Random box deformations at constant volume

[oyin alabi]

Hi,

 

I am working on a simulation that requires the simulation box to undergo random deformations at constant volume, I would like to inquire how to specify the box move types, specifically the aspect and shear at a fixed volume. I have looked at the documentation (https://hoomd-blue.readthedocs.io/en/v4.0.1/module-hpmc-update.html#hoomd.hpmc.update.BoxMC) , and I have included the BoxMC in my code.  Please find below a minimum version of the code.

I'd appreciate any suggestion.

 

Thanks,

Oyin

 

#minimum version of the code

# %% import packages

from __future__ import division

from __future__ import print_function

import hoomd

import gsd.hoomd

import math

import freud

import itertools

import numpy as np

from hoomd import hpmc

import coxeter

 

# %% startup parameters  

T =10000  

m= 4 

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)

 

 

verts = [[0.05, 0.05, 0.05], [0.05, -0.05, 0.05], [0.05, 0.05, -0.05], [0.05, -0.05, -0.05],[-0.05, 0.05, 0.05], [-0.05, -0.05, 0.05], [-0.05, 0.05, -0.05], [-0.05, -0.05, -0.05]]

shape = coxeter.shapes.ConvexPolyhedron(verts)

vol = shape.volume

 

#setup mc integrator  

mc = hoomd.hpmc.integrate.ConvexPolyhedron()

mc.shape['cube'] = dict(vertices=[

    (0.05, 0.05, 0.05),

    (0.05, -0.05, 0.05),

    (0.05, 0.05, -0.05),

    (0.05, -0.05, -0.05),

    (-0.05, 0.05, 0.05),

    (-0.05, -0.05, 0.05),

    (-0.05, 0.05, -0.05),

    (-0.05, -0.05, -0.05),

])

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 = hoomd.logging.Logger()

logger.add(mc, quantities=['type_shapes'])           

 

sim.run(100) 

#box deformation      

Box_shape= hoomd.hpmc.update.BoxMC(trigger=hoomd.trigger.Periodic(10), betaP=hoomd.variant.Constant(1))

sim.operations.updaters.append(Box_shape)

 

#initial box volume

initial_volume_fraction = (sim.state.N_particles * vol/sim.state.box.volume)

print(initial_volume_fraction)

 

gsd_file.log=logger

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

 sim.operations.writers.append(gsd_file)

 

 

#performs a quick compress 

initial_box = sim.state.box

final_box = hoomd.Box.from_box(initial_box)

final_volume_fraction = 0.55              

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) 

 

 

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)

 

#append tune operation to simulation

sim.operations.tuners.append(tune)

sim.run(1000)

 

#check the compress.complete property if it is not true run for another 1000 steps

while not compress.complete and sim.timestep < 1e6:

 

    sim.run(1000)

[Joshua Anderson]

Oyin,

Set the aspect and shear attributes of Box_shape to enable these move types:

https://hoomd-blue.readthedocs.io/en/v4.0.1/module-hpmc-update.html#hoomd.hpmc.update.BoxMC.aspect

https://hoomd-blue.readthedocs.io/en/v4.0.1/module-hpmc-update.html#hoomd.hpmc.update.BoxMC.shear

------

Joshua A. Anderson, Ph.D.

Research Area Specialist, Chemical Engineering, University of Michigan

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[oyin alabi]

Hi,

Thank you for your response. I specified the aspect and shear moves, however I am getting this error "*Warning*: No move types with non-zero weight. UpdaterBoxMC has nothing to do. ".  

Please find below the code. I'd appreciate any suggestion. 

 

Thanks,

Oyin

 

 

# %% import packages

 

from __future__ import division

from __future__ import print_function

 

#import compress_helper

#from compress_helper import length_geom

import hoomd

import gsd.hoomd

import math

#from fresnel import render

#from fresnel import render_movie

import freud

#import matplotlib 

#sim.operations.writers.append(gsd)

 

logger = hoomd.logging.Logger()

logger.add(mc, quantities=['type_shapes'])           

 

sim.run(100) 

       

Box_shape= hoomd.hpmc.update.BoxMC(trigger=hoomd.trigger.Periodic(10), betaP=hoomd.variant.Constant(10.0))

aspect=Box_shape.aspect

aspect.weight= 0.8

aspect.delta=1.2

 

shear=Box_shape.shear

shear.weight= 0.8

shear.delta=1.2

shear.reduce=0.6 

print("shear moves", Box_shape.shear_moves) 

sim.operations.updaters.append(Box_shape)

print("aspect moves", Box_shape.aspect_moves)

print("shear moves", Box_shape.shear_moves) 

 

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 

sim.operations.writers.append(gsd_file)

 

 

#performs a quick compress 

initial_box = sim.state.box

final_box = hoomd.Box.from_box(initial_box)

final_volume_fraction = 0.55              

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) 

 

 

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

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[Joshua Anderson]

Oyin,

aspect and shear are dictionaries. You need to set them to dictionaries with the keys 'weight', 'delta', and 'reduce' as appropriate. Your code adds attributes by these names, which HOOMD-blue does not expect or examine.

------

Joshua A. Anderson, Ph.D.

Research Area Specialist, Chemical Engineering, University of Michigan

To view this discussion on the web visit https://groups.google.com/d/msgid/hoomd-users/CAEPx1Dxz%2B%2BTFJ-_yXf_YFgkARfmbwehx6srvCVP_mLxGyDT6Pg%40mail.gmail.com.

[oyin alabi]

Hi,

Thanks for the suggestion, it works now.

Thanks again,

Oyin

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