forked from lijiext/lammps
Clean up comments
This commit is contained in:
Mingjian Wen
parent
d6f3a95599
commit
16bb8a1439
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@ -41,49 +41,41 @@ using namespace LAMMPS_NS;
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#define MAXLINE 1024
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#define DELTA 4
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#define PGDELTA 1
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#define HALF 0.5
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/* ---------------------------------------------------------------------- */
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PairDRIP::PairDRIP(LAMMPS *lmp) : Pair(lmp)
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{
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// initialize element to parameter maps
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single_enable = 0;
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nelements = 0;
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elements = NULL;
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nparams = maxparam = 0;
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restartinfo = 0;
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params = NULL;
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nearest3neigh = NULL;
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elements = NULL;
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elem2param = NULL;
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map = NULL;
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nelements = 0;
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cutmax = 0.0;
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//j nmax = 0;
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//j maxlocal = 0;
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//j ipage = NULL;
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//j pgsize = oneatom = 0;
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nearest3neigh = NULL;
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}
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/* ---------------------------------------------------------------------- */
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PairDRIP::~PairDRIP()
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{
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// delete [] ipage;
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(cutsq);
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delete [] map;
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}
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if (elements)
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if (elements != NULL) {
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for (int i = 0; i < nelements; i++) delete [] elements[i];
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delete [] elements;
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delete [] elements;
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elements = NULL;
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}
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memory->destroy(params);
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memory->destroy(elem2param);
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if (allocated) delete [] map;
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memory->destroy(nearest3neigh);
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}
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@ -99,7 +91,6 @@ void PairDRIP::init_style()
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error->all(FLERR,"Pair style drip requires atom attribute molecule");
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// need a full neighbor list, including neighbors of ghosts
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int irequest = neighbor->request(this,instance_me);
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neighbor->requests[irequest]->half = 0;
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neighbor->requests[irequest]->full = 1;
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@ -181,7 +172,6 @@ void PairDRIP::coeff(int narg, char **arg)
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}
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}
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read_file(arg[2]);
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int count = 0;
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@ -216,8 +206,8 @@ void PairDRIP::read_file(char *filename)
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int params_per_line = 14;
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char **words = new char*[params_per_line+1];
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memory->sfree(params);
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params = NULL;
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nparams = maxparam = 0;
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int nparams = 0;
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int maxparam = 0;
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// open file on proc 0
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@ -326,9 +316,7 @@ void PairDRIP::read_file(char *filename)
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// set max cutoff
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if(params[nparams].rcut > cutmax) cutmax = params[nparams].rcut;
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nparams++;
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//if(nparams >= pow(atom->ntypes,3)) break;
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}
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memory->destroy(elem2param);
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@ -353,18 +341,15 @@ void PairDRIP::read_file(char *filename)
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void PairDRIP::compute(int eflag, int vflag)
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{
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int i,j,ii,jj,inum,jnum,itype,jtype,k,l,kk,ll;
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tagint itag,jtag;
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double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,fpair1,fpair2, r, rsq;
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double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,r,rsq;
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int *ilist,*jlist,*numneigh,**firstneigh;
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double ni[DIM];
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double dni_dri[DIM][DIM], dni_drnb1[DIM][DIM];
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double dni_drnb2[DIM][DIM], dni_drnb3[DIM][DIM];
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evdwl = 0.0;
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ev_init(eflag,vflag);
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double **x = atom->x;
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@ -381,7 +366,6 @@ void PairDRIP::compute(int eflag, int vflag)
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find_nearest3neigh();
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// loop over neighbors of my atoms
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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itag = tag[i];
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@ -392,8 +376,7 @@ void PairDRIP::compute(int eflag, int vflag)
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jlist = firstneigh[i];
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jnum = numneigh[i];
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// normal and its derivatives w.r.t. atom i and its 3 nearest neighs
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// normal and its derivatives w.r.t. atom i and its 3 nearest neighbors
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calc_normal(i, ni, dni_dri,dni_drnb1, dni_drnb2, dni_drnb3);
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double fi[DIM] = {0., 0., 0.};
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@ -412,7 +395,6 @@ void PairDRIP::compute(int eflag, int vflag)
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Param& p = params[iparam_ij];
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double rcutsq = p.rcutsq;
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// only include the interation between different layers
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if (rsq < rcutsq && atom->molecule[i] != atom->molecule[j]) {
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@ -425,13 +407,14 @@ void PairDRIP::compute(int eflag, int vflag)
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ni, dni_dri, dni_drnb1, dni_drnb2, dni_drnb3, fi, fj);
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if (eflag) evdwl = HALF * (phi_repul + phi_attr);
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else evdwl = 0.0;
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if (evflag) ev_tally(i,j,nlocal,newton_pair, evdwl,0.0,0,0,0,0);
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f[j][0] += fj[0];
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f[j][1] += fj[1];
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f[j][2] += fj[2];
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// *2 since v_tally has a 0.5 coeff
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// multiply 2 since v_tally has a 0.5 coeff
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fj[0] *= 2; fj[1] *= 2; fj[2] *= 2;
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if (vflag_atom) v_tally(j, fj, x[j]);
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@ -442,7 +425,7 @@ void PairDRIP::compute(int eflag, int vflag)
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f[i][1] += fi[1];
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f[i][2] += fi[2];
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// *2 since v_tally has a 0.5 coeff
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// multiply 2 since v_tally has a 0.5 coeff
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fi[0] *= 2; fi[1] *= 2; fi[2] *= 2;
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if (vflag_atom) v_tally(i, fi, x[i]);
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@ -452,45 +435,15 @@ void PairDRIP::compute(int eflag, int vflag)
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if (vflag_fdotr)
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virial_fdotr_compute();
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printf("@@@ evflags in compute\n");
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printf("@@@ eflag_either=%d\n", eflag_either);
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printf("@@@ eflag_global=%d\n", eflag_global);
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printf("@@@ eflag_atom=%d\n", eflag_atom);
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printf("@@@ vflag_either=%d\n", vflag_either);
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printf("@@@ vflag_global=%d\n", vflag_global);
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printf("@@@ vflag_atom=%d\n", vflag_atom);
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printf("@@@ vflag_fdotr=%d\n", vflag_fdotr);
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printf("@@@@@@@@@@@@@@@@@@@@@@@ virial\n");
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printf("%f, %f, %f, %f, %f, %f\n", virial[0], virial[1], virial[2], virial[3], virial[4], virial[5]);
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printf("@@@@@@@@@@@@@@@@@@@@@@@ virial fdotr\n");
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virial[0]= virial[1]= virial[2]= virial[3]= virial[4]= virial[5]=0.;
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virial_fdotr_compute();
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printf("%f, %f, %f, %f, %f, %f\n", virial[0], virial[1], virial[2], virial[3], virial[4], virial[5]);
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printf("@@@@@@@@@@@@@@@@@@@@@@@ virial from atom virial\n");
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int allnum = list->inum + list->gnum;
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double v[6] = {0., 0., 0., 0., 0., 0.};
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for (int kk=0; kk<allnum; kk++) {
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for (int kkk=0; kkk<6; kkk++) {
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v[kkk] += vatom[kk][kkk];
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}
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}
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printf("%f, %f, %f, %f, %f, %f\n", v[0], v[1], v[2], v[3], v[4], v[5]);
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printf("@@@@@@@@@@@@@@@@@@@@@@@ leave compute\n");
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}
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/* ---------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Attractive part, i.e. the r^(-6) part
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------------------------------------------------------------------------- */
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double PairDRIP::calc_attractive(int const i, int const j, Param& p,
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double const rsq, double const * rvec, double * const fi, double * const fj)
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double const rsq, double const * rvec,
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double * const fi, double * const fj)
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{
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double const z0 = p.z0;
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double const A = p.A;
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@ -515,8 +468,10 @@ double PairDRIP::calc_attractive(int const i, int const j, Param& p,
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return phi;
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}
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/* ----------------------------------------------------------------------
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Repulsive part that depends on transverse distance and dihedral angle
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------------------------------------------------------------------------- */
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/* ---------------------------------------------------------------------- */
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double PairDRIP::calc_repulsive(int const i, int const j,
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Param& p, double const rsq, double const * rvec,
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double const * ni, V3 const * dni_dri, V3 const * dni_drnb1,
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@ -526,7 +481,6 @@ double PairDRIP::calc_repulsive(int const i, int const j,
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double **f = atom->f;
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double **x = atom->x;
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// params
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double C0 = p.C0;
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double C2 = p.C2;
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double C4 = p.C4;
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@ -544,8 +498,6 @@ double PairDRIP::calc_repulsive(int const i, int const j,
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int nbj2 = nearest3neigh[j][1];
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int nbj3 = nearest3neigh[j][2];
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double r = sqrt(rsq);
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double fnbi1[DIM];
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double fnbi2[DIM];
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double fnbi3[DIM];
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@ -566,9 +518,9 @@ double PairDRIP::calc_repulsive(int const i, int const j,
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V3 drhosqij_drnb2;
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V3 drhosqij_drnb3;
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double r = sqrt(rsq);
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// derivative of rhosq w.r.t coordinates of atoms i, j, and the nearests 3
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// neighs of i
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// derivative of rhosq w.r.t. atoms i j and the nearests 3 neighs of i
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get_drhosqij(rvec, ni, dni_dri, dni_drnb1, dni_drnb2, dni_drnb3, drhosqij_dri,
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drhosqij_drj, drhosqij_drnb1, drhosqij_drnb2, drhosqij_drnb3);
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@ -588,10 +540,11 @@ double PairDRIP::calc_repulsive(int const i, int const j,
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double dtp;
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double tp = tap(r, cutoff, dtp);
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/* exponential part */
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// exponential part
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double V1 = exp(-lambda * (r - z0));
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double dV1 = -V1 * lambda;
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// total energy
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double phi = tp * V1 * V2;
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for (int k = 0; k < DIM; k++) {
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@ -601,16 +554,15 @@ double PairDRIP::calc_repulsive(int const i, int const j,
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fi[k] += tmp;
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fj[k] -= tmp;
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// the following incldue the transverse decay part tdij and the dihedral part gij
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// contributions from the transverse decay part tdij and the dihedral part gij
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// derivative of V2 contribute to atoms i, j
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fi[k] -= HALF * tp * V1 * ((dtdij + dgij_drhosq) * drhosqij_dri[k] + dgij_dri[k]);
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fj[k] -= HALF * tp * V1 * ((dtdij + dgij_drhosq) * drhosqij_drj[k] + dgij_drj[k]);
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// derivative of V2 contribute to nearest 3 neighs of atom i
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fnbi1[k] =- HALF * tp * V1 * ((dtdij + dgij_drhosq) * drhosqij_drnb1[k] + dgij_drk1[k]);
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fnbi2[k] =- HALF * tp * V1 * ((dtdij + dgij_drhosq) * drhosqij_drnb2[k] + dgij_drk2[k]);
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fnbi3[k] =- HALF * tp * V1 * ((dtdij + dgij_drhosq) * drhosqij_drnb3[k] + dgij_drk3[k]);
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// derivative of V2 contribute to nearest 3 neighs of atom j
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fnbj1[k] =- HALF * tp * V1 * dgij_drl1[k];
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fnbj2[k] =- HALF * tp * V1 * dgij_drl2[k];
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@ -627,8 +579,7 @@ double PairDRIP::calc_repulsive(int const i, int const j,
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}
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if (vflag_atom) {
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// *2 since v_tally has a 0.5 coeff
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// multiply since v_tally has a 0.5 coeff
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for (int k = 0; k < DIM; k++) {
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fnbi1[k]*=2;
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fnbi2[k]*=2;
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@ -649,16 +600,13 @@ double PairDRIP::calc_repulsive(int const i, int const j,
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}
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/* ---------------------------------------------------------------------- */
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void PairDRIP::find_nearest3neigh()
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{
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int i,j,ii,jj,n,allnum,jnum,itype,jtype;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
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int *ilist,*jlist,*numneigh,**firstneigh;
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//int *neighptr;
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double **x = atom->x;
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int *type = atom->type;
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@ -683,12 +631,11 @@ void PairDRIP::find_nearest3neigh()
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jlist = firstneigh[i];
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jnum = numneigh[i];
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// init nb1 to be the 1st nearest neigh, nb3 the 3rd nearest
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int nb1 = -1;
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int nb2 = -1;
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int nb3 = -1;
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double nb1_rsq = 1.1e10;
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double nb1_rsq = 1.0e10 + 1;
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double nb2_rsq = 2.0e10;
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double nb3_rsq = 3.0e10;
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@ -741,13 +688,11 @@ void PairDRIP::find_nearest3neigh()
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} // loop over ii
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}
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/* ---------------------------------------------------------------------- */
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void PairDRIP::calc_normal(int const i, double * const normal,
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V3 *const dn_dri, V3 *const dn_drk1, V3 *const dn_drk2, V3 *const dn_drk3)
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{
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int k1 = nearest3neigh[i][0];
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int k2 = nearest3neigh[i][1];
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int k3 = nearest3neigh[i][2];
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@ -764,9 +709,9 @@ void PairDRIP::calc_normal(int const i, double * const normal,
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deriv_cross(x[k1], x[k2], x[k3], normal, dn_drk1, dn_drk2, dn_drk3);
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}
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/* ---------------------------------------------------------------------- */
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void PairDRIP::get_drhosqij( double const* rij, double const* ni,
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void PairDRIP::get_drhosqij(double const* rij, double const* ni,
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V3 const* dni_dri, V3 const* dni_drn1,
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V3 const* dni_drn2, V3 const* dni_drn3,
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double* const drhosq_dri, double* const drhosq_drj,
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@ -795,12 +740,10 @@ void PairDRIP::get_drhosqij( double const* rij, double const* ni,
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}
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}
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/* ----------------------------------------------------------------------
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derivartive of transverse decay function f(rho) w.r.t. rho
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------------------------------------------------------------------------- */
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/* ---------------------------------------------------------------------- */
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// derivartive of transverse decay function f(rho) w.r.t rho
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double PairDRIP::td(double C0, double C2, double C4, double delta,
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double const* const rvec, double r,
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const double* const n,
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@ -810,7 +753,8 @@ double PairDRIP::td(double C0, double C2, double C4, double delta,
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rho_sq = r * r - n_dot_r * n_dot_r;
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if (rho_sq < 0) { // in case n is [0, 0, 1] and rho_sq is negative due to numerical error
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// in case n is [0, 0, 1] and rho_sq is negative due to numerical error
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if (rho_sq < 0) {
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rho_sq = 0;
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}
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@ -822,9 +766,10 @@ double PairDRIP::td(double C0, double C2, double C4, double delta,
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return td;
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}
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/* ----------------------------------------------------------------------
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derivartive of dihedral angle func gij w.r.t rho, and atom positions
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------------------------------------------------------------------------- */
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/* ---------------------------------------------------------------------- */
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// derivartive of dihedral angle func gij w.r.t rho, and atom positions
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double PairDRIP::dihedral(
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const int i, const int j, Param& p, double const rhosq, double& d_drhosq,
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double* const d_dri, double* const d_drj,
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@ -935,9 +880,10 @@ double PairDRIP::dihedral(
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return dihe;
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}
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/* ----------------------------------------------------------------------
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compute cos(omega_kijl) and the derivateives
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------------------------------------------------------------------------- */
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/* ---------------------------------------------------------------------- */
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// compute cos(omega_kijl) and the derivateives
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double PairDRIP::deriv_cos_omega( double const* rk, double const* ri,
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double const* rj, double const* rl, double* const dcos_drk,
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double* const dcos_dri, double* const dcos_drj, double* const dcos_drl)
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@ -954,10 +900,12 @@ double PairDRIP::deriv_cos_omega( double const* rk, double const* ri,
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double deijl_drl[DIM][DIM];
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// ejik and derivatives (Note the dejik_dri ... returned are actually the transpose)
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// ejik and derivatives
|
||||
// Note the returned dejik_dri ... are actually the transpose
|
||||
deriv_cross(ri, rj, rk, ejik, dejik_dri, dejik_drj, dejik_drk);
|
||||
|
||||
// flip sign because deriv_cross computes rij cross rik, here we need rji cross rik
|
||||
// flip sign
|
||||
// deriv_cross computes rij cross rik, here we need rji cross rik
|
||||
for (int m = 0; m < DIM; m++) {
|
||||
ejik[m] = -ejik[m];
|
||||
for (int n = 0; n < DIM; n++) {
|
||||
|
|
@ -1002,11 +950,8 @@ double PairDRIP::deriv_cos_omega( double const* rk, double const* ri,
|
|||
return cos_omega;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
// tap cutoff function
|
||||
|
||||
double PairDRIP::tap(double r, double cutoff, double& dtap)
|
||||
{
|
||||
double t;
|
||||
|
|
@ -1027,9 +972,8 @@ double PairDRIP::tap(double r, double cutoff, double& dtap)
|
|||
return t;
|
||||
}
|
||||
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
// tap rho
|
||||
|
||||
double PairDRIP::tap_rho(double rhosq, double cut_rhosq, double& drhosq)
|
||||
{
|
||||
double roc_sq;
|
||||
|
|
@ -1047,11 +991,12 @@ double PairDRIP::tap_rho(double rhosq, double cut_rhosq, double& drhosq)
|
|||
}
|
||||
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
// Compute the normalized cross product of two vector rkl, rkm, and the
|
||||
// derivates w.r.t rk, rl, rm.
|
||||
// NOTE, the dcross_drk, dcross_drl, and dcross_drm is actually the transpose
|
||||
// of the actual one.
|
||||
/* ----------------------------------------------------------------------
|
||||
Compute the normalized cross product of two vector rkl, rkm, and the
|
||||
derivates w.r.t rk, rl, rm.
|
||||
NOTE, the returned dcross_drk, dcross_drl, and dcross_drm are actually the
|
||||
transpose.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairDRIP::deriv_cross( double const* rk, double const* rl, double const* rm,
|
||||
double* const cross, V3 *const dcross_drk,
|
||||
|
|
@ -1134,6 +1079,3 @@ void PairDRIP::deriv_cross( double const* rk, double const* rl, double const* rm
|
|||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -11,6 +11,17 @@
|
|||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Mingjian Wen (University of Minnesota)
|
||||
e-mail: wenxx151@umn.edu
|
||||
based on "pair_style kolmogorov/crespi/full" by Wengen Ouyang
|
||||
|
||||
This implements the DRIP model as described in
|
||||
M. Wen, S. Carr, S. Fang, E. Kaxiras, and E. B. Tadmor, Phys. Rev. B, 98,
|
||||
235404 (2018).
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(drip,PairDRIP)
|
||||
|
|
@ -46,70 +57,67 @@ class PairDRIP : public Pair {
|
|||
int ielement,jelement;
|
||||
double C0,C2,C4,C,delta,lambda,A,z0,B,eta,rhocut,rcut;
|
||||
double rhocutsq, rcutsq;
|
||||
double delta2inv,z06;
|
||||
};
|
||||
Param *params; // parameter set for I-J interactions
|
||||
int ** nearest3neigh; // nearest 3 neighbors of atoms
|
||||
char **elements; // names of unique elements
|
||||
int **elem2param; // mapping from element pairs to parameters
|
||||
int *map; // mapping from atom types to elements
|
||||
int nelements; // # of unique elements
|
||||
int nparams; // # of stored parameter sets
|
||||
int maxparam; // max # of parameter sets
|
||||
double cutmax; // max cutoff for all species
|
||||
int ** nearest3neigh; // nearest 3 neighbors of atoms
|
||||
|
||||
void read_file(char * );
|
||||
void allocate();
|
||||
|
||||
// DRIP specific functions
|
||||
double calc_attractive(int const i, int const j, Param& p,
|
||||
double const rsq, double const * rvec, double * const fi, double * const fj);
|
||||
double calc_attractive(int const, int const, Param&, double const,
|
||||
double const *, double * const, double * const);
|
||||
|
||||
double calc_repulsive(int const i, int const j,
|
||||
Param& p, double const rsq, double const * rvec,
|
||||
double const * ni, V3 const * dni_dri,
|
||||
V3 const * dni_drnb1, V3 const * dni_drnb2, V3 const * dni_drnb3,
|
||||
double * const fi, double * const fj);
|
||||
double calc_repulsive(int const , int const ,
|
||||
Param& , double const , double const * ,
|
||||
double const * , V3 const * ,
|
||||
V3 const * , V3 const * , V3 const * ,
|
||||
double * const , double * const );
|
||||
|
||||
|
||||
void find_nearest3neigh();
|
||||
|
||||
|
||||
void calc_normal(int const i, double * const normal,
|
||||
V3 *const dn_dri, V3 *const dn_drk1, V3 *const dn_drk2, V3 *const dn_drk3);
|
||||
void calc_normal(int const , double * const ,
|
||||
V3 *const , V3 *const , V3 *const , V3 *const );
|
||||
|
||||
|
||||
|
||||
void get_drhosqij( double const* rij, double const* ni,
|
||||
V3 const* dni_dri, V3 const* dni_drn1,
|
||||
V3 const* dni_drn2, V3 const* dni_drn3,
|
||||
double* const drhosq_dri, double* const drhosq_drj,
|
||||
double* const drhosq_drn1, double* const drhosq_drn2,
|
||||
double* const drhosq_drn3);
|
||||
void get_drhosqij( double const* , double const* ,
|
||||
V3 const* , V3 const* ,
|
||||
V3 const* , V3 const* ,
|
||||
double* const , double* const ,
|
||||
double* const , double* const ,
|
||||
double* const );
|
||||
|
||||
|
||||
double td(double C0, double C2, double C4, double delta,
|
||||
double const* const rvec, double r,
|
||||
const double* const n,
|
||||
double& rho_sq, double& dtd);
|
||||
double td(double , double , double , double ,
|
||||
double const* const , double ,
|
||||
const double* const ,
|
||||
double& , double& );
|
||||
|
||||
double dihedral(
|
||||
const int i, const int j, Param& p, double const rhosq, double& d_drhosq,
|
||||
double* const d_dri, double* const d_drj,
|
||||
double* const d_drk1, double* const d_drk2, double* const d_drk3,
|
||||
double* const d_drl1, double* const d_drl2, double* const d_drl3);
|
||||
const int , const int , Param& , double const , double& ,
|
||||
double* const , double* const ,
|
||||
double* const , double* const , double* const ,
|
||||
double* const , double* const , double* const );
|
||||
|
||||
double deriv_cos_omega( double const* rk, double const* ri,
|
||||
double const* rj, double const* rl, double* const dcos_drk,
|
||||
double* const dcos_dri, double* const dcos_drj, double* const dcos_drl);
|
||||
double deriv_cos_omega( double const* , double const* ,
|
||||
double const* , double const* , double* const ,
|
||||
double* const , double* const , double* const );
|
||||
|
||||
double tap(double r, double cutoff, double& dtap);
|
||||
double tap(double , double , double& );
|
||||
|
||||
double tap_rho(double rhosq, double cut_rhosq, double& drhosq);
|
||||
double tap_rho(double , double , double& );
|
||||
|
||||
void deriv_cross( double const* rk, double const* rl, double const* rm,
|
||||
double* const cross, V3 *const dcross_drk,
|
||||
V3 *const dcross_drl, V3 *const dcross_drm);
|
||||
void deriv_cross( double const* , double const* , double const* ,
|
||||
double* const , V3 *const ,
|
||||
V3 *const , V3 *const );
|
||||
|
||||
// inline functions
|
||||
inline double dot(double const* x, double const* y) {
|
||||
|
|
@ -123,7 +131,6 @@ void deriv_cross( double const* rk, double const* rl, double const* rm,
|
|||
}
|
||||
}
|
||||
|
||||
|
||||
};
|
||||
|
||||
}
|
||||
|
|
@ -153,7 +160,4 @@ E: No enough neighbors to construct normal
|
|||
Cannot find three neighbors within cutoff of the target atom.
|
||||
Check the configuration.
|
||||
|
||||
|
||||
|
||||
|
||||
*/
|
||||
|
|
|
|||
Loading…
Reference in New Issue