From 4f4b18ab7ea4b70fa69fd9011c57044a2f69808b Mon Sep 17 00:00:00 2001 From: Daniele Date: Thu, 11 Nov 2021 16:06:42 +0100 Subject: [PATCH 01/57] addig smatb pairs --- src/pair_smatb.cpp | 579 ++++++++++++++++++++++++++++++++++++++ src/pair_smatb.h | 98 +++++++ src/pair_smatb_single.cpp | 540 +++++++++++++++++++++++++++++++++++ src/pair_smatb_single.h | 92 ++++++ 4 files changed, 1309 insertions(+) create mode 100644 src/pair_smatb.cpp create mode 100644 src/pair_smatb.h create mode 100644 src/pair_smatb_single.cpp create mode 100644 src/pair_smatb_single.h diff --git a/src/pair_smatb.cpp b/src/pair_smatb.cpp new file mode 100644 index 0000000000..5e2fd5839f --- /dev/null +++ b/src/pair_smatb.cpp @@ -0,0 +1,579 @@ +#include +#include +#include +#include +#include "pair_smatb.h" +#include "atom.h" +#include "force.h" +#include "comm.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "memory.h" +#include "error.h" + +//#define DR_DEBUG +#ifdef DR_DEBUG +#include +#include +#endif //DR_DEBUG + +using namespace LAMMPS_NS; + +#define MAXLINE 1024 + +PairSMATB::PairSMATB(LAMMPS *lmp) + : Pair(lmp), + nmax(0), + on_eb(nullptr), + r0(nullptr), + p(nullptr), + A(nullptr), + q(nullptr), + QSI(nullptr), + cutOffStart(nullptr), + cutOffEnd(nullptr), + cutOffEnd2(nullptr), + a3(nullptr), a4(nullptr), a5(nullptr), + x3(nullptr), x4(nullptr), x5(nullptr) { + single_enable = 0; // 1 if single() routine exists + restartinfo = 1; // 1 if pair style writes restart info + respa_enable = 0; // 1 if inner/middle/outer rRESPA routines + one_coeff = 0; // 1 if allows only one coeff * * call + manybody_flag = 1; // 1 if a manybody potential + no_virial_fdotr_compute = 0; // 1 if does not invoke virial_fdotr_compute() + writedata = 1; // 1 if writes coeffs to data file + ghostneigh = 0; // 1 if pair style needs neighbors of ghosts + + // set comm size needed by this Pair + comm_forward = 1; + comm_reverse = 1; +} + +PairSMATB::~PairSMATB() { + if (copymode) { + return; + } + memory->destroy(on_eb); + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(r0); + memory->destroy(p); + memory->destroy(A); + memory->destroy(q); + memory->destroy(QSI); + memory->destroy(cutOffStart); + memory->destroy(cutOffEnd); + memory->destroy(cutOffEnd2); + memory->destroy(a5); + memory->destroy(a4); + memory->destroy(a5); + memory->destroy(x5); + memory->destroy(x4); + memory->destroy(x3); + } +} + +void PairSMATB::compute(int eflag, int vflag) {//workhorse routine that computes pairwise interactions + //eflag means compute energy + //vflag means compute virial + int i,j,ii,jj,jnum,itype,jtype; + double xtmp,ytmp,ztmp,del[3],fpair; + double dijsq,dij; + double espo, aexpp, qsiexpq, eb_i, Fb, Fr; + double polyval, polyval2, polyval3, polyval4, polyval5; + //sets up the flags for energy caclulations + if (eflag || vflag) { + ev_setup(eflag,vflag); + eng_vdwl = 0; + } else { + evflag = vflag_fdotr = eflag_global = eflag_atom = 0; + } + + // grow on_eb array if necessary + // need to be atom->nmax in length + + if (atom->nmax > nmax) { + nmax = atom->nmax; + memory->grow(on_eb,nmax,"pair_smatb:on_eb"); + } + + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + int nall = nlocal + atom->nghost; + + int newton_pair = force->newton_pair; + + // zero out on_eb + if (newton_pair) { + memset(on_eb, 0, nall * sizeof(on_eb[0])); + } else { + memset(on_eb, 0, nlocal * sizeof(on_eb[0])); + } + + int inum = list->inum; + int *ilist = list->ilist; + int *jlist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + + //FIRST LOOP: CALCULATES the squared bounding energy and accumulate it in on_eb for each atom + for (ii = 0; ii < inum; ++ii) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; ++jj) { + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + del[0] = xtmp - x[j][0]; + del[1] = ytmp - x[j][1]; + del[2] = ztmp - x[j][2]; + dijsq = del[0]*del[0] + del[1]*del[1] + del[2]*del[2]; + + if ( dijsq < cutOffEnd2[itype][jtype] ) { + dij = sqrt (dijsq); + if ( dij < cutOffStart[itype][jtype] ) { + qsiexpq = (QSI[itype][jtype]*QSI[itype][jtype]) * exp(2.0*q[itype][jtype]*(1.0 - dij/r0[itype][jtype])); + } else { + polyval = dij-cutOffEnd[itype][jtype]; + polyval3 = polyval*polyval*polyval; + polyval4 = polyval3*polyval; + polyval5 = polyval4*polyval; + qsiexpq = x5[itype][jtype]*polyval5+x4[itype][jtype]*polyval4+x3[itype][jtype]*polyval3; + qsiexpq = qsiexpq* qsiexpq; + } + on_eb[i]+=qsiexpq; + //if (newton_pair || j < nlocal) { + on_eb[j]+=qsiexpq; + //} + } + } + } + + //communicate the squared bounding energy between the various bins + + comm->reverse_comm_pair(this); + + //Support Loop: take the square root of the bounding energy and accumulate it in the energy accumulator if needed + // the store the reciprocal in on_eb in order to not do it in the SECOND LOOP + + for (ii = 0; ii < inum; ++ii) { + i = ilist[ii]; + if (i < nlocal){ + eb_i=sqrt(on_eb[i]); + if (eb_i!=0.0) { + on_eb[i]=1.0/eb_i; + } else { + on_eb[i] = 0.0; + } + //if needed the bounding energy is accumulated: + if (eflag_either) { + if (eflag_atom) { + eatom[i] -= eb_i; + } + if (eflag_global) { + eng_vdwl -= eb_i; + } + } + } + } + //this communication stores the denominators in the ghosts atoms, this is needed because of how forces are calculated + comm->forward_comm_pair(this); + + //SECOND LOOP: given on_eb[i] calculates forces and energies + for (ii = 0; ii < inum; ++ii) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + + del[0] = xtmp - x[j][0]; + del[1] = ytmp - x[j][1]; + del[2] = ztmp - x[j][2]; + + dijsq = del[0]*del[0] + del[1]*del[1] + del[2]*del[2]; + if ( dijsq < cutOffEnd2[itype][jtype] ) { + dij = sqrt (dijsq); + if ( dij < cutOffStart[itype][jtype] ) { + espo = 1.0 - dij/r0[itype][jtype]; + aexpp = exp(p[itype][jtype]*espo)*A[itype][jtype]; + Fr = (2.0*aexpp)*(p[itype][jtype]/r0[itype][jtype]); + qsiexpq = (QSI[itype][jtype]*QSI[itype][jtype]) * exp(2.0*q[itype][jtype]*espo); + Fb = -qsiexpq * q[itype][jtype]/r0[itype][jtype]; + } else { + polyval = dij-cutOffEnd[itype][jtype]; + polyval2 = polyval*polyval; + polyval3 = polyval2*polyval; + polyval4 = polyval3*polyval; + polyval5 = polyval4*polyval; + aexpp = a5[itype][jtype]*polyval5+a4[itype][jtype]*polyval4+a3[itype][jtype]*polyval3; + Fr = -2.0*(5.0*a5[itype][jtype]*polyval4+4.0*a4[itype][jtype]*polyval3+3.0*a3[itype][jtype]*polyval2); + qsiexpq = x5[itype][jtype]*polyval5+x4[itype][jtype]*polyval4+x3[itype][jtype]*polyval3; + Fb = ((5.0*x5[itype][jtype]*polyval4+4.0*x4[itype][jtype]*polyval3+3.0*x3[itype][jtype]*polyval2))*qsiexpq; + } + //if needed the repulsive energy is accumulated: + if (eflag_either) { + if (eflag_atom) { + eatom[i] += aexpp; + if (newton_pair || j < nlocal) { + eatom[j] += aexpp; + } + } + if (eflag_global) { + if (newton_pair || j < nlocal) { + eng_vdwl += 2.0*(aexpp); + } else { + eng_vdwl += aexpp; + } + } + } + //calculates the module of the pair energy between i and j + fpair = (Fb*(on_eb[i]+on_eb[j]) + Fr)/dij; + + f[i][0] += del[0]*fpair; + f[i][1] += del[1]*fpair; + f[i][2] += del[2]*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= del[0]*fpair; + f[j][1] -= del[1]*fpair; + f[j][2] -= del[2]*fpair; + } + if (vflag_atom) { + ev_tally(i, j, nlocal, newton_pair, + 0.0, 0.0,//Energy is tally'd in the other parts of the potential + fpair, del[0], del[1], del[2]); + } + } + + } + } + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + global settings + ------------------------------------------------------------------------- */ + +void PairSMATB::settings(int narg, char **) {//reads the input script line with arguments you define + if (narg > 0) error->all(FLERR,"Illegal pair_style command: smatb accepts no options"); +} + +/* ---------------------------------------------------------------------- + allocate all arrays + ------------------------------------------------------------------------- */ + +void PairSMATB::allocate() { + int n = atom->ntypes; + int natoms=atom->natoms; + + memory->create(setflag, n+1, n+1, "pair_smatb:setflag"); + for (int i = 1; i <= n; i++) { + for (int j = i; j <= n; j++) { + setflag[i][j] = 0; + } + } + + memory->create(cutsq, n+1, n+1, "pair_smatb:cutsq"); + + + //memory->create is needed to make a false nxn array on a n^2x1 line of data + memory->create(r0, n+1, n+1, "pair_smatb:r0"); + memory->create(p, n+1, n+1, "pair_smatb:p"); + memory->create(A, n+1, n+1, "pair_smatb:A"); + memory->create(q, n+1, n+1, "pair_smatb:q"); + memory->create(QSI, n+1, n+1, "pair_smatb:QSI"); + memory->create(cutOffStart, n+1, n+1, "pair_smatb:cutOffStart"); + memory->create(cutOffEnd, n+1, n+1, "pair_smatb:cutOffEnd"); + memory->create(cutOffEnd2, n+1, n+1, "pair_smatb:cutOffEnd2"); + memory->create(a3, n+1, n+1, "pair_smatb:a1"); + memory->create(a4, n+1, n+1, "pair_smatb:a2"); + memory->create(a5, n+1, n+1, "pair_smatb:a5"); + memory->create(x3, n+1, n+1, "pair_smatb:x1"); + memory->create(x4, n+1, n+1, "pair_smatb:x2"); + memory->create(x5, n+1, n+1, "pair_smatb:x3"); + + allocated = 1; +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs + ------------------------------------------------------------------------- */ + +void PairSMATB::coeff(int narg, char **arg) {//set coefficients for one i,j type pair + if (!allocated) { + allocate(); + } + if (narg != 9) { + error->all(FLERR,"Incorrect args for pair coefficients:\n SMATB needs \"i j r0 p q A QSI CO_start CO_end\""); + } + int ilo,ihi,jlo,jhi; + utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); + utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); + //reading parameters from input + double myr0 = utils::numeric(FLERR,arg[2],false,lmp), + myp = utils::numeric(FLERR,arg[3],false,lmp), + myq = utils::numeric(FLERR,arg[4],false,lmp), + myA = utils::numeric(FLERR,arg[5],false,lmp), + myQSI = utils::numeric(FLERR,arg[6],false,lmp), + mycutOffStart = utils::numeric(FLERR,arg[7],false,lmp), + mycutOffEnd = utils::numeric(FLERR,arg[8],false,lmp); + int count = 0; + + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + r0[i][j] = myr0; + p[i][j] = myp; + A[i][j] = myA; + q[i][j] = myq; + QSI[i][j] = myQSI; + cutOffStart[i][j] = mycutOffStart; + cutOffEnd[i][j] = mycutOffEnd; + + setflag[i][j] = 1; + + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + +} + +/* ---------------------------------------------------------------------- + init specific to this pair style + ------------------------------------------------------------------------- */ +/* + void PairSMATB::init_style() {//initialization specific to this pair style + neighbor->request(this,instance_me); + } +*/ + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i + ------------------------------------------------------------------------- */ + +double PairSMATB::init_one(int i, int j) {//perform initialization for one i,j type pair + if (setflag[i][j] == 0) { + ///@todo implement smatb mixing rules + cutOffStart[i][j] = MIN(cutOffStart[i][i],cutOffStart[j][j]); + cutOffEnd[i][j] = MAX(cutOffEnd[i][i],cutOffEnd[j][j]); + + error->all(FLERR,"All pair coeffs are not set"); + } + //calculating the polynomial linking to zero + double es = cutOffEnd[i][j] - cutOffStart[i][j]; + double es2 = es*es; + double es3 = es2*es; + + //variables for poly for p and A + double expp = A[i][j] * exp(p[i][j]*(1.-cutOffStart[i][j]/r0[i][j])); + double ap = -1./es3; + double bp = p[i][j]/(r0[i][j]*es2); + double cp = -(p[i][j]*p[i][j])/(es*r0[i][j]*r0[i][j]); + + a5[i][j]= expp * (12.*ap + 6.*bp + cp)/(2.*es2); + a4[i][j]= expp * (15.*ap + 7.*bp + cp)/es; + a3[i][j]= expp * (20.*ap + 8.*bp + cp)/2.; + + //variables for poly for q and qsi + double expq = QSI[i][j]*exp(q[i][j]*(1.-cutOffStart[i][j]/r0[i][j])); + double aq = -1/es3; + double bq = q[i][j]/(es2*r0[i][j]); + double cq = -(q[i][j]*q[i][j])/(es*r0[i][j]*r0[i][j]); + + x5[i][j] = expq * (12.*aq + 6.*bq + cq)/(2.*es2); + x4[i][j] = expq * (15.*aq + 7.*bq + cq)/es; + x3[i][j] = expq * (20.*aq + 8.*bq + cq)/2.; + + cutOffEnd2[i][j] = cutOffEnd[i][j] * cutOffEnd[i][j]; + if ( i!=j ) { + setflag[j][i] = 1; + cutOffEnd2[j][i] = cutOffEnd2[i][j]; + + r0[j][i] = r0[i][j]; + p[j][i] = p[i][j]; + q[j][i] = q[i][j]; + A[j][i] = A[i][j]; + QSI[j][i] = QSI[i][j]; + cutOffStart[j][i] = cutOffStart[i][j]; + cutOffEnd[j][i] = cutOffEnd[i][j]; + + a3[j][i] = a3[i][j]; + a4[j][i] = a4[i][j]; + a5[j][i] = a5[i][j]; + x3[j][i] = x3[i][j]; + x4[j][i] = x4[i][j]; + x5[j][i] = x5[i][j]; + } +#ifdef DR_DEBUG + std::cout << i << " " << j <me; + size_t result; + if (me == 0) { + result = fread(&offset_flag,sizeof(int),1,fp); + result = fread(&mix_flag, sizeof(int),1,fp); + result = fread(&tail_flag, sizeof(int),1,fp); + } + MPI_Bcast(&offset_flag, 1,MPI_INT,0,world); + MPI_Bcast(&mix_flag, 1,MPI_INT,0,world); + MPI_Bcast(&tail_flag, 1,MPI_INT,0,world); +} + +void PairSMATB::write_restart(FILE *fp) { + write_restart_settings(fp); + //"I J r0 p q A QSI CO_start CO_end" + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j], sizeof(int), 1,fp); + if (setflag[i][j]) { + fwrite(&r0[i][j], sizeof(double),1,fp); + fwrite(&p[i][j], sizeof(double),1,fp); + fwrite(&q[i][j], sizeof(double),1,fp); + fwrite(&A[i][j], sizeof(double),1,fp); + fwrite(&QSI[i][j], sizeof(double),1,fp); + fwrite(&cutOffStart[i][j],sizeof(double),1,fp); + fwrite(&cutOffEnd[i][j], sizeof(double),1,fp); + } + } + //maybe we need to save also the values of the various polynomials +} + +void PairSMATB::read_restart(FILE *fp) { + read_restart_settings(fp); + allocate(); + size_t result; + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) { + result = fread(&setflag[i][j],sizeof(int),1,fp); + } + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + result = fread(&r0[i][j], sizeof(double),1,fp); + result = fread(&p[i][j], sizeof(double),1,fp); + result = fread(&q[i][j], sizeof(double),1,fp); + result = fread(&A[i][j], sizeof(double),1,fp); + result = fread(&QSI[i][j], sizeof(double),1,fp); + result = fread(&cutOffStart[i][j],sizeof(double),1,fp); + result = fread(&cutOffEnd[i][j], sizeof(double),1,fp); + } + MPI_Bcast(&r0[i][j], 1,MPI_DOUBLE,0,world); + MPI_Bcast(&p[i][j], 1,MPI_DOUBLE,0,world); + MPI_Bcast(&q[i][j], 1,MPI_DOUBLE,0,world); + MPI_Bcast(&A[i][j], 1,MPI_DOUBLE,0,world); + MPI_Bcast(&QSI[i][j], 1,MPI_DOUBLE,0,world); + MPI_Bcast(&cutOffStart[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cutOffEnd[i][j], 1,MPI_DOUBLE,0,world); + } + } +} + +void PairSMATB::write_data(FILE *fp) { + //smatb needs I J r0 p q A QSI CO_start CO_end + for (int i = 1; i <= atom->ntypes; i++) { + fprintf(fp,"%d %g %g %g %g %g %g %g\n", + i, r0[i][i], p[i][i], q[i][i], A[i][i], QSI[i][i], cutOffStart[i][i], cutOffEnd[i][i]); + } +} + +void PairSMATB::write_data_all(FILE *fp) { + for (int i = 1; i <= atom->ntypes; i++) { + for (int j = i; j <= atom->ntypes; j++) { + fprintf(fp,"%d %d %g %g %g %g %g %g %g\n", + i, j, r0[i][j], p[i][j], q[i][j], A[i][j], QSI[i][j], cutOffStart[i][j], cutOffEnd[i][j]); + } + } +} + diff --git a/src/pair_smatb.h b/src/pair_smatb.h new file mode 100644 index 0000000000..3013a1d40e --- /dev/null +++ b/src/pair_smatb.h @@ -0,0 +1,98 @@ +/* -*- 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. + + This style is written by Daniele Rapetti (iximiel@gmail.com) + ------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS +// clang-format off +PairStyle(smatb,PairSMATB) +// clang-format on +#else + +#ifndef LMP_PAIR_SMATB_H +#define LMP_PAIR_SMATB_H + +#include "pair.h" + +namespace LAMMPS_NS { + + + class PairSMATB : public Pair { + public: + PairSMATB(class LAMMPS *); + virtual ~PairSMATB(); + void compute(int, int);//workhorse routine that computes pairwise interactions + /* + void compute_inner(); + void compute_middle(); + void compute_outer(int, int);*/ + void settings(int, char **);//reads the input script line with arguments you define + void coeff(int, char **);//set coefficients for one i,j type pair + //void init_style();//initialization specific to this pair style + double init_one(int, int);//perform initialization for one i,j type pair + //double single(int, int, int, int, double, double, double, double &);//force and energy of a single pairwise interaction between 2 atoms + + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + void write_data(FILE *); + void write_data_all(FILE *); + + virtual int pack_forward_comm(int, int *, double *, int, int *); + virtual void unpack_forward_comm(int, int, double *); + virtual int pack_reverse_comm(int, int, double *); + virtual void unpack_reverse_comm(int, int *, double *); + protected: + virtual void allocate(); + int nmax; // allocated size of per-atom arrays + double *on_eb; //allocated to store up caclulation values + double **r0; // interaction radius, user-given + double **p, **A, **q, **QSI; // parameters user-given + double **cutOffStart, **cutOffEnd;//cut offs, user given + double **cutOffEnd2; //squared cut off end, calculated + double **a3, **a4, **a5; //polynomial for cutoff linking to zero: Ae^p substitution + double **x3, **x4, **x5; //polynomial for cutoff linking to zero: QSIe^q substitution + /* latex form of the potential (R_c is cutOffEnd, \Xi is QSI): + + E_i = + \sum_{j,R_{ij}\leq R_c} A e^{-p \lrt{\frac{R_{ij}}{R_{0}}-1}} + -\sqrt{\sum_{j,R_{ij}\leq R_c}\Xi^2 e^{-2q\lrt{\frac{R_{ij}}{R_{0}}-1}}}. + + NB::this form does not have the polynomial link to 0 for the cut off + */ + }; + +} + +#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: Cannot open EAM potential file %s + + The specified EAM potential file cannot be opened. Check that the + path and name are correct. + +*/ diff --git a/src/pair_smatb_single.cpp b/src/pair_smatb_single.cpp new file mode 100644 index 0000000000..3430ec1e73 --- /dev/null +++ b/src/pair_smatb_single.cpp @@ -0,0 +1,540 @@ +#include +#include +#include +#include +#include "pair_smatb_single.h" +#include "atom.h" +#include "force.h" +#include "comm.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "memory.h" +#include "error.h" + +//#define DR_DEBUG +#ifdef DR_DEBUG +#include +#include +#endif //DR_DEBUG + +using namespace LAMMPS_NS; + +#define MAXLINE 1024 + +PairSMATBSingle::PairSMATBSingle(LAMMPS *lmp) + : Pair(lmp), + nmax(0), + on_eb(nullptr), + r0(0), + p(0), + A(0), + q(0), + QSI(0), + cutOffStart(0), + cutOffEnd(0), + cutOffEnd2(0), + a3(0), a4(0), a5(0), + x3(0), x4(0), x5(0) { + single_enable = 0; // 1 if single() routine exists + restartinfo = 1; // 1 if pair style writes restart info + respa_enable = 0; // 1 if inner/middle/outer rRESPA routines + one_coeff = 0; // 1 if allows only one coeff * * call + manybody_flag = 1; // 1 if a manybody potential + no_virial_fdotr_compute = 0; // 1 if does not invoke virial_fdotr_compute() + writedata = 1; // 1 if writes coeffs to data file + ghostneigh = 0; // 1 if pair style needs neighbors of ghosts + + // set comm size needed by this Pair + comm_forward = 1; + comm_reverse = 1; +} + +PairSMATBSingle::~PairSMATBSingle() { + if (copymode) { + return; + } + memory->destroy(on_eb); + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + } +} + +void PairSMATBSingle::compute(int eflag, int vflag) {//workhorse routine that computes pairwise interactions + //eflag means compute energy + //vflag means compute virial + int i,j,ii,jj,jnum;//,itype,jtype; + double xtmp,ytmp,ztmp,del[3],fpair; + double dijsq,dij; + double espo, aexpp, qsiexpq, eb_i, Fb, Fr; + double polyval, polyval2, polyval3, polyval4, polyval5; + //sets up the flags for energy caclulations + if (eflag || vflag) { + ev_setup(eflag,vflag); + eng_vdwl = 0; + } else { + evflag = vflag_fdotr = eflag_global = eflag_atom = 0; + } + + // grow on_eb array if necessary + // need to be atom->nmax in length + + if (atom->nmax > nmax) { + nmax = atom->nmax; + memory->grow(on_eb,nmax,"pair_smatb:on_eb"); + } + + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + int nall = nlocal + atom->nghost; + + int newton_pair = force->newton_pair; + + // zero out on_eb + if (newton_pair) { + memset(on_eb, 0, nall * sizeof(on_eb[0])); + } else { + memset(on_eb, 0, nlocal * sizeof(on_eb[0])); + } + + int inum = list->inum; + int *ilist = list->ilist; + int *jlist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + + //FIRST LOOP: CALCULATES the squared bounding energy and accumulate it in on_eb for each atom + for (ii = 0; ii < inum; ++ii) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + //itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; ++jj) { + j = jlist[jj]; + j &= NEIGHMASK; + //jtype = type[j]; + del[0] = xtmp - x[j][0]; + del[1] = ytmp - x[j][1]; + del[2] = ztmp - x[j][2]; + dijsq = del[0]*del[0] + del[1]*del[1] + del[2]*del[2]; + + if ( dijsq < cutOffEnd2 ) { + dij = sqrt (dijsq); + if ( dij < cutOffStart ) { + qsiexpq = (QSI*QSI) * exp(2.0*q*(1.0 - dij/r0)); + } else { + polyval = dij-cutOffEnd; + polyval3 = polyval*polyval*polyval; + polyval4 = polyval3*polyval; + polyval5 = polyval4*polyval; + qsiexpq = x5*polyval5+x4*polyval4+x3*polyval3; + qsiexpq = qsiexpq* qsiexpq; + } + on_eb[i]+=qsiexpq; + //if (newton_pair || j < nlocal) { + on_eb[j]+=qsiexpq; + //} + } + } + } + + //communicate the squared bounding energy between the various bins + + comm->reverse_comm_pair(this); + + //Support Loop: take the square root of the bounding energy and accumulate it in the energy accumulator if needed + // the store the reciprocal in on_eb in order to not do it in the SECOND LOOP + + for (ii = 0; ii < inum; ++ii) { + i = ilist[ii]; + if (i < nlocal){ + eb_i=sqrt(on_eb[i]); + if (eb_i!=0.0) { + on_eb[i]=1.0/eb_i; + } else { + on_eb[i] = 0.0; + } + //if needed the bounding energy is accumulated: + if (eflag_either) { + if (eflag_atom) { + eatom[i] -= eb_i; + } + if (eflag_global) { + eng_vdwl -= eb_i; + } + } + } + } + //this communication stores the denominators in the ghosts atoms, this is needed because of how forces are calculated + comm->forward_comm_pair(this); + + //SECOND LOOP: given on_eb[i] calculates forces and energies + for (ii = 0; ii < inum; ++ii) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + //itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + //jtype = type[j]; + + del[0] = xtmp - x[j][0]; + del[1] = ytmp - x[j][1]; + del[2] = ztmp - x[j][2]; + + dijsq = del[0]*del[0] + del[1]*del[1] + del[2]*del[2]; + if ( dijsq < cutOffEnd2 ) { + dij = sqrt (dijsq); + if ( dij < cutOffStart ) { + espo = 1.0 - dij/r0; + aexpp = exp(p*espo)*A; + Fr = (2.0*aexpp)*(p/r0); + qsiexpq = (QSI*QSI) * exp(2.0*q*espo); + Fb = -qsiexpq * q/r0; + } else { + polyval = dij-cutOffEnd; + polyval2 = polyval*polyval; + polyval3 = polyval2*polyval; + polyval4 = polyval3*polyval; + polyval5 = polyval4*polyval; + aexpp = a5*polyval5+a4*polyval4+a3*polyval3; + Fr = -2.0*(5.0*a5*polyval4+4.0*a4*polyval3+3.0*a3*polyval2); + qsiexpq = x5*polyval5+x4*polyval4+x3*polyval3; + Fb = ((5.0*x5*polyval4+4.0*x4*polyval3+3.0*x3*polyval2))*qsiexpq; + } + //if needed the repulsive energy is accumulated: + if (eflag_either) { + if (eflag_atom) { + eatom[i] += aexpp; + if (newton_pair || j < nlocal) { + eatom[j] += aexpp; + } + } + if (eflag_global) { + if (newton_pair || j < nlocal) { + eng_vdwl += 2.0*(aexpp); + } else { + eng_vdwl += aexpp; + } + } + } + //calculates the module of the pair energy between i and j + fpair = (Fb*(on_eb[i]+on_eb[j]) + Fr)/dij; + + f[i][0] += del[0]*fpair; + f[i][1] += del[1]*fpair; + f[i][2] += del[2]*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= del[0]*fpair; + f[j][1] -= del[1]*fpair; + f[j][2] -= del[2]*fpair; + } + if (vflag_atom) { + ev_tally(i, j, nlocal, newton_pair, + 0.0, 0.0,//Energy is tally'd in the other parts of the potential + fpair, del[0], del[1], del[2]); + } + } + + } + } + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + global settings + ------------------------------------------------------------------------- */ + +void PairSMATBSingle::settings(int narg, char **) {//reads the input script line with arguments you define + if (narg > 0) error->all(FLERR,"Illegal pair_style command: smatb accepts no options"); +} + +/* ---------------------------------------------------------------------- + allocate all arrays + ------------------------------------------------------------------------- */ + +void PairSMATBSingle::allocate() { + int n = atom->ntypes; + int natoms=atom->natoms; + + memory->create(setflag, n+1, n+1, "pair_smatb:setflag"); + for (int i = 1; i <= n; i++) { + for (int j = i; j <= n; j++) { + setflag[i][j] = 0; + } + } + + memory->create(cutsq, n+1, n+1, "pair_smatb:cutsq"); + + allocated = 1; +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs + ------------------------------------------------------------------------- */ + +void PairSMATBSingle::coeff(int narg, char **arg) {//set coefficients for one i,j type pair + if (!allocated) { + allocate(); + } + if (narg != 9) { + error->all(FLERR,"Incorrect args for pair coefficients:\n SMATB needs \"i j r0 p q A QSI CO_start CO_end\""); + } + int ilo,ihi,jlo,jhi; + utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); + utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); + //reading parameters from input + double myr0 = utils::numeric(FLERR,arg[2],false,lmp), + myp = utils::numeric(FLERR,arg[3],false,lmp), + myq = utils::numeric(FLERR,arg[4],false,lmp), + myA = utils::numeric(FLERR,arg[5],false,lmp), + myQSI = utils::numeric(FLERR,arg[6],false,lmp), + mycutOffStart = utils::numeric(FLERR,arg[7],false,lmp), + mycutOffEnd = utils::numeric(FLERR,arg[8],false,lmp); + int count = 0; + + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + r0 = myr0; + p = myp; + A = myA; + q = myq; + QSI = myQSI; + cutOffStart = mycutOffStart; + cutOffEnd = mycutOffEnd; + setflag[i][j] = 1; + + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + +} + +/* ---------------------------------------------------------------------- + init specific to this pair style + ------------------------------------------------------------------------- */ +/* + void PairSMATBSingle::init_style() {//initialization specific to this pair style + neighbor->request(this,instance_me); + } +*/ + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i + ------------------------------------------------------------------------- */ + +double PairSMATBSingle::init_one(int i, int j) {//perform initialization for one i,j type pair + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + //calculating the polynomial linking to zero + double es = cutOffEnd - cutOffStart; + double es2 = es*es; + double es3 = es2*es; + + //variables for poly for p and A + double expp = A * exp(p*(1.-cutOffStart/r0)); + double ap = -1./es3; + double bp = p/(r0*es2); + double cp = -(p*p)/(es*r0*r0); + + a5= expp * (12.*ap + 6.*bp + cp)/(2.*es2); + a4= expp * (15.*ap + 7.*bp + cp)/es; + a3= expp * (20.*ap + 8.*bp + cp)/2.; + + //variables for poly for q and qsi + double expq = QSI*exp(q*(1.-cutOffStart/r0)); + double aq = -1/es3; + double bq = q/(es2*r0); + double cq = -(q*q)/(es*r0*r0); + + x5 = expq * (12.*aq + 6.*bq + cq)/(2.*es2); + x4 = expq * (15.*aq + 7.*bq + cq)/es; + x3 = expq * (20.*aq + 8.*bq + cq)/2.; + + cutOffEnd2 = cutOffEnd * cutOffEnd; + if ( i!=j ) { + setflag[j][i] = 1; + cutOffEnd2 = cutOffEnd2; + + r0 = r0; + p = p; + q = q; + A = A; + QSI = QSI; + cutOffStart = cutOffStart; + cutOffEnd = cutOffEnd; + + a3 = a3; + a4 = a4; + a5 = a5; + x3 = x3; + x4 = x4; + x5 = x5; + } +#ifdef DR_DEBUG + std::cout << i << " " << j <me; + size_t result; + if (me == 0) { + result = fread(&offset_flag,sizeof(int),1,fp); + result = fread(&mix_flag, sizeof(int),1,fp); + result = fread(&tail_flag, sizeof(int),1,fp); + } + MPI_Bcast(&offset_flag, 1,MPI_INT,0,world); + MPI_Bcast(&mix_flag, 1,MPI_INT,0,world); + MPI_Bcast(&tail_flag, 1,MPI_INT,0,world); +} + +void PairSMATBSingle::write_restart(FILE *fp) { + write_restart_settings(fp); + //"I J r0 p q A QSI CO_start CO_end" + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j], sizeof(int), 1,fp); + if (setflag[i][j]) { + fwrite(&r0, sizeof(double),1,fp); + fwrite(&p, sizeof(double),1,fp); + fwrite(&q, sizeof(double),1,fp); + fwrite(&A, sizeof(double),1,fp); + fwrite(&QSI, sizeof(double),1,fp); + fwrite(&cutOffStart,sizeof(double),1,fp); + fwrite(&cutOffEnd, sizeof(double),1,fp); + } + } + //maybe we need to save also the values of the various polynomials +} + +void PairSMATBSingle::read_restart(FILE *fp) { + read_restart_settings(fp); + allocate(); + size_t result; + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) { + result = fread(&setflag[i][j],sizeof(int),1,fp); + } + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + result = fread(&r0, sizeof(double),1,fp); + result = fread(&p, sizeof(double),1,fp); + result = fread(&q, sizeof(double),1,fp); + result = fread(&A, sizeof(double),1,fp); + result = fread(&QSI, sizeof(double),1,fp); + result = fread(&cutOffStart,sizeof(double),1,fp); + result = fread(&cutOffEnd, sizeof(double),1,fp); + } + MPI_Bcast(&r0, 1,MPI_DOUBLE,0,world); + MPI_Bcast(&p, 1,MPI_DOUBLE,0,world); + MPI_Bcast(&q, 1,MPI_DOUBLE,0,world); + MPI_Bcast(&A, 1,MPI_DOUBLE,0,world); + MPI_Bcast(&QSI, 1,MPI_DOUBLE,0,world); + MPI_Bcast(&cutOffStart,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cutOffEnd, 1,MPI_DOUBLE,0,world); + } + } +} + +void PairSMATBSingle::write_data(FILE *fp) { + //smatb needs I J r0 p q A QSI CO_start CO_end + for (int i = 1; i <= atom->ntypes; i++) { + fprintf(fp,"%d %g %g %g %g %g %g %g\n", + i, r0, p, q, A, QSI, cutOffStart, cutOffEnd); + } +} + +void PairSMATBSingle::write_data_all(FILE *fp) { + for (int i = 1; i <= atom->ntypes; i++) { + for (int j = i; j <= atom->ntypes; j++) { + fprintf(fp,"%d %d %g %g %g %g %g %g %g\n", + i, j, r0, p, q, A, QSI, cutOffStart, cutOffEnd); + } + } +} + diff --git a/src/pair_smatb_single.h b/src/pair_smatb_single.h new file mode 100644 index 0000000000..774578f395 --- /dev/null +++ b/src/pair_smatb_single.h @@ -0,0 +1,92 @@ +/* -*- 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. + + This style is written by Daniele Rapetti (iximiel@gmail.com) + ------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS +// clang-format off +PairStyle(smatb/single,PairSMATBSingle) +// clang-format on +#else + +#ifndef LMP_PAIR_SMATBSINGLE_H +#define LMP_PAIR_SMATBSINGLE_H + +#include "pair.h" + +namespace LAMMPS_NS { + + + class PairSMATBSingle : public Pair { + public: + // public variables so USER-ATC package can access them + + PairSMATBSingle(class LAMMPS *); + virtual ~PairSMATBSingle(); + void compute(int, int);//workhorse routine that computes pairwise interactions + /* + void compute_inner(); + void compute_middle(); + void compute_outer(int, int);*/ + void settings(int, char **);//reads the input script line with arguments you define + void coeff(int, char **);//set coefficients for one i,j type pair + //void init_style();//initialization specific to this pair style + double init_one(int, int);//perform initialization for one i,j type pair + //double single(int, int, int, int, double, double, double, double &);//force and energy of a single pairwise interaction between 2 atoms + + virtual void write_restart(FILE *); + virtual void read_restart(FILE *); + virtual void write_restart_settings(FILE *); + virtual void read_restart_settings(FILE *); + virtual void write_data(FILE *); + virtual void write_data_all(FILE *); + + virtual int pack_forward_comm(int, int *, double *, int, int *); + virtual void unpack_forward_comm(int, int, double *); + virtual int pack_reverse_comm(int , int , double *); + virtual void unpack_reverse_comm(int , int *, double *); + protected: + virtual void allocate(); + int nmax; // allocated size of per-atom arrays + double *on_eb; //allocated to store up caclulation values + double r0; // interaction radius, user-given + double p, A, q, QSI; // parameters user-given + double cutOffStart, cutOffEnd;//cut offs, user given + double cutOffEnd2; //squared cut off end, calculated + double a3, a4, a5; //polynomial for cutoff linking to zero: Ae^p substitution + double x3, x4, x5; //polynomial for cutoff linking to zero: QSIe^q substitution + }; + +} + +#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: Cannot open EAM potential file %s + + The specified EAM potential file cannot be opened. Check that the + path and name are correct. + +*/ From 1c0e6578b6663b21743dcac0c4982995ea5418b4 Mon Sep 17 00:00:00 2001 From: Daniele Date: Thu, 11 Nov 2021 16:12:26 +0100 Subject: [PATCH 02/57] changed some comments --- src/pair_smatb.cpp | 537 +++++++++++++++++++------------------- src/pair_smatb.h | 80 +++--- src/pair_smatb_single.cpp | 493 +++++++++++++++++----------------- src/pair_smatb_single.h | 82 +++--- 4 files changed, 578 insertions(+), 614 deletions(-) diff --git a/src/pair_smatb.cpp b/src/pair_smatb.cpp index 5e2fd5839f..32e4e91a8d 100644 --- a/src/pair_smatb.cpp +++ b/src/pair_smatb.cpp @@ -1,58 +1,58 @@ +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- +This pair style is written by Daniele Rapetti (iximiel@gmail.com) +------------------------------------------------------------------------- */ +#include "pair_smatb.h" +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" #include #include #include #include -#include "pair_smatb.h" -#include "atom.h" -#include "force.h" -#include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" - -//#define DR_DEBUG -#ifdef DR_DEBUG -#include -#include -#endif //DR_DEBUG using namespace LAMMPS_NS; #define MAXLINE 1024 -PairSMATB::PairSMATB(LAMMPS *lmp) - : Pair(lmp), - nmax(0), - on_eb(nullptr), - r0(nullptr), - p(nullptr), - A(nullptr), - q(nullptr), - QSI(nullptr), - cutOffStart(nullptr), - cutOffEnd(nullptr), - cutOffEnd2(nullptr), - a3(nullptr), a4(nullptr), a5(nullptr), - x3(nullptr), x4(nullptr), x5(nullptr) { - single_enable = 0; // 1 if single() routine exists - restartinfo = 1; // 1 if pair style writes restart info - respa_enable = 0; // 1 if inner/middle/outer rRESPA routines - one_coeff = 0; // 1 if allows only one coeff * * call - manybody_flag = 1; // 1 if a manybody potential - no_virial_fdotr_compute = 0; // 1 if does not invoke virial_fdotr_compute() - writedata = 1; // 1 if writes coeffs to data file - ghostneigh = 0; // 1 if pair style needs neighbors of ghosts +PairSMATB::PairSMATB(LAMMPS *lmp) : + Pair(lmp), nmax(0), on_eb(nullptr), r0(nullptr), p(nullptr), A(nullptr), q(nullptr), + QSI(nullptr), cutOffStart(nullptr), cutOffEnd(nullptr), cutOffEnd2(nullptr), a3(nullptr), + a4(nullptr), a5(nullptr), x3(nullptr), x4(nullptr), x5(nullptr) +{ + single_enable = 0; // 1 if single() routine exists + restartinfo = 1; // 1 if pair style writes restart info + respa_enable = 0; // 1 if inner/middle/outer rRESPA routines + one_coeff = 0; // 1 if allows only one coeff * * call + manybody_flag = 1; // 1 if a manybody potential + no_virial_fdotr_compute = 0; // 1 if does not invoke virial_fdotr_compute() + writedata = 1; // 1 if writes coeffs to data file + ghostneigh = 0; // 1 if pair style needs neighbors of ghosts // set comm size needed by this Pair comm_forward = 1; comm_reverse = 1; } -PairSMATB::~PairSMATB() { - if (copymode) { - return; - } +PairSMATB::~PairSMATB() +{ + if (copymode) { return; } memory->destroy(on_eb); if (allocated) { memory->destroy(setflag); @@ -75,17 +75,18 @@ PairSMATB::~PairSMATB() { } } -void PairSMATB::compute(int eflag, int vflag) {//workhorse routine that computes pairwise interactions +void PairSMATB::compute(int eflag, int vflag) +{ //workhorse routine that computes pairwise interactions //eflag means compute energy //vflag means compute virial - int i,j,ii,jj,jnum,itype,jtype; - double xtmp,ytmp,ztmp,del[3],fpair; - double dijsq,dij; + int i, j, ii, jj, jnum, itype, jtype; + double xtmp, ytmp, ztmp, del[3], fpair; + double dijsq, dij; double espo, aexpp, qsiexpq, eb_i, Fb, Fr; double polyval, polyval2, polyval3, polyval4, polyval5; //sets up the flags for energy caclulations if (eflag || vflag) { - ev_setup(eflag,vflag); + ev_setup(eflag, vflag); eng_vdwl = 0; } else { evflag = vflag_fdotr = eflag_global = eflag_atom = 0; @@ -96,14 +97,14 @@ void PairSMATB::compute(int eflag, int vflag) {//workhorse routine that computes if (atom->nmax > nmax) { nmax = atom->nmax; - memory->grow(on_eb,nmax,"pair_smatb:on_eb"); + memory->grow(on_eb, nmax, "pair_smatb:on_eb"); } double **x = atom->x; double **f = atom->f; - int *type = atom->type; + int *type = atom->type; int nlocal = atom->nlocal; - int nall = nlocal + atom->nghost; + int nall = nlocal + atom->nghost; int newton_pair = force->newton_pair; @@ -122,39 +123,41 @@ void PairSMATB::compute(int eflag, int vflag) {//workhorse routine that computes //FIRST LOOP: CALCULATES the squared bounding energy and accumulate it in on_eb for each atom for (ii = 0; ii < inum; ++ii) { - i = ilist[ii]; - xtmp = x[i][0]; - ytmp = x[i][1]; - ztmp = x[i][2]; + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; itype = type[i]; jlist = firstneigh[i]; jnum = numneigh[i]; for (jj = 0; jj < jnum; ++jj) { - j = jlist[jj]; + j = jlist[jj]; j &= NEIGHMASK; jtype = type[j]; del[0] = xtmp - x[j][0]; del[1] = ytmp - x[j][1]; del[2] = ztmp - x[j][2]; - dijsq = del[0]*del[0] + del[1]*del[1] + del[2]*del[2]; + dijsq = del[0] * del[0] + del[1] * del[1] + del[2] * del[2]; - if ( dijsq < cutOffEnd2[itype][jtype] ) { - dij = sqrt (dijsq); - if ( dij < cutOffStart[itype][jtype] ) { - qsiexpq = (QSI[itype][jtype]*QSI[itype][jtype]) * exp(2.0*q[itype][jtype]*(1.0 - dij/r0[itype][jtype])); - } else { - polyval = dij-cutOffEnd[itype][jtype]; - polyval3 = polyval*polyval*polyval; - polyval4 = polyval3*polyval; - polyval5 = polyval4*polyval; - qsiexpq = x5[itype][jtype]*polyval5+x4[itype][jtype]*polyval4+x3[itype][jtype]*polyval3; - qsiexpq = qsiexpq* qsiexpq; - } - on_eb[i]+=qsiexpq; - //if (newton_pair || j < nlocal) { - on_eb[j]+=qsiexpq; - //} + if (dijsq < cutOffEnd2[itype][jtype]) { + dij = sqrt(dijsq); + if (dij < cutOffStart[itype][jtype]) { + qsiexpq = (QSI[itype][jtype] * QSI[itype][jtype]) * + exp(2.0 * q[itype][jtype] * (1.0 - dij / r0[itype][jtype])); + } else { + polyval = dij - cutOffEnd[itype][jtype]; + polyval3 = polyval * polyval * polyval; + polyval4 = polyval3 * polyval; + polyval5 = polyval4 * polyval; + qsiexpq = x5[itype][jtype] * polyval5 + x4[itype][jtype] * polyval4 + + x3[itype][jtype] * polyval3; + qsiexpq = qsiexpq * qsiexpq; + } + on_eb[i] += qsiexpq; + //if (newton_pair || j < nlocal) { + on_eb[j] += qsiexpq; + //} } } } @@ -167,22 +170,18 @@ void PairSMATB::compute(int eflag, int vflag) {//workhorse routine that computes // the store the reciprocal in on_eb in order to not do it in the SECOND LOOP for (ii = 0; ii < inum; ++ii) { - i = ilist[ii]; - if (i < nlocal){ - eb_i=sqrt(on_eb[i]); - if (eb_i!=0.0) { - on_eb[i]=1.0/eb_i; + i = ilist[ii]; + if (i < nlocal) { + eb_i = sqrt(on_eb[i]); + if (eb_i != 0.0) { + on_eb[i] = 1.0 / eb_i; } else { on_eb[i] = 0.0; } //if needed the bounding energy is accumulated: if (eflag_either) { - if (eflag_atom) { - eatom[i] -= eb_i; - } - if (eflag_global) { - eng_vdwl -= eb_i; - } + if (eflag_atom) { eatom[i] -= eb_i; } + if (eflag_global) { eng_vdwl -= eb_i; } } } } @@ -207,60 +206,63 @@ void PairSMATB::compute(int eflag, int vflag) {//workhorse routine that computes del[1] = ytmp - x[j][1]; del[2] = ztmp - x[j][2]; - dijsq = del[0]*del[0] + del[1]*del[1] + del[2]*del[2]; - if ( dijsq < cutOffEnd2[itype][jtype] ) { - dij = sqrt (dijsq); - if ( dij < cutOffStart[itype][jtype] ) { - espo = 1.0 - dij/r0[itype][jtype]; - aexpp = exp(p[itype][jtype]*espo)*A[itype][jtype]; - Fr = (2.0*aexpp)*(p[itype][jtype]/r0[itype][jtype]); - qsiexpq = (QSI[itype][jtype]*QSI[itype][jtype]) * exp(2.0*q[itype][jtype]*espo); - Fb = -qsiexpq * q[itype][jtype]/r0[itype][jtype]; - } else { - polyval = dij-cutOffEnd[itype][jtype]; - polyval2 = polyval*polyval; - polyval3 = polyval2*polyval; - polyval4 = polyval3*polyval; - polyval5 = polyval4*polyval; - aexpp = a5[itype][jtype]*polyval5+a4[itype][jtype]*polyval4+a3[itype][jtype]*polyval3; - Fr = -2.0*(5.0*a5[itype][jtype]*polyval4+4.0*a4[itype][jtype]*polyval3+3.0*a3[itype][jtype]*polyval2); - qsiexpq = x5[itype][jtype]*polyval5+x4[itype][jtype]*polyval4+x3[itype][jtype]*polyval3; - Fb = ((5.0*x5[itype][jtype]*polyval4+4.0*x4[itype][jtype]*polyval3+3.0*x3[itype][jtype]*polyval2))*qsiexpq; - } - //if needed the repulsive energy is accumulated: - if (eflag_either) { - if (eflag_atom) { - eatom[i] += aexpp; - if (newton_pair || j < nlocal) { - eatom[j] += aexpp; - } - } - if (eflag_global) { - if (newton_pair || j < nlocal) { - eng_vdwl += 2.0*(aexpp); - } else { - eng_vdwl += aexpp; - } - } - } - //calculates the module of the pair energy between i and j - fpair = (Fb*(on_eb[i]+on_eb[j]) + Fr)/dij; + dijsq = del[0] * del[0] + del[1] * del[1] + del[2] * del[2]; + if (dijsq < cutOffEnd2[itype][jtype]) { + dij = sqrt(dijsq); + if (dij < cutOffStart[itype][jtype]) { + espo = 1.0 - dij / r0[itype][jtype]; + aexpp = exp(p[itype][jtype] * espo) * A[itype][jtype]; + Fr = (2.0 * aexpp) * (p[itype][jtype] / r0[itype][jtype]); + qsiexpq = (QSI[itype][jtype] * QSI[itype][jtype]) * exp(2.0 * q[itype][jtype] * espo); + Fb = -qsiexpq * q[itype][jtype] / r0[itype][jtype]; + } else { + polyval = dij - cutOffEnd[itype][jtype]; + polyval2 = polyval * polyval; + polyval3 = polyval2 * polyval; + polyval4 = polyval3 * polyval; + polyval5 = polyval4 * polyval; + aexpp = a5[itype][jtype] * polyval5 + a4[itype][jtype] * polyval4 + + a3[itype][jtype] * polyval3; + Fr = -2.0 * + (5.0 * a5[itype][jtype] * polyval4 + 4.0 * a4[itype][jtype] * polyval3 + + 3.0 * a3[itype][jtype] * polyval2); + qsiexpq = x5[itype][jtype] * polyval5 + x4[itype][jtype] * polyval4 + + x3[itype][jtype] * polyval3; + Fb = ((5.0 * x5[itype][jtype] * polyval4 + 4.0 * x4[itype][jtype] * polyval3 + + 3.0 * x3[itype][jtype] * polyval2)) * + qsiexpq; + } + //if needed the repulsive energy is accumulated: + if (eflag_either) { + if (eflag_atom) { + eatom[i] += aexpp; + if (newton_pair || j < nlocal) { eatom[j] += aexpp; } + } + if (eflag_global) { + if (newton_pair || j < nlocal) { + eng_vdwl += 2.0 * (aexpp); + } else { + eng_vdwl += aexpp; + } + } + } + //calculates the module of the pair energy between i and j + fpair = (Fb * (on_eb[i] + on_eb[j]) + Fr) / dij; - f[i][0] += del[0]*fpair; - f[i][1] += del[1]*fpair; - f[i][2] += del[2]*fpair; - if (newton_pair || j < nlocal) { - f[j][0] -= del[0]*fpair; - f[j][1] -= del[1]*fpair; - f[j][2] -= del[2]*fpair; - } - if (vflag_atom) { - ev_tally(i, j, nlocal, newton_pair, - 0.0, 0.0,//Energy is tally'd in the other parts of the potential - fpair, del[0], del[1], del[2]); - } + f[i][0] += del[0] * fpair; + f[i][1] += del[1] * fpair; + f[i][2] += del[2] * fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= del[0] * fpair; + f[j][1] -= del[1] * fpair; + f[j][2] -= del[2] * fpair; + } + if (vflag_atom) { + ev_tally(i, j, nlocal, newton_pair, 0.0, + 0.0, //Energy is tally'd in the other parts of the potential + fpair, del[0], del[1], del[2]); + } } - } } if (vflag_fdotr) virial_fdotr_compute(); @@ -270,43 +272,42 @@ void PairSMATB::compute(int eflag, int vflag) {//workhorse routine that computes global settings ------------------------------------------------------------------------- */ -void PairSMATB::settings(int narg, char **) {//reads the input script line with arguments you define - if (narg > 0) error->all(FLERR,"Illegal pair_style command: smatb accepts no options"); +void PairSMATB::settings(int narg, char **) +{ //reads the input script line with arguments you define + if (narg > 0) error->all(FLERR, "Illegal pair_style command: smatb accepts no options"); } /* ---------------------------------------------------------------------- allocate all arrays ------------------------------------------------------------------------- */ -void PairSMATB::allocate() { +void PairSMATB::allocate() +{ int n = atom->ntypes; - int natoms=atom->natoms; + int natoms = atom->natoms; - memory->create(setflag, n+1, n+1, "pair_smatb:setflag"); + memory->create(setflag, n + 1, n + 1, "pair_smatb:setflag"); for (int i = 1; i <= n; i++) { - for (int j = i; j <= n; j++) { - setflag[i][j] = 0; - } + for (int j = i; j <= n; j++) { setflag[i][j] = 0; } } - memory->create(cutsq, n+1, n+1, "pair_smatb:cutsq"); - + memory->create(cutsq, n + 1, n + 1, "pair_smatb:cutsq"); //memory->create is needed to make a false nxn array on a n^2x1 line of data - memory->create(r0, n+1, n+1, "pair_smatb:r0"); - memory->create(p, n+1, n+1, "pair_smatb:p"); - memory->create(A, n+1, n+1, "pair_smatb:A"); - memory->create(q, n+1, n+1, "pair_smatb:q"); - memory->create(QSI, n+1, n+1, "pair_smatb:QSI"); - memory->create(cutOffStart, n+1, n+1, "pair_smatb:cutOffStart"); - memory->create(cutOffEnd, n+1, n+1, "pair_smatb:cutOffEnd"); - memory->create(cutOffEnd2, n+1, n+1, "pair_smatb:cutOffEnd2"); - memory->create(a3, n+1, n+1, "pair_smatb:a1"); - memory->create(a4, n+1, n+1, "pair_smatb:a2"); - memory->create(a5, n+1, n+1, "pair_smatb:a5"); - memory->create(x3, n+1, n+1, "pair_smatb:x1"); - memory->create(x4, n+1, n+1, "pair_smatb:x2"); - memory->create(x5, n+1, n+1, "pair_smatb:x3"); + memory->create(r0, n + 1, n + 1, "pair_smatb:r0"); + memory->create(p, n + 1, n + 1, "pair_smatb:p"); + memory->create(A, n + 1, n + 1, "pair_smatb:A"); + memory->create(q, n + 1, n + 1, "pair_smatb:q"); + memory->create(QSI, n + 1, n + 1, "pair_smatb:QSI"); + memory->create(cutOffStart, n + 1, n + 1, "pair_smatb:cutOffStart"); + memory->create(cutOffEnd, n + 1, n + 1, "pair_smatb:cutOffEnd"); + memory->create(cutOffEnd2, n + 1, n + 1, "pair_smatb:cutOffEnd2"); + memory->create(a3, n + 1, n + 1, "pair_smatb:a1"); + memory->create(a4, n + 1, n + 1, "pair_smatb:a2"); + memory->create(a5, n + 1, n + 1, "pair_smatb:a5"); + memory->create(x3, n + 1, n + 1, "pair_smatb:x1"); + memory->create(x4, n + 1, n + 1, "pair_smatb:x2"); + memory->create(x5, n + 1, n + 1, "pair_smatb:x3"); allocated = 1; } @@ -315,28 +316,29 @@ void PairSMATB::allocate() { set coeffs for one or more type pairs ------------------------------------------------------------------------- */ -void PairSMATB::coeff(int narg, char **arg) {//set coefficients for one i,j type pair - if (!allocated) { - allocate(); - } +void PairSMATB::coeff(int narg, char **arg) +{ //set coefficients for one i,j type pair + if (!allocated) { allocate(); } if (narg != 9) { - error->all(FLERR,"Incorrect args for pair coefficients:\n SMATB needs \"i j r0 p q A QSI CO_start CO_end\""); + error->all( + FLERR, + "Incorrect args for pair coefficients:\n SMATB needs \"i j r0 p q A QSI CO_start CO_end\""); } - int ilo,ihi,jlo,jhi; - utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); - utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); + int ilo, ihi, jlo, jhi; + utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error); + utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error); //reading parameters from input - double myr0 = utils::numeric(FLERR,arg[2],false,lmp), - myp = utils::numeric(FLERR,arg[3],false,lmp), - myq = utils::numeric(FLERR,arg[4],false,lmp), - myA = utils::numeric(FLERR,arg[5],false,lmp), - myQSI = utils::numeric(FLERR,arg[6],false,lmp), - mycutOffStart = utils::numeric(FLERR,arg[7],false,lmp), - mycutOffEnd = utils::numeric(FLERR,arg[8],false,lmp); + double myr0 = utils::numeric(FLERR, arg[2], false, lmp), + myp = utils::numeric(FLERR, arg[3], false, lmp), + myq = utils::numeric(FLERR, arg[4], false, lmp), + myA = utils::numeric(FLERR, arg[5], false, lmp), + myQSI = utils::numeric(FLERR, arg[6], false, lmp), + mycutOffStart = utils::numeric(FLERR, arg[7], false, lmp), + mycutOffEnd = utils::numeric(FLERR, arg[8], false, lmp); int count = 0; for (int i = ilo; i <= ihi; i++) { - for (int j = MAX(jlo,i); j <= jhi; j++) { + for (int j = MAX(jlo, i); j <= jhi; j++) { r0[i][j] = myr0; p[i][j] = myp; A[i][j] = myA; @@ -351,8 +353,7 @@ void PairSMATB::coeff(int narg, char **arg) {//set coefficients for one i,j type } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); - + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); } /* ---------------------------------------------------------------------- @@ -368,41 +369,42 @@ void PairSMATB::coeff(int narg, char **arg) {//set coefficients for one i,j type init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ -double PairSMATB::init_one(int i, int j) {//perform initialization for one i,j type pair +double PairSMATB::init_one(int i, int j) +{ //perform initialization for one i,j type pair if (setflag[i][j] == 0) { ///@todo implement smatb mixing rules - cutOffStart[i][j] = MIN(cutOffStart[i][i],cutOffStart[j][j]); - cutOffEnd[i][j] = MAX(cutOffEnd[i][i],cutOffEnd[j][j]); + cutOffStart[i][j] = MIN(cutOffStart[i][i], cutOffStart[j][j]); + cutOffEnd[i][j] = MAX(cutOffEnd[i][i], cutOffEnd[j][j]); - error->all(FLERR,"All pair coeffs are not set"); + error->all(FLERR, "All pair coeffs are not set"); } //calculating the polynomial linking to zero double es = cutOffEnd[i][j] - cutOffStart[i][j]; - double es2 = es*es; - double es3 = es2*es; + double es2 = es * es; + double es3 = es2 * es; //variables for poly for p and A - double expp = A[i][j] * exp(p[i][j]*(1.-cutOffStart[i][j]/r0[i][j])); - double ap = -1./es3; - double bp = p[i][j]/(r0[i][j]*es2); - double cp = -(p[i][j]*p[i][j])/(es*r0[i][j]*r0[i][j]); + double expp = A[i][j] * exp(p[i][j] * (1. - cutOffStart[i][j] / r0[i][j])); + double ap = -1. / es3; + double bp = p[i][j] / (r0[i][j] * es2); + double cp = -(p[i][j] * p[i][j]) / (es * r0[i][j] * r0[i][j]); - a5[i][j]= expp * (12.*ap + 6.*bp + cp)/(2.*es2); - a4[i][j]= expp * (15.*ap + 7.*bp + cp)/es; - a3[i][j]= expp * (20.*ap + 8.*bp + cp)/2.; + a5[i][j] = expp * (12. * ap + 6. * bp + cp) / (2. * es2); + a4[i][j] = expp * (15. * ap + 7. * bp + cp) / es; + a3[i][j] = expp * (20. * ap + 8. * bp + cp) / 2.; //variables for poly for q and qsi - double expq = QSI[i][j]*exp(q[i][j]*(1.-cutOffStart[i][j]/r0[i][j])); - double aq = -1/es3; - double bq = q[i][j]/(es2*r0[i][j]); - double cq = -(q[i][j]*q[i][j])/(es*r0[i][j]*r0[i][j]); + double expq = QSI[i][j] * exp(q[i][j] * (1. - cutOffStart[i][j] / r0[i][j])); + double aq = -1 / es3; + double bq = q[i][j] / (es2 * r0[i][j]); + double cq = -(q[i][j] * q[i][j]) / (es * r0[i][j] * r0[i][j]); + + x5[i][j] = expq * (12. * aq + 6. * bq + cq) / (2. * es2); + x4[i][j] = expq * (15. * aq + 7. * bq + cq) / es; + x3[i][j] = expq * (20. * aq + 8. * bq + cq) / 2.; - x5[i][j] = expq * (12.*aq + 6.*bq + cq)/(2.*es2); - x4[i][j] = expq * (15.*aq + 7.*bq + cq)/es; - x3[i][j] = expq * (20.*aq + 8.*bq + cq)/2.; - cutOffEnd2[i][j] = cutOffEnd[i][j] * cutOffEnd[i][j]; - if ( i!=j ) { + if (i != j) { setflag[j][i] = 1; cutOffEnd2[j][i] = cutOffEnd2[i][j]; @@ -421,26 +423,15 @@ double PairSMATB::init_one(int i, int j) {//perform initialization for one i,j t x4[j][i] = x4[i][j]; x5[j][i] = x5[i][j]; } -#ifdef DR_DEBUG - std::cout << i << " " << j <me; size_t result; if (me == 0) { - result = fread(&offset_flag,sizeof(int),1,fp); - result = fread(&mix_flag, sizeof(int),1,fp); - result = fread(&tail_flag, sizeof(int),1,fp); + result = fread(&offset_flag, sizeof(int), 1, fp); + result = fread(&mix_flag, sizeof(int), 1, fp); + result = fread(&tail_flag, sizeof(int), 1, fp); } - MPI_Bcast(&offset_flag, 1,MPI_INT,0,world); - MPI_Bcast(&mix_flag, 1,MPI_INT,0,world); - MPI_Bcast(&tail_flag, 1,MPI_INT,0,world); + MPI_Bcast(&offset_flag, 1, MPI_INT, 0, world); + MPI_Bcast(&mix_flag, 1, MPI_INT, 0, world); + MPI_Bcast(&tail_flag, 1, MPI_INT, 0, world); } -void PairSMATB::write_restart(FILE *fp) { +void PairSMATB::write_restart(FILE *fp) +{ write_restart_settings(fp); //"I J r0 p q A QSI CO_start CO_end" - int i,j; + int i, j; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - fwrite(&setflag[i][j], sizeof(int), 1,fp); + fwrite(&setflag[i][j], sizeof(int), 1, fp); if (setflag[i][j]) { - fwrite(&r0[i][j], sizeof(double),1,fp); - fwrite(&p[i][j], sizeof(double),1,fp); - fwrite(&q[i][j], sizeof(double),1,fp); - fwrite(&A[i][j], sizeof(double),1,fp); - fwrite(&QSI[i][j], sizeof(double),1,fp); - fwrite(&cutOffStart[i][j],sizeof(double),1,fp); - fwrite(&cutOffEnd[i][j], sizeof(double),1,fp); + fwrite(&r0[i][j], sizeof(double), 1, fp); + fwrite(&p[i][j], sizeof(double), 1, fp); + fwrite(&q[i][j], sizeof(double), 1, fp); + fwrite(&A[i][j], sizeof(double), 1, fp); + fwrite(&QSI[i][j], sizeof(double), 1, fp); + fwrite(&cutOffStart[i][j], sizeof(double), 1, fp); + fwrite(&cutOffEnd[i][j], sizeof(double), 1, fp); } } //maybe we need to save also the values of the various polynomials } -void PairSMATB::read_restart(FILE *fp) { +void PairSMATB::read_restart(FILE *fp) +{ read_restart_settings(fp); allocate(); size_t result; - int i,j; + int i, j; int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) { - result = fread(&setflag[i][j],sizeof(int),1,fp); - } - MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (me == 0) { result = fread(&setflag[i][j], sizeof(int), 1, fp); } + MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world); if (setflag[i][j]) { if (me == 0) { - result = fread(&r0[i][j], sizeof(double),1,fp); - result = fread(&p[i][j], sizeof(double),1,fp); - result = fread(&q[i][j], sizeof(double),1,fp); - result = fread(&A[i][j], sizeof(double),1,fp); - result = fread(&QSI[i][j], sizeof(double),1,fp); - result = fread(&cutOffStart[i][j],sizeof(double),1,fp); - result = fread(&cutOffEnd[i][j], sizeof(double),1,fp); + result = fread(&r0[i][j], sizeof(double), 1, fp); + result = fread(&p[i][j], sizeof(double), 1, fp); + result = fread(&q[i][j], sizeof(double), 1, fp); + result = fread(&A[i][j], sizeof(double), 1, fp); + result = fread(&QSI[i][j], sizeof(double), 1, fp); + result = fread(&cutOffStart[i][j], sizeof(double), 1, fp); + result = fread(&cutOffEnd[i][j], sizeof(double), 1, fp); } - MPI_Bcast(&r0[i][j], 1,MPI_DOUBLE,0,world); - MPI_Bcast(&p[i][j], 1,MPI_DOUBLE,0,world); - MPI_Bcast(&q[i][j], 1,MPI_DOUBLE,0,world); - MPI_Bcast(&A[i][j], 1,MPI_DOUBLE,0,world); - MPI_Bcast(&QSI[i][j], 1,MPI_DOUBLE,0,world); - MPI_Bcast(&cutOffStart[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&cutOffEnd[i][j], 1,MPI_DOUBLE,0,world); + MPI_Bcast(&r0[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&p[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&q[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&A[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&QSI[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cutOffStart[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cutOffEnd[i][j], 1, MPI_DOUBLE, 0, world); } } } -void PairSMATB::write_data(FILE *fp) { +void PairSMATB::write_data(FILE *fp) +{ //smatb needs I J r0 p q A QSI CO_start CO_end for (int i = 1; i <= atom->ntypes; i++) { - fprintf(fp,"%d %g %g %g %g %g %g %g\n", - i, r0[i][i], p[i][i], q[i][i], A[i][i], QSI[i][i], cutOffStart[i][i], cutOffEnd[i][i]); + fprintf(fp, "%d %g %g %g %g %g %g %g\n", i, r0[i][i], p[i][i], q[i][i], A[i][i], QSI[i][i], + cutOffStart[i][i], cutOffEnd[i][i]); } } -void PairSMATB::write_data_all(FILE *fp) { +void PairSMATB::write_data_all(FILE *fp) +{ for (int i = 1; i <= atom->ntypes; i++) { for (int j = i; j <= atom->ntypes; j++) { - fprintf(fp,"%d %d %g %g %g %g %g %g %g\n", - i, j, r0[i][j], p[i][j], q[i][j], A[i][j], QSI[i][j], cutOffStart[i][j], cutOffEnd[i][j]); + fprintf(fp, "%d %d %g %g %g %g %g %g %g\n", i, j, r0[i][j], p[i][j], q[i][j], A[i][j], + QSI[i][j], cutOffStart[i][j], cutOffEnd[i][j]); } } } - diff --git a/src/pair_smatb.h b/src/pair_smatb.h index 3013a1d40e..8a5fdea91f 100644 --- a/src/pair_smatb.h +++ b/src/pair_smatb.h @@ -26,44 +26,45 @@ PairStyle(smatb,PairSMATB) namespace LAMMPS_NS { - - class PairSMATB : public Pair { - public: - PairSMATB(class LAMMPS *); - virtual ~PairSMATB(); - void compute(int, int);//workhorse routine that computes pairwise interactions - /* +class PairSMATB : public Pair { + public: + PairSMATB(class LAMMPS *); + virtual ~PairSMATB(); + void compute(int, int); //workhorse routine that computes pairwise interactions + /* void compute_inner(); void compute_middle(); - void compute_outer(int, int);*/ - void settings(int, char **);//reads the input script line with arguments you define - void coeff(int, char **);//set coefficients for one i,j type pair - //void init_style();//initialization specific to this pair style - double init_one(int, int);//perform initialization for one i,j type pair - //double single(int, int, int, int, double, double, double, double &);//force and energy of a single pairwise interaction between 2 atoms + void compute_outer(int, int); + */ + void settings(int, char **); //reads the input script line with arguments you define + void coeff(int, char **); //set coefficients for one i,j type pair + //void init_style();//initialization specific to this pair style + double init_one(int, int); //perform initialization for one i,j type pair + //double single(int, int, int, int, double, double, double, double &);//force and energy of a single pairwise interaction between 2 atoms - void write_restart(FILE *); - void read_restart(FILE *); - void write_restart_settings(FILE *); - void read_restart_settings(FILE *); - void write_data(FILE *); - void write_data_all(FILE *); + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + void write_data(FILE *); + void write_data_all(FILE *); - virtual int pack_forward_comm(int, int *, double *, int, int *); - virtual void unpack_forward_comm(int, int, double *); - virtual int pack_reverse_comm(int, int, double *); - virtual void unpack_reverse_comm(int, int *, double *); - protected: - virtual void allocate(); - int nmax; // allocated size of per-atom arrays - double *on_eb; //allocated to store up caclulation values - double **r0; // interaction radius, user-given - double **p, **A, **q, **QSI; // parameters user-given - double **cutOffStart, **cutOffEnd;//cut offs, user given - double **cutOffEnd2; //squared cut off end, calculated - double **a3, **a4, **a5; //polynomial for cutoff linking to zero: Ae^p substitution - double **x3, **x4, **x5; //polynomial for cutoff linking to zero: QSIe^q substitution - /* latex form of the potential (R_c is cutOffEnd, \Xi is QSI): + virtual int pack_forward_comm(int, int *, double *, int, int *); + virtual void unpack_forward_comm(int, int, double *); + virtual int pack_reverse_comm(int, int, double *); + virtual void unpack_reverse_comm(int, int *, double *); + + protected: + virtual void allocate(); + int nmax; // allocated size of per-atom arrays + double *on_eb; //allocated to store up caclulation values + double **r0; // interaction radius, user-given + double **p, **A, **q, **QSI; // parameters user-given + double **cutOffStart, **cutOffEnd; //cut offs, user given + double **cutOffEnd2; //squared cut off end, calculated + double **a3, **a4, **a5; //polynomial for cutoff linking to zero: Ae^p substitution + double **x3, **x4, **x5; //polynomial for cutoff linking to zero: QSIe^q substitution + /* latex form of the potential (R_c is cutOffEnd, \Xi is QSI): E_i = \sum_{j,R_{ij}\leq R_c} A e^{-p \lrt{\frac{R_{ij}}{R_{0}}-1}} @@ -71,14 +72,14 @@ namespace LAMMPS_NS { NB::this form does not have the polynomial link to 0 for the cut off */ - }; +}; -} +} // namespace LAMMPS_NS #endif #endif -/* ERROR/WARNING messages: + /* ERROR/WARNING messages: E: Illegal ... command @@ -90,9 +91,4 @@ namespace LAMMPS_NS { Self-explanatory. Check the input script or data file. - E: Cannot open EAM potential file %s - - The specified EAM potential file cannot be opened. Check that the - path and name are correct. - */ diff --git a/src/pair_smatb_single.cpp b/src/pair_smatb_single.cpp index 3430ec1e73..f5b0e340bc 100644 --- a/src/pair_smatb_single.cpp +++ b/src/pair_smatb_single.cpp @@ -1,58 +1,57 @@ +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- +This pair style is written by Daniele Rapetti (iximiel@gmail.com) +------------------------------------------------------------------------- */ +#include "pair_smatb_single.h" +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" #include #include #include #include -#include "pair_smatb_single.h" -#include "atom.h" -#include "force.h" -#include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" - -//#define DR_DEBUG -#ifdef DR_DEBUG -#include -#include -#endif //DR_DEBUG using namespace LAMMPS_NS; #define MAXLINE 1024 -PairSMATBSingle::PairSMATBSingle(LAMMPS *lmp) - : Pair(lmp), - nmax(0), - on_eb(nullptr), - r0(0), - p(0), - A(0), - q(0), - QSI(0), - cutOffStart(0), - cutOffEnd(0), - cutOffEnd2(0), - a3(0), a4(0), a5(0), - x3(0), x4(0), x5(0) { - single_enable = 0; // 1 if single() routine exists - restartinfo = 1; // 1 if pair style writes restart info - respa_enable = 0; // 1 if inner/middle/outer rRESPA routines - one_coeff = 0; // 1 if allows only one coeff * * call - manybody_flag = 1; // 1 if a manybody potential - no_virial_fdotr_compute = 0; // 1 if does not invoke virial_fdotr_compute() - writedata = 1; // 1 if writes coeffs to data file - ghostneigh = 0; // 1 if pair style needs neighbors of ghosts +PairSMATBSingle::PairSMATBSingle(LAMMPS *lmp) : + Pair(lmp), nmax(0), on_eb(nullptr), r0(0), p(0), A(0), q(0), QSI(0), cutOffStart(0), + cutOffEnd(0), cutOffEnd2(0), a3(0), a4(0), a5(0), x3(0), x4(0), x5(0) +{ + single_enable = 0; // 1 if single() routine exists + restartinfo = 1; // 1 if pair style writes restart info + respa_enable = 0; // 1 if inner/middle/outer rRESPA routines + one_coeff = 0; // 1 if allows only one coeff * * call + manybody_flag = 1; // 1 if a manybody potential + no_virial_fdotr_compute = 0; // 1 if does not invoke virial_fdotr_compute() + writedata = 1; // 1 if writes coeffs to data file + ghostneigh = 0; // 1 if pair style needs neighbors of ghosts // set comm size needed by this Pair comm_forward = 1; comm_reverse = 1; } -PairSMATBSingle::~PairSMATBSingle() { - if (copymode) { - return; - } +PairSMATBSingle::~PairSMATBSingle() +{ + if (copymode) { return; } memory->destroy(on_eb); if (allocated) { memory->destroy(setflag); @@ -60,17 +59,18 @@ PairSMATBSingle::~PairSMATBSingle() { } } -void PairSMATBSingle::compute(int eflag, int vflag) {//workhorse routine that computes pairwise interactions +void PairSMATBSingle::compute(int eflag, int vflag) +{ //workhorse routine that computes pairwise interactions //eflag means compute energy //vflag means compute virial - int i,j,ii,jj,jnum;//,itype,jtype; - double xtmp,ytmp,ztmp,del[3],fpair; - double dijsq,dij; + int i, j, ii, jj, jnum; //,itype,jtype; + double xtmp, ytmp, ztmp, del[3], fpair; + double dijsq, dij; double espo, aexpp, qsiexpq, eb_i, Fb, Fr; double polyval, polyval2, polyval3, polyval4, polyval5; //sets up the flags for energy caclulations if (eflag || vflag) { - ev_setup(eflag,vflag); + ev_setup(eflag, vflag); eng_vdwl = 0; } else { evflag = vflag_fdotr = eflag_global = eflag_atom = 0; @@ -81,14 +81,14 @@ void PairSMATBSingle::compute(int eflag, int vflag) {//workhorse routine that co if (atom->nmax > nmax) { nmax = atom->nmax; - memory->grow(on_eb,nmax,"pair_smatb:on_eb"); + memory->grow(on_eb, nmax, "pair_smatb:on_eb"); } double **x = atom->x; double **f = atom->f; - int *type = atom->type; + int *type = atom->type; int nlocal = atom->nlocal; - int nall = nlocal + atom->nghost; + int nall = nlocal + atom->nghost; int newton_pair = force->newton_pair; @@ -107,39 +107,39 @@ void PairSMATBSingle::compute(int eflag, int vflag) {//workhorse routine that co //FIRST LOOP: CALCULATES the squared bounding energy and accumulate it in on_eb for each atom for (ii = 0; ii < inum; ++ii) { - i = ilist[ii]; - xtmp = x[i][0]; - ytmp = x[i][1]; - ztmp = x[i][2]; + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; //itype = type[i]; jlist = firstneigh[i]; jnum = numneigh[i]; for (jj = 0; jj < jnum; ++jj) { - j = jlist[jj]; + j = jlist[jj]; j &= NEIGHMASK; //jtype = type[j]; del[0] = xtmp - x[j][0]; del[1] = ytmp - x[j][1]; del[2] = ztmp - x[j][2]; - dijsq = del[0]*del[0] + del[1]*del[1] + del[2]*del[2]; + dijsq = del[0] * del[0] + del[1] * del[1] + del[2] * del[2]; - if ( dijsq < cutOffEnd2 ) { - dij = sqrt (dijsq); - if ( dij < cutOffStart ) { - qsiexpq = (QSI*QSI) * exp(2.0*q*(1.0 - dij/r0)); - } else { - polyval = dij-cutOffEnd; - polyval3 = polyval*polyval*polyval; - polyval4 = polyval3*polyval; - polyval5 = polyval4*polyval; - qsiexpq = x5*polyval5+x4*polyval4+x3*polyval3; - qsiexpq = qsiexpq* qsiexpq; - } - on_eb[i]+=qsiexpq; - //if (newton_pair || j < nlocal) { - on_eb[j]+=qsiexpq; - //} + if (dijsq < cutOffEnd2) { + dij = sqrt(dijsq); + if (dij < cutOffStart) { + qsiexpq = (QSI * QSI) * exp(2.0 * q * (1.0 - dij / r0)); + } else { + polyval = dij - cutOffEnd; + polyval3 = polyval * polyval * polyval; + polyval4 = polyval3 * polyval; + polyval5 = polyval4 * polyval; + qsiexpq = x5 * polyval5 + x4 * polyval4 + x3 * polyval3; + qsiexpq = qsiexpq * qsiexpq; + } + on_eb[i] += qsiexpq; + //if (newton_pair || j < nlocal) { + on_eb[j] += qsiexpq; + //} } } } @@ -152,22 +152,18 @@ void PairSMATBSingle::compute(int eflag, int vflag) {//workhorse routine that co // the store the reciprocal in on_eb in order to not do it in the SECOND LOOP for (ii = 0; ii < inum; ++ii) { - i = ilist[ii]; - if (i < nlocal){ - eb_i=sqrt(on_eb[i]); - if (eb_i!=0.0) { - on_eb[i]=1.0/eb_i; + i = ilist[ii]; + if (i < nlocal) { + eb_i = sqrt(on_eb[i]); + if (eb_i != 0.0) { + on_eb[i] = 1.0 / eb_i; } else { on_eb[i] = 0.0; } //if needed the bounding energy is accumulated: if (eflag_either) { - if (eflag_atom) { - eatom[i] -= eb_i; - } - if (eflag_global) { - eng_vdwl -= eb_i; - } + if (eflag_atom) { eatom[i] -= eb_i; } + if (eflag_global) { eng_vdwl -= eb_i; } } } } @@ -192,60 +188,57 @@ void PairSMATBSingle::compute(int eflag, int vflag) {//workhorse routine that co del[1] = ytmp - x[j][1]; del[2] = ztmp - x[j][2]; - dijsq = del[0]*del[0] + del[1]*del[1] + del[2]*del[2]; - if ( dijsq < cutOffEnd2 ) { - dij = sqrt (dijsq); - if ( dij < cutOffStart ) { - espo = 1.0 - dij/r0; - aexpp = exp(p*espo)*A; - Fr = (2.0*aexpp)*(p/r0); - qsiexpq = (QSI*QSI) * exp(2.0*q*espo); - Fb = -qsiexpq * q/r0; - } else { - polyval = dij-cutOffEnd; - polyval2 = polyval*polyval; - polyval3 = polyval2*polyval; - polyval4 = polyval3*polyval; - polyval5 = polyval4*polyval; - aexpp = a5*polyval5+a4*polyval4+a3*polyval3; - Fr = -2.0*(5.0*a5*polyval4+4.0*a4*polyval3+3.0*a3*polyval2); - qsiexpq = x5*polyval5+x4*polyval4+x3*polyval3; - Fb = ((5.0*x5*polyval4+4.0*x4*polyval3+3.0*x3*polyval2))*qsiexpq; - } - //if needed the repulsive energy is accumulated: - if (eflag_either) { - if (eflag_atom) { - eatom[i] += aexpp; - if (newton_pair || j < nlocal) { - eatom[j] += aexpp; - } - } - if (eflag_global) { - if (newton_pair || j < nlocal) { - eng_vdwl += 2.0*(aexpp); - } else { - eng_vdwl += aexpp; - } - } - } - //calculates the module of the pair energy between i and j - fpair = (Fb*(on_eb[i]+on_eb[j]) + Fr)/dij; + dijsq = del[0] * del[0] + del[1] * del[1] + del[2] * del[2]; + if (dijsq < cutOffEnd2) { + dij = sqrt(dijsq); + if (dij < cutOffStart) { + espo = 1.0 - dij / r0; + aexpp = exp(p * espo) * A; + Fr = (2.0 * aexpp) * (p / r0); + qsiexpq = (QSI * QSI) * exp(2.0 * q * espo); + Fb = -qsiexpq * q / r0; + } else { + polyval = dij - cutOffEnd; + polyval2 = polyval * polyval; + polyval3 = polyval2 * polyval; + polyval4 = polyval3 * polyval; + polyval5 = polyval4 * polyval; + aexpp = a5 * polyval5 + a4 * polyval4 + a3 * polyval3; + Fr = -2.0 * (5.0 * a5 * polyval4 + 4.0 * a4 * polyval3 + 3.0 * a3 * polyval2); + qsiexpq = x5 * polyval5 + x4 * polyval4 + x3 * polyval3; + Fb = ((5.0 * x5 * polyval4 + 4.0 * x4 * polyval3 + 3.0 * x3 * polyval2)) * qsiexpq; + } + //if needed the repulsive energy is accumulated: + if (eflag_either) { + if (eflag_atom) { + eatom[i] += aexpp; + if (newton_pair || j < nlocal) { eatom[j] += aexpp; } + } + if (eflag_global) { + if (newton_pair || j < nlocal) { + eng_vdwl += 2.0 * (aexpp); + } else { + eng_vdwl += aexpp; + } + } + } + //calculates the module of the pair energy between i and j + fpair = (Fb * (on_eb[i] + on_eb[j]) + Fr) / dij; - f[i][0] += del[0]*fpair; - f[i][1] += del[1]*fpair; - f[i][2] += del[2]*fpair; - if (newton_pair || j < nlocal) { - f[j][0] -= del[0]*fpair; - f[j][1] -= del[1]*fpair; - f[j][2] -= del[2]*fpair; - } - if (vflag_atom) { - ev_tally(i, j, nlocal, newton_pair, - 0.0, 0.0,//Energy is tally'd in the other parts of the potential - fpair, del[0], del[1], del[2]); - } + f[i][0] += del[0] * fpair; + f[i][1] += del[1] * fpair; + f[i][2] += del[2] * fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= del[0] * fpair; + f[j][1] -= del[1] * fpair; + f[j][2] -= del[2] * fpair; + } + if (vflag_atom) { + ev_tally(i, j, nlocal, newton_pair, 0.0, + 0.0, //Energy is tally'd in the other parts of the potential + fpair, del[0], del[1], del[2]); + } } - } } if (vflag_fdotr) virial_fdotr_compute(); @@ -255,26 +248,26 @@ void PairSMATBSingle::compute(int eflag, int vflag) {//workhorse routine that co global settings ------------------------------------------------------------------------- */ -void PairSMATBSingle::settings(int narg, char **) {//reads the input script line with arguments you define - if (narg > 0) error->all(FLERR,"Illegal pair_style command: smatb accepts no options"); +void PairSMATBSingle::settings(int narg, char **) +{ //reads the input script line with arguments you define + if (narg > 0) error->all(FLERR, "Illegal pair_style command: smatb accepts no options"); } /* ---------------------------------------------------------------------- allocate all arrays ------------------------------------------------------------------------- */ -void PairSMATBSingle::allocate() { +void PairSMATBSingle::allocate() +{ int n = atom->ntypes; - int natoms=atom->natoms; + int natoms = atom->natoms; - memory->create(setflag, n+1, n+1, "pair_smatb:setflag"); + memory->create(setflag, n + 1, n + 1, "pair_smatb:setflag"); for (int i = 1; i <= n; i++) { - for (int j = i; j <= n; j++) { - setflag[i][j] = 0; - } + for (int j = i; j <= n; j++) { setflag[i][j] = 0; } } - memory->create(cutsq, n+1, n+1, "pair_smatb:cutsq"); + memory->create(cutsq, n + 1, n + 1, "pair_smatb:cutsq"); allocated = 1; } @@ -283,28 +276,29 @@ void PairSMATBSingle::allocate() { set coeffs for one or more type pairs ------------------------------------------------------------------------- */ -void PairSMATBSingle::coeff(int narg, char **arg) {//set coefficients for one i,j type pair - if (!allocated) { - allocate(); - } +void PairSMATBSingle::coeff(int narg, char **arg) +{ //set coefficients for one i,j type pair + if (!allocated) { allocate(); } if (narg != 9) { - error->all(FLERR,"Incorrect args for pair coefficients:\n SMATB needs \"i j r0 p q A QSI CO_start CO_end\""); + error->all( + FLERR, + "Incorrect args for pair coefficients:\n SMATB needs \"i j r0 p q A QSI CO_start CO_end\""); } - int ilo,ihi,jlo,jhi; - utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); - utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); + int ilo, ihi, jlo, jhi; + utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error); + utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error); //reading parameters from input - double myr0 = utils::numeric(FLERR,arg[2],false,lmp), - myp = utils::numeric(FLERR,arg[3],false,lmp), - myq = utils::numeric(FLERR,arg[4],false,lmp), - myA = utils::numeric(FLERR,arg[5],false,lmp), - myQSI = utils::numeric(FLERR,arg[6],false,lmp), - mycutOffStart = utils::numeric(FLERR,arg[7],false,lmp), - mycutOffEnd = utils::numeric(FLERR,arg[8],false,lmp); + double myr0 = utils::numeric(FLERR, arg[2], false, lmp), + myp = utils::numeric(FLERR, arg[3], false, lmp), + myq = utils::numeric(FLERR, arg[4], false, lmp), + myA = utils::numeric(FLERR, arg[5], false, lmp), + myQSI = utils::numeric(FLERR, arg[6], false, lmp), + mycutOffStart = utils::numeric(FLERR, arg[7], false, lmp), + mycutOffEnd = utils::numeric(FLERR, arg[8], false, lmp); int count = 0; for (int i = ilo; i <= ihi; i++) { - for (int j = MAX(jlo,i); j <= jhi; j++) { + for (int j = MAX(jlo, i); j <= jhi; j++) { r0 = myr0; p = myp; A = myA; @@ -318,8 +312,7 @@ void PairSMATBSingle::coeff(int narg, char **arg) {//set coefficients for one i, } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); - + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); } /* ---------------------------------------------------------------------- @@ -335,35 +328,36 @@ void PairSMATBSingle::coeff(int narg, char **arg) {//set coefficients for one i, init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ -double PairSMATBSingle::init_one(int i, int j) {//perform initialization for one i,j type pair - if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); +double PairSMATBSingle::init_one(int i, int j) +{ //perform initialization for one i,j type pair + if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set"); //calculating the polynomial linking to zero double es = cutOffEnd - cutOffStart; - double es2 = es*es; - double es3 = es2*es; + double es2 = es * es; + double es3 = es2 * es; //variables for poly for p and A - double expp = A * exp(p*(1.-cutOffStart/r0)); - double ap = -1./es3; - double bp = p/(r0*es2); - double cp = -(p*p)/(es*r0*r0); + double expp = A * exp(p * (1. - cutOffStart / r0)); + double ap = -1. / es3; + double bp = p / (r0 * es2); + double cp = -(p * p) / (es * r0 * r0); - a5= expp * (12.*ap + 6.*bp + cp)/(2.*es2); - a4= expp * (15.*ap + 7.*bp + cp)/es; - a3= expp * (20.*ap + 8.*bp + cp)/2.; + a5 = expp * (12. * ap + 6. * bp + cp) / (2. * es2); + a4 = expp * (15. * ap + 7. * bp + cp) / es; + a3 = expp * (20. * ap + 8. * bp + cp) / 2.; //variables for poly for q and qsi - double expq = QSI*exp(q*(1.-cutOffStart/r0)); - double aq = -1/es3; - double bq = q/(es2*r0); - double cq = -(q*q)/(es*r0*r0); + double expq = QSI * exp(q * (1. - cutOffStart / r0)); + double aq = -1 / es3; + double bq = q / (es2 * r0); + double cq = -(q * q) / (es * r0 * r0); + + x5 = expq * (12. * aq + 6. * bq + cq) / (2. * es2); + x4 = expq * (15. * aq + 7. * bq + cq) / es; + x3 = expq * (20. * aq + 8. * bq + cq) / 2.; - x5 = expq * (12.*aq + 6.*bq + cq)/(2.*es2); - x4 = expq * (15.*aq + 7.*bq + cq)/es; - x3 = expq * (20.*aq + 8.*bq + cq)/2.; - cutOffEnd2 = cutOffEnd * cutOffEnd; - if ( i!=j ) { + if (i != j) { setflag[j][i] = 1; cutOffEnd2 = cutOffEnd2; @@ -382,26 +376,15 @@ double PairSMATBSingle::init_one(int i, int j) {//perform initialization for one x4 = x4; x5 = x5; } -#ifdef DR_DEBUG - std::cout << i << " " << j <me; size_t result; if (me == 0) { - result = fread(&offset_flag,sizeof(int),1,fp); - result = fread(&mix_flag, sizeof(int),1,fp); - result = fread(&tail_flag, sizeof(int),1,fp); + result = fread(&offset_flag, sizeof(int), 1, fp); + result = fread(&mix_flag, sizeof(int), 1, fp); + result = fread(&tail_flag, sizeof(int), 1, fp); } - MPI_Bcast(&offset_flag, 1,MPI_INT,0,world); - MPI_Bcast(&mix_flag, 1,MPI_INT,0,world); - MPI_Bcast(&tail_flag, 1,MPI_INT,0,world); + MPI_Bcast(&offset_flag, 1, MPI_INT, 0, world); + MPI_Bcast(&mix_flag, 1, MPI_INT, 0, world); + MPI_Bcast(&tail_flag, 1, MPI_INT, 0, world); } -void PairSMATBSingle::write_restart(FILE *fp) { +void PairSMATBSingle::write_restart(FILE *fp) +{ write_restart_settings(fp); //"I J r0 p q A QSI CO_start CO_end" - int i,j; + int i, j; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - fwrite(&setflag[i][j], sizeof(int), 1,fp); + fwrite(&setflag[i][j], sizeof(int), 1, fp); if (setflag[i][j]) { - fwrite(&r0, sizeof(double),1,fp); - fwrite(&p, sizeof(double),1,fp); - fwrite(&q, sizeof(double),1,fp); - fwrite(&A, sizeof(double),1,fp); - fwrite(&QSI, sizeof(double),1,fp); - fwrite(&cutOffStart,sizeof(double),1,fp); - fwrite(&cutOffEnd, sizeof(double),1,fp); + fwrite(&r0, sizeof(double), 1, fp); + fwrite(&p, sizeof(double), 1, fp); + fwrite(&q, sizeof(double), 1, fp); + fwrite(&A, sizeof(double), 1, fp); + fwrite(&QSI, sizeof(double), 1, fp); + fwrite(&cutOffStart, sizeof(double), 1, fp); + fwrite(&cutOffEnd, sizeof(double), 1, fp); } } //maybe we need to save also the values of the various polynomials } -void PairSMATBSingle::read_restart(FILE *fp) { +void PairSMATBSingle::read_restart(FILE *fp) +{ read_restart_settings(fp); allocate(); size_t result; - int i,j; + int i, j; int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) { - result = fread(&setflag[i][j],sizeof(int),1,fp); - } - MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (me == 0) { result = fread(&setflag[i][j], sizeof(int), 1, fp); } + MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world); if (setflag[i][j]) { if (me == 0) { - result = fread(&r0, sizeof(double),1,fp); - result = fread(&p, sizeof(double),1,fp); - result = fread(&q, sizeof(double),1,fp); - result = fread(&A, sizeof(double),1,fp); - result = fread(&QSI, sizeof(double),1,fp); - result = fread(&cutOffStart,sizeof(double),1,fp); - result = fread(&cutOffEnd, sizeof(double),1,fp); + result = fread(&r0, sizeof(double), 1, fp); + result = fread(&p, sizeof(double), 1, fp); + result = fread(&q, sizeof(double), 1, fp); + result = fread(&A, sizeof(double), 1, fp); + result = fread(&QSI, sizeof(double), 1, fp); + result = fread(&cutOffStart, sizeof(double), 1, fp); + result = fread(&cutOffEnd, sizeof(double), 1, fp); } - MPI_Bcast(&r0, 1,MPI_DOUBLE,0,world); - MPI_Bcast(&p, 1,MPI_DOUBLE,0,world); - MPI_Bcast(&q, 1,MPI_DOUBLE,0,world); - MPI_Bcast(&A, 1,MPI_DOUBLE,0,world); - MPI_Bcast(&QSI, 1,MPI_DOUBLE,0,world); - MPI_Bcast(&cutOffStart,1,MPI_DOUBLE,0,world); - MPI_Bcast(&cutOffEnd, 1,MPI_DOUBLE,0,world); + MPI_Bcast(&r0, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&p, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&q, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&A, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&QSI, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cutOffStart, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cutOffEnd, 1, MPI_DOUBLE, 0, world); } } } -void PairSMATBSingle::write_data(FILE *fp) { +void PairSMATBSingle::write_data(FILE *fp) +{ //smatb needs I J r0 p q A QSI CO_start CO_end for (int i = 1; i <= atom->ntypes; i++) { - fprintf(fp,"%d %g %g %g %g %g %g %g\n", - i, r0, p, q, A, QSI, cutOffStart, cutOffEnd); + fprintf(fp, "%d %g %g %g %g %g %g %g\n", i, r0, p, q, A, QSI, cutOffStart, cutOffEnd); } } -void PairSMATBSingle::write_data_all(FILE *fp) { +void PairSMATBSingle::write_data_all(FILE *fp) +{ for (int i = 1; i <= atom->ntypes; i++) { for (int j = i; j <= atom->ntypes; j++) { - fprintf(fp,"%d %d %g %g %g %g %g %g %g\n", - i, j, r0, p, q, A, QSI, cutOffStart, cutOffEnd); + fprintf(fp, "%d %d %g %g %g %g %g %g %g\n", i, j, r0, p, q, A, QSI, cutOffStart, cutOffEnd); } } } - diff --git a/src/pair_smatb_single.h b/src/pair_smatb_single.h index 774578f395..8eb4b2fdf0 100644 --- a/src/pair_smatb_single.h +++ b/src/pair_smatb_single.h @@ -10,7 +10,7 @@ See the README file in the top-level LAMMPS directory. - This style is written by Daniele Rapetti (iximiel@gmail.com) + This pair style is written by Daniele Rapetti (iximiel@gmail.com) ------------------------------------------------------------------------- */ #ifdef PAIR_CLASS @@ -26,53 +26,51 @@ PairStyle(smatb/single,PairSMATBSingle) namespace LAMMPS_NS { - - class PairSMATBSingle : public Pair { - public: - // public variables so USER-ATC package can access them - - PairSMATBSingle(class LAMMPS *); - virtual ~PairSMATBSingle(); - void compute(int, int);//workhorse routine that computes pairwise interactions - /* +class PairSMATBSingle : public Pair { + public: + PairSMATBSingle(class LAMMPS *); + virtual ~PairSMATBSingle(); + void compute(int, int); //workhorse routine that computes pairwise interactions + /* void compute_inner(); void compute_middle(); - void compute_outer(int, int);*/ - void settings(int, char **);//reads the input script line with arguments you define - void coeff(int, char **);//set coefficients for one i,j type pair - //void init_style();//initialization specific to this pair style - double init_one(int, int);//perform initialization for one i,j type pair - //double single(int, int, int, int, double, double, double, double &);//force and energy of a single pairwise interaction between 2 atoms + void compute_outer(int, int); + */ + void settings(int, char **); //reads the input script line with arguments you define + void coeff(int, char **); //set coefficients for one i,j type pair + //void init_style();//initialization specific to this pair style + double init_one(int, int); //perform initialization for one i,j type pair - virtual void write_restart(FILE *); - virtual void read_restart(FILE *); - virtual void write_restart_settings(FILE *); - virtual void read_restart_settings(FILE *); - virtual void write_data(FILE *); - virtual void write_data_all(FILE *); + virtual void write_restart(FILE *); + virtual void read_restart(FILE *); + virtual void write_restart_settings(FILE *); + virtual void read_restart_settings(FILE *); + virtual void write_data(FILE *); + virtual void write_data_all(FILE *); - virtual int pack_forward_comm(int, int *, double *, int, int *); - virtual void unpack_forward_comm(int, int, double *); - virtual int pack_reverse_comm(int , int , double *); - virtual void unpack_reverse_comm(int , int *, double *); - protected: - virtual void allocate(); - int nmax; // allocated size of per-atom arrays - double *on_eb; //allocated to store up caclulation values - double r0; // interaction radius, user-given - double p, A, q, QSI; // parameters user-given - double cutOffStart, cutOffEnd;//cut offs, user given - double cutOffEnd2; //squared cut off end, calculated - double a3, a4, a5; //polynomial for cutoff linking to zero: Ae^p substitution - double x3, x4, x5; //polynomial for cutoff linking to zero: QSIe^q substitution - }; + virtual int pack_forward_comm(int, int *, double *, int, int *); + virtual void unpack_forward_comm(int, int, double *); + virtual int pack_reverse_comm(int, int, double *); + virtual void unpack_reverse_comm(int, int *, double *); -} + protected: + virtual void allocate(); + int nmax; // allocated size of per-atom arrays + double *on_eb; //allocated to store up caclulation values + double r0; // interaction radius, user-given + double p, A, q, QSI; // parameters user-given + double cutOffStart, cutOffEnd; //cut offs, user given + double cutOffEnd2; //squared cut off end, calculated + double a3, a4, a5; //polynomial for cutoff linking to zero: Ae^p substitution + double x3, x4, x5; //polynomial for cutoff linking to zero: QSIe^q substitution +}; + +} // namespace LAMMPS_NS #endif #endif -/* ERROR/WARNING messages: + /* ERROR/WARNING messages: E: Illegal ... command @@ -83,10 +81,4 @@ namespace LAMMPS_NS { E: Incorrect args for pair coefficients Self-explanatory. Check the input script or data file. - - E: Cannot open EAM potential file %s - - The specified EAM potential file cannot be opened. Check that the - path and name are correct. - */ From bdc4f7fb18ced0cff4b108087c9833ec527fb979 Mon Sep 17 00:00:00 2001 From: Daniele Date: Thu, 11 Nov 2021 16:27:09 +0100 Subject: [PATCH 03/57] styled the headers --- src/pair_smatb.cpp | 2 -- src/pair_smatb.h | 71 +++++++++++++++++++++------------------ src/pair_smatb_single.cpp | 2 -- src/pair_smatb_single.h | 70 +++++++++++++++++++++----------------- 4 files changed, 78 insertions(+), 67 deletions(-) diff --git a/src/pair_smatb.cpp b/src/pair_smatb.cpp index 32e4e91a8d..244194183d 100644 --- a/src/pair_smatb.cpp +++ b/src/pair_smatb.cpp @@ -29,8 +29,6 @@ This pair style is written by Daniele Rapetti (iximiel@gmail.com) using namespace LAMMPS_NS; -#define MAXLINE 1024 - PairSMATB::PairSMATB(LAMMPS *lmp) : Pair(lmp), nmax(0), on_eb(nullptr), r0(nullptr), p(nullptr), A(nullptr), q(nullptr), QSI(nullptr), cutOffStart(nullptr), cutOffEnd(nullptr), cutOffEnd2(nullptr), a3(nullptr), diff --git a/src/pair_smatb.h b/src/pair_smatb.h index 8a5fdea91f..fc4f1f2a9b 100644 --- a/src/pair_smatb.h +++ b/src/pair_smatb.h @@ -29,41 +29,48 @@ namespace LAMMPS_NS { class PairSMATB : public Pair { public: PairSMATB(class LAMMPS *); - virtual ~PairSMATB(); - void compute(int, int); //workhorse routine that computes pairwise interactions - /* - void compute_inner(); - void compute_middle(); - void compute_outer(int, int); - */ - void settings(int, char **); //reads the input script line with arguments you define - void coeff(int, char **); //set coefficients for one i,j type pair - //void init_style();//initialization specific to this pair style - double init_one(int, int); //perform initialization for one i,j type pair - //double single(int, int, int, int, double, double, double, double &);//force and energy of a single pairwise interaction between 2 atoms - - void write_restart(FILE *); - void read_restart(FILE *); - void write_restart_settings(FILE *); - void read_restart_settings(FILE *); - void write_data(FILE *); - void write_data_all(FILE *); - - virtual int pack_forward_comm(int, int *, double *, int, int *); - virtual void unpack_forward_comm(int, int, double *); - virtual int pack_reverse_comm(int, int, double *); - virtual void unpack_reverse_comm(int, int *, double *); + ~PairSMATB() override; + void compute(int, int) override; + void settings(int, char **) override; + void coeff(int, char **) override; + double init_one(int, int) override; + void write_restart(FILE *) override; + void read_restart(FILE *) override; + void write_restart_settings(FILE *) override; + void read_restart_settings(FILE *) override; + void write_data(FILE *) override; + void write_data_all(FILE *) override; + int pack_forward_comm(int, int *, double *, int, int *) override; + void unpack_forward_comm(int, int, double *) override; + int pack_reverse_comm(int, int, double *) override; + void unpack_reverse_comm(int, int *, double *) override; protected: virtual void allocate(); - int nmax; // allocated size of per-atom arrays - double *on_eb; //allocated to store up caclulation values - double **r0; // interaction radius, user-given - double **p, **A, **q, **QSI; // parameters user-given - double **cutOffStart, **cutOffEnd; //cut offs, user given - double **cutOffEnd2; //squared cut off end, calculated - double **a3, **a4, **a5; //polynomial for cutoff linking to zero: Ae^p substitution - double **x3, **x4, **x5; //polynomial for cutoff linking to zero: QSIe^q substitution + // allocated size of per-atom arrays + int nmax; + //allocated to store up caclulation values + double *on_eb{nullptr}; + // interaction radius, user-given + double **r0{nullptr}; + // parameters user-given + double **p{nullptr}; + double **A{nullptr}; + double **q{nullptr}; + double **QSI{nullptr}; + //extremes of the cut off, user given + double **cutOffStart{nullptr}; + double **cutOffEnd{nullptr}; + //squared cut off end, calculated + double **cutOffEnd2{nullptr}; + //polynomial for cutoff linking to zero: Ae^p substitution + double **a3{nullptr}; + double **a4{nullptr}; + double **a5{nullptr}; + //polynomial for cutoff linking to zero: QSIe^q substitution + double **x3{nullptr}; + double **x4{nullptr}; + double **x5{nullptr}; /* latex form of the potential (R_c is cutOffEnd, \Xi is QSI): E_i = diff --git a/src/pair_smatb_single.cpp b/src/pair_smatb_single.cpp index f5b0e340bc..92e55916df 100644 --- a/src/pair_smatb_single.cpp +++ b/src/pair_smatb_single.cpp @@ -29,8 +29,6 @@ This pair style is written by Daniele Rapetti (iximiel@gmail.com) using namespace LAMMPS_NS; -#define MAXLINE 1024 - PairSMATBSingle::PairSMATBSingle(LAMMPS *lmp) : Pair(lmp), nmax(0), on_eb(nullptr), r0(0), p(0), A(0), q(0), QSI(0), cutOffStart(0), cutOffEnd(0), cutOffEnd2(0), a3(0), a4(0), a5(0), x3(0), x4(0), x5(0) diff --git a/src/pair_smatb_single.h b/src/pair_smatb_single.h index 8eb4b2fdf0..4b8fcf70e5 100644 --- a/src/pair_smatb_single.h +++ b/src/pair_smatb_single.h @@ -29,40 +29,48 @@ namespace LAMMPS_NS { class PairSMATBSingle : public Pair { public: PairSMATBSingle(class LAMMPS *); - virtual ~PairSMATBSingle(); - void compute(int, int); //workhorse routine that computes pairwise interactions - /* - void compute_inner(); - void compute_middle(); - void compute_outer(int, int); - */ - void settings(int, char **); //reads the input script line with arguments you define - void coeff(int, char **); //set coefficients for one i,j type pair - //void init_style();//initialization specific to this pair style - double init_one(int, int); //perform initialization for one i,j type pair - - virtual void write_restart(FILE *); - virtual void read_restart(FILE *); - virtual void write_restart_settings(FILE *); - virtual void read_restart_settings(FILE *); - virtual void write_data(FILE *); - virtual void write_data_all(FILE *); - - virtual int pack_forward_comm(int, int *, double *, int, int *); - virtual void unpack_forward_comm(int, int, double *); - virtual int pack_reverse_comm(int, int, double *); - virtual void unpack_reverse_comm(int, int *, double *); + ~PairSMATBSingle() override; + void compute(int, int) override; + void settings(int, char **) override; + void coeff(int, char **) override; + double init_one(int, int) override; + void write_restart(FILE *) override; + void read_restart(FILE *) override; + void write_restart_settings(FILE *) override; + void read_restart_settings(FILE *) override; + void write_data(FILE *) override; + void write_data_all(FILE *) override; + int pack_forward_comm(int, int *, double *, int, int *) override; + void unpack_forward_comm(int, int, double *) override; + int pack_reverse_comm(int, int, double *) override; + void unpack_reverse_comm(int, int *, double *) override; protected: virtual void allocate(); - int nmax; // allocated size of per-atom arrays - double *on_eb; //allocated to store up caclulation values - double r0; // interaction radius, user-given - double p, A, q, QSI; // parameters user-given - double cutOffStart, cutOffEnd; //cut offs, user given - double cutOffEnd2; //squared cut off end, calculated - double a3, a4, a5; //polynomial for cutoff linking to zero: Ae^p substitution - double x3, x4, x5; //polynomial for cutoff linking to zero: QSIe^q substitution + // allocated size of per-atom arrays + int nmax; + //allocated to store up caclulation values + double *on_eb{nullptr}; + // interaction radius, user-given + double r0; + // parameters user-given + double p; + double A; + double q; + double QSI; + //cut offs, user given + double cutOffStart; + double cutOffEnd; + //squared cut off end, calculated + double cutOffEnd2; + //polynomial for cutoff linking to zero: Ae^p substitution + double a3; + double a4; + double a5; + //polynomial for cutoff linking to zero: QSIe^q substitution + double x3; + double x4; + double x5; }; } // namespace LAMMPS_NS From 80efc8839aa81bdc169622deffebaa178c7f8a2f Mon Sep 17 00:00:00 2001 From: Daniele Date: Thu, 11 Nov 2021 16:36:48 +0100 Subject: [PATCH 04/57] fixed a grammar mistake --- src/pair_smatb.cpp | 2 +- src/pair_smatb.h | 2 +- src/pair_smatb_single.cpp | 2 +- src/pair_smatb_single.h | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/pair_smatb.cpp b/src/pair_smatb.cpp index 244194183d..cda65837c8 100644 --- a/src/pair_smatb.cpp +++ b/src/pair_smatb.cpp @@ -82,7 +82,7 @@ void PairSMATB::compute(int eflag, int vflag) double dijsq, dij; double espo, aexpp, qsiexpq, eb_i, Fb, Fr; double polyval, polyval2, polyval3, polyval4, polyval5; - //sets up the flags for energy caclulations + //sets up the flags for energy calculations if (eflag || vflag) { ev_setup(eflag, vflag); eng_vdwl = 0; diff --git a/src/pair_smatb.h b/src/pair_smatb.h index fc4f1f2a9b..d87546ecd1 100644 --- a/src/pair_smatb.h +++ b/src/pair_smatb.h @@ -49,7 +49,7 @@ class PairSMATB : public Pair { virtual void allocate(); // allocated size of per-atom arrays int nmax; - //allocated to store up caclulation values + //allocated to store up calculation values double *on_eb{nullptr}; // interaction radius, user-given double **r0{nullptr}; diff --git a/src/pair_smatb_single.cpp b/src/pair_smatb_single.cpp index 92e55916df..f7910b076a 100644 --- a/src/pair_smatb_single.cpp +++ b/src/pair_smatb_single.cpp @@ -66,7 +66,7 @@ void PairSMATBSingle::compute(int eflag, int vflag) double dijsq, dij; double espo, aexpp, qsiexpq, eb_i, Fb, Fr; double polyval, polyval2, polyval3, polyval4, polyval5; - //sets up the flags for energy caclulations + //sets up the flags for energy calculations if (eflag || vflag) { ev_setup(eflag, vflag); eng_vdwl = 0; diff --git a/src/pair_smatb_single.h b/src/pair_smatb_single.h index 4b8fcf70e5..8d31a7d047 100644 --- a/src/pair_smatb_single.h +++ b/src/pair_smatb_single.h @@ -49,7 +49,7 @@ class PairSMATBSingle : public Pair { virtual void allocate(); // allocated size of per-atom arrays int nmax; - //allocated to store up caclulation values + //allocated to store up calculation values double *on_eb{nullptr}; // interaction radius, user-given double r0; From c488e912e6baae347c57e6b768641a57ba837511 Mon Sep 17 00:00:00 2001 From: Daniele Date: Thu, 11 Nov 2021 17:01:03 +0100 Subject: [PATCH 05/57] adding the pair_smatb to lammps documentation --- doc/src/pair_smatb.rst | 122 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 122 insertions(+) create mode 100644 doc/src/pair_smatb.rst diff --git a/doc/src/pair_smatb.rst b/doc/src/pair_smatb.rst new file mode 100644 index 0000000000..fb42fe0b7a --- /dev/null +++ b/doc/src/pair_smatb.rst @@ -0,0 +1,122 @@ +.. index:: pair_style smatb +.. index:: pair_style smatb/single + +pair_style smatb command +========================= + +Syntax +"""""" + +.. code-block:: LAMMPS + + pair_style style args + +* style = *smatb* +* args = none + +.. parsed-literal:: + + *smatb* + +Examples +"""""""" + +.. code-block:: LAMMPS + + pair_style smatb 2.5 + pair_coeff 1 1 2.88 10.35 4.178 0.210 1.818 4.07293506 4.9883063257983666 + +Description +""""""""""" + +The *lj/cut* styles compute the standard 12/6 Lennard-Jones potential, +given by + +.. math:: + + E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - + \left(\frac{\sigma}{r}\right)^6 \right] + \qquad r < r_c + +:math:`r_c` is the cutoff. + +See the :doc:`lj/cut/coul ` styles to add a Coulombic +pairwise interaction and the :doc:`lj/cut/tip4p ` styles to +add the TIP4P water model. + +Coefficients +"""""""""""" + +The following coefficients must be defined for each pair of atoms types via the +:doc:`pair_coeff ` command as in the examples above, or in the data +file or restart files read by the :doc:`read_data ` or +:doc:`read_restart ` commands, or by mixing as described below: + +* :math:`\epsilon` (energy units) +* :math:`\sigma` (distance units) +* LJ cutoff (distance units) + +Note that :math:`\sigma` is defined in the LJ formula as the zero-crossing +distance for the potential, not as the energy minimum at :math:`2^{\frac{1}{6}} \sigma`. + +The last coefficient is optional. If not specified, the global +LJ cutoff specified in the pair_style command are used. + +---------- + +A version of these styles with a soft core, *lj/cut/soft*, suitable +for use in free energy calculations, is part of the FEP package and +is documented with the :doc:`pair_style */soft ` +styles. + +---------- + +.. include:: accel_styles.rst + +---------- + +Mixing, shift, table, tail correction, restart, rRESPA info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +For atom type pairs I,J and I != J, the epsilon and sigma coefficients +and cutoff distance for all of the lj/cut pair styles can be mixed. +The default mix value is *geometric*. See the "pair_modify" command +for details. + +All of the *lj/cut* pair styles support the +:doc:`pair_modify ` shift option for the energy of the +Lennard-Jones portion of the pair interaction. + +All of the *lj/cut* pair styles support the +:doc:`pair_modify ` tail option for adding a long-range +tail correction to the energy and pressure for the Lennard-Jones +portion of the pair interaction. + +All of the *lj/cut* pair styles write their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do +not need to be specified in an input script that reads a restart file. + +The *lj/cut* pair styles support the use of the +*inner*, *middle*, and *outer* keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be +partitioned by distance at different levels of the rRESPA hierarchy. +The other styles only support the *pair* keyword of run_style respa. +See the :doc:`run_style ` command for details. + +---------- + +Related commands +"""""""""""""""" + +* :doc:`pair_coeff ` +* :doc:`pair_style lj/cut/coul/cut ` +* :doc:`pair_style lj/cut/coul/debye ` +* :doc:`pair_style lj/cut/coul/dsf ` +* :doc:`pair_style lj/cut/coul/long ` +* :doc:`pair_style lj/cut/coul/msm ` +* :doc:`pair_style lj/cut/coul/wolf ` +* :doc:`pair_style lj/cut/tip4p/cut ` +* :doc:`pair_style lj/cut/tip4p/long ` + +Default +""""""" + +none From cfe08ba55f8cb570d8d327821b8cd72e9ee3ac8e Mon Sep 17 00:00:00 2001 From: Daniele Date: Fri, 12 Nov 2021 10:32:04 +0100 Subject: [PATCH 06/57] working on the manual --- doc/src/pair_smatb.rst | 51 +++--------------------------------------- src/pair_smatb.h | 4 ++-- 2 files changed, 5 insertions(+), 50 deletions(-) diff --git a/doc/src/pair_smatb.rst b/doc/src/pair_smatb.rst index fb42fe0b7a..0a54e124e0 100644 --- a/doc/src/pair_smatb.rst +++ b/doc/src/pair_smatb.rst @@ -34,9 +34,9 @@ given by .. math:: - E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - - \left(\frac{\sigma}{r}\right)^6 \right] - \qquad r < r_c + E_i = + \sum_{j,R_{ij}\leq R_c} A e^{-p \left(\frac{R_{ij}}{R_{0}}-1\right)} + -\sqrt{\sum_{j,R_{ij}\leq R_c}\Xi^2 e^{-2q\left(\frac{R_{ij}}{R_{0}}-1\right)}}. :math:`r_c` is the cutoff. @@ -62,43 +62,6 @@ distance for the potential, not as the energy minimum at :math:`2^{\frac{1}{6}} The last coefficient is optional. If not specified, the global LJ cutoff specified in the pair_style command are used. ----------- - -A version of these styles with a soft core, *lj/cut/soft*, suitable -for use in free energy calculations, is part of the FEP package and -is documented with the :doc:`pair_style */soft ` -styles. - ----------- - -.. include:: accel_styles.rst - ----------- - -Mixing, shift, table, tail correction, restart, rRESPA info -""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" - -For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for all of the lj/cut pair styles can be mixed. -The default mix value is *geometric*. See the "pair_modify" command -for details. - -All of the *lj/cut* pair styles support the -:doc:`pair_modify ` shift option for the energy of the -Lennard-Jones portion of the pair interaction. - -All of the *lj/cut* pair styles support the -:doc:`pair_modify ` tail option for adding a long-range -tail correction to the energy and pressure for the Lennard-Jones -portion of the pair interaction. - -All of the *lj/cut* pair styles write their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do -not need to be specified in an input script that reads a restart file. - -The *lj/cut* pair styles support the use of the -*inner*, *middle*, and *outer* keywords of the :doc:`run_style respa ` command, meaning the pairwise forces can be -partitioned by distance at different levels of the rRESPA hierarchy. -The other styles only support the *pair* keyword of run_style respa. See the :doc:`run_style ` command for details. ---------- @@ -107,14 +70,6 @@ Related commands """""""""""""""" * :doc:`pair_coeff ` -* :doc:`pair_style lj/cut/coul/cut ` -* :doc:`pair_style lj/cut/coul/debye ` -* :doc:`pair_style lj/cut/coul/dsf ` -* :doc:`pair_style lj/cut/coul/long ` -* :doc:`pair_style lj/cut/coul/msm ` -* :doc:`pair_style lj/cut/coul/wolf ` -* :doc:`pair_style lj/cut/tip4p/cut ` -* :doc:`pair_style lj/cut/tip4p/long ` Default """"""" diff --git a/src/pair_smatb.h b/src/pair_smatb.h index d87546ecd1..a18392fab1 100644 --- a/src/pair_smatb.h +++ b/src/pair_smatb.h @@ -74,8 +74,8 @@ class PairSMATB : public Pair { /* latex form of the potential (R_c is cutOffEnd, \Xi is QSI): E_i = - \sum_{j,R_{ij}\leq R_c} A e^{-p \lrt{\frac{R_{ij}}{R_{0}}-1}} - -\sqrt{\sum_{j,R_{ij}\leq R_c}\Xi^2 e^{-2q\lrt{\frac{R_{ij}}{R_{0}}-1}}}. + \sum_{j,R_{ij}\leq R_c} A e^{-p \left(\frac{R_{ij}}{R_{0}}-1\right)} + -\sqrt{\sum_{j,R_{ij}\leq R_c}\Xi^2 e^{-2q\left(\frac{R_{ij}}{R_{0}}-1\right)}}. NB::this form does not have the polynomial link to 0 for the cut off */ From bfc34023b1de89080393696fd22149ca5d7a7929 Mon Sep 17 00:00:00 2001 From: Daniele Date: Fri, 12 Nov 2021 12:01:05 +0100 Subject: [PATCH 07/57] working on the documentation --- doc/src/Commands_pair.rst | 2 ++ doc/src/pair_smatb.rst | 67 +++++++++++++++++++++++++++++---------- 2 files changed, 53 insertions(+), 16 deletions(-) diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index 7cf4e7635b..84c414abb2 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -240,6 +240,8 @@ OPT. * :doc:`rebo (io) ` * :doc:`resquared (go) ` * :doc:`sdpd/taitwater/isothermal ` + * :doc:`smatb ` + * :doc:`smatb/single` * :doc:`smd/hertz ` * :doc:`smd/tlsph ` * :doc:`smd/tri_surface ` diff --git a/doc/src/pair_smatb.rst b/doc/src/pair_smatb.rst index 0a54e124e0..ae9317732d 100644 --- a/doc/src/pair_smatb.rst +++ b/doc/src/pair_smatb.rst @@ -4,6 +4,9 @@ pair_style smatb command ========================= +pair_style smatb/single command +=============================== + Syntax """""" @@ -23,26 +26,34 @@ Examples .. code-block:: LAMMPS - pair_style smatb 2.5 + pair_style smatb pair_coeff 1 1 2.88 10.35 4.178 0.210 1.818 4.07293506 4.9883063257983666 Description """"""""""" -The *lj/cut* styles compute the standard 12/6 Lennard-Jones potential, +The *smatb* styles compute the Second Moment Aproximation to the Tight Binding +:ref:`(Cyrot) `, :ref:`(Gupta) `, :ref:`(Rosato) `, given by .. math:: - E_i = - \sum_{j,R_{ij}\leq R_c} A e^{-p \left(\frac{R_{ij}}{R_{0}}-1\right)} - -\sqrt{\sum_{j,R_{ij}\leq R_c}\Xi^2 e^{-2q\left(\frac{R_{ij}}{R_{0}}-1\right)}}. + E_{ik} &= A e^{-p \left(\frac{R_{ik}}{R_{0}}-1\right)} -\sqrt{ + \sum_{j,R_{ij}\leq R_c}\Xi^2 + e^{-2q\left(\frac{R_{ij}}{R_{0}}-1\right)}}.\qquad R_{ij} < R_{sc}\\ + E_{ik} &=\left(a_3\left(R_{ik}-R_c\right)^3 + +a_4\left(R_{ik}-R_c\right)^4 + +a_5\left(R_{ik}-R_c\right)^5\right) -\sqrt{ + \sum_{j,R_{ij}\left( + x_3\left(R_{ij}-R_c\right)^3 + +x_4\left(R_{ij}-R_c\right)^4 + +x_5\left(R_{ij}-R_c\right)^5 + \right)^2}. \qquad R_{sc} < R_{ij} < r_c -:math:`r_c` is the cutoff. +The polynomial coefficients a3, a4, a5, x3, x4, x5 are computed by LAMMPS smoothly +link the two exponential to zero from the inner cutoff :math:`R_{sc}` to the +outer cutoff :math:`R_c`. -See the :doc:`lj/cut/coul ` styles to add a Coulombic -pairwise interaction and the :doc:`lj/cut/tip4p ` styles to -add the TIP4P water model. Coefficients """""""""""" @@ -52,15 +63,24 @@ The following coefficients must be defined for each pair of atoms types via the file or restart files read by the :doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: -* :math:`\epsilon` (energy units) -* :math:`\sigma` (distance units) -* LJ cutoff (distance units) +* :math:`R_{0}` (distance units) +* :math:`p` +* :math:`q` +* :math:`A` (energy units) +* :math:`\Xi` (energy units) +* :math:`R_{cs}` (distance units) +* :math:`R_c` (distance units) -Note that :math:`\sigma` is defined in the LJ formula as the zero-crossing -distance for the potential, not as the energy minimum at :math:`2^{\frac{1}{6}} \sigma`. -The last coefficient is optional. If not specified, the global -LJ cutoff specified in the pair_style command are used. +Note that : when :math:`R_{cs} < R_{ij} < R_c` the exponentials are substituted +by a polynomial in the form: +:math:`P(R_{ij}) = P_3\left(R_{ij}-R_c\right)^3+P_4\left(R_{ij}-R_c\right)^4+P_5\left(R_{ij}-R_c\right)^5`, +where :math:`P_3`, :math:`P_4` nd :math:`P_5` are calculated at the +initialization of the potential in order to guarantee the continuity of the +function, of the first and of the second derivateves in :math:`R_{cs}`, +moreover the vaule of :math:`P(R_{ij})` and of its first and second derivative +is automatically zero in the end of the cutoff :math:`R_c` due to its polynomial +form. See the :doc:`run_style ` command for details. @@ -75,3 +95,18 @@ Default """"""" none + +---------- + +.. _Cyrot: + +**(Cyrot)** Cyrot-Lackmann and Ducastelle, Phys Rev. B, 4, 2406-2412 (1971). + +.. _Gupta: + +**(Gupta)** Gupta ,Phys Rev. B, 23, 6265-6270 (1981). + +.. _Rosato: + +**(Rosato)** Rosato and Guillope and Legrand, Philosophical Magazine A, 59.2, 321-336 (1989). + From fe5f00bbeaf9f354df1fbfd2b3f92dbcc6dbfc77 Mon Sep 17 00:00:00 2001 From: Daniele Date: Fri, 12 Nov 2021 14:37:16 +0100 Subject: [PATCH 08/57] Updating the documentation, now 'make html' do not give errors --- doc/src/Commands_pair.rst | 2 +- doc/src/pair_smatb.rst | 50 +++++++++++++++++++-------------------- doc/src/pair_style.rst | 2 ++ 3 files changed, 28 insertions(+), 26 deletions(-) diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index 84c414abb2..4fc9e083e4 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -241,7 +241,7 @@ OPT. * :doc:`resquared (go) ` * :doc:`sdpd/taitwater/isothermal ` * :doc:`smatb ` - * :doc:`smatb/single` + * :doc:`smatb/single ` * :doc:`smd/hertz ` * :doc:`smd/tlsph ` * :doc:`smd/tri_surface ` diff --git a/doc/src/pair_smatb.rst b/doc/src/pair_smatb.rst index ae9317732d..ac9ecbfb75 100644 --- a/doc/src/pair_smatb.rst +++ b/doc/src/pair_smatb.rst @@ -27,32 +27,32 @@ Examples .. code-block:: LAMMPS pair_style smatb - pair_coeff 1 1 2.88 10.35 4.178 0.210 1.818 4.07293506 4.9883063257983666 + pair_coeff 1 1 2.88 10.35 4.178 0.210 1.818 4.07293506 4.9883063257983666 + Description """"""""""" -The *smatb* styles compute the Second Moment Aproximation to the Tight Binding +The *smatb* styles compute the Second Moment Approximation to the Tight Binding :ref:`(Cyrot) `, :ref:`(Gupta) `, :ref:`(Rosato) `, given by .. math:: - E_{ik} &= A e^{-p \left(\frac{R_{ik}}{R_{0}}-1\right)} -\sqrt{ - \sum_{j,R_{ij}\leq R_c}\Xi^2 - e^{-2q\left(\frac{R_{ij}}{R_{0}}-1\right)}}.\qquad R_{ij} < R_{sc}\\ - E_{ik} &=\left(a_3\left(R_{ik}-R_c\right)^3 - +a_4\left(R_{ik}-R_c\right)^4 - +a_5\left(R_{ik}-R_c\right)^5\right) -\sqrt{ - \sum_{j,R_{ij}\left( - x_3\left(R_{ij}-R_c\right)^3 - +x_4\left(R_{ij}-R_c\right)^4 - +x_5\left(R_{ij}-R_c\right)^5 - \right)^2}. \qquad R_{sc} < R_{ij} < r_c + E_{ik} =\left\lbrace\begin{array}{ll} + A e^{-p \left(\frac{R_{ik}}{R_{0}}-1\right)} + -\sqrt{\sum_{j,R_{ij}\leq R_c}\Xi^2e^{-2q\left(\frac{R_{ij}}{R_{0}}-1\right)}}& R_{ij} < R_{sc}\\ + {\left(a_3\left(R_{ik}-R_c\right)^3+a_4\left(R_{ik}-R_c\right)^4 + +a_5\left(R_{ik}-R_c\right)^5\right) + -\sqrt{\sum_{j,R_{ij}\leq R_c}\left(x_3\left(R_{ij}-R_c\right)^3 + +x_4\left(R_{ij}-R_c\right)^4+x_5\left(R_{ij}-R_c\right)^5\right)^2}} & R_{sc} < R_{ij} < r_c + \end{array} + \right. -The polynomial coefficients a3, a4, a5, x3, x4, x5 are computed by LAMMPS smoothly -link the two exponential to zero from the inner cutoff :math:`R_{sc}` to the -outer cutoff :math:`R_c`. +The polynomial coefficients :math:`a_3`, :math:`a_4`, :math:`a_5`, :math:`x_3`, +:math:`x_4`, :math:`x_5` are computed by LAMMPS smoothly +link the two exponentials and their first and second order derivatives to zero +from the inner cutoff :math:`R_{sc}` to the outer cutoff :math:`R_c`. Coefficients @@ -72,20 +72,20 @@ file or restart files read by the :doc:`read_data ` or * :math:`R_c` (distance units) -Note that : when :math:`R_{cs} < R_{ij} < R_c` the exponentials are substituted -by a polynomial in the form: -:math:`P(R_{ij}) = P_3\left(R_{ij}-R_c\right)^3+P_4\left(R_{ij}-R_c\right)^4+P_5\left(R_{ij}-R_c\right)^5`, -where :math:`P_3`, :math:`P_4` nd :math:`P_5` are calculated at the -initialization of the potential in order to guarantee the continuity of the -function, of the first and of the second derivateves in :math:`R_{cs}`, -moreover the vaule of :math:`P(R_{ij})` and of its first and second derivative -is automatically zero in the end of the cutoff :math:`R_c` due to its polynomial -form. +Note that: :math:`R_{0}` is the nearest neighbour distance, usually coincides +with the diameter of the atoms See the :doc:`run_style ` command for details. ---------- +Mixing info +""""""""""" + +For atom type pairs I,J and I != J the coefficients are not automatically mixed. + +---------- + Related commands """""""""""""""" diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 1cf033ddba..5e9bc918ad 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -304,6 +304,8 @@ accelerated styles exist. * :doc:`rebo ` - second generation REBO potential of Brenner * :doc:`resquared ` - Everaers RE-Squared ellipsoidal potential * :doc:`sdpd/taitwater/isothermal ` - smoothed dissipative particle dynamics for water at isothermal conditions +* :doc:`smatb ` - Second Moment Approximation to the Tight Binding +* :doc:`smatb/single ` - Second Moment Approximation to the Tight Binding for single-element systems * :doc:`smd/hertz ` - * :doc:`smd/tlsph ` - * :doc:`smd/tri_surface ` - From 0eb227e7dea8ab22626fd3d1ba625aed3804a78f Mon Sep 17 00:00:00 2001 From: Daniele Date: Fri, 12 Nov 2021 14:55:48 +0100 Subject: [PATCH 09/57] working on the documentation --- doc/src/pair_smatb.rst | 26 ++++++++++++++------------ 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/doc/src/pair_smatb.rst b/doc/src/pair_smatb.rst index ac9ecbfb75..d79eff5603 100644 --- a/doc/src/pair_smatb.rst +++ b/doc/src/pair_smatb.rst @@ -27,7 +27,7 @@ Examples .. code-block:: LAMMPS pair_style smatb - pair_coeff 1 1 2.88 10.35 4.178 0.210 1.818 4.07293506 4.9883063257983666 + paiR_{c}oeff 1 1 2.88 10.35 4.178 0.210 1.818 4.07293506 4.9883063257983666 Description @@ -41,35 +41,37 @@ given by E_{ik} =\left\lbrace\begin{array}{ll} A e^{-p \left(\frac{R_{ik}}{R_{0}}-1\right)} - -\sqrt{\sum_{j,R_{ij}\leq R_c}\Xi^2e^{-2q\left(\frac{R_{ij}}{R_{0}}-1\right)}}& R_{ij} < R_{sc}\\ - {\left(a_3\left(R_{ik}-R_c\right)^3+a_4\left(R_{ik}-R_c\right)^4 - +a_5\left(R_{ik}-R_c\right)^5\right) - -\sqrt{\sum_{j,R_{ij}\leq R_c}\left(x_3\left(R_{ij}-R_c\right)^3 - +x_4\left(R_{ij}-R_c\right)^4+x_5\left(R_{ij}-R_c\right)^5\right)^2}} & R_{sc} < R_{ij} < r_c + -\sqrt{\sum_{j,R_{ij}\leq R_{c}}\Xi^2e^{-2q\left(\frac{R_{ij}}{R_{0}}-1\right)}}& R_{ij} < R_{sc}\\ + {\left(a_3\left(R_{ik}-R_{c}\right)^3+a_4\left(R_{ik}-R_{c}\right)^4 + +a_5\left(R_{ik}-R_{c}\right)^5\right) + -\sqrt{\sum_{j,R_{ij}\leq R_{c}}\left(x_3\left(R_{ij}-R_{c}\right)^3 + +x_4\left(R_{ij}-R_{c}\right)^4+x_5\left(R_{ij}-R_{c}\right)^5\right)^2}} & R_{sc} < R_{ij} < R_{c} \end{array} \right. The polynomial coefficients :math:`a_3`, :math:`a_4`, :math:`a_5`, :math:`x_3`, :math:`x_4`, :math:`x_5` are computed by LAMMPS smoothly link the two exponentials and their first and second order derivatives to zero -from the inner cutoff :math:`R_{sc}` to the outer cutoff :math:`R_c`. +from the inner cutoff :math:`R_{sc}` to the outer cutoff :math:`R_{c}`. + +:math:`R_{ik}` is the distance between the atom :math:`i` and :math:`k` Coefficients """""""""""" The following coefficients must be defined for each pair of atoms types via the -:doc:`pair_coeff ` command as in the examples above, or in the data +:doc:`paiR_{c}oeff ` command as in the examples above, or in the data file or restart files read by the :doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * :math:`R_{0}` (distance units) -* :math:`p` -* :math:`q` +* :math:`p` (dimensionless) +* :math:`q` (dimensionless) * :math:`A` (energy units) * :math:`\Xi` (energy units) * :math:`R_{cs}` (distance units) -* :math:`R_c` (distance units) +* :math:`R_{c}` (distance units) Note that: :math:`R_{0}` is the nearest neighbour distance, usually coincides @@ -89,7 +91,7 @@ For atom type pairs I,J and I != J the coefficients are not automatically mixed. Related commands """""""""""""""" -* :doc:`pair_coeff ` +* :doc:`paiR_{c}oeff ` Default """"""" From 7a914c84d7ce2f4ae3f9840e104fe143883ddf33 Mon Sep 17 00:00:00 2001 From: Daniele Date: Fri, 12 Nov 2021 16:25:48 +0100 Subject: [PATCH 10/57] again correction in the documentation --- doc/src/pair_smatb.rst | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/doc/src/pair_smatb.rst b/doc/src/pair_smatb.rst index d79eff5603..3b2c578d55 100644 --- a/doc/src/pair_smatb.rst +++ b/doc/src/pair_smatb.rst @@ -27,7 +27,7 @@ Examples .. code-block:: LAMMPS pair_style smatb - paiR_{c}oeff 1 1 2.88 10.35 4.178 0.210 1.818 4.07293506 4.9883063257983666 + pair_coeff 1 1 2.88 10.35 4.178 0.210 1.818 4.07293506 4.9883063257983666 Description @@ -41,11 +41,13 @@ given by E_{ik} =\left\lbrace\begin{array}{ll} A e^{-p \left(\frac{R_{ik}}{R_{0}}-1\right)} - -\sqrt{\sum_{j,R_{ij}\leq R_{c}}\Xi^2e^{-2q\left(\frac{R_{ij}}{R_{0}}-1\right)}}& R_{ij} < R_{sc}\\ + -\sqrt{\sum_{j,R_{ij}\leq R_{c}}\Xi^2 + e^{-2q\left(\frac{R_{ij}}{R_{0}}-1\right)}}& R_{ij} < R_{sc}\\ {\left(a_3\left(R_{ik}-R_{c}\right)^3+a_4\left(R_{ik}-R_{c}\right)^4 +a_5\left(R_{ik}-R_{c}\right)^5\right) -\sqrt{\sum_{j,R_{ij}\leq R_{c}}\left(x_3\left(R_{ij}-R_{c}\right)^3 - +x_4\left(R_{ij}-R_{c}\right)^4+x_5\left(R_{ij}-R_{c}\right)^5\right)^2}} & R_{sc} < R_{ij} < R_{c} + +x_4\left(R_{ij}-R_{c}\right)^4+x_5\left(R_{ij}-R_{c}\right)^5\right)^2}} + & R_{sc} < R_{ij} < R_{c} \end{array} \right. @@ -61,7 +63,7 @@ Coefficients """""""""""" The following coefficients must be defined for each pair of atoms types via the -:doc:`paiR_{c}oeff ` command as in the examples above, or in the data +:doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the :doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: @@ -88,10 +90,15 @@ For atom type pairs I,J and I != J the coefficients are not automatically mixed. ---------- +Restrictions +"""""""""""" + +none + Related commands """""""""""""""" -* :doc:`paiR_{c}oeff ` +* :doc:`pair_coeff ` Default """"""" From b06a70c33c47417e9050270cc93fb28d5f91db29 Mon Sep 17 00:00:00 2001 From: Daniele Date: Thu, 18 Nov 2021 12:40:10 +0100 Subject: [PATCH 11/57] corrected some errors in the manual --- doc/src/pair_smatb.rst | 36 +++++++++++++++++++++--------------- 1 file changed, 21 insertions(+), 15 deletions(-) diff --git a/doc/src/pair_smatb.rst b/doc/src/pair_smatb.rst index 3b2c578d55..ca9a1fde77 100644 --- a/doc/src/pair_smatb.rst +++ b/doc/src/pair_smatb.rst @@ -38,27 +38,33 @@ The *smatb* styles compute the Second Moment Approximation to the Tight Binding given by .. math:: + E_{i} = \sum_{j,R_{ij}\leq R_{c}} \alpha(R_{ij}) - \sqrt{\sum_{j,R_{ij}\leq R_{c}}\Xi^2(R_{ij})} - E_{ik} =\left\lbrace\begin{array}{ll} - A e^{-p \left(\frac{R_{ik}}{R_{0}}-1\right)} - -\sqrt{\sum_{j,R_{ij}\leq R_{c}}\Xi^2 - e^{-2q\left(\frac{R_{ij}}{R_{0}}-1\right)}}& R_{ij} < R_{sc}\\ - {\left(a_3\left(R_{ik}-R_{c}\right)^3+a_4\left(R_{ik}-R_{c}\right)^4 - +a_5\left(R_{ik}-R_{c}\right)^5\right) - -\sqrt{\sum_{j,R_{ij}\leq R_{c}}\left(x_3\left(R_{ij}-R_{c}\right)^3 - +x_4\left(R_{ij}-R_{c}\right)^4+x_5\left(R_{ij}-R_{c}\right)^5\right)^2}} - & R_{sc} < R_{ij} < R_{c} +:math:`R_{ij}` is the distance between the atom :math:`i` and :math:`j`. +And the two functions :math:`\alpha\left(r\right)` and :math:`\Xi\left(r\right)` are: + +.. math:: + \alpha\left(r\right)=\left\lbrace\begin{array}{ll} + A e^{-p \left(\frac{r}{R_{0}}-1\right)} & r < R_{sc}\\ + a_3\left(r-R_{c}\right)^3+a_4\left(r-R_{c}\right)^4 + +a_5\left(r-R_{c}\right)^5& R_{sc} < r < R_{c} \end{array} \right. +.. math:: + \Xi\left(r\right)=\left\lbrace\begin{array}{ll} + \xi e^{-q \left(\frac{r}{R_{0}}-1\right)} & r < R_{sc}\\ + x_3\left(r-R_{c}\right)^3+x_4\left(r-R_{c}\right)^4 + +x_5\left(r-R_{c}\right)^5& R_{sc} < r < R_{c} + \end{array} + \right. + + The polynomial coefficients :math:`a_3`, :math:`a_4`, :math:`a_5`, :math:`x_3`, -:math:`x_4`, :math:`x_5` are computed by LAMMPS smoothly -link the two exponentials and their first and second order derivatives to zero +:math:`x_4`, :math:`x_5` are computed by LAMMPS: the two exponentials and their +first and second order derivatives are smoothly linked to zero, from the inner cutoff :math:`R_{sc}` to the outer cutoff :math:`R_{c}`. -:math:`R_{ik}` is the distance between the atom :math:`i` and :math:`k` - - Coefficients """""""""""" @@ -71,7 +77,7 @@ file or restart files read by the :doc:`read_data ` or * :math:`p` (dimensionless) * :math:`q` (dimensionless) * :math:`A` (energy units) -* :math:`\Xi` (energy units) +* :math:`\xi` (energy units) * :math:`R_{cs}` (distance units) * :math:`R_{c}` (distance units) From a5df4941764d99624c6d801040217646615e8c77 Mon Sep 17 00:00:00 2001 From: Daniele Date: Thu, 18 Nov 2021 14:30:26 +0100 Subject: [PATCH 12/57] added examples --- examples/smatb/AgCuPancake.data | 48 + examples/smatb/dump.smatb | 8600 +++++++++++++++++ examples/smatb/in.smatb.BulkFCC | 27 + examples/smatb/in.smatbNP | 38 + .../smatb/log.27Oct21.smatbAgCuPancake.g++ | 1127 +++ examples/smatb/log.27Oct21.smatbBulkFCC.g++ | 160 + src/pair_smatb.h | 6 +- src/pair_smatb_single.h | 6 +- 8 files changed, 10010 insertions(+), 2 deletions(-) create mode 100644 examples/smatb/AgCuPancake.data create mode 100644 examples/smatb/dump.smatb create mode 100644 examples/smatb/in.smatb.BulkFCC create mode 100644 examples/smatb/in.smatbNP create mode 100644 examples/smatb/log.27Oct21.smatbAgCuPancake.g++ create mode 100644 examples/smatb/log.27Oct21.smatbBulkFCC.g++ diff --git a/examples/smatb/AgCuPancake.data b/examples/smatb/AgCuPancake.data new file mode 100644 index 0000000000..09f732b4e9 --- /dev/null +++ b/examples/smatb/AgCuPancake.data @@ -0,0 +1,48 @@ +# AgCu Pancake : energy should be around -90.16 eV +34 atoms +2 atom types +0 30 xlo xhi +0 30 ylo yhi +0 30 zlo zhi + +Masses + +1 108 # Ag +2 64 # Cu + +Atoms # atomic + +1 1 11.8677744 17.4748811 16.8202155 +2 1 14.4591543 12.6388264 17.3769114 +3 1 19.2905996 14.8698601 15.9074284 +4 1 13.6418392 11.2583912 15.0376329 +5 1 16.5295136 18.8875825 16.3408808 +6 1 11.4394217 12.6680604 13.934792 +7 1 17.1772792 13.4579369 17.0971284 +8 1 11.7477198 12.5836832 16.6835448 +9 1 12.3254647 15.127665 12.9151285 +10 1 11.5595413 17.5592601 14.0713777 +11 1 18.9820568 14.9536515 13.1587506 +12 1 14.5653354 15.1189885 11.12255 +13 1 14.5797485 17.250847 17.5049696 +14 1 13.9305528 12.7833817 12.6633235 +15 1 12.8538576 14.9830633 17.6286053 +16 1 16.7229337 16.4525301 12.4627193 +17 1 14.0512024 17.3954338 12.7914031 +18 1 18.2824041 17.2316517 14.6999911 +19 1 16.2210303 18.9719703 13.5921161 +20 1 17.2517138 16.3080477 17.1761679 +21 1 16.0269821 11.057668 13.3712031 +22 1 16.3354169 10.9735982 16.1199203 +23 1 13.9149278 18.8223918 15.2392839 +24 1 18.1136886 12.5568867 14.5759053 +25 1 16.6484505 13.6019749 12.3834541 +26 1 11.0468778 15.1307677 15.4471491 +27 1 15.4347551 14.8811145 18.8773723 +28 2 15.1502129 14.9589199 16.3394186 +29 2 13.2837251 13.9076768 15.1588849 +30 2 13.4425035 16.3005712 15.2145264 +31 2 15.7534979 16.8960911 14.9738557 +32 2 15.4967806 13.024304 14.8837423 +33 2 14.8498337 15.0410649 13.6605697 +34 2 17.0232044 14.8712576 14.7690776 diff --git a/examples/smatb/dump.smatb b/examples/smatb/dump.smatb new file mode 100644 index 0000000000..7e046da126 --- /dev/null +++ b/examples/smatb/dump.smatb @@ -0,0 +1,8600 @@ +ITEM: TIMESTEP +50 +ITEM: NUMBER OF ATOMS +34 +ITEM: BOX BOUNDS pp pp pp +0.0000000000000000e+00 3.0000000000000000e+01 +0.0000000000000000e+00 3.0000000000000000e+01 +0.0000000000000000e+00 3.0000000000000000e+01 +ITEM: ATOMS id type xs ys zs +6 1 0.370674 0.420404 0.47149 +14 1 0.460672 0.41852 0.432087 +11 1 0.639652 0.504553 0.436168 +21 1 0.540601 0.374123 0.443148 +24 1 0.60701 0.421969 0.486349 +25 1 0.566436 0.459227 0.413766 +32 2 0.519564 0.437082 0.49495 +34 2 0.56935 0.500032 0.491838 +9 1 0.414161 0.497752 0.432411 +10 1 0.374355 0.574559 0.469254 +12 1 0.490502 0.499703 0.37824 +17 1 0.473407 0.578249 0.422754 +33 2 0.497297 0.503375 0.458739 +16 1 0.561339 0.560137 0.419936 +18 1 0.616909 0.575654 0.489699 +19 1 0.537545 0.642161 0.455445 +31 2 0.524729 0.566645 0.49895 +2 1 0.473742 0.420536 0.579327 +4 1 0.450202 0.371666 0.506856 +8 1 0.380988 0.421172 0.560588 +15 1 0.418899 0.498224 0.583519 +29 2 0.437456 0.457696 0.509079 +3 1 0.647934 0.491881 0.524905 +7 1 0.572877 0.44522 0.568745 +22 1 0.539329 0.366444 0.529206 +27 1 0.516313 0.492195 0.622096 +28 2 0.500476 0.497512 0.54372 +1 1 0.393266 0.591305 0.55498 +13 1 0.491759 0.576225 0.582494 +23 1 0.46575 0.63209 0.510436 +26 1 0.358202 0.500111 0.514116 +30 2 0.442022 0.540367 0.508884 +5 1 0.562491 0.628751 0.540272 +20 1 0.580384 0.535563 0.568062 +ITEM: TIMESTEP +100 +ITEM: NUMBER OF ATOMS +34 +ITEM: BOX BOUNDS pp pp pp +0.0000000000000000e+00 3.0000000000000000e+01 +0.0000000000000000e+00 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a/examples/smatb/in.smatb.BulkFCC b/examples/smatb/in.smatb.BulkFCC new file mode 100644 index 0000000000..286ee2accf --- /dev/null +++ b/examples/smatb/in.smatb.BulkFCC @@ -0,0 +1,27 @@ +# -*- lammps -*- + +units metal +atom_style atomic +boundary p p p + +lattice fcc 4.0782 + +region myreg block 0 8 0 8 0 8 + +create_box 1 myreg + +create_atoms 1 box + +mass 1 196.96655 # Au + +pair_style smatb/single +pair_coeff 1 1 2.88 10.35 4.178 0.210 1.818 4.07293506 4.9883063257983666 + +neighbor 8.0 bin +neigh_modify every 1 delay 0 check yes + +thermo 1 +fix boxmin all box/relax iso 1.0 +minimize 1.0e-8 1.0e-10 10000 100000 +unfix boxmin +minimize 1.0e-8 1.0e-10 10000 100000 diff --git a/examples/smatb/in.smatbNP b/examples/smatb/in.smatbNP new file mode 100644 index 0000000000..9a03a3d994 --- /dev/null +++ b/examples/smatb/in.smatbNP @@ -0,0 +1,38 @@ +# -*- lammps -*- + +units metal +atom_style atomic +boundary p p p + +read_data AgCuPancake.data + +pair_style smatb +# NN p q a qsi cutOff_Start cutOff_End +pair_coeff 1 1 2.89 10.85 3.18 0.1031 1.1895 4.08707719 5.0056268338740553 +pair_coeff 1 2 2.725 10.70 2.805 0.0977 1.2275 4.08707719 4.4340500673763259 +pair_coeff 2 2 2.56 10.55 2.43 0.0894 1.2799 3.62038672 4.4340500673763259 + + +neighbor 8.0 bin +neigh_modify every 1 delay 0 check yes + +thermo 1 +minimize 1.0e-8 1.0e-10 10000 100000 + +velocity all create 600.0 761341 rot yes mom yes + +fix 1 all nve +thermo 10 +timestep 0.005 + +#dump 1 all atom 50 dump.smatb + +#dump 2 all image 10 image.*.jpg element element & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 element Si C + +#dump 3 all movie 10 movie.mpg element element & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 element Si C + +run 10000 \ No newline at end of file diff --git a/examples/smatb/log.27Oct21.smatbAgCuPancake.g++ b/examples/smatb/log.27Oct21.smatbAgCuPancake.g++ new file mode 100644 index 0000000000..bd162728f2 --- /dev/null +++ b/examples/smatb/log.27Oct21.smatbAgCuPancake.g++ @@ -0,0 +1,1127 @@ +LAMMPS (27 Oct 2021) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# -*- lammps -*- + +units metal +atom_style atomic +boundary p p p + +read_data AgCuPancake.data +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (30.000000 30.000000 30.000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 34 atoms + read_data CPU = 0.000 seconds + +pair_style smatb +# NN p q a qsi cutOff_Start cutOff_End +pair_coeff 1 1 2.89 10.85 3.18 0.1031 1.1895 4.08707719 5.0056268338740553 +pair_coeff 1 2 2.725 10.70 2.805 0.0977 1.2275 4.08707719 4.4340500673763259 +pair_coeff 2 2 2.56 10.55 2.43 0.0894 1.2799 3.62038672 4.4340500673763259 + + +neighbor 8.0 bin +neigh_modify every 1 delay 0 check yes + +thermo 1 +minimize 1.0e-8 1.0e-10 10000 100000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 13.005627 + ghost atom cutoff = 13.005627 + binsize = 6.5028134, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair smatb, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.186 | 4.186 | 4.186 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -90.165962 0 -90.165962 0.15999216 + 1 0 -90.165962 0 -90.165962 0.016319576 +Loop time of 6.8907e-05 on 1 procs for 1 steps with 34 atoms + +98.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -90.1659620528124 -90.1659620528124 -90.1659622946346 + Force two-norm initial, final = 0.0024917172 0.0017840646 + Force max component initial, final = 0.00098891473 0.00054742198 + Final line search alpha, max atom move = 1.0000000 0.00054742198 + Iterations, force evaluations = 1 2 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.6089e-05 | 5.6089e-05 | 5.6089e-05 | 0.0 | 81.40 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 1.725e-06 | 1.725e-06 | 1.725e-06 | 0.0 | 2.50 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.109e-05 | | | 16.10 + +Nlocal: 34.0000 ave 34 max 34 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 56.0000 ave 56 max 56 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 561.000 ave 561 max 561 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 561 +Ave neighs/atom = 16.500000 +Neighbor list builds = 0 +Dangerous builds = 0 + +velocity all create 600.0 761341 rot yes mom yes + +fix 1 all nve +thermo 10 +timestep 0.005 + +#dump 1 all atom 50 dump.smatb + +#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 element Si C + +#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 element Si C + +run 10000 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Per MPI rank memory allocation (min/avg/max) = 3.061 | 3.061 | 3.061 Mbytes +Step Temp E_pair E_mol TotEng Press + 1 600 -90.165962 0 -87.606611 101.26402 + 10 298.0506 -88.871794 0 -87.600434 548.48617 + 20 248.60946 -88.662484 0 -87.602019 90.486083 + 30 221.44826 -88.545423 0 -87.600817 -508.39815 + 40 228.33268 -88.575214 0 -87.601242 -589.39365 + 50 245.7154 -88.649826 0 -87.601706 65.305495 + 60 273.03023 -88.765916 0 -87.601283 398.01803 + 70 366.50025 -89.166263 0 -87.602925 207.77985 + 80 276.91193 -88.782331 0 -87.60114 8.3684522 + 90 307.868 -88.915252 0 -87.602015 -304.72741 + 100 322.45302 -88.977777 0 -87.602327 -205.15812 + 110 303.31578 -88.896089 0 -87.60227 260.03553 + 120 269.99988 -88.753066 0 -87.601359 351.68785 + 130 286.8011 -88.825253 0 -87.601879 -64.479292 + 140 287.40216 -88.827221 0 -87.601282 -315.09505 + 150 328.85371 -89.004517 0 -87.601764 -298.80386 + 160 284.47173 -88.814826 0 -87.601388 358.1389 + 170 280.279 -88.797886 0 -87.602332 467.92358 + 180 311.43691 -88.931598 0 -87.603138 -77.489811 + 190 193.15923 -88.423986 0 -87.600048 -425.5563 + 200 304.96368 -88.902942 0 -87.602094 -596.60958 + 210 302.68927 -88.892198 0 -87.601051 91.636064 + 220 309.19801 -88.920064 0 -87.601153 621.21354 + 230 380.73063 -89.22681 0 -87.602771 447.14396 + 240 284.74877 -88.816012 0 -87.601392 -119.01968 + 250 238.52309 -88.61849 0 -87.601049 -501.65646 + 260 259.11102 -88.707412 0 -87.602152 -368.93359 + 270 251.74586 -88.674842 0 -87.600999 175.03119 + 280 382.00434 -89.231874 0 -87.602403 290.82425 + 290 310.3687 -88.924886 0 -87.600982 293.57749 + 300 279.433 -88.79349 0 -87.601545 -42.519241 + 310 276.82128 -88.781921 0 -87.601116 -274.91273 + 320 290.86073 -88.842663 0 -87.601972 -251.72319 + 330 247.13231 -88.655944 0 -87.60178 215.5825 + 340 304.78418 -88.902207 0 -87.602125 224.33743 + 350 321.83348 -88.975242 0 -87.602434 -146.36749 + 360 256.1084 -88.693238 0 -87.600785 -243.86723 + 370 333.28383 -89.023692 0 -87.602042 -202.7226 + 380 324.46336 -88.985932 0 -87.601906 338.96104 + 390 297.78689 -88.872153 0 -87.601918 474.90823 + 400 323.523 -88.983153 0 -87.603138 70.699072 + 410 241.32969 -88.630465 0 -87.601053 -335.98449 + 420 216.24017 -88.522752 0 -87.600361 -483.64034 + 430 340.87719 -89.057194 0 -87.603153 -153.19639 + 440 297.22954 -88.871197 0 -87.603339 437.42311 + 450 297.67599 -88.8724 0 -87.602638 411.10618 + 460 347.10992 -89.082494 0 -87.601867 -85.383428 + 470 310.98706 -88.928867 0 -87.602325 -258.83538 + 480 243.70408 -88.64023 0 -87.600689 -209.15529 + 490 202.36375 -88.462523 0 -87.599323 30.433491 + 500 310.02578 -88.925742 0 -87.603301 102.03538 + 510 311.17419 -88.929206 0 -87.601866 141.67864 + 520 338.18968 -89.045078 0 -87.602502 -16.941008 + 530 264.61141 -88.730468 0 -87.601746 187.78747 + 540 304.0748 -88.899894 0 -87.602837 -23.335389 + 550 257.2387 -88.699533 0 -87.60226 -76.623864 + 560 255.29649 -88.689478 0 -87.600489 -157.6005 + 570 296.00752 -88.86567 0 -87.603025 -80.312046 + 580 276.10128 -88.780334 0 -87.6026 53.17176 + 590 308.39452 -88.918678 0 -87.603195 38.274105 + 600 287.50603 -88.829033 0 -87.602652 114.15043 + 610 325.44631 -88.990713 0 -87.602494 -149.00031 + 620 296.79101 -88.868281 0 -87.602294 -31.191595 + 630 233.20643 -88.596762 0 -87.602 51.803242 + 640 366.28772 -89.16588 0 -87.603448 -35.874837 + 650 287.00582 -88.826607 0 -87.602359 108.51296 + 660 250.92942 -88.672951 0 -87.60259 71.245421 + 670 262.05685 -88.719309 0 -87.601484 -45.906179 + 680 325.28482 -88.989008 0 -87.601478 -153.5577 + 690 305.21477 -88.902942 0 -87.601023 86.906849 + 700 311.86315 -88.931883 0 -87.601604 101.32482 + 710 236.96144 -88.61142 0 -87.60064 80.204649 + 720 279.15425 -88.792529 0 -87.601773 -299.79972 + 730 324.76243 -88.988046 0 -87.602745 -190.80505 + 740 263.42453 -88.726147 0 -87.602488 265.91457 + 750 302.62838 -88.893264 0 -87.602377 140.40681 + 760 319.02473 -88.96278 0 -87.601953 31.374117 + 770 250.8839 -88.672034 0 -87.601867 -107.29433 + 780 270.67757 -88.756034 0 -87.601436 -223.11211 + 790 325.22943 -88.989523 0 -87.60223 -7.8218354 + 800 315.84743 -88.949085 0 -87.601811 158.29361 + 810 285.44223 -88.818547 0 -87.600969 348.1465 + 820 273.78228 -88.769575 0 -87.601733 -40.315077 + 830 278.78036 -88.790787 0 -87.601626 -239.09329 + 840 301.53249 -88.887576 0 -87.601364 -210.8338 + 850 299.43388 -88.879524 0 -87.602263 97.287213 + 860 289.9817 -88.83822 0 -87.601278 236.16201 + 870 308.32291 -88.917016 0 -87.601838 26.230231 + 880 286.88415 -88.826564 0 -87.602836 -12.642436 + 890 293.46738 -88.854834 0 -87.603024 -177.77579 + 900 260.54906 -88.713526 0 -87.602132 -138.78025 + 910 310.93853 -88.928482 0 -87.602147 5.3207191 + 920 331.11482 -89.015365 0 -87.602967 181.82814 + 930 278.62443 -88.790683 0 -87.602186 313.60224 + 940 307.93562 -88.915181 0 -87.601656 -139.69608 + 950 291.81836 -88.846372 0 -87.601596 -327.26973 + 960 277.8025 -88.786647 0 -87.601657 -129.44547 + 970 261.49577 -88.717364 0 -87.601931 242.6305 + 980 308.0163 -88.916951 0 -87.603082 169.78602 + 990 290.00437 -88.838536 0 -87.601498 44.660874 + 1000 357.1344 -89.126236 0 -87.602849 -265.91044 + 1010 283.45708 -88.810737 0 -87.601627 -152.47623 + 1020 297.97492 -88.874959 0 -87.603921 70.00523 + 1030 279.12249 -88.792681 0 -87.602061 159.79846 + 1040 312.39383 -88.934418 0 -87.601876 158.68328 + 1050 337.09276 -89.040629 0 -87.602731 -31.702724 + 1060 227.23727 -88.568884 0 -87.599584 -28.800733 + 1070 283.40375 -88.811423 0 -87.60254 -124.80818 + 1080 271.42275 -88.759439 0 -87.601662 -37.628741 + 1090 335.15468 -89.032775 0 -87.603144 -56.099081 + 1100 261.64481 -88.717593 0 -87.601525 176.07594 + 1110 297.2909 -88.870077 0 -87.601957 205.98241 + 1120 290.77288 -88.843161 0 -87.602844 -84.55887 + 1130 317.14042 -88.955942 0 -87.603153 -340.75016 + 1140 359.81744 -89.138017 0 -87.603185 -105.8786 + 1150 209.98715 -88.49576 0 -87.600042 230.91225 + 1160 324.43808 -88.986117 0 -87.602199 217.03324 + 1170 325.4821 -88.990737 0 -87.602366 1.5123229 + 1180 248.5009 -88.662178 0 -87.602177 -119.39002 + 1190 277.64425 -88.787604 0 -87.603289 -117.53181 + 1200 320.04284 -88.968181 0 -87.603011 -25.685206 + 1210 364.27176 -89.157253 0 -87.603421 75.929091 + 1220 234.49906 -88.600929 0 -87.600654 198.93977 + 1230 323.21645 -88.981743 0 -87.603036 -26.795407 + 1240 306.44746 -88.909845 0 -87.602668 -226.30248 + 1250 262.65422 -88.721948 0 -87.601575 -139.61234 + 1260 297.83104 -88.874145 0 -87.603721 127.64441 + 1270 319.69077 -88.967441 0 -87.603773 211.1439 + 1280 322.04803 -88.975391 0 -87.601668 120.21183 + 1290 302.37605 -88.891213 0 -87.601402 -164.43253 + 1300 226.70372 -88.568572 0 -87.601548 -143.94049 + 1310 222.50036 -88.550282 0 -87.601188 -163.7893 + 1320 338.85208 -89.048398 0 -87.602995 -102.76279 + 1330 370.2677 -89.182829 0 -87.603421 202.90736 + 1340 304.48434 -88.900827 0 -87.602023 436.17765 + 1350 271.13466 -88.758223 0 -87.601675 108.36451 + 1360 292.87592 -88.851046 0 -87.601759 -411.70922 + 1370 286.17601 -88.822909 0 -87.602201 -323.81016 + 1380 271.92765 -88.761741 0 -87.60181 -38.742365 + 1390 277.75266 -88.785982 0 -87.601205 391.17924 + 1400 347.88168 -89.086571 0 -87.602652 183.08725 + 1410 295.96621 -88.86433 0 -87.601861 -84.0265 + 1420 261.00333 -88.715462 0 -87.60213 -94.433666 + 1430 244.17278 -88.644119 0 -87.60258 -163.1004 + 1440 301.17108 -88.888009 0 -87.603338 -144.27123 + 1450 356.09498 -89.121777 0 -87.602823 -1.8206165 + 1460 332.86257 -89.021897 0 -87.602043 179.46074 + 1470 276.25226 -88.779864 0 -87.601487 376.39659 + 1480 302.47254 -88.892321 0 -87.602098 -88.155871 + 1490 246.60945 -88.652741 0 -87.600807 -132.37692 + 1500 284.04878 -88.813017 0 -87.601383 -290.0804 + 1510 283.76682 -88.812624 0 -87.602193 -33.272095 + 1520 254.7339 -88.688407 0 -87.601818 248.83014 + 1530 318.68849 -88.962694 0 -87.603302 99.197646 + 1540 322.71768 -88.979845 0 -87.603265 -45.038776 + 1550 243.53105 -88.639953 0 -87.601151 -131.47472 + 1560 267.44357 -88.742006 0 -87.601203 -89.590067 + 1570 286.79346 -88.824365 0 -87.601023 73.346429 + 1580 356.46927 -89.123462 0 -87.602912 -33.880707 + 1590 299.98929 -88.882122 0 -87.602492 136.18054 + 1600 277.07373 -88.785253 0 -87.603371 124.34489 + 1610 295.80216 -88.865226 0 -87.603457 -102.03415 + 1620 289.16666 -88.835667 0 -87.602202 -111.10681 + 1630 287.95146 -88.829784 0 -87.601503 -111.35052 + 1640 286.80875 -88.825858 0 -87.602451 83.844874 + 1650 275.08285 -88.775129 0 -87.60174 129.65013 + 1660 306.29672 -88.908967 0 -87.602432 -114.4214 + 1670 267.75873 -88.744656 0 -87.602508 -25.706225 + 1680 305.78446 -88.906817 0 -87.602467 -59.786573 + 1690 312.45402 -88.935284 0 -87.602484 27.295541 + 1700 279.11278 -88.794103 0 -87.603523 89.965543 + 1710 288.88848 -88.835185 0 -87.602907 46.419876 + 1720 310.9645 -88.928819 0 -87.602373 -93.075985 + 1730 268.93523 -88.747955 0 -87.600789 -91.989455 + 1740 294.57034 -88.858645 0 -87.602131 61.734208 + 1750 321.07641 -88.971939 0 -87.60236 -56.677925 + 1760 316.37702 -88.951114 0 -87.601581 209.15256 + 1770 277.22368 -88.785542 0 -87.603021 36.332449 + 1780 216.82668 -88.526023 0 -87.60113 -65.279021 + 1790 277.5677 -88.785691 0 -87.601702 -267.0748 + 1800 305.49588 -88.906685 0 -87.603566 -121.29205 + 1810 245.19957 -88.647543 0 -87.601624 293.34959 + 1820 344.99793 -89.073805 0 -87.602187 21.468923 + 1830 339.88657 -89.052485 0 -87.60267 -0.74286605 + 1840 246.70406 -88.653429 0 -87.601092 -88.583558 + 1850 324.78426 -88.989278 0 -87.603883 -127.0114 + 1860 288.73025 -88.833258 0 -87.601655 211.26226 + 1870 278.825 -88.791203 0 -87.601851 57.213965 + 1880 259.9335 -88.710377 0 -87.601609 22.449955 + 1890 256.11656 -88.693666 0 -87.601179 -140.61185 + 1900 281.84197 -88.804539 0 -87.602318 -112.01218 + 1910 319.25233 -88.964241 0 -87.602443 -43.005465 + 1920 335.34404 -89.033272 0 -87.602833 152.12463 + 1930 287.22826 -88.826665 0 -87.601468 249.61663 + 1940 310.67727 -88.926909 0 -87.601688 -10.319445 + 1950 283.51674 -88.811636 0 -87.602271 -162.04573 + 1960 279.31371 -88.793728 0 -87.602292 -265.7411 + 1970 256.30742 -88.694226 0 -87.600925 -38.707208 + 1980 333.25931 -89.024082 0 -87.602536 192.87856 + 1990 262.09798 -88.718972 0 -87.600971 283.75345 + 2000 289.03468 -88.834899 0 -87.601997 -87.145015 + 2010 259.61063 -88.707653 0 -87.600262 -260.74116 + 2020 340.97507 -89.056481 0 -87.602023 -187.81852 + 2030 306.81218 -88.910403 0 -87.601669 237.58171 + 2040 252.35573 -88.67799 0 -87.601545 322.76321 + 2050 284.67415 -88.816302 0 -87.602001 -3.8812621 + 2060 309.79645 -88.923171 0 -87.601708 -392.72626 + 2070 310.38253 -88.925966 0 -87.602003 -278.95375 + 2080 230.78966 -88.584789 0 -87.600336 293.00497 + 2090 296.90589 -88.868332 0 -87.601855 299.99507 + 2100 335.41016 -89.032518 0 -87.601798 21.683373 + 2110 288.43159 -88.831561 0 -87.601232 -250.86825 + 2120 220.80849 -88.542642 0 -87.600765 -136.68286 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-87.601508 243.58529 + 9160 268.07276 -88.744717 0 -87.60123 20.079915 + 9170 264.62976 -88.730667 0 -87.601866 -277.89092 + 9180 275.90424 -88.778953 0 -87.60206 -275.66381 + 9190 281.94929 -88.804611 0 -87.601932 13.526196 + 9200 281.13084 -88.801203 0 -87.602016 294.38319 + 9210 314.62854 -88.944577 0 -87.602503 105.79101 + 9220 292.02357 -88.84761 0 -87.601958 -104.69927 + 9230 263.09361 -88.72319 0 -87.600942 -128.10326 + 9240 331.45587 -89.016941 0 -87.603088 -18.190047 + 9250 285.33158 -88.81914 0 -87.602034 227.59969 + 9260 299.98924 -88.882009 0 -87.602379 32.577895 + 9270 308.2903 -88.916567 0 -87.601528 -133.67016 + 9280 282.91862 -88.808383 0 -87.601569 -117.01408 + 9290 262.06397 -88.720688 0 -87.602832 16.64012 + 9300 296.132 -88.866211 0 -87.603035 150.55861 + 9310 273.2275 -88.766914 0 -87.601439 73.160286 + 9320 307.91507 -88.915968 0 -87.602531 -149.79118 + 9330 291.13943 -88.844154 0 -87.602274 -149.00604 + 9340 277.13879 -88.783771 0 -87.601612 -29.054577 + 9350 311.97519 -88.933324 0 -87.602568 44.536142 + 9360 317.72694 -88.957781 0 -87.602489 154.81556 + 9370 235.45594 -88.605049 0 -87.600692 137.48304 + 9380 231.13782 -88.586808 0 -87.60087 -93.891428 + 9390 294.82803 -88.859655 0 -87.602041 -264.31551 + 9400 362.55838 -89.148714 0 -87.60219 -156.86709 + 9410 339.81674 -89.051615 0 -87.602098 271.51139 + 9420 280.89936 -88.800362 0 -87.602162 395.57822 + 9430 305.34246 -88.905082 0 -87.602618 -5.3355995 + 9440 273.25794 -88.76723 0 -87.601625 -302.23068 + 9450 238.78972 -88.619508 0 -87.60093 -319.11968 + 9460 311.18937 -88.929597 0 -87.602192 -0.68489272 + 9470 338.35461 -89.045304 0 -87.602024 211.3674 + 9480 296.18865 -88.865202 0 -87.601785 253.48027 + 9490 287.39009 -88.828514 0 -87.602627 11.560189 + 9500 222.64679 -88.550865 0 -87.601147 -102.26318 + 9510 282.26405 -88.80587 0 -87.601848 -244.32346 + 9520 329.66107 -89.008214 0 -87.602016 -201.7463 + 9530 318.29206 -88.959585 0 -87.601883 338.24867 + 9540 277.64692 -88.786011 0 -87.601685 362.92276 + 9550 299.9758 -88.881901 0 -87.602329 -52.986848 + 9560 264.07935 -88.728095 0 -87.601642 -257.17293 + 9570 271.78597 -88.761247 0 -87.601921 -322.32643 + 9580 293.25633 -88.853227 0 -87.602318 15.509204 + 9590 313.99297 -88.941965 0 -87.602601 203.41962 + 9600 314.0622 -88.942163 0 -87.602504 261.82469 + 9610 290.14214 -88.839283 0 -87.601657 -36.0876 + 9620 308.94913 -88.919943 0 -87.602094 -188.60605 + 9630 283.60522 -88.811507 0 -87.601765 -82.315739 + 9640 261.14737 -88.715734 0 -87.601788 33.628265 + 9650 255.36423 -88.690939 0 -87.601662 191.27378 + 9660 286.57809 -88.824936 0 -87.602513 -9.4340498 + 9670 283.19171 -88.810525 0 -87.602547 -215.96343 + 9680 313.56792 -88.939496 0 -87.601945 -123.18549 + 9690 336.09815 -89.035376 0 -87.601721 60.038925 + 9700 272.18381 -88.76201 0 -87.600987 352.23962 + 9710 297.62806 -88.871878 0 -87.602321 107.42505 + 9720 265.59711 -88.733728 0 -87.600801 -85.858056 + 9730 303.23247 -88.895251 0 -87.601788 -388.61966 + 9740 256.8463 -88.697047 0 -87.601448 -108.71472 + 9750 276.03836 -88.779084 0 -87.601619 213.48947 + 9760 342.20761 -89.06272 0 -87.603005 199.03836 + 9770 333.75262 -89.026471 0 -87.602821 78.008338 + 9780 311.14422 -88.928916 0 -87.601704 -144.25471 + 9790 296.38674 -88.866209 0 -87.601946 -128.04915 + 9800 250.03064 -88.6681 0 -87.601573 5.7582715 + 9810 290.52821 -88.841724 0 -87.602451 136.19024 + 9820 262.7407 -88.722173 0 -87.60143 64.707606 + 9830 299.20995 -88.878061 0 -87.601756 -237.61353 + 9840 315.1346 -88.945859 0 -87.601626 -46.37683 + 9850 288.53998 -88.832109 0 -87.601317 134.10721 + 9860 256.50104 -88.694755 0 -87.600628 104.9712 + 9870 318.6017 -88.961241 0 -87.602219 -31.68379 + 9880 325.37115 -88.990064 0 -87.602165 -78.599349 + 9890 306.49052 -88.909116 0 -87.601755 -49.123798 + 9900 282.88958 -88.80931 0 -87.60262 51.563119 + 9910 299.93938 -88.882506 0 -87.603089 83.125725 + 9920 278.97804 -88.792051 0 -87.602047 22.40744 + 9930 258.23652 -88.702905 0 -87.601375 7.7553914 + 9940 297.88687 -88.872442 0 -87.60178 -90.767726 + 9950 316.93813 -88.953574 0 -87.601647 -139.45285 + 9960 284.60319 -88.815957 0 -87.601958 178.99591 + 9970 267.65923 -88.743258 0 -87.601534 177.69007 + 9980 283.9857 -88.81345 0 -87.602085 -66.889934 + 9990 303.62269 -88.898221 0 -87.603093 -299.83071 + 10000 260.03075 -88.710707 0 -87.601524 -73.881784 + 10001 258.76961 -88.705262 0 -87.601458 -43.203807 +Loop time of 0.17839 on 1 procs for 10000 steps with 34 atoms + +Performance: 24216.636 ns/day, 0.001 hours/ns, 56057.027 timesteps/s +90.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.15624 | 0.15624 | 0.15624 | 0.0 | 87.59 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0036623 | 0.0036623 | 0.0036623 | 0.0 | 2.05 +Output | 0.011836 | 0.011836 | 0.011836 | 0.0 | 6.63 +Modify | 0.0036767 | 0.0036767 | 0.0036767 | 0.0 | 2.06 +Other | | 0.002972 | | | 1.67 + +Nlocal: 34.0000 ave 34 max 34 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 56.0000 ave 56 max 56 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 561.000 ave 561 max 561 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 561 +Ave neighs/atom = 16.500000 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/smatb/log.27Oct21.smatbBulkFCC.g++ b/examples/smatb/log.27Oct21.smatbBulkFCC.g++ new file mode 100644 index 0000000000..0902915117 --- /dev/null +++ b/examples/smatb/log.27Oct21.smatbBulkFCC.g++ @@ -0,0 +1,160 @@ +LAMMPS (27 Oct 2021) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# -*- lammps -*- + +units metal +atom_style atomic +boundary p p p + +lattice fcc 4.0782 +Lattice spacing in x,y,z = 4.0782000 4.0782000 4.0782000 + +region myreg block 0 8 0 8 0 8 + +create_box 1 myreg +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (32.625600 32.625600 32.625600) + 1 by 1 by 1 MPI processor grid + +create_atoms 1 box +Created 2048 atoms + using lattice units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (32.625600 32.625600 32.625600) + create_atoms CPU = 0.001 seconds + +mass 1 196.96655 # Au + +pair_style smatb/single +pair_coeff 1 1 2.88 10.35 4.178 0.210 1.818 4.07293506 4.9883063257983666 + +neighbor 8.0 bin +neigh_modify every 1 delay 0 check yes + +thermo 1 +fix boxmin all box/relax iso 1.0 +minimize 1.0e-8 1.0e-10 10000 100000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12.988306 + ghost atom cutoff = 12.988306 + binsize = 6.4941532, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair smatb/single, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.601 | 6.601 | 6.601 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0 -7800.9629 0 -7800.9629 -17598.853 34727.66 + 1 0 -7801.0757 0 -7801.0757 -17102.698 34717.243 + 2 0 -7801.1852 0 -7801.1852 -16605.672 34706.828 + 3 0 -7801.2915 0 -7801.2915 -16107.773 34696.415 + 4 0 -7801.3946 0 -7801.3946 -15609 34686.004 + 5 0 -7801.4944 0 -7801.4944 -15109.353 34675.595 + 6 0 -7801.5909 0 -7801.5909 -14608.829 34665.188 + 7 0 -7801.6841 0 -7801.6841 -14107.429 34654.783 + 8 0 -7801.7741 0 -7801.7741 -13605.15 34644.38 + 9 0 -7801.8608 0 -7801.8608 -13101.992 34633.98 + 10 0 -7801.9442 0 -7801.9442 -12597.953 34623.581 + 11 0 -7802.0243 0 -7802.0243 -12093.033 34613.185 + 12 0 -7802.1011 0 -7802.1011 -11587.23 34602.79 + 13 0 -7802.1746 0 -7802.1746 -11080.543 34592.398 + 14 0 -7802.2448 0 -7802.2448 -10572.902 34582.008 + 15 0 -7802.3117 0 -7802.3117 -10064.258 34571.62 + 16 0 -7802.3753 0 -7802.3753 -9554.6096 34561.234 + 17 0 -7802.4356 0 -7802.4356 -9043.9555 34550.85 + 18 0 -7802.4925 0 -7802.4925 -8532.2942 34540.468 + 19 0 -7802.5462 0 -7802.5462 -8019.6245 34530.088 + 20 0 -7802.5964 0 -7802.5964 -7505.945 34519.711 + 21 0 -7802.6434 0 -7802.6434 -6991.2543 34509.335 + 22 0 -7802.687 0 -7802.687 -6475.5513 34498.961 + 23 0 -7802.7272 0 -7802.7272 -5958.8344 34488.59 + 24 0 -7802.7641 0 -7802.7641 -5441.1024 34478.221 + 25 0 -7802.7977 0 -7802.7977 -4922.354 34467.853 + 26 0 -7802.8278 0 -7802.8278 -4402.5878 34457.488 + 27 0 -7802.8546 0 -7802.8546 -3881.8024 34447.125 + 28 0 -7802.878 0 -7802.878 -3359.9966 34436.764 + 29 0 -7802.8981 0 -7802.8981 -2837.1689 34426.405 + 30 0 -7802.9147 0 -7802.9147 -2313.3181 34416.048 + 31 0 -7802.928 0 -7802.928 -1788.4427 34405.693 + 32 0 -7802.9378 0 -7802.9378 -1262.5414 34395.34 + 33 0 -7802.9443 0 -7802.9443 -735.61295 34384.99 + 34 0 -7802.9473 0 -7802.9473 -207.6559 34374.641 + 35 0 -7802.9476 0 -7802.9476 0.90227419 34370.559 + 36 0 -7802.9476 0 -7802.9476 0.99992446 34370.557 +Loop time of 0.142744 on 1 procs for 36 steps with 2048 atoms + +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -7800.9628521055 -7802.94781441221 -7802.94781442797 + Force two-norm initial, final = 1144.4464 4.8784902e-06 + Force max component initial, final = 1144.4464 4.8784902e-06 + Final line search alpha, max atom move = 0.015845171 7.7300512e-08 + Iterations, force evaluations = 36 38 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.13461 | 0.13461 | 0.13461 | 0.0 | 94.30 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0012706 | 0.0012706 | 0.0012706 | 0.0 | 0.89 +Output | 0.00066993 | 0.00066993 | 0.00066993 | 0.0 | 0.47 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.006191 | | | 4.34 + +Nlocal: 2048.00 ave 2048 max 2048 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 10147.0 ave 10147 max 10147 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 567296.0 ave 567296 max 567296 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 567296 +Ave neighs/atom = 277.00000 +Neighbor list builds = 0 +Dangerous builds = 0 +unfix boxmin +minimize 1.0e-8 1.0e-10 10000 100000 +Per MPI rank memory allocation (min/avg/max) = 6.601 | 6.601 | 6.601 Mbytes +Step Temp E_pair E_mol TotEng Press + 36 0 -7802.9476 0 -7802.9476 0.99992446 + 37 0 -7802.9476 0 -7802.9476 0.99992446 +Loop time of 0.0105782 on 1 procs for 1 steps with 2048 atoms + +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -7802.94759154184 -7802.94759154184 -7802.94759154185 + Force two-norm initial, final = 4.7040841e-12 1.3779243e-12 + Force max component initial, final = 1.1096422e-13 4.1164848e-14 + Final line search alpha, max atom move = 1.0000000 4.1164848e-14 + Iterations, force evaluations = 1 2 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.010394 | 0.010394 | 0.010394 | 0.0 | 98.25 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 8.6608e-05 | 8.6608e-05 | 8.6608e-05 | 0.0 | 0.82 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 9.804e-05 | | | 0.93 + +Nlocal: 2048.00 ave 2048 max 2048 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 10147.0 ave 10147 max 10147 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 567296.0 ave 567296 max 567296 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 567296 +Ave neighs/atom = 277.00000 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/src/pair_smatb.h b/src/pair_smatb.h index a18392fab1..967a46327f 100644 --- a/src/pair_smatb.h +++ b/src/pair_smatb.h @@ -11,7 +11,11 @@ See the README file in the top-level LAMMPS directory. This style is written by Daniele Rapetti (iximiel@gmail.com) - ------------------------------------------------------------------------- */ +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- +This pair style is written by Daniele Rapetti (iximiel@gmail.com) +------------------------------------------------------------------------- */ #ifdef PAIR_CLASS // clang-format off diff --git a/src/pair_smatb_single.h b/src/pair_smatb_single.h index 8d31a7d047..e8b29d5303 100644 --- a/src/pair_smatb_single.h +++ b/src/pair_smatb_single.h @@ -11,7 +11,11 @@ See the README file in the top-level LAMMPS directory. This pair style is written by Daniele Rapetti (iximiel@gmail.com) - ------------------------------------------------------------------------- */ +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- +This pair style is written by Daniele Rapetti (iximiel@gmail.com) +------------------------------------------------------------------------- */ #ifdef PAIR_CLASS // clang-format off From a759987515c3ba6c3adf9e16a905f43c2c3a1648 Mon Sep 17 00:00:00 2001 From: Daniele Date: Thu, 18 Nov 2021 14:31:21 +0100 Subject: [PATCH 13/57] added examples --- examples/smatb/in.smatbNP | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/examples/smatb/in.smatbNP b/examples/smatb/in.smatbNP index 9a03a3d994..5ccd9c8efb 100644 --- a/examples/smatb/in.smatbNP +++ b/examples/smatb/in.smatbNP @@ -29,10 +29,10 @@ timestep 0.005 #dump 2 all image 10 image.*.jpg element element & # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 element Si C +#dump_modify 2 pad 3 element Ag Cu #dump 3 all movie 10 movie.mpg element element & # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 element Si C +#dump_modify 3 pad 3 element Ag Cu run 10000 \ No newline at end of file From 4646671e700380883bfb196af56958fb6c745fe6 Mon Sep 17 00:00:00 2001 From: Daniele Date: Thu, 18 Nov 2021 14:32:39 +0100 Subject: [PATCH 14/57] added examples --- examples/smatb/{in.smatbNP => in.smatbAgCuPancake} | 0 examples/smatb/{in.smatb.BulkFCC => in.smatbBulkFCC} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename examples/smatb/{in.smatbNP => in.smatbAgCuPancake} (100%) rename examples/smatb/{in.smatb.BulkFCC => in.smatbBulkFCC} (100%) diff --git a/examples/smatb/in.smatbNP b/examples/smatb/in.smatbAgCuPancake similarity index 100% rename from examples/smatb/in.smatbNP rename to examples/smatb/in.smatbAgCuPancake diff --git a/examples/smatb/in.smatb.BulkFCC b/examples/smatb/in.smatbBulkFCC similarity index 100% rename from examples/smatb/in.smatb.BulkFCC rename to examples/smatb/in.smatbBulkFCC From c918b6fbccdb7601d924a430456c43c7e631cb04 Mon Sep 17 00:00:00 2001 From: Daniele Date: Thu, 18 Nov 2021 14:36:38 +0100 Subject: [PATCH 15/57] removed example dump file --- examples/smatb/dump.smatb | 8600 ------------------------------------- 1 file changed, 8600 deletions(-) delete mode 100644 examples/smatb/dump.smatb diff --git a/examples/smatb/dump.smatb b/examples/smatb/dump.smatb deleted file mode 100644 index 7e046da126..0000000000 --- a/examples/smatb/dump.smatb +++ /dev/null @@ -1,8600 +0,0 @@ -ITEM: TIMESTEP -50 -ITEM: NUMBER OF ATOMS -34 -ITEM: BOX BOUNDS pp pp pp -0.0000000000000000e+00 3.0000000000000000e+01 -0.0000000000000000e+00 3.0000000000000000e+01 -0.0000000000000000e+00 3.0000000000000000e+01 -ITEM: ATOMS id type xs ys zs -6 1 0.370674 0.420404 0.47149 -14 1 0.460672 0.41852 0.432087 -11 1 0.639652 0.504553 0.436168 -21 1 0.540601 0.374123 0.443148 -24 1 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0.460621 -12 1 0.473266 0.507517 0.374657 -17 1 0.474906 0.581054 0.426676 -33 2 0.4963 0.497941 0.454293 -16 1 0.561836 0.549966 0.415507 -18 1 0.615347 0.578405 0.488678 -19 1 0.546236 0.632464 0.452171 -31 2 0.525458 0.560755 0.498458 -2 1 0.476732 0.418824 0.584013 -4 1 0.452038 0.374676 0.503232 -8 1 0.39002 0.417584 0.568724 -15 1 0.428242 0.504804 0.588147 -29 2 0.442252 0.459709 0.507229 -3 1 0.6449 0.495803 0.52558 -7 1 0.571582 0.443051 0.5674 -22 1 0.538974 0.360298 0.535376 -27 1 0.508416 0.499506 0.626722 -28 2 0.506826 0.493944 0.544041 -1 1 0.396926 0.58518 0.558996 -13 1 0.493377 0.576296 0.576994 -23 1 0.469537 0.624709 0.509777 -26 1 0.363612 0.501771 0.52269 -30 2 0.449633 0.540412 0.505102 -5 1 0.558086 0.63348 0.540552 -20 1 0.576175 0.541068 0.569562 -ITEM: TIMESTEP -10000 -ITEM: NUMBER OF ATOMS -34 -ITEM: BOX BOUNDS pp pp pp -0.0000000000000000e+00 3.0000000000000000e+01 -0.0000000000000000e+00 3.0000000000000000e+01 -0.0000000000000000e+00 3.0000000000000000e+01 -ITEM: ATOMS id type xs ys zs -6 1 0.37963 0.425224 0.464624 -14 1 0.465316 0.421947 0.423634 -11 1 0.640153 0.495882 0.432425 -21 1 0.535603 0.360033 0.454859 -24 1 0.602336 0.413551 0.482868 -25 1 0.553619 0.446818 0.412929 -32 2 0.5201 0.433105 0.498833 -34 2 0.570134 0.499315 0.490623 -9 1 0.413746 0.506632 0.436245 -10 1 0.380064 0.590256 0.471545 -12 1 0.481405 0.506821 0.375115 -17 1 0.464965 0.586599 0.428656 -33 2 0.494561 0.501177 0.456729 -16 1 0.5581 0.538987 0.407568 -18 1 0.606491 0.576339 0.484863 -19 1 0.540144 0.634853 0.457332 -31 2 0.523698 0.565102 0.494906 -2 1 0.480445 0.42596 0.579585 -4 1 0.449363 0.373429 0.499536 -8 1 0.390355 0.42522 0.553828 -15 1 0.432917 0.503125 0.589959 -29 2 0.441783 0.460946 0.504695 -3 1 0.647053 0.481317 0.526333 -7 1 0.577756 0.4448 0.565506 -22 1 0.537068 0.362471 0.542401 -27 1 0.52694 0.492921 0.62524 -28 2 0.502338 0.501364 0.541346 -1 1 0.394496 0.585836 0.563247 -13 1 0.481699 0.57649 0.584806 -23 1 0.460134 0.630867 0.505452 -26 1 0.364443 0.512817 0.515976 -30 2 0.445487 0.547838 0.506843 -5 1 0.552561 0.628144 0.548219 -20 1 0.584328 0.54742 0.570819 From b4b6ba91e02bcec48b372ad5f508ecb0a58befb4 Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Wed, 20 Apr 2022 18:01:24 -0600 Subject: [PATCH 16/57] Slight adjustment to definition of Sinner and Dinner --- doc/src/compute_sna_atom.rst | 29 ++++++++++++++++------------- doc/src/pair_snap.rst | 10 +++++----- src/ML-SNAP/pair_snap.cpp | 1 - src/ML-SNAP/sna.cpp | 12 ++++++------ 4 files changed, 27 insertions(+), 25 deletions(-) diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst index e43e61cd00..992c87c816 100644 --- a/doc/src/compute_sna_atom.rst +++ b/doc/src/compute_sna_atom.rst @@ -59,9 +59,9 @@ Syntax *bikflag* value = *0* or *1* (only implemented for compute snap) *0* = per-atom bispectrum descriptors are summed over atoms *1* = per-atom bispectrum descriptors are not summed over atoms - *switchinnerflag* values = *rinnerlist* *drinnerlist* - *rinnerlist* = *ntypes* values of rinner (distance units) - *drinnerlist* = *ntypes* values of drinner (distance units) + *switchinnerflag* values = *sinnerlist* *dinnerlist* + *sinnerlist* = *ntypes* values of *Sinner* (distance units) + *dinnerlist* = *ntypes* values of *Dinner* (distance units) Examples """""""" @@ -316,21 +316,24 @@ The keyword *switchinnerflag* activates an additional radial switching function similar to :math:`f_c(r)` above, but acting to switch off smoothly contributions from neighbor atoms at short separation distances. This is useful when SNAP is used in combination with a simple -repulsive potential. The keyword is followed by the *ntypes* -values for :math:`r_{inner}` and the *ntypes* -values for :math:`\Delta r_{inner}`. For a neighbor atom at +repulsive potential. For a neighbor atom at distance :math:`r`, its contribution is scaled by a multiplicative factor :math:`f_{inner}(r)` defined as follows: .. math:: - = & 0, r \leq r_{inner} \\ - f_{inner}(r) = & \frac{1}{2}(1 - \cos(\pi \frac{r-r_{inner}}{\Delta r_{inner}})), r_{inner} < r \leq r_{inner} + \Delta r_{inner} \\ - = & 1, r > r_{inner} + \Delta r_{inner} + = & 0, r \leq S_{inner} - D_{inner} \\ + f_{inner}(r) = & \frac{1}{2}(1 - \cos(\frac{\pi}{2} (1 + \frac{r-S_{inner}}{D_{inner}})), S_{inner} - D_{inner} < r \leq S_{inner} + D_{inner} \\ + = & 1, r > S_{inner} + D_{inner} -The values of :math:`r_{inner}` and :math:`\Delta r_{inner}` are -the arithmetic means of the values for the central atom of type I -and the neighbor atom of type J. +where the switching region is centered at :math:`S_{inner}` and it extends a distance :math:`D_{inner}` +to the left and to the right of this. +The keyword is followed by the *ntypes* +values for :math:`S_{inner}` and the *ntypes* +values for :math:`D_{inner}`. +When the central atom and the neighbor atom have different types, +the values of :math:`S_{inner}` and :math:`D_{inner}` are +the arithmetic means of the values for both types. .. note:: @@ -450,7 +453,7 @@ Default The optional keyword defaults are *rmin0* = 0, *switchflag* = 1, *bzeroflag* = 1, *quadraticflag* = 0, -*bnormflag* = 0, *wselfallflag* = 0 +*bnormflag* = 0, *wselfallflag* = 0, *switchinnerflag* = off, ---------- diff --git a/doc/src/pair_snap.rst b/doc/src/pair_snap.rst index 350561fe4d..f7cc7ff731 100644 --- a/doc/src/pair_snap.rst +++ b/doc/src/pair_snap.rst @@ -136,7 +136,7 @@ keyword/value pair. The required keywords are *rcutfac* and *twojmax*\ . Optional keywords are *rfac0*, *rmin0*, *switchflag*, *bzeroflag*, *quadraticflag*, *chemflag*, *bnormflag*, *wselfallflag*, *switchinnerflag*, -*rinner*, *drinner*, *chunksize*, and *parallelthresh*\ . +*Sinner*, *Dinner*, *chunksize*, and *parallelthresh*\ . The default values for these keywords are @@ -152,6 +152,9 @@ The default values for these keywords are * *chunksize* = 32768 * *parallelthresh* = 8192 +For detailed definitions of all of these keywords, +see the :doc:`compute sna/atom ` doc page. + If *quadraticflag* is set to 1, then the SNAP energy expression includes additional quadratic terms that have been shown to increase the overall accuracy of the potential without much increase in computational cost @@ -194,7 +197,7 @@ pair_coeff command, to avoid ambiguity in the number of coefficients. The keyword *switchinnerflag* activates an additional switching function that smoothly turns off contributions to the SNAP potential from neighbor atoms at short separations. If *switchinnerflag* is set to 1 then -the additional keywords *rinner* and *drinner* must also be provided. +the additional keywords *Sinner* and *Dinner* must also be provided. Each of these is followed by *nelements* values, where *nelements* is the number of unique elements appearing in appearing in the LAMMPS pair_coeff command. The element order should correspond to the order @@ -217,9 +220,6 @@ already large enough to saturate the GPU threads. Extra parallelism will be performed if the *chunksize* (or total number of atoms per GPU) is smaller than *parallelthresh*. -Detailed definitions for all the other keywords -are given on the :doc:`compute sna/atom ` doc page. - .. note:: The previously used *diagonalstyle* keyword was removed in 2019, diff --git a/src/ML-SNAP/pair_snap.cpp b/src/ML-SNAP/pair_snap.cpp index 6a108ad3dd..3ba14c5872 100644 --- a/src/ML-SNAP/pair_snap.cpp +++ b/src/ML-SNAP/pair_snap.cpp @@ -703,7 +703,6 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) if (keywd == "rinner") { keyval = words[iword]; for (int ielem = 0; ielem < nelements; ielem++) { - printf("rinnerelem = %p ielem = %d nelements = %d iword = %d nwords = %d\n",rinnerelem, ielem, nelements, iword, nwords); rinnerelem[ielem] = utils::numeric(FLERR,keyval,false,lmp); iword++; } diff --git a/src/ML-SNAP/sna.cpp b/src/ML-SNAP/sna.cpp index 9d32f4ab9c..717d0014f5 100644 --- a/src/ML-SNAP/sna.cpp +++ b/src/ML-SNAP/sna.cpp @@ -1582,10 +1582,10 @@ double SNA::compute_sfac_inner(double r, double rinner, double drinner) double sfac; if (switch_inner_flag == 0) sfac = 1.0; else if (r >= rinner + drinner) sfac = 1.0; - else if (r <= rinner) sfac = 0.0; + else if (r <= rinner - drinner) sfac = 0.0; else { - double rcutfac = MY_PI / drinner; - sfac = 0.5 * (1.0 - cos((r - rinner) * rcutfac)); + double rcutfac = MY_PI2 / drinner; + sfac = 0.5 * (1.0 - cos(MY_PI2 + (r - rinner) * rcutfac)); } return sfac; } @@ -1597,10 +1597,10 @@ double SNA::compute_dsfac_inner(double r, double rinner, double drinner) double dsfac; if (switch_inner_flag == 0) dsfac = 0.0; else if (r >= rinner + drinner) dsfac = 0.0; - else if (r <= rinner) dsfac = 0.0; + else if (r <= rinner - drinner) dsfac = 0.0; else { - double rcutfac = MY_PI / drinner; - dsfac = 0.5 * sin((r - rinner) * rcutfac) * rcutfac; + double rcutfac = MY_PI2 / drinner; + dsfac = 0.5 * rcutfac * sin(MY_PI2 + (r - rinner) * rcutfac); } return dsfac; } From e8cacc438001d57cd530aae4642cd305de0e6eb5 Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Wed, 20 Apr 2022 18:17:23 -0600 Subject: [PATCH 17/57] Updated example syntax --- doc/src/compute_sna_atom.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst index 992c87c816..eecb3295ab 100644 --- a/doc/src/compute_sna_atom.rst +++ b/doc/src/compute_sna_atom.rst @@ -73,7 +73,7 @@ Examples compute vb all sna/atom 1.4 0.95 6 2.0 1.0 compute snap all snap 1.4 0.95 6 2.0 1.0 compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 chem 2 0 1 - compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 switchinnerflag 1.1 1.3 0.5 0.6 + compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 switchinnerflag 1.35 1.6 0.25 0.3 Description """"""""""" From 4de9ab85ce0aa348606e1293734b0bcf1d076618 Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Thu, 21 Apr 2022 17:30:12 -0600 Subject: [PATCH 18/57] Completed inner cutoff, KOKKOS still in progress --- doc/src/compute_sna_atom.rst | 21 +++--- doc/src/pair_snap.rst | 4 +- src/KOKKOS/pair_snap_kokkos_impl.h | 2 +- src/KOKKOS/sna_kokkos.h | 20 ++++-- src/KOKKOS/sna_kokkos_impl.h | 52 ++++++++++---- src/ML-SNAP/compute_sna_atom.cpp | 43 +++++++++--- src/ML-SNAP/compute_sna_atom.h | 4 +- src/ML-SNAP/compute_snad_atom.cpp | 52 ++++++++++---- src/ML-SNAP/compute_snad_atom.h | 4 +- src/ML-SNAP/compute_snap.cpp | 45 ++++++++---- src/ML-SNAP/compute_snap.h | 4 +- src/ML-SNAP/compute_snav_atom.cpp | 51 ++++++++++---- src/ML-SNAP/compute_snav_atom.h | 4 +- src/ML-SNAP/pair_snap.cpp | 46 ++++++------- src/ML-SNAP/pair_snap.h | 4 +- src/ML-SNAP/sna.cpp | 107 ++++++++++++----------------- src/ML-SNAP/sna.h | 11 ++- 17 files changed, 286 insertions(+), 188 deletions(-) diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst index eecb3295ab..e34c9a8889 100644 --- a/doc/src/compute_sna_atom.rst +++ b/doc/src/compute_sna_atom.rst @@ -33,7 +33,7 @@ Syntax * R_1, R_2,... = list of cutoff radii, one for each type (distance units) * w_1, w_2,... = list of neighbor weights, one for each type * zero or more keyword/value pairs may be appended -* keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag* or *chem* or *bnormflag* or *wselfallflag* or *bikflag* or *switchinnerflag* +* keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag* or *chem* or *bnormflag* or *wselfallflag* or *bikflag* or *switchinnerflag* or *sinner* or *dinner* .. parsed-literal:: @@ -59,8 +59,12 @@ Syntax *bikflag* value = *0* or *1* (only implemented for compute snap) *0* = per-atom bispectrum descriptors are summed over atoms *1* = per-atom bispectrum descriptors are not summed over atoms - *switchinnerflag* values = *sinnerlist* *dinnerlist* + *switchinnerflag* value = *0* or *1* + *0* = do not use inner switching function + *1* = use inner switching function + *sinner* values = *sinnerlist* *sinnerlist* = *ntypes* values of *Sinner* (distance units) + *dinner* values = *dinnerlist* *dinnerlist* = *ntypes* values of *Dinner* (distance units) Examples @@ -73,7 +77,7 @@ Examples compute vb all sna/atom 1.4 0.95 6 2.0 1.0 compute snap all snap 1.4 0.95 6 2.0 1.0 compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 chem 2 0 1 - compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 switchinnerflag 1.35 1.6 0.25 0.3 + compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 switchinnerflag 1 sinner 1.35 1.6 dinner 0.25 0.3 Description """"""""""" @@ -312,7 +316,8 @@ the resulting bispectrum rows are :math:`B_{i,k}` instead of just :math:`B_k`. In this case, the entries in the final column for these rows are set to zero. -The keyword *switchinnerflag* activates an additional radial switching +The keyword *switchinnerflag* with value 1 +activates an additional radial switching function similar to :math:`f_c(r)` above, but acting to switch off smoothly contributions from neighbor atoms at short separation distances. This is useful when SNAP is used in combination with a simple @@ -328,9 +333,9 @@ factor :math:`f_{inner}(r)` defined as follows: where the switching region is centered at :math:`S_{inner}` and it extends a distance :math:`D_{inner}` to the left and to the right of this. -The keyword is followed by the *ntypes* -values for :math:`S_{inner}` and the *ntypes* -values for :math:`D_{inner}`. +With this option, additional keywords *sinner* and *dinner* must be used, +each followed by *ntypes* +values for :math:`S_{inner}` and :math:`D_{inner}`, respectively. When the central atom and the neighbor atom have different types, the values of :math:`S_{inner}` and :math:`D_{inner}` are the arithmetic means of the values for both types. @@ -453,7 +458,7 @@ Default The optional keyword defaults are *rmin0* = 0, *switchflag* = 1, *bzeroflag* = 1, *quadraticflag* = 0, -*bnormflag* = 0, *wselfallflag* = 0, *switchinnerflag* = off, +*bnormflag* = 0, *wselfallflag* = 0, *switchinnerflag* = 0, ---------- diff --git a/doc/src/pair_snap.rst b/doc/src/pair_snap.rst index f7cc7ff731..ebedb288c1 100644 --- a/doc/src/pair_snap.rst +++ b/doc/src/pair_snap.rst @@ -136,7 +136,7 @@ keyword/value pair. The required keywords are *rcutfac* and *twojmax*\ . Optional keywords are *rfac0*, *rmin0*, *switchflag*, *bzeroflag*, *quadraticflag*, *chemflag*, *bnormflag*, *wselfallflag*, *switchinnerflag*, -*Sinner*, *Dinner*, *chunksize*, and *parallelthresh*\ . +*sinner*, *dinner*, *chunksize*, and *parallelthresh*\ . The default values for these keywords are @@ -197,7 +197,7 @@ pair_coeff command, to avoid ambiguity in the number of coefficients. The keyword *switchinnerflag* activates an additional switching function that smoothly turns off contributions to the SNAP potential from neighbor atoms at short separations. If *switchinnerflag* is set to 1 then -the additional keywords *Sinner* and *Dinner* must also be provided. +the additional keywords *sinner* and *dinner* must also be provided. Each of these is followed by *nelements* values, where *nelements* is the number of unique elements appearing in appearing in the LAMMPS pair_coeff command. The element order should correspond to the order diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index 6cf40b31a5..6bc034a163 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -602,7 +602,7 @@ void PairSNAPKokkos::coeff(int narg, char Kokkos::deep_copy(d_map,h_map); snaKK = SNAKokkos(rfac0,twojmax, - rmin0,switchflag,bzeroflag,chemflag,bnormflag,wselfallflag,nelements); + rmin0,switchflag,bzeroflag,chemflag,bnormflag,wselfallflag,nelements,switchinnerflag); snaKK.grow_rij(0,0); snaKK.init(); } diff --git a/src/KOKKOS/sna_kokkos.h b/src/KOKKOS/sna_kokkos.h index c33f5e486e..706f2d2f4c 100644 --- a/src/KOKKOS/sna_kokkos.h +++ b/src/KOKKOS/sna_kokkos.h @@ -103,7 +103,7 @@ inline SNAKokkos(const SNAKokkos& sna, const typename Kokkos::TeamPolicy::member_type& team); inline - SNAKokkos(real_type, int, real_type, int, int, int, int, int, int); +SNAKokkos(real_type, int, real_type, int, int, int, int, int, int, int); KOKKOS_INLINE_FUNCTION ~SNAKokkos(); @@ -192,13 +192,13 @@ inline void compute_deidrj_cpu(const typename Kokkos::TeamPolicy::member_type& team, int, int); // ForceSNAP KOKKOS_INLINE_FUNCTION - real_type compute_sfac(real_type, real_type); // add_uarraytot, compute_duarray + real_type compute_sfac(real_type, real_type, real_type, real_type); // add_uarraytot, compute_duarray KOKKOS_INLINE_FUNCTION - real_type compute_dsfac(real_type, real_type); // compute_duarray + real_type compute_dsfac(real_type, real_type, real_type, real_type); // compute_duarray KOKKOS_INLINE_FUNCTION - void compute_s_dsfac(const real_type, const real_type, real_type&, real_type&); // compute_cayley_klein + void compute_s_dsfac(const real_type, const real_type, const real_type, const real_type, real_type&, real_type&); // compute_cayley_klein #ifdef TIMING_INFO double* timers; @@ -214,6 +214,8 @@ inline t_sna_2i inside; t_sna_2d wj; t_sna_2d rcutij; + t_sna_2d sinnerij; + t_sna_2d dinnerij; t_sna_2i element; t_sna_3d dedr; int natom, nmax; @@ -297,7 +299,7 @@ inline void init_rootpqarray(); // init() KOKKOS_INLINE_FUNCTION - void add_uarraytot(const typename Kokkos::TeamPolicy::member_type& team, int, int, const real_type&, const real_type&, const real_type&, int); // compute_ui + void add_uarraytot(const typename Kokkos::TeamPolicy::member_type& team, int, int, const real_type&, const real_type&, const real_type&, const real_type&, const real_type&, int); // compute_ui KOKKOS_INLINE_FUNCTION void compute_uarray_cpu(const typename Kokkos::TeamPolicy::member_type& team, int, int, @@ -313,13 +315,19 @@ inline KOKKOS_INLINE_FUNCTION void compute_duarray_cpu(const typename Kokkos::TeamPolicy::member_type& team, int, int, const real_type&, const real_type&, const real_type&, // compute_duidrj_cpu - const real_type&, const real_type&, const real_type&, const real_type&, const real_type&); + const real_type&, const real_type&, const real_type&, const real_type&, const real_type&, + const real_type&, const real_type&); // Sets the style for the switching function // 0 = none // 1 = cosine int switch_flag; + // Sets the style for the inner switching function + // 0 = none + // 1 = cosine + int switch_inner_flag; + // Chem snap flags int chem_flag; int bnorm_flag; diff --git a/src/KOKKOS/sna_kokkos_impl.h b/src/KOKKOS/sna_kokkos_impl.h index 550548df55..546c07ee11 100644 --- a/src/KOKKOS/sna_kokkos_impl.h +++ b/src/KOKKOS/sna_kokkos_impl.h @@ -25,12 +25,13 @@ namespace LAMMPS_NS { static const double MY_PI = 3.14159265358979323846; // pi +static const double MY_PI2 = 1.57079632679489661923; // pi/2 template inline SNAKokkos::SNAKokkos(real_type rfac0_in, int twojmax_in, real_type rmin0_in, int switch_flag_in, int bzero_flag_in, - int chem_flag_in, int bnorm_flag_in, int wselfall_flag_in, int nelements_in) + int chem_flag_in, int bnorm_flag_in, int wselfall_flag_in, int nelements_in, int switch_inner_flag_in) { LAMMPS_NS::ExecutionSpace execution_space = ExecutionSpaceFromDevice::space; host_flag = (execution_space == LAMMPS_NS::Host); @@ -40,6 +41,7 @@ SNAKokkos::SNAKokkos(real_type rfac0_in, rfac0 = rfac0_in; rmin0 = rmin0_in; switch_flag = switch_flag_in; + switch_inner_flag = switch_inner_flag_in; bzero_flag = bzero_flag_in; chem_flag = chem_flag_in; @@ -295,6 +297,8 @@ void SNAKokkos::grow_rij(int newnatom, int rij = t_sna_3d(Kokkos::NoInit("sna:rij"),natom,nmax,3); wj = t_sna_2d(Kokkos::NoInit("sna:wj"),natom,nmax); rcutij = t_sna_2d(Kokkos::NoInit("sna:rcutij"),natom,nmax); + sinnerij = t_sna_2d(Kokkos::NoInit("sna:sinnerij"),natom,nmax); + dinnerij = t_sna_2d(Kokkos::NoInit("sna:dinnerij"),natom,nmax); inside = t_sna_2i(Kokkos::NoInit("sna:inside"),natom,nmax); element = t_sna_2i(Kokkos::NoInit("sna:element"),natom,nmax); dedr = t_sna_3d(Kokkos::NoInit("sna:dedr"),natom,nmax,3); @@ -371,6 +375,8 @@ void SNAKokkos::compute_cayley_klein(const const real_type rsq = x * x + y * y + z * z; const real_type r = sqrt(rsq); const real_type rcut = rcutij(iatom, jnbor); + const real_type sinner = sinnerij(iatom, jnbor); + const real_type dinner = dinnerij(iatom, jnbor); const real_type rscale0 = rfac0 * static_cast(MY_PI) / (rcut - rmin0); const real_type theta0 = (r - rmin0) * rscale0; const real_type sn = sin(theta0); @@ -380,7 +386,7 @@ void SNAKokkos::compute_cayley_klein(const const real_type wj_local = wj(iatom, jnbor); real_type sfac, dsfac; - compute_s_dsfac(r, rcut, sfac, dsfac); + compute_s_dsfac(r, rcut, sinner, dinner, sfac, dsfac); sfac *= wj_local; dsfac *= wj_local; @@ -1238,7 +1244,7 @@ void SNAKokkos::compute_ui_cpu(const typen z0 = r / tan(theta0); compute_uarray_cpu(team, iatom, jnbor, x, y, z, z0, r); - add_uarraytot(team, iatom, jnbor, r, wj(iatom,jnbor), rcutij(iatom,jnbor), element(iatom, jnbor)); + add_uarraytot(team, iatom, jnbor, r, wj(iatom,jnbor), rcutij(iatom,jnbor), sinnerij(iatom,jnbor), dinnerij(iatom,jnbor), element(iatom, jnbor)); } /* ---------------------------------------------------------------------- @@ -1541,7 +1547,7 @@ void SNAKokkos::compute_duidrj_cpu(const t z0 = r * cs / sn; dz0dr = z0 / r - (r*rscale0) * (rsq + z0 * z0) / rsq; - compute_duarray_cpu(team, iatom, jnbor, x, y, z, z0, r, dz0dr, wj(iatom,jnbor), rcutij(iatom,jnbor)); + compute_duarray_cpu(team, iatom, jnbor, x, y, z, z0, r, dz0dr, wj(iatom,jnbor), rcutij(iatom,jnbor), sinnerij(iatom,jnbor), dinnerij(iatom,jnbor)); } @@ -1623,9 +1629,10 @@ void SNAKokkos::compute_deidrj_cpu(const t template KOKKOS_INLINE_FUNCTION void SNAKokkos::add_uarraytot(const typename Kokkos::TeamPolicy::member_type& team, int iatom, int jnbor, - const real_type& r, const real_type& wj, const real_type& rcut, int jelem) + const real_type& r, const real_type& wj, const real_type& rcut, + const real_type& sinner, const real_type& dinner, int jelem) { - const real_type sfac = compute_sfac(r, rcut) * wj; + const real_type sfac = compute_sfac(r, rcut, sinner, dinner) * wj; Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,twojmax+1), [&] (const int& j) { @@ -1746,7 +1753,8 @@ KOKKOS_INLINE_FUNCTION void SNAKokkos::compute_duarray_cpu(const typename Kokkos::TeamPolicy::member_type& team, int iatom, int jnbor, const real_type& x, const real_type& y, const real_type& z, const real_type& z0, const real_type& r, const real_type& dz0dr, - const real_type& wj, const real_type& rcut) + const real_type& wj, const real_type& rcut, + const real_type& sinner, const real_type& dinner) { real_type r0inv; real_type a_r, a_i, b_r, b_i; @@ -1872,8 +1880,8 @@ void SNAKokkos::compute_duarray_cpu(const }); } - real_type sfac = compute_sfac(r, rcut); - real_type dsfac = compute_dsfac(r, rcut); + real_type sfac = compute_sfac(r, rcut, sinner, dinner); + real_type dsfac = compute_dsfac(r, rcut, sinner, dinner); sfac *= wj; dsfac *= wj; @@ -2224,7 +2232,7 @@ int SNAKokkos::compute_ncoeff() template KOKKOS_INLINE_FUNCTION -real_type SNAKokkos::compute_sfac(real_type r, real_type rcut) +real_type SNAKokkos::compute_sfac(real_type r, real_type rcut, real_type sinner, real_type dinner) { constexpr real_type one = static_cast(1.0); constexpr real_type zero = static_cast(0.0); @@ -2235,18 +2243,30 @@ real_type SNAKokkos::compute_sfac(real_typ else if (r > rcut) return zero; else { real_type rcutfac = static_cast(MY_PI) / (rcut - rmin0); - return onehalf * (cos((r - rmin0) * rcutfac) + one); + if (switch_inner_flag == 0) + return onehalf * (cos((r - rmin0) * rcutfac) + one); + if (switch_inner_flag == 1) { + if (r >= sinner + dinner) + return onehalf * (cos((r - rmin0) * rcutfac) + one); + else if (r > sinner - dinner) { + real_type rcutfacinner = static_cast(MY_PI2) / dinner; + return onehalf * (cos((r - rmin0) * rcutfac) + one) * + onehalf * (one - cos(static_cast(MY_PI2) + (r - sinner) * rcutfacinner)); + } else return zero; + } + return zero; // dummy return } } - return zero; + return zero; // dummy return } /* ---------------------------------------------------------------------- */ template KOKKOS_INLINE_FUNCTION -real_type SNAKokkos::compute_dsfac(real_type r, real_type rcut) +real_type SNAKokkos::compute_dsfac(real_type r, real_type rcut, real_type sinner, real_type dinner) { + constexpr real_type one = static_cast(1.0); constexpr real_type zero = static_cast(0.0); constexpr real_type onehalf = static_cast(0.5); if (switch_flag == 0) return zero; @@ -2258,12 +2278,12 @@ real_type SNAKokkos::compute_dsfac(real_ty return -onehalf * sin((r - rmin0) * rcutfac) * rcutfac; } } - return zero; + return zero; // dummy return } template KOKKOS_INLINE_FUNCTION -void SNAKokkos::compute_s_dsfac(const real_type r, const real_type rcut, real_type& sfac, real_type& dsfac) { +void SNAKokkos::compute_s_dsfac(const real_type r, const real_type rcut, const real_type sinner, const real_type dinner, real_type& sfac, real_type& dsfac) { constexpr real_type one = static_cast(1.0); constexpr real_type zero = static_cast(0.0); constexpr real_type onehalf = static_cast(0.5); @@ -2356,6 +2376,8 @@ double SNAKokkos::memory_usage() bytes += natom * nmax * sizeof(real_type); // inside bytes += natom * nmax * sizeof(real_type); // wj bytes += natom * nmax * sizeof(real_type); // rcutij + bytes += natom * nmax * sizeof(real_type); // sinnerij + bytes += natom * nmax * sizeof(real_type); // dinnerij return bytes; } diff --git a/src/ML-SNAP/compute_sna_atom.cpp b/src/ML-SNAP/compute_sna_atom.cpp index cec705770d..5f24ebeaa6 100644 --- a/src/ML-SNAP/compute_sna_atom.cpp +++ b/src/ML-SNAP/compute_sna_atom.cpp @@ -32,7 +32,7 @@ using namespace LAMMPS_NS; ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), cutsq(nullptr), list(nullptr), sna(nullptr), - radelem(nullptr), wjelem(nullptr), rinnerelem(nullptr), drinnerelem(nullptr) + radelem(nullptr), wjelem(nullptr), sinnerelem(nullptr), dinnerelem(nullptr) { double rmin0, rfac0; @@ -85,6 +85,11 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) : } } + // set local input checks + + int sinnerflag = 0; + int dinnerflag = 0; + // process optional args int iarg = nargmin; @@ -134,21 +139,37 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) : wselfallflag = atoi(arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"switchinnerflag") == 0) { - if (iarg+1+2*ntypes > narg) + if (iarg+2 > narg) error->all(FLERR,"Illegal compute sna/atom command"); - switchinnerflag = 1; + switchinnerflag = atoi(arg[iarg+1]); + iarg += 2; + } else if (strcmp(arg[iarg],"sinner") == 0) { iarg++; - memory->create(rinnerelem,ntypes+1,"sna/atom:rinnerelem"); - memory->create(drinnerelem,ntypes+1,"sna/atom:drinnerelem"); + if (iarg+ntypes > narg) + error->all(FLERR,"Illegal compute sna/atom command"); + memory->create(sinnerelem,ntypes+1,"sna/atom:sinnerelem"); for (int i = 0; i < ntypes; i++) - rinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp); + sinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp); + sinnerflag = 1; iarg += ntypes; + } else if (strcmp(arg[iarg],"dinner") == 0) { + iarg++; + if (iarg+ntypes > narg) + error->all(FLERR,"Illegal compute sna/atom command"); + memory->create(dinnerelem,ntypes+1,"sna/atom:dinnerelem"); for (int i = 0; i < ntypes; i++) - drinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp); + dinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp); + dinnerflag = 1; iarg += ntypes; } else error->all(FLERR,"Illegal compute sna/atom command"); } + if (switchinnerflag && !(sinnerflag && dinnerflag)) + error->all(FLERR,"Illegal compute sna/atom command: switchinnerflag = 1, missing sinner/dinner keyword"); + + if (!switchinnerflag && (sinnerflag || dinnerflag)) + error->all(FLERR,"Illegal compute sna/atom command: switchinnerflag = 0, unexpected sinner/dinner keyword"); + snaptr = new SNA(lmp, rfac0, twojmax, rmin0, switchflag, bzeroflag, chemflag, bnormflag, wselfallflag, @@ -176,8 +197,8 @@ ComputeSNAAtom::~ComputeSNAAtom() if (chemflag) memory->destroy(map); if (switchinnerflag) { - memory->destroy(rinnerelem); - memory->destroy(drinnerelem); + memory->destroy(sinnerelem); + memory->destroy(dinnerelem); } } @@ -282,8 +303,8 @@ void ComputeSNAAtom::compute_peratom() snaptr->wj[ninside] = wjelem[jtype]; snaptr->rcutij[ninside] = (radi+radelem[jtype])*rcutfac; if (switchinnerflag) { - snaptr->rinnerij[ninside] = 0.5*(rinnerelem[itype]+rinnerelem[jtype]); - snaptr->drinnerij[ninside] = 0.5*(drinnerelem[itype]+drinnerelem[jtype]); + snaptr->sinnerij[ninside] = 0.5*(sinnerelem[itype]+sinnerelem[jtype]); + snaptr->dinnerij[ninside] = 0.5*(dinnerelem[itype]+dinnerelem[jtype]); } if (chemflag) snaptr->element[ninside] = jelem; ninside++; diff --git a/src/ML-SNAP/compute_sna_atom.h b/src/ML-SNAP/compute_sna_atom.h index 5e62fe47d9..a7140c3949 100644 --- a/src/ML-SNAP/compute_sna_atom.h +++ b/src/ML-SNAP/compute_sna_atom.h @@ -45,8 +45,8 @@ class ComputeSNAAtom : public Compute { int *map; // map types to [0,nelements) int nelements, chemflag; int switchinnerflag; - double *rinnerelem; - double *drinnerelem; + double *sinnerelem; + double *dinnerelem; class SNA *snaptr; double cutmax; int quadraticflag; diff --git a/src/ML-SNAP/compute_snad_atom.cpp b/src/ML-SNAP/compute_snad_atom.cpp index 4874a53c9c..838d8a85c9 100644 --- a/src/ML-SNAP/compute_snad_atom.cpp +++ b/src/ML-SNAP/compute_snad_atom.cpp @@ -32,7 +32,7 @@ using namespace LAMMPS_NS; ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), cutsq(nullptr), list(nullptr), snad(nullptr), - radelem(nullptr), wjelem(nullptr), rinnerelem(nullptr), drinnerelem(nullptr) + radelem(nullptr), wjelem(nullptr), sinnerelem(nullptr), dinnerelem(nullptr) { double rfac0, rmin0; int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag; @@ -57,8 +57,8 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) : // process required arguments - memory->create(radelem,ntypes+1,"sna/atom:radelem"); // offset by 1 to match up with types - memory->create(wjelem,ntypes+1,"sna/atom:wjelem"); + memory->create(radelem,ntypes+1,"snad/atom:radelem"); // offset by 1 to match up with types + memory->create(wjelem,ntypes+1,"snad/atom:wjelem"); rcutfac = atof(arg[3]); rfac0 = atof(arg[4]); twojmax = atoi(arg[5]); @@ -71,7 +71,7 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) : double cut; cutmax = 0.0; - memory->create(cutsq,ntypes+1,ntypes+1,"sna/atom:cutsq"); + memory->create(cutsq,ntypes+1,ntypes+1,"snad/atom:cutsq"); for (int i = 1; i <= ntypes; i++) { cut = 2.0*radelem[i]*rcutfac; if (cut > cutmax) cutmax = cut; @@ -82,6 +82,11 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) : } } + // set local input checks + + int sinnerflag = 0; + int dinnerflag = 0; + // process optional args int iarg = nargmin; @@ -131,21 +136,38 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) : wselfallflag = atoi(arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"switchinnerflag") == 0) { - if (iarg+1+2*ntypes > narg) + if (iarg+2 > narg) error->all(FLERR,"Illegal compute snad/atom command"); - switchinnerflag = 1; + switchinnerflag = atoi(arg[iarg+1]); + iarg += 2; + } else if (strcmp(arg[iarg],"sinner") == 0) { iarg++; - memory->create(rinnerelem,ntypes+1,"snad/atom:rinnerelem"); - memory->create(drinnerelem,ntypes+1,"snad/atom:drinnerelem"); + if (iarg+ntypes > narg) + error->all(FLERR,"Illegal compute snad/atom command"); + memory->create(sinnerelem,ntypes+1,"snad/atom:sinnerelem"); for (int i = 0; i < ntypes; i++) - rinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp); + sinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp); + sinnerflag = 1; iarg += ntypes; + } else if (strcmp(arg[iarg],"dinner") == 0) { + iarg++; + if (iarg+ntypes > narg) + error->all(FLERR,"Illegal compute snad/atom command"); + memory->create(dinnerelem,ntypes+1,"snad/atom:dinnerelem"); for (int i = 0; i < ntypes; i++) - drinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp); + dinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp); + dinnerflag = 1; iarg += ntypes; } else error->all(FLERR,"Illegal compute snad/atom command"); } + if (switchinnerflag && !(sinnerflag && dinnerflag)) + error->all(FLERR,"Illegal compute snad/atom command: switchinnerflag = 1, missing sinner/dinner keyword"); + + if (!switchinnerflag && (sinnerflag || dinnerflag)) + error->all(FLERR,"Illegal compute snad/atom command: switchinnerflag = 0, unexpected sinner/dinner keyword"); + + snaptr = new SNA(lmp, rfac0, twojmax, rmin0, switchflag, bzeroflag, chemflag, bnormflag, wselfallflag, @@ -177,8 +199,8 @@ ComputeSNADAtom::~ComputeSNADAtom() if (chemflag) memory->destroy(map); if (switchinnerflag) { - memory->destroy(rinnerelem); - memory->destroy(drinnerelem); + memory->destroy(sinnerelem); + memory->destroy(dinnerelem); } } @@ -190,7 +212,7 @@ void ComputeSNADAtom::init() error->all(FLERR,"Compute snad/atom requires a pair style be defined"); if (cutmax > force->pair->cutforce) - error->all(FLERR,"Compute sna/atom cutoff is longer than pairwise cutoff"); + error->all(FLERR,"Compute snad/atom cutoff is longer than pairwise cutoff"); // need an occasional full neighbor list @@ -299,8 +321,8 @@ void ComputeSNADAtom::compute_peratom() snaptr->wj[ninside] = wjelem[jtype]; snaptr->rcutij[ninside] = (radi+radelem[jtype])*rcutfac; if (switchinnerflag) { - snaptr->rinnerij[ninside] = 0.5*(rinnerelem[itype]+rinnerelem[jtype]); - snaptr->drinnerij[ninside] = 0.5*(drinnerelem[itype]+drinnerelem[jtype]); + snaptr->sinnerij[ninside] = 0.5*(sinnerelem[itype]+sinnerelem[jtype]); + snaptr->dinnerij[ninside] = 0.5*(dinnerelem[itype]+dinnerelem[jtype]); } if (chemflag) snaptr->element[ninside] = jelem; ninside++; diff --git a/src/ML-SNAP/compute_snad_atom.h b/src/ML-SNAP/compute_snad_atom.h index c03458446f..2e2842a0c1 100644 --- a/src/ML-SNAP/compute_snad_atom.h +++ b/src/ML-SNAP/compute_snad_atom.h @@ -47,8 +47,8 @@ class ComputeSNADAtom : public Compute { int *map; // map types to [0,nelements) int nelements, chemflag; int switchinnerflag; - double *rinnerelem; - double *drinnerelem; + double *sinnerelem; + double *dinnerelem; class SNA *snaptr; double cutmax; int quadraticflag; diff --git a/src/ML-SNAP/compute_snap.cpp b/src/ML-SNAP/compute_snap.cpp index 04dac2acba..83f56e338c 100644 --- a/src/ML-SNAP/compute_snap.cpp +++ b/src/ML-SNAP/compute_snap.cpp @@ -35,7 +35,7 @@ enum{SCALAR,VECTOR,ARRAY}; ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), cutsq(nullptr), list(nullptr), snap(nullptr), snapall(nullptr), snap_peratom(nullptr), radelem(nullptr), wjelem(nullptr), - rinnerelem(nullptr), drinnerelem(nullptr), snaptr(nullptr) + sinnerelem(nullptr), dinnerelem(nullptr), snaptr(nullptr) { array_flag = 1; @@ -89,6 +89,11 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) : } } + // set local input checks + + int sinnerflag = 0; + int dinnerflag = 0; + // process optional args int iarg = nargmin; @@ -115,7 +120,7 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) : quadraticflag = atoi(arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"chem") == 0) { - if (iarg+2 > narg) + if (iarg+2+ntypes > narg) error->all(FLERR,"Illegal compute snap command"); chemflag = 1; memory->create(map,ntypes+1,"compute_snap:map"); @@ -143,21 +148,37 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) : bikflag = atoi(arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"switchinnerflag") == 0) { - if (iarg+1+2*ntypes > narg) + if (iarg+2 > narg) error->all(FLERR,"Illegal compute snap command"); - switchinnerflag = 1; + switchinnerflag = atoi(arg[iarg+1]); + iarg += 2; + } else if (strcmp(arg[iarg],"sinner") == 0) { iarg++; - memory->create(rinnerelem,ntypes+1,"snap:rinnerelem"); - memory->create(drinnerelem,ntypes+1,"snap:drinnerelem"); + if (iarg+ntypes > narg) + error->all(FLERR,"Illegal compute snap command"); + memory->create(sinnerelem,ntypes+1,"snap:sinnerelem"); for (int i = 0; i < ntypes; i++) - rinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp); + sinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp); + sinnerflag = 1; iarg += ntypes; + } else if (strcmp(arg[iarg],"dinner") == 0) { + iarg++; + if (iarg+ntypes > narg) + error->all(FLERR,"Illegal compute snap command"); + memory->create(dinnerelem,ntypes+1,"snap:dinnerelem"); for (int i = 0; i < ntypes; i++) - drinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp); + dinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp); + dinnerflag = 1; iarg += ntypes; } else error->all(FLERR,"Illegal compute snap command"); } + if (switchinnerflag && !(sinnerflag && dinnerflag)) + error->all(FLERR,"Illegal compute snap command: switchinnerflag = 1, missing sinner/dinner keyword"); + + if (!switchinnerflag && (sinnerflag || dinnerflag)) + error->all(FLERR,"Illegal compute snap command: switchinnerflag = 0, unexpected sinner/dinner keyword"); + snaptr = new SNA(lmp, rfac0, twojmax, rmin0, switchflag, bzeroflag, chemflag, bnormflag, wselfallflag, @@ -198,8 +219,8 @@ ComputeSnap::~ComputeSnap() if (chemflag) memory->destroy(map); if (switchinnerflag) { - memory->destroy(rinnerelem); - memory->destroy(drinnerelem); + memory->destroy(sinnerelem); + memory->destroy(dinnerelem); } } @@ -353,8 +374,8 @@ void ComputeSnap::compute_array() snaptr->wj[ninside] = wjelem[jtype]; snaptr->rcutij[ninside] = (radi+radelem[jtype])*rcutfac; if (switchinnerflag) { - snaptr->rinnerij[ninside] = 0.5*(rinnerelem[itype]+rinnerelem[jtype]); - snaptr->drinnerij[ninside] = 0.5*(drinnerelem[itype]+drinnerelem[jtype]); + snaptr->sinnerij[ninside] = 0.5*(sinnerelem[itype]+sinnerelem[jtype]); + snaptr->dinnerij[ninside] = 0.5*(dinnerelem[itype]+dinnerelem[jtype]); } if (chemflag) snaptr->element[ninside] = jelem; ninside++; diff --git a/src/ML-SNAP/compute_snap.h b/src/ML-SNAP/compute_snap.h index fa31de747d..bf631539ba 100644 --- a/src/ML-SNAP/compute_snap.h +++ b/src/ML-SNAP/compute_snap.h @@ -47,8 +47,8 @@ class ComputeSnap : public Compute { int *map; // map types to [0,nelements) int nelements, chemflag; int switchinnerflag; - double *rinnerelem; - double *drinnerelem; + double *sinnerelem; + double *dinnerelem; class SNA *snaptr; double cutmax; int quadraticflag; diff --git a/src/ML-SNAP/compute_snav_atom.cpp b/src/ML-SNAP/compute_snav_atom.cpp index d3999381f2..0baa4bc110 100644 --- a/src/ML-SNAP/compute_snav_atom.cpp +++ b/src/ML-SNAP/compute_snav_atom.cpp @@ -31,7 +31,7 @@ using namespace LAMMPS_NS; ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), cutsq(nullptr), list(nullptr), snav(nullptr), - radelem(nullptr), wjelem(nullptr), rinnerelem(nullptr), drinnerelem(nullptr) + radelem(nullptr), wjelem(nullptr), sinnerelem(nullptr), dinnerelem(nullptr) { double rfac0, rmin0; int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag; @@ -56,8 +56,8 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) : // process required arguments - memory->create(radelem,ntypes+1,"sna/atom:radelem"); // offset by 1 to match up with types - memory->create(wjelem,ntypes+1,"sna/atom:wjelem"); + memory->create(radelem,ntypes+1,"snav/atom:radelem"); // offset by 1 to match up with types + memory->create(wjelem,ntypes+1,"snav/atom:wjelem"); rcutfac = atof(arg[3]); rfac0 = atof(arg[4]); twojmax = atoi(arg[5]); @@ -67,7 +67,7 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) : wjelem[i+1] = atof(arg[6+ntypes+i]); // construct cutsq double cut; - memory->create(cutsq,ntypes+1,ntypes+1,"sna/atom:cutsq"); + memory->create(cutsq,ntypes+1,ntypes+1,"snav/atom:cutsq"); for (int i = 1; i <= ntypes; i++) { cut = 2.0*radelem[i]*rcutfac; cutsq[i][i] = cut*cut; @@ -77,6 +77,11 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) : } } + // set local input checks + + int sinnerflag = 0; + int dinnerflag = 0; + // process optional args int iarg = nargmin; @@ -104,7 +109,7 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) : iarg += 2; } else if (strcmp(arg[iarg],"chem") == 0) { if (iarg+2+ntypes > narg) - error->all(FLERR,"Illegal compute sna/atom command"); + error->all(FLERR,"Illegal compute snav/atom command"); chemflag = 1; memory->create(map,ntypes+1,"compute_sna_atom:map"); nelements = utils::inumeric(FLERR,arg[iarg+1],false,lmp); @@ -126,21 +131,37 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) : wselfallflag = atoi(arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"switchinnerflag") == 0) { - if (iarg+1+2*ntypes > narg) + if (iarg+2 > narg) error->all(FLERR,"Illegal compute snav/atom command"); - switchinnerflag = 1; + switchinnerflag = atoi(arg[iarg+1]); + iarg += 2; + } else if (strcmp(arg[iarg],"sinner") == 0) { iarg++; - memory->create(rinnerelem,ntypes+1,"snav/atom:rinnerelem"); - memory->create(drinnerelem,ntypes+1,"snav/atom:drinnerelem"); + if (iarg+ntypes > narg) + error->all(FLERR,"Illegal compute snav/atom command"); + memory->create(sinnerelem,ntypes+1,"snav/atom:sinnerelem"); for (int i = 0; i < ntypes; i++) - rinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp); + sinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp); + sinnerflag = 1; iarg += ntypes; + } else if (strcmp(arg[iarg],"dinner") == 0) { + iarg++; + if (iarg+ntypes > narg) + error->all(FLERR,"Illegal compute snav/atom command"); + memory->create(dinnerelem,ntypes+1,"snav/atom:dinnerelem"); for (int i = 0; i < ntypes; i++) - drinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp); + dinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp); + dinnerflag = 1; iarg += ntypes; } else error->all(FLERR,"Illegal compute snav/atom command"); } + if (switchinnerflag && !(sinnerflag && dinnerflag)) + error->all(FLERR,"Illegal compute snav/atom command: switchinnerflag = 1, missing sinner/dinner keyword"); + + if (!switchinnerflag && (sinnerflag || dinnerflag)) + error->all(FLERR,"Illegal compute snav/atom command: switchinnerflag = 0, unexpected sinner/dinner keyword"); + snaptr = new SNA(lmp, rfac0, twojmax, rmin0, switchflag, bzeroflag, chemflag, bnormflag, wselfallflag, @@ -171,8 +192,8 @@ ComputeSNAVAtom::~ComputeSNAVAtom() if (chemflag) memory->destroy(map); if (switchinnerflag) { - memory->destroy(rinnerelem); - memory->destroy(drinnerelem); + memory->destroy(sinnerelem); + memory->destroy(dinnerelem); } } @@ -291,8 +312,8 @@ void ComputeSNAVAtom::compute_peratom() snaptr->wj[ninside] = wjelem[jtype]; snaptr->rcutij[ninside] = (radi+radelem[jtype])*rcutfac; if (switchinnerflag) { - snaptr->rinnerij[ninside] = 0.5*(rinnerelem[itype]+rinnerelem[jtype]); - snaptr->drinnerij[ninside] = 0.5*(drinnerelem[itype]+drinnerelem[jtype]); + snaptr->sinnerij[ninside] = 0.5*(sinnerelem[itype]+sinnerelem[jtype]); + snaptr->dinnerij[ninside] = 0.5*(dinnerelem[itype]+dinnerelem[jtype]); } if (chemflag) snaptr->element[ninside] = jelem; ninside++; diff --git a/src/ML-SNAP/compute_snav_atom.h b/src/ML-SNAP/compute_snav_atom.h index be442f3a49..335f994323 100644 --- a/src/ML-SNAP/compute_snav_atom.h +++ b/src/ML-SNAP/compute_snav_atom.h @@ -47,8 +47,8 @@ class ComputeSNAVAtom : public Compute { int *map; // map types to [0,nelements) int nelements, chemflag; int switchinnerflag; - double *rinnerelem; - double *drinnerelem; + double *sinnerelem; + double *dinnerelem; class SNA *snaptr; int quadraticflag; }; diff --git a/src/ML-SNAP/pair_snap.cpp b/src/ML-SNAP/pair_snap.cpp index 3ba14c5872..9c076710da 100644 --- a/src/ML-SNAP/pair_snap.cpp +++ b/src/ML-SNAP/pair_snap.cpp @@ -45,8 +45,8 @@ PairSNAP::PairSNAP(LAMMPS *lmp) : Pair(lmp) radelem = nullptr; wjelem = nullptr; coeffelem = nullptr; - rinnerelem = nullptr; - drinnerelem = nullptr; + sinnerelem = nullptr; + dinnerelem = nullptr; beta_max = 0; beta = nullptr; @@ -65,8 +65,8 @@ PairSNAP::~PairSNAP() memory->destroy(coeffelem); if (switchinnerflag) { - memory->destroy(rinnerelem); - memory->destroy(drinnerelem); + memory->destroy(sinnerelem); + memory->destroy(dinnerelem); } memory->destroy(beta); @@ -158,8 +158,8 @@ void PairSNAP::compute(int eflag, int vflag) snaptr->wj[ninside] = wjelem[jelem]; snaptr->rcutij[ninside] = (radi + radelem[jelem])*rcutfac; if (switchinnerflag) { - snaptr->rinnerij[ninside] = 0.5*(rinnerelem[ielem]+rinnerelem[jelem]); - snaptr->drinnerij[ninside] = 0.5*(drinnerelem[ielem]+drinnerelem[jelem]); + snaptr->sinnerij[ninside] = 0.5*(sinnerelem[ielem]+sinnerelem[jelem]); + snaptr->dinnerij[ninside] = 0.5*(dinnerelem[ielem]+dinnerelem[jelem]); } if (chemflag) snaptr->element[ninside] = jelem; ninside++; @@ -331,8 +331,8 @@ void PairSNAP::compute_bispectrum() snaptr->wj[ninside] = wjelem[jelem]; snaptr->rcutij[ninside] = (radi + radelem[jelem])*rcutfac; if (switchinnerflag) { - snaptr->rinnerij[ninside] = 0.5*(rinnerelem[ielem]+rinnerelem[jelem]); - snaptr->drinnerij[ninside] = 0.5*(drinnerelem[ielem]+drinnerelem[jelem]); + snaptr->sinnerij[ninside] = 0.5*(sinnerelem[ielem]+sinnerelem[jelem]); + snaptr->dinnerij[ninside] = 0.5*(dinnerelem[ielem]+dinnerelem[jelem]); } if (chemflag) snaptr->element[ninside] = jelem; ninside++; @@ -516,13 +516,13 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) memory->destroy(radelem); memory->destroy(wjelem); memory->destroy(coeffelem); - memory->destroy(rinnerelem); - memory->destroy(drinnerelem); + memory->destroy(sinnerelem); + memory->destroy(dinnerelem); memory->create(radelem,nelements,"pair:radelem"); memory->create(wjelem,nelements,"pair:wjelem"); memory->create(coeffelem,nelements,ncoeffall,"pair:coeffelem"); - memory->create(rinnerelem,nelements,"pair:rinnerelem"); - memory->create(drinnerelem,nelements,"pair:drinnerelem"); + memory->create(sinnerelem,nelements,"pair:sinnerelem"); + memory->create(dinnerelem,nelements,"pair:dinnerelem"); // initialize checklist for all required nelements @@ -644,8 +644,8 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) // set local input checks - int rinnerflag = 0; - int drinnerflag = 0; + int sinnerflag = 0; + int dinnerflag = 0; // open SNAP parameter file on proc 0 @@ -690,7 +690,7 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) // check for keywords with one value per element - if (keywd == "rinner" || keywd == "drinner") { + if (keywd == "sinner" || keywd == "dinner") { if (words.size() != nelements+1) error->all(FLERR,"Incorrect SNAP parameter file"); @@ -700,20 +700,20 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) int iword = 1; - if (keywd == "rinner") { + if (keywd == "sinner") { keyval = words[iword]; for (int ielem = 0; ielem < nelements; ielem++) { - rinnerelem[ielem] = utils::numeric(FLERR,keyval,false,lmp); + sinnerelem[ielem] = utils::numeric(FLERR,keyval,false,lmp); iword++; } - rinnerflag = 1; - } else if (keywd == "drinner") { + sinnerflag = 1; + } else if (keywd == "dinner") { keyval = words[iword]; for (int ielem = 0; ielem < nelements; ielem++) { - drinnerelem[ielem] = utils::numeric(FLERR,keyval,false,lmp); + dinnerelem[ielem] = utils::numeric(FLERR,keyval,false,lmp); iword++; } - drinnerflag = 1; + dinnerflag = 1; } } else { @@ -765,10 +765,10 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) if (chemflag && nelemtmp != nelements) error->all(FLERR,"Incorrect SNAP parameter file"); - if (switchinnerflag && !(rinnerflag && drinnerflag)) + if (switchinnerflag && !(sinnerflag && dinnerflag)) error->all(FLERR,"Incorrect SNAP parameter file"); - if (!switchinnerflag && (rinnerflag || drinnerflag)) + if (!switchinnerflag && (sinnerflag || dinnerflag)) error->all(FLERR,"Incorrect SNAP parameter file"); } diff --git a/src/ML-SNAP/pair_snap.h b/src/ML-SNAP/pair_snap.h index 77ceeabd4f..f260704801 100644 --- a/src/ML-SNAP/pair_snap.h +++ b/src/ML-SNAP/pair_snap.h @@ -60,8 +60,8 @@ class PairSNAP : public Pair { int twojmax, switchflag, bzeroflag, bnormflag; int chemflag, wselfallflag; int switchinnerflag; // inner cutoff switch - double *rinnerelem; // element inner cutoff - double *drinnerelem; // element inner cutoff range + double *sinnerelem; // element inner cutoff midpoint + double *dinnerelem; // element inner cutoff half-width int chunksize,parallel_thresh; double rfac0, rmin0, wj1, wj2; int rcutfacflag, twojmaxflag; // flags for required parameters diff --git a/src/ML-SNAP/sna.cpp b/src/ML-SNAP/sna.cpp index 717d0014f5..0bd66d0bce 100644 --- a/src/ML-SNAP/sna.cpp +++ b/src/ML-SNAP/sna.cpp @@ -145,8 +145,8 @@ SNA::SNA(LAMMPS* lmp, double rfac0_in, int twojmax_in, inside = nullptr; wj = nullptr; rcutij = nullptr; - rinnerij = nullptr; - drinnerij = nullptr; + sinnerij = nullptr; + dinnerij = nullptr; element = nullptr; nmax = 0; idxz = nullptr; @@ -176,10 +176,8 @@ SNA::~SNA() memory->destroy(inside); memory->destroy(wj); memory->destroy(rcutij); - if (switch_inner_flag) { - memory->destroy(rinnerij); - memory->destroy(drinnerij); - } + memory->destroy(sinnerij); + memory->destroy(dinnerij); if (chem_flag) memory->destroy(element); memory->destroy(ulist_r_ij); memory->destroy(ulist_i_ij); @@ -327,10 +325,8 @@ void SNA::grow_rij(int newnmax) memory->destroy(inside); memory->destroy(wj); memory->destroy(rcutij); - if (switch_inner_flag) { - memory->destroy(rinnerij); - memory->destroy(drinnerij); - } + memory->destroy(sinnerij); + memory->destroy(dinnerij); if (chem_flag) memory->destroy(element); memory->destroy(ulist_r_ij); memory->destroy(ulist_i_ij); @@ -338,10 +334,8 @@ void SNA::grow_rij(int newnmax) memory->create(inside, nmax, "pair:inside"); memory->create(wj, nmax, "pair:wj"); memory->create(rcutij, nmax, "pair:rcutij"); - if (switch_inner_flag) { - memory->create(rinnerij, nmax, "pair:rinnerij"); - memory->create(drinnerij, nmax, "pair:drinnerij"); - } + memory->create(sinnerij, nmax, "pair:sinnerij"); + memory->create(dinnerij, nmax, "pair:dinnerij"); if (chem_flag) memory->create(element, nmax, "sna:element"); memory->create(ulist_r_ij, nmax, idxu_max, "sna:ulist_ij"); memory->create(ulist_i_ij, nmax, idxu_max, "sna:ulist_ij"); @@ -1020,12 +1014,9 @@ void SNA::add_uarraytot(double r, int jj) double sfac; int jelem; - sfac = compute_sfac(r, rcutij[jj]); + sfac = compute_sfac(r, rcutij[jj], sinnerij[jj], dinnerij[jj]); sfac *= wj[jj]; - if (switch_inner_flag) - sfac *= compute_sfac_inner(r, rinnerij[jj], drinnerij[jj]); - if (chem_flag) jelem = element[jj]; else jelem = 0; @@ -1268,14 +1259,8 @@ void SNA::compute_duarray(double x, double y, double z, } } - double sfac = compute_sfac(r, rcut); - double dsfac = compute_dsfac(r, rcut); - - if (switch_inner_flag) { - double sfac_inner = compute_sfac_inner(r, rinnerij[jj], drinnerij[jj]); - dsfac = dsfac*sfac_inner + sfac*compute_dsfac_inner(r, rinnerij[jj], drinnerij[jj]); - sfac *= sfac_inner; - } + double sfac = compute_sfac(r, rcut, sinnerij[jj], dinnerij[jj]); + double dsfac = compute_dsfac(r, rcut, sinnerij[jj], dinnerij[jj]); sfac *= wj; dsfac *= wj; @@ -1339,10 +1324,8 @@ double SNA::memory_usage() bytes += (double)nmax * sizeof(int); // inside bytes += (double)nmax * sizeof(double); // wj bytes += (double)nmax * sizeof(double); // rcutij - if (switch_inner_flag) { - bytes += (double)nmax * sizeof(double); // rinnerij - bytes += (double)nmax * sizeof(double); // drinnerij - } + bytes += (double)nmax * sizeof(double); // sinnerij + bytes += (double)nmax * sizeof(double); // dinnerij if (chem_flag) bytes += (double)nmax * sizeof(int); // element return bytes; @@ -1547,7 +1530,7 @@ void SNA::compute_ncoeff() /* ---------------------------------------------------------------------- */ -double SNA::compute_sfac(double r, double rcut) +double SNA::compute_sfac(double r, double rcut, double sinner, double dinner) { double sfac; if (switch_flag == 0) sfac = 1.0; @@ -1557,14 +1540,22 @@ double SNA::compute_sfac(double r, double rcut) double rcutfac = MY_PI / (rcut - rmin0); sfac = 0.5 * (cos((r - rmin0) * rcutfac) + 1.0); } + + if (switch_inner_flag == 1 && r < sinner + dinner) { + if (r > sinner - dinner) { + double rcutfac = MY_PI2 / dinner; + sfac *= 0.5 * (1.0 - cos(MY_PI2 + (r - sinner) * rcutfac)); + } else sfac = 0.0; + } + return sfac; } /* ---------------------------------------------------------------------- */ -double SNA::compute_dsfac(double r, double rcut) +double SNA::compute_dsfac(double r, double rcut, double sinner, double dinner) { - double dsfac; + double sfac, dsfac, sfac_inner, dsfac_inner; if (switch_flag == 0) dsfac = 0.0; else if (r <= rmin0) dsfac = 0.0; else if (r > rcut) dsfac = 0.0; @@ -1572,36 +1563,26 @@ double SNA::compute_dsfac(double r, double rcut) double rcutfac = MY_PI / (rcut - rmin0); dsfac = -0.5 * sin((r - rmin0) * rcutfac) * rcutfac; } - return dsfac; -} - -/* ---------------------------------------------------------------------- */ - -double SNA::compute_sfac_inner(double r, double rinner, double drinner) -{ - double sfac; - if (switch_inner_flag == 0) sfac = 1.0; - else if (r >= rinner + drinner) sfac = 1.0; - else if (r <= rinner - drinner) sfac = 0.0; - else { - double rcutfac = MY_PI2 / drinner; - sfac = 0.5 * (1.0 - cos(MY_PI2 + (r - rinner) * rcutfac)); - } - return sfac; -} - -/* ---------------------------------------------------------------------- */ - -double SNA::compute_dsfac_inner(double r, double rinner, double drinner) -{ - double dsfac; - if (switch_inner_flag == 0) dsfac = 0.0; - else if (r >= rinner + drinner) dsfac = 0.0; - else if (r <= rinner - drinner) dsfac = 0.0; - else { - double rcutfac = MY_PI2 / drinner; - dsfac = 0.5 * rcutfac * sin(MY_PI2 + (r - rinner) * rcutfac); - } + + // duplicated computation, but rarely visited + + if (switch_inner_flag == 1 && r < sinner + dinner) { + if (r > sinner - dinner) { + if (switch_flag == 0) sfac = 1.0; + else if (r <= rmin0) sfac = 1.0; + else if (r > rcut) sfac = 0.0; + else { + double rcutfac = MY_PI / (rcut - rmin0); + sfac = 0.5 * (cos((r - rmin0) * rcutfac) + 1.0); + } + + double rcutfac = MY_PI2 / dinner; + sfac_inner = 0.5 * (1.0 - cos(MY_PI2 + (r - sinner) * rcutfac)); + dsfac_inner = 0.5 * rcutfac * sin(MY_PI2 + (r - sinner) * rcutfac); + dsfac = dsfac*sfac_inner + sfac*dsfac_inner; + } else dsfac = 0.0; + } + return dsfac; } diff --git a/src/ML-SNAP/sna.h b/src/ML-SNAP/sna.h index 03d77d52b4..6eaf774941 100644 --- a/src/ML-SNAP/sna.h +++ b/src/ML-SNAP/sna.h @@ -56,11 +56,8 @@ class SNA : protected Pointers { void compute_duidrj(int); void compute_dbidrj(); void compute_deidrj(double *); - double compute_sfac(double, double); - double compute_dsfac(double, double); - - double compute_sfac_inner(double, double, double); - double compute_dsfac_inner(double, double, double); + double compute_sfac(double, double, double, double); + double compute_dsfac(double, double, double, double); // public bispectrum data @@ -80,8 +77,8 @@ class SNA : protected Pointers { // only allocated for switch_inner_flag=1 - double *rinnerij; // short inner cutoff list - double *drinnerij;// short inner range list + double *sinnerij; // short inner cutoff midpoint list + double *dinnerij; // short inner half-width list // only allocated for chem_flag=1 From 2c71d0eea25c3d4cf0bec407596e57e81d65c3bc Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Fri, 22 Apr 2022 16:43:19 -0600 Subject: [PATCH 19/57] Ported to KOKKOS, untested --- src/KOKKOS/sna_kokkos_impl.h | 94 +++++++++++++++++++++++++++--------- src/ML-SNAP/sna.cpp | 34 ++++++++----- 2 files changed, 92 insertions(+), 36 deletions(-) diff --git a/src/KOKKOS/sna_kokkos_impl.h b/src/KOKKOS/sna_kokkos_impl.h index 546c07ee11..c9c1bfbb99 100644 --- a/src/KOKKOS/sna_kokkos_impl.h +++ b/src/KOKKOS/sna_kokkos_impl.h @@ -2234,29 +2234,30 @@ template KOKKOS_INLINE_FUNCTION real_type SNAKokkos::compute_sfac(real_type r, real_type rcut, real_type sinner, real_type dinner) { + real_type sfac_outer; constexpr real_type one = static_cast(1.0); constexpr real_type zero = static_cast(0.0); constexpr real_type onehalf = static_cast(0.5); - if (switch_flag == 0) return one; + if (switch_flag == 0) sfac_outer = one; if (switch_flag == 1) { - if (r <= rmin0) return one; + if (r <= rmin0) sfac_outer = one; else if (r > rcut) return zero; else { real_type rcutfac = static_cast(MY_PI) / (rcut - rmin0); - if (switch_inner_flag == 0) - return onehalf * (cos((r - rmin0) * rcutfac) + one); - if (switch_inner_flag == 1) { - if (r >= sinner + dinner) - return onehalf * (cos((r - rmin0) * rcutfac) + one); - else if (r > sinner - dinner) { - real_type rcutfacinner = static_cast(MY_PI2) / dinner; - return onehalf * (cos((r - rmin0) * rcutfac) + one) * - onehalf * (one - cos(static_cast(MY_PI2) + (r - sinner) * rcutfacinner)); - } else return zero; - } - return zero; // dummy return + sfac_outer = onehalf * (cos((r - rmin0) * rcutfac) + one); } } + + if (switch_inner_flag == 0) return sfac_outer; + if (switch_inner_flag == 1) { + if (r >= sinner + dinner) + return sfac_outer; + else if (r > sinner - dinner) { + real_type rcutfac = static_cast(MY_PI2) / dinner; + return sfac_outer * + onehalf * (one - cos(static_cast(MY_PI2) + (r - sinner) * rcutfac)); + } else return zero; + } return zero; // dummy return } @@ -2266,41 +2267,86 @@ template KOKKOS_INLINE_FUNCTION real_type SNAKokkos::compute_dsfac(real_type r, real_type rcut, real_type sinner, real_type dinner) { + real_type sfac_outer, dsfac_outer, sfac_inner, dsfac_inner; constexpr real_type one = static_cast(1.0); constexpr real_type zero = static_cast(0.0); constexpr real_type onehalf = static_cast(0.5); - if (switch_flag == 0) return zero; + if (switch_flag == 0) dsfac_outer = zero; if (switch_flag == 1) { - if (r <= rmin0) return zero; + if (r <= rmin0) dsfac_outer = zero; else if (r > rcut) return zero; else { real_type rcutfac = static_cast(MY_PI) / (rcut - rmin0); - return -onehalf * sin((r - rmin0) * rcutfac) * rcutfac; + dsfac_outer = -onehalf * sin((r - rmin0) * rcutfac) * rcutfac; } } + + if (switch_inner_flag == 0) return dsfac_outer; + if (switch_inner_flag == 1) { + if (r >= sinner + dinner) + return dsfac_outer; + else if (r > sinner - dinner) { + + // calculate sfac_outer + + if (switch_flag == 0) sfac_outer = one; + if (switch_flag == 1) { + if (r <= rmin0) sfac_outer = one; + else if (r > rcut) sfac_outer = zero; + else { + real_type rcutfac = static_cast(MY_PI) / (rcut - rmin0); + sfac_outer = onehalf * (cos((r - rmin0) * rcutfac) + one); + } + } + + // calculate sfac_inner + + real_type rcutfac = static_cast(MY_PI2) / dinner; + sfac_inner = onehalf * (one - cos(static_cast(MY_PI2) + (r - sinner) * rcutfac)); + dsfac_inner = onehalf * rcutfac * sin(static_cast(MY_PI2) + (r - sinner) * rcutfac); + return dsfac_outer * sfac_inner + sfac_outer * dsfac_inner; + + } else return zero; + } return zero; // dummy return } template KOKKOS_INLINE_FUNCTION void SNAKokkos::compute_s_dsfac(const real_type r, const real_type rcut, const real_type sinner, const real_type dinner, real_type& sfac, real_type& dsfac) { + + real_type sfac_outer, dsfac_outer, sfac_inner, dsfac_inner; constexpr real_type one = static_cast(1.0); constexpr real_type zero = static_cast(0.0); constexpr real_type onehalf = static_cast(0.5); - if (switch_flag == 0) { sfac = zero; dsfac = zero; } + + if (switch_flag == 0) { sfac_outer = zero; dsfac_outer = zero; } else if (switch_flag == 1) { - if (r <= rmin0) { sfac = one; dsfac = zero; } - else if (r > rcut) { sfac = zero; dsfac = zero; } + if (r <= rmin0) { sfac_outer = one; dsfac_outer = zero; } + else if (r > rcut) { sfac = zero; dsfac = zero; return; } else { const real_type rcutfac = static_cast(MY_PI) / (rcut - rmin0); const real_type theta0 = (r - rmin0) * rcutfac; const real_type sn = sin(theta0); const real_type cs = cos(theta0); - sfac = onehalf * (cs + one); - dsfac = -onehalf * sn * rcutfac; - + sfac_outer = onehalf * (cs + one); + dsfac_outer = -onehalf * sn * rcutfac; } - } else { sfac = zero; dsfac = zero; } + } else { sfac = zero; dsfac = zero; return; } // dummy return + + if (switch_inner_flag == 0) { sfac = sfac_outer; dsfac = dsfac_outer; return; } + else if (switch_inner_flag == 1) { + if (r >= sinner + dinner) { sfac = sfac_outer; dsfac = dsfac_outer; return; } + else if (r > sinner - dinner) { + real_type rcutfac = static_cast(MY_PI2) / dinner; + sfac_inner = onehalf * (one - cos(static_cast(MY_PI2) + (r - sinner) * rcutfac)); + dsfac_inner = onehalf * rcutfac * sin(static_cast(MY_PI2) + (r - sinner) * rcutfac); + sfac = sfac_outer * sfac_inner; + dsfac = dsfac_outer * sfac_inner + sfac_outer * dsfac_inner; + return; + } else { sfac = zero; dsfac = zero; return; } + } else { sfac = zero; dsfac = zero; return; } // dummy return + } /* ---------------------------------------------------------------------- diff --git a/src/ML-SNAP/sna.cpp b/src/ML-SNAP/sna.cpp index 0bd66d0bce..2b86774d5b 100644 --- a/src/ML-SNAP/sna.cpp +++ b/src/ML-SNAP/sna.cpp @@ -1533,6 +1533,9 @@ void SNA::compute_ncoeff() double SNA::compute_sfac(double r, double rcut, double sinner, double dinner) { double sfac; + + // calculate sfac = sfac_outer + if (switch_flag == 0) sfac = 1.0; else if (r <= rmin0) sfac = 1.0; else if (r > rcut) sfac = 0.0; @@ -1541,6 +1544,8 @@ double SNA::compute_sfac(double r, double rcut, double sinner, double dinner) sfac = 0.5 * (cos((r - rmin0) * rcutfac) + 1.0); } + // calculate sfac *= sfac_inner, rarely visited + if (switch_inner_flag == 1 && r < sinner + dinner) { if (r > sinner - dinner) { double rcutfac = MY_PI2 / dinner; @@ -1555,33 +1560,38 @@ double SNA::compute_sfac(double r, double rcut, double sinner, double dinner) double SNA::compute_dsfac(double r, double rcut, double sinner, double dinner) { - double sfac, dsfac, sfac_inner, dsfac_inner; - if (switch_flag == 0) dsfac = 0.0; - else if (r <= rmin0) dsfac = 0.0; - else if (r > rcut) dsfac = 0.0; + double dsfac, sfac_outer, dsfac_outer, sfac_inner, dsfac_inner; + if (switch_flag == 0) dsfac_outer = 0.0; + else if (r <= rmin0) dsfac_outer = 0.0; + else if (r > rcut) dsfac_outer = 0.0; else { double rcutfac = MY_PI / (rcut - rmin0); - dsfac = -0.5 * sin((r - rmin0) * rcutfac) * rcutfac; + dsfac_outer = -0.5 * sin((r - rmin0) * rcutfac) * rcutfac; } - // duplicated computation, but rarely visited + // some duplicated computation, but rarely visited if (switch_inner_flag == 1 && r < sinner + dinner) { if (r > sinner - dinner) { - if (switch_flag == 0) sfac = 1.0; - else if (r <= rmin0) sfac = 1.0; - else if (r > rcut) sfac = 0.0; + + // calculate sfac_outer + + if (switch_flag == 0) sfac_outer = 1.0; + else if (r <= rmin0) sfac_outer = 1.0; + else if (r > rcut) sfac_outer = 0.0; else { double rcutfac = MY_PI / (rcut - rmin0); - sfac = 0.5 * (cos((r - rmin0) * rcutfac) + 1.0); + sfac_outer = 0.5 * (cos((r - rmin0) * rcutfac) + 1.0); } + // calculate sfac_inner + double rcutfac = MY_PI2 / dinner; sfac_inner = 0.5 * (1.0 - cos(MY_PI2 + (r - sinner) * rcutfac)); dsfac_inner = 0.5 * rcutfac * sin(MY_PI2 + (r - sinner) * rcutfac); - dsfac = dsfac*sfac_inner + sfac*dsfac_inner; + dsfac = dsfac_outer*sfac_inner + sfac_outer*dsfac_inner; } else dsfac = 0.0; - } + } else dsfac = dsfac_outer; return dsfac; } From 9c46acfd625bb27d2aed2692d9dfb0a15e5d2779 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 24 Apr 2022 23:23:01 -0400 Subject: [PATCH 20/57] fix parallel processing bug with shell mkdir command --- src/input.cpp | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/src/input.cpp b/src/input.cpp index 6c4fc56776..a28bd48296 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -1195,11 +1195,9 @@ void Input::shell() if (me == 0) { for (int i = 1; i < narg; i++) { rv = (platform::mkdir(arg[i]) < 0) ? errno : 0; - MPI_Reduce(&rv,&err,1,MPI_INT,MPI_MAX,0,world); - errno = err; - if (err != 0) - error->warning(FLERR, "Shell command 'mkdir {}' failed with error '{}'", - arg[i],utils::getsyserror()); + if (rv != 0) + error->warning(FLERR, "Shell command 'mkdir {}' failed with error '{}'", arg[i], + utils::getsyserror()); } } } else if (strcmp(arg[0],"mv") == 0) { From 28900925f4eebb5e98ed7c0774c2e87e695eeb62 Mon Sep 17 00:00:00 2001 From: Zheng GONG Date: Mon, 25 Apr 2022 05:59:41 +0200 Subject: [PATCH 21/57] Fix the unit for fix/accelerate/cos --- doc/src/fix_accelerate_cos.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/fix_accelerate_cos.rst b/doc/src/fix_accelerate_cos.rst index 46e08e68b4..904e853ad8 100644 --- a/doc/src/fix_accelerate_cos.rst +++ b/doc/src/fix_accelerate_cos.rst @@ -13,7 +13,7 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * accelerate/cos = style name of this fix command -* value = amplitude of acceleration (in unit of force/mass) +* value = amplitude of acceleration (in unit of velocity/time) Examples From a5cd95d6c661f23ea798ad3e46dd1f8f2a94e676 Mon Sep 17 00:00:00 2001 From: Zheng GONG Date: Mon, 25 Apr 2022 06:23:54 +0200 Subject: [PATCH 22/57] Add comment for the units in compute/viscosity --- doc/src/compute_viscosity_cos.rst | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/doc/src/compute_viscosity_cos.rst b/doc/src/compute_viscosity_cos.rst index d08217a590..2f7a09924c 100644 --- a/doc/src/compute_viscosity_cos.rst +++ b/doc/src/compute_viscosity_cos.rst @@ -21,12 +21,13 @@ Examples .. code-block:: LAMMPS + units real compute cos all viscosity/cos variable V equal c_cos[7] - variable A equal 0.02E-5 + variable A equal 0.02E-5 # A/fs^2 variable density equal density variable lz equal lz - variable reciprocalViscosity equal v_V/${A}/v_density*39.4784/v_lz/v_lz*100 + variable reciprocalViscosity equal v_V/${A}/v_density*39.4784/v_lz/v_lz*100 # 1/(Pa*s) Description """"""""""" From 8679266db845eb374b2eea9de11fc71e2001b6fc Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 25 Apr 2022 13:05:43 -0400 Subject: [PATCH 23/57] add container definitions for Fedora 36 and Ubuntu 22.04LTS --- tools/singularity/fedora36_mingw.def | 125 ++++++++++++++++++++++ tools/singularity/ubuntu22.04.def | 149 +++++++++++++++++++++++++++ 2 files changed, 274 insertions(+) create mode 100644 tools/singularity/fedora36_mingw.def create mode 100644 tools/singularity/ubuntu22.04.def diff --git a/tools/singularity/fedora36_mingw.def b/tools/singularity/fedora36_mingw.def new file mode 100644 index 0000000000..79213e9e92 --- /dev/null +++ b/tools/singularity/fedora36_mingw.def @@ -0,0 +1,125 @@ +BootStrap: docker +From: fedora:36 + +%post + dnf -y update + dnf -y install vim-enhanced git file make cmake patch which file Lmod \ + ninja-build clang clang-tools-extra libomp-devel libubsan libasan libtsan \ + diffutils dos2unix findutils rsync python-devel libjpeg-devel libpng-devel \ + ccache gcc-c++ gcc-gfortran gdb valgrind eigen3-devel openblas-devel \ + openmpi-devel mpich-devel fftw-devel voro++-devel gsl-devel hdf5-devel \ + netcdf-devel netcdf-cxx-devel netcdf-mpich-devel netcdf-openmpi-devel \ + readline-devel python3-pyyaml python3-Cython \ + mingw-filesystem-base mingw32-nsis mingw-binutils-generic \ + mingw32-filesystem mingw32-pkg-config \ + mingw64-filesystem mingw64-pkg-config \ + mingw32-crt mingw32-headers mingw32-binutils \ + mingw64-crt mingw64-headers mingw64-binutils \ + mingw32-cpp mingw32-gcc mingw32-gcc-gfortran mingw32-gcc-c++ \ + mingw64-cpp mingw64-gcc mingw64-gcc-gfortran mingw64-gcc-c++ \ + mingw32-libgomp mingw64-libgomp \ + mingw32-winpthreads mingw64-winpthreads \ + mingw32-eigen3 mingw64-eigen3 \ + mingw32-fftw mingw64-fftw \ + mingw32-libjpeg-turbo mingw64-libjpeg-turbo \ + mingw32-libpng mingw64-libpng \ + mingw32-python3 mingw64-python3 \ + mingw32-python3-numpy mingw64-python3-numpy \ + mingw32-python3-pyyaml mingw64-python3-pyyaml \ + mingw32-python3-setuptools mingw64-python3-setuptools \ + mingw32-readline mingw64-readline \ + mingw32-termcap mingw64-termcap \ + mingw32-zlib mingw64-zlib \ + mingw32-zstd mingw64-zstd \ + enchant python3-virtualenv doxygen latexmk \ + texlive-latex-fonts texlive-pslatex texlive-collection-latexrecommended \ + texlive-latex texlive-latexconfig doxygen-latex texlive-collection-latex \ + texlive-latex-bin texlive-lualatex-math texlive-fncychap texlive-tabulary \ + texlive-framed texlive-wrapfig texlive-upquote texlive-capt-of \ + texlive-needspace texlive-titlesec texlive-anysize texlive-dvipng texlive-xindy \ + blas-devel lapack-devel libyaml-devel openkim-models kim-api-devel \ + zstd libzstd-devel yaml-cpp-devel + dnf clean all + + # enable Lmod and load MPI + source /usr/share/lmod/lmod/init/profile + module purge + module load mpi + + # manually install Plumed + mkdir plumed + cd plumed + version=2.7.4 + curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz + tar -xzf plumed.tar.gz + cd plumed-${version} + ./configure --disable-doc --prefix=/usr + make + make install + # fix up installation for CentOS and Fedora + mv -v /usr/lib64/pkgconfig/plumed* /usr/share/pkgconfig/ + cd ../../ + rm -rvf plumed + + # create missing termcap pkgconfig files + cat > /usr/i686-w64-mingw32/sys-root/mingw/lib/pkgconfig/termcap.pc < /usr/x86_64-w64-mingw32/sys-root/mingw/lib/pkgconfig/termcap.pc <$CUSTOM_PROMPT_ENV <$CUSTOM_PROMPT_ENV < Date: Mon, 25 Apr 2022 13:58:41 -0600 Subject: [PATCH 24/57] Updated ML-IAP package --- src/ML-IAP/mliap_descriptor_snap.cpp | 53 +++++++++++++--------------- src/ML-IAP/mliap_descriptor_snap.h | 4 +-- 2 files changed, 27 insertions(+), 30 deletions(-) diff --git a/src/ML-IAP/mliap_descriptor_snap.cpp b/src/ML-IAP/mliap_descriptor_snap.cpp index 7badf7b641..195eaa07fa 100644 --- a/src/ML-IAP/mliap_descriptor_snap.cpp +++ b/src/ML-IAP/mliap_descriptor_snap.cpp @@ -41,8 +41,8 @@ MLIAPDescriptorSNAP::MLIAPDescriptorSNAP(LAMMPS *_lmp, char *paramfilename) : ML radelem = nullptr; wjelem = nullptr; snaptr = nullptr; - rinnerelem = nullptr; - drinnerelem = nullptr; + sinnerelem = nullptr; + dinnerelem = nullptr; read_paramfile(paramfilename); @@ -59,11 +59,8 @@ MLIAPDescriptorSNAP::~MLIAPDescriptorSNAP() memory->destroy(radelem); memory->destroy(wjelem); delete snaptr; - - if (switchinnerflag) { - memory->destroy(rinnerelem); - memory->destroy(drinnerelem); - } + memory->destroy(sinnerelem); + memory->destroy(dinnerelem); } /* ---------------------------------------------------------------------- @@ -94,8 +91,8 @@ void MLIAPDescriptorSNAP::compute_descriptors(class MLIAPData *data) snaptr->wj[ninside] = wjelem[jelem]; snaptr->rcutij[ninside] = sqrt(cutsq[ielem][jelem]); if (switchinnerflag) { - snaptr->rinnerij[ninside] = 0.5 * (rinnerelem[ielem] + rinnerelem[jelem]); - snaptr->drinnerij[ninside] = 0.5 * (drinnerelem[ielem] + drinnerelem[jelem]); + snaptr->sinnerij[ninside] = 0.5 * (sinnerelem[ielem] + sinnerelem[jelem]); + snaptr->dinnerij[ninside] = 0.5 * (dinnerelem[ielem] + dinnerelem[jelem]); } if (chemflag) snaptr->element[ninside] = jelem; ninside++; @@ -150,8 +147,8 @@ void MLIAPDescriptorSNAP::compute_forces(class MLIAPData *data) snaptr->wj[ninside] = wjelem[jelem]; snaptr->rcutij[ninside] = sqrt(cutsq[ielem][jelem]); if (switchinnerflag) { - snaptr->rinnerij[ninside] = 0.5 * (rinnerelem[ielem] + rinnerelem[jelem]); - snaptr->drinnerij[ninside] = 0.5 * (drinnerelem[ielem] + drinnerelem[jelem]); + snaptr->sinnerij[ninside] = 0.5 * (sinnerelem[ielem] + sinnerelem[jelem]); + snaptr->dinnerij[ninside] = 0.5 * (dinnerelem[ielem] + dinnerelem[jelem]); } if (chemflag) snaptr->element[ninside] = jelem; ninside++; @@ -222,8 +219,8 @@ void MLIAPDescriptorSNAP::compute_force_gradients(class MLIAPData *data) snaptr->wj[ninside] = wjelem[jelem]; snaptr->rcutij[ninside] = sqrt(cutsq[ielem][jelem]); if (switchinnerflag) { - snaptr->rinnerij[ninside] = 0.5 * (rinnerelem[ielem] + rinnerelem[jelem]); - snaptr->drinnerij[ninside] = 0.5 * (drinnerelem[ielem] + drinnerelem[jelem]); + snaptr->sinnerij[ninside] = 0.5 * (sinnerelem[ielem] + sinnerelem[jelem]); + snaptr->dinnerij[ninside] = 0.5 * (dinnerelem[ielem] + dinnerelem[jelem]); } if (chemflag) snaptr->element[ninside] = jelem; ninside++; @@ -292,8 +289,8 @@ void MLIAPDescriptorSNAP::compute_descriptor_gradients(class MLIAPData *data) snaptr->wj[ninside] = wjelem[jelem]; snaptr->rcutij[ninside] = sqrt(cutsq[ielem][jelem]); if (switchinnerflag) { - snaptr->rinnerij[ninside] = 0.5 * (rinnerelem[ielem] + rinnerelem[jelem]); - snaptr->drinnerij[ninside] = 0.5 * (drinnerelem[ielem] + drinnerelem[jelem]); + snaptr->sinnerij[ninside] = 0.5 * (sinnerelem[ielem] + sinnerelem[jelem]); + snaptr->dinnerij[ninside] = 0.5 * (dinnerelem[ielem] + dinnerelem[jelem]); } if (chemflag) snaptr->element[ninside] = jelem; ninside++; @@ -364,8 +361,8 @@ void MLIAPDescriptorSNAP::read_paramfile(char *paramfilename) // set local input checks - int rinnerflag = 0; - int drinnerflag = 0; + int sinnerflag = 0; + int dinnerflag = 0; for (int i = 0; i < nelements; i++) delete[] elements[i]; delete[] elements; @@ -414,7 +411,7 @@ void MLIAPDescriptorSNAP::read_paramfile(char *paramfilename) // check for keywords with one value per element if ((keywd == "elems") || (keywd == "radelems") || (keywd == "welems") || - (keywd == "rinnerelems") || (keywd == "drinnerelems")) { + (keywd == "sinnerelems") || (keywd == "dinnerelems")) { if ((nelementsflag == 0) || ((int)words.count() != nelements + 1)) error->all(FLERR, "Incorrect SNAP parameter file"); @@ -433,14 +430,14 @@ void MLIAPDescriptorSNAP::read_paramfile(char *paramfilename) for (int ielem = 0; ielem < nelements; ielem++) wjelem[ielem] = utils::numeric(FLERR, words.next(), false, lmp); wjelemflag = 1; - } else if (keywd == "rinnerelems") { + } else if (keywd == "sinnerelems") { for (int ielem = 0; ielem < nelements; ielem++) - rinnerelem[ielem] = utils::numeric(FLERR, words.next(), false, lmp); - rinnerflag = 1; - } else if (keywd == "drinnerelems") { + sinnerelem[ielem] = utils::numeric(FLERR, words.next(), false, lmp); + sinnerflag = 1; + } else if (keywd == "dinnerelems") { for (int ielem = 0; ielem < nelements; ielem++) - drinnerelem[ielem] = utils::numeric(FLERR, words.next(), false, lmp); - rinnerflag = 1; + dinnerelem[ielem] = utils::numeric(FLERR, words.next(), false, lmp); + dinnerflag = 1; } } else { @@ -457,8 +454,8 @@ void MLIAPDescriptorSNAP::read_paramfile(char *paramfilename) elements = new char *[nelements]; memory->create(radelem, nelements, "mliap_snap_descriptor:radelem"); memory->create(wjelem, nelements, "mliap_snap_descriptor:wjelem"); - memory->create(rinnerelem, nelements, "mliap_snap_descriptor:rinner"); - memory->create(drinnerelem, nelements, "mliap_snap_descriptor:drinner"); + memory->create(sinnerelem, nelements, "mliap_snap_descriptor:sinner"); + memory->create(dinnerelem, nelements, "mliap_snap_descriptor:dinner"); nelementsflag = 1; } else if (keywd == "rcutfac") { rcutfac = utils::numeric(FLERR, keyval, false, lmp); @@ -491,10 +488,10 @@ void MLIAPDescriptorSNAP::read_paramfile(char *paramfilename) !wjelemflag) error->all(FLERR, "Incorrect SNAP parameter file"); - if (switchinnerflag && !(rinnerflag && drinnerflag)) + if (switchinnerflag && !(sinnerflag && dinnerflag)) error->all(FLERR, "Incorrect SNAP parameter file"); - if (!switchinnerflag && (rinnerflag || drinnerflag)) + if (!switchinnerflag && (sinnerflag || dinnerflag)) error->all(FLERR, "Incorrect SNAP parameter file"); // construct cutsq diff --git a/src/ML-IAP/mliap_descriptor_snap.h b/src/ML-IAP/mliap_descriptor_snap.h index 2136eefc5e..b49ff6d2cc 100644 --- a/src/ML-IAP/mliap_descriptor_snap.h +++ b/src/ML-IAP/mliap_descriptor_snap.h @@ -42,8 +42,8 @@ class MLIAPDescriptorSNAP : public MLIAPDescriptor { int switchinnerflag; double rfac0, rmin0; - double* rinnerelem; - double* drinnerelem; + double* sinnerelem; + double* dinnerelem; }; } // namespace LAMMPS_NS From 950b175fcd12bfd4e2c5ab68c886421205d47f43 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 25 Apr 2022 16:23:48 -0400 Subject: [PATCH 25/57] remove invalid [[noreturn]] attribute --- src/utils.h | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/utils.h b/src/utils.h index f7f269a97d..6726240d0d 100644 --- a/src/utils.h +++ b/src/utils.h @@ -56,8 +56,7 @@ namespace utils { * \param cmd name of the failing command * \param error pointer to Error class instance (for abort) or nullptr */ - [[noreturn]] void missing_cmd_args(const std::string &file, int line, const std::string &cmd, - Error *error); + void missing_cmd_args(const std::string &file, int line, const std::string &cmd, Error *error); /* Internal function handling the argument list for logmesg(). */ From bb8e953fb5137663a2c5af46bf4e6d410f9ee680 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Mon, 25 Apr 2022 15:43:08 -0600 Subject: [PATCH 26/57] add support for wildcards in variable vectors --- doc/src/fix_ave_correlate.rst | 30 ++++++++---- doc/src/fix_ave_histo.rst | 49 ++++++++++++------- doc/src/fix_ave_time.rst | 31 ++++++++---- doc/src/thermo_style.rst | 31 +++++++----- .../ELASTIC_T/BORN_MATRIX/Silicon/output.in | 3 +- src/utils.cpp | 28 +++++++++-- 6 files changed, 117 insertions(+), 55 deletions(-) diff --git a/doc/src/fix_ave_correlate.rst b/doc/src/fix_ave_correlate.rst index 23086d465f..d2e9599374 100644 --- a/doc/src/fix_ave_correlate.rst +++ b/doc/src/fix_ave_correlate.rst @@ -25,7 +25,7 @@ Syntax f_ID = global scalar calculated by a fix with ID f_ID[I] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below) v_name = global value calculated by an equal-style variable with name - v_name[I] = Ith component of a vector-style variable with name + v_name[I] = Ith component of a vector-style variable with name, I can include wildcard (see below) * zero or more keyword/arg pairs may be appended * keyword = *type* or *ave* or *start* or *prefactor* or *file* or *overwrite* or *title1* or *title2* or *title3* @@ -105,15 +105,17 @@ individual fixes for info on which ones produce such values. ones that can be used with this fix. Variables of style *atom* cannot be used, since they produce per-atom values. -Note that for values from a compute or fix, the bracketed index I can -be specified using a wildcard asterisk with the index to effectively -specify multiple values. This takes the form "\*" or "\*n" or "n\*" or -"m\*n". If N = the size of the vector (for *mode* = scalar) or the -number of columns in the array (for *mode* = vector), then an asterisk -with no numeric values means all indices from 1 to N. A leading -asterisk means all indices from 1 to n (inclusive). A trailing -asterisk means all indices from n to N (inclusive). A middle asterisk -means all indices from m to n (inclusive). +---------- + +For input values from a compute or fix or variable , the bracketed +index I can be specified using a wildcard asterisk with the index to +effectively specify multiple values. This takes the form "\*" or +"\*n" or "n\*" or "m\*n". If N = the size of the vector (for *mode* = +scalar) or the number of columns in the array (for *mode* = vector), +then an asterisk with no numeric values means all indices from 1 to N. +A leading asterisk means all indices from 1 to n (inclusive). A +trailing asterisk means all indices from n to N (inclusive). A middle +asterisk means all indices from m to n (inclusive). Using a wildcard is the same as if the individual elements of the vector had been listed one by one. E.g. these 2 fix ave/correlate @@ -128,6 +130,14 @@ values. c_myPress[1] c_myPress[2] c_myPress[3] & c_myPress[4] c_myPress[5] c_myPress[6] +.. note:: + + For a vector-style variable, only the wildcard forms "\*n" or + "m\*n" are allowed. You must specify the upper bound, because + vector-style variable lengths are not determined until the variable + is evaluated. If n is specified larger than the vector length + turns out to be, zeroes are output for missing vector values. + ---------- The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what diff --git a/doc/src/fix_ave_histo.rst b/doc/src/fix_ave_histo.rst index 05c63a6faf..3cd1bdf4db 100644 --- a/doc/src/fix_ave_histo.rst +++ b/doc/src/fix_ave_histo.rst @@ -32,7 +32,7 @@ Syntax f_ID = scalar or vector calculated by a fix with ID f_ID[I] = Ith component of vector or Ith column of array calculated by a fix with ID, I can include wildcard (see below) v_name = value(s) calculated by an equal-style or vector-style or atom-style variable with name - v_name[I] = value calculated by a vector-style variable with name + v_name[I] = value calculated by a vector-style variable with name, I can include wildcard (see below) * zero or more keyword/arg pairs may be appended * keyword = *mode* or *file* or *ave* or *start* or *beyond* or *overwrite* or *title1* or *title2* or *title3* @@ -120,15 +120,27 @@ If *mode* = vector, then the input values must be vectors, or arrays with a bracketed term appended, indicating the Ith column of the array is used. -Note that for values from a compute or fix, the bracketed index I can -be specified using a wildcard asterisk with the index to effectively -specify multiple values. This takes the form "\*" or "\*n" or "n\*" or -"m\*n". If N = the size of the vector (for *mode* = scalar) or the -number of columns in the array (for *mode* = vector), then an asterisk -with no numeric values means all indices from 1 to N. A leading -asterisk means all indices from 1 to n (inclusive). A trailing -asterisk means all indices from n to N (inclusive). A middle asterisk -means all indices from m to n (inclusive). +If the fix ave/histo/weight command is used, exactly two values must +be specified. If the values are vectors, they must be the same +length. The first value (a scalar or vector) is what is histogrammed +into bins, in the same manner the fix ave/histo command operates. The +second value (a scalar or vector) is used as a "weight". This means +that instead of each value tallying a "1" to its bin, the +corresponding weight is tallied. E.g. The Nth entry (weight) in the +second vector is tallied to the bin corresponding to the Nth entry in +the first vector. + +---------- + +For input values from a compute or fix or variable, the bracketed +index I can be specified using a wildcard asterisk with the index to +effectively specify multiple values. This takes the form "\*" or +"\*n" or "n\*" or "m\*n". If N = the size of the vector (for *mode* = +scalar) or the number of columns in the array (for *mode* = vector), +then an asterisk with no numeric values means all indices from 1 to N. +A leading asterisk means all indices from 1 to n (inclusive). A +trailing asterisk means all indices from n to N (inclusive). A middle +asterisk means all indices from m to n (inclusive). Using a wildcard is the same as if the individual elements of the vector or columns of the array had been listed one by one. E.g. these @@ -141,15 +153,14 @@ vector or columns of the array had been listed one by one. E.g. these fix 1 all ave/histo 100 1 100 -10.0 10.0 100 c_myCOM[*] file tmp1.com mode vector fix 2 all ave/histo 100 1 100 -10.0 10.0 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector -If the fix ave/histo/weight command is used, exactly two values must -be specified. If the values are vectors, they must be the same -length. The first value (a scalar or vector) is what is histogrammed -into bins, in the same manner the fix ave/histo command operates. The -second value (a scalar or vector) is used as a "weight". This means -that instead of each value tallying a "1" to its bin, the -corresponding weight is tallied. E.g. The Nth entry (weight) in the -second vector is tallied to the bin corresponding to the Nth entry in -the first vector. +.. note:: + + For a vector-style variable, only the wildcard forms "\*n" or + "m\*n" are allowed. You must specify the upper bound, because + vector-style variable lengths are not determined until the variable + is evaluated. If n is specified larger than the vector length"\*n" + or "n\*" or "m\*n". turns out to be, zeroes are output for missing + vector values. ---------- diff --git a/doc/src/fix_ave_time.rst b/doc/src/fix_ave_time.rst index dfa385ea46..f2d634ca75 100644 --- a/doc/src/fix_ave_time.rst +++ b/doc/src/fix_ave_time.rst @@ -25,7 +25,7 @@ Syntax f_ID = global scalar or vector calculated by a fix with ID f_ID[I] = Ith component of global vector or Ith column of global array calculated by a fix with ID, I can include wildcard (see below) v_name = value(s) calculated by an equal-style or vector-style variable with name - v_name[I] = value calculated by a vector-style variable with name + v_name[I] = value calculated by a vector-style variable with name, I can include wildcard (see below) * zero or more keyword/arg pairs may be appended * keyword = *mode* or *file* or *ave* or *start* or *off* or *overwrite* or *title1* or *title2* or *title3* @@ -113,15 +113,17 @@ with a bracketed term appended, indicating the Ith column of the array is used. All vectors must be the same length, which is the length of the vector or number of rows in the array. -Note that for values from a compute or fix, the bracketed index I can -be specified using a wildcard asterisk with the index to effectively -specify multiple values. This takes the form "\*" or "\*n" or "n\*" or -"m\*n". If N = the size of the vector (for *mode* = scalar) or the -number of columns in the array (for *mode* = vector), then an asterisk -with no numeric values means all indices from 1 to N. A leading -asterisk means all indices from 1 to n (inclusive). A trailing -asterisk means all indices from n to N (inclusive). A middle asterisk -means all indices from m to n (inclusive). +---------- + +For input values from a compute or fix or variable, the bracketed +index I can be specified using a wildcard asterisk with the index to +effectively specify multiple values. This takes the form "\*" or +"\*n" or "n\*" or "m\*n". If N = the size of the vector (for *mode* = +scalar) or the number of columns in the array (for *mode* = vector), +then an asterisk with no numeric values means all indices from 1 to N. +A leading asterisk means all indices from 1 to n (inclusive). A +trailing asterisk means all indices from n to N (inclusive). A middle +asterisk means all indices from m to n (inclusive). Using a wildcard is the same as if the individual elements of the vector or columns of the array had been listed one by one. E.g. these @@ -134,6 +136,15 @@ with 3 columns, each of length 50: fix 1 all ave/time 100 1 100 c_myRDF[*] file tmp1.rdf mode vector fix 2 all ave/time 100 1 100 c_myRDF[1] c_myRDF[2] c_myRDF[3] file tmp2.rdf mode vector +.. note:: + + For a vector-style variable, only the wildcard forms "\*n" or + "m\*n" are allowed. You must specify the upper bound, because + vector-style variable lengths are not determined until the variable + is evaluated. If n is specified larger than the vector length"\*n" + or "n\*" or "m\*n". turns out to be, zeroes are output for missing + vector values. + ---------- The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what diff --git a/doc/src/thermo_style.rst b/doc/src/thermo_style.rst index 5d63ed81b6..38f832ba98 100644 --- a/doc/src/thermo_style.rst +++ b/doc/src/thermo_style.rst @@ -85,7 +85,7 @@ Syntax f_ID[I] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below) f_ID[I][J] = I,J component of global array calculated by a fix with ID v_name = value calculated by an equal-style variable with name - v_name[I] = value calculated by a vector-style variable with name + v_name[I] = value calculated by a vector-style variable with name, I can include wildcard (see below) Examples """""""" @@ -348,16 +348,16 @@ dimensions *lx*, *ly*, *lz*, *yz*, *xz*, *xy*\ . ---------- -For output values from a compute or fix, the bracketed index I used to -index a vector, as in *c_ID[I]* or *f_ID[I]*, can be specified -using a wildcard asterisk with the index to effectively specify -multiple values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". -If N = the size of the vector (for *mode* = scalar) or the number of -columns in the array (for *mode* = vector), then an asterisk with no -numeric values means all indices from 1 to N. A leading asterisk -means all indices from 1 to n (inclusive). A trailing asterisk means -all indices from n to N (inclusive). A middle asterisk means all -indices from m to n (inclusive). +For output values from a compute or fix or variable, the bracketed +index I used to index a vector, as in *c_ID[I]* or *f_ID[I]* or +*v_name[I]*, can be specified using a wildcard asterisk with the index +to effectively specify multiple values. This takes the form "\*" or +"\*n" or "n\*" or "m\*n". If N = the size of the vector (for *mode* = +scalar) or the number of columns in the array (for *mode* = vector), +then an asterisk with no numeric values means all indices from 1 to N. +A leading asterisk means all indices from 1 to n (inclusive). A +trailing asterisk means all indices from n to N (inclusive). A middle +asterisk means all indices from m to n (inclusive). Using a wildcard is the same as if the individual elements of the vector had been listed one by one. E.g. these 2 thermo_style commands @@ -372,6 +372,15 @@ creates a global vector with 6 values. c_myTemp[1] c_myTemp[2] c_myTemp[3] & c_myTemp[4] c_myTemp[5] c_myTemp[6] + +.. note:: + + For a vector-style variable, only the wildcard forms "\*n" or + "m\*n" are allowed. You must specify the upper bound, because + vector-style variable lengths are not determined until the variable + is evaluated. If n is specified larger than the vector length + turns out to be, zeroes are output for missing vector values. + ---------- The *c_ID* and *c_ID[I]* and *c_ID[I][J]* keywords allow global values diff --git a/examples/ELASTIC_T/BORN_MATRIX/Silicon/output.in b/examples/ELASTIC_T/BORN_MATRIX/Silicon/output.in index d6a89cff6a..05e007fab6 100644 --- a/examples/ELASTIC_T/BORN_MATRIX/Silicon/output.in +++ b/examples/ELASTIC_T/BORN_MATRIX/Silicon/output.in @@ -136,5 +136,6 @@ variable C46 equal v_F46+v_B[20] variable C56 equal v_F56+v_B[21] thermo ${nthermo} -thermo_style custom step temp pe press density f_avt f_avp f_avpe v_F11 v_F22 v_F33 v_F44 v_F55 v_F66 v_F12 v_F13 v_F23 v_B[1] v_B[2] v_B[3] v_B[4] v_B[5] v_B[6] v_B[7] v_B[8] v_B[12] +thermo_style custom step temp pe press density f_avt f_avp f_avpe v_F11 v_F22 v_F33 v_F44 v_F55 v_F66 v_F12 v_F13 v_F23 v_B[*8] v_B[12] + thermo_modify norm no diff --git a/src/utils.cpp b/src/utils.cpp index 3bc8c761c6..690bb10b2b 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -19,11 +19,13 @@ #include "error.h" #include "fix.h" #include "fmt/chrono.h" +#include "input.h" #include "memory.h" #include "modify.h" #include "text_file_reader.h" #include "universe.h" #include "update.h" +#include "variable.h" #include #include @@ -631,7 +633,7 @@ int utils::expand_args(const char *file, int line, int narg, char **arg, int mod // match compute, fix, or custom property array reference with a '*' wildcard // number range in the first pair of square brackets - if (strmatch(word, "^[cf]_\\w+\\[\\d*\\*\\d*\\]") || + if (strmatch(word, "^[cfv]_\\w+\\[\\d*\\*\\d*\\]") || strmatch(word, "^[id]2_\\w+\\[\\d*\\*\\d*\\]")) { // split off the compute/fix/property ID, the wildcard and trailing text @@ -669,7 +671,7 @@ int utils::expand_args(const char *file, int line, int narg, char **arg, int mod } } - // fix + // fix } else if (word[0] == 'f') { auto fix = lmp->modify->get_fix_by_id(id); @@ -692,8 +694,25 @@ int utils::expand_args(const char *file, int line, int narg, char **arg, int mod } } - // only match custom array reference with a '*' wildcard - // number range in the first pair of square brackets + // vector variable + + } else if (word[0] == 'v') { + int index = lmp->input->variable->find(id.c_str()); + + // check for global vector/array, peratom array, local array + + if (index >= 0) { + if (mode == 0 && lmp->input->variable->vectorstyle(index)) { + utils::bounds(file, line, wc, 1, MAXSMALLINT, nlo, nhi, lmp->error); + if (nhi < MAXSMALLINT) { + nmax = nhi; + expandflag = 1; + } + } + } + + // only match custom array reference with a '*' wildcard + // number range in the first pair of square brackets } else if ((word[0] == 'i') || (word[0] == 'd')) { int flag, cols; @@ -716,6 +735,7 @@ int utils::expand_args(const char *file, int line, int narg, char **arg, int mod if (expandflag) { // expand wild card string to nlo/nhi numbers + utils::bounds(file, line, wc, 1, nmax, nlo, nhi, lmp->error); if (newarg + nhi - nlo + 1 > maxarg) { From 65978c33b604eb5a4a21a5847a4ca5a9ec2b2e86 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Mon, 25 Apr 2022 16:06:52 -0600 Subject: [PATCH 27/57] 2 more doc pages --- doc/src/fix_ave_histo.rst | 10 +++++----- doc/src/fix_ave_time.rst | 19 +++++++++++-------- 2 files changed, 16 insertions(+), 13 deletions(-) diff --git a/doc/src/fix_ave_histo.rst b/doc/src/fix_ave_histo.rst index 3cd1bdf4db..5d36a372c3 100644 --- a/doc/src/fix_ave_histo.rst +++ b/doc/src/fix_ave_histo.rst @@ -144,8 +144,9 @@ asterisk means all indices from m to n (inclusive). Using a wildcard is the same as if the individual elements of the vector or columns of the array had been listed one by one. E.g. these -2 fix ave/histo commands are equivalent, since the :doc:`compute com/chunk ` command creates a global array with -3 columns: +2 fix ave/histo commands are equivalent, since the :doc:`compute +com/chunk ` command creates a global array with 3 +columns: .. code-block:: LAMMPS @@ -158,9 +159,8 @@ vector or columns of the array had been listed one by one. E.g. these For a vector-style variable, only the wildcard forms "\*n" or "m\*n" are allowed. You must specify the upper bound, because vector-style variable lengths are not determined until the variable - is evaluated. If n is specified larger than the vector length"\*n" - or "n\*" or "m\*n". turns out to be, zeroes are output for missing - vector values. + is evaluated. If n is specified larger than the vector length + turns out to be, zeroes are output for missing vector values. ---------- diff --git a/doc/src/fix_ave_time.rst b/doc/src/fix_ave_time.rst index f2d634ca75..2836e11fd0 100644 --- a/doc/src/fix_ave_time.rst +++ b/doc/src/fix_ave_time.rst @@ -127,8 +127,9 @@ asterisk means all indices from m to n (inclusive). Using a wildcard is the same as if the individual elements of the vector or columns of the array had been listed one by one. E.g. these -2 fix ave/time commands are equivalent, since the :doc:`compute rdf ` command creates, in this case, a global array -with 3 columns, each of length 50: +2 fix ave/time commands are equivalent, since the :doc:`compute rdf +` command creates, in this case, a global array with 3 +columns, each of length 50: .. code-block:: LAMMPS @@ -141,9 +142,8 @@ with 3 columns, each of length 50: For a vector-style variable, only the wildcard forms "\*n" or "m\*n" are allowed. You must specify the upper bound, because vector-style variable lengths are not determined until the variable - is evaluated. If n is specified larger than the vector length"\*n" - or "n\*" or "m\*n". turns out to be, zeroes are output for missing - vector values. + is evaluated. If n is specified larger than the vector length + turns out to be, zeroes are output for missing vector values. ---------- @@ -180,9 +180,12 @@ asterisk to effectively specify multiple values. Note that there is a :doc:`compute reduce ` command which can sum per-atom quantities into a global scalar or vector which can thus be accessed by fix ave/time. Or it can be a compute defined -not in your input script, but by :doc:`thermodynamic output ` or other fixes such as :doc:`fix nvt ` or :doc:`fix temp/rescale `. See -the doc pages for these commands which give the IDs of these computes. -Users can also write code for their own compute styles and :doc:`add them to LAMMPS `. +not in your input script, but by :doc:`thermodynamic output +` or other fixes such as :doc:`fix nvt ` or +:doc:`fix temp/rescale `. See the doc pages for +these commands which give the IDs of these computes. Users can also +write code for their own compute styles and :doc:`add them to LAMMPS +`. If a value begins with "f\_", a fix ID must follow which has been previously defined in the input script. If *mode* = scalar, then if From e7a9073ccda9f821b5f4d27fe75decf8bb3a32d5 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Mon, 25 Apr 2022 17:01:15 -0600 Subject: [PATCH 28/57] remove discussion of mode --- doc/src/thermo_style.rst | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/doc/src/thermo_style.rst b/doc/src/thermo_style.rst index 38f832ba98..a5a8935dc4 100644 --- a/doc/src/thermo_style.rst +++ b/doc/src/thermo_style.rst @@ -352,10 +352,9 @@ For output values from a compute or fix or variable, the bracketed index I used to index a vector, as in *c_ID[I]* or *f_ID[I]* or *v_name[I]*, can be specified using a wildcard asterisk with the index to effectively specify multiple values. This takes the form "\*" or -"\*n" or "n\*" or "m\*n". If N = the size of the vector (for *mode* = -scalar) or the number of columns in the array (for *mode* = vector), -then an asterisk with no numeric values means all indices from 1 to N. -A leading asterisk means all indices from 1 to n (inclusive). A +"\*n" or "n\*" or "m\*n". If N = the size of the vector, then an +asterisk with no numeric values means all indices from 1 to N. A +leading asterisk means all indices from 1 to n (inclusive). A trailing asterisk means all indices from n to N (inclusive). A middle asterisk means all indices from m to n (inclusive). From fdb7dfdea7a95da2967bbe2bf118141d249ceb03 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Mon, 25 Apr 2022 17:04:04 -0600 Subject: [PATCH 29/57] also remove mode from fix ave/correlate --- doc/src/fix_ave_correlate.rst | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/doc/src/fix_ave_correlate.rst b/doc/src/fix_ave_correlate.rst index d2e9599374..6653b91d91 100644 --- a/doc/src/fix_ave_correlate.rst +++ b/doc/src/fix_ave_correlate.rst @@ -110,17 +110,16 @@ be used, since they produce per-atom values. For input values from a compute or fix or variable , the bracketed index I can be specified using a wildcard asterisk with the index to effectively specify multiple values. This takes the form "\*" or -"\*n" or "n\*" or "m\*n". If N = the size of the vector (for *mode* = -scalar) or the number of columns in the array (for *mode* = vector), -then an asterisk with no numeric values means all indices from 1 to N. -A leading asterisk means all indices from 1 to n (inclusive). A +"\*n" or "n\*" or "m\*n". If N = the size of the vector, then an +asterisk with no numeric values means all indices from 1 to N. A +leading asterisk means all indices from 1 to n (inclusive). A trailing asterisk means all indices from n to N (inclusive). A middle asterisk means all indices from m to n (inclusive). Using a wildcard is the same as if the individual elements of the vector had been listed one by one. E.g. these 2 fix ave/correlate -commands are equivalent, since the :doc:`compute pressure ` command creates a global vector with 6 -values. +commands are equivalent, since the :doc:`compute pressure +` command creates a global vector with 6 values. .. code-block:: LAMMPS From ba02d90bf1796e549b3f2cba1079ded26ecaa6b6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 26 Apr 2022 09:29:57 -0400 Subject: [PATCH 30/57] add test for new errorurl() utility function --- unittest/utils/test_utils.cpp | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/unittest/utils/test_utils.cpp b/unittest/utils/test_utils.cpp index 900ce6814c..5967ac087a 100644 --- a/unittest/utils/test_utils.cpp +++ b/unittest/utils/test_utils.cpp @@ -746,6 +746,12 @@ TEST(Utils, boundsbig_case3) ASSERT_EQ(nhi, -1); } +TEST(Utils, errorurl) +{ + auto errmesg = utils::errorurl(10); + ASSERT_THAT(errmesg, Eq("\nFor more information see https://docs.lammps.org/err0010")); +} + TEST(Utils, getsyserror) { #if defined(__linux__) From 4691ff06b5a4463ea230ff2a01d9c1af9025e436 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 26 Apr 2022 09:30:10 -0400 Subject: [PATCH 31/57] format --- unittest/cplusplus/test_error_class.cpp | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/unittest/cplusplus/test_error_class.cpp b/unittest/cplusplus/test_error_class.cpp index 27318646be..a94e6a3e41 100644 --- a/unittest/cplusplus/test_error_class.cpp +++ b/unittest/cplusplus/test_error_class.cpp @@ -1,4 +1,4 @@ -// unit tests for issuing command to a LAMMPS instance through the Input class +// unit tests for public member functions of the Error class #include "error.h" #include "info.h" @@ -129,8 +129,7 @@ int main(int argc, char **argv) ::testing::InitGoogleMock(&argc, argv); if (platform::mpi_vendor() == "Open MPI" && !LAMMPS_NS::Info::has_exceptions()) - std::cout << "Warning: using OpenMPI without exceptions. " - "Death tests will be skipped\n"; + std::cout << "Warning: using OpenMPI without exceptions. Death tests will be skipped\n"; // handle arguments passed via environment variable if (const char *var = getenv("TEST_ARGS")) { From 837f9040d848738df2ba8ebd31c57b4f3d22f434 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 26 Apr 2022 09:30:34 -0400 Subject: [PATCH 32/57] add tests for advanced utility functions that require a LAMMPS instance --- unittest/cplusplus/CMakeLists.txt | 4 + unittest/cplusplus/test_advanced_utils.cpp | 194 +++++++++++++++++++++ 2 files changed, 198 insertions(+) create mode 100644 unittest/cplusplus/test_advanced_utils.cpp diff --git a/unittest/cplusplus/CMakeLists.txt b/unittest/cplusplus/CMakeLists.txt index 88f082a204..9199e20792 100644 --- a/unittest/cplusplus/CMakeLists.txt +++ b/unittest/cplusplus/CMakeLists.txt @@ -8,6 +8,10 @@ add_executable(test_input_class test_input_class.cpp) target_link_libraries(test_input_class PRIVATE lammps GTest::GTestMain) add_test(NAME InputClass COMMAND test_input_class) +add_executable(test_advanced_utils test_advanced_utils.cpp) +target_link_libraries(test_advanced_utils PRIVATE lammps GTest::GMock) +add_test(NAME AdvancedUtils COMMAND test_advanced_utils) + add_executable(test_error_class test_error_class.cpp) target_link_libraries(test_error_class PRIVATE lammps GTest::GMock) add_test(NAME ErrorClass COMMAND test_error_class) diff --git a/unittest/cplusplus/test_advanced_utils.cpp b/unittest/cplusplus/test_advanced_utils.cpp new file mode 100644 index 0000000000..3e5a846914 --- /dev/null +++ b/unittest/cplusplus/test_advanced_utils.cpp @@ -0,0 +1,194 @@ +// unit tests for utils:: functions requiring a LAMMPS + +#include "error.h" +#include "input.h" +#include "lammps.h" +#include "utils.h" + +#include "../testing/core.h" +#include "gmock/gmock.h" +#include "gtest/gtest.h" + +#include + +// whether to print verbose output (i.e. not capturing LAMMPS screen output). +bool verbose = false; + +namespace LAMMPS_NS { + +class Advanced_utils : public LAMMPSTest { +protected: + Error *error; + + void SetUp() override + { + testbinary = "AdvancedUtils"; + LAMMPSTest::SetUp(); + error = lmp->error; + } +}; + +TEST_F(Advanced_utils, missing_cmd_args) +{ + auto output = CAPTURE_OUTPUT([&] { + utils::missing_cmd_args(FLERR, "dummy", nullptr); + }); + EXPECT_EQ(output, ""); + + TEST_FAILURE("ERROR: Illegal dummy command: missing argument", + utils::missing_cmd_args(FLERR, "dummy", error);); +}; + +TEST_F(Advanced_utils, logmesg) +{ + auto output = CAPTURE_OUTPUT([&] { + utils::logmesg(lmp, "test message"); + }); + EXPECT_EQ(output, "test message"); + + output = CAPTURE_OUTPUT([&] { + utils::logmesg(lmp, "test message from test {}", testbinary); + }); + EXPECT_EQ(output, "test message from test " + testbinary); +}; + +TEST_F(Advanced_utils, bounds_case1) +{ + int nlo, nhi; + + nlo = nhi = -1; + utils::bounds(FLERR, "9", 0, 10, nlo, nhi, nullptr); + ASSERT_EQ(nlo, 9); + ASSERT_EQ(nhi, 9); + utils::bounds(FLERR, "1", 1, 10, nlo, nhi, nullptr); + ASSERT_EQ(nlo, 1); + ASSERT_EQ(nhi, 1); + utils::bounds(FLERR, "1x", 1, 10, nlo, nhi, nullptr); + ASSERT_EQ(nlo, -1); + ASSERT_EQ(nhi, -1); + utils::bounds(FLERR, "-1", 1, 10, nlo, nhi, nullptr); + ASSERT_EQ(nlo, -1); + ASSERT_EQ(nhi, -1); + utils::bounds(FLERR, "+1", 1, 10, nlo, nhi, nullptr); + ASSERT_EQ(nlo, -1); + ASSERT_EQ(nhi, -1); + utils::bounds(FLERR, "1:3", 1, 10, nlo, nhi, nullptr); + ASSERT_EQ(nlo, -1); + ASSERT_EQ(nhi, -1); +} + +TEST_F(Advanced_utils, bounds_case2) +{ + int nlo, nhi; + + nlo = nhi = -1; + utils::bounds(FLERR, "*", 0, 10, nlo, nhi, nullptr); + ASSERT_EQ(nlo, 0); + ASSERT_EQ(nhi, 10); + utils::bounds(FLERR, "*", -10, 5, nlo, nhi, nullptr); + ASSERT_EQ(nlo, -10); + ASSERT_EQ(nhi, 5); + utils::bounds(FLERR, "?", -10, 5, nlo, nhi, nullptr); + ASSERT_EQ(nlo, -1); + ASSERT_EQ(nhi, -1); +} + +TEST_F(Advanced_utils, bounds_case3) +{ + int nlo, nhi; + + nlo = nhi = -1; + utils::bounds(FLERR, "2*", 0, 10, nlo, nhi, nullptr); + ASSERT_EQ(nlo, 2); + ASSERT_EQ(nhi, 10); + utils::bounds(FLERR, "3*", -10, 5, nlo, nhi, nullptr); + ASSERT_EQ(nlo, 3); + ASSERT_EQ(nhi, 5); + utils::bounds(FLERR, "3*:2", -10, 5, nlo, nhi, nullptr); + ASSERT_EQ(nlo, -1); + ASSERT_EQ(nhi, -1); +} + +TEST_F(Advanced_utils, boundsbig_case1) +{ + bigint nlo, nhi; + + nlo = nhi = -1; + utils::bounds(FLERR, "9", 0, 10, nlo, nhi, nullptr); + ASSERT_EQ(nlo, 9); + ASSERT_EQ(nhi, 9); + utils::bounds(FLERR, "1", 1, 10, nlo, nhi, nullptr); + ASSERT_EQ(nlo, 1); + ASSERT_EQ(nhi, 1); + utils::bounds(FLERR, "1x", 1, 10, nlo, nhi, nullptr); + ASSERT_EQ(nlo, -1); + ASSERT_EQ(nhi, -1); + utils::bounds(FLERR, "-1", 1, 10, nlo, nhi, nullptr); + ASSERT_EQ(nlo, -1); + ASSERT_EQ(nhi, -1); + utils::bounds(FLERR, "+1", 1, 10, nlo, nhi, nullptr); + ASSERT_EQ(nlo, -1); + ASSERT_EQ(nhi, -1); + utils::bounds(FLERR, "1:3", 1, 10, nlo, nhi, nullptr); + ASSERT_EQ(nlo, -1); + ASSERT_EQ(nhi, -1); +} + +TEST_F(Advanced_utils, boundsbig_case2) +{ + bigint nlo, nhi; + + nlo = nhi = -1; + utils::bounds(FLERR, "*", 0, 10, nlo, nhi, nullptr); + ASSERT_EQ(nlo, 0); + ASSERT_EQ(nhi, 10); + utils::bounds(FLERR, "*", -10, 5, nlo, nhi, nullptr); + ASSERT_EQ(nlo, -10); + ASSERT_EQ(nhi, 5); + utils::bounds(FLERR, "?", -10, 5, nlo, nhi, nullptr); + ASSERT_EQ(nlo, -1); + ASSERT_EQ(nhi, -1); +} + +TEST_F(Advanced_utils, boundsbig_case3) +{ + bigint nlo, nhi; + + nlo = nhi = -1; + utils::bounds(FLERR, "2*", 0, 10, nlo, nhi, nullptr); + ASSERT_EQ(nlo, 2); + ASSERT_EQ(nhi, 10); + utils::bounds(FLERR, "3*", -10, 5, nlo, nhi, nullptr); + ASSERT_EQ(nlo, 3); + ASSERT_EQ(nhi, 5); + utils::bounds(FLERR, "3*:2", -10, 5, nlo, nhi, nullptr); + ASSERT_EQ(nlo, -1); + ASSERT_EQ(nhi, -1); +} + +} // namespace LAMMPS_NS + +int main(int argc, char **argv) +{ + MPI_Init(&argc, &argv); + ::testing::InitGoogleMock(&argc, argv); + + if (platform::mpi_vendor() == "Open MPI" && !LAMMPS_NS::Info::has_exceptions()) + std::cout << "Warning: using OpenMPI without exceptions. Death tests will be skipped\n"; + + // handle arguments passed via environment variable + if (const char *var = getenv("TEST_ARGS")) { + std::vector env = utils::split_words(var); + for (auto arg : env) { + if (arg == "-v") { + verbose = true; + } + } + } + + if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true; + + int rv = RUN_ALL_TESTS(); + MPI_Finalize(); + return rv; +} From 26278643d4660fa35f712705378be384914913fb Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Tue, 26 Apr 2022 08:22:00 -0600 Subject: [PATCH 33/57] Port changes to Kokkos --- src/KOKKOS/pair_snap_kokkos.h | 2 ++ src/KOKKOS/pair_snap_kokkos_impl.h | 32 ++++++++++++++++++++++-------- 2 files changed, 26 insertions(+), 8 deletions(-) diff --git a/src/KOKKOS/pair_snap_kokkos.h b/src/KOKKOS/pair_snap_kokkos.h index bdad113c18..1c0bf38699 100644 --- a/src/KOKKOS/pair_snap_kokkos.h +++ b/src/KOKKOS/pair_snap_kokkos.h @@ -280,6 +280,8 @@ inline double dist2(double* x,double* y); Kokkos::View d_radelem; // element radii Kokkos::View d_wjelem; // elements weights Kokkos::View d_coeffelem; // element bispectrum coefficients + Kokkos::View d_sinnerelem; // element inner cutoff midpoint + Kokkos::View d_dinnerelem; // element inner cutoff half-width Kokkos::View d_map; // mapping from atom types to elements Kokkos::View d_ninside; // ninside for all atoms in list Kokkos::View d_beta; // betas for all atoms in list diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index 6bc034a163..7c621176cd 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -578,15 +578,21 @@ void PairSNAPKokkos::coeff(int narg, char d_radelem = Kokkos::View("pair:radelem",nelements); d_wjelem = Kokkos::View("pair:wjelem",nelements); d_coeffelem = Kokkos::View("pair:coeffelem",nelements,ncoeffall); + d_sinnerelem = Kokkos::View("pair:sinnerelem",nelements); + d_dinnerelem = Kokkos::View("pair:dinnerelem",nelements); auto h_radelem = Kokkos::create_mirror_view(d_radelem); auto h_wjelem = Kokkos::create_mirror_view(d_wjelem); auto h_coeffelem = Kokkos::create_mirror_view(d_coeffelem); + auto h_sinnerelem = Kokkos::create_mirror_view(d_sinnerelem); + auto h_dinnerelem = Kokkos::create_mirror_view(d_dinnerelem); auto h_map = Kokkos::create_mirror_view(d_map); for (int ielem = 0; ielem < nelements; ielem++) { h_radelem(ielem) = radelem[ielem]; h_wjelem(ielem) = wjelem[ielem]; + h_sinnerelem(ielem) = sinnerelem[ielem]; + h_dinnerelem(ielem) = dinnerelem[ielem]; for (int jcoeff = 0; jcoeff < ncoeffall; jcoeff++) { h_coeffelem(ielem,jcoeff) = coeffelem[ielem][jcoeff]; } @@ -599,6 +605,8 @@ void PairSNAPKokkos::coeff(int narg, char Kokkos::deep_copy(d_radelem,h_radelem); Kokkos::deep_copy(d_wjelem,h_wjelem); Kokkos::deep_copy(d_coeffelem,h_coeffelem); + Kokkos::deep_copy(d_sinnerelem,h_sinnerelem); + Kokkos::deep_copy(d_dinnerelem,h_dinnerelem); Kokkos::deep_copy(d_map,h_map); snaKK = SNAKokkos(rfac0,twojmax, @@ -724,15 +732,19 @@ void PairSNAPKokkos::operator() (TagPairSN const F_FLOAT dx = x(j,0) - xtmp; const F_FLOAT dy = x(j,1) - ytmp; const F_FLOAT dz = x(j,2) - ztmp; - const int elem_j = d_map[jtype]; + const int jelem = d_map[jtype]; my_sna.rij(ii,offset,0) = static_cast(dx); my_sna.rij(ii,offset,1) = static_cast(dy); my_sna.rij(ii,offset,2) = static_cast(dz); - my_sna.wj(ii,offset) = static_cast(d_wjelem[elem_j]); - my_sna.rcutij(ii,offset) = static_cast((radi + d_radelem[elem_j])*rcutfac); + my_sna.wj(ii,offset) = static_cast(d_wjelem[jelem]); + my_sna.rcutij(ii,offset) = static_cast((radi + d_radelem[jelem])*rcutfac); my_sna.inside(ii,offset) = j; + if (switchinnerflag) { + my_sna.sinnerij(ii,ninside) = 0.5*(d_sinnerelem[ielem] + d_sinnerelem[jelem]); + my_sna.dinnerij(ii,ninside) = 0.5*(d_dinnerelem[ielem] + d_dinnerelem[jelem]); + } if (chemflag) - my_sna.element(ii,offset) = elem_j; + my_sna.element(ii,offset) = jelem; else my_sna.element(ii,offset) = 0; } @@ -1080,18 +1092,22 @@ void PairSNAPKokkos::operator() (TagPairSN const int jtype = type(j); const F_FLOAT rsq = dx*dx + dy*dy + dz*dz; - const int elem_j = d_map[jtype]; + const int jelem = d_map[jtype]; if (rsq < rnd_cutsq(itype,jtype)) { if (final) { my_sna.rij(ii,offset,0) = static_cast(dx); my_sna.rij(ii,offset,1) = static_cast(dy); my_sna.rij(ii,offset,2) = static_cast(dz); - my_sna.wj(ii,offset) = static_cast(d_wjelem[elem_j]); - my_sna.rcutij(ii,offset) = static_cast((radi + d_radelem[elem_j])*rcutfac); + my_sna.wj(ii,offset) = static_cast(d_wjelem[jelem]); + my_sna.rcutij(ii,offset) = static_cast((radi + d_radelem[jelem])*rcutfac); my_sna.inside(ii,offset) = j; + if (switchinnerflag) { + my_sna.sinnerij(ii,ninside) = 0.5*(d_sinnerelem[ielem] + d_sinnerelem[jelem]); + my_sna.dinnerij(ii,ninside) = 0.5*(d_dinnerelem[ielem] + d_dinnerelem[jelem]); + } if (chemflag) - my_sna.element(ii,offset) = elem_j; + my_sna.element(ii,offset) = jelem; else my_sna.element(ii,offset) = 0; } From 7663fc62563f47071ac985052ebef36d1a1c2ba6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 26 Apr 2022 11:08:31 -0400 Subject: [PATCH 34/57] correctly use "type" to detect executables/scripts --- src/ADIOS/Install.sh | 6 +++--- src/ML-IAP/Install.sh | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/ADIOS/Install.sh b/src/ADIOS/Install.sh index ddca8c6efe..bd0acb1414 100644 --- a/src/ADIOS/Install.sh +++ b/src/ADIOS/Install.sh @@ -31,17 +31,17 @@ done if (test $1 = 1) then CONFIGSCRIPT=none - if ( test `which adios2-config 2>> /dev/null` ) then + if ( type adios2-config > /dev/null 2>&1 ) then CONFIGSCRIPT=adios2-config elif ( ! test -z "$ADIOS2_DIR" ) then - if ( test `which $ADIOS2_DIR/bin/adios2-config` ) then + if ( type $ADIOS2_DIR/bin/adios2-config > /dev/null 2>&1 ) then CONFIGSCRIPT=$ADIOS2_DIR/bin/adios2-config else echo "ERROR: ADIOS2_DIR environment variable is set but" \ "\$ADIOS2_DIR/bin/adios2-config does not exist" fi elif ( ! test -z "$ADIOS_DIR" ) then - if ( test `which $ADIOS_DIR/bin/adios2-config` ) then + if ( type $ADIOS_DIR/bin/adios2-config > /dev/null 2>&1 ) then CONFIGSCRIPT=$ADIOS_DIR/bin/adios2-config else echo "ERROR: ADIOS_DIR environment variable is set but" \ diff --git a/src/ML-IAP/Install.sh b/src/ML-IAP/Install.sh index 753dfae358..3a1a7493aa 100755 --- a/src/ML-IAP/Install.sh +++ b/src/ML-IAP/Install.sh @@ -46,7 +46,7 @@ action mliap_model_python_couple.pyx python_impl.cpp # edit 2 Makefile.package files to include/exclude package info if (test $1 = 1) then - if (test "$(type cythonize 2> /dev/null)" != "" && test -e ../python_impl.cpp) then + if (type cythonize > /dev/null 2>&1 && test -e ../python_impl.cpp) then if (test -e ../Makefile.package) then sed -i -e 's|^PKG_INC =[ \t]*|&-DMLIAP_PYTHON |' ../Makefile.package fi @@ -69,7 +69,7 @@ elif (test $1 = 0) then sed -i -e '/^include.*python.*mliap_python.*$/d' ../Makefile.package.settings elif (test $1 = 2) then - if (type cythonize 2>&1 > /dev/null && test -e ../python_impl.cpp) then + if (type cythonize > /dev/null 2>&1 && test -e ../python_impl.cpp) then if (test -e ../Makefile.package) then sed -i -e 's/[^ \t]*-DMLIAP_PYTHON[^ \t]* //g' ../Makefile.package fi From 800e0a73574282b45bc3f01aa07c7eb4fd9eda73 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Tue, 26 Apr 2022 09:34:27 -0600 Subject: [PATCH 35/57] bug fix for new fix adapt angle support --- src/angle.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/angle.cpp b/src/angle.cpp index 6fdb9307cb..0756ce1fbd 100644 --- a/src/angle.cpp +++ b/src/angle.cpp @@ -31,6 +31,7 @@ Angle::Angle(LAMMPS *_lmp) : Pointers(_lmp) energy = 0.0; virial[0] = virial[1] = virial[2] = virial[3] = virial[4] = virial[5] = 0.0; writedata = 1; + reinitflag = 1; allocated = 0; suffix_flag = Suffix::NONE; From 7eb6c2652f43711da97ad0da5ca3861b02bb90ea Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 26 Apr 2022 16:16:44 -0400 Subject: [PATCH 36/57] update advanced utils tests. include test for expand args --- unittest/cplusplus/test_advanced_utils.cpp | 213 +++++++++++---------- 1 file changed, 113 insertions(+), 100 deletions(-) diff --git a/unittest/cplusplus/test_advanced_utils.cpp b/unittest/cplusplus/test_advanced_utils.cpp index 3e5a846914..8c9bb6ea19 100644 --- a/unittest/cplusplus/test_advanced_utils.cpp +++ b/unittest/cplusplus/test_advanced_utils.cpp @@ -3,6 +3,7 @@ #include "error.h" #include "input.h" #include "lammps.h" +#include "memory.h" #include "utils.h" #include "../testing/core.h" @@ -26,6 +27,25 @@ protected: LAMMPSTest::SetUp(); error = lmp->error; } + + void atomic_system() + { + BEGIN_HIDE_OUTPUT(); + command("units real"); + command("lattice sc 1.0 origin 0.125 0.125 0.125"); + command("region box block -2 2 -2 2 -2 2"); + command("create_box 8 box"); + command("create_atoms 1 box"); + command("pair_style zero 3.5"); + command("pair_coeff * *"); + command("mass * 1.0"); + command("region left block -2.0 -1.0 INF INF INF INF"); + command("region right block 0.5 2.0 INF INF INF INF"); + command("region top block INF INF -2.0 -1.0 INF INF"); + command("set region left type 2"); + command("set region right type 3"); + END_HIDE_OUTPUT(); + } }; TEST_F(Advanced_utils, missing_cmd_args) @@ -52,118 +72,111 @@ TEST_F(Advanced_utils, logmesg) EXPECT_EQ(output, "test message from test " + testbinary); }; -TEST_F(Advanced_utils, bounds_case1) +// death tests only. the other cases are tested in the basic utils unit tester +TEST_F(Advanced_utils, bounds_int_fail) { int nlo, nhi; - - nlo = nhi = -1; - utils::bounds(FLERR, "9", 0, 10, nlo, nhi, nullptr); - ASSERT_EQ(nlo, 9); - ASSERT_EQ(nhi, 9); - utils::bounds(FLERR, "1", 1, 10, nlo, nhi, nullptr); - ASSERT_EQ(nlo, 1); - ASSERT_EQ(nhi, 1); - utils::bounds(FLERR, "1x", 1, 10, nlo, nhi, nullptr); - ASSERT_EQ(nlo, -1); - ASSERT_EQ(nhi, -1); - utils::bounds(FLERR, "-1", 1, 10, nlo, nhi, nullptr); - ASSERT_EQ(nlo, -1); - ASSERT_EQ(nhi, -1); - utils::bounds(FLERR, "+1", 1, 10, nlo, nhi, nullptr); - ASSERT_EQ(nlo, -1); - ASSERT_EQ(nhi, -1); - utils::bounds(FLERR, "1:3", 1, 10, nlo, nhi, nullptr); - ASSERT_EQ(nlo, -1); - ASSERT_EQ(nhi, -1); + TEST_FAILURE("ERROR: Invalid range string: 1x ", + utils::bounds(FLERR, "1x", 1, 10, nlo, nhi, error);); + TEST_FAILURE("ERROR: Invalid range string: -1 ", + utils::bounds(FLERR, "-1", 1, 10, nlo, nhi, error);); + TEST_FAILURE("ERROR: Invalid range string: \\+1 ", + utils::bounds(FLERR, "+1", 1, 10, nlo, nhi, error);); + TEST_FAILURE("ERROR: Invalid range string: 1:3 ", + utils::bounds(FLERR, "1:3", 1, 10, nlo, nhi, error);); + TEST_FAILURE("ERROR: Invalid range string: \\? ", + utils::bounds(FLERR, "?", -10, 5, nlo, nhi, error);); + TEST_FAILURE("ERROR: Invalid range string: 3\\*:2 ", + utils::bounds(FLERR, "3*:2", -10, 5, nlo, nhi, error);); } -TEST_F(Advanced_utils, bounds_case2) -{ - int nlo, nhi; - - nlo = nhi = -1; - utils::bounds(FLERR, "*", 0, 10, nlo, nhi, nullptr); - ASSERT_EQ(nlo, 0); - ASSERT_EQ(nhi, 10); - utils::bounds(FLERR, "*", -10, 5, nlo, nhi, nullptr); - ASSERT_EQ(nlo, -10); - ASSERT_EQ(nhi, 5); - utils::bounds(FLERR, "?", -10, 5, nlo, nhi, nullptr); - ASSERT_EQ(nlo, -1); - ASSERT_EQ(nhi, -1); -} - -TEST_F(Advanced_utils, bounds_case3) -{ - int nlo, nhi; - - nlo = nhi = -1; - utils::bounds(FLERR, "2*", 0, 10, nlo, nhi, nullptr); - ASSERT_EQ(nlo, 2); - ASSERT_EQ(nhi, 10); - utils::bounds(FLERR, "3*", -10, 5, nlo, nhi, nullptr); - ASSERT_EQ(nlo, 3); - ASSERT_EQ(nhi, 5); - utils::bounds(FLERR, "3*:2", -10, 5, nlo, nhi, nullptr); - ASSERT_EQ(nlo, -1); - ASSERT_EQ(nhi, -1); -} - -TEST_F(Advanced_utils, boundsbig_case1) +TEST_F(Advanced_utils, bounds_bigint_fail) { bigint nlo, nhi; - - nlo = nhi = -1; - utils::bounds(FLERR, "9", 0, 10, nlo, nhi, nullptr); - ASSERT_EQ(nlo, 9); - ASSERT_EQ(nhi, 9); - utils::bounds(FLERR, "1", 1, 10, nlo, nhi, nullptr); - ASSERT_EQ(nlo, 1); - ASSERT_EQ(nhi, 1); - utils::bounds(FLERR, "1x", 1, 10, nlo, nhi, nullptr); - ASSERT_EQ(nlo, -1); - ASSERT_EQ(nhi, -1); - utils::bounds(FLERR, "-1", 1, 10, nlo, nhi, nullptr); - ASSERT_EQ(nlo, -1); - ASSERT_EQ(nhi, -1); - utils::bounds(FLERR, "+1", 1, 10, nlo, nhi, nullptr); - ASSERT_EQ(nlo, -1); - ASSERT_EQ(nhi, -1); - utils::bounds(FLERR, "1:3", 1, 10, nlo, nhi, nullptr); - ASSERT_EQ(nlo, -1); - ASSERT_EQ(nhi, -1); + TEST_FAILURE("ERROR: Invalid range string: 1x ", + utils::bounds(FLERR, "1x", 1, 10, nlo, nhi, error);); + TEST_FAILURE("ERROR: Invalid range string: -1 ", + utils::bounds(FLERR, "-1", 1, 10, nlo, nhi, error);); + TEST_FAILURE("ERROR: Invalid range string: \\+1 ", + utils::bounds(FLERR, "+1", 1, 10, nlo, nhi, error);); + TEST_FAILURE("ERROR: Invalid range string: 1:3 ", + utils::bounds(FLERR, "1:3", 1, 10, nlo, nhi, error);); + TEST_FAILURE("ERROR: Invalid range string: \\? ", + utils::bounds(FLERR, "?", -10, 5, nlo, nhi, error);); + TEST_FAILURE("ERROR: Invalid range string: 3\\*:2 ", + utils::bounds(FLERR, "3*:2", -10, 5, nlo, nhi, error);); } -TEST_F(Advanced_utils, boundsbig_case2) +TEST_F(Advanced_utils, expand_args) { - bigint nlo, nhi; + atomic_system(); + BEGIN_CAPTURE_OUTPUT(); + command("compute temp all temp"); + command("variable temp vector c_temp"); + command("variable step equal step"); + command("variable pe equal pe"); + command("variable pe equal pe"); + command("variable epair equal epair"); + command("compute gofr all rdf 20 1 1 1 2"); + command("fix 1 all ave/time 1 1 1 v_step v_pe v_epair"); + command("fix 2 all nve"); + command("run 1 post no"); + auto output = END_CAPTURE_OUTPUT(); - nlo = nhi = -1; - utils::bounds(FLERR, "*", 0, 10, nlo, nhi, nullptr); - ASSERT_EQ(nlo, 0); - ASSERT_EQ(nhi, 10); - utils::bounds(FLERR, "*", -10, 5, nlo, nhi, nullptr); - ASSERT_EQ(nlo, -10); - ASSERT_EQ(nhi, 5); - utils::bounds(FLERR, "?", -10, 5, nlo, nhi, nullptr); - ASSERT_EQ(nlo, -1); - ASSERT_EQ(nhi, -1); -} + char **args, **earg; + args = new char *[9]; + args[0] = utils::strdup("v_step"); + args[1] = utils::strdup("c_temp"); + args[2] = utils::strdup("f_1[*]"); + args[3] = utils::strdup("c_temp[*]"); + args[4] = utils::strdup("v_temp[*]"); + args[5] = utils::strdup("c_rdf[*]"); + args[6] = utils::strdup("c_rdf[1][*]"); + args[7] = utils::strdup("c_rdf[*][2]"); + args[8] = utils::strdup("c_rdf[*][*]"); -TEST_F(Advanced_utils, boundsbig_case3) -{ - bigint nlo, nhi; + auto narg = utils::expand_args(FLERR, 9, args, 0, earg, lmp); + EXPECT_EQ(narg, 16); + EXPECT_STREQ(earg[0], "v_step"); + EXPECT_STREQ(earg[1], "c_temp"); + EXPECT_STREQ(earg[2], "f_1[1]"); + EXPECT_STREQ(earg[3], "f_1[2]"); + EXPECT_STREQ(earg[4], "f_1[3]"); + EXPECT_STREQ(earg[5], "c_temp[1]"); + EXPECT_STREQ(earg[6], "c_temp[2]"); + EXPECT_STREQ(earg[7], "c_temp[3]"); + EXPECT_STREQ(earg[8], "c_temp[4]"); + EXPECT_STREQ(earg[9], "c_temp[5]"); + EXPECT_STREQ(earg[10], "c_temp[6]"); + EXPECT_STREQ(earg[11], "v_temp[*]"); + EXPECT_STREQ(earg[12], "c_rdf[*]"); + EXPECT_STREQ(earg[13], "c_rdf[1][*]"); + EXPECT_STREQ(earg[14], "c_rdf[*][2]"); + EXPECT_STREQ(earg[15], "c_rdf[*][*]"); - nlo = nhi = -1; - utils::bounds(FLERR, "2*", 0, 10, nlo, nhi, nullptr); - ASSERT_EQ(nlo, 2); - ASSERT_EQ(nhi, 10); - utils::bounds(FLERR, "3*", -10, 5, nlo, nhi, nullptr); - ASSERT_EQ(nlo, 3); - ASSERT_EQ(nhi, 5); - utils::bounds(FLERR, "3*:2", -10, 5, nlo, nhi, nullptr); - ASSERT_EQ(nlo, -1); - ASSERT_EQ(nhi, -1); + for (int i = 0; i < narg; ++i) + delete[] earg[i]; + lmp->memory->sfree(earg); + + narg = utils::expand_args(FLERR, 9, args, 1, earg, lmp); + EXPECT_EQ(narg, 9); + EXPECT_NE(args, earg); + EXPECT_STREQ(earg[0], "v_step"); + EXPECT_STREQ(earg[1], "c_temp"); + EXPECT_STREQ(earg[2], "f_1[*]"); + EXPECT_STREQ(earg[3], "c_temp[*]"); + EXPECT_STREQ(earg[4], "v_temp[*]"); + EXPECT_STREQ(earg[5], "c_rdf[*]"); + EXPECT_STREQ(earg[6], "c_rdf[1][*]"); + EXPECT_STREQ(earg[7], "c_rdf[*][2]"); + EXPECT_STREQ(earg[8], "c_rdf[*][*]"); + + for (int i = 0; i < 9; ++i) + delete[] args[i]; + delete[] args; + for (int i = 0; i < narg; ++i) + delete[] earg[i]; + lmp->memory->sfree(earg); } } // namespace LAMMPS_NS From 64fff417c37e40c6fc1828f22a40d1acaf0dd995 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 26 Apr 2022 17:25:27 -0400 Subject: [PATCH 37/57] test more bound variants --- unittest/cplusplus/test_advanced_utils.cpp | 49 ++++++++++------------ 1 file changed, 23 insertions(+), 26 deletions(-) diff --git a/unittest/cplusplus/test_advanced_utils.cpp b/unittest/cplusplus/test_advanced_utils.cpp index 8c9bb6ea19..ee39f67f34 100644 --- a/unittest/cplusplus/test_advanced_utils.cpp +++ b/unittest/cplusplus/test_advanced_utils.cpp @@ -124,54 +124,51 @@ TEST_F(Advanced_utils, expand_args) auto output = END_CAPTURE_OUTPUT(); char **args, **earg; - args = new char *[9]; + constexpr int oarg = 9; + args = new char *[oarg]; args[0] = utils::strdup("v_step"); args[1] = utils::strdup("c_temp"); - args[2] = utils::strdup("f_1[*]"); - args[3] = utils::strdup("c_temp[*]"); - args[4] = utils::strdup("v_temp[*]"); + args[2] = utils::strdup("f_1[2*]"); + args[3] = utils::strdup("c_temp[2*4]"); + args[4] = utils::strdup("v_temp[*4]"); args[5] = utils::strdup("c_rdf[*]"); args[6] = utils::strdup("c_rdf[1][*]"); args[7] = utils::strdup("c_rdf[*][2]"); args[8] = utils::strdup("c_rdf[*][*]"); - auto narg = utils::expand_args(FLERR, 9, args, 0, earg, lmp); - EXPECT_EQ(narg, 16); + auto narg = utils::expand_args(FLERR, oarg, args, 0, earg, lmp); + EXPECT_EQ(narg, 12); EXPECT_STREQ(earg[0], "v_step"); EXPECT_STREQ(earg[1], "c_temp"); - EXPECT_STREQ(earg[2], "f_1[1]"); - EXPECT_STREQ(earg[3], "f_1[2]"); - EXPECT_STREQ(earg[4], "f_1[3]"); - EXPECT_STREQ(earg[5], "c_temp[1]"); - EXPECT_STREQ(earg[6], "c_temp[2]"); - EXPECT_STREQ(earg[7], "c_temp[3]"); - EXPECT_STREQ(earg[8], "c_temp[4]"); - EXPECT_STREQ(earg[9], "c_temp[5]"); - EXPECT_STREQ(earg[10], "c_temp[6]"); - EXPECT_STREQ(earg[11], "v_temp[*]"); - EXPECT_STREQ(earg[12], "c_rdf[*]"); - EXPECT_STREQ(earg[13], "c_rdf[1][*]"); - EXPECT_STREQ(earg[14], "c_rdf[*][2]"); - EXPECT_STREQ(earg[15], "c_rdf[*][*]"); + EXPECT_STREQ(earg[2], "f_1[2]"); + EXPECT_STREQ(earg[3], "f_1[3]"); + EXPECT_STREQ(earg[4], "c_temp[2]"); + EXPECT_STREQ(earg[5], "c_temp[3]"); + EXPECT_STREQ(earg[6], "c_temp[4]"); + EXPECT_STREQ(earg[7], "v_temp[*4]"); + EXPECT_STREQ(earg[8], "c_rdf[*]"); + EXPECT_STREQ(earg[9], "c_rdf[1][*]"); + EXPECT_STREQ(earg[10], "c_rdf[*][2]"); + EXPECT_STREQ(earg[11], "c_rdf[*][*]"); for (int i = 0; i < narg; ++i) delete[] earg[i]; lmp->memory->sfree(earg); - narg = utils::expand_args(FLERR, 9, args, 1, earg, lmp); - EXPECT_EQ(narg, 9); + narg = utils::expand_args(FLERR, oarg, args, 1, earg, lmp); + EXPECT_EQ(narg, oarg); EXPECT_NE(args, earg); EXPECT_STREQ(earg[0], "v_step"); EXPECT_STREQ(earg[1], "c_temp"); - EXPECT_STREQ(earg[2], "f_1[*]"); - EXPECT_STREQ(earg[3], "c_temp[*]"); - EXPECT_STREQ(earg[4], "v_temp[*]"); + EXPECT_STREQ(earg[2], "f_1[2*]"); + EXPECT_STREQ(earg[3], "c_temp[2*4]"); + EXPECT_STREQ(earg[4], "v_temp[*4]"); EXPECT_STREQ(earg[5], "c_rdf[*]"); EXPECT_STREQ(earg[6], "c_rdf[1][*]"); EXPECT_STREQ(earg[7], "c_rdf[*][2]"); EXPECT_STREQ(earg[8], "c_rdf[*][*]"); - for (int i = 0; i < 9; ++i) + for (int i = 0; i < oarg; ++i) delete[] args[i]; delete[] args; for (int i = 0; i < narg; ++i) From d8e98cb99db77d4d3b33d610ce4a587ef0caef57 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 26 Apr 2022 17:53:47 -0400 Subject: [PATCH 38/57] make tests more complex and add vector variable expansion --- unittest/cplusplus/test_advanced_utils.cpp | 103 +++++++++++++++------ 1 file changed, 73 insertions(+), 30 deletions(-) diff --git a/unittest/cplusplus/test_advanced_utils.cpp b/unittest/cplusplus/test_advanced_utils.cpp index ee39f67f34..46da2d5d4b 100644 --- a/unittest/cplusplus/test_advanced_utils.cpp +++ b/unittest/cplusplus/test_advanced_utils.cpp @@ -125,55 +125,98 @@ TEST_F(Advanced_utils, expand_args) char **args, **earg; constexpr int oarg = 9; - args = new char *[oarg]; - args[0] = utils::strdup("v_step"); - args[1] = utils::strdup("c_temp"); - args[2] = utils::strdup("f_1[2*]"); - args[3] = utils::strdup("c_temp[2*4]"); - args[4] = utils::strdup("v_temp[*4]"); - args[5] = utils::strdup("c_rdf[*]"); - args[6] = utils::strdup("c_rdf[1][*]"); - args[7] = utils::strdup("c_rdf[*][2]"); - args[8] = utils::strdup("c_rdf[*][*]"); + args = new char *[oarg]; + args[0] = utils::strdup("v_step"); + args[1] = utils::strdup("c_temp"); + args[2] = utils::strdup("f_1[*]"); + args[3] = utils::strdup("c_temp[2*4]"); + args[4] = utils::strdup("v_temp[*4]"); + args[5] = utils::strdup("c_gofr[3*]"); + args[6] = utils::strdup("c_gofr[1][*]"); + args[7] = utils::strdup("c_gofr[*2][2]"); + args[8] = utils::strdup("c_gofr[*][*]"); auto narg = utils::expand_args(FLERR, oarg, args, 0, earg, lmp); - EXPECT_EQ(narg, 12); + EXPECT_EQ(narg, 16); EXPECT_STREQ(earg[0], "v_step"); EXPECT_STREQ(earg[1], "c_temp"); - EXPECT_STREQ(earg[2], "f_1[2]"); - EXPECT_STREQ(earg[3], "f_1[3]"); - EXPECT_STREQ(earg[4], "c_temp[2]"); - EXPECT_STREQ(earg[5], "c_temp[3]"); - EXPECT_STREQ(earg[6], "c_temp[4]"); - EXPECT_STREQ(earg[7], "v_temp[*4]"); - EXPECT_STREQ(earg[8], "c_rdf[*]"); - EXPECT_STREQ(earg[9], "c_rdf[1][*]"); - EXPECT_STREQ(earg[10], "c_rdf[*][2]"); - EXPECT_STREQ(earg[11], "c_rdf[*][*]"); + EXPECT_STREQ(earg[2], "f_1[1]"); + EXPECT_STREQ(earg[3], "f_1[2]"); + EXPECT_STREQ(earg[4], "f_1[3]"); + EXPECT_STREQ(earg[5], "c_temp[2]"); + EXPECT_STREQ(earg[6], "c_temp[3]"); + EXPECT_STREQ(earg[7], "c_temp[4]"); + EXPECT_STREQ(earg[8], "v_temp[1]"); + EXPECT_STREQ(earg[9], "v_temp[2]"); + EXPECT_STREQ(earg[10], "v_temp[3]"); + EXPECT_STREQ(earg[11], "v_temp[4]"); + EXPECT_STREQ(earg[12], "c_gofr[3*]"); + EXPECT_STREQ(earg[13], "c_gofr[1][*]"); + EXPECT_STREQ(earg[14], "c_gofr[*2][2]"); + EXPECT_STREQ(earg[15], "c_gofr[*][*]"); for (int i = 0; i < narg; ++i) delete[] earg[i]; lmp->memory->sfree(earg); narg = utils::expand_args(FLERR, oarg, args, 1, earg, lmp); - EXPECT_EQ(narg, oarg); + EXPECT_EQ(narg, 16); EXPECT_NE(args, earg); EXPECT_STREQ(earg[0], "v_step"); EXPECT_STREQ(earg[1], "c_temp"); - EXPECT_STREQ(earg[2], "f_1[2*]"); + EXPECT_STREQ(earg[2], "f_1[*]"); EXPECT_STREQ(earg[3], "c_temp[2*4]"); EXPECT_STREQ(earg[4], "v_temp[*4]"); - EXPECT_STREQ(earg[5], "c_rdf[*]"); - EXPECT_STREQ(earg[6], "c_rdf[1][*]"); - EXPECT_STREQ(earg[7], "c_rdf[*][2]"); - EXPECT_STREQ(earg[8], "c_rdf[*][*]"); + EXPECT_STREQ(earg[5], "c_gofr[3]"); + EXPECT_STREQ(earg[6], "c_gofr[4]"); + EXPECT_STREQ(earg[7], "c_gofr[5]"); + EXPECT_STREQ(earg[8], "c_gofr[1][*]"); + EXPECT_STREQ(earg[9], "c_gofr[1][2]"); + EXPECT_STREQ(earg[10], "c_gofr[2][2]"); + EXPECT_STREQ(earg[11], "c_gofr[1][*]"); + EXPECT_STREQ(earg[12], "c_gofr[2][*]"); + EXPECT_STREQ(earg[13], "c_gofr[3][*]"); + EXPECT_STREQ(earg[14], "c_gofr[4][*]"); + EXPECT_STREQ(earg[15], "c_gofr[5][*]"); - for (int i = 0; i < oarg; ++i) - delete[] args[i]; - delete[] args; for (int i = 0; i < narg; ++i) delete[] earg[i]; lmp->memory->sfree(earg); + + args[3][9] = '9'; + TEST_FAILURE("ERROR: Numeric index 9 is out of bounds \\(1-6\\).*", + utils::expand_args(FLERR, oarg, args, 0, earg, lmp);); + + args[3][9] = '4'; + args[5][7] = '9'; + TEST_FAILURE("ERROR: Numeric index 9 is out of bounds \\(1-5\\).*", + utils::expand_args(FLERR, oarg, args, 1, earg, lmp);); + + args[5][7] = '3'; + delete[] args[4]; + args[4] = utils::strdup("v_temp[2*]"); + narg = utils::expand_args(FLERR, oarg, args, 0, earg, lmp); + EXPECT_EQ(narg, 13); + EXPECT_STREQ(earg[0], "v_step"); + EXPECT_STREQ(earg[1], "c_temp"); + EXPECT_STREQ(earg[2], "f_1[1]"); + EXPECT_STREQ(earg[3], "f_1[2]"); + EXPECT_STREQ(earg[4], "f_1[3]"); + EXPECT_STREQ(earg[5], "c_temp[2]"); + EXPECT_STREQ(earg[6], "c_temp[3]"); + EXPECT_STREQ(earg[7], "c_temp[4]"); + EXPECT_STREQ(earg[8], "v_temp[2*]"); + EXPECT_STREQ(earg[9], "c_gofr[3*]"); + EXPECT_STREQ(earg[10], "c_gofr[1][*]"); + EXPECT_STREQ(earg[11], "c_gofr[*2][2]"); + EXPECT_STREQ(earg[12], "c_gofr[*][*]"); + + for (int i = 0; i < narg; ++i) + delete[] earg[i]; + lmp->memory->sfree(earg); + for (int i = 0; i < oarg; ++i) + delete[] args[i]; + delete[] args; } } // namespace LAMMPS_NS From d857600d9cecbc937fa39e43a3a7a0decbebde2d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 27 Apr 2022 04:46:18 -0400 Subject: [PATCH 39/57] start documenting functions in the MathSpecial namespace --- doc/doxygen/Doxyfile.in | 4 +++- doc/src/Developer_utils.rst | 17 ++++++++++++++ src/math_special.cpp | 4 ++++ src/math_special.h | 46 ++++++++++++++++++++++++++++++------- 4 files changed, 62 insertions(+), 9 deletions(-) diff --git a/doc/doxygen/Doxyfile.in b/doc/doxygen/Doxyfile.in index d454898f4e..e905d5a64d 100644 --- a/doc/doxygen/Doxyfile.in +++ b/doc/doxygen/Doxyfile.in @@ -2,7 +2,7 @@ DOXYFILE_ENCODING = UTF-8 PROJECT_NAME = "LAMMPS Programmer's Guide" -PROJECT_NUMBER = "24 August 2020" +PROJECT_NUMBER = "4 May 2022" PROJECT_BRIEF = "Documentation of the LAMMPS library interface and Python wrapper" PROJECT_LOGO = lammps-logo.png CREATE_SUBDIRS = NO @@ -437,6 +437,8 @@ INPUT = @LAMMPS_SOURCE_DIR@/utils.cpp \ @LAMMPS_SOURCE_DIR@/math_eigen.h \ @LAMMPS_SOURCE_DIR@/platform.h \ @LAMMPS_SOURCE_DIR@/platform.cpp \ + @LAMMPS_SOURCE_DIR@/math_special.h \ + @LAMMPS_SOURCE_DIR@/math_special.cpp \ # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or # directories that are symbolic links (a Unix file system feature) are excluded diff --git a/doc/src/Developer_utils.rst b/doc/src/Developer_utils.rst index d7b1f077dd..0883d6b3c8 100644 --- a/doc/src/Developer_utils.rst +++ b/doc/src/Developer_utils.rst @@ -246,6 +246,23 @@ Customized standard functions --------------------------- +Special Math functions +---------------------- + +The ``MathSpecial`` namespace implements a selection of custom and optimized +mathematical functions for a variety of applications. + +.. doxygenfunction:: factorial + :project: progguide + +.. doxygenfunction:: exp2_x86 + :project: progguide + +.. doxygenfunction:: fm_exp + :project: progguide + +--------------------------- + Tokenizer classes ----------------- diff --git a/src/math_special.cpp b/src/math_special.cpp index da99c5850a..fd47aec9e9 100644 --- a/src/math_special.cpp +++ b/src/math_special.cpp @@ -706,6 +706,7 @@ static const double fm_exp2_p[] = { double MathSpecial::exp2_x86(double x) { +#if defined(__BYTE_ORDER__) && (__BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__) double ipart, fpart, px, qx; udi_t epart; @@ -726,6 +727,9 @@ double MathSpecial::exp2_x86(double x) x = 1.0 + 2.0*(px/(qx-px)); return epart.f*x; +#else + return pow(2.0, x); +#endif } double MathSpecial::fm_exp(double x) diff --git a/src/math_special.h b/src/math_special.h index fa39d46321..db780a240c 100644 --- a/src/math_special.h +++ b/src/math_special.h @@ -20,20 +20,50 @@ namespace LAMMPS_NS { namespace MathSpecial { - // tabulated factorial function + /*! Fast tabulated factorial function + * + * This function looks up precomputed factorial values for arguments of n = 0 + * to a maximum of 167, which is the maximal value representable by a double + * precision floating point number. For other values of n a NaN value is returned. + * + * \param n argument (valid: 0 <= n <= 167) + * \return value of n! as double precision number or NaN */ - extern double factorial(const int); + extern double factorial(const int n); + + /*! Fast implementation of 2^x without argument checks for little endian CPUs + * + * This function implements an optimized version of pow(2.0, x) that does not + * check for valid arguments and thus may only be used where arguments are well + * behaved. The implementation makes assumptions about the layout of double + * precision floating point numbers in memory and thus will only work on little + * endian CPUs. If little endian cannot be safely detected, the result of + * calling pow(2.0, x) will be returned. This function also is the basis for + * the fast exponential fm_exp(x). + * + * \param x argument + * \return value of 2^x as double precision number */ + + extern double exp2_x86(double x); + + /*! Fast implementation of exp(x) for little endian CPUs + * + * This function implements an optimized version of exp(x) for little endian CPUs. + * It calls the exp2_x86(x) function with a suitable prefactor to x to return exp(x). + * The implementation makes assumptions about the layout of double + * precision floating point numbers in memory and thus will only work on little + * endian CPUs. If little endian cannot be safely detected, the result of + * calling the exp(x) implementation in the libm math library will be returned. + * + * \param x argument + * \return value of e^x as double precision number */ + + extern double fm_exp(double x); // support function for scaled error function complement extern double erfcx_y100(const double y100); - // fast 2**x function without argument checks for little endian CPUs - extern double exp2_x86(double x); - - // fast e**x function for little endian CPUs, falls back to libc on other platforms - extern double fm_exp(double x); - // scaled error function complement exp(x*x)*erfc(x) for coul/long styles static inline double my_erfcx(const double x) From 643977740626be8757fb11f7ca1de6bcc53425f5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 27 Apr 2022 11:55:54 -0400 Subject: [PATCH 40/57] complete documentation of the MathSpecial namespace --- doc/src/Developer_utils.rst | 21 ++++++++ doc/utils/sphinx-config/false_positives.txt | 2 + src/math_special.h | 59 +++++++++++++++++---- 3 files changed, 72 insertions(+), 10 deletions(-) diff --git a/doc/src/Developer_utils.rst b/doc/src/Developer_utils.rst index 0883d6b3c8..0932276a58 100644 --- a/doc/src/Developer_utils.rst +++ b/doc/src/Developer_utils.rst @@ -261,6 +261,27 @@ mathematical functions for a variety of applications. .. doxygenfunction:: fm_exp :project: progguide +.. doxygenfunction:: my_erfcx + :project: progguide + +.. doxygenfunction:: expmsq + :project: progguide + +.. doxygenfunction:: square + :project: progguide + +.. doxygenfunction:: cube + :project: progguide + +.. doxygenfunction:: powsign + :project: progguide + +.. doxygenfunction:: powint + :project: progguide + +.. doxygenfunction:: powsinxx + :project: progguide + --------------------------- Tokenizer classes diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 62983f4f39..c66bb326db 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -890,6 +890,7 @@ Embt emi emol eN +endian energetics energyCorr eng @@ -1067,6 +1068,7 @@ fld floralwhite Florez flv +fm fmackay fmag fmass diff --git a/src/math_special.h b/src/math_special.h index db780a240c..51462922ac 100644 --- a/src/math_special.h +++ b/src/math_special.h @@ -22,7 +22,7 @@ namespace MathSpecial { /*! Fast tabulated factorial function * - * This function looks up precomputed factorial values for arguments of n = 0 + * This function looks up pre-computed factorial values for arguments of n = 0 * to a maximum of 167, which is the maximal value representable by a double * precision floating point number. For other values of n a NaN value is returned. * @@ -53,7 +53,7 @@ namespace MathSpecial { * The implementation makes assumptions about the layout of double * precision floating point numbers in memory and thus will only work on little * endian CPUs. If little endian cannot be safely detected, the result of - * calling the exp(x) implementation in the libm math library will be returned. + * calling the exp(x) implementation in the standard math library will be returned. * * \param x argument * \return value of e^x as double precision number */ @@ -64,7 +64,17 @@ namespace MathSpecial { extern double erfcx_y100(const double y100); - // scaled error function complement exp(x*x)*erfc(x) for coul/long styles + /*! Fast scaled error function complement exp(x*x)*erfc(x) for coul/long styles + * + * This is a portable fast implementation of exp(x*x)*erfc(x) that can be used + * in coul/long pair styles as a replacement for the polynomial expansion that + * is/was widely used. Unlike the polynomial expansion, that is only accurate + * at the level of single precision floating point it provides full double precision + * accuracy, but at comparable speed (unlike the erfc() implementation shipped + * with GNU standard math library). + * + * \param x argument + * \return value of e^(x*x)*erfc(x) */ static inline double my_erfcx(const double x) { @@ -74,7 +84,15 @@ namespace MathSpecial { return 2.0 * exp(x * x) - erfcx_y100(400.0 / (4.0 - x)); } - // exp(-x*x) for coul/long styles + /*! Fast implementation of exp(-x*x) for little endian CPUs for coul/long styles + * + * This function implements an optimized version of exp(-x*x) based on exp2_x86() + * for use with little endian CPUs. If little endian cannot be safely detected, + * the result of calling the exp(-x*x) implementation in the standard math + * library will be returned. + * + * \param x argument + * \return value of e^(-x*x) as double precision number */ static inline double expmsq(double x) { @@ -87,18 +105,34 @@ namespace MathSpecial { #endif } - // x**2, use instead of pow(x,2.0) + /*! Fast inline version of pow(x, 2.0) + * + * \param x argument + * \return x*x */ static inline double square(const double &x) { return x * x; } - // x**3, use instead of pow(x,3.0) + /*! Fast inline version of pow(x, 3.0) + * + * \param x argument + * \return x*x */ + static inline double cube(const double &x) { return x * x * x; } - // return -1.0 for odd n, 1.0 for even n, like pow(-1.0,n) + /* Fast inline version of pow(-1.0, n) + * + * \param n argument (integer) + * \return -1 if n is odd, 1.0 if n is even */ + static inline double powsign(const int n) { return (n & 1) ? -1.0 : 1.0; } - // optimized version of pow(x,n) with n being integer - // up to 10x faster than pow(x,y) + /* Fast inline version of pow(x,n) for integer n + * + * This is a version of pow(x,n) optimized for n being integer. + * Speedups of up to 10x faster than pow(x,y) have been measured. + * + * \param n argument (integer) + * \return value of x^n */ static inline double powint(const double &x, const int n) { @@ -114,7 +148,12 @@ namespace MathSpecial { return (n > 0) ? yy : 1.0 / yy; } - // optimized version of (sin(x)/x)**n with n being a _positive_ integer + /* Fast inline version of (sin(x)/x)^n as used by PPPM kspace styles + * + * This is an optimized function to compute (sin(x)/x)^n as frequently used by PPPM. + * + * \param n argument (integer). Expected to be positive. + * \return value of (sin(x)/x)^n */ static inline double powsinxx(const double &x, int n) { From a3c6baad4ca4ec173dedafbaf87f15d0abcf6b61 Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Wed, 27 Apr 2022 10:58:22 -0600 Subject: [PATCH 41/57] Removed CPU specific options --- src/KOKKOS/pair_snap_kokkos_impl.h | 31 ++++++++++++++++-------------- 1 file changed, 17 insertions(+), 14 deletions(-) diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index 7c621176cd..4d2edf037c 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -89,15 +89,17 @@ PairSNAPKokkos::~PairSNAPKokkos() template void PairSNAPKokkos::init_style() { - if (host_flag) { - if (lmp->kokkos->nthreads > 1) - if (comm->me == 0) - utils::logmesg(lmp,"Pair style snap/kk currently only runs on a single " - "CPU thread, even if more threads are requested\n"); - PairSNAP::init_style(); - return; - } + // Disabled for DEBUGGING on CPU + // if (host_flag) { + // if (lmp->kokkos->nthreads > 1) + // if (comm->me == 0) + // utils::logmesg(lmp,"Pair style snap/kk currently only runs on a single " + // "CPU thread, even if more threads are requested\n"); + + // PairSNAP::init_style(); + // return; + // } if (force->newton_pair == 0) error->all(FLERR,"Pair style SNAP requires newton pair on"); @@ -139,12 +141,13 @@ struct FindMaxNumNeighs { template void PairSNAPKokkos::compute(int eflag_in, int vflag_in) { - if (host_flag) { - atomKK->sync(Host,X_MASK|TYPE_MASK); - PairSNAP::compute(eflag_in,vflag_in); - atomKK->modified(Host,F_MASK); - return; - } + // Disabled for DEBUGGING on CPU + // if (host_flag) { + // atomKK->sync(Host,X_MASK|TYPE_MASK); + // PairSNAP::compute(eflag_in,vflag_in); + // atomKK->modified(Host,F_MASK); + // return; + // } eflag = eflag_in; vflag = vflag_in; From 3b1165ccdc507ac432c6b167b1dcc54361bf4e52 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 27 Apr 2022 15:02:32 -0400 Subject: [PATCH 42/57] update files to be more compatible with LAMMPS' conventions and for code changes --- src/pair_smatb.cpp | 178 +++++++++++++++++++------------------- src/pair_smatb.h | 60 ++++--------- src/pair_smatb_single.cpp | 142 ++++++++++++++---------------- src/pair_smatb_single.h | 25 +----- 4 files changed, 176 insertions(+), 229 deletions(-) diff --git a/src/pair_smatb.cpp b/src/pair_smatb.cpp index cda65837c8..dc1d42d3f7 100644 --- a/src/pair_smatb.cpp +++ b/src/pair_smatb.cpp @@ -12,9 +12,11 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- -This pair style is written by Daniele Rapetti (iximiel@gmail.com) + Contributing author: Daniele Rapetti (iximiel@gmail.com) ------------------------------------------------------------------------- */ + #include "pair_smatb.h" + #include "atom.h" #include "comm.h" #include "error.h" @@ -22,15 +24,15 @@ This pair style is written by Daniele Rapetti (iximiel@gmail.com) #include "memory.h" #include "neigh_list.h" #include "neighbor.h" -#include -#include -#include -#include + +#include using namespace LAMMPS_NS; -PairSMATB::PairSMATB(LAMMPS *lmp) : - Pair(lmp), nmax(0), on_eb(nullptr), r0(nullptr), p(nullptr), A(nullptr), q(nullptr), +/* ---------------------------------------------------------------------- */ + +PairSMATB::PairSMATB(LAMMPS *_lmp) : + Pair(_lmp), nmax(0), on_eb(nullptr), r0(nullptr), p(nullptr), A(nullptr), q(nullptr), QSI(nullptr), cutOffStart(nullptr), cutOffEnd(nullptr), cutOffEnd2(nullptr), a3(nullptr), a4(nullptr), a5(nullptr), x3(nullptr), x4(nullptr), x5(nullptr) { @@ -48,6 +50,8 @@ PairSMATB::PairSMATB(LAMMPS *lmp) : comm_reverse = 1; } +/* ---------------------------------------------------------------------- */ + PairSMATB::~PairSMATB() { if (copymode) { return; } @@ -73,16 +77,16 @@ PairSMATB::~PairSMATB() } } +/* ---------------------------------------------------------------------- */ + void PairSMATB::compute(int eflag, int vflag) -{ //workhorse routine that computes pairwise interactions - //eflag means compute energy - //vflag means compute virial +{ int i, j, ii, jj, jnum, itype, jtype; double xtmp, ytmp, ztmp, del[3], fpair; double dijsq, dij; double espo, aexpp, qsiexpq, eb_i, Fb, Fr; double polyval, polyval2, polyval3, polyval4, polyval5; - //sets up the flags for energy calculations + if (eflag || vflag) { ev_setup(eflag, vflag); eng_vdwl = 0; @@ -91,7 +95,6 @@ void PairSMATB::compute(int eflag, int vflag) } // grow on_eb array if necessary - // need to be atom->nmax in length if (atom->nmax > nmax) { nmax = atom->nmax; @@ -119,7 +122,7 @@ void PairSMATB::compute(int eflag, int vflag) int *numneigh = list->numneigh; int **firstneigh = list->firstneigh; - //FIRST LOOP: CALCULATES the squared bounding energy and accumulate it in on_eb for each atom + // FIRST LOOP: CALCULATES the squared bonding energy and accumulate it in on_eb for each atom for (ii = 0; ii < inum; ++ii) { i = ilist[ii]; xtmp = x[i][0]; @@ -153,19 +156,18 @@ void PairSMATB::compute(int eflag, int vflag) qsiexpq = qsiexpq * qsiexpq; } on_eb[i] += qsiexpq; - //if (newton_pair || j < nlocal) { on_eb[j] += qsiexpq; - //} } } } - //communicate the squared bounding energy between the various bins + // communicate the squared bonding energy between the various bins - comm->reverse_comm_pair(this); + comm->reverse_comm(this); - //Support Loop: take the square root of the bounding energy and accumulate it in the energy accumulator if needed - // the store the reciprocal in on_eb in order to not do it in the SECOND LOOP + // Support Loop: take the square root of the bonding energy and + // accumulate it in the energy accumulator if needed the store the + // reciprocal in on_eb in order to not do it in the SECOND LOOP for (ii = 0; ii < inum; ++ii) { i = ilist[ii]; @@ -176,17 +178,18 @@ void PairSMATB::compute(int eflag, int vflag) } else { on_eb[i] = 0.0; } - //if needed the bounding energy is accumulated: + //if needed the bonding energy is accumulated: if (eflag_either) { if (eflag_atom) { eatom[i] -= eb_i; } if (eflag_global) { eng_vdwl -= eb_i; } } } } - //this communication stores the denominators in the ghosts atoms, this is needed because of how forces are calculated - comm->forward_comm_pair(this); + // this communication stores the denominators in the ghosts atoms, + // this is needed because of how forces are calculated + comm->forward_comm(this); - //SECOND LOOP: given on_eb[i] calculates forces and energies + // SECOND LOOP: given on_eb[i] calculates forces and energies for (ii = 0; ii < inum; ++ii) { i = ilist[ii]; xtmp = x[i][0]; @@ -230,7 +233,7 @@ void PairSMATB::compute(int eflag, int vflag) 3.0 * x3[itype][jtype] * polyval2)) * qsiexpq; } - //if needed the repulsive energy is accumulated: + // if needed the repulsive energy is accumulated: if (eflag_either) { if (eflag_atom) { eatom[i] += aexpp; @@ -244,7 +247,7 @@ void PairSMATB::compute(int eflag, int vflag) } } } - //calculates the module of the pair energy between i and j + // calculates the module of the pair energy between i and j fpair = (Fb * (on_eb[i] + on_eb[j]) + Fr) / dij; f[i][0] += del[0] * fpair; @@ -271,7 +274,7 @@ void PairSMATB::compute(int eflag, int vflag) ------------------------------------------------------------------------- */ void PairSMATB::settings(int narg, char **) -{ //reads the input script line with arguments you define +{ if (narg > 0) error->all(FLERR, "Illegal pair_style command: smatb accepts no options"); } @@ -281,31 +284,27 @@ void PairSMATB::settings(int narg, char **) void PairSMATB::allocate() { - int n = atom->ntypes; - int natoms = atom->natoms; + const int np1 = atom->ntypes + 1; - memory->create(setflag, n + 1, n + 1, "pair_smatb:setflag"); - for (int i = 1; i <= n; i++) { - for (int j = i; j <= n; j++) { setflag[i][j] = 0; } - } + memory->create(setflag, np1, np1, "pair_smatb:setflag"); + for (int i = 1; i < np1; i++) + for (int j = i; j < np1; j++) setflag[i][j] = 0; - memory->create(cutsq, n + 1, n + 1, "pair_smatb:cutsq"); - - //memory->create is needed to make a false nxn array on a n^2x1 line of data - memory->create(r0, n + 1, n + 1, "pair_smatb:r0"); - memory->create(p, n + 1, n + 1, "pair_smatb:p"); - memory->create(A, n + 1, n + 1, "pair_smatb:A"); - memory->create(q, n + 1, n + 1, "pair_smatb:q"); - memory->create(QSI, n + 1, n + 1, "pair_smatb:QSI"); - memory->create(cutOffStart, n + 1, n + 1, "pair_smatb:cutOffStart"); - memory->create(cutOffEnd, n + 1, n + 1, "pair_smatb:cutOffEnd"); - memory->create(cutOffEnd2, n + 1, n + 1, "pair_smatb:cutOffEnd2"); - memory->create(a3, n + 1, n + 1, "pair_smatb:a1"); - memory->create(a4, n + 1, n + 1, "pair_smatb:a2"); - memory->create(a5, n + 1, n + 1, "pair_smatb:a5"); - memory->create(x3, n + 1, n + 1, "pair_smatb:x1"); - memory->create(x4, n + 1, n + 1, "pair_smatb:x2"); - memory->create(x5, n + 1, n + 1, "pair_smatb:x3"); + memory->create(cutsq, np1, np1, "pair_smatb:cutsq"); + memory->create(r0, np1, np1, "pair_smatb:r0"); + memory->create(p, np1, np1, "pair_smatb:p"); + memory->create(A, np1, np1, "pair_smatb:A"); + memory->create(q, np1, np1, "pair_smatb:q"); + memory->create(QSI, np1, np1, "pair_smatb:QSI"); + memory->create(cutOffStart, np1, np1, "pair_smatb:cutOffStart"); + memory->create(cutOffEnd, np1, np1, "pair_smatb:cutOffEnd"); + memory->create(cutOffEnd2, np1, np1, "pair_smatb:cutOffEnd2"); + memory->create(a3, np1, np1, "pair_smatb:a1"); + memory->create(a4, np1, np1, "pair_smatb:a2"); + memory->create(a5, np1, np1, "pair_smatb:a5"); + memory->create(x3, np1, np1, "pair_smatb:x1"); + memory->create(x4, np1, np1, "pair_smatb:x2"); + memory->create(x5, np1, np1, "pair_smatb:x3"); allocated = 1; } @@ -315,26 +314,23 @@ void PairSMATB::allocate() ------------------------------------------------------------------------- */ void PairSMATB::coeff(int narg, char **arg) -{ //set coefficients for one i,j type pair +{ if (!allocated) { allocate(); } - if (narg != 9) { - error->all( - FLERR, - "Incorrect args for pair coefficients:\n SMATB needs \"i j r0 p q A QSI CO_start CO_end\""); - } + if (narg != 9) utils::missing_cmd_args(FLERR, "pair_style smatb", error); + int ilo, ihi, jlo, jhi; utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error); utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error); - //reading parameters from input - double myr0 = utils::numeric(FLERR, arg[2], false, lmp), - myp = utils::numeric(FLERR, arg[3], false, lmp), - myq = utils::numeric(FLERR, arg[4], false, lmp), - myA = utils::numeric(FLERR, arg[5], false, lmp), - myQSI = utils::numeric(FLERR, arg[6], false, lmp), - mycutOffStart = utils::numeric(FLERR, arg[7], false, lmp), - mycutOffEnd = utils::numeric(FLERR, arg[8], false, lmp); - int count = 0; + double myr0 = utils::numeric(FLERR, arg[2], false, lmp); + double myp = utils::numeric(FLERR, arg[3], false, lmp); + double myq = utils::numeric(FLERR, arg[4], false, lmp); + double myA = utils::numeric(FLERR, arg[5], false, lmp); + double myQSI = utils::numeric(FLERR, arg[6], false, lmp); + double mycutOffStart = utils::numeric(FLERR, arg[7], false, lmp); + double mycutOffEnd = utils::numeric(FLERR, arg[8], false, lmp); + + int count = 0; for (int i = ilo; i <= ihi; i++) { for (int j = MAX(jlo, i); j <= jhi; j++) { r0[i][j] = myr0; @@ -354,21 +350,12 @@ void PairSMATB::coeff(int narg, char **arg) if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); } -/* ---------------------------------------------------------------------- - init specific to this pair style - ------------------------------------------------------------------------- */ -/* - void PairSMATB::init_style() {//initialization specific to this pair style - neighbor->request(this,instance_me); - } -*/ - /* ---------------------------------------------------------------------- init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ double PairSMATB::init_one(int i, int j) -{ //perform initialization for one i,j type pair +{ if (setflag[i][j] == 0) { ///@todo implement smatb mixing rules cutOffStart[i][j] = MIN(cutOffStart[i][i], cutOffStart[j][j]); @@ -376,12 +363,12 @@ double PairSMATB::init_one(int i, int j) error->all(FLERR, "All pair coeffs are not set"); } - //calculating the polynomial linking to zero + double es = cutOffEnd[i][j] - cutOffStart[i][j]; double es2 = es * es; double es3 = es2 * es; - //variables for poly for p and A + // variables for poly for p and A double expp = A[i][j] * exp(p[i][j] * (1. - cutOffStart[i][j] / r0[i][j])); double ap = -1. / es3; double bp = p[i][j] / (r0[i][j] * es2); @@ -391,7 +378,7 @@ double PairSMATB::init_one(int i, int j) a4[i][j] = expp * (15. * ap + 7. * bp + cp) / es; a3[i][j] = expp * (20. * ap + 8. * bp + cp) / 2.; - //variables for poly for q and qsi + // variables for poly for q and qsi double expq = QSI[i][j] * exp(q[i][j] * (1. - cutOffStart[i][j] / r0[i][j])); double aq = -1 / es3; double bq = q[i][j] / (es2 * r0[i][j]); @@ -421,7 +408,7 @@ double PairSMATB::init_one(int i, int j) x4[j][i] = x4[i][j]; x5[j][i] = x5[i][j]; } - //returns cutOffEnd to calculate cutforce and cutsq + return cutOffEnd[i][j]; } @@ -474,7 +461,8 @@ void PairSMATB::unpack_reverse_comm(int n, int *list, double *buf) } } -//write binary data of this simulation: +/* ---------------------------------------------------------------------- */ + void PairSMATB::write_restart_settings(FILE *fp) { fwrite(&offset_flag, sizeof(int), 1, fp); @@ -482,6 +470,8 @@ void PairSMATB::write_restart_settings(FILE *fp) fwrite(&tail_flag, sizeof(int), 1, fp); } +/* ---------------------------------------------------------------------- */ + void PairSMATB::read_restart_settings(FILE *fp) { int me = comm->me; @@ -496,12 +486,14 @@ void PairSMATB::read_restart_settings(FILE *fp) MPI_Bcast(&tail_flag, 1, MPI_INT, 0, world); } +/* ---------------------------------------------------------------------- */ + void PairSMATB::write_restart(FILE *fp) { write_restart_settings(fp); - //"I J r0 p q A QSI CO_start CO_end" + int i, j; - for (i = 1; i <= atom->ntypes; i++) + for (i = 1; i <= atom->ntypes; i++) { for (j = i; j <= atom->ntypes; j++) { fwrite(&setflag[i][j], sizeof(int), 1, fp); if (setflag[i][j]) { @@ -514,12 +506,15 @@ void PairSMATB::write_restart(FILE *fp) fwrite(&cutOffEnd[i][j], sizeof(double), 1, fp); } } - //maybe we need to save also the values of the various polynomials + } } +/* ---------------------------------------------------------------------- */ + void PairSMATB::read_restart(FILE *fp) { read_restart_settings(fp); + allocate(); size_t result; @@ -531,13 +526,13 @@ void PairSMATB::read_restart(FILE *fp) MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world); if (setflag[i][j]) { if (me == 0) { - result = fread(&r0[i][j], sizeof(double), 1, fp); - result = fread(&p[i][j], sizeof(double), 1, fp); - result = fread(&q[i][j], sizeof(double), 1, fp); - result = fread(&A[i][j], sizeof(double), 1, fp); - result = fread(&QSI[i][j], sizeof(double), 1, fp); - result = fread(&cutOffStart[i][j], sizeof(double), 1, fp); - result = fread(&cutOffEnd[i][j], sizeof(double), 1, fp); + utils::sfread(FLERR, &r0[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &p[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &q[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &A[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &QSI[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &cutOffStart[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &cutOffEnd[i][j], sizeof(double), 1, fp, nullptr, error); } MPI_Bcast(&r0[i][j], 1, MPI_DOUBLE, 0, world); MPI_Bcast(&p[i][j], 1, MPI_DOUBLE, 0, world); @@ -550,15 +545,18 @@ void PairSMATB::read_restart(FILE *fp) } } +/* ---------------------------------------------------------------------- */ + void PairSMATB::write_data(FILE *fp) { - //smatb needs I J r0 p q A QSI CO_start CO_end for (int i = 1; i <= atom->ntypes; i++) { fprintf(fp, "%d %g %g %g %g %g %g %g\n", i, r0[i][i], p[i][i], q[i][i], A[i][i], QSI[i][i], cutOffStart[i][i], cutOffEnd[i][i]); } } +/* ---------------------------------------------------------------------- */ + void PairSMATB::write_data_all(FILE *fp) { for (int i = 1; i <= atom->ntypes; i++) { diff --git a/src/pair_smatb.h b/src/pair_smatb.h index 967a46327f..abef8f35d0 100644 --- a/src/pair_smatb.h +++ b/src/pair_smatb.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 @@ -9,8 +9,6 @@ the GNU General Public License. See the README file in the top-level LAMMPS directory. - - This style is written by Daniele Rapetti (iximiel@gmail.com) ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- @@ -19,7 +17,7 @@ This pair style is written by Daniele Rapetti (iximiel@gmail.com) #ifdef PAIR_CLASS // clang-format off -PairStyle(smatb,PairSMATB) +PairStyle(smatb,PairSMATB); // clang-format on #else @@ -54,52 +52,28 @@ class PairSMATB : public Pair { // allocated size of per-atom arrays int nmax; //allocated to store up calculation values - double *on_eb{nullptr}; + double *on_eb; // interaction radius, user-given - double **r0{nullptr}; + double **r0; // parameters user-given - double **p{nullptr}; - double **A{nullptr}; - double **q{nullptr}; - double **QSI{nullptr}; + double **p; + double **A; + double **q; + double **QSI; //extremes of the cut off, user given - double **cutOffStart{nullptr}; - double **cutOffEnd{nullptr}; + double **cutOffStart; + double **cutOffEnd; //squared cut off end, calculated - double **cutOffEnd2{nullptr}; + double **cutOffEnd2; //polynomial for cutoff linking to zero: Ae^p substitution - double **a3{nullptr}; - double **a4{nullptr}; - double **a5{nullptr}; + double **a3; + double **a4; + double **a5; //polynomial for cutoff linking to zero: QSIe^q substitution - double **x3{nullptr}; - double **x4{nullptr}; - double **x5{nullptr}; - /* latex form of the potential (R_c is cutOffEnd, \Xi is QSI): - - E_i = - \sum_{j,R_{ij}\leq R_c} A e^{-p \left(\frac{R_{ij}}{R_{0}}-1\right)} - -\sqrt{\sum_{j,R_{ij}\leq R_c}\Xi^2 e^{-2q\left(\frac{R_{ij}}{R_{0}}-1\right)}}. - - NB::this form does not have the polynomial link to 0 for the cut off - */ + double **x3; + double **x4; + double **x5; }; - } // 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. - -*/ diff --git a/src/pair_smatb_single.cpp b/src/pair_smatb_single.cpp index f7910b076a..2d22829ba4 100644 --- a/src/pair_smatb_single.cpp +++ b/src/pair_smatb_single.cpp @@ -12,9 +12,11 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- -This pair style is written by Daniele Rapetti (iximiel@gmail.com) + Contributing author: Daniele Rapetti (iximiel@gmail.com) ------------------------------------------------------------------------- */ + #include "pair_smatb_single.h" + #include "atom.h" #include "comm.h" #include "error.h" @@ -22,15 +24,15 @@ This pair style is written by Daniele Rapetti (iximiel@gmail.com) #include "memory.h" #include "neigh_list.h" #include "neighbor.h" -#include -#include -#include -#include + +#include using namespace LAMMPS_NS; -PairSMATBSingle::PairSMATBSingle(LAMMPS *lmp) : - Pair(lmp), nmax(0), on_eb(nullptr), r0(0), p(0), A(0), q(0), QSI(0), cutOffStart(0), +/* ---------------------------------------------------------------------- */ + +PairSMATBSingle::PairSMATBSingle(LAMMPS *_lmp) : + Pair(_lmp), nmax(0), on_eb(nullptr), r0(0), p(0), A(0), q(0), QSI(0), cutOffStart(0), cutOffEnd(0), cutOffEnd2(0), a3(0), a4(0), a5(0), x3(0), x4(0), x5(0) { single_enable = 0; // 1 if single() routine exists @@ -47,6 +49,8 @@ PairSMATBSingle::PairSMATBSingle(LAMMPS *lmp) : comm_reverse = 1; } +/* ---------------------------------------------------------------------- */ + PairSMATBSingle::~PairSMATBSingle() { if (copymode) { return; } @@ -57,16 +61,16 @@ PairSMATBSingle::~PairSMATBSingle() } } +/* ---------------------------------------------------------------------- */ + void PairSMATBSingle::compute(int eflag, int vflag) -{ //workhorse routine that computes pairwise interactions - //eflag means compute energy - //vflag means compute virial - int i, j, ii, jj, jnum; //,itype,jtype; +{ + int i, j, ii, jj, jnum; double xtmp, ytmp, ztmp, del[3], fpair; double dijsq, dij; double espo, aexpp, qsiexpq, eb_i, Fb, Fr; double polyval, polyval2, polyval3, polyval4, polyval5; - //sets up the flags for energy calculations + if (eflag || vflag) { ev_setup(eflag, vflag); eng_vdwl = 0; @@ -75,7 +79,6 @@ void PairSMATBSingle::compute(int eflag, int vflag) } // grow on_eb array if necessary - // need to be atom->nmax in length if (atom->nmax > nmax) { nmax = atom->nmax; @@ -103,20 +106,18 @@ void PairSMATBSingle::compute(int eflag, int vflag) int *numneigh = list->numneigh; int **firstneigh = list->firstneigh; - //FIRST LOOP: CALCULATES the squared bounding energy and accumulate it in on_eb for each atom + // FIRST LOOP: CALCULATES the squared bonding energy and accumulate it in on_eb for each atom for (ii = 0; ii < inum; ++ii) { i = ilist[ii]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; - //itype = type[i]; jlist = firstneigh[i]; jnum = numneigh[i]; for (jj = 0; jj < jnum; ++jj) { j = jlist[jj]; j &= NEIGHMASK; - //jtype = type[j]; del[0] = xtmp - x[j][0]; del[1] = ytmp - x[j][1]; del[2] = ztmp - x[j][2]; @@ -135,19 +136,18 @@ void PairSMATBSingle::compute(int eflag, int vflag) qsiexpq = qsiexpq * qsiexpq; } on_eb[i] += qsiexpq; - //if (newton_pair || j < nlocal) { on_eb[j] += qsiexpq; - //} } } } - //communicate the squared bounding energy between the various bins + // communicate the squared bonding energy between the various bins - comm->reverse_comm_pair(this); + comm->reverse_comm(this); - //Support Loop: take the square root of the bounding energy and accumulate it in the energy accumulator if needed - // the store the reciprocal in on_eb in order to not do it in the SECOND LOOP + // Support Loop: take the square root of the bonding energy and + // accumulate it in the energy accumulator if needed the store the + // reciprocal in on_eb in order to not do it in the SECOND LOOP for (ii = 0; ii < inum; ++ii) { i = ilist[ii]; @@ -158,29 +158,28 @@ void PairSMATBSingle::compute(int eflag, int vflag) } else { on_eb[i] = 0.0; } - //if needed the bounding energy is accumulated: + //if needed the bonding energy is accumulated: if (eflag_either) { if (eflag_atom) { eatom[i] -= eb_i; } if (eflag_global) { eng_vdwl -= eb_i; } } } } - //this communication stores the denominators in the ghosts atoms, this is needed because of how forces are calculated - comm->forward_comm_pair(this); + // this communication stores the denominators in the ghosts atoms, + // this is needed because of how forces are calculated + comm->forward_comm(this); - //SECOND LOOP: given on_eb[i] calculates forces and energies + // SECOND LOOP: given on_eb[i] calculates forces and energies for (ii = 0; ii < inum; ++ii) { i = ilist[ii]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; - //itype = type[i]; jlist = firstneigh[i]; jnum = numneigh[i]; for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; j &= NEIGHMASK; - //jtype = type[j]; del[0] = xtmp - x[j][0]; del[1] = ytmp - x[j][1]; @@ -206,7 +205,7 @@ void PairSMATBSingle::compute(int eflag, int vflag) qsiexpq = x5 * polyval5 + x4 * polyval4 + x3 * polyval3; Fb = ((5.0 * x5 * polyval4 + 4.0 * x4 * polyval3 + 3.0 * x3 * polyval2)) * qsiexpq; } - //if needed the repulsive energy is accumulated: + // if needed the repulsive energy is accumulated: if (eflag_either) { if (eflag_atom) { eatom[i] += aexpp; @@ -220,7 +219,7 @@ void PairSMATBSingle::compute(int eflag, int vflag) } } } - //calculates the module of the pair energy between i and j + // calculates the module of the pair energy between i and j fpair = (Fb * (on_eb[i] + on_eb[j]) + Fr) / dij; f[i][0] += del[0] * fpair; @@ -247,7 +246,7 @@ void PairSMATBSingle::compute(int eflag, int vflag) ------------------------------------------------------------------------- */ void PairSMATBSingle::settings(int narg, char **) -{ //reads the input script line with arguments you define +{ if (narg > 0) error->all(FLERR, "Illegal pair_style command: smatb accepts no options"); } @@ -275,35 +274,25 @@ void PairSMATBSingle::allocate() ------------------------------------------------------------------------- */ void PairSMATBSingle::coeff(int narg, char **arg) -{ //set coefficients for one i,j type pair +{ if (!allocated) { allocate(); } - if (narg != 9) { - error->all( - FLERR, - "Incorrect args for pair coefficients:\n SMATB needs \"i j r0 p q A QSI CO_start CO_end\""); - } + if (narg != 9) utils::missing_cmd_args(FLERR, "pair_style smatb/single", error); + int ilo, ihi, jlo, jhi; utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error); utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error); - //reading parameters from input - double myr0 = utils::numeric(FLERR, arg[2], false, lmp), - myp = utils::numeric(FLERR, arg[3], false, lmp), - myq = utils::numeric(FLERR, arg[4], false, lmp), - myA = utils::numeric(FLERR, arg[5], false, lmp), - myQSI = utils::numeric(FLERR, arg[6], false, lmp), - mycutOffStart = utils::numeric(FLERR, arg[7], false, lmp), - mycutOffEnd = utils::numeric(FLERR, arg[8], false, lmp); - int count = 0; + r0 = utils::numeric(FLERR, arg[2], false, lmp); + p = utils::numeric(FLERR, arg[3], false, lmp); + q = utils::numeric(FLERR, arg[4], false, lmp); + A = utils::numeric(FLERR, arg[5], false, lmp); + QSI = utils::numeric(FLERR, arg[6], false, lmp); + cutOffStart = utils::numeric(FLERR, arg[7], false, lmp); + cutOffEnd = utils::numeric(FLERR, arg[8], false, lmp); + + int count = 0; for (int i = ilo; i <= ihi; i++) { for (int j = MAX(jlo, i); j <= jhi; j++) { - r0 = myr0; - p = myp; - A = myA; - q = myq; - QSI = myQSI; - cutOffStart = mycutOffStart; - cutOffEnd = mycutOffEnd; setflag[i][j] = 1; count++; @@ -313,21 +302,12 @@ void PairSMATBSingle::coeff(int narg, char **arg) if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); } -/* ---------------------------------------------------------------------- - init specific to this pair style - ------------------------------------------------------------------------- */ -/* - void PairSMATBSingle::init_style() {//initialization specific to this pair style - neighbor->request(this,instance_me); - } -*/ - /* ---------------------------------------------------------------------- init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ double PairSMATBSingle::init_one(int i, int j) -{ //perform initialization for one i,j type pair +{ if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set"); //calculating the polynomial linking to zero double es = cutOffEnd - cutOffStart; @@ -374,7 +354,7 @@ double PairSMATBSingle::init_one(int i, int j) x4 = x4; x5 = x5; } - //returns cutOffEnd to calculate cutforce and cutsq + return cutOffEnd; } @@ -427,6 +407,8 @@ void PairSMATBSingle::unpack_reverse_comm(int n, int *list, double *buf) } } +/* ---------------------------------------------------------------------- */ + //write binary data of this simulation: void PairSMATBSingle::write_restart_settings(FILE *fp) { @@ -435,6 +417,8 @@ void PairSMATBSingle::write_restart_settings(FILE *fp) fwrite(&tail_flag, sizeof(int), 1, fp); } +/* ---------------------------------------------------------------------- */ + void PairSMATBSingle::read_restart_settings(FILE *fp) { int me = comm->me; @@ -449,12 +433,14 @@ void PairSMATBSingle::read_restart_settings(FILE *fp) MPI_Bcast(&tail_flag, 1, MPI_INT, 0, world); } +/* ---------------------------------------------------------------------- */ + void PairSMATBSingle::write_restart(FILE *fp) { write_restart_settings(fp); - //"I J r0 p q A QSI CO_start CO_end" + int i, j; - for (i = 1; i <= atom->ntypes; i++) + for (i = 1; i <= atom->ntypes; i++) { for (j = i; j <= atom->ntypes; j++) { fwrite(&setflag[i][j], sizeof(int), 1, fp); if (setflag[i][j]) { @@ -467,12 +453,15 @@ void PairSMATBSingle::write_restart(FILE *fp) fwrite(&cutOffEnd, sizeof(double), 1, fp); } } - //maybe we need to save also the values of the various polynomials + } } +/* ---------------------------------------------------------------------- */ + void PairSMATBSingle::read_restart(FILE *fp) { read_restart_settings(fp); + allocate(); size_t result; @@ -484,13 +473,13 @@ void PairSMATBSingle::read_restart(FILE *fp) MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world); if (setflag[i][j]) { if (me == 0) { - result = fread(&r0, sizeof(double), 1, fp); - result = fread(&p, sizeof(double), 1, fp); - result = fread(&q, sizeof(double), 1, fp); - result = fread(&A, sizeof(double), 1, fp); - result = fread(&QSI, sizeof(double), 1, fp); - result = fread(&cutOffStart, sizeof(double), 1, fp); - result = fread(&cutOffEnd, sizeof(double), 1, fp); + utils::sfread(FLERR, &r0, sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &p, sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &q, sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &A, sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &QSI, sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &cutOffStart, sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &cutOffEnd, sizeof(double), 1, fp, nullptr, error); } MPI_Bcast(&r0, 1, MPI_DOUBLE, 0, world); MPI_Bcast(&p, 1, MPI_DOUBLE, 0, world); @@ -503,14 +492,17 @@ void PairSMATBSingle::read_restart(FILE *fp) } } +/* ---------------------------------------------------------------------- */ + void PairSMATBSingle::write_data(FILE *fp) { - //smatb needs I J r0 p q A QSI CO_start CO_end for (int i = 1; i <= atom->ntypes; i++) { fprintf(fp, "%d %g %g %g %g %g %g %g\n", i, r0, p, q, A, QSI, cutOffStart, cutOffEnd); } } +/* ---------------------------------------------------------------------- */ + void PairSMATBSingle::write_data_all(FILE *fp) { for (int i = 1; i <= atom->ntypes; i++) { diff --git a/src/pair_smatb_single.h b/src/pair_smatb_single.h index e8b29d5303..e47bf11d46 100644 --- a/src/pair_smatb_single.h +++ b/src/pair_smatb_single.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 @@ -9,8 +9,6 @@ the GNU General Public License. See the README file in the top-level LAMMPS directory. - - This pair style is written by Daniele Rapetti (iximiel@gmail.com) ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- @@ -19,12 +17,12 @@ This pair style is written by Daniele Rapetti (iximiel@gmail.com) #ifdef PAIR_CLASS // clang-format off -PairStyle(smatb/single,PairSMATBSingle) +PairStyle(smatb/single,PairSMATBSingle); // clang-format on #else -#ifndef LMP_PAIR_SMATBSINGLE_H -#define LMP_PAIR_SMATBSINGLE_H +#ifndef LMP_PAIR_SMATB_SINGLE_H +#define LMP_PAIR_SMATB_SINGLE_H #include "pair.h" @@ -76,21 +74,6 @@ class PairSMATBSingle : public Pair { double x4; double x5; }; - } // 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. -*/ From 3cfae26b843442194844008bb14576c25043a4d3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 27 Apr 2022 15:03:12 -0400 Subject: [PATCH 43/57] update docs and make part of SMTBQ package --- doc/src/Packages_details.rst | 12 +++++++----- doc/src/Packages_list.rst | 4 ++-- doc/src/pair_smatb.rst | 16 +++++++++------- doc/utils/sphinx-config/false_positives.txt | 9 +++++++++ 4 files changed, 27 insertions(+), 14 deletions(-) diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 6d2b2f5a68..d2fb35623c 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -2578,18 +2578,20 @@ SMTBQ package **Contents:** -A pair style which implements a Second Moment Tight Binding model with -QEq charge equilibration (SMTBQ) potential for the description of -ionocovalent bonds in oxides. +Pair styles which implement Second Moment Tight Binding models. +One with QEq charge equilibration (SMTBQ) for the description of +ionocovalent bonds in oxides, and two more as plain SMATB models. -**Authors:** Nicolas Salles, Emile Maras, Olivier Politano, and Robert -Tetot (LAAS-CNRS, France). +**Authors:** SMTBQ: Nicolas Salles, Emile Maras, Olivier Politano, and Robert +Tetot (LAAS-CNRS, France); +SMATB: Daniele Rapetti (Politecnico di Torino) **Supporting info:** * src/SMTBQ: filenames -> commands * src/SMTBQ/README * :doc:`pair_style smtbq ` +* :doc:`pair_style smatb `, :doc:`pair_style smatb/single ` * examples/PACKAGES/smtbq ---------- diff --git a/doc/src/Packages_list.rst b/doc/src/Packages_list.rst index 14d76e0ba3..26461b69a0 100644 --- a/doc/src/Packages_list.rst +++ b/doc/src/Packages_list.rst @@ -429,8 +429,8 @@ whether an extra library is needed to build and use the package: - n/a - no * - :ref:`SMTBQ ` - - second moment tight binding potential - - :doc:`pair_style smtbq ` + - second moment tight binding potentials + - :doc:`pair_style smtbq ` :doc:`pair_style smatb ` - PACKAGES/smtbq - no * - :ref:`SPH ` diff --git a/doc/src/pair_smatb.rst b/doc/src/pair_smatb.rst index ca9a1fde77..a9648a38bb 100644 --- a/doc/src/pair_smatb.rst +++ b/doc/src/pair_smatb.rst @@ -60,10 +60,11 @@ And the two functions :math:`\alpha\left(r\right)` and :math:`\Xi\left(r\right)` \right. -The polynomial coefficients :math:`a_3`, :math:`a_4`, :math:`a_5`, :math:`x_3`, -:math:`x_4`, :math:`x_5` are computed by LAMMPS: the two exponentials and their -first and second order derivatives are smoothly linked to zero, -from the inner cutoff :math:`R_{sc}` to the outer cutoff :math:`R_{c}`. +The polynomial coefficients :math:`a_3`, :math:`a_4`, :math:`a_5`, +:math:`x_3`, :math:`x_4`, :math:`x_5` are computed by LAMMPS: the two +exponential terms and their first and second derivatives are smoothly +reduced to zero, from the inner cutoff :math:`R_{sc}` to the outer +cutoff :math:`R_{c}`. Coefficients """""""""""" @@ -78,11 +79,11 @@ file or restart files read by the :doc:`read_data ` or * :math:`q` (dimensionless) * :math:`A` (energy units) * :math:`\xi` (energy units) -* :math:`R_{cs}` (distance units) +* :math:`R_{cs}` (distance units) * :math:`R_{c}` (distance units) -Note that: :math:`R_{0}` is the nearest neighbour distance, usually coincides +Note that: :math:`R_{0}` is the nearest neighbor distance, usually coincides with the diameter of the atoms See the :doc:`run_style ` command for details. @@ -99,7 +100,8 @@ For atom type pairs I,J and I != J the coefficients are not automatically mixed. Restrictions """""""""""" -none +This pair style is part of the SMTBQ package and is only enabled +if LAMMPS is built with that package. See the :doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 62983f4f39..6b489c9cb8 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -693,6 +693,7 @@ DFT dftb dh dhex +di dia diag diagonalization @@ -784,6 +785,7 @@ dtheta dtshrink du dU +Ducastelle Dudarev Duin Dullweber @@ -1246,6 +1248,7 @@ Gubbins Guenole Guericke gui +Guillope Gumbsch Gunsteren Gunzenmuller @@ -1722,6 +1725,7 @@ lebedeva Lebedeva Lebold Lechman +Legrand Lehoucq Leimkuhler Leite @@ -2636,6 +2640,7 @@ Polarizable polarizables polarizer Politano +Politecnico polyA polybond polydisperse @@ -2794,6 +2799,7 @@ Randisi randomizations rann RANN +Rapetti Raphson Rappe Ravelo @@ -2939,6 +2945,7 @@ Rohart Ronchetti Ronevich Rosati +Rosato Rosenberger Rossky rosybrown @@ -3115,6 +3122,7 @@ smallbig smallint Smallint smallsmall +smatb smd SMD smi @@ -3383,6 +3391,7 @@ toolchain topologies Toporov Torder +Torino torsions Tosi Toukmaji From 585b14f08f73c52463ec1aadfcb1bcaaf4db9806 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 27 Apr 2022 15:10:55 -0400 Subject: [PATCH 44/57] fix memory leak --- src/pair_smatb.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/pair_smatb.cpp b/src/pair_smatb.cpp index dc1d42d3f7..7ea630ba44 100644 --- a/src/pair_smatb.cpp +++ b/src/pair_smatb.cpp @@ -68,7 +68,7 @@ PairSMATB::~PairSMATB() memory->destroy(cutOffStart); memory->destroy(cutOffEnd); memory->destroy(cutOffEnd2); - memory->destroy(a5); + memory->destroy(a3); memory->destroy(a4); memory->destroy(a5); memory->destroy(x5); From 2d45e3340fc3515900ad51a29a9990d424aa3af0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 27 Apr 2022 15:14:02 -0400 Subject: [PATCH 45/57] move sources and examples for smatb styles to SMTBQ package folders --- .../{smatb => PACKAGES/smtbq}/AgCuPancake.data | 0 .../smtbq}/in.smatbAgCuPancake | 0 .../{smatb => PACKAGES/smtbq}/in.smatbBulkFCC | 0 .../smtbq}/log.27Oct21.smatbAgCuPancake.g++ | 0 .../smtbq}/log.27Oct21.smatbBulkFCC.g++ | 0 src/.gitignore | 4 ++++ src/SMTBQ/README | 16 ---------------- src/{ => SMTBQ}/pair_smatb.cpp | 0 src/{ => SMTBQ}/pair_smatb.h | 0 src/{ => SMTBQ}/pair_smatb_single.cpp | 0 src/{ => SMTBQ}/pair_smatb_single.h | 0 11 files changed, 4 insertions(+), 16 deletions(-) rename examples/{smatb => PACKAGES/smtbq}/AgCuPancake.data (100%) rename examples/{smatb => PACKAGES/smtbq}/in.smatbAgCuPancake (100%) rename examples/{smatb => PACKAGES/smtbq}/in.smatbBulkFCC (100%) rename examples/{smatb => PACKAGES/smtbq}/log.27Oct21.smatbAgCuPancake.g++ (100%) rename examples/{smatb => PACKAGES/smtbq}/log.27Oct21.smatbBulkFCC.g++ (100%) delete mode 100644 src/SMTBQ/README rename src/{ => SMTBQ}/pair_smatb.cpp (100%) rename src/{ => SMTBQ}/pair_smatb.h (100%) rename src/{ => SMTBQ}/pair_smatb_single.cpp (100%) rename src/{ => SMTBQ}/pair_smatb_single.h (100%) diff --git a/examples/smatb/AgCuPancake.data b/examples/PACKAGES/smtbq/AgCuPancake.data similarity index 100% rename from examples/smatb/AgCuPancake.data rename to examples/PACKAGES/smtbq/AgCuPancake.data diff --git a/examples/smatb/in.smatbAgCuPancake b/examples/PACKAGES/smtbq/in.smatbAgCuPancake similarity index 100% rename from examples/smatb/in.smatbAgCuPancake rename to examples/PACKAGES/smtbq/in.smatbAgCuPancake diff --git a/examples/smatb/in.smatbBulkFCC b/examples/PACKAGES/smtbq/in.smatbBulkFCC similarity index 100% rename from examples/smatb/in.smatbBulkFCC rename to examples/PACKAGES/smtbq/in.smatbBulkFCC diff --git a/examples/smatb/log.27Oct21.smatbAgCuPancake.g++ b/examples/PACKAGES/smtbq/log.27Oct21.smatbAgCuPancake.g++ similarity index 100% rename from examples/smatb/log.27Oct21.smatbAgCuPancake.g++ rename to examples/PACKAGES/smtbq/log.27Oct21.smatbAgCuPancake.g++ diff --git a/examples/smatb/log.27Oct21.smatbBulkFCC.g++ b/examples/PACKAGES/smtbq/log.27Oct21.smatbBulkFCC.g++ similarity index 100% rename from examples/smatb/log.27Oct21.smatbBulkFCC.g++ rename to examples/PACKAGES/smtbq/log.27Oct21.smatbBulkFCC.g++ diff --git a/src/.gitignore b/src/.gitignore index 80b4baa0e5..d5ed0343e7 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -1537,6 +1537,10 @@ /pair_mgpt.h /pair_morse_smooth_linear.cpp /pair_morse_smooth_linear.h +/pair_smatb.cpp +/pair_smatb.h +/pair_smatb_single.cpp +/pair_smatb_single.h /pair_smtbq.cpp /pair_smtbq.h /pair_vashishta*.cpp diff --git a/src/SMTBQ/README b/src/SMTBQ/README deleted file mode 100644 index 594df29ac6..0000000000 --- a/src/SMTBQ/README +++ /dev/null @@ -1,16 +0,0 @@ -This package implements the Second Moment Tight Binding - QEq (SMTB-Q) -potential for the description of ionocovalent bonds in oxides. - -Authors: Nicolas Salles, Emile Maras, Olivier Politano, Robert Tetot -at ICB, Universite de Bourgogne and ICMMO, Universite Paris-Sud. - -Contact emails: lammps@u-bourgogne.fr, nsalles33@gmail.com - -This package is occasionally maintained. - -See the doc page for the pair_style smtbq command to get started. - -There are potential files for this potential in the potentials dir. - -There are example scripts for using this package in -examples/PACKAGES/smtbq. diff --git a/src/pair_smatb.cpp b/src/SMTBQ/pair_smatb.cpp similarity index 100% rename from src/pair_smatb.cpp rename to src/SMTBQ/pair_smatb.cpp diff --git a/src/pair_smatb.h b/src/SMTBQ/pair_smatb.h similarity index 100% rename from src/pair_smatb.h rename to src/SMTBQ/pair_smatb.h diff --git a/src/pair_smatb_single.cpp b/src/SMTBQ/pair_smatb_single.cpp similarity index 100% rename from src/pair_smatb_single.cpp rename to src/SMTBQ/pair_smatb_single.cpp diff --git a/src/pair_smatb_single.h b/src/SMTBQ/pair_smatb_single.h similarity index 100% rename from src/pair_smatb_single.h rename to src/SMTBQ/pair_smatb_single.h From b76594e551a973f535b44d0f0ee8d51505b1e008 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 27 Apr 2022 18:08:05 -0400 Subject: [PATCH 46/57] enforce only newton pair on with smatb pair styles. add unit tests --- doc/src/pair_smatb.rst | 2 + src/MANYBODY/pair_eam.cpp | 3 +- src/SMTBQ/pair_smatb.cpp | 42 ++++---- src/SMTBQ/pair_smatb.h | 1 + src/SMTBQ/pair_smatb_single.cpp | 44 ++++----- src/SMTBQ/pair_smatb_single.h | 1 + .../force-styles/tests/atomic-pair-smatb.yaml | 95 +++++++++++++++++++ .../tests/atomic-pair-smatb_same.yaml | 93 ++++++++++++++++++ .../tests/atomic-pair-smatb_single.yaml | 93 ++++++++++++++++++ 9 files changed, 319 insertions(+), 55 deletions(-) create mode 100644 unittest/force-styles/tests/atomic-pair-smatb.yaml create mode 100644 unittest/force-styles/tests/atomic-pair-smatb_same.yaml create mode 100644 unittest/force-styles/tests/atomic-pair-smatb_single.yaml diff --git a/doc/src/pair_smatb.rst b/doc/src/pair_smatb.rst index a9648a38bb..73f3781f90 100644 --- a/doc/src/pair_smatb.rst +++ b/doc/src/pair_smatb.rst @@ -103,6 +103,8 @@ Restrictions This pair style is part of the SMTBQ package and is only enabled if LAMMPS is built with that package. See the :doc:`Build package ` page for more info. +These pair potentials require the :doc:`newton ` setting to be "on" for pair interactions. + Related commands """""""""""""""" diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp index 77b6d551be..834c71a947 100644 --- a/src/MANYBODY/pair_eam.cpp +++ b/src/MANYBODY/pair_eam.cpp @@ -319,8 +319,7 @@ void PairEAM::compute(int eflag, int vflag) } if (eflag) evdwl = scale[itype][jtype]*phi; - if (evflag) ev_tally(i,j,nlocal,newton_pair, - evdwl,0.0,fpair,delx,dely,delz); + if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz); } } } diff --git a/src/SMTBQ/pair_smatb.cpp b/src/SMTBQ/pair_smatb.cpp index 7ea630ba44..b2cbda0854 100644 --- a/src/SMTBQ/pair_smatb.cpp +++ b/src/SMTBQ/pair_smatb.cpp @@ -110,11 +110,7 @@ void PairSMATB::compute(int eflag, int vflag) int newton_pair = force->newton_pair; // zero out on_eb - if (newton_pair) { - memset(on_eb, 0, nall * sizeof(on_eb[0])); - } else { - memset(on_eb, 0, nlocal * sizeof(on_eb[0])); - } + memset(on_eb, 0, nall * sizeof(double)); int inum = list->inum; int *ilist = list->ilist; @@ -156,14 +152,14 @@ void PairSMATB::compute(int eflag, int vflag) qsiexpq = qsiexpq * qsiexpq; } on_eb[i] += qsiexpq; - on_eb[j] += qsiexpq; + if (newton_pair) on_eb[j] += qsiexpq; } } } // communicate the squared bonding energy between the various bins - comm->reverse_comm(this); + if (newton_pair) comm->reverse_comm(this); // Support Loop: take the square root of the bonding energy and // accumulate it in the energy accumulator if needed the store the @@ -178,7 +174,7 @@ void PairSMATB::compute(int eflag, int vflag) } else { on_eb[i] = 0.0; } - //if needed the bonding energy is accumulated: + // if needed the bonding energy is accumulated: if (eflag_either) { if (eflag_atom) { eatom[i] -= eb_i; } if (eflag_global) { eng_vdwl -= eb_i; } @@ -233,20 +229,7 @@ void PairSMATB::compute(int eflag, int vflag) 3.0 * x3[itype][jtype] * polyval2)) * qsiexpq; } - // if needed the repulsive energy is accumulated: - if (eflag_either) { - if (eflag_atom) { - eatom[i] += aexpp; - if (newton_pair || j < nlocal) { eatom[j] += aexpp; } - } - if (eflag_global) { - if (newton_pair || j < nlocal) { - eng_vdwl += 2.0 * (aexpp); - } else { - eng_vdwl += aexpp; - } - } - } + // calculates the module of the pair energy between i and j fpair = (Fb * (on_eb[i] + on_eb[j]) + Fr) / dij; @@ -258,10 +241,8 @@ void PairSMATB::compute(int eflag, int vflag) f[j][1] -= del[1] * fpair; f[j][2] -= del[2] * fpair; } - if (vflag_atom) { - ev_tally(i, j, nlocal, newton_pair, 0.0, - 0.0, //Energy is tally'd in the other parts of the potential - fpair, del[0], del[1], del[2]); + if (evflag) { + ev_tally(i, j, nlocal, newton_pair, 2.0 * aexpp, 0.0, fpair, del[0], del[1], del[2]); } } } @@ -350,6 +331,15 @@ void PairSMATB::coeff(int narg, char **arg) if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); } +/* ------------------------------------------------------------------------ */ + +void PairSMATB::init_style() +{ + if (force->newton_pair == 0) error->all(FLERR, "Pair style smatb requires newton pair on"); + + neighbor->add_request(this); +} + /* ---------------------------------------------------------------------- init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ diff --git a/src/SMTBQ/pair_smatb.h b/src/SMTBQ/pair_smatb.h index abef8f35d0..198ea10559 100644 --- a/src/SMTBQ/pair_smatb.h +++ b/src/SMTBQ/pair_smatb.h @@ -35,6 +35,7 @@ class PairSMATB : public Pair { void compute(int, int) override; void settings(int, char **) override; void coeff(int, char **) override; + void init_style() override; double init_one(int, int) override; void write_restart(FILE *) override; void read_restart(FILE *) override; diff --git a/src/SMTBQ/pair_smatb_single.cpp b/src/SMTBQ/pair_smatb_single.cpp index 2d22829ba4..759ad4216b 100644 --- a/src/SMTBQ/pair_smatb_single.cpp +++ b/src/SMTBQ/pair_smatb_single.cpp @@ -94,11 +94,7 @@ void PairSMATBSingle::compute(int eflag, int vflag) int newton_pair = force->newton_pair; // zero out on_eb - if (newton_pair) { - memset(on_eb, 0, nall * sizeof(on_eb[0])); - } else { - memset(on_eb, 0, nlocal * sizeof(on_eb[0])); - } + memset(on_eb, 0, nall * sizeof(double)); int inum = list->inum; int *ilist = list->ilist; @@ -136,14 +132,14 @@ void PairSMATBSingle::compute(int eflag, int vflag) qsiexpq = qsiexpq * qsiexpq; } on_eb[i] += qsiexpq; - on_eb[j] += qsiexpq; + if (newton_pair) on_eb[j] += qsiexpq; } } } // communicate the squared bonding energy between the various bins - comm->reverse_comm(this); + if (newton_pair) comm->reverse_comm(this); // Support Loop: take the square root of the bonding energy and // accumulate it in the energy accumulator if needed the store the @@ -158,7 +154,7 @@ void PairSMATBSingle::compute(int eflag, int vflag) } else { on_eb[i] = 0.0; } - //if needed the bonding energy is accumulated: + // if needed the bonding energy is accumulated: if (eflag_either) { if (eflag_atom) { eatom[i] -= eb_i; } if (eflag_global) { eng_vdwl -= eb_i; } @@ -205,20 +201,7 @@ void PairSMATBSingle::compute(int eflag, int vflag) qsiexpq = x5 * polyval5 + x4 * polyval4 + x3 * polyval3; Fb = ((5.0 * x5 * polyval4 + 4.0 * x4 * polyval3 + 3.0 * x3 * polyval2)) * qsiexpq; } - // if needed the repulsive energy is accumulated: - if (eflag_either) { - if (eflag_atom) { - eatom[i] += aexpp; - if (newton_pair || j < nlocal) { eatom[j] += aexpp; } - } - if (eflag_global) { - if (newton_pair || j < nlocal) { - eng_vdwl += 2.0 * (aexpp); - } else { - eng_vdwl += aexpp; - } - } - } + // calculates the module of the pair energy between i and j fpair = (Fb * (on_eb[i] + on_eb[j]) + Fr) / dij; @@ -230,10 +213,8 @@ void PairSMATBSingle::compute(int eflag, int vflag) f[j][1] -= del[1] * fpair; f[j][2] -= del[2] * fpair; } - if (vflag_atom) { - ev_tally(i, j, nlocal, newton_pair, 0.0, - 0.0, //Energy is tally'd in the other parts of the potential - fpair, del[0], del[1], del[2]); + if (evflag) { + ev_tally(i, j, nlocal, newton_pair, 2.0 * aexpp, 0.0, fpair, del[0], del[1], del[2]); } } } @@ -247,7 +228,7 @@ void PairSMATBSingle::compute(int eflag, int vflag) void PairSMATBSingle::settings(int narg, char **) { - if (narg > 0) error->all(FLERR, "Illegal pair_style command: smatb accepts no options"); + if (narg > 0) error->all(FLERR, "Illegal pair_style command: smatb/single accepts no options"); } /* ---------------------------------------------------------------------- @@ -302,6 +283,15 @@ void PairSMATBSingle::coeff(int narg, char **arg) if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); } +/* ------------------------------------------------------------------------ */ + +void PairSMATBSingle::init_style() +{ + if (force->newton_pair == 0) error->all(FLERR, "Pair style smatb/single requires newton pair on"); + + neighbor->add_request(this); +} + /* ---------------------------------------------------------------------- init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ diff --git a/src/SMTBQ/pair_smatb_single.h b/src/SMTBQ/pair_smatb_single.h index e47bf11d46..619192b31f 100644 --- a/src/SMTBQ/pair_smatb_single.h +++ b/src/SMTBQ/pair_smatb_single.h @@ -35,6 +35,7 @@ class PairSMATBSingle : public Pair { void compute(int, int) override; void settings(int, char **) override; void coeff(int, char **) override; + void init_style() override; double init_one(int, int) override; void write_restart(FILE *) override; void read_restart(FILE *) override; diff --git a/unittest/force-styles/tests/atomic-pair-smatb.yaml b/unittest/force-styles/tests/atomic-pair-smatb.yaml new file mode 100644 index 0000000000..1a1bd60d38 --- /dev/null +++ b/unittest/force-styles/tests/atomic-pair-smatb.yaml @@ -0,0 +1,95 @@ +--- +lammps_version: 24 Mar 2022 +date_generated: Wed Apr 27 17:35:13 2022 +epsilon: 6e-12 +skip_tests: single +prerequisites: ! | + pair smatb +pre_commands: ! | + variable units index metal + variable newton_pair delete + variable newton_pair index on +post_commands: ! "" +input_file: in.metal +pair_style: smatb +pair_coeff: ! | + 1 1 2.88 10.35 4.178 0.210 1.818 4.07293506 4.9883063257983666 + 1 2 2.725 10.70 2.805 0.0977 1.2275 4.08707719 4.4340500673763259 + 2 2 2.56 10.55 2.43 0.0894 1.2799 3.62038672 4.4340500673763259 +extract: ! "" +natoms: 32 +init_vdwl: -60.168389119061764 +init_coul: 0 +init_stress: ! |2- + 3.0379713999046641e+02 2.8481689618050700e+02 2.7487901025801546e+02 1.2210883607368261e+01 -4.6310157292178644e+00 4.6132589248268313e-01 +init_forces: ! |2 + 1 1.7537039354439259e+00 7.0360956531760914e+00 -8.4184005958845576e-01 + 2 -9.6588965012743466e-01 -4.2968327220274549e+00 9.9999262128352517e-01 + 3 -2.2460353121901719e+00 1.0242304966158118e+01 -1.8443560888714017e+00 + 4 9.9448733303045811e-01 7.5230397435187024e-01 -6.0766236587933242e-01 + 5 3.2183954634823486e+00 1.5733656263362944e+01 4.7039945398761146e-01 + 6 2.8052970436237228e+00 4.8969292026494609e+00 2.9489788602236294e-01 + 7 -5.7345085273481313e+00 8.6530112130150911e+00 7.7447706601282529e-01 + 8 -2.7028241379012670e+00 -1.2472144397235256e+00 3.5063865351057539e+00 + 9 -2.2386799966388922e+00 -5.1178927074297116e+00 -3.6574951500303547e+00 + 10 -4.0842175514437216e+00 -9.2805347046989155e+00 -9.5216421574104011e+00 + 11 -3.0158013348581383e+00 -9.8825164063184836e+00 4.7066807600425307e+00 + 12 2.9355737505075075e-01 -9.1277559819075993e+00 1.7503554943451509e+00 + 13 6.5442807463873454e-01 3.5771666022763327e-01 -2.9268279206132601e+00 + 14 2.9546102292027019e+00 -2.1076657421595297e+00 2.4027353745102911e+00 + 15 -1.4362459620281001e+00 -1.4469338088460937e-01 1.2638040704141933e+00 + 16 1.1853600123947110e+01 -8.2217359454928722e+00 3.5602820971226925e+00 + 17 2.9760114434025717e+00 9.1510881878371890e+00 2.6527712778949613e+00 + 18 -3.8448816734858200e+00 -3.8596834411195530e-01 -1.5363106241864222e+00 + 19 -5.4287609604186988e+00 8.3639132891808646e-02 1.2597633537120057e+00 + 20 1.8993344143373079e+00 1.7539397493690578e+00 -2.3674883662900768e+00 + 21 9.3202877569111724e+00 1.0161906623748195e+01 2.5117245084501487e+00 + 22 -5.4286006790341602e-02 -4.1235834232008373e-01 -1.6165289278166828e-01 + 23 5.1618239402933046e+00 7.8084801332958875e+00 -7.8617666396584083e+00 + 24 2.1573958095505019e+00 3.3064758348776766e+00 1.0356666170852131e+00 + 25 2.7317865068673508e-01 -6.7983594715200391e-01 -8.4962145425034485e-01 + 26 -6.1973411118185515e+00 -9.9363067654978252e+00 1.1125063212404200e+01 + 27 8.8836361676639608e-01 -2.5101152574520498e+00 -1.5693011315761736e+00 + 28 -1.5415779635281726e+00 3.0301797542504927e-01 1.5248141023284689e+00 + 29 2.7349816106722007e+00 8.8545204263186583e-01 -8.5526109552538948e-02 + 30 -1.0720483420459732e+00 -4.4498068532010109e+00 -2.2225391974890889e+00 + 31 1.1773042862086689e+00 -3.7757672138358065e+00 2.8670718827673392e-01 + 32 -1.0553662576625207e+01 -9.5490168588044995e+00 -4.0724914608207419e+00 +run_vdwl: -60.20669005164827 +run_coul: 0 +run_stress: ! |2- + 3.0366990231859160e+02 2.8472030171897950e+02 2.7473728347285567e+02 1.2172424459197687e+01 -4.6332954461814584e+00 4.7608342060898434e-01 +run_forces: ! |2 + 1 1.7287621761096983e+00 7.0355573735520842e+00 -8.4682174175985714e-01 + 2 -9.6697895447504500e-01 -4.2958415607798441e+00 1.0015306640771833e+00 + 3 -2.2449153785930140e+00 1.0220034215661133e+01 -1.8504820220633480e+00 + 4 9.9601791340276336e-01 7.5369431710262291e-01 -6.0681572641646842e-01 + 5 3.2060009999484147e+00 1.5701015711784372e+01 4.8372081899056063e-01 + 6 2.8080670120413069e+00 4.8912991510058559e+00 2.8963381062351951e-01 + 7 -5.7324770842913582e+00 8.6591358821788482e+00 7.6431887086981398e-01 + 8 -2.7059540524354420e+00 -1.2467200304482609e+00 3.5070033937113965e+00 + 9 -2.2338690489351816e+00 -5.1254178402905834e+00 -3.6627325643998292e+00 + 10 -4.0440304555481070e+00 -9.2663471307481604e+00 -9.4950789175699022e+00 + 11 -3.0095603324750355e+00 -9.8809272965546722e+00 4.6968379350949254e+00 + 12 2.9955821111103709e-01 -9.1186689644052663e+00 1.7487225514885398e+00 + 13 6.4891903429679598e-01 3.5328774712317623e-01 -2.9200027226328809e+00 + 14 2.9573134095573934e+00 -2.0910918248790211e+00 2.3937660891560109e+00 + 15 -1.4362727166791407e+00 -1.4487584341495263e-01 1.2659041092021559e+00 + 16 1.1811093106525520e+01 -8.2096829056411114e+00 3.5467098338575100e+00 + 17 2.9812217984029723e+00 9.1459474011872697e+00 2.6544874139680337e+00 + 18 -3.8455925628350474e+00 -3.8293266140015725e-01 -1.5378864958810305e+00 + 19 -5.4246332382008848e+00 8.2734848602692174e-02 1.2542661008733695e+00 + 20 1.8971229950794164e+00 1.7555326782428182e+00 -2.3672155825569949e+00 + 21 9.3028027186473548e+00 1.0133810518512346e+01 2.5079668062515421e+00 + 22 -5.2108622808623904e-02 -4.0963871892230036e-01 -1.5978127490210359e-01 + 23 5.1748427747828964e+00 7.8093248331208418e+00 -7.8361064692451841e+00 + 24 2.1561221337678749e+00 3.3060392424596703e+00 1.0375590296124864e+00 + 25 2.7439938289817345e-01 -6.7913212538661649e-01 -8.4934088300559951e-01 + 26 -6.1703634942784520e+00 -9.9078856414327738e+00 1.1113100533969693e+01 + 27 8.8899668170198953e-01 -2.5084240247927481e+00 -1.5752281408111217e+00 + 28 -1.5419740545035272e+00 3.0574247513776465e-01 1.5244579333305823e+00 + 29 2.7318838331391233e+00 8.8556581077732033e-01 -8.1366934099631305e-02 + 30 -1.0707952569409716e+00 -4.4481845742260617e+00 -2.2189658111567914e+00 + 31 1.1734335189797629e+00 -3.7753076875705340e+00 2.8648052295520054e-01 + 32 -1.0557032447392665e+01 -9.5476433755557508e+00 -4.0686411315317814e+00 +... diff --git a/unittest/force-styles/tests/atomic-pair-smatb_same.yaml b/unittest/force-styles/tests/atomic-pair-smatb_same.yaml new file mode 100644 index 0000000000..4ecc086a57 --- /dev/null +++ b/unittest/force-styles/tests/atomic-pair-smatb_same.yaml @@ -0,0 +1,93 @@ +--- +lammps_version: 24 Mar 2022 +date_generated: Wed Apr 27 17:51:25 2022 +epsilon: 6e-12 +skip_tests: single +prerequisites: ! | + pair smatb +pre_commands: ! | + variable units index metal + variable newton_pair delete + variable newton_pair index on +post_commands: ! "" +input_file: in.metal +pair_style: smatb +pair_coeff: ! | + * * 2.88 10.35 4.178 0.210 1.818 4.07293506 4.9883063257983666 +extract: ! "" +natoms: 32 +init_vdwl: 15.546009002462199 +init_coul: 0 +init_stress: ! |2- + 7.0981045919895291e+02 6.9464048009855617e+02 6.8185854046738905e+02 1.8940099448628423e+01 -2.3190641785495831e+00 -7.6126579722972734e+00 +init_forces: ! |2 + 1 1.8383788817685609e+00 7.3043414500016803e+00 1.2928059118046571e+00 + 2 -2.6848648395616506e+00 -7.8218002510265290e+00 5.1835989139783809e+00 + 3 -4.1262133070389613e+00 2.0356333849891929e+01 -5.0300134853162675e+00 + 4 2.1640213680130582e+00 -8.2080827254125310e-01 -5.7189855300172958e+00 + 5 5.1336080958834502e+00 1.4999943174537506e+01 4.1898025714112999e+00 + 6 4.5017623545159724e+00 3.6176208409156039e+00 -4.4379897612576352e-01 + 7 -6.2917785937694219e+00 9.6471529013643753e+00 -1.0169471822201503e+00 + 8 -6.9079266006711242e+00 -6.2411913330296631e+00 4.0631933657348354e+00 + 9 1.4448974765969274e+00 -6.3335992210787921e+00 -2.7877666693063965e+00 + 10 -3.2369455571053383e+00 -1.4726480521388170e+01 -1.2343244613879385e+01 + 11 -4.4279873426372749e+00 -5.8875813372324703e+00 4.2645243184789097e+00 + 12 2.7168432086644443e+00 -9.2808529346155240e+00 -4.2510938219210220e-01 + 13 -2.0372275262801081e+00 2.2026130441803748e+00 -4.7893800758259584e+00 + 14 6.1358565129828193e+00 -2.4215787035807863e+00 7.4237482521334002e+00 + 15 -3.2151583983209826e+00 2.8722155568519296e+00 -3.1022228268650602e+00 + 16 1.1834167029249446e+01 -9.9960409045212177e+00 4.0046914221724927e+00 + 17 4.4438667082387253e+00 1.4015434663357324e+01 1.1980157677253445e-01 + 18 -1.5049446792950388e+01 -2.9866974100159291e+00 -7.3487669643132998e+00 + 19 -1.5962776779061105e+01 -7.7159633670829013e+00 4.0578908190472625e+00 + 20 2.6368639403789449e+00 2.1948034299735144e+00 -3.2117143706849434e+00 + 21 1.6938751336137905e+01 5.3405439576559601e+00 3.9965661174944200e-01 + 22 4.6915262682186748e-01 -8.7314686216914801e+00 -1.2388516494108810e+00 + 23 4.7426470160406025e+00 1.2927761843820045e+01 -8.4044784783918658e+00 + 24 1.2732138070191686e+01 9.8600435340252197e+00 8.6676713483852375e+00 + 25 7.4659209593593703e+00 1.1048037573717906e-01 -5.0287486768790597e+00 + 26 -5.0656394516203669e+00 -1.5673717710206070e+01 1.3291597641889949e+01 + 27 4.4816496229054108e+00 -4.8760375214009000e-01 3.1769655817027243e-01 + 28 1.7501136457128652e+00 5.5544282266261300e+00 7.7052630849006061e+00 + 29 4.4375276260835363e+00 1.0588320818463746e+01 -5.0996447319488158e-01 + 30 -4.6722349677858155e+00 -3.1632380030448481e+00 -8.9559874574015321e+00 + 31 -2.1137799706905263e+00 -1.2576277946084598e+01 7.8183097013203859e+00 + 32 -2.0076186352052531e+01 -6.7271373781221957e+00 -2.4442712859248417e+00 +run_vdwl: 15.467597736353799 +run_coul: 0 +run_stress: ! |2- + 7.0958747804689210e+02 6.9441827563947470e+02 6.8163127749154512e+02 1.8878502566994296e+01 -2.3370443631780007e+00 -7.6034095912045760e+00 +run_forces: ! |2 + 1 1.8060069687912315e+00 7.2937921411443272e+00 1.2874043790398257e+00 + 2 -2.6860686380065211e+00 -7.8171831729036949e+00 5.1804211817416146e+00 + 3 -4.1171784798928526e+00 2.0287394801872782e+01 -5.0380109293520263e+00 + 4 2.1656515555309701e+00 -8.1400307560916696e-01 -5.7145340820348807e+00 + 5 5.1215865715331210e+00 1.4962842274862354e+01 4.1990209437793720e+00 + 6 4.5053950543110819e+00 3.6131448405817745e+00 -4.5093219067517526e-01 + 7 -6.2879800842830242e+00 9.6521438182158885e+00 -1.0299290710899491e+00 + 8 -6.9178598166543104e+00 -6.2386160865726810e+00 4.0623272209295660e+00 + 9 1.4558477052948295e+00 -6.3449931159549564e+00 -2.7980116422532566e+00 + 10 -3.1947087252955644e+00 -1.4694132852113814e+01 -1.2296068939837111e+01 + 11 -4.4213006161890327e+00 -5.8917488565993494e+00 4.2536421369191544e+00 + 12 2.7297061846000523e+00 -9.2628857408236485e+00 -4.2352406239391233e-01 + 13 -2.0463406900814625e+00 2.1917055360874724e+00 -4.7773710542900174e+00 + 14 6.1383962160687062e+00 -2.3802746888087309e+00 7.3930657535424977e+00 + 15 -3.2106271078248252e+00 2.8691911150262972e+00 -3.0935315047336651e+00 + 16 1.1775118023237834e+01 -9.9744044265688689e+00 3.9903927678211364e+00 + 17 4.4470872747424268e+00 1.3995945810173936e+01 1.2365235440776301e-01 + 18 -1.5026673304996480e+01 -2.9750422082331016e+00 -7.3424362144564483e+00 + 19 -1.5930045931183475e+01 -7.7015474120118768e+00 4.0406518181177002e+00 + 20 2.6298049917805058e+00 2.2000986429230047e+00 -3.2110928815587529e+00 + 21 1.6909713615092866e+01 5.3101658559139251e+00 4.0868602173987068e-01 + 22 4.7983382632912780e-01 -8.7146552778884860e+00 -1.2319261458206390e+00 + 23 4.7543321502399483e+00 1.2910146662851659e+01 -8.3714393526052007e+00 + 24 1.2703010580857182e+01 9.8446813695739301e+00 8.6611807480415717e+00 + 25 7.4606294163504421e+00 1.1676144511890918e-01 -5.0227835859998491e+00 + 26 -5.0389376565333173e+00 -1.5622579837196479e+01 1.3265181089097052e+01 + 27 4.4802107201737105e+00 -4.8768004812534205e-01 3.0515995799100715e-01 + 28 1.7426613249450380e+00 5.5559456274721297e+00 7.6944148346751184e+00 + 29 4.4190985096740434e+00 1.0572340858974512e+01 -4.9630774662960464e-01 + 30 -4.6643835948427661e+00 -3.1602285684767137e+00 -8.9347962499921074e+00 + 31 -2.1238163435419626e+00 -1.2568441864236553e+01 7.8082109733945497e+00 + 32 -2.0058169700227520e+01 -6.7278835686694558e+00 -2.4407165275151792e+00 +... diff --git a/unittest/force-styles/tests/atomic-pair-smatb_single.yaml b/unittest/force-styles/tests/atomic-pair-smatb_single.yaml new file mode 100644 index 0000000000..c3751fed04 --- /dev/null +++ b/unittest/force-styles/tests/atomic-pair-smatb_single.yaml @@ -0,0 +1,93 @@ +--- +lammps_version: 24 Mar 2022 +date_generated: Wed Apr 27 17:43:01 2022 +epsilon: 6e-12 +skip_tests: single +prerequisites: ! | + pair smatb/single +pre_commands: ! | + variable units index metal + variable newton_pair delete + variable newton_pair index on +post_commands: ! "" +input_file: in.metal +pair_style: smatb/single +pair_coeff: ! | + * * 2.88 10.35 4.178 0.210 1.818 4.07293506 4.9883063257983666 +extract: ! "" +natoms: 32 +init_vdwl: 15.546009002462199 +init_coul: 0 +init_stress: ! |2- + 7.0981045919895291e+02 6.9464048009855617e+02 6.8185854046738905e+02 1.8940099448628423e+01 -2.3190641785495831e+00 -7.6126579722972734e+00 +init_forces: ! |2 + 1 1.8383788817685609e+00 7.3043414500016803e+00 1.2928059118046571e+00 + 2 -2.6848648395616506e+00 -7.8218002510265290e+00 5.1835989139783809e+00 + 3 -4.1262133070389613e+00 2.0356333849891929e+01 -5.0300134853162675e+00 + 4 2.1640213680130582e+00 -8.2080827254125310e-01 -5.7189855300172958e+00 + 5 5.1336080958834502e+00 1.4999943174537506e+01 4.1898025714112999e+00 + 6 4.5017623545159724e+00 3.6176208409156039e+00 -4.4379897612576352e-01 + 7 -6.2917785937694219e+00 9.6471529013643753e+00 -1.0169471822201503e+00 + 8 -6.9079266006711242e+00 -6.2411913330296631e+00 4.0631933657348354e+00 + 9 1.4448974765969274e+00 -6.3335992210787921e+00 -2.7877666693063965e+00 + 10 -3.2369455571053383e+00 -1.4726480521388170e+01 -1.2343244613879385e+01 + 11 -4.4279873426372749e+00 -5.8875813372324703e+00 4.2645243184789097e+00 + 12 2.7168432086644443e+00 -9.2808529346155240e+00 -4.2510938219210220e-01 + 13 -2.0372275262801081e+00 2.2026130441803744e+00 -4.7893800758259584e+00 + 14 6.1358565129828193e+00 -2.4215787035807863e+00 7.4237482521334002e+00 + 15 -3.2151583983209826e+00 2.8722155568519296e+00 -3.1022228268650602e+00 + 16 1.1834167029249446e+01 -9.9960409045212177e+00 4.0046914221724927e+00 + 17 4.4438667082387253e+00 1.4015434663357324e+01 1.1980157677253445e-01 + 18 -1.5049446792950388e+01 -2.9866974100159291e+00 -7.3487669643132998e+00 + 19 -1.5962776779061105e+01 -7.7159633670829013e+00 4.0578908190472625e+00 + 20 2.6368639403789449e+00 2.1948034299735144e+00 -3.2117143706849434e+00 + 21 1.6938751336137905e+01 5.3405439576559601e+00 3.9965661174944195e-01 + 22 4.6915262682186748e-01 -8.7314686216914801e+00 -1.2388516494108810e+00 + 23 4.7426470160406025e+00 1.2927761843820045e+01 -8.4044784783918658e+00 + 24 1.2732138070191686e+01 9.8600435340252197e+00 8.6676713483852375e+00 + 25 7.4659209593593703e+00 1.1048037573717906e-01 -5.0287486768790597e+00 + 26 -5.0656394516203669e+00 -1.5673717710206070e+01 1.3291597641889949e+01 + 27 4.4816496229054108e+00 -4.8760375214009000e-01 3.1769655817027243e-01 + 28 1.7501136457128652e+00 5.5544282266261300e+00 7.7052630849006061e+00 + 29 4.4375276260835363e+00 1.0588320818463746e+01 -5.0996447319488158e-01 + 30 -4.6722349677858155e+00 -3.1632380030448481e+00 -8.9559874574015321e+00 + 31 -2.1137799706905263e+00 -1.2576277946084598e+01 7.8183097013203859e+00 + 32 -2.0076186352052531e+01 -6.7271373781221957e+00 -2.4442712859248417e+00 +run_vdwl: 15.467597736353799 +run_coul: 0 +run_stress: ! |2- + 7.0958747804689210e+02 6.9441827563947470e+02 6.8163127749154512e+02 1.8878502566994296e+01 -2.3370443631780007e+00 -7.6034095912045760e+00 +run_forces: ! |2 + 1 1.8060069687912315e+00 7.2937921411443272e+00 1.2874043790398257e+00 + 2 -2.6860686380065211e+00 -7.8171831729036949e+00 5.1804211817416146e+00 + 3 -4.1171784798928526e+00 2.0287394801872782e+01 -5.0380109293520263e+00 + 4 2.1656515555309701e+00 -8.1400307560916696e-01 -5.7145340820348807e+00 + 5 5.1215865715331210e+00 1.4962842274862354e+01 4.1990209437793720e+00 + 6 4.5053950543110819e+00 3.6131448405817745e+00 -4.5093219067517526e-01 + 7 -6.2879800842830242e+00 9.6521438182158885e+00 -1.0299290710899491e+00 + 8 -6.9178598166543104e+00 -6.2386160865726810e+00 4.0623272209295660e+00 + 9 1.4558477052948295e+00 -6.3449931159549564e+00 -2.7980116422532566e+00 + 10 -3.1947087252955644e+00 -1.4694132852113814e+01 -1.2296068939837111e+01 + 11 -4.4213006161890327e+00 -5.8917488565993494e+00 4.2536421369191544e+00 + 12 2.7297061846000523e+00 -9.2628857408236485e+00 -4.2352406239391233e-01 + 13 -2.0463406900814625e+00 2.1917055360874724e+00 -4.7773710542900174e+00 + 14 6.1383962160687062e+00 -2.3802746888087309e+00 7.3930657535424977e+00 + 15 -3.2106271078248252e+00 2.8691911150262972e+00 -3.0935315047336651e+00 + 16 1.1775118023237834e+01 -9.9744044265688672e+00 3.9903927678211364e+00 + 17 4.4470872747424268e+00 1.3995945810173936e+01 1.2365235440776301e-01 + 18 -1.5026673304996480e+01 -2.9750422082331016e+00 -7.3424362144564483e+00 + 19 -1.5930045931183475e+01 -7.7015474120118768e+00 4.0406518181177002e+00 + 20 2.6298049917805058e+00 2.2000986429230047e+00 -3.2110928815587529e+00 + 21 1.6909713615092866e+01 5.3101658559139251e+00 4.0868602173987068e-01 + 22 4.7983382632912785e-01 -8.7146552778884860e+00 -1.2319261458206390e+00 + 23 4.7543321502399483e+00 1.2910146662851659e+01 -8.3714393526052007e+00 + 24 1.2703010580857182e+01 9.8446813695739301e+00 8.6611807480415717e+00 + 25 7.4606294163504421e+00 1.1676144511890918e-01 -5.0227835859998500e+00 + 26 -5.0389376565333173e+00 -1.5622579837196479e+01 1.3265181089097052e+01 + 27 4.4802107201737105e+00 -4.8768004812534205e-01 3.0515995799100759e-01 + 28 1.7426613249450380e+00 5.5559456274721297e+00 7.6944148346751184e+00 + 29 4.4190985096740434e+00 1.0572340858974512e+01 -4.9630774662960464e-01 + 30 -4.6643835948427661e+00 -3.1602285684767137e+00 -8.9347962499921074e+00 + 31 -2.1238163435419626e+00 -1.2568441864236553e+01 7.8082109733945497e+00 + 32 -2.0058169700227520e+01 -6.7278835686694558e+00 -2.4407165275151792e+00 +... From 55fddf3aac574cead17105c7ec3a950425f9f9b9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 27 Apr 2022 18:26:07 -0400 Subject: [PATCH 47/57] update (tentative) release date --- doc/src/Modify_style.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/src/Modify_style.rst b/doc/src/Modify_style.rst index 0ee600acc5..2ed83ed7c6 100644 --- a/doc/src/Modify_style.rst +++ b/doc/src/Modify_style.rst @@ -250,9 +250,9 @@ on` comments around that block. Error or warning messages and explanations (preferred) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. versionchanged:: 27Apr2022 +.. versionchanged:: 4May2022 -Starting with LAMMPS version 27 April 2022 the LAMMPS developers have +Starting with LAMMPS version 4 May 2022 the LAMMPS developers have agreed on a new policy for error and warning messages. Previously, all error and warning strings were supposed to be listed in From a3e0e1a6ebc3956364c72c23e793e58e9f843ab3 Mon Sep 17 00:00:00 2001 From: megmcca <90424440+megmcca@users.noreply.github.com> Date: Thu, 28 Apr 2022 15:57:53 -0600 Subject: [PATCH 48/57] fixed multielement assignment error --- src/ML-SNAP/pair_snap.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/ML-SNAP/pair_snap.cpp b/src/ML-SNAP/pair_snap.cpp index 6dcdaa67e9..089f594fff 100644 --- a/src/ML-SNAP/pair_snap.cpp +++ b/src/ML-SNAP/pair_snap.cpp @@ -701,15 +701,15 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) int iword = 1; if (keywd == "sinner") { - keyval = words[iword]; for (int ielem = 0; ielem < nelements; ielem++) { + keyval = words[iword]; sinnerelem[ielem] = utils::numeric(FLERR,keyval,false,lmp); iword++; } sinnerflag = 1; } else if (keywd == "dinner") { - keyval = words[iword]; for (int ielem = 0; ielem < nelements; ielem++) { + keyval = words[iword]; dinnerelem[ielem] = utils::numeric(FLERR,keyval,false,lmp); iword++; } From 2292caef3898ee5cfc0cb8a774cd8ec4b23fac5b Mon Sep 17 00:00:00 2001 From: megmcca <90424440+megmcca@users.noreply.github.com> Date: Fri, 29 Apr 2022 07:48:02 -0600 Subject: [PATCH 49/57] updated sinner/dinner log output now logmsg displays all element params for sinner, dinner on same line (replaces only first param + ...) --- src/ML-SNAP/pair_snap.cpp | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/src/ML-SNAP/pair_snap.cpp b/src/ML-SNAP/pair_snap.cpp index 089f594fff..56c3250c3f 100644 --- a/src/ML-SNAP/pair_snap.cpp +++ b/src/ML-SNAP/pair_snap.cpp @@ -688,16 +688,17 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) auto keywd = words[0]; auto keyval = words[1]; - // check for keywords with one value per element + // check for keywords with more than one value per element if (keywd == "sinner" || keywd == "dinner") { if ((int)words.size() != nelements+1) error->all(FLERR,"Incorrect SNAP parameter file"); + + // innerlogstr collects all values of sinner or dinner for log output below - if (comm->me == 0) - utils::logmesg(lmp,"SNAP keyword {} {} ... \n", keywd, keyval); - + std::string innerlogstr; + int iword = 1; if (keywd == "sinner") { @@ -705,6 +706,7 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) keyval = words[iword]; sinnerelem[ielem] = utils::numeric(FLERR,keyval,false,lmp); iword++; + innerlogstr += keyval + " "; } sinnerflag = 1; } else if (keywd == "dinner") { @@ -712,9 +714,13 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) keyval = words[iword]; dinnerelem[ielem] = utils::numeric(FLERR,keyval,false,lmp); iword++; + innerlogstr += keyval + " "; } dinnerflag = 1; } + + if (comm->me == 0) + utils::logmesg(lmp,"SNAP keyword {} {} ... \n", keywd, innerlogstr); } else { From c34efcc718111a91af12e35af72b21635d81830f Mon Sep 17 00:00:00 2001 From: megmcca <90424440+megmcca@users.noreply.github.com> Date: Fri, 29 Apr 2022 07:53:39 -0600 Subject: [PATCH 50/57] fixed multielement assignment error tested in CPU and GPU mode, gets same output for eneriges and forces as build without KOKKOS for various settings of sinner, dinner --- src/KOKKOS/pair_snap_kokkos_impl.h | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index 4d2edf037c..65684d58ba 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -743,8 +743,8 @@ void PairSNAPKokkos::operator() (TagPairSN my_sna.rcutij(ii,offset) = static_cast((radi + d_radelem[jelem])*rcutfac); my_sna.inside(ii,offset) = j; if (switchinnerflag) { - my_sna.sinnerij(ii,ninside) = 0.5*(d_sinnerelem[ielem] + d_sinnerelem[jelem]); - my_sna.dinnerij(ii,ninside) = 0.5*(d_dinnerelem[ielem] + d_dinnerelem[jelem]); + my_sna.sinnerij(ii,offset) = 0.5*(d_sinnerelem[ielem] + d_sinnerelem[jelem]); + my_sna.dinnerij(ii,offset) = 0.5*(d_dinnerelem[ielem] + d_dinnerelem[jelem]); } if (chemflag) my_sna.element(ii,offset) = jelem; @@ -1106,8 +1106,8 @@ void PairSNAPKokkos::operator() (TagPairSN my_sna.rcutij(ii,offset) = static_cast((radi + d_radelem[jelem])*rcutfac); my_sna.inside(ii,offset) = j; if (switchinnerflag) { - my_sna.sinnerij(ii,ninside) = 0.5*(d_sinnerelem[ielem] + d_sinnerelem[jelem]); - my_sna.dinnerij(ii,ninside) = 0.5*(d_dinnerelem[ielem] + d_dinnerelem[jelem]); + my_sna.sinnerij(ii,offset) = 0.5*(d_sinnerelem[ielem] + d_sinnerelem[jelem]); + my_sna.dinnerij(ii,offset) = 0.5*(d_dinnerelem[ielem] + d_dinnerelem[jelem]); } if (chemflag) my_sna.element(ii,offset) = jelem; From 641e769bdea8a5494320462b6d55ca3d088e9fd4 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 29 Apr 2022 09:03:44 -0600 Subject: [PATCH 51/57] Revert a3c6baad4ca4ec173dedafbaf87f15d0abcf6b61 --- src/KOKKOS/pair_snap_kokkos_impl.h | 30 ++++++++++++++---------------- 1 file changed, 14 insertions(+), 16 deletions(-) diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index 65684d58ba..2b49345371 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -90,16 +90,15 @@ template void PairSNAPKokkos::init_style() { - // Disabled for DEBUGGING on CPU - // if (host_flag) { - // if (lmp->kokkos->nthreads > 1) - // if (comm->me == 0) - // utils::logmesg(lmp,"Pair style snap/kk currently only runs on a single " - // "CPU thread, even if more threads are requested\n"); + if (host_flag) { + if (lmp->kokkos->nthreads > 1) + if (comm->me == 0) + utils::logmesg(lmp,"Pair style snap/kk currently only runs on a single " + "CPU thread, even if more threads are requested\n"); - // PairSNAP::init_style(); - // return; - // } + PairSNAP::init_style(); + return; + } if (force->newton_pair == 0) error->all(FLERR,"Pair style SNAP requires newton pair on"); @@ -141,13 +140,12 @@ struct FindMaxNumNeighs { template void PairSNAPKokkos::compute(int eflag_in, int vflag_in) { - // Disabled for DEBUGGING on CPU - // if (host_flag) { - // atomKK->sync(Host,X_MASK|TYPE_MASK); - // PairSNAP::compute(eflag_in,vflag_in); - // atomKK->modified(Host,F_MASK); - // return; - // } + if (host_flag) { + atomKK->sync(Host,X_MASK|TYPE_MASK); + PairSNAP::compute(eflag_in,vflag_in); + atomKK->modified(Host,F_MASK); + return; + } eflag = eflag_in; vflag = vflag_in; From 69a79ba082350f3efc7f440c051ee329bf1ef0c7 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 29 Apr 2022 09:17:24 -0600 Subject: [PATCH 52/57] whitespace --- src/KOKKOS/pair_snap_kokkos_impl.h | 29 ++++++++++++++--------------- 1 file changed, 14 insertions(+), 15 deletions(-) diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index 2b49345371..e39f42058f 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -89,16 +89,15 @@ PairSNAPKokkos::~PairSNAPKokkos() template void PairSNAPKokkos::init_style() { + if (host_flag) { + if (lmp->kokkos->nthreads > 1) + if (comm->me == 0) + utils::logmesg(lmp,"Pair style snap/kk currently only runs on a single " + "CPU thread, even if more threads are requested\n"); - if (host_flag) { - if (lmp->kokkos->nthreads > 1) - if (comm->me == 0) - utils::logmesg(lmp,"Pair style snap/kk currently only runs on a single " - "CPU thread, even if more threads are requested\n"); - - PairSNAP::init_style(); - return; - } + PairSNAP::init_style(); + return; + } if (force->newton_pair == 0) error->all(FLERR,"Pair style SNAP requires newton pair on"); @@ -140,12 +139,12 @@ struct FindMaxNumNeighs { template void PairSNAPKokkos::compute(int eflag_in, int vflag_in) { - if (host_flag) { - atomKK->sync(Host,X_MASK|TYPE_MASK); - PairSNAP::compute(eflag_in,vflag_in); - atomKK->modified(Host,F_MASK); - return; - } + if (host_flag) { + atomKK->sync(Host,X_MASK|TYPE_MASK); + PairSNAP::compute(eflag_in,vflag_in); + atomKK->modified(Host,F_MASK); + return; + } eflag = eflag_in; vflag = vflag_in; From 57098f3df7e94ddeaaed1b4ab5628fcb3df66b6d Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 29 Apr 2022 09:22:14 -0600 Subject: [PATCH 53/57] Remove extra files --- src/MAKE/OPTIONS/Makefile.kokkos_omp_db_asan | 126 ------------------- src/Si.tersoff | 18 --- src/Si.tersoff.mod | 27 ---- src/Si.tersoff.modc | 10 -- 4 files changed, 181 deletions(-) delete mode 100644 src/MAKE/OPTIONS/Makefile.kokkos_omp_db_asan delete mode 100644 src/Si.tersoff delete mode 100644 src/Si.tersoff.mod delete mode 100644 src/Si.tersoff.modc diff --git a/src/MAKE/OPTIONS/Makefile.kokkos_omp_db_asan b/src/MAKE/OPTIONS/Makefile.kokkos_omp_db_asan deleted file mode 100644 index 72427b9e5f..0000000000 --- a/src/MAKE/OPTIONS/Makefile.kokkos_omp_db_asan +++ /dev/null @@ -1,126 +0,0 @@ -# kokkos_omp = KOKKOS/OMP package, MPI with its default compiler - -SHELL = /bin/sh - -# --------------------------------------------------------------------- -# compiler/linker settings -# specify flags and libraries needed for your compiler - -CC = mpicxx -CCFLAGS = -g -O0 -fsanitize=address -SHFLAGS = -fPIC -DEPFLAGS = -M - -LINK = mpicxx -LINKFLAGS = -g -O0 -fsanitize=address -LIB = -SIZE = size - -ARCHIVE = ar -ARFLAGS = -rc -SHLIBFLAGS = -shared -KOKKOS_DEVICES = OpenMP -KOKKOS_DEBUG = yes - -# --------------------------------------------------------------------- -# LAMMPS-specific settings, all OPTIONAL -# specify settings for LAMMPS features you will use -# if you change any -D setting, do full re-compile after "make clean" - -# LAMMPS ifdef settings -# see possible settings in Section 3.5 of the manual - -LMP_INC = -DLAMMPS_GZIP - -# MPI library -# see discussion in Section 3.4 of the manual -# MPI wrapper compiler/linker can provide this info -# can point to dummy MPI library in src/STUBS as in Makefile.serial -# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts -# INC = path for mpi.h, MPI compiler settings -# PATH = path for MPI library -# LIB = name of MPI library - -MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -MPI_PATH = -MPI_LIB = - -# FFT library -# see discussion in Section 3.5.2 of manual -# can be left blank to use provided KISS FFT library -# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings -# PATH = path for FFT library -# LIB = name of FFT library - -FFT_INC = -FFT_PATH = -FFT_LIB = - -# JPEG and/or PNG library -# see discussion in Section 3.5.4 of manual -# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC -# INC = path(s) for jpeglib.h and/or png.h -# PATH = path(s) for JPEG library and/or PNG library -# LIB = name(s) of JPEG library and/or PNG library - -JPG_INC = -JPG_PATH = -JPG_LIB = - -# library for loading shared objects (defaults to -ldl, should be empty on Windows) -# uncomment to change the default - -# override DYN_LIB = - -# --------------------------------------------------------------------- -# build rules and dependencies -# do not edit this section - -include Makefile.package.settings -include Makefile.package - -EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) -EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) -EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB) -EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) -EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) - -# Path to src files - -vpath %.cpp .. -vpath %.h .. - -# Link target - -$(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS) - $(LINK) $(LINKFLAGS) main.o $(EXTRA_PATH) $(LMPLINK) $(EXTRA_LIB) $(LIB) -o $@ - $(SIZE) $@ - -# Library targets - -$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS) - @rm -f ../$(ARLIB) - $(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ) - @rm -f $(ARLIB) - @ln -s ../$(ARLIB) $(ARLIB) - -$(SHLIB): $(OBJ) $(EXTRA_LINK_DEPENDS) - $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o ../$(SHLIB) \ - $(OBJ) $(EXTRA_LIB) $(LIB) - @rm -f $(SHLIB) - @ln -s ../$(SHLIB) $(SHLIB) - -# Compilation rules - -%.o:%.cpp - $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< - -# Individual dependencies - -depend : fastdep.exe $(SRC) - @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 - -fastdep.exe: ../DEPEND/fastdep.c - cc -O -o $@ $< - -sinclude .depend diff --git a/src/Si.tersoff b/src/Si.tersoff deleted file mode 100644 index fa565df42b..0000000000 --- a/src/Si.tersoff +++ /dev/null @@ -1,18 +0,0 @@ -# DATE: 2007-10-25 UNITS: metal CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Tersoff, Phys Rev B, 37, 6991 (1988) - -# Tersoff parameters for various elements and mixtures -# multiple entries can be added to this file, LAMMPS reads the ones it needs -# these entries are in LAMMPS "metal" units: -# A,B = eV; lambda1,lambda2,lambda3 = 1/Angstroms; R,D = Angstroms -# other quantities are unitless - -# This is the Si parameterization from a particular Tersoff paper: -# J. Tersoff, PRB, 37, 6991 (1988) -# See the SiCGe.tersoff file for different Si variants. - -# format of a single entry (one or more lines): -# element 1, element 2, element 3, -# m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A - -Si Si Si 3.0 1.0 1.3258 4.8381 2.0417 0.0000 22.956 - 0.33675 1.3258 95.373 3.0 0.2 3.2394 3264.7 diff --git a/src/Si.tersoff.mod b/src/Si.tersoff.mod deleted file mode 100644 index 016c247638..0000000000 --- a/src/Si.tersoff.mod +++ /dev/null @@ -1,27 +0,0 @@ -# DATE: 2013-07-26 UNITS: metal CONTRIBUTOR: Unknown CITATION: Kumagai, Izumi, Hara and Sakai, Comp Mat Sci, 39, 457 (2007) - -# Modified Tersoff potential (named MOD potential) parameters for various elements and mixtures -# multiple entries can be added to this file, LAMMPS reads the ones it needs -# these entries are in LAMMPS "metal" units: -# A,B = eV; lambda1,lambda2 = 1/Angstroms; R,D = Angstroms -# other quantities are unitless - -# MOD. This is the Si parameterization from the paper: -# [1] T. Kumagai, S. Izumi, S. Hara, S. Sakai, Comp. Mat. Sci., 39, 457 (2007) - -# format of a single entry (one or more lines): -# element 1, element 2, element 3, -# beta, alpha, h, eta, -# beta_ters, lambda2, B, R, D, lambda1, A, n -# c1, c2, c3, c4, c5 - -# Notes -# 1) beta_ters must be equal to 1.0 -# 2) R = (R1+R2)/2, where R1 and R2 determined at [1] (R1 = 2.7A, R2 = 3.3A) -# 3) D = (R2-R1)/2, where R1 and R2 determined at [1] (R1 = 2.7A, R2 = 3.3A) -# 4) n = 1.0/(2*delta), where delta determined at [1] (eta*delta = 0.53298909) - -#mod -Si Si Si 1.0 2.3890327 -.365 1.0 - 1.0 1.345797 121.00047 3.0 0.3 3.2300135 3281.5905 .93810551 - 0.20173476 730418.72 1000000.0 1.0 26.0 diff --git a/src/Si.tersoff.modc b/src/Si.tersoff.modc deleted file mode 100644 index ce184960bf..0000000000 --- a/src/Si.tersoff.modc +++ /dev/null @@ -1,10 +0,0 @@ -# DATE: 2016-11-09 UNITS: metal CONTRIBUTOR: Ganga P Purja Pun (George Mason University, Fairfax) CITATION: Unknown -# -# Format: -# element1 element2 element3 -# beta alpha h eta -# beta_ters lam2 B R D lam1 A -# n c1 c2 c3 c4 c5 C -Si Si Si 3.00000000 1.80536502 -0.38136087 2.16152496 -1 1.39343356 117.78072440 2.87478837 0.33090566 3.18011795 3198.51383127 -1.98633876 0.20123243 614230.04310619 996439.09714140 3.33560562 25.20963770 -0.00592042 From 894b7810b244bbba793db75e77255a907182b109 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 29 Apr 2022 09:32:24 -0600 Subject: [PATCH 54/57] whitespace --- src/KOKKOS/pair_snap_kokkos_impl.h | 4 ++-- src/KOKKOS/sna_kokkos.h | 4 ++-- src/KOKKOS/sna_kokkos_impl.h | 30 +++++++++++++++--------------- 3 files changed, 19 insertions(+), 19 deletions(-) diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index e39f42058f..74264ca47e 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -92,8 +92,8 @@ void PairSNAPKokkos::init_style() if (host_flag) { if (lmp->kokkos->nthreads > 1) if (comm->me == 0) - utils::logmesg(lmp,"Pair style snap/kk currently only runs on a single " - "CPU thread, even if more threads are requested\n"); + utils::logmesg(lmp,"Pair style snap/kk currently only runs on a single " + "CPU thread, even if more threads are requested\n"); PairSNAP::init_style(); return; diff --git a/src/KOKKOS/sna_kokkos.h b/src/KOKKOS/sna_kokkos.h index 4f10a9ac0b..7ed2736947 100644 --- a/src/KOKKOS/sna_kokkos.h +++ b/src/KOKKOS/sna_kokkos.h @@ -315,8 +315,8 @@ inline KOKKOS_INLINE_FUNCTION void compute_duarray_cpu(const typename Kokkos::TeamPolicy::member_type& team, int, int, const real_type&, const real_type&, const real_type&, // compute_duidrj_cpu - const real_type&, const real_type&, const real_type&, const real_type&, const real_type&, - const real_type&, const real_type&); + const real_type&, const real_type&, const real_type&, const real_type&, const real_type&, + const real_type&, const real_type&); // Sets the style for the switching function // 0 = none diff --git a/src/KOKKOS/sna_kokkos_impl.h b/src/KOKKOS/sna_kokkos_impl.h index c9c1bfbb99..77130b9781 100644 --- a/src/KOKKOS/sna_kokkos_impl.h +++ b/src/KOKKOS/sna_kokkos_impl.h @@ -31,7 +31,7 @@ template inline SNAKokkos::SNAKokkos(real_type rfac0_in, int twojmax_in, real_type rmin0_in, int switch_flag_in, int bzero_flag_in, - int chem_flag_in, int bnorm_flag_in, int wselfall_flag_in, int nelements_in, int switch_inner_flag_in) + int chem_flag_in, int bnorm_flag_in, int wselfall_flag_in, int nelements_in, int switch_inner_flag_in) { LAMMPS_NS::ExecutionSpace execution_space = ExecutionSpaceFromDevice::space; host_flag = (execution_space == LAMMPS_NS::Host); @@ -1753,8 +1753,8 @@ KOKKOS_INLINE_FUNCTION void SNAKokkos::compute_duarray_cpu(const typename Kokkos::TeamPolicy::member_type& team, int iatom, int jnbor, const real_type& x, const real_type& y, const real_type& z, const real_type& z0, const real_type& r, const real_type& dz0dr, - const real_type& wj, const real_type& rcut, - const real_type& sinner, const real_type& dinner) + const real_type& wj, const real_type& rcut, + const real_type& sinner, const real_type& dinner) { real_type r0inv; real_type a_r, a_i, b_r, b_i; @@ -2247,15 +2247,15 @@ real_type SNAKokkos::compute_sfac(real_typ sfac_outer = onehalf * (cos((r - rmin0) * rcutfac) + one); } } - + if (switch_inner_flag == 0) return sfac_outer; if (switch_inner_flag == 1) { - if (r >= sinner + dinner) - return sfac_outer; + if (r >= sinner + dinner) + return sfac_outer; else if (r > sinner - dinner) { real_type rcutfac = static_cast(MY_PI2) / dinner; - return sfac_outer * - onehalf * (one - cos(static_cast(MY_PI2) + (r - sinner) * rcutfac)); + return sfac_outer * + onehalf * (one - cos(static_cast(MY_PI2) + (r - sinner) * rcutfac)); } else return zero; } return zero; // dummy return @@ -2283,7 +2283,7 @@ real_type SNAKokkos::compute_dsfac(real_ty if (switch_inner_flag == 0) return dsfac_outer; if (switch_inner_flag == 1) { - if (r >= sinner + dinner) + if (r >= sinner + dinner) return dsfac_outer; else if (r > sinner - dinner) { @@ -2291,12 +2291,12 @@ real_type SNAKokkos::compute_dsfac(real_ty if (switch_flag == 0) sfac_outer = one; if (switch_flag == 1) { - if (r <= rmin0) sfac_outer = one; - else if (r > rcut) sfac_outer = zero; - else { - real_type rcutfac = static_cast(MY_PI) / (rcut - rmin0); - sfac_outer = onehalf * (cos((r - rmin0) * rcutfac) + one); - } + if (r <= rmin0) sfac_outer = one; + else if (r > rcut) sfac_outer = zero; + else { + real_type rcutfac = static_cast(MY_PI) / (rcut - rmin0); + sfac_outer = onehalf * (cos((r - rmin0) * rcutfac) + one); + } } // calculate sfac_inner From 2f8e70818405ddca27ad478456fd495eeb336973 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 29 Apr 2022 09:37:27 -0600 Subject: [PATCH 55/57] more whitespace --- src/KOKKOS/pair_snap_kokkos.h | 16 ++++++++-------- src/KOKKOS/sna_kokkos.h | 25 +++++++++++++------------ 2 files changed, 21 insertions(+), 20 deletions(-) diff --git a/src/KOKKOS/pair_snap_kokkos.h b/src/KOKKOS/pair_snap_kokkos.h index 1c0bf38699..2cd0003478 100644 --- a/src/KOKKOS/pair_snap_kokkos.h +++ b/src/KOKKOS/pair_snap_kokkos.h @@ -73,7 +73,7 @@ struct TagPairSNAPComputeDeidrjCPU{}; template class PairSNAPKokkos : public PairSNAP { -public: + public: enum {EnabledNeighFlags=FULL|HALF|HALFTHREAD}; enum {COUL_FLAG=0}; typedef DeviceType device_type; @@ -228,7 +228,7 @@ public: const F_FLOAT &fx, const F_FLOAT &fy, const F_FLOAT &fz, const F_FLOAT &delx, const F_FLOAT &dely, const F_FLOAT &delz) const; -protected: + protected: typename AT::t_neighbors_2d d_neighbors; typename AT::t_int_1d_randomread d_ilist; typename AT::t_int_1d_randomread d_numneigh; @@ -252,9 +252,9 @@ protected: void allocate() override; //void read_files(char *, char *); /*template -inline int equal(double* x,double* y); + inline int equal(double* x,double* y); template -inline double dist2(double* x,double* y); + inline double dist2(double* x,double* y); double extra_cutoff(); void load_balance(); void set_sna_to_shared(int snaid,int i); @@ -331,10 +331,10 @@ inline double dist2(double* x,double* y); template class PairSNAPKokkosDevice : public PairSNAPKokkos { -private: + private: using Base = PairSNAPKokkos; -public: + public: PairSNAPKokkosDevice(class LAMMPS *); @@ -350,10 +350,10 @@ public: template class PairSNAPKokkosHost : public PairSNAPKokkos { -private: + private: using Base = PairSNAPKokkos; -public: + public: PairSNAPKokkosHost(class LAMMPS *); diff --git a/src/KOKKOS/sna_kokkos.h b/src/KOKKOS/sna_kokkos.h index 7ed2736947..fe70129660 100644 --- a/src/KOKKOS/sna_kokkos.h +++ b/src/KOKKOS/sna_kokkos.h @@ -64,7 +64,7 @@ struct alignas(8) FullHalfMapper { template class SNAKokkos { -public: + public: using real_type = real_type_; using complex = SNAComplex; static constexpr int vector_length = vector_length_; @@ -97,21 +97,22 @@ public: typedef Kokkos::View t_sna_3c3; typedef Kokkos::View t_sna_5c; -inline + inline SNAKokkos() {}; + KOKKOS_INLINE_FUNCTION SNAKokkos(const SNAKokkos& sna, const typename Kokkos::TeamPolicy::member_type& team); -inline -SNAKokkos(real_type, int, real_type, int, int, int, int, int, int, int); + inline + SNAKokkos(real_type, int, real_type, int, int, int, int, int, int, int); KOKKOS_INLINE_FUNCTION ~SNAKokkos(); -inline + inline void build_indexlist(); // SNAKokkos() -inline + inline void init(); // double memory_usage(); @@ -257,7 +258,7 @@ inline int ndoubles; int ntriples; -private: + private: real_type rmin0, rfac0; //use indexlist instead of loops, constructor generates these @@ -266,13 +267,13 @@ private: Kokkos::View idxb; Kokkos::View idxcg_block; -public: + public: Kokkos::View idxu_block; Kokkos::View idxu_half_block; Kokkos::View idxu_cache_block; Kokkos::View idxu_full_half; -private: + private: Kokkos::View idxz_block; Kokkos::View idxb_block; @@ -292,10 +293,10 @@ private: KOKKOS_INLINE_FUNCTION void create_thread_scratch_arrays(const typename Kokkos::TeamPolicy::member_type& team); // SNAKokkos() -inline + inline void init_clebsch_gordan(); // init() -inline + inline void init_rootpqarray(); // init() KOKKOS_INLINE_FUNCTION @@ -310,7 +311,7 @@ inline inline double deltacg(int, int, int); // init_clebsch_gordan -inline + inline int compute_ncoeff(); // SNAKokkos() KOKKOS_INLINE_FUNCTION void compute_duarray_cpu(const typename Kokkos::TeamPolicy::member_type& team, int, int, From df76673beed86f79b9ddd61c7d29ed70850246e0 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Fri, 29 Apr 2022 10:10:36 -0600 Subject: [PATCH 56/57] bdim --> adim in fix adapt --- src/fix_adapt.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp index edaa5c9866..c54e569c3a 100644 --- a/src/fix_adapt.cpp +++ b/src/fix_adapt.cpp @@ -428,7 +428,7 @@ void FixAdapt::init() if (ad->angle == nullptr ) error->all(FLERR,"Fix adapt angle style does not exist"); - void *ptr = ad->angle->extract(ad->aparam,ad->bdim); + void *ptr = ad->angle->extract(ad->aparam,ad->adim); if (ptr == nullptr) error->all(FLERR,"Fix adapt angle style param not supported"); From 37d2d9e013f480afca3cf50ef9f7ee4a32453a31 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 29 Apr 2022 10:56:34 -0600 Subject: [PATCH 57/57] Remove trailing spaces --- doc/src/compute_sna_atom.rst | 4 ++-- src/ML-SNAP/pair_snap.cpp | 6 +++--- src/ML-SNAP/sna.cpp | 12 ++++++------ 3 files changed, 11 insertions(+), 11 deletions(-) diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst index e34c9a8889..54a6df02a2 100644 --- a/doc/src/compute_sna_atom.rst +++ b/doc/src/compute_sna_atom.rst @@ -335,7 +335,7 @@ where the switching region is centered at :math:`S_{inner}` and it extends a dis to the left and to the right of this. With this option, additional keywords *sinner* and *dinner* must be used, each followed by *ntypes* -values for :math:`S_{inner}` and :math:`D_{inner}`, respectively. +values for :math:`S_{inner}` and :math:`D_{inner}`, respectively. When the central atom and the neighbor atom have different types, the values of :math:`S_{inner}` and :math:`D_{inner}` are the arithmetic means of the values for both types. @@ -458,7 +458,7 @@ Default The optional keyword defaults are *rmin0* = 0, *switchflag* = 1, *bzeroflag* = 1, *quadraticflag* = 0, -*bnormflag* = 0, *wselfallflag* = 0, *switchinnerflag* = 0, +*bnormflag* = 0, *wselfallflag* = 0, *switchinnerflag* = 0, ---------- diff --git a/src/ML-SNAP/pair_snap.cpp b/src/ML-SNAP/pair_snap.cpp index 56c3250c3f..07a8237ab5 100644 --- a/src/ML-SNAP/pair_snap.cpp +++ b/src/ML-SNAP/pair_snap.cpp @@ -694,11 +694,11 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) if ((int)words.size() != nelements+1) error->all(FLERR,"Incorrect SNAP parameter file"); - + // innerlogstr collects all values of sinner or dinner for log output below std::string innerlogstr; - + int iword = 1; if (keywd == "sinner") { @@ -718,7 +718,7 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) } dinnerflag = 1; } - + if (comm->me == 0) utils::logmesg(lmp,"SNAP keyword {} {} ... \n", keywd, innerlogstr); diff --git a/src/ML-SNAP/sna.cpp b/src/ML-SNAP/sna.cpp index 2b86774d5b..33937b9c45 100644 --- a/src/ML-SNAP/sna.cpp +++ b/src/ML-SNAP/sna.cpp @@ -1552,7 +1552,7 @@ double SNA::compute_sfac(double r, double rcut, double sinner, double dinner) sfac *= 0.5 * (1.0 - cos(MY_PI2 + (r - sinner) * rcutfac)); } else sfac = 0.0; } - + return sfac; } @@ -1568,14 +1568,14 @@ double SNA::compute_dsfac(double r, double rcut, double sinner, double dinner) double rcutfac = MY_PI / (rcut - rmin0); dsfac_outer = -0.5 * sin((r - rmin0) * rcutfac) * rcutfac; } - - // some duplicated computation, but rarely visited + + // some duplicated computation, but rarely visited if (switch_inner_flag == 1 && r < sinner + dinner) { if (r > sinner - dinner) { // calculate sfac_outer - + if (switch_flag == 0) sfac_outer = 1.0; else if (r <= rmin0) sfac_outer = 1.0; else if (r > rcut) sfac_outer = 0.0; @@ -1585,14 +1585,14 @@ double SNA::compute_dsfac(double r, double rcut, double sinner, double dinner) } // calculate sfac_inner - + double rcutfac = MY_PI2 / dinner; sfac_inner = 0.5 * (1.0 - cos(MY_PI2 + (r - sinner) * rcutfac)); dsfac_inner = 0.5 * rcutfac * sin(MY_PI2 + (r - sinner) * rcutfac); dsfac = dsfac_outer*sfac_inner + sfac_outer*dsfac_inner; } else dsfac = 0.0; } else dsfac = dsfac_outer; - + return dsfac; }