DPDLJ

class hoomd.md.pair.DPDLJ(nlist, kT, default_r_cut=None, mode='none')

Bases: Pair

Dissipative Particle Dynamics with the LJ conservative force.

Parameters:

• nlist (hoomd.md.nlist.NeighborList) – Neighbor list.

• kT (hoomd.variant or float) – Temperature of thermostat $[\mathrm{energy}]$.

• default_r_cut (float) – Default cutoff radius $[\mathrm{length}]$.

• mode (str) – Energy shifting mode.

DPDLJ computes the DPD thermostat combined with the LJ pair force on every particle in the simulation state with:

$$\begin{split} F &= F_{\mathrm{C}}(r) + F_{\mathrm{R,ij}}(r_{ij}) + F_{\mathrm{D,ij}}(v_{ij}), \\ F_{\mathrm{C}}(r) &= \partial U / \partial r, \\ F_{\mathrm{R, ij}}(r_{ij}) &= - \theta_{ij}\sqrt{3} \sqrt{\frac{2k_b\gamma T}{\Delta t}}\cdot w(r_{ij}), \\ F_{\mathrm{D, ij}}(r_{ij}) &= - \gamma w^2(r_{ij}) \left( \hat r_{ij} \circ v_{ij} \right), \\ U(r) &= 4 \varepsilon \left[ \left( \frac{\sigma}{r} \right)^{12} - \left( \frac{\sigma}{r} \right)^{6} \right], \\ w(r_{ij}) &= \begin{cases} \left( 1 - r/r_{\mathrm{cut}} \right) & r < r_{\mathrm{cut}} \\ 0 & r \ge r_{\mathrm{cut}} \\ \end{cases}, \end{split}$$

$\hat r_{ij}$ is a normalized vector from particle i to particle j, $v_{ij} = v_i - v_j$, and $\theta_{ij}$ is a uniformly distributed random number in the range [-1, 1].

C. L. Phillips et. al. 2011 describes the DPD implementation details. Cite it if you utilize the DPD functionality in your work.

To use the DPD thermostat, apply the hoomd.md.methods.ConstantVolume or hoomd.md.methods.ConstantPressure integration method without thermostat along with DPD forces. Use of the DPD thermostat pair force with other integrators will result in nonphysical behavior.

Example:

nl = nlist.Cell()
dpdlj = pair.DPDLJ(nlist=nl, kT=1.0, default_r_cut=2.5)
dpdlj.params[('A', 'A')] = dict(epsilon=1.0, sigma=1.0, gamma=4.5)
dpdlj.params[(['A', 'B'], ['C', 'D'])] = dict(
    epsilon=3.0, sigma=1.0, gamma=1.2)
dpdlj.r_cut[('B', 'B')] = 2.0**(1.0/6.0)

Members inherited from AutotunedObject:

property kernel_parameters

Kernel parameters. Read more...

property is_tuning_complete

Check if kernel parameter tuning is complete. Read more...

tune_kernel_parameters()

Start tuning kernel parameters. Read more...

Members inherited from Force:

additional_energy

Additional energy term. Read more...

additional_virial

Additional virial tensor term $W_\mathrm{additional}$. Read more...

cpu_local_force_arrays

Local force arrays on the CPU. Read more...

energies

Energy contribution $U_i$ from each particle. Read more...

energy

The potential energy $U$ of the system from this force. Read more...

forces

The force $\vec{F}_i$ applied to each particle. Read more...

gpu_local_force_arrays

Local force arrays on the GPU. Read more...

torques

The torque $\vec{\tau}_i$ applied to each particle. Read more...

virials

Virial tensor contribution $W_i$ from each particle. Read more...

Members inherited from Pair:

nlist

Neighbor list used to compute the pair force. Read more...

mode

Energy smoothing/cutoff mode. Read more...

r_cut

Cuttoff radius beyond which the energy and force are 0. Read more...

r_on

Radius at which the XPLOR smoothing function starts. Read more...

compute_energy()

Compute the energy between two sets of particles. Read more...

Members defined in DPDLJ:

params

The DPDLJ potential parameters. The dictionary has the following keys:

• epsilon (float, required) - $\varepsilon$ $[\mathrm{energy}]$

• sigma (float, required) - $\sigma$ $[\mathrm{length}]$

• gamma (float, required) - $\gamma$ $[\mathrm{mass} \cdot \mathrm{time}^{-1}]$

Type: TypeParameter [tuple [particle_type, particle_type], dict]