diff --git a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp new file mode 100644 index 0000000000..3ba892c1e1 --- /dev/null +++ b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp @@ -0,0 +1,1024 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Paul Crozier (SNL) + Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) +------------------------------------------------------------------------- */ + +#include "math.h" +#include "stdio.h" +#include "stdlib.h" +#include "string.h" +#include "pair_lj_charmm_coul_long_soft.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "kspace.h" +#include "update.h" +#include "integrate.h" +#include "respa.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +#define EWALD_F 1.12837917 +#define EWALD_P 0.3275911 +#define A1 0.254829592 +#define A2 -0.284496736 +#define A3 1.421413741 +#define A4 -1.453152027 +#define A5 1.061405429 + +/* ---------------------------------------------------------------------- */ + +PairLJCharmmCoulLongSoft::PairLJCharmmCoulLongSoft(LAMMPS *lmp) : Pair(lmp) +{ + respa_enable = 1; + ewaldflag = pppmflag = 1; + implicit = 0; + mix_flag = ARITHMETIC; + writedata = 1; +} + +/* ---------------------------------------------------------------------- */ + +PairLJCharmmCoulLongSoft::~PairLJCharmmCoulLongSoft() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(epsilon); + memory->destroy(sigma); + memory->destroy(lambda); + memory->destroy(eps14); + memory->destroy(sigma14); + memory->destroy(lj1); + memory->destroy(lj2); + memory->destroy(lj3); + memory->destroy(lj4); + memory->destroy(lj14_1); + memory->destroy(lj14_2); + memory->destroy(lj14_3); + memory->destroy(lj14_4); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairLJCharmmCoulLongSoft::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; + double r,rsq,forcecoul,forcelj,factor_coul,factor_lj; + double grij,expm2,prefactor,t,erfc; + double philj,switch1,switch2; + double denc, denlj, r4sig6; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = ecoul = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **f = atom->f; + double *q = atom->q; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_coul = force->special_coul; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + double qqrd2e = force->qqrd2e; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + qtmp = q[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + factor_coul = special_coul[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cut_bothsq) { + + if (rsq < cut_coulsq) { + r = sqrt(rsq); + grij = g_ewald * r; + expm2 = exp(-grij*grij); + t = 1.0 / (1.0 + EWALD_P*grij); + erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; + + denc = sqrt(lj4[itype][jtype] + rsq); + prefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc); + + forcecoul = prefactor * (erfc + EWALD_F*grij*expm2); + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor; + } else forcecoul = 0.0; + + if (rsq < cut_ljsq) { + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); + + if (rsq > cut_lj_innersq) { + switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) * + (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; + switch2 = 12.0 * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj; + philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * + (1.0/(denlj*denlj) - 1.0/denlj); + forcelj = forcelj*switch1 + philj*switch2; + } + } else forcelj = 0.0; + + fpair = forcecoul + factor_lj*forcelj; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (eflag) { + if (rsq < cut_coulsq) { + prefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / denc; + ecoul = prefactor*erfc; + if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor; + } else ecoul = 0.0; + + if (rsq < cut_ljsq) { + evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * + (1.0/(denlj*denlj) - 1.0/denlj); + if (rsq > cut_lj_innersq) { + switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) * + (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; + evdwl *= switch1; + } + evdwl *= factor_lj; + } else evdwl = 0.0; + } + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,ecoul,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- */ + +void PairLJCharmmCoulLongSoft::compute_inner() +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,fpair; + double rsq,forcecoul,forcelj,factor_coul,factor_lj; + double rsw; + double denc, denlj, r4sig6; + int *ilist,*jlist,*numneigh,**firstneigh; + + double **x = atom->x; + double **f = atom->f; + double *q = atom->q; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_coul = force->special_coul; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + double qqrd2e = force->qqrd2e; + + inum = listinner->inum; + ilist = listinner->ilist; + numneigh = listinner->numneigh; + firstneigh = listinner->firstneigh; + + double cut_out_on = cut_respa[0]; + double cut_out_off = cut_respa[1]; + + double cut_out_diff = cut_out_off - cut_out_on; + double cut_out_on_sq = cut_out_on*cut_out_on; + double cut_out_off_sq = cut_out_off*cut_out_off; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + qtmp = q[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + factor_coul = special_coul[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq < cut_out_off_sq) { + jtype = type[j]; + + denc = sqrt(lj4[itype][jtype] + rsq); + forcecoul = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc); + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*forcecoul; + + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); + + fpair = forcecoul + factor_lj*forcelj; + + if (rsq > cut_out_on_sq) { + rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff; + fpair *= 1.0 + rsw*rsw*(2.0*rsw-3.0); + } + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + } + } + } +} + +/* ---------------------------------------------------------------------- */ + +void PairLJCharmmCoulLongSoft::compute_middle() +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,fpair; + double rsq,forcecoul,forcelj,factor_coul,factor_lj; + double philj,switch1,switch2; + double rsw; + double denc, denlj, r4sig6; + int *ilist,*jlist,*numneigh,**firstneigh; + + double **x = atom->x; + double **f = atom->f; + double *q = atom->q; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_coul = force->special_coul; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + double qqrd2e = force->qqrd2e; + + inum = listmiddle->inum; + ilist = listmiddle->ilist; + numneigh = listmiddle->numneigh; + firstneigh = listmiddle->firstneigh; + + double cut_in_off = cut_respa[0]; + double cut_in_on = cut_respa[1]; + double cut_out_on = cut_respa[2]; + double cut_out_off = cut_respa[3]; + + double cut_in_diff = cut_in_on - cut_in_off; + double cut_out_diff = cut_out_off - cut_out_on; + double cut_in_off_sq = cut_in_off*cut_in_off; + double cut_in_on_sq = cut_in_on*cut_in_on; + double cut_out_on_sq = cut_out_on*cut_out_on; + double cut_out_off_sq = cut_out_off*cut_out_off; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + qtmp = q[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + factor_coul = special_coul[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq < cut_out_off_sq && rsq > cut_in_off_sq) { + jtype = type[j]; + + denc = sqrt(lj4[itype][jtype] + rsq); + forcecoul = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc); + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*forcecoul; + + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); + + if (rsq > cut_lj_innersq) { + switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) * + (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; + switch2 = 12.0 * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj; + philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * + (1.0/(denlj*denlj) - 1.0/denlj); + forcelj = forcelj*switch1 + philj*switch2; + } + + fpair = forcecoul + factor_lj*forcelj; + + if (rsq < cut_in_on_sq) { + rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff; + fpair *= rsw*rsw*(3.0 - 2.0*rsw); + } + if (rsq > cut_out_on_sq) { + rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff; + fpair *= 1.0 + rsw*rsw*(2.0*rsw - 3.0); + } + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + } + } + } +} + +/* ---------------------------------------------------------------------- */ + +void PairLJCharmmCoulLongSoft::compute_outer(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; + double r,rsq,forcecoul,forcelj,factor_coul,factor_lj; + double grij,expm2,fprefactor,eprefactor,t,erfc; + double philj,switch1,switch2; + double rsw; + double denc, denlj, r4sig6; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = ecoul = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = 0; + + double **x = atom->x; + double **f = atom->f; + double *q = atom->q; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_coul = force->special_coul; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + double qqrd2e = force->qqrd2e; + + inum = listouter->inum; + ilist = listouter->ilist; + numneigh = listouter->numneigh; + firstneigh = listouter->firstneigh; + + double cut_in_off = cut_respa[2]; + double cut_in_on = cut_respa[3]; + + double cut_in_diff = cut_in_on - cut_in_off; + double cut_in_off_sq = cut_in_off*cut_in_off; + double cut_in_on_sq = cut_in_on*cut_in_on; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + qtmp = q[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + factor_coul = special_coul[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq < cut_bothsq) { + jtype = type[j]; + + if (rsq < cut_coulsq) { + r = sqrt(rsq); + grij = g_ewald * r; + expm2 = exp(-grij*grij); + t = 1.0 / (1.0 + EWALD_P*grij); + erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; + + denc = sqrt(lj4[itype][jtype] + rsq); + fprefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / + (denc*denc*denc); + + forcecoul = fprefactor * (erfc + EWALD_F*grij*expm2 - 1.0); + + if (rsq > cut_in_off_sq) { + if (rsq < cut_in_on_sq) { + rsw = (r - cut_in_off)/cut_in_diff; + forcecoul += fprefactor*rsw*rsw*(3.0 - 2.0*rsw); + if (factor_coul < 1.0) + forcecoul -= + (1.0-factor_coul)*fprefactor*rsw*rsw*(3.0 - 2.0*rsw); + } else { + forcecoul += fprefactor; + if (factor_coul < 1.0) + forcecoul -= (1.0-factor_coul)*fprefactor; + } + } + } else forcecoul = 0.0; + + if (rsq < cut_ljsq && rsq > cut_in_off_sq) { + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); + + if (rsq > cut_lj_innersq) { + switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) * + (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; + switch2 = 12.0 * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj; + philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * + (1.0/(denlj*denlj) - 1.0/denlj); + forcelj = forcelj*switch1 + philj*switch2; + } + if (rsq < cut_in_on_sq) { + rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff; + forcelj *= rsw*rsw*(3.0 - 2.0*rsw); + } + } else forcelj = 0.0; + + fpair = forcecoul + forcelj; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (eflag) { + if (rsq < cut_coulsq) { + eprefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / denc; + ecoul = eprefactor*erfc; + if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*eprefactor; + } else ecoul = 0.0; + + if (rsq < cut_ljsq) { + evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * + (1.0/(denlj*denlj) - 1.0/denlj); + if (rsq > cut_lj_innersq) { + switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) * + (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; + evdwl *= switch1; + } + evdwl *= factor_lj; + } else evdwl = 0.0; + } + + if (vflag) { + if (rsq < cut_coulsq) { + forcecoul = fprefactor * (erfc + EWALD_F*grij*expm2); + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*fprefactor; + } else forcecoul = 0.0; + + if (rsq <= cut_in_off_sq) { + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); + + if (rsq > cut_lj_innersq) { + switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) * + (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; + switch2 = 12.0 * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj; + philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * + (1.0/(denlj*denlj) - 1.0/denlj); + forcelj = forcelj*switch1 + philj*switch2; + } + } else if (rsq <= cut_in_on_sq) { + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); + if (rsq > cut_lj_innersq) { + switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) * + (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; + switch2 = 12.0 * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj; + philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * + (1.0/(denlj*denlj) - 1.0/denlj); + forcelj = forcelj*switch1 + philj*switch2; + } + } + fpair = forcecoul + factor_lj*forcelj; + } + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,ecoul,fpair,delx,dely,delz); + } + } + } +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairLJCharmmCoulLongSoft::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair: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:cutsq"); + + memory->create(epsilon,n+1,n+1,"pair:epsilon"); + memory->create(sigma,n+1,n+1,"pair:sigma"); + memory->create(lambda,n+1,n+1,"pair:lambda"); + memory->create(eps14,n+1,n+1,"pair:eps14"); + memory->create(sigma14,n+1,n+1,"pair:sigma14"); + memory->create(lj1,n+1,n+1,"pair:lj1"); + memory->create(lj2,n+1,n+1,"pair:lj2"); + memory->create(lj3,n+1,n+1,"pair:lj3"); + memory->create(lj4,n+1,n+1,"pair:lj4"); + memory->create(lj14_1,n+1,n+1,"pair:lj14_1"); + memory->create(lj14_2,n+1,n+1,"pair:lj14_2"); + memory->create(lj14_3,n+1,n+1,"pair:lj14_3"); + memory->create(lj14_4,n+1,n+1,"pair:lj14_4"); +} + +/* ---------------------------------------------------------------------- + global settings + unlike other pair styles, + there are no individual pair settings that these override +------------------------------------------------------------------------- */ + +void PairLJCharmmCoulLongSoft::settings(int narg, char **arg) +{ + if (narg != 5 && narg != 6) error->all(FLERR,"Illegal pair_style command"); + + nlambda = force->numeric(FLERR,arg[0]); + alphalj = force->numeric(FLERR,arg[1]); + alphac = force->numeric(FLERR,arg[2]); + + cut_lj_inner = force->numeric(FLERR,arg[3]); + cut_lj = force->numeric(FLERR,arg[4]); + if (narg == 5) cut_coul = cut_lj; + else cut_coul = force->numeric(FLERR,arg[5]); +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairLJCharmmCoulLongSoft::coeff(int narg, char **arg) +{ + if (narg != 5 && narg != 7) error->all(FLERR,"Illegal pair_coeff command"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(arg[0],atom->ntypes,ilo,ihi); + force->bounds(arg[1],atom->ntypes,jlo,jhi); + + double epsilon_one = force->numeric(FLERR,arg[2]); + double sigma_one = force->numeric(FLERR,arg[3]); + double lambda_one = force->numeric(FLERR,arg[4]); + + double eps14_one = epsilon_one; + double sigma14_one = sigma_one; + if (narg == 7) { + eps14_one = force->numeric(FLERR,arg[5]); + sigma14_one = force->numeric(FLERR,arg[6]); + } + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + epsilon[i][j] = epsilon_one; + sigma[i][j] = sigma_one; + lambda[i][j] = lambda_one; + eps14[i][j] = eps14_one; + sigma14[i][j] = sigma14_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairLJCharmmCoulLongSoft::init_style() +{ + if (!atom->q_flag) + error->all(FLERR, + "Pair style lj/charmm/coul/long/soft requires atom attribute q"); + + // request regular or rRESPA neighbor lists + + int irequest; + + if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + int respa = 0; + if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; + if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; + + if (respa == 0) irequest = neighbor->request(this); + else if (respa == 1) { + irequest = neighbor->request(this); + neighbor->requests[irequest]->id = 1; + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->respainner = 1; + irequest = neighbor->request(this); + neighbor->requests[irequest]->id = 3; + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->respaouter = 1; + } else { + irequest = neighbor->request(this); + neighbor->requests[irequest]->id = 1; + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->respainner = 1; + irequest = neighbor->request(this); + neighbor->requests[irequest]->id = 2; + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->respamiddle = 1; + irequest = neighbor->request(this); + neighbor->requests[irequest]->id = 3; + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->respaouter = 1; + } + + } else irequest = neighbor->request(this); + + // require cut_lj_inner < cut_lj + + if (cut_lj_inner >= cut_lj) + error->all(FLERR,"Pair inner cutoff >= Pair outer cutoff"); + + cut_lj_innersq = cut_lj_inner * cut_lj_inner; + cut_ljsq = cut_lj * cut_lj; + cut_coulsq = cut_coul * cut_coul; + cut_bothsq = MAX(cut_ljsq,cut_coulsq); + + denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) * + (cut_ljsq-cut_lj_innersq); + + // set & error check interior rRESPA cutoffs + + if (strstr(update->integrate_style,"respa") && + ((Respa *) update->integrate)->level_inner >= 0) { + cut_respa = ((Respa *) update->integrate)->cutoff; + if (MIN(cut_lj,cut_coul) < cut_respa[3]) + error->all(FLERR,"Pair cutoff < Respa interior cutoff"); + if (cut_lj_inner < cut_respa[1]) + error->all(FLERR,"Pair inner cutoff < Respa interior cutoff"); + } else cut_respa = NULL; + + // insure use of KSpace long-range solver, set g_ewald + + if (force->kspace == NULL) + error->all(FLERR,"Pair style requires a KSpace style"); + g_ewald = force->kspace->g_ewald; +} + +/* ---------------------------------------------------------------------- + neighbor callback to inform pair style of neighbor list to use + regular or rRESPA +------------------------------------------------------------------------- */ + +void PairLJCharmmCoulLongSoft::init_list(int id, NeighList *ptr) +{ + if (id == 0) list = ptr; + else if (id == 1) listinner = ptr; + else if (id == 2) listmiddle = ptr; + else if (id == 3) listouter = ptr; +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairLJCharmmCoulLongSoft::init_one(int i, int j) +{ + if (setflag[i][j] == 0) { + epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j], + sigma[i][i],sigma[j][j]); + sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]); + if (lambda[i][i] != lambda[j][j]) + error->all(FLERR,"Pair lj/charmm/coul/long/soft different lambda values in mix"); + lambda[i][j] = lambda[i][i]; + eps14[i][j] = mix_energy(eps14[i][i],eps14[j][j], + sigma14[i][i],sigma14[j][j]); + sigma14[i][j] = mix_distance(sigma14[i][i],sigma14[j][j]); + } + + double cut = MAX(cut_lj,cut_coul); + + lj1[i][j] = pow(lambda[i][j], nlambda); + lj2[i][j] = pow(sigma[i][j], 6.0); + lj3[i][j] = alphalj * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]); + lj4[i][j] = alphac * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]); + + // 1-4 interactions unaffected (they're part of the dihedral term) + lj14_1[i][j] = 48.0 * eps14[i][j] * pow(sigma14[i][j],12.0); + lj14_2[i][j] = 24.0 * eps14[i][j] * pow(sigma14[i][j],6.0); + lj14_3[i][j] = 4.0 * eps14[i][j] * pow(sigma14[i][j],12.0); + lj14_4[i][j] = 4.0 * eps14[i][j] * pow(sigma14[i][j],6.0); + + epsilon[j][i] = epsilon[i][j]; + sigma[j][i] = sigma[i][j]; + lambda[j][i] = lambda[i][j]; + lj1[j][i] = lj1[i][j]; + lj2[j][i] = lj2[i][j]; + lj3[j][i] = lj3[i][j]; + lj4[j][i] = lj4[i][j]; + lj14_1[j][i] = lj14_1[i][j]; + lj14_2[j][i] = lj14_2[i][j]; + lj14_3[j][i] = lj14_3[i][j]; + lj14_4[j][i] = lj14_4[i][j]; + + return cut; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJCharmmCoulLongSoft::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + 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(&epsilon[i][j],sizeof(double),1,fp); + fwrite(&sigma[i][j],sizeof(double),1,fp); + fwrite(&lambda[i][j],sizeof(double),1,fp); + fwrite(&eps14[i][j],sizeof(double),1,fp); + fwrite(&sigma14[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairLJCharmmCoulLongSoft::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) 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) { + fread(&epsilon[i][j],sizeof(double),1,fp); + fread(&sigma[i][j],sizeof(double),1,fp); + fread(&lambda[i][j],sizeof(double),1,fp); + fread(&eps14[i][j],sizeof(double),1,fp); + fread(&sigma14[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&lambda[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&eps14[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&sigma14[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJCharmmCoulLongSoft::write_restart_settings(FILE *fp) +{ + fwrite(&nlambda,sizeof(double),1,fp); + fwrite(&alphalj,sizeof(double),1,fp); + fwrite(&alphac,sizeof(double),1,fp); + + fwrite(&cut_lj_inner,sizeof(double),1,fp); + fwrite(&cut_lj,sizeof(double),1,fp); + fwrite(&cut_coul,sizeof(double),1,fp); + fwrite(&offset_flag,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairLJCharmmCoulLongSoft::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&nlambda,sizeof(double),1,fp); + fread(&alphalj,sizeof(double),1,fp); + fread(&alphac,sizeof(double),1,fp); + + fread(&cut_lj_inner,sizeof(double),1,fp); + fread(&cut_lj,sizeof(double),1,fp); + fread(&cut_coul,sizeof(double),1,fp); + fread(&offset_flag,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + } + + MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world); + MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world); + MPI_Bcast(&alphac,1,MPI_DOUBLE,0,world); + + MPI_Bcast(&cut_lj_inner,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_lj,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); + MPI_Bcast(&offset_flag,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); +} + + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairLJCharmmCoulLongSoft::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g %g %g %g %g\n",i,epsilon[i][i],sigma[i][i], + lambda[i][i],eps14[i][i],sigma14[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairLJCharmmCoulLongSoft::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\n",i,j,epsilon[i][j],sigma[i][j], + lambda[i][j],eps14[i][j],sigma14[i][j]); +} + +/* ---------------------------------------------------------------------- */ + +double PairLJCharmmCoulLongSoft::single(int i, int j, int itype, int jtype, + double rsq, + double factor_coul, double factor_lj, + double &fforce) +{ + double r,grij,expm2,t,erfc,prefactor; + double switch1,switch2,forcecoul,forcelj,phicoul,philj; + double denc, denlj, r4sig6; + + if (rsq < cut_coulsq) { + r = sqrt(rsq); + grij = g_ewald * r; + expm2 = exp(-grij*grij); + t = 1.0 / (1.0 + EWALD_P*grij); + erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; + + denc = sqrt(lj4[itype][jtype] + rsq); + prefactor = force->qqrd2e * lj1[itype][jtype] * atom->q[i]*atom->q[j] / + (denc*denc*denc); + + forcecoul = prefactor * (erfc + EWALD_F*grij*expm2); + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor; + } else forcecoul = 0.0; + + if (rsq < cut_ljsq) { + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); + if (rsq > cut_lj_innersq) { + switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) * + (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; + switch2 = 12.0 * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj; + philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * + (1.0/(denlj*denlj) - 1.0/denlj); + forcelj = forcelj*switch1 + philj*switch2; + } + } else forcelj = 0.0; + fforce = forcecoul + factor_lj*forcelj; + + double eng = 0.0; + if (rsq < cut_coulsq) { + prefactor = force->qqrd2e * lj1[itype][jtype] * atom->q[i]*atom->q[j] / denc; + phicoul = prefactor*erfc; + if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor; + eng += phicoul; + } + + if (rsq < cut_ljsq) { + philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * + (1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype]; + if (rsq > cut_lj_innersq) { + switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) * + (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj; + philj *= switch1; + } + eng += factor_lj*philj; + } + + return eng; +} + +/* ---------------------------------------------------------------------- */ + +void *PairLJCharmmCoulLongSoft::extract(const char *str, int &dim) +{ + dim = 2; + if (strcmp(str,"lj14_1") == 0) return (void *) lj14_1; + if (strcmp(str,"lj14_2") == 0) return (void *) lj14_2; + if (strcmp(str,"lj14_3") == 0) return (void *) lj14_3; + if (strcmp(str,"lj14_4") == 0) return (void *) lj14_4; + + if (strcmp(str,"epsilon") == 0) return (void *) epsilon; + if (strcmp(str,"sigma") == 0) return (void *) sigma; + if (strcmp(str,"lambda") == 0) return (void *) lambda; + + dim = 0; + if (strcmp(str,"implicit") == 0) return (void *) &implicit; + if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul; + + return NULL; +} diff --git a/src/USER-FEP/pair_lj_charmm_coul_long_soft.h b/src/USER-FEP/pair_lj_charmm_coul_long_soft.h new file mode 100644 index 0000000000..7e52ec54b5 --- /dev/null +++ b/src/USER-FEP/pair_lj_charmm_coul_long_soft.h @@ -0,0 +1,107 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(lj/charmm/coul/long/soft,PairLJCharmmCoulLongSoft) + +#else + +#ifndef LMP_PAIR_LJ_CHARMM_COUL_LONG_SOFT_H +#define LMP_PAIR_LJ_CHARMM_COUL_LONG_SOFT_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairLJCharmmCoulLongSoft : public Pair { + public: + PairLJCharmmCoulLongSoft(class LAMMPS *); + virtual ~PairLJCharmmCoulLongSoft(); + + virtual void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + void init_style(); + void init_list(int, class NeighList *); + double init_one(int, int); + 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 double single(int, int, int, int, double, double, double, double &); + + void compute_inner(); + void compute_middle(); + virtual void compute_outer(int, int); + virtual void *extract(const char *, int &); + + protected: + int implicit; + double cut_lj_inner,cut_lj; + double cut_lj_innersq,cut_ljsq; + double cut_coul,cut_coulsq; + double cut_bothsq; + double denom_lj; + double **epsilon,**sigma,**eps14,**sigma14,**lambda; + double nlambda, alphalj, alphac; + double **lj1,**lj2,**lj3,**lj4,**offset; + double **lj14_1,**lj14_2,**lj14_3,**lj14_4; + double *cut_respa; + double g_ewald; + + void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair style lj/charmm/coul/long/soft requires atom attribute q + +The atom style defined does not have these attributes. + +E: Pair inner cutoff >= Pair outer cutoff + +The specified cutoffs for the pair style are inconsistent. + +E: Pair cutoff < Respa interior cutoff + +One or more pairwise cutoffs are too short to use with the specified +rRESPA cutoffs. + +E: Pair inner cutoff < Respa interior cutoff + +One or more pairwise cutoffs are too short to use with the specified +rRESPA cutoffs. + +E: Pair style requires a KSpace style + +No kspace style is defined. + +*/