def run_simulation(self, label, liq, AGrad=True):
"""
Submit a simulation to the Work Queue or run it locally.
Inputs:
label = The name of the molecule (and hopefully the folder name that you're running in)
liq = True/false flag indicating whether to run in liquid or gas phase
"""
wq = getWorkQueue()
# Create a dictionary of MD options that the script will read.
md_opts = OrderedDict()
md_opts['temperature'] = self.hfe_temperature
md_opts['pressure'] = self.hfe_pressure
md_opts['minimize'] = True
if liq:
sdnm = 'liq'
md_opts['nequil'] = self.liquid_eq_steps
md_opts['nsteps'] = self.liquid_md_steps
md_opts['timestep'] = self.liquid_timestep
md_opts['sample'] = self.liquid_interval
else:
sdnm = 'gas'
md_opts['nequil'] = self.gas_eq_steps
md_opts['nsteps'] = self.gas_md_steps
md_opts['timestep'] = self.gas_timestep
md_opts['sample'] = self.gas_interval
eng_opts = deepcopy(self.engine_opts)
# Enforce implicit solvent in the liquid simulation.
# We need to be more careful with this when running explicit solvent.
eng_opts['implicit_solvent'] = liq
eng_opts['coords'] = os.path.basename(self.molecules[label])
if not os.path.exists(sdnm):
os.makedirs(sdnm)
os.chdir(sdnm)
if not os.path.exists('md_result.p'):
# Link in a bunch of files... what were these again?
link_dir_contents(os.path.join(self.root,self.rundir),os.getcwd())
# Link in the scripts required to run the simulation
for f in self.scripts:
LinkFile(os.path.join(os.path.split(__file__)[0],"data",f),os.path.join(os.getcwd(),f))
# Link in the coordinate file.
LinkFile(self.molecules[label], './%s' % os.path.basename(self.molecules[label]))
# Store names of previous trajectory files.
self.last_traj += [os.path.join(os.getcwd(), i) for i in self.extra_output]
# Write target, engine and simulation options to disk.
lp_dump((self.OptionDict, eng_opts, md_opts), 'simulation.p')
# Execute the script for running molecular dynamics.
cmdstr = '%s python md_ism_hfe.py %s' % (self.prefix, "-g" if AGrad else "")
if wq == None:
logger.info("Running condensed phase simulation locally.\n")
logger.info("You may tail -f %s/npt.out in another terminal window\n" % os.getcwd())
_exec(cmdstr, copy_stderr=True, outfnm='md.out')
else:
queue_up(wq, command = cmdstr+' &> md.out', tag='%s:%s/%s' % (self.name, label, "liq" if liq else "gas"),
input_files = self.scripts + ['simulation.p', 'forcefield.p', os.path.basename(self.molecules[label])],
output_files = ['md_result.p', 'md.out'] + self.extra_output, tgt=self, verbose=False, print_time=3600)
os.chdir('..')
def run_simulation(self, label, liq, AGrad=True):
"""
Submit a simulation to the Work Queue or run it locally.
Inputs:
label = The name of the molecule (and hopefully the folder name that you're running in)
liq = True/false flag indicating whether to run in liquid or gas phase
"""
wq = getWorkQueue()
# Create a dictionary of MD options that the script will read.
md_opts = OrderedDict()
md_opts['temperature'] = self.hfe_temperature
md_opts['pressure'] = self.hfe_pressure
md_opts['minimize'] = True
if liq:
sdnm = 'liq'
md_opts['nequil'] = self.liquid_eq_steps
md_opts['nsteps'] = self.liquid_md_steps
md_opts['timestep'] = self.liquid_timestep
md_opts['sample'] = self.liquid_interval
else:
sdnm = 'gas'
md_opts['nequil'] = self.gas_eq_steps
md_opts['nsteps'] = self.gas_md_steps
md_opts['timestep'] = self.gas_timestep
md_opts['sample'] = self.gas_interval
eng_opts = deepcopy(self.engine_opts)
# Enforce implicit solvent in the liquid simulation.
# We need to be more careful with this when running explicit solvent.
eng_opts['implicit_solvent'] = liq
eng_opts['coords'] = os.path.basename(self.molecules[label])
if not os.path.exists(sdnm):
os.makedirs(sdnm)
os.chdir(sdnm)
if not os.path.exists('md_result.p'):
# Link in a bunch of files... what were these again?
link_dir_contents(os.path.join(self.root,self.rundir),os.getcwd())
# Link in the scripts required to run the simulation
for f in self.scripts:
LinkFile(os.path.join(os.path.split(__file__)[0],"data",f),os.path.join(os.getcwd(),f))
# Link in the coordinate file.
LinkFile(self.molecules[label], './%s' % os.path.basename(self.molecules[label]))
# Store names of previous trajectory files.
self.last_traj += [os.path.join(os.getcwd(), i) for i in self.extra_output]
# Write target, engine and simulation options to disk.
lp_dump((self.OptionDict, eng_opts, md_opts), 'simulation.p')
# Execute the script for running molecular dynamics.
cmdstr = '%s python md_ism_hfe.py %s' % (self.prefix, "-g" if AGrad else "")
if wq is None:
logger.info("Running condensed phase simulation locally.\n")
logger.info("You may tail -f %s/npt.out in another terminal window\n" % os.getcwd())
_exec(cmdstr, copy_stderr=True, outfnm='md.out')
else:
queue_up(wq, command = cmdstr+' &> md.out', tag='%s:%s/%s' % (self.name, label, "liq" if liq else "gas"),
input_files = self.scripts + ['simulation.p', 'forcefield.p', os.path.basename(self.molecules[label])],
output_files = ['md_result.p', 'md.out'] + self.extra_output, tgt=self, verbose=False, print_time=3600)
os.chdir('..')