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cosmetic changes

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This commit is contained in:
Axel Kohlmeyer
2021-05-04 22:52:24 -04:00
parent cdc3e2bad9
commit 51a84a67f9
2 changed files with 39 additions and 57 deletions
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95
src/MANYBODY/pair_polymorphic.cpp
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@ -211,7 +211,7 @@ void PairPolymorphic::compute(int eflag, int vflag)
if (eta == 1) {
iparam_ii = elem2param[itype][itype];
PairParameters & p = pairParameters[iparam_ii];
PairParameters &p = pairParameters[iparam_ii];
emb = (p.F)->get_vmax();
}
@ -231,13 +231,13 @@ void PairPolymorphic::compute(int eflag, int vflag)
r0 = sqrt(rsq);
iparam_ij = elem2param[itype][jtype];
PairParameters & p = pairParameters[iparam_ij];
PairParameters &p = pairParameters[iparam_ij];
// do not include the neighbor if get_vmax() <= epsilon because the function is near zero
if (eta == 1) {
if (emb > epsilon) {
iparam_jj = elem2param[jtype][jtype];
PairParameters & q = pairParameters[iparam_jj];
PairParameters &q = pairParameters[iparam_jj];
if (rsq < (q.W)->get_xmaxsq() && (q.W)->get_vmax() > epsilon) {
numneighW = numneighW + 1;
firstneighW[numneighW] = j;
@ -301,7 +301,7 @@ void PairPolymorphic::compute(int eflag, int vflag)
if (emb > epsilon) {
iparam_ii = elem2param[itype][itype];
PairParameters & p = pairParameters[iparam_ii];
PairParameters &p = pairParameters[iparam_ii];
// accumulate bondorder zeta for each i-j interaction via loop over k
@ -312,7 +312,7 @@ void PairPolymorphic::compute(int eflag, int vflag)
ktype = map[type[k]];
iparam_kk = elem2param[ktype][ktype];
PairParameters & q = pairParameters[iparam_kk];
PairParameters &q = pairParameters[iparam_kk];
(q.W)->value2(drW[kk],wfac,1,fpair,0);
@ -339,7 +339,7 @@ void PairPolymorphic::compute(int eflag, int vflag)
delr2[2] = -delzW[kk];
iparam_kk = elem2param[ktype][ktype];
PairParameters & q = pairParameters[iparam_kk];
PairParameters &q = pairParameters[iparam_kk];
(q.W)->value2(drW[kk],wfac,0,fpair,1);
fpair = -prefactor*fpair/drW[kk];
@ -362,7 +362,7 @@ void PairPolymorphic::compute(int eflag, int vflag)
jtype = map[type[j]];
iparam_ij = elem2param[itype][jtype];
PairParameters & p = pairParameters[iparam_ij];
PairParameters &p = pairParameters[iparam_ij];
delr1[0] = -delxV[jj];
delr1[1] = -delyV[jj];
@ -379,7 +379,7 @@ void PairPolymorphic::compute(int eflag, int vflag)
if (j == k) continue;
ktype = map[type[k]];
iparam_ijk = elem3param[jtype][itype][ktype];
TripletParameters & trip = tripletParameters[iparam_ijk];
TripletParameters &trip = tripletParameters[iparam_ijk];
if ((trip.G)->get_vmax() <= epsilon) continue;
numneighW1 = numneighW1 + 1;
@ -394,7 +394,7 @@ void PairPolymorphic::compute(int eflag, int vflag)
delr1[2]*delr2[2]) / (r1*r2);
iparam_ik = elem2param[itype][ktype];
PairParameters & q = pairParameters[iparam_ik];
PairParameters &q = pairParameters[iparam_ik];
(q.W)->value2(r2,wfac,1,fpair,0);
(trip.P)->value2(r1-(p.xi)*r2,pfac,1,fpair,0);
@ -428,7 +428,7 @@ void PairPolymorphic::compute(int eflag, int vflag)
k = firstneighW[kk];
ktype = map[type[k]];
iparam_ijk = elem3param[jtype][itype][ktype];
TripletParameters & trip = tripletParameters[iparam_ijk];
TripletParameters &trip = tripletParameters[iparam_ijk];
delr2[0] = -delxW[kk];
delr2[1] = -delyW[kk];
@ -436,7 +436,7 @@ void PairPolymorphic::compute(int eflag, int vflag)
r2 = drW[kk];
iparam_ik = elem2param[itype][ktype];
PairParameters & q = pairParameters[iparam_ik];
PairParameters &q = pairParameters[iparam_ik];
attractive(&p,&q,&trip,prefactor,r1,r2,delr1,delr2,fi,fj,fk);
@ -607,7 +607,7 @@ void PairPolymorphic::read_file(char *file)
tripletParameters = new TripletParameters[ntriple];
for (int i = 0; i < npair; i++) {
PairParameters & p = pairParameters[i];
PairParameters &p = pairParameters[i];
values = reader->next_values(2);
p.cut = values.next_double();
p.cutsq = p.cut*p.cut;
@ -641,28 +641,22 @@ void PairPolymorphic::read_file(char *file)
// start reading tabular functions
double * singletable = new double[nr];
for (int i = 0; i < npair; i++) { // U
PairParameters & p = pairParameters[i];
if (comm->me == 0) {
reader->next_dvector(singletable, nr);
}
PairParameters &p = pairParameters[i];
if (comm->me == 0) reader->next_dvector(singletable, nr);
MPI_Bcast(singletable,nr,MPI_DOUBLE,0,world);
p.U = new TabularFunction;
(p.U)->set_values(nr,0.0,p.cut,singletable);
}
for (int i = 0; i < npair; i++) { // V
PairParameters & p = pairParameters[i];
if (comm->me == 0) {
reader->next_dvector(singletable, nr);
}
PairParameters &p = pairParameters[i];
if (comm->me == 0) reader->next_dvector(singletable, nr);
MPI_Bcast(singletable,nr,MPI_DOUBLE,0,world);
p.V = new TabularFunction;
(p.V)->set_values(nr,0.0,p.cut,singletable);
}
for (int i = 0; i < npair; i++) { // W
PairParameters & p = pairParameters[i];
if (comm->me == 0) {
reader->next_dvector(singletable, nr);
}
PairParameters &p = pairParameters[i];
if (comm->me == 0) reader->next_dvector(singletable, nr);
MPI_Bcast(singletable,nr,MPI_DOUBLE,0,world);
p.W = new TabularFunction;
(p.W)->set_values(nr,0.0,p.cut,singletable);
@ -670,34 +664,30 @@ void PairPolymorphic::read_file(char *file)
cutmax = 0.0;
for (int i = 0; i < npair; i++) {
PairParameters & p = pairParameters[i];
PairParameters &p = pairParameters[i];
if (p.cut > cutmax) cutmax = p.cut;
}
cutmaxsq = cutmax*cutmax;
if (eta != 3) {
for (int j = 0; j < nelements; j++) { // P
if (comm->me == 0) {
reader->next_dvector(singletable, nr);
}
if (comm->me == 0) reader->next_dvector(singletable, nr);
MPI_Bcast(singletable,nr,MPI_DOUBLE,0,world);
for (int i = 0; i < nelements; i++) {
TripletParameters & p = tripletParameters[i*nelements*nelements+j*nelements+j];
TripletParameters &p = tripletParameters[i*nelements*nelements+j*nelements+j];
p.P = new TabularFunction;
(p.P)->set_values(nr,-cutmax,cutmax,singletable);
}
}
for (int j = 0; j < nelements-1; j++) { // P
for (int k = j+1; k < nelements; k++) {
if (comm->me == 0) {
reader->next_dvector(singletable, nr);
}
if (comm->me == 0) reader->next_dvector(singletable, nr);
MPI_Bcast(singletable,nr,MPI_DOUBLE,0,world);
for (int i = 0; i < nelements; i++) {
TripletParameters & p = tripletParameters[i*nelements*nelements+j*nelements+k];
TripletParameters &p = tripletParameters[i*nelements*nelements+j*nelements+k];
p.P = new TabularFunction;
(p.P)->set_values(nr,-cutmax,cutmax,singletable);
TripletParameters & q = tripletParameters[i*nelements*nelements+k*nelements+j];
TripletParameters &q = tripletParameters[i*nelements*nelements+k*nelements+j];
q.P = new TabularFunction;
(q.P)->set_values(nr,-cutmax,cutmax,singletable);
}
@ -706,10 +696,8 @@ void PairPolymorphic::read_file(char *file)
}
if (eta == 3) {
for (int i = 0; i < ntriple; i++) { // P
TripletParameters & p = tripletParameters[i];
if (comm->me == 0) {
reader->next_dvector(singletable, nr);
}
TripletParameters &p = tripletParameters[i];
if (comm->me == 0) reader->next_dvector(singletable, nr);
MPI_Bcast(singletable,nr,MPI_DOUBLE,0,world);
p.P = new TabularFunction;
(p.P)->set_values(nr,-cutmax,cutmax,singletable);
@ -718,10 +706,8 @@ void PairPolymorphic::read_file(char *file)
delete[] singletable;
singletable = new double[ng];
for (int i = 0; i < ntriple; i++) { // G
TripletParameters & p = tripletParameters[i];
if (comm->me == 0) {
reader->next_dvector(singletable, ng);
}
TripletParameters &p = tripletParameters[i];
if (comm->me == 0) reader->next_dvector(singletable, ng);
MPI_Bcast(singletable,ng,MPI_DOUBLE,0,world);
p.G = new TabularFunction;
(p.G)->set_values(ng,-1.0,1.0,singletable);
@ -729,22 +715,18 @@ void PairPolymorphic::read_file(char *file)
delete[] singletable;
singletable = new double[nx];
for (int i = 0; i < npair; i++) { // F
PairParameters & p = pairParameters[i];
if (comm->me == 0) {
reader->next_dvector(singletable, nx);
}
PairParameters &p = pairParameters[i];
if (comm->me == 0) reader->next_dvector(singletable, nx);
MPI_Bcast(singletable,nx,MPI_DOUBLE,0,world);
p.F = new TabularFunction;
(p.F)->set_values(nx,0.0,maxX,singletable);
}
delete[] singletable;
if (comm->me == 0) {
delete reader;
}
if (comm->me == 0) delete reader;
// recalculate cutoffs of all params
for (int i = 0; i < npair; i++) {
PairParameters & p = pairParameters[i];
PairParameters &p = pairParameters[i];
p.cut = (p.U)->get_xmax();
if (p.cut < (p.V)->get_xmax()) p.cut = (p.V)->get_xmax();
if (p.cut < (p.W)->get_xmax()) p.cut = (p.W)->get_xmax();
@ -754,7 +736,7 @@ void PairPolymorphic::read_file(char *file)
// set cutmax to max of all params
cutmax = 0.0;
for (int i = 0; i < npair; i++) {
PairParameters & p = pairParameters[i];
PairParameters &p = pairParameters[i];
if (cutmax < p.cut) cutmax = p.cut;
}
cutmaxsq = cutmax*cutmax;
@ -898,7 +880,7 @@ void PairPolymorphic::write_tables(int npts)
elements[j],comm->me);
fp = fopen(filename.c_str(), "w");
int iparam_ij = elem2param[i][j];
PairParameters & pair = pairParameters[iparam_ij];
PairParameters &pair = pairParameters[iparam_ij];
xmin = (pair.U)->get_xmin();
xmax = (pair.U)->get_xmax();
double xl = xmax - xmin;
@ -909,7 +891,8 @@ void PairPolymorphic::write_tables(int npts)
(pair.U)->value2(x, uf, 1, ufp, 1);
(pair.V)->value2(x, vf, 1, vfp, 1);
(pair.W)->value2(x, wf, 1, wfp, 1);
fprintf(fp,"%12.4f %12.4f %12.4f %12.4f %12.4f %12.4f %12.4f \n",x,uf,vf,wf,ufp,vfp,wfp);
fprintf(fp,"%12.4f %12.4f %12.4f %12.4f %12.4f %12.4f %12.4f \n",
x,uf,vf,wf,ufp,vfp,wfp);
}
fclose(fp);
}
@ -921,7 +904,7 @@ void PairPolymorphic::write_tables(int npts)
elements[k],comm->me);
fp = fopen(filename.c_str(), "w");
int iparam_ij = elem3param[i][j][k];
TripletParameters & pair = tripletParameters[iparam_ij];
TripletParameters &pair = tripletParameters[iparam_ij];
xmin = (pair.P)->get_xmin();
xmax = (pair.P)->get_xmax();
double xl = xmax - xmin;
@ -943,7 +926,7 @@ void PairPolymorphic::write_tables(int npts)
elements[k],comm->me);
fp = fopen(filename.c_str(), "w");
int iparam_ij = elem3param[i][j][k];
TripletParameters & pair = tripletParameters[iparam_ij];
TripletParameters &pair = tripletParameters[iparam_ij];
xmin = (pair.G)->get_xmin();
xmax = (pair.G)->get_xmax();
for (int n = 0; n < npts; n++) {
@ -961,7 +944,7 @@ void PairPolymorphic::write_tables(int npts)
elements[j],comm->me);
fp = fopen(filename.c_str(), "w");
int iparam_ij = elem2param[i][j];
PairParameters & pair = pairParameters[iparam_ij];
PairParameters &pair = pairParameters[iparam_ij];
xmin = (pair.F)->get_xmin();
xmax = (pair.F)->get_xmax();
double xl = xmax - xmin;

1
src/MANYBODY/pair_polymorphic.h
View File

@ -21,7 +21,6 @@ PairStyle(polymorphic,PairPolymorphic)
#define LMP_PAIR_POLYMORPHIC_H
#include "pair.h"
#include <cmath>
namespace LAMMPS_NS {
// forward declaration