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pyne Change Log

Next Version

New Capabilities

Change

  • Update pyne::ValueError to return a pointer to a stored string instead of an out-of-scope string. (#1358)
  • Setting CMP0074 in CMakeLists.txt to allow *_ROOT variables in the CMake command.
  • Change the e_bounds tag unit from eV to MeV (#1353)
  • Add functions to tag the decay_time, source_intensity and version to source.h5m (#1352)

Fix

  • An e_bounds reading problem when old sampler is used without e_bounds text file (#1353)
  • Fix the compatibility problem of transmuters with numpy version v1.19.x
  • Fix to MaterialLibrary.__delitem__ to call the underlying instance.

Maintenance

v0.7.3

Change

  • Update OVA link in the docs (#1348)
  • Bump license date to 2020 (#1348)
  • Add the energy boundaries to photon source file (#1341)
  • Add a new source sampling sampler without e_bounds (#1341)
Fix
  • Compatibility fix with MCNP6 ptracs. (#1336)
  • Add some missing pieces in MaterialLibrary API to match std::unordered_map one (#1350)

v0.7.2

Change

  • Now attribute a number to material when adding them into a material library (#1334)

Fix

  • change the ref address of the materials group in the nuc_data.h5 material_library (to match new format) (#1337)
  • clean the remaining calls to the old material_library write_hdf5 API
Maintenance
  • Add dockerhub authentication for pulling images

v0.7.1

New Capabilities
  • Adding unordered_map like API to MaterialLibrary pointing directly to the nested unordered_map

Maintenance

  • Documentation Changes
    • Update conda install instruction. (#1324)
  • move join_string declaration in utils header to allow amalgamate PyNE to be compiled with clang
  • Fix the incompatibility between MOAB 5.2.0 and test_activation_responses (#1328)
  • Bug fixes
    • Update version numbering for release v0.7.1 (#1326)
  • Improvements in building and testing
    • Update moab version 5.1.0 >> 5.2.1 (#1331)

v0.7.0

IMPORTANT: Python 2 is no longer supported as of this release. Some packages may continue to work,
but there is no longer testing of Python 2 during development.

New Capabilities

  • Subvoxel R2S allows activation and photon source sampling by material within a mesh voxel
    • SubMode parameter in source_sampling
    • Add code for submode: SUBVOXEL
    • Test functions to test SUBVOXEL codes in test_source_sampling.py
    • Add subvoxel r2s workflow support in pyne/scripts/r2s.py
    • Use new sampler for both voxel and sub-voxel R2S.
    • Define cell_mats for subvoxel equals False
    • Function Sampler::mesh_tag_data to be compatible for both DEFAULT and SUBVOXEL mode
  • OpenMC support
    • Add CI test for OpenMC as an optional dependency
    • Add options to install OpenMC Python API
    • Functions to read OpenMC state point file to get meshtally data
  • File scripts/activation_responses.py to get activation responses data for ALARA output file for better visualization. Responses include:
    • decay heat
    • specific activity
    • alpha heat
    • beta heat
    • gamma heat
    • wdr
    • photon_source
    • multiple response in one output.txt file
  • first introduction of GT-CADIS workflows
    • added gtcadis.py script
    • first step for the GT-CADIS workflow, further steps to follow

Enhancements to Previous Capabilities

  • MCNP Support * Default library reading capability from material card, such as nlib, plib and etc. (#1316)

  • Turn off QA warnings by default and enable with env variable 'PYNE_QA_WARN' (#1268)

  • Enhancements of Material and MaterialLibrary capabilities

    • A C++ API for the MaterialLibrary class has been created for direct use in compiled software tools

    • Change the MaterialLibrary Python API to bind to the new c++ one.

    • Overhaul of HDF5 format of Material and MaterialLibrary

      • Capability to read nuclides from a specific path when loading material from an hdf5 file (not necessarily relying on autodetect the nucpath).

      • change the structure of material when written in a hdf5 file:

        /material/
/material/my_mat/
/material/my_mat/composition
/material/my_mat/nuclidelist
/material/my_mat/composition_metadata

        where, /material and /material/my_mat are now HDF5 groups

    • Material I/O formats
      • pyne::Material: capability to form PHITS input material card
      • capability to form a uwuw material name
      • A new argument mult_den (bool) that makes Material class's get_density_frac method (hence also mcnp and phits methods) write atom/mass density if true, otherwise write atom/mass fraction.
      • increased precision of the material density reported in the comment card for an MCNP material to 5 decimal places
      • Adds tests to tests/test:materials.py:test_decay_heat(self) to check more isotopes
      • Adds from_activity() to create or redefine materials using radionuclide activities
  • Bug fixes in serpent support
    • in serpent.py, function VOL_serp2_fix() to correct for _VOL variable being an array. as seen in serpent 2
    • fix error in serpent parse_dep
    • serpent.py function parse_dep. Catches ValueError that occurs when parse_dep attempts to make_mats with a serpent 2 *_dep.m file due to the *_VOL variable not being a float
  • Fixes in examples and tutorials
    • in half_life example, changed nuc_data call in anum to give int data type
    • in Data Sources, rerun example to update output
    • in Chainsolve Transmutation, rerun example to update output
    • pytaps to pymoab update in intro/diffusion tutorials (#1282, #1304)
    • in material_library example, updated import and class usage to reflect MaterialLibrary changes (#1280)
    • Removed QA warnings
    • in ACE Module example, change urllib for requests
    • adds broken yt warning to examples notebooks, updates deprecated urlretrieve to requests (#1295, #1304)
    • remove Origen 2.2: H1 Cross Section for PyNE repo not supporting necessary inputs to reproduce the example.
    • in mesh basic tutorial, add broken yt warning
    • in endf reader example, cross-section plots from ENDF/B-VII.1 and updated module for deprecated urlretrieve to requests (#1297, #1317)
    • change to integer division in example in nuclide naming tutorial, fix typo (#1310)
  • Changes in source sampling for mesh-based Monte Carlo sources
    • Add statistics summary output of find_cell failure in source sampling.
    • Add the ability to allow user turn off the void rejection in source sampling.
    • Add cell_fracs and cell_number tags for both default and subvoxel r2s modes
    • Check for the existence of the e_bounds file. Print error message when it's missing.
    • Check for bias_tag data. Report error when bias tag data are all zero
    • Check 'cell_fracs' tag in source_sampling.cpp when sub_mode is DEFAULT. Prevent wrong use of source.h5m.
    • Fix the problem of reading cell_number_tag with size of 1
    • Change mode range of cell rejection from >3 to >2
    • Sort cell_fracs according to the order of 'idx' and 'vol_frac'. For faster source sampling.
    • Pass cell_list back to Fortran, to speed up source sampling.
    • function to write total photon intensities for subvoxel r2s
    • Removed variables `icl_tmp` and `find_cell` which are not longer needed.
    • MCNP6 version of source.F90
    • Changed source.F90 to use "implicit none" instead of "implicit real"
    • Addition & updates of unit tests for above improvements
  • Improvements in Rigorous-2-Step shutdown dose rate analysis workflow
    • Documentation improvements
    • Provide example files for variety of problems/problem modes
    • Improvements in testing of R2S
      • Use example files for automated testing
    • Streamline code related to addition of subvoxel mode
      • Combine the subvoxel/voxel R2S loops to calculate the total photon source intensities.
      • Keep cell_number, cell_fracs, cell_largest_frac_number and cell_largest_frac tag in r2s step1
      • Use subvoxel and normal r2s compatible workflow parameters
      • Input check of cell_fracs tag under voxel mode. As the cell_fracs tag is there for voxel/sub-voxel mode.
    • Load geom and calculate cell_mats in r2s step2
    • Read decay times from r2s config.ini, and then write them into alara_inp.
    • In R2S step2, add option to write only 'total' to h5 file, reduce the CPU time
    • Error in voxel R2S.
    • Changes in processing of ALARA input/output
      • Change some default names of alara_inp.
      • Decay times in the alara_params.txt.
      • Add input units check to the function utils.py/to_sec
      • Use function utils.py/to_sec to replace alara.py/_TO_SEC
      • Simplify the method to get the list of decay/cooling times
  • Nuclear Data Handling and Reporting
    • Fixed issue where some gamma x-rays where throwing NotANuclide errors because the underlying nuclides were being read & recorded with negative ids. All nuclide ids are now ensured to be positive.
    • Misidentification of descriptive text in (MF,MT)=(1,451) as contents lines.
    • decay_heat() in material.cpp now calls metastable_id to convert zas_id to state_id
    • Fix ENDF parsing of TSL files with short collision time approximation for non-principal atoms.
    • endf.Library._read_headers() and regular expressions in endf.pyx
      • Removed regexps: CONTENTS_R, SPACE66_R, NUMERICAL_DATA_R
      • Added regexps: SPACEINT11_R
      • Added methods: _isContentLine(parts)
    • ENSDF database link to 2019 Oct 4th database
    • Update the C012-n.ace file link.
    • Missing elements name_to_zz dictionary
    • Updated half_life in data.pyx to return nan if isotope not found (#1257)
  • Improvements in Mesh capabilities
    • added mesh tally definitions to tallies
    • store multi particle tally (for Volume and Surface)
    • mcnp can write multi-particle tally
    • Move check of tag_names to mesh.py
    • Fix a problem of creating mesh from reading h5m files in unstructued R2S
    • Default initializer pyne.mesh.Mesh() now raises an exception with info on how to properly make a mesh
    • Move class MeshTally from mcnp.py to mesh.py
    • Change the method of creating meshtally from mcnp meshtal
    • pyne.mesh now takes advantage of PyMOAB instead of PyTAPS:
      • IMeshTag changed to NativeMeshTag, with according tagetype name change: from 'imesh' to 'nat_mesh'
      • write_hdf5(self, filename) -> write_hdf5(self, filename, write_mats)
      • new save(self, filename, write_mats) (alias for write hdf5)
      • new class MeshSetIterator()
      • new get_tag(self, tag_name) and delete_tag(self, tag_name) methods
      • when tagging the root set of a mesh, a new syntax is available:
        • mymesh.mytag[mesh.mesh.getRootSet()] = val can now be written as mymesh.mytag[mymesh] = val
      • direct call to the mesh entities change accordingly for example:
        • getEntSets() -> get_entities_by_type( , )
        • getTagHandle('XXX') -> tag_get_handle(types.XXXXX)
        • iterate() -> mesh_iterate()
        • getAllTags(xx) -> tag_get_tags_on_entity(xx)
        • mesh.destroyTag(self, boolean) -> mesh.delete_tag(self)
        • ... (see PyTAPS and PyMOAB respective documentation)
      • those changes have been propagated in mcnp.py, alara.py, ccc.py, dagmc.pyx, r2s.py, variancereduction.py, expand_tags.py, and their respective tests...

Maintenance

  • Documentation Changes
    • Credit Rochman for allowing redistribute TENDL file
    • Fix various typos
    • automatic deployment of a updated version of the website on tags
    • automatic creation of a new version of the website (not deployed) for verification purposes in pyne.github.com/website_preview
    • New developers guide: The update adds information about creating an environment, updates formatting for more consistency, details considerations and methods to check the version of dependencies, and adds additional links to coding resources.
    • In website index, change C++ API link to "C++ API Documentation" instead of "C++ & Fortran API Documentation"
    • Added publications to bibliography (PR #1256)
    • Adding contributing guide and code of conduct (#1258)
    • Changed Doc and Tutorial mentions of iPython notebooks to Jupyter notebooks (PR #1262)
    • Improvements in documentation for release (#1290 #1285 #1299)
    • Fix broken links (#1311)
    • Update install instructions (#1238 & #1315)
    • Update New Developers Guide
  • Improvements in building and testing
    • require contributor to change CHANGELOG
    • stopped all testing in Python 2 (#1321)
    • now get the base branch name from github and check change against it
      (inspired by https://github.com/NarrativeScience/circleci-orb-ghpr/blob/master/src/commands/get-pr-info.yml)
    • Expand testing matrix to include:
      • python 2 vs 3
      • with vs without PyMOAB
      • with vs without DAGMC
    • Added FindDAGMC.cmake file
    • turn off BLAS/LAPACK & FORTRAN in MOAB build
    • Dockerfile to build many variations of PyNE docker image, with python script CLI
    • Add hdf5-tools as dependency for docker images used in CircleCI, for better nose test comparing h5 files
    • Add future as dependency for docker images used in CircleCI, for python2 and python3 compatibility
    • "--dagmc" flag added to setup.py in order to build PyNE against DAGMC
    • new check won't now be triggered after a merge only on PRs
    • utils.py: updated the download timeout time to 120sec (from 30sec)
    • updated CI to use CircleCI 2.1 workflows: now build separately from tests with state saved between runs
    • test_fluka:
      • added test to check the data tag name of the different tally part and error.
    • revert internal nuc_data_path to origin value after internal data test
    • added DEFINE variable to allow material.cpp amalgamation without decay.cpp
    • now skips endf test when website is not reachable to allow completeness of the other tests.
      • test file for ENDF was wrong
    • Add functions to do file, file block, line, and string almost the same compare functions in pyne/utils.py
    • make data available as replacement for data.pyne.io (#1261, #1265)
    • Removed iPython check from setup.py and added Jupyter to be an optional dependency in documentation (#1273)
    • Install Python dependencies with Pip instead of APT in Dockerfile
    • Remove if block in travis-run-tests.sh (just run nosetests)
    • Deprecating most of the python 2 tests. Only testing python2 with pyMOAB and DAGMC deps.
    • updates tutorials and examples to python3 syntax to avoid failures (#1271)
    • added a welcome bot for first PR, Issue, and merge (#1287)
    • allow spatial solvers to be built in conda environments (#1305)
    • ensure that ENSDF fortran tools are linked correctly. (#1306)
    • allow spatial solvers to be turned on/off at time of setup (#1308)
  • Code cleanup
    • Formatting improvements
    • Compatibility with language updates
      • update the way that collections is imported in preparation for deprecated changes in future python versions
      • removed some imports of collections that were not necessary
      • change return type of method to avoid compiler compatibility issue
      • Convert some code and tests to enable python2/3 compatibility
    • Clean up some hard coded strings in test_source_sampling.py
    • rxname.child() and rxname.parent() now accept str for the z argument in Python 3.
    • dagmc_bridge: added a static DagMC instance
    • cleanup throws return from return (const char *) to simple return (it was suggested that those complicated return might cause seg fault, on some system -- OsX+conda)
    • Fixes string formatting typo in pyne/fortranformat/_parser.py. Entire file is now str.format() (#1275)
    • Remove deprecated file open mode 'U' (#1298)

Fixed:

  • Bug fix in xsdir class for parsing correct ZAID XS (#1314)

v0.5.11

Added:

  • Function to convert unit to s in pyne/alara.py
  • Function to do float match for decay times
  • Add SourceParticle class in pyne/src/source_sampling.
  • Codes to read ALARA output file under subvoxel R2S condition
  • A function to build up a subvoxel_array from mesh and cell_mats information
  • A test function to test the process of reading ALARA output file
  • Test function for subvoxel with (N, 1) condition in test_mesh.py
  • Reshape the array when max_num_cells == 1

Changed:

  • shape of IMeshTag when input value is a (N, 1) array
  • set tag as array rather than number
  • decaygen now gets the include dir based on the compiler path.
  • Build system now explitily looks for C++11 standard compatability.
  • Unit of e_bounds changed from eV to MeV
  • Change loop variables to be v for volume elements and e for energy groups (instead of i & j)
  • Use bias_mode instead of mode to allow for additional mode types in future
  • A parameter in test_alara.py, to test modified match method
  • Correct the wrong mode description comment in pyne/src/source_sampling.h
  • Change the particle_birth return value from std::vectot<double> to SourceParticle object
  • Some code clean up
  • Some clean up of white space

Removed:

  • Code in mesh.py to reshpe a (N,1) to (N, ) array is no longer needed if PR #971 merged

Fixed:

  • decaygen now can properly produce Clang assembly.
  • Build system would always download cram sources, even if they already existed. This has been fixed.
  • ENDF error bounds bug that was preventing nuc_data_make from working.
  • NNDC no longer provides the mednew.dat data set. A fallback has been supplied.

v0.5.10

Fixed:

  • Made SSL context creation Python 2 & 3 Compatible.

v0.5.9

Changed:

  • Downloading files now uses null SSL context.

v0.5.8

Changed:

  • Downloading data now uses HTTP, rather than HTTPS.

v0.5.7

Fixed:

  • Occassional bug with downloading URL fix.

v0.5.6

v0.5.5

v0.5.4