##########################################################################################
################################### RUN no_constraints #################################
# rename first frame set by default to '0'
ENGINE.rename_frame('0', 'no_constraints')
ACN_CONSTRAINT.set_used(False)
EMD_CONSTRAINT.set_used(False)
run_normal(nsteps=1000000, saveFrequency=1000, engineFilePath=engineFilePath)
run_swap(nsteps=100000, saveFrequency=1000, engineFilePath=engineFilePath)
run_normal(nsteps=10000, saveFrequency=1000, engineFilePath=engineFilePath)
##########################################################################################
###################################### RUN with_vdw ####################################
ENGINE.add_frames('with_vdw')
ENGINE.set_used_frame('with_vdw')
ENGINE.reinit_frame('with_vdw')
ACN_CONSTRAINT.set_used(False)
EMD_CONSTRAINT.set_used(True)
run_normal(nsteps=1000000, saveFrequency=1000, engineFilePath=engineFilePath)
run_swap(nsteps=100000, saveFrequency=1000, engineFilePath=engineFilePath)
run_normal(nsteps=10000, saveFrequency=1000, engineFilePath=engineFilePath)
##########################################################################################
################################### RUN all_constraints ################################
ENGINE.add_frames('all_constraints')
ENGINE.set_used_frame('all_constraints')
ENGINE.reinit_frame('all_constraints')
ACN_CONSTRAINT.set_used(True)
EMD_CONSTRAINT.set_used(True)
ACN_CONSTRAINT.set_coordination_number_definition([
ENGINE.set_groups([RO, RLi, RCo])
## run engine
ENGINE.run(numberOfSteps=numberOfSteps, saveFrequency=saveFrequency)
# #################################################################################### #
# ################################## RUN SIMULATION ################################## #
## run normal
normal_run(numberOfSteps=100000, saveFrequency=50000)
PDF_CONSTRAINT.set_adjust_scale_factor((10, 0.7, 1.3))
normal_run(numberOfSteps=250000, saveFrequency=50000)
## add first swapping frame
if not ENGINE.is_frame('swap_1'):
ENGINE.add_frame('swap_1')
## use swap_1 frame and run swapping
ENGINE.set_used_frame('swap_1')
swaps_run(numberOfSteps=200000, saveFrequency=50000)
normal_run(numberOfSteps=250000, saveFrequency=50000)
## add first removing frame
if not ENGINE.is_frame('removes_2'):
ENGINE.add_frame('removes_2')
## use removes_2 frame and run some removes
ENGINE.set_used_frame('removes_2')
for _ in range(20):
# remove as little as possible then try to refine
removes_run(numberOfSteps=100, saveFrequency=100)
normal_run(numberOfSteps=100000, saveFrequency=10000)
swaps_run(numberOfSteps=50000, saveFrequency=10000)
# set number density
ENGINE.set_number_density(.0125)
# save engine
ENGINE.save()
else:
ENGINE = ENGINE.load(engineFilePath)
# get constraints
PDF_CONSTRAINT, EMD_CONSTRAINT, ACNC_CONSTRAINT = ENGINE.constraints
# add multiframe
if not ENGINE.is_frame(multiframe):
ENGINE.add_frame({'name':multiframe, 'frames_name':numberOfFrames})
for sf in ENGINE.frames[multiframe]['frames_name']:
ENGINE.set_used_frame(os.path.join(multiframe, sf))
ENGINE.set_pdb(os.path.join(DIR_PATH, 'multiframe_structure_%s.pdb'%sf))
_usedConstraints, _constraints, _rigidConstraints = ENGINE.initialize_used_constraints(sortConstraints=True)
if not len(_usedConstraints):
LOGGER.warn("@%s No constraints are used. Configuration will be randomized"%ENGINE.usedFrame)
# runtime initialize group selector
ENGINE._Engine__groupSelector._runtime_initialize()
# runtime initialize constraints
_=[c._runtime_initialize() for c in _usedConstraints]
LOGGER.info("@%s Stochastic engine files are created"%ENGINE.usedFrame)
################################################################################
###################### CREATE SOFTGRID WORKERS MANAGEMENT ######################
WM = MultiframeUtils.WorkersManagement()
WM.start(engine=ENGINE, multiframe='size_distribution', orchestrator=None)