forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4297 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
c3414bf5f6
commit
7e402f3871
|
|
@ -11,6 +11,7 @@
|
|||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
#include "string.h"
|
||||
#include "stdlib.h"
|
||||
#include "fix_adapt.h"
|
||||
|
|
@ -148,14 +149,17 @@ void FixAdapt::init()
|
|||
error->all("Fix adapt pair style does not exist");
|
||||
pairindex[m] =
|
||||
pairptr[m]->pre_adapt(param[m],ilo[m],ihi[m],jlo[m],jhi[m]);
|
||||
if (pairindex[m] < 0)
|
||||
error->all("Fix adapt pair style is not compatible");
|
||||
if (pairindex[m] == -1)
|
||||
error->all("Fix adapt pair parameter is not recognized");
|
||||
if (pairindex[m] == -2)
|
||||
error->all("Fix adapt pair types are not valid");
|
||||
|
||||
} else if (which[m] == ATOM) {
|
||||
if (strcmp(param[m],"diameter") == 0) {
|
||||
awhich[m] = DIAMETER;
|
||||
if (!atom->radius_flag)
|
||||
error->all("Fix adapt requires atom attribute radius");
|
||||
} else error->all("Invalid fix adapt atom attribute");
|
||||
} else error->all("Fix adapt atom attribute is not recognized");
|
||||
}
|
||||
|
||||
ivar[m] = input->variable->find(var[m]);
|
||||
|
|
@ -182,14 +186,26 @@ void FixAdapt::pre_force(int vflag)
|
|||
pairptr[m]->adapt(pairindex[m],ilo[m],ihi[m],jlo[m],jhi[m],value);
|
||||
|
||||
else if (which[m] == ATOM) {
|
||||
double *radius = atom->radius;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
// set radius from diameter
|
||||
// set rmass if both rmass and density are defined
|
||||
|
||||
if (awhich[m] == DIAMETER) {
|
||||
int mflag = 0;
|
||||
if (atom->rmass_flag && atom->density_flag) mflag = 1;
|
||||
double PI = 4.0*atan(1.0);
|
||||
|
||||
double *radius = atom->radius;
|
||||
double *rmass = atom->rmass;
|
||||
double *density = atom->density;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit)
|
||||
if (mask[i] & groupbit) {
|
||||
radius[i] = 0.5*value;
|
||||
rmass[i] = 4.0*PI/3.0 * radius[i]*radius[i]*radius[i] * density[i];
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,6 @@
|
|||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "pair.h"
|
||||
#include "pair_soft.h"
|
||||
#include "atom.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
|
|
@ -895,13 +894,6 @@ void Pair::write_file(int narg, char **arg)
|
|||
|
||||
force->init();
|
||||
|
||||
// if pair style = soft, set prefactor to final value
|
||||
|
||||
Pair *spair = force->pair_match("soft",1);
|
||||
if (spair)
|
||||
((PairSoft *) spair)->prefactor[itype][jtype] =
|
||||
((PairSoft *) spair)->prestop[itype][jtype];
|
||||
|
||||
// if pair style = any of EAM, swap in dummy fp vector
|
||||
|
||||
double eamfp[2];
|
||||
|
|
|
|||
|
|
@ -32,7 +32,7 @@ class PairHybrid : public Pair {
|
|||
char **keywords; // style name of each Pair style
|
||||
|
||||
PairHybrid(class LAMMPS *);
|
||||
~PairHybrid();
|
||||
virtual ~PairHybrid();
|
||||
void compute(int, int);
|
||||
void settings(int, char **);
|
||||
virtual void coeff(int, char **);
|
||||
|
|
|
|||
|
|
@ -27,6 +27,7 @@ namespace LAMMPS_NS {
|
|||
class PairHybridOverlay : public PairHybrid {
|
||||
public:
|
||||
PairHybridOverlay(class LAMMPS *);
|
||||
~PairHybridOverlay() {}
|
||||
void coeff(int, char **);
|
||||
|
||||
private:
|
||||
|
|
|
|||
|
|
@ -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,
|
||||
|
|
|
|||
|
|
@ -38,12 +38,13 @@ class PairSoft : public Pair {
|
|||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
int pre_adapt(char *, int, int, int, int);
|
||||
void adapt(int, int, int, int, int, double);
|
||||
double single(int, int, int, int, double, double, double, double &);
|
||||
|
||||
private:
|
||||
double PI;
|
||||
double cut_global;
|
||||
double **prestart,**prestop;
|
||||
double **prefactor;
|
||||
double **cut;
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue