\(\renewcommand{\AA}{\text{Å}}\)

# fix pimd command¶

## Syntax¶

```
fix ID group-ID pimd keyword value ...
```

ID, group-ID are documented in fix command

pimd = style name of this fix command

zero or more keyword/value pairs may be appended

keyword =

*method*or*fmass*or*sp*or*temp*or*nhc**method*value =*pimd*or*nmpimd*or*cmd**fmass*value = scaling factor on mass*sp*value = scaling factor on Planck constant*temp*value = temperature (temperarate units)*nhc*value = Nc = number of chains in Nose-Hoover thermostat

## Examples¶

```
fix 1 all pimd method nmpimd fmass 1.0 sp 2.0 temp 300.0 nhc 4
```

## Description¶

This command performs quantum molecular dynamics simulations based on the Feynman path integral to include effects of tunneling and zero-point motion. In this formalism, the isomorphism of a quantum partition function for the original system to a classical partition function for a ring-polymer system is exploited, to efficiently sample configurations from the canonical ensemble (Feynman). The classical partition function and its components are given by the following equations:

The interested user is referred to any of the numerous references on
this methodology, but briefly, each quantum particle in a path
integral simulation is represented by a ring-polymer of P quasi-beads,
labeled from 1 to P. During the simulation, each quasi-bead interacts
with beads on the other ring-polymers with the same imaginary time
index (the second term in the effective potential above). The
quasi-beads also interact with the two neighboring quasi-beads through
the spring potential in imaginary-time space (first term in effective
potential). To sample the canonical ensemble, a Nose-Hoover massive
chain thermostat is applied (Tuckerman). With the
massive chain algorithm, a chain of NH thermostats is coupled to each
degree of freedom for each quasi-bead. The keyword *temp* sets the
target temperature for the system and the keyword *nhc* sets the
number *Nc* of thermostats in each chain. For example, for a
simulation of N particles with P beads in each ring-polymer, the total
number of NH thermostats would be 3 x N x P x Nc.

Note

This fix implements a complete velocity-verlet integrator combined with NH massive chain thermostat, so no other time integration fix should be used.

The *method* keyword determines what style of PIMD is performed. A
value of *pimd* is standard PIMD. A value of *nmpimd* is for
normal-mode PIMD. A value of *cmd* is for centroid molecular dynamics
(CMD). The difference between the styles is as follows.

In standard PIMD, the value used for a bead’s fictitious mass is arbitrary. A common choice is to use Mi = m/P, which results in the mass of the entire ring-polymer being equal to the real quantum particle. But it can be difficult to efficiently integrate the equations of motion for the stiff harmonic interactions in the ring polymers.

A useful way to resolve this issue is to integrate the equations of motion in a normal mode representation, using Normal Mode Path-Integral Molecular Dynamics (NMPIMD) (Cao1). In NMPIMD, the NH chains are attached to each normal mode of the ring-polymer and the fictitious mass of each mode is chosen as Mk = the eigenvalue of the Kth normal mode for k > 0. The k = 0 mode, referred to as the zero-frequency mode or centroid, corresponds to overall translation of the ring-polymer and is assigned the mass of the real particle.

Motion of the centroid can be effectively uncoupled from the other normal modes by scaling the fictitious masses to achieve a partial adiabatic separation. This is called a Centroid Molecular Dynamics (CMD) approximation (Cao2). The time-evolution (and resulting dynamics) of the quantum particles can be used to obtain centroid time correlation functions, which can be further used to obtain the true quantum correlation function for the original system. The CMD method also uses normal modes to evolve the system, except only the k > 0 modes are thermostatted, not the centroid degrees of freedom.

The keyword *fmass* sets a further scaling factor for the fictitious
masses of beads, which can be used for the Partial Adiabatic CMD
(Hone), or to be set as P, which results in the fictitious
masses to be equal to the real particle masses.

The keyword *sp* is a scaling factor on Planck’s constant, which can
be useful for debugging or other purposes. The default value of 1.0
is appropriate for most situations.

The PIMD algorithm in LAMMPS is implemented as a hyper-parallel scheme as described in (Calhoun). In LAMMPS this is done by using multi-replica feature in LAMMPS, where each quasi-particle system is stored and simulated on a separate partition of processors. The following diagram illustrates this approach. The original system with 2 ring polymers is shown in red. Since each ring has 4 quasi-beads (imaginary time slices), there are 4 replicas of the system, each running on one of the 4 partitions of processors. Each replica (shown in green) owns one quasi-bead in each ring.

To run a PIMD simulation with M quasi-beads in each ring polymer using N MPI tasks for each partition’s domain-decomposition, you would use P = MxN processors (cores) and run the simulation as follows:

```
mpirun -np P lmp_mpi -partition MxN -in script
```

Note that in the LAMMPS input script for a multi-partition simulation, it is often very useful to define a uloop-style variable such as

```
variable ibead uloop M pad
```

where M is the number of quasi-beads (partitions) used in the calculation. The uloop variable can then be used to manage I/O related tasks for each of the partitions, e.g.

```
dump dcd all dcd 10 system_${ibead}.dcd
restart 1000 system_${ibead}.restart1 system_${ibead}.restart2
read_restart system_${ibead}.restart2
```

## Restart, fix_modify, output, run start/stop, minimize info¶

This fix writes the state of the Nose/Hoover thermostat over all quasi-beads to binary restart files. See the read_restart command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion.

None of the fix_modify options are relevant to this fix.

This fix computes a global 3-vector, which can be accessed by various output commands. The three quantities in the global vector are

the total spring energy of the quasi-beads,

the current temperature of the classical system of ring polymers,

the current value of the scalar virial estimator for the kinetic energy of the quantum system (Herman).

The vector values calculated by this fix are “extensive”, except for the temperature, which is “intensive”.

No parameter of this fix can be used with the *start/stop* keywords of
the run command. This fix is not invoked during
energy minimization.

## Restrictions¶

This fix is part of the REPLICA package. It is only enabled if LAMMPS was built with that package. See the Build package page for more info.

Fix pid cannot be used with lj units.

A PIMD simulation can be initialized with a single data file read via the read_data command. However, this means all quasi-beads in a ring polymer will have identical positions and velocities, resulting in identical trajectories for all quasi-beads. To avoid this, users can simply initialize velocities with different random number seeds assigned to each partition, as defined by the uloop variable, e.g.

```
velocity all create 300.0 1234${ibead} rot yes dist gaussian
```

## Default¶

The keyword defaults are method = pimd, fmass = 1.0, sp = 1.0, temp = 300.0, and nhc = 2.

**(Feynman)** R. Feynman and A. Hibbs, Chapter 7, Quantum Mechanics and
Path Integrals, McGraw-Hill, New York (1965).

**(Tuckerman)** M. Tuckerman and B. Berne, J Chem Phys, 99, 2796 (1993).

**(Cao1)** J. Cao and B. Berne, J Chem Phys, 99, 2902 (1993).

**(Cao2)** J. Cao and G. Voth, J Chem Phys, 100, 5093 (1994).

**(Hone)** T. Hone, P. Rossky, G. Voth, J Chem Phys, 124,
154103 (2006).

**(Calhoun)** A. Calhoun, M. Pavese, G. Voth, Chem Phys Letters, 262,
415 (1996).

**(Herman)** M. F. Herman, E. J. Bruskin, B. J. Berne, J Chem Phys, 76, 5150 (1982).