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 npt_simulation(self, temperature, pressure, simnum):
""" Submit a NPT simulation to the Work Queue. """
wq = getWorkQueue()
if not (os.path.exists('npt_result.p') or os.path.exists('npt_result.p.bz2')):
link_dir_contents(os.path.join(self.root,self.rundir),os.getcwd())
if wq == None:
print "Running condensed phase simulation locally."
print "You may tail -f %s/npt.out in another terminal window" % os.getcwd()
# if GoodStep() and (temperature, pressure) in self.DynDict_New:
# self.DynDict[(temperature, pressure)] = self.DynDict_New[(temperature, pressure)]
# if (temperature, pressure) in self.DynDict:
# dynsrc = self.DynDict[(temperature, pressure)]
# dyndest = os.path.join(os.getcwd(), 'liquid.dyn')
# print "Copying .dyn file: %s to %s" % (dynsrc, dyndest)
# shutil.copy2(dynsrc,dyndest)
cmdstr = 'python npt.py gromacs %i %.3f %.3f %.3f %.3f %s --liquid_equ_steps %i &> npt.out' % \
(self.liquid_prod_steps, self.liquid_timestep, self.liquid_interval, temperature, pressure, " --minimize_energy" if self.minimize_energy else "", self.liquid_equ_steps)
_exec(cmdstr)
# self.DynDict_New[(temperature, pressure)] = os.path.join(os.getcwd(),'liquid.dyn')
else:
# This part of the code has never been used before
# Still need to figure out where to specify GROMACS location on each cluster
# queue_up(wq,
# command = 'python npt.py liquid.xyz %.3f %.3f &> npt.out' % (temperature, pressure),
# input_files = ['liquid.xyz','liquid.key','mono.xyz','mono.key','forcebalance.p','npt.py'],
# output_files = ['npt_result.p.bz2', 'npt.py'] + self.FF.fnms,
# tgt=self)
raise RuntimeError('Remote GROMACS execution is not yet enabled')
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('..')
def submit_jobs(self, mvals, AGrad=True, AHess=True):
"""This routine is called by Objective.stage() and will run before "get".
It submits the jobs and the stage() function will wait for jobs
to complete.
Parameters
----------
mvals : list
Mathematical parameter values.
AGrad : Boolean
Switch to turn on analytic gradient.
AHess : Boolean
Switch to turn on analytic Hessian.
Returns
-------
Nothing.
"""
# Set up and run the simulation chain on all points.
for pt in self.points:
# Create subdir
try:
os.makedirs(str(pt.idnr))
except OSError as exception:
if exception.errno != errno.EEXIST:
raise
# Goto subdir
os.chdir(str(pt.idnr))
# Link dir contents from target subdir to current temp directory.
for f in self.scripts:
LinkFile(os.path.join(self.root, self.tempdir, f),
os.path.join(os.getcwd(), f))
link_dir_contents(os.path.join(self.root, self.tgtdir,
str(pt.idnr)), os.getcwd())
# Dump the force field to a pickle file
with wopen('forcebalance.p') as f:
lp_dump((self.FF, mvals, self.OptionDict, AGrad), f)
# Run the simulation chain for point.
cmdstr = ("%s python md_chain.py " % self.mdpfx +
" ".join(self.quantities) + " " +
"--engine %s " % self.engname +
"--length %d " % self.n_sim_chain +
"--name %s " % self.simpfx +
"--temperature %f " % pt.temperature +
"--pressure %f " % pt.pressure +
"--nequil %d " % self.eq_steps +
"--nsteps %d " % self.md_steps)
_exec(cmdstr, copy_stderr=True, outfnm='md_chain.out')
os.chdir('..')
def submit_jobs(self, mvals, AGrad=True, AHess=True):
"""This routine is called by Objective.stage() and will run before "get".
It submits the jobs and the stage() function will wait for jobs
to complete.
Parameters
----------
mvals : list
Mathematical parameter values.
AGrad : Boolean
Switch to turn on analytic gradient.
AHess : Boolean
Switch to turn on analytic Hessian.
Returns
-------
Nothing.
"""
# Set up and run the simulation chain on all points.
for pt in self.points:
# Create subdir
try:
os.makedirs(str(pt.idnr))
except OSError as exception:
if exception.errno != errno.EEXIST:
raise
# Goto subdir
os.chdir(str(pt.idnr))
# Link dir contents from target subdir to current temp directory.
for f in self.scripts:
LinkFile(os.path.join(self.root, self.tempdir, f),
os.path.join(os.getcwd(), f))
link_dir_contents(os.path.join(self.root, self.tgtdir,
str(pt.idnr)), os.getcwd())
# Dump the force field to a pickle file
lp_dump((self.FF, mvals, self.OptionDict, AGrad), 'forcebalance.p')
# Run the simulation chain for point.
cmdstr = ("%s python md_chain.py " % self.mdpfx +
" ".join(self.quantities) + " " +
"--engine %s " % self.engname +
"--length %d " % self.n_sim_chain +
"--name %s " % self.simpfx +
"--temperature %f " % pt.temperature +
"--pressure %f " % pt.pressure +
"--nequil %d " % self.eq_steps +
"--nsteps %d " % self.md_steps)
_exec(cmdstr, copy_stderr=True, outfnm='md_chain.out')
os.chdir('..')
def link_from_tempdir(self, absdestdir):
link_dir_contents(os.path.join(self.root, self.tempdir), absdestdir)
def link_from_tempdir(self,absdestdir):
link_dir_contents(os.path.join(self.root,self.tempdir), absdestdir)
