forked from lijiext/lammps
import updated pair lj/sf/dipole/sf files from sam genheden
(cherry picked from commit ae691ab786)
This commit is contained in:
Axel Kohlmeyer
parent
c3e8cb2f30
commit
8b1ef1c686
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@ -12,7 +12,8 @@
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Mario Orsi (U Southampton), orsimario@gmail.com
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Contributing authors: Mario Orsi (QMUL), m.orsi@qmul.ac.uk
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Samuel Genheden (University of Southampton)
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------------------------------------------------------------------------- */
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#include <math.h>
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@ -34,7 +35,6 @@ using namespace LAMMPS_NS;
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PairLJSFDipoleSF::PairLJSFDipoleSF(LAMMPS *lmp) : Pair(lmp)
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{
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single_enable = 0;
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}
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/* ---------------------------------------------------------------------- */
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@ -55,6 +55,7 @@ PairLJSFDipoleSF::~PairLJSFDipoleSF()
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memory->destroy(lj2);
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memory->destroy(lj3);
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memory->destroy(lj4);
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memory->destroy(scale);
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}
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}
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@ -86,6 +87,7 @@ void PairLJSFDipoleSF::compute(int eflag, int vflag)
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double **torque = atom->torque;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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// The global scaling parameters aren't used anymore
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double *special_coul = force->special_coul;
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double *special_lj = force->special_lj;
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int newton_pair = force->newton_pair;
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@ -234,7 +236,7 @@ void PairLJSFDipoleSF::compute(int eflag, int vflag)
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// total force
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fq = factor_coul*qqrd2e;
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fq = factor_coul*qqrd2e*scale[itype][jtype];
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fx = fq*forcecoulx + delx*forcelj;
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fy = fq*forcecouly + dely*forcelj;
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fz = fq*forcecoulz + delz*forcelj;
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@ -268,7 +270,7 @@ void PairLJSFDipoleSF::compute(int eflag, int vflag)
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ecoul += -q[j] * r3inv * pqfac * pidotr;
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if (mu[j][3] > 0.0 && qtmp != 0.0)
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ecoul += qtmp * r3inv * qpfac * pjdotr;
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ecoul *= factor_coul*qqrd2e;
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ecoul *= factor_coul*qqrd2e*scale[itype][jtype];
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} else ecoul = 0.0;
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if (rsq < cut_ljsq[itype][jtype]) {
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@ -315,6 +317,7 @@ void PairLJSFDipoleSF::allocate()
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memory->create(lj2,n+1,n+1,"pair:lj2");
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memory->create(lj3,n+1,n+1,"pair:lj3");
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memory->create(lj4,n+1,n+1,"pair:lj4");
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memory->create(scale,n+1,n+1,"pair:scale");
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}
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/* ----------------------------------------------------------------------
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@ -352,7 +355,7 @@ void PairLJSFDipoleSF::settings(int narg, char **arg)
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void PairLJSFDipoleSF::coeff(int narg, char **arg)
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{
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if (narg < 4 || narg > 6)
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if (narg < 4 || narg > 7)
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error->all(FLERR,"Incorrect args for pair coefficients");
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if (!allocated) allocate();
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@ -363,10 +366,13 @@ void PairLJSFDipoleSF::coeff(int narg, char **arg)
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double epsilon_one = force->numeric(FLERR,arg[2]);
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double sigma_one = force->numeric(FLERR,arg[3]);
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double scale_one = 1.0;
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if (narg >= 5) scale_one = force->numeric(FLERR,arg[4]);
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double cut_lj_one = cut_lj_global;
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double cut_coul_one = cut_coul_global;
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if (narg >= 5) cut_coul_one = cut_lj_one = force->numeric(FLERR,arg[4]);
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if (narg == 6) cut_coul_one = force->numeric(FLERR,arg[5]);
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if (narg >= 6) cut_coul_one = cut_lj_one = force->numeric(FLERR,arg[5]);
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if (narg == 7) cut_coul_one = force->numeric(FLERR,arg[6]);
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int count = 0;
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for (int i = ilo; i <= ihi; i++) {
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@ -376,6 +382,7 @@ void PairLJSFDipoleSF::coeff(int narg, char **arg)
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cut_lj[i][j] = cut_lj_one;
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cut_coul[i][j] = cut_coul_one;
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setflag[i][j] = 1;
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scale[i][j] = scale_one;
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count++;
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}
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}
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@ -424,6 +431,7 @@ double PairLJSFDipoleSF::init_one(int i, int j)
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lj2[j][i] = lj2[i][j];
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lj3[j][i] = lj3[i][j];
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lj4[j][i] = lj4[i][j];
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scale[j][i] = scale[i][j];
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return cut;
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}
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@ -445,6 +453,7 @@ void PairLJSFDipoleSF::write_restart(FILE *fp)
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fwrite(&sigma[i][j],sizeof(double),1,fp);
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fwrite(&cut_lj[i][j],sizeof(double),1,fp);
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fwrite(&cut_coul[i][j],sizeof(double),1,fp);
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fwrite(&scale[i][j],sizeof(double),1,fp);
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}
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}
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}
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@ -471,11 +480,13 @@ void PairLJSFDipoleSF::read_restart(FILE *fp)
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fread(&sigma[i][j],sizeof(double),1,fp);
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fread(&cut_lj[i][j],sizeof(double),1,fp);
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fread(&cut_coul[i][j],sizeof(double),1,fp);
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fread(&scale[i][j],sizeof(double),1,fp);
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}
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MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&scale[i][j],1,MPI_DOUBLE,0,world);
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}
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}
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}
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@ -506,3 +517,105 @@ void PairLJSFDipoleSF::read_restart_settings(FILE *fp)
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MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world);
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MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
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}
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// PairLJSFDipoleSF: calculation of force is missing (to be implemented)
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double PairLJSFDipoleSF::single(int i, int j, int itype, int jtype, double rsq,
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double factor_coul, double factor_lj,
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double &fforce)
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{
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double r2inv,r6inv;
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double pdotp,pidotr,pjdotr,pre1,delx,dely,delz;
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double rinv, r3inv,r5inv, rcutlj2inv, rcutcoul2inv,rcutlj6inv;
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double qtmp,xtmp,ytmp,ztmp,bfac,pqfac,qpfac, ecoul, evdwl;
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double **x = atom->x;
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double *q = atom->q;
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double **mu = atom->mu;
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qtmp = q[i];
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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r2inv = 1.0/rsq;
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rinv = sqrt(r2inv);
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fforce = 0.0;
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if (rsq < cut_coulsq[itype][jtype]) {
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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// if (qtmp != 0.0 && q[j] != 0.0) {
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// pre1 = qtmp*q[j]*rinv*(r2inv-1.0/cut_coulsq[itype][jtype]);
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// forcecoulx += pre1*delx;
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// forcecouly += pre1*dely;
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// forcecoulz += pre1*delz;
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// }
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if (mu[i][3] > 0.0 && mu[j][3] > 0.0) {
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r3inv = r2inv*rinv;
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r5inv = r3inv*r2inv;
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rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
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pdotp = mu[i][0]*mu[j][0] + mu[i][1]*mu[j][1] + mu[i][2]*mu[j][2];
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pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
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pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
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bfac = 1.0 - 4.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv) +
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3.0*rsq*rsq*rcutcoul2inv*rcutcoul2inv;
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}
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if (mu[i][3] > 0.0 && q[j] != 0.0) {
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r3inv = r2inv*rinv;
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r5inv = r3inv*r2inv;
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pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
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rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
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pqfac = 1.0 - 3.0*rsq*rcutcoul2inv +
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2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
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}
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if (mu[j][3] > 0.0 && qtmp != 0.0) {
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r3inv = r2inv*rinv;
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r5inv = r3inv*r2inv;
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pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
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rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
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qpfac = 1.0 - 3.0*rsq*rcutcoul2inv +
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2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
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}
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}
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if (rsq < cut_ljsq[itype][jtype]) {
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r6inv = r2inv*r2inv*r2inv;
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rcutlj2inv = 1.0 / cut_ljsq[itype][jtype];
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rcutlj6inv = rcutlj2inv * rcutlj2inv * rcutlj2inv;
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}
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double eng = 0.0;
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if (rsq < cut_coulsq[itype][jtype]) {
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ecoul = (1.0-sqrt(rsq)/sqrt(cut_coulsq[itype][jtype]));
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ecoul *= ecoul;
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ecoul *= qtmp * q[j] * rinv;
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if (mu[i][3] > 0.0 && mu[j][3] > 0.0)
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ecoul += bfac * (r3inv*pdotp - 3.0*r5inv*pidotr*pjdotr);
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if (mu[i][3] > 0.0 && q[j] != 0.0)
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ecoul += -q[j] * r3inv * pqfac * pidotr;
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if (mu[j][3] > 0.0 && qtmp != 0.0)
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ecoul += qtmp * r3inv * qpfac * pjdotr;
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ecoul *= factor_coul*force->qqrd2e*scale[itype][jtype];
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eng += ecoul;
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}
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if (rsq < cut_ljsq[itype][jtype]) {
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evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype])+
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rcutlj6inv*(6*lj3[itype][jtype]*rcutlj6inv-3*lj4[itype][jtype])*
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rsq*rcutlj2inv+
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rcutlj6inv*(-7*lj3[itype][jtype]*rcutlj6inv+4*lj4[itype][jtype]);
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eng += evdwl*factor_lj;
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}
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return eng;
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}
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/* ---------------------------------------------------------------------- */
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void *PairLJSFDipoleSF::extract(const char *str, int &dim)
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{
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dim = 2;
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if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
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if (strcmp(str,"sigma") == 0) return (void *) sigma;
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if (strcmp(str,"scale") == 0) return (void *) scale;
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return NULL;
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}
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@ -1,4 +1,4 @@
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/* -*- c++ -*- ----------------------------------------------------------
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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@ -37,6 +37,8 @@ class PairLJSFDipoleSF : public Pair {
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void read_restart(FILE *);
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void write_restart_settings(FILE *);
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void read_restart_settings(FILE *);
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virtual double single(int, int, int, int, double, double, double, double &);
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void *extract(const char *, int &);
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protected:
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double cut_lj_global,cut_coul_global;
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@ -44,6 +46,7 @@ class PairLJSFDipoleSF : public Pair {
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double **cut_coul,**cut_coulsq;
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double **epsilon,**sigma;
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double **lj1,**lj2,**lj3,**lj4;
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double **scale;
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void allocate();
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};
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