def __init__(self, options, tgt_opts, forcefield):
super(Objective, self).__init__(options)
self.set_option(options, 'penalty_type')
self.set_option(options, 'penalty_additive')
self.set_option(options, 'penalty_multiplicative')
self.set_option(options, 'penalty_hyperbolic_b')
self.set_option(options, 'penalty_alpha')
self.set_option(options, 'normalize_weights')
## Work Queue Port (The specific target itself may or may not actually use this.)
self.set_option(options, 'wq_port')
## Asynchronous objective function evaluation (i.e. execute Work Queue and local objective concurrently.)
self.set_option(options, 'asynchronous')
## The list of fitting targets
self.Targets = []
for opts in tgt_opts:
if opts['type'] not in Implemented_Targets:
logger.error(
'The target type \x1b[1;91m%s\x1b[0m is not implemented!\n'
% opts['type'])
raise RuntimeError
if opts["remote"]:
Tgt = forcebalance.target.RemoteTarget(options, opts,
forcefield)
else:
Tgt = Implemented_Targets[opts['type']](options, opts,
forcefield)
self.Targets.append(Tgt)
printcool_dictionary(Tgt.PrintOptionDict,
"Setup for target %s :" % Tgt.name)
if len(set([Tgt.name for Tgt in self.Targets])) != len(
[Tgt.name for Tgt in self.Targets]):
logger.error("The list of target names is not unique!\n")
raise RuntimeError
## The force field (it seems to be everywhere)
self.FF = forcefield
## Initialize the penalty function.
self.Penalty = Penalty(self.penalty_type, forcefield,
self.penalty_additive,
self.penalty_multiplicative,
self.penalty_hyperbolic_b, self.penalty_alpha)
## Obtain the denominator.
if self.normalize_weights:
self.WTot = np.sum([i.weight for i in self.Targets])
else:
self.WTot = 1.0
self.ObjDict = OrderedDict()
self.ObjDict_Last = OrderedDict()
# Create the work queue here.
if self.wq_port != 0:
createWorkQueue(self.wq_port)
logger.info('Work Queue is listening on %d\n' % self.wq_port)
printcool_dictionary(self.PrintOptionDict,
"Setup for objective function :")
def __init__(self, options, tgt_opts, forcefield):
super(Objective, self).__init__(options)
self.set_option(options, 'penalty_type')
self.set_option(options, 'penalty_additive')
self.set_option(options, 'penalty_multiplicative')
self.set_option(options, 'penalty_hyperbolic_b')
self.set_option(options, 'penalty_alpha')
self.set_option(options, 'penalty_power')
self.set_option(options, 'normalize_weights')
## Work Queue Port (The specific target itself may or may not actually use this.)
self.set_option(options, 'wq_port')
## Asynchronous objective function evaluation (i.e. execute Work Queue and local objective concurrently.)
self.set_option(options, 'asynchronous')
## The list of fitting targets
self.Targets = []
for opts in tgt_opts:
if opts['type'] not in Implemented_Targets:
logger.error('The target type \x1b[1;91m%s\x1b[0m is not implemented!\n' % opts['type'])
raise RuntimeError
# Create a target object. This is done by looking up the
# Target class from the Implemented_Targets dictionary
# using opts['type'] as the key. The object is created by
# passing (options, opts, forcefield) to the constructor.
if opts["remote"] and self.wq_port != 0: Tgt = forcebalance.target.RemoteTarget(options, opts, forcefield)
else: Tgt = Implemented_Targets[opts['type']](options,opts,forcefield)
self.Targets.append(Tgt)
printcool_dictionary(Tgt.PrintOptionDict,"Setup for target %s :" % Tgt.name)
if len(set([Tgt.name for Tgt in self.Targets])) != len([Tgt.name for Tgt in self.Targets]):
logger.error("The list of target names is not unique!\n")
raise RuntimeError
## The force field (it seems to be everywhere)
self.FF = forcefield
## Initialize the penalty function.
self.Penalty = Penalty(self.penalty_type,forcefield,self.penalty_additive,
self.penalty_multiplicative,self.penalty_hyperbolic_b,
self.penalty_alpha,self.penalty_power)
## Obtain the denominator.
if self.normalize_weights:
self.WTot = np.sum([i.weight for i in self.Targets])
else:
self.WTot = 1.0
self.ObjDict = OrderedDict()
self.ObjDict_Last = OrderedDict()
# Create the work queue here.
if self.wq_port != 0:
createWorkQueue(self.wq_port)
logger.info('Work Queue is listening on %d\n' % self.wq_port)
printcool_dictionary(self.PrintOptionDict, "Setup for objective function :")
def __init__(self, options, tgt_opts, forcefield):
super(Objective, self).__init__(options)
self.set_option(options, 'penalty_type')
self.set_option(options, 'penalty_additive')
self.set_option(options, 'penalty_multiplicative')
self.set_option(options, 'penalty_hyperbolic_b')
self.set_option(options, 'penalty_alpha')
self.set_option(options, 'normalize_weights')
## Work Queue Port (The specific target itself may or may not actually use this.)
self.set_option(options, 'wq_port')
## Asynchronous objective function evaluation (i.e. execute Work Queue and local objective concurrently.)
self.set_option(options, 'asynchronous')
## The list of fitting targets
self.Targets = []
for opts in tgt_opts:
if opts['type'] not in Implemented_Targets:
raise RuntimeError('The target type \x1b[1;91m%s\x1b[0m is not implemented!' % opts['type'])
Tgt = Implemented_Targets[opts['type']](options,opts,forcefield)
self.Targets.append(Tgt)
printcool_dictionary(Tgt.PrintOptionDict,"Setup for target %s :" % Tgt.name)
if len(set([Tgt.name for Tgt in self.Targets])) != len([Tgt.name for Tgt in self.Targets]):
raise Exception("The list of target names is not unique!")
## The force field (it seems to be everywhere)
self.FF = forcefield
## Initialize the penalty function.
self.Penalty = Penalty(options['penalty_type'],forcefield,options['penalty_additive'],
options['penalty_multiplicative'],options['penalty_hyperbolic_b'],
options['penalty_alpha'])
## Obtain the denominator.
if self.normalize_weights:
self.WTot = sum([i.weight for i in self.Targets])
else:
self.WTot = 1.0
self.ObjDict = OrderedDict()
self.ObjDict_Last = OrderedDict()
# Create the work queue here.
if self.wq_port != 0:
createWorkQueue(self.wq_port)
print('Work Queue is listening on %d' % self.wq_port)
printcool_dictionary(self.PrintOptionDict, "Setup for objective function :")
def __init__(self, options, tgt_opts, forcefield):
super(Objective, self).__init__(options)
self.set_option(options, 'penalty_type')
self.set_option(options, 'penalty_additive')
self.set_option(options, 'penalty_multiplicative')
self.set_option(options, 'penalty_hyperbolic_b')
self.set_option(options, 'penalty_alpha')
self.set_option(options, 'penalty_power')
self.set_option(options, 'normalize_weights')
## Work Queue Port (The specific target itself may or may not actually use this.)
self.set_option(options, 'wq_port')
## Asynchronous objective function evaluation (i.e. execute Work Queue and local objective concurrently.)
self.set_option(options, 'asynchronous')
## The list of fitting targets
self.Targets = []
enable_smirnoff_prints = False # extra prints for SMIRNOFF forcefield
for opts in tgt_opts:
if opts['type'] not in Implemented_Targets:
logger.error(
'The target type \x1b[1;91m%s\x1b[0m is not implemented!\n'
% opts['type'])
raise RuntimeError
elif opts['type'].endswith("SMIRNOFF"):
enable_smirnoff_prints = True
# Create a target object. This is done by looking up the
# Target class from the Implemented_Targets dictionary
# using opts['type'] as the key. The object is created by
# passing (options, opts, forcefield) to the constructor.
if opts["remote"] and self.wq_port != 0:
Tgt = forcebalance.target.RemoteTarget(options, opts,
forcefield)
else:
Tgt = Implemented_Targets[opts['type']](options, opts,
forcefield)
self.Targets.append(Tgt)
printcool_dictionary(Tgt.PrintOptionDict,
"Setup for target %s :" % Tgt.name)
if len(set([Tgt.name for Tgt in self.Targets])) != len(
[Tgt.name for Tgt in self.Targets]):
logger.error("The list of target names is not unique!\n")
raise RuntimeError
if enable_smirnoff_prints:
smirnoff_analyze_parameter_coverage(forcefield, tgt_opts)
## The force field (it seems to be everywhere)
self.FF = forcefield
## Initialize the penalty function.
self.Penalty = Penalty(self.penalty_type, forcefield,
self.penalty_additive,
self.penalty_multiplicative,
self.penalty_hyperbolic_b, self.penalty_alpha,
self.penalty_power)
## Obtain the denominator.
if self.normalize_weights:
self.WTot = np.sum([i.weight for i in self.Targets])
else:
self.WTot = 1.0
self.ObjDict = OrderedDict()
self.ObjDict_Last = OrderedDict()
# Create the work queue here.
if self.wq_port != 0:
createWorkQueue(self.wq_port)
logger.info('Work Queue is listening on %d\n' % self.wq_port)
printcool_dictionary(self.PrintOptionDict,
"Setup for objective function :")