def resume(self, phases=None):
"""
Resume an existing set of alchemical free energy calculations found in current store directory.
Parameters
----------
phases : list of str, optional, default=None
The list of calculation phases (e.g. ['solvent', 'complex']) to resume.
If not specified, all simulations in the store_directory will be resumed.
"""
# If no phases specified, construct a list of phases from the filename prefixes in the store directory.
if phases is None:
phases = utils.find_phases_in_store_directory(
self._store_directory)
self._phases = phases.keys()
# Construct store filenames.
self._store_filenames = {
phase: os.path.join(self._store_directory, phase + '.nc')
for phase in self._phases
}
# Ensure we can resume from each store file, processing override options.
for phase in self._phases:
# TODO: Use resume capabaility of repex to resume and modify any parameters we can change.
store_filename = self._store_filenames[phase]
pass
# Record we are now initialized.
self._initialized = True
return
def resume(self, phases=None):
"""
Resume an existing set of alchemical free energy calculations found in current store directory.
Parameters
----------
phases : list of str, optional, default=None
The list of calculation phases (e.g. ['solvent', 'complex']) to resume.
If not specified, all simulations in the store_directory will be resumed.
"""
# If no phases specified, construct a list of phases from the filename prefixes in the store directory.
if phases is None:
phases = utils.find_phases_in_store_directory(self._store_directory)
self._phases = phases.keys()
# Construct store filenames.
self._store_filenames = { phase : os.path.join(self._store_directory, phase + '.nc') for phase in self._phases }
# Ensure we can resume from each store file, processing override options.
for phase in self._phases:
# TODO: Use resume capabaility of repex to resume and modify any parameters we can change.
store_filename = self._store_filenames[phase]
pass
# Record we are now initialized.
self._initialized = True
return
def print_status(store_directory):
"""
Print a quick summary of simulation progress.
Parameters
----------
store_directory : string
The location of the NetCDF simulation output files.
Returns
-------
success : bool
True is returned on success; False if some files could not be read.
"""
# Get NetCDF files
phases = utils.find_phases_in_store_directory(store_directory)
# Process each netcdf file.
for phase, fullpath in phases.items():
# Check that the file exists.
if not os.path.exists(fullpath):
# Report failure.
logger.info("File %s not found." % fullpath)
logger.info(
"Check to make sure the right directory was specified, and 'yank setup' has been run."
)
return False
# Open NetCDF file for reading.
logger.debug(
"Opening NetCDF trajectory file '%(fullpath)s' for reading..." %
vars())
ncfile = netcdf.Dataset(fullpath, 'r')
# Read dimensions.
niterations = ncfile.variables['positions'].shape[0]
nstates = ncfile.variables['positions'].shape[1]
natoms = ncfile.variables['positions'].shape[2]
# Print summary.
logger.info("%s" % phase)
logger.info(" %8d iterations completed" % niterations)
logger.info(" %8d alchemical states" % nstates)
logger.info(" %8d atoms" % natoms)
# TODO: Print average ns/day and estimated completion time.
# Close file.
ncfile.close()
return True
def print_status(store_directory):
"""
Print a quick summary of simulation progress.
Parameters
----------
store_directory : string
The location of the NetCDF simulation output files.
Returns
-------
success : bool
True is returned on success; False if some files could not be read.
"""
# Get NetCDF files
phases = utils.find_phases_in_store_directory(store_directory)
# Process each netcdf file.
for phase, fullpath in phases.items():
# Check that the file exists.
if not os.path.exists(fullpath):
# Report failure.
logger.info("File %s not found." % fullpath)
logger.info("Check to make sure the right directory was specified, and 'yank setup' has been run.")
return False
# Open NetCDF file for reading.
logger.debug("Opening NetCDF trajectory file '%(fullpath)s' for reading..." % vars())
ncfile = netcdf.Dataset(fullpath, 'r')
# Read dimensions.
niterations = ncfile.variables['positions'].shape[0]
nstates = ncfile.variables['positions'].shape[1]
natoms = ncfile.variables['positions'].shape[2]
# Print summary.
logger.info("%s" % phase)
logger.info(" %8d iterations completed" % niterations)
logger.info(" %8d alchemical states" % nstates)
logger.info(" %8d atoms" % natoms)
# TODO: Print average ns/day and estimated completion time.
# Close file.
ncfile.close()
return True
