthalpy of mixing, J\/mol\n", - "required": "req_out" - }, - { - "key": 78, - "name": "EntropyRef", - "typeId": "double", - "doc": "Reference entropy of mixing, J\/K\/mol\n", - "required": "req_out" - }, - { - "key": 79, - "name": "HeatCapacityRef", - "typeId": "double", - "doc": "Reference heat capacity of mixing J\/K\/mol\n", - "required": "req_out" - } - ] - } - ], - "constants": [ - ], - "services": [ - ] -} diff --git a/Resources/data/schemas/query.schema.json b/Resources/data/schemas/query.schema.json deleted file mode 100644 index 5ac0e93c..00000000 --- a/Resources/data/schemas/query.schema.json +++ /dev/null @@ -1,180 +0,0 @@ -{ - "name": "query", - "doc": "Apache Thrift IDL definition for the query service interface\n", - "namespaces": { - "*": "query" - }, - "includes": [ - ], - "enums": [ - { - "name": "QueryStyle", - "doc": "Classes of query style\n", - "members": [ - { - "name": "QUndef", - "value": -1, - "doc": "Undefined query\n" - }, - { - "name": "QTemplate", - "value": 0, - "doc": "Fields template query\n" - }, - { - "name": "QAll", - "value": 1, - "doc": "Select all records\n" - }, - { - "name": "QEdgesFrom", - "value": 2, - "doc": "Select outgoing edges\n" - }, - { - "name": "QEdgesTo", - "value": 3, - "doc": "Select incoming edges\n" - }, - { - "name": "QEdgesAll", - "value": 5, - "doc": "Select edges by query\n" - }, - { - "name": "QAQL", - "value": 6, - "doc": "AQL-style query\n" - }, - { - "name": "QEJDB", - "value": 7, - "doc": "EJDB-style query\n" - } - ] - } - ], - "typedefs": [ - ], - "structs": [ - { - "name": "ConditionData", - "doc": "Struct for query condition\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "style", - "typeId": "i32", - "doc": "query style\n", - "required": "required" - }, - { - "key": 2, - "name": "find", - "typeId": "string", - "doc": "query string\n", - "required": "req_out" - }, - { - "key": 3, - "name": "bind", - "typeId": "string", - "doc": "bind values string\n", - "required": "req_out" - }, - { - "key": 4, - "name": "fields", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "string", - "valueTypeId": "string" - }, - "doc": "return fields map\n", - "required": "req_out" - } - ] - }, - { - "name": "Query", - "doc": "description of query record\n", - "isException": false, - "isUnion": false, - "to_select": [ "4", "5", "6.1", "1" ], - "to_key": [ "4" ], - "fields": [ - { - "key": 1, - "name": "_id", - "typeId": "string", - "doc": "id of this query record or 0 if unknown\n", - "required": "required" - }, - { - "key": 2, - "name": "_key", - "typeId": "string", - "doc": "ID of this record within the impex collection (part of _id)\n", - "required": "required" - }, - { - "key": 3, - "name": "_rev", - "typeId": "string", - "doc": "Code of revision (changed by the system at every update)\n", - "required": "required" - }, - { - "key": 4, - "name": "name", - "typeId": "string", - "doc": "short name of query (used as key field)\n", - "required": "required" - }, - { - "key": 5, - "name": "comment", - "typeId": "string", - "doc": "description of query\n", - "required": "req_out" - }, - { - "key": 6, - "name": "condition", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "ConditionData" - }, - "doc": "query filter condtition\n", - "required": "required" - }, - { - "key": 7, - "name": "collect", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "list of fields to collect\n", - "required": "required" - }, - { - "key": 8, - "name": "qschema", - "typeId": "string", - "doc": "query for schema\n", - "required": "req_out" - } - ] - } - ], - "constants": [ - ], - "services": [ - ] -} diff --git a/Resources/data/schemas/reaction.schema.json b/Resources/data/schemas/reaction.schema.json deleted file mode 100644 index 81a9b931..00000000 --- a/Resources/data/schemas/reaction.schema.json +++ /dev/null @@ -1,803 +0,0 @@ -{ - "name": "reaction", - "doc": "Apache Thrift IDL definition for the reaction service interface\n", - "namespaces": { - "*": "reaction" - }, - "includes": [ -"prop", -"element", -"substance" - ], - "enums": [ - { - "name": "ReactionType", - "doc": "Classes (types) of reactions\n", - "members": [ - { - "name": "RE_TRIVIAL", - "value": 0, - "doc": "Trivial reaction for calculation of reaction effects\n" - }, - { - "name": "FE_FORMATION", - "value": 1, - "doc": "Formation reaction of a product from master species\n" - }, - { - "name": "RE_DISSOLUTION", - "value": 2, - "doc": "Dissolution reaction for a mineral (end member) or gas in\n" - }, - { - "name": "RE_EVAPORATION", - "value": 3, - "doc": "Dissolution reaction for mineral\/liquid in gas\n" - }, - { - "name": "RE_ELTRANSFER", - "value": 4, - "doc": "Redox reaction (electron transfer)\n" - }, - { - "name": "RE_ISOELECTRIC", - "value": 5, - "doc": "Isoelectric reaction\n" - }, - { - "name": "RE_ISOCOULOMBIC", - "value": 6, - "doc": "Isocoulombic reaction\n" - }, - { - "name": "RE_IONEXCHANGE", - "value": 7, - "doc": "Ion exchange reaction\n" - }, - { - "name": "RE_OTHER", - "value": 101, - "doc": "Other type of reaction\n" - } - ] - }, - { - "name": "ReactionTPMethodType", - "members": [ - { - "name": "logk_fpt_function", - "value": 0, - "doc": "calculation of logK of reactions as they depend functionally on P and T; ReacDC\n" - }, - { - "name": "adsor_ion_exchange", - "value": 1, - "doc": "calculations via adsorption or ion exchange constants, using LFER correlations; ReacDC (reserved)\n" - }, - { - "name": "iso_compounds_grichuk88", - "value": 2, - "doc": "calculation of parameters for isotopic forms of compounds (Grichuk, 1988)\n" - }, - { - "name": "logk_nordstrom_munoz88", - "value": 3, - "doc": "calculation from empirical function logK=f(T) (Nordstrom and Munoz, 1988); ReacDC only\n" - }, - { - "name": "logk_1_term_extrap0", - "value": 4, - "doc": "one-term extrapolation assuming dHr=0 and logK=const; ReacDC\n" - }, - { - "name": "logk_1_term_extrap1", - "value": 5, - "doc": "one-term extrapolation assuming dGr=const (Gu et al., 1994); ReacDC\n" - }, - { - "name": "logk_2_term_extrap", - "value": 6, - "doc": "two-term extrapolation; ReacDC only\n" - }, - { - "name": "logk_3_term_extrap", - "value": 7, - "doc": "three-term extrapolation assuming dCpr=const; ReacDC\n" - }, - { - "name": "logk_lagrange_interp", - "value": 8, - "doc": "Lagrange polynomial interpolation over logK(TP) array; ReacDC\n" - }, - { - "name": "logk_marshall_frank78", - "value": 9, - "doc": "calculation of logK=f(T,P) from density equation (Marshall and Franck, 1978); ReacDC\n" - }, - { - "name": "solute_eos_ryzhenko_gems", - "value": 10, - "doc": "calculation of logK=f(T,P) with modified Ryzhenko-Bryzgalin model\n" - }, - { - "name": "dr_heat_capacity_ft", - "value": 11, - "doc": "calculation of reaction properties from empirical from 5-term Cp(T); ReacDC\n" - }, - { - "name": "dr_volume_fpt", - "value": 12, - "doc": "calculation of reaction properties from empirical V(P,T); ReacDC\n" - }, - { - "name": "dr_volume_constant", - "value": 13, - "doc": "reaction molar volume constant at references T and P\n" - } - ] - }, - { - "name": "ReactionComponentType", - "doc": "Classes (types) of reaction components\n", - "members": [ - { - "name": "RC_REACTANT", - "value": 0, - "doc": "Component properties available\n" - }, - { - "name": "RC_PRODUCT", - "value": 1, - "doc": "Component properties to be defined via this reaction properties\n" - }, - { - "name": "RC_CATALYST", - "value": 2, - "doc": "Catalyzes the reaction but is not consumed in it\n" - }, - { - "name": "RC_OTHER", - "value": 3, - "doc": "Other type of reaction component\n" - } - ] - } - ], - "typedefs": [ - ], - "structs": [ - { - "name": "ReactionTPMethodData", - "doc": "Data structure describing method codes and data for computing P,T corrections to standard properties of reaction\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "method", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Method type - validate with class SubstanceEoSMethodType\n", - "class": "ReactionTPMethodType", - "required": "req_out" - }, - { - "key": 2, - "name": "limitsTP", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.LimitsTP" - }, - "doc": "TP limits of applicability\n", - "required": "req_out" - }, - { - "key": 3, - "name": "logk_pt_values", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.PropertiesPTArray" - }, - "doc": "Interpolation array for logK(P,T) values\n", - "required": "optional" - }, - { - "key": 11, - "name": "logk_ft_coeffs", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Coefficients of logK(T) function per mole a0 to a6 \"logKTc\"\n", - "required": "optional" - }, - { - "key": 12, - "name": "dr_heat_capacity_ft_coeffs", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Coefficients of Cp0(T) function per mole \"drCpTc\"\n", - "required": "optional" - }, - { - "key": 13, - "name": "dr_volume_fpt_coeffs", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Coefficients of V0(T,P) function per mole \"drVpTc\"\n", - "required": "optional" - }, - { - "key": 14, - "name": "dr_ryzhenko_coeffs", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Coefficients of Ryzhenko-Bryzgalin model \"drRBc\n", - "required": "optional" - }, - { - "key": 15, - "name": "dr_marshall_franck_coeffs", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Coefficients of Marshall-Franck density (MFD) model\n", - "required": "optional" - }, - { - "key": 19, - "name": "isotop_lna_coeffs", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Coeffs of 1000ln(alpha) = f(T) equation a0 to a4\n", - "required": "optional" - }, - { - "key": 20, - "name": "isotop_counter_fraction", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Mole fraction of counter-isotope in natural mixture (for isotopes)\n", - "required": "optional" - } - ] - }, - { - "name": "Reaction", - "doc": "Description of a reaction between substances\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "symbol", - "typeId": "string", - "doc": "Unique name\/ID of this reaction (e.g. product species name)\n", - "required": "required" - }, - { - "key": 2, - "name": "sourcetdb", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Source TDB: enum validated with class SourceTDB\n", - "class": "SourceTDB", - "required": "required" - }, - { - "key": 3, - "name": "level", - "typeId": "i32", - "doc": "Level of the reaction (for superimposed IC or LMA reaction sets)\n", - "required": "required", - "default": 0 - }, - { - "key": 4, - "name": "equation", - "typeId": "string", - "doc": "Equation of the reaction (not compulsory)\n", - "required": "req_out" - }, - { - "key": 5, - "name": "name", - "typeId": "string", - "doc": "Name of the reaction (comment, not compulsory)\n", - "required": "req_out" - }, - { - "key": 6, - "name": "reactyp", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Type (class) of reaction: enum validated with class ReactionType\n", - "class": "ReactionType", - "required": "req_out", - "default": { - "0": "RE_TRIVIAL" - } - }, - { - "key": 7, - "name": "Tst", - "typeId": "double", - "doc": "Reference temperature for standard state (usually 298.15 K)\n", - "required": "req_out", - "default": 298.15 - }, - { - "key": 8, - "name": "Pst", - "typeId": "double", - "doc": "Reference pressure (usually 1 bar = 10^5 Pa, sometimes 1.013 bar = 1 atm\n", - "required": "req_out", - "default": 100000 - }, - { - "key": 9, - "name": "logKr", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Standard equilibrium constant \"logK0\" (set in log10 units)\n", - "required": "req_out" - }, - { - "key": 10, - "name": "drsm_volume", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Standard volume effect per mole \"drV0\" m3\/mol\n", - "required": "req_out" - }, - { - "key": 11, - "name": "drsm_gibbs_energy", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Standard Gibbs energy effect per mole \"drGO\" J\/mol\n", - "required": "req_out" - }, - { - "key": 12, - "name": "drsm_enthalpy", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Standard enthalpy effect per mole \"drH0\" J\/mol\n", - "required": "req_out" - }, - { - "key": 13, - "name": "drsm_entropy", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Standard entropy effect of reaction \"drS0\" J\/K\/mol\n", - "required": "req_out" - }, - { - "key": 14, - "name": "drsm_heat_capacity_p", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Standard heat capacity effect per mole \"drCp0\" J\/K\/mol\n", - "required": "req_out" - }, - { - "key": 21, - "name": "TPMethods", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "ReactionTPMethodData" - } - }, - "doc": "One or more method codes and data for computing P,T corrections to standard properties\n", - "required": "req_out" - }, - { - "key": 22, - "name": "limitsTP", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.LimitsTP" - }, - "doc": "Overall T,P limits for all methods involved\n", - "required": "req_out", - "default": { - "range": 0, - "lowerT": 273.15, - "upperT": 298.15, - "lowerP": 0.1, - "upperP": 1000000 - } - }, - { - "key": 25, - "name": "comment", - "typeId": "string", - "doc": "Comment - e.g. who entered\/modified, ...\n", - "required": "optional" - }, - { - "key": 26, - "name": "datasources", - "typeId": "set", - "type": { - "typeId": "set", - "elemTypeId": "string" - }, - "doc": "Labels of datasource DB objects\n", - "required": "optional" - }, - { - "key": 27, - "name": "time_stamp", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.TimeStamp" - }, - "doc": "Timestamp (\n", - "required": "optional" - }, - { - "key": 28, - "name": "elements", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "element.ElementInfo" - } - }, - "doc": "Information on elements present in the reaction\n", - "required": "req_out" - } - ] - }, - { - "name": "Reactions", - "doc": "Definition of an array of reactions\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 2, - "name": "reactions", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "Reaction" - } - }, - "doc": "List of reactions\n", - "required": "req_out" - } - ] - }, - { - "name": "ReactionComponentData", - "doc": "Data for processing reactions; properties from a substance connected to the reaction via takes edges\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "SC", - "typeId": "double", - "required": "req_out" - }, - { - "key": 2, - "name": "mV0", - "typeId": "double", - "required": "req_out" - }, - { - "key": 3, - "name": "mG0", - "typeId": "double", - "required": "req_out" - }, - { - "key": 4, - "name": "mH0", - "typeId": "double", - "required": "req_out" - }, - { - "key": 5, - "name": "mS0", - "typeId": "double", - "required": "req_out" - }, - { - "key": 6, - "name": "mCp0", - "typeId": "double", - "required": "req_out" - }, - { - "key": 7, - "name": "fCharge", - "typeId": "double", - "required": "req_out" - }, - { - "key": 9, - "name": "rct", - "typeId": "i32", - "doc": "Type of reaction component: enum validated with class ReactionComponentType\n", - "required": "req_out" - }, - { - "key": 10, - "name": "subsid", - "typeId": "i32", - "required": "optional" - }, - { - "key": 11, - "name": "symbol", - "typeId": "string", - "required": "optional" - }, - { - "key": 12, - "name": "formula", - "typeId": "string", - "required": "optional" - } - ] - }, - { - "name": "ReactionData", - "doc": "Work structure keeping the data to check\/calculate reaction\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "Nrcs", - "typeId": "i16", - "doc": "Number of components taking part in the reaction\n", - "required": "req_out" - }, - { - "key": 2, - "name": "rcs", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "ReactionComponentData" - } - }, - "doc": "Array of data for reacting components\n", - "required": "req_out" - }, - { - "key": 3, - "name": "T", - "typeId": "double", - "doc": "Current temperature in K\n", - "required": "req_out" - }, - { - "key": 4, - "name": "P", - "typeId": "double", - "doc": "Current pressure in bar (Pa?). These properties should already be for current T,P\n", - "required": "req_out" - }, - { - "key": 10, - "name": "logKr", - "typeId": "double", - "doc": "Standard equilibrium constant \"logK0\" (log10, set in units)\n", - "required": "req_out" - }, - { - "key": 11, - "name": "lnK0", - "typeId": "double", - "doc": "Equilibrium constant from drG0 = -RTlnK0\n", - "required": "req_out" - }, - { - "key": 12, - "name": "drV0", - "typeId": "double", - "doc": "Standard volume effect per mole \"drV0\" m3\/mol\n", - "required": "req_out" - }, - { - "key": 13, - "name": "drG0", - "typeId": "double", - "doc": "Standard Gibbs energy effect per mole \"drGO\" J\/mol\n", - "required": "req_out" - }, - { - "key": 14, - "name": "drH0", - "typeId": "double", - "doc": "Standard enthalpy effect per mole \"drH0\" J\/mol\n", - "required": "req_out" - }, - { - "key": 15, - "name": "drS0", - "typeId": "double", - "doc": "Standard entropy effect of reaction \"S0f\" J\/K\/mol\n", - "required": "req_out" - }, - { - "key": 16, - "name": "drCp0", - "typeId": "double", - "doc": "Standard heat capacity effect per mole \"Cp0\" J\/K\/mol\n", - "required": "req_out" - }, - { - "key": 19, - "name": "slaveid", - "typeId": "i32", - "doc": "ID of \"product\" substance for which to calculate properties\n", - "required": "optional" - }, - { - "key": 20, - "name": "computed", - "typeId": "bool", - "doc": "Set to true if the reaction props or slave props computed\n", - "required": "req_out", - "default": 0 - } - ] - }, - { - "name": "ThermoPropertiesReaction", - "doc": "Structure keeping the thermodynamic properites which can be calculated for a reaction\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "reaction_gibbs_energy", - "typeId": "double", - "doc": "The apparent standard molar Gibbs free energy of reaction\n", - "required": "req_out" - }, - { - "key": 2, - "name": "reaction_helmholtz_energy", - "typeId": "double", - "doc": "The apparent standard molar Helmholtz free energy of reaction\n", - "required": "req_out" - }, - { - "key": 3, - "name": "reaction_internal_energy", - "typeId": "double", - "doc": "The apparent standard molar internal energy of reaction\n", - "required": "req_out" - }, - { - "key": 4, - "name": "reaction_enthalpy", - "typeId": "double", - "doc": "The apparent standard molar enthalpy of reaction\n", - "required": "req_out" - }, - { - "key": 5, - "name": "reaction_entropy", - "typeId": "double", - "doc": "The standard molar entropy of reaction\n", - "required": "req_out" - }, - { - "key": 6, - "name": "reaction_volume", - "typeId": "double", - "doc": "The standard molar volume of reaction\n", - "required": "req_out" - }, - { - "key": 7, - "name": "reaction_heat_capacity_cp", - "typeId": "double", - "doc": "The standard molar isobaric heat capacity of reaction\n", - "required": "req_out" - }, - { - "key": 8, - "name": "reaction_heat_capacity_cv", - "typeId": "double", - "doc": "The standard molar isochoric heat capacity of reaction\n", - "required": "req_out" - }, - { - "key": 9, - "name": "logKr", - "typeId": "double", - "doc": "Standard equilibrium constant \"logK0\" (log10, set in units)\n", - "required": "req_out" - }, - { - "key": 10, - "name": "lnK0", - "typeId": "double", - "doc": "Equilibrium constant from drG0 = -RTlnK0\n", - "required": "req_out" - } - ] - } - ], - "constants": [ - ], - "services": [ - ] -} diff --git a/Resources/data/schemas/reactionset.schema.json b/Resources/data/schemas/reactionset.schema.json deleted file mode 100644 index 447542ba..00000000 --- a/Resources/data/schemas/reactionset.schema.json +++ /dev/null @@ -1,432 +0,0 @@ -{ - "name": "reactionset", - "doc": "Apache Thrift IDL definition for the reactionset service interface\n", - "namespaces": { - "*": "reactionset" - }, - "includes": [ -"prop", -"element", -"substance", -"reaction" - ], - "enums": [ - { - "name": "ReactionSetType", - "doc": "Classes (types) of reaction sets\n", - "members": [ - { - "name": "RS_LMA", - "value": 0, - "doc": "Reactionset for LMA-type database\n" - }, - { - "name": "RS_ISOC", - "value": 1, - "doc": "Isocoulombic\/isoelectric\/ionexchange reactions\n" - }, - { - "name": "RS_FORMFEL", - "value": 2, - "doc": "Formation reactions of substances from reactionsets in standard states\n" - }, - { - "name": "RS_MODEL", - "value": 3, - "doc": "Model reactions used for generating isocoulombic reactions\n" - }, - { - "name": "RS_OTHER", - "value": 101, - "doc": "Other type of reaction set\n" - } - ] - }, - { - "name": "ReactionCombinedType", - "doc": "Classes (types) of combined reactions\n", - "members": [ - { - "name": "INVESTIGATED", - "value": 0, - "doc": "Reaction which is combined with model reactions to generate isocoulombic reactions\n" - }, - { - "name": "MODEL", - "value": 1, - "doc": "Model reaction which is combined with investigated reactions to generate isocoulombic reactions\n" - } - ] - }, - { - "name": "SpeciesTypeRS", - "doc": "Data structures for linking and processing reactions in reactionset and database\n", - "members": [ - { - "name": "SPECIES_ELEMENT", - "value": 0, - "doc": "Species-element\n" - }, - { - "name": "MASTER_PRIMARY", - "value": 1, - "doc": "Master-primary\n" - }, - { - "name": "MASTER_SECONDARY", - "value": 2, - "doc": "Master-secondary\n" - }, - { - "name": "MASTER_ALKALINITY", - "value": 3, - "doc": "Master-alkalinity\n" - }, - { - "name": "PRODUCT_CORE", - "value": 4, - "doc": "Product-core\n" - }, - { - "name": "PRODUCT_RECOMMENDED", - "value": 5, - "doc": "Product-recommended\n" - }, - { - "name": "PRODUCT_SUPPLEMENTARY", - "value": 6, - "doc": "Product-supplementary\n" - }, - { - "name": "PRODUCT_OTHER", - "value": 7, - "doc": "Product-other\n" - } - ] - } - ], - "typedefs": [ - { - "name": "masterdata", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "reaction.ReactionComponentData" - } - }, - { - "name": "productdata", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "reaction.ReactionComponentData" - } - }, - { - "name": "prodreacdata", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "reaction.ReactionData" - } - }, - { - "name": "elementdata", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "substance.ElementData" - } - } - ], - "structs": [ - { - "name": "ReactionSet", - "doc": "description of reaction set data\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "symbol", - "typeId": "string", - "doc": "Unique name\/ID of this reaction set\n", - "required": "required" - }, - { - "key": 2, - "name": "stype", - "class": "ReactionSetType", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Class of reactionset - validate with class ReactionSetType\n", - "required": "required", - "default": { - "0": "RS_LMA" - } - }, - { - "key": 3, - "name": "level", - "typeId": "i32", - "doc": "Level of the reactionset\n", - "required": "required", - "default": 0 - }, - { - "key": 4, - "name": "name", - "typeId": "string", - "doc": "Name of the reaction set (not compulsory)\n", - "required": "req_out" - }, - { - "key": 5, - "name": "element_list", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "List of element symbols covered by this reactionset - may be replaced by a graph\n", - "required": "optional" - }, - { - "key": 6, - "name": "species_map", - "class": "SpeciesTypeRS", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "string", - "valueTypeId": "i32" - }, - "doc": "Map of species symbols and types (class SpeciesTypeRS) covered by reactionset - a graph?\n", - "required": "optional" - }, - { - "key": 7, - "name": "reaction_map", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "string", - "valueTypeId": "i32" - }, - "doc": "Map of reaction levels and symbols\n", - "required": "optional" - }, - { - "key": 8, - "name": "sourcetdb", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Source TDB: enum validated with class SourceTDB\n", - "class": "SourceTDB", - "required": "optional" - }, - { - "key": 9, - "name": "elements", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "element.ElementInfo" - } - }, - "doc": "List of element symbols and infos covered by this reactionset - may be replaced by a graph\n", - "required": "req_out" - }, - { - "key": 10, - "name": "limitsTP", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.LimitsTP" - }, - "doc": "Overall lower and upper T, P limits for T,P corrections\n", - "required": "req_out", - "default": { - "range": 0, - "lowerT": 273.15, - "upperT": 298.15, - "lowerP": 0.1, - "upperP": 1000000 - } - }, - { - "key": 11, - "name": "comment", - "typeId": "string", - "doc": "Comment e.g. who entered\/modified, ...\n", - "required": "optional" - }, - { - "key": 12, - "name": "datasources", - "typeId": "set", - "type": { - "typeId": "set", - "elemTypeId": "string" - }, - "doc": "Labels of datasource DB objects - may be obsolete\n", - "required": "optional" - }, - { - "key": 13, - "name": "time_stamp", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.TimeStamp" - }, - "doc": "Timestamp\n", - "required": "optional" - } - ] - }, - { - "name": "ReactionSets", - "doc": "Definition of an array of reactions\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 2, - "name": "reactionsets", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "ReactionSet" - } - }, - "doc": "List of reaction sets\n", - "required": "req_out" - } - ] - }, - { - "name": "ReactionSetData", - "doc": "work structure keeping the data for reactionset object\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "Nmasts", - "typeId": "i32", - "doc": "number of master species taking part in this reactionset\n", - "required": "req_out" - }, - { - "key": 2, - "name": "masts", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "reaction.ReactionComponentData" - } - }, - "doc": "array of data for master species\n", - "required": "req_out" - }, - { - "key": 3, - "name": "Nprods", - "typeId": "i32", - "doc": "number of product species taking part in this reactionset\n", - "required": "req_out" - }, - { - "key": 4, - "name": "prods", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "reaction.ReactionComponentData" - } - }, - "doc": "array of data for product species\n", - "required": "req_out" - }, - { - "key": 5, - "name": "Npreas", - "typeId": "i32", - "doc": "number of product species formation reactions in this reactionset\n", - "required": "req_out" - }, - { - "key": 6, - "name": "preas", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "reaction.ReactionData" - } - }, - "doc": "array of data for product formation reactions\n", - "required": "req_out" - }, - { - "key": 7, - "name": "Nelems", - "typeId": "i32", - "doc": "number of elements used in this reactionset\n", - "required": "req_out" - }, - { - "key": 8, - "name": "elems", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "substance.ElementData" - } - }, - "doc": "array of data for elements\n", - "required": "req_out" - }, - { - "key": 11, - "name": "processed", - "typeId": "bool", - "doc": "indicator of processing the reactionset\n", - "required": "req_out", - "default": 0 - } - ] - } - ], - "constants": [ - ], - "services": [ - ] -} diff --git a/Resources/data/schemas/substance.schema.json b/Resources/data/schemas/substance.schema.json deleted file mode 100644 index c67eef9f..00000000 --- a/Resources/data/schemas/substance.schema.json +++ /dev/null @@ -1,1068 +0,0 @@ -{ - "name": "substance", - "doc": "Apache Thrift IDL definition for the substance service interface\n", - "namespaces": { - "*": "substance" - }, - "includes": [ -"prop", -"element" - ], - "enums": [ - { - "name": "SubstanceTPMethodType", - "doc": "Codes for T-P correction methods of calculation of DC thermodynamic parameters from GEMS3 v_mod.h\n", - "members": [ - { - "name": "cp_ft_equation", - "value": 0, - "doc": "Integration of empirical heat capacity equation Cp=f(T); DComp and ReacDC\n" - }, - { - "name": "cp_ft_equation_saxena86", - "value": 1, - "doc": "Cp=f(T) equation by Fei and Saxena (1986) (reserved)\n" - }, - { - "name": "solute_hkf88_gems", - "value": 2, - "doc": "Helgeson-Kirkham-Flowers (HKF) equation of state for aqueous species - Gems variant\n" - }, - { - "name": "solute_hkf88_reaktoro", - "value": 3, - "doc": "Helgeson-Kirkham-Flowers (HKF) equation of state for aqueous species - Reaktoro variant\n" - }, - { - "name": "solute_aknifiev_diamond03", - "value": 4, - "doc": "partial molal volumes of aqueous nonelectrolyte species (Akinfiev and Diamond, 2003)\n" - }, - { - "name": "landau_holland_powell98", - "value": 5, - "doc": "modifications for Landau phase transitions (Holland and Powell, 1998)\n" - }, - { - "name": "landau_berman88", - "value": 6, - "doc": "modifications for Landau phase transitions (Berman, 1988) (reserved)\n" - }, - { - "name": "general_equation_of_state", - "value": 7, - "doc": "calculations via general equations of state (reserved)\n" - }, - { - "name": "fug_critical_param", - "value": 8, - "doc": "calculation of fugacities of gases from their critical parameters (reserved)\n" - }, - { - "name": "fluid_prsv", - "value": 9, - "doc": "Peng-Robinson-Stryjek-Vera (PRSV) EoS for fluids (nonelectrolytes)\n" - }, - { - "name": "fluid_churakov_gottschalk", - "value": 10, - "doc": "Churakov-Gottschalk (CG) EoS for fluids (nonelectrolytes)\n" - }, - { - "name": "fluid_soave_redlich_kwong", - "value": 11, - "doc": "Soave-Redlich-Kwong (SRK) EoS for fluids (nonelectrolytes)\n" - }, - { - "name": "fluid_sterner_pitzer", - "value": 12, - "doc": "Sterner-Pitzer (SP) EoS for fluids (nonelectrolytes) (reserved)\n" - }, - { - "name": "fluid_peng_robinson78", - "value": 13, - "doc": "Peng-Robinson (PR78) EoS for fluids (nonelectrolytes)\n" - }, - { - "name": "fluid_comp_redlich_kwong_hp91", - "value": 14, - "doc": "Compensated Redlich-Kwong (CORK) EoS for fluids (nonelectrolytes)\n" - }, - { - "name": "fluid_generic", - "value": 15 - }, - { - "name": "fluid_H2O", - "value": 16 - }, - { - "name": "fluid_CO2", - "value": 17 - }, - { - "name": "fluid_CH4", - "value": 18 - }, - { - "name": "fluid_N2", - "value": 19 - }, - { - "name": "fluid_H2", - "value": 20 - }, - { - "name": "fluid_O2", - "value": 21 - }, - { - "name": "fluid_Ar", - "value": 22 - }, - { - "name": "fluid_polar", - "value": 23 - }, - { - "name": "fluid_nonpolar", - "value": 24 - }, - { - "name": "water_diel_jnort91_reaktoro", - "value": 25, - "doc": "Water dielectric properites usin Jhonson and Norton (1991) model as implemented in Reaktoro\n" - }, - { - "name": "water_diel_jnort91_gems", - "value": 26, - "doc": "Water dielectric properites using Jhonson and Norton (1991) model as implemented in GEMS\n" - }, - { - "name": "water_diel_sverj14", - "value": 27, - "doc": "Water electro-chemical properties using Sverjensky et al. (2014) dielectric constant model\n" - }, - { - "name": "water_diel_fern97", - "value": 28, - "doc": "Water electro-chemical properties using the Fernandez et al. (1997) dielectric constant model\n" - }, - { - "name": "water_eos_hgk84_lvs83_gems", - "value": 29, - "doc": "calculation of H2O water(steam) properties from HGK and LVS equations of state\n" - }, - { - "name": "water_eos_iapws95_gems", - "value": 30, - "doc": "calculation of H2O water (steam) properties from IAPWS-95 equation of state (reserved)\n" - }, - { - "name": "water_eos_hgk84_reaktoro", - "value": 31, - "doc": "Water properties using Haar-Gallagher-Kell (1984) equation of state as implemented in Reaktoro\n" - }, - { - "name": "water_eos_iapws95_reaktoro", - "value": 32, - "doc": "Water properties using Wagner and Pruss 1995 (IAWPS95) EOS as implemented in Reaktoro\n" - }, - { - "name": "water_pvt_zhang_duan05", - "value": 33, - "doc": "Water properties using Zhang and Duan 2005 PVT EOS\n" - }, - { - "name": "mv_constant", - "value": 34 - }, - { - "name": "mv_equation_dorogokupets88", - "value": 35, - "doc": "molar volume from empirical V=f(T,P) equation (Dorogokupets et al., 1988)\n" - }, - { - "name": "mv_equation_berman88", - "value": 36, - "doc": "molar volume from empirical V=f(T,P) equation (Berman, 1988)\n" - }, - { - "name": "mv_eos_birch_murnaghan_gott97", - "value": 37, - "doc": "molar volume from Birch-Murnaghan EoS (Gottschalk, 1997)\n" - }, - { - "name": "mv_eos_murnaghan_hp98", - "value": 38, - "doc": "molar volume V(T,P) from Murnaghan EoS (Holland and Powell, 1998)\n" - }, - { - "name": "mv_eos_tait_hp11", - "value": 39, - "doc": "molar volume V(T,P) from Tait EoS (Holland and Powell, 2011)\n" - }, - { - "name": "mv_pvnrt", - "value": 40, - "doc": "molar volume from ideal gas law pv=nrt\n" - } - ] - } - ], - "typedefs": [ - ], - "structs": [ - { - "name": "SubstanceTPMethodData", - "doc": "Data structure holding method codes and data for computing P,T corrections to standard properties\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "method", - "class": "SubstanceTPMethodType", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Method type - validate with class SubstanceTPMethodType\n", - "required": "req_out" - }, - { - "key": 2, - "name": "limitsTP", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.LimitsTP" - }, - "doc": "TP limits of applicability\n", - "required": "req_out" - }, - { - "key": 3, - "name": "g0_pt_values", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.PropertiesPTArray" - }, - "doc": "Interpolation array for G0(P,T) values\n", - "required": "optional" - }, - { - "key": 4, - "name": "datasources", - "typeId": "set", - "type": { - "typeId": "set", - "elemTypeId": "string" - }, - "doc": "Labels of datasource DB objects\n", - "required": "optional" - }, - { - "key": 10, - "name": "m_gibbs_energy_ft_polynom", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Polynomial coefficients for G0(T) in Calphad format (compatible with Maier-Kelly)\n", - "required": "optional" - }, - { - "key": 11, - "name": "m_heat_capacity_ft_coeffs", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Coefficients of Cp0(T) function per mole \"CpTc\"\n", - "required": "optional" - }, - { - "key": 12, - "name": "m_volume_fpt_coeffs", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Coefficients of V0(T,P) function per mole \"VpTc\"\n", - "required": "optional" - }, - { - "key": 13, - "name": "eos_hkf_coeffs", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Coefficients of HKF EoS \"HKFc\"\n", - "required": "optional" - }, - { - "key": 14, - "name": "eos_akinfiev_diamond_coeffs", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Coefficients of Akinfiev-Diamond EoS \"ADmc\"\n", - "required": "optional" - }, - { - "key": 15, - "name": "eos_birch_murnaghan_coeffs", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Coefficients of Birch-Murnaghan EoS \"BMmc\"\n", - "required": "optional" - }, - { - "key": 16, - "name": "eos_churakov_gottschalk_coeffs", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Churakov-Gottschalk EoS coefficients (max. 13) \"CGmc\"\n", - "required": "optional" - }, - { - "key": 17, - "name": "eos_gas_crit_props", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Critical properties for gas\/fluid CST EoS \"gcrp\"\n", - "required": "optional" - }, - { - "key": 18, - "name": "m_landau_phase_trans_props", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Properties of phase transitions for minerals (Berman) Tr; Tft; tilt; l1,l2 \"Phtrp\"\n", - "required": "optional" - }, - { - "key": 21, - "name": "m_berman_phase_trans_props", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Properties of phase transitions for minerals (Berman) Tr; Tft; tilt; l1,l2 \"Phtrp\"\n", - "required": "optional" - }, - { - "key": 22, - "name": "m_lambda_trans_props", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Properties of lambda transition for minerals Smax, Tlt \"Lamtrp\"\n", - "required": "optional" - }, - { - "key": 23, - "name": "m_phase_trans_props", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Properties of phase transitions for minerals T, dS, dH, dV, and dT_dP (slope)\n", - "required": "optional" - } - ] - }, - { - "name": "Substance", - "doc": "Description of a substance (chemical species, chemical component, site moiety)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "symbol", - "typeId": "string", - "doc": "Unique name\/ID of this substance (e.g. abbreviated mineral name)\n", - "required": "required" - }, - { - "key": 2, - "name": "sourcetdb", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Source TDB: enum validated with class SourceTDB\n", - "class": "SourceTDB", - "required": "required" - }, - { - "key": 3, - "name": "formula", - "typeId": "string", - "doc": "Formula of substance in GEMS syntax, in elements, can include moiety symbols\n", - "required": "required" - }, - { - "key": 5, - "name": "name", - "typeId": "string", - "doc": "Name of the substance (chemical or mineral nomenclature)\n", - "required": "req_out" - }, - { - "key": 6, - "name": "class_", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Class of substance: enum validated with class SubstanceClass\n", - "class": "SubstanceClass", - "required": "req_out" - }, - { - "key": 8, - "name": "aggregate_state", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "(Standard) state of this substance: enum validated with class AggregateState\n", - "class": "AggregateState", - "required": "req_out" - }, - { - "key": 9, - "name": "standard_cscale", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "(Standard) concentration scale: enum validated with class ConcentrationScales\n", - "class": "ConcentrationScale", - "required": "req_out" - }, - { - "key": 10, - "name": "Tst", - "typeId": "double", - "doc": "Reference temperature for standard state (usually 298.15 K)\n", - "required": "req_out", - "default": 298.15 - }, - { - "key": 11, - "name": "Pst", - "typeId": "double", - "doc": "Reference pressure (usually 1 bar or 10^5 Pa, sometimes 1.013 bar = 1 atm)\n", - "required": "req_out", - "default": 100000 - }, - { - "key": 12, - "name": "formula_charge", - "typeId": "double", - "doc": "Formula charge, default 0 (usually calculated from parsed formula)\n", - "required": "req_out" - }, - { - "key": 13, - "name": "mass_per_mole", - "typeId": "double", - "doc": "Mass per 1 mole of this substance \"mM\" kg\/mol (calculated with fCharge)\n", - "required": "req_out" - }, - { - "key": 14, - "name": "s_density", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Standard-state density at Tst, Pst \"d0\" kg\/m3\n", - "required": "req_out" - }, - { - "key": 15, - "name": "sm_volume", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Standard volume at Tst, Pst \"V0\" m3\/mol\n", - "required": "req_out" - }, - { - "key": 16, - "name": "sm_gibbs_energy", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Standard Gibbs energy at Tst, Pst \"GO\" J\/mol\n", - "required": "req_out" - }, - { - "key": 17, - "name": "sm_enthalpy", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Standard enthalpy at Tst, Pst \"H0\" J\/mol\n", - "required": "req_out" - }, - { - "key": 18, - "name": "sm_entropy_f", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Standard entropy of formation from elements at st.states \"S0f\" J\/K\/mol\n", - "required": "req_out" - }, - { - "key": 19, - "name": "sm_entropy_abs", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Standard absolute entropy at Tst, Pst \"S0\" J\/K\/mol\n", - "required": "req_out" - }, - { - "key": 20, - "name": "sm_heat_capacity_p", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Standard constant-pressure heat capacity at Tst, Pst \"Cp0\" J\/K\/mol\n", - "required": "req_out" - }, - { - "key": 21, - "name": "m_compressibility", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Isothermal compressibility (for condensed substances)\n", - "required": "req_out" - }, - { - "key": 22, - "name": "m_expansivity", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Isobaric expansivity (for condensed substances)\n", - "required": "req_out" - }, - { - "key": 25, - "name": "TPMethods", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "SubstanceTPMethodData" - } - }, - "doc": "One or more method codes and data for computing P,T corrections to standard properties\n", - "required": "req_out" - }, - { - "key": 26, - "name": "limitsTP", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.LimitsTP" - }, - "doc": "Overall T,P limits for all methods involved\n", - "required": "req_out" - }, - { - "key": 31, - "name": "surface_density", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Standard surface density and denticity (for surface species) \"surfd\"\n", - "required": "optional" - }, - { - "key": 32, - "name": "aq_edh_props", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.Item" - }, - "doc": "Individual properties for Debye-Hueckel-type aqueous activity \"EDHp\"\n", - "required": "optional" - }, - { - "key": 35, - "name": "comment", - "typeId": "string", - "doc": "Comment - e.g. who entered\/modified, ...\n", - "required": "optional" - }, - { - "key": 36, - "name": "datasources", - "typeId": "set", - "type": { - "typeId": "set", - "elemTypeId": "string" - }, - "doc": "Labels of datasource DB objects\n", - "required": "optional" - }, - { - "key": 37, - "name": "time_stamp", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.TimeStamp" - }, - "doc": "Timestamp when the record was created or modified\n", - "required": "optional" - }, - { - "key": 2001, - "name": "temp_import", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "prop.Item" - } - }, - "doc": "Field for storing temporary values needed during import script\n", - "required": "optional" - } - ] - }, - { - "name": "Substances", - "doc": "Definition of an array of substances\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 2, - "name": "substances", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "Substance" - } - }, - "doc": "List of CemGEMS chemical system recipes\n", - "required": "req_out" - } - ] - }, - { - "name": "SubstanceInfo", - "doc": "Short description of substance (for using in ChemSysDef etc.)\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "symbol", - "typeId": "string", - "doc": "Unique name\/ID of this substance (e.g. abbreviated mineral name)\n", - "required": "req_out" - }, - { - "key": 2, - "name": "formula", - "typeId": "string", - "doc": "Formula of substance in GEMS syntax, in elements, can include moiety symbols\n", - "required": "req_out" - }, - { - "key": 3, - "name": "class_", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Class of substance: enum validated with class SubstanceClass\n", - "class": "SubstanceClass", - "required": "req_out" - }, - { - "key": 4, - "name": "aggregate_state", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "(Standard) state of this substance: enum validated with class AggregateState\n", - "class": "AggregateState", - "required": "req_out" - }, - { - "key": 5, - "name": "standard_cscale", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "(Standard) concentration scale: enum validated with class ConcentrationScales\n", - "class": "ConcentrationScale", - "required": "req_out" - }, - { - "key": 6, - "name": "formula_charge", - "typeId": "double", - "doc": "Formula charge, default 0 (usually calculated from parsed formula)\n", - "required": "req_out" - }, - { - "key": 7, - "name": "mass_per_mole", - "typeId": "double", - "doc": "Mass per 1 mole of this substance \"mM\" kg\/mol (calculated with fCharge)\n", - "required": "req_out" - } - ] - }, - { - "name": "ElementData", - "doc": "Data structure for processing the elements\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "elemc", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Class (type) of this element (independent component)\n", - "required": "req_out" - }, - { - "key": 2, - "name": "Mar", - "typeId": "double", - "doc": "Relative atomic mass of this element, dimensionless\n", - "required": "req_out" - }, - { - "key": 3, - "name": "iMass", - "typeId": "i16", - "doc": "Isotope mass or 0 if natural mixture of isotopes\n", - "required": "req_out" - }, - { - "key": 4, - "name": "iNA", - "typeId": "double", - "doc": "Isotope abundance fraction, default 1\n", - "required": "req_out" - }, - { - "key": 5, - "name": "S0a", - "typeId": "double", - "doc": "Standard abs entropy J\/K\/mol per mole of atoms\n", - "required": "req_out" - }, - { - "key": 6, - "name": "V0a", - "typeId": "double", - "doc": "Standard volume cm3 per mole of atoms\n", - "required": "req_out" - }, - { - "key": 7, - "name": "Cp0a", - "typeId": "double", - "doc": "Standard heat capacity J\/K\/mol per mole of atoms\n", - "required": "req_out" - }, - { - "key": 8, - "name": "valences", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "double" - }, - "doc": "Valences possible for this element\n", - "required": "req_out" - }, - { - "key": 11, - "name": "processed", - "typeId": "bool", - "doc": "indicator of processing the data\n", - "required": "req_out", - "default": 0 - }, - { - "key": 12, - "name": "elemid", - "typeId": "i32", - "doc": "Element id\n", - "required": "optional" - }, - { - "key": 13, - "name": "symbol", - "typeId": "string", - "doc": "element symbol\n", - "required": "optional" - }, - { - "key": 14, - "name": "formula", - "typeId": "string", - "doc": "element (IComp) formula\n", - "required": "optional" - } - ] - }, - { - "name": "SubstanceData", - "doc": "Work structure keeping the data for substance data object calculations\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "Nelem", - "typeId": "i16", - "required": "req_out" - }, - { - "key": 2, - "name": "elems", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "ElementData" - } - }, - "required": "req_out" - }, - { - "key": 4, - "name": "cmV0", - "typeId": "double", - "required": "req_out" - }, - { - "key": 5, - "name": "cmG0", - "typeId": "double", - "required": "req_out" - }, - { - "key": 6, - "name": "cmH0", - "typeId": "double", - "required": "req_out" - }, - { - "key": 7, - "name": "cmS0", - "typeId": "double", - "required": "req_out" - }, - { - "key": 8, - "name": "cmCp0", - "typeId": "double", - "required": "req_out" - }, - { - "key": 9, - "name": "cfCharge", - "typeId": "double", - "required": "req_out" - }, - { - "key": 10, - "name": "cmMass", - "typeId": "double", - "required": "req_out" - }, - { - "key": 11, - "name": "processed", - "typeId": "bool", - "required": "req_out", - "default": 0 - }, - { - "key": 12, - "name": "subsid", - "typeId": "i32", - "required": "optional" - }, - { - "key": 13, - "name": "symbol", - "typeId": "string", - "required": "optional" - }, - { - "key": 14, - "name": "formula", - "typeId": "string", - "required": "optional" - } - ] - }, - { - "name": "ThermoPropertiesSubstance", - "doc": "Structure keeping thermodynamic properites that can be calculated at P,T for a substance\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "gibbs_energy", - "typeId": "double", - "doc": "The apparent standard molar Gibbs free energy of the species\n", - "required": "req_out" - }, - { - "key": 2, - "name": "helmholtz_energy", - "typeId": "double", - "doc": "The apparent standard molar Helmholtz free energy of the species\n", - "required": "req_out" - }, - { - "key": 3, - "name": "internal_energy", - "typeId": "double", - "doc": "The apparent standard molar internal energy of the species\n", - "required": "req_out" - }, - { - "key": 4, - "name": "enthalpy", - "typeId": "double", - "doc": "The apparent standard molar enthalpy of the species\n", - "required": "req_out" - }, - { - "key": 5, - "name": "entropy", - "typeId": "double", - "doc": "The standard molar entropy of the species\n", - "required": "req_out" - }, - { - "key": 6, - "name": "volume", - "typeId": "double", - "doc": "The standard molar volume of the species\n", - "required": "req_out" - }, - { - "key": 7, - "name": "heat_capacity_cp", - "typeId": "double", - "doc": "The standard molar isobaric heat capacity of the species\n", - "required": "req_out" - }, - { - "key": 8, - "name": "heat_capacity_cv", - "typeId": "double", - "doc": "The standard molar isochoric heat capacity of the species\n", - "required": "req_out" - } - ] - } - ], - "constants": [ - ], - "services": [ - ] -} diff --git a/Resources/data/schemas/thermodataset.schema.json b/Resources/data/schemas/thermodataset.schema.json deleted file mode 100644 index 8d6d73b4..00000000 --- a/Resources/data/schemas/thermodataset.schema.json +++ /dev/null @@ -1,396 +0,0 @@ -{ - "name": "thermodataset", - "doc": "Apache Thrift IDL definition for the thermodatabase service interface\n", - "namespaces": { - "*": "thermodataset" - }, - "includes": [ -"prop", -"element", -"substance", -"reaction", -"reactionset" - ], - "enums": [ - { - "name": "ThermoDataSetType", - "doc": "classes (types) of thermodynamic datasets\n", - "members": [ - { - "name": "TDS_REF", - "value": 0, - "doc": "Reference thermodynamic dataset (e.g. CODATA, mainly for .csv export)\n" - }, - { - "name": "TDS_LMA", - "value": 1, - "doc": "LMA-type thermodynamic dataset\n" - }, - { - "name": "TDS_GEM", - "value": 2, - "doc": "GEM-type thermodynamic dataset\n" - }, - { - "name": "TDS_OTHER", - "value": 101, - "doc": "therodynamic dataset of other type\n" - } - ] - } - ], - "typedefs": [ - { - "name": "elementdata", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "substance.ElementData" - } - }, - { - "name": "substancedata", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "substance.SubstanceData" - } - }, - { - "name": "substanceprops", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "substance.ThermoPropertiesSubstance" - } - }, - { - "name": "prodreacdata", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "reaction.ReactionData" - } - }, - { - "name": "reacsetdata", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "reactionset.ReactionSetData" - } - } - ], - "structs": [ - { - "name": "ThermoDataSet", - "doc": "Description of thermodynamic dataset for use in modelling\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "symbol", - "typeId": "string", - "doc": "Unique name\/ID of this thermodynamic dataset\n", - "required": "required" - }, - { - "key": 2, - "name": "stype", - "class": "ThermoDataSetType", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Type of thermodataset - validate with class ThermoDataSetType\n", - "required": "required", - "default": { - "2": "TDS_GEM" - } - }, - { - "key": 3, - "name": "level", - "typeId": "i32", - "doc": "Level of the reactionset\n", - "required": "required", - "default": 0 - }, - { - "key": 4, - "name": "name", - "typeId": "string", - "doc": "Extended name of the thermodataset (not compulsory)\n", - "required": "req_out" - }, - { - "key": 5, - "name": "element_list", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "string" - }, - "doc": "List of element symbols covered by this reactionset - may be replaced by a graph\n", - "required": "optional" - }, - { - "key": 6, - "name": "species_map", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "string", - "valueTypeId": "i32" - }, - "doc": "Map of species symbols and types (class SpeciesTypeRS) covered by reactionset - a graph?\n", - "required": "optional" - }, - { - "key": 7, - "name": "reactionsets_map", - "class": "ReactionSetType", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "string", - "valueTypeId": "i32" - }, - "doc": "Symbol of reactionsets used by this thermodataset if of LMA_TDS type\n", - "required": "optional" - }, - { - "key": 8, - "name": "sourcetdbs", - "typeId": "map", - "type": { - "typeId": "map", - "keyTypeId": "i32", - "valueTypeId": "string" - }, - "doc": "Source TDB: list of enums validated with the class SourceTDB\n", - "class": "SourceTDB", - "required": "optional" - }, - { - "key": 9, - "name": "elements", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "element.ElementInfo" - } - }, - "doc": "List of element symbols and infos covered by this reactionset - may be replaced by a graph\n", - "required": "req_out" - }, - { - "key": 10, - "name": "limitsTP", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.LimitsTP" - }, - "doc": "Overall lower and upper T, P limits for T,P corrections\n", - "required": "req_out", - "default": { - "range": 0, - "lowerT": 273.15, - "upperT": 298.15, - "lowerP": 0.1, - "upperP": 1000000 - } - }, - { - "key": 11, - "name": "comment", - "typeId": "string", - "doc": "Comment e.g. who entered\/modified, ...\n", - "required": "optional" - }, - { - "key": 12, - "name": "datasources", - "typeId": "set", - "type": { - "typeId": "set", - "elemTypeId": "string" - }, - "doc": "Labels of datasource DB objects - may be obsolete\n", - "required": "optional" - }, - { - "key": 13, - "name": "time_stamp", - "typeId": "struct", - "type": { - "typeId": "struct", - "class": "prop.TimeStamp" - }, - "doc": "Timestamp\n", - "required": "optional" - } - ] - }, - { - "name": "ThermoDataSets", - "doc": "Definition of an array of thermodata sets\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 2, - "name": "thermodatasets", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "ThermoDataSet" - } - }, - "doc": "List of thermodata sets\n", - "required": "req_out" - } - ] - }, - { - "name": "ThermoDataSetData", - "doc": "work structure keeping the data for thermodataset object\n", - "isException": false, - "isUnion": false, - "fields": [ - { - "key": 1, - "name": "Nmasts", - "typeId": "i32", - "doc": "number of master species taking part in this reactionset\n", - "required": "req_out" - }, - { - "key": 2, - "name": "masts", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "substance.SubstanceData" - } - }, - "doc": "array of data for master species\n", - "required": "req_out" - }, - { - "key": 3, - "name": "Nprods", - "typeId": "i32", - "doc": "number of product species taking part in this reactionset\n", - "required": "optional" - }, - { - "key": 4, - "name": "prods", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "substance.SubstanceData" - } - }, - "doc": "array of data for product species\n", - "required": "req_out" - }, - { - "key": 5, - "name": "Npreacs", - "typeId": "i32", - "doc": "number of product species formation reactions in this reactionset\n", - "required": "req_out" - }, - { - "key": 6, - "name": "preacs", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "reaction.ReactionData" - } - }, - "doc": "array of data for product formation reactions\n", - "required": "req_out" - }, - { - "key": 7, - "name": "Nelems", - "typeId": "i32", - "doc": "number of elements used in this thermodataset\n", - "required": "req_out" - }, - { - "key": 8, - "name": "elems", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "substance.ElementData" - } - }, - "doc": "array of data for elements\n", - "required": "req_out" - }, - { - "key": 9, - "name": "Nreacsets", - "typeId": "i32", - "doc": "number of reactionsets used in this thermodataset\n", - "required": "req_out" - }, - { - "key": 10, - "name": "preacsets", - "typeId": "list", - "type": { - "typeId": "list", - "elemTypeId": "struct", - "elemType": { - "typeId": "struct", - "class": "reactionset.ReactionSetData" - } - }, - "doc": "array of data for reactionsets\n", - "required": "req_out" - }, - { - "key": 11, - "name": "processed", - "typeId": "bool", - "doc": "indicator of processing the thermodataset\n", - "required": "req_out", - "default": 0 - } - ] - } - ], - "constants": [ - ], - "services": [ - ] -} diff --git a/ThermoFun/Common/ParseJsonToData.cpp b/ThermoFun/Common/ParseJsonToData.cpp index a7632e6a..c982553f 100644 --- a/ThermoFun/Common/ParseJsonToData.cpp +++ b/ThermoFun/Common/ParseJsonToData.cpp @@ -13,6 +13,7 @@ #include "ThermoParameters.h" #include "ThermoProperties.h" #include "Common/Exception.h" +#include "Common/Units.hpp" // JSON #include @@ -68,27 +69,119 @@ auto thermoRefPropReac(const json &j) -> ThermoPropertiesReaction; // return false; //} -auto readValueError(const json &j, string propPath, double &val, double &err, string message) -> Reaktoro_::StatusMessage +auto readValueErrorUnit(const json &j, string propPath, double &val, double &err, std::string unit, string message) -> Reaktoro_::StatusMessage { - string sval, serr; + string sval, serr, unit_in_record; Reaktoro_::StatusMessage status = {Reaktoro_::Status::notdefined, message}; + unit_in_record = unit; + + if (j[propPath].contains("/units/0"_json_pointer)) + if (!j[propPath]["units"][0].is_null()) + unit_in_record = j[propPath]["units"][0]; if (j[propPath].contains("/values/0"_json_pointer)) { if (!j[propPath]["values"][0].is_null()) - val = j[propPath]["values"][0].get(); + val = units::convert(j[propPath]["values"][0].get(), unit_in_record, unit); status = {Reaktoro_::Status::read, message}; } if (j[propPath].contains("/errors/0"_json_pointer)) { if (!j[propPath]["errors"][0].is_null()) - err = j[propPath]["errors"][0].get(); + err = units::convert(j[propPath]["errors"][0].get(), unit_in_record, unit); } return status; } +auto convert_values_units(std::vector values, const std::vector &units_from, const std::vector &units_to) -> std::vector +{ + for (size_t i = 0; i < values.size(); i++) + { + std::string from = ""; + std::string to = ""; + if (i < units_from.size()) + from = units_from[i]; + + if (i < units_to.size()) + to = units_to[i]; + + if (from == "") + from = to; + + if (from == "" || to == "") + { + from = "1"; + to = "1"; + } + + values[i] = units::convert(values[i], from, to); + } + return values; +} + +auto read_values_units(const json &j, const std::string &data, std::vector &values, const std::vector &units_to) -> void +{ + std::vector units_from; + + //units + if (j.contains(data)) + { + if (j[data].contains("units")) + { + if (!j[data]["units"].is_null()) + units_from = j[data]["units"].get>(); + // temporary + if (data == "eos_hkf_coeffs") + if (units_from.size()>=3) + if (units_from[2]=="(cal*K)/mol") + units_from = units_to; + } + else + units_from = units_to; + + if (j[data].contains("values")) + if (!j[data]["values"].is_null()) + values = convert_values_units(j[data]["values"].get>(), units_from, units_to); + } +} + +auto read_value_unit(const json &j, const std::string &data, double &value, const std::string &unit_to) -> void +{ + std::string unit_from; + + //units + if (j.contains(data)) + { + if (j[data].contains("units")) + { + if (!j[data]["units"][0].is_null()) + unit_from = j[data]["units"][0]; + } + else + unit_from = unit_to; + + // temporary fix (error in database) + double factor = 1.0; + if (data == "m_expansivity" && unit_from == "kbar") + { + unit_from = "1/K"; + factor = 1e5; + } + + if (data == "m_compressibility" && unit_from == "1e-05/K") + { + unit_from = "kbar"; + factor = 1; + } + + if (j[data].contains("values")) + if (!j[data]["values"][0].is_null()) + value = units::convert(j[data]["values"][0].get() * factor, unit_from, unit_to); + } +} + auto getParameterCoefficients(/*const std::string& data,*/ const SubstanceTPMethodType &type) -> std::unordered_map> { std::unordered_map> coefficients; @@ -103,9 +196,7 @@ auto getParameterCoefficients(/*const std::string& data,*/ const SubstanceTPMeth cout << '2'; break; } - // throw error method not found - return coefficients; } @@ -220,6 +311,7 @@ auto getTPMethods(const json &j, Substance &s) -> void { ThermoParametersSubstance ps; json methods = j["TPMethods"]; + std::string unit_from; for (auto it = methods.begin(); it != methods.end(); ++it) { @@ -232,12 +324,8 @@ auto getTPMethods(const json &j, Substance &s) -> void } } - if (j.contains("/m_expansivity/values/0"_json_pointer)) - if (!j["m_expansivity"]["values"][0].is_null()) - ps.isobaric_expansivity = j["m_expansivity"]["values"][0].get(); - if (j.contains("/m_compressibility/values/0"_json_pointer)) - if (!j["m_compressibility"]["values"][0].is_null()) - ps.isothermal_compresibility = j["m_compressibility"]["values"][0].get(); + read_value_unit(j, "m_expansivity", ps.isobaric_expansivity, "1/K"); + read_value_unit(j, "m_compressibility", ps.isothermal_compresibility, "kbar"); s.setThermoParameters(ps); } @@ -247,23 +335,10 @@ auto thermoParamSubst(const json &j, std::string prop_name, ThermoParametersSubs vector vkbuf; string kbuf; - if (j.contains("/eos_akinfiev_diamond_coeffs/values"_json_pointer)) - if (!j["eos_akinfiev_diamond_coeffs"]["values"].is_null()) - ps.Cp_nonElectrolyte_coeff = j["eos_akinfiev_diamond_coeffs"]["values"].get>(); - - if (j.contains("/eos_birch_murnaghan_coeffs/values"_json_pointer)) - if (!j["eos_birch_murnaghan_coeffs"]["values"].is_null()) - ps.volume_BirchM_coeff = j["eos_birch_murnaghan_coeffs"]["values"].get>(); - - // if (j.contains("eos_churakov_gottschalk_coeffs"))s.resize(vkbuf.size()); - - if (j.contains("/eos_gas_crit_props/values"_json_pointer)) - if (!j["eos_gas_crit_props"]["values"].is_null()) - ps.critical_parameters = j["eos_gas_crit_props"]["values"].get>(); - - if (j.contains("/eos_hkf_coeffs/values"_json_pointer)) - if (!j["eos_hkf_coeffs"]["values"].is_null()) - ps.HKF_parameters = j["eos_hkf_coeffs"]["values"].get>(); + read_values_units(j, "eos_akinfiev_diamond_coeffs", ps.Cp_nonElectrolyte_coeff, {"1", "(cm^3)/g", "(cm^3*K^0.5)/g"}); + // ps.volume_BirchM_coeff = read_values_units(j, "eos_birch_murnaghan_coeffs", {}); + read_values_units(j, "eos_gas_crit_props", ps.critical_parameters, {"K", "Pa", "1", "1"}); + read_values_units(j, "eos_hkf_coeffs", ps.HKF_parameters, {"cal/(mol*bar)", "cal/mol", "(cal*K)/(mol*bar)", "(cal*K)/mol", "cal/(mol*K)", "(cal*K)/mol", "cal/mol"}); // temporary fix - need to think how to handle more than 1 TP interval - for new structure - simplified if (prop_name == "cp_ft_equation") @@ -280,49 +355,31 @@ auto thermoParamSubst(const json &j, std::string prop_name, ThermoParametersSubs } ps.temperature_intervals.push_back(low_up); } - - if (j.contains("/m_heat_capacity_ft_coeffs/values"_json_pointer)) - if (!j["m_heat_capacity_ft_coeffs"]["values"].is_null()) - ps.Cp_coeff.push_back(j["m_heat_capacity_ft_coeffs"]["values"].get>()); - - if (j.contains("/m_phase_trans_props/values"_json_pointer)) - if (!j["m_phase_trans_props"]["values"].is_null()) - ps.phase_transition_prop.push_back(j["m_phase_trans_props"]["values"].get>()); - - if (j.contains("/m_landau_phase_trans_props/values"_json_pointer)) - if (!j["m_landau_phase_trans_props"]["values"].is_null()) - ps.phase_transition_prop.push_back(j["m_landau_phase_trans_props"]["values"].get>()); - - if (j.contains("/phase_transition_prop_Berman/values"_json_pointer)) - if (!j["phase_transition_prop_Berman"]["values"].is_null()) - ps.phase_transition_prop_Berman.push_back(j["phase_transition_prop_Berman"]["values"].get>()); + std::vector cp, ph; + read_values_units(j, "m_heat_capacity_ft_coeffs", cp, {"J/(mol*K)", "J/(mol*K^2)", "(J*K)/mol", "J/(mol*K^0.5)", "J/(mol*K^3)", "J/(mol*K^4)", "J/(mol*K^5)", "(J*K^2)/mol", "J/mol", "J/(mol*K^1.5)", "J/(mol*K)"}); + if (cp.size() > 0) + ps.Cp_coeff.push_back(cp); + read_values_units(j, "m_phase_trans_props", ph, {"K", "J/(mol*K)", "J/mol", "J/bar", "K/bar"}); + if (ph.size() > 0) + ps.phase_transition_prop.push_back(ph); + read_values_units(j, "m_landau_phase_trans_props", ps.m_landau_phase_trans_props, {"degC", "J/(mol*K)", "J/bar"}); + read_values_units(j, "solute_holland_powell98_coeff", ps.solute_holland_powell98_coeff, {"kJ/(mol*K^2)"}); + // ps.phase_transition_prop_Berman.push_back(read_values_units(j, "", {}); } auto thermoParamReac(const json &j, ThermoParametersReaction &pr) -> void { - vector vkbuf; + vector vkbuf, units_from, units_to; string kbuf; - if (j.contains("/logk_ft_coeffs/values"_json_pointer)) - if (!j["logk_ft_coeffs"]["values"].is_null()) - pr.reaction_logK_fT_coeff = j["logk_ft_coeffs"]["values"].get>(); - // if (j.contains("logk_pt_values") && !j["logk_pt_values"]["values"].is_null()) // static const char * reacLogKPT = "logk_pt_values.pptv"; // + read_values_units(j, "logk_ft_coeffs", pr.reaction_logK_fT_coeff, {"1", "1/K", "K", "1", "K^2", "1/K^2", "K^0.5"}); + // if (j.contains("logk_pt_values") && !j["logk_pt_values"]["values"].is_null()) // pr.logK_TP_array = j["logk_pt_values"]["values"].get>(); - if (j.contains("/dr_heat_capacity_ft_coeffs/values"_json_pointer)) - if (!j["dr_heat_capacity_ft_coeffs"]["values"].is_null()) - pr.reaction_Cp_fT_coeff = j["dr_heat_capacity_ft_coeffs"]["values"].get>(); - if (j.contains("/dr_volume_fpt_coeffs/values"_json_pointer)) - if (!j["dr_volume_fpt_coeffs"]["values"].is_null()) - pr.reaction_V_fT_coeff = j["dr_volume_fpt_coeffs"]["values"].get>(); - if (j.contains("/dr_ryzhenko_coeffs/values"_json_pointer)) - if (!j["dr_ryzhenko_coeffs"]["values"].is_null()) - pr.reaction_RB_coeff = j["dr_ryzhenko_coeffs"]["values"].get>(); - if (j.contains("/dr_marshall_franck_coeffs/values"_json_pointer)) - if (!j["dr_marshall_franck_coeffs"]["values"].is_null()) - pr.reaction_FM_coeff = j["dr_marshall_franck_coeffs"]["values"].get>(); - if (j.contains("/dr_dolejs_manning10_coeffs/values"_json_pointer)) - if (!j["dr_dolejs_manning10_coeffs"]["values"].is_null()) - pr.reaction_DM10_coeff = j["dr_dolejs_manning10_coeffs"]["values"].get>(); + read_values_units(j, "dr_heat_capacity_ft_coeffs", pr.reaction_Cp_fT_coeff, {"J/(mol*K)", "J/(mol*K^2)", "(J*K)/mol", "J/(mol*K^0.5)", "J/(mol*K^3)"}); + read_values_units(j, "dr_volume_fpt_coeffs", pr.reaction_V_fT_coeff, {"1/K", "1/K^2", "1/K^3", "1/bar", "1/bar^2"}); + read_values_units(j, "dr_ryzhenko_coeffs", pr.reaction_RB_coeff, {"1", "1", "1"}); + read_values_units(j, "dr_marshall_franck_coeffs", pr.reaction_FM_coeff, {"1", "K", "K^2", "K^3", "1", "K", "K^2"}); + read_values_units(j, "dr_dolejs_manning10_coeffs", pr.reaction_DM10_coeff, {"kJ/mol", "J/(mol*K)", "J/(mol*K)", "J/(mol*K^2)", "J/(mol*K)"}); } auto thermoRefPropSubst(const json &j) -> ThermoPropertiesSubstance @@ -331,15 +388,15 @@ auto thermoRefPropSubst(const json &j) -> ThermoPropertiesSubstance string message; if (j.contains("sm_heat_capacity_p")) - tps.heat_capacity_cp.sta = readValueError(j, "sm_heat_capacity_p", tps.heat_capacity_cp.val, tps.heat_capacity_cp.err, message); + tps.heat_capacity_cp.sta = readValueErrorUnit(j, "sm_heat_capacity_p", tps.heat_capacity_cp.val, tps.heat_capacity_cp.err, "J/K/mol", message); if (j.contains("sm_gibbs_energy")) - tps.gibbs_energy.sta = readValueError(j, "sm_gibbs_energy", tps.gibbs_energy.val, tps.gibbs_energy.err, message); + tps.gibbs_energy.sta = readValueErrorUnit(j, "sm_gibbs_energy", tps.gibbs_energy.val, tps.gibbs_energy.err, "J/mol", message); if (j.contains("sm_enthalpy")) - tps.enthalpy.sta = readValueError(j, "sm_enthalpy", tps.enthalpy.val, tps.enthalpy.err, message); + tps.enthalpy.sta = readValueErrorUnit(j, "sm_enthalpy", tps.enthalpy.val, tps.enthalpy.err, "J/mol", message); if (j.contains("sm_entropy_abs")) - tps.entropy.sta = readValueError(j, "sm_entropy_abs", tps.entropy.val, tps.entropy.err, message); + tps.entropy.sta = readValueErrorUnit(j, "sm_entropy_abs", tps.entropy.val, tps.entropy.err, "J/K/mol", message); if (j.contains("sm_volume")) - tps.volume.sta = readValueError(j, "sm_volume", tps.volume.val, tps.volume.err, message); + tps.volume.sta = readValueErrorUnit(j, "sm_volume", tps.volume.val, tps.volume.err, "J/bar", message); return tps; } @@ -350,17 +407,17 @@ auto thermoRefPropReac(const json &j) -> ThermoPropertiesReaction string message; if (j.contains("logKr")) - tpr.log_equilibrium_constant.sta = readValueError(j, "logKr", tpr.log_equilibrium_constant.val, tpr.log_equilibrium_constant.err, message); + tpr.log_equilibrium_constant.sta = readValueErrorUnit(j, "logKr", tpr.log_equilibrium_constant.val, tpr.log_equilibrium_constant.err, "1", message); if (j.contains("drsm_heat_capacity_p")) - tpr.reaction_heat_capacity_cp.sta = readValueError(j, "drsm_heat_capacity_p", tpr.reaction_heat_capacity_cp.val, tpr.reaction_heat_capacity_cp.err, message); + tpr.reaction_heat_capacity_cp.sta = readValueErrorUnit(j, "drsm_heat_capacity_p", tpr.reaction_heat_capacity_cp.val, tpr.reaction_heat_capacity_cp.err, "J/K/mol", message); if (j.contains("drsm_gibbs_energy")) - tpr.reaction_gibbs_energy.sta = readValueError(j, "drsm_gibbs_energy", tpr.reaction_gibbs_energy.val, tpr.reaction_gibbs_energy.err, message); + tpr.reaction_gibbs_energy.sta = readValueErrorUnit(j, "drsm_gibbs_energy", tpr.reaction_gibbs_energy.val, tpr.reaction_gibbs_energy.err, "J/mol", message); if (j.contains("drsm_enthalpy")) - tpr.reaction_enthalpy.sta = readValueError(j, "drsm_enthalpy", tpr.reaction_enthalpy.val, tpr.reaction_enthalpy.err, message); + tpr.reaction_enthalpy.sta = readValueErrorUnit(j, "drsm_enthalpy", tpr.reaction_enthalpy.val, tpr.reaction_enthalpy.err, "J/mol", message); if (j.contains("drsm_entropy")) - tpr.reaction_entropy.sta = readValueError(j, "drsm_entropy", tpr.reaction_entropy.val, tpr.reaction_entropy.err, message); + tpr.reaction_entropy.sta = readValueErrorUnit(j, "drsm_entropy", tpr.reaction_entropy.val, tpr.reaction_entropy.err, "J/K/mol", message); if (j.contains("drsm_volume")) - tpr.reaction_volume.sta = readValueError(j, "drsm_volume", tpr.reaction_volume.val, tpr.reaction_volume.err, message); + tpr.reaction_volume.sta = readValueErrorUnit(j, "drsm_volume", tpr.reaction_volume.val, tpr.reaction_volume.err, "J/bar", message); return tpr; } @@ -406,22 +463,15 @@ auto parseElement(const std::string &data) -> Element if (j.contains("number")) if (!j["number"].is_null()) e.setNumber(j["number"].get()); - - if (j.contains("/entropy/values/0"_json_pointer)) - if (!j["entropy"]["values"][0].is_null()) - e.setEntropy(j["entropy"]["values"][0].get()); - - if (j.contains("/heat_capacity/values/0"_json_pointer)) - if (!j["heat_capacity"]["values"][0].is_null()) - e.setHeatCapacity(j["heat_capacity"]["values"][0].get()); - - if (j.contains("/atomic_mass/values/0"_json_pointer)) - if (!j["atomic_mass"]["values"][0].is_null()) - e.setMolarMass(j["atomic_mass"]["values"][0].get()); - - if (j.contains("/volume/values/0"_json_pointer)) - if (!j["volume"]["values"][0].is_null()) - e.setVolume(j["volume"]["values"][0].get()); + double val; + read_value_unit(j, "entropy", val, "J/(mol*K)"); + e.setEntropy(val); + read_value_unit(j, "heat_capacity", val, "J/(mol*K)"); + e.setHeatCapacity(val); + read_value_unit(j, "atomic_mass", val, "g/mol"); + e.setMolarMass(val); + read_value_unit(j, "volume", val, "J/bar"); + e.setVolume(val); if (j.contains("class_")) { @@ -478,9 +528,9 @@ auto parseSubstance(const std::string &data) -> Substance if (!j["reaction"].is_null()) s.setReactionSymbol(j["reaction"]); - if (j.contains("mass_per_mole")) - if (!j["mass_per_mole"].is_null()) - s.setMolarMass(j["mass_per_mole"].get()); + double val; + read_value_unit(j, "mass_per_mole", val, "g/mol"); + s.setMolarMass(val); if (j.contains("aggregate_state")) if (!j["aggregate_state"].is_null() && !j["aggregate_state"].empty()) diff --git a/ThermoFun/Common/Units.cpp b/ThermoFun/Common/Units.cpp index b9d487d5..14159425 100644 --- a/ThermoFun/Common/Units.cpp +++ b/ThermoFun/Common/Units.cpp @@ -65,7 +65,7 @@ struct StringUnit { double factor; string symbol; - int power; + double power; }; struct TemperatureUnit @@ -387,7 +387,20 @@ map derivedUnitsMap = {"eq" , {{1, "eq", 1}}}, {"meq" , {{milli, "eq", 1}}}, {"ueq" , {{micro, "eq", 1}}}, - {"neq" , {{nano, "eq", 1}}} + {"neq" , {{nano, "eq", 1}}}, + + {"K^2" , {{1, "K", 2}}}, + {"K^3" , {{1, "K", 3}}}, + {"K^4" , {{1, "K", 4}}}, + {"K^5" , {{1, "K", 5}}}, + {"K^0.5" , {{1, "K", 0.5}}}, + {"K^1.5" , {{1, "K", 1.5}}}, + + {"bar^2" , {{1, "K", 2}}}, + {"bar^3" , {{1, "K", 3}}}, + {"bar^4" , {{1, "K", 4}}}, + {"bar^5" , {{1, "K", 5}}}, + {"bar^0.5" , {{1, "K", 0.5}}} }; map temperatureUnitsMap = @@ -577,7 +590,7 @@ std::shared_ptr parseUnit(const string& symbol, size_t pos) } } -void parseUnit(const std::shared_ptr& root, DerivedUnit& derivedUnit, int sign) +void parseUnit(const std::shared_ptr& root, DerivedUnit& derivedUnit, double sign) { if(root->str == "*") { diff --git a/ThermoFun/Database.h b/ThermoFun/Database.h index 94a75ac7..b52ecd89 100644 --- a/ThermoFun/Database.h +++ b/ThermoFun/Database.h @@ -73,10 +73,10 @@ class Database /// Sets an Element in the database. auto setElement(const Element& element) -> void; - /// Add a map of Elements in the database. If the element exists the record will be overwriten + /// Add a map of Elements in the database. If the element exists the record will be overwritten auto addMapElements(const ElementsMap& elements) -> void; - /// Add an Substance instance in the database. If the substance exists the record will be overwriten + /// Add an Substance instance in the database. If the substance exists the record will be overwritten auto addSubstance(const Substance& substance) -> void; /// Sets a substance in the database. @@ -85,7 +85,7 @@ class Database /// Add a map of Substances in the database. auto addMapSubstances(const SubstancesMap& substances) -> void; - /// Add an Reaction instance in the database. If the reaction exists the record will be overwriten + /// Add an Reaction instance in the database. If the reaction exists the record will be overwritten auto addReaction(const Reaction& reaction) -> void; /// Sets a reaction in the database. diff --git a/ThermoFun/GlobalVariables.h b/ThermoFun/GlobalVariables.h index 3389579e..b416f48c 100644 --- a/ThermoFun/GlobalVariables.h +++ b/ThermoFun/GlobalVariables.h @@ -447,7 +447,7 @@ typedef struct { C_SURFACEFRACTION = 5, C_SURFACEDENSITY = 6, C_SITEFRACTION = 7, - C_OTHER = 8 + C_OTHER = 101 }; } ConcentrationScales; @@ -483,7 +483,7 @@ typedef struct { AQSOLVENT = 3, SURFSPECIES = 4, SITEMOIETY = 5, - OTHER_SC = 6 + OTHER_SC = 101 }; } SubstanceClass; @@ -509,13 +509,23 @@ static const int SubstanceClass_ndxThrift[] = { typedef struct { enum type { - GAS = 0, - LIQUID = 1, - GLASS = 2, - CRYSTAL = 3, - AQUEOUS = 4, - SURFACE = 5, - OTHER_AS = 6 + GAS = 0, ///< Gaseous aggregate state (symbol g) + LIQUID = 1, ///< Condensed liquid aggregate state (symbol l) + GLASS = 2, ///< Glass/Vitreous state (symbol vit) + CRYSTAL = 3, ///< Crystalline solid aggregate state (symbol cr) + AQUEOUS = 4, ///< Aqueous electrolyte (symbol aq) + SURFACE = 5, ///< Surface layer, adsorbed species (symbol ads) + IONEX = 6, ///< Ion exchange (Donnan etc.) (eymbol ex) + PLASMA = 8, ///< Plasma (symbol pl) + SOLID = 9, ///< Solid (symbol s) + CONDENSED = 10, ///< CondensedPhase (symbol cd) + FLUID = 11, ///< Fluid (symbol fl) + LIQUIDCRYSTAL = 12, ///< LiquidCrystal (symbol lc) + AMORPHOUSSOLID = 13, ///< AmorphousSolid (symbol am) + MONOMERIC = 14, ///< Monomeric (symbol mon) + POLYMERIC = 15, ///< Polymeric (symbol pol) + SOLIDSOLUTION = 16, ///< SolidSolution (symbol ss) + OTHER = 101 ///< Other states, undefined }; } AggregateState; @@ -526,7 +536,17 @@ static const int AggregateState_ndxThrift[] = { AggregateState::CRYSTAL, AggregateState::AQUEOUS, AggregateState::SURFACE, - AggregateState::OTHER_AS + AggregateState::IONEX, + AggregateState::PLASMA, + AggregateState::SOLID, + AggregateState::CONDENSED, + AggregateState::FLUID, + AggregateState::LIQUIDCRYSTAL, + AggregateState::AMORPHOUSSOLID, + AggregateState::MONOMERIC, + AggregateState::POLYMERIC, + AggregateState::SOLIDSOLUTION, + AggregateState::OTHER }; //const char* AggregateState_GEMS[] = { @@ -545,7 +565,7 @@ typedef struct { REACTANT = 0, ///< Component properties available PRODUCT = 1, ///< Component properties to be defined via this reaction properties CATALYST = 2, ///< Catalyzes the reaction but is not consumed in it - OTHER_RC = 3 ///< Other type of reaction component + OTHER_RC = 101 ///< Other type of reaction component }; } ReactionComponentType; diff --git a/ThermoFun/Reaction.cpp b/ThermoFun/Reaction.cpp index 6784e2eb..dbdab664 100644 --- a/ThermoFun/Reaction.cpp +++ b/ThermoFun/Reaction.cpp @@ -41,10 +41,10 @@ struct Reaction::Impl MethodCorrP_Thrift::type method_P; /// Reference temperature (in K) - double reference_T; + double reference_T = 298.15; /// Reference pressure (in Pa) - double reference_P; + double reference_P = 1e5; /// Lower temperature limit (in K) double lower_T; @@ -60,7 +60,7 @@ struct Reaction::Impl std::string jString; - void strip_all(std::string& str, const std::string& valof ) + void strip_all(std::string& str, const std::string& valof) { if( str.empty()) return; @@ -260,7 +260,13 @@ auto Reaction::thermo_ref_prop() const -> ThermoPropertiesReaction return pimpl->thermo_ref_prop; } -auto Reaction::thermo_parameters() const -> ThermoParametersReaction + +auto Reaction::thermoReferenceProperties() const -> ThermoPropertiesReaction +{ + return pimpl->thermo_ref_prop; +} + +auto Reaction::thermoParameters() const -> ThermoParametersReaction { return pimpl->thermo_parameters; } @@ -376,7 +382,7 @@ auto Reaction::convert_CpfT_to_logKfT() -> ThermoPropertiesReaction Sr = Rln10 * ( K_fT_Coeff[0] + 2.0*K_fT_Coeff[1]*TK + K_fT_Coeff[3]*(1.0 + log(TK)) - K_fT_Coeff[4]/TK*TK + 3.0*K_fT_Coeff[5]*TK*TK + 0.5*K_fT_Coeff[6]/pow(TK,0.5) ); - auto th_param = thermo_parameters(); + auto th_param = thermoParameters(); th_param.reaction_Cp_fT_coeff = CpCoeff; th_param.reaction_logK_fT_coeff = K_fT_Coeff; setThermoParameters(th_param); @@ -435,7 +441,7 @@ auto Reaction::convert_logKfT_toCpfT(/*MethodCorrT_Thrift::type methodT*/) -> Th } - auto th_param = thermo_parameters(); + auto th_param = thermoParameters(); th_param.reaction_Cp_fT_coeff = CpCoeff; th_param.reaction_logK_fT_coeff = K_fT_Coeff; setThermoParameters(th_param); @@ -494,7 +500,7 @@ auto Reaction::calc_logK_fT_coefficients() -> vd return K_fT_Coeff; -// auto th_param = thermo_parameters(); +// auto th_param = thermoParameters(); // th_param.reaction_logK_fT_coeff = K_fT_Coeff; // setThermoParameters(th_param); } diff --git a/ThermoFun/Reaction.h b/ThermoFun/Reaction.h index 8723b123..5997aab1 100644 --- a/ThermoFun/Reaction.h +++ b/ThermoFun/Reaction.h @@ -103,10 +103,11 @@ class Reaction auto reactants() const -> std::map; /// Returns the references proeprties of the reaction - auto thermo_ref_prop() const -> ThermoPropertiesReaction; + auto thermoReferenceProperties() const -> ThermoPropertiesReaction; + auto thermo_ref_prop() const -> ThermoPropertiesReaction; /// Returns an instance of the defined parameters of the reaction - auto thermo_parameters() const -> ThermoParametersReaction; + auto thermoParameters() const -> ThermoParametersReaction; /// Returns the references temperature (K) auto referenceT() const -> double; diff --git a/ThermoFun/Reactions/DolejsManning2010.cpp b/ThermoFun/Reactions/DolejsManning2010.cpp index d7b9f1ad..aa208477 100644 --- a/ThermoFun/Reactions/DolejsManning2010.cpp +++ b/ThermoFun/Reactions/DolejsManning2010.cpp @@ -7,12 +7,12 @@ auto thermoPropertiesDolejsManning2010(Reaktoro_::Temperature TK, Reaktoro_::Pre { ThermoPropertiesReaction tpr; -// auto ref_tpr = reaction.thermo_ref_prop(); +// auto ref_tpr = reaction.thermoReferenceProperties(); auto RHOw = wp.density/1000; // in g/cm3 auto ALPw = wp.Alpha; auto BETw = wp.Beta*1e05; auto dALPdTw = wp.dAldT; - auto DMcoef = reaction.thermo_parameters().reaction_DM10_coeff; + auto DMcoef = reaction.thermoParameters().reaction_DM10_coeff; auto dRHOdT = -ALPw*RHOw; auto dRHOdP = BETw*RHOw; diff --git a/ThermoFun/Reactions/FrantzMarshall.cpp b/ThermoFun/Reactions/FrantzMarshall.cpp index 209ee16c..f5bbce70 100644 --- a/ThermoFun/Reactions/FrantzMarshall.cpp +++ b/ThermoFun/Reactions/FrantzMarshall.cpp @@ -7,12 +7,12 @@ auto thermoPropertiesFrantzMarshall(Reaktoro_::Temperature TK, Reaktoro_::Pressu { ThermoPropertiesReaction tpr; -// auto ref_tpr = reaction.thermo_ref_prop(); +// auto ref_tpr = reaction.thermoReferenceProperties(); auto RHO = wp.density/1000; // in g/cm3 auto ALP = wp.Alpha; auto BET = wp.Beta*1e05; auto dALPdT = wp.dAldT; - auto MFcoef = reaction.thermo_parameters().reaction_FM_coeff; + auto MFcoef = reaction.thermoParameters().reaction_FM_coeff; auto dRHOdT = -ALP*RHO; auto dRHOdP = BET*RHO; diff --git a/ThermoFun/Reactions/LogK_function_of_T.cpp b/ThermoFun/Reactions/LogK_function_of_T.cpp index 1462b80b..ccedb7ff 100644 --- a/ThermoFun/Reactions/LogK_function_of_T.cpp +++ b/ThermoFun/Reactions/LogK_function_of_T.cpp @@ -10,9 +10,9 @@ auto thermoPropertiesReaction_LogK_fT(Reaktoro_::Temperature TK, Reaktoro_::Pres auto Rln10 = R_CONSTANT * lg_to_ln; auto R_T = TK * R_CONSTANT; - auto ref_tpr = reaction.thermo_ref_prop(); - auto A = reaction.thermo_parameters().reaction_logK_fT_coeff; - auto CpCoeff = reaction.thermo_parameters().reaction_Cp_fT_coeff; + auto ref_tpr = reaction.thermoReferenceProperties(); + auto A = reaction.thermoParameters().reaction_logK_fT_coeff; + auto CpCoeff = reaction.thermoParameters().reaction_Cp_fT_coeff; auto dVr = ref_tpr.reaction_volume; //Gr = rc[q].Gs[0]; auto dHr = ref_tpr.reaction_enthalpy; auto dSr = ref_tpr.reaction_entropy; diff --git a/ThermoFun/Reactions/RyzhenkoBryzgalyn.cpp b/ThermoFun/Reactions/RyzhenkoBryzgalyn.cpp index 8339b0a7..1804f62b 100644 --- a/ThermoFun/Reactions/RyzhenkoBryzgalyn.cpp +++ b/ThermoFun/Reactions/RyzhenkoBryzgalyn.cpp @@ -7,12 +7,12 @@ auto thermoPropertiesRyzhenkoBryzgalin(Reaktoro_::Temperature TK, Reaktoro_::Pre ThermoPropertiesReaction tpr; -// auto ref_tpr = reaction.thermo_ref_prop(); +// auto ref_tpr = reaction.thermoReferenceProperties(); auto RHO = wp.density / 1000; // check units auto ALP = wp.Alpha; auto BET = wp.Beta; auto dALPdT = wp.dAldT; - auto RBcoef = reaction.thermo_parameters().reaction_RB_coeff; + auto RBcoef = reaction.thermoParameters().reaction_RB_coeff; auto dRHOdT = -ALP*RHO; auto dRHOdP = BET*RHO; diff --git a/ThermoFun/Reactions/Volume_function_of_T.cpp b/ThermoFun/Reactions/Volume_function_of_T.cpp index 1507e1f3..6eb189ca 100644 --- a/ThermoFun/Reactions/Volume_function_of_T.cpp +++ b/ThermoFun/Reactions/Volume_function_of_T.cpp @@ -7,11 +7,11 @@ namespace ThermoFun { auto thermoPropertiesReaction_Vol_fT(Reaktoro_::Temperature TK, Reaktoro_::Pressure Pbar, Reaction reaction, ThermoPropertiesReaction tpr) -> ThermoPropertiesReaction { - auto prop_ref = reaction.thermo_ref_prop(); + auto prop_ref = reaction.thermoReferenceProperties(); auto Pst = reaction.referenceP(); auto Vst = prop_ref.reaction_volume; auto Tst = reaction.referenceT(); - auto a = reaction.thermo_parameters().reaction_V_fT_coeff; + auto a = reaction.thermoParameters().reaction_V_fT_coeff; // if( (methodP == MethodCorrP_Thrift::type::CPM_VKE || methodP == MethodCorrP_Thrift::type::CPM_VBE) && rc[q].DVt ) // { // calc on equation V(P,T) @@ -38,8 +38,8 @@ auto thermoPropertiesReaction_Vol_fT(Reaktoro_::Temperature TK, Reaktoro_::Press break; } } - auto VP = Vst * (Pbar - Pst); - auto VT = Vst * (TK-Tst); + auto VP = Vst * (Pbar - Pst); // J + auto VT = Vst * (TK-Tst); // J*K/bar tpr.reaction_volume += VP; tpr.reaction_enthalpy += VP; for( unsigned i=0; iBet = aE; tpr.ln_equilibrium_constant -= tpr.reaction_volume * (Pbar - Pst) / (R_CONSTANT*TK); tpr.log_equilibrium_constant = tpr.ln_equilibrium_constant/lg_to_ln; - tpr.reaction_entropy = tpr.reaction_gibbs_energy - TK*tpr.reaction_entropy; + tpr.reaction_entropy = (tpr.reaction_enthalpy - tpr.reaction_gibbs_energy)/TK; tpr.reaction_internal_energy = tpr.reaction_enthalpy - Pbar*tpr.reaction_volume; tpr.reaction_helmholtz_energy = tpr.reaction_internal_energy - TK*tpr.reaction_entropy; diff --git a/ThermoFun/Substances/Solids/SolidHPLandau.cpp b/ThermoFun/Substances/Solids/SolidHPLandau.cpp index b4779951..b583dd31 100644 --- a/ThermoFun/Substances/Solids/SolidHPLandau.cpp +++ b/ThermoFun/Substances/Solids/SolidHPLandau.cpp @@ -9,12 +9,13 @@ namespace ThermoFun { auto thermoPropertiesHPLandau(Reaktoro_::Temperature TK, Reaktoro_::Pressure Pbar, Substance subst, ThermoPropertiesSubstance tps) -> ThermoPropertiesSubstance { Reaktoro_::ThermoScalar Tcr, Qq, dQq; - vector transProp= subst.thermoParameters().phase_transition_prop[0]; + vector transProp = subst.thermoParameters().m_landau_phase_trans_props; // auto (P/1000) = Reaktoro::Pressure (p.val /1000); // in kbar auto TrK = subst.referenceT(); if (transProp.size() < 3) { + std::cout << transProp.size() << " " << std::endl; errorModelParameters("transition properties", "HP Landau", __LINE__, __FILE__); } @@ -24,7 +25,7 @@ auto thermoPropertiesHPLandau(Reaktoro_::Temperature TK, Reaktoro_::Pressure Pba auto Vmax = transProp[2]; auto k298 = subst.thermoParameters().isothermal_compresibility; // This is the bulk modulus k in kbar at 298 K! - auto a0 = subst.thermoParameters().isobaric_expansivity; // This is the a parameter (at one bar) in 1/K ! + auto a0 = subst.thermoParameters().isobaric_expansivity*1e-05; // This is the a parameter (at one bar) in 1/K! if ( Smax <= 0) Smax = 1.0e-20; diff --git a/ThermoFun/Substances/Solids/SolidMurnaghanHP98.cpp b/ThermoFun/Substances/Solids/SolidMurnaghanHP98.cpp index 8e84e9ca..ab8c8012 100644 --- a/ThermoFun/Substances/Solids/SolidMurnaghanHP98.cpp +++ b/ThermoFun/Substances/Solids/SolidMurnaghanHP98.cpp @@ -13,7 +13,7 @@ auto thermoPropertiesMinMurnaghanEOSHP98(Reaktoro_::Temperature TK, Reaktoro_::P auto P_Pst = Pbar - Pst; auto T_Tst = TK -Tst; auto k0 = subst.thermoParameters().isothermal_compresibility; // bulk modulus k in kbar at 298 K - auto a0 = subst.thermoParameters().isobaric_expansivity; // in 1/K + auto a0 = subst.thermoParameters().isobaric_expansivity*1e-05; // in 1/K auto dg = tps.gibbs_energy; auto ds = tps.entropy; diff --git a/ThermoFun/ThermoEngine.cpp b/ThermoFun/ThermoEngine.cpp index f75c1968..91a1f441 100644 --- a/ThermoFun/ThermoEngine.cpp +++ b/ThermoFun/ThermoEngine.cpp @@ -16,9 +16,10 @@ #include -namespace ThermoFun { +namespace ThermoFun +{ -bool iequals(const string& a, const string& b) +bool iequals(const string &a, const string &b) { size_t sz = a.size(); if (b.size() != sz) @@ -30,9 +31,9 @@ bool iequals(const string& a, const string& b) } const std::map implemented_conventions = { -{"Benson-Helgeson", "aparent-properties" }, -{"Berman-Brown", "aparent-properties" }, -{"steam-tables", "water-properties" }}; + {"Benson-Helgeson", "aparent-properties"}, + {"Berman-Brown", "aparent-properties"}, + {"steam-tables", "water-properties"}}; /// /// \brief The ThermoPreferences struct holds preferences such as the calculation methods for the current substance @@ -40,31 +41,31 @@ const std::map implemented_conventions = { struct ThermoPreferences { Substance workSubstance; - Reaction workReaction; + Reaction workReaction; MethodGenEoS_Thrift::type method_genEOS; - MethodCorrT_Thrift::type method_T; - MethodCorrP_Thrift::type method_P; + MethodCorrT_Thrift::type method_T; + MethodCorrP_Thrift::type method_P; int solventState = 0; // 0: liquid; 1: vapor - bool isHydrogen = false; - bool isH2Ovapor = false; - bool isH2OSolvent = false; - bool isReacDC = false; + bool isHydrogen = false; + bool isH2Ovapor = false; + bool isH2OSolvent = false; + bool isReacDC = false; bool isReacFromReactants = false; }; using ThermoPropertiesSubstanceFunction = - std::function; + std::function; using ElectroPropertiesSolventFunction = - std::function; + std::function; using PropertiesSolventFunction = - std::function; + std::function; using ThermoPropertiesReactionFunction = - std::function; + std::function; struct ThermoEngine::Impl { @@ -74,43 +75,44 @@ struct ThermoEngine::Impl std::string solventSymbol = "H2O@"; // default const std::map conventions = { - {"aparent-properties", "Benson-Helgeson" }, - {"water-properties", "" }}; + {"aparent-properties", "Benson-Helgeson"}, + {"water-properties", ""}}; ThermoPropertiesSubstanceFunction thermo_properties_substance_fn; - ElectroPropertiesSolventFunction electro_properties_solvent_fn; + ElectroPropertiesSolventFunction electro_properties_solvent_fn; - PropertiesSolventFunction properties_solvent_fn; + PropertiesSolventFunction properties_solvent_fn; - ThermoPropertiesReactionFunction thermo_properties_reaction_fn; + ThermoPropertiesReactionFunction thermo_properties_reaction_fn; Impl() - {} + { + } - Impl(const Database& database) - : database(database) + Impl(const Database &database) + : database(database) { - thermo_properties_substance_fn = [=](double T, double P_, double &P, std::string symbol) - { auto x = P_; + thermo_properties_substance_fn = [=](double T, double P_, double &P, std::string symbol) { + auto x = P_; return thermoPropertiesSubstance(T, P, symbol); }; thermo_properties_substance_fn = memoize(thermo_properties_substance_fn); - electro_properties_solvent_fn = [=](double T, double P_, double &P, std::string symbol) - { auto x = P_; + electro_properties_solvent_fn = [=](double T, double P_, double &P, std::string symbol) { + auto x = P_; return electroPropertiesSolvent(T, P, symbol); }; electro_properties_solvent_fn = memoize(electro_properties_solvent_fn); - properties_solvent_fn = [=](double T, double P_, double &P, std::string symbol) - { auto x = P_; + properties_solvent_fn = [=](double T, double P_, double &P, std::string symbol) { + auto x = P_; return propertiesSolvent(T, P, symbol); }; properties_solvent_fn = memoize(properties_solvent_fn); - thermo_properties_reaction_fn = [=](double T, double P_, double &P, std::string symbol) - { auto x = P_; + thermo_properties_reaction_fn = [=](double T, double P_, double &P, std::string symbol) { + auto x = P_; return thermoPropertiesReaction(T, P, symbol); }; thermo_properties_reaction_fn = memoize(thermo_properties_reaction_fn); @@ -119,15 +121,17 @@ struct ThermoEngine::Impl auto toSteamTables(ThermoPropertiesSubstance &tps) -> void { // Auxiliary data from Helgeson and Kirkham (1974), on page 1098 - const auto Str = 15.1320 * cal_to_J; // unit: J/(mol*K) + const auto Str = 15.1320 * cal_to_J; // unit: J/(mol*K) const auto Gtr = -56290.0 * cal_to_J; // unit: J/mol const auto Htr = -68767.0 * cal_to_J; // unit: J/mol const auto Utr = -67887.0 * cal_to_J; // unit: J/mol const auto Atr = -55415.0 * cal_to_J; // unit: J/mol - tps.gibbs_energy -=Gtr; tps.enthalpy -=Htr; - tps.entropy -=Str; tps.helmholtz_energy -=Atr; - tps.internal_energy -=Utr; + tps.gibbs_energy -= Gtr; + tps.enthalpy -= Htr; + tps.entropy -= Str; + tps.helmholtz_energy -= Atr; + tps.internal_energy -= Utr; } auto toBermanBrown(ThermoPropertiesSubstance &tps, const Substance &subst) -> void @@ -135,24 +139,17 @@ struct ThermoEngine::Impl const auto Tr = subst.referenceT(); FormulaProperites prop = ThermoFun::ChemicalFormula::calcThermo(subst.formula()); const auto entropyElements = prop.elemental_entropy; - tps.gibbs_energy -= (Tr*entropyElements); + tps.gibbs_energy -= (Tr * entropyElements); } - auto getThermoPreferencesReaction(std::string symbolReaction) -> ThermoPreferences + auto getThermoPreferencesReaction(const Reaction &reaction) -> ThermoPreferences { ThermoPreferences preferences; - // if the thermoPropertiesReacton function is called using a reaction equation - if (!database.containsReaction(symbolReaction) && (symbolReaction.find("=") != std::string::npos)) - { - Reaction reaction; - reaction.fromEquation(symbolReaction); - database.addReaction(reaction); - } - preferences.workReaction = database.getReaction(symbolReaction); - preferences.method_genEOS = preferences.workReaction.methodGenEOS(); - preferences.method_T = preferences.workReaction.method_T(); - preferences.method_P = preferences.workReaction.method_P(); + preferences.workReaction = reaction; + preferences.method_genEOS = preferences.workReaction.methodGenEOS(); + preferences.method_T = preferences.workReaction.method_T(); + preferences.method_P = preferences.workReaction.method_P(); // if no method is present try to calculate properties of reaction from reactants if ((!preferences.method_genEOS && !preferences.method_P && !preferences.method_T)) @@ -161,13 +158,13 @@ struct ThermoEngine::Impl return preferences; } - auto getThermoPreferencesSubstance(std::string substance) -> ThermoPreferences + auto getThermoPreferencesSubstance(const Substance &substance) -> ThermoPreferences { ThermoPreferences preferences; - preferences.workSubstance = database.getSubstance(substance); - preferences.method_genEOS = preferences.workSubstance.methodGenEOS(); - preferences.method_T = preferences.workSubstance.method_T(); - preferences.method_P = preferences.workSubstance.method_P(); + preferences.workSubstance = substance; + preferences.method_genEOS = preferences.workSubstance.methodGenEOS(); + preferences.method_T = preferences.workSubstance.method_T(); + preferences.method_P = preferences.workSubstance.method_P(); // check for H+ if (preferences.workSubstance.symbol() == "H+") @@ -189,13 +186,13 @@ struct ThermoEngine::Impl // set solvent state if (preferences.workSubstance.aggregateState() == AggregateState::type::GAS) - preferences.solventState = 1; // vapor + preferences.solventState = 1; // vapor else - preferences.solventState = 0; // liquid + preferences.solventState = 0; // liquid // check if the substance is reaction dependent if ((preferences.workSubstance.thermoCalculationType() == SubstanceThermoCalculationType::type::REACDC) || - (!preferences.method_genEOS && !preferences.method_P && !preferences.method_T)) + (!preferences.method_genEOS && !preferences.method_P && !preferences.method_T)) preferences.isReacDC = true; else preferences.isReacDC = false; @@ -206,7 +203,12 @@ struct ThermoEngine::Impl auto thermoPropertiesSubstance(double T, double &P, std::string substance) -> ThermoPropertiesSubstance { - ThermoPreferences pref = getThermoPreferencesSubstance(substance); + return thermoPropertiesSubstance(T, P, database.getSubstance(substance)); + } + + auto thermoPropertiesSubstance(double T, double &P, const Substance &substance) -> ThermoPropertiesSubstance + { + ThermoPreferences pref = getThermoPreferencesSubstance(substance); ThermoPropertiesSubstance tps; if (pref.isHydrogen) @@ -219,7 +221,7 @@ struct ThermoEngine::Impl if (!pref.isH2OSolvent && !pref.isH2Ovapor) { // metohd EOS - switch( pref.method_genEOS ) + switch (pref.method_genEOS) { case MethodGenEoS_Thrift::type::CTPM_CPT: { @@ -256,7 +258,7 @@ struct ThermoEngine::Impl } // method T - switch ( pref.method_T ) + switch (pref.method_T) { case MethodCorrT_Thrift::type::CTM_CHP: { @@ -274,18 +276,13 @@ struct ThermoEngine::Impl } // method P - switch ( pref.method_P ) + switch (pref.method_P) { case MethodCorrP_Thrift::type::CPM_AKI: { double Pr = database.getSubstance(solventSymbol).referenceP(); double Tr = database.getSubstance(solventSymbol).referenceT(); - tps = SoluteAkinfievDiamondEOS(pref.workSubstance).thermoProperties(T, P, tps, thermo_properties_substance_fn(T, P, P, solventSymbol), - WaterIdealGasWoolley(database.getSubstance(solventSymbol)).thermoProperties(T, P), - properties_solvent_fn(T, P, P, solventSymbol), - thermo_properties_substance_fn(Tr, Pr, Pr, solventSymbol), - WaterIdealGasWoolley(database.getSubstance(solventSymbol)).thermoProperties(Tr, Pr), - properties_solvent_fn(Tr, Pr, Pr, solventSymbol)); + tps = SoluteAkinfievDiamondEOS(pref.workSubstance).thermoProperties(T, P, tps, thermo_properties_substance_fn(T, P, P, solventSymbol), WaterIdealGasWoolley(database.getSubstance(solventSymbol)).thermoProperties(T, P), properties_solvent_fn(T, P, P, solventSymbol), thermo_properties_substance_fn(Tr, Pr, Pr, solventSymbol), WaterIdealGasWoolley(database.getSubstance(solventSymbol)).thermoProperties(Tr, Pr), properties_solvent_fn(Tr, Pr, Pr, solventSymbol)); break; } case MethodCorrP_Thrift::type::CPM_CEH: @@ -351,7 +348,7 @@ struct ThermoEngine::Impl if (pref.isH2OSolvent || pref.isH2Ovapor) { - switch(pref.method_T) + switch (pref.method_T) { case MethodCorrT_Thrift::type::CTM_WAT: { @@ -374,7 +371,7 @@ struct ThermoEngine::Impl break; } default: - switch( pref.method_genEOS ) + switch (pref.method_genEOS) { case MethodGenEoS_Thrift::type::CTPM_CPT: { @@ -387,20 +384,25 @@ struct ThermoEngine::Impl // // Exception // errorMethodNotFound("substance", pref.workSubstance.symbol(), __LINE__); } - } /// Convetion convert - if (pref.isH2OSolvent) { - if (iequals(conventions.at("water-properties"),"steam-tables")) { + if (pref.isH2OSolvent) + { + if (iequals(conventions.at("water-properties"), "steam-tables")) + { toSteamTables(tps); } - } else { - if (iequals(conventions.at("aparent-properties"),"Berman-Brown")) { + } + else + { + if (iequals(conventions.at("aparent-properties"), "Berman-Brown")) + { toBermanBrown(tps, pref.workSubstance); } } - } else // substance properties calculated using the properties of a reaction + } + else // substance properties calculated using the properties of a reaction { tps = reacDCthermoProperties(T, P, pref.workSubstance); } @@ -409,13 +411,18 @@ struct ThermoEngine::Impl auto electroPropertiesSolvent(double T, double &P, std::string solvent) -> ElectroPropertiesSolvent { - ThermoPreferences pref = getThermoPreferencesSubstance(solvent); - PropertiesSolvent ps = properties_solvent_fn(T, P, P, solvent); /*propertiesSolvent(T, P, solvent);*/ + return electroPropertiesSolvent(T, P, database.getSubstance(solvent)); + } + + auto electroPropertiesSolvent(double T, double &P, const Substance &solvent) -> ElectroPropertiesSolvent + { + ThermoPreferences pref = getThermoPreferencesSubstance(solvent); + PropertiesSolvent ps = propertiesSolvent(T, P, solvent); ElectroPropertiesSolvent eps; if (pref.isH2OSolvent) { - switch(pref.method_genEOS) + switch (pref.method_genEOS) { case MethodGenEoS_Thrift::type::CTPM_WJNR: { @@ -424,35 +431,40 @@ struct ThermoEngine::Impl } case MethodGenEoS_Thrift::type::CTPM_WJNG: { - eps = WaterJNgems(pref.workSubstance).electroPropertiesSolvent(T, P/*, ps*/ ); + eps = WaterJNgems(pref.workSubstance).electroPropertiesSolvent(T, P /*, ps*/); break; } case MethodGenEoS_Thrift::type::CTPM_WSV14: { - eps = WaterElectroSverjensky2014(pref.workSubstance).electroPropertiesSolvent(T, P/*, ps*/); + eps = WaterElectroSverjensky2014(pref.workSubstance).electroPropertiesSolvent(T, P /*, ps*/); break; } case MethodGenEoS_Thrift::type::CTPM_WF97: { - eps = WaterElectroFernandez1997(pref.workSubstance).electroPropertiesSolvent(T, P/*, ps*/); + eps = WaterElectroFernandez1997(pref.workSubstance).electroPropertiesSolvent(T, P /*, ps*/); break; } - // default: - // // Exception - // errorMethodNotFound("solvent", pref.workSubstance.symbol(), __LINE__); + // default: + // // Exception + // errorMethodNotFound("solvent", pref.workSubstance.symbol(), __LINE__); } } return eps; } auto propertiesSolvent(double T, double &P, std::string solvent) -> PropertiesSolvent + { + return propertiesSolvent(T, P, database.getSubstance(solvent)); + } + + auto propertiesSolvent(double T, double &P, const Substance &solvent) -> PropertiesSolvent { ThermoPreferences pref = getThermoPreferencesSubstance(solvent); PropertiesSolvent ps; if (pref.isH2OSolvent) { - switch(pref.method_T) + switch (pref.method_T) { case MethodCorrT_Thrift::type::CTM_WAT: { @@ -484,11 +496,11 @@ struct ThermoEngine::Impl auto reacDCthermoProperties(double T, double &P, Substance subst) -> ThermoPropertiesSubstance { - ThermoPropertiesSubstance tps, reacTps; - ThermoPropertiesReaction tpr; - string reactionSymbol = subst.reactionSymbol(); - Reaction reaction; - std::map reactants; + ThermoPropertiesSubstance tps, reacTps; + ThermoPropertiesReaction tpr; + string reactionSymbol = subst.reactionSymbol(); + Reaction reaction; + std::map reactants; if (!reactionSymbol.empty()) { @@ -496,42 +508,43 @@ struct ThermoEngine::Impl tpr = thermo_properties_reaction_fn(T, P, P, reactionSymbol); /*thermoPropertiesReaction(T, P, reactionSymbol);*/ - tps.enthalpy = tpr.reaction_enthalpy; - tps.entropy = tpr.reaction_entropy; - tps.gibbs_energy = tpr.reaction_gibbs_energy; + tps.enthalpy = tpr.reaction_enthalpy; + tps.entropy = tpr.reaction_entropy; + tps.gibbs_energy = tpr.reaction_gibbs_energy; tps.heat_capacity_cp = tpr.reaction_heat_capacity_cp; tps.heat_capacity_cv = tpr.reaction_heat_capacity_cv; tps.helmholtz_energy = tpr.reaction_helmholtz_energy; - tps.internal_energy = tpr.reaction_internal_energy; - tps.volume = tpr.reaction_volume; + tps.internal_energy = tpr.reaction_internal_energy; + tps.volume = tpr.reaction_volume; reactants = reaction.reactants(); - for(auto reactant : reactants) + for (auto reactant : reactants) { if (reactant.first != subst.symbol()) { - reacTps = thermo_properties_substance_fn(T,P,P, reactant.first); /* thermoPropertiesSubstance(T, P, reactant.first);*/ - tps.enthalpy -= reacTps.enthalpy*reactant.second; - tps.entropy -= reacTps.entropy*reactant.second; - tps.gibbs_energy -= reacTps.gibbs_energy*reactant.second; - tps.heat_capacity_cp -= reacTps.heat_capacity_cp*reactant.second; - tps.heat_capacity_cv -= reacTps.heat_capacity_cv*reactant.second; - tps.helmholtz_energy -= reacTps.helmholtz_energy*reactant.second; - tps.internal_energy -= reacTps.internal_energy*reactant.second; - tps.volume -= reacTps.volume*reactant.second; + reacTps = thermo_properties_substance_fn(T, P, P, reactant.first); /* thermoPropertiesSubstance(T, P, reactant.first);*/ + tps.enthalpy -= reacTps.enthalpy * reactant.second; + tps.entropy -= reacTps.entropy * reactant.second; + tps.gibbs_energy -= reacTps.gibbs_energy * reactant.second; + tps.heat_capacity_cp -= reacTps.heat_capacity_cp * reactant.second; + tps.heat_capacity_cv -= reacTps.heat_capacity_cv * reactant.second; + tps.helmholtz_energy -= reacTps.helmholtz_energy * reactant.second; + tps.internal_energy -= reacTps.internal_energy * reactant.second; + tps.volume -= reacTps.volume * reactant.second; } } - tps.enthalpy = tps.enthalpy/reactants[subst.symbol()]; - tps.entropy = tps.entropy/reactants[subst.symbol()]; - tps.gibbs_energy = tps.gibbs_energy/reactants[subst.symbol()]; - tps.heat_capacity_cp = tps.heat_capacity_cp/reactants[subst.symbol()]; - tps.heat_capacity_cv = tps.heat_capacity_cv/reactants[subst.symbol()]; - tps.helmholtz_energy = tps.helmholtz_energy/reactants[subst.symbol()]; - tps.internal_energy = tps.internal_energy/reactants[subst.symbol()]; - tps.volume = tps.volume/reactants[subst.symbol()]; - } else + tps.enthalpy = tps.enthalpy / reactants[subst.symbol()]; + tps.entropy = tps.entropy / reactants[subst.symbol()]; + tps.gibbs_energy = tps.gibbs_energy / reactants[subst.symbol()]; + tps.heat_capacity_cp = tps.heat_capacity_cp / reactants[subst.symbol()]; + tps.heat_capacity_cv = tps.heat_capacity_cv / reactants[subst.symbol()]; + tps.helmholtz_energy = tps.helmholtz_energy / reactants[subst.symbol()]; + tps.internal_energy = tps.internal_energy / reactants[subst.symbol()]; + tps.volume = tps.volume / reactants[subst.symbol()]; + } + else { errorReactionNotDefined(subst.symbol(), __LINE__, __FILE__); } @@ -539,13 +552,24 @@ struct ThermoEngine::Impl return tps; } - auto thermoPropertiesReaction (double T, double &P, std::string reaction) -> ThermoPropertiesReaction + auto thermoPropertiesReaction(double T, double &P, std::string symbol) -> ThermoPropertiesReaction + { + // if the thermoPropertiesReaction function is called using a reaction equation + if (!database.containsReaction(symbol) && (symbol.find("=") != std::string::npos)) + { + Reaction reaction; + reaction.fromEquation(symbol); + return thermoPropertiesReaction(T, P, reaction); + //database.addReaction(reaction); + } + return thermoPropertiesReaction(T, P, database.getReaction(symbol)); + } + + auto thermoPropertiesReaction(double T, double &P, const Reaction &reaction) -> ThermoPropertiesReaction { ThermoPropertiesReaction tpr; ThermoPreferences pref = getThermoPreferencesReaction(reaction); -// auto reac = database.getReaction(reaction); -// auto methodT = reac.method_T(); -// auto methodP = reac.method_P(); + if (!pref.isReacFromReactants) { switch (pref.method_genEOS) @@ -586,12 +610,11 @@ struct ThermoEngine::Impl // calc_r_interp( q, p, CE, CV ); break; } - // default: - // // Exception - // errorMethodNotFound("reaction", reac.name(), __LINE__); + // default: + // // Exception + // errorMethodNotFound("reaction", reac.name(), __LINE__); } - switch (pref.method_P) { @@ -605,57 +628,61 @@ struct ThermoEngine::Impl case MethodCorrP_Thrift::type::CPM_NUL: case MethodCorrP_Thrift::type::CPM_CON: { - auto Pref = pref.workReaction.referenceP()/1e5; - auto P_ = P/1e5; - auto VP = tpr.reaction_volume * (P_-Pref); + auto Pref = pref.workReaction.referenceP() / 1e5; + auto P_ = P / 1e5; + auto VP = tpr.reaction_volume * (P_ - Pref); tpr.reaction_gibbs_energy += VP; tpr.reaction_enthalpy += VP; - auto Vref = pref.workReaction.thermo_ref_prop().reaction_volume; - tpr.log_equilibrium_constant -= Vref *(P_-Pref)/(R_CONSTANT*T)/lg_to_ln; - tpr.reaction_entropy = (tpr.reaction_enthalpy - tpr.reaction_gibbs_energy)/T; - tpr.reaction_internal_energy = tpr.reaction_enthalpy - P_*tpr.reaction_volume; - tpr.reaction_helmholtz_energy = tpr.reaction_internal_energy - T*tpr.reaction_entropy; + auto Vref = pref.workReaction.thermoReferenceProperties().reaction_volume; + tpr.log_equilibrium_constant -= Vref * (P_ - Pref) / (R_CONSTANT * T) / lg_to_ln; + tpr.reaction_entropy = (tpr.reaction_enthalpy - tpr.reaction_gibbs_energy) / T; + tpr.reaction_internal_energy = tpr.reaction_enthalpy - P_ * tpr.reaction_volume; + tpr.reaction_helmholtz_energy = tpr.reaction_internal_energy - T * tpr.reaction_entropy; //dU/dT=C (v) break; } - // default: - // // Exception - // errorMethodNotFound("reaction", reac.name(), __LINE__); + // default: + // // Exception + // errorMethodNotFound("reaction", reac.name(), __LINE__); } - // make a new method P ??? - // line 1571 m_reac2.cpp - // if(( rc[q].pstate[0] == CP_GAS || rc[q].pstate[0] == CP_GASI ) && aW.twp->P > 0.0 ) - // { // molar volume from the ideal gas law - // aW.twp->dV = T / aW.twp->P * R_CONSTANT; - // } + // make a new method P ??? + // line 1571 m_reac2.cpp + // if(( rc[q].pstate[0] == CP_GAS || rc[q].pstate[0] == CP_GASI ) && aW.twp->P > 0.0 ) + // { // molar volume from the ideal gas law + // aW.twp->dV = T / aW.twp->P * R_CONSTANT; + // } // // Calculating pressure correction to logK - // aW.twp->lgK -= aW.twp->dV * (aW.twp->P - aW.twp->Pst) / aW.twp->RT / lg_to_ln; - } else + // aW.twp->lgK -= aW.twp->dV * (aW.twp->P - aW.twp->Pst) / aW.twp->RT / lg_to_ln; + } + else tpr = thermoPropertiesReactionFromReactants(T, P, reaction); - return tpr; + return tpr; } - auto thermoPropertiesReactionFromReactants (double T, double &P, std::string symbol) -> ThermoPropertiesReaction + auto thermoPropertiesReactionFromReactants(double T, double &P, std::string symbol) -> ThermoPropertiesReaction { - ThermoPropertiesReaction tpr; - tpr.reaction_heat_capacity_cp = 0.0; - tpr.reaction_gibbs_energy = 0.0; - tpr.reaction_enthalpy = 0.0; - tpr.reaction_entropy = 0.0; - tpr.reaction_volume = 0.0; - tpr.ln_equilibrium_constant = 0.0; - tpr.log_equilibrium_constant = 0.0; + return thermoPropertiesReactionFromReactants(T, P, database.getReaction(symbol)); + } + + auto thermoPropertiesReactionFromReactants(double T, double &P, const Reaction& reaction) -> ThermoPropertiesReaction + { + ThermoPropertiesReaction tpr; + tpr.reaction_heat_capacity_cp = 0.0; + tpr.reaction_gibbs_energy = 0.0; + tpr.reaction_enthalpy = 0.0; + tpr.reaction_entropy = 0.0; + tpr.reaction_volume = 0.0; + tpr.ln_equilibrium_constant = 0.0; + tpr.log_equilibrium_constant = 0.0; tpr.reaction_heat_capacity_cv = 0.0; - tpr.reaction_internal_energy = 0.0; + tpr.reaction_internal_energy = 0.0; tpr.reaction_helmholtz_energy = 0.0; - - Reaction reaction = database.getReaction(symbol); - string message = "Calculated from the reaction components: " + reaction.symbol() + "; "; + string message = "Calculated from the reaction components: " + reaction.symbol() + "; "; for (auto &reactant : reaction.reactants()) { @@ -664,9 +691,9 @@ struct ThermoEngine::Impl auto s = database.getSubstance(substance); // check if substance is correctly defined - if (!s.methodGenEOS() && !s.method_P() && !s.method_T() && s.reactionSymbol() == symbol) + if (!s.methodGenEOS() && !s.method_P() && !s.method_T() && s.reactionSymbol() == reaction.symbol()) { - errorMethodNotFound("reaction", symbol, __LINE__, __FILE__); + errorMethodNotFound("reaction", reaction.symbol(), __LINE__, __FILE__); } auto tps = thermo_properties_substance_fn(T, P,P, substance); /*thermoPropertiesSubstance(T, P, substance);*/ @@ -695,16 +722,19 @@ struct ThermoEngine::Impl }; ThermoEngine::ThermoEngine(const std::string filename) -: pimpl(new Impl(*(new const Database(filename)))) -{} + : pimpl(new Impl(*(new const Database(filename)))) +{ +} -ThermoEngine::ThermoEngine(const Database& database) -: pimpl(new Impl(database)) -{} +ThermoEngine::ThermoEngine(const Database &database) + : pimpl(new Impl(database)) +{ +} -ThermoEngine::ThermoEngine(const ThermoEngine& other) -: pimpl(new Impl(*other.pimpl)) -{} +ThermoEngine::ThermoEngine(const ThermoEngine &other) + : pimpl(new Impl(*other.pimpl)) +{ +} auto ThermoEngine::thermoPropertiesSubstance(double T, double &P, std::string substance) -> ThermoPropertiesSubstance { @@ -721,28 +751,53 @@ auto ThermoEngine::propertiesSolvent(double T, double &P, std::string solvent) - return pimpl->properties_solvent_fn(T, P, P, solvent); } +auto ThermoEngine::thermoPropertiesSubstance(double T, double &P, const Substance& substance) -> ThermoPropertiesSubstance +{ + return pimpl->thermoPropertiesSubstance(T, P, substance); +} + +auto ThermoEngine::electroPropertiesSolvent(double T, double &P, const Substance& solvent) -> ElectroPropertiesSolvent +{ + return pimpl->electroPropertiesSolvent(T, P, solvent); +} + +auto ThermoEngine::propertiesSolvent(double T, double &P, const Substance& solvent) -> PropertiesSolvent +{ + return pimpl->propertiesSolvent(T, P, solvent); +} + // Reaction -auto ThermoEngine::thermoPropertiesReaction (double T, double &P, std::string reaction) -> ThermoPropertiesReaction +auto ThermoEngine::thermoPropertiesReaction(double T, double &P, std::string reaction) -> ThermoPropertiesReaction { return pimpl->thermo_properties_reaction_fn(T, P, P, reaction); } -auto ThermoEngine::thermoPropertiesReactionFromReactants (double T, double &P, std::string symbol) -> ThermoPropertiesReaction +auto ThermoEngine::thermoPropertiesReactionFromReactants(double T, double &P, std::string symbol) -> ThermoPropertiesReaction { return pimpl->thermoPropertiesReactionFromReactants(T, P, symbol); } +auto ThermoEngine::thermoPropertiesReaction(double T, double &P, const Reaction& reaction) -> ThermoPropertiesReaction +{ + return pimpl->thermoPropertiesReaction(T, P, reaction); +} + +auto ThermoEngine::thermoPropertiesReactionFromReactants(double T, double &P, const Reaction& reaction) -> ThermoPropertiesReaction +{ + return pimpl->thermoPropertiesReactionFromReactants(T, P, reaction); +} + auto ThermoEngine::setSolventSymbol(const std::string solvent_symbol) -> void { pimpl->solventSymbol = solvent_symbol; } -auto ThermoEngine::solventSymbol( ) const -> std::string +auto ThermoEngine::solventSymbol() const -> std::string { return pimpl->solventSymbol; } -auto ThermoEngine::database() -> const Database +auto ThermoEngine::database() const -> const Database & { return pimpl->database; } diff --git a/ThermoFun/ThermoEngine.h b/ThermoFun/ThermoEngine.h index 4eca1ea2..38a23261 100644 --- a/ThermoFun/ThermoEngine.h +++ b/ThermoFun/ThermoEngine.h @@ -6,12 +6,14 @@ #include #include -namespace ThermoFun { +namespace ThermoFun +{ // Forward declarations class Database; class Solvent; class Substance; +class Reaction; class Element; struct ThermoPreferences; struct ThermoPropertiesSubstance; @@ -27,8 +29,8 @@ struct PropertiesSolvent; class ThermoEngine { friend class Interface; -public: +public: /** * @brief Construct a new Thermo Engine object * @@ -37,19 +39,19 @@ class ThermoEngine explicit ThermoEngine(const std::string filename); /// Construct a Thermo instance with given Database instance - ThermoEngine(const Database& database); + ThermoEngine(const Database &database); /// Construct a copy of an ThermoEngine instance - ThermoEngine(const ThermoEngine& other); + ThermoEngine(const ThermoEngine &other); /// Sets the symbol of the solvent which is used to calculate properties using the thermo instance auto setSolventSymbol(const std::string solvent_symbol) -> void; /// Returns the symbol of the solvent which is used to calculate properties using the thermo instance - auto solventSymbol( ) const -> std::string; + auto solventSymbol() const -> std::string; /// Returns the instance of the database present inside thermo - auto database() -> const Database; + auto database() const -> const Database &; /** * @brief appendData append records to the database from a file @@ -71,32 +73,62 @@ class ThermoEngine /// @param T The temperature value (in units of K) /// @param P The pressure value (in units of Pa) /// @param substance The symbol of the substance - auto thermoPropertiesSubstance (double T, double &P, std::string substance) -> ThermoPropertiesSubstance; + auto thermoPropertiesSubstance(double T, double &P, std::string substance) -> ThermoPropertiesSubstance; + + /// Calculate the thermodynamic properties of a substance. + /// @param T The temperature value (in units of K) + /// @param P The pressure value (in units of Pa) + /// @param substance substance object + auto thermoPropertiesSubstance(double T, double &P, const Substance& substance) -> ThermoPropertiesSubstance; /// Calculate the electro-chemical properties of a substance. /// @param T The temperature value (in units of K) /// @param P The pressure value (in units of Pa) - /// @param substance The symbol of the substance + /// @param solvent The symbol of the substance solvent auto electroPropertiesSolvent(double T, double &P, std::string solvent) -> ElectroPropertiesSolvent; + /// Calculate the electro-chemical properties of a substance. + /// @param T The temperature value (in units of K) + /// @param P The pressure value (in units of Pa) + /// @param solvent substance solvent object + auto electroPropertiesSolvent(double T, double &P, const Substance& solvent) -> ElectroPropertiesSolvent; + /// Calculate the physical properties of a substance. /// @param T The temperature value (in units of K) /// @param P The pressure value (in units of Pa) - /// @param solvent The symbol of the solvent + /// @param solvent The symbol of the substance solvent auto propertiesSolvent(double T, double &P, std::string solvent) -> PropertiesSolvent; + /// Calculate the physical properties of a substance. + /// @param T The temperature value (in units of K) + /// @param P The pressure value (in units of Pa) + /// @param solvent substance solvent object + auto propertiesSolvent(double T, double &P, const Substance& solvent) -> PropertiesSolvent; + // Reaction /// Calculate the thermodynamic properties of a reaction. /// @param T The temperature value (in units of K) /// @param P The pressure value (in units of Pa) /// @param reaction The symbol of the reaction - auto thermoPropertiesReaction (double T, double &P, std::string reaction) -> ThermoPropertiesReaction; + auto thermoPropertiesReaction(double T, double &P, std::string reaction) -> ThermoPropertiesReaction; + + /// Calculate the thermodynamic properties of a reaction. + /// @param T The temperature value (in units of K) + /// @param P The pressure value (in units of Pa) + /// @param reaction the reaction object + auto thermoPropertiesReaction(double T, double &P, const Reaction& reaction) -> ThermoPropertiesReaction; /// Calculate the thermodynamic properties of a reaction from the substances participating in the reaction. /// @param T The temperature value (in units of K) /// @param P The pressure value (in units of Pa) /// @param reaction The symbol of the reaction - auto thermoPropertiesReactionFromReactants (double T, double &P, std::string symbol) -> ThermoPropertiesReaction; + auto thermoPropertiesReactionFromReactants(double T, double &P, std::string reaction) -> ThermoPropertiesReaction; + + /// Calculate the thermodynamic properties of a reaction from the substances participating in the reaction. + /// @param T The temperature value (in units of K) + /// @param P The pressure value (in units of Pa) + /// @param reaction the reaction object + auto thermoPropertiesReactionFromReactants(double T, double &P, const Reaction& reaction) -> ThermoPropertiesReaction; /// Pareses a given substance formula present in the database /// @param formula diff --git a/ThermoFun/ThermoParameters.h b/ThermoFun/ThermoParameters.h index afc2b259..c14656f3 100644 --- a/ThermoFun/ThermoParameters.h +++ b/ThermoFun/ThermoParameters.h @@ -97,6 +97,9 @@ struct ThermoParametersSubstance /// Properties of phase transition (Berman): Tr; Tft; tilt; l1,l2 (reserved) vvd phase_transition_prop_Berman; + // HP Landau + vd m_landau_phase_trans_props; + // ParamsHKF HKF_param; /// Empirical coefficients of HKF EOS (a1, a2, a3, a4, c1, c2, w0) diff --git a/ci/travis/install.sh b/ci/travis/install.sh index 004cb0a1..c76ca37a 100644 --- a/ci/travis/install.sh +++ b/ci/travis/install.sh @@ -30,4 +30,4 @@ cmake -GNinja \ ninja install conda list cd .. -pytest -ra -vv --color=yes . +if [ $TRAVIS_OS_NAME = "linux" ]; then pytest -ra -vv --color=yes .; fi diff --git a/pytests/test-aq17-gem-lma-thermofun.json b/pytests/test-aq17-gem-lma-thermofun.json new file mode 100644 index 00000000..2b20d611 --- /dev/null +++ b/pytests/test-aq17-gem-lma-thermofun.json @@ -0,0 +1,38796 @@ +{ + "datasources": [ + "db.thermohub.org" + ], + "date": "08.02.2020 20:38:27", + "elements": [ + { + "atomic_mass": { + "name": "M0i", + "values": [ + 0 + ] + }, + "class_": { + "4": "CHARGE" + }, + "datasources": [ + "AQ17" + ], + "entropy": { + "name": "S0i", + "values": [ + -65.3399963378906 + ] + }, + "symbol": "Zz" + }, + { + "atomic_mass": { + "name": "M0i", + "values": [ + 1.00794994831085 + ] + }, + "class_": { + "0": "ELEMENT" + }, + "datasources": [ + "AQ17" + ], + "entropy": { + "name": "S0i", + "values": [ + 65.3399963378906 + ] + }, + "symbol": "H" + }, + { + "atomic_mass": { + "name": "M0i", + "values": [ + 12.0108003616333 + ] + }, + "class_": { + "0": "ELEMENT" + }, + "datasources": [ + "AQ17" + ], + "entropy": { + "name": "S0i", + "values": [ + 5.73999977111816 + ] + }, + "symbol": "C" + }, + { + "atomic_mass": { + "name": "M0i", + "values": [ + 15.999400138855 + ] + }, + "class_": { + "0": "ELEMENT" + }, + "datasources": [ + "AQ17" + ], + "entropy": { + "name": "S0i", + "values": [ + 102.569000244141 + ] + }, + "symbol": "O" + }, + { + "atomic_mass": { + "name": "M0i", + "values": [ + 22.9897994995117 + ] + }, + "class_": { + "0": "ELEMENT" + }, + "datasources": [ + "AQ17" + ], + "entropy": { + "name": "S0i", + "values": [ + 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and Powell (1991)" + ], + "formula": "O|0|2", + "formula_charge": 0, + "m_compressibility": { + "units": [ + "1e-05/K" + ], + "values": [ + 0 + ] + }, + "m_expansivity": { + "units": [ + "kbar" + ], + "values": [ + 0 + ] + }, + "name": "Oxygen (O2)", + "reaction": "O2", + "sm_enthalpy": { + "units": [ + "J/mol" + ], + "values": [ + 0 + ] + }, + "sm_entropy_abs": { + "units": [ + "J/(mol*K)" + ], + "values": [ + 205.19999694824 + ] + }, + "sm_gibbs_energy": { + "units": [ + "J/mol" + ], + "values": [ + 0 + ] + }, + "sm_heat_capacity_p": { + "errors": [ + 0 + ], + "units": [ + "J/(mol*K)" + ], + "values": [ + 29.345325469971 + ] + }, + "sm_volume": { + "errors": [ + 0 + ], + "units": [ + "J/bar" + ], + "values": [ + 2478.9699707031 + ] + }, + "symbol": "O2" + } + ], + "thermodataset": [ + "AQ17" + ] +} \ No newline at end of file diff --git a/pytests/test-database-thermofun.json b/pytests/test-database-thermofun.json index fd9dd870..f499a0f5 100644 --- a/pytests/test-database-thermofun.json +++ b/pytests/test-database-thermofun.json @@ -87,6 +87,156 @@ "[1992JOH/OEL]" ] }, + { + "name": "Quartz (q)", + "symbol": "Quartz", + "formula": "SiO2", + "formula_charge": 0, + "aggregate_state": { + "3": "AS_CRYSTAL" + }, + "class_": { + "0": "SC_COMPONENT" + }, + "Tst": 298.15, + "Pst": 100000, + "TPMethods": [ + { + "method": { + "0": "cp_ft_equation" + }, + "limitsTP": { + "range": true, + "lowerT": 273.15, + "upperT": 2273.15 + }, + "m_heat_capacity_ft_coeffs": { + "values": [ + 110.69999694824, + -0.0051890001632273, + 0, + -1128.3000488281, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0 + ], + "units": [ + "J/(mol*K)", + "J/(mol*K^2)", + "(J*K)/mol", + "J/(mol*K^0.5)", + "J/(mol*K^3)", + "J/(mol*K^4)", + "J/(mol*K^5)", + "(J*K^2)/mol", + "J/mol", + "J/(mol*K^1.5)", + "J/(mol*K)" + ], + "names": [ + "a0", + "a1", + "a2", + "a3", + "a4", + "a5", + "a6", + "a7", + "a8", + "a9", + "a10" + ] + } + }, + { + "method": { + "5": "landau_holland_powell98" + }, + "m_landau_phase_trans_props": { + "values": [ + 573.84997558594, + 4.9499998092651, + 0.11879999935627 + ] + } + }, + { + "method": { + "38": "mv_eos_murnaghan_hp98" + } + } + ], + "sm_heat_capacity_p": { + "values": [ + 44.89091873169 + ], + "errors": [ + 0 + ], + "units": [ + "J/(mol*K)" + ] + }, + "sm_gibbs_energy": { + "values": [ + -856433 + ], + "units": [ + "J/mol" + ] + }, + "sm_enthalpy": { + "values": [ + -910830 + ], + "units": [ + "J/mol" + ] + }, + "sm_entropy_abs": { + "values": [ + 41.5 + ], + "units": [ + "J/(mol*K)" + ] + }, + "sm_volume": { + "values": [ + 2.2688000202179 + ], + "errors": [ + 0 + ], + "units": [ + "J/bar" + ] + }, + "m_compressibility": { + "values": [ + 750 + ], + "units": [ + "1e-05/K" + ] + }, + "m_expansivity": { + "values": [ + 0.0000064999999267457 + ], + "units": [ + "kbar" + ] + }, + "datasources": [ + "[1998HOL/POW]" + ] + }, { "name": "Al(OH)2+", "symbol": "Al(OH)2+", @@ -112,16 +262,17 @@ 6.4145998954773, -27091, 16.743900299072, - -10465, + -43785.56, 53240, 0 ], "units": [ "cal/(mol*bar)", "cal/mol", + "(cal*K)/(mol*bar)", "(cal*K)/mol", "cal/(mol*K)", - "(cal*K)/mol", + "(J*K)/mol", "cal/mol" ], "names": [ @@ -456,13 +607,16 @@ }, "drsm_heat_capacity_p": { "values": [ - -2598.484998 + -2.598484998 ], "status": [ {} ], "errors": [ 0 + ], + "units": [ + "kJ/(mol*K)" ] }, "drsm_gibbs_energy": { diff --git a/pytests/test-thermoengine-thermofun.json b/pytests/test-thermoengine-thermofun.json index 0201d2e9..d5809357 100644 --- a/pytests/test-thermoengine-thermofun.json +++ b/pytests/test-thermoengine-thermofun.json @@ -509,6 +509,290 @@ "[1998SHO/EA]" ] }, + { + "name": "CO2 (aq)", + "symbol": "CO2@", + "formula": "CO2@", + "formula_charge": 0, + "aggregate_state": { + "4": "AS_AQUEOUS" + }, + "class_": { + "2": "SC_AQSOLUTE" + }, + "Tst": 298.15, + "Pst": 100000, + "TPMethods": [ + { + "method": { + "0": "cp_ft_equation" + }, + "limitsTP": { + "range": true, + "lowerT": 273.15, + "upperT": 1773.15 + }, + "m_heat_capacity_ft_coeffs": { + "values": [ + 65.68229675293, + 0.011197299696505, + 280403, + -599.12902832031, + -0.0000039157198443718, + 0, + 0, + 0, + 0, + 0, + 0, + 0 + ], + "units": [ + "J/(mol*K)", + "J/(mol*K^2)", + "(J*K)/mol", + "J/(mol*K^0.5)", + "J/(mol*K^3)", + "J/(mol*K^4)", + "J/(mol*K^5)", + "(J*K^2)/mol", + "J/mol", + "J/(mol*K^1.5)", + "J/(mol*K)" + ], + "names": [ + "a0", + "a1", + "a2", + "a3", + "a4", + "a5", + "a6", + "a7", + "a8", + "a9", + "a10" + ] + } + }, + { + "method": { + "4": "solute_aknifiev_diamond03" + }, + "eos_akinfiev_diamond_coeffs": { + "values": [ + -0.08500000089407, + -8.8320999145508, + 11.268400192261, + 0, + 0, + 0, + 0 + ] + } + } + ], + "sm_heat_capacity_p": { + "values": [ + 209.74876403809 + ], + "errors": [ + 0 + ], + "units": [ + "J/(mol*K)" + ] + }, + "sm_gibbs_energy": { + "values": [ + -386030 + ], + "units": [ + "J/mol" + ] + }, + "sm_enthalpy": { + "values": [ + -413337 + ], + "units": [ + "J/mol" + ] + }, + "sm_entropy_abs": { + "values": [ + 119.29000091553 + ], + "units": [ + "J/(mol*K)" + ] + }, + "sm_volume": { + "values": [ + 3.2702753543854 + ], + "errors": [ + 0 + ], + "units": [ + "J/bar" + ] + }, + "datasources": [ + "[2017MIR/WAG]", + "[2003AKI/DIA]" + ] + }, + { + "name": "Quartz (q)", + "symbol": "Quartz", + "formula": "SiO2", + "formula_charge": 0, + "aggregate_state": { + "3": "AS_CRYSTAL" + }, + "class_": { + "0": "SC_COMPONENT" + }, + "Tst": 298.15, + "Pst": 100000, + "TPMethods": [ + { + "method": { + "0": "cp_ft_equation" + }, + "limitsTP": { + "range": true, + "lowerT": 273.15, + "upperT": 2273.15 + }, + "m_heat_capacity_ft_coeffs": { + "values": [ + 110.69999694824, + -0.0051890001632273, + 0, + -1128.3000488281, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0 + ], + "units": [ + "J/(mol*K)", + "J/(mol*K^2)", + "(J*K)/mol", + "J/(mol*K^0.5)", + "J/(mol*K^3)", + "J/(mol*K^4)", + "J/(mol*K^5)", + "(J*K^2)/mol", + "J/mol", + "J/(mol*K^1.5)", + "J/(mol*K)" + ], + "names": [ + "a0", + "a1", + "a2", + "a3", + "a4", + "a5", + "a6", + "a7", + "a8", + "a9", + "a10" + ] + } + }, + { + "method": { + "5": "landau_holland_powell98" + }, + "m_landau_phase_trans_props": { + "values": [ + 573.84997558594, + 4.9499998092651, + 0.11879999935627 + ] + } + }, + { + "method": { + "38": "mv_eos_murnaghan_hp98" + } + } + ], + "sm_heat_capacity_p": { + "values": [ + 44.89091873169 + ], + "errors": [ + 0 + ], + "units": [ + "J/(mol*K)" + ] + }, + "sm_gibbs_energy": { + "values": [ + -856433 + ], + "units": [ + "J/mol" + ] + }, + "sm_enthalpy": { + "values": [ + -910830 + ], + "units": [ + "J/mol" + ] + }, + "sm_entropy_abs": { + "values": [ + 41.5 + ], + "units": [ + "J/(mol*K)" + ] + }, + "sm_volume": { + "values": [ + 2.2688000202179 + ], + "errors": [ + 0 + ], + "units": [ + "J/bar" + ] + }, + "m_compressibility": { + "values": [ + 750 + ], + "units": [ + "1e-05/K" + ] + }, + "m_expansivity": { + "values": [ + 0.0000064999999267457 + ], + "units": [ + "kbar" + ] + }, + "datasources": [ + "[1998HOL/POW]" + ] + }, { "name": "Ca+2 ion", "symbol": "Ca+2", @@ -853,21 +1137,422 @@ "datasources": [ "[1998SHO/EA]" ] - } - ], - "reactions": [ + }, { - "symbol": "Meionite-Ca", - "equation": "Ca4Al6Si6O24(CO3) + 25H+ = HCO3- + 6H4SiO4@ + 4Ca+2 + 6Al+3", - "reactants": [ - { - "symbol": "Meionite-Ca", - "coefficient": -1 - }, - { - "symbol": "Ca+2", - "coefficient": 4 - }, + "Pst": 100000, + "TPMethods": [ + { + "eos_hkf_coeffs": { + "names": [ + "a1", + "a2", + "a3", + "a4", + "c1", + "c2", + "wref" + ], + "units": [ + "cal/(mol*bar)", + "cal/mol", + "(cal*K)/mol", + "cal/(mol*K)", + "(cal*K)/mol", + "cal/mol" + ], + "values": [ + 0.18999999761581, + 170, + 20, + -27000, + 29.10000038147, + -512000, + 12910, + 0 + ] + }, + "method": { + "3": "solute_hkf88_reaktoro" + } + } + ], + "Tst": 298.15, + "aggregate_state": { + "4": "AS_AQUEOUS" + }, + "class_": { + "2": "SC_AQSOLUTE" + }, + "datasources": [ + "" + ], + "formula": "SiO2@", + "formula_charge": 0, + "name": "SiO2 (aq)", + "sm_enthalpy": { + "units": [ + "J/mol" + ], + "values": [ + -878357 + ] + }, + "sm_entropy_abs": { + "units": [ + "J/(mol*K)" + ], + "values": [ + 75.311996459961 + ] + }, + "sm_gibbs_energy": { + "units": [ + "J/mol" + ], + "values": [ + -834041 + ] + }, + "sm_heat_capacity_p": { + "errors": [ + 0 + ], + "units": [ + "J/(mol*K)" + ], + "values": [ + -318.48419189453 + ] + }, + "sm_volume": { + "errors": [ + 0 + ], + "units": [ + "J/bar" + ], + "values": [ + 1.6063253879547 + ] + }, + "symbol": "SiO2@" + }, + { + "Pst": 100000, + "TPMethods": [ + { + "eos_hkf_coeffs": { + "names": [ + "a1", + "a2", + "a3", + "a4", + "c1", + "c2", + "wref" + ], + "units": [ + "cal/(mol*bar)", + "cal/mol", + "(cal*K)/mol", + "cal/(mol*K)", + "(cal*K)/mol", + "cal/mol" + ], + "values": [ + 0.29936000704765, + 497.86999511719, + 23.59049987793, + -29848, + 12.994000434876, + -47579, + 127920, + 0 + ] + }, + "method": { + "3": "solute_hkf88_reaktoro" + } + } + ], + "Tst": 298.15, + "aggregate_state": { + "4": "AS_AQUEOUS" + }, + "class_": { + "2": "SC_AQSOLUTE" + }, + "datasources": [ + "" + ], + "formula": "HCO3-", + "formula_charge": -1, + "name": "HCO3- bicarbonate ion", + "sm_enthalpy": { + "units": [ + "J/mol" + ], + "values": [ + -690463 + ] + }, + "sm_entropy_abs": { + "units": [ + "J/(mol*K)" + ], + "values": [ + 96.625 + ] + }, + "sm_gibbs_energy": { + "units": [ + "J/mol" + ], + "values": [ + -586855 + ] + }, + "sm_heat_capacity_p": { + "errors": [ + 0 + ], + "units": [ + "J/(mol*K)" + ], + "values": [ + -34.845699310303 + ] + }, + "sm_volume": { + "errors": [ + 0 + ], + "units": [ + "J/bar" + ], + "values": [ + 2.420910358429 + ] + }, + "symbol": "HCO3-" + }, + { + "Pst": 100000, + "TPMethods": [ + { + "limitsTP": { + "lowerT": 273.15, + "range": true, + "upperT": 2273.15 + }, + "m_heat_capacity_ft_coeffs": { + "names": [ + "a0", + "a1", + "a2", + "a3", + "a4", + "a5", + "a6", + "a7", + "a8", + "a9", + "a10" + ], + "units": [ + "J/(mol*K)", + "J/(mol*K^2)", + "(J*K)/mol", + "J/(mol*K^0.5)", + "J/(mol*K^3)", + "J/(mol*K^4)", + "J/(mol*K^5)", + "(J*K^2)/mol", + "J/mol", + "J/(mol*K^1.5)", + "J/(mol*K)" + ], + "values": [ + 1359, + 0.036442000418901, + -8594700, + -9598.2001953125, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0 + ] + }, + "method": { + "0": "cp_ft_equation" + } + }, + { + "method": { + "38": "mv_eos_murnaghan_hp98" + } + } + ], + "Tst": 298.15, + "aggregate_state": { + "3": "AS_CRYSTAL" + }, + "class_": { + "0": "SC_COMPONENT" + }, + "datasources": [ + "Holland and Powell (2002)" + ], + "formula": "Ca4Al6Si6O24(CO3)", + "formula_charge": 0, + "m_compressibility": { + "units": [ + "1e-05/K" + ], + "values": [ + 870 + ] + }, + "m_expansivity": { + "units": [ + "kbar" + ], + "values": [ + 3.1600000511389e-05 + ] + }, + "name": "Meionite-Ca (me)", + "reaction": "Meionite-Ca", + "sm_enthalpy": { + "units": [ + "J/mol" + ], + "values": [ + -13843570 + ] + }, + "sm_entropy_abs": { + "units": [ + "J/(mol*K)" + ], + "values": [ + 752 + ] + }, + "sm_gibbs_energy": { + "units": [ + "J/mol" + ], + "values": [ + -13106507 + ] + }, + "sm_heat_capacity_p": { + "errors": [ + 0 + ], + "units": [ + "J/(mol*K)" + ], + "values": [ + 717.31079101562 + ] + }, + "sm_volume": { + "errors": [ + 0 + ], + "units": [ + "J/bar" + ], + "values": [ + 33.985000610352 + ] + }, + "symbol": "Meionite-Ca" + }, + { + "Pst": 100000, + "Tst": 298.15, + "aggregate_state": { + "4": "AS_AQUEOUS" + }, + "class_": { + "2": "SC_AQSOLUTE" + }, + "datasources": [ + "" + ], + "formula": "H4SiO4@", + "formula_charge": 0, + "name": "H4SiO4 (aq)", + "reaction": "H4SiO4@", + "sm_enthalpy": { + "units": [ + "J/mol" + ], + "values": [ + -1450119 + ] + }, + "sm_entropy_abs": { + "units": [ + "J/(mol*K)" + ], + "values": [ + 215.158 + ] + }, + "sm_gibbs_energy": { + "units": [ + "J/mol" + ], + "values": [ + -1308407 + ] + }, + "sm_heat_capacity_p": { + "errors": [ + 0 + ], + "units": [ + "J/(mol*K)" + ], + "values": [ + -167.762 + ] + }, + "sm_volume": { + "errors": [ + 0 + ], + "units": [ + "J/bar" + ], + "values": [ + 5.22 + ] + }, + "symbol": "H4SiO4@" + } + ], + "reactions": [ + { + "symbol": "Meionite-Ca", + "equation": "Ca4Al6Si6O24(CO3) + 25H+ = HCO3- + 6H4SiO4@ + 4Ca+2 + 6Al+3", + "reactants": [ + { + "symbol": "Meionite-Ca", + "coefficient": -1 + }, + { + "symbol": "Ca+2", + "coefficient": 4 + }, { "symbol": "H+", "coefficient": -25 @@ -892,24 +1577,6 @@ "upperP": 1000000, "upperT": 298.15 }, - "TPMethods": [ - { - "method": { - "7": "logk_3_term_extrap" - }, - "logk_ft_coeffs": { - "values": [ - 0, - 0, - 49480.5741302139, - -135.727504800267, - 0, - 0, - 0 - ] - } - } - ], "logKr": { "values": [ 80.875017 @@ -978,6 +1645,116 @@ }, "references": [] }, + { + "TPMethods": [ + { + "logk_ft_coeffs": { + "values": [ + 0, + 0, + 0, + 0, + 0, + 0, + 0 + ] + }, + "method": { + "4": "logk_1_term_extrap0" + } + } + ], + "datasources": null, + "drsm_enthalpy": { + "errors": [ + 400 + ], + "status": [ + {} + ], + "values": [ + 0 + ] + }, + "drsm_entropy": { + "errors": [ + 0.2 + ], + "status": [ + {} + ], + "values": [ + 0 + ] + }, + "drsm_gibbs_energy": { + "errors": [ + 200 + ], + "status": [ + {} + ], + "values": [ + 0 + ] + }, + "drsm_heat_capacity_p": { + "errors": [ + 0 + ], + "status": [ + {} + ], + "values": [ + 0 + ] + }, + "drsm_volume": { + "errors": [ + 0 + ], + "status": [ + {} + ], + "values": [ + 0 + ] + }, + "equation": "H4SiO4@ = SiO2@ + 2H2O@", + "limitsTP": { + "lowerP": 0.1, + "lowerT": 273.15, + "range": false, + "upperP": 5000000000, + "upperT": 1073.15 + }, + "logKr": { + "errors": [ + 0.035038 + ], + "status": [ + {} + ], + "values": [ + 0 + ] + }, + "reactants": [ + { + "coefficient": -1, + "symbol": "H4SiO4@" + }, + { + "coefficient": 1, + "symbol": "SiO2@" + }, + { + "coefficient": 2, + "symbol": "H2O@" + } + ], + "symbol": "H4SiO4@" + }, { "symbol": "Gedrite-Mg", "equation": "Mg5Al4Si6O22(OH)2 + 22H+ = 5Mg+2 + 6H4SiO4@ + 4Al+3", diff --git a/pytests/test_database.py b/pytests/test_database.py index d422b4b8..28cadfd7 100644 --- a/pytests/test_database.py +++ b/pytests/test_database.py @@ -25,9 +25,20 @@ def test_parsing_substance(self): assert self.database.getSubstance("Al(OH)2+").thermoReferenceProperties().entropy.val == -27.530000686646 # J/(mol*K) assert self.database.getSubstance("Al(OH)2+").thermoReferenceProperties().heat_capacity_cp.val == 40.865230560303 # J/(mol*K) assert self.database.getSubstance("Al(OH)2+").thermoReferenceProperties().volume.val == 0.38507527112961 # J/bar + assert self.database.getSubstance("Al(OH)2+").thermoParameters().HKF_parameters[0] == 0.24940000474453003 # "cal/(mol*bar)" + assert self.database.getSubstance("Al(OH)2+").thermoParameters().HKF_parameters[1] == -169.08999633789 + assert self.database.getSubstance("Al(OH)2+").thermoParameters().HKF_parameters[2] == 6.4145998954773 + assert self.database.getSubstance("Al(OH)2+").thermoParameters().HKF_parameters[3] == -27091 + assert self.database.getSubstance("Al(OH)2+").thermoParameters().HKF_parameters[4] == 16.743900299072 + assert self.database.getSubstance("Al(OH)2+").thermoParameters().HKF_parameters[5] == -10465 + assert self.database.getSubstance("Al(OH)2+").thermoParameters().HKF_parameters[6] == 53240 + assert self.database.getSubstance("Quartz").thermoParameters().m_landau_phase_trans_props[2] == 0.11879999935626999 + def test_parsing_reaction(self): + assert self.database.getReaction("Meionite-Ca").thermoReferenceProperties().log_equilibrium_constant.val == 80.875017 # "1" + assert self.database.getReaction("Meionite-Ca").thermoReferenceProperties().reaction_heat_capacity_cp.val == -2598.4849980000004 # J/(mol*K) def test_append_data(self): self.database.appendData('pytests/Substances/Solute/test-hkf-thermofun.json') assert self.database.getSubstance("SiO2@").name() == "SiO2 (aq)" assert self.database.getSubstance("SiO2@").thermoReferenceProperties().gibbs_energy.val == -833411 - assert self.database.numberOfSubstances() == 6 \ No newline at end of file + assert self.database.numberOfSubstances() == 7 \ No newline at end of file diff --git a/pytests/test_thermoengine.py b/pytests/test_thermoengine.py index 98d97889..b3a235ca 100644 --- a/pytests/test_thermoengine.py +++ b/pytests/test_thermoengine.py @@ -7,9 +7,32 @@ class TestThermoEngine(unittest.TestCase): def setUp(self): self.engine = thermofun.ThermoEngine('pytests/test-thermoengine-thermofun.json') + self.engine2 = thermofun.ThermoEngine('pytests/test-aq17-gem-lma-thermofun.json') + + def test_properties_substance(self): + assert self.engine.thermoPropertiesSubstance(873.15, 5000e5, "Quartz").gibbs_energy.val == pytest.approx(-889055.513, 1e-5, 1e-14) + assert self.engine.thermoPropertiesSubstance(873.15, 5000e5, "Quartz").volume.val == pytest.approx(2.3183336, 1e-5, 1e-14) + assert self.engine.thermoPropertiesSubstance(873.15, 5000e5, "Quartz").entropy.val == pytest.approx(105.5428, 1e-5, 1e-14) + assert self.engine.thermoPropertiesSubstance(873.15, 5000e5, "Quartz").heat_capacity_cp.val == pytest.approx(75.14837, 1e-5, 1e-14) + assert self.engine.thermoPropertiesSubstance(873.15, 5000e5, "CO2@").gibbs_energy.val == pytest.approx(-485154.6363, 1e-5, 1e-14) + assert self.engine.thermoPropertiesSubstance(873.15, 5000e5, "CO2@").volume.val == pytest.approx(3.43432, 1e-5, 1e-14) + assert self.engine.thermoPropertiesSubstance(873.15, 5000e5, "CO2@").entropy.val == pytest.approx(239.07241, 1e-5, 1e-14) + assert self.engine.thermoPropertiesSubstance(873.15, 5000e5, "CO2@").heat_capacity_cp.val == pytest.approx(71.9893685, 1e-5, 1e-14) def test_properties_reaction_from_equation(self): assert self.engine.thermoPropertiesReaction(298.15, 1e5, "Cal = Ca+2 + CO3-2").log_equilibrium_constant.val == pytest.approx(-8.48014, 1e-5, 1e-14) assert self.engine.thermoPropertiesReaction(298.15, 1e5, "Al+3 + 4 H2O@ + 0Ca+2= 1Al(OH)4- + 4 \n H+").log_equilibrium_constant.val == pytest.approx(-22.3085, 1e-5, 1e-14) + assert self.engine.thermoPropertiesReaction(423.15, 0, "Cal = Ca+2 + CO3-2").log_equilibrium_constant.val == pytest.approx(-10.10169, 1e-5, 1e-14) + assert self.engine.thermoPropertiesReaction(873.15, 3000e5, "Cal = Ca+2 + CO3-2").reaction_heat_capacity_cp.val == pytest.approx(-718.75763, 1e-5, 1e-14) assert self.engine.thermoPropertiesReaction(348.15, 1e5, "Cal = Ca+2 + CO3-2").reaction_gibbs_energy.ddt == pytest.approx( -self.engine.thermoPropertiesReaction(348.15, 1e5, "Cal = Ca+2 + CO3-2").reaction_entropy.val, 1e-5, 1e-14) + + def test_properties_reaction(self): + assert self.engine2.thermoPropertiesReaction(298.15, 1e5, "Meionite-Ca").log_equilibrium_constant.val == pytest.approx(80.873916, 1e-5, 1e-14) + assert self.engine2.thermoPropertiesReaction(423.15, 0, "Meionite-Ca").log_equilibrium_constant.val == pytest.approx(28.243799, 1e-5, 1e-14) + assert self.engine2.thermoPropertiesReaction(298.15, 0, "Meionite-Ca + 25H+ = HCO3- + 6H4SiO4@ + 4Ca+2 + 6Al+3").log_equilibrium_constant.val == pytest.approx(80.873916, 1e-5, 1e-14) + assert self.engine2.thermoPropertiesReaction(873.15, 5000e5, "Meionite-Ca + 25H+ = HCO3- + 6H4SiO4@ + 4Ca+2 + 6Al+3").reaction_heat_capacity_cp.val == pytest.approx(-1072.969936, 1e-5, 1e-14) + assert self.engine2.thermoPropertiesReaction(873.15, 5000e5, "Meionite-Ca + 25H+ = HCO3- + 6H4SiO4@ + 4Ca+2 + 6Al+3").reaction_entropy.val == pytest.approx(-1704.130129, 1e-5, 1e-14) + assert self.engine2.thermoPropertiesReaction(873.15, 5000e5, "Meionite-Ca + 25H+ = HCO3- + 6H4SiO4@ + 4Ca+2 + 6Al+3").reaction_volume.val == pytest.approx(-60.00281, 1e-5, 1e-14) + assert self.engine2.thermoPropertiesReaction(873.15, 5000e5, "Meionite-Ca + 25H+ = HCO3- + 6H4SiO4@ + 4Ca+2 + 6Al+3").reaction_enthalpy.val == pytest.approx(-1139970.03233, 1e-5, 1e-14) + diff --git a/python/pyThermoFun/PyThermoFun.cpp b/python/pyThermoFun/PyThermoFun.cpp index aa78cbbc..e123c942 100644 --- a/python/pyThermoFun/PyThermoFun.cpp +++ b/python/pyThermoFun/PyThermoFun.cpp @@ -29,6 +29,9 @@ PYBIND11_MODULE(PyThermoFun, m) exportThermoPropertiesReaction(m); exportElectroPropertiesSolvent(m); exportPropertiesSolvent(m); + // Parameters + exportThermoParametersReaction(m); + exportThermoParametersSubstance(m); // Core module exportThermoEngine(m); exportThermoBatch(m); diff --git a/python/pyThermoFun/PyThermoFun.hpp b/python/pyThermoFun/PyThermoFun.hpp index 5d619fb6..940b542c 100644 --- a/python/pyThermoFun/PyThermoFun.hpp +++ b/python/pyThermoFun/PyThermoFun.hpp @@ -29,6 +29,9 @@ namespace ThermoFun { void exportThermoPropertiesReaction(py::module& m); void exportElectroPropertiesSolvent(py::module& m); void exportPropertiesSolvent(py::module& m); + // Parameters + void exportThermoParametersReaction(py::module& m); + void exportThermoParametersSubstance(py::module& m); // Core module void exportThermoEngine(py::module& m); void exportThermoBatch(py::module& m); diff --git a/python/pyThermoFun/pyReaction.cpp b/python/pyThermoFun/pyReaction.cpp index 224e79f9..1a636e04 100644 --- a/python/pyThermoFun/pyReaction.cpp +++ b/python/pyThermoFun/pyReaction.cpp @@ -38,7 +38,7 @@ void exportReaction(py::module& m) .def("setEquation", &Reaction::setEquation,"Set the equation of the Reaction") .def("setReactants", &Reaction::setReactants,"Set map of reactant symbols") .def("setReferenceT", &Reaction::setReferenceT,"Set reference temperature fo the standard properties of reaction (K)") - .def("setReferenceP", &Reaction::setReferenceP,"Set references pressure for the standard proeprties of reaction (Pa)") + .def("setReferenceP", &Reaction::setReferenceP,"Set references pressure for the standard properties of reaction (Pa)") .def("setLowerT", &Reaction::setLowerT,"Set upper temperature limit of the correction method (K)") .def("setLowerP", &Reaction::setLowerP,"Set upper presure limit of the correction method (Pa)") .def("setUpperT", &Reaction::setUpperT,"Set lower temperature limit of the correction method (K)") @@ -46,16 +46,16 @@ void exportReaction(py::module& m) .def("setMethodGenEoS", &Reaction::setMethodGenEoS,"Set the code for general EOS calculation method") .def("setMethod_T", &Reaction::setMethod_T,"Set the code for the temperature correction method") .def("setMethod_P", &Reaction::setMethod_P,"Set the code for the pressure correction method") - .def("setThermoReferenceProperties", &Reaction::setThermoReferenceProperties,"Set the references proeprties of reaction") - .def("setThermoParameters", &Reaction::setThermoParameters,"Set the parameters used for calculating the proeprties of reaction at T and P") + .def("setThermoReferenceProperties", &Reaction::setThermoReferenceProperties,"Set the references properties of reaction") + .def("setThermoParameters", &Reaction::setThermoParameters,"Set the parameters used for calculating the properties of reaction at T and P") .def("setJsonString", &Reaction::setJsonString, "Set the record as a json string") .def("fromEquation", &Reaction::fromEquation, "Initialize the reaction using a reaction equation") .def("name", &Reaction::name,"Returns the name of the chemical Reaction") .def("symbol", &Reaction::symbol,"Returns the symbol of the Reaction") .def("equation", &Reaction::equation,"Returns the equation of the Reaction") .def("reactants", &Reaction::reactants,"Returns the map of reactants symbols and their coefficients") - .def("thermo_ref_prop", &Reaction::thermo_ref_prop,"Returns the references proeprties of the reaction") - .def("thermo_parameters", &Reaction::thermo_parameters,"Returns an instance of the defined parameters of the reaction") + .def("thermoReferenceProperties", &Reaction::thermoReferenceProperties,"Returns the references properties of the reaction") + .def("thermoParameters", &Reaction::thermoParameters,"Returns an instance of the defined parameters of the reaction") .def("referenceT", &Reaction::referenceT,"Returns the references temperature (K)") .def("referenceP", &Reaction::referenceP,"Returns the references pressure (Pa)") .def("lowerT", &Reaction::lowerT,"Return upper temperature limit of the correction method (K)") diff --git a/python/pyThermoFun/pyThermoEngine.cpp b/python/pyThermoFun/pyThermoEngine.cpp index 65e60015..77aaea25 100644 --- a/python/pyThermoFun/pyThermoEngine.cpp +++ b/python/pyThermoFun/pyThermoEngine.cpp @@ -24,6 +24,8 @@ namespace py = pybind11; // ThermoFun includes #include #include +#include +#include #include namespace ThermoFun { @@ -33,6 +35,18 @@ void exportThermoEngine(py::module& m) auto appendData1 = static_cast(&ThermoEngine::appendData); auto appendData2 = static_cast, std::string)>(&ThermoEngine::appendData); + auto thermoPropertiesSubstance1 = static_cast(&ThermoEngine::thermoPropertiesSubstance); + auto electroPropertiesSolvent1 = static_cast(&ThermoEngine::electroPropertiesSolvent); + auto propertiesSolvent1 = static_cast(&ThermoEngine::propertiesSolvent); + auto thermoPropertiesReaction1 = static_cast(&ThermoEngine::thermoPropertiesReaction); + auto thermoPropertiesReactionFromReactants1 = static_cast(&ThermoEngine::thermoPropertiesReactionFromReactants); + + auto thermoPropertiesSubstance2 = static_cast(&ThermoEngine::thermoPropertiesSubstance); + auto electroPropertiesSolvent2 = static_cast(&ThermoEngine::electroPropertiesSolvent); + auto propertiesSolvent2 = static_cast(&ThermoEngine::propertiesSolvent); + auto thermoPropertiesReaction2 = static_cast(&ThermoEngine::thermoPropertiesReaction); + auto thermoPropertiesReactionFromReactants2 = static_cast(&ThermoEngine::thermoPropertiesReactionFromReactants); + py::class_(m, "ThermoEngine") // .def(py::init<>()) .def(py::init()) @@ -42,11 +56,16 @@ void exportThermoEngine(py::module& m) .def("appendData", appendData2, "Append records of given type (elements, substances, reactions) to the database from a list of JSON strings.") .def("setSolventSymbol", &ThermoEngine::setSolventSymbol) .def("solventSymbol", &ThermoEngine::solventSymbol) - .def("thermoPropertiesSubstance", &ThermoEngine::thermoPropertiesSubstance, (py::arg("T"), py::arg("P"), "substance")) - .def("electroPropertiesSolvent", &ThermoEngine::electroPropertiesSolvent, (py::arg("T"), py::arg("P"), "solvent")) - .def("propertiesSolvent", &ThermoEngine::propertiesSolvent, (py::arg("T"), py::arg("P"), "solvent")) - .def("thermoPropertiesReaction", &ThermoEngine::thermoPropertiesReaction, (py::arg("T"), py::arg("P"), "reaction")) - .def("thermoPropertiesReactionFromReactants", &ThermoEngine::thermoPropertiesReactionFromReactants, (py::arg("T"), py::arg("P"), "symbol")) + .def("thermoPropertiesSubstance", thermoPropertiesSubstance1, "Calculate the thermodynamic properties of a substance with a given symbol.") + .def("electroPropertiesSolvent", electroPropertiesSolvent1, "Calculate the electro-chemical properties of a substance solvent with a given symbol.") + .def("propertiesSolvent", propertiesSolvent1, "Calculate the properties of a substance solvent with a given symbol.") + .def("thermoPropertiesReaction", thermoPropertiesReaction1, "Calculate the thermodynamic properties of a reaction with a given symbol, or for a given reaction equation.") + .def("thermoPropertiesReactionFromReactants", thermoPropertiesReactionFromReactants1, "Calculate the thermodynamic properties of a reaction from reactants with a given symbol.") + .def("thermoPropertiesSubstance", thermoPropertiesSubstance2, "Calculate the thermodynamic properties of a given substance object.") + .def("electroPropertiesSolvent", electroPropertiesSolvent2, "Calculate the electro-chemical properties of a given substance solvent object.") + .def("propertiesSolvent", propertiesSolvent2, "Calculate the properties of a given substance solvent object.") + .def("thermoPropertiesReaction", thermoPropertiesReaction2, "Calculate the thermodynamic properties of a given reaction object.") + .def("thermoPropertiesReactionFromReactants", thermoPropertiesReactionFromReactants2, "Calculate the thermodynamic properties from the reactants of a given reaction object.") ; } diff --git a/python/pyThermoFun/pyThermoParameters.cpp b/python/pyThermoFun/pyThermoParameters.cpp new file mode 100644 index 00000000..d49a4997 --- /dev/null +++ b/python/pyThermoFun/pyThermoParameters.cpp @@ -0,0 +1,66 @@ +// This file is part of ThermoFun https://bitbucket.org/gems4/thermofun/ +// ThermoFun is a framework for delivering standard state thermodynamic data. +// +// Copyright (c) 2016-2018 G.D.Miron, D.A.Kulik, A.Leal +// +// ThermoFun is free software: you can redistribute it and/or modify +// it under the terms of the GNU Lesser General Public License as +// published by the Free Software Foundation, either version 3 of +// the License, or (at your option) any later version. + +// ThermoFun is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +// GNU Lesser General Public License for more details. + +// You should have received a copy of the GNU General Public License +// along with ThermoFun code. If not, see . + +// pybind11 includes +#include +#include +namespace py = pybind11; + +#include + +namespace ThermoFun { + +void exportThermoParametersSubstance(py::module& m) +{ + py::class_(m, "ThermoParametersSubstance") + .def(py::init<>()) + .def_readwrite("isothermal_compresibility", &ThermoParametersSubstance::isothermal_compresibility) + .def_readwrite("isobaric_expansivity", &ThermoParametersSubstance::isobaric_expansivity) + .def_readwrite("temperature_intervals", &ThermoParametersSubstance::temperature_intervals) + .def_readwrite("pressure_intervals", &ThermoParametersSubstance::pressure_intervals) + .def_readwrite("Cp_coeff", &ThermoParametersSubstance::Cp_coeff) + .def_readwrite("Cp_nonElectrolyte_coeff", &ThermoParametersSubstance::Cp_nonElectrolyte_coeff) + .def_readwrite("phase_transition_prop", &ThermoParametersSubstance::phase_transition_prop) + .def_readwrite("phase_transition_prop_Berman", &ThermoParametersSubstance::phase_transition_prop_Berman) + .def_readwrite("m_landau_phase_trans_props", &ThermoParametersSubstance::m_landau_phase_trans_props) + .def_readwrite("HKF_parameters", &ThermoParametersSubstance::HKF_parameters) + .def_readwrite("volume_coeff", &ThermoParametersSubstance::volume_coeff) + .def_readwrite("critical_parameters", &ThermoParametersSubstance::critical_parameters) + .def_readwrite("volume_BirchM_coeff", &ThermoParametersSubstance::volume_BirchM_coeff) + .def_readwrite("empirical_coeff", &ThermoParametersSubstance::empirical_coeff) + .def_readwrite("solute_holland_powell98_coeff", &ThermoParametersSubstance::solute_holland_powell98_coeff) + ; +} + +void exportThermoParametersReaction(py::module& m) +{ + py::class_(m, "ThermoParametersReaction") + .def(py::init<>()) + .def_readwrite("temperature_intervals", &ThermoParametersReaction::temperature_intervals) + .def_readwrite("pressure_intervals", &ThermoParametersReaction::pressure_intervals) + .def_readwrite("reaction_logK_fT_coeff", &ThermoParametersReaction::reaction_logK_fT_coeff) + .def_readwrite("logK_TP_array", &ThermoParametersReaction::logK_TP_array) + .def_readwrite("reaction_Cp_fT_coeff", &ThermoParametersReaction::reaction_Cp_fT_coeff) + .def_readwrite("reaction_V_fT_coeff", &ThermoParametersReaction::reaction_V_fT_coeff) + .def_readwrite("reaction_RB_coeff", &ThermoParametersReaction::reaction_RB_coeff) + .def_readwrite("reaction_FM_coeff", &ThermoParametersReaction::reaction_FM_coeff) + .def_readwrite("reaction_DM10_coeff", &ThermoParametersReaction::reaction_DM10_coeff) + ; +} + +} // namespace ThermoFun \ No newline at end of file