Rigid body

[Al ehmn]

Hi , Dear HOMMD-blue users, I am trying to use   hoomd.group.rigid() to simulate my systems,

my script looks like this:

import hoomd

import hoomd.md

import hoomd.deprecated

hoomd.context.initialize()

hoomd.deprecated.init.read_xml(filename="b.xml")

nl = hoomd.md.nlist.cell();

slj =hoomd.md.pair.slj(r_cut=3.0, nlist=nl, d_max = 2.0)

slj.pair_coeff.set('A', 'A', epsilon=1.0, sigma=1.0,  r_cut=2.5)

slj.pair_coeff.set('A', 'B', epsilon=1.0, sigma=1.0,  r_cut=2**(1.0/6.0))

slj.pair_coeff.set('B', 'B', epsilon=1.0, sigma=1.0,  r_cut=2.5)

fene =hoomd.md.bond.fene()

fene.bond_coeff.set('A-A', k=30.0, r0=1.5, sigma=1.0, epsilon= 1.0)

fene.bond_coeff.set('A-B', k=30.0, r0=1.5, sigma=1.0, epsilon= 1.0)

fene.bond_coeff.set('B-B', k=30.0, r0=1.5, sigma=1.0, epsilon= 1.0)

all =hoomd.group.all()

rigid=hoomd.group.rigid()

nonrigid =hoomd.group.nonrigid()

hoomd.md.integrate.mode_standard(dt=0.005)

integrator_nonrigid =hoomd.md.integrate.brownian(group=nonrigid, kT=1.0, seed=5)

integrator_rigid =hoomd.md.integrate.brownian(group=rigid,       kT=1.0, seed=6)

integrator_nonrigid.set_gamma('B', gamma=5.0)

integrator_rigid.set_gamma('A', gamma=5.0)

hoomd.analyze.log(filename="log-output.log",

                  quantities=['potential_energy', 'temperature','pressure'],

                  period=50000,

                  overwrite=True);

xml=hoomd.deprecated.dump.xml(group=hoomd.group.all(), filename="particles", period=1e2)

xml.set_params(type=True, position=True, bond=True, image=True, mass=True, velocity=True)

xml=hoomd.deprecated.dump.xml(group=hoomd.group.all(), filename="particles", period=1e2)

xml.set_params(type=True, position=True, bond=True, image=True, mass=True, velocity=True)

# integrate NVT for a bunch of time steps

hoomd.run(3e3);

and I got the error:

a.py:010  |  nl = hoomd.md.nlist.cell();

a.py:015  |  slj =hoomd.md.pair.slj(r_cut=3.0, nlist=nl, d_max = 2.0)

a.py:016  |  slj.pair_coeff.set('A', 'A', epsilon=1.0, sigma=1.0,  r_cut=2.5)

a.py:017  |  slj.pair_coeff.set('A', 'B', epsilon=1.0, sigma=1.0,  r_cut=2**(1.0/6.0))

a.py:018  |  slj.pair_coeff.set('B', 'B', epsilon=1.0, sigma=1.0,  r_cut=2.5)

a.py:024  |  fene =hoomd.md.bond.fene()

a.py:025  |  fene.bond_coeff.set('A-A', k=30.0, r0=1.5, sigma=1.0, epsilon= 1.0)

a.py:026  |  fene.bond_coeff.set('A-B', k=30.0, r0=1.5, sigma=1.0, epsilon= 1.0)

a.py:027  |  fene.bond_coeff.set('B-B', k=30.0, r0=1.5, sigma=1.0, epsilon= 1.0)

a.py:033  |  all =hoomd.group.all()

a.py:035  |  rigid=hoomd.group.rigid()

notice(2): Group "rigid" created containing 2488 particles

a.py:036  |  nonrigid =hoomd.group.nonrigid()

notice(2): Group "nonrigid" created containing 5598 particles

a.py:037  |  hoomd.md.integrate.mode_standard(dt=0.005)

a.py:044  |  integrator_nonrigid =hoomd.md.integrate.brownian(group=nonrigid, kT=1.0, seed=5)

notice(2): integrate.langevin/bd is using specified gamma values

a.py:045  |  integrator_rigid =hoomd.md.integrate.brownian(group=rigid,       kT=1.0, seed=6)

notice(2): integrate.langevin/bd is using specified gamma values

**ERROR**: Particle 1 belongs to a rigid body, but is not its center particle.

This integration method does not operate on constituent particles.

Traceback (most recent call last):

  File "a.py", line 45, in <module>

    integrator_rigid =hoomd.md.integrate.brownian(group=rigid,       kT=1.0, seed=6)

  File "/home/sql/anaconda3/envs/deepmd/lib/python3.6/site-packages/hoomd/md/integrate.py", line 1196, in __init__

    self.cpp_method.validateGroup()

RuntimeError: Error initializing integration method

It seems the rigid body must have a center beads, can anyone help me on this ? Thanks in advance !

[Joshua Anderson]

Al ehmn,

Use rigid=hoomd.group.rigid_center()

See the section "Integrating Bodies" in the documentation for more information: https://hoomd-blue.readthedocs.io/en/v2.9.6/module-md-constrain.html#hoomd.md.constrain.rigid
------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan

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[Al ehmn]

Thank you very much for your kind help. 

[Yulin Luo]

Hi  Al ehmn:

    
I have a problem similar to yours, I create the initial configuration by "read_xml", and I am trying to use   hoomd.group.rigid() to simulate my systems,too.

After the "read_xml", how should I use the "rigid = hoomd.group.rigid_center()"? 

In other words, do I still need to specify the position of the rigid_center?

Could you please help me with this issue? Thanks in advance.

Best,

Yulin