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Better compute_pressure hybrid and doc

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This commit is contained in:
Julien Devemy
2019-06-25 12:01:29 +02:00
parent 7fab12c36f
commit 6a6d08e18e
2 changed files with 42 additions and 16 deletions
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8
doc/src/compute_pressure.txt
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@ -16,12 +16,13 @@ ID, group-ID are documented in "compute"_compute.html command
pressure = style name of this compute command
temp-ID = ID of compute that calculates temperature, can be NULL if not needed
zero or more keywords may be appended
keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} :ul
keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} or {hybridpair} :ul
[Examples:]
compute 1 all pressure thermo_temp
compute 1 all pressure NULL pair bond :pre
compute 1 all pressure NULL pair bond
compute 1 all pressure NULL hybridpair lj/cut :pre
[Description:]
@ -67,6 +68,9 @@ extra keywords are listed, then only those components are summed to
compute temperature or ke and/or the virial. The {virial} keyword
means include all terms except the kinetic energy {ke}.
The {hybridpair} keyword means to only include contribution
from a subpair in a {hybrid} or {hybrid/overlay} pair style.
Details of how LAMMPS computes the virial efficiently for the entire
system, including for many-body potentials and accounting for the
effects of periodic boundary conditions are discussed in

50
src/compute_pressure.cpp
View File

@ -81,8 +81,37 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) :
int iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"ke") == 0) keflag = 1;
else if (strcmp(arg[iarg],"hybridpair") == 0)
hybridpairflag = force->inumeric(FLERR, arg[++iarg]);
else if (strcmp(arg[iarg],"hybridpair") == 0) {
int n = strlen(arg[++iarg]) + 1;
if (lmp->suffix) n += strlen(lmp->suffix) + 1;
pstyle = new char[n];
strcpy(pstyle,arg[iarg++]);
nsub = 0;
if (narg > iarg) {
if (isdigit(arg[iarg][0])) {
nsub = force->inumeric(FLERR,arg[iarg]);
++iarg;
if (nsub <= 0)
error->all(FLERR,"Illegal compute pressure command");
}
}
// check if pair style with and without suffix exists
hybridpair = (Pair *) force->pair_match(pstyle,1,nsub);
if (!hybridpair && lmp->suffix) {
strcat(pstyle,"/");
strcat(pstyle,lmp->suffix);
hybridpair = (Pair *) force->pair_match(pstyle,1,nsub);
}
if (!hybridpair)
error->all(FLERR,"Unrecognized pair style in compute pressure command");
hybridpairflag = 1;
}
else if (strcmp(arg[iarg],"pair") == 0) pairflag = 1;
else if (strcmp(arg[iarg],"bond") == 0) bondflag = 1;
else if (strcmp(arg[iarg],"angle") == 0) angleflag = 1;
@ -144,12 +173,7 @@ void ComputePressure::init()
nvirial = 0;
vptr = NULL;
if (hybridpairflag > 0 && force->pair) {
if (strstr(force->pair_style, "hybrid")) {
PairHybrid *ph = (PairHybrid *) force->pair;
if (hybridpairflag <= ph->nstyles) nvirial++;
}
}
if (hybridpairflag && force->pair) nvirial++;
if (pairflag && force->pair) nvirial++;
if (bondflag && atom->molecular && force->bond) nvirial++;
if (angleflag && atom->molecular && force->angle) nvirial++;
@ -162,12 +186,10 @@ void ComputePressure::init()
if (nvirial) {
vptr = new double*[nvirial];
nvirial = 0;
if (hybridpairflag > 0 && force->pair) {
if (strstr(force->pair_style, "hybrid")) {
PairHybrid *ph = (PairHybrid *) force->pair;
if (hybridpairflag <= ph->nstyles)
vptr[nvirial++] = ph->styles[hybridpairflag-1]->virial;
}
if (hybridpairflag && force->pair) {
PairHybrid *ph = (PairHybrid *) force->pair;
ph->no_virial_fdotr_compute = 1;
vptr[nvirial++] = hybridpair->virial;
}
if (pairflag && force->pair) vptr[nvirial++] = force->pair->virial;
if (bondflag && force->bond) vptr[nvirial++] = force->bond->virial;