def create_engine():
# create engine
ENGINE = Engine(path=None)
ENGINE.set_pdb(pdbPath)
# initialize constraints
B_CONSTRAINT = BondConstraint()
BA_CONSTRAINT = BondsAngleConstraint()
IA_CONSTRAINT = ImproperAngleConstraint()
# add constraints
ENGINE.add_constraints([B_CONSTRAINT])
B_CONSTRAINT.create_bonds_by_definition( bondsDefinition={"THF": [('O' ,'C1' , 1.20, 1.70),
('O' ,'C4' , 1.20, 1.70),
('C1','C2' , 1.25, 1.90),
('C2','C3' , 1.25, 1.90),
('C3','C4' , 1.25, 1.90),
('C1','H11', 0.88, 1.16),('C1','H12', 0.88, 1.16),
('C2','H21', 0.88, 1.16),('C2','H22', 0.88, 1.16),
('C3','H31', 0.88, 1.16),('C3','H32', 0.88, 1.16),
('C4','H41', 0.88, 1.16),('C4','H42', 0.88, 1.16)] })
ENGINE.add_constraints([BA_CONSTRAINT])
BA_CONSTRAINT.create_angles_by_definition( anglesDefinition={"THF": [ ('O' ,'C1' ,'C4' , 105, 125),
('C1' ,'O' ,'C2' , 100, 120),
('C4' ,'O' ,'C3' , 100, 120),
('C2' ,'C1' ,'C3' , 95 , 115),
('C3' ,'C2' ,'C4' , 95 , 115),
# H-C-H angle
('C1' ,'H11','H12', 98 , 118),
('C2' ,'H21','H22', 98 , 118),
('C3' ,'H31','H32', 98 , 118),
('C4' ,'H41','H42', 98 , 118),
# 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' , 103, 123),
('C1' ,'H12','C2' , 103, 123),
('C2' ,'H21','C1' , 103, 123),
('C2' ,'H21','C3' , 103, 123),
('C2' ,'H22','C1' , 103, 123),
('C2' ,'H22','C3' , 103, 123),
('C3' ,'H31','C2' , 103, 123),
('C3' ,'H31','C4' , 103, 123),
('C3' ,'H32','C2' , 103, 123),
('C3' ,'H32','C4' , 103, 123),
('C4' ,'H41','C3' , 103, 123),
('C4' ,'H42','C3' , 103, 123) ] })
ENGINE.add_constraints([IA_CONSTRAINT])
IA_CONSTRAINT.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()
# set moves generators
# set all move generators to Translation with a maximum amplutide of 0.3 A
[g.set_move_generator(TranslationGenerator(amplitude=0.3)) for g in ENGINE.groups]
# set randomly 25% of the translation amplitude to 10A
[g.set_move_generator(TranslationGenerator(amplitude=10.)) for g in ENGINE.groups if np.random.random()>0.25]
# return engine
return ENGINE
# Create plotting styles
#styles = ['-','--','-.',':']
colors = ["b", 'g', 'r', 'c', 'm', 'y']
markers = ["", '.', '+', '^', '|']
INTRA_STYLES = [r[0] + r[1] for r in itertools.product(['--'], colors)]
INTRA_STYLES = [r[0] + r[1] for r in itertools.product(markers, INTRA_STYLES)]
INTER_STYLES = [r[0] + r[1] for r in itertools.product(['-'], colors)]
INTER_STYLES = [r[0] + r[1] for r in itertools.product(markers, INTER_STYLES)]
trajectories = ["atomsTraj.xyz", "exploreTraj.xyz"]
pdbPath = "CO2.pdb"
expDataPath = "Xrays.gr"
# create engine
ENGINE = Engine(path=None)
ENGINE.set_pdb(pdbPath)
PDF_CONSTRAINT = PairDistributionConstraint(experimentalData=expDataPath,
weighting="atomicNumber")
ENGINE.add_constraints([PDF_CONSTRAINT])
ENGINE.initialize_used_constraints()
ENGINE.set_chi_square()
def create_figure(PDF, show=False, savePath=None):
# get output
output = PDF.get_constraint_value()
# create figure
FIG = plt.figure()
FIG.patch.set_facecolor('white')
grid = gridspec.GridSpec(nrows=2, ncols=2)
grid.update(left=0.05, right=0.95, wspace=0.05)
# fullrmc library imports
from fullrmc.Globals import LOGGER
from fullrmc.Engine import Engine
from fullrmc.Constraints.BondConstraints import BondConstraint
from fullrmc.Constraints.AngleConstraints import BondsAngleConstraint
##########################################################################################
################################## 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 constraints
B_CONSTRAINT = BondConstraint()
BA_CONSTRAINT = BondsAngleConstraint()
ENGINE.add_constraints([B_CONSTRAINT, BA_CONSTRAINT])
B_CONSTRAINT.create_bonds_by_definition(bondsDefinition={
"TIP": [('OH2', 'H1', 0.8, 1.1), ('OH2', 'H2', 0.8, 1.1)]
})
BA_CONSTRAINT.create_angles_by_definition(
anglesDefinition={"TIP": [('OH2', 'H1', 'H2', 80, 120)]})
# set TranslationGenerator move generators amplitude
[g.moveGenerator.set_amplitude(0.025) for g in ENGINE.groups]
# standard libraries imports
import os
import itertools
# external libraries imports
import matplotlib.pyplot as plt
# fullrmc library imports
from fullrmc.Engine import Engine
from fullrmc.Constraints.PairCorrelationConstraints import PairDistributionConstraint
ENGINE = Engine(path=None)
ENGINE.set_pdb('system.pdb')
PDF_CONSTRAINT = PairDistributionConstraint(experimentalData="experimental.gr",
weighting="atomicNumber")
ENGINE.add_constraints([PDF_CONSTRAINT])
# Create plotting styles
colors = ["b", 'g', 'r', 'c', 'm', 'y']
markers = ["", '.', '+', '^', '|']
STYLE = [r[0] + r[1] for r in itertools.product(['-'], colors)]
STYLE = [r[0] + r[1] for r in itertools.product(markers, STYLE)]
def plot(PDF, figName, imgpath, show=False, save=True):
# plot
output = PDF.get_constraint_value()
plt.plot(PDF.experimentalDistances,
PDF.experimentalPDF,
'ro',
label="experimental",
from fullrmc.Generators.Translations import TranslationGenerator
from fullrmc.Generators.Swaps import SwapPositionsGenerator
# #################################################################################### #
# ############################# DECLARE USEFUL VARIABLES ############################# #
experimentalDataPath = "pdf.exp"
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),
sqFileName = "experimental.fq"
pdbFileName = "system.pdb"
# engine variables
grExpPath = os.path.join(DIR_PATH, grFileName)
sqExpPath = os.path.join(DIR_PATH, sqFileName)
pdbPath = os.path.join(DIR_PATH, pdbFileName)
engineFilePath = os.path.join(DIR_PATH, engineFileName)
# set some useful flags
FRESH_START = True
# check Engine exists, if not build it otherwise load it.
ENGINE = Engine(path=None)
if not ENGINE.is_engine(engineFilePath) or FRESH_START:
# create engine
ENGINE = Engine(path=engineFilePath, freshStart=True)
ENGINE.set_pdb(pdbFileName)
# 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
pdbFileName = "SiOx.pdb"
engineFileName = "SiOx.rmc"
multiframe = 'size_distribution'
numberOfFrames = 10
FRESH_START = False
# engine variables
grExpPath = os.path.join(DIR_PATH, grFileName)
pdbPath = os.path.join(DIR_PATH, pdbFileName)
engineFilePath = os.path.join(DIR_PATH, engineFileName)
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()
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