Integrators

VelocityVerlet(force, M, Δt)

Set up the velocity Verlet integrator.

Fields

• force - In place gradient of the potential
• M - Mass (either scalar or vector)
• Δt - Time step

PositionVerlet(force, M, Δt)

Set up the position Verlet integrator.

Fields

• force - In place gradient of the potential
• M - Mass (either scalar or vector)
• Δt - Time step

EM(force, β, Δt)

Set up the EM integrator for overdamped Langevin.

Fields

• force - In place gradient of the potential
• β - Inverse temperature
• Δt - Time step

BBK(force, β, γ, M, Δt)

Set up the BBK integrator for inertial Langevin.

Fields

• force - In place gradient of the potential
• β - Inverse temperature
• γ - Damping Coefficient
• M - Mass (either scalar or vector)
• Δt - Time step

VEC(force, β, γ, M, Δt)

Set up the Vanden-Eijnden Ciccotti integrator for inertial Langevin. Taken from "Second-order integrators for Langevin equations with holonomic constraints" doi: 10.1016/j.cplett.2006.07.086

Fields

• force - In place gradient of the potential
• β - Inverse temperature
• γ - Damping Coefficient
• M - Mass (either scalar or vector)
• Δt - Time step

GJ(force, β, γ, M, Δt, type)

Set up the various GJ integrator for inertial Langevin. Use type to select the approriate integrator

Fields

• force - In place gradient of the potential
• β - Inverse temperature
• γ - Damping Coefficient
• M - Mass (either scalar or vector)
• Δt - Time step
• type - Choice of the integrator should be one of "I","II","III","IV","V","VI"

GJF(force, β, γ, M, Δt)

Set up the G-JF integrator for inertial Langevin.

Fields

• force - In place gradient of the potential
• β - Inverse temperature
• γ - Damping Coefficient
• M - Mass (either scalar or vector)
• Δt - Time step

BAOAB(force, β, γ, M, Δt)

Set up the BAOAB integrator for inertial Langevin.

Fields

• force - In place gradient of the potential
• β - Inverse temperature
• γ - Damping Coefficient
• M - Mass (either scalar or vector)
• Δt - Time step

OBABO(force, β, γ, M, Δt)

Set up the OBABO integrator for inertial Langevin.

Fields

• force - In place gradient of the potential
• β - Inverse temperature
• γ - Damping Coefficient
• M - Mass (either scalar or vector)
• Δt - Time step

ABOBA(force, β, γ, M, Δt)

Set up the ABOBA integrator for inertial Langevin.

Fields

• force - In place gradient of the potential
• β - Inverse temperature
• γ - Damping Coefficient
• M - Mass (either scalar or vector)
• Δt - Time step

BBK_Kernel(force, β, γ, M, Δt)

Set up the BBK_Kernel integrator for generalized Langevin.

Adapted from Iterative Reconstruction of Memory Kernels Gerhard Jung,,†,‡ Martin Hanke,,§ and Friederike Schmid*,†

Fields

• force - In place gradient of the potential
• β - Inverse temperature
• γ - Damping Coefficient
• M - Mass (either scalar or vector)
• Δt - Time step

GJF_Kernel(force, β, γ, M, Δt)

Set up the G-JF integrator for inertial Langevin.

Adapted from Iterative Reconstruction of Memory Kernels Gerhard Jung,,†,‡ Martin Hanke,,§ and Friederike Schmid*,†

Fields

• force - In place gradient of the potential
• β - Inverse temperature
• γ - Damping Coefficient
• M - Mass (either scalar or vector)
• Δt - Time step

EM_Hidden(force, β, Δt)

Set up the EM_Hidden integrator for underdamped Langevin with hidden variables.

Fields

• force - In place gradient of the potential
• A - Friction matrix
• C - diffusion matrix
• Δt - Time step

ABOBA_Hidden(force, β, γ, M, Δt)

Set up the ABOBA_Hidden integrator for underdamped Langevin with hidden variables.

Fields

• force - In place gradient of the potential
• β - Inverse temperature
• γ - Damping Coefficient
• M - Mass (either scalar or vector)
• Δt - Time step