def energies(top, gro, mdp, gmx_path=GMX_PATH, grosuff='', grompp_check=False):
"""Compute single-point energies using GROMACS.
Args:
top (str):
gro (str):
mdp (str):
gmx_path (str):
grosuff (str):
grompp_check (bool):
Returns:
e_out:
ener_xvg:
"""
if not os.path.isfile(mdp):
logger.error("Can't find mdp file %s to compute energies" % (mdp))
mdp = os.path.abspath(mdp)
directory, _ = os.path.split(os.path.abspath(top))
tpr = os.path.join(directory, 'topol.tpr')
ener = os.path.join(directory, 'ener.edr')
ener_xvg = os.path.join(directory, 'energy.xvg')
conf = os.path.join(directory, 'confout.gro')
mdout = os.path.join(directory, 'mdout.mdp')
state = os.path.join(directory, 'state.cpt')
traj = os.path.join(directory, 'traj.trr')
log = os.path.join(directory, 'md.log')
stdout_path = os.path.join(directory, 'gromacs_stdout.txt')
stderr_path = os.path.join(directory, 'gromacs_stderr.txt')
grompp_bin, mdrun_bin, genergy_bin = binaries(gmx_path, grosuff)
# Run grompp.
grompp_bin.extend(['-f', mdp, '-c', gro, '-p', top, '-o', tpr, '-po', mdout, '-maxwarn', '5'])
proc = run_subprocess(grompp_bin, 'gromacs', stdout_path, stderr_path)
if proc.returncode != 0:
logger.error('grompp failed. See %s' % stderr_path)
# Run single-point calculation with mdrun.
mdrun_bin.extend(['-nt', '1', '-s', tpr, '-o', traj, '-cpo', state, '-c', conf, '-e', ener, '-g', log])
proc = run_subprocess(mdrun_bin, 'gromacs', stdout_path, stderr_path)
if proc.returncode != 0:
logger.error('mdrun failed. See %s' % stderr_path)
# Extract energies using g_energy
select = " ".join(map(str, range(1, 20))) + " 0 "
genergy_bin.extend(['-f', ener, '-o', ener_xvg, '-dp'])
proc = run_subprocess(genergy_bin, 'gromacs', stdout_path, stderr_path, stdin=select)
if proc.returncode != 0:
logger.error('g_energy failed. See %s' % stderr_path)
return _group_energy_terms(ener_xvg)
def energies(top, gro, mdp, gmx_path=GMX_PATH, grosuff='', grompp_check=False):
"""Compute single-point energies using GROMACS.
Args:
top (str):
gro (str):
mdp (str):
gmx_path (str):
grosuff (str):
grompp_check (bool):
Returns:
e_out:
ener_xvg:
"""
if not os.path.isfile(mdp):
logger.error("Can't find mdp file %s to compute energies" % (mdp))
mdp = os.path.abspath(mdp)
directory, _ = os.path.split(os.path.abspath(top))
tpr = os.path.join(directory, 'topol.tpr')
ener = os.path.join(directory, 'ener.edr')
ener_xvg = os.path.join(directory, 'energy.xvg')
conf = os.path.join(directory, 'confout.gro')
mdout = os.path.join(directory, 'mdout.mdp')
state = os.path.join(directory, 'state.cpt')
traj = os.path.join(directory, 'traj.trr')
log = os.path.join(directory, 'md.log')
stdout_path = os.path.join(directory, 'gromacs_stdout.txt')
stderr_path = os.path.join(directory, 'gromacs_stderr.txt')
grompp_bin, mdrun_bin, genergy_bin = binaries(gmx_path, grosuff)
# Run grompp.
grompp_bin.extend(['-f', mdp, '-c', gro, '-p', top, '-o', tpr, '-po', mdout, '-maxwarn', '5'])
proc = run_subprocess(grompp_bin, 'gromacs', stdout_path, stderr_path)
if proc.returncode != 0:
logger.error('grompp failed. See %s' % stderr_path)
# Run single-point calculation with mdrun.
mdrun_bin.extend(['-nt', '1', '-s', tpr, '-o', traj, '-cpo', state, '-c', conf, '-e', ener, '-g', log])
proc = run_subprocess(mdrun_bin, 'gromacs', stdout_path, stderr_path)
if proc.returncode != 0:
logger.error('mdrun failed. See %s' % stderr_path)
# Extract energies using g_energy
select = " ".join(map(str, range(1, 20))) + " 0 "
genergy_bin.extend(['-f', ener, '-o', ener_xvg, '-dp'])
proc = run_subprocess(genergy_bin, 'gromacs', stdout_path, stderr_path, stdin=select)
if proc.returncode != 0:
logger.error('g_energy failed. See %s' % stderr_path)
return _group_energy_terms(ener_xvg)
def amber_energies(prmtop, crd, input, amb_path):
"""Compute single-point energies using AMBER.
Args:
prmtop (str):
crd (str):
input (str)
amb_path (str):
Returns:
e_out:
ener_xvg:
"""
logger.info('Evaluating energy of {0}'.format(crd))
directory, _ = os.path.split(os.path.abspath(prmtop))
if not prmtop:
prmtop = os.path.join(directory, 'parm.prmtop')
if not crd:
crd = os.path.join(directory, 'ener.edr')
mdout = os.path.join(directory, 'amber.out')
stdout_path = os.path.join(directory, 'amber_stdout.txt')
stderr_path = os.path.join(directory, 'amber_stderr.txt')
# did they give a path, or the name of the file?
islastbin = os.path.basename(os.path.normpath(amb_path))
if islastbin == 'sander':
amber_bin = amb_path
else:
amber_bin = os.path.join(amb_path, 'sander')
if not which(amber_bin):
raise IOError('Unable to find AMBER executable (sander).')
# run sander
cmd = [amber_bin, '-i', input, '-c', crd, '-p', prmtop, '-o', mdout, '-O']
proc = run_subprocess(cmd, 'amber', stdout_path, stderr_path)
if proc.returncode != 0:
logger.error('sander failed. See %s' % stderr_path)
# Extract energies from amber output
return _group_energy_terms(mdout)
def amber_energies(prmtop, crd, input, amb_path):
"""Compute single-point energies using AMBER.
Args:
prmtop (str):
crd (str):
input (str)
amb_path (str):
Returns:
e_out:
ener_xvg:
"""
logger.info("Evaluating energy of {0}".format(crd))
directory, _ = os.path.split(os.path.abspath(prmtop))
if not prmtop:
prmtop = os.path.join(directory, "parm.prmtop")
if not crd:
crd = os.path.join(directory, "ener.edr")
mdout = os.path.join(directory, "amber.out")
stdout_path = os.path.join(directory, "amber_stdout.txt")
stderr_path = os.path.join(directory, "amber_stderr.txt")
# did they give a path, or the name of the file?
islastbin = os.path.basename(os.path.normpath(amb_path))
if islastbin == "sander":
amber_bin = amb_path
else:
amber_bin = os.path.join(amb_path, "sander")
if not which(amber_bin):
raise IOError("Unable to find AMBER executable (sander).")
# run sander
cmd = [amber_bin, "-i", input, "-c", crd, "-p", prmtop, "-o", mdout, "-O"]
proc = run_subprocess(cmd, "amber", stdout_path, stderr_path)
if proc.returncode != 0:
logger.error("sander failed. See %s" % stderr_path)
# Extract energies from amber output
return _group_energy_terms(mdout)
def energies(inpfile, crm_path):
"""Compute single-point energies using CHARMM.
Args:
inpfile (str)
crm_path (str):
Returns:
e_out:
ener_xvg:
"""
logger.info('Evaluating energy of {0}'.format(inpfile))
# find the directory the input file is in.
directory, _ = os.path.split(os.path.abspath(inpfile))
# create files for output
stdout_path = os.path.join(directory, 'charmm_stdout.txt')
stderr_path = os.path.join(directory, 'charmm_stderr.txt')
# delete previous stdout and stderr
if os.path.isfile(stdout_path):
os.remove(stdout_path)
if os.path.isfile(stderr_path):
os.remove(stderr_path)
if not which(crm_path):
raise IOError('Unable to find CHARMM executable (charmm).')
if os.path.isdir(crm_path):
charmm_bin = os.path.join(crm_path, 'charmm')
else:
charmm_bin = crm_path
# run charmm - this assumes all files required in the input file are present
cmd = [charmm_bin, '-i', inpfile]
proc = run_subprocess(cmd, 'charmm', stdout_path, stderr_path)
if proc.returncode != 0:
logger.error('charmm failed. See %s' % stderr_path)
# Extract energies from charmm output
return _group_energy_terms(stdout_path)
def charmm_energies(inpfile, crm_path):
"""Compute single-point energies using CHARMM.
Args:
inpfile (str)
crm_path (str):
Returns:
e_out:
ener_xvg:
"""
logger.info('Evaluating energy of {0}'.format(inpfile))
# find the directory the input file is in.
directory, _ = os.path.split(os.path.abspath(inpfile))
# create files for output
stdout_path = os.path.join(directory, 'charmm_stdout.txt')
stderr_path = os.path.join(directory, 'charmm_stderr.txt')
# delete previous stdout and stderr
if os.path.isfile(stdout_path):
os.remove(stdout_path)
if os.path.isfile(stderr_path):
os.remove(stderr_path)
if not which(crm_path):
raise IOError('Unable to find CHARMM executable (charmm).')
if os.path.isdir(crm_path):
charmm_bin = os.path.join(crm_path, 'charmm')
else:
charmm_bin = crm_path
# run charmm - this assumes all files required in the input file are present
cmd = [charmm_bin, '-i', inpfile]
proc = run_subprocess(cmd, 'charmm', stdout_path, stderr_path)
if proc.returncode != 0:
logger.error('charmm failed. See %s' % stderr_path)
# Extract energies from charmm output
return _group_energy_terms(stdout_path)
def energies(prmtop, crd, input, amb_path):
"""Compute single-point energies using AMBER.
Args:
prmtop (str):
crd (str):
input (str)
amb_path (str):
Returns:
e_out:
ener_xvg:
"""
logger.info('Evaluating energy of {0}'.format(crd))
directory, _ = os.path.split(os.path.abspath(prmtop))
if not prmtop:
prmtop = os.path.join(directory, 'parm.prmtop')
if not crd:
crd = os.path.join(directory, 'ener.edr')
mdout = os.path.join(directory, 'amber.out')
stdout_path = os.path.join(directory, 'amber_stdout.txt')
stderr_path = os.path.join(directory, 'amber_stderr.txt')
# Did they give a path, or the name of the file?
islastbin = os.path.basename(os.path.normpath(amb_path))
if islastbin == 'sander':
amber_bin = amb_path
else:
amber_bin = os.path.join(amb_path, 'sander')
if not which(amber_bin):
raise IOError('Unable to find AMBER executable (sander).')
# Run sander.
cmd = [amber_bin, '-i', input, '-c', crd, '-p', prmtop, '-o', mdout, '-O']
proc = run_subprocess(cmd, 'amber', stdout_path, stderr_path)
if proc.returncode != 0:
logger.error('sander failed. See %s' % stderr_path)
return _group_energy_terms(mdout)
def energies(input_file, lmp_path=None):
"""Evaluate energies of LAMMPS files
Args:
input_file = path to input file (expects data file in same folder)
lmp_path = path to LAMMPS binaries
"""
if lmp_path is None and LMP_PATH is not None:
lmp_path = LMP_PATH
elif LMP_PATH is None:
raise IOError('Unable to find LAMMPS executables.')
logger.info('Evaluating energy of {0}'.format(input_file))
directory, input_file = os.path.split(os.path.abspath(input_file))
stdout_path = os.path.join(directory, 'lammps_stdout.txt')
stderr_path = os.path.join(directory, 'lammps_stderr.txt')
# TODO: Read energy info from stdout in memory instead of from log files.
try:
os.remove(stdout_path)
except FileNotFoundError:
pass
try:
os.remove(stderr_path)
except FileNotFoundError:
pass
# Step into the directory.
saved_path = os.getcwd()
os.chdir(directory)
cmd = [lmp_path, '-in', input_file]
proc = run_subprocess(cmd, 'lammps', stdout_path, stderr_path)
if proc.returncode != 0:
logger.error('LAMMPS failed. See %s/lammps_stderr.txt' % directory)
# Step back out.
os.chdir(saved_path)
return _group_energy_terms(stdout_path)
def energies(input_file, lmp_path=None):
"""Evaluate energies of LAMMPS files
Args:
input_file = path to input file (expects data file in same folder)
lmp_path = path to LAMMPS binaries
"""
if lmp_path is None:
lmp_path = LMP_PATH
logger.info('Evaluating energy of {0}'.format(input_file))
directory, input_file = os.path.split(os.path.abspath(input_file))
stdout_path = os.path.join(directory, 'lammps_stdout.txt')
stderr_path = os.path.join(directory, 'lammps_stderr.txt')
# TODO: Read energy info from stdout in memory instead of from log files.
try:
os.remove(stdout_path)
except FileNotFoundError:
pass
try:
os.remove(stderr_path)
except FileNotFoundError:
pass
# Step into the directory.
saved_path = os.getcwd()
os.chdir(directory)
cmd = [lmp_path, '-in', input_file]
proc = run_subprocess(cmd, 'lammps', stdout_path, stderr_path)
if proc.returncode != 0:
logger.error('LAMMPS failed. See %s/lammps_stderr.txt' % directory)
# Step back out.
os.chdir(saved_path)
return _group_energy_terms(stdout_path)