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