Release 1.3.0

.gitignore

@@ -36,3 +36,10 @@ docs/source/generated/
 
 #VSCode
 .vscode/
+
+# unittests
+puffin_unittest_scratch/
+
+# puffin instance
+puffin.yaml
+puffin.sh

CHANGELOG.rst

@@ -1,6 +1,30 @@
 Changelog
 =========
 
+Release 1.3.0
+-------------
+
+New Features:
+    - Store found elementary step even if none of the endpoints corresponds to the initial starting structures
+    - Add restart information with valid TS for jobs trying to find new elementary steps, where the IRC failed to produce different endpoints
+    - Consider potential surface structures for label determination of new structures
+    - Logic to transfer indices information and other complex properties from reactants to products
+    - Save close lying spin multiplicities and allow to manipulate exact spin propensity
+      check behavior with added settings
+
+New Jobs:
+    - Microkinetic modeling with the program Reaction Mechanism Simulator.
+
+New interfaced programs
+    - AMS via SCINE AMS Wrapper
+    - MRCC (release version March 2022)
+
+Bug fixes:
+    - Ensure that `only_distance_connectivity` is adhered in all reaction jobs
+
+Other:
+    - Update address in license
+
 Release 1.2.0
 -------------
 

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group
 
 Redistribution and use in source and binary forms, with or without modification,
 are permitted provided that the following conditions are met:

README.rst

@@ -6,7 +6,7 @@
 Introduction
 ------------
 
-SCINE Puffin is a calculation handler for SCINE Chemoton. Thus, it bridges the gap between high level exploration jobs for reaction networks and  basic quantum chemical calculations. Making use of the abstractions defined the SCINE Core and SCINE Utilities  modules it provides the means to define and execute jobs that generate new data for reaction networks. SCINE Puffin is designed as an instanced runner that, once bootstrapped, continuously processes requested jobs. It is built to work in containerized environments (Docker, Singularity).
+SCINE Puffin is a calculation handler for SCINE Chemoton. Thus, it bridges the gap between high level exploration jobs for reaction networks and  basic quantum chemical calculations. Making use of the abstractions defined the SCINE Core and SCINE Utilities  modules it provides the means to define and execute jobs that generate new data for reaction networks. SCINE Puffin is designed as an instanced runner that, once bootstrapped, continuously processes requested jobs. It is built to work in containerized environments (Docker, Apptainer/Singularity).
 
 License and Copyright Information
 ---------------------------------

conanfile.txt

@@ -0,0 +1,18 @@
+[requires]
+scine_utilities/9.0.0@
+scine_molassembler/2.0.1@
+scine_database/1.3.0@
+scine_xtb_wrapper/3.0.0@
+scine_sparrow/5.0.0@
+scine_readuct/5.1.0@
+
+[options]
+scine_utilities:python=True
+scine_molassembler:python=True
+scine_database:python=True
+scine_sparrow:python=True
+scine_xtb_wrapper:python=True
+scine_readuct:python=True
+
+[generators]
+virtualenv_python

container/singularity/README.rst → container/apptainer/README.rst

@@ -2,39 +2,40 @@ Basic Container Usage
 ---------------------
 
 In essence, these two commands should be enough to run a basic ``Puffin``
-instance inside a Singularity image.
+instance inside an Apptainer (formerly Singularity) image.
 One to build the container:
+
 .. code-block:: bash
 
-   singularity build puffin.sif puffin.def
+   apptainer build puffin.sif puffin.def
 
 and one to run the generated image:
 
 .. code-block:: bash
 
-   singularity run puffin.sif
+   apptainer run puffin.sif
 
 The build command may require slight alterations to the ``.def`` file first, as
 the file may reference a user's SSH keys in order to allow the cloning of some
 ``SCINE`` repositories.
 For some users the ``--fakeroot`` option may be more comfortable than using a
 ``sudo`` preface, but keep in mind that this option is not guaranteed to work,
 depending on the subordinate UID mapping configured for you on the machine you're working on.
-Also, it may be required to make Singularity build the image in
+Also, it may be required to make Apptainer build the image in
 a custom temporary directory if the default ``/tmp`` is not big enough.
 A slightly different build command may thus look like this:
 
 .. code-block:: bash
 
-   SINGULARITY_TMPDIR=/scratch/tmp singularity build --fakeroot puffin.sif puffin.def
+   APPTAINER_TMPDIR=/scratch/tmp apptainer build --fakeroot puffin.sif puffin.def
 
 The run command will have to be changed depending on the use case.
 It may be required to change some of the settings of the Puffin
 instance running inside the container. To this end, environment variables for
 Puffin can be set. These variables need to be present inside the container.
-With Singularity versions greater than 3.6 it is possible to use the
-``--env`` or ``--env-file`` argument to the run command. The more general way is
-setting ``SINGULARITYENV_`` variables on the host machine.
+It is possible to use the ``--env`` or ``--env-file`` argument to the run command.
+However, the more general way is setting ``APPTAINERENV_`` variables on the host
+machine.
 
 Furthermore it is required to mount two folders into the image, both are scratch
 direcories, one for ``.log`` and ``.pid`` files (``/socket``) and one for the
@@ -44,10 +45,10 @@ A more complete run could thus look like this:
 
 .. code-block:: bash
 
-   singularity build puffin.sif puffin.def
-   export SINGULARITYENV_PUFFIN_DATABASE_NAME=ath_dft
-   export SINGULARITYENV_PUFFIN_DATABASE_PORT=27001
-   export SINGULARITYENV_PUFFIN_DATABASE_IP=129.132.118.83
-   singularity run --bind /scratch/puffin:/socket \
+   apptainer build puffin.sif puffin.def
+   export APPTAINERENV_PUFFIN_DATABASE_NAME=ath_dft
+   export APPTAINERENV_PUFFIN_DATABASE_PORT=27001
+   export APPTAINERENV_PUFFIN_DATABASE_IP=129.132.118.83
+   apptainer run --bind /scratch/puffin:/socket \
                    --bind /scratch/puffin/jobs:/jobs \
                    puffin.sif

container/singularity/puffin.def → container/apptainer/puffin.def

@@ -42,11 +42,12 @@ From: ubuntu:focal
     echo 'export MKLROOT=/opt/intel/oneapi/mkl/latest' >>$SINGULARITY_ENVIRONMENT
 
     # Install Cython
-    pip3 install Cython pythran
+    pip3 install Cython==0.29.36 pythran
 
     # Install numpy
     git clone https://github.com/numpy/numpy.git numpy
     cd numpy
+    git checkout v1.24.2
     git submodule update --init
     cp site.cfg.example site.cfg
     echo "\n[mkl]" >> site.cfg
@@ -62,6 +63,7 @@ From: ubuntu:focal
     # Install scipy
     git clone https://github.com/scipy/scipy.git scipy
     cd scipy
+    git checkout v1.10.1
     git submodule update --init
     python3 setup.py build
     python3 setup.py install

container/docker/Dockerfile

@@ -30,28 +30,31 @@ ENV LD_LIBRARY_PATH=/opt/intel/oneapi/mkl/latest/lib/intel64:$LD_LIBRARY_PATH
 ENV MKLROOT=/opt/intel/oneapi/mkl/latest
 
 # Install Cython
-RUN pip3 install Cython pythran
+RUN pip3 install Cython==0.29.36 pythran
 
 # Install numpy
+WORKDIR /
 RUN git clone https://github.com/numpy/numpy.git numpy
-RUN cd numpy ; \
-  cp site.cfg.example site.cfg ; \
+WORKDIR /numpy
+RUN git checkout v1.24.2
+RUN git submodule update --init
+RUN cp site.cfg.example site.cfg ; \
   echo "\n[mkl]" >> site.cfg ; \
   echo "include_dirs = /opt/intel/oneapi/mkl/latest/lib/intel64/" >> site.cfg ; \
   echo "library_dirs = /opt/intel/oneapi/mkl/latest/lib/intel64/" >> site.cfg ; \
   echo "mkl_libs = mkl_rt" >> site.cfg ; \
   echo "lapack_libs =" >> site.cfg
-RUN cd numpy ; git submodule update --init
-RUN cd numpy ; python3 setup.py build --fcompiler=gnu95
-RUN cd numpy ; python3 setup.py install
-RUN rm -rf numpy
+RUN python3 setup.py build --fcompiler=gnu95
+RUN python3 setup.py install
 
 # Install scipy
+WORKDIR /
 RUN git clone https://github.com/scipy/scipy.git scipy
-RUN cd scipy ; git submodule update --init
-RUN cd scipy ; python3 setup.py build
-RUN cd scipy ; python3 setup.py install
-RUN rm -rf scipy
+WORKDIR /scipy
+RUN git checkout v1.10.1
+RUN git submodule update --init
+RUN python3 setup.py build
+RUN python3 setup.py install
 
 # Install MongoDB C++ bindings
 RUN wget https://github.com/mongodb/mongo-c-driver/releases/download/1.17.3/mongo-c-driver-1.17.3.tar.gz

docs/source/conf.py

@@ -58,7 +58,7 @@
 
 # General information about the project.
 project = 'scine_puffin'
-copyright = '2022, ETH Zurich, Laboratory for Physical Chemistry, Reiher Group'
+copyright = 'ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group'
 author = 'Reiher Group'
 
 # The version info for the project you're documenting, acts as replacement for

docs/source/programs.rst

@@ -27,6 +27,10 @@ SCINE: Sparrow
 ``````````````
 .. autoclass:: scine_puffin.programs.sparrow.Sparrow
 
+SCINE: Parrot
+`````````````
+.. autoclass:: scine_puffin.programs.parrot.Parrot
+
 Serenity
 ````````
 .. autoclass:: scine_puffin.programs.serenity.Serenity

requirements-dev.txt

@@ -3,10 +3,6 @@ matplotlib
 pytest
 coverage
 recommonmark
-sphinx
-sphinx_rtd_theme
-sphinx_autodoc_typehints
-sphinx_copybutton
 numpydoc
 pylint
 pylint-exit

requirements.txt

@@ -1,7 +1,13 @@
 gitpython
 numpy
 psutil
+pymatgen
 python-daemon
 pyyaml
 scipy
 setproctitle
+sphinx
+sphinx_rtd_theme
+sphinx_autodoc_typehints
+sphinx_copybutton
+salib

scine_puffin/__init__.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 __copyright__ = """ This code is licensed under the 3-clause BSD license.
-Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
 See LICENSE.txt for details.
 """
 

scine_puffin/__main__.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 __copyright__ = """ This code is licensed under the 3-clause BSD license.
-Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
 See LICENSE.txt for details.
 """
 

scine_puffin/_version.py

@@ -1,6 +1,6 @@
 __copyright__ = """ This code is licensed under the 3-clause BSD license.
-Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
 See LICENSE.txt for details.
 """
 
-__version__ = "1.2.0"
+__version__ = "1.3.0"

scine_puffin/bootstrap.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 __copyright__ = """ This code is licensed under the 3-clause BSD license.
-Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
 See LICENSE.txt for details.
 """
 import os
@@ -62,15 +62,18 @@ def bootstrap(config: Configuration):
 
     # Install minimal requirement
     print("")
-    print("Building SCINE Utils from sources.")
+    print("Building SCINE Core/Utils from sources.")
     print("")
+    core_build_dir = os.path.join(build_dir, "core")
+    core = Utils(config.programs()["core"])
+    core.install(core_build_dir, install_dir, config["resources"]["cores"])
     utils_build_dir = os.path.join(build_dir, "utils")
     utils = Utils(config.programs()["utils"])
     utils.install(utils_build_dir, install_dir, config["resources"]["cores"])
 
     # Install all other programs
     for program_name, settings in config.programs().items():
-        if program_name == "utils" or not settings["available"]:
+        if program_name in ['core', 'utils'] or not settings["available"]:
             continue
         print("")
         print("Preparing " + program_name.capitalize() + "...")
@@ -101,6 +104,22 @@ def bootstrap(config: Configuration):
             "python" + str(python_version[0]) + "." + str(python_version[1]),
             "site-packages",
         )
+        + ":"
+        + os.path.join(
+            install_dir,
+            "local",
+            "lib",
+            "python" + str(python_version[0]) + "." + str(python_version[1]),
+            "dist-packages",
+        )
+        + ":"
+        + os.path.join(
+            install_dir,
+            "local",
+            "lib64",
+            "python" + str(python_version[0]) + "." + str(python_version[1]),
+            "dist-packages",
+        )
     )
     env["PATH"] = os.path.join(install_dir, "bin")
     env["LD_LIBRARY_PATH"] = os.path.join(install_dir, "lib") + ":" + os.path.join(install_dir, "lib64")