thermalize_particle_momenta assigns velocities and angular momentum to constituent particles.

[joaander]

Description

thermalize_particle_momenta, when given the All filter, will assign non-zero values to the velocities and angular momenta of rigid body constituent particles. hoomd.md.constrain.Rigid does not overwrite these values, though perhaps it should (see #278). Regardless, to behave consistently with ThermodynamicQuantities, thermalize_particle_momenta should assign 0's to constituent particle velocities and angular momenta:

hoomd-blue/hoomd/ParticleGroup.cc

Lines 824 to 863 in 925a739

	for (unsigned int group_idx = 0; group_idx < group_size; group_idx++)
	{
	unsigned int j = this->getMemberIndex(group_idx);
	unsigned int ptag = h_tag.data[j];
	// Seed the RNG
	hoomd::RandomGenerator rng(hoomd::Seed(hoomd::RNGIdentifier::ParticleGroupThermalize,
	timestep,
	m_sysdef->getSeed()),
	hoomd::Counter(ptag));
	// Generate a random velocity
	Scalar mass = h_vel.data[j].w;
	Scalar sigma = slow::sqrt(kT / mass);
	hoomd::NormalDistribution<Scalar> normal(sigma);
	h_vel.data[j].x = normal(rng);
	h_vel.data[j].y = normal(rng);
	if (n_dimensions > 2)
	h_vel.data[j].z = normal(rng);
	else
	h_vel.data[j].z = 0; // For 2D systems
	tot_momentum += mass * vec3<Scalar>(h_vel.data[j]);
	// Generate random angular momentum if the particle has rotational degrees of freedom.
	vec3<Scalar> p_vec(0, 0, 0);
	quat<Scalar> q(h_orientation.data[j]);
	vec3<Scalar> I(h_inertia.data[j]);
	if (I.x > 0)
	p_vec.x = hoomd::NormalDistribution<Scalar>(slow::sqrt(kT * I.x))(rng);
	if (I.y > 0)
	p_vec.y = hoomd::NormalDistribution<Scalar>(slow::sqrt(kT * I.y))(rng);
	if (I.z > 0)
	p_vec.z = hoomd::NormalDistribution<Scalar>(slow::sqrt(kT * I.z))(rng);
	// Store the angular momentum quaternion
	quat<Scalar> p = Scalar(2.0) * q * p_vec;
	h_angmom.data[j] = quat_to_scalar4(p);
	}

Script

import hoomd

snapshot = hoomd.Snapshot()
snapshot.configuration.box = (10, 10, 10, 0, 0, 0)
snapshot.particles.N = 4
snapshot.particles.types = ['A']
snapshot.particles.body[:] = [0, 0, 2, 2]
snapshot.particles.moment_inertia[:] = [[1,1,1]] * 4

sim = hoomd.Simulation(device=hoomd.device.CPU())
sim.create_state_from_snapshot(snapshot)

sim.state.thermalize_particle_momenta(filter=hoomd.filter.All(), kT=1.0)
thermalized_snapshot = sim.state.get_snapshot()
print(thermalized_snapshot.particles.velocity)
print(thermalized_snapshot.particles.angmom)

Input files

No response

Output

[[-0.66990062  0.13619617  0.63650922]
 [-1.00984745 -0.81729512  1.43739685]
 [ 0.77239644  0.5919247  -0.56883137]
 [ 0.90735163  0.08917425 -1.5050747 ]]
[[ 0.         -0.80604741  0.73100313  1.6675459 ]
 [ 0.         -1.39461841 -3.73358298 -1.2261137 ]
 [ 0.          2.98269913 -0.46326691  1.24673851]
 [ 0.          2.23798918  0.51482892  2.8423569 ]]

Expected output

I expected 0 velocity and angular momentum for particles 1 and 3.

Platform

CPU, GPU, Linux, macOS

Installation method

Compiled from source

HOOMD-blue version

3.8.1

Python version

3.10.6