-n 1 ${PROGRAM[@]} --junitxml=$PLUGIN_MPI_TEST_XML : \
-n 1 ${PROGRAM[@]}
fi
-
-# Run Python acceptance tests.
-python -m pytest python_packaging/test --junitxml=$PY_ACCEPTANCE_TEST_XML --threads=2
-
-# Note: Multiple pytest processes getting --junitxml output file argument
-# may cause problems, so we set the option on only one of the launched processes.
-# See also Multiple Instruction Multiple Data Model for OpenMPI mpirun:
-# https://www.open-mpi.org/doc/v3.0/man1/mpiexec.1.php
-PROGRAM=(`which python` -m mpi4py -m pytest \
- -p no:cacheprovider \
- $PWD/python_packaging/test \
- --threads=1)
-# shellcheck disable=SC2068
-if [ -x `which mpiexec` ]; then
- PYTHONDONTWRITEBYTECODE=1 \
- mpiexec --allow-run-as-root \
- -x OMP_NUM_THREADS=1 \
- --mca opal_warn_on_missing_libcuda 0 \
- --mca orte_base_help_aggregate 0 \
- -n 1 ${PROGRAM[@]} --junitxml=$PLUGIN_MPI_TEST_XML : \
- -n 1 ${PROGRAM[@]}
-fi
+++ /dev/null
-========================
-Python packaging roadmap
-========================
-
-Describe functional goals, feature tracking, and associated tests.
-
-Functionality to build
-======================
-
-General tool implementation sequence
-------------------------------------
-
-1. Tools in ``operation`` submodule wrap Python code with compliant interface
-2. ``commandline_operation()`` provides UI for (nearly) arbitrary CLI tools
-3. ``tool`` submodule provides trivially wrapped ``gmx`` tools with well-defined inputs and outputs
-
-Simulation tool implementation sequence
----------------------------------------
-
-1. ``mdrun``
-2. ``modify_input``
-3. ``make_input``
-
-Data flow
----------
-
-* ``result()`` methods force data locality for use by non-API calls
-* output properties allow proxied access to (fault tolerant, portable) result futures
-* ``logical_and()``, etc. allow manipulation of data / signals "in flight"
-
-Data flow topology tools
-------------------------
-
-* implicit scatter / map
-* implicit broadcast
-* ``gather()`` makes results local
-* ``reduce()`` allows operation across an ensemble (implicit allReduce where appropriate)
-
-Control flow
-------------
-
-* ``subgraph`` allows several operations to be bundled with a scope that allows
- user-declared data persistence (e.g. when used in a loop)
-* ``while_loop`` allows repeated execution of a subgraph, subject to a declared
- condition of the subgraph state/output, managing accessibilty of data handles
- internal and external to the graph
-
-Execution environment
----------------------
-
-1. Top level module function ``run()`` launches work to produce requested data
-2. Infrastructure manages / negotiates dispatching or allocation of available resources
-
-Packaging
----------
-
-1. Python package can be installed from GROMACS source directory after GROMACS installation.
-2. Python package can be installed by a user from a hand-built GROMACS installation.
-3. Python package can be installed from a Linux binary GROMACS distribution using
- appropriate optimized binary libraries.
-
-Installation procedures are testable with Dockerfiles in a Docker-based CI environment.
-Ref: https://github.com/kassonlab/gmxapi/blob/master/ci_scripts/test_installers.sh
-
-Typing
-------
-
-In addition to basic scalar types,
-some structured data types are immediately necessary.
-
-* gmxapi.NDArray supports an N-dimensional array of a single scalar gmxapi data type
- (with sufficient metadata for common array view APIs)
-* gmxapi.Map supports an associative container with key strings and Variant values
-
-NDArray is immediately necessary to disambiguate non-scalar parameters/inputs from
-implicit data flow topological operations.
-
-Data structures currently coupled to file formats should be decomposable into
-Maps with well-specified schema, but in the absence of more complete API data
-abstractions we just use filename Strings as the API-level content of
-input/output data handles. (Suggest: no need for file objects at
-the higher-level API if read_Xfiletype(/write_Yfiletype) operations
-produce(/consume) named and typed data objects of specified API types.)
-
-The API specification should be clear about policies for narrowing and widening
-of scalar types.
-
-Sequence
-========
-
-Features development sequence based on functional priorities and dependencies.
-
-* fr1: wrap importable Python code.
-* fr2: output proxy establishes execution dependency (superseded by fr3)
-* fr3: output proxy can be used as input
-* fr4: dimensionality and typing of named data causes generation of correct work topologies
-* fr5: explicit many-to-one or many-to-many data flow
-* fr7: Python bindings for launching simulations
-* fr8: gmx.mdrun understands ensemble work
-* fr9: MD plugins
-* fr10: fused operations for use in looping constructs
-* fr11: Python access to TPR file contents
-* fr12: Simulation checkpoint handling
-* fr13: ``run`` module function simplifies user experience
-* fr14: Easy access to GROMACS run time parameters
-* fr15: Simulation input modification
-* fr16: Create simulation input from simulation output
-* fr17: Prepare simulation input from multiple sources
-* fr18: GROMACS CLI tools receive improved Python-level support over generic commandline_operations
-* fr19: GROMACS CLI tools receive improved C++-level support over generic commandline_operations
-* fr20: Python bindings use C++ API for expressing user interface
-* fr21 User insulated from filesystem paths
-* fr22 MPI-based ensemble management from Python
-* fr23 Ensemble simulations can themselves use MPI
-
-Expectations on Mark for Q1-Q2 2019 GROMACS master changes
-==========================================================
-
-* Broker and implement build system amenable to multiple use
- cases. Need to be able to build and deploy python module from single
- source repo that is usable (i.e. can run the acceptance tests).
-
- - Some kind of nested structure likely appropriate, perhaps
- structured as nested CMake projects that in principle could stand
- alone. That's probably workable because nested projects can see
- the parent project's cache variables (TODO check this)
- - probably a top-level project coordinating a libgromacs build and a
- python module build, with the former typically feeding the latter
- - the libgromacs build may be able to leverage independent efforts
- towards a multi-configuration build (so SIMD/MPI/GPU agnostic)
- - top-level project offers much the same UI as now, passing much of
- it through to the libgromacs project
- - top-level project offers the option to find a Python (or be told
- which to use), to find a libgromacs (or be told, or be told to
- build), to build any necessary wrapper binaries (ie. classical gmx
- and mdrun), and to deploy all linked artefacts to
- CMAKE_INSTALL_PREFIX or the appropriate Python site-packages
- - the top-level project will be used by e.g. setup.py wrapper
- from scikit-build/distutils
- - requires reform of compiler flags handling
- - probably requires some re-organization of external dependencies
- of libgromacs
- - follow online "Modern CMake" best practices as far as practicable
- - library should be available for static linking with position
- independent code to allow a single shared object to be built for
- the Python module.
-
-* Dissolve boundary between libgmxapi and libgromacs
-
- - no effort on form and stability of the C++ headers and library in
- 2019, beyond what facilitates implementing the Python interface
- in GROMACS 2020
- - existing libgromacs declarations of "public API" and installed
- headers removed
-
-* libgromacs to be able to be use an MPI communicator passed in,
- rather than hard-coding MPI_COMM_WORLD anywhere. It is likely that
- existing wrapper binaries can use the same mechanism to pass
- MPI_COMM_WORLD to libgromacs.
-
-* UI helpers should express.
- - preferred name for datum as a string: ``nsteps``, ``tau-t``, etc.
- - setter (function object, pointer to a builder method, )
- - typing and type discovery (could be deducible from setter, but something to allow user input checking, or determination
- of the suitability of a data source to provide the given input)
- - help text: can be recycled to provide auto-extracted documentation, command-line help, and annotation in Python docstrings.
- - for CLI: short name for flag. E.g. 'p' for "topology_file"
- - for compatibility: deprecated / alternate names. E.g. "nstlist" for "neighbor_list_rebuild_interval", or "orire" for
- "enable_orientation_restraints"
- - default values
-
-Possible GROMACS source changes whose impact is currently unknown
-=================================================================
-* gmx::Any (which is a flavour of C++17 std::any) type could be
- helpful at API boundary. Also perhaps a flavour of C++17
- std::optional or std::variant.
-
-Additional goals
-================
-
-Some project goals are integrations or optimizations that are explicitly hidden from the user
-and not testable in a high level script, but should be reflected as milestones in a roadmap.
-
-GROMACS source changes deferred to later in 2019
-================================================
-* Build system works also from tarball
-* Build system can produce maximally static artefacts (for performance
- on HPC infrastructure)
-* express grompp and mdrun options handling with gmx::Options to
- prepare for future dictionary-like handling in Python without
- serializing a .tpr file
They can be specified as arguments to the Docker containers based on `ci.dockerfile`
* `run_flake8` runs the Flake8 Python linting tool on the `gmxapi` package sources.
-* `run_acceptace_test` runs the test suite in the higher level `test` directory.
* `run_gmxapi_unittest` runs single-threaded tests for the gmxapi Python package.
* `run_sample_test` runs the tests for the sample_restraint MD plugin API client code.
* `run_full` runs all of the above tests.
+++ /dev/null
-#!/bin/bash
-# Entry point script for Docker containers.
-# Additional arguments are passed along to pytest.
-# See README.md and the gmxapi/ci-<option> Docker images.
-
-# TODO: (#2756) Centrally manage dependencies on the GROMACS installation.
-# The gmxapi package, virtualenv, or test infrastructure should have an
-# internal mechanism for tracking the correct GROMACS installation.
-source /usr/local/gromacs/bin/GMXRC
-
-pytest $HOME/test $@
source /usr/local/gromacs/bin/GMXRC
pytest $HOME/gmxapi/test
-pytest $HOME/test
pytest $HOME/sample_restraint/tests
mpiexec -n 2 `which python` -m mpi4py -m pytest $HOME/gmxapi/test
mpiexec -n 2 `which python` -m mpi4py -m pytest $HOME/sample_restraint/tests
-mpiexec -n 2 `which python` -m mpi4py -m pytest $HOME/test
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2019,2020, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS 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 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS 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 Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-"""Configuration and fixtures for pytest."""
-
-import json
-import logging
-import os
-
-import pytest
-
-pytest_plugins = ('gmxapi.testsupport',)
-
-
-@pytest.fixture(scope='class')
-def spc_water_box(gmxcli, remove_tempdir):
- """Provide a TPR input file for a simple simulation.
-
- Prepare the MD input in a freshly created working directory.
- """
- import gmxapi as gmx
- # TODO: Remove this import when the the spc_water_box fixture is migrated to gmxapi.testsupport
- from gmxapi.testsupport import _cleandir
-
- # TODO: (#2896) Fetch MD input from package / library data.
- # Example:
- # import pkg_resources
- # # Note: importing pkg_resources means setuptools is required for running this test.
- # # Get or build TPR file from data bundled via setup(package_data=...)
- # # Ref https://setuptools.readthedocs.io/en/latest/setuptools.html#including-data-files
- # from gmx.data import tprfilename
-
- with _cleandir(remove_tempdir) as tempdir:
-
- testdir = os.path.dirname(__file__)
- with open(os.path.join(testdir, 'testdata.json'), 'r') as fh:
- testdata = json.load(fh)
-
- # TODO: (#2756) Don't rely on so many automagical behaviors (as described in comments below)
-
- structurefile = os.path.join(tempdir, 'structure.gro')
- # We let `gmx solvate` use the default solvent. Otherwise, we would do
- # gro_input = testdata['solvent_structure']
- # with open(structurefile, 'w') as fh:
- # fh.write('\n'.join(gro_input))
- # fh.write('\n')
-
- topfile = os.path.join(tempdir, 'topology.top')
- top_input = testdata['solvent_topology']
- # `gmx solvate` will append a line to the provided file with the molecule count,
- # so we strip the last line from the input topology.
- with open(topfile, 'w') as fh:
- fh.write('\n'.join(top_input[:-1]))
- fh.write('\n')
-
- assert os.path.exists(topfile)
- solvate = gmx.commandline_operation(gmxcli,
- arguments=['solvate', '-box', '5', '5', '5'],
- # We use the default solvent instead of specifying one.
- # input_files={'-cs': structurefile},
- output_files={'-p': topfile,
- '-o': structurefile,
- }
- )
- assert os.path.exists(topfile)
-
- if solvate.output.returncode.result() != 0:
- logging.debug(solvate.output.erroroutput.result())
- raise RuntimeError('solvate failed in spc_water_box testing fixture.')
-
- # Choose an exactly representable dt of 2^-9 ps (approximately 0.002)
- dt = 2.**-9.
- mdp_input = [('integrator', 'md'),
- ('dt', dt),
- ('cutoff-scheme', 'Verlet'),
- ('nsteps', 2),
- ('nstxout', 1),
- ('nstvout', 1),
- ('nstfout', 1),
- ('tcoupl', 'v-rescale'),
- ('tc-grps', 'System'),
- ('tau-t', 1),
- ('ref-t', 298)]
- mdp_input = '\n'.join([' = '.join([str(item) for item in kvpair]) for kvpair in mdp_input])
- mdpfile = os.path.join(tempdir, 'md.mdp')
- with open(mdpfile, 'w') as fh:
- fh.write(mdp_input)
- fh.write('\n')
- tprfile = os.path.join(tempdir, 'topol.tpr')
- # We don't use mdout_mdp, but if we don't specify it to grompp,
- # it will be created in the current working directory.
- mdout_mdp = os.path.join(tempdir, 'mdout.mdp')
-
- grompp = gmx.commandline_operation(gmxcli, 'grompp',
- input_files={
- '-f': mdpfile,
- '-p': solvate.output.file['-p'],
- '-c': solvate.output.file['-o'],
- '-po': mdout_mdp,
- },
- output_files={'-o': tprfile})
- tprfilename = grompp.output.file['-o'].result()
- if grompp.output.returncode.result() != 0:
- logging.debug(grompp.output.erroroutput.result())
- raise RuntimeError('grompp failed in spc_water_box testing fixture.')
-
- # TODO: more inspection of grompp errors...
- assert os.path.exists(tprfilename)
- yield tprfilename
+++ /dev/null
-[pytest]
-junit_family=xunit2
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2019,2020, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS 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 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS 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 Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-"""Reusable definitions for test modules.
-
-Define the ``withmpi_only`` test decorator.
-"""
-
-import pytest
-
-# TODO: (#3718) Normalize the handling of run-time arguments.
-from gmxapi.simulation.mdrun import ResourceManager as _ResourceManager
-_ResourceManager.mdrun_kwargs = {'threads': 2}
-
-withmpi_only = None
-
-try:
- from mpi4py import MPI
- withmpi_only = \
- pytest.mark.skipif(not MPI.Is_initialized() or MPI.COMM_WORLD.Get_size() < 2,
- reason="Test requires at least 2 MPI ranks, "
- + "but MPI is not initialized or context is too small.")
-except ImportError:
- withmpi_only = pytest.mark.skip(reason="Test requires at least 2 MPI ranks, but mpi4py is not available.")
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2019,2020, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS 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 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS 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 Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-"""Test gmxapi functionality described in roadmap.rst."""
-
-import gmxapi as gmx
-
-
-def test_fr1():
- """FR1: Wrap importable Python code.
-
- gmxapi compatible operations are implemented with simple machinery that allows
- compartmentalized progress on functionality to be highly decoupled from
- implementing user-facing tools. Tools are provided in `gmx.operation` and
- demonstrated by implementing `gmx.commandline_operation`.
- """
- # commandline_operation helper creates a set of operations
- # that includes the discovery and execution of the program
- # named in `executable`.
- operation = gmx.commandline_operation(executable='true')
- operation.run()
- assert operation.output.returncode.result() == 0
-
- operation = gmx.commandline_operation(executable='false')
- operation.run()
- assert operation.output.returncode.result() == 1
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2019,2020, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS 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 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS 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 Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-"""Test gmxapi functionality described in roadmap.rst."""
-
-import os
-import shutil
-import stat
-import tempfile
-
-import gmxapi as gmx
-
-
-def test_fr3():
- """FR3: Output proxy can be used as input."""
- with tempfile.TemporaryDirectory() as directory:
- file1 = os.path.join(directory, 'input')
- file2 = os.path.join(directory, 'output')
-
- # Make a shell script that acts like the type of tool we are wrapping.
- scriptname = os.path.join(directory, 'clicommand.sh')
- with open(scriptname, 'w') as fh:
- fh.write('\n'.join(['#!' + shutil.which('bash'),
- '# Concatenate an input file and a string argument to an output file.',
- '# Mock a utility with the tested syntax.',
- '# clicommand.sh "some words" -i inputfile -o outputfile',
- 'echo $1 | cat $3 - > $5\n']))
- os.chmod(scriptname, stat.S_IRWXU)
-
- line1 = 'first line'
- filewriter1 = gmx.commandline_operation(scriptname,
- arguments=[line1],
- input_files={'-i': os.devnull},
- output_files={'-o': file1})
-
- line2 = 'second line'
- filewriter2 = gmx.commandline_operation(scriptname,
- arguments=[line2],
- input_files={'-i': filewriter1.output.file['-o']},
- output_files={'-o': file2})
-
- filewriter2.run()
- # Check that the files have the expected lines
- with open(file1, 'r') as fh:
- lines = [text.rstrip() for text in fh]
- assert len(lines) == 1
- assert lines[0] == line1
- with open(file2, 'r') as fh:
- lines = [text.rstrip() for text in fh]
- assert len(lines) == 2
- assert lines[0] == line1
- assert lines[1] == line2
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2019, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS 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 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS 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 Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-"""Test gmxapi functionality described in roadmap.rst."""
-
-import pytest
-
-import gmxapi as gmx
-from gmxapi.version import has_feature
-
-@pytest.mark.skipif(not has_feature('fr4'),
- reason="Feature level not met.")
-def test_fr4():
- """FR4: Dimensionality and typing of named data causes generation of correct work topologies."""
- N = 10
- simulation_input = gmx.read_tpr(initial_tpr)
-
- # Array inputs imply array outputs.
- input_array = gmx.modify_input(
- simulation_input, params={'tau-t': [t / 10.0 for t in range(N)]})
-
- md = gmx.mdrun(input_array) # An array of simulations
-
- rmsf = gmx.commandline_operation(
- 'gmx',
- 'rmsf',
- input={
- '-f': md.output.trajectory,
- '-s': initial_tpr
- },
- output={'-o': gmx.FileName(suffix='.xvg')})
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2019, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS 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 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS 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 Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-"""Test gmxapi functionality described in roadmap.rst."""
-
-import pytest
-
-import gmxapi as gmx
-from gmxapi.version import has_feature
-
-@pytest.mark.skipif(not has_feature('fr5'),
- reason="Feature level not met.")
-def test_fr5():
- """FR5: Explicit many-to-one or many-to-many data flow.
-
- Test operations for manipulating the data flow graph topology.
-
- Check for expected default behavior and explicit behavior of data flow (graph
- edges) with respect to scatter, gather, map, reduce, and broadcast.
- """
- output_files = gmx.gather(rmsf.output.file['-o'])
- gmx.run()
-
- print('Output file list:')
- print(', '.join(output_files.result()))
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2019,2020, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS 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 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS 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 Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-"""Test gmxapi functionality described in roadmap.rst."""
-
-import pytest
-
-import gmxapi as gmx
-
-
-@pytest.mark.usefixtures('cleandir')
-def test_fr7(spc_water_box):
- """FR7: Python bindings for launching simulations.
-
- gmx.mdrun uses bindings to C++ API to launch simulations.
- """
- md = gmx.mdrun(spc_water_box)
- md.run()
- # Note: can't verify that this is accomplished with C++ integration without
- # exploring implementation details.
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2019,2020, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS 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 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS 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 Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-"""Test gmxapi functionality described in roadmap.rst."""
-
-import pytest
-
-import gmxapi as gmx
-from gmxapi.version import has_feature
-
-# Ref https://gitlab.com/gromacs/gromacs/-/issues/3192
-@pytest.mark.skipif(not has_feature('fr8'),
- reason="Feature level not met.")
-def test_fr8(spc_water_box):
- """FR8: gmx.mdrun understands ensemble work."""
- md = gmx.mdrun([spc_water_box, spc_water_box])
- md.run()
- # Maybe assert that two trajectory files with unique filesystem locations are produced?
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2019, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS 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 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS 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 Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-"""Test gmxapi functionality described in roadmap.rst."""
-
-import pytest
-
-import gmxapi as gmx
-from gmxapi.version import has_feature
-
-@pytest.mark.skipif(not has_feature('fr9'),
- reason="Feature level not met.")
-def test_fr9():
- """FR9: *gmx.mdrun supports interface for binding MD plugins*
-
- (requires interaction with library development)
- """
- import sample_restraint
-
- starting_structure = 'input_conf.gro'
- topology_file = 'input.top'
- run_parameters = 'params.mdp'
-
- initial_tpr = gmx.commandline_operation(
- 'gmx',
- 'grompp',
- input={
- '-f': run_parameters,
- '-c': starting_structure,
- '-p': topology_file
- },
- output={'-o': gmx.OutputFile('.tpr')})
-
- simulation_input = gmx.read_tpr(initial_tpr.output.file['-o'])
-
- # Prepare a simple harmonic restraint between atoms 1 and 4
- restraint_params = {'sites': [1, 4],
- 'R0': 2.0,
- 'k': 10000.0}
-
- restraint = sample_restraint.harmonic_restraint(input=restraint_params)
-
- md = gmx.mdrun(input=simulation_input, potential=sample_restraint)
-
- #md.run()
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2019, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS 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 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS 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 Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-"""Test gmxapi functionality described in roadmap.rst."""
-
-import pytest
-
-import gmxapi as gmx
-from gmxapi.version import has_feature
-
-@pytest.mark.skipif(not has_feature('fr10'),
- reason="Feature level not met.")
-def test_fr10():
- """FR10: 10: fused operations for use in looping constructs
-
- * gmx.subgraph fuses operations
- * gmx.while creates an operation wrapping a dynamic number of iterations of a subgraph
- """
- train = gmx.subgraph(variables={'conformation': initial_input})
- with train:
- myplugin.training_restraint(
- label='training_potential',
- params=my_dict_params)
- modified_input = gmx.modify_input(
- input=initial_input, structure=train.conformation)
- md = gmx.mdrun(input=modified_input, potential=train.training_potential)
- # Alternate syntax to facilitate adding multiple potentials:
- # md.interface.potential.add(train.training_potential)
- brer_tools.training_analyzer(
- label='is_converged',
- params=train.training_potential.output.alpha)
- train.conformation = md.output.conformation
-
- train_loop = gmx.while_loop(
- operation=train,
- condition=gmx.logical_not(train.is_converged))
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2019, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS 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 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS 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 Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-"""Test gmxapi functionality described in roadmap.rst."""
-
-import pytest
-
-import gmxapi as gmx
-from gmxapi.version import has_feature
-
-@pytest.mark.skipif(not has_feature('fr11'),
- reason="Feature level not met.")
-def test_fr11():
- """FR11: Python access to TPR file contents.
-
- * gmx.read_tpr utility provides access to TPR file contents
- * gmx.read_tpr operation produces output consumable by gmx.mdrun
- * gmx.mdrun produces gromacs.read_tpr node for tpr filename kwargs
- """
- simulation_input = gmx.read_tpr(initial_tpr)
- nsteps = simulation_input.params('nsteps')
- md = gmx.mdrun(simulation_input)
- assert md.output.trajectory.step.result() == nsteps
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2019, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS 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 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS 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 Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-"""Test gmxapi functionality described in roadmap.rst."""
-
-import pytest
-
-import gmxapi as gmx
-from gmxapi.version import has_feature
-
-@pytest.mark.skipif(not has_feature('fr12'),
- reason="Feature level not met.")
-def test_fr12():
- """FR12: Simulation checkpoint handling
-
- * gmx.mdrun is properly restartable
-
- This should be invisible to the user, and requires introspection and testing infrastructure to properly test (TBD).
- """
- from gmxapi import testsupport
-
- simulation_input = gmx.read_tpr(initial_tpr)
- md = gmx.mdrun(simulation_input, label='md')
- interrupting_context = testsupport.interrupted_md(md)
- with interrupting_context as session:
- first_half_md = session.md.run()
- md = gmx.mdrun(first_half_md, context=testsupport.inspect)
- testsupport.verify_restart(md)
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2019, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS 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 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS 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 Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-"""Test gmxapi functionality described in roadmap.rst."""
-
-import pytest
-
-import gmxapi as gmx
-from gmxapi.version import has_feature
-
-@pytest.mark.skipif(not has_feature('fr13'),
- reason="Feature level not met.")
-def test_fr13():
- """FR13: ``run`` module function simplifies user experience
-
- * gmx.run finds and runs operations to produce expected output files
- * gmx.run handles ensemble work topologies
- * gmx.run handles multi-process execution
- * gmx.run safety checks to avoid data loss / corruption
- """
- # commandline_operation helper creates a set of operations
- # that includes the discovery and execution of the program
- # named in `executable`.
- md = gmx.mdrun([tprfilename, tprfilename])
- gmx.run()
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2019, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS 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 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS 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 Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-"""Test gmxapi functionality described in roadmap.rst."""
-
-import pytest
-
-import gmxapi as gmx
-from gmxapi.version import has_feature
-
-@pytest.mark.skipif(not has_feature('fr14'),
- reason="Feature level not met.")
-def test_fr14():
- """FR14: Easy access to GROMACS run time parameters
-
- *gmx.run conveys run-time parameters to execution context*
-
- (requires interaction with library development)
-
- TODO: find human readable parameter names to complement short CLI flags.
- """
- gmx.run(work, tmpi=20, grid=gmx.NDArray([3, 3, 2]), ntomp_pme=1, npme=2, ntomp=1)
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2019,2020, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS 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 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS 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 Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-"""Test gmxapi functionality described in roadmap.rst."""
-
-import logging
-
-import pytest
-
-import gmxapi as gmx
-
-# Configure the `logging` module before proceeding any further.
-gmx.logger.setLevel(logging.WARNING)
-
-try:
- from mpi4py import MPI
- rank_number = MPI.COMM_WORLD.Get_rank()
-except ImportError:
- rank_number = 0
- rank_tag = ''
- MPI = None
-else:
- rank_tag = 'rank{}:'.format(rank_number)
-
-# Use this formatter to improve the caplog log records.
-formatter = logging.Formatter(rank_tag + '%(name)s:%(levelname)s: %(message)s')
-
-@pytest.mark.usefixtures('cleandir')
-def test_fr15(spc_water_box, caplog):
- """FR15: Simulation input modification.
-
- * *gmx.modify_input produces new (tpr) simulation input in data flow operation*
- (requires interaction with library development)
- """
- try:
- from mpi4py import MPI
- current_rank = MPI.COMM_WORLD.Get_rank()
- ensemble_size = MPI.COMM_WORLD.Get_size()
- except ImportError:
- current_rank = 0
- ensemble_size = 1
-
- with caplog.at_level(logging.DEBUG):
- caplog.handler.setFormatter(formatter)
- with caplog.at_level(logging.WARNING, 'gmxapi'), \
- caplog.at_level(logging.DEBUG, 'gmxapi.mdrun'), \
- caplog.at_level(logging.DEBUG, 'gmxapi.modify_input'), \
- caplog.at_level(logging.DEBUG, 'gmxapi.read_tpr'), \
- caplog.at_level(logging.DEBUG, 'gmxapi.simulation'):
-
- initial_input = gmx.read_tpr([spc_water_box for _ in range(ensemble_size)])
- parameters = list([{'ld-seed': i} for i in range(ensemble_size)])
- param_sweep = gmx.modify_input(input=initial_input,
- parameters=parameters
- )
- md = gmx.mdrun(param_sweep)
- # TODO: (#3179) Handle ensembles of size 1 more elegantly.
- if md.output.ensemble_width > 1:
- result_list = md.output.parameters['ld-seed'].result()
- else:
- result_list = [md.output.parameters['ld-seed'].result()]
- for expected, actual in zip(parameters, result_list):
- assert expected['ld-seed'] == actual
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2019, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS 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 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS 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 Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-"""Test gmxapi functionality described in roadmap.rst."""
-
-import pytest
-
-import gmxapi as gmx
-from gmxapi.version import has_feature
-
-@pytest.mark.skipif(not has_feature('fr16'),
- reason="Feature level not met.")
-def test_fr16():
- """FR16: Create simulation input from simulation output.
-
- *gmx.make_input handles state from checkpoints*
- (requires interaction with library development)
- """
- initial_input = gmx.read_tpr(tpr_filename)
- md = gmx.mdrun(initial_input)
- stage2_input = gmx.make_input(topology=initial_input,
- conformation=md.output,
- parameters=stage2_params,
- simulation_state=md.output)
- md = gmx.mdrun(stage2_input)
- md.run()
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2019, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS 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 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS 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 Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-"""Test gmxapi functionality described in roadmap.rst."""
-
-import pytest
-
-import gmxapi as gmx
-from gmxapi.version import has_feature
-
-@pytest.mark.skipif(not has_feature('fr17'),
- reason="Feature level not met.")
-def test_fr17():
- """FR17: Prepare simulation input from multiple sources
-
- gmx.write_tpr (a facility used to implement higher-level functionality)
- merges tpr data (e.g. inputrec, structure, topology) into new file(s)
- """
- gmx.fileio.write_tpr(filename=managed_filename, input=stage2_input)
- for key, value in gmx.fileio.read_tpr(managed_filename)['input']:
- assert stage2_input[key] == value
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2019, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS 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 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS 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 Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-"""Test gmxapi functionality described in roadmap.rst."""
-
-import pytest
-
-import gmxapi as gmx
-from gmxapi.version import has_feature
-
-@pytest.mark.skipif(not has_feature('fr18'),
- reason="Feature level not met.")
-def test_fr18():
- """FR18: GROMACS CLI tools receive improved Python-level support over generic commandline_operations
-
- * gmx.tool provides wrapping of unmigrated gmx CLI tools
- """
- rmsf = gmx.tool.rmsf(trajectory=md.output.trajectory,
- structure=initial_tpr)
- output_files = gmx.gather(rmsf.output.file).result()
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2019, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS 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 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS 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 Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-"""Test gmxapi functionality described in roadmap.rst."""
-
-import pytest
-
-import gmxapi as gmx
-from gmxapi.version import has_feature
-
-@pytest.mark.skipif(not has_feature('fr19'),
- reason="Feature level not met.")
-def test_fr19():
- """FR19: GROMACS CLI tools receive improved C++-level support over generic commandline_operations
-
- gmx.tool uses Python bindings on C++ API for CLI modules (not testable at the UI level)
- """
- rmsf = gmx.rmsf(trajectory=md.output.trajectory,
- structure=initial_tpr)
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2019, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS 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 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS 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 Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-"""Test gmxapi functionality described in roadmap.rst."""
-
-import pytest
-
-import gmxapi as gmx
-from gmxapi.version import has_feature
-
-@pytest.mark.skipif(not has_feature('fr20'),
- reason="Feature level not met.")
-def test_fr20():
- """FR20: Python bindings use C++ API for expressing user interface
-
- gmx.tool operations are migrated to updated Options infrastructure
- (requires interaction with library development)
- """
- analysis = gmx.rmsf(trajectory=md.output.trajectory,
- topology=initial_input)
- file_list = gmx.fileio.write_xvg(analysis.output).result()
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2019, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS 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 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS 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 Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-"""Test gmxapi functionality described in roadmap.rst."""
-
-import pytest
-
-import gmxapi as gmx
-from gmxapi.version import has_feature
-
-@pytest.mark.skipif(not has_feature('fr21'),
- reason="Feature level not met.")
-def test_fr21():
- """FR21: User insulated from filesystem paths.
-
- gmx.context manages data placement according to where operations run
- """
- output_files = gmx.gather(rmsf.output.file).result()
- testsupport.verify_unique_xvg_files(output_files)
- # Verify completeness of project sustainability goal in code review.
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2019, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS 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 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS 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 Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-"""Test gmxapi functionality described in roadmap.rst."""
-
-import pytest
-
-import gmxapi as gmx
-from gmxapi.version import has_feature
-
-from pytesthelpers import withmpi_only
-
-@withmpi_only
-@pytest.mark.skipif(not has_feature('fr22'),
- reason="Feature level not met.")
-def test_fr22():
- """FR22: MPI-based ensemble management from Python
-
- gmx.context can own an MPI communicator and run ensembles of simulations.
- """
- from mpi4py import MPI
- comm_world = MPI.COMM_WORLD
-
- group2 = comm_world.Get_group().Incl([0,1])
- ensemble_comm = comm_world.Create_group(group2)
-
- md = gmx.mdrun([tpr_filename for _ in range(2)])
-
- with gmx.get_context(md, communicator=ensemble_comm) as session:
- session.run()
-
- ensemble_comm.Free()
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2019, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS 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 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS 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 Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-"""Test gmxapi functionality described in roadmap.rst."""
-
-import pytest
-
-import gmxapi as gmx
-from gmxapi.version import has_feature
-
-from pytesthelpers import withmpi_only
-
-@withmpi_only
-@pytest.mark.skipif(not has_feature('fr23'),
- reason="Feature level not met.")
-def test_fr23():
- """FR23: Ensemble simulations can themselves use MPI
-
- *GROMACS simulation can use a set of subcommunicators from the comm owned by the client.*
- (requires interaction with library development)
- """
- from mpi4py import MPI
- comm_world = MPI.COMM_WORLD
-
- md = gmx.mdrun([tpr_filename for _ in range(2)])
-
- with gmx.get_context(md, communicator=comm_world) as session:
- session.run()
-
- md = gmx.mdrun([tpr_filename for _ in range(4)])
-
-
- with gmx.get_context(md, communicator=comm_world) as session:
- session.run()
+++ /dev/null
-{
- "datasource": {
- "solvent_topology": "src/testutils/simulationdatabase/spc216.top",
- "solvent_structure": "src/testutils/simulationdatabase/spc216.gro"
- },
- "solvent_topology": [
- "#include \"oplsaa.ff/forcefield.itp\"",
- "",
- "; Include water topology",
- "#include \"oplsaa.ff/tip3p.itp\"",
- "",
- "[ system ]",
- "; Name",
- "spc2",
- "",
- "[ molecules ]",
- "; Compound #mols",
- "SOL 216"
- ],
- "solvent_structure": [
- "216 water molecules",
- " 648",
- " 1SOL OW 1 0.005 0.600 0.244 0.1823 -0.4158 0.4875",
- " 1SOL HW1 2 -0.017 0.690 0.270 -1.7457 -0.5883 -0.4604",
- " 1SOL HW2 3 0.051 0.610 0.161 2.5085 -0.1501 1.7627",
- " 2SOL OW 4 0.155 0.341 0.735 0.6282 0.4390 0.0015",
- " 2SOL HW1 5 0.140 0.284 0.660 -0.3206 0.0700 0.4631",
- " 2SOL HW2 6 0.081 0.402 0.734 -0.1556 -0.4529 1.4404",
- " 3SOL OW 7 1.853 0.500 0.554 0.0780 0.6477 0.1596",
- " 3SOL HW1 8 1.788 0.505 0.484 -0.5409 -1.2601 0.5636",
- " 3SOL HW2 9 1.809 0.533 0.632 -0.0335 0.4430 0.1829",
- " 4SOL OW 10 0.732 1.356 1.314 0.3818 -0.1526 0.0053",
- " 4SOL HW1 11 0.724 1.291 1.245 -0.6376 0.1642 -0.1766",
- " 4SOL HW2 12 0.767 1.434 1.270 0.7292 -0.2888 0.0444",
- " 5SOL OW 13 1.746 1.593 0.575 -0.4779 -0.0868 0.0596",
- " 5SOL HW1 14 1.735 1.666 0.637 0.2545 -0.2925 0.4446",
- " 5SOL HW2 15 1.708 1.518 0.621 1.8857 -0.6672 1.1321",
- " 6SOL OW 16 1.759 0.582 0.800 0.1066 0.3638 0.1453",
- " 6SOL HW1 17 1.673 0.542 0.815 0.2653 -0.5059 -1.2580",
- " 6SOL HW2 18 1.787 0.608 0.888 -0.6999 -1.1652 0.8946",
- " 7SOL OW 19 0.965 0.529 0.941 0.0464 0.6791 -0.5470",
- " 7SOL HW1 20 0.912 0.531 1.020 0.7588 -0.9814 -0.0074",
- " 7SOL HW2 21 0.902 0.533 0.869 -0.5440 3.3012 0.0802",
- " 8SOL OW 22 0.091 0.598 1.836 0.0326 0.2995 0.5048",
- " 8SOL HW1 23 0.091 0.507 1.806 -1.9591 0.6076 -0.4926",
- " 8SOL HW2 24 0.174 0.634 1.804 0.0499 -0.6923 -0.5988",
- " 9SOL OW 25 0.796 1.279 0.780 0.0287 0.9120 0.0338",
- " 9SOL HW1 26 0.731 1.331 0.734 -0.7066 0.7743 0.9173",
- " 9SOL HW2 27 0.799 1.196 0.733 0.1127 1.1975 -0.4621",
- " 10SOL OW 28 0.737 0.813 0.145 -0.2045 -0.2755 -0.1129",
- " 10SOL HW1 29 0.765 0.723 0.130 2.0853 0.6254 -1.4381",
- " 10SOL HW2 30 0.771 0.835 0.231 0.8150 -0.0891 -0.5595",
- " 11SOL OW 31 0.547 1.092 0.477 0.7492 -0.2399 -0.7211",
- " 11SOL HW1 32 0.529 1.089 0.571 -1.6704 -1.5609 -1.1701",
- " 11SOL HW2 33 0.463 1.072 0.436 1.8685 -0.1447 -3.1641",
- " 12SOL OW 34 0.729 1.093 1.672 -0.3320 -0.4160 -0.1770",
- " 12SOL HW1 35 0.781 1.129 1.744 -3.0691 0.8046 1.2710",
- " 12SOL HW2 36 0.762 1.004 1.660 -0.3590 -0.9619 3.2122",
- " 13SOL OW 37 0.570 1.373 1.080 0.5042 -0.2319 -0.2229",
- " 13SOL HW1 38 0.625 1.297 1.099 -1.3369 -1.5288 0.0461",
- " 13SOL HW2 39 0.544 1.361 0.988 -1.9170 -1.3747 0.5551",
- " 14SOL OW 40 1.431 1.407 1.448 -0.0622 0.3206 -0.1113",
- " 14SOL HW1 41 1.471 1.367 1.526 -0.0250 -0.0867 -0.3344",
- " 14SOL HW2 42 1.398 1.332 1.397 -0.3689 0.6034 -0.3325",
- " 15SOL OW 43 0.544 0.321 1.628 0.2713 0.2958 -0.0287",
- " 15SOL HW1 44 0.458 0.278 1.627 0.2912 0.2480 0.2043",
- " 15SOL HW2 45 0.579 0.307 1.540 0.4867 -0.5991 0.1932",
- " 16SOL OW 46 1.482 0.418 0.684 0.2029 0.6095 -0.1120",
- " 16SOL HW1 47 1.396 0.411 0.641 -0.0022 0.9048 0.2426",
- " 16SOL HW2 48 1.490 0.336 0.734 -0.2046 0.9013 0.4457",
- " 17SOL OW 49 0.383 1.854 0.680 -0.5139 0.5358 0.4888",
- " 17SOL HW1 50 0.421 1.821 0.599 0.7665 0.7680 0.9853",
- " 17SOL HW2 51 0.458 1.885 0.731 -1.3106 0.4418 1.7385",
- " 18SOL OW 52 1.132 1.589 1.714 0.2895 -0.1975 -0.0185",
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- ""
- ]
-}
-
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff