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first complete implementation of AGNI pair style

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This commit is contained in:
Axel Kohlmeyer
2016-11-11 17:32:47 -05:00
parent e453adaf81
commit 9b0987d8c4
2 changed files with 74 additions and 96 deletions
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166
src/USER-MISC/pair_agni.cpp
View File

@ -31,10 +31,11 @@
#include "memory.h"
#include "error.h"
#include "citeme.h"
#include "math_special.h"
#include "math_const.h"
using namespace LAMMPS_NS;
#define AGNI_VERSION 1
using namespace MathSpecial;
static const char cite_pair_agni[] =
"pair agni command:\n\n"
@ -61,10 +62,14 @@ static const char cite_pair_agni[] =
" publisher = {APS}\n"
"}\n\n";
#define AGNI_VERSION 1
#define MAXLINE 10240
#define MAXWORD 40
#define DELTA 4
struct _3vec {
double x,y,z;
};
typedef struct _3vec _3vec_t;
/* ---------------------------------------------------------------------- */
@ -79,6 +84,7 @@ PairAGNI::PairAGNI(LAMMPS *lmp) : Pair(lmp)
nelements = 0;
elements = NULL;
elem2param = NULL;
nparams = 0;
params = NULL;
map = NULL;
@ -119,24 +125,17 @@ PairAGNI::~PairAGNI()
void PairAGNI::compute(int eflag, int vflag)
{
int i,j,k,ii,jj,kk,inum,jnum,jnumm1;
int itype,jtype,ktype,ijparam,ikparam,ijkparam;
tagint itag,jtag;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,rsq1,rsq2;
double delr1[3],delr2[3],fj[3],fk[3];
int i,j,k,ii,jj,inum,jnum,itype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
tagint *tag = atom->tag;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
@ -144,18 +143,22 @@ void PairAGNI::compute(int eflag, int vflag)
firstneigh = list->firstneigh;
double fxtmp,fytmp,fztmp;
_3vec_t *V;
// loop over full neighbor list of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
itag = tag[i];
itype = map[type[i]];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
fxtmp = fytmp = fztmp = 0.0;
const Param &iparam = params[elem2param[itype]];
V = new _3vec_t[iparam.numeta];
memset(V,0,iparam.numeta *sizeof(_3vec_t));
jlist = firstneigh[i];
jnum = numneigh[i];
@ -168,23 +171,42 @@ void PairAGNI::compute(int eflag, int vflag)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = map[type[j]];
// ijparam = elem2param[itype][jtype];
if (rsq < params[ijparam].cutsq) {
// XXX compute force
fxtmp += delx*fpair;
fytmp += dely*fpair;
fztmp += delz*fpair;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
0,0.0,fpair,delx,dely,delz);
if ((rsq > 0.0) && (rsq < iparam.cutsq)) {
const double r = sqrt(rsq);
const double cF = 0.5*(cos((MathConst::MY_PI*r)/iparam.cut)+1.0);
const double wX = cF*delx/r;
const double wY = cF*dely/r;
const double wZ = cF*delz/r;
for (k = 0; k < iparam.numeta; ++k) {
const double e = exp(-(iparam.eta[k]*rsq));
V[k].x += wX*e;
V[k].y += wY*e;
V[k].z += wZ*e;
}
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
for (j = 0; j < iparam.numtrain; ++j) {
double kx = 0.0;
double ky = 0.0;
double kz = 0.0;
for(int k = 0; k < iparam.numeta; ++k) {
const double xu = iparam.xU[k][j];
kx += square(V[k].x - xu);
ky += square(V[k].y - xu);
kz += square(V[k].z - xu);
}
const double e = -0.5/(square(iparam.sigma));
fxtmp += iparam.alpha[j]*exp(kx*e);
fytmp += iparam.alpha[j]*exp(ky*e);
fztmp += iparam.alpha[j]*exp(kz*e);
}
f[i][0] += fxtmp + iparam.b;
f[i][1] += fytmp + iparam.b;
f[i][2] += fztmp + iparam.b;
delete [] V;
}
if (vflag_fdotr) virial_fdotr_compute();
@ -315,7 +337,8 @@ void PairAGNI::read_file(char *file)
params = NULL;
nparams = 0;
// open file on proc 0
// open file on proc 0 only
// then read line by line and broadcast the line to all MPI ranks
FILE *fp;
if (comm->me == 0) {
@ -327,11 +350,7 @@ void PairAGNI::read_file(char *file)
}
}
// read each set of params from potential file
// one set of params can span multiple lines
// store params if all 3 element tags are in element list
int i,j,n,nwords,curparam,wantdata,numdata;
int i,j,n,nwords,curparam,wantdata;
char line[MAXLINE],*ptr;
int eof = 0;
char **words = new char*[MAXWORD+1];
@ -386,8 +405,8 @@ void PairAGNI::read_file(char *file)
for (i = 0; i < nparams; ++i) {
for (j = 0; j < nelements; ++j)
if (strcmp(words[i+1],elements[j]) == 0) break;
if (j == nelements) params[nparams].ielement = params[nparams].jelement = -1;
else params[nparams].ielement = params[nparams].jelement = j;
if (j == nelements) params[i].ielement = -1;
else params[i].ielement = j;
}
} else if (params && (nwords == 2) && (strcmp(words[0],"interaction") == 0)) {
for (i = 0; i < nparams; ++i)
@ -443,32 +462,25 @@ void PairAGNI::read_file(char *file)
void PairAGNI::setup_params()
{
int i,j,k,m,n;
int i,m,n;
double rtmp;
#if 0
// set elem2param for all triplet combinations
// must be a single exact match to lines read from file
// do not allow for ACB in place of ABC
// set elem2param for all elements
memory->destroy(elem2param);
memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param");
memory->create(elem2param,nelements,"pair:elem2param");
for (i = 0; i < nelements; i++)
for (j = 0; j < nelements; j++)
for (k = 0; k < nelements; k++) {
n = -1;
for (m = 0; m < nparams; m++) {
if (i == params[m].ielement && j == params[m].jelement &&
k == params[m].kelement) {
if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
n = m;
}
}
if (n < 0) error->all(FLERR,"Potential file is missing an entry");
elem2param[i][j][k] = n;
for (i = 0; i < nelements; i++) {
n = -1;
for (m = 0; m < nparams; m++) {
if (i == params[m].ielement) {
if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
n = m;
}
}
if (n < 0) error->all(FLERR,"Potential file is missing an entry");
elem2param[i] = n;
}
// compute parameter values derived from inputs
@ -476,45 +488,11 @@ void PairAGNI::setup_params()
// calculations. cut must remain unchanged as it is a potential parameter
// (cut = a*sigma)
for (m = 0; m < nparams; m++) {
params[m].cut = params[m].sigma*params[m].littlea;
rtmp = params[m].cut;
if (params[m].tol > 0.0) {
if (params[m].tol > 0.01) params[m].tol = 0.01;
if (params[m].gamma < 1.0)
rtmp = rtmp +
params[m].gamma * params[m].sigma / log(params[m].tol);
else rtmp = rtmp +
params[m].sigma / log(params[m].tol);
}
params[m].cutsq = rtmp * rtmp;
params[m].sigma_gamma = params[m].sigma*params[m].gamma;
params[m].lambda_epsilon = params[m].lambda*params[m].epsilon;
params[m].lambda_epsilon2 = 2.0*params[m].lambda*params[m].epsilon;
params[m].c1 = params[m].biga*params[m].epsilon *
params[m].powerp*params[m].bigb *
pow(params[m].sigma,params[m].powerp);
params[m].c2 = params[m].biga*params[m].epsilon*params[m].powerq *
pow(params[m].sigma,params[m].powerq);
params[m].c3 = params[m].biga*params[m].epsilon*params[m].bigb *
pow(params[m].sigma,params[m].powerp+1.0);
params[m].c4 = params[m].biga*params[m].epsilon *
pow(params[m].sigma,params[m].powerq+1.0);
params[m].c5 = params[m].biga*params[m].epsilon*params[m].bigb *
pow(params[m].sigma,params[m].powerp);
params[m].c6 = params[m].biga*params[m].epsilon *
pow(params[m].sigma,params[m].powerq);
}
// set cutmax to max of all params
cutmax = 0.0;
for (m = 0; m < nparams; m++) {
rtmp = sqrt(params[m].cutsq);
rtmp = params[m].cut;
params[m].cutsq = rtmp * rtmp;
if (rtmp > cutmax) cutmax = rtmp;
}
#endif
}

4
src/USER-MISC/pair_agni.h
View File

@ -38,14 +38,14 @@ class PairAGNI : public Pair {
double cut,cutsq;
double *eta,**xU,*yU,*alpha;
double sigma,lambda,b;
int numeta,numtrain;
int ielement,jelement;
int numeta,numtrain,ielement;
};
protected:
double cutmax; // max cutoff for all elements
int nelements; // # of unique atom type labels
char **elements; // names of unique elements
int *elem2param; // mapping from element pairs to parameters
int *map; // mapping from atom types to elements
int nparams; // # of stored parameter sets
Param *params; // parameter set for an I-J interaction