git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -5,7 +5,7 @@
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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@ -57,13 +57,13 @@ void Replicate::command(int narg, char **arg)
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// error and warning checks
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if (nx <= 0 || ny <= 0 || nz <= 0)
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if (nx <= 0 || ny <= 0 || nz <= 0)
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error->all(FLERR,"Illegal replicate command");
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if (domain->dimension == 2 && nz != 1)
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error->all(FLERR,"Cannot replicate 2d simulation in z dimension");
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if ((nx > 1 && domain->xperiodic == 0) ||
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if ((nx > 1 && domain->xperiodic == 0) ||
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(ny > 1 && domain->yperiodic == 0) ||
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(nz > 1 && domain->zperiodic == 0)) {
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(nz > 1 && domain->zperiodic == 0)) {
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if (comm->me == 0)
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error->warning(FLERR,"Replicating in a non-periodic dimension");
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}
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@ -137,9 +137,9 @@ void Replicate::command(int narg, char **arg)
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atom->tag[i] = 0;
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if (nrep*old->natoms < 0 || nrep*old->natoms > MAXBIGINT ||
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nrep*old->nbonds < 0 || nrep*old->nbonds > MAXBIGINT ||
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nrep*old->nangles < 0 || nrep*old->nangles > MAXBIGINT ||
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nrep*old->ndihedrals < 0 || nrep*old->ndihedrals > MAXBIGINT ||
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nrep*old->nbonds < 0 || nrep*old->nbonds > MAXBIGINT ||
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nrep*old->nangles < 0 || nrep*old->nangles > MAXBIGINT ||
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nrep*old->ndihedrals < 0 || nrep*old->ndihedrals > MAXBIGINT ||
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nrep*old->nimpropers < 0 || nrep*old->nimpropers > MAXBIGINT)
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error->all(FLERR,"Replicated system is too big");
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@ -156,7 +156,7 @@ void Replicate::command(int narg, char **arg)
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atom->nangletypes = old->nangletypes;
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atom->ndihedraltypes = old->ndihedraltypes;
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atom->nimpropertypes = old->nimpropertypes;
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atom->bond_per_atom = old->bond_per_atom;
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atom->angle_per_atom = old->angle_per_atom;
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atom->dihedral_per_atom = old->dihedral_per_atom;
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@ -270,77 +270,77 @@ void Replicate::command(int narg, char **arg)
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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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for (iz = 0; iz < nz; iz++) {
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// while loop over one proc's atom list
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// while loop over one proc's atom list
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m = 0;
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while (m < n) {
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image = (512 << 20) | (512 << 10) | 512;
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if (triclinic == 0) {
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x[0] = buf[m+1] + ix*old_xprd;
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x[1] = buf[m+2] + iy*old_yprd;
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x[2] = buf[m+3] + iz*old_zprd;
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} else {
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x[0] = buf[m+1] + ix*old_xprd + iy*old_xy + iz*old_xz;
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x[1] = buf[m+2] + iy*old_yprd + iz*old_yz;
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x[2] = buf[m+3] + iz*old_zprd;
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}
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domain->remap(x,image);
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if (triclinic) {
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domain->x2lamda(x,lamda);
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coord = lamda;
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} else coord = x;
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m = 0;
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while (m < n) {
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image = (512 << 20) | (512 << 10) | 512;
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if (triclinic == 0) {
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x[0] = buf[m+1] + ix*old_xprd;
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x[1] = buf[m+2] + iy*old_yprd;
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x[2] = buf[m+3] + iz*old_zprd;
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} else {
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x[0] = buf[m+1] + ix*old_xprd + iy*old_xy + iz*old_xz;
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x[1] = buf[m+2] + iy*old_yprd + iz*old_yz;
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x[2] = buf[m+3] + iz*old_zprd;
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}
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domain->remap(x,image);
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if (triclinic) {
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domain->x2lamda(x,lamda);
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coord = lamda;
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} else coord = x;
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if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
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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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if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
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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]);
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i = atom->nlocal - 1;
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if (tag_enable)
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atom_offset = iz*ny*nx*maxtag + iy*nx*maxtag + ix*maxtag;
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else atom_offset = 0;
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mol_offset = iz*ny*nx*maxmol + iy*nx*maxmol + ix*maxmol;
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i = atom->nlocal - 1;
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if (tag_enable)
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atom_offset = iz*ny*nx*maxtag + iy*nx*maxtag + ix*maxtag;
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else atom_offset = 0;
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mol_offset = iz*ny*nx*maxmol + iy*nx*maxmol + ix*maxmol;
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atom->x[i][0] = x[0];
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atom->x[i][1] = x[1];
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atom->x[i][2] = x[2];
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atom->x[i][0] = x[0];
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atom->x[i][1] = x[1];
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atom->x[i][2] = x[2];
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atom->tag[i] += atom_offset;
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atom->image[i] = image;
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atom->tag[i] += atom_offset;
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atom->image[i] = image;
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if (atom->molecular) {
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if (atom->molecule[i] > 0)
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atom->molecule[i] += mol_offset;
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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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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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}
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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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}
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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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}
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}
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} else m += static_cast<int> (buf[m]);
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}
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}
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if (atom->molecular) {
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if (atom->molecule[i] > 0)
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atom->molecule[i] += mol_offset;
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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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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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}
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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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}
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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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}
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}
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} else m += static_cast<int> (buf[m]);
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}
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}
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}
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}
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}
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@ -363,7 +363,7 @@ void Replicate::command(int narg, char **arg)
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if (natoms != atom->natoms)
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error->all(FLERR,"Replicate did not assign all atoms correctly");
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if (me == 0) {
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if (atom->nbonds) {
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if (screen) fprintf(screen," " BIGINT_FORMAT " bonds\n",atom->nbonds);
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@ -371,21 +371,21 @@ void Replicate::command(int narg, char **arg)
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}
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if (atom->nangles) {
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if (screen) fprintf(screen," " BIGINT_FORMAT " angles\n",
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atom->nangles);
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atom->nangles);
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if (logfile) fprintf(logfile," " BIGINT_FORMAT " angles\n",
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atom->nangles);
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atom->nangles);
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}
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if (atom->ndihedrals) {
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if (screen) fprintf(screen," " BIGINT_FORMAT " dihedrals\n",
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atom->ndihedrals);
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atom->ndihedrals);
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if (logfile) fprintf(logfile," " BIGINT_FORMAT " dihedrals\n",
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atom->ndihedrals);
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atom->ndihedrals);
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}
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if (atom->nimpropers) {
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if (screen) fprintf(screen," " BIGINT_FORMAT " impropers\n",
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atom->nimpropers);
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atom->nimpropers);
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if (logfile) fprintf(logfile," " BIGINT_FORMAT " impropers\n",
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atom->nimpropers);
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atom->nimpropers);
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}
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}
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Block a user