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. - */