structurePdbPath = "system.pdb"
engineSavePath = "system.rmc"
FRESH_START = False
# #################################################################################### #
# ################################### CREATE ENGINE ################################## #
ENGINE = Engine(path=None)
if not ENGINE.is_engine(engineSavePath) or FRESH_START:
ENGINE = Engine(path=engineSavePath, freshStart=True)
ENGINE.set_pdb(structurePdbPath)
## create and add pair distribution constraint
PDF_CONSTRAINT = PairDistributionConstraint(
experimentalData=experimentalDataPath, weighting="atomicNumber")
ENGINE.add_constraints([PDF_CONSTRAINT])
## create and add intermolecular distances constraint
EMD_CONSTRAINT = InterMolecularDistanceConstraint()
ENGINE.add_constraints([EMD_CONSTRAINT])
EMD_CONSTRAINT.set_type_definition("element")
EMD_CONSTRAINT.set_pairs_distance([
('Co', 'Co', 2.00),
('Co', 'Mn', 2.00),
('Co', 'Ni', 2.00),
('Co', 'Li', 2.00),
('Co', 'O', 1.7),
('Mn', 'Mn', 2.00),
('Mn', 'Li', 2.00),
('Mn', 'Ni', 2.00),
('Mn', 'O', 1.7),
('Ni', 'Ni', 2.00),
('Ni', 'Li', 2.00),
('Ni', 'O', 1.7),
################################## SHUT DOWN LOGGING ###################################
LOGGER.set_minimum_level(sys.maxint, stdoutFlag=True, fileFlag=True)
##########################################################################################
##################################### CREATE ENGINE ####################################
# parameters
NSTEPS = 10000
pdbPath = 'system.pdb'
expData = 'experimental.gr'
# initialize engine
ENGINE = Engine(path=None)
ENGINE.set_pdb(pdbPath)
# create constraints
PDF_CONSTRAINT = PairDistributionConstraint(experimentalData=expData,
weighting="atomicNumber")
EMD_CONSTRAINT = InterMolecularDistanceConstraint()
B_CONSTRAINT = BondConstraint()
BA_CONSTRAINT = BondsAngleConstraint()
IA_CONSTRAINT = ImproperAngleConstraint()
# add constraints to engine
ENGINE.add_constraints([
PDF_CONSTRAINT, EMD_CONSTRAINT, B_CONSTRAINT, BA_CONSTRAINT, IA_CONSTRAINT
])
# initialize constraints definitions
B_CONSTRAINT.create_bonds_by_definition(
bondsDefinition={
"THF": [('O', 'C1', 1.22,
1.70), ('O', 'C4', 1.22, 1.70), (
'C1', 'C2', 1.25,
1.90), ('C2', 'C3', 1.25, 1.90), (
'C3', 'C4', 1.25,
# add G(r) constraint
PDF_CONSTRAINT = PairDistributionConstraint(experimentalData=grExpPath,
weighting="atomicNumber")
ENGINE.add_constraints([PDF_CONSTRAINT])
# Rebin S(Q) experimental data and build constraint
Sq = np.transpose(rebin(np.loadtxt(sqExpPath),
bin=0.05)).astype(FLOAT_TYPE)
RSF_CONSTRAINT = ReducedStructureFactorConstraint(experimentalData=Sq,
weighting="atomicNumber")
ENGINE.add_constraints([RSF_CONSTRAINT])
# add coordination number constraint and set to un-used
ACN_CONSTRAINT = AtomicCoordinationNumberConstraint()
ENGINE.add_constraints([ACN_CONSTRAINT])
ACN_CONSTRAINT.set_used(False)
# add inter-molecular distance constraint
EMD_CONSTRAINT = InterMolecularDistanceConstraint(defaultDistance=2.2,
flexible=True)
ENGINE.add_constraints([EMD_CONSTRAINT])
# save engine
ENGINE.save()
else:
ENGINE = ENGINE.load(engineFilePath)
# unpack constraints before fitting in case tweaking is needed
PDF_CONSTRAINT, RSF_CONSTRAINT, ACN_CONSTRAINT, EMD_CONSTRAINT = ENGINE.constraints
##########################################################################################
##################################### DIFFERENT RUNS ###################################
def run_normal(nsteps, saveFrequency, engineFilePath):
ENGINE.set_groups_as_atoms()
ENGINE.run(numberOfSteps=nsteps,
saveFrequency=saveFrequency,
##########################################################################################
##################################### CREATE ENGINE ####################################
# file names
expDataPath = "Xrays.gr"
pdbPath = "CO2.pdb"
enginePath = "CO2.rmc"
FRESH_START = False
ENGINE = Engine(path=None)
if not ENGINE.is_engine(enginePath) or FRESH_START:
# initialize engine
ENGINE = Engine(path=enginePath, freshStart=True)
ENGINE.set_pdb(pdbPath)
PDF_CONSTRAINT = PairDistributionConstraint(experimentalData=expDataPath,
weighting="atomicNumber")
IMD_CONSTRAINT = InterMolecularDistanceConstraint(defaultDistance=1.4)
B_CONSTRAINT = BondConstraint()
BA_CONSTRAINT = BondsAngleConstraint()
# add constraints
ENGINE.add_constraints(
[PDF_CONSTRAINT, IMD_CONSTRAINT, B_CONSTRAINT, BA_CONSTRAINT])
B_CONSTRAINT.create_bonds_by_definition(bondsDefinition={
"CO2": [('C', 'O1', 0.52, 1.4), ('C', 'O2', 0.52, 1.4)]
})
BA_CONSTRAINT.create_angles_by_definition(
anglesDefinition={"CO2": [('C', 'O1', 'O2', 170, 180)]})
# initialize constraints data
ENGINE.initialize_used_constraints()
# save engine
ENGINE.save()
else:
ENGINE = Engine(path=None)
if not ENGINE.is_engine(engineFilePath) or FRESH_START:
# create engine
ENGINE = Engine(path=engineFilePath, freshStart=True)
ENGINE.set_pdb(pdbPath)
# create and add pair distribution constraint to the engine
PDF_CONSTRAINT = PairDistributionConstraint(experimentalData=grExpPath, weighting="atomicNumber")
# shape function parameters
params = {'rmin':0., 'rmax':None, 'dr':0.5,
'qmin':0.0001, 'qmax':0.6, 'dq':0.005,
'updateFreq':1000}
PDF_CONSTRAINT.set_shape_function_parameters(params)
ENGINE.add_constraints([PDF_CONSTRAINT])
# Intermolecular constraint
EMD_CONSTRAINT = InterMolecularDistanceConstraint()
ENGINE.add_constraints([EMD_CONSTRAINT])
EMD_CONSTRAINT.set_type_definition("element")
EMD_CONSTRAINT.set_pairs_distance([('Si','Si',1.75), ('O','O',1.10), ('Si','O',1.30)])
# coordination number constraint
ACNC_CONSTRAINT = AtomicCoordinationNumberConstraint()
ENGINE.add_constraints([ACNC_CONSTRAINT])
ACNC_CONSTRAINT.set_coordination_number_definition( coordNumDef=[('Si','Si',1.8,2.8,3,6), ])
# initialize constraints
_ = ENGINE.initialize_used_constraints()
# set number density
ENGINE.set_number_density(.0125)
# save engine
ENGINE.save()
else:
ENGINE = ENGINE.load(engineFilePath)
from fullrmc.Core.MoveGenerator import MoveGeneratorCollector
from fullrmc.Constraints.DistanceConstraints import InterMolecularDistanceConstraint
from fullrmc.Generators.Rotations import RotationGenerator
from fullrmc.Generators.Translations import TranslationTowardsCenterGenerator
##########################################################################################
################################## SHUT DOWN LOGGING ###################################
LOGGER.set_minimum_level(sys.maxint, stdoutFlag=True, fileFlag=True)
##########################################################################################
##################################### CREATE ENGINE ####################################
pdbPath = "system.pdb"
ENGINE = Engine(path=None)
ENGINE.set_pdb(pdbPath)
# add inter-molecular distance constraint
EMD_CONSTRAINT = InterMolecularDistanceConstraint(defaultDistance=1.75)
ENGINE.add_constraints([EMD_CONSTRAINT])
##########################################################################################
#################################### DIFFERENT RUNS ####################################
def move_towards():
# set only one molecule group
ENGINE.set_groups_as_molecules()
secMolIdxs = ENGINE.groups[1].indexes
ENGINE.set_groups(ENGINE.groups[0])
# set move generator
for g in ENGINE.groups:
t = TranslationTowardsCenterGenerator(center={'indexes': secMolIdxs},
amplitude=0.15,
angle=90)
def run_engine(PDF=True,
IMD=True,
B=True,
BA=True,
IA=True,
molecular=True,
nsteps=10000,
ncores=1):
ENGINE = Engine(path=None)
ENGINE.set_pdb(pdbPath)
# create experimental constraints
if PDF:
C = PairDistributionConstraint(experimentalData=expPath,
weighting="atomicNumber")
ENGINE.add_constraints(C)
# create and define molecular constraints
if IMD:
C = InterMolecularDistanceConstraint(defaultDistance=1.5)
ENGINE.add_constraints(C)
if B:
C = BondConstraint()
ENGINE.add_constraints(C)
C.create_bonds_by_definition(
bondsDefinition={
"THF": [('O', 'C1', 1.29,
1.70), ('O', 'C4', 1.29,
1.70), ('C1', 'C2', 1.29,
1.70), ('C2', 'C3', 1.29,
1.70), ('C3', 'C4', 1.29,
1.70),
('C1', 'H11', 0.58,
1.15), ('C1', 'H12', 0.58,
1.15), ('C2', 'H21', 0.58,
1.15), ('C2', 'H22', 0.58, 1.15),
('C3', 'H31', 0.58,
1.15), ('C3', 'H32', 0.58,
1.15), ('C4', 'H41', 0.58,
1.15), ('C4', 'H42', 0.58, 1.15)]
})
if BA:
C = BondsAngleConstraint()
ENGINE.add_constraints(C)
C.create_angles_by_definition(
anglesDefinition={
"THF": [
('O', 'C1', 'C4', 95, 135),
('C1', 'O', 'C2', 95, 135),
('C4', 'O', 'C3', 95, 135),
('C2', 'C1', 'C3', 90, 120),
('C3', 'C2', 'C4', 90, 120),
# H-C-H angle
('C1', 'H11', 'H12', 95, 125),
('C2', 'H21', 'H22', 95, 125),
('C3', 'H31', 'H32', 95, 125),
('C4', 'H41', 'H42', 95, 125),
# H-C-O angle
('C1', 'H11', 'O', 100, 120),
('C1', 'H12', 'O', 100, 120),
('C4', 'H41', 'O', 100, 120),
('C4', 'H42', 'O', 100, 120),
# H-C-C
('C1', 'H11', 'C2', 80, 123),
('C1', 'H12', 'C2', 80, 123),
('C2', 'H21', 'C1', 80, 123),
('C2', 'H21', 'C3', 80, 123),
('C2', 'H22', 'C1', 80, 123),
('C2', 'H22', 'C3', 80, 123),
('C3', 'H31', 'C2', 80, 123),
('C3', 'H31', 'C4', 80, 123),
('C3', 'H32', 'C2', 80, 123),
('C3', 'H32', 'C4', 80, 123),
('C4', 'H41', 'C3', 80, 123),
('C4', 'H42', 'C3', 80, 123)
]
})
if IA:
C = ImproperAngleConstraint()
ENGINE.add_constraints(C)
C.create_angles_by_definition(
anglesDefinition={
"THF": [('C2', 'O', 'C1', 'C4', -15,
15), ('C3', 'O', 'C1', 'C4', -15, 15)]
})
# initialize constraints data
ENGINE.initialize_used_constraints()
# run engine
if molecular:
ENGINE.set_groups_as_molecules()
print 'molecular, %s atoms, %s steps, %2s cores' % (
ENGINE.numberOfAtoms, nsteps, ncores),
tic = time.time()
ENGINE.run(numberOfSteps=nsteps,
saveFrequency=2 * nsteps,
restartPdb=None,
ncores=ncores)
elapsed = float(time.time() - tic) / float(nsteps)
print ' -- > %s seconds per step' % (elapsed, )
else:
ENGINE.set_groups_as_atoms()
print 'atomic , %s atoms, %s steps, %2s cores' % (
ENGINE.numberOfAtoms, nsteps, ncores),
tic = time.time()
ENGINE.run(numberOfSteps=nsteps,
saveFrequency=2 * nsteps,
restartPdb=None,
ncores=ncores)
elapsed = float(time.time() - tic) / float(nsteps)
print ' -- > %s seconds per step' % (elapsed, )
# return elapsed time
return elapsed
ENGINE = Engine(path=None)
if freshStart or not ENGINE.is_engine(engineFilePath):
# create engine
ENGINE = Engine(path=engineFilePath, freshStart=True)
ENGINE.set_pdb(pdbFileName)
## create experimental constraints
#PDF_CONSTRAINT = PairDistributionConstraint(experimentalData=expPath, weighting="atomicNumber")
_, _, _, gr = convert_Gr_to_gr(np.loadtxt(expPath), minIndex=[4, 5, 6])
dataWeights = np.ones(gr.shape[0])
dataWeights[:np.nonzero(gr[:, 1] > 0)[0][0]] = 0
PDF_CONSTRAINT = PairCorrelationConstraint(
experimentalData=gr.astype(FLOAT_TYPE),
weighting="atomicNumber",
dataWeights=dataWeights)
# create and define molecular constraints
EMD_CONSTRAINT = InterMolecularDistanceConstraint(defaultDistance=1.5)
B_CONSTRAINT = BondConstraint()
BA_CONSTRAINT = BondsAngleConstraint()
IA_CONSTRAINT = ImproperAngleConstraint()
# add constraints to engine
ENGINE.add_constraints([
PDF_CONSTRAINT, EMD_CONSTRAINT, B_CONSTRAINT, BA_CONSTRAINT,
IA_CONSTRAINT
])
# initialize constraints definitions
B_CONSTRAINT.create_bonds_by_definition(
bondsDefinition={
"THF": [('O', 'C1', 1.29, 1.70), (
'O', 'C4', 1.29,
1.70), ('C1', 'C2', 1.29, 1.70), (
'C2', 'C3', 1.29,
# add G(r) constraint
PDF_CONSTRAINT = PairDistributionConstraint(experimentalData=grExpPath,
weighting="atomicNumber")
ENGINE.add_constraints([PDF_CONSTRAINT])
# Rebin S(Q) experimental data and build constraint
Sq = np.transpose(rebin(np.loadtxt(sqExpPath),
bin=0.05)).astype(FLOAT_TYPE)
RSF_CONSTRAINT = ReducedStructureFactorConstraint(experimentalData=Sq,
weighting="atomicNumber")
ENGINE.add_constraints([RSF_CONSTRAINT])
# add coordination number constraint and set to un-used
ACN_CONSTRAINT = AtomicCoordinationNumberConstraint()
ENGINE.add_constraints([ACN_CONSTRAINT])
#ACN_CONSTRAINT.set_used(False)
# add inter-molecular distance constraint
EMD_CONSTRAINT = InterMolecularDistanceConstraint(defaultDistance=2.2,
flexible=True)
ENGINE.add_constraints([EMD_CONSTRAINT])
# save engine
ENGINE.save()
else:
ENGINE = ENGINE.load(engineFilePath)
# unpack constraints before fitting in case tweaking is needed
PDF_CONSTRAINT, RSF_CONSTRAINT, ACN_CONSTRAINT, EMD_CONSTRAINT = ENGINE.constraints
##########################################################################################
##################################### DIFFERENT RUNS ###################################
def run_normal(nsteps, saveFrequency, engineFilePath):
ENGINE.set_groups_as_atoms()
ENGINE.run(numberOfSteps=nsteps, saveFrequency=saveFrequency)