def run(self, force=False, **gmxargs):
"""Analyze trajectory and write energy files.
:Arguments:
- *force*: do analysis and overwrite existing files
- *gmxargs*: additional keyword arguments for :func:`gromacs.g_energy`
"""
if not self.check_file_exists(self.parameters.filenames['Energy'], resolve='warning') or force:
logger.info("Analyzing energy file...")
gromacs.g_energy(s=self.simulation.tpr, f=self.simulation.edr,
o=self.parameters.filenames['Energy'],
input=self.terms + [0], **gmxargs)
def run(self, force=False, **gmxargs):
"""Analyze trajectory and write energy files.
:Arguments:
- *force*: do analysis and overwrite existing files
- *gmxargs*: additional keyword arguments for :func:`gromacs.g_energy`
"""
if not self.check_file_exists(self.parameters.filenames['Energy'], resolve='warning') or force:
logger.info("Analyzing energy file...")
gromacs.g_energy(s=self.simulation.tpr, f=self.simulation.edr,
o=self.parameters.filenames['Energy'],
input=self.terms + [0], **gmxargs)
def rerun_energy(s, o, prefix):
e = prefix + '.edr'
rc, output, junk = gromacs.mdrun(v=True, s=s, rerun=o, e=e, stdout=False, stderr=False)
assert rc == 0, "mdrun failed"
xvg = prefix + '.xvg'
rc, output, junk = gromacs.g_energy(f=e, o=xvg,
input=("Proper-Dih.", "Improper-Dih.", "CMAP-Dih.",
"LJ-14", "Coulomb-14", "LJ-(SR)", "Coulomb-(SR)",
"Coul.-recip.", "Potential"), stdout=False, stderr=False)
assert rc == 0, "g_energy failed"
return XVG(xvg).to_df()
def rerun_energy(s, o, prefix):
e = prefix + '.edr'
rc, output, junk = gromacs.mdrun(v=True,
s=s,
rerun=o,
e=e,
stdout=False,
stderr=False)
assert rc == 0, "mdrun failed"
xvg = prefix + '.xvg'
rc, output, junk = gromacs.g_energy(
f=e,
o=xvg,
input=("Proper-Dih.", "Improper-Dih.", "CMAP-Dih.", "LJ-14",
"Coulomb-14", "LJ-(SR)", "Coulomb-(SR)", "Coul.-recip.",
"Potential"),
stdout=False,
stderr=False)
assert rc == 0, "g_energy failed"
return XVG(xvg).to_df()
def get_observables(edr, observables=None, **kwargs):
"""Run :program:`g_energy` to get thermodynamic averages.
:Arguments:
*edr*
Gromacs energy file
*observables*
list of energy (thermodynamic) averages to be computed;
the default (for ``None``) is ::
["Pressure", "Volume", "Density", "Temperature"]
*kwargs*
other keywords are passed to
:class:`gromacs.tools.G_energy`; for instance, *b* sets
the start time (in ps) and *o* sets the output file name
:Returns: :class:`~numpy.core.records.recarray` with the
observable name in the first column ("*Energy*") and
subsequent columns containing the exact averages
produced by :program:`g_energy`.
"""
if observables is None:
observables = ["Pressure", "Volume", "Density", "Temperature"]
logger.info("Analyzing observables %(observables)r in energy file %(edr)r...", vars())
kwargs['input'] = observables
kwargs['f'] = edr
kwargs['stdout'] = False # required for processing
kwargs['stderr'] = False # suppress stderr
fd, kwargs['o'] = tempfile.mkstemp(suffix=".xvg")
try:
rc, data, stderr = gromacs.g_energy(**kwargs)
if rc != 0:
logger.error("g_energy failed")
raise GromacsError("g_energy failed --- see output below:\n\n" + stderr + data)
finally:
unlink_gmx(kwargs['o'])
return parse_energy(data)
