/* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/ Sandia National Laboratories LAMMPS development team: developers@lammps.org 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: Christoph Scherer (MPIP Mainz) scherer@mpip-mainz.mpg.de ------------------------------------------------------------------------- */ #include "pair_threebody_table.h" #include "atom.h" #include "comm.h" #include "error.h" #include "force.h" #include "math_const.h" #include "memory.h" #include "neigh_list.h" #include "neighbor.h" #include "potential_file_reader.h" #include "table_file_reader.h" #include #include using namespace LAMMPS_NS; using MathConst::MY_PI; #define DELTA 4 /* ---------------------------------------------------------------------- */ PairThreebodyTable::PairThreebodyTable(LAMMPS *lmp) : Pair(lmp), params(nullptr), neighshort(nullptr) { single_enable = 0; restartinfo = 0; one_coeff = 1; manybody_flag = 1; centroidstressflag = CENTROID_NOTAVAIL; maxshort = 10; } /* ---------------------------------------------------------------------- check if allocated, since class can be destructed when incomplete ------------------------------------------------------------------------- */ PairThreebodyTable::~PairThreebodyTable() { if (copymode) return; for (int m = 0; m < nparams; m++) free_param(¶ms[m]); // free_param will call free_table memory->sfree(params); memory->destroy(elem3param); if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); memory->destroy(neighshort); } } /* ---------------------------------------------------------------------- */ void PairThreebodyTable::compute(int eflag, int vflag) { int i, j, k, ii, jj, kk, inum, jnum, jnumm1; int itype, jtype, ktype, ijparam, ijkparam; tagint itag, jtag; double xtmp, ytmp, ztmp, delx, dely, delz, evdwl; double rsq, rsq1, rsq2; double delr1[3], delr2[3], fi[3], fj[3], fk[3]; int *ilist, *jlist, *numneigh, **firstneigh; evdwl = 0.0; ev_init(eflag, vflag); double **x = atom->x; double **f = atom->f; tagint *tag = atom->tag; int *type = atom->type; inum = list->inum; ilist = list->ilist; numneigh = list->numneigh; firstneigh = list->firstneigh; double fxtmp, fytmp, fztmp; // 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; // two-body interactions, skip half of them jlist = firstneigh[i]; jnum = numneigh[i]; int numshort = 0; for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; 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 = map[type[j]]; ijparam = elem3param[itype][jtype][jtype]; if (rsq >= params[ijparam].cutsq) { continue; } else { neighshort[numshort++] = j; if (numshort >= maxshort) { maxshort += maxshort / 2; memory->grow(neighshort, maxshort, "pair:neighshort"); } } 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; } //two-body interactions are not computed } jnumm1 = numshort - 1; for (jj = 0; jj < jnumm1; jj++) { j = neighshort[jj]; jtype = map[type[j]]; ijparam = elem3param[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]; double fjxtmp, fjytmp, fjztmp; fjxtmp = fjytmp = fjztmp = 0.0; for (kk = jj + 1; kk < numshort; kk++) { k = neighshort[kk]; ktype = map[type[k]]; ijkparam = elem3param[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]; threebody(¶ms[ijkparam], rsq1, rsq2, delr1, delr2, fi, fj, fk, eflag, evdwl); fxtmp += fi[0]; fytmp += fi[1]; fztmp += fi[2]; fjxtmp += fj[0]; fjytmp += fj[1]; fjztmp += 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); } f[j][0] += fjxtmp; f[j][1] += fjytmp; f[j][2] += fjztmp; } f[i][0] += fxtmp; f[i][1] += fytmp; f[i][2] += fztmp; } if (vflag_fdotr) virial_fdotr_compute(); } /* ---------------------------------------------------------------------- */ void PairThreebodyTable::allocate() { allocated = 1; int np1 = atom->ntypes + 1; memory->create(setflag, np1, np1, "pair:setflag"); memory->create(cutsq, np1, np1, "pair:cutsq"); memory->create(neighshort, maxshort, "pair:neighshort"); map = new int[np1]; } /* ---------------------------------------------------------------------- global settings ------------------------------------------------------------------------- */ void PairThreebodyTable::settings(int narg, char ** /*arg*/) { if (narg != 0) error->all(FLERR, "Illegal pair_style command"); } /* ---------------------------------------------------------------------- set coeffs for one or more type pairs ------------------------------------------------------------------------- */ void PairThreebodyTable::coeff(int narg, char **arg) { if (!allocated) allocate(); map_element2type(narg - 3, arg + 3); // read potential file and initialize potential parameters if (params) { for (int m = 0; m < nparams; m++) free_param(¶ms[m]); // free_param will call free_table memory->sfree(params); params = nullptr; } read_file(arg[2]); setup_params(); } /* ---------------------------------------------------------------------- init specific to this pair style ------------------------------------------------------------------------- */ void PairThreebodyTable::init_style() { if (atom->tag_enable == 0) error->all(FLERR, "Pair style threebody/table requires atom IDs"); if (force->newton_pair == 0) error->all(FLERR, "Pair style threebody/table requires newton pair on"); // need a full neighbor list neighbor->add_request(this, NeighConst::REQ_FULL); } /* ---------------------------------------------------------------------- init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ double PairThreebodyTable::init_one(int i, int j) { if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set"); return cutmax; } /* ---------------------------------------------------------------------- */ void PairThreebodyTable::read_file(char *file) { params = nullptr; nparams = maxparam = 0; // open file on proc 0 if (comm->me == 0) { PotentialFileReader reader(lmp, file, "threebody", unit_convert_flag); char *line; while ((line = reader.next_line(NPARAMS_PER_LINE))) { try { ValueTokenizer values(line); std::string iname = values.next_string(); std::string jname = values.next_string(); std::string kname = values.next_string(); // ielement,jelement,kelement = 1st args // if all 3 args are in element list, then parse this line // else skip to next entry in file int ielement, jelement, kelement; for (ielement = 0; ielement < nelements; ielement++) if (iname == elements[ielement]) break; if (ielement == nelements) continue; for (jelement = 0; jelement < nelements; jelement++) if (jname == elements[jelement]) break; if (jelement == nelements) continue; for (kelement = 0; kelement < nelements; kelement++) if (kname == elements[kelement]) 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"); // make certain all addional allocated storage is initialized // to avoid false positives when checking with valgrind memset(params + nparams, 0, DELTA * sizeof(Param)); } params[nparams].ielement = ielement; params[nparams].jelement = jelement; params[nparams].kelement = kelement; // if jelement = kelement, symmetric is true, if not then it is false params[nparams].symmetric = false; if (params[nparams].jelement == params[nparams].kelement) params[nparams].symmetric = true; // read cut off params[nparams].cut = values.next_double(); // read parameters of angle table std::string name = values.next_string(); params[nparams].tablenamelength = name.length() + 1; params[nparams].tablename = utils::strdup(name); name = values.next_string(); params[nparams].keywordlength = name.length() + 1; params[nparams].keyword = utils::strdup(name); name = values.next_string(); if (name != "linear") error->all(FLERR, "Unknown table style {} in threebody table", name); params[nparams].tablength = values.next_int(); } catch (TokenizerException &e) { error->one(FLERR, e.what()); } if (params[nparams].cut < 0.0 || params[nparams].tablength < 0.0) error->one(FLERR, "Illegal threebody/table parameters"); nparams++; } } MPI_Bcast(&nparams, 1, MPI_INT, 0, world); MPI_Bcast(&maxparam, 1, MPI_INT, 0, world); if (comm->me != 0) params = (Param *) memory->srealloc(params, maxparam * sizeof(Param), "pair:params"); MPI_Bcast(params, maxparam * sizeof(Param), MPI_BYTE, 0, world); // for each set of parameters, broadcast table name and keyword and read threebody table for (int m = 0; m < nparams; ++m) { if (comm->me != 0) { params[m].tablename = new char[params[m].tablenamelength]; params[m].keyword = new char[params[m].keywordlength]; } MPI_Bcast(params[m].tablename, params[m].tablenamelength, MPI_CHAR, 0, world); MPI_Bcast(params[m].keyword, params[m].keywordlength, MPI_CHAR, 0, world); // initialize threebodytable memory->create(params[m].mltable, 1, "param:threebodytable"); null_table(params[m].mltable); //call read_table to read corresponding tabulated threebody file (only called by process 0) if (comm->me == 0) { read_table(params[m].mltable, params[m].tablename, params[m].keyword, params[m].symmetric); } // broadcast read in threebodytable to all processes bcast_table(params[m].mltable, params[m].symmetric); // error check on table parameters if (params[m].mltable->ninput <= 1) error->one(FLERR, "Invalid threebody table length"); } } /* ---------------------------------------------------------------------- */ void PairThreebodyTable::setup_params() { int i, j, k, m, n; double rtmp; // set elem3param 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(elem3param); memory->create(elem3param, nelements, nelements, nelements, "pair:elem3param"); 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 a duplicate entry for: {} {} {}", elements[i], elements[j], elements[k]); n = m; } } if (n < 0) error->all(FLERR, "Potential file is missing an entry for: {} {} {}", elements[i], elements[j], elements[k]); elem3param[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) for (m = 0; m < nparams; m++) { rtmp = params[m].cut; params[m].cutsq = rtmp * rtmp; } // 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; } } /* ---------------------------------------------------------------------- read table file, only called by proc 0 ------------------------------------------------------------------------- */ void PairThreebodyTable::read_table(Table *tb, char *file, char *keyword, bool symmetric) { TableFileReader reader(lmp, file, "threebodytable"); char *line = reader.find_section_start(keyword); if (!line) error->one(FLERR, "Did not find keyword in table file"); // read args on 2nd line of section // allocate table arrays for file values line = reader.next_line(); param_extract(tb, line); // if it is a symmetric threebody interaction, less table entries are required if (symmetric) { memory->create(tb->r12file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:r12file"); memory->create(tb->r13file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:r13file"); memory->create(tb->thetafile, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:thetafile"); memory->create(tb->f11file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:f11file"); memory->create(tb->f12file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:f12file"); memory->create(tb->f21file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:f21file"); memory->create(tb->f22file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:f22file"); memory->create(tb->f31file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:f31file"); memory->create(tb->f32file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:f32file"); memory->create(tb->efile, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:efile"); } // else, more (full) table entries are required else { memory->create(tb->r12file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:r12file"); memory->create(tb->r13file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:r13file"); memory->create(tb->thetafile, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:thetafile"); memory->create(tb->f11file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:f11file"); memory->create(tb->f12file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:f12file"); memory->create(tb->f21file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:f21file"); memory->create(tb->f22file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:f22file"); memory->create(tb->f31file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:f31file"); memory->create(tb->f32file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:f32file"); memory->create(tb->efile, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:efile"); } // read threebody table values from file int cerror = 0; reader.skip_line(); // if it is a symmetric threebody interaction, less table entries are required if (symmetric) { for (int i = 0; i < tb->ninput * tb->ninput * (tb->ninput + 1); i++) { line = reader.next_line(11); try { ValueTokenizer values(line); values.next_int(); tb->r12file[i] = values.next_double(); tb->r13file[i] = values.next_double(); tb->thetafile[i] = values.next_double(); tb->f11file[i] = values.next_double(); tb->f12file[i] = values.next_double(); tb->f21file[i] = values.next_double(); tb->f22file[i] = values.next_double(); tb->f31file[i] = values.next_double(); tb->f32file[i] = values.next_double(); tb->efile[i] = values.next_double(); } catch (TokenizerException &) { ++cerror; } } } else { for (int i = 0; i < 2 * tb->ninput * tb->ninput * tb->ninput; i++) { line = reader.next_line(11); try { ValueTokenizer values(line); values.next_int(); tb->r12file[i] = values.next_double(); tb->r13file[i] = values.next_double(); tb->thetafile[i] = values.next_double(); tb->f11file[i] = values.next_double(); tb->f12file[i] = values.next_double(); tb->f21file[i] = values.next_double(); tb->f22file[i] = values.next_double(); tb->f31file[i] = values.next_double(); tb->f32file[i] = values.next_double(); tb->efile[i] = values.next_double(); } catch (TokenizerException &) { ++cerror; } } } // warn if data was read incompletely, e.g. columns were missing if (cerror) error->warning(FLERR, "{} of {} lines in table incomplete or could not be parsed", cerror, tb->ninput); } /* ---------------------------------------------------------------------- extract attributes from parameter line in table section format of line: N value FP fplo fphi EQ theta0 N is required, other params are optional only called by read_table, only called by proc 0 ------------------------------------------------------------------------- */ void PairThreebodyTable::param_extract(Table *tb, char *line) { tb->ninput = 0; tb->rmin = 0.0; tb->rmax = 0.0; try { ValueTokenizer values(line); while (values.has_next()) { std::string word = values.next_string(); if (word == "N") { tb->ninput = values.next_int(); } else if (word == "rmin") { tb->rmin = values.next_double(); } else if (word == "rmax") { tb->rmax = values.next_double(); } else { error->one(FLERR, "Invalid keyword {} in angle table parameters", word); } } } catch (TokenizerException &e) { error->one(FLERR, e.what()); } if (tb->ninput == 0) error->one(FLERR, "threebodytable parameters did not set N"); if (tb->rmin == 0.0) error->one(FLERR, "threebodytable parameters did not set rmin"); if (tb->rmax == 0.0) error->one(FLERR, "threebodytable parameters did not set rmax"); } /* ---------------------------------------------------------------------- broadcast read-in table info from proc 0 to other procs this function communicates these values in Table: ninput,afile,efile,ffile,fpflag,fplo,fphi,theta0 ------------------------------------------------------------------------- */ void PairThreebodyTable::bcast_table(Table *tb, bool symmetric) { MPI_Bcast(&tb->ninput, 1, MPI_INT, 0, world); int me; MPI_Comm_rank(world, &me); if (me > 0) { // if it is a symmetric threebody interaction, less table entries are required if (symmetric) { memory->create(tb->r12file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:r12file"); memory->create(tb->r13file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:r13file"); memory->create(tb->thetafile, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:thetafile"); memory->create(tb->f11file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:f11file"); memory->create(tb->f12file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:f12file"); memory->create(tb->f21file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:f21file"); memory->create(tb->f22file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:f22file"); memory->create(tb->f31file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:f31file"); memory->create(tb->f32file, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:f32file"); memory->create(tb->efile, tb->ninput * tb->ninput * (tb->ninput + 1), "mltable:efile"); } // else, more (full) table entries are required else { memory->create(tb->r12file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:r12file"); memory->create(tb->r13file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:r13file"); memory->create(tb->thetafile, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:thetafile"); memory->create(tb->f11file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:f11file"); memory->create(tb->f12file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:f12file"); memory->create(tb->f21file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:f21file"); memory->create(tb->f22file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:f22file"); memory->create(tb->f31file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:f31file"); memory->create(tb->f32file, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:f32file"); memory->create(tb->efile, 2 * tb->ninput * tb->ninput * tb->ninput, "mltable:efile"); } } // if it is a symmetric threebody interaction, less table entries are required if (symmetric) { MPI_Bcast(tb->r12file, tb->ninput * tb->ninput * (tb->ninput + 1), MPI_DOUBLE, 0, world); MPI_Bcast(tb->r13file, tb->ninput * tb->ninput * (tb->ninput + 1), MPI_DOUBLE, 0, world); MPI_Bcast(tb->thetafile, tb->ninput * tb->ninput * (tb->ninput + 1), MPI_DOUBLE, 0, world); MPI_Bcast(tb->f11file, tb->ninput * tb->ninput * (tb->ninput + 1), MPI_DOUBLE, 0, world); MPI_Bcast(tb->f12file, tb->ninput * tb->ninput * (tb->ninput + 1), MPI_DOUBLE, 0, world); MPI_Bcast(tb->f21file, tb->ninput * tb->ninput * (tb->ninput + 1), MPI_DOUBLE, 0, world); MPI_Bcast(tb->f22file, tb->ninput * tb->ninput * (tb->ninput + 1), MPI_DOUBLE, 0, world); MPI_Bcast(tb->f31file, tb->ninput * tb->ninput * (tb->ninput + 1), MPI_DOUBLE, 0, world); MPI_Bcast(tb->f32file, tb->ninput * tb->ninput * (tb->ninput + 1), MPI_DOUBLE, 0, world); MPI_Bcast(tb->efile, tb->ninput * tb->ninput * (tb->ninput + 1), MPI_DOUBLE, 0, world); } // else, more (full) table entries are required else { MPI_Bcast(tb->r12file, 2 * tb->ninput * tb->ninput * tb->ninput, MPI_DOUBLE, 0, world); MPI_Bcast(tb->r13file, 2 * tb->ninput * tb->ninput * tb->ninput, MPI_DOUBLE, 0, world); MPI_Bcast(tb->thetafile, 2 * tb->ninput * tb->ninput * tb->ninput, MPI_DOUBLE, 0, world); MPI_Bcast(tb->f11file, 2 * tb->ninput * tb->ninput * tb->ninput, MPI_DOUBLE, 0, world); MPI_Bcast(tb->f12file, 2 * tb->ninput * tb->ninput * tb->ninput, MPI_DOUBLE, 0, world); MPI_Bcast(tb->f21file, 2 * tb->ninput * tb->ninput * tb->ninput, MPI_DOUBLE, 0, world); MPI_Bcast(tb->f22file, 2 * tb->ninput * tb->ninput * tb->ninput, MPI_DOUBLE, 0, world); MPI_Bcast(tb->f31file, 2 * tb->ninput * tb->ninput * tb->ninput, MPI_DOUBLE, 0, world); MPI_Bcast(tb->f32file, 2 * tb->ninput * tb->ninput * tb->ninput, MPI_DOUBLE, 0, world); MPI_Bcast(tb->efile, 2 * tb->ninput * tb->ninput * tb->ninput, MPI_DOUBLE, 0, world); } MPI_Bcast(&tb->rmin, 1, MPI_DOUBLE, 0, world); MPI_Bcast(&tb->rmax, 1, MPI_DOUBLE, 0, world); } /* ---------------------------------------------------------------------- */ void PairThreebodyTable::free_param(Param *pm) { // call free_table to destroy associated threebodytables free_table(pm->mltable); // then destroy associated threebodytable delete[] pm->tablename; delete[] pm->keyword; memory->sfree(pm->mltable); } /* ---------------------------------------------------------------------- */ void PairThreebodyTable::free_table(Table *tb) { memory->destroy(tb->r12file); memory->destroy(tb->r13file); memory->destroy(tb->thetafile); memory->destroy(tb->f11file); memory->destroy(tb->f12file); memory->destroy(tb->f21file); memory->destroy(tb->f22file); memory->destroy(tb->f31file); memory->destroy(tb->f32file); memory->destroy(tb->efile); } /* ---------------------------------------------------------------------- */ void PairThreebodyTable::null_table(Table *tb) { tb->r12file = tb->r13file = tb->thetafile = nullptr; tb->f11file = tb->f12file = nullptr; tb->f21file = tb->f22file = nullptr; tb->f31file = tb->f32file = nullptr; tb->efile = nullptr; } /* ---------------------------------------------------------------------- calculate potential u and force f at angle x ------------------------------------------------------------------------- */ void PairThreebodyTable::uf_lookup(Param *pm, double r12, double r13, double theta, double &f11, double &f12, double &f21, double &f22, double &f31, double &f32, double &u) { int i, itable, nr12, nr13, ntheta; double dr, dtheta; dr = (pm->mltable->rmax - pm->mltable->rmin) / (pm->mltable->ninput - 1); dtheta = (180.0 - 0.0) / (pm->mltable->ninput * 2); //lookup scheme // if it is a symmetric threebody interaction, less table entries are required if (pm->symmetric) { nr12 = (r12 - pm->mltable->rmin + 0.5 * dr - 0.00000001) / dr; if (r12 == (pm->mltable->rmin - 0.5 * dr)) nr12 = 0; nr13 = (r13 - pm->mltable->rmin + 0.5 * dr - 0.00000001) / dr; if (r13 == (pm->mltable->rmin - 0.5 * dr)) nr13 = 0; nr13 -= nr12; ntheta = (theta - 0.00000001) / dtheta; if (theta >= 180.0) ntheta = (pm->mltable->ninput * 2) - 1; itable = 0; for (i = 0; i < nr12; i++) itable += (pm->mltable->ninput - i); itable += nr13; itable *= (pm->mltable->ninput * 2); itable += ntheta; } else { // else, more (full) table entries are required nr12 = (r12 - pm->mltable->rmin + 0.5 * dr - 0.00000001) / dr; if (r12 == (pm->mltable->rmin - 0.5 * dr)) nr12 = 0; nr13 = (r13 - pm->mltable->rmin + 0.5 * dr - 0.00000001) / dr; if (r13 == (pm->mltable->rmin - 0.5 * dr)) nr13 = 0; ntheta = (theta - 0.00000001) / dtheta; if (theta >= 180.0) ntheta = (pm->mltable->ninput * 2) - 1; itable = nr12 * (pm->mltable->ninput); itable += nr13; itable *= (pm->mltable->ninput * 2); itable += ntheta; } f11 = pm->mltable->f11file[itable]; f12 = pm->mltable->f12file[itable]; f21 = pm->mltable->f21file[itable]; f22 = pm->mltable->f22file[itable]; f31 = pm->mltable->f31file[itable]; f32 = pm->mltable->f32file[itable]; u = pm->mltable->efile[itable]; } /* ---------------------------------------------------------------------- */ void PairThreebodyTable::threebody(Param *paramijk, double rsq1, double rsq2, double *delr1, double *delr2, double *fi, double *fj, double *fk, int eflag, double &eng) { double r12, r13, theta, rinv, cs; double f11, f12, f21, f22, f31, f32, u, temp; bool swapped; double dr; dr = (paramijk->mltable->rmax - paramijk->mltable->rmin) / (paramijk->mltable->ninput - 1); //if swap indices or not swapped = false; r12 = sqrt(rsq1); r13 = sqrt(rsq2); rinv = 1.0 / (r12 * r13); cs = (delr1[0] * delr2[0] + delr1[1] * delr2[1] + delr1[2] * delr2[2]) * rinv; //compute angle between r12 and r13 in degrees theta = acos(cs) * 180.0 / MY_PI; //if r12 > r13 swap them, as in lookup table always r13 > r12 do to symmetry reasons if (r12 > r13) { temp = r12; r12 = r13; r13 = temp; swapped = true; } //look up forces and energy in table belonging to parameter set paramijk //only do lookup and add three-body interactions if r12 and r13 are both between rmin and rmax if ((r12 >= (paramijk->mltable->rmin - 0.5 * dr)) && (r13 <= (paramijk->mltable->rmax + 0.5 * dr)) && (r13 >= (paramijk->mltable->rmin - 0.5 * dr)) && (r13 <= (paramijk->mltable->rmax + 0.5 * dr))) { uf_lookup(paramijk, r12, r13, theta, f11, f12, f21, f22, f31, f32, u); } else { f11 = f12 = f21 = f22 = f31 = f32 = u = 0.0; } // if the indices have been swapped, swap them back if (swapped) { temp = r12; r12 = r13; r13 = temp; temp = f11; f11 = f12; f12 = temp; temp = f21; f21 = f31; f31 = temp; temp = f22; f22 = -f32; f32 = -temp; } fi[0] = delr1[0] * f11 + delr2[0] * f12; fi[1] = delr1[1] * f11 + delr2[1] * f12; fi[2] = delr1[2] * f11 + delr2[2] * f12; fj[0] = delr1[0] * f21 + (delr2[0] - delr1[0]) * f22; fj[1] = delr1[1] * f21 + (delr2[1] - delr1[1]) * f22; fj[2] = delr1[2] * f21 + (delr2[2] - delr1[2]) * f22; fk[0] = delr2[0] * f31 + (delr2[0] - delr1[0]) * f32; fk[1] = delr2[1] * f31 + (delr2[1] - delr1[1]) * f32; fk[2] = delr2[2] * f31 + (delr2[2] - delr1[2]) * f32; if (eflag) eng = u; }