From 1ae62793ebeb62182452935ca45b6e1586c416f0 Mon Sep 17 00:00:00 2001 From: Christoph Scherer Date: Thu, 26 May 2022 13:12:50 +0200 Subject: [PATCH 01/34] src/MANYBODY/pair_sw.h: made read_file(char *) virtual to allow overriding --- src/MANYBODY/pair_sw.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/MANYBODY/pair_sw.h b/src/MANYBODY/pair_sw.h index 84088926b1..8bae7e5282 100644 --- a/src/MANYBODY/pair_sw.h +++ b/src/MANYBODY/pair_sw.h @@ -55,7 +55,7 @@ class PairSW : public Pair { void settings(int, char **) override; virtual void allocate(); - void read_file(char *); + virtual void read_file(char *); virtual void setup_params(); void twobody(Param *, double, double &, int, double &); virtual void threebody(Param *, Param *, Param *, double, double, double *, double *, double *, From 1cfba3d8bbdd418d06c86a01e955e9d678645ea8 Mon Sep 17 00:00:00 2001 From: Christoph Scherer Date: Thu, 26 May 2022 13:21:47 +0200 Subject: [PATCH 02/34] src/MANYBODY/pair_sw_3b_table.h, src/MANYBODY/pair_sw_3b_table.cpp: added pair style sw/3b/table which is a modification of the SW pair style with tabulated angular potentials --- src/MANYBODY/pair_sw_3b_table.cpp | 783 ++++++++++++++++++++++++++++++ src/MANYBODY/pair_sw_3b_table.h | 127 +++++ 2 files changed, 910 insertions(+) create mode 100644 src/MANYBODY/pair_sw_3b_table.cpp create mode 100644 src/MANYBODY/pair_sw_3b_table.h diff --git a/src/MANYBODY/pair_sw_3b_table.cpp b/src/MANYBODY/pair_sw_3b_table.cpp new file mode 100644 index 0000000000..d9ef723123 --- /dev/null +++ b/src/MANYBODY/pair_sw_3b_table.cpp @@ -0,0 +1,783 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, 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: Christoph Scherer (MPIP Mainz) + scherer@mpip-mainz.mpg.de +------------------------------------------------------------------------- */ + +#include "pair_sw_3b_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 "table_file_reader.h" +#include "potential_file_reader.h" + +#include +#include + + +using namespace LAMMPS_NS; + +using MathConst::DEG2RAD; +using MathConst::MY_PI; +using MathConst::RAD2DEG; + +#define DELTA 4 + +enum { LINEAR, SPLINE }; + +#define SMALL 0.001 +#define TINY 1.E-10 + +/* ---------------------------------------------------------------------- */ + +PairSW3BTable::PairSW3BTable(LAMMPS *lmp) : PairSW(lmp) +{ + single_enable = 0; + restartinfo = 0; + one_coeff = 1; + manybody_flag = 1; + centroidstressflag = CENTROID_NOTAVAIL; + unit_convert_flag = utils::get_supported_conversions(utils::ENERGY); + + params = nullptr; + extended_params = nullptr; + + maxshort = 10; + neighshort = nullptr; +} + +/* ---------------------------------------------------------------------- + check if allocated, since class can be destructed when incomplete +------------------------------------------------------------------------- */ + +PairSW3BTable::~PairSW3BTable() +{ + if (copymode) return; + + for (int m = 0; m < nparams; m++) free_param(&extended_params[m]); // free_param will call free_table + memory->destroy(params); + memory->destroy(extended_params); + memory->destroy(elem3param); + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(neighshort); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairSW3BTable::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 *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; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + 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; + } + + twobody(¶ms[ijparam],rsq,fpair,eflag,evdwl); + + fxtmp += delx*fpair; + fytmp += dely*fpair; + fztmp += delz*fpair; + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,0.0,fpair,delx,dely,delz); + } + + 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]]; + ikparam = elem3param[itype][ktype][ktype]; + 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[ijparam],¶ms[ikparam],¶ms[ijkparam], &extended_params[ijkparam], + rsq1,rsq2,delr1,delr2,fj,fk,eflag,evdwl); + + fxtmp -= fj[0] + fk[0]; + fytmp -= fj[1] + fk[1]; + fztmp -= fj[2] + fk[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 PairSW3BTable::read_file(char *file) +{ + memory->sfree(params); + params = nullptr; + memory->sfree(extended_params); + extended_params = nullptr; + nparams = maxparam = 0; + + // open file on proc 0 + + if (comm->me == 0) { + PotentialFileReader reader(lmp, file, "sw", unit_convert_flag); + char *line; + + // transparently convert units for supported conversions + + int unit_convert = reader.get_unit_convert(); + double conversion_factor = utils::get_conversion_factor(utils::ENERGY, + unit_convert); + + 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"); + extended_params = (Param_Extension *) memory->srealloc(extended_params,maxparam*sizeof(Param_Extension), + "pair:extended_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; + params[nparams].epsilon = values.next_double(); + params[nparams].sigma = values.next_double(); + params[nparams].littlea = values.next_double(); + params[nparams].lambda = values.next_double(); + params[nparams].gamma = values.next_double(); + params[nparams].costheta = values.next_double(); + params[nparams].biga = values.next_double(); + params[nparams].bigb = values.next_double(); + params[nparams].powerp = values.next_double(); + params[nparams].powerq = values.next_double(); + params[nparams].tol = values.next_double(); + + // read parameters of angle table + std::string tablename_string = values.next_string(); + extended_params[nparams].tablenamelength = tablename_string.length()+1; + memory->create(extended_params[nparams].tablename, extended_params[nparams].tablenamelength, "extended_params.tablename"); + for (int x = 0; x < extended_params[nparams].tablenamelength; ++x) { + extended_params[nparams].tablename[x] = tablename_string[x]; + } + std::string keyword_string = values.next_string(); + extended_params[nparams].keywordlength = keyword_string.length()+1; + memory->create(extended_params[nparams].keyword, extended_params[nparams].keywordlength, "extended_params.keyword"); + for (int x = 0; x < extended_params[nparams].keywordlength; ++x) { + extended_params[nparams].keyword[x] = keyword_string[x]; + } + std::string tablestyle_string = values.next_string(); + char *tablestyle; + memory->create(tablestyle, (tablestyle_string.length()+1), "tablestyle"); + for (int x = 0; x < (tablestyle_string.length()+1); ++x) { + tablestyle[x] = tablestyle_string[x]; + } + if (strcmp(tablestyle,"linear") == 0) extended_params[nparams].tabstyle = LINEAR; + else if (strcmp(tablestyle,"spline") == 0) extended_params[nparams].tabstyle = SPLINE; + else error->all(FLERR,"Unknown table style of angle table file"); + extended_params[nparams].tablength = values.next_int(); + + } catch (TokenizerException &e) { + error->one(FLERR, e.what()); + } + + if (unit_convert) { + params[nparams].epsilon *= conversion_factor; + } + + if (params[nparams].epsilon < 0.0 || params[nparams].sigma < 0.0 || + params[nparams].littlea < 0.0 || params[nparams].lambda < 0.0 || + params[nparams].gamma < 0.0 || params[nparams].biga < 0.0 || + params[nparams].bigb < 0.0 || params[nparams].powerp < 0.0 || + params[nparams].powerq < 0.0 || params[nparams].tol < 0.0 || + extended_params[nparams].tabstyle < 0.0 || extended_params[nparams].tablength < 0.0) + error->one(FLERR,"Illegal Stillinger-Weber parameter"); + + 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"); + extended_params = (Param_Extension *) memory->srealloc(extended_params,maxparam*sizeof(Param_Extension), "pair:extended_params"); + } + + MPI_Bcast(params, maxparam*sizeof(Param), MPI_BYTE, 0, world); + MPI_Bcast(extended_params, maxparam*sizeof(Param_Extension), MPI_BYTE, 0, world); + + // for each set of parameters, broadcast table name and keyword and read angle table + for (int m = 0; m < nparams; ++m){ + if (comm->me != 0) { + memory->create(extended_params[m].tablename, extended_params[m].tablenamelength, "extended_params.tablename"); + } + MPI_Bcast(&extended_params[m].tablename, extended_params[m].tablenamelength, MPI_CHAR, 0, world); + if (comm->me != 0) { + memory->create(extended_params[m].keyword, extended_params[m].keywordlength, "extended_params.keyword"); + } + MPI_Bcast(&extended_params[m].keyword, extended_params[m].keywordlength, MPI_CHAR, 0, world); + + // initialize angtable + memory->create(extended_params[m].angtable,1,"extended_params:angtable"); + null_table(extended_params[m].angtable); + + // call read_table to read corresponding tabulated angle file (only called by process 0) + if (comm->me == 0) read_table(extended_params[m].angtable,extended_params[m].tablename,extended_params[m].keyword); + + // broadcast read in angtable to all processes + bcast_table(extended_params[m].angtable); + + // the following table manipulations are done in all processes + // error check on table parameters + if (extended_params[m].angtable->ninput <= 1) error->one(FLERR,"Invalid angle table length"); + + // error check on parameter range of angle table + double alo,ahi; + alo = extended_params[m].angtable->afile[0]; + ahi = extended_params[m].angtable->afile[extended_params[m].angtable->ninput-1]; + if (fabs(alo-0.0) > TINY || fabs(ahi-180.0) > TINY) + error->all(FLERR,"Angle table must range from 0 to 180 degrees"); + + // convert theta from degrees to radians + for (int i = 0; i < extended_params[m].angtable->ninput; ++i){ + extended_params[m].angtable->afile[i] *= MY_PI/180.0; + extended_params[m].angtable->ffile[i] *= 180.0/MY_PI; + } + + // spline read-in table and compute a,e,f vectors within table + spline_table(extended_params[m].angtable); + // compute_table needs parameter params[m].length for this specific interaction as + // read in value length from .sw file can be different from value in angle table file + compute_table(extended_params[m].angtable,extended_params[m].tablength); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairSW3BTable::threebody(Param *paramij, Param *paramik, Param *paramijk, Param_Extension *extended_paramijk, + double rsq1, double rsq2, + double *delr1, double *delr2, + double *fj, double *fk, int eflag, double &eng) +{ + double r1,rinvsq1,rainv1,gsrainv1,gsrainvsq1,expgsrainv1; + double r2,rinvsq2,rainv2,gsrainv2,gsrainvsq2,expgsrainv2; + double rinv12,cs,facexp; + double ftheta,facradtable,frad1table,frad2table,var; + double acosprime,gradj1,gradj2,gradk1,gradk2,fprimetheta; + + r1 = sqrt(rsq1); + rinvsq1 = 1.0/rsq1; + rainv1 = 1.0/(r1 - paramij->cut); + gsrainv1 = paramij->sigma_gamma * rainv1; + gsrainvsq1 = gsrainv1*rainv1/r1; + expgsrainv1 = exp(gsrainv1); + + r2 = sqrt(rsq2); + rinvsq2 = 1.0/rsq2; + rainv2 = 1.0/(r2 - paramik->cut); + gsrainv2 = paramik->sigma_gamma * rainv2; + gsrainvsq2 = gsrainv2*rainv2/r2; + expgsrainv2 = exp(gsrainv2); + + facexp = expgsrainv1*expgsrainv2; + + rinv12 = 1.0/(r1*r2); + cs = (delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2]) * rinv12; + + var = acos(cs); + + // look up energy (f(theta), ftheta) and force (df(theta)/dtheta, fprimetheta) at + // angle theta (var) in angle table belonging to parameter set paramijk + uf_lookup(extended_paramijk, var, ftheta, fprimetheta); + + acosprime = 1.0 / (sqrt(1 - cs*cs ) ); + + facradtable = facexp*ftheta; + frad1table = facradtable*gsrainvsq1; + frad2table = facradtable*gsrainvsq2; + gradj1 = acosprime * cs * rinvsq1 * facexp * fprimetheta; + gradj2 = acosprime * rinv12 * facexp * fprimetheta; + gradk1 = acosprime * cs * rinvsq2 * facexp * fprimetheta; + gradk2 = acosprime * rinv12 * facexp * fprimetheta; + + fj[0] = delr1[0]*(frad1table+gradj1)-delr2[0]*gradj2; + fj[1] = delr1[1]*(frad1table+gradj1)-delr2[1]*gradj2; + fj[2] = delr1[2]*(frad1table+gradj1)-delr2[2]*gradj2; + + fk[0] = delr2[0]*(frad2table+gradk1)-delr1[0]*gradk2; + fk[1] = delr2[1]*(frad2table+gradk1)-delr1[1]*gradk2; + fk[2] = delr2[2]*(frad2table+gradk1)-delr1[2]*gradk2; + + if (eflag) eng = facradtable; +} + +/* ---------------------------------------------------------------------- + read table file, only called by proc 0 +------------------------------------------------------------------------- */ + +void PairSW3BTable::read_table(Table *tb, char *file, char *keyword) +{ + TableFileReader reader(lmp, file, "angle"); + + 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); + memory->create(tb->afile, tb->ninput, "angle:afile"); + memory->create(tb->efile, tb->ninput, "angle:efile"); + memory->create(tb->ffile, tb->ninput, "angle:ffile"); + + // read a,e,f table values from file + + int cerror = 0; + reader.skip_line(); + for (int i = 0; i < tb->ninput; i++) { + line = reader.next_line(4); + try { + ValueTokenizer values(line); + values.next_int(); + tb->afile[i] = values.next_double(); + tb->efile[i] = values.next_double(); + tb->ffile[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); +} + +/* ---------------------------------------------------------------------- + build spline representation of e,f over entire range of read-in table + this function sets these values in e2file,f2file +------------------------------------------------------------------------- */ + +void PairSW3BTable::spline_table(Table *tb) +{ + memory->create(tb->e2file, tb->ninput, "angle:e2file"); + memory->create(tb->f2file, tb->ninput, "angle:f2file"); + + double ep0 = -tb->ffile[0]; + double epn = -tb->ffile[tb->ninput - 1]; + spline(tb->afile, tb->efile, tb->ninput, ep0, epn, tb->e2file); + + if (tb->fpflag == 0) { + tb->fplo = (tb->ffile[1] - tb->ffile[0]) / (tb->afile[1] - tb->afile[0]); + tb->fphi = (tb->ffile[tb->ninput - 1] - tb->ffile[tb->ninput - 2]) / + (tb->afile[tb->ninput - 1] - tb->afile[tb->ninput - 2]); + } + + double fp0 = tb->fplo; + double fpn = tb->fphi; + spline(tb->afile, tb->ffile, tb->ninput, fp0, fpn, tb->f2file); +} + +/* ---------------------------------------------------------------------- + compute a,e,f vectors from splined values +------------------------------------------------------------------------- */ + +void PairSW3BTable::compute_table(Table *tb,int length) +{ + // delta = table spacing in angle for N-1 bins + + int tlm1 = length - 1; + tb->delta = MY_PI / tlm1; + tb->invdelta = 1.0 / tb->delta; + tb->deltasq6 = tb->delta * tb->delta / 6.0; + + // N-1 evenly spaced bins in angle from 0 to PI + // ang,e,f = value at lower edge of bin + // de,df values = delta values of e,f + // ang,e,f are N in length so de,df arrays can compute difference + + memory->create(tb->ang, length, "angle:ang"); + memory->create(tb->e, length, "angle:e"); + memory->create(tb->de, length, "angle:de"); + memory->create(tb->f, length, "angle:f"); + memory->create(tb->df, length, "angle:df"); + memory->create(tb->e2, length, "angle:e2"); + memory->create(tb->f2, length, "angle:f2"); + + double a; + for (int i = 0; i < length; i++) { + a = i * tb->delta; + tb->ang[i] = a; + tb->e[i] = splint(tb->afile, tb->efile, tb->e2file, tb->ninput, a); + tb->f[i] = splint(tb->afile, tb->ffile, tb->f2file, tb->ninput, a); + } + + 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]; + } + // get final elements from linear extrapolation + tb->de[tlm1] = 2.0 * tb->de[tlm1 - 1] - tb->de[tlm1 - 2]; + tb->df[tlm1] = 2.0 * tb->df[tlm1 - 1] - tb->df[tlm1 - 2]; + + double ep0 = -tb->f[0]; + double epn = -tb->f[tlm1]; + spline(tb->ang, tb->e, length, ep0, epn, tb->e2); + spline(tb->ang, tb->f, length, tb->fplo, tb->fphi, tb->f2); +} + +/* ---------------------------------------------------------------------- + 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 PairSW3BTable::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->afile, tb->ninput, "angle:afile"); + memory->create(tb->efile, tb->ninput, "angle:efile"); + memory->create(tb->ffile, tb->ninput, "angle:ffile"); + } + + MPI_Bcast(tb->afile, 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->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); + } + MPI_Bcast(&tb->theta0, 1, MPI_DOUBLE, 0, world); +} + +/* ---------------------------------------------------------------------- */ + +void PairSW3BTable::null_table(Table *tb) +{ + tb->afile = tb->efile = tb->ffile = nullptr; + tb->e2file = tb->f2file = nullptr; + tb->ang = tb->e = tb->de = nullptr; + tb->f = tb->df = tb->e2 = tb->f2 = nullptr; +} + +/* ---------------------------------------------------------------------- */ + +void PairSW3BTable::free_table(Table *tb) +{ + memory->destroy(tb->afile); + memory->destroy(tb->efile); + memory->destroy(tb->ffile); + memory->destroy(tb->e2file); + memory->destroy(tb->f2file); + + memory->destroy(tb->ang); + memory->destroy(tb->e); + memory->destroy(tb->de); + memory->destroy(tb->f); + memory->destroy(tb->df); + memory->destroy(tb->e2); + memory->destroy(tb->f2); +} + +/* ---------------------------------------------------------------------- */ + +void PairSW3BTable::free_param(Param_Extension *pm) +{ + // call free_table to destroy associated angle table + free_table(pm->angtable); + // then destroy associated angle table + memory->sfree(pm->angtable); +} + +/* ---------------------------------------------------------------------- + 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 PairSW3BTable::param_extract(Table *tb, char *line) +{ + tb->ninput = 0; + tb->fpflag = 0; + tb->theta0 = MY_PI; + + 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 == "FP") { + tb->fpflag = 1; + tb->fplo = values.next_double(); + tb->fphi = values.next_double(); + tb->fplo *= RAD2DEG * RAD2DEG; + tb->fphi *= RAD2DEG * RAD2DEG; + } else if (word == "EQ") { + tb->theta0 = DEG2RAD * values.next_double(); + } else { + error->one(FLERR, "Invalid keyword in angle table parameters"); + } + } + } catch (TokenizerException &e) { + error->one(FLERR, e.what()); + } + + if (tb->ninput == 0) error->one(FLERR, "Angle table parameters did not set N"); +} + +/* ---------------------------------------------------------------------- + spline and splint routines modified from Numerical Recipes +------------------------------------------------------------------------- */ + +void PairSW3BTable::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 > 0.99e300) + 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 > 0.99e300) + 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 PairSW3BTable::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; +} + +/* ---------------------------------------------------------------------- + calculate potential u and force f at angle x +------------------------------------------------------------------------- */ + +void PairSW3BTable::uf_lookup(Param_Extension *pm, double x, double &u, double &f) +{ + if (!std::isfinite(x)) { error->one(FLERR, "Illegal angle in angle style table"); } + + double fraction,a,b; + + // invdelta is based on tablength-1 + int itable = static_cast(x * pm->angtable->invdelta); + if (itable < 0) itable = 0; + if (itable >= pm->tablength) itable = pm->tablength - 1; + + if (pm->tabstyle == LINEAR) { + fraction = (x - pm->angtable->ang[itable]) * pm->angtable->invdelta; + u = pm->angtable->e[itable] + fraction*pm->angtable->de[itable]; + f = pm->angtable->f[itable] + fraction*pm->angtable->df[itable]; + } else if (pm->tabstyle == SPLINE) { + fraction = (x - pm->angtable->ang[itable]) * pm->angtable->invdelta; + + b = (x - pm->angtable->ang[itable]) * pm->angtable->invdelta; + a = 1.0 - b; + u = a * pm->angtable->e[itable] + b * pm->angtable->e[itable+1] + + ((a * a * a - a) * pm->angtable->e2[itable] + (b * b * b - b) * pm->angtable->e2[itable+1]) * + pm->angtable->deltasq6; + f = a * pm->angtable->f[itable] + b * pm->angtable->f[itable+1] + + ((a * a * a - a) * pm->angtable->f2[itable] + (b * b * b - b) * pm->angtable->f2[itable+1]) * + pm->angtable->deltasq6; + } +} diff --git a/src/MANYBODY/pair_sw_3b_table.h b/src/MANYBODY/pair_sw_3b_table.h new file mode 100644 index 0000000000..3f537d432c --- /dev/null +++ b/src/MANYBODY/pair_sw_3b_table.h @@ -0,0 +1,127 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, 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 +// clang-format off +PairStyle(sw/3b/table,PairSW3BTable); +// clang-format on +#else + +#ifndef LMP_PAIR_SW_3B_TABLE_H +#define LMP_PAIR_SW_3B_TABLE_H + +#include "pair_sw.h" + +namespace LAMMPS_NS { + +class PairSW3BTable : public PairSW { + public: + PairSW3BTable(class LAMMPS *); + ~PairSW3BTable() override; + void compute(int, int) override; + + static constexpr int NPARAMS_PER_LINE = 18; + + // use struct Table from class AngleTable + struct Table { + int ninput, fpflag; + double fplo, fphi, theta0; + double *afile, *efile, *ffile; + double *e2file, *f2file; + double delta, invdelta, deltasq6; + double *ang, *e, *de, *f, *df, *e2, *f2; + }; + + struct Param_Extension { + int tablenamelength; // length of table name + char *tablename; // name of associated angular table + int keywordlength; // length of key in table + char *keyword; // key in table + int tabstyle,tablength; // length of interpolation table (not ninput) and style + Table *angtable; // angle table + }; + + protected: + Param_Extension *extended_params; // parameter set for an I-J-K interaction + + void read_file(char *) override; + void threebody(Param *, Param *, Param *, Param_Extension*, double, double, double *, double *, double *, + double *, int, double &); + + void read_table(Table *, char *, char *); + void spline_table(Table *); + void compute_table(Table *,int length); + void bcast_table(Table *); + void null_table(Table *); + void free_table(Table *); + void free_param(Param_Extension *); + void param_extract(Table *, char *); + void spline(double *, double *, int, double, double, double *); + double splint(double *, double *, double *, int, double); + void uf_lookup(Param_Extension *, double, double &, double &); +}; + +} // namespace LAMMPS_NS + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair style Stillinger-Weber requires atom IDs + +This is a requirement to use the SW potential. + +E: Pair style Stillinger-Weber requires newton pair on + +See the newton command. This is a restriction to use the SW +potential. + +E: All pair coeffs are not set + +All pair coefficients must be set in the data file or by the +pair_coeff command before running a simulation. + +E: Cannot open Stillinger-Weber potential file %s + +The specified SW potential file cannot be opened. Check that the path +and name are correct. + +E: Incorrect format in Stillinger-Weber potential file + +Incorrect number of words per line in the potential file. + +E: Illegal Stillinger-Weber parameter + +One or more of the coefficients defined in the potential file is +invalid. + +E: Potential file has duplicate entry + +The potential file has more than one entry for the same element. + +E: Potential file is missing an entry + +The potential file does not have a needed entry. + +*/ From 0e114b10415ffd682937c91bb91c412ac7c3e9f6 Mon Sep 17 00:00:00 2001 From: Christoph Scherer Date: Thu, 26 May 2022 13:35:40 +0200 Subject: [PATCH 03/34] doc/src/pair_sw_3b_table.rst: documentation for added pair style sw/3b/table --- doc/src/pair_sw_3b_table.rst | 309 +++++++++++++++++++++++++++++++++++ 1 file changed, 309 insertions(+) create mode 100644 doc/src/pair_sw_3b_table.rst diff --git a/doc/src/pair_sw_3b_table.rst b/doc/src/pair_sw_3b_table.rst new file mode 100644 index 0000000000..6ee13eb095 --- /dev/null +++ b/doc/src/pair_sw_3b_table.rst @@ -0,0 +1,309 @@ +.. index:: pair_style sw_table + +pair_style sw/3b/table command +=========================== + +Syntax +"""""" + +.. code-block:: LAMMPS + + pair_style style + +* style = *sw/3b/table* + + +Examples +"""""""" + +.. code-block:: LAMMPS + + pair_style sw/3b/table + pair_coeff * * spce.sw type + pair_coeff * * GaN.sw Ga N Ga + + +Description +""""""""""" + +The *sw/3b/table* style is a modification of the original :doc:`pair_style sw `. It has been +developed for coarse-grained simulations (of water) (:ref:`Scherer1 `), +but can be employed for all kinds of systems. It computes a modified 3-body :ref:`Stillinger-Weber ` +potential for the energy E of a system of atoms as + +.. math:: + + E & = \sum_i \sum_{j > i} \phi_2 (r_{ij}) + + \sum_i \sum_{j \neq i} \sum_{k > j} + \phi_3 (r_{ij}, r_{ik}, \theta_{ijk}) \\ + \phi_2(r_{ij}) & = A_{ij} \epsilon_{ij} \left[ B_{ij} (\frac{\sigma_{ij}}{r_{ij}})^{p_{ij}} - + (\frac{\sigma_{ij}}{r_{ij}})^{q_{ij}} \right] + \exp \left( \frac{\sigma_{ij}}{r_{ij} - a_{ij} \sigma_{ij}} \right) \\ + \phi_3(r_{ij},r_{ik},\theta_{ijk}) & = f^{\textrm{3b}}\left(\theta_{ijk}\right) + \exp \left( \frac{\gamma_{ij} \sigma_{ij}}{r_{ij} - a_{ij} \sigma_{ij}} \right) + \exp \left( \frac{\gamma_{ik} \sigma_{ik}}{r_{ik} - a_{ik} \sigma_{ik}} \right) + +where :math:`\phi_2` is a two-body term and :math:`\phi_3` is a +three-body term. The summations in the formula are over all neighbors J +and K of atom I within a cutoff distance :math:`a \sigma`. +In contrast to the original *sw* style, *sw/3b/table* allows for a flexible +three-body term :math:`f^{\textrm{3b}}\left(\theta_{ijk}\right)` which is read in +as a tabulated interaction. It can be parametrized with the csg_fmatch app of VOTCA +as available at: . + +Only a single pair_coeff command is used with the *sw/3b/table* style +which specifies a modified Stillinger-Weber potential file with parameters for all +needed elements. These are mapped to LAMMPS atom types by specifying +N_el additional arguments after the ".sw" filename in the pair_coeff command, +where N_el is the number of LAMMPS atom types: + +* ".sw" filename +* N_el element names = mapping of SW elements to atom types + +See the :doc:`pair_coeff ` page for alternate ways +to specify the path for the potential file. + +As an example, imagine a file SiC.sw has Stillinger-Weber values for +Si and C. If your LAMMPS simulation has 4 atoms types and you want +the first 3 to be Si, and the fourth to be C, you would use the following +pair_coeff command: + +.. code-block:: LAMMPS + + pair_coeff * * SiC.sw Si Si Si C + +The first 2 arguments must be \* \* so as to span all LAMMPS atom types. +The first three Si arguments map LAMMPS atom types 1,2,3 to the Si +element in the SW file. The final C argument maps LAMMPS atom type 4 +to the C element in the SW file. If a mapping value is specified as +NULL, the mapping is not performed. This can be used when a *sw/3b/table* +potential is used as part of the *hybrid* pair style. The NULL values +are placeholders for atom types that will be used with other +potentials. + +The (modified) Stillinger-Weber files have a ".sw" suffix. Lines that are not blank or +comments (starting with #) define parameters for a triplet of +elements. The parameters in a single entry correspond to the two-body +and three-body coefficients in the formula above. Here, also the suffix +".sw" is used though the original Stillinger-Weber file format is supplemented +with four additional lines per parameter block to specify the tabulated +three-body interaction. A single entry then contains: + +* element 1 (the center atom in a 3-body interaction) +* element 2 +* element 3 +* :math:`\epsilon` (energy units) +* :math:`\sigma` (distance units) +* a +* :math:`\lambda` +* :math:`\gamma` +* :math:`\cos\theta_0` +* A +* B +* p +* q +* tol +* filename +* keyword +* style +* N + +The A, B, p, and q parameters are used only for two-body interactions. +The :math:`\lambda` and :math:`\cos\theta_0` parameters, only used +for three-body interactions in the original Stillinger-Weber style, are read +in but ignored in this modified pair style. The :math:`\epsilon` parameter is only used +for two-body interactions in this modified pair style and not for the three-body +terms. The :math:`\sigma` and *a* parameters are used for both two-body and three-body +interactions. :math:`\gamma` is used only in the three-body +interactions, but is defined for pairs of atoms. The non-annotated +parameters are unitless. + +LAMMPS introduces an additional performance-optimization parameter tol +that is used for both two-body and three-body interactions. In the +Stillinger-Weber potential, the interaction energies become negligibly +small at atomic separations substantially less than the theoretical +cutoff distances. LAMMPS therefore defines a virtual cutoff distance +based on a user defined tolerance tol. The use of the virtual cutoff +distance in constructing atom neighbor lists can significantly reduce +the neighbor list sizes and therefore the computational cost. LAMMPS +provides a *tol* value for each of the three-body entries so that they +can be separately controlled. If tol = 0.0, then the standard +Stillinger-Weber cutoff is used. + +The additional parameters *filename*, *keyword*, *style*, and *N* refer to +the tabulated angular potential :math:`f^{\textrm{3b}}\left(\theta_{ijk}\right)`. +The tabulated angular potential has to be of the format as used in the +:doc:`angle_style table ` command: + +An interpolation tables of length *N* is created. The +interpolation is done in one of 2 *styles*: *linear* or *spline*. +For the *linear* style, the angle is used to find 2 surrounding table +values from which an energy or its derivative is computed by linear +interpolation. For the *spline* style, a cubic spline coefficients are computed and +stored at each of the *N* values in the table. The angle is used to +find the appropriate set of coefficients which are used to evaluate a +cubic polynomial which computes the energy or derivative. + +The *filename* specifies the file containing the tabulated energy and +derivative values of :math:`f^{\textrm{3b}}\left(\theta_{ijk}\right)`. +The *keyword* then specifies a section of the file. The +format of this file is as follows (without the +parenthesized comments): + +.. parsed-literal:: + + # Angle potential for harmonic (one or more comment or blank lines) + + HAM (keyword is the first text on line) + N 181 FP 0 0 EQ 90.0 (N, FP, EQ parameters) + (blank line) + 1 0.0 200.5 2.5 (index, angle, energy, derivative) + 2 1.0 198.0 2.5 + ... + 181 180.0 0.0 0.0 + +A section begins with a non-blank line whose first character is not a +"#"; blank lines or lines starting with "#" can be used as comments +between sections. The first line begins with a keyword which +identifies the section. The next line lists (in any +order) one or more parameters for the table. Each parameter is a +keyword followed by one or more numeric values. + +The parameter "N" is required and its value is the number of table +entries that follow. Note that this may be different than the *N* +specified in the Stillinger-Weber potential file. Let +Nsw = *N* in the ".sw" file, and Nfile = "N" in the +tabulated angular file. What LAMMPS does is a preliminary interpolation by +creating splines using the Nfile tabulated values as nodal points. It +uses these to interpolate as needed to generate energy and derivative +values at Ntable different points. The resulting tables of length +Nsw are then used as described above, when computing energy and +force for individual angles and their atoms. This means that if you +want the interpolation tables of length Nsw to match exactly what +is in the tabulated file (with effectively no preliminary +interpolation), you should set Nsw = Nfile. + +The "FP" parameter is optional. If used, it is followed by two values +fplo and fphi, which are the second derivatives at the innermost and +outermost angle settings. These values are needed by the spline +construction routines. If not specified by the "FP" parameter, they +are estimated (less accurately) by the first two and last two +derivative values in the table. + +The "EQ" parameter is also optional. If used, it is followed by a the +equilibrium angle value, which is used, for example, by the :doc:`fix shake ` command. If not used, the equilibrium angle is +set to 180.0. + +Following a blank line, the next N lines of the angular table file list the tabulated values. +On each line, the first value is the index from 1 to N, the second value is +the angle value (in degrees), the third value is the energy (in energy +units), and the fourth is -dE/d(theta) (also in energy units). The third +term is the energy of the 3-atom configuration for the specified +angle. The last term is the derivative of the energy with respect to +the angle (in degrees, not radians). Thus the units of the last term +are still energy, not force. The angle values must increase from one +line to the next. The angle values must also begin with 0.0 and end +with 180.0, i.e. span the full range of possible angles. + +Note that one angular potential file can contain many sections, each with a tabulated +potential. LAMMPS reads the file section by section until it finds +one that matches the specified *keyword* of appropriate section of the ".sw" file. + +The Stillinger-Weber potential file must contain entries for all the +elements listed in the pair_coeff command. It can also contain +entries for additional elements not being used in a particular +simulation; LAMMPS ignores those entries. + +For a single-element simulation, only a single entry is required +(e.g. SiSiSi). For a two-element simulation, the file must contain 8 +entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that +specify SW parameters for all permutations of the two elements +interacting in three-body configurations. Thus for 3 elements, 27 +entries would be required, etc. + +As annotated above, the first element in the entry is the center atom +in a three-body interaction. Thus an entry for SiCC means a Si atom +with 2 C atoms as neighbors. The parameter values used for the +two-body interaction come from the entry where the second and third +elements are the same. Thus the two-body parameters for Si +interacting with C, comes from the SiCC entry. The three-body +angular potential :math:`f^{\textrm{3b}}\left(\theta_{ijk}\right)` +can in principle be specific to the three elements of the +configuration. However, the user must ensure that it makes physically sense. +Note also that the function :math:`\phi_3` contains two exponential +screening factors with parameter values from the ij pair and ik +pairs. So :math:`\phi_3` for a C atom bonded to a Si atom and a second C atom +will depend on the three-body parameters for the CSiC entry, and also +on the two-body parameters for the CCC and CSiSi entries. Since the +order of the two neighbors is arbitrary, the three-body parameters +and the tabulated angular potential for +entries CSiC and CCSi should be the same. Similarly, the two-body +parameters for entries SiCC and CSiSi should also be the same. The +parameters used only for two-body interactions (A, B, p, and q) in +entries whose second and third element are different (e.g. SiCSi) are not +used for anything and can be set to 0.0 if desired. +This is also true for the parameters in :math:`\phi_3` that are +taken from the ij and ik pairs (:math:`\sigma`, *a*, :math:`\gamma`) + +---------- + +.. include:: accel_styles.rst + +.. note:: + + When using the INTEL package with this style, there is an additional + 5 to 10 percent performance improvement when the Stillinger-Weber + parameters p and q are set to 4 and 0 respectively. These + parameters are common for modeling silicon and water. + +---------- + +Mixing, shift, table, tail correction, restart, rRESPA info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +For atom type pairs I,J and I != J, where types I and J correspond to +two different element types, mixing is performed by LAMMPS as +described above from values in the potential file, but not for the +tabulated angular potential file. + +This pair style does not support the :doc:`pair_modify ` +shift, table, and tail options. + +This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. +Thus, you need to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file. + +This pair style can only be used via the *pair* keyword of the +:doc:`run_style respa ` command. It does not support the +*inner*, *middle*, *outer* keywords. + +---------- + +Restrictions +"""""""""""" + +This is a user pair style. For more information, see :ref:`Scherer1 `. It is only enabled +if LAMMPS was explicitly built with it. + +This pair style requires the :doc:`newton ` setting to be "on" +for pair interactions. + +For an example of an extended Stillinger-Weber potential file, have a look at the tutorial +in the tutorial folder. + +Related commands +"""""""""""""""" + +:doc:`pair_coeff ` + + +---------- + +.. _Stillinger2: + +**(Stillinger)** Stillinger and Weber, Phys Rev B, 31, 5262 (1985). + +.. _Scherer1: + +**(Scherer1)** C. Scherer and D. Andrienko, Phys. Chem. Chem. Phys. 20, 22387-22394 (2018). + From 770454cb8b0f39d718e04ead699a7d8f5328fb29 Mon Sep 17 00:00:00 2001 From: Christoph Scherer Date: Thu, 26 May 2022 14:00:06 +0200 Subject: [PATCH 04/34] examples/PACKAGES/pair_sw_3b_table: added example for new pair style sw/3b/table --- examples/PACKAGES/pair_sw_3b_table/README | 41 + examples/PACKAGES/pair_sw_3b_table/run.sh | 5 + examples/PACKAGES/pair_sw_3b_table/spce.data | 1015 ++++++++++++++ examples/PACKAGES/pair_sw_3b_table/spce.in | 45 + examples/PACKAGES/pair_sw_3b_table/spce.sw | 18 + .../PACKAGES/pair_sw_3b_table/table_CG_CG.txt | 1203 +++++++++++++++++ .../pair_sw_3b_table/table_CG_CG_CG.txt | 1004 ++++++++++++++ 7 files changed, 3331 insertions(+) create mode 100644 examples/PACKAGES/pair_sw_3b_table/README create mode 100755 examples/PACKAGES/pair_sw_3b_table/run.sh create mode 100644 examples/PACKAGES/pair_sw_3b_table/spce.data create mode 100644 examples/PACKAGES/pair_sw_3b_table/spce.in create mode 100644 examples/PACKAGES/pair_sw_3b_table/spce.sw create mode 100644 examples/PACKAGES/pair_sw_3b_table/table_CG_CG.txt create mode 100644 examples/PACKAGES/pair_sw_3b_table/table_CG_CG_CG.txt diff --git a/examples/PACKAGES/pair_sw_3b_table/README b/examples/PACKAGES/pair_sw_3b_table/README new file mode 100644 index 0000000000..9d158bf392 --- /dev/null +++ b/examples/PACKAGES/pair_sw_3b_table/README @@ -0,0 +1,41 @@ +Example for pair style sw/table +================================ + +This example contains all required input files for the simulation of CG SPC/E water with +the user pair style sw/table, as well as a run.sh script. + +To run the example, you have to compile LAMMPS with the MANYBODY package, including pair_sw_3b_table.h and pair_sw_3b_table.h. + +Running the simulation, you will reproduce results of the following publication: + +C. Scherer, and D. Andrienko, Understanding three-body contributions to coarse-grained force fields, Phys. Chem. Chem. Phys, 20(34):22387–22394, 2018, http://xlink.rsc.org/?DOI=C8CP00746B + +Here, a water molecule is represented by one coarse-grained (CG) bead. The +two-body (table_CG_CG.txt) and three-body angular (table_CG_CG_CG.txt) interaction potentials +have been parametrized with force-matching (FM) with the VOTCA package (https://gitlab.mpcdf.mpg.de/votca/votca). +For more details, have a look at the publication. For a example on the parametrization, have a look at +https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/guide and +https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/spce/3body_sw. + +The folder contains the LAMMPS data file (spce.data) with the starting configuration +of 1000 CG water molecules, an input file (spce.in) and a (modified) Stillinger-Weber file (spce.sw). + +The lammps input file contains the lines specifying the pair style and coefficients: + +- pair_style hybrid/overlay table linear 1200 sw/3b/table - use a combination of pair_style table with 1200 linear table entries and the pair_style sw/3b/table +- pair_coeff 1 1 table table_CG_CG.txt VOTCA - set the table name and keyword for the pair_style table +- pair_coeff * * sw/3b/table spce.sw type - set the name of the Stillinger-Weber file for the pair_style sw/3b/table + +A hybrid pair style is used, where pair forces are calculated as a tabulated interaction (table_CG_CG.txt) and the +pair style sw/table is only used to calculate the three-body forces. Therefore, in the Stillinger-Weber file all +parameters refering to two-body interactions are set to zero. As explained in the documentation of this pair +style, the .sw file contains the +additional lines refering to the tabulated angular potential: + +- table_CG_CG_CG.txt - file name of tabulated angular potential +- VOTCA - keyword for tabulated angular potential +- linear - angular table is of linear style +- 1001 - 1001 table entries + +The LAMMPS simulation is a standard nvt simulation. A dump file is output with the positions and forces every 10 time steps. +You can calculate the pair distribution and compare it to the one(s) in the publicattion. diff --git a/examples/PACKAGES/pair_sw_3b_table/run.sh b/examples/PACKAGES/pair_sw_3b_table/run.sh new file mode 100755 index 0000000000..8f64855b13 --- /dev/null +++ b/examples/PACKAGES/pair_sw_3b_table/run.sh @@ -0,0 +1,5 @@ +#! /bin/bash -e + +#run the LAMMPS simulation (needs a current LAMMPS version compiled with the user pair_style sw/table) +lmp < spce.in > spce.out + diff --git a/examples/PACKAGES/pair_sw_3b_table/spce.data b/examples/PACKAGES/pair_sw_3b_table/spce.data new file mode 100644 index 0000000000..a56ab1b10c --- /dev/null +++ b/examples/PACKAGES/pair_sw_3b_table/spce.data @@ -0,0 +1,1015 @@ +Data File for CG Water + +1000 atoms +1 atom types + +0 31.0648 xlo xhi +0 31.0648 ylo yhi +0 31.0648 zlo zhi + +Masses + +1 18.0154 + +Atoms + +1 1 18.26 24.7 15.77 +2 1 12.63 1.42 27.01 +3 1 10.39 29.11 13.56 +4 1 26.47 16.64 7.23 +5 1 10.66 23.41 27.33 +6 1 19.08 3.2 21.63 +7 1 11.17 26.19 1.44 +8 1 4.61 4.04 25.72 +9 1 4.61 22.91 8.33 +10 1 30.61 22.71 25.18 +11 1 6.38 18.92 16.87 +12 1 17.83 12.53 11.09 +13 1 14.89 2.43 22.44 +14 1 28.36 30.9 26.38 +15 1 25.73 28.56 8.32 +16 1 19.61 20.22 4.43 +17 1 25.96 30.32 24.22 +18 1 14.51 17.35 16.41 +19 1 30.23 17.26 10.71 +20 1 22.68 23.23 2.3 +21 1 10.89 15.76 14.33 +22 1 1.46 20.46 12.48 +23 1 12.73 19.57 2.71 +24 1 1.21 12.02 9.88 +25 1 2.63 14.4 23.71 +26 1 16.91 20.37 4.73 +27 1 28.02 7.7 30.08 +28 1 21.22 22.47 19.66 +29 1 14.0 28.15 0.14 +30 1 19.62 19.73 1.11 +31 1 28.29 24.36 10.15 +32 1 14.05 1.1 17.64 +33 1 12.2 23.75 24.83 +34 1 24.56 26.02 13.57 +35 1 12.13 8.39 7.17 +36 1 20.47 22.28 25.02 +37 1 11.06 7.63 24.11 +38 1 6.52 22.64 30.46 +39 1 16.51 24.78 18.58 +40 1 30.18 20.56 29.19 +41 1 25.26 7.8 25.98 +42 1 20.37 4.16 3.88 +43 1 18.85 27.34 27.83 +44 1 17.72 29.84 12.78 +45 1 19.26 14.48 19.38 +46 1 29.73 4.46 4.96 +47 1 9.52 26.27 30.33 +48 1 6.55 9.25 20.32 +49 1 10.49 1.91 23.31 +50 1 17.63 1.17 14.48 +51 1 1.56 25.17 4.69 +52 1 9.08 10.39 2.29 +53 1 25.92 7.4 21.53 +54 1 25.3 5.14 28.4 +55 1 5.63 23.26 19.85 +56 1 9.6 9.85 24.85 +57 1 3.32 2.77 9.12 +58 1 28.54 15.28 22.18 +59 1 20.45 8.24 18.25 +60 1 12.86 3.73 11.61 +61 1 7.42 12.05 13.54 +62 1 1.73 28.54 25.27 +63 1 3.25 22.18 23.7 +64 1 3.27 25.38 2.24 +65 1 13.46 15.67 19.28 +66 1 31.0 6.91 13.61 +67 1 4.85 27.3 12.67 +68 1 24.48 13.52 4.98 +69 1 23.93 29.62 19.71 +70 1 5.03 13.35 19.5 +71 1 24.58 13.46 19.59 +72 1 7.42 6.82 9.03 +73 1 28.76 15.1 3.33 +74 1 12.38 17.21 6.63 +75 1 15.75 21.23 27.02 +76 1 4.58 5.06 28.19 +77 1 26.04 23.3 25.38 +78 1 30.02 7.27 9.52 +79 1 6.93 10.03 24.54 +80 1 5.61 26.93 27.34 +81 1 29.12 19.12 5.54 +82 1 18.44 27.8 14.75 +83 1 14.1 23.13 9.78 +84 1 24.12 5.55 20.72 +85 1 2.52 10.99 18.44 +86 1 1.76 6.41 21.47 +87 1 25.22 9.56 30.66 +88 1 11.87 13.25 9.12 +89 1 19.46 0.3 22.07 +90 1 28.82 12.29 11.36 +91 1 28.47 30.29 14.09 +92 1 25.51 20.94 24.33 +93 1 1.14 25.4 8.76 +94 1 1.33 27.98 3.09 +95 1 20.57 26.97 -0.04 +96 1 22.73 1.18 0.62 +97 1 19.16 16.99 30.52 +98 1 0.39 9.65 9.02 +99 1 4.41 7.21 3.22 +100 1 11.07 30.64 25.91 +101 1 7.93 25.84 26.26 +102 1 26.76 2.51 2.93 +103 1 30.8 18.15 18.49 +104 1 10.2 7.46 30.44 +105 1 4.77 20.39 26.99 +106 1 25.27 26.77 1.64 +107 1 28.51 13.99 9.33 +108 1 13.86 8.04 24.9 +109 1 30.67 29.88 23.01 +110 1 29.49 30.58 30.02 +111 1 28.74 5.08 30.95 +112 1 13.21 4.31 30.96 +113 1 5.27 3.66 5.02 +114 1 29.43 7.99 17.07 +115 1 4.19 1.37 16.63 +116 1 1.27 27.81 16.56 +117 1 30.64 5.73 25.91 +118 1 10.33 5.33 26.48 +119 1 11.56 21.77 14.77 +120 1 26.46 27.17 5.7 +121 1 14.85 25.79 8.64 +122 1 22.62 6.18 17.61 +123 1 3.45 18.53 11.84 +124 1 11.65 18.17 15.97 +125 1 23.16 17.0 1.5 +126 1 18.92 16.01 3.98 +127 1 30.05 0.25 5.23 +128 1 26.06 11.96 21.96 +129 1 16.82 2.0 10.25 +130 1 19.58 2.63 24.75 +131 1 20.09 14.75 26.62 +132 1 3.14 0.05 26.13 +133 1 4.86 11.79 12.99 +134 1 1.86 11.32 28.57 +135 1 8.82 28.6 6.22 +136 1 20.85 24.68 23.87 +137 1 7.58 25.15 3.44 +138 1 23.46 9.13 8.11 +139 1 6.45 10.24 27.37 +140 1 15.06 10.35 26.71 +141 1 13.8 18.39 26.5 +142 1 5.11 7.7 5.83 +143 1 23.27 23.16 6.67 +144 1 6.33 1.31 11.37 +145 1 14.66 22.28 21.43 +146 1 7.9 8.65 0.61 +147 1 21.83 3.67 26.17 +148 1 1.41 23.66 11.09 +149 1 10.19 17.23 22.71 +150 1 29.53 27.31 23.19 +151 1 28.69 11.38 2.33 +152 1 1.07 2.97 14.53 +153 1 23.47 30.53 14.32 +154 1 1.59 18.83 14.75 +155 1 20.38 30.6 24.38 +156 1 19.81 29.95 27.9 +157 1 12.68 27.59 26.46 +158 1 20.46 9.14 29.06 +159 1 8.69 13.98 24.71 +160 1 0.72 9.29 30.28 +161 1 11.81 20.55 12.28 +162 1 23.8 13.8 9.4 +163 1 13.63 0.51 0.95 +164 1 2.33 6.68 14.95 +165 1 15.98 6.35 25.28 +166 1 7.38 14.88 18.44 +167 1 17.07 20.48 29.16 +168 1 14.53 1.49 8.4 +169 1 28.45 1.21 20.58 +170 1 0.07 5.28 29.45 +171 1 26.0 9.98 15.37 +172 1 14.56 6.91 14.46 +173 1 20.6 9.09 23.04 +174 1 26.02 4.59 0.14 +175 1 5.21 21.9 17.55 +176 1 2.44 7.72 1.47 +177 1 1.25 30.0 13.48 +178 1 27.27 23.13 14.61 +179 1 24.04 15.61 21.64 +180 1 25.13 5.24 17.43 +181 1 4.2 15.98 12.34 +182 1 26.92 13.54 12.87 +183 1 3.38 19.38 9.08 +184 1 27.75 25.03 2.15 +185 1 26.13 20.68 16.54 +186 1 8.3 14.6 13.49 +187 1 3.04 22.87 29.93 +188 1 9.5 26.41 21.23 +189 1 6.53 2.16 2.75 +190 1 6.37 29.04 2.63 +191 1 26.58 4.38 19.69 +192 1 28.44 6.56 14.66 +193 1 25.55 11.1 28.03 +194 1 25.5 18.39 28.73 +195 1 27.67 23.47 5.65 +196 1 13.69 14.81 16.17 +197 1 22.97 27.61 24.11 +198 1 2.06 18.58 30.22 +199 1 2.07 7.13 29.2 +200 1 13.0 7.26 17.76 +201 1 10.04 16.22 30.62 +202 1 6.54 9.8 17.47 +203 1 5.65 12.68 0.64 +204 1 20.84 20.25 23.02 +205 1 22.48 27.63 21.48 +206 1 15.61 22.73 5.36 +207 1 3.52 30.36 6.24 +208 1 6.38 17.25 26.36 +209 1 14.13 10.57 22.63 +210 1 10.22 25.11 3.64 +211 1 16.63 14.7 25.08 +212 1 3.51 29.69 2.76 +213 1 19.2 11.9 21.44 +214 1 30.8 23.85 14.75 +215 1 21.02 14.34 12.4 +216 1 2.75 22.13 27.29 +217 1 29.27 14.29 6.8 +218 1 8.44 20.67 5.23 +219 1 9.42 20.06 22.95 +220 1 30.83 10.64 19.73 +221 1 19.33 14.14 8.94 +222 1 14.18 11.32 18.19 +223 1 26.55 2.39 28.55 +224 1 6.83 16.57 8.9 +225 1 13.98 8.79 1.97 +226 1 4.94 3.0 23.16 +227 1 25.39 29.46 0.63 +228 1 15.32 16.43 2.45 +229 1 5.26 29.73 29.87 +230 1 26.92 14.84 19.93 +231 1 11.87 30.08 4.52 +232 1 7.17 6.71 2.23 +233 1 10.46 1.13 18.11 +234 1 28.59 20.57 25.68 +235 1 26.54 4.84 8.44 +236 1 16.46 18.37 26.15 +237 1 30.53 0.74 15.31 +238 1 27.25 6.31 27.09 +239 1 22.42 1.65 3.87 +240 1 17.85 3.77 8.02 +241 1 11.82 8.23 11.15 +242 1 8.62 27.66 15.87 +243 1 25.19 1.89 18.37 +244 1 14.0 21.96 30.21 +245 1 29.3 1.73 28.29 +246 1 9.35 24.02 12.03 +247 1 1.05 21.5 0.35 +248 1 21.87 20.54 2.54 +249 1 10.59 15.98 17.51 +250 1 22.76 6.0 9.32 +251 1 0.31 9.13 11.87 +252 1 29.16 25.13 18.29 +253 1 1.23 29.08 7.75 +254 1 30.01 28.49 26.21 +255 1 1.87 5.92 5.03 +256 1 1.15 10.27 22.35 +257 1 11.83 10.31 5.16 +258 1 20.89 8.28 8.14 +259 1 13.48 11.78 28.37 +260 1 6.82 10.48 10.25 +261 1 7.34 4.49 18.73 +262 1 5.49 22.37 14.23 +263 1 12.31 21.05 27.47 +264 1 24.09 17.4 8.65 +265 1 22.03 11.54 20.98 +266 1 16.68 13.17 0.68 +267 1 5.52 1.47 8.78 +268 1 14.95 11.83 7.95 +269 1 5.9 10.66 7.12 +270 1 10.06 11.28 30.73 +271 1 17.72 10.71 27.46 +272 1 13.6 6.23 10.82 +273 1 23.42 30.72 9.31 +274 1 23.27 4.25 3.8 +275 1 13.79 8.37 21.07 +276 1 5.01 30.13 12.61 +277 1 26.04 24.45 17.25 +278 1 22.59 14.31 0.81 +279 1 23.74 10.37 17.17 +280 1 23.4 8.52 12.55 +281 1 10.53 23.97 21.96 +282 1 0.69 13.92 28.42 +283 1 6.94 6.27 15.01 +284 1 29.8 20.92 3.41 +285 1 10.19 20.68 19.0 +286 1 26.38 25.4 28.89 +287 1 12.34 26.9 8.27 +288 1 15.0 7.69 6.4 +289 1 24.75 13.1 2.24 +290 1 4.5 20.58 6.78 +291 1 23.27 18.25 11.48 +292 1 25.92 26.39 22.66 +293 1 24.63 4.21 6.52 +294 1 16.68 15.05 15.6 +295 1 26.39 16.17 29.89 +296 1 10.12 6.21 8.63 +297 1 14.41 14.67 12.23 +298 1 19.59 3.47 1.47 +299 1 28.21 22.43 18.25 +300 1 27.87 29.74 11.47 +301 1 22.53 24.1 13.94 +302 1 12.55 1.58 29.82 +303 1 17.45 21.28 8.34 +304 1 16.3 10.75 16.22 +305 1 16.34 13.25 17.65 +306 1 8.44 4.52 0.93 +307 1 17.47 23.79 2.3 +308 1 29.04 26.8 5.13 +309 1 13.13 11.34 24.9 +310 1 24.33 13.0 13.32 +311 1 8.21 29.74 24.23 +312 1 21.79 28.0 5.85 +313 1 13.74 20.08 10.26 +314 1 20.92 24.38 6.01 +315 1 9.83 29.56 17.99 +316 1 26.66 30.76 2.95 +317 1 24.34 3.08 1.67 +318 1 28.09 10.69 23.33 +319 1 7.08 25.28 0.77 +320 1 15.34 1.12 29.82 +321 1 26.07 12.55 7.74 +322 1 16.85 0.81 21.24 +323 1 9.96 0.57 6.36 +324 1 29.4 2.54 1.18 +325 1 5.81 1.0 5.42 +326 1 25.16 24.89 11.15 +327 1 15.43 24.93 13.71 +328 1 24.6 10.06 10.58 +329 1 20.4 12.04 15.51 +330 1 15.72 18.9 0.21 +331 1 16.5 17.21 28.81 +332 1 16.79 3.11 12.74 +333 1 22.75 6.22 6.6 +334 1 8.09 19.86 30.92 +335 1 24.15 8.75 23.65 +336 1 12.24 30.51 15.39 +337 1 8.15 26.8 18.69 +338 1 0.1 15.0 15.49 +339 1 29.84 15.71 30.0 +340 1 15.39 18.25 11.17 +341 1 1.2 15.49 18.8 +342 1 27.55 9.81 17.9 +343 1 18.93 8.9 10.06 +344 1 28.35 12.36 4.82 +345 1 11.21 13.71 30.62 +346 1 2.5 16.67 16.33 +347 1 0.47 4.2 6.99 +348 1 23.72 4.38 12.28 +349 1 16.59 3.54 16.9 +350 1 17.31 17.81 15.8 +351 1 11.58 0.3 21.21 +352 1 23.67 21.91 15.84 +353 1 7.74 2.78 23.52 +354 1 14.34 9.65 4.52 +355 1 23.35 10.88 14.55 +356 1 3.51 10.03 20.99 +357 1 14.63 21.34 1.75 +358 1 24.37 8.39 2.96 +359 1 14.8 15.5 30.48 +360 1 2.59 1.32 12.76 +361 1 0.16 13.81 25.49 +362 1 11.26 10.11 27.84 +363 1 27.8 18.65 15.07 +364 1 5.07 5.43 21.33 +365 1 14.06 5.26 19.67 +366 1 3.76 18.23 19.36 +367 1 26.68 27.25 10.67 +368 1 7.72 19.58 13.64 +369 1 29.48 16.94 16.45 +370 1 28.18 13.38 30.28 +371 1 29.97 10.41 16.17 +372 1 11.97 28.73 29.31 +373 1 14.88 0.79 25.43 +374 1 8.98 23.85 7.66 +375 1 4.78 8.21 9.79 +376 1 21.74 20.61 28.64 +377 1 20.36 18.75 17.92 +378 1 12.61 21.65 23.18 +379 1 6.36 29.76 8.49 +380 1 12.51 26.69 18.69 +381 1 22.2 17.41 6.86 +382 1 11.7 6.53 21.66 +383 1 4.62 16.22 3.24 +384 1 0.76 13.73 0.83 +385 1 21.91 13.43 5.67 +386 1 17.36 6.16 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24.88 25.38 7.35 +977 1 28.18 14.89 14.6 +978 1 7.84 30.36 4.39 +979 1 14.54 9.59 14.4 +980 1 27.63 12.3 15.83 +981 1 11.15 14.17 27.97 +982 1 25.27 20.88 8.35 +983 1 17.06 14.76 27.78 +984 1 3.9 14.79 15.06 +985 1 13.81 3.82 17.03 +986 1 28.55 24.1 26.15 +987 1 29.28 21.79 15.76 +988 1 15.05 30.12 27.83 +989 1 15.42 3.77 6.76 +990 1 22.65 12.12 11.24 +991 1 11.29 4.96 2.18 +992 1 2.15 7.43 7.57 +993 1 30.21 10.13 26.21 +994 1 24.42 22.18 4.42 +995 1 8.68 14.72 22.08 +996 1 23.1 6.9 27.1 +997 1 18.71 27.2 21.72 +998 1 14.12 12.7 30.76 +999 1 18.81 6.5 10.98 +1000 1 26.66 15.4 4.83 diff --git a/examples/PACKAGES/pair_sw_3b_table/spce.in b/examples/PACKAGES/pair_sw_3b_table/spce.in new file mode 100644 index 0000000000..85303bf0d1 --- /dev/null +++ b/examples/PACKAGES/pair_sw_3b_table/spce.in @@ -0,0 +1,45 @@ +log none + +#SPC/E water + +units real +atom_style atomic + +read_data spce.data + +#hybrid pair style consisting of +#pair_style table to read in CG pair potential +#pair_style sw/table for tabulated sw interactions +pair_style hybrid/overlay table linear 1200 sw/3b/table + +#pair coefficients +pair_coeff 1 1 table table_CG_CG.txt VOTCA +pair_coeff * * sw/3b/table spce.sw type + +#nvt run with nose-hoover thermostat +#time coupling of 100 ts for thermostat +#target T is 300 K +fix 1 all nvt temp 300.0 300.0 200.0 + +#create initial velocities +velocity all create 300 432567 dist uniform +#remove center of mass linear momentum +velocity all zero linear + +#remove center of mass linear momentum every 1000 time steps in each cartesian direction +fix remove all momentum 1000 linear 1 1 1 + +#timestep of 2 fs +timestep 2.0 + +#print out thermodynamic info every 100 ts +thermo 100 + +#run 10000 ts +run 10000 + +#write out dump file every 10 ts for 100000 ts +dump 2 all custom 10 spce.dump id type x y z fx fy fz +run 100000 + +undump 2 diff --git a/examples/PACKAGES/pair_sw_3b_table/spce.sw b/examples/PACKAGES/pair_sw_3b_table/spce.sw new file mode 100644 index 0000000000..8b0fd70f61 --- /dev/null +++ b/examples/PACKAGES/pair_sw_3b_table/spce.sw @@ -0,0 +1,18 @@ +type +type +type +1 #epsilon in kcal/mol +1 #sigma in dimensionless +3.7 # a in Ang +1.0 #lambda dimensionless +0.8 #gamma in Ang +0.0 #costheta0 dimensionless +0 #two body part A=0 +0 #two body part B=0 +0 #two body part p=0 +0 #two body part q=0 +0.0 # use the standard Stillinger-Weber cutoff +table_CG_CG_CG.txt +VOTCA +linear +1001 diff --git a/examples/PACKAGES/pair_sw_3b_table/table_CG_CG.txt b/examples/PACKAGES/pair_sw_3b_table/table_CG_CG.txt new file mode 100644 index 0000000000..f4ccdd4b4e --- /dev/null +++ b/examples/PACKAGES/pair_sw_3b_table/table_CG_CG.txt @@ -0,0 +1,1203 @@ +VOTCA +N 1200 R 0.010000 12.000000 + +1 1.0000000000e-02 1.5390100510e+15 2.1517330910e+16 +2 2.0000000000e-02 1.3370836560e+15 1.8774943350e+16 +3 3.0000000000e-02 1.1616510900e+15 1.6231560530e+16 +4 4.0000000000e-02 1.0092362200e+15 1.4101892510e+16 +5 5.0000000000e-02 8.7681900090e+14 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1.79820e+02 1.9164432e+00 -1.1540710e-02 +1001 1.80000e+02 1.9185186e+00 -1.1513008e-02 From 27524742e571a8d690b1868378ff9ce5a5ec82ed Mon Sep 17 00:00:00 2001 From: Christoph Scherer Date: Thu, 26 May 2022 14:14:08 +0200 Subject: [PATCH 05/34] src/MANYBODY/pair_3b_table.h, src/MANYBODY/pair_3b_table.cpp: added pair style for generic fully tabulated three-body forces which has been developed for simulations with Kernel-based machine learning potentials. --- src/MANYBODY/pair_3b_table.cpp | 861 +++++++++++++++++++++++++++++++++ src/MANYBODY/pair_3b_table.h | 138 ++++++ 2 files changed, 999 insertions(+) create mode 100644 src/MANYBODY/pair_3b_table.cpp create mode 100644 src/MANYBODY/pair_3b_table.h diff --git a/src/MANYBODY/pair_3b_table.cpp b/src/MANYBODY/pair_3b_table.cpp new file mode 100644 index 0000000000..a2227d5161 --- /dev/null +++ b/src/MANYBODY/pair_3b_table.cpp @@ -0,0 +1,861 @@ +/* ---------------------------------------------------------------------- + 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: Christoph Scherer (MPIP Mainz) + scherer@mpip-mainz.mpg.de +------------------------------------------------------------------------- */ + +#include "pair_3b_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 "table_file_reader.h" +#include "potential_file_reader.h" + +#include +#include +// +#include + +using namespace LAMMPS_NS; +using MathConst::MY_PI; + +#define DELTA 4 + +enum{LINEAR}; + +#define SMALL 0.001 +#define TINY 1.E-10 + +/* ---------------------------------------------------------------------- */ + +Pair3BTable::Pair3BTable(LAMMPS *lmp) : Pair(lmp) +{ + single_enable = 0; + restartinfo = 0; + one_coeff = 1; + manybody_flag = 1; + centroidstressflag = CENTROID_NOTAVAIL; + unit_convert_flag = utils::get_supported_conversions(utils::ENERGY); + + params = nullptr; + + maxshort = 10; + neighshort = nullptr; +} + +/* ---------------------------------------------------------------------- + check if allocated, since class can be destructed when incomplete +------------------------------------------------------------------------- */ + +Pair3BTable::~Pair3BTable() +{ + 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 Pair3BTable::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],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; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + 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]]; + ikparam = elem3param[itype][ktype][ktype]; + 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[ijparam],¶ms[ikparam],¶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 Pair3BTable::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"); + memory->create(neighshort,maxshort,"pair:neighshort"); + map = new int[n+1]; +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void Pair3BTable::settings(int narg, char **arg) +{ + //one mre additional argument: number of table entries + if (narg != 0) error->all(FLERR,"Illegal pair_style command"); +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void Pair3BTable::coeff(int narg, char **arg) +{ + if (!allocated) allocate(); + + map_element2type(narg-3,arg+3); + + // read potential file and initialize potential parameters + + read_file(arg[2]); + setup_params(); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void Pair3BTable::init_style() +{ + if (atom->tag_enable == 0) + error->all(FLERR,"Pair style 3b/table requires atom IDs"); + if (force->newton_pair == 0) + error->all(FLERR,"Pair style 3b/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 Pair3BTable::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + return cutmax; +} + +/* ---------------------------------------------------------------------- */ + +void Pair3BTable::read_file(char *file) +{ + memory->sfree(params); + params = nullptr; + nparams = maxparam = 0; + + // open file on proc 0 + + if (comm->me == 0) { + PotentialFileReader reader(lmp, file, "3b", unit_convert_flag); + char *line; + + // transparently convert units for supported conversions + + int unit_convert = reader.get_unit_convert(); + double conversion_factor = utils::get_conversion_factor(utils::ENERGY, + unit_convert); + + 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 tablename_string = values.next_string(); + params[nparams].tablenamelength = tablename_string.length()+1; + memory->create(params[nparams].tablename, params[nparams].tablenamelength, "params.tablename"); + for (int x = 0; x < params[nparams].tablenamelength; ++x) { + params[nparams].tablename[x] = tablename_string[x]; + } + std::string keyword_string = values.next_string(); + params[nparams].keywordlength = keyword_string.length()+1; + memory->create(params[nparams].keyword, params[nparams].keywordlength, "params.keyword"); + for (int x = 0; x < params[nparams].keywordlength; ++x) { + params[nparams].keyword[x] = keyword_string[x]; + } + std::string tablestyle_string = values.next_string(); + char *tablestyle; + memory->create(tablestyle, (tablestyle_string.length()+1), "tablestyle"); + for (int x = 0; x < (tablestyle_string.length()+1); ++x) { + tablestyle[x] = tablestyle_string[x]; + } + if (strcmp(tablestyle,"linear") == 0) params[nparams].tabstyle = LINEAR; + else error->all(FLERR,"Unknown table style in 3b table"); + 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 3b/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 3b table + for (int m = 0; m < nparams; ++m){ + if (comm->me != 0) { + memory->create(params[m].tablename, params[m].tablenamelength, "params.tablename"); + } + MPI_Bcast(¶ms[m].tablename, params[m].tablenamelength, MPI_CHAR, 0, world); + if (comm->me != 0) { + memory->create(params[m].keyword, params[m].keywordlength, "params.keyword"); + } + MPI_Bcast(¶ms[m].keyword, params[m].keywordlength, MPI_CHAR, 0, world); + + // initialize 3btable + memory->create(params[m].mltable,1,"param:3btable"); + null_table(params[m].mltable); + + //call read_table to read corresponding tabulated 3b 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 3btable 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 3b table length"); + } +} + + +/* ---------------------------------------------------------------------- */ + +void Pair3BTable::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 duplicate entry"); + n = m; + } + } + if (n < 0) error->all(FLERR,"Potential file is missing an entry"); + 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 Pair3BTable::read_table(Table *tb, char *file, char *keyword, bool symmetric) +{ + TableFileReader reader(lmp, file, "3body"); + + 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 3body interaction, less table entries are required + if (symmetric == true){ + 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 3b table values from file + + int cerror = 0; + reader.skip_line(); + // if it is a symmetric 3body interaction, less table entries are required + if (symmetric == true){ + 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 Pair3BTable::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"); + } + } + } catch (TokenizerException &e) { + error->one(FLERR, e.what()); + } + + if (tb->ninput == 0) error->one(FLERR, "3body table parameters did not set N"); + if (tb->rmin == 0.0) error->one(FLERR, "3body table parameters did not set rmin"); + if (tb->rmax == 0.0) error->one(FLERR, "3body table 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 Pair3BTable::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 3body interaction, less table entries are required + if (symmetric == true){ + 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 3body interaction, less table entries are required + if (symmetric == true){ + 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 Pair3BTable::free_param(Param *pm) +{ + // call free_table to destroy associated 3btable + free_table(pm->mltable); + // then destroy associated 3btable + memory->sfree(pm->mltable); +} + +/* ---------------------------------------------------------------------- */ + +void Pair3BTable::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 Pair3BTable::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 Pair3BTable::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 (pm->tabstyle == LINEAR) { + // if it is a symmetric 3body interaction, less table entries are required + if (pm->symmetric == true){ + 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 = 79; + } + itable = 0; + for (i=0; imltable->ninput-i); + } + itable += nr13; + itable *= (pm->mltable->ninput*2); + itable += ntheta; + } + // else, more (full) table entries are required + else{ + 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 = 79; + } + 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]; + } +} + +/* ---------------------------------------------------------------------- */ + +void Pair3BTable::threebody(Param *paramij, Param *paramik, 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 tehm back + if (swapped == true){ + 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; + + double epsilon = 0.5; + double epsilon2 = epsilon*epsilon; + + if (eflag) eng = u; +} diff --git a/src/MANYBODY/pair_3b_table.h b/src/MANYBODY/pair_3b_table.h new file mode 100644 index 0000000000..a864a9602c --- /dev/null +++ b/src/MANYBODY/pair_3b_table.h @@ -0,0 +1,138 @@ +/* -*- 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(3b/table,Pair3BTable) + +#else + +#ifndef LMP_PAIR_3B_TABLE_H +#define LMP_PAIR_3B_TABLE_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class Pair3BTable : public Pair { + public: + Pair3BTable(class LAMMPS *); + ~Pair3BTable() override; + void compute(int, int) override; + void coeff(int, char **) override; + double init_one(int, int) override; + void init_style() override; + + static constexpr int NPARAMS_PER_LINE = 8; + + // no write or read from binary restart file + + // struct for 3b/table + struct Table { + int ninput; + double rmin,rmax; + double *r12file,*r13file,*thetafile,*f11file,*f12file,*f21file,*f22file,*f31file,*f32file,*efile; + }; + + struct Param { + double cut,cutsq; + int ielement,jelement,kelement; + bool symmetric; // whether it is a symmetric table or not + int tablenamelength; // length of table name + char *tablename; // name of associated angular table + int keywordlength; // length of key in table + char *keyword; // key in table + int tabstyle,tablength; // length of interpolation table (not ninput) and style + Table *mltable; // 3b Table + }; + + protected: + double cutmax; // max cutoff for all elements + Param *params; // parameter set for an I-J-K interaction + int maxshort; // size of short neighbor list array + int *neighshort; // short neighbor list array + + void settings(int, char **) override; + virtual void allocate(); + void read_file(char *); + virtual void setup_params(); + void threebody(Param *, Param *, Param *, double, double, double *, double *, + double *, double *, double *, int, double &); + + void read_table(Table *, char *, char *, bool); + void bcast_table(Table *, bool); + void null_table(Table *); + + void free_table(Table *); + void free_param(Param *); + + void param_extract(Table *, char *); + + void uf_lookup(Param *, double, double, double, double &, double &, double &, double &, double &, double &, double &); +}; + +} + + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair style 3b/table requires atom IDs + +This is a requirement to use the 3b/table potential. + +E: Pair style 3b/table requires newton pair on + +See the newton command. This is a restriction to use the 3b/table +potential. + +E: All pair coeffs are not set + +All pair coefficients must be set in the data file or by the +pair_coeff command before running a simulation. + +E: Cannot open 3b/table potential file %s + +The specified 3b/table potential file cannot be opened. Check that the path +and name are correct. + +E: Incorrect format in 3b/table potential file + +Incorrect number of words per line in the potential file. + +E: Illegal 3b/table parameter + +One or more of the coefficients defined in the potential file is +invalid. + +E: Potential file has duplicate entry + +The potential file has more than one entry for the same element. + +E: Potential file is missing an entry + +The potential file does not have a needed entry. + +*/ From f9fbc7f94b6e1168f02dea1e807362285858d405 Mon Sep 17 00:00:00 2001 From: Christoph Scherer Date: Thu, 26 May 2022 14:17:36 +0200 Subject: [PATCH 06/34] doc/src/pair_3b_table.rst: documentation for added pair style 3b/table --- doc/src/pair_3b_table.rst | 265 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 265 insertions(+) create mode 100644 doc/src/pair_3b_table.rst diff --git a/doc/src/pair_3b_table.rst b/doc/src/pair_3b_table.rst new file mode 100644 index 0000000000..77d2dc7f1b --- /dev/null +++ b/doc/src/pair_3b_table.rst @@ -0,0 +1,265 @@ +.. index:: pair_style 3b_table + +pair_style 3b/table command +=========================== + +Syntax +"""""" + +.. code-block:: LAMMPS + + pair_style style + +* style = *3b/table* + + +Examples +"""""""" + +.. code-block:: LAMMPS + + pair_style 3b/table + pair_coeff * * spce.3b type + pair_coeff * * GaN.3b Ga N Ga + + +Description +""""""""""" + +The *3b/table* style is a pair style for generic tabulated three-body interactions. +It has been developed for (coarse-grained) simulations (of water) +with Kernel-based machine learning (ML) potentials (:ref:`Scherer2 `). +As for the pair style :doc:`pair_style sw ` +or :doc:`pair_style sw/table `, the energy of a system +is computed as a sum over three-body terms: + +.. math:: + + E = \sum_i \sum_{j \neq i} \sum_{k > j} \phi_3 (r_{ij}, r_{ik}, \theta_{ijk}) + +The summations in the formula are over all neighbors J +and K of atom I within a cutoff distance :math:`cut`. +In contrast to the Stillinger-Weber potential, all forces are not calculated analytically, but +read in from a three-body force/energy table which can be generated with +the csg_ml app of VOTCA as available at: . + +Only a single pair_coeff command is used with the *3b/table* style +which specifies a three-body potential (".3b") file with parameters for all +needed elements. These are then mapped to LAMMPS atom types by specifying +N_el additional arguments after the ".3b" filename in the pair_coeff command, +where N_el is the number of LAMMPS atom types: + +* ".3b" filename +* N_el element names = mapping of 3b elements to atom types + +See the :doc:`pair_coeff ` page for alternate ways +to specify the path for the potential file. + +As an example, imagine a file SiC.3b has three-body values for +Si and C. If your LAMMPS simulation has 4 atoms types and you want +the first 3 to be Si, and the fourth to be C, you would use the following +pair_coeff command: + +.. code-block:: LAMMPS + + pair_coeff * * SiC.3b Si Si Si C + +The first 2 arguments must be \* \* so as to span all LAMMPS atom types. +The first three Si arguments map LAMMPS atom types 1,2,3 to the Si +element in the ".3b" file. The final C argument maps LAMMPS atom type 4 +to the C element in the 3b file. If a mapping value is specified as +NULL, the mapping is not performed. This can be used when a *3b/table* +potential is used as part of the *hybrid* pair style. The NULL values +are placeholders for atom types that will be used with other +potentials. + +The three-body files have a ".3b" suffix. Lines that are not blank or +comments (starting with #) define parameters for a triplet of +elements. The parameters in a single entry specify to the +(three-body) cutoff distance and the tabulated +three-body interaction. A single entry then contains: + +* element 1 (the center atom in a 3-body interaction) +* element 2 +* element 3 +* cut (distance units) +* filename +* keyword +* style +* N + +The parameter :math:`cut` is the (three-body) cutoff distance. +When set to 0, no interaction is calculated for this element triplet. +The parameters *filename*, *keyword*, *style*, and *N* refer to +the tabulated three-body potential. + +The tabulation is done on a three-dimensional grid of the two distances +:math:`r_{ij}` and :math:`r_{ik}` as well as the angle :math:`\theta_{ijk}` +which is constructed in the following way. There are two different cases. +If element 2 and element 3 are of the same type (e.g. SiCC), the distance +:math:`r_{ij}` is varied in "N" steps from rmin to rmax and the distance +:math:`r_{ik}` is varied from :math:`r_{ij}` to rmax. This can be done, +due to the symmetry of the triplet. If element 2 and element 3 are not +of the same type (e.g. SiCSi), there is no additional symmetry and the +distance :math:`r_{ik}` is also varied from rmin to rmax in "N" steps. +The angle :math:`\theta_{ijk}` is alsways varied in "2N" steps from +(0.0 + 180.0/(4N)) to (180.0 - 180.0/(4N)). Therefore, the total number +of table entries is "M = N * N * (N+1)" for the symmetric (element 2 and element 3 +are of the same type) and "M = 2 * N * N * N" for the general case +(element 2 and element 3 are not of the same type). + +The forces on all three particles I, J, and K of a triplet +of this type of thre-body interaction potential +(:math:`\phi_3 (r_{ij}, r_{ik}, \theta_{ijk})`) lie within +the plane defined by the three inter-particle distance vectors +:math:`{\mathbf r}_{ij}`, :math:`{\mathbf r}_{ik}`, and :math:`{\mathbf r}_{jk}`. +This property is used to project the forces onto the inter-particle +distance vectors as follows + +.. math:: + + \begin{pmatrix} + {\mathbf f}_{i} \\ + {\mathbf f}_{j} \\ + {\mathbf f}_{k} \\ + \end{pmatrix} = + \begin{pmatrix} + f_{i1} & f_{i2} & 0 \\ + f_{j1} & 0 & f_{j2} \\ + 0 & f_{k1} & f_{k2} \\ + \end{pmatrix} + \begin{pmatrix} + {\mathbf r}_{ij} \\ + {\mathbf r}_{ik} \\ + {\mathbf r}_{jk} \\ + \end{pmatrix} + +and then tabulate the 6 force constants :math:`f_{i1}`, :math:`f_{i2}`, :math:`f_{j1}`, +:math:`f_{j2}`, :math:`f_{k1}`, and :math:`f_{k2}`, as well as the energy of a triplet e. +Due to symmetry reasons, the following relations hold: :math:`f_{i1}=-f_{j1}`, +:math:`f_{i2}=-f_{k1}`, and :math:`f_{j2}=-f_{k2}`. As in this pair style the +forces are read in directly, a correct MD simulation is also performed in the case that +the triplet energies are set to e=0. + +The *filename* specifies the file containing the tabulated energy and +derivative values of :math:`\phi_3 (r_{ij}, r_{ik}, \theta_{ijk})`. +The *keyword* then specifies a section of the file. The +format of this file is as follows (without the +parenthesized comments): + +.. parsed-literal:: + + # Tabulated three-body potential for spce water (one or more comment or blank lines) + + ENTRY1 (keyword is the first text on line) + N 12 rmin 2.55 rmax 3.65 (N, rmin, rmax parameters) + (blank line) + 1 2.55 2.55 3.75 -867.212 -611.273 867.212 21386.8 611.273 -21386.8 0.0 (index, r_ij, r_ik, theta, f_i1, f_i2, f_j1, f_j2, f_k1, f_k2, e) + 2 2.55 2.55 11.25 -621.539 -411.189 621.539 5035.95 411.189 -5035.95 0.0 + ... + 1872 3.65 3.65 176.25 -0.00215132 -0.00412886 0.00215137 0.00111754 0.00412895 -0.00111757 0.0 + +A section begins with a non-blank line whose first character is not a +"#"; blank lines or lines starting with "#" can be used as comments +between sections. The first line begins with a keyword which +identifies the section. The next line lists (in any +order) one or more parameters for the table. Each parameter is a +keyword followed by one or more numeric values. + +The parameter "N" is required. It should be the same than the parameter "N" of the ".3b" file, +otherwise its value is overwritten. "N" determines the number of table +entries "M" that follow: "M = N * N * (N+1)" (symmetric triplet, e.g. SiCC) or +"M = 2 * N * N * N" (asymmetric triplet, e.g. SiCSi). Therefore "M = 12 * 12 * 13 = 1872" +in the above symmetric example. The parameters "rmin" and "rmax" are also required +and determine the minimum and maximum of the inter-particle distances +:math:`r_{ij}` and :math:`r_{ik}`. + +Following a blank line, the next M lines of the angular table file list the tabulated values. +On each line, the first value is the index from 1 to M, the second value is the distance +:math:`r_{ij}`, the third value is the distance :math:`r_{ik}`, the fourth value +is the angle :math:`\theta_{ijk})`, the next six values are the force constants :math:`f_{i1}`, +:math:`f_{i2}`, :math:`f_{j1}`, :math:`f_{j2}`, :math:`f_{k1}`, and :math:`f_{k2}`, and the +last value is the energy e. + +Note that one three-body potential file can contain many sections, each with a tabulated +potential. LAMMPS reads the file section by section until it finds +one that matches the specified *keyword* of appropriate section of the ".3b" file. + +At the moment, only the *style* *linear* is allowed and implemented. After reading in the +force table, it is internally stored in LAMMPS as a lookup table. For each triplet +configuration occuring in the simulation within the cutoff distance, +the next nearest tabulated triplet configuration is looked up. No interpolation is done. +This allows for a very efficient force calculation +with the stored force constants and energies. Due to the know table structure, the lookup +can be done efficiently. It has been tested (:ref:`Scherer2 `) that with a reasonably +small bin size, the accuracy and speed is comparable to that of a Stillinger-Weber potential +with tabulated three-body interactions (:doc:`pair_style sw/table `) while +the table format of this pair style allows for more flexible three-body interactions. + +As for the Stillinger-Weber potential, the three-body potential file must contain entries for all the +elements listed in the pair_coeff command. It can also contain +entries for additional elements not being used in a particular +simulation; LAMMPS ignores those entries. + +For a single-element simulation, only a single entry is required +(e.g. SiSiSi). For a two-element simulation, the file must contain 8 +entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that +specify 3b parameters for all permutations of the two elements +interacting in three-body configurations. Thus for 3 elements, 27 +entries would be required, etc. + +As annotated above, the first element in the entry is the center atom +in a three-body interaction. Thus an entry for SiCC means a Si atom +with 2 C atoms as neighbors. The tabulated three-body forces can in +principle be specific to the three elements of the configuration. +However, the user must ensure that it makes physically sense. +E.g., the tabulated three-body forces for the +entries CSiC and CCSi should be the same exchanging :math:`r_{ij}` with +r_{ik}, :math:`f_{j1}` with :math:`f_{k1}`, +and :math:`f_{j2}` with :math:`f_{k2}`. + + +---------- + +Mixing, shift, table, tail correction, restart, rRESPA info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +As all interactions are tabulated, no mixing is performed. + +This pair style does not support the :doc:`pair_modify ` +shift, table, and tail options. + +This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. +Thus, you need to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file. + +This pair style can only be used via the *pair* keyword of the +:doc:`run_style respa ` command. It does not support the +*inner*, *middle*, *outer* keywords. + +---------- + +Restrictions +"""""""""""" + +This is a user pair style. For more information, see :ref:`Scherer2 `. It is only enabled +if LAMMPS was explicitly built with it. + +This pair style requires the :doc:`newton ` setting to be "on" +for pair interactions. + +For an example of a three-body potential file, have a look at the tutorial +in the tutorial folder. + +Related commands +"""""""""""""""" + +:doc:`pair_coeff ` + + +---------- + +.. _Scherer2: + +**(Scherer2)** C. Scherer, R. Scheid, D. Andrienko, and T. Bereau, J. Chem. Theor. Comp. 16, 3194–3204 (2020). + From 18c9960db033fb24e035b80ef7c090614be4c82f Mon Sep 17 00:00:00 2001 From: Christoph Scherer Date: Thu, 26 May 2022 14:25:24 +0200 Subject: [PATCH 07/34] examples/pair_sw_3b_table/README: minor correction --- examples/PACKAGES/pair_sw_3b_table/README | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/PACKAGES/pair_sw_3b_table/README b/examples/PACKAGES/pair_sw_3b_table/README index 9d158bf392..690adbc30a 100644 --- a/examples/PACKAGES/pair_sw_3b_table/README +++ b/examples/PACKAGES/pair_sw_3b_table/README @@ -4,7 +4,7 @@ Example for pair style sw/table This example contains all required input files for the simulation of CG SPC/E water with the user pair style sw/table, as well as a run.sh script. -To run the example, you have to compile LAMMPS with the MANYBODY package, including pair_sw_3b_table.h and pair_sw_3b_table.h. +To run the example, you have to compile LAMMPS with the MANYBODY package, including pair_sw_3b_table.h and pair_sw_3b_table.cpp. Running the simulation, you will reproduce results of the following publication: From b8dfb23ede3dd7f781264baec0b902c99baa24e2 Mon Sep 17 00:00:00 2001 From: Christoph Scherer Date: Thu, 26 May 2022 14:32:12 +0200 Subject: [PATCH 08/34] examples/PACKAGES/pair_sw_3b_table/README: corrections in the text --- examples/PACKAGES/pair_sw_3b_table/README | 29 +++++++++++------------ 1 file changed, 14 insertions(+), 15 deletions(-) diff --git a/examples/PACKAGES/pair_sw_3b_table/README b/examples/PACKAGES/pair_sw_3b_table/README index 690adbc30a..2d00030fea 100644 --- a/examples/PACKAGES/pair_sw_3b_table/README +++ b/examples/PACKAGES/pair_sw_3b_table/README @@ -1,8 +1,8 @@ -Example for pair style sw/table -================================ +Example for pair style sw/3b/table + This example contains all required input files for the simulation of CG SPC/E water with -the user pair style sw/table, as well as a run.sh script. +the user pair style sw/3b/table, as well as a run.sh script. To run the example, you have to compile LAMMPS with the MANYBODY package, including pair_sw_3b_table.h and pair_sw_3b_table.cpp. @@ -10,10 +10,10 @@ Running the simulation, you will reproduce results of the following publication: C. Scherer, and D. Andrienko, Understanding three-body contributions to coarse-grained force fields, Phys. Chem. Chem. Phys, 20(34):22387–22394, 2018, http://xlink.rsc.org/?DOI=C8CP00746B -Here, a water molecule is represented by one coarse-grained (CG) bead. The -two-body (table_CG_CG.txt) and three-body angular (table_CG_CG_CG.txt) interaction potentials -have been parametrized with force-matching (FM) with the VOTCA package (https://gitlab.mpcdf.mpg.de/votca/votca). -For more details, have a look at the publication. For a example on the parametrization, have a look at +Here, a water molecule is represented by one coarse-grained (CG) bead. +The two-body (table_CG_CG.txt) and three-body angular (table_CG_CG_CG.txt) interaction potentials have been parametrized with force-matching (FM) with the VOTCA package (https://gitlab.mpcdf.mpg.de/votca/votca). +For more details, have a look at the publication. +For a example on the parametrization, have a look at https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/guide and https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/spce/3body_sw. @@ -22,20 +22,19 @@ of 1000 CG water molecules, an input file (spce.in) and a (modified) Stillinger- The lammps input file contains the lines specifying the pair style and coefficients: -- pair_style hybrid/overlay table linear 1200 sw/3b/table - use a combination of pair_style table with 1200 linear table entries and the pair_style sw/3b/table +- pair_style hybrid/overlay table linear 1200 sw/3b/table - use a combination of pair style table with 1200 linear table entries and the pair style sw/3b/table - pair_coeff 1 1 table table_CG_CG.txt VOTCA - set the table name and keyword for the pair_style table -- pair_coeff * * sw/3b/table spce.sw type - set the name of the Stillinger-Weber file for the pair_style sw/3b/table +- pair_coeff * * sw/3b/table spce.sw type - set the name of the Stillinger-Weber file for the pair style sw/3b/table -A hybrid pair style is used, where pair forces are calculated as a tabulated interaction (table_CG_CG.txt) and the -pair style sw/table is only used to calculate the three-body forces. Therefore, in the Stillinger-Weber file all -parameters refering to two-body interactions are set to zero. As explained in the documentation of this pair -style, the .sw file contains the -additional lines refering to the tabulated angular potential: +A hybrid pair style is used, where pair forces are calculated as a tabulated interaction (table_CG_CG.txt) and the pair style sw/3b/table is only used to calculate the three-body forces. +Therefore, in the Stillinger-Weber file all parameters refering to two-body interactions are set to zero. +As explained in the documentation of this pair style, the .sw file contains the additional lines refering to the tabulated angular potential: - table_CG_CG_CG.txt - file name of tabulated angular potential - VOTCA - keyword for tabulated angular potential - linear - angular table is of linear style - 1001 - 1001 table entries -The LAMMPS simulation is a standard nvt simulation. A dump file is output with the positions and forces every 10 time steps. +The LAMMPS simulation is a standard nvt simulation. +A dump file is output with the positions and forces every 10 time steps. You can calculate the pair distribution and compare it to the one(s) in the publicattion. From e890e5718e9a980fa7013d5ad2d0881836aae960 Mon Sep 17 00:00:00 2001 From: Christoph Scherer Date: Thu, 26 May 2022 14:45:22 +0200 Subject: [PATCH 09/34] examples/PACKAGES/pair_3b_table: added example for new pair style 3b/table --- examples/PACKAGES/pair_3b_table/1-1-1.table | 1875 +++++++++ examples/PACKAGES/pair_3b_table/1-1-2.table | 3459 +++++++++++++++++ .../PACKAGES/pair_3b_table/CG-CG-CG.dist.new | 63 + .../PACKAGES/pair_3b_table/CG-CG.dist.new | 301 ++ examples/PACKAGES/pair_3b_table/README | 65 + .../pair_3b_table/calculate_distributions.xml | 29 + examples/PACKAGES/pair_3b_table/run.sh | 8 + examples/PACKAGES/pair_3b_table/spce.3b | 8 + examples/PACKAGES/pair_3b_table/spce.data | 1015 +++++ examples/PACKAGES/pair_3b_table/spce.in | 43 + examples/PACKAGES/pair_3b_table/spce_2.3b | 71 + examples/PACKAGES/pair_3b_table/spce_2.data | 1016 +++++ examples/PACKAGES/pair_3b_table/spce_2.in | 43 + .../PACKAGES/pair_3b_table/table_CG_CG.txt | 1203 ++++++ 14 files changed, 9199 insertions(+) create mode 100644 examples/PACKAGES/pair_3b_table/1-1-1.table create mode 100644 examples/PACKAGES/pair_3b_table/1-1-2.table create mode 100644 examples/PACKAGES/pair_3b_table/CG-CG-CG.dist.new create mode 100644 examples/PACKAGES/pair_3b_table/CG-CG.dist.new create mode 100644 examples/PACKAGES/pair_3b_table/README create mode 100644 examples/PACKAGES/pair_3b_table/calculate_distributions.xml create mode 100755 examples/PACKAGES/pair_3b_table/run.sh create mode 100644 examples/PACKAGES/pair_3b_table/spce.3b create mode 100644 examples/PACKAGES/pair_3b_table/spce.data create mode 100644 examples/PACKAGES/pair_3b_table/spce.in create mode 100644 examples/PACKAGES/pair_3b_table/spce_2.3b create mode 100644 examples/PACKAGES/pair_3b_table/spce_2.data create mode 100644 examples/PACKAGES/pair_3b_table/spce_2.in create mode 100644 examples/PACKAGES/pair_3b_table/table_CG_CG.txt diff --git a/examples/PACKAGES/pair_3b_table/1-1-1.table b/examples/PACKAGES/pair_3b_table/1-1-1.table new file mode 100644 index 0000000000..76d8f8a9ec --- /dev/null +++ b/examples/PACKAGES/pair_3b_table/1-1-1.table @@ -0,0 +1,1875 @@ +ENTRY1 +N 12 rmin 2.55 rmax 3.65 + +1 2.55 2.55 3.75 -867.212 -611.273 867.212 21386.8 611.273 -21386.8 0.0 +2 2.55 2.55 11.25 -621.539 -411.189 621.539 5035.95 411.189 -5035.95 0.0 +3 2.55 2.55 18.75 -394.167 -243.287 394.167 1722.21 243.287 -1722.21 0.0 +4 2.55 2.55 26.25 -218.789 -127.402 218.789 560.206 127.402 -560.206 0.0 +5 2.55 2.55 33.75 -104.252 -59.5774 104.252 156.639 59.5774 -156.639 0.0 +6 2.55 2.55 41.25 -41.0722 -24.6716 41.072 36.4446 24.6716 -36.4446 0.0 +7 2.55 2.55 48.75 -12.357 -8.38061 12.3571 7.1117 8.38062 -7.1117 0.0 +8 2.55 2.55 56.25 -2.29912 -1.68047 2.29907 0.91657 1.68048 -0.916568 0.0 +9 2.55 2.55 63.75 -0.0509977 0.327321 0.0509129 -0.304729 -0.327319 0.30474 0.0 +10 2.55 2.55 71.25 0.0345509 0.431792 -0.0345867 -0.382614 -0.431782 0.382616 0.0 +11 2.55 2.55 78.75 -0.00019898 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0.997098635 i +14.25 0.9980037804 i +14.3 1.013908132 i +14.35 1.001934888 i +14.4 1.006664102 i +14.45 0.991726169 i +14.5 0.9912580833 i +14.55 1.008190614 i +14.6 0.9970967502 i +14.65 0.9958736094 i +14.7 0.9903643889 i +14.75 0.9965217067 i +14.8 0.998001776 i +14.85 1.000587917 i +14.9 0.9950512374 i +14.95 0.9958385369 i +15 1.001436413 i diff --git a/examples/PACKAGES/pair_3b_table/README b/examples/PACKAGES/pair_3b_table/README new file mode 100644 index 0000000000..d01c00afdd --- /dev/null +++ b/examples/PACKAGES/pair_3b_table/README @@ -0,0 +1,65 @@ +Example for pair style 3b/table + + +This example contains all required input files for the simulation of CG SPC/E water with +the user pair style 3b/table, as well as a run.sh script. + +To run the example, you have to compile LAMMPS with the MANYBODY package, including pair_3b_table.h and pair_3b_table.cpp. + +Running the simulations, you will reproduce results of the following publication: + +C. Scherer, R. Scheid, D. Andrienko, and T. Bereau, Kernel-Based Machine Learning for Efficient Simulations of Molecular Liquids, J. Chem. Theor. Comp., 16(5):3194–3204, 2020, https://doi.org/10.1021/acs.jctc.9b01256 + +Here, a water molecule is represented by one coarse-grained (CG) bead. The example contains +two parts. +The three-body (force) tables for both parts (1-1-1.table and 1-1-2.table) have been parametrized with the kernel-based machine learning (ML) with the VOTCA package (https://gitlab.mpcdf.mpg.de/votca/votca). +For a general description of the table format have a look at the documentation of this pair style. +For a example on the parametrization, have a look at https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/guide and +https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/ml. +In both cases, the parametrization has been done according to the three-body forces of the FM tabulated Stillinger-Weber (sw/3b/table) potential with the covariant meshing technique with the settings files used in https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/ml/3body/with_binning. + +For the first part of example, the folder contains the contains the LAMMPS data file (spce.data) with the starting configuration of 1000 CG water molecules, an input file (spce.in) and a three-body file (spce.3b). + +The lammps input file contains the lines specifying the pair style and coefficients: + +- pair_style hybrid/overlay table linear 1200 3b/table - use a combination of pair style table with 1200 linear table entries and the pair style 3b/table +- pair_coeff 1 1 table table_CG_CG.txt VOTCA - set the table name and keyword for the pair style table +- pair_coeff * * 3b/table spce.3b type - set the name of 3body file and bead type for the pair style 3b/table + +A hybrid pair style is used, where pair forces are calculated as a tabulated interaction (table_CG_CG.txt) and the pair style 3b/table is only used to calculate the three-body forces. +The tabulated pair interaction is the same as in the example of the sw/3b/table pair style: examples/PACKAGES/pair_sw_3b_table + +To run the simulation, one needs an additional 3body file (spce.3b). +It has the following structure: + +- type - relates to keyword type in LAMMPS input file +- type - relates to keyword type in LAMMPS input file +- type - relates to keyword type in LAMMPS input file +- 3.7 - cutoff in Ang +- 1-1-1.table - name of 3-body force table +- ENTRY1 - keyword in 3-body force table for this interaction +- linear - interpolation is linear +- 12 - number of grid points in radial direction (automatically sets grid size, in this case to 1872) + +As there is only one atom type (1), the force table is symmetric and contains "M = N * N * (N+1)" (12 * 12 * 13 = 1872) entries. + +The LAMMPS simulation is a standard nvt simulation. A dump file is output with the positions and forces every 10 time steps. +You can calculate the pair distribution and compare it to the ones in the publication. + +For the second part of the example, have a look at the LAMMPS data file (spce_2.data), the input file (spce_2.in) and the three-body file (spce_2.3b). +Running the second part, you will in fact perform the same MD simulation as in the first part of the example. However, the atom type of the first 100 CG water molecules has been changed from 1 to 2. +This is done to demonstrate how to run a simulation with different atom types. + +Again, lammps input file (spce_2.in) contains the lines specifying the pair style and coefficients: + +- pair_style hybrid/overlay table linear 1200 3b/table - use a combination of pair style table with 1200 linear table entries and the pair style 3b/table +- pair_coeff 1 1 table table_CG_CG.txt VOTCA - set the table name and keyword for the pair style table +- pair_coeff * * 3b/table spce_2.3b type1 type2 - set the name of 3body file and bead type for the pair style 3b/table + +Now, the atom type 1 is mapped to the element type1 and the atom type 2 is mapped to the element type2 in the 3body file (spce_2.3b). +For this (artificial) two-element simulation, the 3body file now contain 8 entries for: type1 type1 type1, type1 type1 type2, type1 type2 type1, type1 type2 type2, type2 type1 type1, type2 type1 type2, type2 type2 type1, type2 type2 type2. +Each entry has the same structure as above. However, entries where the second and the third element are different require a different force table (1-1-2.table) instead of (1-1-1.table). +1-1-2.table contains exactly the force constants as 1-1-1.table. +However it has to have the asymmetric structure where both interparticle distances (r_ij and r_ik) are varied from rmin to rmax and therefore contains "M = 2 * N * N * N" (2 * 12 * 12 * 12 = 3456) entries. + +Now run the simulation. The theromodynamic output, as well as, the pair correlation function should be exactly the same as for the first part of the example. diff --git a/examples/PACKAGES/pair_3b_table/calculate_distributions.xml b/examples/PACKAGES/pair_3b_table/calculate_distributions.xml new file mode 100644 index 0000000000..f2510d4f21 --- /dev/null +++ b/examples/PACKAGES/pair_3b_table/calculate_distributions.xml @@ -0,0 +1,29 @@ + + + grid + + + + + CG-CG + 1 + 1 + 0.0 + 15.0 + 0.05 + + + + + + CG-CG-CG + 1 + 1 + 1 + 1 + 0.0 + 3.1 + 0.05 + 3.7 + + diff --git a/examples/PACKAGES/pair_3b_table/run.sh b/examples/PACKAGES/pair_3b_table/run.sh new file mode 100755 index 0000000000..c87c01e23e --- /dev/null +++ b/examples/PACKAGES/pair_3b_table/run.sh @@ -0,0 +1,8 @@ +#! /bin/bash -e + +#run the LAMMPS simulation of the first part of the tutorial (needs a current LAMMPS version compiled with the user pair_style 3b/table) +lmp < spce.in > spce.out + +#run the LAMMPS simulation of the second part of the tutorial (needs a current LAMMPS version compiled with the user pair_style 3b/table) +lmp < spce_2.in > spce_2.out + diff --git a/examples/PACKAGES/pair_3b_table/spce.3b b/examples/PACKAGES/pair_3b_table/spce.3b new file mode 100644 index 0000000000..07f9b66433 --- /dev/null +++ b/examples/PACKAGES/pair_3b_table/spce.3b @@ -0,0 +1,8 @@ +type +type +type +3.7 # cut in Ang +1-1-1.table +ENTRY1 +linear +12 diff --git a/examples/PACKAGES/pair_3b_table/spce.data b/examples/PACKAGES/pair_3b_table/spce.data new file mode 100644 index 0000000000..a56ab1b10c --- /dev/null +++ b/examples/PACKAGES/pair_3b_table/spce.data @@ -0,0 +1,1015 @@ +Data File for CG Water + +1000 atoms +1 atom types + +0 31.0648 xlo xhi +0 31.0648 ylo yhi +0 31.0648 zlo zhi + +Masses + +1 18.0154 + +Atoms + +1 1 18.26 24.7 15.77 +2 1 12.63 1.42 27.01 +3 1 10.39 29.11 13.56 +4 1 26.47 16.64 7.23 +5 1 10.66 23.41 27.33 +6 1 19.08 3.2 21.63 +7 1 11.17 26.19 1.44 +8 1 4.61 4.04 25.72 +9 1 4.61 22.91 8.33 +10 1 30.61 22.71 25.18 +11 1 6.38 18.92 16.87 +12 1 17.83 12.53 11.09 +13 1 14.89 2.43 22.44 +14 1 28.36 30.9 26.38 +15 1 25.73 28.56 8.32 +16 1 19.61 20.22 4.43 +17 1 25.96 30.32 24.22 +18 1 14.51 17.35 16.41 +19 1 30.23 17.26 10.71 +20 1 22.68 23.23 2.3 +21 1 10.89 15.76 14.33 +22 1 1.46 20.46 12.48 +23 1 12.73 19.57 2.71 +24 1 1.21 12.02 9.88 +25 1 2.63 14.4 23.71 +26 1 16.91 20.37 4.73 +27 1 28.02 7.7 30.08 +28 1 21.22 22.47 19.66 +29 1 14.0 28.15 0.14 +30 1 19.62 19.73 1.11 +31 1 28.29 24.36 10.15 +32 1 14.05 1.1 17.64 +33 1 12.2 23.75 24.83 +34 1 24.56 26.02 13.57 +35 1 12.13 8.39 7.17 +36 1 20.47 22.28 25.02 +37 1 11.06 7.63 24.11 +38 1 6.52 22.64 30.46 +39 1 16.51 24.78 18.58 +40 1 30.18 20.56 29.19 +41 1 25.26 7.8 25.98 +42 1 20.37 4.16 3.88 +43 1 18.85 27.34 27.83 +44 1 17.72 29.84 12.78 +45 1 19.26 14.48 19.38 +46 1 29.73 4.46 4.96 +47 1 9.52 26.27 30.33 +48 1 6.55 9.25 20.32 +49 1 10.49 1.91 23.31 +50 1 17.63 1.17 14.48 +51 1 1.56 25.17 4.69 +52 1 9.08 10.39 2.29 +53 1 25.92 7.4 21.53 +54 1 25.3 5.14 28.4 +55 1 5.63 23.26 19.85 +56 1 9.6 9.85 24.85 +57 1 3.32 2.77 9.12 +58 1 28.54 15.28 22.18 +59 1 20.45 8.24 18.25 +60 1 12.86 3.73 11.61 +61 1 7.42 12.05 13.54 +62 1 1.73 28.54 25.27 +63 1 3.25 22.18 23.7 +64 1 3.27 25.38 2.24 +65 1 13.46 15.67 19.28 +66 1 31.0 6.91 13.61 +67 1 4.85 27.3 12.67 +68 1 24.48 13.52 4.98 +69 1 23.93 29.62 19.71 +70 1 5.03 13.35 19.5 +71 1 24.58 13.46 19.59 +72 1 7.42 6.82 9.03 +73 1 28.76 15.1 3.33 +74 1 12.38 17.21 6.63 +75 1 15.75 21.23 27.02 +76 1 4.58 5.06 28.19 +77 1 26.04 23.3 25.38 +78 1 30.02 7.27 9.52 +79 1 6.93 10.03 24.54 +80 1 5.61 26.93 27.34 +81 1 29.12 19.12 5.54 +82 1 18.44 27.8 14.75 +83 1 14.1 23.13 9.78 +84 1 24.12 5.55 20.72 +85 1 2.52 10.99 18.44 +86 1 1.76 6.41 21.47 +87 1 25.22 9.56 30.66 +88 1 11.87 13.25 9.12 +89 1 19.46 0.3 22.07 +90 1 28.82 12.29 11.36 +91 1 28.47 30.29 14.09 +92 1 25.51 20.94 24.33 +93 1 1.14 25.4 8.76 +94 1 1.33 27.98 3.09 +95 1 20.57 26.97 -0.04 +96 1 22.73 1.18 0.62 +97 1 19.16 16.99 30.52 +98 1 0.39 9.65 9.02 +99 1 4.41 7.21 3.22 +100 1 11.07 30.64 25.91 +101 1 7.93 25.84 26.26 +102 1 26.76 2.51 2.93 +103 1 30.8 18.15 18.49 +104 1 10.2 7.46 30.44 +105 1 4.77 20.39 26.99 +106 1 25.27 26.77 1.64 +107 1 28.51 13.99 9.33 +108 1 13.86 8.04 24.9 +109 1 30.67 29.88 23.01 +110 1 29.49 30.58 30.02 +111 1 28.74 5.08 30.95 +112 1 13.21 4.31 30.96 +113 1 5.27 3.66 5.02 +114 1 29.43 7.99 17.07 +115 1 4.19 1.37 16.63 +116 1 1.27 27.81 16.56 +117 1 30.64 5.73 25.91 +118 1 10.33 5.33 26.48 +119 1 11.56 21.77 14.77 +120 1 26.46 27.17 5.7 +121 1 14.85 25.79 8.64 +122 1 22.62 6.18 17.61 +123 1 3.45 18.53 11.84 +124 1 11.65 18.17 15.97 +125 1 23.16 17.0 1.5 +126 1 18.92 16.01 3.98 +127 1 30.05 0.25 5.23 +128 1 26.06 11.96 21.96 +129 1 16.82 2.0 10.25 +130 1 19.58 2.63 24.75 +131 1 20.09 14.75 26.62 +132 1 3.14 0.05 26.13 +133 1 4.86 11.79 12.99 +134 1 1.86 11.32 28.57 +135 1 8.82 28.6 6.22 +136 1 20.85 24.68 23.87 +137 1 7.58 25.15 3.44 +138 1 23.46 9.13 8.11 +139 1 6.45 10.24 27.37 +140 1 15.06 10.35 26.71 +141 1 13.8 18.39 26.5 +142 1 5.11 7.7 5.83 +143 1 23.27 23.16 6.67 +144 1 6.33 1.31 11.37 +145 1 14.66 22.28 21.43 +146 1 7.9 8.65 0.61 +147 1 21.83 3.67 26.17 +148 1 1.41 23.66 11.09 +149 1 10.19 17.23 22.71 +150 1 29.53 27.31 23.19 +151 1 28.69 11.38 2.33 +152 1 1.07 2.97 14.53 +153 1 23.47 30.53 14.32 +154 1 1.59 18.83 14.75 +155 1 20.38 30.6 24.38 +156 1 19.81 29.95 27.9 +157 1 12.68 27.59 26.46 +158 1 20.46 9.14 29.06 +159 1 8.69 13.98 24.71 +160 1 0.72 9.29 30.28 +161 1 11.81 20.55 12.28 +162 1 23.8 13.8 9.4 +163 1 13.63 0.51 0.95 +164 1 2.33 6.68 14.95 +165 1 15.98 6.35 25.28 +166 1 7.38 14.88 18.44 +167 1 17.07 20.48 29.16 +168 1 14.53 1.49 8.4 +169 1 28.45 1.21 20.58 +170 1 0.07 5.28 29.45 +171 1 26.0 9.98 15.37 +172 1 14.56 6.91 14.46 +173 1 20.6 9.09 23.04 +174 1 26.02 4.59 0.14 +175 1 5.21 21.9 17.55 +176 1 2.44 7.72 1.47 +177 1 1.25 30.0 13.48 +178 1 27.27 23.13 14.61 +179 1 24.04 15.61 21.64 +180 1 25.13 5.24 17.43 +181 1 4.2 15.98 12.34 +182 1 26.92 13.54 12.87 +183 1 3.38 19.38 9.08 +184 1 27.75 25.03 2.15 +185 1 26.13 20.68 16.54 +186 1 8.3 14.6 13.49 +187 1 3.04 22.87 29.93 +188 1 9.5 26.41 21.23 +189 1 6.53 2.16 2.75 +190 1 6.37 29.04 2.63 +191 1 26.58 4.38 19.69 +192 1 28.44 6.56 14.66 +193 1 25.55 11.1 28.03 +194 1 25.5 18.39 28.73 +195 1 27.67 23.47 5.65 +196 1 13.69 14.81 16.17 +197 1 22.97 27.61 24.11 +198 1 2.06 18.58 30.22 +199 1 2.07 7.13 29.2 +200 1 13.0 7.26 17.76 +201 1 10.04 16.22 30.62 +202 1 6.54 9.8 17.47 +203 1 5.65 12.68 0.64 +204 1 20.84 20.25 23.02 +205 1 22.48 27.63 21.48 +206 1 15.61 22.73 5.36 +207 1 3.52 30.36 6.24 +208 1 6.38 17.25 26.36 +209 1 14.13 10.57 22.63 +210 1 10.22 25.11 3.64 +211 1 16.63 14.7 25.08 +212 1 3.51 29.69 2.76 +213 1 19.2 11.9 21.44 +214 1 30.8 23.85 14.75 +215 1 21.02 14.34 12.4 +216 1 2.75 22.13 27.29 +217 1 29.27 14.29 6.8 +218 1 8.44 20.67 5.23 +219 1 9.42 20.06 22.95 +220 1 30.83 10.64 19.73 +221 1 19.33 14.14 8.94 +222 1 14.18 11.32 18.19 +223 1 26.55 2.39 28.55 +224 1 6.83 16.57 8.9 +225 1 13.98 8.79 1.97 +226 1 4.94 3.0 23.16 +227 1 25.39 29.46 0.63 +228 1 15.32 16.43 2.45 +229 1 5.26 29.73 29.87 +230 1 26.92 14.84 19.93 +231 1 11.87 30.08 4.52 +232 1 7.17 6.71 2.23 +233 1 10.46 1.13 18.11 +234 1 28.59 20.57 25.68 +235 1 26.54 4.84 8.44 +236 1 16.46 18.37 26.15 +237 1 30.53 0.74 15.31 +238 1 27.25 6.31 27.09 +239 1 22.42 1.65 3.87 +240 1 17.85 3.77 8.02 +241 1 11.82 8.23 11.15 +242 1 8.62 27.66 15.87 +243 1 25.19 1.89 18.37 +244 1 14.0 21.96 30.21 +245 1 29.3 1.73 28.29 +246 1 9.35 24.02 12.03 +247 1 1.05 21.5 0.35 +248 1 21.87 20.54 2.54 +249 1 10.59 15.98 17.51 +250 1 22.76 6.0 9.32 +251 1 0.31 9.13 11.87 +252 1 29.16 25.13 18.29 +253 1 1.23 29.08 7.75 +254 1 30.01 28.49 26.21 +255 1 1.87 5.92 5.03 +256 1 1.15 10.27 22.35 +257 1 11.83 10.31 5.16 +258 1 20.89 8.28 8.14 +259 1 13.48 11.78 28.37 +260 1 6.82 10.48 10.25 +261 1 7.34 4.49 18.73 +262 1 5.49 22.37 14.23 +263 1 12.31 21.05 27.47 +264 1 24.09 17.4 8.65 +265 1 22.03 11.54 20.98 +266 1 16.68 13.17 0.68 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1 13.13 11.34 24.9 +310 1 24.33 13.0 13.32 +311 1 8.21 29.74 24.23 +312 1 21.79 28.0 5.85 +313 1 13.74 20.08 10.26 +314 1 20.92 24.38 6.01 +315 1 9.83 29.56 17.99 +316 1 26.66 30.76 2.95 +317 1 24.34 3.08 1.67 +318 1 28.09 10.69 23.33 +319 1 7.08 25.28 0.77 +320 1 15.34 1.12 29.82 +321 1 26.07 12.55 7.74 +322 1 16.85 0.81 21.24 +323 1 9.96 0.57 6.36 +324 1 29.4 2.54 1.18 +325 1 5.81 1.0 5.42 +326 1 25.16 24.89 11.15 +327 1 15.43 24.93 13.71 +328 1 24.6 10.06 10.58 +329 1 20.4 12.04 15.51 +330 1 15.72 18.9 0.21 +331 1 16.5 17.21 28.81 +332 1 16.79 3.11 12.74 +333 1 22.75 6.22 6.6 +334 1 8.09 19.86 30.92 +335 1 24.15 8.75 23.65 +336 1 12.24 30.51 15.39 +337 1 8.15 26.8 18.69 +338 1 0.1 15.0 15.49 +339 1 29.84 15.71 30.0 +340 1 15.39 18.25 11.17 +341 1 1.2 15.49 18.8 +342 1 27.55 9.81 17.9 +343 1 18.93 8.9 10.06 +344 1 28.35 12.36 4.82 +345 1 11.21 13.71 30.62 +346 1 2.5 16.67 16.33 +347 1 0.47 4.2 6.99 +348 1 23.72 4.38 12.28 +349 1 16.59 3.54 16.9 +350 1 17.31 17.81 15.8 +351 1 11.58 0.3 21.21 +352 1 23.67 21.91 15.84 +353 1 7.74 2.78 23.52 +354 1 14.34 9.65 4.52 +355 1 23.35 10.88 14.55 +356 1 3.51 10.03 20.99 +357 1 14.63 21.34 1.75 +358 1 24.37 8.39 2.96 +359 1 14.8 15.5 30.48 +360 1 2.59 1.32 12.76 +361 1 0.16 13.81 25.49 +362 1 11.26 10.11 27.84 +363 1 27.8 18.65 15.07 +364 1 5.07 5.43 21.33 +365 1 14.06 5.26 19.67 +366 1 3.76 18.23 19.36 +367 1 26.68 27.25 10.67 +368 1 7.72 19.58 13.64 +369 1 29.48 16.94 16.45 +370 1 28.18 13.38 30.28 +371 1 29.97 10.41 16.17 +372 1 11.97 28.73 29.31 +373 1 14.88 0.79 25.43 +374 1 8.98 23.85 7.66 +375 1 4.78 8.21 9.79 +376 1 21.74 20.61 28.64 +377 1 20.36 18.75 17.92 +378 1 12.61 21.65 23.18 +379 1 6.36 29.76 8.49 +380 1 12.51 26.69 18.69 +381 1 22.2 17.41 6.86 +382 1 11.7 6.53 21.66 +383 1 4.62 16.22 3.24 +384 1 0.76 13.73 0.83 +385 1 21.91 13.43 5.67 +386 1 17.36 6.16 4.12 +387 1 0.34 28.1 11.89 +388 1 2.43 26.92 20.47 +389 1 0.99 22.41 4.14 +390 1 23.77 24.66 24.16 +391 1 22.41 7.79 20.57 +392 1 16.4 22.82 23.46 +393 1 24.68 28.28 17.44 +394 1 14.99 26.21 27.12 +395 1 0.75 13.41 7.7 +396 1 16.43 5.69 21.09 +397 1 19.5 6.71 27.89 +398 1 14.32 17.4 22.9 +399 1 29.04 27.81 19.17 +400 1 9.52 19.68 10.69 +401 1 5.33 27.17 17.3 +402 1 5.2 12.64 9.11 +403 1 9.8 6.14 19.74 +404 1 9.86 22.71 1.2 +405 1 0.84 12.31 14.9 +406 1 18.79 12.07 17.76 +407 1 27.21 25.79 14.27 +408 1 6.11 1.01 19.83 +409 1 8.44 5.68 12.85 +410 1 22.42 26.4 1.81 +411 1 24.0 20.11 18.63 +412 1 2.32 26.11 12.18 +413 1 26.06 7.28 15.77 +414 1 9.96 9.13 19.49 +415 1 10.74 12.01 25.79 +416 1 30.39 1.07 11.77 +417 1 9.49 20.19 26.63 +418 1 15.99 30.59 6.78 +419 1 11.0 30.74 0.96 +420 1 23.67 30.14 22.75 +421 1 24.14 9.9 19.82 +422 1 5.88 5.5 7.25 +423 1 3.45 10.72 9.52 +424 1 11.78 25.26 29.31 +425 1 15.95 27.28 17.71 +426 1 17.99 16.5 8.95 +427 1 28.47 0.47 23.29 +428 1 14.06 1.39 12.17 +429 1 19.28 23.85 8.27 +430 1 13.62 4.42 14.21 +431 1 2.98 9.89 12.04 +432 1 7.35 14.53 10.79 +433 1 15.55 0.87 3.17 +434 1 7.7 24.24 23.88 +435 1 17.61 8.64 6.93 +436 1 5.17 26.9 3.74 +437 1 1.06 17.17 27.8 +438 1 18.8 9.64 19.81 +439 1 8.36 1.64 0.63 +440 1 13.68 14.97 7.75 +441 1 29.56 0.55 17.98 +442 1 3.01 24.45 14.3 +443 1 11.98 7.48 26.92 +444 1 19.13 24.44 27.57 +445 1 11.75 14.57 11.88 +446 1 13.1 4.54 22.64 +447 1 7.2 21.26 28.21 +448 1 24.85 22.96 28.77 +449 1 15.0 23.95 16.32 +450 1 24.6 14.43 15.56 +451 1 3.05 13.66 17.69 +452 1 3.0 3.39 6.37 +453 1 24.92 22.04 13.42 +454 1 21.24 2.56 17.68 +455 1 19.69 0.3 11.75 +456 1 5.73 29.89 26.41 +457 1 7.62 30.1 0.37 +458 1 14.62 28.23 20.86 +459 1 8.72 5.14 23.94 +460 1 9.94 25.78 9.45 +461 1 17.3 4.53 0.74 +462 1 17.58 12.58 14.58 +463 1 8.64 2.55 20.15 +464 1 21.07 10.96 26.32 +465 1 27.85 4.23 10.9 +466 1 20.41 29.07 20.84 +467 1 9.35 12.65 10.7 +468 1 9.88 0.73 3.41 +469 1 26.64 20.78 1.33 +470 1 25.47 19.72 10.96 +471 1 1.01 5.01 12.19 +472 1 10.11 27.98 23.8 +473 1 17.51 0.24 28.51 +474 1 21.85 14.89 8.07 +475 1 18.22 12.88 29.4 +476 1 10.97 16.02 2.55 +477 1 4.3 25.33 5.86 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28.53 17.74 8.3 +857 1 28.99 9.49 7.65 +858 1 11.37 3.77 18.66 +859 1 11.01 23.57 6.0 +860 1 7.29 17.47 30.27 +861 1 18.92 10.24 0.36 +862 1 22.76 24.44 27.3 +863 1 14.27 13.05 5.04 +864 1 3.42 14.59 30.9 +865 1 9.31 22.34 24.75 +866 1 25.78 16.96 15.63 +867 1 7.18 22.01 12.25 +868 1 5.0 18.29 28.57 +869 1 23.36 20.87 22.7 +870 1 13.16 10.8 10.17 +871 1 6.42 24.78 7.47 +872 1 28.86 3.89 20.92 +873 1 4.8 3.05 13.07 +874 1 27.07 3.53 5.63 +875 1 13.11 28.33 23.92 +876 1 14.84 13.88 20.8 +877 1 15.81 7.0 16.91 +878 1 23.41 25.39 20.56 +879 1 26.08 0.43 14.19 +880 1 6.28 17.41 19.28 +881 1 2.74 4.79 19.54 +882 1 20.98 26.42 10.11 +883 1 24.18 28.48 29.18 +884 1 12.74 29.99 12.8 +885 1 27.22 16.82 18.13 +886 1 2.08 19.98 18.27 +887 1 22.0 23.67 17.16 +888 1 17.83 3.01 29.13 +889 1 9.59 26.62 13.51 +890 1 11.48 2.18 13.45 +891 1 13.57 15.29 26.47 +892 1 1.72 0.72 9.92 +893 1 2.14 30.76 17.27 +894 1 17.9 15.88 1.47 +895 1 13.47 5.84 28.76 +896 1 8.96 22.14 21.0 +897 1 12.96 24.15 0.94 +898 1 26.13 23.25 8.89 +899 1 6.01 28.65 6.08 +900 1 22.88 20.21 6.1 +901 1 30.34 20.77 10.49 +902 1 12.19 28.16 10.6 +903 1 5.8 5.33 30.84 +904 1 29.83 26.29 15.91 +905 1 18.28 0.14 5.58 +906 1 1.91 17.34 5.88 +907 1 24.05 18.42 22.53 +908 1 10.82 21.55 3.57 +909 1 11.29 26.73 5.6 +910 1 21.34 14.41 3.22 +911 1 12.61 18.99 24.17 +912 1 25.02 18.6 25.9 +913 1 29.0 21.05 13.14 +914 1 17.72 27.28 30.27 +915 1 30.56 24.81 23.12 +916 1 17.09 20.05 24.02 +917 1 7.35 6.83 21.31 +918 1 3.39 22.32 21.05 +919 1 2.28 29.8 30.23 +920 1 5.29 25.66 14.8 +921 1 26.16 30.72 21.04 +922 1 21.63 6.32 11.68 +923 1 15.45 18.06 4.65 +924 1 5.76 28.33 24.04 +925 1 15.08 29.21 16.09 +926 1 18.76 6.14 6.94 +927 1 22.31 30.25 26.46 +928 1 18.49 22.04 30.93 +929 1 11.15 16.42 9.89 +930 1 4.34 7.98 30.25 +931 1 9.29 29.92 8.58 +932 1 22.97 27.09 8.04 +933 1 20.71 16.7 15.75 +934 1 30.36 7.49 5.24 +935 1 29.56 19.54 0.83 +936 1 30.71 14.04 20.91 +937 1 19.36 4.06 27.14 +938 1 23.41 10.8 2.14 +939 1 1.51 1.32 0.44 +940 1 8.16 14.39 1.63 +941 1 20.66 6.74 4.62 +942 1 20.78 26.26 3.85 +943 1 5.11 15.12 21.64 +944 1 12.53 20.03 17.67 +945 1 28.63 18.4 12.56 +946 1 1.95 21.69 8.08 +947 1 21.53 0.93 7.84 +948 1 2.69 22.51 17.17 +949 1 19.29 22.12 6.05 +950 1 23.68 2.14 11.01 +951 1 27.14 17.8 3.72 +952 1 2.22 14.81 3.31 +953 1 23.1 6.43 14.62 +954 1 0.22 12.59 3.57 +955 1 13.21 22.86 3.67 +956 1 13.45 2.1 20.14 +957 1 12.52 17.12 0.46 +958 1 3.07 27.45 9.03 +959 1 15.33 10.95 11.78 +960 1 0.05 4.26 9.75 +961 1 23.05 16.98 24.69 +962 1 16.15 16.28 6.51 +963 1 30.05 28.87 9.61 +964 1 6.67 29.5 16.95 +965 1 21.95 14.44 14.94 +966 1 22.58 22.47 30.33 +967 1 21.34 19.29 9.9 +968 1 29.31 21.79 20.79 +969 1 5.55 2.56 30.23 +970 1 25.88 3.17 22.22 +971 1 22.38 18.32 30.08 +972 1 6.27 19.24 8.86 +973 1 0.34 24.29 1.49 +974 1 20.49 24.13 0.25 +975 1 2.94 1.41 2.74 +976 1 24.88 25.38 7.35 +977 1 28.18 14.89 14.6 +978 1 7.84 30.36 4.39 +979 1 14.54 9.59 14.4 +980 1 27.63 12.3 15.83 +981 1 11.15 14.17 27.97 +982 1 25.27 20.88 8.35 +983 1 17.06 14.76 27.78 +984 1 3.9 14.79 15.06 +985 1 13.81 3.82 17.03 +986 1 28.55 24.1 26.15 +987 1 29.28 21.79 15.76 +988 1 15.05 30.12 27.83 +989 1 15.42 3.77 6.76 +990 1 22.65 12.12 11.24 +991 1 11.29 4.96 2.18 +992 1 2.15 7.43 7.57 +993 1 30.21 10.13 26.21 +994 1 24.42 22.18 4.42 +995 1 8.68 14.72 22.08 +996 1 23.1 6.9 27.1 +997 1 18.71 27.2 21.72 +998 1 14.12 12.7 30.76 +999 1 18.81 6.5 10.98 +1000 1 26.66 15.4 4.83 diff --git a/examples/PACKAGES/pair_3b_table/spce.in b/examples/PACKAGES/pair_3b_table/spce.in new file mode 100644 index 0000000000..c5b72c4f9a --- /dev/null +++ b/examples/PACKAGES/pair_3b_table/spce.in @@ -0,0 +1,43 @@ +log none + +units real +atom_style atomic + +read_data spce.data + +#hybrid pair style consisting of +#pair_style table to read in CG pair potential +#pair_style 3b/table for tabulated 3b interactions +pair_style hybrid/overlay table linear 1200 3b/table + +#pair coefficients +pair_coeff 1 1 table table_CG_CG.txt VOTCA +pair_coeff * * 3b/table spce.3b type + +#nvt run with nose-hoover thermostat +#time coupling of 100 ts for thermostat +#target T is 300 K +fix 1 all nvt temp 300.0 300.0 200.0 + +#create initial velocities +velocity all create 300 432567 dist uniform +#remove center of mass linear momentum +velocity all zero linear + +#remove center of mass linear momentum every 1000 time steps in each cartesian direction +fix remove all momentum 1000 linear 1 1 1 + +#timestep of 2 fs +timestep 2.0 + +#print out thermodynamic info every 100 ts +thermo 100 + +#run 10000 ts +run 10000 + +#write out dump file every 10 ts for 100000 ts +dump 2 all custom 10 spce.dump id type x y z fx fy fz +run 100000 + +undump 2 diff --git a/examples/PACKAGES/pair_3b_table/spce_2.3b b/examples/PACKAGES/pair_3b_table/spce_2.3b new file mode 100644 index 0000000000..52fcd1e5e9 --- /dev/null +++ b/examples/PACKAGES/pair_3b_table/spce_2.3b @@ -0,0 +1,71 @@ +type1 +type1 +type1 +3.7 # cut in Ang +1-1-1.table +ENTRY1 +linear +12 +type1 +type1 +type2 +3.7 # cut in Ang +1-1-2.table +ENTRY1 +linear +12 +type1 +type2 +type1 +3.7 # cut in Ang +1-1-2.table +ENTRY1 +linear +12 +type1 +type2 +type2 +3.7 # cut in Ang +1-1-1.table +ENTRY1 +linear +12 +type2 +type1 +type1 +3.7 # cut in Ang +1-1-1.table +ENTRY1 +linear +12 +type2 +type1 +type2 +3.7 # cut in Ang +1-1-2.table +ENTRY1 +linear +12 +type2 +type2 +type1 +3.7 # cut in Ang +1-1-2.table +ENTRY1 +linear +12 +type2 +type2 +type2 +3.7 # cut in Ang +1-1-1.table +ENTRY1 +linear +12 + + + + + + + diff --git a/examples/PACKAGES/pair_3b_table/spce_2.data b/examples/PACKAGES/pair_3b_table/spce_2.data new file mode 100644 index 0000000000..a0dbff24e5 --- /dev/null +++ b/examples/PACKAGES/pair_3b_table/spce_2.data @@ -0,0 +1,1016 @@ +Data File for CG Water + +1000 atoms +2 atom types + +0 31.0648 xlo xhi +0 31.0648 ylo yhi +0 31.0648 zlo zhi + +Masses + +1 18.0154 +2 18.0154 + +Atoms + +1 2 18.26 24.7 15.77 +2 2 12.63 1.42 27.01 +3 2 10.39 29.11 13.56 +4 2 26.47 16.64 7.23 +5 2 10.66 23.41 27.33 +6 2 19.08 3.2 21.63 +7 2 11.17 26.19 1.44 +8 2 4.61 4.04 25.72 +9 2 4.61 22.91 8.33 +10 2 30.61 22.71 25.18 +11 2 6.38 18.92 16.87 +12 2 17.83 12.53 11.09 +13 2 14.89 2.43 22.44 +14 2 28.36 30.9 26.38 +15 2 25.73 28.56 8.32 +16 2 19.61 20.22 4.43 +17 2 25.96 30.32 24.22 +18 2 14.51 17.35 16.41 +19 2 30.23 17.26 10.71 +20 2 22.68 23.23 2.3 +21 2 10.89 15.76 14.33 +22 2 1.46 20.46 12.48 +23 2 12.73 19.57 2.71 +24 2 1.21 12.02 9.88 +25 2 2.63 14.4 23.71 +26 2 16.91 20.37 4.73 +27 2 28.02 7.7 30.08 +28 2 21.22 22.47 19.66 +29 2 14.0 28.15 0.14 +30 2 19.62 19.73 1.11 +31 2 28.29 24.36 10.15 +32 2 14.05 1.1 17.64 +33 2 12.2 23.75 24.83 +34 2 24.56 26.02 13.57 +35 2 12.13 8.39 7.17 +36 2 20.47 22.28 25.02 +37 2 11.06 7.63 24.11 +38 2 6.52 22.64 30.46 +39 2 16.51 24.78 18.58 +40 2 30.18 20.56 29.19 +41 2 25.26 7.8 25.98 +42 2 20.37 4.16 3.88 +43 2 18.85 27.34 27.83 +44 2 17.72 29.84 12.78 +45 2 19.26 14.48 19.38 +46 2 29.73 4.46 4.96 +47 2 9.52 26.27 30.33 +48 2 6.55 9.25 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2.14 30.76 17.27 +894 1 17.9 15.88 1.47 +895 1 13.47 5.84 28.76 +896 1 8.96 22.14 21.0 +897 1 12.96 24.15 0.94 +898 1 26.13 23.25 8.89 +899 1 6.01 28.65 6.08 +900 1 22.88 20.21 6.1 +901 1 30.34 20.77 10.49 +902 1 12.19 28.16 10.6 +903 1 5.8 5.33 30.84 +904 1 29.83 26.29 15.91 +905 1 18.28 0.14 5.58 +906 1 1.91 17.34 5.88 +907 1 24.05 18.42 22.53 +908 1 10.82 21.55 3.57 +909 1 11.29 26.73 5.6 +910 1 21.34 14.41 3.22 +911 1 12.61 18.99 24.17 +912 1 25.02 18.6 25.9 +913 1 29.0 21.05 13.14 +914 1 17.72 27.28 30.27 +915 1 30.56 24.81 23.12 +916 1 17.09 20.05 24.02 +917 1 7.35 6.83 21.31 +918 1 3.39 22.32 21.05 +919 1 2.28 29.8 30.23 +920 1 5.29 25.66 14.8 +921 1 26.16 30.72 21.04 +922 1 21.63 6.32 11.68 +923 1 15.45 18.06 4.65 +924 1 5.76 28.33 24.04 +925 1 15.08 29.21 16.09 +926 1 18.76 6.14 6.94 +927 1 22.31 30.25 26.46 +928 1 18.49 22.04 30.93 +929 1 11.15 16.42 9.89 +930 1 4.34 7.98 30.25 +931 1 9.29 29.92 8.58 +932 1 22.97 27.09 8.04 +933 1 20.71 16.7 15.75 +934 1 30.36 7.49 5.24 +935 1 29.56 19.54 0.83 +936 1 30.71 14.04 20.91 +937 1 19.36 4.06 27.14 +938 1 23.41 10.8 2.14 +939 1 1.51 1.32 0.44 +940 1 8.16 14.39 1.63 +941 1 20.66 6.74 4.62 +942 1 20.78 26.26 3.85 +943 1 5.11 15.12 21.64 +944 1 12.53 20.03 17.67 +945 1 28.63 18.4 12.56 +946 1 1.95 21.69 8.08 +947 1 21.53 0.93 7.84 +948 1 2.69 22.51 17.17 +949 1 19.29 22.12 6.05 +950 1 23.68 2.14 11.01 +951 1 27.14 17.8 3.72 +952 1 2.22 14.81 3.31 +953 1 23.1 6.43 14.62 +954 1 0.22 12.59 3.57 +955 1 13.21 22.86 3.67 +956 1 13.45 2.1 20.14 +957 1 12.52 17.12 0.46 +958 1 3.07 27.45 9.03 +959 1 15.33 10.95 11.78 +960 1 0.05 4.26 9.75 +961 1 23.05 16.98 24.69 +962 1 16.15 16.28 6.51 +963 1 30.05 28.87 9.61 +964 1 6.67 29.5 16.95 +965 1 21.95 14.44 14.94 +966 1 22.58 22.47 30.33 +967 1 21.34 19.29 9.9 +968 1 29.31 21.79 20.79 +969 1 5.55 2.56 30.23 +970 1 25.88 3.17 22.22 +971 1 22.38 18.32 30.08 +972 1 6.27 19.24 8.86 +973 1 0.34 24.29 1.49 +974 1 20.49 24.13 0.25 +975 1 2.94 1.41 2.74 +976 1 24.88 25.38 7.35 +977 1 28.18 14.89 14.6 +978 1 7.84 30.36 4.39 +979 1 14.54 9.59 14.4 +980 1 27.63 12.3 15.83 +981 1 11.15 14.17 27.97 +982 1 25.27 20.88 8.35 +983 1 17.06 14.76 27.78 +984 1 3.9 14.79 15.06 +985 1 13.81 3.82 17.03 +986 1 28.55 24.1 26.15 +987 1 29.28 21.79 15.76 +988 1 15.05 30.12 27.83 +989 1 15.42 3.77 6.76 +990 1 22.65 12.12 11.24 +991 1 11.29 4.96 2.18 +992 1 2.15 7.43 7.57 +993 1 30.21 10.13 26.21 +994 1 24.42 22.18 4.42 +995 1 8.68 14.72 22.08 +996 1 23.1 6.9 27.1 +997 1 18.71 27.2 21.72 +998 1 14.12 12.7 30.76 +999 1 18.81 6.5 10.98 +1000 1 26.66 15.4 4.83 diff --git a/examples/PACKAGES/pair_3b_table/spce_2.in b/examples/PACKAGES/pair_3b_table/spce_2.in new file mode 100644 index 0000000000..55db11b7cb --- /dev/null +++ b/examples/PACKAGES/pair_3b_table/spce_2.in @@ -0,0 +1,43 @@ +log none + +units real +atom_style atomic + +read_data spce_2.data + +#hybrid pair style consisting of +#pair_style table to read in CG pair potential +#pair_style 3b/table for tabulated 3b interactions +pair_style hybrid/overlay table linear 1200 3b/table + +#pair coefficients +pair_coeff * * table table_CG_CG.txt VOTCA +pair_coeff * * 3b/table spce_2.3b type1 type2 + +#nvt run with nose-hoover thermostat +#time coupling of 100 ts for thermostat +#target T is 300 K +fix 1 all nvt temp 300.0 300.0 200.0 + +#create initial velocities +velocity all create 300 432567 dist uniform +#remove center of mass linear momentum +velocity all zero linear + +#remove center of mass linear momentum every 1000 time steps in each cartesian direction +fix remove all momentum 1000 linear 1 1 1 + +#timestep of 2 fs +timestep 2.0 + +#print out thermodynamic info every 100 ts +thermo 100 + +#run 10000 ts +run 10000 + +#write out dump file every 10 ts for 100000 ts +dump 2 all custom 10 spce_2.dump id type x y z fx fy fz +run 100000 + +undump 2 diff --git a/examples/PACKAGES/pair_3b_table/table_CG_CG.txt b/examples/PACKAGES/pair_3b_table/table_CG_CG.txt new file mode 100644 index 0000000000..f4ccdd4b4e --- /dev/null +++ b/examples/PACKAGES/pair_3b_table/table_CG_CG.txt @@ -0,0 +1,1203 @@ +VOTCA +N 1200 R 0.010000 12.000000 + +1 1.0000000000e-02 1.5390100510e+15 2.1517330910e+16 +2 2.0000000000e-02 1.3370836560e+15 1.8774943350e+16 +3 3.0000000000e-02 1.1616510900e+15 1.6231560530e+16 +4 4.0000000000e-02 1.0092362200e+15 1.4101892510e+16 +5 5.0000000000e-02 8.7681900090e+14 1.2251648380e+16 +6 6.0000000000e-02 7.6177563290e+14 1.0644166230e+16 +7 7.0000000000e-02 6.6182657340e+14 9.2475943770e+15 +8 8.0000000000e-02 5.7499136800e+14 8.0342602660e+15 +9 9.0000000000e-02 4.9954940840e+14 6.9801221150e+15 +10 1.0000000000e-01 4.3400583970e+14 6.0642925570e+15 +11 1.1000000000e-01 3.7706193970e+14 5.2686247630e+15 +12 1.2000000000e-01 3.2758938550e+14 4.5773528620e+15 +13 1.3000000000e-01 2.8460789650e+14 3.9767795520e+15 +14 1.4000000000e-01 2.4726581000e+14 3.4550046890e+15 +15 1.5000000000e-01 2.1482320610e+14 3.0016894950e+15 +16 1.6000000000e-01 1.8663724620e+14 2.6078516910e+15 +17 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6.5247449720e-05 +1190 1.1900000000e+01 9.9027914890e-07 5.7253374050e-05 +1191 1.1910000000e+01 4.7794482020e-07 4.6374107540e-05 +1192 1.1920000000e+01 7.9430367210e-08 3.3872879470e-05 +1193 1.1930000000e+01 -1.9586145530e-07 2.1091406450e-05 +1194 1.1940000000e+01 -3.5038203430e-07 9.1537875640e-06 +1195 1.1950000000e+01 -3.9696232700e-07 -9.8173844310e-07 +1196 1.1960000000e+01 -3.5733509120e-07 -8.5097413050e-06 +1197 1.1970000000e+01 -2.6065437280e-07 -1.1346751290e-05 +1198 1.1980000000e+01 -1.4201270800e-07 -1.1393547340e-05 +1199 1.1990000000e+01 -4.0956496040e-08 -8.7451546660e-06 +1200 1.2000000000e+01 0.0000000000e+00 -1.0906638080e-06 From 48f477e4b4fe4ba38735b6113c9c18c6e65c1a7d Mon Sep 17 00:00:00 2001 From: Christoph Scherer Date: Thu, 26 May 2022 15:19:41 +0200 Subject: [PATCH 10/34] Update pair_sw_3b_table.rst Small correction --- doc/src/pair_sw_3b_table.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/src/pair_sw_3b_table.rst b/doc/src/pair_sw_3b_table.rst index 6ee13eb095..7c648446a5 100644 --- a/doc/src/pair_sw_3b_table.rst +++ b/doc/src/pair_sw_3b_table.rst @@ -1,7 +1,7 @@ -.. index:: pair_style sw_table +.. index:: pair_style sw_3b_table pair_style sw/3b/table command -=========================== +============================== Syntax """""" From 2a7407aa38abc38a6b66d9c11b1bdf819cbed74b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 26 May 2022 11:41:51 -0400 Subject: [PATCH 11/34] programming style updates --- doc/src/pair_3b_table.rst | 18 ++--- doc/src/pair_sw_3b_table.rst | 4 +- src/.gitignore | 4 + src/MANYBODY/pair_3b_table.cpp | 71 +++++++--------- src/MANYBODY/pair_3b_table.h | 99 ++++++----------------- src/MANYBODY/pair_sw_3b_table.cpp | 130 ++++++++++++------------------ src/MANYBODY/pair_sw_3b_table.h | 84 ++++--------------- 7 files changed, 137 insertions(+), 273 deletions(-) diff --git a/doc/src/pair_3b_table.rst b/doc/src/pair_3b_table.rst index 77d2dc7f1b..ae5e6c2a50 100644 --- a/doc/src/pair_3b_table.rst +++ b/doc/src/pair_3b_table.rst @@ -29,7 +29,7 @@ Description The *3b/table* style is a pair style for generic tabulated three-body interactions. It has been developed for (coarse-grained) simulations (of water) with Kernel-based machine learning (ML) potentials (:ref:`Scherer2 `). -As for the pair style :doc:`pair_style sw ` +As for the pair style :doc:`pair_style sw ` or :doc:`pair_style sw/table `, the energy of a system is computed as a sum over three-body terms: @@ -39,7 +39,7 @@ is computed as a sum over three-body terms: The summations in the formula are over all neighbors J and K of atom I within a cutoff distance :math:`cut`. -In contrast to the Stillinger-Weber potential, all forces are not calculated analytically, but +In contrast to the Stillinger-Weber potential, all forces are not calculated analytically, but read in from a three-body force/energy table which can be generated with the csg_ml app of VOTCA as available at: . @@ -63,7 +63,7 @@ pair_coeff command: .. code-block:: LAMMPS pair_coeff * * SiC.3b Si Si Si C - + The first 2 arguments must be \* \* so as to span all LAMMPS atom types. The first three Si arguments map LAMMPS atom types 1,2,3 to the Si element in the ".3b" file. The final C argument maps LAMMPS atom type 4 @@ -75,7 +75,7 @@ potentials. The three-body files have a ".3b" suffix. Lines that are not blank or comments (starting with #) define parameters for a triplet of -elements. The parameters in a single entry specify to the +elements. The parameters in a single entry specify to the (three-body) cutoff distance and the tabulated three-body interaction. A single entry then contains: @@ -100,18 +100,18 @@ If element 2 and element 3 are of the same type (e.g. SiCC), the distance :math:`r_{ij}` is varied in "N" steps from rmin to rmax and the distance :math:`r_{ik}` is varied from :math:`r_{ij}` to rmax. This can be done, due to the symmetry of the triplet. If element 2 and element 3 are not -of the same type (e.g. SiCSi), there is no additional symmetry and the +of the same type (e.g. SiCSi), there is no additional symmetry and the distance :math:`r_{ik}` is also varied from rmin to rmax in "N" steps. The angle :math:`\theta_{ijk}` is alsways varied in "2N" steps from (0.0 + 180.0/(4N)) to (180.0 - 180.0/(4N)). Therefore, the total number -of table entries is "M = N * N * (N+1)" for the symmetric (element 2 and element 3 +of table entries is "M = N * N * (N+1)" for the symmetric (element 2 and element 3 are of the same type) and "M = 2 * N * N * N" for the general case (element 2 and element 3 are not of the same type). The forces on all three particles I, J, and K of a triplet -of this type of thre-body interaction potential +of this type of thre-body interaction potential (:math:`\phi_3 (r_{ij}, r_{ik}, \theta_{ijk})`) lie within -the plane defined by the three inter-particle distance vectors +the plane defined by the three inter-particle distance vectors :math:`{\mathbf r}_{ij}`, :math:`{\mathbf r}_{ik}`, and :math:`{\mathbf r}_{jk}`. This property is used to project the forces onto the inter-particle distance vectors as follows @@ -215,7 +215,7 @@ principle be specific to the three elements of the configuration. However, the user must ensure that it makes physically sense. E.g., the tabulated three-body forces for the entries CSiC and CCSi should be the same exchanging :math:`r_{ij}` with -r_{ik}, :math:`f_{j1}` with :math:`f_{k1}`, +r_{ik}, :math:`f_{j1}` with :math:`f_{k1}`, and :math:`f_{j2}` with :math:`f_{k2}`. diff --git a/doc/src/pair_sw_3b_table.rst b/doc/src/pair_sw_3b_table.rst index 7c648446a5..97fcb63e34 100644 --- a/doc/src/pair_sw_3b_table.rst +++ b/doc/src/pair_sw_3b_table.rst @@ -112,7 +112,7 @@ The A, B, p, and q parameters are used only for two-body interactions. The :math:`\lambda` and :math:`\cos\theta_0` parameters, only used for three-body interactions in the original Stillinger-Weber style, are read in but ignored in this modified pair style. The :math:`\epsilon` parameter is only used -for two-body interactions in this modified pair style and not for the three-body +for two-body interactions in this modified pair style and not for the three-body terms. The :math:`\sigma` and *a* parameters are used for both two-body and three-body interactions. :math:`\gamma` is used only in the three-body interactions, but is defined for pairs of atoms. The non-annotated @@ -235,7 +235,7 @@ screening factors with parameter values from the ij pair and ik pairs. So :math:`\phi_3` for a C atom bonded to a Si atom and a second C atom will depend on the three-body parameters for the CSiC entry, and also on the two-body parameters for the CCC and CSiSi entries. Since the -order of the two neighbors is arbitrary, the three-body parameters +order of the two neighbors is arbitrary, the three-body parameters and the tabulated angular potential for entries CSiC and CCSi should be the same. Similarly, the two-body parameters for entries SiCC and CSiSi should also be the same. The diff --git a/src/.gitignore b/src/.gitignore index 6657256e8f..de157734fc 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -997,6 +997,8 @@ /neb.h /netcdf_units.cpp /netcdf_units.h +/pair_3b_table.cpp +/pair_3b_table.h /pair_adp.cpp /pair_adp.h /pair_agni.cpp @@ -1291,6 +1293,8 @@ /pair_sph_taitwater_morris.h /pair_sw.cpp /pair_sw.h +/pair_sw_3b_table.cpp +/pair_sw_3b_table.h /pair_sw_mod.cpp /pair_sw_mod.h /pair_tersoff.cpp diff --git a/src/MANYBODY/pair_3b_table.cpp b/src/MANYBODY/pair_3b_table.cpp index a2227d5161..fd91713af8 100644 --- a/src/MANYBODY/pair_3b_table.cpp +++ b/src/MANYBODY/pair_3b_table.cpp @@ -1,6 +1,6 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://www.lammps.org/ Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract @@ -46,19 +46,15 @@ enum{LINEAR}; /* ---------------------------------------------------------------------- */ -Pair3BTable::Pair3BTable(LAMMPS *lmp) : Pair(lmp) +Pair3BTable::Pair3BTable(LAMMPS *lmp) : Pair(lmp), params(nullptr), neighshort(nullptr) { single_enable = 0; restartinfo = 0; one_coeff = 1; manybody_flag = 1; centroidstressflag = CENTROID_NOTAVAIL; - unit_convert_flag = utils::get_supported_conversions(utils::ENERGY); - - params = nullptr; maxshort = 10; - neighshort = nullptr; } /* ---------------------------------------------------------------------- @@ -85,9 +81,9 @@ Pair3BTable::~Pair3BTable() void Pair3BTable::compute(int eflag, int vflag) { int i,j,k,ii,jj,kk,inum,jnum,jnumm1; - int itype,jtype,ktype,ijparam,ikparam,ijkparam; + int itype,jtype,ktype,ijparam,ijkparam; tagint itag,jtag; - double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; + 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; @@ -99,8 +95,6 @@ void Pair3BTable::compute(int eflag, int vflag) 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; @@ -178,7 +172,6 @@ void Pair3BTable::compute(int eflag, int vflag) for (kk = jj+1; kk < numshort; kk++) { k = neighshort[kk]; ktype = map[type[k]]; - ikparam = elem3param[itype][ktype][ktype]; ijkparam = elem3param[itype][jtype][ktype]; delr2[0] = x[k][0] - xtmp; @@ -186,8 +179,7 @@ void Pair3BTable::compute(int eflag, int vflag) delr2[2] = x[k][2] - ztmp; rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2]; - threebody(¶ms[ijparam],¶ms[ikparam],¶ms[ijkparam], - rsq1,rsq2,delr1,delr2,fi,fj,fk,eflag,evdwl); + threebody(¶ms[ijkparam],rsq1,rsq2,delr1,delr2,fi,fj,fk,eflag,evdwl); fxtmp += fi[0]; fytmp += fi[1]; @@ -230,9 +222,8 @@ void Pair3BTable::allocate() global settings ------------------------------------------------------------------------- */ -void Pair3BTable::settings(int narg, char **arg) +void Pair3BTable::settings(int narg, char ** /*arg*/) { - //one mre additional argument: number of table entries if (narg != 0) error->all(FLERR,"Illegal pair_style command"); } @@ -290,15 +281,9 @@ void Pair3BTable::read_file(char *file) // open file on proc 0 if (comm->me == 0) { - PotentialFileReader reader(lmp, file, "3b", unit_convert_flag); + PotentialFileReader reader(lmp, file, "3b/table", unit_convert_flag); char *line; - // transparently convert units for supported conversions - - int unit_convert = reader.get_unit_convert(); - double conversion_factor = utils::get_conversion_factor(utils::ENERGY, - unit_convert); - while ((line = reader.next_line(NPARAMS_PER_LINE))) { try { ValueTokenizer values(line); @@ -348,22 +333,22 @@ void Pair3BTable::read_file(char *file) std::string tablename_string = values.next_string(); params[nparams].tablenamelength = tablename_string.length()+1; memory->create(params[nparams].tablename, params[nparams].tablenamelength, "params.tablename"); - for (int x = 0; x < params[nparams].tablenamelength; ++x) { + for (int x = 0; x < params[nparams].tablenamelength; ++x) { params[nparams].tablename[x] = tablename_string[x]; } std::string keyword_string = values.next_string(); params[nparams].keywordlength = keyword_string.length()+1; memory->create(params[nparams].keyword, params[nparams].keywordlength, "params.keyword"); - for (int x = 0; x < params[nparams].keywordlength; ++x) { + for (int x = 0; x < params[nparams].keywordlength; ++x) { params[nparams].keyword[x] = keyword_string[x]; } std::string tablestyle_string = values.next_string(); char *tablestyle; memory->create(tablestyle, (tablestyle_string.length()+1), "tablestyle"); - for (int x = 0; x < (tablestyle_string.length()+1); ++x) { + for (int x = 0; x < ((int)tablestyle_string.length()+1); ++x) { tablestyle[x] = tablestyle_string[x]; - } - if (strcmp(tablestyle,"linear") == 0) params[nparams].tabstyle = LINEAR; + } + if (strcmp(tablestyle,"linear") == 0) params[nparams].tabstyle = LINEAR; else error->all(FLERR,"Unknown table style in 3b table"); params[nparams].tablength = values.next_int(); @@ -406,7 +391,7 @@ void Pair3BTable::read_file(char *file) if (comm->me == 0){ read_table(params[m].mltable,params[m].tablename,params[m].keyword,params[m].symmetric); } - + // broadcast read in 3btable to all processes bcast_table(params[m].mltable,params[m].symmetric); @@ -484,7 +469,7 @@ void Pair3BTable::read_table(Table *tb, char *file, char *keyword, bool symmetri line = reader.next_line(); param_extract(tb, line); - + // if it is a symmetric 3body interaction, less table entries are required if (symmetric == true){ memory->create(tb->r12file,tb->ninput*tb->ninput*(tb->ninput+1),"mltable:r12file"); @@ -721,7 +706,8 @@ void Pair3BTable::null_table(Table *tb) calculate potential u and force f at angle x ------------------------------------------------------------------------- */ -void Pair3BTable::uf_lookup(Param *pm, double r12, double r13, double theta, double &f11, double &f12, double &f21, double &f22, double &f31, double &f32, double &u) +void Pair3BTable::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; @@ -780,15 +766,13 @@ void Pair3BTable::uf_lookup(Param *pm, double r12, double r13, double theta, dou f22=pm->mltable->f22file[itable]; f31=pm->mltable->f31file[itable]; f32=pm->mltable->f32file[itable]; - } + } } /* ---------------------------------------------------------------------- */ -void Pair3BTable::threebody(Param *paramij, Param *paramik, Param *paramijk, - double rsq1, double rsq2, - double *delr1, double *delr2, - double *fi, double *fj, double *fk, int eflag, double &eng) +void Pair3BTable::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; @@ -807,7 +791,7 @@ void Pair3BTable::threebody(Param *paramij, Param *paramik, Param *paramijk, //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 swap them, as in lookup table always r13 > r12 do to symmetry reasons if (r12 > r13){ temp = r12; r12 = r13; @@ -818,15 +802,17 @@ void Pair3BTable::threebody(Param *paramij, Param *paramik, Param *paramijk, //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)) ){ + + 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{ + } else{ f11 = f12 = f21 = f22 = f31 = f32 = u = 0.0; } - // if the indices have been swapped, swap tehm back + // if the indices have been swapped, swap them back if (swapped == true){ temp = r12; r12 = r13; @@ -854,8 +840,5 @@ void Pair3BTable::threebody(Param *paramij, Param *paramik, Param *paramijk, fk[1] = delr2[1]*f31+(delr2[1]-delr1[1])*f32; fk[2] = delr2[2]*f31+(delr2[2]-delr1[2])*f32; - double epsilon = 0.5; - double epsilon2 = epsilon*epsilon; - if (eflag) eng = u; } diff --git a/src/MANYBODY/pair_3b_table.h b/src/MANYBODY/pair_3b_table.h index a864a9602c..a250fe1b2a 100644 --- a/src/MANYBODY/pair_3b_table.h +++ b/src/MANYBODY/pair_3b_table.h @@ -1,6 +1,6 @@ /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories + https://www.lammps.org/ Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #ifdef PAIR_CLASS - -PairStyle(3b/table,Pair3BTable) - +// clang-format off +PairStyle(3b/table,Pair3BTable); +// clang-format on #else #ifndef LMP_PAIR_3B_TABLE_H @@ -40,34 +40,35 @@ class Pair3BTable : public Pair { // struct for 3b/table struct Table { int ninput; - double rmin,rmax; - double *r12file,*r13file,*thetafile,*f11file,*f12file,*f21file,*f22file,*f31file,*f32file,*efile; + double rmin, rmax; + double *r12file, *r13file, *thetafile, *f11file, *f12file, *f21file, *f22file, *f31file, + *f32file, *efile; }; struct Param { - double cut,cutsq; - int ielement,jelement,kelement; - bool symmetric; // whether it is a symmetric table or not - int tablenamelength; // length of table name - char *tablename; // name of associated angular table - int keywordlength; // length of key in table - char *keyword; // key in table - int tabstyle,tablength; // length of interpolation table (not ninput) and style - Table *mltable; // 3b Table + double cut, cutsq; + int ielement, jelement, kelement; + bool symmetric; // whether it is a symmetric table or not + int tablenamelength; // length of table name + char *tablename; // name of associated angular table + int keywordlength; // length of key in table + char *keyword; // key in table + int tabstyle, tablength; // length of interpolation table (not ninput) and style + Table *mltable; // 3b Table }; protected: - double cutmax; // max cutoff for all elements - Param *params; // parameter set for an I-J-K interaction - int maxshort; // size of short neighbor list array - int *neighshort; // short neighbor list array + double cutmax; // max cutoff for all elements + Param *params; // parameter set for an I-J-K interaction + int maxshort; // size of short neighbor list array + int *neighshort; // short neighbor list array void settings(int, char **) override; virtual void allocate(); void read_file(char *); virtual void setup_params(); - void threebody(Param *, Param *, Param *, double, double, double *, double *, - double *, double *, double *, int, double &); + void threebody(Param *, double, double, double *, double *, double *, double *, double *, int, + double &); void read_table(Table *, char *, char *, bool); void bcast_table(Table *, bool); @@ -78,61 +79,11 @@ class Pair3BTable : public Pair { void param_extract(Table *, char *); - void uf_lookup(Param *, double, double, double, double &, double &, double &, double &, double &, double &, double &); + void uf_lookup(Param *, double, double, double, double &, double &, double &, double &, double &, + double &, double &); }; -} - +} // namespace LAMMPS_NS #endif #endif - -/* ERROR/WARNING messages: - -E: Illegal ... command - -Self-explanatory. Check the input script syntax and compare to the -documentation for the command. You can use -echo screen as a -command-line option when running LAMMPS to see the offending line. - -E: Incorrect args for pair coefficients - -Self-explanatory. Check the input script or data file. - -E: Pair style 3b/table requires atom IDs - -This is a requirement to use the 3b/table potential. - -E: Pair style 3b/table requires newton pair on - -See the newton command. This is a restriction to use the 3b/table -potential. - -E: All pair coeffs are not set - -All pair coefficients must be set in the data file or by the -pair_coeff command before running a simulation. - -E: Cannot open 3b/table potential file %s - -The specified 3b/table potential file cannot be opened. Check that the path -and name are correct. - -E: Incorrect format in 3b/table potential file - -Incorrect number of words per line in the potential file. - -E: Illegal 3b/table parameter - -One or more of the coefficients defined in the potential file is -invalid. - -E: Potential file has duplicate entry - -The potential file has more than one entry for the same element. - -E: Potential file is missing an entry - -The potential file does not have a needed entry. - -*/ diff --git a/src/MANYBODY/pair_sw_3b_table.cpp b/src/MANYBODY/pair_sw_3b_table.cpp index d9ef723123..1eac9d87a7 100644 --- a/src/MANYBODY/pair_sw_3b_table.cpp +++ b/src/MANYBODY/pair_sw_3b_table.cpp @@ -33,7 +33,6 @@ #include #include - using namespace LAMMPS_NS; using MathConst::DEG2RAD; @@ -44,25 +43,13 @@ using MathConst::RAD2DEG; enum { LINEAR, SPLINE }; -#define SMALL 0.001 -#define TINY 1.E-10 +static constexpr double TINY = 1.0e-10; /* ---------------------------------------------------------------------- */ -PairSW3BTable::PairSW3BTable(LAMMPS *lmp) : PairSW(lmp) +PairSW3BTable::PairSW3BTable(LAMMPS *lmp) : PairSW(lmp), table_params(nullptr) { - single_enable = 0; - restartinfo = 0; - one_coeff = 1; - manybody_flag = 1; - centroidstressflag = CENTROID_NOTAVAIL; - unit_convert_flag = utils::get_supported_conversions(utils::ENERGY); - - params = nullptr; - extended_params = nullptr; - - maxshort = 10; - neighshort = nullptr; + unit_convert_flag = utils::NOCONVERT; } /* ---------------------------------------------------------------------- @@ -73,9 +60,9 @@ PairSW3BTable::~PairSW3BTable() { if (copymode) return; - for (int m = 0; m < nparams; m++) free_param(&extended_params[m]); // free_param will call free_table + for (int m = 0; m < nparams; m++) free_param(&table_params[m]); // free_param will call free_table memory->destroy(params); - memory->destroy(extended_params); + memory->destroy(table_params); memory->destroy(elem3param); if (allocated) { @@ -201,8 +188,8 @@ void PairSW3BTable::compute(int eflag, int vflag) delr2[2] = x[k][2] - ztmp; rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2]; - threebody(¶ms[ijparam],¶ms[ikparam],¶ms[ijkparam], &extended_params[ijkparam], - rsq1,rsq2,delr1,delr2,fj,fk,eflag,evdwl); + threebody_table(¶ms[ijparam],¶ms[ikparam],&table_params[ijkparam], + rsq1,rsq2,delr1,delr2,fj,fk,eflag,evdwl); fxtmp -= fj[0] + fk[0]; fytmp -= fj[1] + fk[1]; @@ -234,22 +221,16 @@ void PairSW3BTable::read_file(char *file) { memory->sfree(params); params = nullptr; - memory->sfree(extended_params); - extended_params = nullptr; + memory->sfree(table_params); + table_params = nullptr; nparams = maxparam = 0; // open file on proc 0 if (comm->me == 0) { - PotentialFileReader reader(lmp, file, "sw", unit_convert_flag); + PotentialFileReader reader(lmp, file, "sw/3b", unit_convert_flag); char *line; - // transparently convert units for supported conversions - - int unit_convert = reader.get_unit_convert(); - double conversion_factor = utils::get_conversion_factor(utils::ENERGY, - unit_convert); - while ((line = reader.next_line(NPARAMS_PER_LINE))) { try { ValueTokenizer values(line); @@ -279,8 +260,8 @@ void PairSW3BTable::read_file(char *file) maxparam += DELTA; params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), "pair:params"); - extended_params = (Param_Extension *) memory->srealloc(extended_params,maxparam*sizeof(Param_Extension), - "pair:extended_params"); + table_params = (ParamTable *) memory->srealloc(table_params,maxparam*sizeof(ParamTable), + "pair:table_params"); // make certain all addional allocated storage is initialized // to avoid false positives when checking with valgrind @@ -305,42 +286,38 @@ void PairSW3BTable::read_file(char *file) // read parameters of angle table std::string tablename_string = values.next_string(); - extended_params[nparams].tablenamelength = tablename_string.length()+1; - memory->create(extended_params[nparams].tablename, extended_params[nparams].tablenamelength, "extended_params.tablename"); - for (int x = 0; x < extended_params[nparams].tablenamelength; ++x) { - extended_params[nparams].tablename[x] = tablename_string[x]; + table_params[nparams].tablenamelength = tablename_string.length()+1; + memory->create(table_params[nparams].tablename, table_params[nparams].tablenamelength, "table_params.tablename"); + for (int i = 0; i < table_params[nparams].tablenamelength; ++i) { + table_params[nparams].tablename[i] = tablename_string[i]; } std::string keyword_string = values.next_string(); - extended_params[nparams].keywordlength = keyword_string.length()+1; - memory->create(extended_params[nparams].keyword, extended_params[nparams].keywordlength, "extended_params.keyword"); - for (int x = 0; x < extended_params[nparams].keywordlength; ++x) { - extended_params[nparams].keyword[x] = keyword_string[x]; + table_params[nparams].keywordlength = keyword_string.length()+1; + memory->create(table_params[nparams].keyword, table_params[nparams].keywordlength, "table_params.keyword"); + for (int i = 0; i < table_params[nparams].keywordlength; ++i) { + table_params[nparams].keyword[i] = keyword_string[i]; } std::string tablestyle_string = values.next_string(); char *tablestyle; memory->create(tablestyle, (tablestyle_string.length()+1), "tablestyle"); - for (int x = 0; x < (tablestyle_string.length()+1); ++x) { - tablestyle[x] = tablestyle_string[x]; - } - if (strcmp(tablestyle,"linear") == 0) extended_params[nparams].tabstyle = LINEAR; - else if (strcmp(tablestyle,"spline") == 0) extended_params[nparams].tabstyle = SPLINE; + for (int i = 0; i < ((int)tablestyle_string.length()+1); ++i) { + tablestyle[i] = tablestyle_string[i]; + } + if (strcmp(tablestyle,"linear") == 0) table_params[nparams].tabstyle = LINEAR; + else if (strcmp(tablestyle,"spline") == 0) table_params[nparams].tabstyle = SPLINE; else error->all(FLERR,"Unknown table style of angle table file"); - extended_params[nparams].tablength = values.next_int(); + table_params[nparams].tablength = values.next_int(); } catch (TokenizerException &e) { error->one(FLERR, e.what()); } - if (unit_convert) { - params[nparams].epsilon *= conversion_factor; - } - if (params[nparams].epsilon < 0.0 || params[nparams].sigma < 0.0 || params[nparams].littlea < 0.0 || params[nparams].lambda < 0.0 || params[nparams].gamma < 0.0 || params[nparams].biga < 0.0 || params[nparams].bigb < 0.0 || params[nparams].powerp < 0.0 || params[nparams].powerq < 0.0 || params[nparams].tol < 0.0 || - extended_params[nparams].tabstyle < 0.0 || extended_params[nparams].tablength < 0.0) + table_params[nparams].tabstyle < 0.0 || table_params[nparams].tablength < 0.0) error->one(FLERR,"Illegal Stillinger-Weber parameter"); nparams++; @@ -352,64 +329,63 @@ void PairSW3BTable::read_file(char *file) if (comm->me != 0) { params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), "pair:params"); - extended_params = (Param_Extension *) memory->srealloc(extended_params,maxparam*sizeof(Param_Extension), "pair:extended_params"); + table_params = (ParamTable *) memory->srealloc(table_params,maxparam*sizeof(ParamTable), "pair:table_params"); } MPI_Bcast(params, maxparam*sizeof(Param), MPI_BYTE, 0, world); - MPI_Bcast(extended_params, maxparam*sizeof(Param_Extension), MPI_BYTE, 0, world); + MPI_Bcast(table_params, maxparam*sizeof(ParamTable), MPI_BYTE, 0, world); // for each set of parameters, broadcast table name and keyword and read angle table for (int m = 0; m < nparams; ++m){ if (comm->me != 0) { - memory->create(extended_params[m].tablename, extended_params[m].tablenamelength, "extended_params.tablename"); + memory->create(table_params[m].tablename, table_params[m].tablenamelength, "table_params.tablename"); } - MPI_Bcast(&extended_params[m].tablename, extended_params[m].tablenamelength, MPI_CHAR, 0, world); + MPI_Bcast(&table_params[m].tablename, table_params[m].tablenamelength, MPI_CHAR, 0, world); if (comm->me != 0) { - memory->create(extended_params[m].keyword, extended_params[m].keywordlength, "extended_params.keyword"); + memory->create(table_params[m].keyword, table_params[m].keywordlength, "table_params.keyword"); } - MPI_Bcast(&extended_params[m].keyword, extended_params[m].keywordlength, MPI_CHAR, 0, world); + MPI_Bcast(&table_params[m].keyword, table_params[m].keywordlength, MPI_CHAR, 0, world); // initialize angtable - memory->create(extended_params[m].angtable,1,"extended_params:angtable"); - null_table(extended_params[m].angtable); + memory->create(table_params[m].angtable,1,"table_params:angtable"); + null_table(table_params[m].angtable); // call read_table to read corresponding tabulated angle file (only called by process 0) - if (comm->me == 0) read_table(extended_params[m].angtable,extended_params[m].tablename,extended_params[m].keyword); + if (comm->me == 0) read_table(table_params[m].angtable,table_params[m].tablename,table_params[m].keyword); // broadcast read in angtable to all processes - bcast_table(extended_params[m].angtable); + bcast_table(table_params[m].angtable); // the following table manipulations are done in all processes // error check on table parameters - if (extended_params[m].angtable->ninput <= 1) error->one(FLERR,"Invalid angle table length"); + if (table_params[m].angtable->ninput <= 1) error->one(FLERR,"Invalid angle table length"); // error check on parameter range of angle table double alo,ahi; - alo = extended_params[m].angtable->afile[0]; - ahi = extended_params[m].angtable->afile[extended_params[m].angtable->ninput-1]; + alo = table_params[m].angtable->afile[0]; + ahi = table_params[m].angtable->afile[table_params[m].angtable->ninput-1]; if (fabs(alo-0.0) > TINY || fabs(ahi-180.0) > TINY) error->all(FLERR,"Angle table must range from 0 to 180 degrees"); // convert theta from degrees to radians - for (int i = 0; i < extended_params[m].angtable->ninput; ++i){ - extended_params[m].angtable->afile[i] *= MY_PI/180.0; - extended_params[m].angtable->ffile[i] *= 180.0/MY_PI; + for (int i = 0; i < table_params[m].angtable->ninput; ++i){ + table_params[m].angtable->afile[i] *= MY_PI/180.0; + table_params[m].angtable->ffile[i] *= 180.0/MY_PI; } // spline read-in table and compute a,e,f vectors within table - spline_table(extended_params[m].angtable); + spline_table(table_params[m].angtable); // compute_table needs parameter params[m].length for this specific interaction as - // read in value length from .sw file can be different from value in angle table file - compute_table(extended_params[m].angtable,extended_params[m].tablength); + // read in value length from .sw file can be different from value in angle table file + compute_table(table_params[m].angtable,table_params[m].tablength); } } /* ---------------------------------------------------------------------- */ -void PairSW3BTable::threebody(Param *paramij, Param *paramik, Param *paramijk, Param_Extension *extended_paramijk, - double rsq1, double rsq2, - double *delr1, double *delr2, - double *fj, double *fk, int eflag, double &eng) +void PairSW3BTable::threebody_table(Param *paramij, Param *paramik, ParamTable *table_paramijk, + double rsq1, double rsq2, double *delr1, double *delr2, + double *fj, double *fk, int eflag, double &eng) { double r1,rinvsq1,rainv1,gsrainv1,gsrainvsq1,expgsrainv1; double r2,rinvsq2,rainv2,gsrainv2,gsrainvsq2,expgsrainv2; @@ -440,7 +416,7 @@ void PairSW3BTable::threebody(Param *paramij, Param *paramik, Param *paramijk, P // look up energy (f(theta), ftheta) and force (df(theta)/dtheta, fprimetheta) at // angle theta (var) in angle table belonging to parameter set paramijk - uf_lookup(extended_paramijk, var, ftheta, fprimetheta); + uf_lookup(table_paramijk, var, ftheta, fprimetheta); acosprime = 1.0 / (sqrt(1 - cs*cs ) ); @@ -469,7 +445,7 @@ void PairSW3BTable::threebody(Param *paramij, Param *paramik, Param *paramijk, P void PairSW3BTable::read_table(Table *tb, char *file, char *keyword) { - TableFileReader reader(lmp, file, "angle"); + TableFileReader reader(lmp, file, "3b/table"); char *line = reader.find_section_start(keyword); @@ -642,7 +618,7 @@ void PairSW3BTable::free_table(Table *tb) /* ---------------------------------------------------------------------- */ -void PairSW3BTable::free_param(Param_Extension *pm) +void PairSW3BTable::free_param(ParamTable *pm) { // call free_table to destroy associated angle table free_table(pm->angtable); @@ -753,7 +729,7 @@ double PairSW3BTable::splint(double *xa, double *ya, double *y2a, int n, double calculate potential u and force f at angle x ------------------------------------------------------------------------- */ -void PairSW3BTable::uf_lookup(Param_Extension *pm, double x, double &u, double &f) +void PairSW3BTable::uf_lookup(ParamTable *pm, double x, double &u, double &f) { if (!std::isfinite(x)) { error->one(FLERR, "Illegal angle in angle style table"); } diff --git a/src/MANYBODY/pair_sw_3b_table.h b/src/MANYBODY/pair_sw_3b_table.h index 3f537d432c..187b815c1c 100644 --- a/src/MANYBODY/pair_sw_3b_table.h +++ b/src/MANYBODY/pair_sw_3b_table.h @@ -32,7 +32,7 @@ class PairSW3BTable : public PairSW { static constexpr int NPARAMS_PER_LINE = 18; - // use struct Table from class AngleTable + // use struct Table as in class AngleTable struct Table { int ninput, fpflag; double fplo, fphi, theta0; @@ -41,87 +41,37 @@ class PairSW3BTable : public PairSW { double delta, invdelta, deltasq6; double *ang, *e, *de, *f, *df, *e2, *f2; }; - - struct Param_Extension { - int tablenamelength; // length of table name - char *tablename; // name of associated angular table - int keywordlength; // length of key in table - char *keyword; // key in table - int tabstyle,tablength; // length of interpolation table (not ninput) and style - Table *angtable; // angle table + + struct ParamTable { + int tablenamelength; // length of table name + char *tablename; // name of associated angular table + int keywordlength; // length of key in table + char *keyword; // key in table + int tabstyle, tablength; // length of interpolation table (not ninput) and style + Table *angtable; // angle table }; - + protected: - Param_Extension *extended_params; // parameter set for an I-J-K interaction - + ParamTable *table_params; // tabulated parameter set for an I-J-K interaction + void read_file(char *) override; - void threebody(Param *, Param *, Param *, Param_Extension*, double, double, double *, double *, double *, - double *, int, double &); + void threebody_table(Param *, Param *, ParamTable *, double, double, double *, double *, + double *, double *, int, double &); void read_table(Table *, char *, char *); void spline_table(Table *); - void compute_table(Table *,int length); + void compute_table(Table *, int length); void bcast_table(Table *); void null_table(Table *); void free_table(Table *); - void free_param(Param_Extension *); + void free_param(ParamTable *); void param_extract(Table *, char *); void spline(double *, double *, int, double, double, double *); double splint(double *, double *, double *, int, double); - void uf_lookup(Param_Extension *, double, double &, double &); + void uf_lookup(ParamTable *, double, double &, double &); }; } // namespace LAMMPS_NS #endif #endif - -/* ERROR/WARNING messages: - -E: Illegal ... command - -Self-explanatory. Check the input script syntax and compare to the -documentation for the command. You can use -echo screen as a -command-line option when running LAMMPS to see the offending line. - -E: Incorrect args for pair coefficients - -Self-explanatory. Check the input script or data file. - -E: Pair style Stillinger-Weber requires atom IDs - -This is a requirement to use the SW potential. - -E: Pair style Stillinger-Weber requires newton pair on - -See the newton command. This is a restriction to use the SW -potential. - -E: All pair coeffs are not set - -All pair coefficients must be set in the data file or by the -pair_coeff command before running a simulation. - -E: Cannot open Stillinger-Weber potential file %s - -The specified SW potential file cannot be opened. Check that the path -and name are correct. - -E: Incorrect format in Stillinger-Weber potential file - -Incorrect number of words per line in the potential file. - -E: Illegal Stillinger-Weber parameter - -One or more of the coefficients defined in the potential file is -invalid. - -E: Potential file has duplicate entry - -The potential file has more than one entry for the same element. - -E: Potential file is missing an entry - -The potential file does not have a needed entry. - -*/ From d9b560e70be3a31ee4886713dabcd1442d6bc289 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 26 May 2022 12:08:21 -0400 Subject: [PATCH 12/34] properly integrate into manual --- doc/src/Commands_pair.rst | 2 + doc/src/pair_3b_table.rst | 36 +++++++-------- doc/src/pair_style.rst | 2 + doc/src/pair_sw_3b_table.rst | 50 +++++++++++---------- doc/utils/sphinx-config/false_positives.txt | 7 +++ 5 files changed, 56 insertions(+), 41 deletions(-) diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index c5782f5e04..21a84a2518 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -34,6 +34,7 @@ OPT. * * * + * :doc:`3b/table ` * :doc:`adp (ko) ` * :doc:`agni (o) ` * :doc:`airebo (io) ` @@ -269,6 +270,7 @@ OPT. * :doc:`spin/neel ` * :doc:`srp ` * :doc:`sw (giko) ` + * :doc:`sw/3b/table ` * :doc:`sw/mod (o) ` * :doc:`table (gko) ` * :doc:`table/rx (k) ` diff --git a/doc/src/pair_3b_table.rst b/doc/src/pair_3b_table.rst index ae5e6c2a50..0a239883e4 100644 --- a/doc/src/pair_3b_table.rst +++ b/doc/src/pair_3b_table.rst @@ -1,4 +1,4 @@ -.. index:: pair_style 3b_table +.. index:: pair_style 3b/table pair_style 3b/table command =========================== @@ -26,22 +26,22 @@ Examples Description """"""""""" -The *3b/table* style is a pair style for generic tabulated three-body interactions. -It has been developed for (coarse-grained) simulations (of water) -with Kernel-based machine learning (ML) potentials (:ref:`Scherer2 `). -As for the pair style :doc:`pair_style sw ` -or :doc:`pair_style sw/table `, the energy of a system -is computed as a sum over three-body terms: +The *3b/table* style is a pair style for generic tabulated three-body +interactions. It has been developed for (coarse-grained) simulations +(of water) with Kernel-based machine learning (ML) potentials +(:ref:`Scherer2 `). As for the pair style :doc:`pair_style sw +` or :doc:`pair_style sw/3b/table `, the energy of +a system is computed as a sum over three-body terms: .. math:: E = \sum_i \sum_{j \neq i} \sum_{k > j} \phi_3 (r_{ij}, r_{ik}, \theta_{ijk}) -The summations in the formula are over all neighbors J -and K of atom I within a cutoff distance :math:`cut`. -In contrast to the Stillinger-Weber potential, all forces are not calculated analytically, but -read in from a three-body force/energy table which can be generated with -the csg_ml app of VOTCA as available at: . +The summations in the formula are over all neighbors J and K of atom I +within a cutoff distance :math:`cut`. In contrast to the +Stillinger-Weber potential, all forces are not calculated analytically, +but read in from a three-body force/energy table which can be generated +with the csg_ml app of VOTCA as available at: https://gitlab.mpcdf.mpg.de/votca/votca. Only a single pair_coeff command is used with the *3b/table* style which specifies a three-body potential (".3b") file with parameters for all @@ -102,14 +102,14 @@ If element 2 and element 3 are of the same type (e.g. SiCC), the distance due to the symmetry of the triplet. If element 2 and element 3 are not of the same type (e.g. SiCSi), there is no additional symmetry and the distance :math:`r_{ik}` is also varied from rmin to rmax in "N" steps. -The angle :math:`\theta_{ijk}` is alsways varied in "2N" steps from +The angle :math:`\theta_{ijk}` is always varied in "2N" steps from (0.0 + 180.0/(4N)) to (180.0 - 180.0/(4N)). Therefore, the total number of table entries is "M = N * N * (N+1)" for the symmetric (element 2 and element 3 are of the same type) and "M = 2 * N * N * N" for the general case (element 2 and element 3 are not of the same type). The forces on all three particles I, J, and K of a triplet -of this type of thre-body interaction potential +of this type of three-body interaction potential (:math:`\phi_3 (r_{ij}, r_{ik}, \theta_{ijk})`) lie within the plane defined by the three inter-particle distance vectors :math:`{\mathbf r}_{ij}`, :math:`{\mathbf r}_{ik}`, and :math:`{\mathbf r}_{jk}`. @@ -187,13 +187,13 @@ one that matches the specified *keyword* of appropriate section of the ".3b" fil At the moment, only the *style* *linear* is allowed and implemented. After reading in the force table, it is internally stored in LAMMPS as a lookup table. For each triplet -configuration occuring in the simulation within the cutoff distance, +configuration occurring in the simulation within the cutoff distance, the next nearest tabulated triplet configuration is looked up. No interpolation is done. This allows for a very efficient force calculation with the stored force constants and energies. Due to the know table structure, the lookup can be done efficiently. It has been tested (:ref:`Scherer2 `) that with a reasonably small bin size, the accuracy and speed is comparable to that of a Stillinger-Weber potential -with tabulated three-body interactions (:doc:`pair_style sw/table `) while +with tabulated three-body interactions (:doc:`pair_style sw/table `) while the table format of this pair style allows for more flexible three-body interactions. As for the Stillinger-Weber potential, the three-body potential file must contain entries for all the @@ -254,12 +254,12 @@ in the tutorial folder. Related commands """""""""""""""" -:doc:`pair_coeff ` +:doc:`pair_coeff `, :doc:`pair sw/3b/table ` ---------- .. _Scherer2: -**(Scherer2)** C. Scherer, R. Scheid, D. Andrienko, and T. Bereau, J. Chem. Theor. Comp. 16, 3194–3204 (2020). +**(Scherer2)** C. Scherer, R. Scheid, D. Andrienko, and T. Bereau, J. Chem. Theor. Comp. 16, 3194-3204 (2020). diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 2bcd66590d..d24596e2fa 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -112,6 +112,7 @@ accelerated styles exist. * :doc:`hybrid/scaled ` - multiple styles of scaled superposed pairwise interactions * :doc:`zero ` - neighbor list but no interactions +* :doc:`3b/table ` - generic tabulated three-body potential * :doc:`adp ` - angular dependent potential (ADP) of Mishin * :doc:`agni ` - AGNI machine-learning potential * :doc:`airebo ` - AIREBO potential of Stuart @@ -348,6 +349,7 @@ accelerated styles exist. * :doc:`spin/neel ` - * :doc:`srp ` - * :doc:`sw ` - Stillinger-Weber 3-body potential +* :doc:`sw/3b/table ` - Stillinger-Weber potential with tabulated 3-body term * :doc:`sw/mod ` - modified Stillinger-Weber 3-body potential * :doc:`table ` - tabulated pair potential * :doc:`table/rx ` - diff --git a/doc/src/pair_sw_3b_table.rst b/doc/src/pair_sw_3b_table.rst index 97fcb63e34..2d57803a61 100644 --- a/doc/src/pair_sw_3b_table.rst +++ b/doc/src/pair_sw_3b_table.rst @@ -1,4 +1,4 @@ -.. index:: pair_style sw_3b_table +.. index:: pair_style sw/3b/table pair_style sw/3b/table command ============================== @@ -26,10 +26,12 @@ Examples Description """"""""""" -The *sw/3b/table* style is a modification of the original :doc:`pair_style sw `. It has been -developed for coarse-grained simulations (of water) (:ref:`Scherer1 `), -but can be employed for all kinds of systems. It computes a modified 3-body :ref:`Stillinger-Weber ` -potential for the energy E of a system of atoms as +The *sw/3b/table* style is a modification of the original +:doc:`pair_style sw `. It has been developed for coarse-grained +simulations (of water) (:ref:`Scherer1 `), but can be employed +for all kinds of systems. It computes a modified 3-body +:ref:`Stillinger-Weber ` potential for the energy E of a +system of atoms as .. math:: @@ -48,8 +50,8 @@ three-body term. The summations in the formula are over all neighbors J and K of atom I within a cutoff distance :math:`a \sigma`. In contrast to the original *sw* style, *sw/3b/table* allows for a flexible three-body term :math:`f^{\textrm{3b}}\left(\theta_{ijk}\right)` which is read in -as a tabulated interaction. It can be parametrized with the csg_fmatch app of VOTCA -as available at: . +as a tabulated interaction. It can be parameterized with the csg_fmatch app of VOTCA +as available at: https://gitlab.mpcdf.mpg.de/votca/votca. Only a single pair_coeff command is used with the *sw/3b/table* style which specifies a modified Stillinger-Weber potential file with parameters for all @@ -191,19 +193,21 @@ are estimated (less accurately) by the first two and last two derivative values in the table. The "EQ" parameter is also optional. If used, it is followed by a the -equilibrium angle value, which is used, for example, by the :doc:`fix shake ` command. If not used, the equilibrium angle is -set to 180.0. +equilibrium angle value, which is used, for example, by the :doc:`fix +shake ` command. If not used, the equilibrium angle is set to +180.0. -Following a blank line, the next N lines of the angular table file list the tabulated values. -On each line, the first value is the index from 1 to N, the second value is -the angle value (in degrees), the third value is the energy (in energy -units), and the fourth is -dE/d(theta) (also in energy units). The third -term is the energy of the 3-atom configuration for the specified -angle. The last term is the derivative of the energy with respect to -the angle (in degrees, not radians). Thus the units of the last term -are still energy, not force. The angle values must increase from one -line to the next. The angle values must also begin with 0.0 and end -with 180.0, i.e. span the full range of possible angles. +Following a blank line, the next N lines of the angular table file list +the tabulated values. On each line, the first value is the index from 1 +to N, the second value is the angle value (in degrees), the third value +is the energy (in energy units), and the fourth is -dE/d(theta) (also in +energy units). The third term is the energy of the 3-atom configuration +for the specified angle. The last term is the derivative of the energy +with respect to the angle (in degrees, not radians). Thus the units of +the last term are still energy, not force. The angle values must +increase from one line to the next. The angle values must also begin +with 0.0 and end with 180.0, i.e. span the full range of possible +angles. Note that one angular potential file can contain many sections, each with a tabulated potential. LAMMPS reads the file section by section until it finds @@ -282,8 +286,8 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" -This is a user pair style. For more information, see :ref:`Scherer1 `. It is only enabled -if LAMMPS was explicitly built with it. +This is a user pair style. For more information, see :ref:`Scherer1 +`. It is only enabled if LAMMPS was explicitly built with it. This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. @@ -294,12 +298,12 @@ in the tutorial folder. Related commands """""""""""""""" -:doc:`pair_coeff ` +:doc:`pair_coeff `, :doc:`pair_style sw `, :doc:`pair_style 3b/table ` ---------- -.. _Stillinger2: +.. _Stillinger3: **(Stillinger)** Stillinger and Weber, Phys Rev B, 31, 5262 (1985). diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index c8450c570b..083d25bd2f 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -94,6 +94,7 @@ amu Amzallag analytical Anders +Andrienko Andzelm Ang anglegrad @@ -239,6 +240,7 @@ benchmarking Bennet Berardi Beraun +Bereau berendsen Berendsen berger @@ -560,6 +562,7 @@ Crozier Cryst Crystallogr Csanyi +csg csh cshrc CSiC @@ -873,6 +876,7 @@ Eindhoven Eisenforschung Ejtehadi El +el elaplong elastance Electroneg @@ -1081,6 +1085,7 @@ fm fmackay fmag fmass +fmatch fmm fmt fmtlib @@ -2405,6 +2410,7 @@ Nstep Nsteplast Nstop nsub +Nsw Nswap nt Nt @@ -3034,6 +3040,7 @@ scalexz scaleyz Scalfi Schaik +Scheid Schilfgarde Schimansky Schiotz From 3ecb6bb54af747034da79c865492b415480537a5 Mon Sep 17 00:00:00 2001 From: Christoph Scherer Date: Fri, 27 May 2022 12:34:53 +0200 Subject: [PATCH 13/34] Update pair_3b_table.cpp Added (forgotten) line "u=pm->mltable->efile[itable];" to compute energy due to read in table values --- src/MANYBODY/pair_3b_table.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/MANYBODY/pair_3b_table.cpp b/src/MANYBODY/pair_3b_table.cpp index fd91713af8..6e908d6816 100644 --- a/src/MANYBODY/pair_3b_table.cpp +++ b/src/MANYBODY/pair_3b_table.cpp @@ -766,6 +766,7 @@ void Pair3BTable::uf_lookup(Param *pm, double r12, double r13, double theta, dou f22=pm->mltable->f22file[itable]; f31=pm->mltable->f31file[itable]; f32=pm->mltable->f32file[itable]; + u=pm->mltable->efile[itable]; } } From cfb3d6bdf87faa3f3eeaf1dbf79be8aa5c1aa771 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 27 May 2022 07:48:00 -0400 Subject: [PATCH 14/34] simplify, remove inactive code, plug memory leaks --- src/MANYBODY/pair_3b_table.cpp | 111 ++++++++++++++---------------- src/MANYBODY/pair_sw_3b_table.cpp | 15 ++-- 2 files changed, 56 insertions(+), 70 deletions(-) diff --git a/src/MANYBODY/pair_3b_table.cpp b/src/MANYBODY/pair_3b_table.cpp index 6e908d6816..00af61ee82 100644 --- a/src/MANYBODY/pair_3b_table.cpp +++ b/src/MANYBODY/pair_3b_table.cpp @@ -39,11 +39,6 @@ using MathConst::MY_PI; #define DELTA 4 -enum{LINEAR}; - -#define SMALL 0.001 -#define TINY 1.E-10 - /* ---------------------------------------------------------------------- */ Pair3BTable::Pair3BTable(LAMMPS *lmp) : Pair(lmp), params(nullptr), neighshort(nullptr) @@ -342,14 +337,9 @@ void Pair3BTable::read_file(char *file) for (int x = 0; x < params[nparams].keywordlength; ++x) { params[nparams].keyword[x] = keyword_string[x]; } - std::string tablestyle_string = values.next_string(); - char *tablestyle; - memory->create(tablestyle, (tablestyle_string.length()+1), "tablestyle"); - for (int x = 0; x < ((int)tablestyle_string.length()+1); ++x) { - tablestyle[x] = tablestyle_string[x]; - } - if (strcmp(tablestyle,"linear") == 0) params[nparams].tabstyle = LINEAR; - else error->all(FLERR,"Unknown table style in 3b table"); + auto tablestyle = values.next_string(); + if (tablestyle != "linear") + error->all(FLERR,"Unknown table style {} in 3b table", tablestyle); params[nparams].tablength = values.next_int(); } catch (TokenizerException &e) { @@ -672,6 +662,8 @@ void Pair3BTable::free_param(Param *pm) // call free_table to destroy associated 3btable free_table(pm->mltable); // then destroy associated 3btable + memory->sfree(pm->tablename); + memory->sfree(pm->keyword); memory->sfree(pm->mltable); } @@ -716,58 +708,55 @@ void Pair3BTable::uf_lookup(Param *pm, double r12, double r13, double theta, dou //lookup scheme - if (pm->tabstyle == LINEAR) { - // if it is a symmetric 3body interaction, less table entries are required - if (pm->symmetric == true){ - 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 = 79; - } - itable = 0; - for (i=0; imltable->ninput-i); - } - itable += nr13; - itable *= (pm->mltable->ninput*2); - itable += ntheta; + // if it is a symmetric 3body interaction, less table entries are required + if (pm->symmetric == true){ + 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 = 79; + } + itable = 0; + for (i=0; imltable->ninput-i); + } + itable += nr13; + itable *= (pm->mltable->ninput*2); + itable += ntheta; + } else { // else, more (full) table entries are required - else{ - 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 = 79; - } - itable = nr12*(pm->mltable->ninput); - itable += nr13; - itable *= (pm->mltable->ninput*2); - itable += ntheta; + nr12 = (r12 - pm->mltable->rmin + 0.5*dr - 0.00000001)/dr; + if (r12 == (pm->mltable->rmin - 0.5*dr)){ + nr12 = 0; } - - 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]; + 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 = 79; + } + 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]; } /* ---------------------------------------------------------------------- */ diff --git a/src/MANYBODY/pair_sw_3b_table.cpp b/src/MANYBODY/pair_sw_3b_table.cpp index 1eac9d87a7..a614e428e0 100644 --- a/src/MANYBODY/pair_sw_3b_table.cpp +++ b/src/MANYBODY/pair_sw_3b_table.cpp @@ -297,15 +297,10 @@ void PairSW3BTable::read_file(char *file) for (int i = 0; i < table_params[nparams].keywordlength; ++i) { table_params[nparams].keyword[i] = keyword_string[i]; } - std::string tablestyle_string = values.next_string(); - char *tablestyle; - memory->create(tablestyle, (tablestyle_string.length()+1), "tablestyle"); - for (int i = 0; i < ((int)tablestyle_string.length()+1); ++i) { - tablestyle[i] = tablestyle_string[i]; - } - if (strcmp(tablestyle,"linear") == 0) table_params[nparams].tabstyle = LINEAR; - else if (strcmp(tablestyle,"spline") == 0) table_params[nparams].tabstyle = SPLINE; - else error->all(FLERR,"Unknown table style of angle table file"); + auto tablestyle = values.next_string(); + if (tablestyle == "linear") table_params[nparams].tabstyle = LINEAR; + else if (tablestyle == "spline") table_params[nparams].tabstyle = SPLINE; + else error->all(FLERR,"Unknown table style {} of 3b/table file", tablestyle); table_params[nparams].tablength = values.next_int(); } catch (TokenizerException &e) { @@ -623,6 +618,8 @@ void PairSW3BTable::free_param(ParamTable *pm) // call free_table to destroy associated angle table free_table(pm->angtable); // then destroy associated angle table + memory->sfree(pm->keyword); + memory->sfree(pm->tablename); memory->sfree(pm->angtable); } From 25f24fbab120740ed572fee9ffaf18e185b738ed Mon Sep 17 00:00:00 2001 From: Christoph Scherer Date: Wed, 1 Jun 2022 14:11:32 +0200 Subject: [PATCH 15/34] Update and rename pair_sw_3b_table.h to pair_sw_angle_table.h Renamed header file from sw/3b/table to sw/angle/table --- .../{pair_sw_3b_table.h => pair_sw_angle_table.h} | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) rename src/MANYBODY/{pair_sw_3b_table.h => pair_sw_angle_table.h} (91%) diff --git a/src/MANYBODY/pair_sw_3b_table.h b/src/MANYBODY/pair_sw_angle_table.h similarity index 91% rename from src/MANYBODY/pair_sw_3b_table.h rename to src/MANYBODY/pair_sw_angle_table.h index 187b815c1c..6257d18283 100644 --- a/src/MANYBODY/pair_sw_3b_table.h +++ b/src/MANYBODY/pair_sw_angle_table.h @@ -13,21 +13,21 @@ #ifdef PAIR_CLASS // clang-format off -PairStyle(sw/3b/table,PairSW3BTable); +PairStyle(sw/angle/table,PairSWAngleTable); // clang-format on #else -#ifndef LMP_PAIR_SW_3B_TABLE_H -#define LMP_PAIR_SW_3B_TABLE_H +#ifndef LMP_PAIR_SW_ANGLE_TABLE_H +#define LMP_PAIR_SW_ANGLE_TABLE_H #include "pair_sw.h" namespace LAMMPS_NS { -class PairSW3BTable : public PairSW { +class PairSWAngleTable : public PairSW { public: - PairSW3BTable(class LAMMPS *); - ~PairSW3BTable() override; + PairSWAngleTable(class LAMMPS *); + ~PairSWAngleTable() override; void compute(int, int) override; static constexpr int NPARAMS_PER_LINE = 18; From 8dfa4a8682644bbd52620953a62c94238c81d649 Mon Sep 17 00:00:00 2001 From: Christoph Scherer Date: Wed, 1 Jun 2022 14:20:30 +0200 Subject: [PATCH 16/34] Update and rename pair_sw_3b_table.cpp to pair_sw_angle_table.cpp Changed .cpp file for pair style sw/3b/table to sw/angle/table --- ...w_3b_table.cpp => pair_sw_angle_table.cpp} | 40 +++++++++---------- 1 file changed, 20 insertions(+), 20 deletions(-) rename src/MANYBODY/{pair_sw_3b_table.cpp => pair_sw_angle_table.cpp} (95%) diff --git a/src/MANYBODY/pair_sw_3b_table.cpp b/src/MANYBODY/pair_sw_angle_table.cpp similarity index 95% rename from src/MANYBODY/pair_sw_3b_table.cpp rename to src/MANYBODY/pair_sw_angle_table.cpp index a614e428e0..fbef0a6dd9 100644 --- a/src/MANYBODY/pair_sw_3b_table.cpp +++ b/src/MANYBODY/pair_sw_angle_table.cpp @@ -17,7 +17,7 @@ scherer@mpip-mainz.mpg.de ------------------------------------------------------------------------- */ -#include "pair_sw_3b_table.h" +#include "pair_sw_angle_table.h" #include "atom.h" #include "comm.h" @@ -47,7 +47,7 @@ static constexpr double TINY = 1.0e-10; /* ---------------------------------------------------------------------- */ -PairSW3BTable::PairSW3BTable(LAMMPS *lmp) : PairSW(lmp), table_params(nullptr) +PairSWAngleTable::PairSWAngleTable(LAMMPS *lmp) : PairSW(lmp), table_params(nullptr) { unit_convert_flag = utils::NOCONVERT; } @@ -56,7 +56,7 @@ PairSW3BTable::PairSW3BTable(LAMMPS *lmp) : PairSW(lmp), table_params(nullptr) check if allocated, since class can be destructed when incomplete ------------------------------------------------------------------------- */ -PairSW3BTable::~PairSW3BTable() +PairSWAngleTable::~PairSWAngleTable() { if (copymode) return; @@ -74,7 +74,7 @@ PairSW3BTable::~PairSW3BTable() /* ---------------------------------------------------------------------- */ -void PairSW3BTable::compute(int eflag, int vflag) +void PairSWAngleTable::compute(int eflag, int vflag) { int i,j,k,ii,jj,kk,inum,jnum,jnumm1; int itype,jtype,ktype,ijparam,ikparam,ijkparam; @@ -217,7 +217,7 @@ void PairSW3BTable::compute(int eflag, int vflag) /* ---------------------------------------------------------------------- */ -void PairSW3BTable::read_file(char *file) +void PairSWAngleTable::read_file(char *file) { memory->sfree(params); params = nullptr; @@ -228,7 +228,7 @@ void PairSW3BTable::read_file(char *file) // open file on proc 0 if (comm->me == 0) { - PotentialFileReader reader(lmp, file, "sw/3b", unit_convert_flag); + PotentialFileReader reader(lmp, file, "sw/angle/table", unit_convert_flag); char *line; while ((line = reader.next_line(NPARAMS_PER_LINE))) { @@ -300,7 +300,7 @@ void PairSW3BTable::read_file(char *file) auto tablestyle = values.next_string(); if (tablestyle == "linear") table_params[nparams].tabstyle = LINEAR; else if (tablestyle == "spline") table_params[nparams].tabstyle = SPLINE; - else error->all(FLERR,"Unknown table style {} of 3b/table file", tablestyle); + else error->all(FLERR,"Unknown table style {} of angle table file", tablestyle); table_params[nparams].tablength = values.next_int(); } catch (TokenizerException &e) { @@ -378,7 +378,7 @@ void PairSW3BTable::read_file(char *file) /* ---------------------------------------------------------------------- */ -void PairSW3BTable::threebody_table(Param *paramij, Param *paramik, ParamTable *table_paramijk, +void PairSWAngleTable::threebody_table(Param *paramij, Param *paramik, ParamTable *table_paramijk, double rsq1, double rsq2, double *delr1, double *delr2, double *fj, double *fk, int eflag, double &eng) { @@ -438,9 +438,9 @@ void PairSW3BTable::threebody_table(Param *paramij, Param *paramik, ParamTable * read table file, only called by proc 0 ------------------------------------------------------------------------- */ -void PairSW3BTable::read_table(Table *tb, char *file, char *keyword) +void PairSWAngleTable::read_table(Table *tb, char *file, char *keyword) { - TableFileReader reader(lmp, file, "3b/table"); + TableFileReader reader(lmp, file, "angle table"); char *line = reader.find_section_start(keyword); @@ -484,7 +484,7 @@ void PairSW3BTable::read_table(Table *tb, char *file, char *keyword) this function sets these values in e2file,f2file ------------------------------------------------------------------------- */ -void PairSW3BTable::spline_table(Table *tb) +void PairSWAngleTable::spline_table(Table *tb) { memory->create(tb->e2file, tb->ninput, "angle:e2file"); memory->create(tb->f2file, tb->ninput, "angle:f2file"); @@ -508,7 +508,7 @@ void PairSW3BTable::spline_table(Table *tb) compute a,e,f vectors from splined values ------------------------------------------------------------------------- */ -void PairSW3BTable::compute_table(Table *tb,int length) +void PairSWAngleTable::compute_table(Table *tb,int length) { // delta = table spacing in angle for N-1 bins @@ -558,7 +558,7 @@ void PairSW3BTable::compute_table(Table *tb,int length) ninput,afile,efile,ffile,fpflag,fplo,fphi,theta0 ------------------------------------------------------------------------- */ -void PairSW3BTable::bcast_table(Table *tb) +void PairSWAngleTable::bcast_table(Table *tb) { MPI_Bcast(&tb->ninput, 1, MPI_INT, 0, world); @@ -584,7 +584,7 @@ void PairSW3BTable::bcast_table(Table *tb) /* ---------------------------------------------------------------------- */ -void PairSW3BTable::null_table(Table *tb) +void PairSWAngleTable::null_table(Table *tb) { tb->afile = tb->efile = tb->ffile = nullptr; tb->e2file = tb->f2file = nullptr; @@ -594,7 +594,7 @@ void PairSW3BTable::null_table(Table *tb) /* ---------------------------------------------------------------------- */ -void PairSW3BTable::free_table(Table *tb) +void PairSWAngleTable::free_table(Table *tb) { memory->destroy(tb->afile); memory->destroy(tb->efile); @@ -613,7 +613,7 @@ void PairSW3BTable::free_table(Table *tb) /* ---------------------------------------------------------------------- */ -void PairSW3BTable::free_param(ParamTable *pm) +void PairSWAngleTable::free_param(ParamTable *pm) { // call free_table to destroy associated angle table free_table(pm->angtable); @@ -631,7 +631,7 @@ void PairSW3BTable::free_param(ParamTable *pm) only called by read_table, only called by proc 0 ------------------------------------------------------------------------- */ -void PairSW3BTable::param_extract(Table *tb, char *line) +void PairSWAngleTable::param_extract(Table *tb, char *line) { tb->ninput = 0; tb->fpflag = 0; @@ -668,7 +668,7 @@ void PairSW3BTable::param_extract(Table *tb, char *line) spline and splint routines modified from Numerical Recipes ------------------------------------------------------------------------- */ -void PairSW3BTable::spline(double *x, double *y, int n, double yp1, double ypn, double *y2) +void PairSWAngleTable::spline(double *x, double *y, int n, double yp1, double ypn, double *y2) { int i, k; double p, qn, sig, un; @@ -700,7 +700,7 @@ void PairSW3BTable::spline(double *x, double *y, int n, double yp1, double ypn, } /* ---------------------------------------------------------------------- */ -double PairSW3BTable::splint(double *xa, double *ya, double *y2a, int n, double x) +double PairSWAngleTable::splint(double *xa, double *ya, double *y2a, int n, double x) { int klo, khi, k; double h, b, a, y; @@ -726,7 +726,7 @@ double PairSW3BTable::splint(double *xa, double *ya, double *y2a, int n, double calculate potential u and force f at angle x ------------------------------------------------------------------------- */ -void PairSW3BTable::uf_lookup(ParamTable *pm, double x, double &u, double &f) +void PairSWAngleTable::uf_lookup(ParamTable *pm, double x, double &u, double &f) { if (!std::isfinite(x)) { error->one(FLERR, "Illegal angle in angle style table"); } From ebce66389e1d37b05689fd279625b1cfebb193b7 Mon Sep 17 00:00:00 2001 From: Christoph Scherer Date: Wed, 1 Jun 2022 14:24:40 +0200 Subject: [PATCH 17/34] Update and rename pair_sw_3b_table.rst to pair_sw_angle_table.rst changed documentation and file name from sw/3b/table to sw/angle/table --- ...sw_3b_table.rst => pair_sw_angle_table.rst} | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) rename doc/src/{pair_sw_3b_table.rst => pair_sw_angle_table.rst} (96%) diff --git a/doc/src/pair_sw_3b_table.rst b/doc/src/pair_sw_angle_table.rst similarity index 96% rename from doc/src/pair_sw_3b_table.rst rename to doc/src/pair_sw_angle_table.rst index 2d57803a61..a50b7eaaf5 100644 --- a/doc/src/pair_sw_3b_table.rst +++ b/doc/src/pair_sw_angle_table.rst @@ -1,6 +1,6 @@ -.. index:: pair_style sw/3b/table +.. index:: pair_style sw/angle/table -pair_style sw/3b/table command +pair_style sw/angle/table command ============================== Syntax @@ -10,7 +10,7 @@ Syntax pair_style style -* style = *sw/3b/table* +* style = *sw/angle/table* Examples @@ -18,7 +18,7 @@ Examples .. code-block:: LAMMPS - pair_style sw/3b/table + pair_style sw/angle/table pair_coeff * * spce.sw type pair_coeff * * GaN.sw Ga N Ga @@ -26,7 +26,7 @@ Examples Description """"""""""" -The *sw/3b/table* style is a modification of the original +The *sw/angle/table* style is a modification of the original :doc:`pair_style sw `. It has been developed for coarse-grained simulations (of water) (:ref:`Scherer1 `), but can be employed for all kinds of systems. It computes a modified 3-body @@ -48,12 +48,12 @@ system of atoms as where :math:`\phi_2` is a two-body term and :math:`\phi_3` is a three-body term. The summations in the formula are over all neighbors J and K of atom I within a cutoff distance :math:`a \sigma`. -In contrast to the original *sw* style, *sw/3b/table* allows for a flexible +In contrast to the original *sw* style, *sw/angle/table* allows for a flexible three-body term :math:`f^{\textrm{3b}}\left(\theta_{ijk}\right)` which is read in as a tabulated interaction. It can be parameterized with the csg_fmatch app of VOTCA as available at: https://gitlab.mpcdf.mpg.de/votca/votca. -Only a single pair_coeff command is used with the *sw/3b/table* style +Only a single pair_coeff command is used with the *sw/angle/table* style which specifies a modified Stillinger-Weber potential file with parameters for all needed elements. These are mapped to LAMMPS atom types by specifying N_el additional arguments after the ".sw" filename in the pair_coeff command, @@ -78,7 +78,7 @@ The first 2 arguments must be \* \* so as to span all LAMMPS atom types. The first three Si arguments map LAMMPS atom types 1,2,3 to the Si element in the SW file. The final C argument maps LAMMPS atom type 4 to the C element in the SW file. If a mapping value is specified as -NULL, the mapping is not performed. This can be used when a *sw/3b/table* +NULL, the mapping is not performed. This can be used when a *sw/angle/table* potential is used as part of the *hybrid* pair style. The NULL values are placeholders for atom types that will be used with other potentials. @@ -298,7 +298,7 @@ in the tutorial folder. Related commands """""""""""""""" -:doc:`pair_coeff `, :doc:`pair_style sw `, :doc:`pair_style 3b/table ` +:doc:`pair_coeff `, :doc:`pair_style sw `, :doc:`pair_style threebody/table ` ---------- From 5756dedfed15bdabdfa8dde85b34edf33f45b7ad Mon Sep 17 00:00:00 2001 From: Christoph Scherer Date: Wed, 1 Jun 2022 15:52:46 +0200 Subject: [PATCH 18/34] Update and rename pair_3b_table.h to pair_threebody_table.h changed pair style and file name of header file from 3b/table to threebody/table --- .../{pair_3b_table.h => pair_threebody_table.h} | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) rename src/MANYBODY/{pair_3b_table.h => pair_threebody_table.h} (88%) diff --git a/src/MANYBODY/pair_3b_table.h b/src/MANYBODY/pair_threebody_table.h similarity index 88% rename from src/MANYBODY/pair_3b_table.h rename to src/MANYBODY/pair_threebody_table.h index a250fe1b2a..218bfeebd8 100644 --- a/src/MANYBODY/pair_3b_table.h +++ b/src/MANYBODY/pair_threebody_table.h @@ -13,21 +13,21 @@ #ifdef PAIR_CLASS // clang-format off -PairStyle(3b/table,Pair3BTable); +PairStyle(threebody/table,PairThreebodyTable); // clang-format on #else -#ifndef LMP_PAIR_3B_TABLE_H -#define LMP_PAIR_3B_TABLE_H +#ifndef LMP_PAIR_THREEBODY_TABLE_H +#define LMP_PAIR_THREEBODY_TABLE_H #include "pair.h" namespace LAMMPS_NS { -class Pair3BTable : public Pair { +class PairThreebodyTable : public Pair { public: - Pair3BTable(class LAMMPS *); - ~Pair3BTable() override; + PairThreebodyTable(class LAMMPS *); + ~PairThreebodyTable() override; void compute(int, int) override; void coeff(int, char **) override; double init_one(int, int) override; @@ -37,7 +37,7 @@ class Pair3BTable : public Pair { // no write or read from binary restart file - // struct for 3b/table + // struct for threebody/table struct Table { int ninput; double rmin, rmax; @@ -54,7 +54,7 @@ class Pair3BTable : public Pair { int keywordlength; // length of key in table char *keyword; // key in table int tabstyle, tablength; // length of interpolation table (not ninput) and style - Table *mltable; // 3b Table + Table *mltable; // threebody table }; protected: From 187ccdd2223bb5cd2101e57789d45c5a8276f0fb Mon Sep 17 00:00:00 2001 From: Christoph Scherer Date: Wed, 1 Jun 2022 16:03:06 +0200 Subject: [PATCH 19/34] Update and rename pair_3b_table.cpp to pair_threebody_table.cpp changed pair 3b/table to pair threebody/table including name of .cpp file --- ..._3b_table.cpp => pair_threebody_table.cpp} | 84 +++++++++---------- 1 file changed, 42 insertions(+), 42 deletions(-) rename src/MANYBODY/{pair_3b_table.cpp => pair_threebody_table.cpp} (90%) diff --git a/src/MANYBODY/pair_3b_table.cpp b/src/MANYBODY/pair_threebody_table.cpp similarity index 90% rename from src/MANYBODY/pair_3b_table.cpp rename to src/MANYBODY/pair_threebody_table.cpp index 00af61ee82..201e2a77a2 100644 --- a/src/MANYBODY/pair_3b_table.cpp +++ b/src/MANYBODY/pair_threebody_table.cpp @@ -16,7 +16,7 @@ scherer@mpip-mainz.mpg.de ------------------------------------------------------------------------- */ -#include "pair_3b_table.h" +#include "pair_threebody_table.h" #include "atom.h" #include "comm.h" @@ -41,7 +41,7 @@ using MathConst::MY_PI; /* ---------------------------------------------------------------------- */ -Pair3BTable::Pair3BTable(LAMMPS *lmp) : Pair(lmp), params(nullptr), neighshort(nullptr) +PairThreebodyTable::PairThreebodyTable(LAMMPS *lmp) : Pair(lmp), params(nullptr), neighshort(nullptr) { single_enable = 0; restartinfo = 0; @@ -56,7 +56,7 @@ Pair3BTable::Pair3BTable(LAMMPS *lmp) : Pair(lmp), params(nullptr), neighshort(n check if allocated, since class can be destructed when incomplete ------------------------------------------------------------------------- */ -Pair3BTable::~Pair3BTable() +PairThreebodyTable::~PairThreebodyTable() { if (copymode) return; @@ -73,7 +73,7 @@ Pair3BTable::~Pair3BTable() /* ---------------------------------------------------------------------- */ -void Pair3BTable::compute(int eflag, int vflag) +void PairThreebodyTable::compute(int eflag, int vflag) { int i,j,k,ii,jj,kk,inum,jnum,jnumm1; int itype,jtype,ktype,ijparam,ijkparam; @@ -202,7 +202,7 @@ void Pair3BTable::compute(int eflag, int vflag) /* ---------------------------------------------------------------------- */ -void Pair3BTable::allocate() +void PairThreebodyTable::allocate() { allocated = 1; int n = atom->ntypes; @@ -217,7 +217,7 @@ void Pair3BTable::allocate() global settings ------------------------------------------------------------------------- */ -void Pair3BTable::settings(int narg, char ** /*arg*/) +void PairThreebodyTable::settings(int narg, char ** /*arg*/) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); } @@ -226,7 +226,7 @@ void Pair3BTable::settings(int narg, char ** /*arg*/) set coeffs for one or more type pairs ------------------------------------------------------------------------- */ -void Pair3BTable::coeff(int narg, char **arg) +void PairThreebodyTable::coeff(int narg, char **arg) { if (!allocated) allocate(); @@ -242,12 +242,12 @@ void Pair3BTable::coeff(int narg, char **arg) init specific to this pair style ------------------------------------------------------------------------- */ -void Pair3BTable::init_style() +void PairThreebodyTable::init_style() { if (atom->tag_enable == 0) - error->all(FLERR,"Pair style 3b/table requires atom IDs"); + error->all(FLERR,"Pair style threebody/table requires atom IDs"); if (force->newton_pair == 0) - error->all(FLERR,"Pair style 3b/table requires newton pair on"); + error->all(FLERR,"Pair style threebody/table requires newton pair on"); // need a full neighbor list @@ -258,7 +258,7 @@ void Pair3BTable::init_style() init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ -double Pair3BTable::init_one(int i, int j) +double PairThreebodyTable::init_one(int i, int j) { if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); @@ -267,7 +267,7 @@ double Pair3BTable::init_one(int i, int j) /* ---------------------------------------------------------------------- */ -void Pair3BTable::read_file(char *file) +void PairThreebodyTable::read_file(char *file) { memory->sfree(params); params = nullptr; @@ -276,7 +276,7 @@ void Pair3BTable::read_file(char *file) // open file on proc 0 if (comm->me == 0) { - PotentialFileReader reader(lmp, file, "3b/table", unit_convert_flag); + PotentialFileReader reader(lmp, file, "threebody", unit_convert_flag); char *line; while ((line = reader.next_line(NPARAMS_PER_LINE))) { @@ -339,7 +339,7 @@ void Pair3BTable::read_file(char *file) } auto tablestyle = values.next_string(); if (tablestyle != "linear") - error->all(FLERR,"Unknown table style {} in 3b table", tablestyle); + error->all(FLERR,"Unknown table style {} in threebody table", tablestyle); params[nparams].tablength = values.next_int(); } catch (TokenizerException &e) { @@ -347,7 +347,7 @@ void Pair3BTable::read_file(char *file) } if (params[nparams].cut < 0.0 || params[nparams].tablength < 0.0) - error->one(FLERR,"Illegal 3b/table parameters"); + error->one(FLERR,"Illegal threebody/table parameters"); nparams++; } @@ -362,7 +362,7 @@ void Pair3BTable::read_file(char *file) MPI_Bcast(params, maxparam*sizeof(Param), MPI_BYTE, 0, world); - // for each set of parameters, broadcast table name and keyword and read 3b table + // 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) { memory->create(params[m].tablename, params[m].tablenamelength, "params.tablename"); @@ -373,27 +373,27 @@ void Pair3BTable::read_file(char *file) } MPI_Bcast(¶ms[m].keyword, params[m].keywordlength, MPI_CHAR, 0, world); - // initialize 3btable - memory->create(params[m].mltable,1,"param:3btable"); + // initialize threebodytable + memory->create(params[m].mltable,1,"param:threebodytable"); null_table(params[m].mltable); - //call read_table to read corresponding tabulated 3b file (only called by process 0) + //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 3btable to all processes + // 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 3b table length"); + if (params[m].mltable->ninput <= 1) error->one(FLERR,"Invalid threebody table length"); } } /* ---------------------------------------------------------------------- */ -void Pair3BTable::setup_params() +void PairThreebodyTable::setup_params() { int i,j,k,m,n; double rtmp; @@ -446,9 +446,9 @@ void Pair3BTable::setup_params() read table file, only called by proc 0 ------------------------------------------------------------------------- */ -void Pair3BTable::read_table(Table *tb, char *file, char *keyword, bool symmetric) +void PairThreebodyTable::read_table(Table *tb, char *file, char *keyword, bool symmetric) { - TableFileReader reader(lmp, file, "3body"); + TableFileReader reader(lmp, file, "threebodytable"); char *line = reader.find_section_start(keyword); @@ -460,7 +460,7 @@ void Pair3BTable::read_table(Table *tb, char *file, char *keyword, bool symmetri line = reader.next_line(); param_extract(tb, line); - // if it is a symmetric 3body interaction, less table entries are required + // if it is a symmetric threebody interaction, less table entries are required if (symmetric == true){ 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"); @@ -488,11 +488,11 @@ void Pair3BTable::read_table(Table *tb, char *file, char *keyword, bool symmetri } - // read 3b table values from file + // read threebody table values from file int cerror = 0; reader.skip_line(); - // if it is a symmetric 3body interaction, less table entries are required + // if it is a symmetric threebody interaction, less table entries are required if (symmetric == true){ for (int i = 0; i < tb->ninput*tb->ninput*(tb->ninput+1); i++) { line = reader.next_line(11); @@ -551,7 +551,7 @@ void Pair3BTable::read_table(Table *tb, char *file, char *keyword, bool symmetri only called by read_table, only called by proc 0 ------------------------------------------------------------------------- */ -void Pair3BTable::param_extract(Table *tb, char *line) +void PairThreebodyTable::param_extract(Table *tb, char *line) { tb->ninput = 0; tb->rmin = 0.0; @@ -577,9 +577,9 @@ void Pair3BTable::param_extract(Table *tb, char *line) error->one(FLERR, e.what()); } - if (tb->ninput == 0) error->one(FLERR, "3body table parameters did not set N"); - if (tb->rmin == 0.0) error->one(FLERR, "3body table parameters did not set rmin"); - if (tb->rmax == 0.0) error->one(FLERR, "3body table parameters did not set rmax"); + 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"); } @@ -589,14 +589,14 @@ void Pair3BTable::param_extract(Table *tb, char *line) ninput,afile,efile,ffile,fpflag,fplo,fphi,theta0 ------------------------------------------------------------------------- */ -void Pair3BTable::bcast_table(Table *tb, bool symmetric) +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 3body interaction, less table entries are required + // if it is a symmetric threebody interaction, less table entries are required if (symmetric == true){ 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"); @@ -624,7 +624,7 @@ void Pair3BTable::bcast_table(Table *tb, bool symmetric) } } - // if it is a symmetric 3body interaction, less table entries are required + // if it is a symmetric threebody interaction, less table entries are required if (symmetric == true){ 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); @@ -657,11 +657,11 @@ void Pair3BTable::bcast_table(Table *tb, bool symmetric) /* ---------------------------------------------------------------------- */ -void Pair3BTable::free_param(Param *pm) +void PairThreebodyTable::free_param(Param *pm) { - // call free_table to destroy associated 3btable + // call free_table to destroy associated threebodytable free_table(pm->mltable); - // then destroy associated 3btable + // then destroy associated threebodytable memory->sfree(pm->tablename); memory->sfree(pm->keyword); memory->sfree(pm->mltable); @@ -669,7 +669,7 @@ void Pair3BTable::free_param(Param *pm) /* ---------------------------------------------------------------------- */ -void Pair3BTable::free_table(Table *tb) +void PairThreebodyTable::free_table(Table *tb) { memory->destroy(tb->r12file); memory->destroy(tb->r13file); @@ -685,7 +685,7 @@ void Pair3BTable::free_table(Table *tb) /* ---------------------------------------------------------------------- */ -void Pair3BTable::null_table(Table *tb) +void PairThreebodyTable::null_table(Table *tb) { tb->r12file = tb->r13file = tb->thetafile = nullptr; tb->f11file = tb->f12file = nullptr; @@ -698,7 +698,7 @@ void Pair3BTable::null_table(Table *tb) calculate potential u and force f at angle x ------------------------------------------------------------------------- */ -void Pair3BTable::uf_lookup(Param *pm, double r12, double r13, double theta, double &f11, double &f12, +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; @@ -708,7 +708,7 @@ void Pair3BTable::uf_lookup(Param *pm, double r12, double r13, double theta, dou //lookup scheme - // if it is a symmetric 3body interaction, less table entries are required + // if it is a symmetric threebody interaction, less table entries are required if (pm->symmetric == true){ nr12 = (r12 - pm->mltable->rmin + 0.5*dr - 0.00000001)/dr; if (r12 == (pm->mltable->rmin - 0.5*dr)){ @@ -761,7 +761,7 @@ void Pair3BTable::uf_lookup(Param *pm, double r12, double r13, double theta, dou /* ---------------------------------------------------------------------- */ -void Pair3BTable::threebody(Param *paramijk, double rsq1, double rsq2, double *delr1, double *delr2, +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; From a833baac806b7b8a166209c007b8b0f31ba32a57 Mon Sep 17 00:00:00 2001 From: Christoph Scherer Date: Wed, 1 Jun 2022 16:04:09 +0200 Subject: [PATCH 20/34] Update pair_sw_angle_table.cpp Minor correction in pair_sw_angle_table.cpp --- src/MANYBODY/pair_sw_angle_table.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/MANYBODY/pair_sw_angle_table.cpp b/src/MANYBODY/pair_sw_angle_table.cpp index fbef0a6dd9..5da277bc05 100644 --- a/src/MANYBODY/pair_sw_angle_table.cpp +++ b/src/MANYBODY/pair_sw_angle_table.cpp @@ -228,7 +228,7 @@ void PairSWAngleTable::read_file(char *file) // open file on proc 0 if (comm->me == 0) { - PotentialFileReader reader(lmp, file, "sw/angle/table", unit_convert_flag); + PotentialFileReader reader(lmp, file, "sw", unit_convert_flag); char *line; while ((line = reader.next_line(NPARAMS_PER_LINE))) { @@ -440,7 +440,7 @@ void PairSWAngleTable::threebody_table(Param *paramij, Param *paramik, ParamTabl void PairSWAngleTable::read_table(Table *tb, char *file, char *keyword) { - TableFileReader reader(lmp, file, "angle table"); + TableFileReader reader(lmp, file, "angletable"); char *line = reader.find_section_start(keyword); From c1e301ac1af0a13726476b9e0a9233e42db8f65b Mon Sep 17 00:00:00 2001 From: Christoph Scherer Date: Wed, 1 Jun 2022 16:11:47 +0200 Subject: [PATCH 21/34] Update pair_3b_table.rst changed documentation and file name from pair style 3b/table to threebody/table --- doc/src/pair_3b_table.rst | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/doc/src/pair_3b_table.rst b/doc/src/pair_3b_table.rst index 0a239883e4..569979f78d 100644 --- a/doc/src/pair_3b_table.rst +++ b/doc/src/pair_3b_table.rst @@ -1,7 +1,7 @@ -.. index:: pair_style 3b/table +.. index:: pair_style threebody/table -pair_style 3b/table command -=========================== +pair_style threebody/table command +================================== Syntax """""" @@ -10,7 +10,7 @@ Syntax pair_style style -* style = *3b/table* +* style = *threebody/table* Examples @@ -18,7 +18,7 @@ Examples .. code-block:: LAMMPS - pair_style 3b/table + pair_style threebody/table pair_coeff * * spce.3b type pair_coeff * * GaN.3b Ga N Ga @@ -26,11 +26,11 @@ Examples Description """"""""""" -The *3b/table* style is a pair style for generic tabulated three-body +The *threebody/table* style is a pair style for generic tabulated three-body interactions. It has been developed for (coarse-grained) simulations (of water) with Kernel-based machine learning (ML) potentials (:ref:`Scherer2 `). As for the pair style :doc:`pair_style sw -` or :doc:`pair_style sw/3b/table `, the energy of +` or :doc:`pair_style sw/threebody/table `, the energy of a system is computed as a sum over three-body terms: .. math:: @@ -43,14 +43,14 @@ Stillinger-Weber potential, all forces are not calculated analytically, but read in from a three-body force/energy table which can be generated with the csg_ml app of VOTCA as available at: https://gitlab.mpcdf.mpg.de/votca/votca. -Only a single pair_coeff command is used with the *3b/table* style -which specifies a three-body potential (".3b") file with parameters for all +Only a single pair_coeff command is used with the *threebody/table* style +which specifies a threebody potential (".3b") file with parameters for all needed elements. These are then mapped to LAMMPS atom types by specifying N_el additional arguments after the ".3b" filename in the pair_coeff command, where N_el is the number of LAMMPS atom types: * ".3b" filename -* N_el element names = mapping of 3b elements to atom types +* N_el element names = mapping of threebody elements to atom types See the :doc:`pair_coeff ` page for alternate ways to specify the path for the potential file. @@ -67,8 +67,8 @@ pair_coeff command: The first 2 arguments must be \* \* so as to span all LAMMPS atom types. The first three Si arguments map LAMMPS atom types 1,2,3 to the Si element in the ".3b" file. The final C argument maps LAMMPS atom type 4 -to the C element in the 3b file. If a mapping value is specified as -NULL, the mapping is not performed. This can be used when a *3b/table* +to the C element in the threebody file. If a mapping value is specified as +NULL, the mapping is not performed. This can be used when a *threebody/table* potential is used as part of the *hybrid* pair style. The NULL values are placeholders for atom types that will be used with other potentials. @@ -193,7 +193,7 @@ This allows for a very efficient force calculation with the stored force constants and energies. Due to the know table structure, the lookup can be done efficiently. It has been tested (:ref:`Scherer2 `) that with a reasonably small bin size, the accuracy and speed is comparable to that of a Stillinger-Weber potential -with tabulated three-body interactions (:doc:`pair_style sw/table `) while +with tabulated three-body interactions (:doc:`pair_style sw/angle/table `) while the table format of this pair style allows for more flexible three-body interactions. As for the Stillinger-Weber potential, the three-body potential file must contain entries for all the @@ -204,7 +204,7 @@ simulation; LAMMPS ignores those entries. For a single-element simulation, only a single entry is required (e.g. SiSiSi). For a two-element simulation, the file must contain 8 entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that -specify 3b parameters for all permutations of the two elements +specify threebody parameters for all permutations of the two elements interacting in three-body configurations. Thus for 3 elements, 27 entries would be required, etc. @@ -254,7 +254,7 @@ in the tutorial folder. Related commands """""""""""""""" -:doc:`pair_coeff `, :doc:`pair sw/3b/table ` +:doc:`pair_coeff `, :doc:`pair sw/angle/table ` ---------- From 64d67f7604479649e7b0d2d05251c56fcaf283f8 Mon Sep 17 00:00:00 2001 From: Christoph Scherer Date: Wed, 1 Jun 2022 16:12:13 +0200 Subject: [PATCH 22/34] Update pair_sw_angle_table.rst pair_sw_angle_table.rst: minor correction --- doc/src/pair_sw_angle_table.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/pair_sw_angle_table.rst b/doc/src/pair_sw_angle_table.rst index a50b7eaaf5..cc2bbba08f 100644 --- a/doc/src/pair_sw_angle_table.rst +++ b/doc/src/pair_sw_angle_table.rst @@ -1,7 +1,7 @@ .. index:: pair_style sw/angle/table pair_style sw/angle/table command -============================== +================================= Syntax """""" From f6fab8365a65655c2a2a746aaadac88d93254b5c Mon Sep 17 00:00:00 2001 From: Christoph Scherer Date: Wed, 1 Jun 2022 16:14:37 +0200 Subject: [PATCH 23/34] Update Commands_pair.rst Commands_pair.rst: update due to name change from 3b/table to threebody/table and sw/3b/table to sw/angle/table --- doc/src/Commands_pair.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index 21a84a2518..f902b40b29 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -34,7 +34,6 @@ OPT. * * * - * :doc:`3b/table ` * :doc:`adp (ko) ` * :doc:`agni (o) ` * :doc:`airebo (io) ` @@ -270,7 +269,7 @@ OPT. * :doc:`spin/neel ` * :doc:`srp ` * :doc:`sw (giko) ` - * :doc:`sw/3b/table ` + * :doc:`sw/angle/table ` * :doc:`sw/mod (o) ` * :doc:`table (gko) ` * :doc:`table/rx (k) ` @@ -281,6 +280,7 @@ OPT. * :doc:`tersoff/table (o) ` * :doc:`tersoff/zbl (gko) ` * :doc:`thole ` + * :doc:`threebody/table ` * :doc:`tip4p/cut (o) ` * :doc:`tip4p/long (o) ` * :doc:`tip4p/long/soft (o) ` From 3a19b1eb4b9728c973f9eb78269e75387211cf08 Mon Sep 17 00:00:00 2001 From: Christoph Scherer Date: Wed, 1 Jun 2022 16:16:13 +0200 Subject: [PATCH 24/34] Update pair_style.rst pair_style.rst: update due to name changes from 3b/table to threebody/table and sw/3b/table to sw/angle/table --- doc/src/pair_style.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index d24596e2fa..7e9414cee9 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -112,7 +112,6 @@ accelerated styles exist. * :doc:`hybrid/scaled ` - multiple styles of scaled superposed pairwise interactions * :doc:`zero ` - neighbor list but no interactions -* :doc:`3b/table ` - generic tabulated three-body potential * :doc:`adp ` - angular dependent potential (ADP) of Mishin * :doc:`agni ` - AGNI machine-learning potential * :doc:`airebo ` - AIREBO potential of Stuart @@ -349,7 +348,7 @@ accelerated styles exist. * :doc:`spin/neel ` - * :doc:`srp ` - * :doc:`sw ` - Stillinger-Weber 3-body potential -* :doc:`sw/3b/table ` - Stillinger-Weber potential with tabulated 3-body term +* :doc:`sw/angle/table ` - Stillinger-Weber potential with tabulated angular term * :doc:`sw/mod ` - modified Stillinger-Weber 3-body potential * :doc:`table ` - tabulated pair potential * :doc:`table/rx ` - @@ -360,6 +359,7 @@ accelerated styles exist. * :doc:`tersoff/table ` - * :doc:`tersoff/zbl ` - Tersoff/ZBL 3-body potential * :doc:`thole ` - Coulomb interactions with thole damping +* :doc:`threebody/table ` - generic tabulated three-body potential * :doc:`tip4p/cut ` - Coulomb for TIP4P water w/out LJ * :doc:`tip4p/long ` - long-range Coulomb for TIP4P water w/out LJ * :doc:`tip4p/long/soft ` - From e8d9bf05075df7c7fdd12d28486d0d115a16aeb2 Mon Sep 17 00:00:00 2001 From: schererc Date: Wed, 1 Jun 2022 16:30:37 +0200 Subject: [PATCH 25/34] examples/PACKAGES: renamed pair_3b_table to pair_threebody_table including all input and documentation files --- .../1-1-1.table | 0 .../1-1-2.table | 0 .../CG-CG-CG.dist.new | 0 .../CG-CG.dist.new | 0 .../README | 30 +++++++++---------- .../calculate_distributions.xml | 0 .../run.sh | 0 .../spce.3b | 0 .../spce.data | 0 .../spce.in | 6 ++-- .../spce_2.3b | 0 .../spce_2.data | 0 .../spce_2.in | 6 ++-- .../table_CG_CG.txt | 0 14 files changed, 21 insertions(+), 21 deletions(-) rename examples/PACKAGES/{pair_3b_table => pair_threebody_table}/1-1-1.table (100%) rename examples/PACKAGES/{pair_3b_table => pair_threebody_table}/1-1-2.table (100%) rename examples/PACKAGES/{pair_3b_table => pair_threebody_table}/CG-CG-CG.dist.new (100%) rename examples/PACKAGES/{pair_3b_table => pair_threebody_table}/CG-CG.dist.new (100%) rename examples/PACKAGES/{pair_3b_table => pair_threebody_table}/README (66%) rename examples/PACKAGES/{pair_3b_table => pair_threebody_table}/calculate_distributions.xml (100%) rename examples/PACKAGES/{pair_3b_table => pair_threebody_table}/run.sh (100%) rename examples/PACKAGES/{pair_3b_table => pair_threebody_table}/spce.3b (100%) rename examples/PACKAGES/{pair_3b_table => pair_threebody_table}/spce.data (100%) rename examples/PACKAGES/{pair_3b_table => pair_threebody_table}/spce.in (83%) rename examples/PACKAGES/{pair_3b_table => pair_threebody_table}/spce_2.3b (100%) rename examples/PACKAGES/{pair_3b_table => pair_threebody_table}/spce_2.data (100%) rename examples/PACKAGES/{pair_3b_table => pair_threebody_table}/spce_2.in (82%) rename examples/PACKAGES/{pair_3b_table => pair_threebody_table}/table_CG_CG.txt (100%) diff --git a/examples/PACKAGES/pair_3b_table/1-1-1.table b/examples/PACKAGES/pair_threebody_table/1-1-1.table similarity index 100% rename from examples/PACKAGES/pair_3b_table/1-1-1.table rename to examples/PACKAGES/pair_threebody_table/1-1-1.table diff --git a/examples/PACKAGES/pair_3b_table/1-1-2.table b/examples/PACKAGES/pair_threebody_table/1-1-2.table similarity index 100% rename from examples/PACKAGES/pair_3b_table/1-1-2.table rename to examples/PACKAGES/pair_threebody_table/1-1-2.table diff --git a/examples/PACKAGES/pair_3b_table/CG-CG-CG.dist.new b/examples/PACKAGES/pair_threebody_table/CG-CG-CG.dist.new similarity index 100% rename from examples/PACKAGES/pair_3b_table/CG-CG-CG.dist.new rename to examples/PACKAGES/pair_threebody_table/CG-CG-CG.dist.new diff --git a/examples/PACKAGES/pair_3b_table/CG-CG.dist.new b/examples/PACKAGES/pair_threebody_table/CG-CG.dist.new similarity index 100% rename from examples/PACKAGES/pair_3b_table/CG-CG.dist.new rename to examples/PACKAGES/pair_threebody_table/CG-CG.dist.new diff --git a/examples/PACKAGES/pair_3b_table/README b/examples/PACKAGES/pair_threebody_table/README similarity index 66% rename from examples/PACKAGES/pair_3b_table/README rename to examples/PACKAGES/pair_threebody_table/README index d01c00afdd..3897f80a81 100644 --- a/examples/PACKAGES/pair_3b_table/README +++ b/examples/PACKAGES/pair_threebody_table/README @@ -1,10 +1,10 @@ -Example for pair style 3b/table +Example for pair style threebody/table This example contains all required input files for the simulation of CG SPC/E water with -the user pair style 3b/table, as well as a run.sh script. +the user pair style threebody/table, as well as a run.sh script. -To run the example, you have to compile LAMMPS with the MANYBODY package, including pair_3b_table.h and pair_3b_table.cpp. +To run the example, you have to compile LAMMPS with the MANYBODY package, including pair_threebody_table.h and pair_threebody_table.cpp. Running the simulations, you will reproduce results of the following publication: @@ -16,20 +16,20 @@ The three-body (force) tables for both parts (1-1-1.table and 1-1-2.table) have For a general description of the table format have a look at the documentation of this pair style. For a example on the parametrization, have a look at https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/guide and https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/ml. -In both cases, the parametrization has been done according to the three-body forces of the FM tabulated Stillinger-Weber (sw/3b/table) potential with the covariant meshing technique with the settings files used in https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/ml/3body/with_binning. +In both cases, the parametrization is done according to a sample system, using the three-body forces of a Stillinger-Weber potential with tabulated angular forces (sw/angle/table). These then are learned with the covariant meshing technique with the settings files used in https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/ml/3body/with_binning. -For the first part of example, the folder contains the contains the LAMMPS data file (spce.data) with the starting configuration of 1000 CG water molecules, an input file (spce.in) and a three-body file (spce.3b). +For the first part of example, the folder contains the contains the LAMMPS data file (spce.data) with the starting configuration of 1000 CG water molecules, an input file (spce.in) and a threebody file (spce.3b). The lammps input file contains the lines specifying the pair style and coefficients: -- pair_style hybrid/overlay table linear 1200 3b/table - use a combination of pair style table with 1200 linear table entries and the pair style 3b/table +- pair_style hybrid/overlay table linear 1200 threebody/table - use a combination of pair style table with 1200 linear table entries and the pair style threebody/table - pair_coeff 1 1 table table_CG_CG.txt VOTCA - set the table name and keyword for the pair style table -- pair_coeff * * 3b/table spce.3b type - set the name of 3body file and bead type for the pair style 3b/table +- pair_coeff * * threebody/table spce.3b type - set the name of threebody file and bead type for the pair style threebody/table -A hybrid pair style is used, where pair forces are calculated as a tabulated interaction (table_CG_CG.txt) and the pair style 3b/table is only used to calculate the three-body forces. -The tabulated pair interaction is the same as in the example of the sw/3b/table pair style: examples/PACKAGES/pair_sw_3b_table +A hybrid pair style is used, where pair forces are calculated as a tabulated interaction (table_CG_CG.txt) and the pair style threebody/table is only used to calculate the three-body forces. +The tabulated pair interaction is the same as in the example of the sw/angle/table pair style: examples/PACKAGES/pair_sw_angle_table -To run the simulation, one needs an additional 3body file (spce.3b). +To run the simulation, one needs an additional threebody file (spce.3b). It has the following structure: - type - relates to keyword type in LAMMPS input file @@ -46,18 +46,18 @@ As there is only one atom type (1), the force table is symmetric and contains "M The LAMMPS simulation is a standard nvt simulation. A dump file is output with the positions and forces every 10 time steps. You can calculate the pair distribution and compare it to the ones in the publication. -For the second part of the example, have a look at the LAMMPS data file (spce_2.data), the input file (spce_2.in) and the three-body file (spce_2.3b). +For the second part of the example, have a look at the LAMMPS data file (spce_2.data), the input file (spce_2.in) and the threebody file (spce_2.3b). Running the second part, you will in fact perform the same MD simulation as in the first part of the example. However, the atom type of the first 100 CG water molecules has been changed from 1 to 2. This is done to demonstrate how to run a simulation with different atom types. Again, lammps input file (spce_2.in) contains the lines specifying the pair style and coefficients: -- pair_style hybrid/overlay table linear 1200 3b/table - use a combination of pair style table with 1200 linear table entries and the pair style 3b/table +- pair_style hybrid/overlay table linear 1200 threebody/table - use a combination of pair style table with 1200 linear table entries and the pair style threebody/table - pair_coeff 1 1 table table_CG_CG.txt VOTCA - set the table name and keyword for the pair style table -- pair_coeff * * 3b/table spce_2.3b type1 type2 - set the name of 3body file and bead type for the pair style 3b/table +- pair_coeff * * threebody/table spce_2.3b type1 type2 - set the name of threebody file and bead type for the pair style threebody/table -Now, the atom type 1 is mapped to the element type1 and the atom type 2 is mapped to the element type2 in the 3body file (spce_2.3b). -For this (artificial) two-element simulation, the 3body file now contain 8 entries for: type1 type1 type1, type1 type1 type2, type1 type2 type1, type1 type2 type2, type2 type1 type1, type2 type1 type2, type2 type2 type1, type2 type2 type2. +Now, the atom type 1 is mapped to the element type1 and the atom type 2 is mapped to the element type2 in the threebody file (spce_2.3b). +For this (artificial) two-element simulation, the threebody file now contain 8 entries for: type1 type1 type1, type1 type1 type2, type1 type2 type1, type1 type2 type2, type2 type1 type1, type2 type1 type2, type2 type2 type1, type2 type2 type2. Each entry has the same structure as above. However, entries where the second and the third element are different require a different force table (1-1-2.table) instead of (1-1-1.table). 1-1-2.table contains exactly the force constants as 1-1-1.table. However it has to have the asymmetric structure where both interparticle distances (r_ij and r_ik) are varied from rmin to rmax and therefore contains "M = 2 * N * N * N" (2 * 12 * 12 * 12 = 3456) entries. diff --git a/examples/PACKAGES/pair_3b_table/calculate_distributions.xml b/examples/PACKAGES/pair_threebody_table/calculate_distributions.xml similarity index 100% rename from examples/PACKAGES/pair_3b_table/calculate_distributions.xml rename to examples/PACKAGES/pair_threebody_table/calculate_distributions.xml diff --git a/examples/PACKAGES/pair_3b_table/run.sh b/examples/PACKAGES/pair_threebody_table/run.sh similarity index 100% rename from examples/PACKAGES/pair_3b_table/run.sh rename to examples/PACKAGES/pair_threebody_table/run.sh diff --git a/examples/PACKAGES/pair_3b_table/spce.3b b/examples/PACKAGES/pair_threebody_table/spce.3b similarity index 100% rename from examples/PACKAGES/pair_3b_table/spce.3b rename to examples/PACKAGES/pair_threebody_table/spce.3b diff --git a/examples/PACKAGES/pair_3b_table/spce.data b/examples/PACKAGES/pair_threebody_table/spce.data similarity index 100% rename from examples/PACKAGES/pair_3b_table/spce.data rename to examples/PACKAGES/pair_threebody_table/spce.data diff --git a/examples/PACKAGES/pair_3b_table/spce.in b/examples/PACKAGES/pair_threebody_table/spce.in similarity index 83% rename from examples/PACKAGES/pair_3b_table/spce.in rename to examples/PACKAGES/pair_threebody_table/spce.in index c5b72c4f9a..2ca97708c6 100644 --- a/examples/PACKAGES/pair_3b_table/spce.in +++ b/examples/PACKAGES/pair_threebody_table/spce.in @@ -7,12 +7,12 @@ read_data spce.data #hybrid pair style consisting of #pair_style table to read in CG pair potential -#pair_style 3b/table for tabulated 3b interactions -pair_style hybrid/overlay table linear 1200 3b/table +#pair_style threebody/table for tabulated threebody interactions +pair_style hybrid/overlay table linear 1200 threebody/table #pair coefficients pair_coeff 1 1 table table_CG_CG.txt VOTCA -pair_coeff * * 3b/table spce.3b type +pair_coeff * * threebody/table spce.3b type #nvt run with nose-hoover thermostat #time coupling of 100 ts for thermostat diff --git a/examples/PACKAGES/pair_3b_table/spce_2.3b b/examples/PACKAGES/pair_threebody_table/spce_2.3b similarity index 100% rename from examples/PACKAGES/pair_3b_table/spce_2.3b rename to examples/PACKAGES/pair_threebody_table/spce_2.3b diff --git a/examples/PACKAGES/pair_3b_table/spce_2.data b/examples/PACKAGES/pair_threebody_table/spce_2.data similarity index 100% rename from examples/PACKAGES/pair_3b_table/spce_2.data rename to examples/PACKAGES/pair_threebody_table/spce_2.data diff --git a/examples/PACKAGES/pair_3b_table/spce_2.in b/examples/PACKAGES/pair_threebody_table/spce_2.in similarity index 82% rename from examples/PACKAGES/pair_3b_table/spce_2.in rename to examples/PACKAGES/pair_threebody_table/spce_2.in index 55db11b7cb..e05df5d719 100644 --- a/examples/PACKAGES/pair_3b_table/spce_2.in +++ b/examples/PACKAGES/pair_threebody_table/spce_2.in @@ -7,12 +7,12 @@ read_data spce_2.data #hybrid pair style consisting of #pair_style table to read in CG pair potential -#pair_style 3b/table for tabulated 3b interactions -pair_style hybrid/overlay table linear 1200 3b/table +#pair_style threebody/table for tabulated threebody interactions +pair_style hybrid/overlay table linear 1200 threebody/table #pair coefficients pair_coeff * * table table_CG_CG.txt VOTCA -pair_coeff * * 3b/table spce_2.3b type1 type2 +pair_coeff * * threebody/table spce_2.3b type1 type2 #nvt run with nose-hoover thermostat #time coupling of 100 ts for thermostat diff --git a/examples/PACKAGES/pair_3b_table/table_CG_CG.txt b/examples/PACKAGES/pair_threebody_table/table_CG_CG.txt similarity index 100% rename from examples/PACKAGES/pair_3b_table/table_CG_CG.txt rename to examples/PACKAGES/pair_threebody_table/table_CG_CG.txt From 95a979c657e3697884e15412e8c2cfcafe88442e Mon Sep 17 00:00:00 2001 From: schererc Date: Wed, 1 Jun 2022 16:34:10 +0200 Subject: [PATCH 26/34] examples/PACKAGES: rename pair_sw_3b_table to pair_sw_angle_table including all input and documentation files --- .../{pair_sw_3b_table => pair_sw_angle_table}/README | 12 ++++++------ .../{pair_sw_3b_table => pair_sw_angle_table}/run.sh | 0 .../spce.data | 0 .../spce.in | 6 +++--- .../spce.sw | 0 .../table_CG_CG.txt | 0 .../table_CG_CG_CG.txt | 0 7 files changed, 9 insertions(+), 9 deletions(-) rename examples/PACKAGES/{pair_sw_3b_table => pair_sw_angle_table}/README (80%) rename examples/PACKAGES/{pair_sw_3b_table => pair_sw_angle_table}/run.sh (100%) rename examples/PACKAGES/{pair_sw_3b_table => pair_sw_angle_table}/spce.data (100%) rename examples/PACKAGES/{pair_sw_3b_table => pair_sw_angle_table}/spce.in (82%) rename examples/PACKAGES/{pair_sw_3b_table => pair_sw_angle_table}/spce.sw (100%) rename examples/PACKAGES/{pair_sw_3b_table => pair_sw_angle_table}/table_CG_CG.txt (100%) rename examples/PACKAGES/{pair_sw_3b_table => pair_sw_angle_table}/table_CG_CG_CG.txt (100%) diff --git a/examples/PACKAGES/pair_sw_3b_table/README b/examples/PACKAGES/pair_sw_angle_table/README similarity index 80% rename from examples/PACKAGES/pair_sw_3b_table/README rename to examples/PACKAGES/pair_sw_angle_table/README index 2d00030fea..54e665ff6c 100644 --- a/examples/PACKAGES/pair_sw_3b_table/README +++ b/examples/PACKAGES/pair_sw_angle_table/README @@ -1,10 +1,10 @@ -Example for pair style sw/3b/table +Example for pair style sw/angle/table This example contains all required input files for the simulation of CG SPC/E water with -the user pair style sw/3b/table, as well as a run.sh script. +the user pair style sw/angle/table, as well as a run.sh script. -To run the example, you have to compile LAMMPS with the MANYBODY package, including pair_sw_3b_table.h and pair_sw_3b_table.cpp. +To run the example, you have to compile LAMMPS with the MANYBODY package, including pair_sw_angle_table.h and pair_sw_angle_table.cpp. Running the simulation, you will reproduce results of the following publication: @@ -22,11 +22,11 @@ of 1000 CG water molecules, an input file (spce.in) and a (modified) Stillinger- The lammps input file contains the lines specifying the pair style and coefficients: -- pair_style hybrid/overlay table linear 1200 sw/3b/table - use a combination of pair style table with 1200 linear table entries and the pair style sw/3b/table +- pair_style hybrid/overlay table linear 1200 sw/angle/table - use a combination of pair style table with 1200 linear table entries and the pair style sw/angle/table - pair_coeff 1 1 table table_CG_CG.txt VOTCA - set the table name and keyword for the pair_style table -- pair_coeff * * sw/3b/table spce.sw type - set the name of the Stillinger-Weber file for the pair style sw/3b/table +- pair_coeff * * sw/angle/table spce.sw type - set the name of the Stillinger-Weber file for the pair style sw/angle/table -A hybrid pair style is used, where pair forces are calculated as a tabulated interaction (table_CG_CG.txt) and the pair style sw/3b/table is only used to calculate the three-body forces. +A hybrid pair style is used, where pair forces are calculated as a tabulated interaction (table_CG_CG.txt) and the pair style sw/angle/table is only used to calculate the three-body forces. Therefore, in the Stillinger-Weber file all parameters refering to two-body interactions are set to zero. As explained in the documentation of this pair style, the .sw file contains the additional lines refering to the tabulated angular potential: diff --git a/examples/PACKAGES/pair_sw_3b_table/run.sh b/examples/PACKAGES/pair_sw_angle_table/run.sh similarity index 100% rename from examples/PACKAGES/pair_sw_3b_table/run.sh rename to examples/PACKAGES/pair_sw_angle_table/run.sh diff --git a/examples/PACKAGES/pair_sw_3b_table/spce.data b/examples/PACKAGES/pair_sw_angle_table/spce.data similarity index 100% rename from examples/PACKAGES/pair_sw_3b_table/spce.data rename to examples/PACKAGES/pair_sw_angle_table/spce.data diff --git a/examples/PACKAGES/pair_sw_3b_table/spce.in b/examples/PACKAGES/pair_sw_angle_table/spce.in similarity index 82% rename from examples/PACKAGES/pair_sw_3b_table/spce.in rename to examples/PACKAGES/pair_sw_angle_table/spce.in index 85303bf0d1..8b1ef719a6 100644 --- a/examples/PACKAGES/pair_sw_3b_table/spce.in +++ b/examples/PACKAGES/pair_sw_angle_table/spce.in @@ -9,12 +9,12 @@ read_data spce.data #hybrid pair style consisting of #pair_style table to read in CG pair potential -#pair_style sw/table for tabulated sw interactions -pair_style hybrid/overlay table linear 1200 sw/3b/table +#pair_style sw/angle/table for sw interactions with tabulated angular potential +pair_style hybrid/overlay table linear 1200 sw/angle/table #pair coefficients pair_coeff 1 1 table table_CG_CG.txt VOTCA -pair_coeff * * sw/3b/table spce.sw type +pair_coeff * * sw/angle/table spce.sw type #nvt run with nose-hoover thermostat #time coupling of 100 ts for thermostat diff --git a/examples/PACKAGES/pair_sw_3b_table/spce.sw b/examples/PACKAGES/pair_sw_angle_table/spce.sw similarity index 100% rename from examples/PACKAGES/pair_sw_3b_table/spce.sw rename to examples/PACKAGES/pair_sw_angle_table/spce.sw diff --git a/examples/PACKAGES/pair_sw_3b_table/table_CG_CG.txt b/examples/PACKAGES/pair_sw_angle_table/table_CG_CG.txt similarity index 100% rename from examples/PACKAGES/pair_sw_3b_table/table_CG_CG.txt rename to examples/PACKAGES/pair_sw_angle_table/table_CG_CG.txt diff --git a/examples/PACKAGES/pair_sw_3b_table/table_CG_CG_CG.txt b/examples/PACKAGES/pair_sw_angle_table/table_CG_CG_CG.txt similarity index 100% rename from examples/PACKAGES/pair_sw_3b_table/table_CG_CG_CG.txt rename to examples/PACKAGES/pair_sw_angle_table/table_CG_CG_CG.txt From b85b3e1f4c7969548726c2440bb43bc9ffb0218b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 1 Jun 2022 12:06:56 -0400 Subject: [PATCH 27/34] fix doc file names and links --- doc/src/{pair_3b_table.rst => pair_threebody_table.rst} | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) rename doc/src/{pair_3b_table.rst => pair_threebody_table.rst} (98%) diff --git a/doc/src/pair_3b_table.rst b/doc/src/pair_threebody_table.rst similarity index 98% rename from doc/src/pair_3b_table.rst rename to doc/src/pair_threebody_table.rst index 569979f78d..5e2503fc3f 100644 --- a/doc/src/pair_3b_table.rst +++ b/doc/src/pair_threebody_table.rst @@ -29,9 +29,8 @@ Description The *threebody/table* style is a pair style for generic tabulated three-body interactions. It has been developed for (coarse-grained) simulations (of water) with Kernel-based machine learning (ML) potentials -(:ref:`Scherer2 `). As for the pair style :doc:`pair_style sw -` or :doc:`pair_style sw/threebody/table `, the energy of -a system is computed as a sum over three-body terms: +(:ref:`Scherer2 `). As for many other MANYBODY package pair styles +the energy of a system is computed as a sum over three-body terms: .. math:: From 8e9071b01f00c44d41060e08d3ceb234e9ccdd47 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 1 Jun 2022 14:22:53 -0400 Subject: [PATCH 28/34] move and update threebody/table examples --- doc/utils/sphinx-config/false_positives.txt | 1 + .../1-1-1.table | 0 .../1-1-2.table | 0 .../README | 0 .../spce.data => manybody_table/data.spce} | 0 .../spce_2.data => manybody_table/data.spce2} | 0 examples/PACKAGES/manybody_table/in.spce | 21 ++ examples/PACKAGES/manybody_table/in.spce2 | 22 ++ .../manybody_table/log.1Jun22.spce.g++.1 | 88 +++++ .../manybody_table/log.1Jun22.spce.g++.4 | 88 +++++ .../manybody_table/log.1Jun22.spce2.g++.1 | 89 ++++++ .../manybody_table/log.1Jun22.spce2.g++.4 | 89 ++++++ .../spce.3b | 0 .../spce_2.3b => manybody_table/spce2.3b} | 0 .../table_CG_CG.txt | 0 .../pair_threebody_table/CG-CG-CG.dist.new | 63 ---- .../pair_threebody_table/CG-CG.dist.new | 301 ------------------ .../calculate_distributions.xml | 29 -- examples/PACKAGES/pair_threebody_table/run.sh | 8 - .../PACKAGES/pair_threebody_table/spce.in | 43 --- .../PACKAGES/pair_threebody_table/spce_2.in | 43 --- 21 files changed, 398 insertions(+), 487 deletions(-) rename examples/PACKAGES/{pair_threebody_table => manybody_table}/1-1-1.table (100%) rename examples/PACKAGES/{pair_threebody_table => manybody_table}/1-1-2.table (100%) rename examples/PACKAGES/{pair_threebody_table => manybody_table}/README (100%) rename examples/PACKAGES/{pair_threebody_table/spce.data => manybody_table/data.spce} (100%) rename examples/PACKAGES/{pair_threebody_table/spce_2.data => manybody_table/data.spce2} (100%) create mode 100644 examples/PACKAGES/manybody_table/in.spce create mode 100644 examples/PACKAGES/manybody_table/in.spce2 create mode 100644 examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.1 create mode 100644 examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.4 create mode 100644 examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.1 create mode 100644 examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.4 rename examples/PACKAGES/{pair_threebody_table => manybody_table}/spce.3b (100%) rename examples/PACKAGES/{pair_threebody_table/spce_2.3b => manybody_table/spce2.3b} (100%) rename examples/PACKAGES/{pair_threebody_table => manybody_table}/table_CG_CG.txt (100%) delete mode 100644 examples/PACKAGES/pair_threebody_table/CG-CG-CG.dist.new delete mode 100644 examples/PACKAGES/pair_threebody_table/CG-CG.dist.new delete mode 100644 examples/PACKAGES/pair_threebody_table/calculate_distributions.xml delete mode 100755 examples/PACKAGES/pair_threebody_table/run.sh delete mode 100644 examples/PACKAGES/pair_threebody_table/spce.in delete mode 100644 examples/PACKAGES/pair_threebody_table/spce_2.in diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 36efbe5e45..667d988433 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -3220,6 +3220,7 @@ statvolt stdin stdio stdlib +stdout steelblue Stegailov Steinbach diff --git a/examples/PACKAGES/pair_threebody_table/1-1-1.table b/examples/PACKAGES/manybody_table/1-1-1.table similarity index 100% rename from examples/PACKAGES/pair_threebody_table/1-1-1.table rename to examples/PACKAGES/manybody_table/1-1-1.table diff --git a/examples/PACKAGES/pair_threebody_table/1-1-2.table b/examples/PACKAGES/manybody_table/1-1-2.table similarity index 100% rename from examples/PACKAGES/pair_threebody_table/1-1-2.table rename to examples/PACKAGES/manybody_table/1-1-2.table diff --git a/examples/PACKAGES/pair_threebody_table/README b/examples/PACKAGES/manybody_table/README similarity index 100% rename from examples/PACKAGES/pair_threebody_table/README rename to examples/PACKAGES/manybody_table/README diff --git a/examples/PACKAGES/pair_threebody_table/spce.data b/examples/PACKAGES/manybody_table/data.spce similarity index 100% rename from examples/PACKAGES/pair_threebody_table/spce.data rename to examples/PACKAGES/manybody_table/data.spce diff --git a/examples/PACKAGES/pair_threebody_table/spce_2.data b/examples/PACKAGES/manybody_table/data.spce2 similarity index 100% rename from examples/PACKAGES/pair_threebody_table/spce_2.data rename to examples/PACKAGES/manybody_table/data.spce2 diff --git a/examples/PACKAGES/manybody_table/in.spce b/examples/PACKAGES/manybody_table/in.spce new file mode 100644 index 0000000000..6c6c6f2050 --- /dev/null +++ b/examples/PACKAGES/manybody_table/in.spce @@ -0,0 +1,21 @@ +units real +atom_style atomic + +# data file with one atom type +read_data data.spce + +pair_style hybrid/overlay table linear 1200 threebody/table + +#pair coefficients +pair_coeff 1 1 table table_CG_CG.txt VOTCA +pair_coeff * * threebody/table spce.3b type + +fix 1 all nvt temp 300.0 300.0 200.0 + +velocity all create 300 432567 dist uniform loop geom mom yes +timestep 2.0 + +thermo 100 +#dump 2 all custom 100 dump.spce id type x y z fx fy fz + +run 1000 diff --git a/examples/PACKAGES/manybody_table/in.spce2 b/examples/PACKAGES/manybody_table/in.spce2 new file mode 100644 index 0000000000..c8656c105f --- /dev/null +++ b/examples/PACKAGES/manybody_table/in.spce2 @@ -0,0 +1,22 @@ +units real +atom_style atomic + +# data file with two atom types +read_data data.spce2 + +pair_style hybrid/overlay table linear 1200 threebody/table + +#pair coefficients +pair_coeff * * table table_CG_CG.txt VOTCA +pair_coeff * * threebody/table spce2.3b type1 type2 + +fix 1 all nvt temp 300.0 300.0 200.0 + +velocity all create 300 432567 dist uniform loop geom mom yes +timestep 2.0 + +thermo 100 +#dump 2 all custom 100 dump.spce2 id type x y z fx fy fz + +run 1000 + diff --git a/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.1 b/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.1 new file mode 100644 index 0000000000..3489ad5d7a --- /dev/null +++ b/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.1 @@ -0,0 +1,88 @@ +LAMMPS (4 May 2022) + using 1 OpenMP thread(s) per MPI task +units real +atom_style atomic + +# data file with one atom type +read_data data.spce +Reading data file ... + orthogonal box = (0 0 0) to (31.0648 31.0648 31.0648) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1000 atoms + read_data CPU = 0.001 seconds + +pair_style hybrid/overlay table linear 1200 threebody/table + +#pair coefficients +pair_coeff 1 1 table table_CG_CG.txt VOTCA +pair_coeff * * threebody/table spce.3b type + +fix 1 all nvt temp 300.0 300.0 200.0 + +velocity all create 300 432567 dist uniform loop geom mom yes +timestep 2.0 + +thermo 100 +#dump 2 all custom 100 dump.spce id type x y z fx fy fz + +run 1000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair table, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair threebody/table, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.487 | 5.487 | 5.487 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -5377.8719 0 -4484.5232 -320.10184 + 100 296.01121 -5418.505 0 -4537.0342 -223.39972 + 200 295.27654 -5430.3033 0 -4551.0202 794.29126 + 300 302.16526 -5445.8048 0 -4546.0083 -11.568299 + 400 308.59003 -5434.7181 0 -4515.7896 1.7337645 + 500 295.346 -5436.0896 0 -4556.5996 778.73307 + 600 293.14671 -5422.6082 0 -4549.6673 -148.64256 + 700 307.63238 -5465.187 0 -4549.1103 285.18556 + 800 313.16537 -5466.4124 0 -4533.8594 489.99301 + 900 303.42954 -5506.3208 0 -4602.7595 360.05608 + 1000 299.50926 -5446.8981 0 -4555.0107 993.95615 +Loop time of 5.12079 on 1 procs for 1000 steps with 1000 atoms + +Performance: 33.745 ns/day, 0.711 hours/ns, 195.282 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.8109 | 4.8109 | 4.8109 | 0.0 | 93.95 +Neigh | 0.27061 | 0.27061 | 0.27061 | 0.0 | 5.28 +Comm | 0.020092 | 0.020092 | 0.020092 | 0.0 | 0.39 +Output | 0.00020325 | 0.00020325 | 0.00020325 | 0.0 | 0.00 +Modify | 0.011643 | 0.011643 | 0.011643 | 0.0 | 0.23 +Other | | 0.007324 | | | 0.14 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5900 ave 5900 max 5900 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 191126 ave 191126 max 191126 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 382252 ave 382252 max 382252 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 382252 +Ave neighs/atom = 382.252 +Neighbor list builds = 27 +Dangerous builds = 0 +Total wall time: 0:00:05 diff --git a/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.4 b/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.4 new file mode 100644 index 0000000000..e5985ae51e --- /dev/null +++ b/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.4 @@ -0,0 +1,88 @@ +LAMMPS (4 May 2022) + using 1 OpenMP thread(s) per MPI task +units real +atom_style atomic + +# data file with one atom type +read_data data.spce +Reading data file ... + orthogonal box = (0 0 0) to (31.0648 31.0648 31.0648) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 1000 atoms + read_data CPU = 0.001 seconds + +pair_style hybrid/overlay table linear 1200 threebody/table + +#pair coefficients +pair_coeff 1 1 table table_CG_CG.txt VOTCA +pair_coeff * * threebody/table spce.3b type + +fix 1 all nvt temp 300.0 300.0 200.0 + +velocity all create 300 432567 dist uniform loop geom mom yes +timestep 2.0 + +thermo 100 +#dump 2 all custom 100 dump.spce id type x y z fx fy fz + +run 1000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair table, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair threebody/table, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.87 | 3.87 | 3.87 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -5377.8719 0 -4484.5232 -320.10184 + 100 296.01121 -5418.505 0 -4537.0342 -223.39972 + 200 295.27654 -5430.3033 0 -4551.0202 794.29126 + 300 302.16526 -5445.8048 0 -4546.0083 -11.568299 + 400 308.59003 -5434.7181 0 -4515.7896 1.7337642 + 500 295.346 -5436.0896 0 -4556.5996 778.73304 + 600 293.14648 -5422.6082 0 -4549.6681 -148.67071 + 700 307.6975 -5465.3018 0 -4549.0312 287.70203 + 800 314.09436 -5467.6073 0 -4532.2879 522.73489 + 900 300.85843 -5503.7551 0 -4607.85 491.78041 + 1000 302.84638 -5468.3331 0 -4566.5083 338.05123 +Loop time of 1.45119 on 4 procs for 1000 steps with 1000 atoms + +Performance: 119.075 ns/day, 0.202 hours/ns, 689.091 timesteps/s +98.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.2376 | 1.256 | 1.2833 | 1.5 | 86.55 +Neigh | 0.06865 | 0.06984 | 0.071283 | 0.4 | 4.81 +Comm | 0.084664 | 0.1133 | 0.13329 | 5.4 | 7.81 +Output | 0.0001668 | 0.00034177 | 0.00086454 | 0.0 | 0.02 +Modify | 0.0069024 | 0.0071705 | 0.0074503 | 0.3 | 0.49 +Other | | 0.004489 | | | 0.31 + +Nlocal: 250 ave 257 max 240 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +Nghost: 3488.75 ave 3504 max 3478 min +Histogram: 1 1 0 0 0 1 0 0 0 1 +Neighs: 47828 ave 49169 max 45782 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +FullNghs: 95656 ave 98253 max 91425 min +Histogram: 1 0 0 0 0 1 0 0 1 1 + +Total # of neighbors = 382624 +Ave neighs/atom = 382.624 +Neighbor list builds = 27 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.1 b/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.1 new file mode 100644 index 0000000000..12503118e0 --- /dev/null +++ b/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.1 @@ -0,0 +1,89 @@ +LAMMPS (4 May 2022) + using 1 OpenMP thread(s) per MPI task +units real +atom_style atomic + +# data file with two atom types +read_data data.spce2 +Reading data file ... + orthogonal box = (0 0 0) to (31.0648 31.0648 31.0648) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1000 atoms + read_data CPU = 0.001 seconds + +pair_style hybrid/overlay table linear 1200 threebody/table + +#pair coefficients +pair_coeff * * table table_CG_CG.txt VOTCA +pair_coeff * * threebody/table spce2.3b type1 type2 + +fix 1 all nvt temp 300.0 300.0 200.0 + +velocity all create 300 432567 dist uniform loop geom mom yes +timestep 2.0 + +thermo 100 +#dump 2 all custom 100 dump.spce2 id type x y z fx fy fz + +run 1000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair table, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair threebody/table, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.487 | 5.487 | 5.487 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -5377.8719 0 -4484.5232 -320.10184 + 100 296.01121 -5418.505 0 -4537.0342 -223.39972 + 200 295.27654 -5430.3033 0 -4551.0202 794.29126 + 300 302.16526 -5445.8048 0 -4546.0083 -11.568299 + 400 308.59003 -5434.7181 0 -4515.7896 1.7337645 + 500 295.346 -5436.0896 0 -4556.5996 778.73307 + 600 293.14671 -5422.6082 0 -4549.6673 -148.64256 + 700 307.63238 -5465.187 0 -4549.1103 285.18556 + 800 313.16537 -5466.4124 0 -4533.8594 489.99301 + 900 303.42954 -5506.3208 0 -4602.7595 360.05608 + 1000 299.50926 -5446.8981 0 -4555.0107 993.95615 +Loop time of 5.16704 on 1 procs for 1000 steps with 1000 atoms + +Performance: 33.443 ns/day, 0.718 hours/ns, 193.534 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.8574 | 4.8574 | 4.8574 | 0.0 | 94.01 +Neigh | 0.27015 | 0.27015 | 0.27015 | 0.0 | 5.23 +Comm | 0.020112 | 0.020112 | 0.020112 | 0.0 | 0.39 +Output | 0.0002118 | 0.0002118 | 0.0002118 | 0.0 | 0.00 +Modify | 0.011792 | 0.011792 | 0.011792 | 0.0 | 0.23 +Other | | 0.007409 | | | 0.14 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5900 ave 5900 max 5900 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 191126 ave 191126 max 191126 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 382252 ave 382252 max 382252 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 382252 +Ave neighs/atom = 382.252 +Neighbor list builds = 27 +Dangerous builds = 0 + +Total wall time: 0:00:05 diff --git a/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.4 b/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.4 new file mode 100644 index 0000000000..23f3348c34 --- /dev/null +++ b/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.4 @@ -0,0 +1,89 @@ +LAMMPS (4 May 2022) + using 1 OpenMP thread(s) per MPI task +units real +atom_style atomic + +# data file with two atom types +read_data data.spce2 +Reading data file ... + orthogonal box = (0 0 0) to (31.0648 31.0648 31.0648) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 1000 atoms + read_data CPU = 0.002 seconds + +pair_style hybrid/overlay table linear 1200 threebody/table + +#pair coefficients +pair_coeff * * table table_CG_CG.txt VOTCA +pair_coeff * * threebody/table spce2.3b type1 type2 + +fix 1 all nvt temp 300.0 300.0 200.0 + +velocity all create 300 432567 dist uniform loop geom mom yes +timestep 2.0 + +thermo 100 +#dump 2 all custom 100 dump.spce2 id type x y z fx fy fz + +run 1000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair table, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair threebody/table, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.87 | 3.87 | 3.87 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -5377.8719 0 -4484.5232 -320.10184 + 100 296.01121 -5418.505 0 -4537.0342 -223.39972 + 200 295.27654 -5430.3033 0 -4551.0202 794.29126 + 300 302.16526 -5445.8048 0 -4546.0083 -11.568299 + 400 308.59003 -5434.7181 0 -4515.7896 1.7337642 + 500 295.346 -5436.0896 0 -4556.5996 778.73304 + 600 293.14648 -5422.6082 0 -4549.6681 -148.67071 + 700 307.6975 -5465.3018 0 -4549.0312 287.70203 + 800 314.09436 -5467.6073 0 -4532.2879 522.73489 + 900 300.85843 -5503.7551 0 -4607.85 491.78041 + 1000 302.84638 -5468.3331 0 -4566.5083 338.05123 +Loop time of 1.4686 on 4 procs for 1000 steps with 1000 atoms + +Performance: 117.663 ns/day, 0.204 hours/ns, 680.919 timesteps/s +98.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.2491 | 1.2757 | 1.3162 | 2.3 | 86.87 +Neigh | 0.06817 | 0.069468 | 0.071025 | 0.5 | 4.73 +Comm | 0.069929 | 0.11236 | 0.14069 | 8.1 | 7.65 +Output | 0.00016417 | 0.00050711 | 0.0015318 | 0.0 | 0.03 +Modify | 0.0057514 | 0.0061681 | 0.0066503 | 0.5 | 0.42 +Other | | 0.004366 | | | 0.30 + +Nlocal: 250 ave 257 max 240 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +Nghost: 3488.75 ave 3504 max 3478 min +Histogram: 1 1 0 0 0 1 0 0 0 1 +Neighs: 47828 ave 49169 max 45782 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +FullNghs: 95656 ave 98253 max 91425 min +Histogram: 1 0 0 0 0 1 0 0 1 1 + +Total # of neighbors = 382624 +Ave neighs/atom = 382.624 +Neighbor list builds = 27 +Dangerous builds = 0 + +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/pair_threebody_table/spce.3b b/examples/PACKAGES/manybody_table/spce.3b similarity index 100% rename from examples/PACKAGES/pair_threebody_table/spce.3b rename to examples/PACKAGES/manybody_table/spce.3b diff --git a/examples/PACKAGES/pair_threebody_table/spce_2.3b b/examples/PACKAGES/manybody_table/spce2.3b similarity index 100% rename from examples/PACKAGES/pair_threebody_table/spce_2.3b rename to examples/PACKAGES/manybody_table/spce2.3b diff --git a/examples/PACKAGES/pair_threebody_table/table_CG_CG.txt b/examples/PACKAGES/manybody_table/table_CG_CG.txt similarity index 100% rename from examples/PACKAGES/pair_threebody_table/table_CG_CG.txt rename to examples/PACKAGES/manybody_table/table_CG_CG.txt diff --git a/examples/PACKAGES/pair_threebody_table/CG-CG-CG.dist.new b/examples/PACKAGES/pair_threebody_table/CG-CG-CG.dist.new deleted file mode 100644 index 7009d77ec6..0000000000 --- a/examples/PACKAGES/pair_threebody_table/CG-CG-CG.dist.new +++ /dev/null @@ -1,63 +0,0 @@ -0 0 i -0.05 0 i -0.1 0 i -0.15 0 i -0.2 0 i -0.25 0 i -0.3 0 i -0.35 0 i -0.4 0 i -0.45 0 i -0.5 0 i -0.55 0 i -0.6 0 i -0.65 0 i -0.7 0.001948589708 i -0.75 0.04587304938 i -0.8 0.2676063199 i -0.85 0.5482844291 i -0.9 0.6484744166 i -0.95 0.6004903951 i -1 0.4988389653 i -1.05 0.4309630905 i -1.1 0.4329116802 i -1.15 0.4468765731 i -1.2 0.4768361398 i -1.25 0.4997320689 i -1.3 0.5256320738 i -1.35 0.5270935161 i -1.4 0.5542925807 i -1.45 0.5859571635 i -1.5 0.5850640599 i -1.55 0.5951317734 i -1.6 0.6080411802 i -1.65 0.6103145349 i -1.7 0.6252537226 i -1.75 0.6264715912 i -1.8 0.6312618742 i -1.85 0.6111264472 i -1.9 0.5870938408 i -1.95 0.5864443109 i -2 0.5615186009 i -2.05 0.5516944611 i -2.1 0.5181624799 i -2.15 0.5016806586 i -2.2 0.4791906857 i -2.25 0.4356721823 i -2.3 0.4166734326 i -2.35 0.4014906711 i -2.4 0.3701508533 i -2.45 0.3518016336 i -2.5 0.32533329 i -2.55 0.3129922219 i -2.6 0.2849812448 i -2.65 0.2464965981 i -2.7 0.2347238686 i -2.75 0.1968887518 i -2.8 0.1679846711 i -2.85 0.1487423477 i -2.9 0.115372749 i -2.95 0.0894727441 i -3 0.0654401377 i -3.05 0.04424922462 i -3.1 0.02127210431 i diff --git a/examples/PACKAGES/pair_threebody_table/CG-CG.dist.new b/examples/PACKAGES/pair_threebody_table/CG-CG.dist.new deleted file mode 100644 index 20086f12e2..0000000000 --- a/examples/PACKAGES/pair_threebody_table/CG-CG.dist.new +++ /dev/null @@ -1,301 +0,0 @@ -0 0 i -0.05 0 i -0.1 0 i -0.15 0 i -0.2 0 i -0.25 0 i -0.3 0 i -0.35 0 i -0.4 0 i -0.45 0 i -0.5 0 i -0.55 0 i -0.6 0 i -0.65 0 i -0.7 0 i -0.75 0 i -0.8 0 i -0.85 0 i -0.9 0 i -0.95 0 i -1 0 i -1.05 0 i -1.1 0 i -1.15 0 i -1.2 0 i -1.25 0 i -1.3 0 i -1.35 0 i -1.4 0 i -1.45 0 i -1.5 0 i -1.55 0 i -1.6 0 i -1.65 0 i -1.7 0 i -1.75 0 i -1.8 0 i -1.85 0 i -1.9 0 i -1.95 0 i -2 0 i -2.05 0 i -2.1 0 i -2.15 0 i -2.2 0 i -2.25 0 i -2.3 0 i -2.35 0 i -2.4 0 i -2.45 0.006868969636 i -2.5 0.06691209899 i -2.55 0.3369686231 i -2.6 1.016837547 i -2.65 1.941722496 i -2.7 2.810156047 i -2.75 3.109238091 i -2.8 2.992426567 i -2.85 2.654848044 i -2.9 2.142463942 i -2.95 1.78347485 i -3 1.474515791 i -3.05 1.214450999 i -3.1 1.145558566 i -3.15 1.05605496 i -3.2 0.9416308652 i -3.25 0.9061891875 i -3.3 0.8518932332 i -3.35 0.8345267201 i -3.4 0.7974243251 i -3.45 0.7759630924 i -3.5 0.8025159274 i -3.55 0.7814715757 i -3.6 0.8367247283 i -3.65 0.8466756241 i -3.7 0.8260987595 i -3.75 0.8875703499 i -3.8 0.8908815678 i -3.85 0.8893512455 i -3.9 0.9034838101 i -3.95 0.975136055 i -4 0.9693174253 i -4.05 0.9333220268 i -4.1 0.9786753242 i -4.15 1.02432124 i -4.2 0.9877232079 i -4.25 1.042558817 i -4.3 1.016224537 i -4.35 1.041869238 i -4.4 1.064875454 i -4.45 1.028884843 i -4.5 1.030581768 i -4.55 1.048458215 i -4.6 1.089257872 i -4.65 1.094290276 i -4.7 1.084997348 i -4.75 1.070629827 i -4.8 1.084744429 i -4.85 1.082526933 i -4.9 1.06079278 i -4.95 1.0471637 i -5 1.062609545 i -5.05 1.040979202 i -5.1 1.030405966 i -5.15 1.010273278 i -5.2 1.023613984 i -5.25 0.9909597269 i -5.3 1.015757348 i -5.35 1.006532346 i -5.4 0.9437414066 i -5.45 0.961407175 i -5.5 0.9391385986 i -5.55 0.9337672098 i -5.6 0.9434633573 i -5.65 0.9427075195 i -5.7 0.9256975468 i -5.75 0.969172923 i -5.8 0.9108617596 i -5.85 0.9316750162 i -5.9 0.9343951559 i -5.95 0.9320676092 i -6 0.9648657983 i -6.05 0.9452822858 i -6.1 0.9782890038 i -6.15 0.9800447499 i -6.2 1.000311384 i -6.25 0.9763785285 i -6.3 1.003683553 i -6.35 0.9945134274 i -6.4 1.018437926 i -6.45 1.022248288 i -6.5 1.016480477 i -6.55 1.022988268 i -6.6 1.012956154 i -6.65 1.03627509 i -6.7 1.053539045 i -6.75 1.033851978 i -6.8 1.030805888 i -6.85 1.025729717 i -6.9 1.050384748 i -6.95 1.025204169 i -7 1.032609309 i -7.05 1.03922794 i -7.1 1.029667001 i -7.15 1.034097295 i -7.2 0.9966052515 i -7.25 0.998595277 i -7.3 1.020333466 i -7.35 1.012277485 i -7.4 1.008970678 i -7.45 0.9878317879 i -7.5 1.022664977 i -7.55 1.017638075 i -7.6 0.9861398784 i -7.65 1.015262635 i -7.7 1.001623523 i -7.75 1.003549644 i -7.8 0.9805591545 i -7.85 1.007394142 i -7.9 0.9803367825 i -7.95 0.9888274034 i -8 0.9665658006 i -8.05 0.9611406547 i -8.1 0.9696011841 i -8.15 0.9612879559 i -8.2 0.9740415393 i -8.25 0.9570782131 i -8.3 0.970292395 i -8.35 0.9968930245 i -8.4 1.002925264 i -8.45 0.9971135902 i -8.5 0.9944668799 i -8.55 0.9901215978 i -8.6 0.9963226014 i -8.65 1.002471928 i -8.7 0.9972859678 i -8.75 1.000461709 i -8.8 1.007456373 i -8.85 0.9975337886 i -8.9 1.006881375 i -8.95 1.003898668 i -9 1.01939082 i -9.05 1.027863733 i -9.1 1.0126874 i -9.15 1.002986797 i -9.2 1.014592881 i -9.25 0.996218997 i -9.3 1.01434386 i -9.35 1.009318782 i -9.4 1.002409715 i -9.45 1.00752861 i -9.5 1.003738731 i -9.55 1.00546252 i -9.6 1.004475552 i -9.65 1.01401835 i -9.7 0.9999605344 i -9.75 0.9928909486 i -9.8 0.9909424428 i -9.85 0.9900750302 i -9.9 0.9919391121 i -9.95 0.9982970715 i -10 0.9898116624 i -10.05 0.9900764439 i -10.1 0.9969278915 i -10.15 0.9995371762 i -10.2 0.9830245195 i -10.25 0.9985185237 i -10.3 1.011778325 i -10.35 0.987729726 i -10.4 0.9792899029 i -10.45 1.005757012 i -10.5 1.011427913 i -10.55 1.01826943 i -10.6 1.018069644 i -10.65 1.009052089 i -10.7 1.012454415 i -10.75 1.014373714 i -10.8 1.003033618 i -10.85 1.00581897 i -10.9 0.9943814535 i -10.95 0.9987325036 i -11 0.9983875703 i -11.05 1.00760791 i -11.1 1.002375405 i -11.15 1.019653897 i -11.2 1.012683264 i -11.25 1.011799775 i -11.3 0.9985755313 i -11.35 1.004657344 i -11.4 1.011546083 i -11.45 1.006280333 i -11.5 0.9938523349 i -11.55 0.9903439726 i -11.6 0.9903610229 i -11.65 0.9993250672 i -11.7 1.000612865 i -11.75 0.985843493 i -11.8 0.9935396204 i -11.85 0.9961212519 i -11.9 0.9881008469 i -11.95 0.9912340172 i -12 0.9932581399 i -12.05 1.005031664 i -12.1 1.000283189 i -12.15 0.9957382812 i -12.2 0.9905217757 i -12.25 1.005650661 i -12.3 0.9983867528 i -12.35 1.008547414 i -12.4 1.004989106 i -12.45 1.011715734 i -12.5 1.003525112 i -12.55 0.9923659728 i -12.6 0.9925939594 i -12.65 0.993670768 i -12.7 1.006897619 i -12.75 0.9910443316 i -12.8 1.003773488 i -12.85 1.003254426 i -12.9 1.003173391 i -12.95 1.003485179 i -13 0.9982555554 i -13.05 0.9907591011 i -13.1 0.9928898602 i -13.15 0.9995581937 i -13.2 1.004068838 i -13.25 1.001772811 i -13.3 1.002046922 i -13.35 1.000603255 i -13.4 1.011323585 i -13.45 1.009060732 i -13.5 1.013946339 i -13.55 1.005578858 i -13.6 0.9982940357 i -13.65 1.003923923 i -13.7 1.010292528 i -13.75 1.004609556 i -13.8 0.9928580994 i -13.85 1.003973204 i -13.9 0.99837917 i -13.95 0.9980455921 i -14 0.9986529903 i -14.05 0.9917965086 i -14.1 1.00095185 i -14.15 0.9970089013 i -14.2 0.997098635 i -14.25 0.9980037804 i -14.3 1.013908132 i -14.35 1.001934888 i -14.4 1.006664102 i -14.45 0.991726169 i -14.5 0.9912580833 i -14.55 1.008190614 i -14.6 0.9970967502 i -14.65 0.9958736094 i -14.7 0.9903643889 i -14.75 0.9965217067 i -14.8 0.998001776 i -14.85 1.000587917 i -14.9 0.9950512374 i -14.95 0.9958385369 i -15 1.001436413 i diff --git a/examples/PACKAGES/pair_threebody_table/calculate_distributions.xml b/examples/PACKAGES/pair_threebody_table/calculate_distributions.xml deleted file mode 100644 index f2510d4f21..0000000000 --- a/examples/PACKAGES/pair_threebody_table/calculate_distributions.xml +++ /dev/null @@ -1,29 +0,0 @@ - - - grid - - - - - CG-CG - 1 - 1 - 0.0 - 15.0 - 0.05 - - - - - - CG-CG-CG - 1 - 1 - 1 - 1 - 0.0 - 3.1 - 0.05 - 3.7 - - diff --git a/examples/PACKAGES/pair_threebody_table/run.sh b/examples/PACKAGES/pair_threebody_table/run.sh deleted file mode 100755 index c87c01e23e..0000000000 --- a/examples/PACKAGES/pair_threebody_table/run.sh +++ /dev/null @@ -1,8 +0,0 @@ -#! /bin/bash -e - -#run the LAMMPS simulation of the first part of the tutorial (needs a current LAMMPS version compiled with the user pair_style 3b/table) -lmp < spce.in > spce.out - -#run the LAMMPS simulation of the second part of the tutorial (needs a current LAMMPS version compiled with the user pair_style 3b/table) -lmp < spce_2.in > spce_2.out - diff --git a/examples/PACKAGES/pair_threebody_table/spce.in b/examples/PACKAGES/pair_threebody_table/spce.in deleted file mode 100644 index 2ca97708c6..0000000000 --- a/examples/PACKAGES/pair_threebody_table/spce.in +++ /dev/null @@ -1,43 +0,0 @@ -log none - -units real -atom_style atomic - -read_data spce.data - -#hybrid pair style consisting of -#pair_style table to read in CG pair potential -#pair_style threebody/table for tabulated threebody interactions -pair_style hybrid/overlay table linear 1200 threebody/table - -#pair coefficients -pair_coeff 1 1 table table_CG_CG.txt VOTCA -pair_coeff * * threebody/table spce.3b type - -#nvt run with nose-hoover thermostat -#time coupling of 100 ts for thermostat -#target T is 300 K -fix 1 all nvt temp 300.0 300.0 200.0 - -#create initial velocities -velocity all create 300 432567 dist uniform -#remove center of mass linear momentum -velocity all zero linear - -#remove center of mass linear momentum every 1000 time steps in each cartesian direction -fix remove all momentum 1000 linear 1 1 1 - -#timestep of 2 fs -timestep 2.0 - -#print out thermodynamic info every 100 ts -thermo 100 - -#run 10000 ts -run 10000 - -#write out dump file every 10 ts for 100000 ts -dump 2 all custom 10 spce.dump id type x y z fx fy fz -run 100000 - -undump 2 diff --git a/examples/PACKAGES/pair_threebody_table/spce_2.in b/examples/PACKAGES/pair_threebody_table/spce_2.in deleted file mode 100644 index e05df5d719..0000000000 --- a/examples/PACKAGES/pair_threebody_table/spce_2.in +++ /dev/null @@ -1,43 +0,0 @@ -log none - -units real -atom_style atomic - -read_data spce_2.data - -#hybrid pair style consisting of -#pair_style table to read in CG pair potential -#pair_style threebody/table for tabulated threebody interactions -pair_style hybrid/overlay table linear 1200 threebody/table - -#pair coefficients -pair_coeff * * table table_CG_CG.txt VOTCA -pair_coeff * * threebody/table spce_2.3b type1 type2 - -#nvt run with nose-hoover thermostat -#time coupling of 100 ts for thermostat -#target T is 300 K -fix 1 all nvt temp 300.0 300.0 200.0 - -#create initial velocities -velocity all create 300 432567 dist uniform -#remove center of mass linear momentum -velocity all zero linear - -#remove center of mass linear momentum every 1000 time steps in each cartesian direction -fix remove all momentum 1000 linear 1 1 1 - -#timestep of 2 fs -timestep 2.0 - -#print out thermodynamic info every 100 ts -thermo 100 - -#run 10000 ts -run 10000 - -#write out dump file every 10 ts for 100000 ts -dump 2 all custom 10 spce_2.dump id type x y z fx fy fz -run 100000 - -undump 2 From edea4fa9a2fbdf660fc5df54133938c5a7c10aa9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 1 Jun 2022 14:23:30 -0400 Subject: [PATCH 29/34] fix memory allocation/communication issues. avoid memory leaks. --- src/MANYBODY/pair_threebody_table.cpp | 68 ++++++++++++--------------- 1 file changed, 31 insertions(+), 37 deletions(-) diff --git a/src/MANYBODY/pair_threebody_table.cpp b/src/MANYBODY/pair_threebody_table.cpp index 201e2a77a2..1ce68dbf69 100644 --- a/src/MANYBODY/pair_threebody_table.cpp +++ b/src/MANYBODY/pair_threebody_table.cpp @@ -31,8 +31,6 @@ #include #include -// -#include using namespace LAMMPS_NS; using MathConst::MY_PI; @@ -205,12 +203,12 @@ void PairThreebodyTable::compute(int eflag, int vflag) void PairThreebodyTable::allocate() { allocated = 1; - int n = atom->ntypes; + int np1 = atom->ntypes + 1; - memory->create(setflag,n+1,n+1,"pair:setflag"); - memory->create(cutsq,n+1,n+1,"pair:cutsq"); + memory->create(setflag,np1,np1,"pair:setflag"); + memory->create(cutsq,np1,np1,"pair:cutsq"); memory->create(neighshort,maxshort,"pair:neighshort"); - map = new int[n+1]; + map = new int[np1]; } /* ---------------------------------------------------------------------- @@ -234,6 +232,11 @@ void PairThreebodyTable::coeff(int narg, char **arg) // 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(); } @@ -269,7 +272,6 @@ double PairThreebodyTable::init_one(int i, int j) void PairThreebodyTable::read_file(char *file) { - memory->sfree(params); params = nullptr; nparams = maxparam = 0; @@ -325,21 +327,17 @@ void PairThreebodyTable::read_file(char *file) params[nparams].cut = values.next_double(); // read parameters of angle table - std::string tablename_string = values.next_string(); - params[nparams].tablenamelength = tablename_string.length()+1; - memory->create(params[nparams].tablename, params[nparams].tablenamelength, "params.tablename"); - for (int x = 0; x < params[nparams].tablenamelength; ++x) { - params[nparams].tablename[x] = tablename_string[x]; - } - std::string keyword_string = values.next_string(); - params[nparams].keywordlength = keyword_string.length()+1; - memory->create(params[nparams].keyword, params[nparams].keywordlength, "params.keyword"); - for (int x = 0; x < params[nparams].keywordlength; ++x) { - params[nparams].keyword[x] = keyword_string[x]; - } - auto tablestyle = values.next_string(); - if (tablestyle != "linear") - error->all(FLERR,"Unknown table style {} in threebody table", tablestyle); + 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) { @@ -356,29 +354,25 @@ void PairThreebodyTable::read_file(char *file) 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"); - } - + 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) { - memory->create(params[m].tablename, params[m].tablenamelength, "params.tablename"); + params[m].tablename = new char[params[m].tablenamelength]; + params[m].keyword = new char[params[m].keywordlength]; } - MPI_Bcast(¶ms[m].tablename, params[m].tablenamelength, MPI_CHAR, 0, world); - if (comm->me != 0) { - memory->create(params[m].keyword, params[m].keywordlength, "params.keyword"); - } - MPI_Bcast(¶ms[m].keyword, params[m].keywordlength, MPI_CHAR, 0, world); + + 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){ + if (comm->me == 0) { read_table(params[m].mltable,params[m].tablename,params[m].keyword,params[m].symmetric); } @@ -570,7 +564,7 @@ void PairThreebodyTable::param_extract(Table *tb, char *line) } else if (word == "rmax") { tb->rmax = values.next_double(); } else { - error->one(FLERR, "Invalid keyword in angle table parameters"); + error->one(FLERR, "Invalid keyword {} in angle table parameters", word); } } } catch (TokenizerException &e) { @@ -659,11 +653,11 @@ void PairThreebodyTable::bcast_table(Table *tb, bool symmetric) void PairThreebodyTable::free_param(Param *pm) { - // call free_table to destroy associated threebodytable + // call free_table to destroy associated threebodytables free_table(pm->mltable); // then destroy associated threebodytable - memory->sfree(pm->tablename); - memory->sfree(pm->keyword); + delete[] pm->tablename; + delete[] pm->keyword; memory->sfree(pm->mltable); } From b9b0d7207c495add938df885d5b22028939612cb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 1 Jun 2022 14:24:23 -0400 Subject: [PATCH 30/34] apply clang-format --- src/MANYBODY/pair_threebody_table.cpp | 385 ++++++++++++-------------- 1 file changed, 183 insertions(+), 202 deletions(-) diff --git a/src/MANYBODY/pair_threebody_table.cpp b/src/MANYBODY/pair_threebody_table.cpp index 1ce68dbf69..14f3c261d9 100644 --- a/src/MANYBODY/pair_threebody_table.cpp +++ b/src/MANYBODY/pair_threebody_table.cpp @@ -26,8 +26,8 @@ #include "memory.h" #include "neigh_list.h" #include "neighbor.h" -#include "table_file_reader.h" #include "potential_file_reader.h" +#include "table_file_reader.h" #include #include @@ -39,7 +39,8 @@ using MathConst::MY_PI; /* ---------------------------------------------------------------------- */ -PairThreebodyTable::PairThreebodyTable(LAMMPS *lmp) : Pair(lmp), params(nullptr), neighshort(nullptr) +PairThreebodyTable::PairThreebodyTable(LAMMPS *lmp) : + Pair(lmp), params(nullptr), neighshort(nullptr) { single_enable = 0; restartinfo = 0; @@ -58,7 +59,7 @@ PairThreebodyTable::~PairThreebodyTable() { if (copymode) return; - for (int m = 0; m < nparams; m++) free_param(¶ms[m]); // free_param will call free_table + for (int m = 0; m < nparams; m++) free_param(¶ms[m]); // free_param will call free_table memory->sfree(params); memory->destroy(elem3param); @@ -73,16 +74,16 @@ PairThreebodyTable::~PairThreebodyTable() 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; + 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); + ev_init(eflag, vflag); double **x = atom->x; double **f = atom->f; @@ -94,7 +95,7 @@ void PairThreebodyTable::compute(int eflag, int vflag) numneigh = list->numneigh; firstneigh = list->firstneigh; - double fxtmp,fytmp,fztmp; + double fxtmp, fytmp, fztmp; // loop over full neighbor list of my atoms @@ -120,7 +121,7 @@ void PairThreebodyTable::compute(int eflag, int vflag) delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; + rsq = delx * delx + dely * dely + delz * delz; jtype = map[type[j]]; ijparam = elem3param[itype][jtype][jtype]; @@ -129,16 +130,16 @@ void PairThreebodyTable::compute(int eflag, int vflag) } else { neighshort[numshort++] = j; if (numshort >= maxshort) { - maxshort += maxshort/2; - memory->grow(neighshort,maxshort,"pair:neighshort"); + maxshort += maxshort / 2; + memory->grow(neighshort, maxshort, "pair:neighshort"); } } jtag = tag[j]; if (itag > jtag) { - if ((itag+jtag) % 2 == 0) continue; + if ((itag + jtag) % 2 == 0) continue; } else if (itag < jtag) { - if ((itag+jtag) % 2 == 1) continue; + if ((itag + jtag) % 2 == 1) continue; } else { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp && x[j][1] < ytmp) continue; @@ -157,12 +158,12 @@ void PairThreebodyTable::compute(int eflag, int vflag) 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]; + rsq1 = delr1[0] * delr1[0] + delr1[1] * delr1[1] + delr1[2] * delr1[2]; - double fjxtmp,fjytmp,fjztmp; + double fjxtmp, fjytmp, fjztmp; fjxtmp = fjytmp = fjztmp = 0.0; - for (kk = jj+1; kk < numshort; kk++) { + for (kk = jj + 1; kk < numshort; kk++) { k = neighshort[kk]; ktype = map[type[k]]; ijkparam = elem3param[itype][jtype][ktype]; @@ -170,9 +171,9 @@ void PairThreebodyTable::compute(int eflag, int vflag) 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]; + 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); + threebody(¶ms[ijkparam], rsq1, rsq2, delr1, delr2, fi, fj, fk, eflag, evdwl); fxtmp += fi[0]; fytmp += fi[1]; @@ -184,7 +185,7 @@ void PairThreebodyTable::compute(int eflag, int vflag) 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 (evflag) ev_tally3(i, j, k, evdwl, 0.0, fj, fk, delr1, delr2); } f[j][0] += fjxtmp; f[j][1] += fjytmp; @@ -205,9 +206,9 @@ 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"); + memory->create(setflag, np1, np1, "pair:setflag"); + memory->create(cutsq, np1, np1, "pair:cutsq"); + memory->create(neighshort, maxshort, "pair:neighshort"); map = new int[np1]; } @@ -217,7 +218,7 @@ void PairThreebodyTable::allocate() void PairThreebodyTable::settings(int narg, char ** /*arg*/) { - if (narg != 0) error->all(FLERR,"Illegal pair_style command"); + if (narg != 0) error->all(FLERR, "Illegal pair_style command"); } /* ---------------------------------------------------------------------- @@ -228,12 +229,12 @@ void PairThreebodyTable::coeff(int narg, char **arg) { if (!allocated) allocate(); - map_element2type(narg-3,arg+3); + 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 + for (int m = 0; m < nparams; m++) free_param(¶ms[m]); // free_param will call free_table memory->sfree(params); params = nullptr; } @@ -247,10 +248,9 @@ void PairThreebodyTable::coeff(int narg, char **arg) void PairThreebodyTable::init_style() { - if (atom->tag_enable == 0) - error->all(FLERR,"Pair style threebody/table requires atom IDs"); + 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"); + error->all(FLERR, "Pair style threebody/table requires newton pair on"); // need a full neighbor list @@ -263,7 +263,7 @@ void PairThreebodyTable::init_style() double PairThreebodyTable::init_one(int i, int j) { - if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set"); return cutmax; } @@ -308,13 +308,12 @@ void PairThreebodyTable::read_file(char *file) if (nparams == maxparam) { maxparam += DELTA; - params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), - "pair:params"); + 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)); + memset(params + nparams, 0, DELTA * sizeof(Param)); } params[nparams].ielement = ielement; @@ -328,16 +327,15 @@ void PairThreebodyTable::read_file(char *file) // read parameters of angle table std::string name = values.next_string(); - params[nparams].tablenamelength = name.length()+1; + params[nparams].tablenamelength = name.length() + 1; params[nparams].tablename = utils::strdup(name); name = values.next_string(); - params[nparams].keywordlength = name.length()+1; + 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); + if (name != "linear") error->all(FLERR, "Unknown table style {} in threebody table", name); params[nparams].tablength = values.next_int(); } catch (TokenizerException &e) { @@ -345,7 +343,7 @@ void PairThreebodyTable::read_file(char *file) } if (params[nparams].cut < 0.0 || params[nparams].tablength < 0.0) - error->one(FLERR,"Illegal threebody/table parameters"); + error->one(FLERR, "Illegal threebody/table parameters"); nparams++; } @@ -354,42 +352,42 @@ void PairThreebodyTable::read_file(char *file) 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); + 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){ + 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"); + 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); + 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); + 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"); + if (params[m].mltable->ninput <= 1) error->one(FLERR, "Invalid threebody table length"); } } - /* ---------------------------------------------------------------------- */ void PairThreebodyTable::setup_params() { - int i,j,k,m,n; + int i, j, k, m, n; double rtmp; // set elem3param for all triplet combinations @@ -397,24 +395,22 @@ void PairThreebodyTable::setup_params() // do not allow for ACB in place of ABC memory->destroy(elem3param); - memory->create(elem3param,nelements,nelements,nelements,"pair: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 duplicate entry"); + 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"); + if (n < 0) error->all(FLERR, "Potential file is missing an entry"); elem3param[i][j][k] = n; } - // compute parameter values derived from inputs // set cutsq using shortcut to reduce neighbor list for accelerated @@ -426,7 +422,6 @@ void PairThreebodyTable::setup_params() params[m].cutsq = rtmp * rtmp; } - // set cutmax to max of all params cutmax = 0.0; @@ -455,40 +450,39 @@ void PairThreebodyTable::read_table(Table *tb, char *file, char *keyword, bool s param_extract(tb, line); // if it is a symmetric threebody interaction, less table entries are required - if (symmetric == true){ - 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"); + if (symmetric == true) { + 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"); + 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 == true){ - for (int i = 0; i < tb->ninput*tb->ninput*(tb->ninput+1); i++) { + if (symmetric == true) { + for (int i = 0; i < tb->ninput * tb->ninput * (tb->ninput + 1); i++) { line = reader.next_line(11); try { ValueTokenizer values(line); @@ -507,9 +501,8 @@ void PairThreebodyTable::read_table(Table *tb, char *file, char *keyword, bool s ++cerror; } } - } - else{ - for (int i = 0; i < 2*tb->ninput*tb->ninput*tb->ninput; i++) { + } else { + for (int i = 0; i < 2 * tb->ninput * tb->ninput * tb->ninput; i++) { line = reader.next_line(11); try { ValueTokenizer values(line); @@ -576,7 +569,6 @@ void PairThreebodyTable::param_extract(Table *tb, char *line) 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: @@ -585,68 +577,69 @@ void PairThreebodyTable::param_extract(Table *tb, char *line) void PairThreebodyTable::bcast_table(Table *tb, bool symmetric) { - MPI_Bcast(&tb->ninput,1,MPI_INT,0,world); + 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 == true){ - 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"); + if (symmetric == true) { + 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"); + 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 == true){ - 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); + if (symmetric == true) { + 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); + 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); + MPI_Bcast(&tb->rmin, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&tb->rmax, 1, MPI_DOUBLE, 0, world); } /* ---------------------------------------------------------------------- */ @@ -692,91 +685,79 @@ void PairThreebodyTable::null_table(Table *tb) 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) +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); + 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 == true){ - 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; - } + if (pm->symmetric == true) { + 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 = 79; - } + ntheta = (theta - 0.00000001) / dtheta; + if (theta == 180.0) { ntheta = 79; } itable = 0; - for (i=0; imltable->ninput-i); - } + for (i = 0; i < nr12; i++) { itable += (pm->mltable->ninput - i); } itable += nr13; - itable *= (pm->mltable->ninput*2); + 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 = 79; - } - itable = nr12*(pm->mltable->ninput); + 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 = 79; } + itable = nr12 * (pm->mltable->ninput); itable += nr13; - itable *= (pm->mltable->ninput*2); + 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]; + 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) +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 r12, r13, theta, rinv, cs; - double f11,f12,f21,f22,f31,f32,u,temp; + double f11, f12, f21, f22, f31, f32, u, temp; bool swapped; double dr; - dr = (paramijk->mltable->rmax - paramijk->mltable->rmin)/(paramijk->mltable->ninput-1); + 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; + 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; + 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){ + if (r12 > r13) { temp = r12; r12 = r13; r13 = temp; @@ -787,17 +768,17 @@ void PairThreebodyTable::threebody(Param *paramijk, double rsq1, double rsq2, do //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)) ){ + 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{ + } else { f11 = f12 = f21 = f22 = f31 = f32 = u = 0.0; } // if the indices have been swapped, swap them back - if (swapped == true){ + if (swapped == true) { temp = r12; r12 = r13; r13 = temp; @@ -812,17 +793,17 @@ void PairThreebodyTable::threebody(Param *paramijk, double rsq1, double rsq2, do 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; + 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; + 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; + 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; } From 8a055fdcfa3121b4fbba915b4563e66811997ea9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 1 Jun 2022 15:04:07 -0400 Subject: [PATCH 31/34] merge with third manybody table example and provide updated log files --- examples/PACKAGES/manybody_table/README | 101 +- examples/PACKAGES/manybody_table/in.spce_sw | 20 + .../manybody_table/log.1Jun22.spce.g++.1 | 16 +- .../manybody_table/log.1Jun22.spce.g++.4 | 18 +- .../manybody_table/log.1Jun22.spce2.g++.1 | 18 +- .../manybody_table/log.1Jun22.spce2.g++.4 | 20 +- .../manybody_table/log.1Jun22.spce_sw.g++.1 | 87 ++ .../manybody_table/log.1Jun22.spce_sw.g++.4 | 87 ++ .../spce.sw | 0 .../table_CG_CG_CG.txt | 0 examples/PACKAGES/pair_sw_angle_table/README | 40 - examples/PACKAGES/pair_sw_angle_table/run.sh | 5 - .../PACKAGES/pair_sw_angle_table/spce.data | 1015 -------------- examples/PACKAGES/pair_sw_angle_table/spce.in | 45 - .../pair_sw_angle_table/table_CG_CG.txt | 1203 ----------------- 15 files changed, 276 insertions(+), 2399 deletions(-) create mode 100644 examples/PACKAGES/manybody_table/in.spce_sw create mode 100644 examples/PACKAGES/manybody_table/log.1Jun22.spce_sw.g++.1 create mode 100644 examples/PACKAGES/manybody_table/log.1Jun22.spce_sw.g++.4 rename examples/PACKAGES/{pair_sw_angle_table => manybody_table}/spce.sw (100%) rename examples/PACKAGES/{pair_sw_angle_table => manybody_table}/table_CG_CG_CG.txt (100%) delete mode 100644 examples/PACKAGES/pair_sw_angle_table/README delete mode 100755 examples/PACKAGES/pair_sw_angle_table/run.sh delete mode 100644 examples/PACKAGES/pair_sw_angle_table/spce.data delete mode 100644 examples/PACKAGES/pair_sw_angle_table/spce.in delete mode 100644 examples/PACKAGES/pair_sw_angle_table/table_CG_CG.txt diff --git a/examples/PACKAGES/manybody_table/README b/examples/PACKAGES/manybody_table/README index 3897f80a81..385695e0e0 100644 --- a/examples/PACKAGES/manybody_table/README +++ b/examples/PACKAGES/manybody_table/README @@ -1,65 +1,56 @@ -Example for pair style threebody/table +Three examples inputs for pair styles threebody/table (in.spce and +in.spce2) and sw/angle/table (in.spce_sw). All inputs are for the +simulation of coarse-grained SPC/E water. +A water molecule is represented by one coarse-grained (CG) bead. -This example contains all required input files for the simulation of CG SPC/E water with -the user pair style threebody/table, as well as a run.sh script. - -To run the example, you have to compile LAMMPS with the MANYBODY package, including pair_threebody_table.h and pair_threebody_table.cpp. - -Running the simulations, you will reproduce results of the following publication: - -C. Scherer, R. Scheid, D. Andrienko, and T. Bereau, Kernel-Based Machine Learning for Efficient Simulations of Molecular Liquids, J. Chem. Theor. Comp., 16(5):3194–3204, 2020, https://doi.org/10.1021/acs.jctc.9b01256 - -Here, a water molecule is represented by one coarse-grained (CG) bead. The example contains -two parts. -The three-body (force) tables for both parts (1-1-1.table and 1-1-2.table) have been parametrized with the kernel-based machine learning (ML) with the VOTCA package (https://gitlab.mpcdf.mpg.de/votca/votca). -For a general description of the table format have a look at the documentation of this pair style. -For a example on the parametrization, have a look at https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/guide and +For the two threebody/table examples the three-body (force) tables are +in the files 1-1-1.table and 1-1-2.table. These have been parametrized +with the kernel-based machine learning (ML) with the VOTCA package +(https://gitlab.mpcdf.mpg.de/votca/votca). For a example on the +parametrization, have a look at +https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/guide +and https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/ml. -In both cases, the parametrization is done according to a sample system, using the three-body forces of a Stillinger-Weber potential with tabulated angular forces (sw/angle/table). These then are learned with the covariant meshing technique with the settings files used in https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/ml/3body/with_binning. -For the first part of example, the folder contains the contains the LAMMPS data file (spce.data) with the starting configuration of 1000 CG water molecules, an input file (spce.in) and a threebody file (spce.3b). +In both cases, the parametrization is done according to a sample system, +using the three-body forces of a Stillinger-Weber potential with +tabulated angular forces (sw/angle/table) (see in.spce_sw). These then +are learned with the covariant meshing technique with the settings files +used in +https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/ml/3body/with_binning. -The lammps input file contains the lines specifying the pair style and coefficients: +The first example, in.spce uses the LAMMPS data file (data.spce) with +the starting configuration of 1000 CG water molecules, and a threebody +file (spce.3b) which loads the 1-1-1.table file. -- pair_style hybrid/overlay table linear 1200 threebody/table - use a combination of pair style table with 1200 linear table entries and the pair style threebody/table -- pair_coeff 1 1 table table_CG_CG.txt VOTCA - set the table name and keyword for the pair style table -- pair_coeff * * threebody/table spce.3b type - set the name of threebody file and bead type for the pair style threebody/table +A hybrid/overlay pair style is used to sum a tabulated pairwise +interaction (table_CG_CG.txt) with the tabulated threebody interactions. +The tabulated pair interaction is the effectively the same as in the +what is used by the in.spce_sw input using sw/angle/table pair style. -A hybrid pair style is used, where pair forces are calculated as a tabulated interaction (table_CG_CG.txt) and the pair style threebody/table is only used to calculate the three-body forces. -The tabulated pair interaction is the same as in the example of the sw/angle/table pair style: examples/PACKAGES/pair_sw_angle_table +IMPORTANT NOTE: The threebody tables are parameterized without storing +energies (the last column of the threebody table files is zero). This +is due to a current limitation of the paramerization procedure. -To run the simulation, one needs an additional threebody file (spce.3b). -It has the following structure: +This in.spce2 example uses the data.spce2 file and the threebody input +spce2.3b. This is essentially the same simulation as in in.spce only +the atom type of the first 100 CG water molecules has been changed from +1 to 2. This is done to demonstrate how to run a simulation with +different atom types. -- type - relates to keyword type in LAMMPS input file -- type - relates to keyword type in LAMMPS input file -- type - relates to keyword type in LAMMPS input file -- 3.7 - cutoff in Ang -- 1-1-1.table - name of 3-body force table -- ENTRY1 - keyword in 3-body force table for this interaction -- linear - interpolation is linear -- 12 - number of grid points in radial direction (automatically sets grid size, in this case to 1872) +For this (artificial) two-element simulation, the threebody file now +contain 8 entries for: type1 type1 type1, type1 type1 type2, type1 type2 +type1, type1 type2 type2, type2 type1 type1, type2 type1 type2, type2 +type2 type1, type2 type2 type2. Each entry has the same structure as +above. However, entries where the second and the third element are +different require a different force table (1-1-2.table) instead of +(1-1-1.table). 1-1-2.table contains exactly the force constants as +1-1-1.table. However it has to have the asymmetric structure where both +interparticle distances (r_ij and r_ik) are varied from rmin to rmax and +therefore contains "M = 2 * N * N * N" (2 * 12 * 12 * 12 = 3456) +entries. -As there is only one atom type (1), the force table is symmetric and contains "M = N * N * (N+1)" (12 * 12 * 13 = 1872) entries. - -The LAMMPS simulation is a standard nvt simulation. A dump file is output with the positions and forces every 10 time steps. -You can calculate the pair distribution and compare it to the ones in the publication. - -For the second part of the example, have a look at the LAMMPS data file (spce_2.data), the input file (spce_2.in) and the threebody file (spce_2.3b). -Running the second part, you will in fact perform the same MD simulation as in the first part of the example. However, the atom type of the first 100 CG water molecules has been changed from 1 to 2. -This is done to demonstrate how to run a simulation with different atom types. - -Again, lammps input file (spce_2.in) contains the lines specifying the pair style and coefficients: - -- pair_style hybrid/overlay table linear 1200 threebody/table - use a combination of pair style table with 1200 linear table entries and the pair style threebody/table -- pair_coeff 1 1 table table_CG_CG.txt VOTCA - set the table name and keyword for the pair style table -- pair_coeff * * threebody/table spce_2.3b type1 type2 - set the name of threebody file and bead type for the pair style threebody/table - -Now, the atom type 1 is mapped to the element type1 and the atom type 2 is mapped to the element type2 in the threebody file (spce_2.3b). -For this (artificial) two-element simulation, the threebody file now contain 8 entries for: type1 type1 type1, type1 type1 type2, type1 type2 type1, type1 type2 type2, type2 type1 type1, type2 type1 type2, type2 type2 type1, type2 type2 type2. -Each entry has the same structure as above. However, entries where the second and the third element are different require a different force table (1-1-2.table) instead of (1-1-1.table). -1-1-2.table contains exactly the force constants as 1-1-1.table. -However it has to have the asymmetric structure where both interparticle distances (r_ij and r_ik) are varied from rmin to rmax and therefore contains "M = 2 * N * N * N" (2 * 12 * 12 * 12 = 3456) entries. - -Now run the simulation. The theromodynamic output, as well as, the pair correlation function should be exactly the same as for the first part of the example. +The third example, in.spce_sw, contains the analytical twobody interactions +and replaces the threebody term of the Stillinger-Weber potential with an +angle/table style potential which is stored in the table_CG_CG_CG.txt file. diff --git a/examples/PACKAGES/manybody_table/in.spce_sw b/examples/PACKAGES/manybody_table/in.spce_sw new file mode 100644 index 0000000000..bb0a097743 --- /dev/null +++ b/examples/PACKAGES/manybody_table/in.spce_sw @@ -0,0 +1,20 @@ +units real +atom_style atomic + +read_data data.spce + +pair_style hybrid/overlay table linear 1200 sw/angle/table + +pair_coeff 1 1 table table_CG_CG.txt VOTCA +pair_coeff * * sw/angle/table spce.sw type + +fix 1 all nvt temp 300.0 300.0 200.0 + +velocity all create 300 432567 dist uniform mom yes + +timestep 2.0 + +thermo 100 +#dump 2 all custom 10 spce_sw.dump id type x y z fx fy fz + +run 1000 diff --git a/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.1 b/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.1 index 3489ad5d7a..ec20bd3ced 100644 --- a/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.1 +++ b/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.1 @@ -57,20 +57,20 @@ Per MPI rank memory allocation (min/avg/max) = 5.487 | 5.487 | 5.487 Mbytes 800 313.16537 -5466.4124 0 -4533.8594 489.99301 900 303.42954 -5506.3208 0 -4602.7595 360.05608 1000 299.50926 -5446.8981 0 -4555.0107 993.95615 -Loop time of 5.12079 on 1 procs for 1000 steps with 1000 atoms +Loop time of 5.15787 on 1 procs for 1000 steps with 1000 atoms -Performance: 33.745 ns/day, 0.711 hours/ns, 195.282 timesteps/s +Performance: 33.502 ns/day, 0.716 hours/ns, 193.879 timesteps/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 4.8109 | 4.8109 | 4.8109 | 0.0 | 93.95 -Neigh | 0.27061 | 0.27061 | 0.27061 | 0.0 | 5.28 -Comm | 0.020092 | 0.020092 | 0.020092 | 0.0 | 0.39 -Output | 0.00020325 | 0.00020325 | 0.00020325 | 0.0 | 0.00 -Modify | 0.011643 | 0.011643 | 0.011643 | 0.0 | 0.23 -Other | | 0.007324 | | | 0.14 +Pair | 4.8428 | 4.8428 | 4.8428 | 0.0 | 93.89 +Neigh | 0.27527 | 0.27527 | 0.27527 | 0.0 | 5.34 +Comm | 0.020461 | 0.020461 | 0.020461 | 0.0 | 0.40 +Output | 0.00020949 | 0.00020949 | 0.00020949 | 0.0 | 0.00 +Modify | 0.01198 | 0.01198 | 0.01198 | 0.0 | 0.23 +Other | | 0.007163 | | | 0.14 Nlocal: 1000 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.4 b/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.4 index e5985ae51e..48b37d55fe 100644 --- a/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.4 +++ b/examples/PACKAGES/manybody_table/log.1Jun22.spce.g++.4 @@ -57,20 +57,20 @@ Per MPI rank memory allocation (min/avg/max) = 3.87 | 3.87 | 3.87 Mbytes 800 314.09436 -5467.6073 0 -4532.2879 522.73489 900 300.85843 -5503.7551 0 -4607.85 491.78041 1000 302.84638 -5468.3331 0 -4566.5083 338.05123 -Loop time of 1.45119 on 4 procs for 1000 steps with 1000 atoms +Loop time of 1.60997 on 4 procs for 1000 steps with 1000 atoms -Performance: 119.075 ns/day, 0.202 hours/ns, 689.091 timesteps/s -98.3% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 107.331 ns/day, 0.224 hours/ns, 621.131 timesteps/s +94.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.2376 | 1.256 | 1.2833 | 1.5 | 86.55 -Neigh | 0.06865 | 0.06984 | 0.071283 | 0.4 | 4.81 -Comm | 0.084664 | 0.1133 | 0.13329 | 5.4 | 7.81 -Output | 0.0001668 | 0.00034177 | 0.00086454 | 0.0 | 0.02 -Modify | 0.0069024 | 0.0071705 | 0.0074503 | 0.3 | 0.49 -Other | | 0.004489 | | | 0.31 +Pair | 1.28 | 1.2942 | 1.3018 | 0.8 | 80.38 +Neigh | 0.069763 | 0.070222 | 0.070788 | 0.2 | 4.36 +Comm | 0.19379 | 0.20979 | 0.23226 | 3.6 | 13.03 +Output | 0.0001711 | 0.00046947 | 0.0013621 | 0.0 | 0.03 +Modify | 0.021613 | 0.030016 | 0.038718 | 4.8 | 1.86 +Other | | 0.005309 | | | 0.33 Nlocal: 250 ave 257 max 240 min Histogram: 1 0 0 0 0 1 0 0 1 1 diff --git a/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.1 b/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.1 index 12503118e0..d6432a1c07 100644 --- a/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.1 +++ b/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.1 @@ -57,20 +57,20 @@ Per MPI rank memory allocation (min/avg/max) = 5.487 | 5.487 | 5.487 Mbytes 800 313.16537 -5466.4124 0 -4533.8594 489.99301 900 303.42954 -5506.3208 0 -4602.7595 360.05608 1000 299.50926 -5446.8981 0 -4555.0107 993.95615 -Loop time of 5.16704 on 1 procs for 1000 steps with 1000 atoms +Loop time of 5.16365 on 1 procs for 1000 steps with 1000 atoms -Performance: 33.443 ns/day, 0.718 hours/ns, 193.534 timesteps/s -99.7% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 33.465 ns/day, 0.717 hours/ns, 193.661 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 4.8574 | 4.8574 | 4.8574 | 0.0 | 94.01 -Neigh | 0.27015 | 0.27015 | 0.27015 | 0.0 | 5.23 -Comm | 0.020112 | 0.020112 | 0.020112 | 0.0 | 0.39 -Output | 0.0002118 | 0.0002118 | 0.0002118 | 0.0 | 0.00 -Modify | 0.011792 | 0.011792 | 0.011792 | 0.0 | 0.23 -Other | | 0.007409 | | | 0.14 +Pair | 4.8443 | 4.8443 | 4.8443 | 0.0 | 93.81 +Neigh | 0.27931 | 0.27931 | 0.27931 | 0.0 | 5.41 +Comm | 0.020302 | 0.020302 | 0.020302 | 0.0 | 0.39 +Output | 0.00022712 | 0.00022712 | 0.00022712 | 0.0 | 0.00 +Modify | 0.011944 | 0.011944 | 0.011944 | 0.0 | 0.23 +Other | | 0.007616 | | | 0.15 Nlocal: 1000 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.4 b/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.4 index 23f3348c34..70fb163b67 100644 --- a/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.4 +++ b/examples/PACKAGES/manybody_table/log.1Jun22.spce2.g++.4 @@ -10,7 +10,7 @@ Reading data file ... 1 by 2 by 2 MPI processor grid reading atoms ... 1000 atoms - read_data CPU = 0.002 seconds + read_data CPU = 0.004 seconds pair_style hybrid/overlay table linear 1200 threebody/table @@ -57,20 +57,20 @@ Per MPI rank memory allocation (min/avg/max) = 3.87 | 3.87 | 3.87 Mbytes 800 314.09436 -5467.6073 0 -4532.2879 522.73489 900 300.85843 -5503.7551 0 -4607.85 491.78041 1000 302.84638 -5468.3331 0 -4566.5083 338.05123 -Loop time of 1.4686 on 4 procs for 1000 steps with 1000 atoms +Loop time of 1.54853 on 4 procs for 1000 steps with 1000 atoms -Performance: 117.663 ns/day, 0.204 hours/ns, 680.919 timesteps/s -98.1% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 111.590 ns/day, 0.215 hours/ns, 645.773 timesteps/s +96.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.2491 | 1.2757 | 1.3162 | 2.3 | 86.87 -Neigh | 0.06817 | 0.069468 | 0.071025 | 0.5 | 4.73 -Comm | 0.069929 | 0.11236 | 0.14069 | 8.1 | 7.65 -Output | 0.00016417 | 0.00050711 | 0.0015318 | 0.0 | 0.03 -Modify | 0.0057514 | 0.0061681 | 0.0066503 | 0.5 | 0.42 -Other | | 0.004366 | | | 0.30 +Pair | 1.2599 | 1.2908 | 1.3259 | 2.1 | 83.36 +Neigh | 0.069097 | 0.071294 | 0.075502 | 0.9 | 4.60 +Comm | 0.12731 | 0.15884 | 0.19196 | 5.7 | 10.26 +Output | 0.00017674 | 0.0026016 | 0.0098653 | 8.2 | 0.17 +Modify | 0.0093453 | 0.011999 | 0.014575 | 2.3 | 0.77 +Other | | 0.01295 | | | 0.84 Nlocal: 250 ave 257 max 240 min Histogram: 1 0 0 0 0 1 0 0 1 1 diff --git a/examples/PACKAGES/manybody_table/log.1Jun22.spce_sw.g++.1 b/examples/PACKAGES/manybody_table/log.1Jun22.spce_sw.g++.1 new file mode 100644 index 0000000000..e64d577fae --- /dev/null +++ b/examples/PACKAGES/manybody_table/log.1Jun22.spce_sw.g++.1 @@ -0,0 +1,87 @@ +LAMMPS (4 May 2022) + using 1 OpenMP thread(s) per MPI task +units real +atom_style atomic + +read_data data.spce +Reading data file ... + orthogonal box = (0 0 0) to (31.0648 31.0648 31.0648) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1000 atoms + read_data CPU = 0.001 seconds + +pair_style hybrid/overlay table linear 1200 sw/angle/table + +pair_coeff 1 1 table table_CG_CG.txt VOTCA +pair_coeff * * sw/angle/table spce.sw type + +fix 1 all nvt temp 300.0 300.0 200.0 + +velocity all create 300 432567 dist uniform mom yes + +timestep 2.0 + +thermo 100 +#dump 2 all custom 10 spce_sw.dump id type x y z fx fy fz + +run 1000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair table, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair sw/angle/table, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.487 | 5.487 | 5.487 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -4572.9581 0 -3679.6093 -402.23914 + 100 286.5642 -4508.6912 0 -3655.352 -610.63256 + 200 291.59063 -4465.6368 0 -3597.3297 -218.54913 + 300 298.40301 -4460.64 0 -3572.0468 302.96636 + 400 305.99618 -4460.1128 0 -3548.9084 -68.022415 + 500 301.94233 -4440.337 0 -3541.2043 179.36975 + 600 308.95709 -4485.8412 0 -3565.8197 -95.917517 + 700 291.69015 -4489.4465 0 -3620.843 -56.044939 + 800 294.95653 -4496.904 0 -3618.5738 563.3456 + 900 295.50533 -4478.1134 0 -3598.149 89.234288 + 1000 308.63559 -4471.1612 0 -3552.0971 906.33706 +Loop time of 5.39753 on 1 procs for 1000 steps with 1000 atoms + +Performance: 32.015 ns/day, 0.750 hours/ns, 185.270 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.0954 | 5.0954 | 5.0954 | 0.0 | 94.40 +Neigh | 0.26201 | 0.26201 | 0.26201 | 0.0 | 4.85 +Comm | 0.020497 | 0.020497 | 0.020497 | 0.0 | 0.38 +Output | 0.00021869 | 0.00021869 | 0.00021869 | 0.0 | 0.00 +Modify | 0.011849 | 0.011849 | 0.011849 | 0.0 | 0.22 +Other | | 0.007577 | | | 0.14 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5862 ave 5862 max 5862 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 191262 ave 191262 max 191262 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 382524 ave 382524 max 382524 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 382524 +Ave neighs/atom = 382.524 +Neighbor list builds = 26 +Dangerous builds = 0 +Total wall time: 0:00:05 diff --git a/examples/PACKAGES/manybody_table/log.1Jun22.spce_sw.g++.4 b/examples/PACKAGES/manybody_table/log.1Jun22.spce_sw.g++.4 new file mode 100644 index 0000000000..b439b82286 --- /dev/null +++ b/examples/PACKAGES/manybody_table/log.1Jun22.spce_sw.g++.4 @@ -0,0 +1,87 @@ +LAMMPS (4 May 2022) + using 1 OpenMP thread(s) per MPI task +units real +atom_style atomic + +read_data data.spce +Reading data file ... + orthogonal box = (0 0 0) to (31.0648 31.0648 31.0648) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 1000 atoms + read_data CPU = 0.001 seconds + +pair_style hybrid/overlay table linear 1200 sw/angle/table + +pair_coeff 1 1 table table_CG_CG.txt VOTCA +pair_coeff * * sw/angle/table spce.sw type + +fix 1 all nvt temp 300.0 300.0 200.0 + +velocity all create 300 432567 dist uniform mom yes + +timestep 2.0 + +thermo 100 +#dump 2 all custom 10 spce_sw.dump id type x y z fx fy fz + +run 1000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair table, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair sw/angle/table, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.87 | 3.87 | 3.87 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 300 -4572.9581 0 -3679.6093 -402.23914 + 100 286.5642 -4508.6912 0 -3655.352 -610.63256 + 200 291.59063 -4465.6368 0 -3597.3297 -218.54913 + 300 298.40301 -4460.64 0 -3572.0468 302.96636 + 400 305.99618 -4460.1128 0 -3548.9084 -68.022415 + 500 301.94233 -4440.337 0 -3541.2043 179.36975 + 600 308.95709 -4485.8412 0 -3565.8197 -95.917517 + 700 291.69015 -4489.4465 0 -3620.843 -56.044939 + 800 294.95653 -4496.904 0 -3618.5738 563.3456 + 900 295.50533 -4478.1134 0 -3598.149 89.234292 + 1000 308.63559 -4471.1612 0 -3552.0971 906.33708 +Loop time of 1.57073 on 4 procs for 1000 steps with 1000 atoms + +Performance: 110.012 ns/day, 0.218 hours/ns, 636.646 timesteps/s +97.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.3064 | 1.3347 | 1.3706 | 2.0 | 84.97 +Neigh | 0.065344 | 0.070299 | 0.07737 | 1.7 | 4.48 +Comm | 0.117 | 0.15297 | 0.18685 | 6.5 | 9.74 +Output | 0.00016937 | 0.00055648 | 0.0017097 | 0.0 | 0.04 +Modify | 0.0073414 | 0.0079027 | 0.0085343 | 0.6 | 0.50 +Other | | 0.0043 | | | 0.27 + +Nlocal: 250 ave 254 max 247 min +Histogram: 1 1 0 0 0 1 0 0 0 1 +Nghost: 3473.25 ave 3490 max 3450 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +Neighs: 47815.5 ave 48520 max 47134 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +FullNghs: 95631 ave 97203 max 94083 min +Histogram: 1 0 1 0 0 0 1 0 0 1 + +Total # of neighbors = 382524 +Ave neighs/atom = 382.524 +Neighbor list builds = 26 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/pair_sw_angle_table/spce.sw b/examples/PACKAGES/manybody_table/spce.sw similarity index 100% rename from examples/PACKAGES/pair_sw_angle_table/spce.sw rename to examples/PACKAGES/manybody_table/spce.sw diff --git a/examples/PACKAGES/pair_sw_angle_table/table_CG_CG_CG.txt b/examples/PACKAGES/manybody_table/table_CG_CG_CG.txt similarity index 100% rename from examples/PACKAGES/pair_sw_angle_table/table_CG_CG_CG.txt rename to examples/PACKAGES/manybody_table/table_CG_CG_CG.txt diff --git a/examples/PACKAGES/pair_sw_angle_table/README b/examples/PACKAGES/pair_sw_angle_table/README deleted file mode 100644 index 54e665ff6c..0000000000 --- a/examples/PACKAGES/pair_sw_angle_table/README +++ /dev/null @@ -1,40 +0,0 @@ -Example for pair style sw/angle/table - - -This example contains all required input files for the simulation of CG SPC/E water with -the user pair style sw/angle/table, as well as a run.sh script. - -To run the example, you have to compile LAMMPS with the MANYBODY package, including pair_sw_angle_table.h and pair_sw_angle_table.cpp. - -Running the simulation, you will reproduce results of the following publication: - -C. Scherer, and D. Andrienko, Understanding three-body contributions to coarse-grained force fields, Phys. Chem. Chem. Phys, 20(34):22387–22394, 2018, http://xlink.rsc.org/?DOI=C8CP00746B - -Here, a water molecule is represented by one coarse-grained (CG) bead. -The two-body (table_CG_CG.txt) and three-body angular (table_CG_CG_CG.txt) interaction potentials have been parametrized with force-matching (FM) with the VOTCA package (https://gitlab.mpcdf.mpg.de/votca/votca). -For more details, have a look at the publication. -For a example on the parametrization, have a look at -https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/guide and -https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/spce/3body_sw. - -The folder contains the LAMMPS data file (spce.data) with the starting configuration -of 1000 CG water molecules, an input file (spce.in) and a (modified) Stillinger-Weber file (spce.sw). - -The lammps input file contains the lines specifying the pair style and coefficients: - -- pair_style hybrid/overlay table linear 1200 sw/angle/table - use a combination of pair style table with 1200 linear table entries and the pair style sw/angle/table -- pair_coeff 1 1 table table_CG_CG.txt VOTCA - set the table name and keyword for the pair_style table -- pair_coeff * * sw/angle/table spce.sw type - set the name of the Stillinger-Weber file for the pair style sw/angle/table - -A hybrid pair style is used, where pair forces are calculated as a tabulated interaction (table_CG_CG.txt) and the pair style sw/angle/table is only used to calculate the three-body forces. -Therefore, in the Stillinger-Weber file all parameters refering to two-body interactions are set to zero. -As explained in the documentation of this pair style, the .sw file contains the additional lines refering to the tabulated angular potential: - -- table_CG_CG_CG.txt - file name of tabulated angular potential -- VOTCA - keyword for tabulated angular potential -- linear - angular table is of linear style -- 1001 - 1001 table entries - -The LAMMPS simulation is a standard nvt simulation. -A dump file is output with the positions and forces every 10 time steps. -You can calculate the pair distribution and compare it to the one(s) in the publicattion. diff --git a/examples/PACKAGES/pair_sw_angle_table/run.sh b/examples/PACKAGES/pair_sw_angle_table/run.sh deleted file mode 100755 index 8f64855b13..0000000000 --- a/examples/PACKAGES/pair_sw_angle_table/run.sh +++ /dev/null @@ -1,5 +0,0 @@ -#! /bin/bash -e - -#run the LAMMPS simulation (needs a current LAMMPS version compiled with the user pair_style sw/table) -lmp < spce.in > spce.out - diff --git a/examples/PACKAGES/pair_sw_angle_table/spce.data b/examples/PACKAGES/pair_sw_angle_table/spce.data deleted file mode 100644 index a56ab1b10c..0000000000 --- a/examples/PACKAGES/pair_sw_angle_table/spce.data +++ /dev/null @@ -1,1015 +0,0 @@ -Data File for CG Water - -1000 atoms -1 atom types - -0 31.0648 xlo xhi -0 31.0648 ylo yhi -0 31.0648 zlo zhi - -Masses - -1 18.0154 - -Atoms - -1 1 18.26 24.7 15.77 -2 1 12.63 1.42 27.01 -3 1 10.39 29.11 13.56 -4 1 26.47 16.64 7.23 -5 1 10.66 23.41 27.33 -6 1 19.08 3.2 21.63 -7 1 11.17 26.19 1.44 -8 1 4.61 4.04 25.72 -9 1 4.61 22.91 8.33 -10 1 30.61 22.71 25.18 -11 1 6.38 18.92 16.87 -12 1 17.83 12.53 11.09 -13 1 14.89 2.43 22.44 -14 1 28.36 30.9 26.38 -15 1 25.73 28.56 8.32 -16 1 19.61 20.22 4.43 -17 1 25.96 30.32 24.22 -18 1 14.51 17.35 16.41 -19 1 30.23 17.26 10.71 -20 1 22.68 23.23 2.3 -21 1 10.89 15.76 14.33 -22 1 1.46 20.46 12.48 -23 1 12.73 19.57 2.71 -24 1 1.21 12.02 9.88 -25 1 2.63 14.4 23.71 -26 1 16.91 20.37 4.73 -27 1 28.02 7.7 30.08 -28 1 21.22 22.47 19.66 -29 1 14.0 28.15 0.14 -30 1 19.62 19.73 1.11 -31 1 28.29 24.36 10.15 -32 1 14.05 1.1 17.64 -33 1 12.2 23.75 24.83 -34 1 24.56 26.02 13.57 -35 1 12.13 8.39 7.17 -36 1 20.47 22.28 25.02 -37 1 11.06 7.63 24.11 -38 1 6.52 22.64 30.46 -39 1 16.51 24.78 18.58 -40 1 30.18 20.56 29.19 -41 1 25.26 7.8 25.98 -42 1 20.37 4.16 3.88 -43 1 18.85 27.34 27.83 -44 1 17.72 29.84 12.78 -45 1 19.26 14.48 19.38 -46 1 29.73 4.46 4.96 -47 1 9.52 26.27 30.33 -48 1 6.55 9.25 20.32 -49 1 10.49 1.91 23.31 -50 1 17.63 1.17 14.48 -51 1 1.56 25.17 4.69 -52 1 9.08 10.39 2.29 -53 1 25.92 7.4 21.53 -54 1 25.3 5.14 28.4 -55 1 5.63 23.26 19.85 -56 1 9.6 9.85 24.85 -57 1 3.32 2.77 9.12 -58 1 28.54 15.28 22.18 -59 1 20.45 8.24 18.25 -60 1 12.86 3.73 11.61 -61 1 7.42 12.05 13.54 -62 1 1.73 28.54 25.27 -63 1 3.25 22.18 23.7 -64 1 3.27 25.38 2.24 -65 1 13.46 15.67 19.28 -66 1 31.0 6.91 13.61 -67 1 4.85 27.3 12.67 -68 1 24.48 13.52 4.98 -69 1 23.93 29.62 19.71 -70 1 5.03 13.35 19.5 -71 1 24.58 13.46 19.59 -72 1 7.42 6.82 9.03 -73 1 28.76 15.1 3.33 -74 1 12.38 17.21 6.63 -75 1 15.75 21.23 27.02 -76 1 4.58 5.06 28.19 -77 1 26.04 23.3 25.38 -78 1 30.02 7.27 9.52 -79 1 6.93 10.03 24.54 -80 1 5.61 26.93 27.34 -81 1 29.12 19.12 5.54 -82 1 18.44 27.8 14.75 -83 1 14.1 23.13 9.78 -84 1 24.12 5.55 20.72 -85 1 2.52 10.99 18.44 -86 1 1.76 6.41 21.47 -87 1 25.22 9.56 30.66 -88 1 11.87 13.25 9.12 -89 1 19.46 0.3 22.07 -90 1 28.82 12.29 11.36 -91 1 28.47 30.29 14.09 -92 1 25.51 20.94 24.33 -93 1 1.14 25.4 8.76 -94 1 1.33 27.98 3.09 -95 1 20.57 26.97 -0.04 -96 1 22.73 1.18 0.62 -97 1 19.16 16.99 30.52 -98 1 0.39 9.65 9.02 -99 1 4.41 7.21 3.22 -100 1 11.07 30.64 25.91 -101 1 7.93 25.84 26.26 -102 1 26.76 2.51 2.93 -103 1 30.8 18.15 18.49 -104 1 10.2 7.46 30.44 -105 1 4.77 20.39 26.99 -106 1 25.27 26.77 1.64 -107 1 28.51 13.99 9.33 -108 1 13.86 8.04 24.9 -109 1 30.67 29.88 23.01 -110 1 29.49 30.58 30.02 -111 1 28.74 5.08 30.95 -112 1 13.21 4.31 30.96 -113 1 5.27 3.66 5.02 -114 1 29.43 7.99 17.07 -115 1 4.19 1.37 16.63 -116 1 1.27 27.81 16.56 -117 1 30.64 5.73 25.91 -118 1 10.33 5.33 26.48 -119 1 11.56 21.77 14.77 -120 1 26.46 27.17 5.7 -121 1 14.85 25.79 8.64 -122 1 22.62 6.18 17.61 -123 1 3.45 18.53 11.84 -124 1 11.65 18.17 15.97 -125 1 23.16 17.0 1.5 -126 1 18.92 16.01 3.98 -127 1 30.05 0.25 5.23 -128 1 26.06 11.96 21.96 -129 1 16.82 2.0 10.25 -130 1 19.58 2.63 24.75 -131 1 20.09 14.75 26.62 -132 1 3.14 0.05 26.13 -133 1 4.86 11.79 12.99 -134 1 1.86 11.32 28.57 -135 1 8.82 28.6 6.22 -136 1 20.85 24.68 23.87 -137 1 7.58 25.15 3.44 -138 1 23.46 9.13 8.11 -139 1 6.45 10.24 27.37 -140 1 15.06 10.35 26.71 -141 1 13.8 18.39 26.5 -142 1 5.11 7.7 5.83 -143 1 23.27 23.16 6.67 -144 1 6.33 1.31 11.37 -145 1 14.66 22.28 21.43 -146 1 7.9 8.65 0.61 -147 1 21.83 3.67 26.17 -148 1 1.41 23.66 11.09 -149 1 10.19 17.23 22.71 -150 1 29.53 27.31 23.19 -151 1 28.69 11.38 2.33 -152 1 1.07 2.97 14.53 -153 1 23.47 30.53 14.32 -154 1 1.59 18.83 14.75 -155 1 20.38 30.6 24.38 -156 1 19.81 29.95 27.9 -157 1 12.68 27.59 26.46 -158 1 20.46 9.14 29.06 -159 1 8.69 13.98 24.71 -160 1 0.72 9.29 30.28 -161 1 11.81 20.55 12.28 -162 1 23.8 13.8 9.4 -163 1 13.63 0.51 0.95 -164 1 2.33 6.68 14.95 -165 1 15.98 6.35 25.28 -166 1 7.38 14.88 18.44 -167 1 17.07 20.48 29.16 -168 1 14.53 1.49 8.4 -169 1 28.45 1.21 20.58 -170 1 0.07 5.28 29.45 -171 1 26.0 9.98 15.37 -172 1 14.56 6.91 14.46 -173 1 20.6 9.09 23.04 -174 1 26.02 4.59 0.14 -175 1 5.21 21.9 17.55 -176 1 2.44 7.72 1.47 -177 1 1.25 30.0 13.48 -178 1 27.27 23.13 14.61 -179 1 24.04 15.61 21.64 -180 1 25.13 5.24 17.43 -181 1 4.2 15.98 12.34 -182 1 26.92 13.54 12.87 -183 1 3.38 19.38 9.08 -184 1 27.75 25.03 2.15 -185 1 26.13 20.68 16.54 -186 1 8.3 14.6 13.49 -187 1 3.04 22.87 29.93 -188 1 9.5 26.41 21.23 -189 1 6.53 2.16 2.75 -190 1 6.37 29.04 2.63 -191 1 26.58 4.38 19.69 -192 1 28.44 6.56 14.66 -193 1 25.55 11.1 28.03 -194 1 25.5 18.39 28.73 -195 1 27.67 23.47 5.65 -196 1 13.69 14.81 16.17 -197 1 22.97 27.61 24.11 -198 1 2.06 18.58 30.22 -199 1 2.07 7.13 29.2 -200 1 13.0 7.26 17.76 -201 1 10.04 16.22 30.62 -202 1 6.54 9.8 17.47 -203 1 5.65 12.68 0.64 -204 1 20.84 20.25 23.02 -205 1 22.48 27.63 21.48 -206 1 15.61 22.73 5.36 -207 1 3.52 30.36 6.24 -208 1 6.38 17.25 26.36 -209 1 14.13 10.57 22.63 -210 1 10.22 25.11 3.64 -211 1 16.63 14.7 25.08 -212 1 3.51 29.69 2.76 -213 1 19.2 11.9 21.44 -214 1 30.8 23.85 14.75 -215 1 21.02 14.34 12.4 -216 1 2.75 22.13 27.29 -217 1 29.27 14.29 6.8 -218 1 8.44 20.67 5.23 -219 1 9.42 20.06 22.95 -220 1 30.83 10.64 19.73 -221 1 19.33 14.14 8.94 -222 1 14.18 11.32 18.19 -223 1 26.55 2.39 28.55 -224 1 6.83 16.57 8.9 -225 1 13.98 8.79 1.97 -226 1 4.94 3.0 23.16 -227 1 25.39 29.46 0.63 -228 1 15.32 16.43 2.45 -229 1 5.26 29.73 29.87 -230 1 26.92 14.84 19.93 -231 1 11.87 30.08 4.52 -232 1 7.17 6.71 2.23 -233 1 10.46 1.13 18.11 -234 1 28.59 20.57 25.68 -235 1 26.54 4.84 8.44 -236 1 16.46 18.37 26.15 -237 1 30.53 0.74 15.31 -238 1 27.25 6.31 27.09 -239 1 22.42 1.65 3.87 -240 1 17.85 3.77 8.02 -241 1 11.82 8.23 11.15 -242 1 8.62 27.66 15.87 -243 1 25.19 1.89 18.37 -244 1 14.0 21.96 30.21 -245 1 29.3 1.73 28.29 -246 1 9.35 24.02 12.03 -247 1 1.05 21.5 0.35 -248 1 21.87 20.54 2.54 -249 1 10.59 15.98 17.51 -250 1 22.76 6.0 9.32 -251 1 0.31 9.13 11.87 -252 1 29.16 25.13 18.29 -253 1 1.23 29.08 7.75 -254 1 30.01 28.49 26.21 -255 1 1.87 5.92 5.03 -256 1 1.15 10.27 22.35 -257 1 11.83 10.31 5.16 -258 1 20.89 8.28 8.14 -259 1 13.48 11.78 28.37 -260 1 6.82 10.48 10.25 -261 1 7.34 4.49 18.73 -262 1 5.49 22.37 14.23 -263 1 12.31 21.05 27.47 -264 1 24.09 17.4 8.65 -265 1 22.03 11.54 20.98 -266 1 16.68 13.17 0.68 -267 1 5.52 1.47 8.78 -268 1 14.95 11.83 7.95 -269 1 5.9 10.66 7.12 -270 1 10.06 11.28 30.73 -271 1 17.72 10.71 27.46 -272 1 13.6 6.23 10.82 -273 1 23.42 30.72 9.31 -274 1 23.27 4.25 3.8 -275 1 13.79 8.37 21.07 -276 1 5.01 30.13 12.61 -277 1 26.04 24.45 17.25 -278 1 22.59 14.31 0.81 -279 1 23.74 10.37 17.17 -280 1 23.4 8.52 12.55 -281 1 10.53 23.97 21.96 -282 1 0.69 13.92 28.42 -283 1 6.94 6.27 15.01 -284 1 29.8 20.92 3.41 -285 1 10.19 20.68 19.0 -286 1 26.38 25.4 28.89 -287 1 12.34 26.9 8.27 -288 1 15.0 7.69 6.4 -289 1 24.75 13.1 2.24 -290 1 4.5 20.58 6.78 -291 1 23.27 18.25 11.48 -292 1 25.92 26.39 22.66 -293 1 24.63 4.21 6.52 -294 1 16.68 15.05 15.6 -295 1 26.39 16.17 29.89 -296 1 10.12 6.21 8.63 -297 1 14.41 14.67 12.23 -298 1 19.59 3.47 1.47 -299 1 28.21 22.43 18.25 -300 1 27.87 29.74 11.47 -301 1 22.53 24.1 13.94 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15.29 26.47 -892 1 1.72 0.72 9.92 -893 1 2.14 30.76 17.27 -894 1 17.9 15.88 1.47 -895 1 13.47 5.84 28.76 -896 1 8.96 22.14 21.0 -897 1 12.96 24.15 0.94 -898 1 26.13 23.25 8.89 -899 1 6.01 28.65 6.08 -900 1 22.88 20.21 6.1 -901 1 30.34 20.77 10.49 -902 1 12.19 28.16 10.6 -903 1 5.8 5.33 30.84 -904 1 29.83 26.29 15.91 -905 1 18.28 0.14 5.58 -906 1 1.91 17.34 5.88 -907 1 24.05 18.42 22.53 -908 1 10.82 21.55 3.57 -909 1 11.29 26.73 5.6 -910 1 21.34 14.41 3.22 -911 1 12.61 18.99 24.17 -912 1 25.02 18.6 25.9 -913 1 29.0 21.05 13.14 -914 1 17.72 27.28 30.27 -915 1 30.56 24.81 23.12 -916 1 17.09 20.05 24.02 -917 1 7.35 6.83 21.31 -918 1 3.39 22.32 21.05 -919 1 2.28 29.8 30.23 -920 1 5.29 25.66 14.8 -921 1 26.16 30.72 21.04 -922 1 21.63 6.32 11.68 -923 1 15.45 18.06 4.65 -924 1 5.76 28.33 24.04 -925 1 15.08 29.21 16.09 -926 1 18.76 6.14 6.94 -927 1 22.31 30.25 26.46 -928 1 18.49 22.04 30.93 -929 1 11.15 16.42 9.89 -930 1 4.34 7.98 30.25 -931 1 9.29 29.92 8.58 -932 1 22.97 27.09 8.04 -933 1 20.71 16.7 15.75 -934 1 30.36 7.49 5.24 -935 1 29.56 19.54 0.83 -936 1 30.71 14.04 20.91 -937 1 19.36 4.06 27.14 -938 1 23.41 10.8 2.14 -939 1 1.51 1.32 0.44 -940 1 8.16 14.39 1.63 -941 1 20.66 6.74 4.62 -942 1 20.78 26.26 3.85 -943 1 5.11 15.12 21.64 -944 1 12.53 20.03 17.67 -945 1 28.63 18.4 12.56 -946 1 1.95 21.69 8.08 -947 1 21.53 0.93 7.84 -948 1 2.69 22.51 17.17 -949 1 19.29 22.12 6.05 -950 1 23.68 2.14 11.01 -951 1 27.14 17.8 3.72 -952 1 2.22 14.81 3.31 -953 1 23.1 6.43 14.62 -954 1 0.22 12.59 3.57 -955 1 13.21 22.86 3.67 -956 1 13.45 2.1 20.14 -957 1 12.52 17.12 0.46 -958 1 3.07 27.45 9.03 -959 1 15.33 10.95 11.78 -960 1 0.05 4.26 9.75 -961 1 23.05 16.98 24.69 -962 1 16.15 16.28 6.51 -963 1 30.05 28.87 9.61 -964 1 6.67 29.5 16.95 -965 1 21.95 14.44 14.94 -966 1 22.58 22.47 30.33 -967 1 21.34 19.29 9.9 -968 1 29.31 21.79 20.79 -969 1 5.55 2.56 30.23 -970 1 25.88 3.17 22.22 -971 1 22.38 18.32 30.08 -972 1 6.27 19.24 8.86 -973 1 0.34 24.29 1.49 -974 1 20.49 24.13 0.25 -975 1 2.94 1.41 2.74 -976 1 24.88 25.38 7.35 -977 1 28.18 14.89 14.6 -978 1 7.84 30.36 4.39 -979 1 14.54 9.59 14.4 -980 1 27.63 12.3 15.83 -981 1 11.15 14.17 27.97 -982 1 25.27 20.88 8.35 -983 1 17.06 14.76 27.78 -984 1 3.9 14.79 15.06 -985 1 13.81 3.82 17.03 -986 1 28.55 24.1 26.15 -987 1 29.28 21.79 15.76 -988 1 15.05 30.12 27.83 -989 1 15.42 3.77 6.76 -990 1 22.65 12.12 11.24 -991 1 11.29 4.96 2.18 -992 1 2.15 7.43 7.57 -993 1 30.21 10.13 26.21 -994 1 24.42 22.18 4.42 -995 1 8.68 14.72 22.08 -996 1 23.1 6.9 27.1 -997 1 18.71 27.2 21.72 -998 1 14.12 12.7 30.76 -999 1 18.81 6.5 10.98 -1000 1 26.66 15.4 4.83 diff --git a/examples/PACKAGES/pair_sw_angle_table/spce.in b/examples/PACKAGES/pair_sw_angle_table/spce.in deleted file mode 100644 index 8b1ef719a6..0000000000 --- a/examples/PACKAGES/pair_sw_angle_table/spce.in +++ /dev/null @@ -1,45 +0,0 @@ -log none - -#SPC/E water - -units real -atom_style atomic - -read_data spce.data - -#hybrid pair style consisting of -#pair_style table to read in CG pair potential -#pair_style sw/angle/table for sw interactions with tabulated angular potential -pair_style hybrid/overlay table linear 1200 sw/angle/table - -#pair coefficients -pair_coeff 1 1 table table_CG_CG.txt VOTCA -pair_coeff * * sw/angle/table spce.sw type - -#nvt run with nose-hoover thermostat -#time coupling of 100 ts for thermostat -#target T is 300 K -fix 1 all nvt temp 300.0 300.0 200.0 - -#create initial velocities -velocity all create 300 432567 dist uniform -#remove center of mass linear momentum -velocity all zero linear - -#remove center of mass linear momentum every 1000 time steps in each cartesian direction -fix remove all momentum 1000 linear 1 1 1 - -#timestep of 2 fs -timestep 2.0 - -#print out thermodynamic info every 100 ts -thermo 100 - -#run 10000 ts -run 10000 - -#write out dump file every 10 ts for 100000 ts -dump 2 all custom 10 spce.dump id type x y z fx fy fz -run 100000 - -undump 2 diff --git a/examples/PACKAGES/pair_sw_angle_table/table_CG_CG.txt b/examples/PACKAGES/pair_sw_angle_table/table_CG_CG.txt deleted file mode 100644 index f4ccdd4b4e..0000000000 --- a/examples/PACKAGES/pair_sw_angle_table/table_CG_CG.txt +++ /dev/null @@ -1,1203 +0,0 @@ -VOTCA -N 1200 R 0.010000 12.000000 - -1 1.0000000000e-02 1.5390100510e+15 2.1517330910e+16 -2 2.0000000000e-02 1.3370836560e+15 1.8774943350e+16 -3 3.0000000000e-02 1.1616510900e+15 1.6231560530e+16 -4 4.0000000000e-02 1.0092362200e+15 1.4101892510e+16 -5 5.0000000000e-02 8.7681900090e+14 1.2251648380e+16 -6 6.0000000000e-02 7.6177563290e+14 1.0644166230e+16 -7 7.0000000000e-02 6.6182657340e+14 9.2475943770e+15 -8 8.0000000000e-02 5.7499136800e+14 8.0342602660e+15 -9 9.0000000000e-02 4.9954940840e+14 6.9801221150e+15 -10 1.0000000000e-01 4.3400583970e+14 6.0642925570e+15 -11 1.1000000000e-01 3.7706193970e+14 5.2686247630e+15 -12 1.2000000000e-01 3.2758938550e+14 4.5773528620e+15 -13 1.3000000000e-01 2.8460789650e+14 3.9767795520e+15 -14 1.4000000000e-01 2.4726581000e+14 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-1.8421787100e-04 -1170 1.1700000000e+01 -1.2510893210e-05 -2.1616290120e-04 -1171 1.1710000000e+01 -1.0294430290e-05 -2.3233687030e-04 -1172 1.1720000000e+01 -7.9678780230e-06 -2.3227402260e-04 -1173 1.1730000000e+01 -5.6486954130e-06 -2.3150892740e-04 -1174 1.1740000000e+01 -3.4322545090e-06 -2.1621802220e-04 -1175 1.1750000000e+01 -1.3934204810e-06 -1.9466108350e-04 -1176 1.1760000000e+01 4.1185956270e-07 -1.6850313820e-04 -1177 1.1770000000e+01 1.9449594820e-06 -1.3936779990e-04 -1178 1.1780000000e+01 3.1829692270e-06 -1.0873702930e-04 -1179 1.1790000000e+01 4.1170826780e-06 -7.7937096740e-05 -1180 1.1800000000e+01 4.7509787070e-06 -4.8134899120e-05 -1181 1.1810000000e+01 5.0991788260e-06 -2.0329557190e-05 -1182 1.1820000000e+01 5.1853377300e-06 4.6534024350e-06 -1183 1.1830000000e+01 5.0405482780e-06 2.6153287390e-05 -1184 1.1840000000e+01 4.7017245850e-06 4.3667703640e-05 -1185 1.1850000000e+01 4.2099998780e-06 5.6852853570e-05 -1186 1.1860000000e+01 3.6091206690e-06 6.5520030940e-05 -1187 1.1870000000e+01 2.9438377600e-06 6.8044387790e-05 -1188 1.1880000000e+01 2.2582945630e-06 6.8005776470e-05 -1189 1.1890000000e+01 1.5944132410e-06 6.5247449720e-05 -1190 1.1900000000e+01 9.9027914890e-07 5.7253374050e-05 -1191 1.1910000000e+01 4.7794482020e-07 4.6374107540e-05 -1192 1.1920000000e+01 7.9430367210e-08 3.3872879470e-05 -1193 1.1930000000e+01 -1.9586145530e-07 2.1091406450e-05 -1194 1.1940000000e+01 -3.5038203430e-07 9.1537875640e-06 -1195 1.1950000000e+01 -3.9696232700e-07 -9.8173844310e-07 -1196 1.1960000000e+01 -3.5733509120e-07 -8.5097413050e-06 -1197 1.1970000000e+01 -2.6065437280e-07 -1.1346751290e-05 -1198 1.1980000000e+01 -1.4201270800e-07 -1.1393547340e-05 -1199 1.1990000000e+01 -4.0956496040e-08 -8.7451546660e-06 -1200 1.2000000000e+01 0.0000000000e+00 -1.0906638080e-06 From 7d31544cc25c5dc43f20b776e0aff4ec44fc4a99 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 1 Jun 2022 15:04:28 -0400 Subject: [PATCH 32/34] simplify and avoid memory access and leak issues in parallel --- src/MANYBODY/pair_sw_angle_table.cpp | 53 +++++++++++++--------------- 1 file changed, 25 insertions(+), 28 deletions(-) diff --git a/src/MANYBODY/pair_sw_angle_table.cpp b/src/MANYBODY/pair_sw_angle_table.cpp index 5da277bc05..d66a959d52 100644 --- a/src/MANYBODY/pair_sw_angle_table.cpp +++ b/src/MANYBODY/pair_sw_angle_table.cpp @@ -219,10 +219,13 @@ void PairSWAngleTable::compute(int eflag, int vflag) void PairSWAngleTable::read_file(char *file) { - memory->sfree(params); - params = nullptr; - memory->sfree(table_params); - table_params = nullptr; + if (params) { + for (int m = 0; m < nparams; m++) free_param(&table_params[m]); // free_param will call free_table + memory->destroy(params); + memory->destroy(table_params); + memory->destroy(elem3param); + } + nparams = maxparam = 0; // open file on proc 0 @@ -285,22 +288,18 @@ void PairSWAngleTable::read_file(char *file) params[nparams].tol = values.next_double(); // read parameters of angle table - std::string tablename_string = values.next_string(); - table_params[nparams].tablenamelength = tablename_string.length()+1; - memory->create(table_params[nparams].tablename, table_params[nparams].tablenamelength, "table_params.tablename"); - for (int i = 0; i < table_params[nparams].tablenamelength; ++i) { - table_params[nparams].tablename[i] = tablename_string[i]; - } - std::string keyword_string = values.next_string(); - table_params[nparams].keywordlength = keyword_string.length()+1; - memory->create(table_params[nparams].keyword, table_params[nparams].keywordlength, "table_params.keyword"); - for (int i = 0; i < table_params[nparams].keywordlength; ++i) { - table_params[nparams].keyword[i] = keyword_string[i]; - } - auto tablestyle = values.next_string(); - if (tablestyle == "linear") table_params[nparams].tabstyle = LINEAR; - else if (tablestyle == "spline") table_params[nparams].tabstyle = SPLINE; - else error->all(FLERR,"Unknown table style {} of angle table file", tablestyle); + std::string name = values.next_string(); + table_params[nparams].tablenamelength = name.length()+1; + table_params[nparams].tablename = utils::strdup(name); + + name = values.next_string(); + table_params[nparams].keywordlength = name.length()+1; + table_params[nparams].keyword = utils::strdup(name); + + name = values.next_string(); + if (name == "linear") table_params[nparams].tabstyle = LINEAR; + else if (name == "spline") table_params[nparams].tabstyle = SPLINE; + else error->all(FLERR,"Unknown table style {} of angle table file", name); table_params[nparams].tablength = values.next_int(); } catch (TokenizerException &e) { @@ -333,13 +332,11 @@ void PairSWAngleTable::read_file(char *file) // for each set of parameters, broadcast table name and keyword and read angle table for (int m = 0; m < nparams; ++m){ if (comm->me != 0) { - memory->create(table_params[m].tablename, table_params[m].tablenamelength, "table_params.tablename"); + table_params[m].tablename = new char[table_params[m].tablenamelength]; + table_params[m].keyword = new char[table_params[m].keywordlength]; } - MPI_Bcast(&table_params[m].tablename, table_params[m].tablenamelength, MPI_CHAR, 0, world); - if (comm->me != 0) { - memory->create(table_params[m].keyword, table_params[m].keywordlength, "table_params.keyword"); - } - MPI_Bcast(&table_params[m].keyword, table_params[m].keywordlength, MPI_CHAR, 0, world); + MPI_Bcast(table_params[m].tablename, table_params[m].tablenamelength, MPI_CHAR, 0, world); + MPI_Bcast(table_params[m].keyword, table_params[m].keywordlength, MPI_CHAR, 0, world); // initialize angtable memory->create(table_params[m].angtable,1,"table_params:angtable"); @@ -618,8 +615,8 @@ void PairSWAngleTable::free_param(ParamTable *pm) // call free_table to destroy associated angle table free_table(pm->angtable); // then destroy associated angle table - memory->sfree(pm->keyword); - memory->sfree(pm->tablename); + delete[] pm->keyword; + delete[] pm->tablename; memory->sfree(pm->angtable); } From 217b07020452f55c6fc5d4014ccb51640858c581 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 1 Jun 2022 15:31:49 -0400 Subject: [PATCH 33/34] add unit tests --- unittest/force-styles/tests/1-1-1.table | 1875 +++++++++ unittest/force-styles/tests/1-1-2.table | 3459 +++++++++++++++++ .../tests/atomic-pair-sw_angle_table.yaml | 97 + .../tests/atomic-pair-threebody_table.yaml | 98 + unittest/force-styles/tests/spce.sw | 18 + unittest/force-styles/tests/spce2.3b | 71 + unittest/force-styles/tests/table_CG_CG.txt | 1203 ++++++ .../force-styles/tests/table_CG_CG_CG.txt | 1004 +++++ 8 files changed, 7825 insertions(+) create mode 100644 unittest/force-styles/tests/1-1-1.table create mode 100644 unittest/force-styles/tests/1-1-2.table create mode 100644 unittest/force-styles/tests/atomic-pair-sw_angle_table.yaml create mode 100644 unittest/force-styles/tests/atomic-pair-threebody_table.yaml create mode 100644 unittest/force-styles/tests/spce.sw create mode 100644 unittest/force-styles/tests/spce2.3b create mode 100644 unittest/force-styles/tests/table_CG_CG.txt create mode 100644 unittest/force-styles/tests/table_CG_CG_CG.txt diff --git a/unittest/force-styles/tests/1-1-1.table b/unittest/force-styles/tests/1-1-1.table new file mode 100644 index 0000000000..76d8f8a9ec --- /dev/null +++ b/unittest/force-styles/tests/1-1-1.table @@ -0,0 +1,1875 @@ +ENTRY1 +N 12 rmin 2.55 rmax 3.65 + +1 2.55 2.55 3.75 -867.212 -611.273 867.212 21386.8 611.273 -21386.8 0.0 +2 2.55 2.55 11.25 -621.539 -411.189 621.539 5035.95 411.189 -5035.95 0.0 +3 2.55 2.55 18.75 -394.167 -243.287 394.167 1722.21 243.287 -1722.21 0.0 +4 2.55 2.55 26.25 -218.789 -127.402 218.789 560.206 127.402 -560.206 0.0 +5 2.55 2.55 33.75 -104.252 -59.5774 104.252 156.639 59.5774 -156.639 0.0 +6 2.55 2.55 41.25 -41.0722 -24.6716 41.072 36.4446 24.6716 -36.4446 0.0 +7 2.55 2.55 48.75 -12.357 -8.38061 12.3571 7.1117 8.38062 -7.1117 0.0 +8 2.55 2.55 56.25 -2.29912 -1.68047 2.29907 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0.00140212 0.000784814 0.00329161 -0.000784826 0.0 +3454 3.65 3.65 161.25 -0.00190979 -0.00380299 0.00190977 0.000966445 0.00380303 -0.000966483 0.0 +3455 3.65 3.65 168.75 -0.00211603 -0.00404799 0.00211605 0.00107292 0.004048 -0.00107292 0.0 +3456 3.65 3.65 176.25 -0.00215132 -0.00412886 0.00215137 0.00111754 0.00412895 -0.00111757 0.0 diff --git a/unittest/force-styles/tests/atomic-pair-sw_angle_table.yaml b/unittest/force-styles/tests/atomic-pair-sw_angle_table.yaml new file mode 100644 index 0000000000..b8eae7848b --- /dev/null +++ b/unittest/force-styles/tests/atomic-pair-sw_angle_table.yaml @@ -0,0 +1,97 @@ +--- +lammps_version: 4 May 2022 +tags: generated +date_generated: Wed Jun 1 15:17:22 2022 +epsilon: 1e-12 +skip_tests: single +prerequisites: ! | + pair sw/angle/table + pair table +pre_commands: ! | + variable units index real + variable newton_pair delete + variable newton_pair index on + shell cp ${input_dir}/table_CG_CG_CG.txt . +post_commands: ! "" +input_file: in.metal +pair_style: hybrid/overlay table linear 1200 sw/angle/table +pair_coeff: ! | + * * table ${input_dir}/table_CG_CG.txt VOTCA + * * sw/angle/table ${input_dir}/spce.sw type type +extract: ! "" +natoms: 32 +init_vdwl: 2428.9633428241673 +init_coul: 0 +init_stress: ! |2- + 2.1799808252981104e+04 2.2098847758334741e+04 1.5227317495796946e+04 5.5915487284825185e+03 4.2330141376182507e+02 -2.1635648030093221e+03 +init_forces: ! |2 + 1 -3.5272456427265922e+02 4.7896703188444229e+02 7.6160632749768567e+01 + 2 -2.2734507500176406e+01 -1.5821645847684510e+02 1.1028261572305695e+02 + 3 -3.6932223674029137e+02 1.7315628979419187e+03 -5.2288079251214720e+02 + 4 3.1116044194470057e+01 -3.1009878149268530e+01 -6.8414290700926671e+01 + 5 1.2157567668233901e+03 1.3361425827696451e+03 -2.4428700622833938e+02 + 6 2.1498603159595226e+02 1.2379258234822432e+01 -1.8192892150594932e+02 + 7 -5.8065242995364076e+02 6.3615913954340272e+02 -5.8940661342540871e+01 + 8 -2.9330102622037936e+02 -1.4478456371145094e+02 3.4992669050834974e+02 + 9 5.4581529315399578e+01 -1.0085658890730177e+02 -4.3539166606697755e+01 + 10 -7.5328757518773557e+02 -1.9208550331031577e+03 -5.9929086772884966e+02 + 11 -6.2073979508185595e+01 -9.3172505877146349e+01 8.8201736909256510e+01 + 12 5.2022495622775352e+02 -6.4668600468680108e+02 -1.8086255931588799e+01 + 13 -1.4637585277113917e+02 -2.4193749312797078e+01 -1.3497675472534843e+02 + 14 2.2785633726795228e+02 -1.4050021950202930e+02 4.2957377860079254e+02 + 15 -4.1589593903912913e+01 5.6849936807240290e+01 -5.3315771137404397e+01 + 16 5.0207265346701280e+02 -4.3553084670415353e+02 2.2270110539464073e+02 + 17 2.7243217976852867e+02 6.7842110608020960e+02 -1.8488293016613730e+02 + 18 -1.6339467540544510e+03 -8.6208840396403559e+02 -5.2809809085219297e+02 + 19 -1.8146991394127588e+03 -1.4248970633821093e+03 1.6246778777497133e+02 + 20 5.0143947854312678e+01 3.0349353798587607e+01 -7.6753179337391444e+01 + 21 1.1359392702527382e+03 6.7780617382057903e+02 -2.1777379118829096e+01 + 22 2.6318213617558456e+01 -1.1442799194941128e+02 -4.0723882345600529e+01 + 23 1.0173532367943421e+03 1.4870722398544501e+03 -3.3061556638580618e+02 + 24 1.8951324945224176e+03 1.3655558041004167e+03 6.3746947970957035e+02 + 25 2.1139286860441129e+02 -1.4343085616543428e+02 -2.4472193090284622e+02 + 26 -6.6054117554868481e+02 -1.7214679588856484e+03 1.1872792057456782e+03 + 27 3.8554823693482177e+02 -2.4263768110018356e+02 -1.4505783275426307e+01 + 28 -1.6156920382667545e+02 3.2681073686927527e+02 4.0195534333261003e+02 + 29 1.0269877810330740e+03 1.0972018261937728e+03 -4.9239365569732279e+01 + 30 -7.7183246664884393e+01 -1.1163723935859770e+02 -5.6015149765282524e+02 + 31 2.7330076741933460e+01 -6.2134053241130312e+02 3.7926314422192496e+02 + 32 -1.8451713394504984e+03 -9.7754451225108528e+02 -6.8151426644039077e+01 +run_vdwl: 2428.764401023566 +run_coul: 0 +run_stress: ! 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| + pair threebody/table + pair table +pre_commands: ! | + variable units index real + variable newton_pair delete + variable newton_pair index on + shell cp ${input_dir}/1-1-1.table . + shell cp ${input_dir}/1-1-2.table . +post_commands: ! "" +input_file: in.metal +pair_style: hybrid/overlay table linear 1200 threebody/table +pair_coeff: ! | + * * table ${input_dir}/table_CG_CG.txt VOTCA + * * threebody/table ${input_dir}/spce2.3b type1 type2 +extract: ! "" +natoms: 32 +init_vdwl: 1491.9850663210582 +init_coul: 0 +init_stress: ! |2- + 2.1388163370760823e+04 2.1664558645983379e+04 1.4729243404366314e+04 5.6495516964437775e+03 5.1637900223635859e+02 -2.2491014848350428e+03 +init_forces: ! |2 + 1 -3.4809429741393029e+02 4.6567597414239913e+02 9.4441973687110405e+01 + 2 -1.8412192720214428e+01 -1.6122507911305391e+02 1.1798397229543718e+02 + 3 -3.6959552927057359e+02 1.7366664628134174e+03 -5.2433878744101696e+02 + 4 1.9704833162904933e+01 -2.8473480842310366e+01 -7.6632873700899410e+01 + 5 1.2286660791793993e+03 1.3189646599149826e+03 -2.5750328829062335e+02 + 6 2.3230773636573508e+02 1.3236909769358112e+01 -1.6536673989911372e+02 + 7 -5.9250555047871524e+02 6.4419772822168966e+02 -7.3421471775369668e+01 + 8 -2.7993451614515635e+02 -1.3398848087050882e+02 3.4786818228776917e+02 + 9 6.0102535250319256e+01 -8.2958743522890487e+01 -4.2554780357129808e+01 + 10 -7.7091710125156442e+02 -1.9316366702146124e+03 -5.7574889508217711e+02 + 11 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mode 100644 index 0000000000..52fcd1e5e9 --- /dev/null +++ b/unittest/force-styles/tests/spce2.3b @@ -0,0 +1,71 @@ +type1 +type1 +type1 +3.7 # cut in Ang +1-1-1.table +ENTRY1 +linear +12 +type1 +type1 +type2 +3.7 # cut in Ang +1-1-2.table +ENTRY1 +linear +12 +type1 +type2 +type1 +3.7 # cut in Ang +1-1-2.table +ENTRY1 +linear +12 +type1 +type2 +type2 +3.7 # cut in Ang +1-1-1.table +ENTRY1 +linear +12 +type2 +type1 +type1 +3.7 # cut in Ang +1-1-1.table +ENTRY1 +linear +12 +type2 +type1 +type2 +3.7 # cut in Ang +1-1-2.table +ENTRY1 +linear +12 +type2 +type2 +type1 +3.7 # cut in Ang +1-1-2.table +ENTRY1 +linear +12 +type2 +type2 +type2 +3.7 # cut in Ang +1-1-1.table +ENTRY1 +linear +12 + + + + + + + diff --git a/unittest/force-styles/tests/table_CG_CG.txt b/unittest/force-styles/tests/table_CG_CG.txt new file mode 100644 index 0000000000..f4ccdd4b4e --- /dev/null +++ b/unittest/force-styles/tests/table_CG_CG.txt @@ -0,0 +1,1203 @@ +VOTCA +N 1200 R 0.010000 12.000000 + +1 1.0000000000e-02 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1.78920e+02 1.9058572e+00 -1.2111194e-02 +996 1.79100e+02 1.9080222e+00 -1.1928418e-02 +997 1.79280e+02 1.9101574e+00 -1.1778874e-02 +998 1.79460e+02 1.9122686e+00 -1.1662552e-02 +999 1.79640e+02 1.9143619e+00 -1.1579483e-02 +1000 1.79820e+02 1.9164432e+00 -1.1540710e-02 +1001 1.80000e+02 1.9185186e+00 -1.1513008e-02 From 7a02043f18d58fcc7842798b0e1cfca06ed5e934 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 2 Jun 2022 12:11:10 -0400 Subject: [PATCH 34/34] update docs to list examples and include links to the tutorials --- doc/src/pair_sw_angle_table.rst | 224 +++++++++++++++-------------- doc/src/pair_threebody_table.rst | 237 +++++++++++++++++-------------- 2 files changed, 238 insertions(+), 223 deletions(-) diff --git a/doc/src/pair_sw_angle_table.rst b/doc/src/pair_sw_angle_table.rst index cc2bbba08f..6431917d67 100644 --- a/doc/src/pair_sw_angle_table.rst +++ b/doc/src/pair_sw_angle_table.rst @@ -20,7 +20,12 @@ Examples pair_style sw/angle/table pair_coeff * * spce.sw type - pair_coeff * * GaN.sw Ga N Ga + +Used in example input script: + + .. parsed-literal:: + + examples/PACKAGES/manybody_table/in.spce_sw Description @@ -47,27 +52,29 @@ system of atoms as where :math:`\phi_2` is a two-body term and :math:`\phi_3` is a three-body term. The summations in the formula are over all neighbors J -and K of atom I within a cutoff distance :math:`a \sigma`. -In contrast to the original *sw* style, *sw/angle/table* allows for a flexible -three-body term :math:`f^{\textrm{3b}}\left(\theta_{ijk}\right)` which is read in -as a tabulated interaction. It can be parameterized with the csg_fmatch app of VOTCA -as available at: https://gitlab.mpcdf.mpg.de/votca/votca. +and K of atom I within a cutoff distance :math:`a \sigma`. In contrast +to the original *sw* style, *sw/angle/table* allows for a flexible +three-body term :math:`f^{\textrm{3b}}\left(\theta_{ijk}\right)` which +is read in as a tabulated interaction. It can be parameterized with the +csg_fmatch app of VOTCA as available at: +https://gitlab.mpcdf.mpg.de/votca/votca. Only a single pair_coeff command is used with the *sw/angle/table* style -which specifies a modified Stillinger-Weber potential file with parameters for all -needed elements. These are mapped to LAMMPS atom types by specifying -N_el additional arguments after the ".sw" filename in the pair_coeff command, -where N_el is the number of LAMMPS atom types: +which specifies a modified Stillinger-Weber potential file with +parameters for all needed elements. These are mapped to LAMMPS atom +types by specifying N_el additional arguments after the ".sw" filename +in the pair_coeff command, where N_el is the number of LAMMPS atom +types: * ".sw" filename * N_el element names = mapping of SW elements to atom types -See the :doc:`pair_coeff ` page for alternate ways -to specify the path for the potential file. +See the :doc:`pair_coeff ` page for alternate ways to +specify the path for the potential file. -As an example, imagine a file SiC.sw has Stillinger-Weber values for -Si and C. If your LAMMPS simulation has 4 atoms types and you want -the first 3 to be Si, and the fourth to be C, you would use the following +As an example, imagine a file SiC.sw has Stillinger-Weber values for Si +and C. If your LAMMPS simulation has 4 atoms types and you want the +first 3 to be Si, and the fourth to be C, you would use the following pair_coeff command: .. code-block:: LAMMPS @@ -76,20 +83,20 @@ pair_coeff command: The first 2 arguments must be \* \* so as to span all LAMMPS atom types. The first three Si arguments map LAMMPS atom types 1,2,3 to the Si -element in the SW file. The final C argument maps LAMMPS atom type 4 -to the C element in the SW file. If a mapping value is specified as -NULL, the mapping is not performed. This can be used when a *sw/angle/table* +element in the SW file. The final C argument maps LAMMPS atom type 4 to +the C element in the SW file. If a mapping value is specified as NULL, +the mapping is not performed. This can be used when a *sw/angle/table* potential is used as part of the *hybrid* pair style. The NULL values -are placeholders for atom types that will be used with other -potentials. +are placeholders for atom types that will be used with other potentials. -The (modified) Stillinger-Weber files have a ".sw" suffix. Lines that are not blank or -comments (starting with #) define parameters for a triplet of -elements. The parameters in a single entry correspond to the two-body -and three-body coefficients in the formula above. Here, also the suffix -".sw" is used though the original Stillinger-Weber file format is supplemented -with four additional lines per parameter block to specify the tabulated -three-body interaction. A single entry then contains: +The (modified) Stillinger-Weber files have a ".sw" suffix. Lines that +are not blank or comments (starting with #) define parameters for a +triplet of elements. The parameters in a single entry correspond to the +two-body and three-body coefficients in the formula above. Here, also +the suffix ".sw" is used though the original Stillinger-Weber file +format is supplemented with four additional lines per parameter block to +specify the tabulated three-body interaction. A single entry then +contains: * element 1 (the center atom in a 3-body interaction) * element 2 @@ -111,11 +118,12 @@ three-body interaction. A single entry then contains: * N The A, B, p, and q parameters are used only for two-body interactions. -The :math:`\lambda` and :math:`\cos\theta_0` parameters, only used -for three-body interactions in the original Stillinger-Weber style, are read -in but ignored in this modified pair style. The :math:`\epsilon` parameter is only used -for two-body interactions in this modified pair style and not for the three-body -terms. The :math:`\sigma` and *a* parameters are used for both two-body and three-body +The :math:`\lambda` and :math:`\cos\theta_0` parameters, only used for +three-body interactions in the original Stillinger-Weber style, are read +in but ignored in this modified pair style. The :math:`\epsilon` +parameter is only used for two-body interactions in this modified pair +style and not for the three-body terms. The :math:`\sigma` and *a* +parameters are used for both two-body and three-body interactions. :math:`\gamma` is used only in the three-body interactions, but is defined for pairs of atoms. The non-annotated parameters are unitless. @@ -132,25 +140,25 @@ provides a *tol* value for each of the three-body entries so that they can be separately controlled. If tol = 0.0, then the standard Stillinger-Weber cutoff is used. -The additional parameters *filename*, *keyword*, *style*, and *N* refer to -the tabulated angular potential :math:`f^{\textrm{3b}}\left(\theta_{ijk}\right)`. -The tabulated angular potential has to be of the format as used in the -:doc:`angle_style table ` command: +The additional parameters *filename*, *keyword*, *style*, and *N* refer +to the tabulated angular potential +:math:`f^{\textrm{3b}}\left(\theta_{ijk}\right)`. The tabulated angular +potential has to be of the format as used in the :doc:`angle_style table +` command: -An interpolation tables of length *N* is created. The -interpolation is done in one of 2 *styles*: *linear* or *spline*. -For the *linear* style, the angle is used to find 2 surrounding table -values from which an energy or its derivative is computed by linear -interpolation. For the *spline* style, a cubic spline coefficients are computed and -stored at each of the *N* values in the table. The angle is used to -find the appropriate set of coefficients which are used to evaluate a -cubic polynomial which computes the energy or derivative. +An interpolation tables of length *N* is created. The interpolation is +done in one of 2 *styles*: *linear* or *spline*. For the *linear* +style, the angle is used to find 2 surrounding table values from which +an energy or its derivative is computed by linear interpolation. For the +*spline* style, a cubic spline coefficients are computed and stored at +each of the *N* values in the table. The angle is used to find the +appropriate set of coefficients which are used to evaluate a cubic +polynomial which computes the energy or derivative. The *filename* specifies the file containing the tabulated energy and derivative values of :math:`f^{\textrm{3b}}\left(\theta_{ijk}\right)`. -The *keyword* then specifies a section of the file. The -format of this file is as follows (without the -parenthesized comments): +The *keyword* then specifies a section of the file. The format of this +file is as follows (without the parenthesized comments): .. parsed-literal:: @@ -166,31 +174,30 @@ parenthesized comments): A section begins with a non-blank line whose first character is not a "#"; blank lines or lines starting with "#" can be used as comments -between sections. The first line begins with a keyword which -identifies the section. The next line lists (in any -order) one or more parameters for the table. Each parameter is a -keyword followed by one or more numeric values. +between sections. The first line begins with a keyword which identifies +the section. The next line lists (in any order) one or more parameters +for the table. Each parameter is a keyword followed by one or more +numeric values. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the *N* -specified in the Stillinger-Weber potential file. Let -Nsw = *N* in the ".sw" file, and Nfile = "N" in the -tabulated angular file. What LAMMPS does is a preliminary interpolation by -creating splines using the Nfile tabulated values as nodal points. It -uses these to interpolate as needed to generate energy and derivative -values at Ntable different points. The resulting tables of length -Nsw are then used as described above, when computing energy and -force for individual angles and their atoms. This means that if you -want the interpolation tables of length Nsw to match exactly what -is in the tabulated file (with effectively no preliminary -interpolation), you should set Nsw = Nfile. +specified in the Stillinger-Weber potential file. Let Nsw = *N* in the +".sw" file, and Nfile = "N" in the tabulated angular file. What LAMMPS +does is a preliminary interpolation by creating splines using the Nfile +tabulated values as nodal points. It uses these to interpolate as +needed to generate energy and derivative values at Ntable different +points. The resulting tables of length Nsw are then used as described +above, when computing energy and force for individual angles and their +atoms. This means that if you want the interpolation tables of length +Nsw to match exactly what is in the tabulated file (with effectively no +preliminary interpolation), you should set Nsw = Nfile. The "FP" parameter is optional. If used, it is followed by two values fplo and fphi, which are the second derivatives at the innermost and outermost angle settings. These values are needed by the spline -construction routines. If not specified by the "FP" parameter, they -are estimated (less accurately) by the first two and last two -derivative values in the table. +construction routines. If not specified by the "FP" parameter, they are +estimated (less accurately) by the first two and last two derivative +values in the table. The "EQ" parameter is also optional. If used, it is followed by a the equilibrium angle value, which is used, for example, by the :doc:`fix @@ -209,14 +216,15 @@ increase from one line to the next. The angle values must also begin with 0.0 and end with 180.0, i.e. span the full range of possible angles. -Note that one angular potential file can contain many sections, each with a tabulated -potential. LAMMPS reads the file section by section until it finds -one that matches the specified *keyword* of appropriate section of the ".sw" file. +Note that one angular potential file can contain many sections, each +with a tabulated potential. LAMMPS reads the file section by section +until it finds one that matches the specified *keyword* of appropriate +section of the ".sw" file. The Stillinger-Weber potential file must contain entries for all the -elements listed in the pair_coeff command. It can also contain -entries for additional elements not being used in a particular -simulation; LAMMPS ignores those entries. +elements listed in the pair_coeff command. It can also contain entries +for additional elements not being used in a particular simulation; +LAMMPS ignores those entries. For a single-element simulation, only a single entry is required (e.g. SiSiSi). For a two-element simulation, the file must contain 8 @@ -225,40 +233,31 @@ specify SW parameters for all permutations of the two elements interacting in three-body configurations. Thus for 3 elements, 27 entries would be required, etc. -As annotated above, the first element in the entry is the center atom -in a three-body interaction. Thus an entry for SiCC means a Si atom -with 2 C atoms as neighbors. The parameter values used for the -two-body interaction come from the entry where the second and third -elements are the same. Thus the two-body parameters for Si -interacting with C, comes from the SiCC entry. The three-body -angular potential :math:`f^{\textrm{3b}}\left(\theta_{ijk}\right)` -can in principle be specific to the three elements of the -configuration. However, the user must ensure that it makes physically sense. -Note also that the function :math:`\phi_3` contains two exponential -screening factors with parameter values from the ij pair and ik -pairs. So :math:`\phi_3` for a C atom bonded to a Si atom and a second C atom -will depend on the three-body parameters for the CSiC entry, and also -on the two-body parameters for the CCC and CSiSi entries. Since the -order of the two neighbors is arbitrary, the three-body parameters -and the tabulated angular potential for -entries CSiC and CCSi should be the same. Similarly, the two-body +As annotated above, the first element in the entry is the center atom in +a three-body interaction. Thus an entry for SiCC means a Si atom with 2 +C atoms as neighbors. The parameter values used for the two-body +interaction come from the entry where the second and third elements are +the same. Thus the two-body parameters for Si interacting with C, comes +from the SiCC entry. The three-body angular potential +:math:`f^{\textrm{3b}}\left(\theta_{ijk}\right)` can in principle be +specific to the three elements of the configuration. However, the user +must ensure that it makes physically sense. Note also that the function +:math:`\phi_3` contains two exponential screening factors with parameter +values from the ij pair and ik pairs. So :math:`\phi_3` for a C atom +bonded to a Si atom and a second C atom will depend on the three-body +parameters for the CSiC entry, and also on the two-body parameters for +the CCC and CSiSi entries. Since the order of the two neighbors is +arbitrary, the three-body parameters and the tabulated angular potential +for entries CSiC and CCSi should be the same. Similarly, the two-body parameters for entries SiCC and CSiSi should also be the same. The parameters used only for two-body interactions (A, B, p, and q) in -entries whose second and third element are different (e.g. SiCSi) are not -used for anything and can be set to 0.0 if desired. -This is also true for the parameters in :math:`\phi_3` that are -taken from the ij and ik pairs (:math:`\sigma`, *a*, :math:`\gamma`) +entries whose second and third element are different (e.g. SiCSi) are +not used for anything and can be set to 0.0 if desired. This is also +true for the parameters in :math:`\phi_3` that are taken from the ij and +ik pairs (:math:`\sigma`, *a*, :math:`\gamma`) ----------- - -.. include:: accel_styles.rst - -.. note:: - - When using the INTEL package with this style, there is an additional - 5 to 10 percent performance improvement when the Stillinger-Weber - parameters p and q are set to 4 and 0 respectively. These - parameters are common for modeling silicon and water. +Additional input files and reference data can be found at: +https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-tutorials/spce/3body_sw ---------- @@ -266,16 +265,17 @@ Mixing, shift, table, tail correction, restart, rRESPA info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" For atom type pairs I,J and I != J, where types I and J correspond to -two different element types, mixing is performed by LAMMPS as -described above from values in the potential file, but not for the -tabulated angular potential file. +two different element types, mixing is performed by LAMMPS as described +above from values in the potential file, but not for the tabulated +angular potential file. This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. -This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. -Thus, you need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. +This pair style does not write its information to :doc:`binary restart +files `, since it is stored in potential files. Thus, you need +to re-specify the pair_style and pair_coeff commands in an input script +that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the @@ -286,15 +286,13 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" -This is a user pair style. For more information, see :ref:`Scherer1 -`. It is only enabled if LAMMPS was explicitly built with it. +This pair style is part of the MANYBODY package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` page for more info. This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. -For an example of an extended Stillinger-Weber potential file, have a look at the tutorial -in the tutorial folder. - Related commands """""""""""""""" diff --git a/doc/src/pair_threebody_table.rst b/doc/src/pair_threebody_table.rst index 5e2503fc3f..68661270c9 100644 --- a/doc/src/pair_threebody_table.rst +++ b/doc/src/pair_threebody_table.rst @@ -19,18 +19,28 @@ Examples .. code-block:: LAMMPS pair_style threebody/table - pair_coeff * * spce.3b type - pair_coeff * * GaN.3b Ga N Ga + pair_coeff * * spce2.3b type1 type2 + pair_style hybrid/overlay table linear 1200 threebody/table + pair_coeff 1 1 table table_CG_CG.txt VOTCA + pair_coeff * * threebody/table spce.3b type + +Used in example input scripts: + + .. parsed-literal:: + + examples/PACKAGES/manybody_table/in.spce + examples/PACKAGES/manybody_table/in.spce2 Description """"""""""" -The *threebody/table* style is a pair style for generic tabulated three-body -interactions. It has been developed for (coarse-grained) simulations -(of water) with Kernel-based machine learning (ML) potentials -(:ref:`Scherer2 `). As for many other MANYBODY package pair styles -the energy of a system is computed as a sum over three-body terms: +The *threebody/table* style is a pair style for generic tabulated +three-body interactions. It has been developed for (coarse-grained) +simulations (of water) with Kernel-based machine learning (ML) +potentials (:ref:`Scherer2 `). As for many other MANYBODY +package pair styles the energy of a system is computed as a sum over +three-body terms: .. math:: @@ -40,24 +50,25 @@ The summations in the formula are over all neighbors J and K of atom I within a cutoff distance :math:`cut`. In contrast to the Stillinger-Weber potential, all forces are not calculated analytically, but read in from a three-body force/energy table which can be generated -with the csg_ml app of VOTCA as available at: https://gitlab.mpcdf.mpg.de/votca/votca. +with the csg_ml app of VOTCA as available at: +https://gitlab.mpcdf.mpg.de/votca/votca. -Only a single pair_coeff command is used with the *threebody/table* style -which specifies a threebody potential (".3b") file with parameters for all -needed elements. These are then mapped to LAMMPS atom types by specifying -N_el additional arguments after the ".3b" filename in the pair_coeff command, -where N_el is the number of LAMMPS atom types: +Only a single pair_coeff command is used with the *threebody/table* +style which specifies a threebody potential (".3b") file with parameters +for all needed elements. These are then mapped to LAMMPS atom types by +specifying N_el additional arguments after the ".3b" filename in the +pair_coeff command, where N_el is the number of LAMMPS atom types: * ".3b" filename * N_el element names = mapping of threebody elements to atom types -See the :doc:`pair_coeff ` page for alternate ways -to specify the path for the potential file. +See the :doc:`pair_coeff ` page for alternate ways to +specify the path for the potential file. -As an example, imagine a file SiC.3b has three-body values for -Si and C. If your LAMMPS simulation has 4 atoms types and you want -the first 3 to be Si, and the fourth to be C, you would use the following -pair_coeff command: +As an example, imagine a file SiC.3b has three-body values for Si and C. +If your LAMMPS simulation has 4 atoms types and you want the first 3 to +be Si, and the fourth to be C, you would use the following pair_coeff +command: .. code-block:: LAMMPS @@ -66,17 +77,17 @@ pair_coeff command: The first 2 arguments must be \* \* so as to span all LAMMPS atom types. The first three Si arguments map LAMMPS atom types 1,2,3 to the Si element in the ".3b" file. The final C argument maps LAMMPS atom type 4 -to the C element in the threebody file. If a mapping value is specified as -NULL, the mapping is not performed. This can be used when a *threebody/table* -potential is used as part of the *hybrid* pair style. The NULL values -are placeholders for atom types that will be used with other -potentials. +to the C element in the threebody file. If a mapping value is specified +as NULL, the mapping is not performed. This can be used when a +*threebody/table* potential is used as part of the *hybrid* pair style. +The NULL values are placeholders for atom types that will be used with +other potentials. The three-body files have a ".3b" suffix. Lines that are not blank or comments (starting with #) define parameters for a triplet of -elements. The parameters in a single entry specify to the -(three-body) cutoff distance and the tabulated -three-body interaction. A single entry then contains: +elements. The parameters in a single entry specify to the (three-body) +cutoff distance and the tabulated three-body interaction. A single entry +then contains: * element 1 (the center atom in a 3-body interaction) * element 2 @@ -87,33 +98,33 @@ three-body interaction. A single entry then contains: * style * N -The parameter :math:`cut` is the (three-body) cutoff distance. -When set to 0, no interaction is calculated for this element triplet. -The parameters *filename*, *keyword*, *style*, and *N* refer to -the tabulated three-body potential. +The parameter :math:`cut` is the (three-body) cutoff distance. When set +to 0, no interaction is calculated for this element triplet. The +parameters *filename*, *keyword*, *style*, and *N* refer to the +tabulated three-body potential. The tabulation is done on a three-dimensional grid of the two distances -:math:`r_{ij}` and :math:`r_{ik}` as well as the angle :math:`\theta_{ijk}` -which is constructed in the following way. There are two different cases. -If element 2 and element 3 are of the same type (e.g. SiCC), the distance -:math:`r_{ij}` is varied in "N" steps from rmin to rmax and the distance -:math:`r_{ik}` is varied from :math:`r_{ij}` to rmax. This can be done, -due to the symmetry of the triplet. If element 2 and element 3 are not -of the same type (e.g. SiCSi), there is no additional symmetry and the -distance :math:`r_{ik}` is also varied from rmin to rmax in "N" steps. -The angle :math:`\theta_{ijk}` is always varied in "2N" steps from -(0.0 + 180.0/(4N)) to (180.0 - 180.0/(4N)). Therefore, the total number -of table entries is "M = N * N * (N+1)" for the symmetric (element 2 and element 3 -are of the same type) and "M = 2 * N * N * N" for the general case -(element 2 and element 3 are not of the same type). +:math:`r_{ij}` and :math:`r_{ik}` as well as the angle +:math:`\theta_{ijk}` which is constructed in the following way. There +are two different cases. If element 2 and element 3 are of the same +type (e.g. SiCC), the distance :math:`r_{ij}` is varied in "N" steps +from rmin to rmax and the distance :math:`r_{ik}` is varied from +:math:`r_{ij}` to rmax. This can be done, due to the symmetry of the +triplet. If element 2 and element 3 are not of the same type +(e.g. SiCSi), there is no additional symmetry and the distance +:math:`r_{ik}` is also varied from rmin to rmax in "N" steps. The angle +:math:`\theta_{ijk}` is always varied in "2N" steps from (0.0 + +180.0/(4N)) to (180.0 - 180.0/(4N)). Therefore, the total number of +table entries is "M = N * N * (N+1)" for the symmetric (element 2 and +element 3 are of the same type) and "M = 2 * N * N * N" for the general +case (element 2 and element 3 are not of the same type). -The forces on all three particles I, J, and K of a triplet -of this type of three-body interaction potential -(:math:`\phi_3 (r_{ij}, r_{ik}, \theta_{ijk})`) lie within -the plane defined by the three inter-particle distance vectors -:math:`{\mathbf r}_{ij}`, :math:`{\mathbf r}_{ik}`, and :math:`{\mathbf r}_{jk}`. -This property is used to project the forces onto the inter-particle -distance vectors as follows +The forces on all three particles I, J, and K of a triplet of this type +of three-body interaction potential (:math:`\phi_3 (r_{ij}, r_{ik}, +\theta_{ijk})`) lie within the plane defined by the three inter-particle +distance vectors :math:`{\mathbf r}_{ij}`, :math:`{\mathbf r}_{ik}`, and +:math:`{\mathbf r}_{jk}`. This property is used to project the forces +onto the inter-particle distance vectors as follows .. math:: @@ -133,18 +144,18 @@ distance vectors as follows {\mathbf r}_{jk} \\ \end{pmatrix} -and then tabulate the 6 force constants :math:`f_{i1}`, :math:`f_{i2}`, :math:`f_{j1}`, -:math:`f_{j2}`, :math:`f_{k1}`, and :math:`f_{k2}`, as well as the energy of a triplet e. -Due to symmetry reasons, the following relations hold: :math:`f_{i1}=-f_{j1}`, -:math:`f_{i2}=-f_{k1}`, and :math:`f_{j2}=-f_{k2}`. As in this pair style the -forces are read in directly, a correct MD simulation is also performed in the case that -the triplet energies are set to e=0. +and then tabulate the 6 force constants :math:`f_{i1}`, :math:`f_{i2}`, +:math:`f_{j1}`, :math:`f_{j2}`, :math:`f_{k1}`, and :math:`f_{k2}`, as +well as the energy of a triplet e. Due to symmetry reasons, the +following relations hold: :math:`f_{i1}=-f_{j1}`, +:math:`f_{i2}=-f_{k1}`, and :math:`f_{j2}=-f_{k2}`. As in this pair +style the forces are read in directly, a correct MD simulation is also +performed in the case that the triplet energies are set to e=0. The *filename* specifies the file containing the tabulated energy and -derivative values of :math:`\phi_3 (r_{ij}, r_{ik}, \theta_{ijk})`. -The *keyword* then specifies a section of the file. The -format of this file is as follows (without the -parenthesized comments): +derivative values of :math:`\phi_3 (r_{ij}, r_{ik}, \theta_{ijk})`. The +*keyword* then specifies a section of the file. The format of this file +is as follows (without the parenthesized comments): .. parsed-literal:: @@ -160,45 +171,51 @@ parenthesized comments): A section begins with a non-blank line whose first character is not a "#"; blank lines or lines starting with "#" can be used as comments -between sections. The first line begins with a keyword which -identifies the section. The next line lists (in any -order) one or more parameters for the table. Each parameter is a -keyword followed by one or more numeric values. +between sections. The first line begins with a keyword which identifies +the section. The next line lists (in any order) one or more parameters +for the table. Each parameter is a keyword followed by one or more +numeric values. -The parameter "N" is required. It should be the same than the parameter "N" of the ".3b" file, -otherwise its value is overwritten. "N" determines the number of table -entries "M" that follow: "M = N * N * (N+1)" (symmetric triplet, e.g. SiCC) or -"M = 2 * N * N * N" (asymmetric triplet, e.g. SiCSi). Therefore "M = 12 * 12 * 13 = 1872" -in the above symmetric example. The parameters "rmin" and "rmax" are also required +The parameter "N" is required. It should be the same than the parameter +"N" of the ".3b" file, otherwise its value is overwritten. "N" +determines the number of table entries "M" that follow: "M = N * N * +(N+1)" (symmetric triplet, e.g. SiCC) or "M = 2 * N * N * N" (asymmetric +triplet, e.g. SiCSi). Therefore "M = 12 * 12 * 13 = 1872" in the above +symmetric example. The parameters "rmin" and "rmax" are also required and determine the minimum and maximum of the inter-particle distances :math:`r_{ij}` and :math:`r_{ik}`. -Following a blank line, the next M lines of the angular table file list the tabulated values. -On each line, the first value is the index from 1 to M, the second value is the distance -:math:`r_{ij}`, the third value is the distance :math:`r_{ik}`, the fourth value -is the angle :math:`\theta_{ijk})`, the next six values are the force constants :math:`f_{i1}`, -:math:`f_{i2}`, :math:`f_{j1}`, :math:`f_{j2}`, :math:`f_{k1}`, and :math:`f_{k2}`, and the -last value is the energy e. +Following a blank line, the next M lines of the angular table file list +the tabulated values. On each line, the first value is the index from 1 +to M, the second value is the distance :math:`r_{ij}`, the third value +is the distance :math:`r_{ik}`, the fourth value is the angle +:math:`\theta_{ijk})`, the next six values are the force constants +:math:`f_{i1}`, :math:`f_{i2}`, :math:`f_{j1}`, :math:`f_{j2}`, +:math:`f_{k1}`, and :math:`f_{k2}`, and the last value is the energy e. -Note that one three-body potential file can contain many sections, each with a tabulated -potential. LAMMPS reads the file section by section until it finds -one that matches the specified *keyword* of appropriate section of the ".3b" file. +Note that one three-body potential file can contain many sections, each +with a tabulated potential. LAMMPS reads the file section by section +until it finds one that matches the specified *keyword* of appropriate +section of the ".3b" file. -At the moment, only the *style* *linear* is allowed and implemented. After reading in the -force table, it is internally stored in LAMMPS as a lookup table. For each triplet -configuration occurring in the simulation within the cutoff distance, -the next nearest tabulated triplet configuration is looked up. No interpolation is done. -This allows for a very efficient force calculation -with the stored force constants and energies. Due to the know table structure, the lookup -can be done efficiently. It has been tested (:ref:`Scherer2 `) that with a reasonably -small bin size, the accuracy and speed is comparable to that of a Stillinger-Weber potential -with tabulated three-body interactions (:doc:`pair_style sw/angle/table `) while -the table format of this pair style allows for more flexible three-body interactions. +At the moment, only the *style* *linear* is allowed and +implemented. After reading in the force table, it is internally stored +in LAMMPS as a lookup table. For each triplet configuration occurring in +the simulation within the cutoff distance, the next nearest tabulated +triplet configuration is looked up. No interpolation is done. This +allows for a very efficient force calculation with the stored force +constants and energies. Due to the know table structure, the lookup can +be done efficiently. It has been tested (:ref:`Scherer2 `) +that with a reasonably small bin size, the accuracy and speed is +comparable to that of a Stillinger-Weber potential with tabulated +three-body interactions (:doc:`pair_style sw/angle/table +`) while the table format of this pair style allows +for more flexible three-body interactions. -As for the Stillinger-Weber potential, the three-body potential file must contain entries for all the -elements listed in the pair_coeff command. It can also contain -entries for additional elements not being used in a particular -simulation; LAMMPS ignores those entries. +As for the Stillinger-Weber potential, the three-body potential file +must contain entries for all the elements listed in the pair_coeff +command. It can also contain entries for additional elements not being +used in a particular simulation; LAMMPS ignores those entries. For a single-element simulation, only a single entry is required (e.g. SiSiSi). For a two-element simulation, the file must contain 8 @@ -207,16 +224,17 @@ specify threebody parameters for all permutations of the two elements interacting in three-body configurations. Thus for 3 elements, 27 entries would be required, etc. -As annotated above, the first element in the entry is the center atom -in a three-body interaction. Thus an entry for SiCC means a Si atom -with 2 C atoms as neighbors. The tabulated three-body forces can in -principle be specific to the three elements of the configuration. -However, the user must ensure that it makes physically sense. -E.g., the tabulated three-body forces for the -entries CSiC and CCSi should be the same exchanging :math:`r_{ij}` with -r_{ik}, :math:`f_{j1}` with :math:`f_{k1}`, -and :math:`f_{j2}` with :math:`f_{k2}`. +As annotated above, the first element in the entry is the center atom in +a three-body interaction. Thus an entry for SiCC means a Si atom with 2 +C atoms as neighbors. The tabulated three-body forces can in principle +be specific to the three elements of the configuration. However, the +user must ensure that it makes physically sense. E.g., the tabulated +three-body forces for the entries CSiC and CCSi should be the same +exchanging :math:`r_{ij}` with r_{ik}, :math:`f_{j1}` with +:math:`f_{k1}`, and :math:`f_{j2}` with :math:`f_{k2}`. +Additional input files and reference data can be found at: +https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-tutorials/ml ---------- @@ -228,9 +246,10 @@ As all interactions are tabulated, no mixing is performed. This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. -This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. -Thus, you need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. +This pair style does not write its information to :doc:`binary restart +files `, since it is stored in potential files. Thus, you need +to re-specify the pair_style and pair_coeff commands in an input script +that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the @@ -241,15 +260,13 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" -This is a user pair style. For more information, see :ref:`Scherer2 `. It is only enabled -if LAMMPS was explicitly built with it. +This pair style is part of the MANYBODY package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` page for more info. This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. -For an example of a three-body potential file, have a look at the tutorial -in the tutorial folder. - Related commands """"""""""""""""