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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4297 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2010-06-18 16:33:00 +00:00
parent c3414bf5f6
commit 7e402f3871
6 changed files with 69 additions and 62 deletions
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87
src/pair_soft.cpp
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@ -14,6 +14,7 @@
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_soft.h"
#include "atom.h"
#include "comm.h"
@ -43,8 +44,6 @@ PairSoft::~PairSoft()
memory->destroy_2d_int_array(setflag);
memory->destroy_2d_double_array(cutsq);
memory->destroy_2d_double_array(prestart);
memory->destroy_2d_double_array(prestop);
memory->destroy_2d_double_array(prefactor);
memory->destroy_2d_double_array(cut);
}
@ -63,21 +62,6 @@ void PairSoft::compute(int eflag, int vflag)
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
// set current prefactor
// for minimization, set to prestop
// for dynamics, ramp from prestart to prestop
// for 0-step dynamics, set to prestart
double delta = update->ntimestep - update->beginstep;
if (update->whichflag == 2) delta = 1.0;
else if (update->nsteps) delta /= update->endstep - update->beginstep;
else delta = 0.0;
int ntypes = atom->ntypes;
for (i = 1; i <= ntypes; i++)
for (j = 1; j <= ntypes; j++)
prefactor[i][j] = prestart[i][j] +
delta * (prestop[i][j] - prestart[i][j]);
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
@ -161,20 +145,8 @@ void PairSoft::allocate()
cutsq = memory->create_2d_double_array(n+1,n+1,"pair:cutsq");
prestart = memory->create_2d_double_array(n+1,n+1,"pair:prestart");
prestop = memory->create_2d_double_array(n+1,n+1,"pair:prestop");
prefactor = memory->create_2d_double_array(n+1,n+1,"pair:prefactor");
cut = memory->create_2d_double_array(n+1,n+1,"pair:cut");
// init prestart and prestop to 0.0
// since pair_hybrid can use all types even if pair_soft sub-class
// never sets them
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++) {
prestart[i][j] = 0.0;
prestop[i][j] = 0.0;
}
}
/* ----------------------------------------------------------------------
@ -203,24 +175,22 @@ void PairSoft::settings(int narg, char **arg)
void PairSoft::coeff(int narg, char **arg)
{
if (narg < 4 || narg > 5) error->all("Incorrect args for pair coefficients");
if (narg < 3 || narg > 4) error->all("Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
double prestart_one = force->numeric(arg[2]);
double prestop_one = force->numeric(arg[3]);
double prefactor_one = force->numeric(arg[2]);
double cut_one = cut_global;
if (narg == 5) cut_one = force->numeric(arg[4]);
if (narg == 4) cut_one = force->numeric(arg[3]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
prestart[i][j] = prestart_one;
prestop[i][j] = prestop_one;
prefactor[i][j] = prefactor_one;
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
@ -239,13 +209,11 @@ double PairSoft::init_one(int i, int j)
// always mix prefactors geometrically
if (setflag[i][j] == 0) {
prestart[i][j] = sqrt(prestart[i][i]*prestart[j][j]);
prestop[i][j] = sqrt(prestop[i][i]*prestop[j][j]);
prefactor[i][j] = sqrt(prefactor[i][i]*prefactor[j][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
prestart[j][i] = prestart[i][j];
prestop[j][i] = prestop[i][j];
prefactor[j][i] = prefactor[i][j];
cut[j][i] = cut[i][j];
return cut[i][j];
@ -264,8 +232,7 @@ void PairSoft::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&prestart[i][j],sizeof(double),1,fp);
fwrite(&prestop[i][j],sizeof(double),1,fp);
fwrite(&prefactor[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
@ -289,12 +256,10 @@ void PairSoft::read_restart(FILE *fp)
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&prestart[i][j],sizeof(double),1,fp);
fread(&prestop[i][j],sizeof(double),1,fp);
fread(&prefactor[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&prestart[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&prestop[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&prefactor[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
@ -324,6 +289,38 @@ void PairSoft::read_restart_settings(FILE *fp)
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
}
/* ----------------------------------------------------------------------
check if name is recognized, return integer index for that name
if name not recognized, return -1
if type pair setting, return -2 if no type pairs are set
------------------------------------------------------------------------- */
int PairSoft::pre_adapt(char *name, int ilo, int ihi, int jlo, int jhi)
{
int count = 0;
for (int i = ilo; i <= ihi; i++)
for (int j = MAX(jlo,i); j <= jhi; j++)
count++;
if (count == 0) return -2;
if (strcmp(name,"a") == 0) return 0;
return -1;
}
/* ----------------------------------------------------------------------
adapt parameter indexed by which
change all pair variables affected by the reset parameter
if type pair setting, set I-J and J-I coeffs
------------------------------------------------------------------------- */
void PairSoft::adapt(int which, int ilo, int ihi, int jlo, int jhi,
double value)
{
for (int i = ilo; i <= ihi; i++)
for (int j = MAX(jlo,i); j <= jhi; j++)
prefactor[i][j] = prefactor[j][i] = value;
}
/* ---------------------------------------------------------------------- */
double PairSoft::single(int i, int j, int itype, int jtype, double rsq,