'bondlist' option for replicate command
generalizes the command to work for periodic systems
This commit is contained in:
jrgissing
@ -55,10 +55,16 @@ void Replicate::command(int narg, char **arg)
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int ny = utils::inumeric(FLERR,arg[1],false,lmp);
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int nz = utils::inumeric(FLERR,arg[2],false,lmp);
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int nrep = nx*ny*nz;
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allnrep[0] = nx;
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allnrep[1] = ny;
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allnrep[2] = nz;
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int bbox_flag = 0;
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if (narg == 4)
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int bondlist_flag = 0;
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if (narg == 4) {
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if (strcmp(arg[3],"bbox") == 0) bbox_flag = 1;
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if (strcmp(arg[3],"bondlist") == 0) bondlist_flag = 1;
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}
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// error and warning checks
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@ -81,9 +87,9 @@ void Replicate::command(int narg, char **arg)
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MPI_Barrier(world);
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double time1 = platform::walltime();
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// maxtag = largest atom tag across all existing atoms
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// maxtag = original largest atom tag across all existing atoms
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tagint maxtag = 0;
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maxtag = 0;
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if (atom->tag_enable) {
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for (i = 0; i < atom->nlocal; i++) maxtag = MAX(atom->tag[i],maxtag);
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tagint maxtag_all;
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@ -154,7 +160,7 @@ void Replicate::command(int narg, char **arg)
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// atom = new replicated atom class
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// also set atomKK for Kokkos version of Atom class
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Atom *old = atom;
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old = atom;
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atomKK = nullptr;
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if (lmp->kokkos) atom = atomKK = new AtomKokkos(lmp);
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else atom = new Atom(lmp);
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@ -229,6 +235,11 @@ void Replicate::command(int narg, char **arg)
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double old_xprd = domain->xprd;
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double old_yprd = domain->yprd;
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double old_zprd = domain->zprd;
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double old_center[3];
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for (i = 0; i < 3; i++) {
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old_prd_half[i] = domain->prd_half[i];
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old_center[i] = 0.5*(domain->boxlo[i]+domain->boxhi[i]);
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}
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double old_xy = domain->xy;
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double old_xz = domain->xz;
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double old_yz = domain->yz;
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@ -339,13 +350,13 @@ void Replicate::command(int narg, char **arg)
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AtomVec *avec = atom->avec;
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int ix,iy,iz;
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tagint atom_offset,mol_offset;
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tagint atom_offset,mol_offset,atom0tag;
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imageint image;
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double x[3],lamda[3];
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double x[3],lamda[3],shiftsign[3];
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double *coord;
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int tag_enable = atom->tag_enable;
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if (bbox_flag) {
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if (bbox_flag || bondlist_flag) {
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// allgather size of buf on each proc
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@ -418,10 +429,23 @@ void Replicate::command(int narg, char **arg)
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int num_replicas_added = 0;
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// let's repurpose the old atom class to allow atom->map for all atoms
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// tag and x for the whole system (before replication) stored in 'old'
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m = 0;
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old->nlocal = 0;
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while (m < size_buf_all) m += old_avec->unpack_restart(&buf_all[m],old);
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old->map_init();
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old->map_set();
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for (ix = 0; ix < nx; ix++) {
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for (iy = 0; iy < ny; iy++) {
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for (iz = 0; iz < nz; iz++) {
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thisrep[0] = ix;
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thisrep[1] = iy;
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thisrep[2] = iz;
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// domain->remap() overwrites coordinates, so always recompute here
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if (triclinic) {
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@ -567,6 +591,10 @@ void Replicate::command(int narg, char **arg)
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m = 0;
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while (m < size_buf_all) {
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for (j = 0; j < 3; j++) {
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if (buf_all[m+j+1] > old_center[j]) shiftsign[j] = 1;
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else shiftsign[j] = -1;
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}
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image = ((imageint) IMGMAX << IMG2BITS) |
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((imageint) IMGMAX << IMGBITS) | IMGMAX;
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if (triclinic == 0) {
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@ -588,7 +616,7 @@ void Replicate::command(int narg, char **arg)
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coord[1] >= sublo[1] && coord[1] < subhi[1] &&
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coord[2] >= sublo[2] && coord[2] < subhi[2]) {
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m += avec->unpack_restart(&buf_all[m]);
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m += avec->unpack_restart(&buf_all[m],atom);
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i = atom->nlocal - 1;
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if (tag_enable)
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@ -600,6 +628,7 @@ void Replicate::command(int narg, char **arg)
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atom->x[i][1] = x[1];
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atom->x[i][2] = x[2];
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atom0tag = atom->tag[i];
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atom->tag[i] += atom_offset;
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atom->image[i] = image;
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@ -608,27 +637,50 @@ void Replicate::command(int narg, char **arg)
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atom->molecule[i] += mol_offset;
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if (atom->molecular == Atom::MOLECULAR) {
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if (atom->avec->bonds_allow)
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for (j = 0; j < atom->num_bond[i]; j++)
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atom->bond_atom[i][j] += atom_offset;
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for (j = 0; j < atom->num_bond[i]; j++) {
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if (bondlist_flag)
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newtag(atom0tag,atom->bond_atom[i][j],shiftsign);
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else atom->bond_atom[i][j] += atom_offset;
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}
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if (atom->avec->angles_allow)
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for (j = 0; j < atom->num_angle[i]; j++) {
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atom->angle_atom1[i][j] += atom_offset;
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atom->angle_atom2[i][j] += atom_offset;
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atom->angle_atom3[i][j] += atom_offset;
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if (bondlist_flag) {
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newtag(atom0tag,atom->angle_atom1[i][j],shiftsign);
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newtag(atom0tag,atom->angle_atom2[i][j],shiftsign);
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newtag(atom0tag,atom->angle_atom3[i][j],shiftsign);
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} else {
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atom->angle_atom1[i][j] += atom_offset;
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atom->angle_atom2[i][j] += atom_offset;
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atom->angle_atom3[i][j] += atom_offset;
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}
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}
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if (atom->avec->dihedrals_allow)
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for (j = 0; j < atom->num_dihedral[i]; j++) {
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atom->dihedral_atom1[i][j] += atom_offset;
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atom->dihedral_atom2[i][j] += atom_offset;
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atom->dihedral_atom3[i][j] += atom_offset;
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atom->dihedral_atom4[i][j] += atom_offset;
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if (bondlist_flag) {
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newtag(atom0tag,atom->dihedral_atom1[i][j],shiftsign);
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newtag(atom0tag,atom->dihedral_atom2[i][j],shiftsign);
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newtag(atom0tag,atom->dihedral_atom3[i][j],shiftsign);
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newtag(atom0tag,atom->dihedral_atom4[i][j],shiftsign);
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} else {
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atom->dihedral_atom1[i][j] += atom_offset;
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atom->dihedral_atom2[i][j] += atom_offset;
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atom->dihedral_atom3[i][j] += atom_offset;
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atom->dihedral_atom4[i][j] += atom_offset;
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}
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}
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if (atom->avec->impropers_allow)
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for (j = 0; j < atom->num_improper[i]; j++) {
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atom->improper_atom1[i][j] += atom_offset;
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atom->improper_atom2[i][j] += atom_offset;
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atom->improper_atom3[i][j] += atom_offset;
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atom->improper_atom4[i][j] += atom_offset;
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if (bondlist_flag) {
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newtag(atom0tag,atom->improper_atom1[i][j],shiftsign);
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newtag(atom0tag,atom->improper_atom2[i][j],shiftsign);
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newtag(atom0tag,atom->improper_atom3[i][j],shiftsign);
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newtag(atom0tag,atom->improper_atom4[i][j],shiftsign);
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} else {
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atom->improper_atom1[i][j] += atom_offset;
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atom->improper_atom2[i][j] += atom_offset;
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atom->improper_atom3[i][j] += atom_offset;
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atom->improper_atom4[i][j] += atom_offset;
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}
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}
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}
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}
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@ -689,7 +741,7 @@ void Replicate::command(int narg, char **arg)
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coord[1] >= sublo[1] && coord[1] < subhi[1] &&
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coord[2] >= sublo[2] && coord[2] < subhi[2]) {
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m += avec->unpack_restart(&buf[m]);
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m += avec->unpack_restart(&buf[m],atom);
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i = atom->nlocal - 1;
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if (tag_enable)
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@ -739,7 +791,7 @@ void Replicate::command(int narg, char **arg)
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}
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}
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}
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} // if (bbox_flag)
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} // if (bbox_flag || bondlist_flag)
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// free communication buffer and old atom class
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@ -801,3 +853,25 @@ void Replicate::command(int narg, char **arg)
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if (me == 0)
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utils::logmesg(lmp," replicate CPU = {:.3f} seconds\n",platform::walltime()-time1);
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}
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/* ----------------------------------------------------------------------
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find new tag for the atom 'atom2bond' bonded to atom 'atom0'
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for bondlist option, useful for periodic loops or inconsistent image flags
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reassign bond if > old boxlength / 2
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------------------------------------------------------------------------- */
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void Replicate::newtag(int atom0tag, int &tag2bond, double shiftsign[]) {
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double del[3];
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int rep2bond[3], repshift[3] = {0, 0, 0};
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int atom0 = old->map(atom0tag);
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int atom2bond = old->map(tag2bond);
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for (int i = 0; i < 3; i++) {
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del[i] = fabs(old->x[atom0][i] - old->x[atom2bond][i]);
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if (del[i] > old_prd_half[i]) repshift[i] = shiftsign[i];
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rep2bond[i] = thisrep[i] + repshift[i];
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if (rep2bond[i] >= allnrep[i]) rep2bond[i] = 0;
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if (rep2bond[i] < 0) rep2bond[i] = allnrep[i]-1;
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}
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tag2bond = (tag2bond + rep2bond[2]*allnrep[1]*allnrep[0]*maxtag
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+ rep2bond[1]*allnrep[0]*maxtag + rep2bond[0]*maxtag);
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}
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