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456 lines
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<div class="section" id="run-style-command">
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<span id="index-0"></span><h1>run_style command<a class="headerlink" href="#run-style-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>run_style style args
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</pre></div>
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</div>
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<ul class="simple">
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<li>style = <em>verlet</em> or <em>verlet/split</em> or <em>respa</em> or <em>respa/omp</em></li>
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</ul>
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<pre class="literal-block">
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<em>verlet</em> args = none
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<em>verlet/split</em> args = none
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<em>respa</em> 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 = <em>bond</em> or <em>angle</em> or <em>dihedral</em> or <em>improper</em> or
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<em>pair</em> or <em>inner</em> or <em>middle</em> or <em>outer</em> or <em>hybrid</em> or <em>kspace</em>
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<em>bond</em> value = M
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M = which level (1-N) to compute bond forces in
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<em>angle</em> value = M
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M = which level (1-N) to compute angle forces in
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<em>dihedral</em> value = M
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M = which level (1-N) to compute dihedral forces in
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<em>improper</em> value = M
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M = which level (1-N) to compute improper forces in
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<em>pair</em> value = M
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M = which level (1-N) to compute pair forces in
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<em>inner</em> 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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<em>middle</em> 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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<em>outer</em> value = M
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M = which level (1-N) to compute pair outer forces in
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<em>hybrid</em> 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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<em>kspace</em> 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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</div>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><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></div>
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</div>
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<div class="highlight-python"><div class="highlight"><pre>run_style respa 3 4 2 bond 1 hybrid 2 2 1 kspace 3
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>Choose the style of time integrator used for molecular dynamics
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simulations performed by LAMMPS.</p>
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<p>The <em>verlet</em> style is a standard velocity-Verlet integrator.</p>
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<hr class="docutils" />
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<p>The <em>verlet/split</em> 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 class="reference internal" href="Section_start.html#start-7"><span>Section_start 6</span></a> for an
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explanation of the -partition command-line switch.</p>
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<p>Specifically, this style performs all computation except the
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<a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> portion of the force field on the 1st
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partition. This include the <a class="reference internal" href="pair_style.html"><em>pair style</em></a>, <a class="reference internal" href="bond_style.html"><em>bond style</em></a>, <a class="reference internal" href="neighbor.html"><em>neighbor list building</em></a>,
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<a class="reference internal" href="fix.html"><em>fixes</em></a> including time intergration, and output. The
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<a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> portion of the calculation is
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performed on the 2nd partition.</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.</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.</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 class="reference internal" href="processors.html"><em>processors</em></a> command with its <em>part</em> keyword for a way
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to control this, e.g.</p>
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<div class="highlight-python"><div class="highlight"><pre>procssors * * * part 1 2 multiple
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</pre></div>
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</div>
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<p>You can also use the <a class="reference internal" href="partition.html"><em>partition</em></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:</p>
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<div class="highlight-python"><div class="highlight"><pre>partition yes 1 processors 3 4 5
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partition yes 2 processors 3 1 5
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</pre></div>
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</div>
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<p>When you run in 2-partition mode with the <em>verlet/split</em> 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.</p>
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<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
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performance details of the speed-up offered by the <em>verlet/split</em>
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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 class="reference internal" href="processors.html"><em>processors</em></a> command has
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options to support this, and strategies are discussed in
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<a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual.</p>
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<hr class="docutils" />
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<p>The <em>respa</em> style implements the rRESPA multi-timescale integrator
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<a class="reference internal" href="#tuckerman"><span>(Tuckerman)</span></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.</p>
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<p>The <a class="reference internal" href="timestep.html"><em>timestep</em></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 class="reference internal" href="neigh_modify.html"><em>neigh_modify</em></a>
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parameters, <a class="reference internal" href="dump.html"><em>dump</em></a> every N timesteps, etc) refer to the
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outermost timesteps.</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.</p>
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<p>The <em>inner</em> and <em>middle</em> 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 <em>inner</em> 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.</p>
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<p>Only some pair potentials support the use of the <em>inner</em> and <em>middle</em>
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and <em>outer</em> keywords. If not, only the <em>pair</em> 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</p>
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<p>Another option for using pair potentials with rRESPA is with the
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<em>hybrid</em> keyword, which requires the use of the <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid or hybrid/overlay</em></a> 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 <em>hybrid</em> 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 <em>hybrid</em> keyword
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operates on pair style computations, it is mututally exclusive with
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either the <em>pair</em> or the <em>inner</em>/<em>middle</em>/<em>outer</em> keywords.</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 <em>a priori</em>
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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.</p>
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<p>With that caveat, a few rules-of-thumb may be useful in selecting
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<em>respa</em> 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 <em>respa</em> style without SHAKE in biomolecular
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simulations:</p>
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<div class="highlight-python"><div class="highlight"><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></div>
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</div>
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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 <em>verlet</em> style with a 0.5 fmsec
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timestep.</p>
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<p>If SHAKE is used with the <em>respa</em> 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:</p>
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<div class="highlight-python"><div class="highlight"><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></div>
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</div>
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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 <em>verlet</em> style with SHAKE and a
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2.0 fmsec timestep.</p>
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<p>For non-biomolecular simulations, the <em>respa</em> 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:</p>
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<div class="highlight-python"><div class="highlight"><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></div>
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</div>
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<hr class="docutils" />
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<p>The <em>respa/omp</em> styles is a variant of <em>respa</em> adapted for use with
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pair, bond, angle, dihedral, improper, or kspace styles with an <em>omp</em>
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suffix. It is functionally equivalent to <em>respa</em> but performs additional
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operations required for managing <em>omp</em> styles. For more on <em>omp</em> styles
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see the <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></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.</p>
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<p>You can specify <em>respa/omp</em> explicitly in your input script, or
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you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a>
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when you invoke LAMMPS, or you can use the <a class="reference internal" href="suffix.html"><em>suffix</em></a>
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command in your input script.</p>
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<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
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more instructions on how to use the accelerated styles effectively.</p>
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</div>
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<hr class="docutils" />
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<div class="section" id="restrictions">
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<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
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<p>The <em>verlet/split</em> style can only be used if LAMMPS was built with the
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REPLICA package. Correspondingly the <em>respa/omp</em> style is available only
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if the USER-OMP package was included. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
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section for more info on packages.</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.</p>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
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<p><a class="reference internal" href="timestep.html"><em>timestep</em></a>, <a class="reference internal" href="run.html"><em>run</em></a></p>
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</div>
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<div class="section" id="default">
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<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>run_style verlet
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</pre></div>
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</div>
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<hr class="docutils" />
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<p id="tuckerman"><strong>(Tuckerman)</strong> Tuckerman, Berne and Martyna, J Chem Phys, 97, p 1990
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(1992).</p>
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