('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),
('Li', 'Li', 2.40),
('Li', 'O', 1.8),
('O', 'O', 1.20),
])
## save engine
ENGINE.save()
else:
ENGINE = ENGINE.load(engineSavePath)
## unpack constraints before fitting in case tweaking is needed
PDF_CONSTRAINT, EMD_CONSTRAINT = ENGINE.constraints
# #################################################################################### #
# ############################### DEFINE DIFFERENT RUNS ############################## #
def normal_run(numberOfSteps=100000, saveFrequency=10000):
## reset groups as atoms
ENGINE.set_groups_as_atoms()
## run engine
ENGINE.run(numberOfSteps=numberOfSteps, saveFrequency=saveFrequency)
def swaps_run(numberOfSteps=100000, saveFrequency=10000):
## reset groups as atoms
INTER_STYLES = [r[0] + r[1]for r in itertools.product(markers, INTER_STYLES)]
# dirname
DIR_PATH = os.path.dirname( os.path.realpath(__file__) )
engineFilePath = os.path.join(DIR_PATH, "CO2.rmc")
# load
ENGINE = Engine(path=None)
result, mes = ENGINE.is_engine(engineFilePath, mes=True)
if not result:
print mes
exit()
# load engine and get pdf constraint engine
ENGINE = ENGINE.load(engineFilePath)
PDF_CONSTRAINT = ENGINE.constraints[0]
def create_figure(PDF):
# 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)
totalAx = plt.subplot(grid[0, :])
lowRAx = plt.subplot(grid[1, 0])
highRAx = plt.subplot(grid[1, 1])
# set axis ticks
highRAx.get_yaxis().set_ticks([])
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.load(enginePath)
# unpack constraints before fitting in case tweaking is needed
PDF_CONSTRAINT, IMD_CONSTRAINT, B_CONSTRAINT, BA_CONSTRAINT = ENGINE.constraints
# set all constraints as used. Used value is True by default!
# Now you know you can deactivate any constraint at any time though.
PDF_CONSTRAINT.set_used(True)
IMD_CONSTRAINT.set_used(True)
B_CONSTRAINT.set_used(True)
BA_CONSTRAINT.set_used(True)
##########################################################################################
##################################### DIFFERENT RUNS ###################################
def run_atoms(ENGINE, rang=None, recur=None, xyzFrequency=500):
ENGINE.set_groups(None)