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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8159 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2012-05-23 15:51:56 +00:00
parent 7941aa48cc
commit 144f2f2fd6
23 changed files with 250 additions and 246 deletions
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18
src/USER-CG-CMM/pair_lj_sdk_coul_long.cpp
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@ -175,12 +175,10 @@ void PairLJSDKCoulLong::eval()
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (EFLAG)
ecoul = prefactor*erfc;
if (EFLAG) ecoul = prefactor*erfc;
if (factor_coul < 1.0) {
forcecoul -= (1.0-factor_coul)*prefactor;
if (EFLAG)
ecoul -= (1.0-factor_coul)*prefactor;
if (EFLAG) ecoul -= (1.0-factor_coul)*prefactor;
}
} else {
union_int_float_t rsq_lookup;
@ -190,14 +188,12 @@ void PairLJSDKCoulLong::eval()
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (EFLAG)
ecoul = qtmp*q[j] * table;
if (EFLAG) ecoul = qtmp*q[j] * (etable[itable] + fraction*detable[itable]);
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
if (EFLAG)
ecoul -= (1.0-factor_coul)*prefactor;
if (EFLAG) ecoul -= (1.0-factor_coul)*prefactor;
}
}
}
@ -231,8 +227,7 @@ void PairLJSDKCoulLong::eval()
- lj4[itype][jtype]) - offset[itype][jtype];
}
forcelj *= factor_lj;
if (EFLAG)
evdwl *= factor_lj;
if (EFLAG) evdwl *= factor_lj;
}
fpair = (forcecoul + forcelj) * r2inv;
@ -247,8 +242,7 @@ void PairLJSDKCoulLong::eval()
}
if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
evdwl,ecoul,fpair,delx,dely,delz);
evdwl,ecoul,fpair,delx,dely,delz);
}
}
f[i][0] += fxtmp;

2
src/USER-OMP/improper_class2_omp.cpp
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@ -79,7 +79,7 @@ void ImproperClass2OMP::compute(int eflag, int vflag)
} // end of omp parallel region
}
template <const int EVFLAG, const int EFLAG, const int NEWTON_BOND>
template <int EVFLAG, int EFLAG, int NEWTON_BOND>
void ImproperClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
{
int i1,i2,i3,i4,i,j,k,n,type;

1
src/USER-OMP/pair_buck_coul_omp.cpp
View File

@ -39,6 +39,7 @@ PairBuckCoulOMP::PairBuckCoulOMP(LAMMPS *lmp) :
{
suffix_flag |= Suffix::OMP;
respa_enable = 0;
cut_respa = NULL;
}
/* ---------------------------------------------------------------------- */

1
src/USER-OMP/pair_coul_long_omp.cpp
View File

@ -38,6 +38,7 @@ PairCoulLongOMP::PairCoulLongOMP(LAMMPS *lmp) :
{
suffix_flag |= Suffix::OMP;
respa_enable = 0;
cut_respa = NULL;
}
/* ---------------------------------------------------------------------- */

1
src/USER-OMP/pair_lj96_cut_omp.cpp
View File

@ -30,6 +30,7 @@ PairLJ96CutOMP::PairLJ96CutOMP(LAMMPS *lmp) :
{
suffix_flag |= Suffix::OMP;
respa_enable = 0;
cut_respa = NULL;
}
/* ---------------------------------------------------------------------- */

179
src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp
View File

@ -23,14 +23,6 @@
#include "suffix.h"
using namespace LAMMPS_NS;
#define EWALD_F 1.12837917
#define EWALD_P 0.3275911
#define A1 0.254829592
#define A2 -0.284496736
#define A3 1.421413741
#define A4 -1.453152027
#define A5 1.061405429
/* ---------------------------------------------------------------------- */
PairLJCharmmCoulLongOMP::PairLJCharmmCoulLongOMP(LAMMPS *lmp) :
@ -38,6 +30,7 @@ PairLJCharmmCoulLongOMP::PairLJCharmmCoulLongOMP(LAMMPS *lmp) :
{
suffix_flag |= Suffix::OMP;
respa_enable = 0;
cut_respa = NULL;
}
/* ---------------------------------------------------------------------- */
@ -84,101 +77,121 @@ void PairLJCharmmCoulLongOMP::compute(int eflag, int vflag)
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
void PairLJCharmmCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
{
int i,j,ii,jj,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double fraction,table;
double r,rsq,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double philj,switch1,switch2;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = ecoul = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const int * const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_coul = force->special_coul;
const double * const special_lj = force->special_lj;
const double qqrd2e = force->qqrd2e;
double fxtmp,fytmp,fztmp;
const double inv_denom_lj = 1.0/denom_lj;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
const int * const ilist = list->ilist;
const int * const numneigh = list->numneigh;
const int * const * const firstneigh = list->firstneigh;
const int nlocal = atom->nlocal;
// loop over neighbors of my atoms
for (ii = iifrom; ii < iito; ++ii) {
for (int ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
const int i = ilist[ii];
const int itype = type[i];
const double qtmp = q[i];
const double xtmp = x[i][0];
const double ytmp = x[i][1];
const double ztmp = x[i][2];
double fxtmp,fytmp,fztmp;
fxtmp=fytmp=fztmp=0.0;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
const int * const jlist = firstneigh[i];
const int jnum = numneigh[i];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
for (int jj = 0; jj < jnum; jj++) {
double forcecoul, forcelj, evdwl, ecoul;
forcecoul = forcelj = evdwl = ecoul = 0.0;
const int sbindex = sbmask(jlist[jj]);
const int j = jlist[jj] & NEIGHMASK;
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
const double delz = ztmp - x[j][2];
const double rsq = delx*delx + dely*dely + delz*delz;
const int jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
const double r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor = qqrd2e * qtmp*q[j]/r;
const double A1 = 0.254829592;
const double A2 = -0.284496736;
const double A3 = 1.421413741;
const double A4 = -1.453152027;
const double A5 = 1.061405429;
const double EWALD_F = 1.12837917;
const double INV_EWALD_P = 1.0/0.3275911;
const double r = sqrt(rsq);
const double grij = g_ewald * r;
const double expm2 = exp(-grij*grij);
const double t = INV_EWALD_P / (INV_EWALD_P + grij);
const double erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
const double prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
if (EFLAG) ecoul = prefactor*erfc;
if (sbindex) {
const double adjust = (1.0-special_coul[sbindex])*prefactor;
forcecoul -= adjust;
if (EFLAG) ecoul -= adjust;
}
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
const int itable = (rsq_lookup.i & ncoulmask) >> ncoulshiftbits;
const double fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
const double table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
if (EFLAG) ecoul = qtmp*q[j] * (etable[itable] + fraction*detable[itable]);
if (sbindex) {
const double table2 = ctable[itable] + fraction*dctable[itable];
const double prefactor = qtmp*q[j] * table2;
const double adjust = (1.0-special_coul[sbindex])*prefactor;
forcecoul -= adjust;
if (EFLAG) ecoul -= adjust;
}
}
} else forcecoul = 0.0;
}
if (rsq < cut_ljsq) {
r6inv = r2inv*r2inv*r2inv;
jtype = type[j];
const double r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
switch2 = 12.0*rsq * (cut_ljsq-rsq) *
(rsq-cut_lj_innersq) / denom_lj;
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
forcelj = forcelj*switch1 + philj*switch2;
}
forcelj *= factor_lj;
} else forcelj = 0.0;
if (EFLAG) evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
fpair = (forcecoul + forcelj) * r2inv;
if (rsq > cut_lj_innersq) {
const double drsq = cut_ljsq - rsq;
const double cut2 = (rsq - cut_lj_innersq) * drsq;
const double switch1 = drsq * (drsq*drsq + 3.0*cut2) * inv_denom_lj;
const double switch2 = 12.0*rsq * cut2 * inv_denom_lj;
if (EFLAG) {
forcelj = forcelj*switch1 + evdwl*switch2;
evdwl *= switch1;
} else {
const double philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
forcelj = forcelj*switch1 + philj*switch2;
}
}
if (sbindex) {
const double factor_lj = special_lj[sbindex];
forcelj *= factor_lj;
if (EFLAG) evdwl *= factor_lj;
}
}
const double fpair = (forcecoul + forcelj) * r2inv;
fxtmp += delx*fpair;
fytmp += dely*fpair;
@ -189,29 +202,7 @@ void PairLJCharmmCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
f[j][2] -= delz*fpair;
}
if (EFLAG) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
ecoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
ecoul = qtmp*q[j] * table;
}
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (rsq < cut_ljsq) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
evdwl *= switch1;
}
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}

1
src/USER-OMP/pair_lj_coul_omp.cpp
View File

@ -39,6 +39,7 @@ PairLJCoulOMP::PairLJCoulOMP(LAMMPS *lmp) :
{
suffix_flag |= Suffix::OMP;
respa_enable = 0;
cut_respa = NULL;
}
/* ---------------------------------------------------------------------- */

1
src/USER-OMP/pair_lj_cut_coul_long_omp.cpp
View File

@ -38,6 +38,7 @@ PairLJCutCoulLongOMP::PairLJCutCoulLongOMP(LAMMPS *lmp) :
{
suffix_flag |= Suffix::OMP;
respa_enable = 0;
cut_respa = NULL;
}
/* ---------------------------------------------------------------------- */

2
src/USER-OMP/pair_lj_cut_coul_long_tip4p_omp.cpp
View File

@ -145,7 +145,7 @@ void PairLJCutCoulLongTIP4POMP::compute(int eflag, int vflag)
/* ---------------------------------------------------------------------- */
template <const int CTABLE, const int EVFLAG, const int EFLAG, const int VFLAG>
template <int CTABLE, int EVFLAG, int EFLAG, int VFLAG>
void PairLJCutCoulLongTIP4POMP::eval(int iifrom, int iito, ThrData * const thr)
{
int i,j,ii,jj,jnum,itype,jtype,itable;

2
src/USER-OMP/pair_lj_cut_coul_pppm_tip4p_omp.cpp
View File

@ -167,7 +167,7 @@ void PairLJCutCoulPPPMTIP4POMP::compute(int eflag, int vflag)
/* ---------------------------------------------------------------------- */
template <const int CTABLE, const int EVFLAG, const int EFLAG, const int VFLAG>
template <int CTABLE, int EVFLAG, int EFLAG, int VFLAG>
void PairLJCutCoulPPPMTIP4POMP::eval(int iifrom, int iito, ThrData * const thr)
{
int i,j,ii,jj,jnum,itype,jtype,itable;

2
src/USER-OMP/pair_lj_cut_coul_pppm_tip4p_omp.h
View File

@ -48,7 +48,7 @@ class PairLJCutCoulPPPMTIP4POMP : public PairLJCutCoulLongTIP4P, public ThrOMP {
void find_M_permissive(int, int &, int &, double *);
private:
template <const int, const int, const int, const int>
template <int, int, int, int>
void eval(int ifrom, int ito, ThrData * const thr);
class PPPMTIP4PProxy *kspace;

1
src/USER-OMP/pair_lj_cut_omp.cpp
View File

@ -30,6 +30,7 @@ PairLJCutOMP::PairLJCutOMP(LAMMPS *lmp) :
{
suffix_flag |= Suffix::OMP;
respa_enable = 0;
cut_respa = NULL;
}
/* ---------------------------------------------------------------------- */

119
src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp
View File

@ -25,15 +25,6 @@
#include "suffix.h"
using namespace LAMMPS_NS;
using namespace LJSDKParms;
#define EWALD_F 1.12837917
#define EWALD_P 0.3275911
#define A1 0.254829592
#define A2 -0.284496736
#define A3 1.421413741
#define A4 -1.453152027
#define A5 1.061405429
/* ---------------------------------------------------------------------- */
PairLJSDKCoulLongOMP::PairLJSDKCoulLongOMP(LAMMPS *lmp) :
@ -87,91 +78,90 @@ void PairLJSDKCoulLongOMP::compute(int eflag, int vflag)
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
void PairLJSDKCoulLongOMP::eval_thr(int iifrom, int iito, ThrData * const thr)
{
int i,ii,j,jj,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double fraction,table;
double r,rsq,r2inv,forcecoul,forcelj,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const int * const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_coul = force->special_coul;
const double * const special_lj = force->special_lj;
const double qqrd2e = force->qqrd2e;
double fxtmp,fytmp,fztmp;
const int * const ilist = list->ilist;
const int * const numneigh = list->numneigh;
const int * const * const firstneigh = list->firstneigh;
const int nlocal = atom->nlocal;
// loop over neighbors of my atoms
for (ii = iifrom; ii < iito; ++ii) {
for (int ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
const int i = ilist[ii];
const int itype = type[i];
const double qtmp = q[i];
const double xtmp = x[i][0];
const double ytmp = x[i][1];
const double ztmp = x[i][2];
double fxtmp,fytmp,fztmp;
fxtmp=fytmp=fztmp=0.0;
const int itype = type[i];
const int * const jlist = firstneigh[i];
const int jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
for (int jj = 0; jj < jnum; jj++) {
double forcecoul, forcelj, evdwl, ecoul;
forcecoul = forcelj = evdwl = ecoul = 0.0;
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
const int sbindex = sbmask(jlist[jj]);
const int j = jlist[jj] & NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
const double delz = ztmp - x[j][2];
const double rsq = delx*delx + dely*dely + delz*delz;
const int jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
const double r2inv = 1.0/rsq;
const int ljt = lj_type[itype][jtype];
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor = qqrd2e * qtmp*q[j]/r;
const double A1 = 0.254829592;
const double A2 = -0.284496736;
const double A3 = 1.421413741;
const double A4 = -1.453152027;
const double A5 = 1.061405429;
const double EWALD_F = 1.12837917;
const double INV_EWALD_P = 1.0/0.3275911;
const double r = sqrt(rsq);
const double grij = g_ewald * r;
const double expm2 = exp(-grij*grij);
const double t = INV_EWALD_P / (INV_EWALD_P + grij);
const double erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
const double prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (EFLAG)
ecoul = prefactor*erfc;
if (factor_coul < 1.0) {
forcecoul -= (1.0-factor_coul)*prefactor;
if (EFLAG)
ecoul -= (1.0-factor_coul)*prefactor;
if (EFLAG) ecoul = prefactor*erfc;
if (sbindex) {
const double adjust = (1.0-special_coul[sbindex])*prefactor;
forcecoul -= adjust;
if (EFLAG) ecoul -= adjust;
}
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
const int itable = (rsq_lookup.i & ncoulmask) >> ncoulshiftbits;
const double fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
const double table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (EFLAG)
ecoul = qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
if (EFLAG)
ecoul -= (1.0-factor_coul)*prefactor;
if (EFLAG) ecoul = qtmp*q[j] * (etable[itable] + fraction*detable[itable]);
if (sbindex) {
const double table2 = ctable[itable] + fraction*dctable[itable];
const double prefactor = qtmp*q[j] * table2;
const double adjust = (1.0-special_coul[sbindex])*prefactor;
forcecoul -= adjust;
if (EFLAG) ecoul -= adjust;
}
}
}
@ -204,12 +194,16 @@ void PairLJSDKCoulLongOMP::eval_thr(int iifrom, int iito, ThrData * const thr)
evdwl = r6inv*(lj3[itype][jtype]*r6inv
- lj4[itype][jtype]) - offset[itype][jtype];
}
forcelj *= factor_lj;
if (EFLAG)
evdwl *= factor_lj;
if (sbindex) {
const double factor_lj = special_lj[sbindex];
forcelj *= factor_lj;
if (EFLAG) evdwl *= factor_lj;
}
}
fpair = (forcecoul + forcelj) * r2inv;
const double fpair = (forcecoul + forcelj) * r2inv;
fxtmp += delx*fpair;
fytmp += dely*fpair;
@ -222,7 +216,6 @@ void PairLJSDKCoulLongOMP::eval_thr(int iifrom, int iito, ThrData * const thr)
if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;

15
src/XTC/dump_xtc.cpp
View File

@ -189,21 +189,6 @@ void DumpXTC::write_header(bigint nbig)
/* ---------------------------------------------------------------------- */
int DumpXTC::count()
{
if (igroup == 0) return atom->nlocal;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int m = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) m++;
return m;
}
/* ---------------------------------------------------------------------- */
void DumpXTC::pack(int *ids)
{
int m,n;

3
src/XTC/dump_xtc.h
View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
@ -49,7 +49,6 @@ class DumpXTC : public Dump {
int modify_param(int, char **);
void openfile();
void write_header(bigint);
int count();
void pack(int *);
void write_data(int, double *);
bigint memory_usage();

16
src/dump.cpp
View File

@ -66,6 +66,7 @@ Dump::Dump(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
flush_flag = 1;
format = NULL;
format_user = NULL;
format_default = NULL;
clearstep = 0;
sort_flag = 0;
append_flag = 0;
@ -223,6 +224,21 @@ void Dump::init()
/* ---------------------------------------------------------------------- */
int Dump::count()
{
if (igroup == 0) return atom->nlocal;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int m = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) m++;
return m;
}
/* ---------------------------------------------------------------------- */
void Dump::write()
{
// if file per timestep, open new file

2
src/dump.h
View File

@ -102,7 +102,7 @@ class Dump : protected Pointers {
virtual void openfile();
virtual int modify_param(int, char **) {return 0;}
virtual void write_header(bigint) = 0;
virtual int count() = 0;
virtual int count();
virtual void pack(int *) = 0;
virtual void write_data(int, double *) = 0;

15
src/dump_atom.cpp
View File

@ -145,21 +145,6 @@ void DumpAtom::write_header(bigint ndump)
/* ---------------------------------------------------------------------- */
int DumpAtom::count()
{
if (igroup == 0) return atom->nlocal;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int m = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) m++;
return m;
}
/* ---------------------------------------------------------------------- */
void DumpAtom::pack(int *ids)
{
(this->*pack_choice)(ids);

1
src/dump_atom.h
View File

@ -37,7 +37,6 @@ class DumpAtom : public Dump {
void init_style();
int modify_param(int, char **);
void write_header(bigint);
int count();
void pack(int *);
void write_data(int, double *);

15
src/dump_dcd.cpp
View File

@ -174,21 +174,6 @@ void DumpDCD::write_header(bigint n)
/* ---------------------------------------------------------------------- */
int DumpDCD::count()
{
if (igroup == 0) return atom->nlocal;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int m = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) m++;
return m;
}
/* ---------------------------------------------------------------------- */
void DumpDCD::pack(int *ids)
{
int m,n;

5
src/dump_dcd.h
View File

@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
@ -20,9 +20,7 @@ DumpStyle(dcd,DumpDCD)
#ifndef LMP_DUMP_DCD_H
#define LMP_DUMP_DCD_H
#include "stdio.h"
#include "dump.h"
#include "inttypes.h"
namespace LAMMPS_NS {
@ -41,7 +39,6 @@ class DumpDCD : public Dump {
void init_style();
void openfile();
void write_header(bigint);
int count();
void pack(int *);
void write_data(int, double *);
int modify_param(int, char **);

83
src/dump_xyz.cpp
View File

@ -17,6 +17,7 @@
#include "group.h"
#include "error.h"
#include "memory.h"
#include "update.h"
using namespace LAMMPS_NS;
@ -31,10 +32,30 @@ DumpXYZ::DumpXYZ(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
sort_flag = 1;
sortcol = 0;
char *str = (char *) "%d %g %g %g";
if (format_default) delete [] format_default;
char *str = (char *) "%s %g %g %g";
int n = strlen(str) + 1;
format_default = new char[n];
strcpy(format_default,str);
ntypes = atom->ntypes;
typenames = NULL;
}
/* ---------------------------------------------------------------------- */
DumpXYZ::~DumpXYZ()
{
delete[] format_default;
format_default = NULL;
if (typenames) {
for (int i = 1; i <= ntypes; i++)
delete [] typenames[i];
delete [] typenames;
typenames = NULL;
}
}
/* ---------------------------------------------------------------------- */
@ -51,6 +72,17 @@ void DumpXYZ::init_style()
strcpy(format,str);
strcat(format,"\n");
// initialize typenames array to be backward compatible by default
// a 32-bit int can be maximally 10 digits plus sign
if (typenames == NULL) {
typenames = new char*[ntypes+1];
for (int itype = 1; itype <= ntypes; itype++) {
typenames[itype] = new char[12];
sprintf(typenames[itype],"%d",itype);
}
}
// open single file, one time only
if (multifile == 0) openfile();
@ -58,31 +90,45 @@ void DumpXYZ::init_style()
/* ---------------------------------------------------------------------- */
int DumpXYZ::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"element") == 0) {
if (narg < ntypes+1)
error->all(FLERR, "Dump modify element names do not match atom types");
if (typenames) {
for (int i = 1; i <= ntypes; i++)
delete [] typenames[i];
delete [] typenames;
typenames = NULL;
}
typenames = new char*[ntypes+1];
for (int itype = 1; itype <= ntypes; itype++) {
int n = strlen(arg[itype]) + 1;
typenames[itype] = new char[n];
strcpy(typenames[itype],arg[itype]);
}
return ntypes+1;
}
return 0;
}
/* ---------------------------------------------------------------------- */
void DumpXYZ::write_header(bigint n)
{
if (me == 0) {
fprintf(fp,BIGINT_FORMAT "\n",n);
fprintf(fp,"Atoms\n");
fprintf(fp,"Atoms. Timestep: " BIGINT_FORMAT "\n",update->ntimestep);
}
}
/* ---------------------------------------------------------------------- */
int DumpXYZ::count()
{
if (igroup == 0) return atom->nlocal;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int m = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) m++;
return m;
}
/* ---------------------------------------------------------------------- */
void DumpXYZ::pack(int *ids)
{
int m,n;
@ -112,7 +158,8 @@ void DumpXYZ::write_data(int n, double *mybuf)
int m = 0;
for (int i = 0; i < n; i++) {
fprintf(fp,format,
static_cast<int> (mybuf[m+1]),mybuf[m+2],mybuf[m+3],mybuf[m+4]);
typenames[static_cast<int> (mybuf[m+1])],
mybuf[m+2],mybuf[m+3],mybuf[m+4]);
m += size_one;
}
}

11
src/dump_xyz.h
View File

@ -27,14 +27,17 @@ namespace LAMMPS_NS {
class DumpXYZ : public Dump {
public:
DumpXYZ(class LAMMPS *, int, char**);
~DumpXYZ() {}
~DumpXYZ();
private:
void init_style();
void write_header(bigint);
int count();
void pack(int *);
void write_data(int, double *);
int modify_param(int, char **);
int ntypes;
char **typenames;
};
}
@ -55,4 +58,8 @@ E: Invalid dump xyz filename
Filenames used with the dump xyz style cannot be binary or cause files
to be written by each processor.
E: Dump modify element names do not match atom types
Number of element names must equal number of atom types.
*/