diff --git a/lib/meam/Makefile.lammps b/lib/meam/Makefile.lammps index a712df2d6..fa62c997d 100644 --- a/lib/meam/Makefile.lammps +++ b/lib/meam/Makefile.lammps @@ -1,5 +1,5 @@ # Settings that the LAMMPS build will import when this package library is used meam_SYSINC = meam_SYSLIB = -lgfortran -meam_SYSPATH = +meam_SYSPATH = diff --git a/src/pair_table.cpp b/src/pair_table.cpp index 17e9058b6..664db4766 100644 --- a/src/pair_table.cpp +++ b/src/pair_table.cpp @@ -1,957 +1,962 @@ /* ---------------------------------------------------------------------- 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: Paul Crozier (SNL) ------------------------------------------------------------------------- */ #include "mpi.h" #include "math.h" #include "stdlib.h" #include "string.h" +#include "ctype.h" #include "pair_table.h" #include "atom.h" #include "force.h" #include "comm.h" #include "neigh_list.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; enum{NONE,RLINEAR,RSQ,BMP}; #define MAXLINE 1024 /* ---------------------------------------------------------------------- */ PairTable::PairTable(LAMMPS *lmp) : Pair(lmp) { ntables = 0; tables = NULL; } /* ---------------------------------------------------------------------- */ PairTable::~PairTable() { for (int m = 0; m < ntables; m++) free_table(&tables[m]); memory->sfree(tables); if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); memory->destroy(tabindex); } } /* ---------------------------------------------------------------------- */ void PairTable::compute(int eflag, int vflag) { int i,j,ii,jj,inum,jnum,itype,jtype,itable; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; double rsq,factor_lj,fraction,value,a,b; int *ilist,*jlist,*numneigh,**firstneigh; Table *tb; union_int_float_t rsq_lookup; int tlm1 = tablength - 1; evdwl = 0.0; if (eflag || vflag) ev_setup(eflag,vflag); else evflag = vflag_fdotr = 0; double **x = atom->x; double **f = atom->f; int *type = atom->type; int nlocal = atom->nlocal; double *special_lj = force->special_lj; int newton_pair = force->newton_pair; inum = list->inum; ilist = list->ilist; numneigh = list->numneigh; firstneigh = list->firstneigh; // loop over neighbors of my atoms for (ii = 0; ii < inum; ii++) { i = ilist[ii]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; itype = type[i]; jlist = firstneigh[i]; jnum = numneigh[i]; for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; factor_lj = special_lj[sbmask(j)]; j &= NEIGHMASK; delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx*delx + dely*dely + delz*delz; jtype = type[j]; if (rsq < cutsq[itype][jtype]) { tb = &tables[tabindex[itype][jtype]]; if (rsq < tb->innersq) error->one(FLERR,"Pair distance < table inner cutoff"); if (tabstyle == LOOKUP) { itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta); if (itable >= tlm1) error->one(FLERR,"Pair distance > table outer cutoff"); fpair = factor_lj * tb->f[itable]; } else if (tabstyle == LINEAR) { itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta); if (itable >= tlm1) error->one(FLERR,"Pair distance > table outer cutoff"); fraction = (rsq - tb->rsq[itable]) * tb->invdelta; value = tb->f[itable] + fraction*tb->df[itable]; fpair = factor_lj * value; } else if (tabstyle == SPLINE) { itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta); if (itable >= tlm1) error->one(FLERR,"Pair distance > table outer cutoff"); b = (rsq - tb->rsq[itable]) * tb->invdelta; a = 1.0 - b; value = a * tb->f[itable] + b * tb->f[itable+1] + ((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) * tb->deltasq6; fpair = factor_lj * value; } else { rsq_lookup.f = rsq; itable = rsq_lookup.i & tb->nmask; itable >>= tb->nshiftbits; fraction = (rsq_lookup.f - tb->rsq[itable]) * tb->drsq[itable]; value = tb->f[itable] + fraction*tb->df[itable]; fpair = factor_lj * value; } f[i][0] += delx*fpair; f[i][1] += dely*fpair; f[i][2] += delz*fpair; if (newton_pair || j < nlocal) { f[j][0] -= delx*fpair; f[j][1] -= dely*fpair; f[j][2] -= delz*fpair; } if (eflag) { if (tabstyle == LOOKUP) evdwl = tb->e[itable]; else if (tabstyle == LINEAR || tabstyle == BITMAP) evdwl = tb->e[itable] + fraction*tb->de[itable]; else evdwl = a * tb->e[itable] + b * tb->e[itable+1] + ((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) * tb->deltasq6; evdwl *= factor_lj; } if (evflag) ev_tally(i,j,nlocal,newton_pair, evdwl,0.0,fpair,delx,dely,delz); } } } if (vflag_fdotr) virial_fdotr_compute(); } /* ---------------------------------------------------------------------- allocate all arrays ------------------------------------------------------------------------- */ void PairTable::allocate() { allocated = 1; int nt = atom->ntypes; memory->create(setflag,nt+1,nt+1,"pair:setflag"); for (int i = 1; i <= nt; i++) for (int j = i; j <= nt; j++) setflag[i][j] = 0; memory->create(cutsq,nt+1,nt+1,"pair:cutsq"); memory->create(tabindex,nt+1,nt+1,"pair:tabindex"); } /* ---------------------------------------------------------------------- global settings ------------------------------------------------------------------------- */ void PairTable::settings(int narg, char **arg) { if (narg != 2) error->all(FLERR,"Illegal pair_style command"); // new settings if (strcmp(arg[0],"lookup") == 0) tabstyle = LOOKUP; else if (strcmp(arg[0],"linear") == 0) tabstyle = LINEAR; else if (strcmp(arg[0],"spline") == 0) tabstyle = SPLINE; else if (strcmp(arg[0],"bitmap") == 0) tabstyle = BITMAP; else error->all(FLERR,"Unknown table style in pair_style command"); tablength = force->inumeric(arg[1]); if (tablength < 2) error->all(FLERR,"Illegal number of pair table entries"); // delete old tables, since cannot just change settings for (int m = 0; m < ntables; m++) free_table(&tables[m]); memory->sfree(tables); if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); memory->destroy(tabindex); } allocated = 0; ntables = 0; tables = NULL; } /* ---------------------------------------------------------------------- set coeffs for one or more type pairs ------------------------------------------------------------------------- */ void PairTable::coeff(int narg, char **arg) { if (narg != 4 && narg != 5) error->all(FLERR,"Illegal pair_coeff command"); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; force->bounds(arg[0],atom->ntypes,ilo,ihi); force->bounds(arg[1],atom->ntypes,jlo,jhi); int me; MPI_Comm_rank(world,&me); tables = (Table *) memory->srealloc(tables,(ntables+1)*sizeof(Table),"pair:tables"); Table *tb = &tables[ntables]; null_table(tb); if (me == 0) read_table(tb,arg[2],arg[3]); bcast_table(tb); // set table cutoff if (narg == 5) tb->cut = force->numeric(arg[4]); else if (tb->rflag) tb->cut = tb->rhi; else tb->cut = tb->rfile[tb->ninput-1]; // error check on table parameters // insure cutoff is within table // for BITMAP tables, file values can be in non-ascending order if (tb->ninput <= 1) error->one(FLERR,"Invalid pair table length"); double rlo,rhi; if (tb->rflag == 0) { rlo = tb->rfile[0]; rhi = tb->rfile[tb->ninput-1]; } else { rlo = tb->rlo; rhi = tb->rhi; } if (tb->cut <= rlo || tb->cut > rhi) error->all(FLERR,"Invalid pair table cutoff"); if (rlo <= 0.0) error->all(FLERR,"Invalid pair table cutoff"); // match = 1 if don't need to spline read-in tables // this is only the case if r values needed by final tables // exactly match r values read from file // for tabstyle SPLINE, always need to build spline tables tb->match = 0; if (tabstyle == LINEAR && tb->ninput == tablength && tb->rflag == RSQ && tb->rhi == tb->cut) tb->match = 1; if (tabstyle == BITMAP && tb->ninput == 1 << tablength && tb->rflag == BMP && tb->rhi == tb->cut) tb->match = 1; if (tb->rflag == BMP && tb->match == 0) error->all(FLERR,"Bitmapped table in file does not match requested table"); // spline read-in values and compute r,e,f vectors within table if (tb->match == 0) spline_table(tb); compute_table(tb); // store ptr to table in tabindex int count = 0; for (int i = ilo; i <= ihi; i++) { for (int j = MAX(jlo,i); j <= jhi; j++) { tabindex[i][j] = ntables; setflag[i][j] = 1; count++; } } if (count == 0) error->all(FLERR,"Illegal pair_coeff command"); ntables++; } /* ---------------------------------------------------------------------- init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ double PairTable::init_one(int i, int j) { if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); tabindex[j][i] = tabindex[i][j]; return tables[tabindex[i][j]].cut; } /* ---------------------------------------------------------------------- read a table section from a tabulated potential file only called by proc 0 this function sets these values in Table: ninput,rfile,efile,ffile,rflag,rlo,rhi,fpflag,fplo,fphi,ntablebits ------------------------------------------------------------------------- */ void PairTable::read_table(Table *tb, char *file, char *keyword) { char line[MAXLINE]; // open file FILE *fp = fopen(file,"r"); if (fp == NULL) { char str[128]; sprintf(str,"Cannot open file %s",file); error->one(FLERR,str); } // loop until section found with matching keyword while (1) { if (fgets(line,MAXLINE,fp) == NULL) error->one(FLERR,"Did not find keyword in table file"); if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line if (line[0] == '#') continue; // comment - if (strstr(line,keyword) == line) break; // matching keyword + int i = 0; + while (isalnum(line[i]) || line[i] == '_') i++; + char *word = new char[i]; + strncpy(word,&line[0],i); + if (strcmp(word,keyword) == 0) break; // matching keyword fgets(line,MAXLINE,fp); // no match, skip section param_extract(tb,line); fgets(line,MAXLINE,fp); for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp); } // read args on 2nd line of section // allocate table arrays for file values fgets(line,MAXLINE,fp); param_extract(tb,line); memory->create(tb->rfile,tb->ninput,"pair:rfile"); memory->create(tb->efile,tb->ninput,"pair:efile"); memory->create(tb->ffile,tb->ninput,"pair:ffile"); // setup bitmap parameters for table to read in tb->ntablebits = 0; int masklo,maskhi,nmask,nshiftbits; if (tb->rflag == BMP) { while (1 << tb->ntablebits < tb->ninput) tb->ntablebits++; if (1 << tb->ntablebits != tb->ninput) error->one(FLERR,"Bitmapped table is incorrect length in table file"); init_bitmap(tb->rlo,tb->rhi,tb->ntablebits,masklo,maskhi,nmask,nshiftbits); } // read r,e,f table values from file // if rflag set, compute r // if rflag not set, use r from file int itmp; double rtmp; union_int_float_t rsq_lookup; fgets(line,MAXLINE,fp); for (int i = 0; i < tb->ninput; i++) { fgets(line,MAXLINE,fp); sscanf(line,"%d %lg %lg %lg",&itmp,&rtmp,&tb->efile[i],&tb->ffile[i]); if (tb->rflag == RLINEAR) rtmp = tb->rlo + (tb->rhi - tb->rlo)*i/(tb->ninput-1); else if (tb->rflag == RSQ) { rtmp = tb->rlo*tb->rlo + (tb->rhi*tb->rhi - tb->rlo*tb->rlo)*i/(tb->ninput-1); rtmp = sqrt(rtmp); } else if (tb->rflag == BMP) { rsq_lookup.i = i << nshiftbits; rsq_lookup.i |= masklo; if (rsq_lookup.f < tb->rlo*tb->rlo) { rsq_lookup.i = i << nshiftbits; rsq_lookup.i |= maskhi; } rtmp = sqrtf(rsq_lookup.f); } tb->rfile[i] = rtmp; } // close file fclose(fp); } /* ---------------------------------------------------------------------- broadcast read-in table info from proc 0 to other procs this function communicates these values in Table: ninput,rfile,efile,ffile,rflag,rlo,rhi,fpflag,fplo,fphi ------------------------------------------------------------------------- */ void PairTable::bcast_table(Table *tb) { MPI_Bcast(&tb->ninput,1,MPI_INT,0,world); int me; MPI_Comm_rank(world,&me); if (me > 0) { memory->create(tb->rfile,tb->ninput,"pair:rfile"); memory->create(tb->efile,tb->ninput,"pair:efile"); memory->create(tb->ffile,tb->ninput,"pair:ffile"); } MPI_Bcast(tb->rfile,tb->ninput,MPI_DOUBLE,0,world); MPI_Bcast(tb->efile,tb->ninput,MPI_DOUBLE,0,world); MPI_Bcast(tb->ffile,tb->ninput,MPI_DOUBLE,0,world); MPI_Bcast(&tb->rflag,1,MPI_INT,0,world); if (tb->rflag) { MPI_Bcast(&tb->rlo,1,MPI_DOUBLE,0,world); MPI_Bcast(&tb->rhi,1,MPI_DOUBLE,0,world); } MPI_Bcast(&tb->fpflag,1,MPI_INT,0,world); if (tb->fpflag) { MPI_Bcast(&tb->fplo,1,MPI_DOUBLE,0,world); MPI_Bcast(&tb->fphi,1,MPI_DOUBLE,0,world); } } /* ---------------------------------------------------------------------- build spline representation of e,f over entire range of read-in table this function sets these values in Table: e2file,f2file ------------------------------------------------------------------------- */ void PairTable::spline_table(Table *tb) { memory->create(tb->e2file,tb->ninput,"pair:e2file"); memory->create(tb->f2file,tb->ninput,"pair:f2file"); double ep0 = - tb->ffile[0]; double epn = - tb->ffile[tb->ninput-1]; spline(tb->rfile,tb->efile,tb->ninput,ep0,epn,tb->e2file); if (tb->fpflag == 0) { tb->fplo = (tb->ffile[1] - tb->ffile[0]) / (tb->rfile[1] - tb->rfile[0]); tb->fphi = (tb->ffile[tb->ninput-1] - tb->ffile[tb->ninput-2]) / (tb->rfile[tb->ninput-1] - tb->rfile[tb->ninput-2]); } double fp0 = tb->fplo; double fpn = tb->fphi; spline(tb->rfile,tb->ffile,tb->ninput,fp0,fpn,tb->f2file); } /* ---------------------------------------------------------------------- extract attributes from parameter line in table section format of line: N value R/RSQ/BITMAP lo hi FP fplo fphi N is required, other params are optional ------------------------------------------------------------------------- */ void PairTable::param_extract(Table *tb, char *line) { tb->ninput = 0; tb->rflag = NONE; tb->fpflag = 0; char *word = strtok(line," \t\n\r\f"); while (word) { if (strcmp(word,"N") == 0) { word = strtok(NULL," \t\n\r\f"); tb->ninput = atoi(word); } else if (strcmp(word,"R") == 0 || strcmp(word,"RSQ") == 0 || strcmp(word,"BITMAP") == 0) { if (strcmp(word,"R") == 0) tb->rflag = RLINEAR; else if (strcmp(word,"RSQ") == 0) tb->rflag = RSQ; else if (strcmp(word,"BITMAP") == 0) tb->rflag = BMP; word = strtok(NULL," \t\n\r\f"); tb->rlo = atof(word); word = strtok(NULL," \t\n\r\f"); tb->rhi = atof(word); } else if (strcmp(word,"FP") == 0) { tb->fpflag = 1; word = strtok(NULL," \t\n\r\f"); tb->fplo = atof(word); word = strtok(NULL," \t\n\r\f"); tb->fphi = atof(word); } else { printf("WORD: %s\n",word); error->one(FLERR,"Invalid keyword in pair table parameters"); } word = strtok(NULL," \t\n\r\f"); } if (tb->ninput == 0) error->one(FLERR,"Pair table parameters did not set N"); } /* ---------------------------------------------------------------------- compute r,e,f vectors from splined values ------------------------------------------------------------------------- */ void PairTable::compute_table(Table *tb) { int tlm1 = tablength-1; // inner = inner table bound // cut = outer table bound // delta = table spacing in rsq for N-1 bins double inner; if (tb->rflag) inner = tb->rlo; else inner = tb->rfile[0]; tb->innersq = inner*inner; tb->delta = (tb->cut*tb->cut - tb->innersq) / tlm1; tb->invdelta = 1.0/tb->delta; // direct lookup tables // N-1 evenly spaced bins in rsq from inner to cut // e,f = value at midpt of bin // e,f are N-1 in length since store 1 value at bin midpt // f is converted to f/r when stored in f[i] // e,f are never a match to read-in values, always computed via spline interp if (tabstyle == LOOKUP) { memory->create(tb->e,tlm1,"pair:e"); memory->create(tb->f,tlm1,"pair:f"); double r,rsq; for (int i = 0; i < tlm1; i++) { rsq = tb->innersq + (i+0.5)*tb->delta; r = sqrt(rsq); tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r); tb->f[i] = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r)/r; } } // linear tables // N-1 evenly spaced bins in rsq from inner to cut // rsq,e,f = value at lower edge of bin // de,df values = delta from lower edge to upper edge of bin // rsq,e,f are N in length so de,df arrays can compute difference // f is converted to f/r when stored in f[i] // e,f can match read-in values, else compute via spline interp if (tabstyle == LINEAR) { memory->create(tb->rsq,tablength,"pair:rsq"); memory->create(tb->e,tablength,"pair:e"); memory->create(tb->f,tablength,"pair:f"); memory->create(tb->de,tlm1,"pair:de"); memory->create(tb->df,tlm1,"pair:df"); double r,rsq; for (int i = 0; i < tablength; i++) { rsq = tb->innersq + i*tb->delta; r = sqrt(rsq); tb->rsq[i] = rsq; if (tb->match) { tb->e[i] = tb->efile[i]; tb->f[i] = tb->ffile[i]/r; } else { tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r); tb->f[i] = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r)/r; } } for (int i = 0; i < tlm1; i++) { tb->de[i] = tb->e[i+1] - tb->e[i]; tb->df[i] = tb->f[i+1] - tb->f[i]; } } // cubic spline tables // N-1 evenly spaced bins in rsq from inner to cut // rsq,e,f = value at lower edge of bin // e2,f2 = spline coefficient for each bin // rsq,e,f,e2,f2 are N in length so have N-1 spline bins // f is converted to f/r after e is splined // e,f can match read-in values, else compute via spline interp if (tabstyle == SPLINE) { memory->create(tb->rsq,tablength,"pair:rsq"); memory->create(tb->e,tablength,"pair:e"); memory->create(tb->f,tablength,"pair:f"); memory->create(tb->e2,tablength,"pair:e2"); memory->create(tb->f2,tablength,"pair:f2"); tb->deltasq6 = tb->delta*tb->delta / 6.0; double r,rsq; for (int i = 0; i < tablength; i++) { rsq = tb->innersq + i*tb->delta; r = sqrt(rsq); tb->rsq[i] = rsq; if (tb->match) { tb->e[i] = tb->efile[i]; tb->f[i] = tb->ffile[i]/r; } else { tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r); tb->f[i] = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r); } } // ep0,epn = dh/dg at inner and at cut // h(r) = e(r) and g(r) = r^2 // dh/dg = (de/dr) / 2r = -f/2r double ep0 = - tb->f[0] / (2.0 * sqrt(tb->innersq)); double epn = - tb->f[tlm1] / (2.0 * tb->cut); spline(tb->rsq,tb->e,tablength,ep0,epn,tb->e2); // fp0,fpn = dh/dg at inner and at cut // h(r) = f(r)/r and g(r) = r^2 // dh/dg = (1/r df/dr - f/r^2) / 2r // dh/dg in secant approx = (f(r2)/r2 - f(r1)/r1) / (g(r2) - g(r1)) double fp0,fpn; double secant_factor = 0.1; if (tb->fpflag) fp0 = (tb->fplo/sqrt(tb->innersq) - tb->f[0]/tb->innersq) / (2.0 * sqrt(tb->innersq)); else { double rsq1 = tb->innersq; double rsq2 = rsq1 + secant_factor*tb->delta; fp0 = (splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,sqrt(rsq2)) / sqrt(rsq2) - tb->f[0] / sqrt(rsq1)) / (secant_factor*tb->delta); } if (tb->fpflag && tb->cut == tb->rfile[tb->ninput-1]) fpn = (tb->fphi/tb->cut - tb->f[tlm1]/(tb->cut*tb->cut)) / (2.0 * tb->cut); else { double rsq2 = tb->cut * tb->cut; double rsq1 = rsq2 - secant_factor*tb->delta; fpn = (tb->f[tlm1] / sqrt(rsq2) - splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,sqrt(rsq1)) / sqrt(rsq1)) / (secant_factor*tb->delta); } for (int i = 0; i < tablength; i++) tb->f[i] /= sqrt(tb->rsq[i]); spline(tb->rsq,tb->f,tablength,fp0,fpn,tb->f2); } // bitmapped linear tables // 2^N bins from inner to cut, spaced in bitmapped manner // f is converted to f/r when stored in f[i] // e,f can match read-in values, else compute via spline interp if (tabstyle == BITMAP) { double r; union_int_float_t rsq_lookup; int masklo,maskhi; // linear lookup tables of length ntable = 2^n // stored value = value at lower edge of bin init_bitmap(inner,tb->cut,tablength,masklo,maskhi,tb->nmask,tb->nshiftbits); int ntable = 1 << tablength; int ntablem1 = ntable - 1; memory->create(tb->rsq,ntable,"pair:rsq"); memory->create(tb->e,ntable,"pair:e"); memory->create(tb->f,ntable,"pair:f"); memory->create(tb->de,ntable,"pair:de"); memory->create(tb->df,ntable,"pair:df"); memory->create(tb->drsq,ntable,"pair:drsq"); union_int_float_t minrsq_lookup; minrsq_lookup.i = 0 << tb->nshiftbits; minrsq_lookup.i |= maskhi; for (int i = 0; i < ntable; i++) { rsq_lookup.i = i << tb->nshiftbits; rsq_lookup.i |= masklo; if (rsq_lookup.f < tb->innersq) { rsq_lookup.i = i << tb->nshiftbits; rsq_lookup.i |= maskhi; } r = sqrtf(rsq_lookup.f); tb->rsq[i] = rsq_lookup.f; if (tb->match) { tb->e[i] = tb->efile[i]; tb->f[i] = tb->ffile[i]/r; } else { tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r); tb->f[i] = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r)/r; } minrsq_lookup.f = MIN(minrsq_lookup.f,rsq_lookup.f); } tb->innersq = minrsq_lookup.f; for (int i = 0; i < ntablem1; i++) { tb->de[i] = tb->e[i+1] - tb->e[i]; tb->df[i] = tb->f[i+1] - tb->f[i]; tb->drsq[i] = 1.0/(tb->rsq[i+1] - tb->rsq[i]); } // get the delta values for the last table entries // tables are connected periodically between 0 and ntablem1 tb->de[ntablem1] = tb->e[0] - tb->e[ntablem1]; tb->df[ntablem1] = tb->f[0] - tb->f[ntablem1]; tb->drsq[ntablem1] = 1.0/(tb->rsq[0] - tb->rsq[ntablem1]); // get the correct delta values at itablemax // smallest r is in bin itablemin // largest r is in bin itablemax, which is itablemin-1, // or ntablem1 if itablemin=0 // deltas at itablemax only needed if corresponding rsq < cut*cut // if so, compute deltas between rsq and cut*cut // if tb->match, data at cut*cut is unavailable, so we'll take // deltas at itablemax-1 as a good approximation double e_tmp,f_tmp; int itablemin = minrsq_lookup.i & tb->nmask; itablemin >>= tb->nshiftbits; int itablemax = itablemin - 1; if (itablemin == 0) itablemax = ntablem1; int itablemaxm1 = itablemax - 1; if (itablemax == 0) itablemaxm1 = ntablem1; rsq_lookup.i = itablemax << tb->nshiftbits; rsq_lookup.i |= maskhi; if (rsq_lookup.f < tb->cut*tb->cut) { if (tb->match) { tb->de[itablemax] = tb->de[itablemaxm1]; tb->df[itablemax] = tb->df[itablemaxm1]; tb->drsq[itablemax] = tb->drsq[itablemaxm1]; } else { rsq_lookup.f = tb->cut*tb->cut; r = sqrtf(rsq_lookup.f); e_tmp = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r); f_tmp = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r)/r; tb->de[itablemax] = e_tmp - tb->e[itablemax]; tb->df[itablemax] = f_tmp - tb->f[itablemax]; tb->drsq[itablemax] = 1.0/(rsq_lookup.f - tb->rsq[itablemax]); } } } } /* ---------------------------------------------------------------------- set all ptrs in a table to NULL, so can be freed safely ------------------------------------------------------------------------- */ void PairTable::null_table(Table *tb) { tb->rfile = tb->efile = tb->ffile = NULL; tb->e2file = tb->f2file = NULL; tb->rsq = tb->drsq = tb->e = tb->de = NULL; tb->f = tb->df = tb->e2 = tb->f2 = NULL; } /* ---------------------------------------------------------------------- free all arrays in a table ------------------------------------------------------------------------- */ void PairTable::free_table(Table *tb) { memory->destroy(tb->rfile); memory->destroy(tb->efile); memory->destroy(tb->ffile); memory->destroy(tb->e2file); memory->destroy(tb->f2file); memory->destroy(tb->rsq); memory->destroy(tb->drsq); memory->destroy(tb->e); memory->destroy(tb->de); memory->destroy(tb->f); memory->destroy(tb->df); memory->destroy(tb->e2); memory->destroy(tb->f2); } /* ---------------------------------------------------------------------- spline and splint routines modified from Numerical Recipes ------------------------------------------------------------------------- */ void PairTable::spline(double *x, double *y, int n, double yp1, double ypn, double *y2) { int i,k; double p,qn,sig,un; double *u = new double[n]; if (yp1 > 0.99e30) y2[0] = u[0] = 0.0; else { y2[0] = -0.5; u[0] = (3.0/(x[1]-x[0])) * ((y[1]-y[0]) / (x[1]-x[0]) - yp1); } for (i = 1; i < n-1; i++) { sig = (x[i]-x[i-1]) / (x[i+1]-x[i-1]); p = sig*y2[i-1] + 2.0; y2[i] = (sig-1.0) / p; u[i] = (y[i+1]-y[i]) / (x[i+1]-x[i]) - (y[i]-y[i-1]) / (x[i]-x[i-1]); u[i] = (6.0*u[i] / (x[i+1]-x[i-1]) - sig*u[i-1]) / p; } if (ypn > 0.99e30) qn = un = 0.0; else { qn = 0.5; un = (3.0/(x[n-1]-x[n-2])) * (ypn - (y[n-1]-y[n-2]) / (x[n-1]-x[n-2])); } y2[n-1] = (un-qn*u[n-2]) / (qn*y2[n-2] + 1.0); for (k = n-2; k >= 0; k--) y2[k] = y2[k]*y2[k+1] + u[k]; delete [] u; } /* ---------------------------------------------------------------------- */ double PairTable::splint(double *xa, double *ya, double *y2a, int n, double x) { int klo,khi,k; double h,b,a,y; klo = 0; khi = n-1; while (khi-klo > 1) { k = (khi+klo) >> 1; if (xa[k] > x) khi = k; else klo = k; } h = xa[khi]-xa[klo]; a = (xa[khi]-x) / h; b = (x-xa[klo]) / h; y = a*ya[klo] + b*ya[khi] + ((a*a*a-a)*y2a[klo] + (b*b*b-b)*y2a[khi]) * (h*h)/6.0; return y; } /* ---------------------------------------------------------------------- proc 0 writes to restart file ------------------------------------------------------------------------- */ void PairTable::write_restart(FILE *fp) { write_restart_settings(fp); } /* ---------------------------------------------------------------------- proc 0 reads from restart file, bcasts ------------------------------------------------------------------------- */ void PairTable::read_restart(FILE *fp) { read_restart_settings(fp); allocate(); } /* ---------------------------------------------------------------------- proc 0 writes to restart file ------------------------------------------------------------------------- */ void PairTable::write_restart_settings(FILE *fp) { fwrite(&tabstyle,sizeof(int),1,fp); fwrite(&tablength,sizeof(int),1,fp); } /* ---------------------------------------------------------------------- proc 0 reads from restart file, bcasts ------------------------------------------------------------------------- */ void PairTable::read_restart_settings(FILE *fp) { if (comm->me == 0) { fread(&tabstyle,sizeof(int),1,fp); fread(&tablength,sizeof(int),1,fp); } MPI_Bcast(&tabstyle,1,MPI_INT,0,world); MPI_Bcast(&tablength,1,MPI_INT,0,world); } /* ---------------------------------------------------------------------- */ double PairTable::single(int i, int j, int itype, int jtype, double rsq, double factor_coul, double factor_lj, double &fforce) { int itable; double fraction,value,a,b,phi; int tlm1 = tablength - 1; Table *tb = &tables[tabindex[itype][jtype]]; if (rsq < tb->innersq) error->one(FLERR,"Pair distance < table inner cutoff"); if (tabstyle == LOOKUP) { itable = static_cast<int> ((rsq-tb->innersq) * tb->invdelta); if (itable >= tlm1) error->one(FLERR,"Pair distance > table outer cutoff"); fforce = factor_lj * tb->f[itable]; } else if (tabstyle == LINEAR) { itable = static_cast<int> ((rsq-tb->innersq) * tb->invdelta); if (itable >= tlm1) error->one(FLERR,"Pair distance > table outer cutoff"); fraction = (rsq - tb->rsq[itable]) * tb->invdelta; value = tb->f[itable] + fraction*tb->df[itable]; fforce = factor_lj * value; } else if (tabstyle == SPLINE) { itable = static_cast<int> ((rsq-tb->innersq) * tb->invdelta); if (itable >= tlm1) error->one(FLERR,"Pair distance > table outer cutoff"); b = (rsq - tb->rsq[itable]) * tb->invdelta; a = 1.0 - b; value = a * tb->f[itable] + b * tb->f[itable+1] + ((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) * tb->deltasq6; fforce = factor_lj * value; } else { union_int_float_t rsq_lookup; rsq_lookup.f = rsq; itable = rsq_lookup.i & tb->nmask; itable >>= tb->nshiftbits; fraction = (rsq_lookup.f - tb->rsq[itable]) * tb->drsq[itable]; value = tb->f[itable] + fraction*tb->df[itable]; fforce = factor_lj * value; } if (tabstyle == LOOKUP) phi = tb->e[itable]; else if (tabstyle == LINEAR || tabstyle == BITMAP) phi = tb->e[itable] + fraction*tb->de[itable]; else phi = a * tb->e[itable] + b * tb->e[itable+1] + ((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) * tb->deltasq6; return factor_lj*phi; } /* ---------------------------------------------------------------------- return the Coulomb cutoff for tabled potentials called by KSpace solvers which require that all pairwise cutoffs be the same loop over all tables not just those indexed by tabindex[i][j] since no way to know which tables are active since pair::init() not yet called ------------------------------------------------------------------------- */ void *PairTable::extract(const char *str, int &dim) { if (strcmp(str,"cut_coul") != 0) return NULL; if (ntables == 0) error->all(FLERR,"All pair coeffs are not set"); double cut_coul = tables[0].cut; for (int m = 1; m < ntables; m++) if (tables[m].cut != cut_coul) error->all(FLERR, "Pair table cutoffs must all be equal to use with KSpace"); dim = 0; return &tables[0].cut; }