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merge with ORIGIN

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This commit is contained in:
Steve Plimpton
2023-07-10 12:57:57 -07:00
parent 07f42930ff 9db5d45232
commit 4ab95611db
6 changed files with 85 additions and 46 deletions
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29
src/OPENMP/npair_half_bin_newton_tri_omp.cpp
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@ -18,6 +18,7 @@
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "force.h"
#include "molecule.h"
#include "domain.h"
#include "my_page.h"
@ -40,6 +41,7 @@ void NPairHalfBinNewtonTriOmp::build(NeighList *list)
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
const int molecular = atom->molecular;
const int moltemplate = (molecular == Atom::TEMPLATE) ? 1 : 0;
const double delta = 0.01 * force->angstrom;
NPAIR_OMP_INIT;
#if defined(_OPENMP)
@ -48,7 +50,7 @@ void NPairHalfBinNewtonTriOmp::build(NeighList *list)
NPAIR_OMP_SETUP(nlocal);
int i,j,k,n,itype,jtype,ibin,which,imol,iatom;
tagint tagprev;
tagint itag,jtag,tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
@ -79,6 +81,7 @@ void NPairHalfBinNewtonTriOmp::build(NeighList *list)
n = 0;
neighptr = ipage.vget();
itag = tag[i];
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
@ -98,12 +101,22 @@ void NPairHalfBinNewtonTriOmp::build(NeighList *list)
ibin = atom2bin[i];
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) {
if (x[j][1] < ytmp) continue;
if (x[j][1] == ytmp) {
if (x[j][0] < xtmp) continue;
if (x[j][0] == xtmp && j <= i) continue;
if (j <= i) continue;
if (j >= nlocal) {
jtag = tag[j];
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
if ((itag+jtag) % 2 == 1) continue;
} else {
if (fabs(x[j][2]-ztmp) > delta) {
if (x[j][2] < ztmp) continue;
} else if (fabs(x[j][1]-ytmp) > delta) {
if (x[j][1] < ytmp) continue;
} else {
if (x[j][0] < xtmp) continue;
}
}
}
@ -119,7 +132,7 @@ void NPairHalfBinNewtonTriOmp::build(NeighList *list)
if (molecular != Atom::ATOMIC) {
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >=0)
else if (imol >= 0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);

24
src/OPENMP/npair_half_nsq_newton_omp.cpp
View File

@ -15,14 +15,16 @@
#include "omp_compat.h"
#include "npair_half_nsq_newton_omp.h"
#include "npair_omp.h"
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "group.h"
#include "molecule.h"
#include "domain.h"
#include "my_page.h"
#include "error.h"
#include "neigh_list.h"
using namespace LAMMPS_NS;
@ -42,6 +44,8 @@ void NPairHalfNsqNewtonOmp::build(NeighList *list)
const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
const int molecular = atom->molecular;
const int moltemplate = (molecular == Atom::TEMPLATE) ? 1 : 0;
const double delta = 0.01 * force->angstrom;
const int triclinic = domain->triclinic;
NPAIR_OMP_INIT;
#if defined(_OPENMP)
@ -49,8 +53,8 @@ void NPairHalfNsqNewtonOmp::build(NeighList *list)
#endif
NPAIR_OMP_SETUP(nlocal);
int i,j,n,itype,jtype,itag,jtag,which,imol,iatom;
tagint tagprev;
int i,j,n,itype,jtype,which,imol,iatom;
tagint itag,jtag,tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
@ -106,6 +110,14 @@ void NPairHalfNsqNewtonOmp::build(NeighList *list)
if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
if ((itag+jtag) % 2 == 1) continue;
} else if (triclinic) {
if (fabs(x[j][2]-ztmp) > delta) {
if (x[j][2] < ztmp) continue;
} else if (fabs(x[j][1]-ytmp) > delta) {
if (x[j][1] < ytmp) continue;
} else {
if (x[j][0] < xtmp) continue;
}
} else {
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) {
@ -127,7 +139,7 @@ void NPairHalfNsqNewtonOmp::build(NeighList *list)
if (molecular != Atom::ATOMIC) {
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >=0)
else if (imol >= 0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);

13
src/OPENMP/npair_halffull_newton_omp.cpp
View File

@ -15,7 +15,9 @@
#include "npair_halffull_newton_omp.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "my_page.h"
#include "neigh_list.h"
#include "npair_omp.h"
@ -38,6 +40,8 @@ NPairHalffullNewtonOmp::NPairHalffullNewtonOmp(LAMMPS *lmp) : NPair(lmp) {}
void NPairHalffullNewtonOmp::build(NeighList *list)
{
const int inum_full = list->listfull->inum;
const double delta = 0.01 * force->angstrom;
const int triclinic = domain->triclinic;
NPAIR_OMP_INIT;
#if defined(_OPENMP)
@ -83,8 +87,17 @@ void NPairHalffullNewtonOmp::build(NeighList *list)
for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (j < nlocal) {
if (i > j) continue;
} else if (triclinic) {
if (fabs(x[j][2]-ztmp) > delta) {
if (x[j][2] < ztmp) continue;
} else if (fabs(x[j][1]-ytmp) > delta) {
if (x[j][1] < ytmp) continue;
} else {
if (x[j][0] < xtmp) continue;
}
} else {
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) {

8
src/npair_half_bin_newton_tri.cpp
View File

@ -40,9 +40,9 @@ void NPairHalfBinNewtonTri::build(NeighList *list)
tagint itag,jtag,tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
double delta = 0.01 * force->angstrom;
const double delta = 0.01 * force->angstrom;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
@ -85,7 +85,7 @@ void NPairHalfBinNewtonTri::build(NeighList *list)
// loop over all atoms in bins in stencil
// for triclinic, bin stencil is full in all 3 dims
// must use itag/jtag to eliminate half the I/J interactions
// cannot use I/J coord comparision
// cannot use I/J exact coord comparision
// b/c transforming orthog -> lambda -> orthog for ghost atoms
// with an added PBC offset can shift all 3 coords by epsilon

33
src/npair_half_nsq_newton.cpp
View File

@ -13,15 +13,16 @@
------------------------------------------------------------------------- */
#include "npair_half_nsq_newton.h"
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "group.h"
#include "molecule.h"
#include "domain.h"
#include "my_page.h"
#include "error.h"
#include "neigh_list.h"
using namespace LAMMPS_NS;
@ -42,9 +43,9 @@ void NPairHalfNsqNewton::build(NeighList *list)
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
double delta = 0.01 * force->angstrom;
int triclinic = domain->triclinic;
const double delta = 0.01 * force->angstrom;
const int triclinic = domain->triclinic;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
@ -92,7 +93,7 @@ void NPairHalfNsqNewton::build(NeighList *list)
// use itag/jtap comparision to eliminate half the interactions
// itag = jtag is possible for long cutoffs that include images of self
// for triclinic, must use delta to eliminate half the I/J interactions
// cannot use direct I/J coord comparision as for orthog
// cannot use I/J exact coord comparision as for orthog
// b/c transforming orthog -> lambda -> orthog for ghost atoms
// with an added PBC offset can shift all 3 coords by epsilon
@ -105,15 +106,15 @@ void NPairHalfNsqNewton::build(NeighList *list)
if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
if ((itag+jtag) % 2 == 1) continue;
} else if (triclinic) {
if (fabs(x[j][2]-ztmp) > delta) {
if (x[j][2] < ztmp) continue;
} else if (fabs(x[j][1]-ytmp) > delta) {
if (x[j][1] < ytmp) continue;
} else {
if (x[j][0] < xtmp) continue;
}
} else {
} else if (triclinic) {
if (fabs(x[j][2]-ztmp) > delta) {
if (x[j][2] < ztmp) continue;
} else if (fabs(x[j][1]-ytmp) > delta) {
if (x[j][1] < ytmp) continue;
} else {
if (x[j][0] < xtmp) continue;
}
} else {
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) {
if (x[j][1] < ytmp) continue;

24
src/npair_halffull_newton.cpp
View File

@ -39,8 +39,8 @@ void NPairHalffullNewton::build(NeighList *list)
int *neighptr, *jlist;
double xtmp, ytmp, ztmp;
double delta = 0.01 * force->angstrom;
int triclinic = domain->triclinic;
const double delta = 0.01 * force->angstrom;
const int triclinic = domain->triclinic;
double **x = atom->x;
int nlocal = atom->nlocal;
@ -72,7 +72,7 @@ void NPairHalffullNewton::build(NeighList *list)
// loop over full neighbor list
// use i < j < nlocal to eliminate half the local/local interactions
// for triclinic, must use delta to eliminate half the local/ghost interactions
// cannot use direct I/J coord comparision as for orthog
// cannot use I/J exact coord comparision as for orthog
// b/c transforming orthog -> lambda -> orthog for ghost atoms
// with an added PBC offset can shift all 3 coords by epsilon
@ -82,17 +82,17 @@ void NPairHalffullNewton::build(NeighList *list)
for (jj = 0; jj < jnum; jj++) {
joriginal = jlist[jj];
j = joriginal & NEIGHMASK;
if (j < nlocal) {
if (i > j) continue;
} else if (triclinic) {
if (fabs(x[j][2]-ztmp) > delta) {
if (x[j][2] < ztmp) continue;
} else if (fabs(x[j][1]-ytmp) > delta) {
if (x[j][1] < ytmp) continue;
} else {
if (x[j][0] < xtmp) continue;
}
if (fabs(x[j][2]-ztmp) > delta) {
if (x[j][2] < ztmp) continue;
} else if (fabs(x[j][1]-ytmp) > delta) {
if (x[j][1] < ytmp) continue;
} else {
if (x[j][0] < xtmp) continue;
}
} else {
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) {
@ -100,7 +100,7 @@ void NPairHalffullNewton::build(NeighList *list)
if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
}
neighptr[n++] = joriginal;
}