added comm_forward of atom::special for ghost atoms
This commit is contained in:
phankl
@ -32,6 +32,7 @@
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#include <cmath>
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#include <cstring>
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#include <unordered_map>
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using namespace LAMMPS_NS;
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using namespace MathConst;
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@ -57,6 +58,8 @@ PairMesoCNT::PairMesoCNT(LAMMPS *lmp) : Pair(lmp)
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no_virial_fdotr_compute = 0;
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writedata = 0;
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ghostneigh = 0;
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comm_forward = 2;
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}
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/* ----------------------------------------------------------------------
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@ -557,51 +560,39 @@ void PairMesoCNT::bond_neigh()
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int *type = atom->type;
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tagint *tag = atom->tag;
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tagint **bond_atom = atom->bond_atom;
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int **nspecial = atom->nspecial;
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tagint **special = atom->special;
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printf("nlocal: %d, nghost: %d\n", nlocal, nghost);
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printf("local atoms: ");
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for (int j = 0; j < nlocal; j++)
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printf("%d ", tag[j]);
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printf("\n");
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printf("ghost atoms: ");
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for (int j = nlocal; j < nlocal+nghost; j++)
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if (j == nlocal-1)
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printf("%d | ", tag[j]);
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else
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printf("%d ", tag[j]);
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printf("\n");
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printf("map(tag): ");
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for (int j = 0; j < nlocal+nghost; j++)
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if (j == nlocal-1)
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printf("%d | ", atom->map(tag[j]));
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else
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printf("%d ", atom->map(tag[j]));
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printf("\n");
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printf("bond_atom: ");
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for (int j = 0; j < nlocal+nghost; j++)
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if (j == nlocal-1)
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printf("%d | ", atom->map(tag[j]));
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else
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printf("%d ", bond_atom[j][0]);
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printf("\n");
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printf("nspecial: ");
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for (int j = 0; j < nlocal+nghost; j++)
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if (j == nlocal-1)
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printf("(%d, %d, %d) | ", nspecial[j][0], nspecial[j][1], nspecial[j][2]);
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else
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printf("(%d, %d, %d) ", nspecial[j][0], nspecial[j][1], nspecial[j][2]);
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printf("\n");
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printf("special: ");
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for (int j = 0; j < nlocal+nghost; j++)
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if (j == nlocal-1)
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printf("(%d, %d) | ", special[j][0], special[j][1]);
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else
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printf("(%d, %d) ", special[j][0], special[j][1]);
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printf("\n");
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comm->forward_comm(this);
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if (comm->me == 0) {
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printf("nlocal: %d, nghost: %d\n", nlocal, nghost);
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printf("tag: ");
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for (int j = 0; j < nlocal+nghost; j++)
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if (j == nlocal-1)
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printf("%d | ", tag[j]);
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else
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printf("%d ", tag[j]);
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printf("\n");
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printf("image: ");
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for (int j = 0; j < nlocal+nghost; j++) {
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int i1 = (atom->image[j] & IMGMASK) - IMGMAX;
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int i2 = (atom->image[j] >> IMGBITS & IMGMASK) - IMGMAX;
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int i3 = (atom->image[j] >> IMG2BITS) - IMGMAX;
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if (j == nlocal-1)
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printf("(%d %d %d)| ", i1, i2, i3);
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else
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printf("(%d %d %d)", i1, i2, i3);
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}
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printf("\n");
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printf("special: ");
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for (int j = 0; j < nlocal+nghost; j++)
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if (j == nlocal-1)
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printf("(%d, %d) | ", special[j][0], special[j][1]);
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else
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printf("(%d, %d) ", special[j][0], special[j][1]);
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printf("\n");
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}
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int *numneigh = list->numneigh;
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int *numneigh_max;
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@ -651,11 +642,9 @@ void PairMesoCNT::bond_neigh()
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// split neighbor list into neighbor chains based on bond topology
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int **chainid, **chainpos, **bonded_atom1, **bonded_atom2;
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int **chainid, **chainpos;
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memory->create_ragged(chainid, nbondlist, reduced_nlist, "pair:chainid");
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memory->create_ragged(chainpos, nbondlist, reduced_nlist, "pair:chainpos");
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memory->create_ragged(bonded_atom1, nbondlist, reduced_nlist, "pair::bonded_atom1");
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memory->create_ragged(bonded_atom2, nbondlist, reduced_nlist, "pair::bonded_atom2");
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memory->create(numchainlist, nbondlist, "pair:numchainlist");
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bool empty_neigh = true;
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@ -666,32 +655,16 @@ void PairMesoCNT::bond_neigh()
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empty_neigh = false;
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for (int j = 0; j < reduced_nlist[i]; j++) {
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int jj = reduced_neighlist[i][j];
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int jtag = tag[jj];
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int jbond = bond_atom[atom->map(jtag)][0];
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bonded_atom1[i][j] = -1;
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bonded_atom2[i][j] = -1;
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chainid[i][j] = -1;
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bool newchain = true;
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for (int k = 0; k < j; k++) {
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int kk = reduced_neighlist[i][k];
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int ktag = tag[kk];
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int kbond = bond_atom[atom->map(ktag)][0];
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// check if atoms are bonded
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if (jtag == kbond || jbond == ktag) {
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if (bonded_atom1[i][j] == -1) bonded_atom1[i][j] = k;
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else bonded_atom2[i][j] = k;
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if (bonded_atom1[i][k] == -1) bonded_atom1[i][k] = j;
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else bonded_atom2[i][k] = j;
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}
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}
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}
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// map local ids to reduced neighbor list ids
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std::unordered_map<int, int> reduced_map;
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for (int j = 0; j < reduced_nlist[i]; j++) {
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reduced_map[reduced_neighlist[i][j]] = j;
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chainid[i][j] = -1;
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printf("(%d, %d, %d) ", j, reduced_neighlist[i][j], tag[reduced_neighlist[i][j]]);
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}
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printf("\n");
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// assign chain ids and positions
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for (int j = 0; j < reduced_nlist[i]; j++) {
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@ -707,45 +680,82 @@ void PairMesoCNT::bond_neigh()
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// down the chain
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int current_atom = j;
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int next_atom = bonded_atom1[i][j];
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while (next_atom != -1) {
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chainid[i][next_atom] = numchainlist[i];
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chainpos[i][next_atom] = chainpos[i][current_atom] - 1;
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if (bonded_atom1[i][next_atom] != current_atom) {
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current_atom = next_atom;
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next_atom = bonded_atom1[i][next_atom];
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int curr_local = reduced_neighlist[i][j];
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int next_local = atom->map(special[curr_local][0]);
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int curr_reduced, next_reduced;
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printf("up: ");
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while (next_local != -1) {
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printf("%d %d ", curr_local, next_local);
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try {
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curr_reduced = reduced_map.at(curr_local);
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next_reduced = reduced_map.at(next_local);
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}
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catch (const std::out_of_range& e) {
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break;
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}
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printf("| ");
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chainid[i][next_reduced] = numchainlist[i];
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chainpos[i][next_reduced] = chainpos[i][curr_reduced] - 1;
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if (special[next_local][0] != tag[curr_local]) {
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curr_local = next_local;
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next_local = atom->map(special[next_local][0]);
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}
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else {
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current_atom = next_atom;
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next_atom = bonded_atom2[i][next_atom];
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curr_local = next_local;
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next_local = atom->map(special[next_local][1]);
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}
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}
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printf("\n");
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// up the chain
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current_atom = j;
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next_atom = bonded_atom2[i][j];
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while (next_atom != -1) {
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chainid[i][next_atom] = numchainlist[i];
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chainpos[i][next_atom] = chainpos[i][current_atom] + 1;
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if (bonded_atom1[i][next_atom] != current_atom) {
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current_atom = next_atom;
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next_atom = bonded_atom1[i][next_atom];
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curr_local = reduced_neighlist[i][j];
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next_local = atom->map(special[curr_local][1]);
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printf("down: ");
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while (next_local != -1) {
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printf("%d %d ", curr_local, next_local);
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try {
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curr_reduced = reduced_map.at(curr_local);
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next_reduced = reduced_map.at(next_local);
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}
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catch (const std::out_of_range& e) {
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break;
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}
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printf("| ");
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chainid[i][next_reduced] = numchainlist[i];
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chainpos[i][next_reduced] = chainpos[i][curr_reduced] + 1;
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if (special[next_local][0] != tag[curr_local]) {
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curr_local = next_local;
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next_local = atom->map(special[next_local][0]);
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}
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else {
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current_atom = next_atom;
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next_atom = bonded_atom2[i][next_atom];
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curr_local = next_local;
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next_local = atom->map(special[next_local][1]);
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}
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}
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numchainlist[i]++;
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}
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}
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// destroy temporary arrays
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memory->destroy(bonded_atom1);
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memory->destroy(bonded_atom2);
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printf("bond: %d\n", i);
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printf("tag: ");
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for (int j = 0; j < reduced_nlist[i]; j++)
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printf("%d ", tag[reduced_neighlist[i][j]]);
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printf("\n");
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printf("chainid: ");
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for (int j = 0; j < reduced_nlist[i]; j++)
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printf("%d ", chainid[i][j]);
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printf("\n");
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printf("chainpos: ");
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for (int j = 0; j < reduced_nlist[i]; j++)
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printf("%d ", chainpos[i][j]);
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printf("\n");
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fflush(stdout);
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}
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// count neighbor chain lengths per bond
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@ -884,6 +894,37 @@ void PairMesoCNT::neigh_common(int i1, int i2, int &numred, int *redlist)
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}
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}
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/* ---------------------------------------------------------------------- */
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int PairMesoCNT::pack_forward_comm(int n, int *list, double *buf,
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int /*pbc_flag*/, int * /*pbc*/)
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{
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int i,j,m;
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m = 0;
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = ubuf(atom->special[j][0]).d;
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buf[m++] = ubuf(atom->special[j][1]).d;
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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void PairMesoCNT::unpack_forward_comm(int n, int first, double *buf)
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{
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int i,m,last;
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m = 0;
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last = first + n;
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for (i = first; i < last; i++) {
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atom->special[i][0] = (tagint) ubuf(buf[m++]).i;
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atom->special[i][1] = (tagint) ubuf(buf[m++]).i;
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}
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}
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/* ----------------------------------------------------------------------
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count neighbor chains of given bond
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------------------------------------------------------------------------- */
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@ -31,6 +31,9 @@ class PairMesoCNT : public Pair {
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void coeff(int, char **) override;
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void init_style() override;
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double init_one(int, int) override;
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int pack_forward_comm(int, int *, double *, int, int *) override;
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void unpack_forward_comm(int, int, double *) override;
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protected:
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int nend_types;
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