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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@371 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2007-03-08 00:54:02 +00:00
parent a70ee2eadc
commit 9e1f8bcd6a
64 changed files with 1785 additions and 772 deletions
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95
src/replicate.cpp
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@ -27,7 +27,8 @@
using namespace LAMMPS_NS;
#define LB_FACTOR 1.1
#define MAXATOMS 0x7FFFFFFF
#define MAXATOMS 0x7FFFFFFF
#define EPSILON 1.0e-6
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
@ -92,7 +93,7 @@ void Replicate::command(int narg, char **arg)
// unmap existing atoms via image flags
for (i = 0; i < atom->nlocal; i++)
domain->unmap(atom->x[i][0],atom->x[i][1],atom->x[i][2],atom->image[i]);
domain->unmap(atom->x[i],atom->image[i]);
// communication buffer for all my atom's info
// max_size = largest buffer needed by any proc
@ -157,15 +158,24 @@ void Replicate::command(int narg, char **arg)
// store old simulation box
int triclinic = domain->triclinic;
double old_xprd = domain->xprd;
double old_yprd = domain->yprd;
double old_zprd = domain->zprd;
double old_xy = domain->xy;
double old_xz = domain->xz;
double old_yz = domain->yz;
// setup new simulation box
domain->boxxhi = domain->boxxlo + nx*old_xprd;
domain->boxyhi = domain->boxylo + ny*old_yprd;
domain->boxzhi = domain->boxzlo + nz*old_zprd;
if (triclinic) {
domain->xy *= ny;
domain->xz *= nz;
domain->yz *= nz;
}
// new problem setup using new box boundaries
@ -175,20 +185,12 @@ void Replicate::command(int narg, char **arg)
atom->allocate_type_arrays();
atom->avec->grow(n);
domain->print_box(" ");
domain->set_initial_box();
domain->set_global_box();
comm->set_procs();
domain->set_local_box();
// sub xyz lo/hi = new processor sub-domain
double subxlo = domain->subxlo;
double subxhi = domain->subxhi;
double subylo = domain->subylo;
double subyhi = domain->subyhi;
double subzlo = domain->subzlo;
double subzhi = domain->subzhi;
// copy type arrays to new atom class
if (atom->mass) {
@ -206,12 +208,41 @@ void Replicate::command(int narg, char **arg)
}
}
// set bounds for my proc
// if periodic and I am lo/hi proc, adjust bounds by EPSILON
// insures all replicated atoms will be owned even with round-off
double sublo[3],subhi[3];
if (triclinic == 0) {
sublo[0] = domain->sublo[0]; subhi[0] = domain->subhi[0];
sublo[1] = domain->sublo[1]; subhi[1] = domain->subhi[1];
sublo[2] = domain->sublo[2]; subhi[2] = domain->subhi[2];
} else {
sublo[0] = domain->sublo_lamda[0]; subhi[0] = domain->subhi_lamda[0];
sublo[1] = domain->sublo_lamda[1]; subhi[1] = domain->subhi_lamda[1];
sublo[2] = domain->sublo_lamda[2]; subhi[2] = domain->subhi_lamda[2];
}
if (domain->xperiodic) {
if (comm->myloc[0] == 0) sublo[0] -= EPSILON;
if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] += EPSILON;
}
if (domain->yperiodic) {
if (comm->myloc[1] == 0) sublo[1] -= EPSILON;
if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] += EPSILON;
}
if (domain->zperiodic) {
if (comm->myloc[2] == 0) sublo[2] -= EPSILON;
if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] += EPSILON;
}
// loop over all procs
// if this iteration of loop is me:
// pack my unmapped atom data into buf
// bcast it to all other procs
// for each atom in buf, each proc performs 3d replicate loop:
// xnew,ynew,znew = new replicated position
// performs 3d replicate loop with while loop over atoms in buf
// x = new replicated position
// unpack atom into new atom class from buf if I own it
// adjust tag, mol #, coord, topology info as needed
@ -219,7 +250,8 @@ void Replicate::command(int narg, char **arg)
AtomVec *avec = atom->avec;
int ix,iy,iz,image,atom_offset,mol_offset;
double xnew,ynew,znew;
double x[3],lamda[3];
double *coord;
int tag_enable = atom->tag_enable;
for (int iproc = 0; iproc < nprocs; iproc++) {
@ -234,17 +266,29 @@ void Replicate::command(int narg, char **arg)
for (iy = 0; iy < ny; iy++) {
for (iz = 0; iz < nz; iz++) {
// while loop over one proc's atom list
m = 0;
while (m < n) {
xnew = buf[m+1] + ix*old_xprd;
ynew = buf[m+2] + iy*old_yprd;
znew = buf[m+3] + iz*old_zprd;
image = (512 << 20) | (512 << 10) | 512;
domain->remap(xnew,ynew,znew,image);
if (triclinic == 0) {
x[0] = buf[m+1] + ix*old_xprd;
x[1] = buf[m+2] + iy*old_yprd;
x[2] = buf[m+3] + iz*old_zprd;
} else {
x[0] = buf[m+1] + ix*old_xprd + iy*old_xy + iz*old_xz;
x[1] = buf[m+2] + iy*old_yprd + iz*old_yz;
x[2] = buf[m+3] + iz*old_zprd;
}
domain->remap(x,image);
if (triclinic) {
domain->x2lamda(x,lamda);
coord = lamda;
} else coord = x;
if (xnew >= subxlo && xnew < subxhi &&
ynew >= subylo && ynew < subyhi &&
znew >= subzlo && znew < subzhi) {
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1] &&
coord[2] >= sublo[2] && coord[2] < subhi[2]) {
m += avec->unpack_restart(&buf[m]);
@ -254,9 +298,9 @@ void Replicate::command(int narg, char **arg)
else atom_offset = 0;
mol_offset = iz*ny*nx*maxmol + iy*nx*maxmol + ix*maxmol;
atom->x[i][0] = xnew;
atom->x[i][1] = ynew;
atom->x[i][2] = znew;
atom->x[i][0] = x[0];
atom->x[i][1] = x[1];
atom->x[i][2] = x[2];
atom->tag[i] += atom_offset;
atom->image[i] = image;
@ -289,8 +333,7 @@ void Replicate::command(int narg, char **arg)
}
}
} else m += static_cast<int> (buf[m]);
} // end of while loop over one proc's atom list
}
}
}
}