/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, 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.
// We don't want Python users to create invalid params objects, so don't
// export a constructor until we can default initialize a valid one.
// mdparams.def(py::init());
- mdparams.def("extract",
- [](const GmxMdParams& self) {
- py::dict dictionary;
- for (const auto& key : gmxapicompat::keys(self))
- {
- try
- {
- // TODO: More complete typing and dispatching.
- // This only handles the two types described in the initial implementation.
- // Less trivial types (strings, maps, arrays) warrant additional
- // design discussion before being exposed through an interface
- // like this one.
- // Also reference https://gitlab.com/gromacs/gromacs/-/issues/2993
-
- // We can use templates and/or tag dispatch in a more complete
- // future implementation.
- const auto& paramType = gmxapicompat::mdParamToType(key);
- if (paramType == GmxapiType::FLOAT64)
- {
- dictionary[key.c_str()] = extractParam(self, key, double());
- }
- else if (paramType == GmxapiType::INT64)
- {
- dictionary[key.c_str()] = extractParam(self, key, int64_t());
- }
- }
- catch (const gmxapicompat::ValueError& e)
- {
- throw gmxapi::ProtocolError(std::string("Unknown parameter: ") + key);
- }
- }
- return dictionary;
- },
- "Get a dictionary of the parameters.");
+ mdparams.def(
+ "extract",
+ [](const GmxMdParams& self) {
+ py::dict dictionary;
+ for (const auto& key : gmxapicompat::keys(self))
+ {
+ try
+ {
+ // TODO: More complete typing and dispatching.
+ // This only handles the two types described in the initial implementation.
+ // Less trivial types (strings, maps, arrays) warrant additional
+ // design discussion before being exposed through an interface
+ // like this one.
+ // Also reference https://gitlab.com/gromacs/gromacs/-/issues/2993
+
+ // We can use templates and/or tag dispatch in a more complete
+ // future implementation.
+ const auto& paramType = gmxapicompat::mdParamToType(key);
+ if (paramType == GmxapiType::FLOAT64)
+ {
+ dictionary[key.c_str()] = extractParam(self, key, double());
+ }
+ else if (paramType == GmxapiType::INT64)
+ {
+ dictionary[key.c_str()] = extractParam(self, key, int64_t());
+ }
+ }
+ catch (const gmxapicompat::ValueError& e)
+ {
+ throw gmxapi::ProtocolError(std::string("Unknown parameter: ") + key);
+ }
+ }
+ return dictionary;
+ },
+ "Get a dictionary of the parameters.");
// Overload a setter for each known type and None
- mdparams.def("set",
- [](GmxMdParams* self, const std::string& key, int64_t value) {
- gmxapicompat::setParam(self, key, value);
- },
- py::arg("key").none(false),
- py::arg("value").none(false),
- "Use a dictionary to update simulation parameters.");
- mdparams.def("set",
- [](GmxMdParams* self, const std::string& key, double value) {
- gmxapicompat::setParam(self, key, value);
- },
- py::arg("key").none(false),
- py::arg("value").none(false),
- "Use a dictionary to update simulation parameters.");
- mdparams.def("set",
- [](GmxMdParams* self, const std::string& key, py::none) {
- // unsetParam(self, key);
- },
- py::arg("key").none(false),
- py::arg("value"),
- "Use a dictionary to update simulation parameters.");
+ mdparams.def(
+ "set",
+ [](GmxMdParams* self, const std::string& key, int64_t value) {
+ gmxapicompat::setParam(self, key, value);
+ },
+ py::arg("key").none(false),
+ py::arg("value").none(false),
+ "Use a dictionary to update simulation parameters.");
+ mdparams.def(
+ "set",
+ [](GmxMdParams* self, const std::string& key, double value) {
+ gmxapicompat::setParam(self, key, value);
+ },
+ py::arg("key").none(false),
+ py::arg("value").none(false),
+ "Use a dictionary to update simulation parameters.");
+ mdparams.def(
+ "set",
+ [](GmxMdParams* self, const std::string& key, py::none) {
+ // unsetParam(self, key);
+ },
+ py::arg("key").none(false),
+ py::arg("value"),
+ "Use a dictionary to update simulation parameters.");
py::class_<TprReadHandle> tprfile(module, "TprFile");
py::arg("filename"),
"Get a handle to a TPR file resource for a given file name.");
- module.def("write_tprfile",
- [](std::string filename, const GmxMdParams& parameterObject) {
- auto tprReadHandle = gmxapicompat::getSourceFileHandle(parameterObject);
- auto params = gmxapicompat::getMdParams(tprReadHandle);
- auto structure = gmxapicompat::getStructureSource(tprReadHandle);
- auto state = gmxapicompat::getSimulationState(tprReadHandle);
- auto topology = gmxapicompat::getTopologySource(tprReadHandle);
- gmxapicompat::writeTprFile(filename, *params, *structure, *state, *topology);
- },
- py::arg("filename").none(false),
- py::arg("parameters"),
- "Write a new TPR file with the provided data.");
-
- module.def("copy_tprfile",
- [](const gmxapicompat::TprReadHandle& input, std::string outFile) {
- return gmxapicompat::copy_tprfile(input, outFile);
- },
- py::arg("source"),
- py::arg("destination"),
- "Copy a TPR file from ``source`` to ``destination``.");
-
- module.def("rewrite_tprfile",
- [](std::string input, std::string output, double end_time) {
- return gmxapicompat::rewrite_tprfile(input, output, end_time);
- },
- py::arg("source"),
- py::arg("destination"),
- py::arg("end_time"),
- "Copy a TPR file from ``source`` to ``destination``, replacing `nsteps` with "
- "``end_time``.");
+ module.def(
+ "write_tprfile",
+ [](std::string filename, const GmxMdParams& parameterObject) {
+ auto tprReadHandle = gmxapicompat::getSourceFileHandle(parameterObject);
+ auto params = gmxapicompat::getMdParams(tprReadHandle);
+ auto structure = gmxapicompat::getStructureSource(tprReadHandle);
+ auto state = gmxapicompat::getSimulationState(tprReadHandle);
+ auto topology = gmxapicompat::getTopologySource(tprReadHandle);
+ gmxapicompat::writeTprFile(filename, *params, *structure, *state, *topology);
+ },
+ py::arg("filename").none(false),
+ py::arg("parameters"),
+ "Write a new TPR file with the provided data.");
+
+ module.def(
+ "copy_tprfile",
+ [](const gmxapicompat::TprReadHandle& input, std::string outFile) {
+ return gmxapicompat::copy_tprfile(input, outFile);
+ },
+ py::arg("source"),
+ py::arg("destination"),
+ "Copy a TPR file from ``source`` to ``destination``.");
+
+ module.def(
+ "rewrite_tprfile",
+ [](std::string input, std::string output, double end_time) {
+ return gmxapicompat::rewrite_tprfile(input, output, end_time);
+ },
+ py::arg("source"),
+ py::arg("destination"),
+ py::arg("end_time"),
+ "Copy a TPR file from ``source`` to ``destination``, replacing `nsteps` with "
+ "``end_time``.");
}
} // end namespace gmxpy
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2019,2020,2021, 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.
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.
+
+@pytest.fixture(scope='session')
+def spc_water_box_collection(gmxcli, remove_tempdir):
+ """Provide a collection of simulation input items for a simple simulation.
Prepare the MD input in a freshly created working directory.
+ Solvate a 5nm cubic box with spc water. Return a dictionary of the artifacts produced.
"""
import gmxapi as gmx
# TODO: Remove this import when the the spc_water_box fixture is migrated to gmxapi.testsupport
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.
+ dt = 2. ** -9.
mdp_input = [('integrator', 'md'),
('dt', dt),
('cutoff-scheme', 'Verlet'),
# TODO: more inspection of grompp errors...
assert os.path.exists(tprfilename)
- yield tprfilename
+ collection = {
+ 'tpr_filename': tprfilename,
+ 'mdp_input_filename': mdpfile,
+ 'mdp_output_filename': mdout_mdp,
+ 'topology_filename': solvate.output.file['-p'].result(),
+ 'gro_filename': solvate.output.file['-o'].result(),
+ 'mdp_input_list': mdp_input
+ }
+ yield collection
+
+
+@pytest.fixture(scope='session')
+def spc_water_box(spc_water_box_collection):
+ """Provide a TPR input file for a simple simulation."""
+ yield spc_water_box_collection['tpr_filename']
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2019, by the GROMACS development team, led by
+# Copyright (c) 2019,2021, 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.
assert tpr_source.output.parameters['nsteps'].result() == 2
-@pytest.mark.usefixtures('cleandir')
-def test_core_tprcopy_alt(spc_water_box):
- """Test gmx.core.copy_tprfile() for update of end_time.
-
- Set a new end time that is 5000 steps later than the original. Read dt
- from file to avoid floating point round-off errors.
-
- Transitively test gmx.fileio.read_tpr()
- """
- tpr_filename = spc_water_box
- additional_steps = 5000
- sim_input = read_tpr(tpr_filename)
- params = sim_input.parameters.extract()
- dt = params['dt']
- nsteps = params['nsteps']
- init_step = params['init-step']
- initial_endtime = (init_step + nsteps) * dt
- new_endtime = initial_endtime + additional_steps*dt
- _, temp_filename = tempfile.mkstemp(suffix='.tpr')
- gmxapi._gmxapi.rewrite_tprfile(source=tpr_filename, destination=temp_filename, end_time=new_endtime)
- tprfile = TprFile(temp_filename, 'r')
- with tprfile as fh:
- params = read_tpr(fh).parameters.extract()
- dt = params['dt']
- nsteps = params['nsteps']
- init_step = params['init-step']
- assert (init_step + nsteps) * dt == new_endtime
-
- os.unlink(temp_filename)
-
-
@pytest.mark.usefixtures('cleandir')
def test_write_tpr_file(spc_water_box):
"""Test gmx.fileio.write_tpr_file() using gmx.core API.
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2021, 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._gmxapi file I/O routines."""
+import os
+import tempfile
+
+import pytest
+import gmxapi
+import gmxapi.simulation.fileio
+from gmxapi import _gmxapi
+
+
+@pytest.mark.usefixtures('cleandir')
+def test_core_read_tpr(spc_water_box):
+ tpr_filehandle: _gmxapi.TprFile = _gmxapi.read_tprfile(os.fsencode(spc_water_box))
+ parameters: _gmxapi.SimulationParameters = tpr_filehandle.params()
+ assert 'nsteps' in parameters.extract()
+ assert 'foo' not in parameters.extract()
+ assert parameters.extract()['nsteps'] == 2
+
+
+@pytest.mark.usefixtures('cleandir')
+def test_core_rewrite_tprfile(spc_water_box):
+ """Test _gmxapi.rewrite_tprfile for update of end_time.
+
+ Set a new end time that is 5000 steps later than the original. Read dt
+ from file to avoid floating point round-off errors.
+
+ Transitively test gmx.fileio.read_tpr()
+ """
+ tpr_filename = spc_water_box
+ additional_steps = 5000
+ tpr_filehandle: _gmxapi.TprFile = _gmxapi.read_tprfile(os.fsencode(spc_water_box))
+ params = tpr_filehandle.params().extract()
+ dt = params['dt']
+ nsteps = params['nsteps']
+ init_step = params['init-step']
+ initial_endtime = (init_step + nsteps) * dt
+ new_endtime = initial_endtime + additional_steps * dt
+ _, temp_filename = tempfile.mkstemp(suffix='.tpr')
+ _gmxapi.rewrite_tprfile(source=tpr_filename, destination=temp_filename, end_time=new_endtime)
+ tprfile = gmxapi.simulation.fileio.TprFile(temp_filename, 'r')
+ with tprfile as fh:
+ params = gmxapi.simulation.fileio.read_tpr(fh).parameters.extract()
+ dt = params['dt']
+ nsteps = params['nsteps']
+ init_step = params['init-step']
+ assert (init_step + nsteps) * dt == new_endtime
+
+ os.unlink(temp_filename)
+
+
+@pytest.mark.usefixtures('cleandir')
+def test_core_read_and_write_tpr_file(spc_water_box):
+ """Test gmx.fileio.write_tpr_file() using gmx.core API.
+ """
+ additional_steps = 5000
+
+ tpr_filehandle: _gmxapi.TprFile = _gmxapi.read_tprfile(os.fsencode(spc_water_box))
+ sim_input: _gmxapi.SimulationParameters = tpr_filehandle.params()
+ params: dict = sim_input.extract()
+ nsteps = params['nsteps']
+ init_step = params['init-step']
+
+ # Choose a new nsteps to check integer parameter setting.
+ new_nsteps = init_step + additional_steps
+ # Choose a new dt to check floating point parameter setting
+ new_dt = params['dt'] * 2.
+
+ sim_input.set('nsteps', new_nsteps)
+ sim_input.set('dt', new_dt)
+
+ _, temp_filename = tempfile.mkstemp(suffix='.tpr')
+ _gmxapi.write_tprfile(temp_filename, sim_input)
+
+ tprfile = gmxapi.simulation.fileio.TprFile(temp_filename, 'r')
+ with tprfile as fh:
+ params = gmxapi.simulation.fileio.read_tpr(fh).parameters.extract()
+ # Note that we have chosen an exactly representable dt for spc_water_box.
+ # Otherwise, we would have to use pytest.approx with a suitable tolerance.
+ assert params['dt'] == new_dt
+ assert params['nsteps'] != nsteps
+ assert params['nsteps'] == new_nsteps
+
+ os.unlink(temp_filename)
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff