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Modularize writing of position and image in dump_h5md.

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This commit is contained in:
Pierre de Buyl
2014-08-20 16:08:49 +02:00
committed by Pierre de Buyl
parent 4d6ef607b7
commit 692b14eb74
2 changed files with 86 additions and 33 deletions
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109
src/USER-H5MD/dump_h5md.cpp
View File

@ -37,7 +37,7 @@ using namespace LAMMPS_NS;
DumpH5MD::DumpH5MD(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
{
if (narg != 5) error->all(FLERR,"Illegal dump xtc command");
if (narg<6) error->all(FLERR,"Illegal dump h5md command");
if (binary || compressed || multifile || multiproc)
error->all(FLERR,"Invalid dump h5md filename");
@ -48,13 +48,40 @@ DumpH5MD::DumpH5MD(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
flush_flag = 0;
unwrap_flag = 0;
every_dump = force->inumeric(FLERR,arg[3]);
every_position = every_image = -1;
int iarg=5;
size_one=0;
while (iarg<narg) {
if (strcmp(arg[iarg], "position")==0) {
if (iarg+1>=narg) {
error->all(FLERR, "Invalid number of arguments in dump h5md");
}
every_position = atoi(arg[iarg+1]);
iarg+=2;
size_one+=domain->dimension;
} else if (strcmp(arg[iarg], "image")==0) {
if (iarg+1>=narg) {
error->all(FLERR, "Invalid number of arguments in dump h5md");
}
every_image = atoi(arg[iarg+1]);
iarg+=2;
size_one+=domain->dimension;
} else {
error->all(FLERR, "Invalid argument to dump h5md");
}
}
// allocate global array for atom coords
bigint n = group->count(igroup);
natoms = static_cast<int> (n);
memory->create(dump_position,domain->dimension*natoms,"dump:position");
memory->create(dump_image,domain->dimension*natoms,"dump:image");
if (every_position>0)
memory->create(dump_position,domain->dimension*natoms,"dump:position");
if (every_image>0)
memory->create(dump_image,domain->dimension*natoms,"dump:image");
openfile();
ntotal = 0;
@ -64,8 +91,10 @@ DumpH5MD::DumpH5MD(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
DumpH5MD::~DumpH5MD()
{
memory->destroy(dump_position);
memory->destroy(dump_image);
if (every_position>0)
memory->destroy(dump_position);
if (every_image>0)
memory->destroy(dump_image);
}
/* ---------------------------------------------------------------------- */
@ -102,9 +131,12 @@ void DumpH5MD::openfile()
delete [] group_name;
dims[0] = natoms;
dims[1] = domain->dimension;
particles_data.position = h5md_create_time_data(particles_data.group, "position", 2, dims, H5T_NATIVE_DOUBLE, NULL);
h5md_create_box(&particles_data, dims[1], boundary, true, NULL);
particles_data.image = h5md_create_time_data(particles_data.group, "image", 2, dims, H5T_NATIVE_INT, NULL);
if (every_position>0) {
particles_data.position = h5md_create_time_data(particles_data.group, "position", 2, dims, H5T_NATIVE_DOUBLE, NULL);
h5md_create_box(&particles_data, dims[1], boundary, true, NULL);
}
if (every_image>0)
particles_data.image = h5md_create_time_data(particles_data.group, "image", 2, dims, H5T_NATIVE_INT, NULL);
}
for (int i=0; i<3; i++) {
delete [] boundary[i];
@ -144,12 +176,16 @@ void DumpH5MD::pack(tagint *ids)
int iy = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
int iz = (image[i] >> IMG2BITS) - IMGMAX;
buf[m++] = (x[i][0] + ix * xprd);
buf[m++] = (x[i][1] + iy * yprd);
if (dim>2) buf[m++] = (x[i][2] + iz * zprd);
buf[m++] = ix;
buf[m++] = iy;
if (dim>2) buf[m++] = iz;
if (every_position>0 && update->ntimestep % (every_position*every_dump) == 0) {
buf[m++] = (x[i][0] + ix * xprd);
buf[m++] = (x[i][1] + iy * yprd);
if (dim>2) buf[m++] = (x[i][2] + iz * zprd);
}
if (every_image>0 && update->ntimestep % (every_image*every_dump) == 0) {
buf[m++] = ix;
buf[m++] = iy;
if (dim>2) buf[m++] = iz;
}
ids[n++] = tag[i];
}
@ -159,12 +195,16 @@ void DumpH5MD::pack(tagint *ids)
int ix = (image[i] & IMGMASK) - IMGMAX;
int iy = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
int iz = (image[i] >> IMG2BITS) - IMGMAX;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
if (dim>2) buf[m++] = x[i][2];
buf[m++] = ix;
buf[m++] = iy;
if (dim>2) buf[m++] = iz;
if (every_position>0 && update->ntimestep % (every_position*every_dump) == 0) {
buf[m++] = x[i][0];
buf[m++] = x[i][1];
if (dim>2) buf[m++] = x[i][2];
}
if (every_image>0 && update->ntimestep % (every_image*every_dump) == 0) {
buf[m++] = ix;
buf[m++] = iy;
if (dim>2) buf[m++] = iz;
}
ids[n++] = tag[i];
}
}
@ -181,12 +221,14 @@ void DumpH5MD::write_data(int n, double *mybuf)
int k = dim*ntotal;
int k_image = dim*ntotal;
for (int i = 0; i < n; i++) {
for (int j=0; j<dim; j++) {
dump_position[k++] = mybuf[m++];
}
for (int j=0; j<dim; j++) {
dump_image[k_image++] = mybuf[m++];
}
if (every_position>0 && update->ntimestep % (every_position*every_dump) == 0)
for (int j=0; j<dim; j++) {
dump_position[k++] = mybuf[m++];
}
if (every_image>0 && update->ntimestep % (every_image*every_dump) == 0)
for (int j=0; j<dim; j++) {
dump_image[k_image++] = mybuf[m++];
}
ntotal++;
}
@ -221,11 +263,14 @@ void DumpH5MD::write_frame()
double edges[3];
local_step = update->ntimestep;
local_time = local_step * update->dt;
h5md_append(particles_data.position, dump_position, local_step, local_time);
edges[0] = boxxhi - boxxlo;
edges[1] = boxyhi - boxylo;
edges[2] = boxzhi - boxzlo;
h5md_append(particles_data.box_edges, edges, local_step, local_time);
h5md_append(particles_data.image, dump_image, local_step, local_time);
if (every_position>0 && local_step % (every_position*every_dump) == 0) {
h5md_append(particles_data.position, dump_position, local_step, local_time);
edges[0] = boxxhi - boxxlo;
edges[1] = boxyhi - boxylo;
edges[2] = boxzhi - boxzlo;
h5md_append(particles_data.box_edges, edges, local_step, local_time);
}
if (every_image>0 && local_step % (every_image*every_dump) == 0)
h5md_append(particles_data.image, dump_image, local_step, local_time);
}

10
src/USER-H5MD/dump_h5md.h
View File

@ -38,9 +38,12 @@ class DumpH5MD : public Dump {
h5md_file datafile;
h5md_particles_group particles_data;
// data arrays
// data arrays and intervals
int every_dump;
double *dump_position;
int every_position;
int *dump_image;
int every_image;
void init_style();
int modify_param(int, char **);
@ -65,6 +68,11 @@ Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Invalid number of arguments in dump h5md
Make sure that each data item (position, etc.) is followed by a dump
interval.
E: Dump h5md requires sorting by atom ID
Use the dump_modify sort command to enable this.