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#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright 2021- The GROMACS Authors
# and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
# Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
#
# 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
# https://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 https://www.gromacs.org.
#
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out https://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"] * 2.0
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)
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