jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13758 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2015-07-28 17:40:16 +00:00
parent 737f6dc86b
commit 1ff053ef7a
9 changed files with 217 additions and 52 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
doc/Section_packages.html
View File

@ -42,7 +42,7 @@ packages, more details are provided.
</H4>
<P>The current list of standard packages is as follows:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD >Package</TD><TD > Description</TD><TD > Author(s)</TD><TD > Doc page</TD><TD > Example</TD><TD > Library</TD></TR>
<TR ALIGN="center"><TD >ASPHERE</TD><TD > aspherical particles</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_14">Section_howto 6.14</A></TD><TD > ellipse</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >BODY</TD><TD > body-style particles</TD><TD > -</TD><TD > <A HREF = "body.html">body</A></TD><TD > body</TD><TD > -</TD></TR>
@ -119,7 +119,7 @@ on how to build LAMMPS with both kinds of auxiliary libraries.
</H4>
<P>The current list of user-contributed packages is as follows:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD >Package</TD><TD > Description</TD><TD > Author(s)</TD><TD > Doc page</TD><TD > Example</TD><TD > Pic/movie</TD><TD > Library</TD></TR>
<TR ALIGN="center"><TD >USER-ATC</TD><TD > atom-to-continuum coupling</TD><TD > Jones & Templeton & Zimmerman (1)</TD><TD > <A HREF = "fix_atc.html">fix atc</A></TD><TD > USER/atc</TD><TD > <A HREF = "http://lammps.sandia.gov/pictures.html#atc">atc</A></TD><TD > lib/atc</TD></TR>
<TR ALIGN="center"><TD >USER-AWPMD</TD><TD > wave-packet MD</TD><TD > Ilya Valuev (JIHT)</TD><TD > <A HREF = "pair_awpmd.html">pair_style awpmd/cut</A></TD><TD > USER/awpmd</TD><TD > -</TD><TD > lib/awpmd</TD></TR>

2
doc/balance.html
View File

@ -152,7 +152,7 @@ partitioning of the simulation box across processors (one sub-box for
each of 16 processors); the middle diagram is after a "grid" method
has been applied.
</P>
<CENTER><A HREF = "JPG/balance_uniform.jpg"><IMG SRC = "JPG/balance_uniform_small.jpg"></A><A HREF = "JGP/balance_nonuniform.jpg"><IMG SRC = "JPG/balance_nonuniform_small.jpg"></A><A HREF = "JPG/balance_rcb.jpg"><IMG SRC = "JPG/balance_rcb_small.jpg"></A>
<CENTER><A HREF = "JPG/balance_uniform.jpg"><IMG SRC = "JPG/balance_uniform_small.jpg"></A><A HREF = "JPG/balance_nonuniform.jpg"><IMG SRC = "JPG/balance_nonuniform_small.jpg"></A><A HREF = "JPG/balance_rcb.jpg"><IMG SRC = "JPG/balance_rcb_small.jpg"></A>
</CENTER>
<P>The <I>rcb</I> style is a "tiling" method which does not produce a logical
3d grid of processors. Rather it tiles the simulation domain with

2
doc/balance.txt
View File

@ -142,7 +142,7 @@ partitioning of the simulation box across processors (one sub-box for
each of 16 processors); the middle diagram is after a "grid" method
has been applied.
:c,image(JPG/balance_uniform_small.jpg,JPG/balance_uniform.jpg),image(JPG/balance_nonuniform_small.jpg,JGP/balance_nonuniform.jpg),image(JPG/balance_rcb_small.jpg,JPG/balance_rcb.jpg)
:c,image(JPG/balance_uniform_small.jpg,JPG/balance_uniform.jpg),image(JPG/balance_nonuniform_small.jpg,JPG/balance_nonuniform.jpg),image(JPG/balance_rcb_small.jpg,JPG/balance_rcb.jpg)
The {rcb} style is a "tiling" method which does not produce a logical
3d grid of processors. Rather it tiles the simulation domain with

11
doc/pair_hybrid.html
View File

@ -190,6 +190,17 @@ potentials.
</P>
<HR>
<P>Different force fields (e.g. CHARMM vs AMBER) may have different rules
for applying these factors to modulate the strength of pairwise
interactions bewteen pairs of atoms that are also 1-2, 1-3, and 1-4
neighbors in the molecular bond topology. Specific
<A HREF = "special_bonds.html">special_bonds</A> settings can be assigned to
different pair hybrid sub-styles via the <A HREF = "pair_modify.html">pair_modify
special</A> special command, using its <I>pair</I> keyword
and optional <I>special</I> argument. This allows multiple force fields to
be used to a model a hybrid system. See the
<A HREF = "special_bonds.html">special_bonds</A> doc page for details.
</P>
<P>The potential energy contribution to the overall system due to an
individual sub-style can be accessed and output via the <A HREF = "compute_pair.html">compute
pair</A> command.

11
doc/pair_hybrid.txt
View File

@ -184,6 +184,17 @@ potentials.
:line
Different force fields (e.g. CHARMM vs AMBER) may have different rules
for applying these factors to modulate the strength of pairwise
interactions bewteen pairs of atoms that are also 1-2, 1-3, and 1-4
neighbors in the molecular bond topology. Specific
"special_bonds"_special_bonds.html settings can be assigned to
different pair hybrid sub-styles via the "pair_modify
special"_pair_modify.html special command, using its {pair} keyword
and optional {special} argument. This allows multiple force fields to
be used to a model a hybrid system. See the
"special_bonds"_special_bonds.html doc page for details.
The potential energy contribution to the overall system due to an
individual sub-style can be accessed and output via the "compute
pair"_compute_pair.html command.

87
doc/pair_modify.html
View File

@ -19,9 +19,12 @@
<LI>keyword = <I>pair</I> or <I>shift</I> or <I>mix</I> or <I>table</I> or <I>table/disp</I> or <I>tabinner</I> or <I>tabinner/disp</I> or <I>tail</I> or <I>compute</I>
<PRE> <I>pair</I> values = sub-style N
<PRE> <I>pair</I> values = sub-style N special which w1 wt2 wt3
sub-style = sub-style of <A HREF = "pair_hybrid.html">pair hybrid</A>
N = which instance of sub-style (only if sub-style is used multiple times)
special = optional if want to override <A HREF = "special_bonds.html">special_bonds</A> settings for sub-style
which = <I>lj/coul</I> or <I>lj</I> or <I>coul</I>
w1,w2,w3 = weights from 0.0 to 1.0 inclusive
<I>mix</I> value = <I>geometric</I> or <I>arithmetic</I> or <I>sixthpower</I>
<I>shift</I> value = <I>yes</I> or <I>no</I>
<I>table</I> value = N
@ -48,19 +51,15 @@ pair_modify table 12
<P>Modify the parameters of the currently defined pair style. Not all
parameters are relevant to all pair styles.
</P>
<P>If used, the <I>pair</I> keyword must appear first in the list of keywords.
It can only be used with the <A HREF = "pair_hybrid.html">hybrid and
hybrid/overlay</A> pair styles. It means that the
following parameters will only be modified for the specified
sub-style, which must be a sub-style defined by the <A HREF = "pair_hybrid.html">pair_style
hybrid</A> command. If the sub-style is defined
multiple times, then an additional numeric argument <I>N</I> must also be
specified which is a number from 1 to M where M is the number of times
the sub-style was listed in the <A HREF = "pair_hybrid.html">pair_style hybrid</A>
command. The extra number indicates which instance of the sub-style
these modifications apply to. Note that if the <I>pair</I> keyword is not
used, and the pair style is <I>hybrid</I> or <I>hybrid/overlay</I>, the
pair_modify keywords will be applied to all sub-styles.
<P>If used, the <I>pair</I> keyword and its optional <I>special</I> arguments must
appear first in the list of keywords. It can only be used with the
<A HREF = "pair_hybrid.html">hybrid and hybrid/overlay</A> pair styles and when used
it means that all the following parameters will only be modified for
the specified sub-style. If the <I>pair</I> keyword is not used, and the
pair style is <I>hybrid</I> or <I>hybrid/overlay</I>, all the following
parameters keywords will be applied to all sub-styles. A more detailed
explanation of the <I>pair</I> keyword syntax, including its optional
<I>special</I> argument are given below.
</P>
<P>The <I>mix</I> keyword affects pair coefficients for interactions between
atoms of type I and J, when I != J and the coefficients are not
@ -202,6 +201,66 @@ a pair style will not work, because the
<A HREF = "kspace_style.html">kspace_style</A> command requires a Kspace-compatible
pair style be defined.
</P>
<HR>
<H4>Use of the pair keyword
</H4>
<P>If used, the <I>pair</I> keyword and its optional <I>special</I> arguments must
appear first in the list of keywords. It can only be used with the
<A HREF = "pair_hybrid.html">hybrid and hybrid/overlay</A> pair styles and when used
it means that all the following parameters will only be modified for
the specified sub-style. If the <I>pair</I> keyword is not used, and the
pair style is <I>hybrid</I> or <I>hybrid/overlay</I>, all the following
parameters keywords will be applied to all sub-styles. A more detailed
explanation of the <I>pair</I> keyword syntax, including its optional
<I>special</I> argument are given below.
</P>
<P>As mentioned above, the <I>pair</I> keyword can only be used with the
<A HREF = "pair_hybrid.html">hybrid and hybrid/overlay</A> pair styles, and must
come first in the list of keywords. If used, the subsequent keywords
will only be applied to the specified sub-style. If the sub-style is
defined multiple times, then an additional numeric argument <I>N</I> must
also be specified, which is a number from 1 to M where M is the number
of times the sub-style was listed in the <A HREF = "pair_hybrid.html">pair_style
hybrid</A> command. The extra number indicates which
instance of the sub-style the pair_modify keywords will be applied to.
</P>
<P>If the optional <I>special</I> argument is used, then the settings of the
<A HREF = "special_bonds.html">special_bonds</A> command are overridden for the
specified sub-style. The <I>special</I> argument requires 4 additional
arguments: <I>which</I> and w1,w2,w3. These are analogous to arguments in
the <A HREF = "special_bonds.html">special_bonds</A> command. The <I>which</I> argument
can be <I>lj</I> to change the Lennard-Jones settings, <I>coul</I> to change the
Coulombic settings, or <I>lj/coul</I> to change both to the same values.
The w1,w2,w3 arguments are numeric weights from 0.0 to 1.0 inclusive,
for the 1-2, 1-3, and 1-4 bond topology neighbors. For example, these
commands
</P>
<PRE>special_bonds lj/coul 0.0 0.0 0.1
pair_hybrid lj/charmm/coul/charmm 8.0 10.0 lj/cut/coul/cut 10.0
pair_modify pair lj/charmm/coul/charmm special lj/coul 0.0 0.0 0.0
pair_modify pair lj/cut/coul/cut special lj 0.0 0.0 0.5
pair_modify pair lj/cut/coul/cut special coul 0.0 0.0 0.8333
</PRE>
<P>show how to use both the CHARMM and AMBER force fields in a single
simulation. The first pair modify command sets the special bonds to
CHARMM values (all 0.0). The latter 2 pair modify commands set the
standard AMBER values for LJ and Coulombic weights.
</P>
<P>IMPORTANT NOTE: The global settings specified by the
<A HREF = "special_bonds.html">special_bonds</A> command affect the construction of
neighbor lists. Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors)
exclude those pairs from the neighbor list entirely. Weights of 1.0
store the neighbor with no weight flag applied. Neither of these
neighbor effects can be changed by setting a sub-style weight to a
non-zero or non-one value. Thus an error is generated if the new
sub-style value is not 0.0 (or 1.0) and the global setting is 0.0 (or
1.0). Note that as in the example above, the global factor can simply
be set a value other than 0.0 or 1.0, then overridden by any of the
sub-styles to a value that is 0.0 or 1.0.
</P>
<HR>
<P><B>Restrictions:</B> none
</P>
<P>You cannot use <I>shift</I> yes with <I>tail</I> yes, since those are

87
doc/pair_modify.txt
View File

@ -14,9 +14,12 @@ pair_modify keyword values ... :pre
one or more keyword/value pairs may be listed :ulb,l
keyword = {pair} or {shift} or {mix} or {table} or {table/disp} or {tabinner} or {tabinner/disp} or {tail} or {compute} :l
{pair} values = sub-style N
{pair} values = sub-style N special which w1 wt2 wt3
sub-style = sub-style of "pair hybrid"_pair_hybrid.html
N = which instance of sub-style (only if sub-style is used multiple times)
special = optional if want to override "special_bonds"_special_bonds.html settings for sub-style
which = {lj/coul} or {lj} or {coul}
w1,w2,w3 = weights from 0.0 to 1.0 inclusive
{mix} value = {geometric} or {arithmetic} or {sixthpower}
{shift} value = {yes} or {no}
{table} value = N
@ -42,19 +45,15 @@ pair_modify table 12 :pre
Modify the parameters of the currently defined pair style. Not all
parameters are relevant to all pair styles.
If used, the {pair} keyword must appear first in the list of keywords.
It can only be used with the "hybrid and
hybrid/overlay"_pair_hybrid.html pair styles. It means that the
following parameters will only be modified for the specified
sub-style, which must be a sub-style defined by the "pair_style
hybrid"_pair_hybrid.html command. If the sub-style is defined
multiple times, then an additional numeric argument {N} must also be
specified which is a number from 1 to M where M is the number of times
the sub-style was listed in the "pair_style hybrid"_pair_hybrid.html
command. The extra number indicates which instance of the sub-style
these modifications apply to. Note that if the {pair} keyword is not
used, and the pair style is {hybrid} or {hybrid/overlay}, the
pair_modify keywords will be applied to all sub-styles.
If used, the {pair} keyword and its optional {special} arguments must
appear first in the list of keywords. It can only be used with the
"hybrid and hybrid/overlay"_pair_hybrid.html pair styles and when used
it means that all the following parameters will only be modified for
the specified sub-style. If the {pair} keyword is not used, and the
pair style is {hybrid} or {hybrid/overlay}, all the following
parameters keywords will be applied to all sub-styles. A more detailed
explanation of the {pair} keyword syntax, including its optional
{special} argument are given below.
The {mix} keyword affects pair coefficients for interactions between
atoms of type I and J, when I != J and the coefficients are not
@ -196,6 +195,66 @@ a pair style will not work, because the
"kspace_style"_kspace_style.html command requires a Kspace-compatible
pair style be defined.
:line
Use of the pair keyword :h4
If used, the {pair} keyword and its optional {special} arguments must
appear first in the list of keywords. It can only be used with the
"hybrid and hybrid/overlay"_pair_hybrid.html pair styles and when used
it means that all the following parameters will only be modified for
the specified sub-style. If the {pair} keyword is not used, and the
pair style is {hybrid} or {hybrid/overlay}, all the following
parameters keywords will be applied to all sub-styles. A more detailed
explanation of the {pair} keyword syntax, including its optional
{special} argument are given below.
As mentioned above, the {pair} keyword can only be used with the
"hybrid and hybrid/overlay"_pair_hybrid.html pair styles, and must
come first in the list of keywords. If used, the subsequent keywords
will only be applied to the specified sub-style. If the sub-style is
defined multiple times, then an additional numeric argument {N} must
also be specified, which is a number from 1 to M where M is the number
of times the sub-style was listed in the "pair_style
hybrid"_pair_hybrid.html command. The extra number indicates which
instance of the sub-style the pair_modify keywords will be applied to.
If the optional {special} argument is used, then the settings of the
"special_bonds"_special_bonds.html command are overridden for the
specified sub-style. The {special} argument requires 4 additional
arguments: {which} and w1,w2,w3. These are analogous to arguments in
the "special_bonds"_special_bonds.html command. The {which} argument
can be {lj} to change the Lennard-Jones settings, {coul} to change the
Coulombic settings, or {lj/coul} to change both to the same values.
The w1,w2,w3 arguments are numeric weights from 0.0 to 1.0 inclusive,
for the 1-2, 1-3, and 1-4 bond topology neighbors. For example, these
commands
special_bonds lj/coul 0.0 0.0 0.1
pair_hybrid lj/charmm/coul/charmm 8.0 10.0 lj/cut/coul/cut 10.0
pair_modify pair lj/charmm/coul/charmm special lj/coul 0.0 0.0 0.0
pair_modify pair lj/cut/coul/cut special lj 0.0 0.0 0.5
pair_modify pair lj/cut/coul/cut special coul 0.0 0.0 0.8333 :pre
show how to use both the CHARMM and AMBER force fields in a single
simulation. The first pair modify command sets the special bonds to
CHARMM values (all 0.0). The latter 2 pair modify commands set the
standard AMBER values for LJ and Coulombic weights.
IMPORTANT NOTE: The global settings specified by the
"special_bonds"_special_bonds.html command affect the construction of
neighbor lists. Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors)
exclude those pairs from the neighbor list entirely. Weights of 1.0
store the neighbor with no weight flag applied. Neither of these
neighbor effects can be changed by setting a sub-style weight to a
non-zero or non-one value. Thus an error is generated if the new
sub-style value is not 0.0 (or 1.0) and the global setting is 0.0 (or
1.0). Note that as in the example above, the global factor can simply
be set a value other than 0.0 or 1.0, then overridden by any of the
sub-styles to a value that is 0.0 or 1.0.
:line
[Restrictions:] none
You cannot use {shift} yes with {tail} yes, since those are

33
doc/run_style.html
View File

@ -24,7 +24,7 @@
n1, n2, ... = loop factor between rRESPA levels (N-1 values)
zero or more keyword/value pairings may be appended to the loop factors
keyword = <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I> or
<I>pair</I> or <I>inner</I> or <I>middle</I> or <I>outer</I> or <I>kspace</I>
<I>pair</I> or <I>inner</I> or <I>middle</I> or <I>outer</I> or <I>hybrid</I> or <I>kspace</I>
<I>bond</I> value = M
M = which level (1-N) to compute bond forces in
<I>angle</I> value = M
@ -47,6 +47,10 @@
cut2 = outer cutoff between pair middle and pair outer (distance units)
<I>outer</I> value = M
M = which level (1-N) to compute pair outer forces in
<I>hybrid</I> 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
...
<I>kspace</I> value = M
M = which level (1-N) to compute kspace forces in
</PRE>
@ -58,6 +62,8 @@
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>
<PRE>run_style respa 3 4 2 bond 1 hybrid 2 2 1 kspace 3
</PRE>
<P><B>Description:</B>
</P>
<P>Choose the style of time integrator used for molecular dynamics
@ -168,7 +174,17 @@ compute forces for all pairs from 5.0 outward, with those from 5.0 to
and <I>outer</I> keywords. If not, only the <I>pair</I> 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.
details.i
</P>
<P>Another variant to use pair potentials in rRESPA is with the <I>hybrid</I>
keyword, which requires the use of a <A HREF = "pair_hybrid.html">hybrid pair_style</A>
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 <I>hybrid</I> designates
pair force computations, it is mututally exclusive with either the <I>pair</I>
or the <I>inner</I>/<I>middle</I>/<I>outer</I> 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
@ -237,16 +253,12 @@ run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3
<P>The <I>respa/omp</I> styles is a variant of <I>respa</I> adapted for use with
pair, bond, angle, dihedral, improper, or kspace styles with an <I>omp</I>
suffix. It is functionally to <I>respa</I> but performs additional required
operations. For more on <I>omp</I> styles see the
<A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual.
suffix. It is functionally equivalent to <I>respa</I> but performs additional
operations required for managing <I>omp</I> styles. For more on <I>omp</I> styles
see the <A HREF = "Section_accelerate.html">Section_accelerate</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>The <I>respa/omp</I> style is part of the USER-OMP packages. It is only
enabled if LAMMPS was built with this package included. See the
<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
</P>
<P>You can specify <I>respa/omp</I> explicitly in your input script, or
you can use the <A HREF = "Section_start.html#start_7">-suffix command-line switch</A>
when you invoke LAMMPS, or you can use the <A HREF = "suffix.html">suffix</A>
@ -260,7 +272,8 @@ more instructions on how to use the accelerated styles effectively.
<P><B>Restrictions:</B>
</P>
<P>The <I>verlet/split</I> style can only be used if LAMMPS was built with the
REPLICA package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
REPLICA package. Correspondingly the <I>respa/omp</I> style is available only
if the USER-OMP package was included. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info on packages.
</P>
<P>Whenever using rRESPA, the user should experiment with trade-offs in

32
doc/run_style.txt
View File

@ -20,7 +20,7 @@ style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l
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 {kspace}
{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
@ -43,6 +43,10 @@ style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l
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
@ -52,6 +56,7 @@ style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l
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:]
@ -163,7 +168,17 @@ 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.
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
@ -232,16 +247,12 @@ run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3 :pre
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 to {respa} but performs additional required
operations. For more on {omp} styles see the
"Section_accelerate"_Section_accelerate.html of the manual.
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.
The {respa/omp} style is part of the USER-OMP packages. It is only
enabled if LAMMPS was built with this package included. See the
"Making LAMMPS"_Section_start.html#start_3 section for more info.
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
@ -255,7 +266,8 @@ more instructions on how to use the accelerated styles effectively.
[Restrictions:]
The {verlet/split} style can only be used if LAMMPS was built with the
REPLICA package. See the "Making LAMMPS"_Section_start.html#start_3
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