run_style command
Syntax
run_style style args
style = verlet or verlet/split or respa or respa/omp
verlet args = none verlet/split args = none respa args = N n1 n2 ... keyword values ... N = # of levels of rRESPA n1, n2, ... = loop factor between rRESPA levels (N-1 values) zero or more keyword/value pairings may be appended to the loop factors keyword = bond or angle or dihedral or improper or pair or inner or middle or outer or hybrid or kspace bond value = M M = which level (1-N) to compute bond forces in angle value = M M = which level (1-N) to compute angle forces in dihedral value = M M = which level (1-N) to compute dihedral forces in improper value = M M = which level (1-N) to compute improper forces in pair value = M M = which level (1-N) to compute pair forces in inner values = M cut1 cut2 M = which level (1-N) to compute pair inner forces in cut1 = inner cutoff between pair inner and pair middle or outer (distance units) cut2 = outer cutoff between pair inner and pair middle or outer (distance units) middle values = M cut1 cut2 M = which level (1-N) to compute pair middle forces in cut1 = inner cutoff between pair middle and pair outer (distance units) cut2 = outer cutoff between pair middle and pair outer (distance units) outer value = M M = which level (1-N) to compute pair outer forces in hybrid values = M1 M2 ... (as many values as there are hybrid sub-styles M1 = which level (1-N) to compute the first pair_style hybrid sub-style in M2 = which level (1-N) to compute the second pair_style hybrid sub-style in M3,etc kspace value = M M = which level (1-N) to compute kspace forces in
Examples
run_style verlet
run_style respa 4 2 2 2 bond 1 dihedral 2 pair 3 kspace 4
run_style respa 4 2 2 2 bond 1 dihedral 2 inner 3 5.0 6.0 outer 4 kspace 4
run_style respa 3 4 2 bond 1 hybrid 2 2 1 kspace 3
Description
Choose the style of time integrator used for molecular dynamics simulations performed by LAMMPS.
The verlet style is a standard velocity-Verlet integrator.
The verlet/split style is also a velocity-Verlet integrator, but it splits the force calculation within each timestep over 2 partitions of processors. See Section 2.7 for an explanation of the -partition command-line switch.
Specifically, this style performs all computation except the kspace_style portion of the force field on the 1st partition. This include the pair style, bond style, neighbor list building, fixes including time intergration, and output. The kspace_style portion of the calculation is performed on the 2nd partition.
This is most useful for the PPPM kspace_style when its performance on a large number of processors degrades due to the cost of communication in its 3d FFTs. In this scenario, splitting your P total processors into 2 subsets of processors, P1 in the 1st partition and P2 in the 2nd partition, can enable your simulation to run faster. This is because the long-range forces in PPPM can be calculated at the same time as pair-wise and bonded forces are being calculated, and the FFTs can actually speed up when running on fewer processors.
To use this style, you must define 2 partitions where P1 is a multiple of P2. Typically having P1 be 3x larger than P2 is a good choice. The 3d processor layouts in each partition must overlay in the following sense. If P1 is a Px1 by Py1 by Pz1 grid, and P2 = Px2 by Py2 by Pz2, then Px1 must be an integer multiple of Px2, and similarly for Py1 a multiple of Py2, and Pz1 a multiple of Pz2.
Typically the best way to do this is to let the 1st partition choose its onn optimal layout, then require the 2nd partition’s layout to match the integer multiple constraint. See the processors command with its part keyword for a way to control this, e.g.
procssors * * * part 1 2 multiple
You can also use the partition command to explicitly specity the processor layout on each partition. E.g. for 2 partitions of 60 and 15 processors each:
partition yes 1 processors 3 4 5
partition yes 2 processors 3 1 5
When you run in 2-partition mode with the verlet/split style, the thermodyanmic data for the entire simulation will be output to the log and screen file of the 1st partition, which are log.lammps.0 and screen.0 by default; see the -plog and -pscreen command-line switches to change this. The log and screen file for the 2nd partition will not contain thermodynamic output beyone the 1st timestep of the run.
See Section 5 of the manual for performance details of the speed-up offered by the verlet/split style. One important performance consideration is the assignemnt of logical processors in the 2 partitions to the physical cores of a parallel machine. The processors command has options to support this, and strategies are discussed in Section 5 of the manual.
The respa style implements the rRESPA multi-timescale integrator (Tuckerman) with N hierarchical levels, where level 1 is the innermost loop (shortest timestep) and level N is the outermost loop (largest timestep). The loop factor arguments specify what the looping factor is between levels. N1 specifies the number of iterations of level 1 for a single iteration of level 2, N2 is the iterations of level 2 per iteration of level 3, etc. N-1 looping parameters must be specified.
The timestep command sets the timestep for the outermost rRESPA level. Thus if the example command above for a 4-level rRESPA had an outer timestep of 4.0 fmsec, the inner timestep would be 8x smaller or 0.5 fmsec. All other LAMMPS commands that specify number of timesteps (e.g. neigh_modify parameters, dump every N timesteps, etc) refer to the outermost timesteps.
The rRESPA keywords enable you to specify at what level of the hierarchy various forces will be computed. If not specified, the defaults are that bond forces are computed at level 1 (innermost loop), angle forces are computed where bond forces are, dihedral forces are computed where angle forces are, improper forces are computed where dihedral forces are, pair forces are computed at the outermost level, and kspace forces are computed where pair forces are. The inner, middle, outer forces have no defaults.
For fixes that support it, the rRESPA level at which a given fix is active, can be selected through the fix_modify command.
The inner and middle keywords take additional arguments for cutoffs that are used by the pairwise force computations. If the 2 cutoffs for inner are 5.0 and 6.0, this means that all pairs up to 6.0 apart are computed by the inner force. Those between 5.0 and 6.0 have their force go ramped to 0.0 so the overlap with the next regime (middle or outer) is smooth. The next regime (middle or outer) will compute forces for all pairs from 5.0 outward, with those from 5.0 to 6.0 having their value ramped in an inverse manner.
Only some pair potentials support the use of the inner and middle and outer keywords. If not, only the pair keyword can be used with that pair style, meaning all pairwise forces are computed at the same rRESPA level. See the doc pages for individual pair styles for details.i
Another option for using pair potentials with rRESPA is with the hybrid keyword, which requires the use of the pair_style hybrid or hybrid/overlay command. In this scenario, different sub-styles of the hybrid pair style are evaluated at different rRESPA levels. This can be useful, for example, to set different timesteps for hybrid coarse-grained/all-atom models. The hybrid keyword requires as many level assignments as there are hybrid substyles, which assigns each sub-style to a rRESPA level, following their order of definition in the pair_style command. Since the hybrid keyword operates on pair style computations, it is mututally exclusive with either the pair or the inner/middle/outer keywords.
When using rRESPA (or for any MD simulation) care must be taken to choose a timestep size(s) that insures the Hamiltonian for the chosen ensemble is conserved. For the constant NVE ensemble, total energy must be conserved. Unfortunately, it is difficult to know a priori how well energy will be conserved, and a fairly long test simulation (~10 ps) is usually necessary in order to verify that no long-term drift in energy occurs with the trial set of parameters.
With that caveat, a few rules-of-thumb may be useful in selecting respa settings. The following applies mostly to biomolecular simulations using the CHARMM or a similar all-atom force field, but the concepts are adaptable to other problems. Without SHAKE, bonds involving hydrogen atoms exhibit high-frequency vibrations and require a timestep on the order of 0.5 fmsec in order to conserve energy. The relatively inexpensive force computations for the bonds, angles, impropers, and dihedrals can be computed on this innermost 0.5 fmsec step. The outermost timestep cannot be greater than 4.0 fmsec without risking energy drift. Smooth switching of forces between the levels of the rRESPA hierarchy is also necessary to avoid drift, and a 1-2 angstrom “healing distance” (the distance between the outer and inner cutoffs) works reasonably well. We thus recommend the following settings for use of the respa style without SHAKE in biomolecular simulations:
timestep 4.0
run_style respa 4 2 2 2 inner 2 4.5 6.0 middle 3 8.0 10.0 outer 4
With these settings, users can expect good energy conservation and roughly a 2.5 fold speedup over the verlet style with a 0.5 fmsec timestep.
If SHAKE is used with the respa style, time reversibility is lost, but substantially longer time steps can be achieved. For biomolecular simulations using the CHARMM or similar all-atom force field, bonds involving hydrogen atoms exhibit high frequency vibrations and require a time step on the order of 0.5 fmsec in order to conserve energy. These high frequency modes also limit the outer time step sizes since the modes are coupled. It is therefore desirable to use SHAKE with respa in order to freeze out these high frequency motions and increase the size of the time steps in the respa hierarchy. The following settings can be used for biomolecular simulations with SHAKE and rRESPA:
fix 2 all shake 0.000001 500 0 m 1.0 a 1
timestep 4.0
run_style respa 2 2 inner 1 4.0 5.0 outer 2
With these settings, users can expect good energy conservation and roughly a 1.5 fold speedup over the verlet style with SHAKE and a 2.0 fmsec timestep.
For non-biomolecular simulations, the respa style can be advantageous if there is a clear separation of time scales - fast and slow modes in the simulation. Even a LJ system can benefit from rRESPA if the interactions are divided by the inner, middle and outer keywords. A 2-fold or more speedup can be obtained while maintaining good energy conservation. In real units, for a pure LJ fluid at liquid density, with a sigma of 3.0 angstroms, and epsilon of 0.1 Kcal/mol, the following settings seem to work well:
timestep 36.0
run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3
The respa/omp styles is a variant of respa adapted for use with pair, bond, angle, dihedral, improper, or kspace styles with an omp suffix. It is functionally equivalent to respa but performs additional operations required for managing omp styles. For more on omp styles see the Section 5 of the manual. Accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.
You can specify respa/omp explicitly in your input script, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.
Restrictions
The verlet/split style can only be used if LAMMPS was built with the REPLICA package. Correspondingly the respa/omp style is available only if the USER-OMP package was included. See the Making LAMMPS section for more info on packages.
Whenever using rRESPA, the user should experiment with trade-offs in speed and accuracy for their system, and verify that they are conserving energy to adequate precision.
Default
run_style verlet
(Tuckerman) Tuckerman, Berne and Martyna, J Chem Phys, 97, p 1990 (1992).