/* ---------------------------------------------------------------------- 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: Greg Wagner (SNL) ------------------------------------------------------------------------- */ #include "pair_meamc.h" #include #include #include #include "meam.h" #include "atom.h" #include "force.h" #include "comm.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; #define MAXLINE 1024 static const int nkeywords = 21; static const char *keywords[] = { "Ec","alpha","rho0","delta","lattce", "attrac","repuls","nn2","Cmin","Cmax","rc","delr", "augt1","gsmooth_factor","re","ialloy", "mixture_ref_t","erose_form","zbl", "emb_lin_neg","bkgd_dyn"}; /* ---------------------------------------------------------------------- */ PairMEAMC::PairMEAMC(LAMMPS *lmp) : Pair(lmp) { single_enable = 0; restartinfo = 0; one_coeff = 1; manybody_flag = 1; allocated = 0; nelements = 0; elements = NULL; mass = NULL; meam_inst = new MEAM(memory); // set comm size needed by this Pair comm_forward = 38; comm_reverse = 30; } /* ---------------------------------------------------------------------- free all arrays check if allocated, since class can be destructed when incomplete ------------------------------------------------------------------------- */ PairMEAMC::~PairMEAMC() { delete meam_inst; for (int i = 0; i < nelements; i++) delete [] elements[i]; delete [] elements; delete [] mass; if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); delete [] map; } } /* ---------------------------------------------------------------------- */ void PairMEAMC::compute(int eflag, int vflag) { int i,ii,n,inum_half,errorflag; int *ilist_half,*numneigh_half,**firstneigh_half; int *numneigh_full,**firstneigh_full; ev_init(eflag,vflag); // neighbor list info inum_half = listhalf->inum; ilist_half = listhalf->ilist; numneigh_half = listhalf->numneigh; firstneigh_half = listhalf->firstneigh; numneigh_full = listfull->numneigh; firstneigh_full = listfull->firstneigh; // strip neighbor lists of any special bond flags before using with MEAM // necessary before doing neigh_f2c and neigh_c2f conversions each step if (neighbor->ago == 0) { neigh_strip(inum_half,ilist_half,numneigh_half,firstneigh_half); neigh_strip(inum_half,ilist_half,numneigh_full,firstneigh_full); } // check size of scrfcn based on half neighbor list int nlocal = atom->nlocal; int nall = nlocal + atom->nghost; n = 0; for (ii = 0; ii < inum_half; ii++) n += numneigh_half[ilist_half[ii]]; meam_inst->meam_dens_setup(atom->nmax, nall, n); double **x = atom->x; double **f = atom->f; int *type = atom->type; int ntype = atom->ntypes; // 3 stages of MEAM calculation // loop over my atoms followed by communication int offset = 0; errorflag = 0; for (ii = 0; ii < inum_half; ii++) { i = ilist_half[ii]; meam_inst->meam_dens_init(i,ntype,type,map,x, numneigh_half[i],firstneigh_half[i], numneigh_full[i],firstneigh_full[i], offset); offset += numneigh_half[i]; } comm->reverse_comm_pair(this); meam_inst->meam_dens_final(nlocal,eflag_either,eflag_global,eflag_atom, &eng_vdwl,eatom,ntype,type,map,errorflag); if (errorflag) { char str[128]; sprintf(str,"MEAM library error %d",errorflag); error->one(FLERR,str); } comm->forward_comm_pair(this); offset = 0; // vptr is first value in vatom if it will be used by meam_force() // else vatom may not exist, so pass dummy ptr double **vptr; if (vflag_atom) vptr = vatom; else vptr = NULL; for (ii = 0; ii < inum_half; ii++) { i = ilist_half[ii]; meam_inst->meam_force(i,eflag_either,eflag_global,eflag_atom, vflag_atom,&eng_vdwl,eatom,ntype,type,map,x, numneigh_half[i],firstneigh_half[i], numneigh_full[i],firstneigh_full[i], offset,f,vptr); offset += numneigh_half[i]; } if (vflag_fdotr) virial_fdotr_compute(); } /* ---------------------------------------------------------------------- */ void PairMEAMC::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 PairMEAMC::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); } /* ---------------------------------------------------------------------- set coeffs for one or more type pairs ------------------------------------------------------------------------- */ void PairMEAMC::coeff(int narg, char **arg) { int m,n; if (!allocated) allocate(); if (narg < 6) 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 MEAM element names between 2 filenames // nelements = # of MEAM elements // elements = list of unique element names if (nelements) { for (int i = 0; i < nelements; i++) delete [] elements[i]; delete [] elements; delete [] mass; } nelements = narg - 4 - atom->ntypes; if (nelements < 1) error->all(FLERR,"Incorrect args for pair coefficients"); if (nelements > maxelt) error->all(FLERR,"Too many elements extracted from MEAM library. " "Increase 'maxelt' in meam.h and recompile."); elements = new char*[nelements]; mass = new double[nelements]; for (int i = 0; i < nelements; i++) { n = strlen(arg[i+3]) + 1; elements[i] = new char[n]; strcpy(elements[i],arg[i+3]); } // read MEAM library and parameter files // pass all parameters to MEAM package // tell MEAM package that setup is done read_files(arg[2],arg[2+nelements+1]); meam_inst->meam_setup_done(&cutmax); // read args that map atom types to MEAM elements // map[i] = which element the Ith atom type is, -1 if not mapped for (int i = 4 + nelements; i < narg; i++) { m = i - (4+nelements) + 1; int j; for (j = 0; j < nelements; j++) if (strcmp(arg[i],elements[j]) == 0) break; if (j < nelements) map[m] = j; else if (strcmp(arg[i],"NULL") == 0) map[m] = -1; else error->all(FLERR,"Incorrect args for pair coefficients"); } // 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 // set mass for i,i in atom class 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; if (i == j) atom->set_mass(FLERR,i,mass[map[i]]); count++; } if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } /* ---------------------------------------------------------------------- init specific to this pair style ------------------------------------------------------------------------- */ void PairMEAMC::init_style() { if (force->newton_pair == 0) error->all(FLERR,"Pair style MEAM requires newton pair on"); // need full and half neighbor list int irequest_full = neighbor->request(this,instance_me); neighbor->requests[irequest_full]->id = 1; neighbor->requests[irequest_full]->half = 0; neighbor->requests[irequest_full]->full = 1; int irequest_half = neighbor->request(this,instance_me); neighbor->requests[irequest_half]->id = 2; } /* ---------------------------------------------------------------------- neighbor callback to inform pair style of neighbor list to use half or full ------------------------------------------------------------------------- */ void PairMEAMC::init_list(int id, NeighList *ptr) { if (id == 1) listfull = ptr; else if (id == 2) listhalf = ptr; } /* ---------------------------------------------------------------------- init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ double PairMEAMC::init_one(int /*i*/, int /*j*/) { return cutmax; } /* ---------------------------------------------------------------------- */ void PairMEAMC::read_files(char *globalfile, char *userfile) { // open global meamf file on proc 0 FILE *fp; if (comm->me == 0) { fp = force->open_potential(globalfile); if (fp == NULL) { char str[128]; snprintf(str,128,"Cannot open MEAM potential file %s",globalfile); error->one(FLERR,str); } } // allocate parameter arrays int params_per_line = 19; lattice_t *lat = new lattice_t[nelements]; int *ielement = new int[nelements]; int *ibar = new int[nelements]; double *z = new double[nelements]; double *atwt = new double[nelements]; double *alpha = new double[nelements]; double *b0 = new double[nelements]; double *b1 = new double[nelements]; double *b2 = new double[nelements]; double *b3 = new double[nelements]; double *alat = new double[nelements]; double *esub = new double[nelements]; double *asub = new double[nelements]; double *t0 = new double[nelements]; double *t1 = new double[nelements]; double *t2 = new double[nelements]; double *t3 = new double[nelements]; double *rozero = new double[nelements]; bool *found = new bool[nelements]; for (int i = 0; i < nelements; i++) found[i] = false; // read each set of params from global MEAM file // one set of params can span multiple lines // store params if element name is in element list // if element name appears multiple times, only store 1st entry int i,n,nwords; char **words = new char*[params_per_line+1]; char line[MAXLINE],*ptr; int eof = 0; int nset = 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 MEAM potential file"); // words = ptrs to all words in line // strip single and double quotes from words nwords = 0; words[nwords++] = strtok(line,"' \t\n\r\f"); while ((words[nwords++] = strtok(NULL,"' \t\n\r\f"))) continue; // skip if element name isn't in element list for (i = 0; i < nelements; i++) if (strcmp(words[0],elements[i]) == 0) break; if (i >= nelements) continue; // skip if element already appeared if (found[i] == true) continue; found[i] = true; // map lat string to an integer if (!MEAM::str_to_lat(words[1], true, lat[i])) error->all(FLERR,"Unrecognized lattice type in MEAM file 1"); // store parameters z[i] = atof(words[2]); ielement[i] = atoi(words[3]); atwt[i] = atof(words[4]); alpha[i] = atof(words[5]); b0[i] = atof(words[6]); b1[i] = atof(words[7]); b2[i] = atof(words[8]); b3[i] = atof(words[9]); alat[i] = atof(words[10]); esub[i] = atof(words[11]); asub[i] = atof(words[12]); t0[i] = atof(words[13]); t1[i] = atof(words[14]); t2[i] = atof(words[15]); t3[i] = atof(words[16]); rozero[i] = atof(words[17]); ibar[i] = atoi(words[18]); if (!isone(t0[i])) error->all(FLERR,"Unsupported parameter in MEAM potential file"); nset++; } // error if didn't find all elements in file if (nset != nelements) error->all(FLERR,"Did not find all elements in MEAM library file"); // pass element parameters to MEAM package meam_inst->meam_setup_global(nelements,lat,z,ielement,atwt,alpha,b0,b1,b2,b3, alat,esub,asub,t0,t1,t2,t3,rozero,ibar); // set element masses for (i = 0; i < nelements; i++) mass[i] = atwt[i]; // clean-up memory delete [] words; delete [] lat; delete [] ielement; delete [] ibar; delete [] z; delete [] atwt; delete [] alpha; delete [] b0; delete [] b1; delete [] b2; delete [] b3; delete [] alat; delete [] esub; delete [] asub; delete [] t0; delete [] t1; delete [] t2; delete [] t3; delete [] rozero; delete [] found; // done if user param file is NULL if (strcmp(userfile,"NULL") == 0) return; // open user param file on proc 0 if (comm->me == 0) { fp = force->open_potential(userfile); if (fp == NULL) { char str[128]; snprintf(str,128,"Cannot open MEAM potential file %s",userfile); error->one(FLERR,str); } } // read settings // pass them one at a time to MEAM package // match strings to list of corresponding ints int which; double value; lattice_t latt; int nindex,index[3]; int maxparams = 6; char **params = new char*[maxparams]; int nparams; 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'; nparams = atom->count_words(line); if (nparams == 0) continue; // words = ptrs to all words in line nparams = 0; params[nparams++] = strtok(line,"=(), '\t\n\r\f"); while (nparams < maxparams && (params[nparams++] = strtok(NULL,"=(), '\t\n\r\f"))) continue; nparams--; for (which = 0; which < nkeywords; which++) if (strcmp(params[0],keywords[which]) == 0) break; if (which == nkeywords) { char str[128]; snprintf(str,128,"Keyword %s in MEAM parameter file not recognized", params[0]); error->all(FLERR,str); } nindex = nparams - 2; for (i = 0; i < nindex; i++) index[i] = atoi(params[i+1]) - 1; // map lattce_meam value to an integer if (which == 4) { if (!MEAM::str_to_lat(params[nparams-1], false, latt)) error->all(FLERR,"Unrecognized lattice type in MEAM file 2"); value = latt; } else value = atof(params[nparams-1]); // pass single setting to MEAM package int errorflag = 0; meam_inst->meam_setup_param(which,value,nindex,index,&errorflag); if (errorflag) { char str[128]; sprintf(str,"MEAM library error %d",errorflag); error->all(FLERR,str); } } delete [] params; } /* ---------------------------------------------------------------------- */ int PairMEAMC::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { int i,j,k,m; m = 0; for (i = 0; i < n; i++) { j = list[i]; buf[m++] = meam_inst->rho0[j]; buf[m++] = meam_inst->rho1[j]; buf[m++] = meam_inst->rho2[j]; buf[m++] = meam_inst->rho3[j]; buf[m++] = meam_inst->frhop[j]; buf[m++] = meam_inst->gamma[j]; buf[m++] = meam_inst->dgamma1[j]; buf[m++] = meam_inst->dgamma2[j]; buf[m++] = meam_inst->dgamma3[j]; buf[m++] = meam_inst->arho2b[j]; buf[m++] = meam_inst->arho1[j][0]; buf[m++] = meam_inst->arho1[j][1]; buf[m++] = meam_inst->arho1[j][2]; buf[m++] = meam_inst->arho2[j][0]; buf[m++] = meam_inst->arho2[j][1]; buf[m++] = meam_inst->arho2[j][2]; buf[m++] = meam_inst->arho2[j][3]; buf[m++] = meam_inst->arho2[j][4]; buf[m++] = meam_inst->arho2[j][5]; for (k = 0; k < 10; k++) buf[m++] = meam_inst->arho3[j][k]; buf[m++] = meam_inst->arho3b[j][0]; buf[m++] = meam_inst->arho3b[j][1]; buf[m++] = meam_inst->arho3b[j][2]; buf[m++] = meam_inst->t_ave[j][0]; buf[m++] = meam_inst->t_ave[j][1]; buf[m++] = meam_inst->t_ave[j][2]; buf[m++] = meam_inst->tsq_ave[j][0]; buf[m++] = meam_inst->tsq_ave[j][1]; buf[m++] = meam_inst->tsq_ave[j][2]; } return m; } /* ---------------------------------------------------------------------- */ void PairMEAMC::unpack_forward_comm(int n, int first, double *buf) { int i,k,m,last; m = 0; last = first + n; for (i = first; i < last; i++) { meam_inst->rho0[i] = buf[m++]; meam_inst->rho1[i] = buf[m++]; meam_inst->rho2[i] = buf[m++]; meam_inst->rho3[i] = buf[m++]; meam_inst->frhop[i] = buf[m++]; meam_inst->gamma[i] = buf[m++]; meam_inst->dgamma1[i] = buf[m++]; meam_inst->dgamma2[i] = buf[m++]; meam_inst->dgamma3[i] = buf[m++]; meam_inst->arho2b[i] = buf[m++]; meam_inst->arho1[i][0] = buf[m++]; meam_inst->arho1[i][1] = buf[m++]; meam_inst->arho1[i][2] = buf[m++]; meam_inst->arho2[i][0] = buf[m++]; meam_inst->arho2[i][1] = buf[m++]; meam_inst->arho2[i][2] = buf[m++]; meam_inst->arho2[i][3] = buf[m++]; meam_inst->arho2[i][4] = buf[m++]; meam_inst->arho2[i][5] = buf[m++]; for (k = 0; k < 10; k++) meam_inst->arho3[i][k] = buf[m++]; meam_inst->arho3b[i][0] = buf[m++]; meam_inst->arho3b[i][1] = buf[m++]; meam_inst->arho3b[i][2] = buf[m++]; meam_inst->t_ave[i][0] = buf[m++]; meam_inst->t_ave[i][1] = buf[m++]; meam_inst->t_ave[i][2] = buf[m++]; meam_inst->tsq_ave[i][0] = buf[m++]; meam_inst->tsq_ave[i][1] = buf[m++]; meam_inst->tsq_ave[i][2] = buf[m++]; } } /* ---------------------------------------------------------------------- */ int PairMEAMC::pack_reverse_comm(int n, int first, double *buf) { int i,k,m,last; m = 0; last = first + n; for (i = first; i < last; i++) { buf[m++] = meam_inst->rho0[i]; buf[m++] = meam_inst->arho2b[i]; buf[m++] = meam_inst->arho1[i][0]; buf[m++] = meam_inst->arho1[i][1]; buf[m++] = meam_inst->arho1[i][2]; buf[m++] = meam_inst->arho2[i][0]; buf[m++] = meam_inst->arho2[i][1]; buf[m++] = meam_inst->arho2[i][2]; buf[m++] = meam_inst->arho2[i][3]; buf[m++] = meam_inst->arho2[i][4]; buf[m++] = meam_inst->arho2[i][5]; for (k = 0; k < 10; k++) buf[m++] = meam_inst->arho3[i][k]; buf[m++] = meam_inst->arho3b[i][0]; buf[m++] = meam_inst->arho3b[i][1]; buf[m++] = meam_inst->arho3b[i][2]; buf[m++] = meam_inst->t_ave[i][0]; buf[m++] = meam_inst->t_ave[i][1]; buf[m++] = meam_inst->t_ave[i][2]; buf[m++] = meam_inst->tsq_ave[i][0]; buf[m++] = meam_inst->tsq_ave[i][1]; buf[m++] = meam_inst->tsq_ave[i][2]; } return m; } /* ---------------------------------------------------------------------- */ void PairMEAMC::unpack_reverse_comm(int n, int *list, double *buf) { int i,j,k,m; m = 0; for (i = 0; i < n; i++) { j = list[i]; meam_inst->rho0[j] += buf[m++]; meam_inst->arho2b[j] += buf[m++]; meam_inst->arho1[j][0] += buf[m++]; meam_inst->arho1[j][1] += buf[m++]; meam_inst->arho1[j][2] += buf[m++]; meam_inst->arho2[j][0] += buf[m++]; meam_inst->arho2[j][1] += buf[m++]; meam_inst->arho2[j][2] += buf[m++]; meam_inst->arho2[j][3] += buf[m++]; meam_inst->arho2[j][4] += buf[m++]; meam_inst->arho2[j][5] += buf[m++]; for (k = 0; k < 10; k++) meam_inst->arho3[j][k] += buf[m++]; meam_inst->arho3b[j][0] += buf[m++]; meam_inst->arho3b[j][1] += buf[m++]; meam_inst->arho3b[j][2] += buf[m++]; meam_inst->t_ave[j][0] += buf[m++]; meam_inst->t_ave[j][1] += buf[m++]; meam_inst->t_ave[j][2] += buf[m++]; meam_inst->tsq_ave[j][0] += buf[m++]; meam_inst->tsq_ave[j][1] += buf[m++]; meam_inst->tsq_ave[j][2] += buf[m++]; } } /* ---------------------------------------------------------------------- memory usage of local atom-based arrays ------------------------------------------------------------------------- */ double PairMEAMC::memory_usage() { double bytes = 11 * meam_inst->nmax * sizeof(double); bytes += (3 + 6 + 10 + 3 + 3 + 3) * meam_inst->nmax * sizeof(double); bytes += 3 * meam_inst->maxneigh * sizeof(double); return bytes; } /* ---------------------------------------------------------------------- strip special bond flags from neighbor list entries are not used with MEAM need to do here so Fortran lib doesn't see them done once per reneighbor so that neigh_f2c and neigh_c2f don't see them ------------------------------------------------------------------------- */ void PairMEAMC::neigh_strip(int inum, int *ilist, int *numneigh, int **firstneigh) { int i,j,ii,jnum; int *jlist; for (ii = 0; ii < inum; ii++) { i = ilist[ii]; jlist = firstneigh[i]; jnum = numneigh[i]; for (j = 0; j < jnum; j++) jlist[j] &= NEIGHMASK; } }