1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
|
#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright 2019- 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.
"""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, tmp_path_factory):
"""Provide a TPR input file for a simple simulation.
Prepare the MD input in a freshly created working directory.
"""
import gmxapi.runtime
from gmxapi.testsupport import scoped_chdir
# 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 scoped_chdir(tmp_path_factory.mktemp("spc_water_box")) 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)
assert gmxapi.version.api_is_at_least(0, 3, 1)
solvate = gmxapi.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.stderr.result())
raise RuntimeError("solvate failed in spc_water_box testing fixture.")
# Choose an exactly representable dt of 2^-9 ps (approximately 0.002)
dt = 2.0**-9.0
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 = gmxapi.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.stderr.result())
raise RuntimeError("grompp failed in spc_water_box testing fixture.")
# TODO: more inspection of grompp errors...
assert os.path.exists(tprfilename)
yield tprfilename
|
