diff --git a/src/MOLECULE/Install.sh b/src/MOLECULE/Install.sh index 58deb45525..5a30b0e86b 100644 --- a/src/MOLECULE/Install.sh +++ b/src/MOLECULE/Install.sh @@ -35,6 +35,7 @@ if (test $1 = 1) then cp pair_hbond_dreiding_morse.cpp .. cp pair_lj_charmm_coul_charmm.cpp .. cp pair_lj_charmm_coul_charmm_implicit.cpp .. + cp pair_lj_cut_tip4p_cut.cpp .. cp angle_charmm.h .. cp angle_cosine.h .. @@ -69,6 +70,7 @@ if (test $1 = 1) then cp pair_hbond_dreiding_morse.h .. cp pair_lj_charmm_coul_charmm.h .. cp pair_lj_charmm_coul_charmm_implicit.h .. + cp pair_lj_cut_tip4p_cut.h .. elif (test $1 = 0) then @@ -105,6 +107,7 @@ elif (test $1 = 0) then rm -f ../pair_hbond_dreiding_morse.cpp rm -f ../pair_lj_charmm_coul_charmm.cpp rm -f ../pair_lj_charmm_coul_charmm_implicit.cpp + rm -f ../pair_lj_cut_tip4p_cut.cpp rm -f ../angle_charmm.h rm -f ../angle_cosine.h @@ -139,5 +142,6 @@ elif (test $1 = 0) then rm -f ../pair_hbond_dreiding_morse.h rm -f ../pair_lj_charmm_coul_charmm.h rm -f ../pair_lj_charmm_coul_charmm_implicit.h + rm -f ../pair_lj_cut_tip4p_cut.h fi diff --git a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp new file mode 100644 index 0000000000..4bd52d293e --- /dev/null +++ b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp @@ -0,0 +1,669 @@ +/* ---------------------------------------------------------------------- + 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: Pavel Elkind (Gothenburg University) +------------------------------------------------------------------------- */ + +#include "math.h" +#include "stdlib.h" +#include "pair_lj_cut_tip4p_cut.h" +#include "atom.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "domain.h" +#include "angle.h" +#include "bond.h" +#include "comm.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +PairLJCutTIP4PCut::PairLJCutTIP4PCut(LAMMPS *lmp) : Pair(lmp) +{ + single_enable = 0; + + nmax = 0; + hneigh = NULL; + newsite = NULL; + + // TIP4P cannot compute virial as F dot r + // due to finding bonded H atoms which are not near O atom + + no_virial_fdotr_compute = 1; +} + +/* ---------------------------------------------------------------------- */ + +PairLJCutTIP4PCut::~PairLJCutTIP4PCut() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut_lj); + memory->destroy(cut_ljsq); + memory->destroy(epsilon); + memory->destroy(sigma); + memory->destroy(lj1); + memory->destroy(lj2); + memory->destroy(lj3); + memory->destroy(lj4); + memory->destroy(offset); + } + + memory->destroy(hneigh); + memory->destroy(newsite); +} + +/* ---------------------------------------------------------------------- */ + +void PairLJCutTIP4PCut::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul; + double rsq,r2inv,r6inv,forcecoul,forcelj,factor_lj,factor_coul; + int *ilist,*jlist,*numneigh,**firstneigh; + + int key; + int n,vlist[6]; + int iH1,iH2,jH1,jH2; + double cforce; + double fO[3],fH[3],fd[3],v[6],xH1[3],xH2[3]; + double *x1,*x2; + + evdwl = ecoul = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + // reallocate hneigh & newsite if necessary + // initialize hneigh[0] to -1 on steps when reneighboring occurred + // initialize hneigh[2] to 0 every step + + int nlocal = atom->nlocal; + int nall = nlocal + atom->nghost; + + if (atom->nmax > nmax) { + nmax = atom->nmax; + memory->destroy(hneigh); + memory->create(hneigh,nmax,3,"pair:hneigh"); + memory->destroy(newsite); + memory->create(newsite,nmax,3,"pair:newsite"); + } + if (neighbor->ago == 0) + for (i = 0; i < nall; i++) hneigh[i][0] = -1; + for (i = 0; i < nall; i++) hneigh[i][2] = 0; + + double **f = atom->f; + double **x = atom->x; + double *q = atom->q; + int *type = atom->type; + double *special_lj = force->special_lj; + double *special_coul = force->special_coul; + 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]; + + if (itype == typeO) { + if (hneigh[i][0] < 0) { + hneigh[i][0] = iH1 = atom->map(atom->tag[i] + 1); + hneigh[i][1] = iH2 = atom->map(atom->tag[i] + 2); + hneigh[i][2] = 1; + if (iH1 == -1 || iH2 == -1) + error->one(FLERR,"TIP4P hydrogen is missing"); + if (atom->type[iH1] != typeH || atom->type[iH2] != typeH) + error->one(FLERR,"TIP4P hydrogen has incorrect atom type"); + compute_newsite(x[i],x[iH1],x[iH2],newsite[i]); + } else { + iH1 = hneigh[i][0]; + iH2 = hneigh[i][1]; + if (hneigh[i][2] == 0) { + hneigh[i][2] = 1; + compute_newsite(x[i],x[iH1],x[iH2],newsite[i]); + } + } + x1 = newsite[i]; + } else x1 = x[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]; + + // LJ interaction based on true rsq + + if (rsq < cut_ljsq[itype][jtype]) { + r2inv = 1.0/rsq; + r6inv = r2inv*r2inv*r2inv; + forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); + forcelj *= factor_lj * r2inv; + + f[i][0] += delx*forcelj; + f[i][1] += dely*forcelj; + f[i][2] += delz*forcelj; + f[j][0] -= delx*forcelj; + f[j][1] -= dely*forcelj; + f[j][2] -= delz*forcelj; + + if (eflag) { + evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) - + offset[itype][jtype]; + evdwl *= factor_lj; + } else evdwl = 0.0; + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,0.0,forcelj,delx,dely,delz); + } + + // adjust rsq and delxyz for off-site O charge(s) if necessary + // but only if they are within reach + + if (rsq < cut_coulsqplus) { + if (itype == typeO || jtype == typeO) { + + // if atom J = water O, set x2 = offset charge site + // else x2 = x of atom J + + if (jtype == typeO) { + if (hneigh[j][0] < 0) { + hneigh[j][0] = jH1 = atom->map(atom->tag[j] + 1); + hneigh[j][1] = jH2 = atom->map(atom->tag[j] + 2); + hneigh[j][2] = 1; + if (jH1 == -1 || jH2 == -1) + error->one(FLERR,"TIP4P hydrogen is missing"); + if (atom->type[jH1] != typeH || atom->type[jH2] != typeH) + error->one(FLERR,"TIP4P hydrogen has incorrect atom type"); + compute_newsite(x[j],x[jH1],x[jH2],newsite[j]); + } else { + jH1 = hneigh[j][0]; + jH2 = hneigh[j][1]; + if (hneigh[j][2] == 0) { + hneigh[j][2] = 1; + compute_newsite(x[j],x[jH1],x[jH2],newsite[j]); + } + } + x2 = newsite[j]; + } else x2 = x[j]; + + delx = x1[0] - x2[0]; + dely = x1[1] - x2[1]; + delz = x1[2] - x2[2]; + rsq = delx*delx + dely*dely + delz*delz; + } + + // Coulombic interaction based on modified rsq + + if (rsq < cut_coulsq) { + r2inv = 1.0 / rsq; + forcecoul = qqrd2e * qtmp * q[j] * sqrt(r2inv); + cforce = factor_coul * forcecoul * r2inv; + + // if i,j are not O atoms, force is applied directly; + // if i or j are O atoms, force is on fictitious atom & partitioned + // force partitioning due to Feenstra, J Comp Chem, 20, 786 (1999) + // f_f = fictitious force, fO = f_f (1 - 2 alpha), fH = alpha f_f + // preserves total force and torque on water molecule + // virial = sum(r x F) where each water's atoms are near xi and xj + // vlist stores 2,4,6 atoms whose forces contribute to virial + + n = 0; + key = 0; + + if (itype != typeO) { + f[i][0] += delx * cforce; + f[i][1] += dely * cforce; + f[i][2] += delz * cforce; + + if (vflag) { + v[0] = x[i][0] * delx * cforce; + v[1] = x[i][1] * dely * cforce; + v[2] = x[i][2] * delz * cforce; + v[3] = x[i][0] * dely * cforce; + v[4] = x[i][0] * delz * cforce; + v[5] = x[i][1] * delz * cforce; + } + vlist[n++] = i; + + } else { + key++; + + fd[0] = delx*cforce; + fd[1] = dely*cforce; + fd[2] = delz*cforce; + + fO[0] = fd[0]*(1.0 - alpha); + fO[1] = fd[1]*(1.0 - alpha); + fO[2] = fd[2]*(1.0 - alpha); + + fH[0] = 0.5 * alpha * fd[0]; + fH[1] = 0.5 * alpha * fd[1]; + fH[2] = 0.5 * alpha * fd[2]; + + f[i][0] += fO[0]; + f[i][1] += fO[1]; + f[i][2] += fO[2]; + + f[iH1][0] += fH[0]; + f[iH1][1] += fH[1]; + f[iH1][2] += fH[2]; + + f[iH2][0] += fH[0]; + f[iH2][1] += fH[1]; + f[iH2][2] += fH[2]; + + if(vflag) { + domain->closest_image(x[i],x[iH1],xH1); + domain->closest_image(x[i],x[iH2],xH2); + + v[0] = x[i][0]*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0]; + v[1] = x[i][1]*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1]; + v[2] = x[i][2]*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2]; + v[3] = x[i][0]*fO[1] + xH1[0]*fH[1] + xH2[0]*fH[1]; + v[4] = x[i][0]*fO[2] + xH1[0]*fH[2] + xH2[0]*fH[2]; + v[5] = x[i][1]*fO[2] + xH1[1]*fH[2] + xH2[1]*fH[2]; + } + vlist[n++] = i; + vlist[n++] = iH1; + vlist[n++] = iH2; + } + + if (jtype != typeO) { + f[j][0] -= delx * cforce; + f[j][1] -= dely * cforce; + f[j][2] -= delz * cforce; + + if (vflag) { + v[0] -= x[j][0] * delx * cforce; + v[1] -= x[j][1] * dely * cforce; + v[2] -= x[j][2] * delz * cforce; + v[3] -= x[j][0] * dely * cforce; + v[4] -= x[j][0] * delz * cforce; + v[5] -= x[j][1] * delz * cforce; + } + vlist[n++] = j; + + } else { + key += 2; + + fd[0] = -delx*cforce; + fd[1] = -dely*cforce; + fd[2] = -delz*cforce; + + fO[0] = fd[0]*(1 - alpha); + fO[1] = fd[1]*(1 - alpha); + fO[2] = fd[2]*(1 - alpha); + + fH[0] = 0.5 * alpha * fd[0]; + fH[1] = 0.5 * alpha * fd[1]; + fH[2] = 0.5 * alpha * fd[2]; + + f[j][0] += fO[0]; + f[j][1] += fO[1]; + f[j][2] += fO[2]; + + f[jH1][0] += fH[0]; + f[jH1][1] += fH[1]; + f[jH1][2] += fH[2]; + + f[jH2][0] += fH[0]; + f[jH2][1] += fH[1]; + f[jH2][2] += fH[2]; + + if (vflag) { + domain->closest_image(x[j],x[jH1],xH1); + domain->closest_image(x[j],x[jH2],xH2); + + v[0] += x[j][0]*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0]; + v[1] += x[j][1]*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1]; + v[2] += x[j][2]*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2]; + v[3] += x[j][0]*fO[1] + xH1[0]*fH[1] + xH2[0]*fH[1]; + v[4] += x[j][0]*fO[2] + xH1[0]*fH[2] + xH2[0]*fH[2]; + v[5] += x[j][1]*fO[2] + xH1[1]*fH[2] + xH2[1]*fH[2]; + } + vlist[n++] = j; + vlist[n++] = jH1; + vlist[n++] = jH2; + } + + if (eflag) { + ecoul = qqrd2e * qtmp * q[j] * sqrt(r2inv); + ecoul *= factor_coul; + } else ecoul = 0.0; + + if (evflag) ev_tally_tip4p(key,vlist,v,ecoul,alpha); + } + } + } + } +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairLJCutTIP4PCut::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(cut_lj,n+1,n+1,"pair:cut_lj"); + memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq"); + memory->create(epsilon,n+1,n+1,"pair:epsilon"); + memory->create(sigma,n+1,n+1,"pair:sigma"); + 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(offset,n+1,n+1,"pair:offset"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairLJCutTIP4PCut::settings(int narg, char **arg) +{ + if (narg != 7) error->all(FLERR,"Illegal pair_style command"); + + typeO = force->inumeric(arg[0]); + typeH = force->inumeric(arg[1]); + typeB = force->inumeric(arg[2]); + typeA = force->inumeric(arg[3]); + qdist = force->numeric(arg[4]); + + cut_lj_global = force->numeric(arg[5]); + cut_coul = force->numeric(arg[6]); + cut_coulsq = cut_coul * cut_coul; + cut_coulsqplus = (cut_coul + 2.0*qdist) * (cut_coul + 2.0*qdist); + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i+1; j <= atom->ntypes; j++) + if (setflag[i][j]) cut_lj[i][j] = cut_lj_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairLJCutTIP4PCut::coeff(int narg, char **arg) +{ + if (narg != 4) error->all(FLERR,"Incorrect args for pair coefficients"); + 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(arg[2]); + double sigma_one = force->numeric(arg[3]); + + 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; + cut_lj[i][j] = cut_lj_global; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairLJCutTIP4PCut::init_style() +{ + if (atom->tag_enable == 0) + error->all(FLERR,"Pair style lj/cut/coul/cut/tip4p requires atom IDs"); + if (!force->newton_pair) + error->all(FLERR, + "Pair style lj/cut/coul/cut/tip4p requires newton pair on"); + if (!atom->q_flag) + error->all(FLERR, + "Pair style lj/cut/coul/cut/tip4p requires atom attribute q"); + if (force->bond == NULL) + error->all(FLERR,"Must use a bond style with TIP4P potential"); + if (force->angle == NULL) + error->all(FLERR,"Must use an angle style with TIP4P potential"); + + neighbor->request(this); + + // set alpha parameter + + double theta = force->angle->equilibrium_angle(typeA); + double blen = force->bond->equilibrium_distance(typeB); + alpha = qdist / (cos(0.5*theta) * blen); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairLJCutTIP4PCut::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]); + cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]); + } + + // include TIP4P qdist in full cutoff, qdist = 0.0 if not TIP4P + + double cut = MAX(cut_lj[i][j],cut_coul+2.0*qdist); + cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j]; + + lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0); + lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0); + lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0); + lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0); + + if (offset_flag) { + double ratio = sigma[i][j] / cut_lj[i][j]; + offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0)); + } else offset[i][j] = 0.0; + + cut_ljsq[j][i] = cut_ljsq[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]; + offset[j][i] = offset[i][j]; + + // check that LJ epsilon = 0.0 for water H + // set LJ cutoff to 0.0 for any interaction involving water H + // so LJ term isn't calculated in compute() + + if ((i == typeH && epsilon[i][i] != 0.0) || + (j == typeH && epsilon[j][j] != 0.0)) + error->all(FLERR,"Water H epsilon must be 0.0 for " + "pair style lj/cut/coul/long/tip4p"); + + if (i == typeH || j == typeH) + cut_ljsq[j][i] = cut_ljsq[i][j] = 0.0; + + return cut; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJCutTIP4PCut::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(&cut_lj[i][j],sizeof(double),1,fp); + } + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairLJCutTIP4PCut::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(&cut_lj[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(&cut_lj[i][j],1,MPI_DOUBLE,0,world); + } + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJCutTIP4PCut::write_restart_settings(FILE *fp) +{ + fwrite(&typeO,sizeof(int),1,fp); + fwrite(&typeH,sizeof(int),1,fp); + fwrite(&typeB,sizeof(int),1,fp); + fwrite(&typeA,sizeof(int),1,fp); + fwrite(&qdist,sizeof(double),1,fp); + fwrite(&cut_lj_global,sizeof(double),1,fp); + fwrite(&cut_coul,sizeof(double),1,fp); + fwrite(&cut_coulsq,sizeof(double),1,fp); + fwrite(&cut_coulsqplus,sizeof(double),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairLJCutTIP4PCut::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&typeO,sizeof(int),1,fp); + fread(&typeH,sizeof(int),1,fp); + fread(&typeB,sizeof(int),1,fp); + fread(&typeA,sizeof(int),1,fp); + fread(&qdist,sizeof(double),1,fp); + fread(&cut_lj_global,sizeof(double),1,fp); + fread(&cut_coul,sizeof(double),1,fp); + fread(&cut_coulsq,sizeof(double),1,fp); + fread(&cut_coulsqplus,sizeof(double),1,fp); + } + + MPI_Bcast(&typeO,1,MPI_INT,0,world); + MPI_Bcast(&typeH,1,MPI_INT,0,world); + MPI_Bcast(&typeB,1,MPI_INT,0,world); + MPI_Bcast(&typeA,1,MPI_INT,0,world); + MPI_Bcast(&qdist,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_coulsq,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_coulsqplus,1,MPI_DOUBLE,0,world); +} + +/* ---------------------------------------------------------------------- + compute position xM of fictitious charge site for O atom and 2 H atoms + return it as xM +------------------------------------------------------------------------- */ + +void PairLJCutTIP4PCut::compute_newsite(double *xO, double *xH1, + double *xH2, double *xM) +{ + double delx1 = xH1[0] - xO[0]; + double dely1 = xH1[1] - xO[1]; + double delz1 = xH1[2] - xO[2]; + domain->minimum_image(delx1,dely1,delz1); + + double delx2 = xH2[0] - xO[0]; + double dely2 = xH2[1] - xO[1]; + double delz2 = xH2[2] - xO[2]; + domain->minimum_image(delx2,dely2,delz2); + + xM[0] = xO[0] + alpha * 0.5 * (delx1 + delx2); + xM[1] = xO[1] + alpha * 0.5 * (dely1 + dely2); + xM[2] = xO[2] + alpha * 0.5 * (delz1 + delz2); +} + +/* ---------------------------------------------------------------------- + memory usage of hneigh +------------------------------------------------------------------------- */ + +double PairLJCutTIP4PCut::memory_usage() +{ + double bytes = maxeatom * sizeof(double); + bytes += maxvatom*6 * sizeof(double); + bytes += 2 * nmax * sizeof(double); + return bytes; +} diff --git a/src/MOLECULE/pair_lj_cut_tip4p_cut.h b/src/MOLECULE/pair_lj_cut_tip4p_cut.h new file mode 100644 index 0000000000..5aaacbed78 --- /dev/null +++ b/src/MOLECULE/pair_lj_cut_tip4p_cut.h @@ -0,0 +1,66 @@ +/* ---------------------------------------------------------------------- + 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/cut/tip4p/cut,PairLJCutTIP4PCut) + +#else + +#ifndef LMP_PAIR_LJ_CUT_TIP4P_CUT_H +#define LMP_PAIR_LJ_CUT_TIP4P_CUT_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairLJCutTIP4PCut : public Pair { + public: + PairLJCutTIP4PCut(class LAMMPS *); + virtual ~PairLJCutTIP4PCut(); + virtual void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + void init_style(); + double init_one(int, int); + virtual void write_restart_settings(FILE *); + virtual void read_restart_settings(FILE *); + void write_restart(FILE *); + void read_restart(FILE *); + double memory_usage(); + + protected: + double cut_lj_global,cut_coul_global; + double cut_coul,cut_coulsq; + double cut_coulsqplus; // extended value for cut_coulsq + double **cut_lj,**cut_ljsq; + double **epsilon,**sigma; + double **lj1,**lj2,**lj3,**lj4,**offset; + + int typeH,typeO; // atom types of TIP4P water H and O atoms + int typeA,typeB; // angle and bond types of TIP4P water + double alpha; // geometric constraint parameter for TIP4P + double qdist; + + int nmax; // info on off-oxygen charge sites + int **hneigh; // 0,1 = indices of 2 H associated with O + // 2 = 0 if site loc not yet computed, 1 if yes + double **newsite; // locations of charge sites + + void allocate(); + void compute_newsite(double *, double *, double *, double *); +}; +} + +#endif +#endif