<p>Choose the style of time integrator used for molecular dynamics
simulations performed by LAMMPS.</p>
<p>The <em>verlet</em> style is a standard velocity-Verlet integrator.</p>
<hrclass="docutils"/>
<p>The <em>verlet/split</em> style is also a velocity-Verlet integrator, but it
splits the force calculation within each timestep over 2 partitions of
processors. See <aclass="reference internal"href="Section_start.html#start-7"><spanclass="std std-ref">Section 2.7</span></a> for an
explanation of the -partition command-line switch.</p>
<p>Specifically, this style performs all computation except the
<aclass="reference internal"href="kspace_style.html"><spanclass="doc">kspace_style</span></a> portion of the force field on the 1st
partition. This include the <aclass="reference internal"href="pair_style.html"><spanclass="doc">pair style</span></a>, <aclass="reference internal"href="bond_style.html"><spanclass="doc">bond style</span></a>, <aclass="reference internal"href="neighbor.html"><spanclass="doc">neighbor list building</span></a>,
<aclass="reference internal"href="fix.html"><spanclass="doc">fixes</span></a> including time intergration, and output. The
<aclass="reference internal"href="kspace_style.html"><spanclass="doc">kspace_style</span></a> portion of the calculation is
performed on the 2nd partition.</p>
<p>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.</p>
<p>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.</p>
<p>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
<aclass="reference internal"href="processors.html"><spanclass="doc">processors</span></a> command with its <em>part</em> keyword for a way
to control this, e.g.</p>
<preclass="literal-block">
procssors * * * part 1 2 multiple
</pre>
<p>You can also use the <aclass="reference internal"href="partition.html"><spanclass="doc">partition</span></a> command to explicitly
specity the processor layout on each partition. E.g. for 2 partitions
<p>When you run in 2-partition mode with the <em>verlet/split</em> 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 <aclass="reference internal"href="Section_start.html#start-7"><spanclass="std std-ref">-plog and -pscreen command-line switches</span></a> to change this. The log and
screen file for the 2nd partition will not contain thermodynamic
output beyone the 1st timestep of the run.</p>
<p>See <aclass="reference internal"href="Section_accelerate.html"><spanclass="doc">Section 5</span></a> of the manual for
performance details of the speed-up offered by the <em>verlet/split</em>
style. One important performance consideration is the assignemnt of
logical processors in the 2 partitions to the physical cores of a
parallel machine. The <aclass="reference internal"href="processors.html"><spanclass="doc">processors</span></a> command has
options to support this, and strategies are discussed in
<aclass="reference internal"href="Section_accelerate.html"><spanclass="doc">Section 5</span></a> of the manual.</p>
<hrclass="docutils"/>
<p>The <em>respa</em> style implements the rRESPA multi-timescale integrator
<aclass="reference internal"href="#tuckerman"><spanclass="std std-ref">(Tuckerman)</span></a> 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.</p>
<p>The <aclass="reference internal"href="timestep.html"><spanclass="doc">timestep</span></a> 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. <aclass="reference internal"href="neigh_modify.html"><spanclass="doc">neigh_modify</span></a>
parameters, <aclass="reference internal"href="dump.html"><spanclass="doc">dump</span></a> every N timesteps, etc) refer to the
outermost timesteps.</p>
<p>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.</p>
<p>For fixes that support it, the rRESPA level at which a given fix is
active, can be selected through the <aclass="reference internal"href="fix_modify.html"><spanclass="doc">fix_modify</span></a> command.</p>
<p>The <em>inner</em> and <em>middle</em> keywords take additional arguments for
cutoffs that are used by the pairwise force computations. If the 2
cutoffs for <em>inner</em> 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.</p>
<p>Only some pair potentials support the use of the <em>inner</em> and <em>middle</em>
and <em>outer</em> keywords. If not, only the <em>pair</em> 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</p>
<p>Another option for using pair potentials with rRESPA is with the
<em>hybrid</em> keyword, which requires the use of the <aclass="reference internal"href="pair_hybrid.html"><spanclass="doc">pair_style hybrid or hybrid/overlay</span></a> 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 <em>hybrid</em> 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 <em>hybrid</em> keyword
operates on pair style computations, it is mututally exclusive with
either the <em>pair</em> or the <em>inner</em>/<em>middle</em>/<em>outer</em> keywords.</p>
<p>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 <em>a priori</em>
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.</p>
<p>With that caveat, a few rules-of-thumb may be useful in selecting
<em>respa</em> 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 <em>respa</em> style without SHAKE in biomolecular
<p>The <em>respa/omp</em> styles is a variant of <em>respa</em> adapted for use with
pair, bond, angle, dihedral, improper, or kspace styles with an <em>omp</em>
suffix. It is functionally equivalent to <em>respa</em> but performs additional
operations required for managing <em>omp</em> styles. For more on <em>omp</em> styles
see the <aclass="reference internal"href="Section_accelerate.html"><spanclass="doc">Section 5</span></a> of the manual.
Accelerated styles take the same arguments and should produce the same
results, except for round-off and precision issues.</p>
<p>You can specify <em>respa/omp</em> explicitly in your input script, or
you can use the <aclass="reference internal"href="Section_start.html#start-7"><spanclass="std std-ref">-suffix command-line switch</span></a>
when you invoke LAMMPS, or you can use the <aclass="reference internal"href="suffix.html"><spanclass="doc">suffix</span></a>
command in your input script.</p>
<p>See <aclass="reference internal"href="Section_accelerate.html"><spanclass="doc">Section 5</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hrclass="docutils"/>
<divclass="section"id="restrictions">
<h2>Restrictions</h2>
<p>The <em>verlet/split</em> style can only be used if LAMMPS was built with the
REPLICA package. Correspondingly the <em>respa/omp</em> style is available only
if the USER-OMP package was included. See the <aclass="reference internal"href="Section_start.html#start-3"><spanclass="std std-ref">Making LAMMPS</span></a>
section for more info on packages.</p>
<p>Whenever using rRESPA, the user should experiment with trade-offs in
speed and accuracy for their system, and verify that they are
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