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used domain->closest_image to find proper local ids for bonded atoms, method works

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phankl
2022-05-05 11:41:30 +01:00
parent 30f66c6438
commit ee6e47388a
1 changed files with 37 additions and 9 deletions
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46
src/MESONT/pair_mesocnt.cpp
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@ -20,6 +20,7 @@
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "math_const.h"
@ -564,6 +565,19 @@ void PairMesoCNT::bond_neigh()
comm->forward_comm(this);
// create version of atom->special with local ids and correct images
int atom1, atom2;
int **special_local;
memory->create(special_local, nlocal+nghost, 2, "pair:special_local");
for (int i = 0; i < nlocal+nghost; i++) {
atom1 = atom->map(special[i][0]);
atom2 = atom->map(special[i][1]);
special_local[i][0] = domain->closest_image(i, atom1);
special_local[i][1] = domain->closest_image(i, atom2);
printf("atom1: %d, atom2: %d, closest1: %d, closest2: %d\n", atom1, atom2, special_local[i][0], special_local[i][1]);
}
if (comm->me == 0) {
printf("nlocal: %d, nghost: %d\n", nlocal, nghost);
printf("tag: ");
@ -573,9 +587,23 @@ void PairMesoCNT::bond_neigh()
else
printf("%d ", tag[j]);
printf("\n");
printf("sametag: ");
for (int j = 0; j < nlocal+nghost; j++)
if (j == nlocal-1)
printf("%d | ", atom->sametag[j]);
else
printf("%d ", atom->sametag[j]);
printf("\n");
printf("x: ");
for (int j = 0; j < nlocal+nghost; j++) {
if (j == nlocal-1)
printf("%f | ", atom->x[j][0]);
else
printf("%f ", atom->x[j][0]);
}
printf("\n");
printf("image: ");
for (int j = 0; j < nlocal+nghost; j++) {
int i1 = (atom->image[j] & IMGMASK) - IMGMAX;
int i2 = (atom->image[j] >> IMGBITS & IMGMASK) - IMGMAX;
int i3 = (atom->image[j] >> IMG2BITS) - IMGMAX;
@ -681,7 +709,7 @@ void PairMesoCNT::bond_neigh()
// down the chain
int curr_local = reduced_neighlist[i][j];
int next_local = atom->map(special[curr_local][0]);
int next_local = special_local[curr_local][0];
int curr_reduced, next_reduced;
printf("up: ");
@ -698,13 +726,13 @@ void PairMesoCNT::bond_neigh()
chainid[i][next_reduced] = numchainlist[i];
chainpos[i][next_reduced] = chainpos[i][curr_reduced] - 1;
if (special[next_local][0] != tag[curr_local]) {
if (special_local[next_local][0] != curr_local) {
curr_local = next_local;
next_local = atom->map(special[next_local][0]);
next_local = special_local[next_local][0];
}
else {
curr_local = next_local;
next_local = atom->map(special[next_local][1]);
next_local = special_local[next_local][1];
}
}
printf("\n");
@ -712,7 +740,7 @@ void PairMesoCNT::bond_neigh()
// up the chain
curr_local = reduced_neighlist[i][j];
next_local = atom->map(special[curr_local][1]);
next_local = special_local[curr_local][1];
printf("down: ");
while (next_local != -1) {
@ -728,13 +756,13 @@ void PairMesoCNT::bond_neigh()
chainid[i][next_reduced] = numchainlist[i];
chainpos[i][next_reduced] = chainpos[i][curr_reduced] + 1;
if (special[next_local][0] != tag[curr_local]) {
if (special_local[next_local][0] != curr_local) {
curr_local = next_local;
next_local = atom->map(special[next_local][0]);
next_local = special_local[next_local][0];
}
else {
curr_local = next_local;
next_local = atom->map(special[next_local][1]);
next_local = special_local[next_local][1];
}
}