Error: Unable to cast Python instance to C++ type
oyin alabi
@FlowProject.pre.isfile('Compression_c1.gsd')
@FlowProject.post.isfile('trajectory_c.gsd')
@FlowProject.operation
def equilibrate(job):
with job:
d = job.sp.d
a = job.sp.a
k = job.sp.k
InertiaTarget= job.sp.InertiaTarget
## dumping period during compression
dump_period = job.sp.dump_period
## logging period during compression
log_period = job.sp.log_period
run_steps = job.sp.run_steps
## random seed
seed = job.sp.seed
## packing fraction
## run afterward
#setup mc integrator
mc = hoomd.hpmc.integrate.ConvexPolyhedron()
cpu = hoomd.device.CPU()
sim = hoomd.Simulation(device=cpu,seed=1)
#read state file
sim.create_state_from_gsd(filename='Compression_c1.gsd')
mc = hoomd.hpmc.integrate.ConvexPolyhedron()
sim.operations.integrator = mc
logger = hoomd.logging.Logger()
logger.add(mc, quantities=['type_shapes'])
sim.run(100)
overlaps = mc.overlaps
print("overlaps",overlaps)
Biased_move = hoomd.hpmc.shape_move.Biased(mc=mc, k=k, default_step_size= 0.01, InertiaTarget=InertiaTarget, vertex_move_probability = 0.1)
Biased_move.volume['A'] = 1
updater = hoomd.hpmc.update.Shape(shape_move=Biased_move, trigger=hoomd.trigger.Periodic(1))
updater.shape_move = Biased_move
sim.operations.updaters.append(updater)
#%%Equilibrate the sys
gsd_file = hoomd.write.GSD(trigger=hoomd.trigger.Periodic(1000),filename='trajectory_c.gsd',mode='wb')
logger = hoomd.logging.Logger()
gsd_file.log=logger
logger.add(mc, quantities=['type_shapes'])
sim.operations.writers.append(gsd_file)
tune = hoomd.hpmc.tune.MoveSize.scale_solver(
moves=['a', 'd'],
target=0.2,
trigger=hoomd.trigger.And([
hoomd.trigger.Periodic(100),
hoomd.trigger.Before(sim.timestep + 5000)
]))
sim.operations.tuners.append(tune)
sim.run(run_steps)
from __future__ import division
from __future__ import print_function
import numpy as np
import copy
import math
import itertools
from collections import OrderedDict
import garnett
import signac
import freud
import gsd
import gsd.hoomd
import coxeter
import hoomd
from hoomd import hpmc
from flow import FlowProject
#from flow import with_job
# project = signac.get_project()
@FlowProject.post.isfile("lattice_c.gsd")
@FlowProject.post.isfile("Compression_c.gsd")
@FlowProject.operation
def initialize(job):
with job:
N_particles = job.sp.N_particles
## m parameter
m = job.sp.m
## step sizes
d = job.sp.d
a = job.sp.a
T = job.sp.T
k = job.sp.k
InertiaTarget= job.sp.InertiaTarget
# seed
seed = job.sp.seed
## equilibration time
equil_steps = job.sp.equil_steps
seed = 1
#setup initial spacing with no overlaps
spacing = 1.2
K = math.ceil(N_particles**(1 / 3))
L = K * spacing
x = np.linspace(-L / 2, L / 2, K, endpoint=False)
position = list(itertools.product(x, repeat=3))
position = position[0:N_particles]
orientation = [(1, 0, 0, 0)] * N_particles
#define initial snapshot state
snapshot = gsd.hoomd.Snapshot()
snapshot.particles.N = N_particles
snapshot.configuration.box = [L, L, L,0, 0, 0]
snapshot.particles.typeid = [0] * N_particles
snapshot.particles.types = ['A']
snapshot.particles.position = position
snapshot.particles.orientation = orientation
with gsd.hoomd.open(name='lattice_c.gsd', mode='wb') as f:
f.append(snapshot)
#define computation device to store the state
cpu = hoomd.device.CPU()
sim = hoomd.Simulation(device=cpu,seed=seed)
verts=[
(0.21148922, 0.22627276, 0.77175814),
(0.33755697, -0.95091281, 0.31423103),
(0.27022411, 0.62174096, -0.83995131),
(0.43026415, 0.82755934, 0.51838333),
(0.34515256, 0.12072877, 0.93284621),
(-0.92738684, -0.33247756, -0.82156785),
(0.33699158, 0.29175872, 0.22843193),
(-0.8563681, 0.88964499, 0.59505754),
(0.2283875, 0.56205495, -0.86597468),
(0.20049869, -0.67177166, 0.33690927),
(-0.82489381, 0.13129898, -0.71304647),
(0.93007831, -0.97913281, 0.15260125),
(0.16171859, 0.60549746, 0.18660708),
(-0.56605983, -0.4376672, -0.80355261),
(-0.8542315, 0.59777026, 0.54903978),
(-0.78070602, -0.6196942, 0.30881963),
(0.6553524, 0.39294286, -0.90164643),
(0.65043392, -0.96413667, 0.25880116),
(0.30577482, 0.62580161, 0.24217116),
(0.15274576, -0.50988537, -0.70052125),
(0.12438968, 0.36590175, 0.62994281),
(0.38698022, 0.22453555, -0.85110107),
(-0.80355275, 0.44346009, 0.88224876),
(0.26313235, -0.73589295, 0.33647919),
(-0.92072183, -0.8748703, 0.20241242),
(-0.97819777, -0.82760802, 0.13292609),
(0.11923232, -0.65643469, -0.66725997),
(0.88294149, 0.17092129, 0.92493397),
(0.17553081, -0.90884513, 0.77924176),
(0.22442608, 0.96223872, 0.45966687),
(0.76130224, -0.28672245, 0.18463901),
(-0.55113045, -0.77260838, -0.89789975)]
shape = coxeter.shapes.ConvexPolyhedron(verts)
vol = shape.volume
# get a scaling factor to set the volume to one
scale = vol**(1.0/3.0)
# re-scale all of the vertices
verts /= scale
# re-create the shape with the scaled vertices
shape = coxeter.shapes.ConvexPolyhedron(verts)
vol = shape.volume
# check that the volume of the new particle is actually one
print("initial particle volume",vol)
#setup mc integrator
mc = hoomd.hpmc.integrate.ConvexPolyhedron();
mc.shape['A'] = dict(vertices=verts)
mc.d['A'] = d
mc.a['A'] = a
cpu = hoomd.device.CPU()
sim = hoomd.Simulation(device=cpu,seed=seed)
#read state file
sim.create_state_from_gsd(filename='lattice_c.gsd')
sim.operations.integrator = mc
#sim.operations.writers.append(gsd)
logger = hoomd.logging.Logger()
logger.add(mc, quantities=['type_shapes'])
sim.run(100)
overlaps = mc.overlaps
print(overlaps)
initial_volume_fraction = (sim.state.N_particles * vol/sim.state.box.volume)
print(initial_volume_fraction)
gsd_file = hoomd.write.GSD(trigger=hoomd.trigger.Periodic(10),filename='Compression_c.gsd',mode='wb')
gsd_file.log=logger
logger.add(mc, quantities=['type_shapes'])
sim.operations.writers.append(gsd_file)
initial_box = sim.state.box
final_box = hoomd.Box.from_box(initial_box)
final_volume_fraction = 0.1 #change accordingly
final_box.volume = sim.state.N_particles * vol / final_volume_fraction
compress = hoomd.hpmc.update.QuickCompress(trigger=hoomd.trigger.Periodic(10),target_box=final_box)
logger.add(compress)
#add compress operation to simulation
sim.operations.updaters.append(compress)
Biased_move = hoomd.hpmc.shape_move.Biased(mc=mc, k=k, default_step_size= 0.01, InertiaTarget =InertiaTarget, vertex_move_probability = 0.1)
Biased_move.volume['A'] = 1
updater = hoomd.hpmc.update.Shape(shape_move=Biased_move, trigger=hoomd.trigger.Periodic(1))
updater.shape_move = Biased_move
sim.operations.updaters.append(updater)
logger.add(Biased_move)
#sim.operations.updaters.add(sim.operations, vertex_move)
logger.add(mc, quantities=['type_shapes'])
tune = hoomd.hpmc.tune.MoveSize.scale_solver(moves=['a', 'd'],
target=0.2,
trigger= hoomd.trigger.Periodic(10),
max_translation_move=0.2,
max_rotation_move=0.2)
#add tune operation to simulation
sim.operations.tuners.append(tune)
# InertiaTarget loop
#check the InertiaTarget is met if not run for another 1000 step
inertia=0.1
j = 0
while (abs(inertia-InertiaTarget) > 0.025):
sim.run(1000)
newverts=mc.shape['A']
print(mc.shape['A'])
shape = coxeter.shapes.ConvexPolyhedron(newverts['vertices'])
moment_of_inertia=shape.inertia_tensor.round(3)
inertia= np.trace(moment_of_inertia)
vol=shape.volume
print('Tr(I):',inertia)
j += 1
sim.run(50000)
shapemove = updater.shape_moves
print("shape_moves", shapemove)
Biased_sm= mc.shape['A']
print (Biased_sm)
hoomd.write.GSD.write(state=sim.state, mode='wb', filename='Compression_c.gsd')
@FlowProject.label()
def initialized(job):
try :
with open(job.fn('Compression_c.gsd')) as temp_file :
return True
except :
return False
@FlowProject.pre.isfile('Compression_c.gsd')
@FlowProject.post.isfile('Compression_c1.gsd')
@FlowProject.operation
def compress1(job):
with job:
d = job.sp.d
a = job.sp.a
## dumping period during compression
dump_period = job.sp.dump_period
## logging period during compression
log_period = job.sp.log_period
## random seed
seed = job.sp.seed
## packing fraction
phi = job.sp.phi
## run afterward
run_steps = job.sp.run_steps
T = job.sp.T
seed = 1 #chnage this to an iN_particlesut if I get signac running
#setup initial spacing with no overlaps
InertiaTarget=job.sp.InertiaTarget
k = job.sp.k
mc = hoomd.hpmc.integrate.ConvexPolyhedron()
Biased_move = hoomd.hpmc.shape_move.Biased(mc=mc, k=k, default_step_size= 0.01, InertiaTarget=InertiaTarget, vertex_move_probability = 0.1)
Biased_move.volume['A'] = 1
updater = hoomd.hpmc.update.Shape(shape_move=Biased_move, trigger=hoomd.trigger.Periodic(1))
updater.shape_move = Biased_move
#define computation device to store the state
cpu = hoomd.device.CPU()
sim = hoomd.Simulation(device=cpu,seed=seed)
#read state file
sim.create_state_from_gsd(filename='Compression_c.gsd')
sim.operations.updaters.append(updater)
sim.operations.integrator = mc
logger = hoomd.logging.Logger()
logger.add(mc, quantities=['type_shapes'])
vol=1
initial_volume_fraction = (sim.state.N_particles * vol/sim.state.box.volume)
N_particles = sim.state.N_particles
print(initial_volume_fraction)
gsd_file = hoomd.write.GSD(trigger=hoomd.trigger.Periodic(10),filename='Compression_c1.gsd',mode='wb')
gsd_file.log=logger
logger.add(mc, quantities=['type_shapes'])
sim.operations.writers.append(gsd_file)
initial_box = sim.state.box
final_box = hoomd.Box.from_box(initial_box)
final_volume_fraction = phi #change accordingly
final_box.volume = sim.state.N_particles * vol / final_volume_fraction
print(initial_box.Lx,final_box.Ly)
compress = hoomd.hpmc.update.QuickCompress(trigger=hoomd.trigger.Periodic(10),target_box=final_box)
logger.add(compress)
#add compress operation to simulation
sim.operations.updaters.append(compress)
print('The packing fraction is', sim.state.N_particles * vol/sim.state.box.volume)
hoomd.write.GSD.write(state=sim.state, mode='wb', filename='Compression_c1.gsd')
@FlowProject.label
def compressed1(job) :
try :
with open(job.fn('Compression_c1.gsd')) as temp_file :
return True
except :
return False
@FlowProject.pre.isfile('Compression_c1.gsd')
@FlowProject.post.isfile('trajectory_c.gsd')
@FlowProject.operation
def equilibrate(job):
with job:
d = job.sp.d
a = job.sp.a
k = job.sp.k
InertiaTarget= job.sp.InertiaTarget
## dumping period during compression
dump_period = job.sp.dump_period
## logging period during compression
log_period = job.sp.log_period
run_steps = job.sp.run_steps
## random seed
seed = job.sp.seed
## packing fraction
## run afterward
#setup mc integrator
mc = hoomd.hpmc.integrate.ConvexPolyhedron()
cpu = hoomd.device.CPU()
sim = hoomd.Simulation(device=cpu,seed=1)
#read state file
sim.create_state_from_gsd(filename='Compression_c1.gsd')
mc = hoomd.hpmc.integrate.ConvexPolyhedron()
sim.operations.integrator = mc
logger = hoomd.logging.Logger()
logger.add(mc, quantities=['type_shapes'])
sim.run(100)
overlaps = mc.overlaps
print("overlaps",overlaps)
Biased_move = hoomd.hpmc.shape_move.Biased(mc=mc, k=k, default_step_size= 0.01, InertiaTarget=InertiaTarget, vertex_move_probability = 0.1)
Biased_move.volume['A'] = 1
updater = hoomd.hpmc.update.Shape(shape_move=Biased_move, trigger=hoomd.trigger.Periodic(1))
updater.shape_move = Biased_move
sim.operations.updaters.append(updater)
#%%Equilibrate the sys
gsd_file = hoomd.write.GSD(trigger=hoomd.trigger.Periodic(1000),filename='trajectory_c.gsd',mode='wb')
logger = hoomd.logging.Logger()
gsd_file.log=logger
logger.add(mc, quantities=['type_shapes'])
sim.operations.writers.append(gsd_file)
tune = hoomd.hpmc.tune.MoveSize.scale_solver(
moves=['a', 'd'],
target=0.2,
trigger=hoomd.trigger.And([
hoomd.trigger.Periodic(100),
hoomd.trigger.Before(sim.timestep + 5000)
]))
sim.operations.tuners.append(tune)
sim.run(run_steps)
Thanks,
Oyin
Joshua Anderson
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oyin alabi
import argparse
from hashlib import sha1
import signac
import numpy as np
import random
def main(args, random_seed) :
project = signac.get_project()
m = 4
for N_particles in [432]:
for phi in [0.6] :
for rep in range(args.num_replicas) :
statepoint = dict(
m = m,
# number of particles
N_particles= 2* m**3,
## trans and rot moves
d = 0.15,
a = 0.2,
T = 10000,
## packing fraction
phi = 0.55,
rep = rep,
## dumping period during compression
dump_period = 1e6,
## logging period during compression
log_period = 1e6,
## equilibration time
equil_steps = 1e5,
## run steps
run_steps = 1e6,
# random seed
seed = random.randint(1,1e6))
project.open_job(statepoint).init()
seeds = []
for job in project.find_jobs() :
seeds.append(job.statepoint()['seed'])
if (len(seeds) == len(set(seeds))) :
print("all random seed numbers are unique!")
else :
print("all random seed numbers are not unique!")
if __name__ == '__main__' :
parser = argparse.ArgumentParser(
description="Initialize the data space.")
parser.add_argument(
'--random',
type=str,
help="A string to generate a random seed.")
parser.add_argument(
'-n', '--num-replicas',
type=int,
default=1,
help="Initialize multiple replications.")
args = parser.parse_args()
# Generate an integer from the random str.
try :
random_seed = args.random
except ValueError :
random_seed = sha1(args.random.encode().hexdigest(), 16) % (10 ** 8)
main(args, random_seed)
Here is the operations code
#k = job.sp.k
#InertiaTarget= job.sp.InertiaTarget
mc = hoomd.hpmc.integrate.ConvexPolyhedron()
mc.shape['A'] = dict(vertices=verts)
mc.d['A'] = d
mc.a['A'] = a
#read state file
sim.create_state_from_gsd(filename='lattice_c.gsd')
sim.operations.integrator = mc
#sim.operations.writers.append(gsd)
logger = hoomd.logging.Logger()
logger.add(mc, quantities=['type_shapes'])
sim.run(100)
overlaps = mc.overlaps
print(overlaps)
initial_volume_fraction = (sim.state.N_particles * vol/sim.state.box.volume)
print(initial_volume_fraction)
gsd_file = hoomd.write.GSD(trigger=hoomd.trigger.Periodic(10),filename='Compression_c.gsd',mode='wb')
gsd_file.log=logger
logger.add(mc, quantities=['type_shapes'])
sim.operations.writers.append(gsd_file)
initial_box = sim.state.box
final_box = hoomd.Box.from_box(initial_box)
final_volume_fraction = 0.1 #change accordingly
final_box.volume = sim.state.N_particles * vol / final_volume_fraction
compress = hoomd.hpmc.update.QuickCompress(trigger=hoomd.trigger.Periodic(10),target_box=final_box)
logger.add(compress)
#add compress operation to simulation
sim.operations.updaters.append(compress)
default_step_size= 0.01
nselect=1
vertex_move = hpmc.shape_move.Vertex(vertex_move_probability = 1)
vertex_move.volume['A'] = 1
updater = hpmc.update.Shape(shape_move=vertex_move, trigger=hoomd.trigger.Periodic(1))
updater.shape_move = vertex_move
logger.add(vertex_move)
#sim.operations.updaters.add(sim.operations, vertex_move)
logger.add(mc, quantities=['type_shapes'])
tune = hoomd.hpmc.tune.MoveSize.scale_solver(moves=['a', 'd'],
target=0.2,
trigger= hoomd.trigger.Periodic(10),
max_translation_move=0.2,
max_rotation_move=0.2)
sim.run(50000)
shapemove = updater.shape_moves
print("shape_moves", shapemove)
vertex_move= mc.shape['A']
print (vertex_move)
default_step_size= 0.01
nselect=1
vertex_move = hpmc.shape_move.Vertex(vertex_move_probability = 1)
vertex_move.volume['A'] = 1
updater = hpmc.update.Shape(shape_move=vertex_move, trigger=hoomd.trigger.Periodic(1))
updater.shape_move = vertex_move
## dumping period during compression
dump_period = job.sp.dump_period
## logging period during compression
log_period = job.sp.log_period
run_steps = job.sp.run_steps
## random seed
seed = job.sp.seed
## packing fraction
## run afterward
#setup mc integrator
mc = hoomd.hpmc.integrate.ConvexPolyhedron()
cpu = hoomd.device.CPU()
sim = hoomd.Simulation(device=cpu,seed=1)
#read state file
sim.create_state_from_gsd(filename='Compression_c1.gsd')
mc = hoomd.hpmc.integrate.ConvexPolyhedron()
n_verts= mc.shape['A']
mc.shape['A'] = dict(vertices=n_verts['vertices']) # Because the vertex has changed I can't use the initial vertices so I tried this out
sim.operations.integrator = mc
logger = hoomd.logging.Logger()
logger.add(mc, quantities=['type_shapes'])
nselect=1
vertex_move = hpmc.shape_move.Vertex(default_step_size= 0.01, vertex_move_probability = 1)
vertex_move.volume['A'] = 1
updater = hpmc.update.Shape(shape_move=vertex_move, trigger=hoomd.trigger.Periodic(1))
updater.shape_move = vertex_move
sim.operations.updaters.append(updater)
#%%Equilibrate the sys
gsd_file = hoomd.write.GSD(trigger=hoomd.trigger.Periodic(1000),filename='trajectory_c.gsd',mode='wb')
logger = hoomd.logging.Logger()
gsd_file.log=logger
logger.add(mc, quantities=['type_shapes'])
sim.operations.writers.append(gsd_file)
tune = hoomd.hpmc.tune.MoveSize.scale_solver(
moves=['a', 'd'],
target=0.2,
trigger=hoomd.trigger.And([
hoomd.trigger.Periodic(100),
hoomd.trigger.Before(sim.timestep + 5000)
]))
sim.operations.tuners.append(tune)
sim.run(run_steps) #here is the part that gives the error
@FlowProject.pre.isfile('trajectory_c.gsd')
@FlowProject.post.isfile('Simf_c.gsd')
@FlowProject.operation
def equilibrate1(job):
traj = gsd.hoomd.open('trajectory_c.gsd') #open previous trajectory
num_frames= len(traj)
solid = freud.order.SolidLiquid(l=6, q_threshold=0.7, solid_threshold=6)
is_solid = []
for frame in traj:
solid.compute(system=(frame.configuration.box, frame.particles.position),
neighbors=dict(mode='nearest', num_neighbors=8))
is_solid.append(solid.num_connections > solid.solid_threshold)
num_solid = np.array([np.sum(a) for a in is_solid])
np.savetxt('num_parts.csv',num_solid, delimiter= ',')
print(num_solid)
gsd_file = hoomd.write.GSD( trigger=hoomd.trigger.Periodic(10), mode='wb', filename='Simf_c.gsd', log=logger) #save for next part
gsd_file.log =logger
logger.add(mc, quantities=['type_shapes'])
sim.operations.writers.append(gsd_file)
sim.run(T)
num_overlaps = mc.overlaps #The integrator performs the MC steps(i.e altering a,d), then it checks for overlaps
print('overlaps=',num_overlaps)
from garnett.reader import GSDHOOMDFileReader
from garnett.writer import PosFileWriter
gsd_reader = GSDHOOMDFileReader()
writer = PosFileWriter()
with open('Simf_c.gsd', 'rb') as gsdfile:
traj = gsd_reader.read(gsdfile)
with open('Simf_c.pos', 'w', encoding='utf-8') as posfile:
writer.write(traj, posfile)
gsd_reader = GSDHOOMDFileReader()
writer = PosFileWriter()
with open('Compression_c1.gsd', 'rb') as gsdfile:
traj = gsd_reader.read(gsdfile)
with open('Compression_c1.pos', 'w', encoding='utf-8') as posfile:
writer.write(traj, posfile)
if __name__ == '__main__':
from flow import FlowProject
FlowProject().main()
And Here is the error message
Error message
(base) tola@lasiurus:~/Downloads/hoomd2/hoomd-blue/build/my_project$ python SigVertSm.py run --progress
Using environment configuration: StandardEnvironment
0%| | 0/1 [00:00<?, ?it/s]
Traceback (most recent call last):
File "/home/tola/miniconda3/lib/python3.8/site-packages/flow/project.py", line 3475, in _execute_operation
self._operations[operation.name](*operation._jobs)
File "/home/tola/miniconda3/lib/python3.8/site-packages/flow/project.py", line 625, in __call__
return self._op_func(*jobs)
File "SigVertSm.py", line 316, in equilibrate
sim.run(run_steps)
File "/home/tola/miniconda3/lib/python3.8/site-packages/hoomd/simulation.py", line 453, in run
self.operations._schedule()
File "/home/tola/miniconda3/lib/python3.8/site-packages/hoomd/operations.py", line 184, in _schedule
self.integrator._attach()
File "/home/tola/miniconda3/lib/python3.8/site-packages/hoomd/hpmc/integrate.py", line 425, in _attach
super()._attach()
File "/home/tola/miniconda3/lib/python3.8/site-packages/hoomd/operation.py", line 395, in _attach
super()._attach()
File "/home/tola/miniconda3/lib/python3.8/site-packages/hoomd/operation.py", line 226, in _attach
self._apply_typeparam_dict(self._cpp_obj, self._simulation)
File "/home/tola/miniconda3/lib/python3.8/site-packages/hoomd/operation.py", line 255, in _apply_typeparam_dict
typeparam._attach(cpp_obj, simulation.state)
File "/home/tola/miniconda3/lib/python3.8/site-packages/hoomd/data/typeparam.py", line 171, in _attach
self.param_dict._attach(cpp_obj, self.name,
File "/home/tola/miniconda3/lib/python3.8/site-packages/hoomd/data/parameterdicts.py", line 515, in _attach
self._single_setitem(key, parameters[key])
File "/home/tola/miniconda3/lib/python3.8/site-packages/hoomd/data/parameterdicts.py", line 458, in _single_setitem
getattr(self._cpp_obj, self._setter)(key, item)
RuntimeError: Unable to cast Python instance to C++ type (compile in debug mode for details)
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "SigVertSm.py", line 357, in <module>
FlowProject().main()
File "/home/tola/miniconda3/lib/python3.8/site-packages/flow/project.py", line 5132, in main
args.func(args)
File "/home/tola/miniconda3/lib/python3.8/site-packages/flow/project.py", line 4844, in _main_run
run()
File "/home/tola/miniconda3/lib/python3.8/site-packages/flow/project.py", line 3720, in run
self._run_operations(
File "/home/tola/miniconda3/lib/python3.8/site-packages/flow/project.py", line 3305, in _run_operations
self._execute_operation(operation, timeout, pretend)
File "/home/tola/miniconda3/lib/python3.8/site-packages/flow/project.py", line 3477, in _execute_operation
raise UserOperationError(execution_error_message) from error
flow.errors.UserOperationError: An exception was raised during operation equilibrate for job or aggregate with id 9a1c427d69e72f81804ae08dca35cb48.
I'd appraciate any suggestion.
Thanks,
Oyin
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Brandon Butler
Hey Ovin,
Thanks for moving to hoomd version 3.11.0. However, this really isn't a minimal example. You are using signac in the example and it looks like there is a lot of code likely not related to the problem. It is helpful to people on the list if a bug is shown in a minimal script. That is a script that contains the minimal complexity, but still errors. While this takes some effort on the person asking's side, it greatly aids though attempting to help debug you script.
Best,
File "/home/tola/miniconda3/lib/python3.8/site-packages/hoomd/data/parameterdicts.py",line 515, in _attach
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Brandon Butler
MolSSI Fellow
PhD Candidate, Chemical Engineering and Scientific Computing | Glotzer Lab, University of Michigan
Email: butl...@umich.edu
oyin alabi
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oyin alabi
Although I am not getting any errors, I am unable to get the current vertices for use in the equilbrate section of the code. Is there a way to extract the current vertices from the code below after the vertex move and use them in the next step? Please find below the minimal version.
Thanks,
Oyin
from __future__ import division
from __future__ import print_function
import numpy as np
import copy
import math
import itertools
from collections import OrderedDict
import garnett
import gsd.hoomd
import coxeter
import hoomd
from hoomd import hpmc
T =10000
m= 2
N_particles= 2* m**3
seed = 1
#setup
spacing = 1.2
K = math.ceil(N_particles**(1 / 3))
L = K * spacing
x = np.linspace(-L / 2, L / 2, K, endpoint=False)
position = list(itertools.product(x, repeat=3))
position = position[0:N_particles]
orientation = [(1, 0, 0, 0)] * N_particles
#define initial snapshot state
snapshot = gsd.hoomd.Snapshot()
snapshot.particles.N = N_particles
snapshot.configuration.box = [L, L, L,0, 0, 0]
snapshot.particles.typeid = [0] * N_particles
snapshot.particles.position = position
snapshot.particles.orientation = orientation
with gsd.hoomd.open(name='lattice_c.gsd', mode='wb') as f:
f.append(snapshot)
sim = hoomd.Simulation(device=cpu,seed=seed)
verts = [[0.5, 0.5, 0.5], [0.5, -0.5, 0.5], [0.5, 0.5, -0.5], [0.5, -0.5, -0.5],[-0.5, 0.5, 0.5], [-0.5, -0.5, 0.5], [-0.5, 0.5, -0.5], [-0.5, -0.5, -0.5]]
shape = coxeter.shapes.ConvexPolyhedron(verts)
vol = shape.volume
mc = hoomd.hpmc.integrate.ConvexPolyhedron();
(0.5, 0.5, 0.5),
(0.5, -0.5, 0.5),
(0.5, 0.5, -0.5),
(0.5, -0.5, -0.5),
(-0.5, 0.5, 0.5),
(-0.5, -0.5, 0.5),
(-0.5, 0.5, -0.5),
(-0.5, -0.5, -0.5)
])
mc.d['cube'] = 0.15
mc.a['cube'] = 0.2
#read state file
sim.create_state_from_gsd(filename='lattice_c.gsd')
sim.operations.integrator = mc
logger.add(mc, quantities=['type_shapes'])
sim.run(100)
overlaps = mc.overlaps
print(overlaps)
initial_volume_fraction = (sim.state.N_particles * vol/sim.state.box.volume)
print(initial_volume_fraction)
gsd_file.log=logger
logger.add(mc, quantities=['type_shapes'])
sim.operations.writers.append(gsd_file)
initial_box = sim.state.box
final_box = hoomd.Box.from_box(initial_box)
final_box.volume = sim.state.N_particles * vol / final_volume_fraction
compress = hoomd.hpmc.update.QuickCompress(trigger=hoomd.trigger.Periodic(10),target_box=final_box)
logger.add(compress)
#add compress operation to simulation
sim.operations.updaters.append(compress)
nselect =0.01
cube_verts = [ (0.5, 0.5, 0.5), (0.5, -0.5, 0.5), (0.5, 0.5, -0.5), (0.5, -0.5, -0.5), (-0.5, 0.5, 0.5), (-0.5, -0.5, 0.5), (-0.5, 0.5, -0.5), (-0.5, -0.5, -0.5)]
mc.shape['cube'] = dict(vertices=np.asarray([ (0.5, 0.5, 0.5), (0.5, -0.5, 0.5), (0.5, 0.5, -0.5), (0.5, -0.5, -0.5), (-0.5, 0.5, 0.5), (-0.5, -0.5, 0.5), (-0.5, 0.5, -0.5), (-0.5, -0.5, -0.5)]))
"VERTEX MOVES"
vertex_move = hoomd.hpmc.shape_move.Vertex(default_step_size= 0.01, vertex_move_probability = 1)
vertex_move.volume['cube'] = 1
updater = hoomd.hpmc.update.Shape(shape_move=vertex_move, trigger=hoomd.trigger.Periodic(1))
updater.shape_move = vertex_move
sim.operations.updaters.append(updater)
logger.add(vertex_move)
logger.add(mc, quantities=['type_shapes'])
tune = hoomd.hpmc.tune.MoveSize.scale_solver(moves=['a', 'd'],
target=0.2,
trigger= hoomd.trigger.Periodic(10),
max_translation_move=0.2,
max_rotation_move=0.2)
#add tune operation to simulation
sim.operations.tuners.append(tune)
shapemove = updater.shape_moves
print("shape_moves", shapemove)
print (vertex_sm)
hoomd.write.GSD.write(state=sim.state, mode='wb', filename='simulation.gsd')
Brandon Butler
Oyin,
Does "mc.shape['cube']" not work?
Also you have logger.add(mc, ["type_shapes"]) multiple times. You only need it once. You also only need to set the mc.shape values once.
Best,
Brandon
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oyin alabi
Hi,
from __future__ import division
from __future__ import print_function
import numpy as np
import copy
import math
import itertools
from collections import OrderedDict
import garnett
import signac
import freud
import gsd
import gsd.hoomd
import coxeter
import hoomd
from hoomd import hpmc
# %% startup parameters
T =10000
m= 2
N_particles= 2* m**3
seed = 1
#setup initial spacing with no overlaps
spacing = 1.2
K = math.ceil(N_particles**(1 / 3))
L = K * spacing
x = np.linspace(-L / 2, L / 2, K, endpoint=False)
position = list(itertools.product(x, repeat=3))
position = position[0:N_particles]
orientation = [(1, 0, 0, 0)] * N_particles
#define initial snapshot state
snapshot = gsd.hoomd.Snapshot()
snapshot.particles.N = N_particles
snapshot.configuration.box = [L, L, L,0, 0, 0]
snapshot.particles.typeid = [0] * N_particles
snapshot.particles.types = ['cube']
snapshot.particles.position = position
snapshot.particles.orientation = orientation
with gsd.hoomd.open(name='lattice_c.gsd', mode='wb') as f:
f.append(snapshot)
#define computation device to store the state
cpu = hoomd.device.CPU()
sim = hoomd.Simulation(device=cpu,seed=seed)
# %% particle volume using coxeter
cube_verts = [ (0.5, 0.5, 0.5), (0.5, -0.5, 0.5), (0.5, 0.5, -0.5), (0.5, -0.5, -0.5), (-0.5, 0.5, 0.5), (-0.5, -0.5, 0.5), (-0.5, 0.5, -0.5), (-0.5, -0.5, -0.5)]
shape = coxeter.shapes.ConvexPolyhedron(cube_verts)
vol = shape.volume
#setup mc integrator
mc = hoomd.hpmc.integrate.ConvexPolyhedron()
mc.shape['cube'] = dict(vertices=[
(0.5, 0.5, 0.5),
(0.5, -0.5, 0.5),
(0.5, 0.5, -0.5),
(0.5, -0.5, -0.5),
(-0.5, 0.5, 0.5),
(-0.5, -0.5, 0.5),
(-0.5, 0.5, -0.5),
(-0.5, -0.5, -0.5)
])
mc.d['cube'] = 0.15
mc.a['cube'] = 0.2
#read state file
sim.create_state_from_gsd(filename='lattice_c.gsd')
sim.operations.integrator = mc
#sim.operations.writers.append(gsd)
sim.run(100)
overlaps = mc.overlaps
print(overlaps)
initial_volume_fraction = (sim.state.N_particles * vol/sim.state.box.volume)
print(initial_volume_fraction)
gsd_file = hoomd.write.GSD(trigger=hoomd.trigger.Periodic(10),filename='Compression_c.gsd',mode='wb') #added a file to just record compression and on
gsd_file.log=logger
logger.add(mc, quantities=['type_shapes'])
sim.operations.writers.append(gsd_file)
initial_box = sim.state.box
final_box = hoomd.Box.from_box(initial_box)
final_volume_fraction = 0.7 #change accordingly
final_box.volume = sim.state.N_particles * vol / final_volume_fraction
compress = hoomd.hpmc.update.QuickCompress(trigger=hoomd.trigger.Periodic(10),target_box=final_box)
logger.add(compress)
#add compress operation to simulation
sim.operations.updaters.append(compress)
"VERTEX MOVES"
nselect =0.0005
"VERTEX MOVES"
vertex_move = hoomd.hpmc.shape_move.Vertex(default_step_size= 0.01, vertex_move_probability = 1)
vertex_move.volume['cube'] = 1
updater = hoomd.hpmc.update.Shape(shape_move=vertex_move, trigger=hoomd.trigger.Periodic(1))
updater.shape_move = vertex_move
sim.operations.updaters.append(updater)
logger.add(vertex_move)
logger.add(mc, quantities=['type_shapes'])
tune = hoomd.hpmc.tune.MoveSize.scale_solver(moves=['a', 'd'],
target=0.2,
trigger= hoomd.trigger.Periodic(10),
max_translation_move=0.2,
max_rotation_move=0.2)
#add tune operation to simulation
sim.operations.tuners.append(tune)
sim.run(1000)
shapemove = updater.shape_moves
print("shape_moves", shapemove)
vertex_sm= mc.shape['cube']
print (vertex_sm)
hoomd.write.GSD.write(state=sim.state, mode='wb', filename='simulation.gsd')
#%%
from __future__ import division
from __future__ import print_function
import numpy as np
import copy
import math
import itertools
from collections import OrderedDict
import garnett
import freud
import gsd
import gsd.hoomd
import coxeter
import hoomd
from hoomd import hpmc
cpu = hoomd.device.CPU()
sim = hoomd.Simulation(device=cpu, seed=20)
mc = hoomd.hpmc.integrate.ConvexPolyhedron()
'''mc.shape['cube'] = dict(vertices=[
(-0.5, 0, 0),
(0.5, 0, 0),
(0, -0.5, 0),
(0, 0.5, 0),
(0, 0, -0.5),
(0, 0, 0.5),
])'''// Is there a way to extract the current vertices from the code above
sim.operations.integrator = mc
sim.create_state_from_gsd(filename='simulation.gsd')
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Brandon Butler
I am assuming that you have two files, and the second is the one you want to keep the shape from the first. This is not clear in your example and perhaps labeling them in the future would help. Given this information, however, I know your problem. You need to read the type_shape value from the GSD file (with the gsd package) and read the last frames 'particles/type_shapes' value which will be a JSON valid string in gsd.fl or a tuple of dictionaries in gsd.hoomd. You can use the vertices from that for your initial shape in the second file.
Best,
Brandon
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oyin alabi
vertex_move = hoomd.hpmc.shape_move.Vertex(default_step_size= 0.01, vertex_move_probability = 1)
sim = hoomd.Simulation(device=cpu, seed=1)
sim.operations.integrator = mc
mc = hoomd.hpmc.integrate.ConvexPolyhedron()
sim.create_state_from_gsd('simulation.gsd')
traj = gsd.hoomd.open('simulation.gsd', 'rb')
#append vertices
vertices=[]
traj2=traj[-1].particles.type_shapes
print(traj2)
#traj2.append(vertices) I am wondering if there is a way I can append the vertices as a list
mc.shape['cube'] = dict(vertices=vertices)
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Brandon Butler
I think you mean access the vertices, not append them. Given your code mc.shape["cube"] = {"vertices": traj2[0]["vertices"]} should work. This isn't really a HOOMD question though. I would recommend one of many Python tutorials to help familiarize yourself with Python as a programming language.
Best,
Brandon
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