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
|
#
# 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.
"""Test gmx.fileio submodule"""
import os
import tempfile
import gmxapi
import pytest
from gmxapi.simulation.fileio import TprFile
from gmxapi.simulation.fileio import read_tpr
from gmxapi.exceptions import UsageError
@pytest.mark.usefixtures("cleandir")
def test_tprfile_read_old(spc_water_box):
tpr_filename = spc_water_box
with pytest.raises(UsageError):
TprFile(tpr_filename, "x")
with pytest.raises(UsageError):
TprFile()
tprfile = TprFile(tpr_filename, "r")
with tprfile as fh:
cpp_object = fh._tprFileHandle
assert cpp_object is not None
params = cpp_object.params().extract()
assert "nsteps" in params
assert "foo" not in params
@pytest.mark.usefixtures("cleandir")
def test_read_tpr(spc_water_box):
tpr_filename = spc_water_box
tpr_source = gmxapi.read_tpr(tpr_filename)
assert "parameters" in tpr_source.output
assert hasattr(tpr_source.output, "parameters")
parameters = tpr_source.output.parameters.result()
assert "nsteps" in parameters
assert "foo" not in parameters
assert parameters["nsteps"] == 2
assert tpr_source.output.parameters["nsteps"].result() == 2
@pytest.mark.usefixtures("cleandir")
def test_write_tpr_file(spc_water_box):
"""Test gmx.fileio.write_tpr_file() using gmx.core API."""
tpr_filename = spc_water_box
additional_steps = 5000
sim_input = read_tpr(tpr_filename)
params = sim_input.parameters.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.parameters.set("nsteps", new_nsteps)
sim_input.parameters.set("dt", new_dt)
_, temp_filename = tempfile.mkstemp(suffix=".tpr")
gmxapi.simulation.fileio.write_tpr_file(temp_filename, input=sim_input)
tprfile = TprFile(temp_filename, "r")
with tprfile as fh:
params = 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)
|
