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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1167 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2007-11-14 16:03:22 +00:00
parent 00d255c902
commit 088bba6dfb
3 changed files with 105 additions and 65 deletions
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160
src/KSPACE/pair_lj_cut_coul_long_tip4p.cpp
View File

@ -54,6 +54,16 @@ PairLJCutCoulLongTIP4P::PairLJCutCoulLongTIP4P(LAMMPS *lmp) :
PairLJCutCoulLong(lmp) PairLJCutCoulLong(lmp)
{ {
single_enable = 0; single_enable = 0;
nmax = 0;
ftmp = NULL;
}
/* ---------------------------------------------------------------------- */
PairLJCutCoulLongTIP4P::~PairLJCutCoulLongTIP4P()
{
memory->destroy_2d_double_array(ftmp);
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -72,24 +82,34 @@ void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
double *x1,*x2; double *x1,*x2;
double fO[3],fH[3]; double fO[3],fH[3];
int *ilist,*jlist,*numneigh,**firstneigh; int *ilist,*jlist,*numneigh,**firstneigh;
double **f;
float rsq; float rsq;
int *int_rsq = (int *) &rsq; int *int_rsq = (int *) &rsq;
eng_vdwl = eng_coul = 0.0; // grow temporary force array if necessary
if (vflag) for (i = 0; i < 6; i++) virial[i] = tvirial[i] = 0.0;
if (vflag == 2) { if (atom->nmax > nmax) {
//f = update->f_pair; memory->destroy_2d_double_array(ftmp);
f = atom->f; nmax = atom->nmax;
tf = atom->f; ftmp = memory->create_2d_double_array(nmax,3,"pair:ftmp");
} }
else f = atom->f;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
eng_vdwl = eng_coul = 0.0;
if (vflag) {
for (i = 0; i < 6; i++) virial[i] = virialtmp[i] = 0.0;
for (i = 0; i < nall; ++i) {
ftmp[i][0] = 0.0;
ftmp[i][1] = 0.0;
ftmp[i][2] = 0.0;
}
}
double **f = atom->f;
double **x = atom->x; double **x = atom->x;
double *q = atom->q; double *q = atom->q;
int *type = atom->type; int *type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
double *special_coul = force->special_coul; double *special_coul = force->special_coul;
double *special_lj = force->special_lj; double *special_lj = force->special_lj;
double qqrd2e = force->qqrd2e; double qqrd2e = force->qqrd2e;
@ -208,17 +228,18 @@ void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
f[i][0] += delx * cforce; f[i][0] += delx * cforce;
f[i][1] += dely * cforce; f[i][1] += dely * cforce;
f[i][2] += delz * cforce; f[i][2] += delz * cforce;
} else {
tf[i][0] += delx * cforce;
tf[i][1] += dely * cforce;
tf[i][2] += delz * cforce;
tvirial[0] += 0.5 * delx * delx * cforce; } else {
tvirial[1] += 0.5 * dely * dely * cforce; ftmp[i][0] += delx * cforce;
tvirial[2] += 0.5 * delz * delz * cforce; ftmp[i][1] += dely * cforce;
tvirial[3] += 0.5 * dely * delx * cforce; ftmp[i][2] += delz * cforce;
tvirial[4] += 0.5 * delz * delx * cforce;
tvirial[5] += 0.5 * delz * dely * cforce; virialtmp[0] += 0.5 * delx * delx * cforce;
virialtmp[1] += 0.5 * dely * dely * cforce;
virialtmp[2] += 0.5 * delz * delz * cforce;
virialtmp[3] += 0.5 * dely * delx * cforce;
virialtmp[4] += 0.5 * delz * delx * cforce;
virialtmp[5] += 0.5 * delz * dely * cforce;
} }
} else { } else {
@ -244,17 +265,17 @@ void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
f[iH2][2] += fH[2]; f[iH2][2] += fH[2];
} else { } else {
tf[i][0] += fO[0]; ftmp[i][0] += fO[0];
tf[i][1] += fO[1]; ftmp[i][1] += fO[1];
tf[i][2] += fO[2]; ftmp[i][2] += fO[2];
tf[iH1][0] += fH[0]; ftmp[iH1][0] += fH[0];
tf[iH1][1] += fH[1]; ftmp[iH1][1] += fH[1];
tf[iH1][2] += fH[2]; ftmp[iH1][2] += fH[2];
tf[iH2][0] += fH[0]; ftmp[iH2][0] += fH[0];
tf[iH2][1] += fH[1]; ftmp[iH2][1] += fH[1];
tf[iH2][2] += fH[2]; ftmp[iH2][2] += fH[2];
delx1 = x[i][0] - x2[0]; delx1 = x[i][0] - x2[0];
dely1 = x[i][1] - x2[1]; dely1 = x[i][1] - x2[1];
@ -271,12 +292,12 @@ void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
delz3 = x[iH2][2] - x2[2]; delz3 = x[iH2][2] - x2[2];
domain->minimum_image(delx3,dely3,delz3); domain->minimum_image(delx3,dely3,delz3);
tvirial[0] += 0.5 * (delx1 * fO[0] + (delx2 + delx3) * fH[0]); virialtmp[0] += 0.5 * (delx1 * fO[0] + (delx2 + delx3) * fH[0]);
tvirial[1] += 0.5 * (dely1 * fO[1] + (dely2 + dely3) * fH[1]); virialtmp[1] += 0.5 * (dely1 * fO[1] + (dely2 + dely3) * fH[1]);
tvirial[2] += 0.5 * (delz1 * fO[2] + (delz2 + delz3) * fH[2]); virialtmp[2] += 0.5 * (delz1 * fO[2] + (delz2 + delz3) * fH[2]);
tvirial[3] += 0.5 * (dely1 * fO[0] + (dely2 + dely3) * fH[0]); virialtmp[3] += 0.5 * (dely1 * fO[0] + (dely2 + dely3) * fH[0]);
tvirial[4] += 0.5 * (delz1 * fO[0] + (delz2 + delz3) * fH[0]); virialtmp[4] += 0.5 * (delz1 * fO[0] + (delz2 + delz3) * fH[0]);
tvirial[5] += 0.5 * (delz1 * fO[1] + (delz2 + delz3) * fH[1]); virialtmp[5] += 0.5 * (delz1 * fO[1] + (delz2 + delz3) * fH[1]);
} }
} }
@ -285,17 +306,18 @@ void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
f[j][0] -= delx * cforce; f[j][0] -= delx * cforce;
f[j][1] -= dely * cforce; f[j][1] -= dely * cforce;
f[j][2] -= delz * cforce; f[j][2] -= delz * cforce;
} else {
tf[j][0] -= delx * cforce;
tf[j][1] -= dely * cforce;
tf[j][2] -= delz * cforce;
tvirial[0] += 0.5 * delx * delx * cforce; } else {
tvirial[1] += 0.5 * dely * dely * cforce; ftmp[j][0] -= delx * cforce;
tvirial[2] += 0.5 * delz * delz * cforce; ftmp[j][1] -= dely * cforce;
tvirial[3] += 0.5 * dely * delx * cforce; ftmp[j][2] -= delz * cforce;
tvirial[4] += 0.5 * delz * delx * cforce;
tvirial[5] += 0.5 * delz * dely * cforce; virialtmp[0] += 0.5 * delx * delx * cforce;
virialtmp[1] += 0.5 * dely * dely * cforce;
virialtmp[2] += 0.5 * delz * delz * cforce;
virialtmp[3] += 0.5 * dely * delx * cforce;
virialtmp[4] += 0.5 * delz * delx * cforce;
virialtmp[5] += 0.5 * delz * dely * cforce;
} }
} else { } else {
@ -323,17 +345,17 @@ void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
f[jH2][2] += fH[2]; f[jH2][2] += fH[2];
} else { } else {
tf[j][0] += fO[0]; ftmp[j][0] += fO[0];
tf[j][1] += fO[1]; ftmp[j][1] += fO[1];
tf[j][2] += fO[2]; ftmp[j][2] += fO[2];
tf[jH1][0] += fH[0]; ftmp[jH1][0] += fH[0];
tf[jH1][1] += fH[1]; ftmp[jH1][1] += fH[1];
tf[jH1][2] += fH[2]; ftmp[jH1][2] += fH[2];
tf[jH2][0] += fH[0]; ftmp[jH2][0] += fH[0];
tf[jH2][1] += fH[1]; ftmp[jH2][1] += fH[1];
tf[jH2][2] += fH[2]; ftmp[jH2][2] += fH[2];
delx1 = x[j][0] - x1[0]; delx1 = x[j][0] - x1[0];
dely1 = x[j][1] - x1[1]; dely1 = x[j][1] - x1[1];
@ -350,12 +372,12 @@ void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
delz3 = x[jH2][2] - x1[2]; delz3 = x[jH2][2] - x1[2];
domain->minimum_image(delx3,dely3,delz3); domain->minimum_image(delx3,dely3,delz3);
tvirial[0] += 0.5 * (delx1 * fO[0] + (delx2 + delx3) * fH[0]); virialtmp[0] += 0.5 * (delx1 * fO[0] + (delx2 + delx3) * fH[0]);
tvirial[1] += 0.5 * (dely1 * fO[1] + (dely2 + dely3) * fH[1]); virialtmp[1] += 0.5 * (dely1 * fO[1] + (dely2 + dely3) * fH[1]);
tvirial[2] += 0.5 * (delz1 * fO[2] + (delz2 + delz3) * fH[2]); virialtmp[2] += 0.5 * (delz1 * fO[2] + (delz2 + delz3) * fH[2]);
tvirial[3] += 0.5 * (dely1 * fO[0] + (dely2 + dely3) * fH[0]); virialtmp[3] += 0.5 * (dely1 * fO[0] + (dely2 + dely3) * fH[0]);
tvirial[4] += 0.5 * (delz1 * fO[0] + (delz2 + delz3) * fH[0]); virialtmp[4] += 0.5 * (delz1 * fO[0] + (delz2 + delz3) * fH[0]);
tvirial[5] += 0.5 * (delz1 * fO[1] + (delz2 + delz3) * fH[1]); virialtmp[5] += 0.5 * (delz1 * fO[1] + (delz2 + delz3) * fH[1]);
} }
} }
@ -373,9 +395,15 @@ void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
} }
} }
} }
if (vflag == 2) { if (vflag == 2) {
virial_compute(); virial_compute();
for (int i = 0; i < 6; i++) virial[i] += tvirial[i]; for (int i = 0; i < 6; i++) virial[i] += virialtmp[i];
for (int i = 0; i < nall; i++) {
f[i][0] += ftmp[i][0];
f[i][1] += ftmp[i][1];
f[i][2] += ftmp[i][2];
}
} }
} }
@ -587,3 +615,13 @@ void *PairLJCutCoulLongTIP4P::extract(char *str)
else if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul; else if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
return NULL; return NULL;
} }
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairLJCutCoulLongTIP4P::memory_usage()
{
double bytes = 3 * nmax * sizeof(double);
return bytes;
}

8
src/KSPACE/pair_lj_cut_coul_long_tip4p.h
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@ -21,20 +21,24 @@ namespace LAMMPS_NS {
class PairLJCutCoulLongTIP4P : public PairLJCutCoulLong { class PairLJCutCoulLongTIP4P : public PairLJCutCoulLong {
public: public:
PairLJCutCoulLongTIP4P(class LAMMPS *); PairLJCutCoulLongTIP4P(class LAMMPS *);
~PairLJCutCoulLongTIP4P();
void compute(int, int); void compute(int, int);
void settings(int, char **); void settings(int, char **);
void init_style(); void init_style();
void write_restart_settings(FILE *fp); void write_restart_settings(FILE *fp);
void read_restart_settings(FILE *fp); void read_restart_settings(FILE *fp);
void *extract(char *); void *extract(char *);
double memory_usage();
private: private:
int typeH,typeO; // atom types of TIP4P water H and O atoms int typeH,typeO; // atom types of TIP4P water H and O atoms
int typeA,typeB; // angle and bond types of TIP4P water int typeA,typeB; // angle and bond types of TIP4P water
double qdist; // distance from O site to negative charge double qdist; // distance from O site to negative charge
double alpha; // geometric constraint parameter for TIP4P double alpha; // geometric constraint parameter for TIP4P
double **tf;
double tvirial[6]; int nmax;
double **ftmp;
double virialtmp[6];
void find_M(int, int &, int &, double *); void find_M(int, int &, int &, double *);
}; };

2
src/style_kspace.h
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@ -28,7 +28,6 @@ KSpaceStyle(pppm/tip4p,PPPMTIP4P)
#include "pair_coul_long.h" #include "pair_coul_long.h"
#include "pair_lj_cut_coul_long.h" #include "pair_lj_cut_coul_long.h"
#include "pair_lj_cut_coul_long_tip4p.h" #include "pair_lj_cut_coul_long_tip4p.h"
#include "pair_new.h"
#include "pair_lj_charmm_coul_long.h" #include "pair_lj_charmm_coul_long.h"
#endif #endif
@ -37,6 +36,5 @@ PairStyle(buck/coul/long,PairBuckCoulLong)
PairStyle(coul/long,PairCoulLong) PairStyle(coul/long,PairCoulLong)
PairStyle(lj/cut/coul/long,PairLJCutCoulLong) PairStyle(lj/cut/coul/long,PairLJCutCoulLong)
PairStyle(lj/cut/coul/long/tip4p,PairLJCutCoulLongTIP4P) PairStyle(lj/cut/coul/long/tip4p,PairLJCutCoulLongTIP4P)
PairStyle(lj/cut/coul/long/tip4p2,PairLJCutCoulLongTIP4P2)
PairStyle(lj/charmm/coul/long,PairLJCharmmCoulLong) PairStyle(lj/charmm/coul/long,PairLJCharmmCoulLong)
#endif #endif