forked from lijiext/lammps
292 lines
13 KiB
Plaintext
292 lines
13 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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run_style command :h3
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[Syntax:]
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run_style style args :pre
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style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l
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{verlet} args = none
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{verlet/split} args = none
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{respa} args = N n1 n2 ... keyword values ...
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N = # of levels of rRESPA
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n1, n2, ... = loop factor between rRESPA levels (N-1 values)
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zero or more keyword/value pairings may be appended to the loop factors
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keyword = {bond} or {angle} or {dihedral} or {improper} or
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{pair} or {inner} or {middle} or {outer} or {hybrid} or {kspace}
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{bond} value = M
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M = which level (1-N) to compute bond forces in
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{angle} value = M
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M = which level (1-N) to compute angle forces in
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{dihedral} value = M
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M = which level (1-N) to compute dihedral forces in
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{improper} value = M
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M = which level (1-N) to compute improper forces in
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{pair} value = M
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M = which level (1-N) to compute pair forces in
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{inner} values = M cut1 cut2
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M = which level (1-N) to compute pair inner forces in
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cut1 = inner cutoff between pair inner and
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pair middle or outer (distance units)
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cut2 = outer cutoff between pair inner and
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pair middle or outer (distance units)
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{middle} values = M cut1 cut2
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M = which level (1-N) to compute pair middle forces in
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cut1 = inner cutoff between pair middle and pair outer (distance units)
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cut2 = outer cutoff between pair middle and pair outer (distance units)
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{outer} value = M
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M = which level (1-N) to compute pair outer forces in
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{hybrid} values = M1 M2 ... (as many values as there are hybrid sub-styles
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M1 = which level (1-N) to compute the first pair_style hybrid sub-style in
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M2 = which level (1-N) to compute the second pair_style hybrid sub-style in
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M3,etc
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{kspace} value = M
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M = which level (1-N) to compute kspace forces in :pre
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:ule
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[Examples:]
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run_style verlet
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run_style respa 4 2 2 2 bond 1 dihedral 2 pair 3 kspace 4
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run_style respa 4 2 2 2 bond 1 dihedral 2 inner 3 5.0 6.0 outer 4 kspace 4 :pre
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run_style respa 3 4 2 bond 1 hybrid 2 2 1 kspace 3 :pre
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[Description:]
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Choose the style of time integrator used for molecular dynamics
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simulations performed by LAMMPS.
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The {verlet} style is a standard velocity-Verlet integrator.
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:line
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The {verlet/split} style is also a velocity-Verlet integrator, but it
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splits the force calculation within each timestep over 2 partitions of
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processors. See "Section_start 6"_Section_start.html#start_7 for an
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explanation of the -partition command-line switch.
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Specifically, this style performs all computation except the
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"kspace_style"_kspace_style.html portion of the force field on the 1st
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partition. This include the "pair style"_pair_style.html, "bond
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style"_bond_style.html, "neighbor list building"_neighbor.html,
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"fixes"_fix.html including time intergration, and output. The
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"kspace_style"_kspace_style.html portion of the calculation is
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performed on the 2nd partition.
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This is most useful for the PPPM kspace_style when its performance on
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a large number of processors degrades due to the cost of communication
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in its 3d FFTs. In this scenario, splitting your P total processors
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into 2 subsets of processors, P1 in the 1st partition and P2 in the
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2nd partition, can enable your simulation to run faster. This is
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because the long-range forces in PPPM can be calculated at the same
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time as pair-wise and bonded forces are being calculated, and the FFTs
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can actually speed up when running on fewer processors.
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To use this style, you must define 2 partitions where P1 is a multiple
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of P2. Typically having P1 be 3x larger than P2 is a good choice.
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The 3d processor layouts in each partition must overlay in the
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following sense. If P1 is a Px1 by Py1 by Pz1 grid, and P2 = Px2 by
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Py2 by Pz2, then Px1 must be an integer multiple of Px2, and similarly
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for Py1 a multiple of Py2, and Pz1 a multiple of Pz2.
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Typically the best way to do this is to let the 1st partition choose
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its onn optimal layout, then require the 2nd partition's layout to
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match the integer multiple constraint. See the
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"processors"_processors.html command with its {part} keyword for a way
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to control this, e.g.
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procssors * * * part 1 2 multiple :pre
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You can also use the "partition"_partition.html command to explicitly
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specity the processor layout on each partition. E.g. for 2 partitions
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of 60 and 15 processors each:
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partition yes 1 processors 3 4 5
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partition yes 2 processors 3 1 5 :pre
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When you run in 2-partition mode with the {verlet/split} style, the
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thermodyanmic data for the entire simulation will be output to the log
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and screen file of the 1st partition, which are log.lammps.0 and
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screen.0 by default; see the "-plog and -pscreen command-line
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switches"Section_start.html#start_7 to change this. The log and
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screen file for the 2nd partition will not contain thermodynamic
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output beyone the 1st timestep of the run.
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See "Section_accelerate"_Section_accelerate.html of the manual for
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performance details of the speed-up offered by the {verlet/split}
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style. One important performance consideration is the assignemnt of
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logical processors in the 2 partitions to the physical cores of a
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parallel machine. The "processors"_processors.html command has
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options to support this, and strategies are discussed in
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"Section_accelerate"_Section_accelerate.html of the manual.
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:line
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The {respa} style implements the rRESPA multi-timescale integrator
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"(Tuckerman)"_#Tuckerman with N hierarchical levels, where level 1 is
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the innermost loop (shortest timestep) and level N is the outermost
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loop (largest timestep). The loop factor arguments specify what the
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looping factor is between levels. N1 specifies the number of
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iterations of level 1 for a single iteration of level 2, N2 is the
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iterations of level 2 per iteration of level 3, etc. N-1 looping
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parameters must be specified.
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The "timestep"_timestep.html command sets the timestep for the
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outermost rRESPA level. Thus if the example command above for a
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4-level rRESPA had an outer timestep of 4.0 fmsec, the inner timestep
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would be 8x smaller or 0.5 fmsec. All other LAMMPS commands that
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specify number of timesteps (e.g. "neigh_modify"_neigh_modify.html
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parameters, "dump"_dump.html every N timesteps, etc) refer to the
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outermost timesteps.
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The rRESPA keywords enable you to specify at what level of the
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hierarchy various forces will be computed. If not specified, the
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defaults are that bond forces are computed at level 1 (innermost
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loop), angle forces are computed where bond forces are, dihedral
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forces are computed where angle forces are, improper forces are
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computed where dihedral forces are, pair forces are computed at the
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outermost level, and kspace forces are computed where pair forces are.
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The inner, middle, outer forces have no defaults.
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The {inner} and {middle} keywords take additional arguments for
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cutoffs that are used by the pairwise force computations. If the 2
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cutoffs for {inner} are 5.0 and 6.0, this means that all pairs up to
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6.0 apart are computed by the inner force. Those between 5.0 and 6.0
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have their force go ramped to 0.0 so the overlap with the next regime
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(middle or outer) is smooth. The next regime (middle or outer) will
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compute forces for all pairs from 5.0 outward, with those from 5.0 to
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6.0 having their value ramped in an inverse manner.
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Only some pair potentials support the use of the {inner} and {middle}
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and {outer} keywords. If not, only the {pair} keyword can be used
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with that pair style, meaning all pairwise forces are computed at the
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same rRESPA level. See the doc pages for individual pair styles for
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details.i
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Another option for using pair potentials with rRESPA is with the
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{hybrid} keyword, which requires the use of the "pair_style hybrid or
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hybrid/overlay"_pair_hybrid.html command. In this scenario, different
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sub-styles of the hybrid pair style are evaluated at different rRESPA
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levels. This can be useful, for example, to set different timesteps
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for hybrid coarse-grained/all-atom models. The {hybrid} keyword
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requires as many level assignments as there are hybrid substyles,
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which assigns each sub-style to a rRESPA level, following their order
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of definition in the pair_style command. Since the {hybrid} keyword
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operates on pair style computations, it is mututally exclusive with
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either the {pair} or the {inner}/{middle}/{outer} keywords.
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When using rRESPA (or for any MD simulation) care must be taken to
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choose a timestep size(s) that insures the Hamiltonian for the chosen
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ensemble is conserved. For the constant NVE ensemble, total energy
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must be conserved. Unfortunately, it is difficult to know {a priori}
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how well energy will be conserved, and a fairly long test simulation
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(~10 ps) is usually necessary in order to verify that no long-term
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drift in energy occurs with the trial set of parameters.
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With that caveat, a few rules-of-thumb may be useful in selecting
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{respa} settings. The following applies mostly to biomolecular
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simulations using the CHARMM or a similar all-atom force field, but
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the concepts are adaptable to other problems. Without SHAKE, bonds
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involving hydrogen atoms exhibit high-frequency vibrations and require
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a timestep on the order of 0.5 fmsec in order to conserve energy. The
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relatively inexpensive force computations for the bonds, angles,
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impropers, and dihedrals can be computed on this innermost 0.5 fmsec
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step. The outermost timestep cannot be greater than 4.0 fmsec without
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risking energy drift. Smooth switching of forces between the levels
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of the rRESPA hierarchy is also necessary to avoid drift, and a 1-2
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angstrom "healing distance" (the distance between the outer and inner
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cutoffs) works reasonably well. We thus recommend the following
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settings for use of the {respa} style without SHAKE in biomolecular
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simulations:
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timestep 4.0
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run_style respa 4 2 2 2 inner 2 4.5 6.0 middle 3 8.0 10.0 outer 4 :pre
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With these settings, users can expect good energy conservation and
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roughly a 2.5 fold speedup over the {verlet} style with a 0.5 fmsec
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timestep.
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If SHAKE is used with the {respa} style, time reversibility is lost,
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but substantially longer time steps can be achieved. For biomolecular
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simulations using the CHARMM or similar all-atom force field, bonds
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involving hydrogen atoms exhibit high frequency vibrations and require
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a time step on the order of 0.5 fmsec in order to conserve energy.
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These high frequency modes also limit the outer time step sizes since
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the modes are coupled. It is therefore desirable to use SHAKE with
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respa in order to freeze out these high frequency motions and increase
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the size of the time steps in the respa hierarchy. The following
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settings can be used for biomolecular simulations with SHAKE and
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rRESPA:
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fix 2 all shake 0.000001 500 0 m 1.0 a 1
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timestep 4.0
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run_style respa 2 2 inner 1 4.0 5.0 outer 2 :pre
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With these settings, users can expect good energy conservation and
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roughly a 1.5 fold speedup over the {verlet} style with SHAKE and a
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2.0 fmsec timestep.
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For non-biomolecular simulations, the {respa} style can be
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advantageous if there is a clear separation of time scales - fast and
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slow modes in the simulation. Even a LJ system can benefit from
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rRESPA if the interactions are divided by the inner, middle and outer
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keywords. A 2-fold or more speedup can be obtained while maintaining
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good energy conservation. In real units, for a pure LJ fluid at
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liquid density, with a sigma of 3.0 angstroms, and epsilon of 0.1
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Kcal/mol, the following settings seem to work well:
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timestep 36.0
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run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3 :pre
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:line
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The {respa/omp} styles is a variant of {respa} adapted for use with
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pair, bond, angle, dihedral, improper, or kspace styles with an {omp}
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suffix. It is functionally equivalent to {respa} but performs additional
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operations required for managing {omp} styles. For more on {omp} styles
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see the "Section_accelerate"_Section_accelerate.html of the manual.
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Accelerated styles take the same arguments and should produce the same
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results, except for round-off and precision issues.
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You can specify {respa/omp} explicitly in your input script, or
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you can use the "-suffix command-line switch"_Section_start.html#start_7
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when you invoke LAMMPS, or you can use the "suffix"_suffix.html
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command in your input script.
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See "Section_accelerate"_Section_accelerate.html of the manual for
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more instructions on how to use the accelerated styles effectively.
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:line
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[Restrictions:]
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The {verlet/split} style can only be used if LAMMPS was built with the
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REPLICA package. Correspondingly the {respa/omp} style is available only
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if the USER-OMP package was included. See the "Making LAMMPS"_Section_start.html#start_3
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section for more info on packages.
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Whenever using rRESPA, the user should experiment with trade-offs in
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speed and accuracy for their system, and verify that they are
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conserving energy to adequate precision.
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[Related commands:]
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"timestep"_timestep.html, "run"_run.html
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[Default:]
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run_style verlet :pre
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:line
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:link(Tuckerman)
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[(Tuckerman)] Tuckerman, Berne and Martyna, J Chem Phys, 97, p 1990
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(1992).
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