diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp new file mode 100644 index 0000000000..1130479d3f --- /dev/null +++ b/src/MANYBODY/pair_nb3b_harmonic.cpp @@ -0,0 +1,532 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Todd R. Zeitler (SNL) + (based on Stillinger-Weber pair style) +------------------------------------------------------------------------- */ + +#include "math.h" +#include "stdio.h" +#include "stdlib.h" +#include "string.h" +#include "pair_nb3b_harmonic.h" +#include "atom.h" +#include "neighbor.h" +#include "neigh_request.h" +#include "force.h" +#include "comm.h" +#include "memory.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +#define MAXLINE 1024 +#define DELTA 4 +#define SMALL 0.001 +#define PI 3.141592653589793238462643383279 + +/* ---------------------------------------------------------------------- */ + +PairNb3bHarmonic::PairNb3bHarmonic(LAMMPS *lmp) : Pair(lmp) +{ + single_enable = 0; + one_coeff = 1; + manybody_flag = 1; + + nelements = 0; + elements = NULL; + nparams = maxparam = 0; + params = NULL; + elem2param = NULL; +} + +/* ---------------------------------------------------------------------- + check if allocated, since class can be destructed when incomplete +------------------------------------------------------------------------- */ + +PairNb3bHarmonic::~PairNb3bHarmonic() +{ + if (elements) + for (int i = 0; i < nelements; i++) delete [] elements[i]; + delete [] elements; + memory->destroy(params); + memory->destroy(elem2param); + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + delete [] map; + } +} + +/* ---------------------------------------------------------------------- */ + +void PairNb3bHarmonic::compute(int eflag, int vflag) +{ + int i,j,k,ii,jj,kk,inum,jnum,jnumm1,itag,jtag; + int itype,jtype,ktype,ijparam,ikparam,ijkparam; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; + double rsq,rsq1,rsq2; + double delr1[3],delr2[3],fj[3],fk[3]; + 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; + int *tag = atom->tag; + int *type = atom->type; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // 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]; + + // two-body interactions, skip half of them + + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + jtag = tag[j]; + + if (itag > jtag) { + if ((itag+jtag) % 2 == 0) continue; + } else if (itag < jtag) { + if ((itag+jtag) % 2 == 1) continue; + } else { + if (x[j][2] < ztmp) continue; + if (x[j][2] == ztmp && x[j][1] < ytmp) continue; + if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue; + } + + jtype = map[type[j]]; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + ijparam = elem2param[itype][jtype][jtype]; + if (rsq > params[ijparam].cutsq) continue; + + } + + jnumm1 = jnum - 1; + + for (jj = 0; jj < jnumm1; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + jtype = map[type[j]]; + ijparam = elem2param[itype][jtype][jtype]; + delr1[0] = x[j][0] - xtmp; + delr1[1] = x[j][1] - ytmp; + delr1[2] = x[j][2] - ztmp; + rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2]; + if (rsq1 > params[ijparam].cutsq) continue; + + for (kk = jj+1; kk < jnum; kk++) { + k = jlist[kk]; + k &= NEIGHMASK; + ktype = map[type[k]]; + ikparam = elem2param[itype][ktype][ktype]; + ijkparam = elem2param[itype][jtype][ktype]; + + delr2[0] = x[k][0] - xtmp; + delr2[1] = x[k][1] - ytmp; + delr2[2] = x[k][2] - ztmp; + rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2]; + if (rsq2 > params[ikparam].cutsq) continue; + + threebody(¶ms[ijparam],¶ms[ikparam],¶ms[ijkparam], + rsq1,rsq2,delr1,delr2,fj,fk,eflag,evdwl); + + f[i][0] -= fj[0] + fk[0]; + f[i][1] -= fj[1] + fk[1]; + f[i][2] -= fj[2] + fk[2]; + f[j][0] += fj[0]; + f[j][1] += fj[1]; + f[j][2] += fj[2]; + f[k][0] += fk[0]; + f[k][1] += fk[1]; + f[k][2] += fk[2]; + + if (evflag) ev_tally3(i,j,k,evdwl,0.0,fj,fk,delr1,delr2); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- */ + +void PairNb3bHarmonic::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + map = new int[n+1]; +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairNb3bHarmonic::settings(int narg, char **arg) +{ + if (narg != 0) error->all(FLERR,"Illegal pair_style command"); +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairNb3bHarmonic::coeff(int narg, char **arg) +{ + int i,j,n; + + if (!allocated) allocate(); + + if (narg != 3 + atom->ntypes) + error->all(FLERR,"Incorrect args for pair coefficients"); + + // insure I,J args are * * + + if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) + error->all(FLERR,"Incorrect args for pair coefficients"); + + // read args that map atom types to elements in potential file + // map[i] = which element the Ith atom type is, -1 if NULL + // nelements = # of unique elements + // elements = list of element names + + if (elements) { + for (i = 0; i < nelements; i++) delete [] elements[i]; + delete [] elements; + } + elements = new char*[atom->ntypes]; + for (i = 0; i < atom->ntypes; i++) elements[i] = NULL; + + nelements = 0; + for (i = 3; i < narg; i++) { + if (strcmp(arg[i],"NULL") == 0) { + map[i-2] = -1; + continue; + } + for (j = 0; j < nelements; j++) + if (strcmp(arg[i],elements[j]) == 0) break; + map[i-2] = j; + if (j == nelements) { + n = strlen(arg[i]) + 1; + elements[j] = new char[n]; + strcpy(elements[j],arg[i]); + nelements++; + } + } + + // read potential file and initialize potential parameters + + read_file(arg[2]); + setup(); + + // clear setflag since coeff() called once with I,J = * * + + n = atom->ntypes; + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + // set setflag i,j for type pairs where both are mapped to elements + + int count = 0; + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + if (map[i] >= 0 && map[j] >= 0) { + setflag[i][j] = 1; + count++; + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairNb3bHarmonic::init_style() +{ + if (atom->tag_enable == 0) + error->all(FLERR,"Pair style nb3b/harmonic requires atom IDs"); + if (force->newton_pair == 0) + error->all(FLERR,"Pair style nb3b/harmonic requires newton pair on"); + + // need a full neighbor list + + int irequest = neighbor->request(this); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairNb3bHarmonic::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + return cutmax; +} + +/* ---------------------------------------------------------------------- */ + +void PairNb3bHarmonic::read_file(char *file) +{ + int params_per_line = 6; + char **words = new char*[params_per_line+1]; + + memory->sfree(params); + params = NULL; + nparams = maxparam = 0; + + // open file on proc 0 + + FILE *fp; + if (comm->me == 0) { + fp = open_potential(file); + if (fp == NULL) { + char str[128]; + sprintf(str,"Cannot open nb3b/harmonic potential file %s",file); + error->one(FLERR,str); + } + } + + // 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 n,nwords,ielement,jelement,kelement; + char line[MAXLINE],*ptr; + int eof = 0; + + while (1) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fp); + if (ptr == NULL) { + eof = 1; + fclose(fp); + } else n = strlen(line) + 1; + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(&n,1,MPI_INT,0,world); + MPI_Bcast(line,n,MPI_CHAR,0,world); + + // strip comment, skip line if blank + + if (ptr = strchr(line,'#')) *ptr = '\0'; + nwords = atom->count_words(line); + if (nwords == 0) continue; + + // concatenate additional lines until have params_per_line words + + while (nwords < params_per_line) { + n = strlen(line); + if (comm->me == 0) { + ptr = fgets(&line[n],MAXLINE-n,fp); + if (ptr == NULL) { + eof = 1; + fclose(fp); + } else n = strlen(line) + 1; + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(&n,1,MPI_INT,0,world); + MPI_Bcast(line,n,MPI_CHAR,0,world); + if (ptr = strchr(line,'#')) *ptr = '\0'; + nwords = atom->count_words(line); + } + + if (nwords != params_per_line) + error->all(FLERR,"Incorrect format in nb3b/harmonic potential file"); + + // words = ptrs to all words in line + + nwords = 0; + words[nwords++] = strtok(line," \t\n\r\f"); + while (words[nwords++] = strtok(NULL," \t\n\r\f")) continue; + + // ielement,jelement,kelement = 1st args + // if all 3 args are in element list, then parse this line + // else skip to next entry in file + + for (ielement = 0; ielement < nelements; ielement++) + if (strcmp(words[0],elements[ielement]) == 0) break; + if (ielement == nelements) continue; + for (jelement = 0; jelement < nelements; jelement++) + if (strcmp(words[1],elements[jelement]) == 0) break; + if (jelement == nelements) continue; + for (kelement = 0; kelement < nelements; kelement++) + if (strcmp(words[2],elements[kelement]) == 0) break; + if (kelement == nelements) continue; + + // load up parameter settings and error check their values + + if (nparams == maxparam) { + maxparam += DELTA; + params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), + "pair:params"); + } + + params[nparams].ielement = ielement; + params[nparams].jelement = jelement; + params[nparams].kelement = kelement; + params[nparams].k_theta = atof(words[3]); + params[nparams].theta0 = atof(words[4]); + params[nparams].cutoff = atof(words[5]); + + if (params[nparams].k_theta < 0.0 || params[nparams].theta0 < 0.0 || + params[nparams].cutoff < 0.0) + error->all(FLERR,"Illegal nb3b/harmonic parameter"); + + nparams++; + } + + delete [] words; +} + +/* ---------------------------------------------------------------------- */ + +void PairNb3bHarmonic::setup() +{ + int i,j,k,m,n; + double rtmp; + + // 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 + + memory->destroy(elem2param); + memory->create(elem2param,nelements,nelements,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; + } + + // compute parameter values derived from inputs + + // set cutsq using shortcut to reduce neighbor list for accelerated + // 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].cutoff; + params[m].cutsq = params[m].cut * params[m].cut; + + params[m].theta0 = params[m].theta0 / 180.0 * PI; + + } + + // set cutmax to max of all params + + cutmax = 0.0; + for (m = 0; m < nparams; m++) { + rtmp = sqrt(params[m].cutsq); + if (rtmp > cutmax) cutmax = rtmp; + } +} + +/* ---------------------------------------------------------------------- */ + + +void PairNb3bHarmonic::threebody(Param *paramij, Param *paramik, + Param *paramijk, + double rsq1, double rsq2, + double *delr1, double *delr2, + double *fj, double *fk, int eflag, double &eng) +{ + double dtheta,tk; + double r1,r2,c,s,a,a11,a12,a22; + + // angle (cos and sin) + + r1 = sqrt(rsq1); + r2 = sqrt(rsq2); + + c = delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2]; + c /= r1*r2; + + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + + s = sqrt(1.0 - c*c); + if (s < SMALL) s = SMALL; + s = 1.0/s; + + // force & energy + + dtheta = acos(c) - paramijk->theta0; + tk = paramijk->k_theta * dtheta; + + if (eflag) eng = tk*dtheta; + + a = -2.0 * tk * s; + a11 = a*c / rsq1; + a12 = -a / (r1*r2); + a22 = a*c / rsq2; + + fj[0] = a11*delr1[0] + a12*delr2[0]; + fj[1] = a11*delr1[1] + a12*delr2[1]; + fj[2] = a11*delr1[2] + a12*delr2[2]; + fk[0] = a22*delr2[0] + a12*delr1[0]; + fk[1] = a22*delr2[1] + a12*delr1[1]; + fk[2] = a22*delr2[2] + a12*delr1[2]; +} + diff --git a/src/MANYBODY/pair_nb3b_harmonic.h b/src/MANYBODY/pair_nb3b_harmonic.h new file mode 100644 index 0000000000..5d126ae09a --- /dev/null +++ b/src/MANYBODY/pair_nb3b_harmonic.h @@ -0,0 +1,64 @@ +/* --*- c++ -*- --------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(nb3b/harmonic,PairNb3bHarmonic) + +#else + +#ifndef LMP_PAIR_NB3B_HARMONIC_H +#define LMP_PAIR_NB3B_HARMONIC_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairNb3bHarmonic : public Pair { + public: + PairNb3bHarmonic(class LAMMPS *); + virtual ~PairNb3bHarmonic(); + virtual void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + double init_one(int, int); + void init_style(); + + protected: + struct Param { + double k_theta, theta0, cutoff; + double cut,cutsq; + int ielement,jelement,kelement; + }; + + double cutmax; // max cutoff for all elements + int nelements; // # of unique elements + char **elements; // names of unique elements + int ***elem2param; // mapping from element triplets to parameters + int *map; // mapping from atom types to elements + int nparams; // # of stored parameter sets + int maxparam; // max # of parameter sets + Param *params; // parameter set for an I-J-K interaction + + void allocate(); + void read_file(char *); + void setup(); + void twobody(Param *, double, double &, int, double &); + void threebody(Param *, Param *, Param *, double, double, double *, double *, + double *, double *, int, double &); +}; + +} + +#endif +#endif