avoid replicated code, consolidate variables and element mapping
This commit is contained in:
Axel Kohlmeyer
@ -22,21 +22,19 @@
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#include "pair_tersoff_table.h"
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#include <cmath>
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#include <cstring>
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#include "atom.h"
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#include "neighbor.h"
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#include "comm.h"
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#include "error.h"
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#include "force.h"
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#include "memory.h"
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#include "neigh_list.h"
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#include "neigh_request.h"
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#include "force.h"
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#include "comm.h"
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#include "memory.h"
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#include "tokenizer.h"
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#include "neighbor.h"
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#include "potential_file_reader.h"
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#include "tokenizer.h"
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#include "error.h"
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#include <cmath>
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#include <cstring>
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using namespace LAMMPS_NS;
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@ -64,11 +62,7 @@ PairTersoffTable::PairTersoffTable(LAMMPS *lmp) : Pair(lmp)
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centroidstressflag = CENTROID_NOTAVAIL;
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unit_convert_flag = utils::get_supported_conversions(utils::ENERGY);
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nelements = 0;
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elements = nullptr;
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nparams = maxparam = 0;
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params = nullptr;
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elem2param = nullptr;
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allocated = 0;
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preGtetaFunction = preGtetaFunctionDerived = nullptr;
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@ -88,17 +82,12 @@ PairTersoffTable::PairTersoffTable(LAMMPS *lmp) : Pair(lmp)
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PairTersoffTable::~PairTersoffTable()
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{
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if (elements)
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for (int i = 0; i < nelements; i++) delete [] elements[i];
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delete [] elements;
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memory->destroy(params);
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memory->destroy(elem2param);
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memory->destroy(elem3param);
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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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deallocateGrids();
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deallocatePreLoops();
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@ -177,7 +166,7 @@ void PairTersoffTable::compute(int eflag, int vflag)
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r_ij = dr_ij[0]*dr_ij[0] + dr_ij[1]*dr_ij[1] + dr_ij[2]*dr_ij[2];
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jtype = map[type[j]];
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ijparam = elem2param[itype][jtype][jtype];
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ijparam = elem3param[itype][jtype][jtype];
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if (r_ij > params[ijparam].cutsq) continue;
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@ -208,8 +197,8 @@ void PairTersoffTable::compute(int eflag, int vflag)
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k = jlist[neighbor_k];
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k &= NEIGHMASK;
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ktype = map[type[k]];
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ikparam = elem2param[itype][ktype][ktype];
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ijkparam = elem2param[itype][jtype][ktype];
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ikparam = elem3param[itype][ktype][ktype];
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ijkparam = elem3param[itype][jtype][ktype];
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dr_ik[0] = xtmp -x[k][0];
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dr_ik[1] = ytmp -x[k][1];
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@ -264,7 +253,7 @@ void PairTersoffTable::compute(int eflag, int vflag)
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r_ij = dr_ij[0]*dr_ij[0] + dr_ij[1]*dr_ij[1] + dr_ij[2]*dr_ij[2];
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jtype = map[type[j]];
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ijparam = elem2param[itype][jtype][jtype];
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ijparam = elem3param[itype][jtype][jtype];
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if (r_ij > params[ijparam].cutsq) continue;
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@ -308,8 +297,8 @@ void PairTersoffTable::compute(int eflag, int vflag)
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k = jlist[neighbor_k];
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k &= NEIGHMASK;
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ktype = map[type[k]];
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ikparam = elem2param[itype][ktype][ktype];
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ijkparam = elem2param[itype][jtype][ktype];
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ikparam = elem3param[itype][ktype][ktype];
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ijkparam = elem3param[itype][jtype][ktype];
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dr_ik[0] = xtmp -x[k][0];
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dr_ik[1] = ytmp -x[k][1];
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@ -333,8 +322,8 @@ void PairTersoffTable::compute(int eflag, int vflag)
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k = jlist[neighbor_k];
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k &= NEIGHMASK;
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ktype = map[type[k]];
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ikparam = elem2param[itype][ktype][ktype];
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ijkparam = elem2param[itype][jtype][ktype];
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ikparam = elem3param[itype][ktype][ktype];
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ijkparam = elem3param[itype][jtype][ktype];
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dr_ik[0] = xtmp -x[k][0];
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dr_ik[1] = ytmp -x[k][1];
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@ -392,8 +381,8 @@ void PairTersoffTable::compute(int eflag, int vflag)
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k = jlist[neighbor_k];
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k &= NEIGHMASK;
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ktype = map[type[k]];
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ikparam = elem2param[itype][ktype][ktype];
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ijkparam = elem2param[itype][jtype][ktype];
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ikparam = elem3param[itype][ktype][ktype];
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ijkparam = elem3param[itype][jtype][ktype];
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dr_ik[0] = xtmp -x[k][0];
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dr_ik[1] = ytmp -x[k][1];
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@ -457,8 +446,8 @@ void PairTersoffTable::compute(int eflag, int vflag)
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k = jlist[neighbor_k];
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k &= NEIGHMASK;
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ktype = map[type[k]];
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ikparam = elem2param[itype][ktype][ktype];
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ijkparam = elem2param[itype][jtype][ktype];
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ikparam = elem3param[itype][ktype][ktype];
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ijkparam = elem3param[itype][jtype][ktype];
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dr_ik[0] = xtmp -x[k][0];
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dr_ik[1] = ytmp -x[k][1];
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@ -608,7 +597,7 @@ void PairTersoffTable::allocateGrids(void)
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r = -1.0;
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deltaArgumentGtetaFunction = 1.0 / GRIDDENSITY_GTETA;
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int iparam = elem2param[i][i][i];
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int iparam = elem3param[i][i][i];
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double c = params[iparam].c;
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double d = params[iparam].d;
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double h = params[iparam].h;
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@ -628,7 +617,7 @@ void PairTersoffTable::allocateGrids(void)
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for (i=0; i<nelements; i++) {
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int iparam = elem2param[i][i][i];
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int iparam = elem3param[i][i][i];
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double c = params[iparam].c;
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double d = params[iparam].d;
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double beta = params[iparam].beta;
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@ -639,7 +628,7 @@ void PairTersoffTable::allocateGrids(void)
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for (j=0; j<nelements; j++) {
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for (k=0; k<nelements; k++) {
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int ijparam = elem2param[i][j][k];
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int ijparam = elem3param[i][j][k];
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double cutoffR = params[ijparam].cutoffR;
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double cutoffS = params[ijparam].cutoffS;
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@ -660,7 +649,7 @@ void PairTersoffTable::allocateGrids(void)
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for (i=0; i<nelements; i++) {
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for (j=0; j<nelements; j++) {
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for (j=0; j<nelements; j++) {
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int ijparam = elem2param[i][j][j];
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int ijparam = elem3param[i][j][j];
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double cutoffR = params[ijparam].cutoffR;
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double cutoffS = params[ijparam].cutoffS;
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@ -693,7 +682,7 @@ void PairTersoffTable::allocateGrids(void)
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for (i=0; i<nelements; i++) {
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int iparam = elem2param[i][i][i];
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int iparam = elem3param[i][i][i];
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double c = params[iparam].c;
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double d = params[iparam].d;
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double beta = params[iparam].beta;
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@ -743,72 +732,17 @@ void PairTersoffTable::settings(int narg, char **/*arg*/)
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void PairTersoffTable::coeff(int narg, char **arg)
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{
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int i,j,n;
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if (!allocated) allocate();
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if (narg != 3 + atom->ntypes)
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error->all(FLERR,"Incorrect args for pair coefficients");
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// insure I,J args are * *
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if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
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error->all(FLERR,"Incorrect args for pair coefficients");
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// read args that map atom types to elements in potential file
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// map[i] = which element the Ith atom type is, -1 if "NULL"
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// nelements = # of unique elements
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// elements = list of element names
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if (elements) {
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for (i = 0; i < nelements; i++) delete [] elements[i];
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delete [] elements;
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}
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elements = new char*[atom->ntypes];
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for (i = 0; i < atom->ntypes; i++) elements[i] = nullptr;
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nelements = 0;
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for (i = 3; i < narg; i++) {
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if (strcmp(arg[i],"NULL") == 0) {
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map[i-2] = -1;
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continue;
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}
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for (j = 0; j < nelements; j++)
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if (strcmp(arg[i],elements[j]) == 0) break;
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map[i-2] = j;
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if (j == nelements) {
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n = strlen(arg[i]) + 1;
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elements[j] = new char[n];
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strcpy(elements[j],arg[i]);
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nelements++;
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}
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}
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map_element2type(narg-3,arg+3);
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// read potential file and initialize potential parameters
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read_file(arg[2]);
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setup_params();
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// clear setflag since coeff() called once with I,J = * *
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n = atom->ntypes;
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for (int i = 1; i <= n; i++)
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for (int j = i; j <= n; j++)
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setflag[i][j] = 0;
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// set setflag i,j for type pairs where both are mapped to elements
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int count = 0;
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for (int i = 1; i <= n; i++)
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for (int j = i; j <= n; j++)
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if (map[i] >= 0 && map[j] >= 0) {
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setflag[i][j] = 1;
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count++;
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}
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if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
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// allocate tables and internal structures
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allocatePreLoops();
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allocateGrids();
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}
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@ -966,12 +900,12 @@ void PairTersoffTable::setup_params()
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{
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int i,j,k,m,n;
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// set elem2param for all triplet combinations
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// set elem3param for all triplet combinations
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// must be a single exact match to lines read from file
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// do not allow for ACB in place of ABC
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memory->destroy(elem2param);
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memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param");
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memory->destroy(elem3param);
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memory->create(elem3param,nelements,nelements,nelements,"pair:elem3param");
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for (i = 0; i < nelements; i++)
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for (j = 0; j < nelements; j++)
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@ -985,7 +919,7 @@ void PairTersoffTable::setup_params()
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}
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}
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if (n < 0) error->all(FLERR,"Potential file is missing an entry");
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elem2param[i][j][k] = n;
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elem3param[i][j][k] = n;
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}
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// set cutoff square
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