def _runtime_initialize(self):
"""
Automatically sets the selector order at the engine runtime.
"""
diffs = np.array([(np.sum(self.engine.realCoordinates[g.indexes], axis=0)/len(g))-self.__center for g in self.engine.groups], dtype=FLOAT_TYPE)
dists = np.array([np.sqrt(np.add.reduce(diff**2)) for diff in diffs])
order = np.argsort(dists).astype(INT_TYPE)
if self.__expand:
order = [o for o in reversed(order)]
# set order
self.set_order(order)
# set groups move generators
if self.__adjustMoveGenerators:
from fullrmc.Core.MoveGenerator import MoveGeneratorCollector
from fullrmc.Generators.Rotations import RotationGenerator
from fullrmc.Generators.Translations import TranslationTowardsCenterGenerator
TG_amp = self.__generatorsParams['TG']['amplitude']
TG_ang = self.__generatorsParams['TG']['angle']
TG_dam = self.__generatorsParams['TG']['damping']
RG_ang = self.__generatorsParams['RG']['amplitude']
maxDist = FLOAT_TYPE(np.max(dists))
TG_ampInterval = TG_amp-TG_amp*TG_dam
for idx in range(len(self.engine.groups)):
g = self.engine.groups[idx]
damping = ((maxDist-dists[idx])/maxDist)*TG_ampInterval
coll = [TranslationTowardsCenterGenerator(center={"fixed":self.__center}, amplitude=TG_amp-damping, angle=TG_ang, direction=not self.__expand)]
if len(g) > 1:
coll.append(RotationGenerator(amplitude=RG_ang))
mg = MoveGeneratorCollector(collection=coll, randomize=True)
g.set_move_generator( mg )
def run_molecules(ENGINE,
rang=5,
recur=100,
refine=False,
explore=True,
exportPdb=False,
xyzFrequency=500):
ENGINE.set_groups_as_molecules()
[
g.set_move_generator(
MoveGeneratorCollector(collection=[
TranslationGenerator(amplitude=0.2),
RotationGenerator(amplitude=2)
],
randomize=True)) for g in ENGINE.groups
]
# number of steps
nsteps = 20 * len(ENGINE.groups)
# set selector
gs = RecursiveGroupSelector(RandomSelector(ENGINE),
recur=recur,
refine=refine,
explore=explore)
ENGINE.set_group_selector(gs)
for stepIdx in range(rang):
LOGGER.info("Running 'molecules' mode step %i" % (stepIdx))
ENGINE.run(numberOfSteps=nsteps,
saveFrequency=nsteps,
xyzFrequency=xyzFrequency,
xyzPath="moleculeTraj.xyz",
restartPdb=None)
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)
r = RotationGenerator(amplitude=10)
mg = MoveGeneratorCollector(collection=[t, r],
randomize=True,
weights=[(0, 1), (1, 5)])
g.set_move_generator(mg)
# set runtime parameters
nsteps = 1000
xyzFrequency = 1
# run engine
xyzPath = "trajectory.xyz"
if os.path.isfile(xyzPath): os.remove(xyzPath)
ENGINE.run(numberOfSteps=nsteps,
saveFrequency=2 * nsteps,
xyzFrequency=xyzFrequency,
xyzPath=xyzPath,
restartPdb=None)
def shrink(ENGINE, newDim):
ENGINE.set_groups_as_molecules()
[
g.set_move_generator(
MoveGeneratorCollector(collection=[
TranslationGenerator(amplitude=0.2),
RotationGenerator(amplitude=5)
],
randomize=True)) for g in ENGINE.groups
]
# get groups order
centers = [
np.sum(ENGINE.realCoordinates[g.indexes], axis=0) / len(g)
for g in ENGINE.groups
]
distances = [np.sqrt(np.add.reduce(c**2)) for c in centers]
order = np.argsort(distances)
# change boundary conditions
bcFrom = str([list(bc) for bc in ENGINE.boundaryConditions.get_vectors()])
ENGINE.set_boundary_conditions(newDim)
bcTo = str([list(bc) for bc in ENGINE.boundaryConditions.get_vectors()])
LOGGER.info("boundary conditions changed from %s to %s" % (bcFrom, bcTo))
# set selector
recur = 200
gs = RecursiveGroupSelector(DefinedOrderSelector(ENGINE, order=order),
recur=recur,
refine=True)
ENGINE.set_group_selector(gs)
# number of steps
nsteps = recur * len(ENGINE.groups)
for stepIdx in range(10):
LOGGER.info("Running 'shrink' mode step %i" % (stepIdx))
ENGINE.run(numberOfSteps=nsteps, saveFrequency=nsteps)
fname = "shrink_" + str(newDim).replace(".", "p")
def random():
# run engine random rotations
xyzPath="random.xyz"
print("Random rotation")
if os.path.isfile(xyzPath): os.remove(xyzPath)
[g.set_move_generator(RotationGenerator(amplitude=10)) for g in ENGINE.groups]
ENGINE.run(numberOfSteps=nsteps, saveFrequency=2*nsteps, xyzFrequency=xyzFrequency, xyzPath=xyzPath, restartPdb=None)
def explore(ENGINE, nsteps=1000, rang=3):
# create group of single molecule
ENGINE.set_groups_as_molecules()
ENGINE.set_groups(ENGINE.groups[0])
# set move generator
[
g.set_move_generator(
MoveGeneratorCollector(collection=[
TranslationGenerator(amplitude=0.5),
RotationGenerator(amplitude=5)
],
randomize=True)) for g in ENGINE.groups
]
# set selector
recur = nsteps
gs = RecursiveGroupSelector(RandomSelector(ENGINE),
recur=recur,
refine=False,
explore=True)
# run
for step in range(rang):
ENGINE.run(numberOfSteps=nsteps, saveFrequency=2 * nsteps)