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""" test run for gromacs calculator """
import pytest
from ase.calculators.gromacs import parse_gromacs_version, get_gromacs_version
sample_header = """\
blahblah...
Command line:
gmx --version
GROMACS version: 2020.1-Ubuntu-2020.1-1
Precision: single
blahblah...
"""
def test_parse_gromacs_version():
assert parse_gromacs_version(sample_header) == '2020.1-Ubuntu-2020.1-1'
@pytest.mark.calculator('gromacs')
def test_get_gromacs_version(factory):
exe = factory.factory.executable
# XXX Can we do this in a different way?
version = get_gromacs_version(exe)
# Hmm. Version could be any string.
assert isinstance(version, str) and len(version) > 0
data = """HISE for testing
20
3HISE N 1 1.966 1.938 1.722
3HISE H1 2 2.053 1.892 1.711
3HISE H2 3 1.893 1.882 1.683
3HISE H3 4 1.969 2.026 1.675
3HISE CA 5 1.939 1.960 1.866
3HISE HA 6 1.934 1.869 1.907
3HISE CB 7 2.055 2.041 1.927
3HISE HB1 8 2.141 2.007 1.890
3HISE HB2 9 2.043 2.137 1.903
3HISE ND1 10 1.962 2.069 2.161
3HISE CG 11 2.065 2.032 2.077
3HISE CE1 12 2.000 2.050 2.287
3HISE HE1 13 1.944 2.069 2.368
3HISE NE2 14 2.123 2.004 2.287
3HISE HE2 15 2.177 1.981 2.369
3HISE CD2 16 2.166 1.991 2.157
3HISE HD2 17 2.256 1.958 2.128
3HISE C 18 1.806 2.032 1.888
3HISE OT1 19 1.736 2.000 1.987
3HISE OT2 20 1.770 2.057 2.016
4.00000 4.00000 4.00000"""
@pytest.mark.calculator_lite
@pytest.mark.calculator('gromacs')
def test_gromacs(factory):
GRO_INIT_FILE = 'hise_box.gro'
# write structure file
with open(GRO_INIT_FILE, 'w') as outfile:
outfile.write(data)
calc = factory.calc(
force_field='charmm27',
define='-DFLEXIBLE',
integrator='cg',
nsteps='10000',
nstfout='10',
nstlog='10',
nstenergy='10',
nstlist='10',
ns_type='grid',
pbc='xyz',
rlist='0.7',
coulombtype='PME-Switch',
rcoulomb='0.6',
vdwtype='shift',
rvdw='0.6',
rvdw_switch='0.55',
DispCorr='Ener')
calc.set_own_params_runs(
'init_structure', GRO_INIT_FILE)
calc.generate_topology_and_g96file()
calc.write_input()
calc.generate_gromacs_run_file()
calc.run()
atoms = calc.get_atoms()
final_energy = calc.get_potential_energy(atoms)
# e.g., -4.17570101 eV = -402.893902 kJ / mol by Gromacs 2019.1 double precision
final_energy_ref = -4.175
tolerance = 0.010
assert abs(final_energy - final_energy_ref) < tolerance
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