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299 lines
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>run_style command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>run_style style args
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</PRE>
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<UL><LI>style = <I>verlet</I> or <I>verlet/split</I> or <I>respa</I> or <I>respa/omp</I>
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<PRE> <I>verlet</I> args = none
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<I>verlet/split</I> args = none
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<I>respa</I> 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 = <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I> or
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<I>pair</I> or <I>inner</I> or <I>middle</I> or <I>outer</I> or <I>hybrid</I> or <I>kspace</I>
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<I>bond</I> value = M
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M = which level (1-N) to compute bond forces in
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<I>angle</I> value = M
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M = which level (1-N) to compute angle forces in
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<I>dihedral</I> value = M
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M = which level (1-N) to compute dihedral forces in
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<I>improper</I> value = M
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M = which level (1-N) to compute improper forces in
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<I>pair</I> value = M
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M = which level (1-N) to compute pair forces in
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<I>inner</I> 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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<I>middle</I> 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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<I>outer</I> value = M
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M = which level (1-N) to compute pair outer forces in
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<I>hybrid</I> 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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...
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<I>kspace</I> value = M
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M = which level (1-N) to compute kspace forces in
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>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
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</PRE>
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<PRE>run_style respa 3 4 2 bond 1 hybrid 2 2 1 kspace 3
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Choose the style of time integrator used for molecular dynamics
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simulations performed by LAMMPS.
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</P>
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<P>The <I>verlet</I> style is a standard velocity-Verlet integrator.
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</P>
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<HR>
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<P>The <I>verlet/split</I> 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 <A HREF = "Section_start.html#start_7">Section_start 6</A> for an
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explanation of the -partition command-line switch.
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</P>
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<P>Specifically, this style performs all computation except the
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<A HREF = "kspace_style.html">kspace_style</A> portion of the force field on the 1st
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partition. This include the <A HREF = "pair_style.html">pair style</A>, <A HREF = "bond_style.html">bond
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style</A>, <A HREF = "neighbor.html">neighbor list building</A>,
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<A HREF = "fix.html">fixes</A> including time intergration, and output. The
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<A HREF = "kspace_style.html">kspace_style</A> portion of the calculation is
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performed on the 2nd partition.
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</P>
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<P>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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</P>
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<P>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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</P>
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<P>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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<A HREF = "processors.html">processors</A> command with its <I>part</I> keyword for a way
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to control this, e.g.
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</P>
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<PRE>procssors * * * part 1 2 multiple
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</PRE>
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<P>You can also use the <A HREF = "partition.html">partition</A> 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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</P>
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<PRE>partition yes 1 processors 3 4 5
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partition yes 2 processors 3 1 5
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</PRE>
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<P>When you run in 2-partition mode with the <I>verlet/split</I> 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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</P>
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<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
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performance details of the speed-up offered by the <I>verlet/split</I>
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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 <A HREF = "processors.html">processors</A> command has
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options to support this, and strategies are discussed in
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<A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual.
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</P>
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<HR>
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<P>The <I>respa</I> style implements the rRESPA multi-timescale integrator
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<A HREF = "#Tuckerman">(Tuckerman)</A> 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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</P>
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<P>The <A HREF = "timestep.html">timestep</A> 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. <A HREF = "neigh_modify.html">neigh_modify</A>
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parameters, <A HREF = "dump.html">dump</A> every N timesteps, etc) refer to the
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outermost timesteps.
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</P>
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<P>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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</P>
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<P>The <I>inner</I> and <I>middle</I> 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 <I>inner</I> 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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</P>
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<P>Only some pair potentials support the use of the <I>inner</I> and <I>middle</I>
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and <I>outer</I> keywords. If not, only the <I>pair</I> 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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</P>
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<P>Another variant to use pair potentials in rRESPA is with the <I>hybrid</I>
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keyword, which requires the use of a <A HREF = "pair_hybrid.html">hybrid pair_style</A>
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In this scenario, different sub-styles of the hybrid pair style are
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evaluated at different rRESPA levels. Thus the hybrid keyword requires
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as many level assignments as there are hybrid substyles which designate
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the respective sub-styles to the rRESPA level according to their order
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of definition in the pair_style command. Since the <I>hybrid</I> designates
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pair force computations, it is mututally exclusive with either the <I>pair</I>
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or the <I>inner</I>/<I>middle</I>/<I>outer</I> keywords.
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</P>
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<P>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 <I>a priori</I>
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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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</P>
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<P>With that caveat, a few rules-of-thumb may be useful in selecting
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<I>respa</I> 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 <I>respa</I> style without SHAKE in biomolecular
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simulations:
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</P>
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<PRE>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
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</PRE>
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<P>With these settings, users can expect good energy conservation and
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roughly a 2.5 fold speedup over the <I>verlet</I> style with a 0.5 fmsec
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timestep.
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</P>
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<P>If SHAKE is used with the <I>respa</I> 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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</P>
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<PRE>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
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</PRE>
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<P>With these settings, users can expect good energy conservation and
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roughly a 1.5 fold speedup over the <I>verlet</I> style with SHAKE and a
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2.0 fmsec timestep.
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</P>
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<P>For non-biomolecular simulations, the <I>respa</I> 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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</P>
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<PRE>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
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</PRE>
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<HR>
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<P>The <I>respa/omp</I> styles is a variant of <I>respa</I> adapted for use with
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pair, bond, angle, dihedral, improper, or kspace styles with an <I>omp</I>
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suffix. It is functionally equivalent to <I>respa</I> but performs additional
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operations required for managing <I>omp</I> styles. For more on <I>omp</I> styles
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see the <A HREF = "Section_accelerate.html">Section_accelerate</A> 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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</P>
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<P>You can specify <I>respa/omp</I> explicitly in your input script, or
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you can use the <A HREF = "Section_start.html#start_7">-suffix command-line switch</A>
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when you invoke LAMMPS, or you can use the <A HREF = "suffix.html">suffix</A>
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command in your input script.
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</P>
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<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
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more instructions on how to use the accelerated styles effectively.
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</P>
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<HR>
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<P><B>Restrictions:</B>
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</P>
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<P>The <I>verlet/split</I> style can only be used if LAMMPS was built with the
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REPLICA package. Correspondingly the <I>respa/omp</I> style is available only
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if the USER-OMP package was included. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
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section for more info on packages.
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</P>
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<P>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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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "timestep.html">timestep</A>, <A HREF = "run.html">run</A>
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</P>
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<P><B>Default:</B>
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</P>
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<PRE>run_style verlet
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</PRE>
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<HR>
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<A NAME = "Tuckerman"></A>
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<P><B>(Tuckerman)</B> Tuckerman, Berne and Martyna, J Chem Phys, 97, p 1990
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(1992).
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</P>
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</HTML>
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