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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3295 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2009-11-02 20:59:26 +00:00
parent 8b7d3712b5
commit 32adc325aa
5 changed files with 56 additions and 14 deletions
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16
src/USER-CG-CMM/pair_cmm_common.cpp
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@ -41,8 +41,7 @@ PairCMMCommon::PairCMMCommon(class LAMMPS *lmp) : Pair(lmp)
* clean up common arrays *
* ---------------------------------------------------------------------- */
PairCMMCommon::~PairCMMCommon()
{
PairCMMCommon::~PairCMMCommon() {
if (allocated) {
memory->destroy_2d_int_array(setflag);
memory->destroy_2d_int_array(cg_type);
@ -447,16 +446,21 @@ double PairCMMCommon::eval_single(int coul_type, int i, int j, int itype, int jt
const double ratio = sigma[itype][jtype]/sqrt(rsq);
const double eps = epsilon[itype][jtype];
lj_force = cgpref*eps * rsq * (cgpow1*pow(ratio,cgpow1)
- cgpow2*pow(ratio,cgpow2));
lj_force = cgpref*eps * (cgpow1*pow(ratio,cgpow1)
- cgpow2*pow(ratio,cgpow2))/rsq;
lj_erg = cgpref*eps * (pow(ratio,cgpow1) - pow(ratio,cgpow2));
}
if (rsq < cut_coul[itype][jtype]) {
if(coul_type == CG_COUL_LONG) {
error->all("single energy computation with coulomb not supported by CG potentials.");
error->all("single energy computation with long-range coulomb not supported by CG potentials.");
} else if ((coul_type == CG_COUL_CUT) || (coul_type == CG_COUL_DEBYE)) {
error->all("single energy computation with coulomb not supported by CG potentials.");
const double r2inv = 1.0/rsq;
const double rinv = sqrt(r2inv);
const double qscreen=exp(-kappa*sqrt(rsq));
coul_force = force->qqrd2e * atom->q[i]*atom->q[j]*rinv * qscreen * (kappa + rinv);
coul_erg = force->qqrd2e * atom->q[i]*atom->q[j]*rinv * qscreen;
// error->all("single energy computation with coulomb not supported by CG potentials.");
} else if (coul_type == CG_COUL_NONE) {
; // do nothing
} else {

14
src/USER-CG-CMM/pair_cmm_common.h
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@ -10,7 +10,7 @@
/* ----------------------------------------------------------------------
Common functionality for the CMM coarse grained MD potentials.
Contributing author: Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>
Contributing author: Axel Kohlmeyer <akohlmey@gmail.com>
------------------------------------------------------------------------- */
#ifndef PAIR_CMM_COMMON_H
@ -247,11 +247,11 @@ namespace LAMMPS_NS {
if ((COUL_TYPE == CG_COUL_CUT) || (COUL_TYPE == CG_COUL_DEBYE)) {
if (rsq < cut_coulsq[itype][jtype]) {
double r=sqrt(rsq);
double screen=exp(-kappa*r);
double qscreen=exp(-kappa*r);
forcecoul = factor_coul * qqrd2e
* qtmp * q[j] * screen * (kappa + 1.0/r);
* qtmp * q[j] * qscreen * (kappa + 1.0/r);
if (EFLAG) ecoul=factor_coul*qqrd2e
* qtmp*q[j] * screen / r;
* qtmp*q[j] * qscreen / r;
}
}
@ -644,11 +644,11 @@ namespace LAMMPS_NS {
if ((COUL_TYPE == CG_COUL_CUT) || (COUL_TYPE == CG_COUL_DEBYE)) {
if (rsq < cut_coulsq[itype][jtype]) {
double r=sqrt(rsq);
double screen=exp(-kappa*r);
double qscreen=exp(-kappa*r);
forcecoul = factor_coul * qqrd2e
* qtmp * q[j] * screen * (kappa + 1.0/r);
* qtmp * q[j] * qscreen * (kappa + 1.0/r);
if (EFLAG) ecoul=factor_coul*qqrd2e
* qtmp*q[j] * screen / r;
* qtmp*q[j] * qscreen / r;
}
}

1
src/finish.cpp
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@ -82,7 +82,6 @@ void Finish::end(int flag)
// overall loop time
// use actual natoms, in case atoms were lost
natoms;
double rlocal = atom->nlocal;
MPI_Allreduce(&rlocal,&natoms,1,MPI_DOUBLE,MPI_SUM,world);

38
src/pair.cpp
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@ -390,6 +390,44 @@ void Pair::ev_tally(int i, int j, int nlocal, int newton_pair,
}
}
/* ----------------------------------------------------------------------
tally eng_vdwl and virial into global and per-atom accumulators
can use this version with full neighbor lists
------------------------------------------------------------------------- */
void Pair::ev_tally_full(int i, double evdwl, double ecoul, double fpair,
double delx, double dely, double delz)
{
if (eflag_either) {
if (eflag_global) {
eng_vdwl += 0.5*evdwl;
eng_coul += 0.5*ecoul;
}
if (eflag_atom) eatom[i] += 0.5 * (evdwl + ecoul);
}
if (vflag_either) {
if (vflag_global) {
virial[0] += 0.5*delx*delx*fpair;
virial[1] += 0.5*dely*dely*fpair;
virial[2] += 0.5*delz*delz*fpair;
virial[3] += 0.5*delx*dely*fpair;
virial[4] += 0.5*delx*delz*fpair;
virial[5] += 0.5*dely*delz*fpair;
}
}
if (vflag_atom) {
vatom[i][0] += 0.5*delx*delx*fpair;
vatom[i][1] += 0.5*dely*dely*fpair;
vatom[i][2] += 0.5*delz*delz*fpair;
vatom[i][3] += 0.5*delx*dely*fpair;
vatom[i][4] += 0.5*delx*delz*fpair;
vatom[i][5] += 0.5*dely*delz*fpair;
}
}
/* ----------------------------------------------------------------------
tally eng_vdwl and virial into global and per-atom accumulators
for virial, have delx,dely,delz and fx,fy,fz

1
src/pair.h
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@ -121,6 +121,7 @@ class Pair : protected Pointers {
void ev_setup(int, int);
void ev_tally(int, int, int, int, double, double, double,
double, double, double);
void ev_tally_full(int, double, double, double, double, double, double);
void ev_tally_xyz(int, int, int, int, double, double,
double, double, double, double, double, double);
void ev_tally3(int, int, int, double, double,