struct sockaddr_in make_address(char *address, uint16_t port){
struct sockaddr_in addr;
struct hostent *hostinfo;
addr.sin_family = AF_INET;
addr.sin_port = htons (port);
hostinfo = gethostbyname(address);
if(hostinfo == NULL)HERR("gethostbyname");
addr.sin_addr = *(struct in_addr*) hostinfo->h_addr;
return addr;
}
/* ------- begin -------------------------- writeAtmos_p.c --- */
void writeAtmos_p(void)
{
/* Write atmos arrays. This has now been modified and writes the interpolated
arrays, from depth_refine. With that, now this is the only viable option
to write the atmos data, as there is no option to save in memory and
writeAtmos_all used to write from the input file, not the interpolated
quantities
IMPORTANT: at the moment this is a trimmed version, only writing z to save
space and computational time.
*/
const char routineName[] = "writeAtmos_p";
hsize_t offset[] = {0, 0, 0, 0};
hsize_t count[] = {1, 1, 1, 1};
hsize_t dims[4];
hid_t file_dspace, mem_dspace;
/* Memory dataspace */
dims[0] = atmos.Nspace;
if (( mem_dspace = H5Screate_simple(1, dims, NULL) ) < 0)
HERR(routineName);
/* File dataspace */
offset[0] = mpi.ix;
offset[1] = mpi.iy;
offset[2] = mpi.zcut;
count[2] = atmos.Nspace;
if (( file_dspace = H5Dget_space(io.in_atmos_T) ) < 0) HERR(routineName);
if (( H5Sselect_hyperslab(file_dspace, H5S_SELECT_SET, offset,
NULL, count, NULL) ) < 0) HERR(routineName);
if (( H5Dwrite(io.in_atmos_T, H5T_NATIVE_DOUBLE, mem_dspace,
file_dspace, H5P_DEFAULT, atmos.T) ) < 0) HERR(routineName);
if (( H5Dwrite(io.in_atmos_vz, H5T_NATIVE_DOUBLE, mem_dspace,
file_dspace, H5P_DEFAULT, geometry.vel) ) < 0) HERR(routineName);
if (( H5Dwrite(io.in_atmos_z, H5T_NATIVE_DOUBLE, mem_dspace,
file_dspace, H5P_DEFAULT, geometry.height) ) < 0) HERR(routineName);
/* release dataspace resources */
if (( H5Sclose(mem_dspace) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
return;
}
/* ------- begin -------------------------- readMolPops_p.c -- */
void readMolPops(Molecule *molecule) {
/* --- Read populations from file.
Note: readPopulations only reads the true populations and not
the LTE populations.
-- -------------- */
const char routineName[] = "readMolPops";
char group_name[ARR_STRLEN], *atmosID;
int nz, nlevel;
H5T_class_t type_class;
size_t attr_size;
hsize_t offset[] = {0, 0, 0, 0};
hsize_t count[] = {1, 1, 1, 1};
hsize_t dims[4];
hid_t ncid, file_dspace, mem_dspace, pop_var;
/* --- Open molecule group --- */
sprintf(group_name, "molecule_%s", molecule->ID);
if (( ncid = H5Gopen(io.aux_ncid, group_name, H5P_DEFAULT) ) < 0)
HERR(routineName);
/* --- Consistency checks --- */
/* Check that atmosID is the same */
if (( H5LTget_attribute_info(io.aux_ncid, "/", "atmosID", NULL, &type_class,
&attr_size) ) < 0) HERR(routineName);
atmosID = (char *) malloc(attr_size + 1);
if (( H5LTget_attribute_string(io.aux_ncid, "/", "atmosID", atmosID) ) < 0)
HERR(routineName);
if (!strstr(atmosID, atmos.ID)) {
sprintf(messageStr,
"Indata file was calculated for different atmosphere (%s) than current",
atmosID);
Error(WARNING, routineName, messageStr);
}
free(atmosID);
/* Check that dimension sizes match */
if (( H5LTget_attribute_int(ncid, ".", "nlevel_vibr", &nlevel) ) < 0)
HERR(routineName);
if (nlevel != molecule->Nv) {
sprintf(messageStr,
"Number of levels mismatch: expected %d, found %d.",
molecule->Nv, (int)nlevel);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
if (( H5LTget_attribute_int(io.aux_ncid, ".", "nz", &nz) ) < 0)
HERR(routineName);
if (nz < atmos.Nspace) {
sprintf(messageStr,
"Number of depth points mismatch: expected %ld, found %d.",
atmos.Nspace, (int)nz);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
/* --- Read data --- */
if (( pop_var = H5Dopen2(ncid, POP_NAME, H5P_DEFAULT)) < 0)
HERR(routineName);
dims[0] = molecule->Nv;
dims[1] = atmos.Nspace;
if (( mem_dspace = H5Screate_simple(2, dims, NULL) ) < 0) HERR(routineName);
/* File dataspace */
offset[0] = 0;
offset[1] = mpi.ix;
offset[2] = mpi.iy;
offset[3] = mpi.zcut;
count[0] = molecule->Nv;
count[3] = atmos.Nspace;
if (( file_dspace = H5Dget_space(pop_var) ) < 0) HERR(routineName);
if (( H5Sselect_hyperslab(file_dspace, H5S_SELECT_SET, offset,
NULL, count, NULL) ) < 0) HERR(routineName);
if (( H5Dread(pop_var, H5T_NATIVE_DOUBLE, mem_dspace,
file_dspace, H5P_DEFAULT, molecule->nv[0]) ) < 0) HERR(routineName);
if (( H5Sclose(mem_dspace) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
if (( H5Dclose(pop_var) ) < 0) HERR(routineName);
return;
}
/* ------- begin -------------------------- readPopulations_p.c -- */
void readPopulations(Atom *atom) {
/* --- Read populations from file.
Note: readPopulations only reads the true populations and not
the LTE populations.
Note2: This routine will not work yet in HFD5. Access to the aux file
needs to be better regulated in OLD_POPULATIONS cases (ie, append
and read/write acess). The code below assumes the file is already
open, which may not be the case.
-- -------------- */
const char routineName[] = "readPopulations_p";
char group_name[ARR_STRLEN], *atmosID;
int nz, nlevel;
H5T_class_t type_class;
size_t attr_size;
hsize_t offset[] = {0, 0, 0, 0};
hsize_t count[] = {1, 1, 1, 1};
hsize_t dims[4];
hid_t ncid, file_dspace, mem_dspace, pop_var;
/* --- Open atom group --- */
sprintf(group_name,(atom->ID[1] == ' ') ? "atom_%.1s" : "atom_%.2s", atom->ID);
if (( ncid = H5Gopen(io.aux_ncid, group_name, H5P_DEFAULT) ) < 0)
HERR(routineName);
/* --- Consistency checks --- */
/* Check that atmosID is the same */
if (( H5LTget_attribute_info(io.aux_ncid, "/", "atmosID", NULL, &type_class,
&attr_size) ) < 0) HERR(routineName);
atmosID = (char *) malloc(attr_size + 1);
if (( H5LTget_attribute_string(io.aux_ncid, "/", "atmosID", atmosID) ) < 0)
HERR(routineName);
if (!strstr(atmosID, atmos.ID)) {
sprintf(messageStr,
"Indata file was calculated for different atmosphere (%s) than current",
atmosID);
Error(WARNING, routineName, messageStr);
}
free(atmosID);
/* Check that dimension sizes match */
if (( H5LTget_attribute_int(ncid, ".", "nlevel", &nlevel) ) < 0)
HERR(routineName);
if (nlevel != atom->Nlevel) {
sprintf(messageStr,
"Number of levels mismatch: expected %d, found %d.",
atom->Nlevel, (int)nlevel);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
if (( H5LTget_attribute_int(io.aux_ncid, ".", "nz", &nz) ) < 0)
HERR(routineName);
if (nz < atmos.Nspace) {
sprintf(messageStr,
"Number of depth points mismatch: expected %ld, found %d.",
atmos.Nspace, (int)nz);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
/* --- Read data --- */
if (( pop_var = H5Dopen2(ncid, POP_NAME, H5P_DEFAULT)) < 0)
HERR(routineName);
dims[0] = atom->Nlevel;
dims[1] = atmos.Nspace;
if (( mem_dspace = H5Screate_simple(2, dims, NULL) ) < 0) HERR(routineName);
/* File dataspace */
offset[0] = 0;
offset[1] = mpi.ix;
offset[2] = mpi.iy;
offset[3] = mpi.zcut;
count[0] = atom->Nlevel;
count[3] = atmos.Nspace;
if (( file_dspace = H5Dget_space(pop_var) ) < 0) HERR(routineName);
if (( H5Sselect_hyperslab(file_dspace, H5S_SELECT_SET, offset,
NULL, count, NULL) ) < 0) HERR(routineName);
if (( H5Dread(pop_var, H5T_NATIVE_DOUBLE, mem_dspace,
file_dspace, H5P_DEFAULT, atom->n[0]) ) < 0) HERR(routineName);
if (( H5Sclose(mem_dspace) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
if (( H5Dclose(pop_var) ) < 0) HERR(routineName);
return;
}
/* ------- begin -------------------------- writeAux_p.c --- */
void writeAux_p(void) {
/* this will write: populations, radrates, coll, damping */
const char routineName[] = "writeAux_p";
int nact, kr;
hsize_t offset[] = {0, 0, 0, 0};
hsize_t count[] = {1, 1, 1, 1};
hsize_t dims[4];
hid_t file_dspace, mem_dspace;
Atom *atom;
Molecule *molecule;
AtomicLine *line;
AtomicContinuum *continuum;
/* --- ATOMS --- */
for (nact = 0; nact < atmos.Nactiveatom; nact++) {
atom = atmos.activeatoms[nact];
/* Write populations */
/* Memory dataspace */
dims[0] = atom->Nlevel;
dims[1] = atmos.Nspace;
/* File dataspace */
offset[0] = 0;
offset[1] = mpi.ix;
offset[2] = mpi.iy;
offset[3] = mpi.zcut;
count[0] = atom->Nlevel;
count[3] = atmos.Nspace;
if (input.p15d_wpop) {
if (( mem_dspace = H5Screate_simple(2, dims, NULL) ) < 0)
HERR(routineName);
if (( file_dspace = H5Dget_space(io.aux_atom_pop[nact]) ) < 0)
HERR(routineName);
if (( H5Sselect_hyperslab(file_dspace, H5S_SELECT_SET, offset,
NULL, count, NULL) ) < 0) HERR(routineName);
if (( H5Dwrite(io.aux_atom_pop[nact], H5T_NATIVE_DOUBLE, mem_dspace,
file_dspace, H5P_DEFAULT, atom->n[0]) ) < 0) HERR(routineName);
if (( H5Dwrite(io.aux_atom_poplte[nact], H5T_NATIVE_DOUBLE, mem_dspace,
file_dspace, H5P_DEFAULT, atom->nstar[0]) ) < 0) HERR(routineName);
if (( H5Sclose(mem_dspace) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
}
if (input.p15d_wrates) {
/* Write radiative rates */
dims[0] = atmos.Nspace;
count[0] = 1;
if (( mem_dspace = H5Screate_simple(1, dims, NULL) ) < 0)
HERR(routineName);
if (( file_dspace = H5Dget_space(io.aux_atom_RijL[nact]) ) < 0)
HERR(routineName);
for (kr=0; kr < atom->Nline; kr++) {
offset[0] = kr;
line = &atom->line[kr];
if (( H5Sselect_hyperslab(file_dspace, H5S_SELECT_SET, offset,
NULL, count, NULL) ) < 0) HERR(routineName);
if (( H5Dwrite(io.aux_atom_RijL[nact], H5T_NATIVE_DOUBLE, mem_dspace,
file_dspace, H5P_DEFAULT, line->Rij) ) < 0) HERR(routineName);
if (( H5Dwrite(io.aux_atom_RjiL[nact], H5T_NATIVE_DOUBLE, mem_dspace,
file_dspace, H5P_DEFAULT, line->Rji) ) < 0) HERR(routineName);
}
for (kr=0; kr < atom->Ncont; kr++) {
offset[0] = kr;
continuum = &atom->continuum[kr];
if (( H5Sselect_hyperslab(file_dspace, H5S_SELECT_SET, offset,
NULL, count, NULL) ) < 0) HERR(routineName);
if (( H5Dwrite(io.aux_atom_RijC[nact], H5T_NATIVE_DOUBLE, mem_dspace,
file_dspace, H5P_DEFAULT, continuum->Rij) ) < 0) HERR(routineName);
if (( H5Dwrite(io.aux_atom_RjiC[nact], H5T_NATIVE_DOUBLE, mem_dspace,
file_dspace, H5P_DEFAULT, continuum->Rji) ) < 0) HERR(routineName);
}
if (( H5Sclose(mem_dspace) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
}
}
/* --- MOLECULES --- */
for (nact = 0; nact < atmos.Nactivemol; nact++) {
molecule = atmos.activemols[nact];
if (input.p15d_wpop) {
/* Write populations */
dims[0] = molecule->Nv;
dims[1] = atmos.Nspace;
if (( mem_dspace = H5Screate_simple(2, dims, NULL) ) < 0)
HERR(routineName);
offset[0] = 0;
offset[1] = mpi.ix;
offset[2] = mpi.iy;
offset[3] = mpi.zcut;
count[0] = molecule->Nv;
count[3] = atmos.Nspace;
if (( file_dspace = H5Dget_space(io.aux_mol_pop[nact]) ) < 0)
HERR(routineName);
if (( H5Sselect_hyperslab(file_dspace, H5S_SELECT_SET, offset,
NULL, count, NULL) ) < 0) HERR(routineName);
if (( H5Dwrite(io.aux_mol_pop[nact], H5T_NATIVE_DOUBLE, mem_dspace,
file_dspace, H5P_DEFAULT, molecule->nv[0]) ) < 0) HERR(routineName);
if (( H5Dwrite(io.aux_mol_poplte[nact], H5T_NATIVE_DOUBLE, mem_dspace,
file_dspace, H5P_DEFAULT, molecule->nvstar[0]) ) < 0) HERR(routineName);
if (( H5Sclose(mem_dspace) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
}
}
return;
}
/* ------- begin -------------------------- init_aux_new.c -- --- */
void init_aux_new(void) {
/* Creates the HDF5 file for the auxiliary data */
const char routineName[] = "init_aux_new";
unsigned int *tmp;
double *tmp_double;
int i;
hid_t plist, ncid, file_dspace, ncid_atom, ncid_mol;
hid_t id_x, id_y, id_z, id_n, id_tmp;
hsize_t dims[4];
char group_name[ARR_STRLEN];
Atom *atom;
Molecule *molecule;
/* Create the file */
if (( plist = H5Pcreate(H5P_FILE_ACCESS) ) < 0) HERR(routineName);
if (( H5Pset_fapl_mpio(plist, mpi.comm, mpi.info) ) < 0) HERR(routineName);
if (( ncid = H5Fcreate(AUX_FILE, H5F_ACC_TRUNC, H5P_DEFAULT,
plist) ) < 0) HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
/* --- Definitions for the root group --- */
/* dimensions as attributes */
if (( H5LTset_attribute_int(ncid, "/", "nx", &mpi.nx, 1) ) < 0)
HERR(routineName);
if (( H5LTset_attribute_int(ncid, "/", "ny", &mpi.ny, 1) ) < 0)
HERR(routineName);
if (( H5LTset_attribute_int(ncid, "/", "nz", (int *) &infile.nz, 1 )) < 0)
HERR(routineName);
/* attributes */
if (( H5LTset_attribute_string(ncid, "/", "atmosID", atmos.ID)) < 0)
HERR(routineName);
if (( H5LTset_attribute_string(ncid, "/", "rev_id", mpi.rev_id) ) < 0)
HERR(routineName);
/* Create arrays for multiple-atom/molecule output */
io.aux_atom_ncid = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_mol_ncid = (hid_t *) malloc(atmos.Nactivemol * sizeof(hid_t));
if (input.p15d_wpop) {
io.aux_atom_pop = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_poplte = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_mol_pop = (hid_t *) malloc(atmos.Nactivemol * sizeof(hid_t));
io.aux_mol_poplte = (hid_t *) malloc(atmos.Nactivemol * sizeof(hid_t));
}
if (input.p15d_wrates) {
io.aux_atom_RijL = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_RjiL = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_RijC = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_RjiC = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
}
/* Fill value */
if (( plist = H5Pcreate(H5P_DATASET_CREATE) ) < 0) HERR(routineName);
if (( H5Pset_fill_value(plist, H5T_NATIVE_FLOAT, &FILLVALUE) ) < 0)
HERR(routineName);
if (( H5Pset_alloc_time(plist, H5D_ALLOC_TIME_EARLY) ) < 0) HERR(routineName);
if (( H5Pset_fill_time(plist, H5D_FILL_TIME_ALLOC) ) < 0) HERR(routineName);
/* --- Group loop over active ATOMS --- */
for (i=0; i < atmos.Nactiveatom; i++) {
atom = atmos.activeatoms[i];
/* Get group name */
sprintf(group_name, (atom->ID[1] == ' ') ? "atom_%.1s" : "atom_%.2s",
atom->ID);
if (( ncid_atom = H5Gcreate(ncid, group_name, H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT) ) < 0) HERR(routineName);
io.aux_atom_ncid[i] = ncid_atom;
/* --- dimensions as attributes --- */
if (( H5LTset_attribute_int(ncid_atom, ".", "nlevel",
&atom->Nlevel, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_atom, ".", "nline",
&atom->Nline, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_atom, ".", "ncontinuum",
&atom->Ncont, 1)) < 0) HERR(routineName);
/* --- dimension datasets --- */
dims[0] = mpi.nx;
if (( H5LTmake_dataset(ncid_atom, X_NAME, 1, dims, H5T_NATIVE_DOUBLE,
geometry.xscale) ) < 0) HERR(routineName);
if (( id_x = H5Dopen2(ncid_atom, X_NAME, H5P_DEFAULT)) < 0) HERR(routineName);
dims[0] = mpi.ny;
if (( H5LTmake_dataset(ncid_atom, Y_NAME, 1, dims, H5T_NATIVE_DOUBLE,
geometry.yscale) ) < 0) HERR(routineName);
if (( id_y = H5Dopen2(ncid_atom, Y_NAME, H5P_DEFAULT)) < 0) HERR(routineName);
dims[0] = infile.nz;
tmp_double = (double *) calloc(infile.nz , sizeof(double));
if (( H5LTmake_dataset(ncid_atom, ZOUT_NAME, 1, dims, H5T_NATIVE_DOUBLE,
tmp_double) ) < 0) HERR(routineName);
free(tmp_double);
if (( id_z = H5Dopen2(ncid_atom, ZOUT_NAME, H5P_DEFAULT)) < 0) HERR(routineName);
dims[0] = atom->Nlevel;
tmp = (unsigned int *) calloc(atom->Nlevel , sizeof(unsigned int));
if (( H5LTmake_dataset(ncid_atom, LEVEL_NAME, 1, dims, H5T_NATIVE_UINT,
tmp) ) < 0) HERR(routineName);
free(tmp);
dims[0] = atom->Nline;
tmp = (unsigned int *) calloc(atom->Nline , sizeof(unsigned int));
if (( H5LTmake_dataset(ncid_atom, LINE_NAME, 1, dims, H5T_NATIVE_UINT,
tmp) ) < 0) HERR(routineName);
free(tmp);
if (atom->Ncont > 0) {
dims[0] = atom->Ncont;
tmp = (unsigned int *) calloc(atom->Ncont , sizeof(unsigned int));
if (( H5LTmake_dataset(ncid_atom, CONT_NAME, 1, dims, H5T_NATIVE_UINT,
tmp) ) < 0) HERR(routineName);
free(tmp);
}
/* For compatibility with netCDF readers, only use dataset as dimension */
if (( H5LTset_attribute_string(ncid_atom, ZOUT_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atom, LEVEL_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atom, LINE_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
if (atom->Ncont > 0) {
if (( H5LTset_attribute_string(ncid_atom, CONT_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
}
/* --- variables --- */
dims[0] = atom->Nlevel;
dims[1] = mpi.nx;
dims[2] = mpi.ny;
dims[3] = infile.nz;
/* Populations */
if (input.p15d_wpop) {
if (( file_dspace = H5Screate_simple(4, dims, NULL) ) < 0)
HERR(routineName);
if (( id_n = H5Dopen2(ncid_atom, LEVEL_NAME,
H5P_DEFAULT)) < 0) HERR(routineName);
if (atom->n != NULL) {
if (( id_tmp = H5Dcreate(ncid_atom, POP_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT,
plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
if (( H5LTset_attribute_float(ncid_atom, POP_NAME, "_FillValue",
&FILLVALUE, 1) ) < 0) HERR(routineName);
io.aux_atom_pop[i] = id_tmp;
}
if (atom->nstar != NULL) {
if (( id_tmp = H5Dcreate(ncid_atom, POPLTE_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT,
plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
if (( H5LTset_attribute_float(ncid_atom, POPLTE_NAME, "_FillValue",
&FILLVALUE, 1) ) < 0) HERR(routineName);
io.aux_atom_poplte[i] = id_tmp;
}
if (( H5Dclose(id_n) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
}
if (input.p15d_wrates) {
/* Radiative rates */
dims[0] = atom->Nline;
dims[1] = mpi.nx;
dims[2] = mpi.ny;
dims[3] = infile.nz;
if (( file_dspace = H5Screate_simple(4, dims, NULL) ) < 0) HERR(routineName);
if (( id_n = H5Dopen2(ncid_atom, LINE_NAME,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( id_tmp = H5Dcreate(ncid_atom, RIJ_L_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
if (( H5LTset_attribute_float(ncid_atom, RIJ_L_NAME, "_FillValue",
&FILLVALUE, 1) ) < 0) HERR(routineName);
io.aux_atom_RijL[i] = id_tmp;
if (( id_tmp = H5Dcreate(ncid_atom, RJI_L_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
if (( H5LTset_attribute_float(ncid_atom, RJI_L_NAME, "_FillValue",
&FILLVALUE, 1) ) < 0) HERR(routineName);
io.aux_atom_RjiL[i] = id_tmp;
if (( H5Dclose(id_n) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
if (atom->Ncont > 0) {
dims[0] = atom->Ncont;
if (( file_dspace = H5Screate_simple(4, dims, NULL) ) < 0)
HERR(routineName);
if (( id_n = H5Dopen2(ncid_atom, CONT_NAME,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( id_tmp = H5Dcreate(ncid_atom, RIJ_C_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
if (( H5LTset_attribute_float(ncid_atom, RIJ_C_NAME, "_FillValue",
&FILLVALUE, 1) ) < 0) HERR(routineName);
io.aux_atom_RijC[i] = id_tmp;
if (( id_tmp = H5Dcreate(ncid_atom, RJI_C_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
if (( H5LTset_attribute_float(ncid_atom, RJI_C_NAME, "_FillValue",
&FILLVALUE, 1) ) < 0) HERR(routineName);
io.aux_atom_RjiC[i] = id_tmp;
if (( H5Dclose(id_n) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
}
}
if (( H5Dclose(id_x) ) < 0) HERR(routineName);
if (( H5Dclose(id_y) ) < 0) HERR(routineName);
if (( H5Dclose(id_z) ) < 0) HERR(routineName);
} /* end active ATOMS loop */
/* --- Group loop over active MOLECULES --- */
for (i=0; i < atmos.Nactivemol; i++) {
molecule = atmos.activemols[i];
/* Get group name */
sprintf( group_name, "molecule_%s", molecule->ID);
if (( ncid_mol = H5Gcreate(ncid, group_name, H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT) ) < 0) HERR(routineName);
io.aux_mol_ncid[i] = ncid_mol;
/* --- dimensions as attributes --- */
if (( H5LTset_attribute_int(ncid_mol, ".", "nlevel_vibr",
&molecule->Nv, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mol, ".", "nline_molecule",
&molecule->Nrt, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mol, ".", "nJ",
&molecule->NJ, 1)) < 0) HERR(routineName);
/* --- dimension datasets --- */
dims[0] = mpi.nx;
if (( H5LTmake_dataset(ncid_mol, X_NAME, 1, dims, H5T_NATIVE_DOUBLE,
geometry.xscale) ) < 0) HERR(routineName);
if (( id_x = H5Dopen2(ncid_mol, X_NAME, H5P_DEFAULT)) < 0) HERR(routineName);
dims[0] = mpi.ny;
if (( H5LTmake_dataset(ncid_mol, Y_NAME, 1, dims, H5T_NATIVE_DOUBLE,
geometry.yscale) ) < 0) HERR(routineName);
if (( id_y = H5Dopen2(ncid_mol, Y_NAME, H5P_DEFAULT)) < 0) HERR(routineName);
dims[0] = infile.nz;
tmp_double = (double *) calloc(infile.nz , sizeof(double));
if (( H5LTmake_dataset(ncid_mol, ZOUT_NAME, 1, dims, H5T_NATIVE_DOUBLE,
tmp_double) ) < 0) HERR(routineName);
free(tmp_double);
if (( id_z = H5Dopen2(ncid_mol, ZOUT_NAME, H5P_DEFAULT)) < 0) HERR(routineName);
dims[0] = molecule->Nv;
tmp = (unsigned int *) calloc(molecule->Nv, sizeof(unsigned int));
if (( H5LTmake_dataset(ncid_mol, VLEVEL_NAME, 1, dims, H5T_NATIVE_UINT,
tmp) ) < 0) HERR(routineName);
free(tmp);
dims[0] = molecule->Nrt;
tmp = (unsigned int *) calloc(molecule->Nrt, sizeof(unsigned int));
if (( H5LTmake_dataset(ncid_mol, VLINE_NAME, 1, dims, H5T_NATIVE_UINT,
tmp) ) < 0) HERR(routineName);
free(tmp);
dims[0] = molecule->NJ;
tmp = (unsigned int *) calloc(molecule->NJ, sizeof(unsigned int));
if (( H5LTmake_dataset(ncid_mol, NJ_NAME, 1, dims, H5T_NATIVE_UINT,
tmp) ) < 0) HERR(routineName);
free(tmp);
/* For compatibility with netCDF readers, only use dataset as dimension */
if (( H5LTset_attribute_string(ncid_mol, ZOUT_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_mol, VLEVEL_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_mol, VLINE_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_mol, NJ_NAME, "NAME",
NETCDF_COMPAT) ) < 0) HERR(routineName);
/* --- variables --- */
dims[0] = molecule->Nv;
dims[1] = mpi.nx;
dims[2] = mpi.ny;
dims[3] = infile.nz;
/* Populations */
if (input.p15d_wpop) {
if (( file_dspace = H5Screate_simple(4, dims, NULL) ) < 0)
HERR(routineName);
if (( id_n = H5Dopen2(ncid_mol, VLEVEL_NAME,
H5P_DEFAULT)) < 0) HERR(routineName);
if (molecule->nv != NULL) {
if (( id_tmp = H5Dcreate(ncid_mol, POP_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
io.aux_mol_pop[i] = id_tmp;
}
if (molecule->nvstar != NULL) {
if (( id_tmp = H5Dcreate(ncid_mol, POPLTE_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist,
H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_n, 0)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_x, 1)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_y, 2)) < 0) HERR(routineName);
if (( H5DSattach_scale(id_tmp, id_z, 3)) < 0) HERR(routineName);
io.aux_mol_poplte[i] = id_tmp;
}
if (( H5Dclose(id_n) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
// TODO: molecule->Ediss, molecule->Tmin, molecule->Tmax
}
if (( H5Dclose(id_x) ) < 0) HERR(routineName);
if (( H5Dclose(id_y) ) < 0) HERR(routineName);
if (( H5Dclose(id_z) ) < 0) HERR(routineName);
} /* end active MOLECULES loop */
io.aux_ncid = ncid; /* Copy stuff to the IO data struct */
if (( H5Pclose(plist) ) < 0) HERR(routineName); /* Free hdf5 resources */
/* Flush ensures file is created in case of crash */
if (( H5Fflush(ncid, H5F_SCOPE_LOCAL) ) < 0) HERR(routineName);
return;
}
/* ------- begin -------------------------- writeAux_all.c --- */
void writeAux_all(void) {
const char routineName[] = "writeAux_all";
hsize_t offset[] = {0, 0, 0, 0};
hsize_t count[] = {1, 1, 1, 1};
hsize_t dims[4];
hid_t file_dspace, mem_dspace;
Atom *atom;
Molecule *molecule;
int nact, task;
long ind = 0;
/* ATOM loop */
for (nact = 0; nact < atmos.Nactiveatom; nact++) {
atom = atmos.activeatoms[nact];
ind = 0; /* Index of each task inside variables */
for (task = 0; task < mpi.Ntasks; task++) {
/* If there was a crash, no data were written into buffer variables */
if (mpi.convergence[task] < 0) continue;
/* Memory dataspace */
dims[0] = atom->Nlevel;
dims[1] = infile.nz - mpi.zcut_hist[task];
if (( mem_dspace = H5Screate_simple(2, dims, NULL) ) < 0)
HERR(routineName);
/* File dataspace */
offset[0] = 0;
offset[1] = mpi.taskmap[task + mpi.my_start][0];
offset[2] = mpi.taskmap[task + mpi.my_start][1];
offset[3] = mpi.zcut_hist[task];
count[0] = atom->Nlevel;
count[1] = 1;
count[2] = 1;
count[3] = infile.nz - mpi.zcut_hist[task];
if (input.p15d_wpop) {
if (( file_dspace = H5Dget_space(io.aux_atom_pop[nact]) ) < 0)
HERR(routineName);
if (( H5Sselect_hyperslab(file_dspace, H5S_SELECT_SET, offset,
NULL, count, NULL) ) < 0) HERR(routineName);
if (( H5Dwrite(io.aux_atom_pop[nact], H5T_NATIVE_DOUBLE,
mem_dspace, file_dspace, H5P_DEFAULT,
&iobuf.n[nact][ind * atom->Nlevel]) ) < 0) HERR(routineName);
if (( H5Dwrite(io.aux_atom_poplte[nact], H5T_NATIVE_DOUBLE,
mem_dspace, file_dspace, H5P_DEFAULT,
&iobuf.nstar[nact][ind * atom->Nlevel]) ) < 0) HERR(routineName);
/* release dataspace resources */
if (( H5Sclose(mem_dspace) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
}
if (input.p15d_wrates) {
/* Memory dataspace */
dims[0] = atom->Nline;
if (( mem_dspace = H5Screate_simple(2, dims, NULL) ) < 0)
HERR(routineName);
count[0] = atom->Nline;
if (( file_dspace = H5Dget_space(io.aux_atom_RijL[nact]) ) < 0)
HERR(routineName);
if (( H5Sselect_hyperslab(file_dspace, H5S_SELECT_SET, offset,
NULL, count, NULL) ) < 0) HERR(routineName);
if (( H5Dwrite(io.aux_atom_RijL[nact], H5T_NATIVE_DOUBLE,
mem_dspace, file_dspace, H5P_DEFAULT,
&iobuf.RijL[nact][ind * atom->Nline]) ) < 0) HERR(routineName);
if (( H5Dwrite(io.aux_atom_RjiL[nact], H5T_NATIVE_DOUBLE,
mem_dspace, file_dspace, H5P_DEFAULT,
&iobuf.RjiL[nact][ind * atom->Nline]) ) < 0) HERR(routineName);
/* release dataspace resources */
if (( H5Sclose(mem_dspace) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
if (atom->Ncont > 0) {
/* Memory dataspace */
dims[0] = atom->Ncont;
if (( mem_dspace = H5Screate_simple(2, dims, NULL) ) < 0)
HERR(routineName);
count[0] = atom->Ncont;
if (( file_dspace = H5Dget_space(io.aux_atom_RijC[nact]) ) < 0)
HERR(routineName);
if (( H5Sselect_hyperslab(file_dspace, H5S_SELECT_SET, offset,
NULL, count, NULL) ) < 0) HERR(routineName);
if (( H5Dwrite(io.aux_atom_RijC[nact], H5T_NATIVE_DOUBLE,
mem_dspace, file_dspace, H5P_DEFAULT,
&iobuf.RijC[nact][ind * atom->Ncont]) ) < 0) HERR(routineName);
if (( H5Dwrite(io.aux_atom_RjiC[nact], H5T_NATIVE_DOUBLE,
mem_dspace, file_dspace, H5P_DEFAULT,
&iobuf.RjiC[nact][ind * atom->Ncont]) ) < 0) HERR(routineName);
/* release dataspace resources */
if (( H5Sclose(mem_dspace) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
}
}
ind += count[3];
}
}
/* MOLECULE loop */
for (nact = 0; nact < atmos.Nactivemol; nact++) {
molecule = atmos.activemols[nact];
ind = 0; /* Index of each task inside variables */
for (task = 0; task < mpi.Ntasks; task++) {
/* If there was a crash, no data were written into buffer variables */
if (mpi.convergence[task] < 0) continue;
if (input.p15d_wpop) {
/* Memory dataspace */
dims[0] = molecule->Nv;
dims[1] = infile.nz - mpi.zcut_hist[task];
if (( mem_dspace = H5Screate_simple(2, dims, NULL) ) < 0)
HERR(routineName);
/* File dataspace */
offset[0] = 0;
offset[1] = mpi.taskmap[task + mpi.my_start][0];
offset[2] = mpi.taskmap[task + mpi.my_start][1];
offset[3] = mpi.zcut_hist[task];
count[0] = molecule->Nv;
count[3] = infile.nz - mpi.zcut_hist[task];
if (( file_dspace = H5Dget_space(io.aux_mol_pop[nact]) ) < 0)
HERR(routineName);
if (( H5Sselect_hyperslab(file_dspace, H5S_SELECT_SET, offset,
NULL, count, NULL) ) < 0) HERR(routineName);
if (( H5Dwrite(io.aux_mol_pop[nact], H5T_NATIVE_DOUBLE,
mem_dspace, file_dspace, H5P_DEFAULT,
&iobuf.nv[nact][ind * molecule->Nv]) ) < 0) HERR(routineName);
if (( H5Dwrite(io.aux_mol_poplte[nact], H5T_NATIVE_DOUBLE,
mem_dspace, file_dspace, H5P_DEFAULT,
&iobuf.nvstar[nact][ind * molecule->Nv]) ) < 0) HERR(routineName);
/* release dataspace resources */
if (( H5Sclose(mem_dspace) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
}
ind += count[3];
}
}
return;
}
/* ------- begin -------------------------- close_hdf5_aux.c --- */
void close_hdf5_aux(void)
/* Closes the aux file */
{
const char routineName[] = "close_hdf5_aux";
Atom *atom;
int i;
/* Close all datasets and groups */
for (i=0; i < atmos.Nactiveatom; i++) {
atom = atmos.activeatoms[i];
if (input.p15d_wpop) {
if (( H5Dclose(io.aux_atom_pop[i]) ) < 0) HERR(routineName);
if (( H5Dclose(io.aux_atom_poplte[i]) ) < 0) HERR(routineName);
}
if (input.p15d_wrates) {
if (( H5Dclose(io.aux_atom_RijL[i]) ) < 0) HERR(routineName);
if (( H5Dclose(io.aux_atom_RjiL[i]) ) < 0) HERR(routineName);
if (atom->Ncont > 0) {
if (( H5Dclose(io.aux_atom_RijC[i]) ) < 0) HERR(routineName);
if (( H5Dclose(io.aux_atom_RjiC[i]) ) < 0) HERR(routineName);
}
}
if (( H5Gclose(io.aux_atom_ncid[i]) ) < 0) HERR(routineName);
}
for (i=0; i < atmos.Nactivemol; i++) {
if (input.p15d_wpop) {
if (( H5Dclose(io.aux_mol_pop[i]) ) < 0) HERR(routineName);
if (( H5Dclose(io.aux_mol_poplte[i]) ) < 0) HERR(routineName);
}
if (( H5Gclose(io.aux_mol_ncid[i]) ) < 0) HERR(routineName);
}
/* Close file */
if (( H5Fclose(io.aux_ncid) ) < 0) HERR(routineName);
return;
}
/* ------- begin -------------------- init_aux_existing.c --- */
void init_aux_existing(void) {
const char routineName[] = "init_aux_existing";
int i, nlevel, nline, ncont;
size_t attr_size;
hid_t ncid, ncid_atom, ncid_mol, plist;
H5T_class_t type_class;
char group_name[ARR_STRLEN], *atmosID;
Atom *atom;
Molecule *molecule;
/* Open the file with parallel MPI-IO access */
if (( plist = H5Pcreate(H5P_FILE_ACCESS )) < 0) HERR(routineName);
if (( H5Pset_fapl_mpio(plist, mpi.comm, mpi.info) ) < 0) HERR(routineName);
if (( ncid = H5Fopen(AUX_FILE, H5F_ACC_RDWR, plist) ) < 0)
HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
io.aux_ncid = ncid;
/* --- Consistency checks --- */
/* Check that atmosID is the same */
if (( H5LTget_attribute_info(ncid, "/", "atmosID", NULL, &type_class,
&attr_size) ) < 0) HERR(routineName);
atmosID = (char *) malloc(attr_size + 1);
if (( H5LTget_attribute_string(ncid, "/", "atmosID", atmosID) ) < 0)
HERR(routineName);
if (!strstr(atmosID, atmos.ID)) {
sprintf(messageStr,
"Indata file was calculated for different atmosphere (%s) than current",
atmosID);
Error(WARNING, routineName, messageStr);
}
free(atmosID);
/* Create arrays for multiple-atom/molecule output */
io.aux_atom_ncid = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_mol_ncid = (hid_t *) malloc(atmos.Nactivemol * sizeof(hid_t));
if (input.p15d_wpop) {
io.aux_atom_pop = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_poplte = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_mol_pop = (hid_t *) malloc(atmos.Nactivemol * sizeof(hid_t));
io.aux_mol_poplte = (hid_t *) malloc(atmos.Nactivemol * sizeof(hid_t));
}
if (input.p15d_wrates) {
io.aux_atom_RijL = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_RjiL = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_RijC = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_RjiC = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
}
/* --- Group loop over active ATOMS --- */
for (i=0; i < atmos.Nactiveatom; i++) {
atom = atmos.activeatoms[i];
/* --- Get ncid of the atom group --- */
sprintf(group_name,(atom->ID[1] == ' ') ? "atom_%.1s" : "atom_%.2s", atom->ID);
if (( io.aux_atom_ncid[i] = H5Gopen(io.aux_ncid, group_name,
H5P_DEFAULT) ) < 0) HERR(routineName);
ncid_atom = io.aux_atom_ncid[i];
/* Check that dimension sizes match */
if (( H5LTget_attribute_int(ncid_atom, ".", "nlevel", &nlevel) ) < 0)
HERR(routineName);
if (nlevel != atom->Nlevel) {
sprintf(messageStr,
"Number of levels mismatch: expected %d, found %d.",
atom->Nlevel, (int)nlevel);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
if (( H5LTget_attribute_int(ncid_atom, ".", "nline", &nline) ) < 0)
HERR(routineName);
if (nline != atom->Nline) {
sprintf(messageStr,
"Number of lines mismatch: expected %d, found %d.",
atom->Nline, (int)nline);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
if (( H5LTget_attribute_int(ncid_atom, ".", "ncontinuum", &ncont) ) < 0)
HERR(routineName);
if (ncont != atom->Ncont) {
sprintf(messageStr,
"Number of continua mismatch: expected %d, found %d.",
atom->Ncont, (int)ncont);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
/* --- Open datasets collectively ---*/
if (input.p15d_wpop) {
if (( io.aux_atom_pop[i] = H5Dopen(ncid_atom, POP_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.aux_atom_poplte[i] = H5Dopen(ncid_atom, POPLTE_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
}
if (input.p15d_wrates) {
if (( io.aux_atom_RijL[i] = H5Dopen(ncid_atom, RIJ_L_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.aux_atom_RjiL[i] = H5Dopen(ncid_atom, RJI_L_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (atom->Ncont > 0) {
if (( io.aux_atom_RijC[i] = H5Dopen(ncid_atom, RIJ_C_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.aux_atom_RjiC[i] = H5Dopen(ncid_atom, RJI_C_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
}
}
} /* end active ATOMS loop */
/* --- Group loop over active MOLECULES --- */
for (i=0; i < atmos.Nactivemol; i++) {
molecule = atmos.activemols[i];
/* --- Get ncid of the molecule group --- */
sprintf( group_name, "molecule_%s", molecule->ID);
if (( io.aux_mol_ncid[i] = H5Gopen(io.aux_ncid, group_name,
H5P_DEFAULT) ) < 0) HERR(routineName);
ncid_mol = io.aux_mol_ncid[i];
/* Check that dimension sizes match */
if (( H5LTget_attribute_int(ncid_mol, ".", "nlevel_vibr", &nlevel) ) < 0)
HERR(routineName);
if (nlevel != molecule->Nv) {
sprintf(messageStr,
"Number of levels mismatch: expected %d, found %d.",
molecule->Nv, (int)nlevel);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
if (( H5LTget_attribute_int(ncid_mol, ".", "nline_molecule", &nline) ) < 0)
HERR(routineName);
if (nline != molecule->Nrt) {
sprintf(messageStr,
"Number of lines mismatch: expected %d, found %d.",
molecule->Nrt, (int)nline);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
if (( H5LTget_attribute_int(ncid_mol, ".", "nJ", &ncont) ) < 0)
HERR(routineName);
if (ncont != molecule->NJ) {
sprintf(messageStr,
"Number of J mismatch: expected %d, found %d.",
molecule->NJ, (int)ncont);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
/* --- Open datasets collectively ---*/
if (input.p15d_wpop) {
if (( io.aux_mol_pop[i] = H5Dopen(ncid_mol, POP_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.aux_mol_poplte[i] = H5Dopen(ncid_mol, POPLTE_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
}
} /* end active MOLECULES loop */
return;
}
/* ------- begin -------------------------- readConvergence.c --- */
void readConvergence(void) {
/* This is a self-contained function to read the convergence matrix,
written by RH. */
const char routineName[] = "readConvergence";
char *atmosID;
int ncid, ncid_mpi, nx, ny;
size_t attr_size;
hid_t plist;
H5T_class_t type_class;
mpi.rh_converged = matrix_int(mpi.nx, mpi.ny);
/* --- Open the inputdata file --- */
if (( plist = H5Pcreate(H5P_FILE_ACCESS )) < 0) HERR(routineName);
if (( H5Pset_fapl_mpio(plist, mpi.comm, mpi.info) ) < 0) HERR(routineName);
if (( ncid = H5Fopen(INPUTDATA_FILE, H5F_ACC_RDWR, plist) ) < 0)
HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
/* Get ncid of the MPI group */
if (( ncid_mpi = H5Gopen(ncid, "mpi", H5P_DEFAULT) ) < 0) HERR(routineName);
/* --- Consistency checks --- */
/* Check that atmosID is the same */
if (( H5LTget_attribute_info(ncid, "/", "atmosID", NULL, &type_class,
&attr_size) ) < 0) HERR(routineName);
atmosID = (char *) malloc(attr_size + 1);
if (( H5LTget_attribute_string(ncid, "/", "atmosID", atmosID) ) < 0)
HERR(routineName);
if (!strstr(atmosID, atmos.ID)) {
sprintf(messageStr,
"Indata file was calculated for different atmosphere (%s) than current",
atmosID);
Error(WARNING, routineName, messageStr);
}
free(atmosID);
/* Check that dimension sizes match */
if (( H5LTget_attribute_int(ncid, "/", "nx", &nx) ) < 0) HERR(routineName);
if (nx != mpi.nx) {
sprintf(messageStr,
"Number of x points mismatch: expected %d, found %d.",
mpi.nx, (int)nx);
Error(WARNING, routineName, messageStr);
}
if (( H5LTget_attribute_int(ncid, "/", "ny", &ny) ) < 0) HERR(routineName);
if (ny != mpi.ny) {
sprintf(messageStr,
"Number of y points mismatch: expected %d, found %d.",
mpi.ny, (int)ny);
Error(WARNING, routineName, messageStr);
}
/* --- Read variable --- */
if (( H5LTread_dataset_int(ncid_mpi, CONV_NAME,
mpi.rh_converged[0]) ) < 0) HERR(routineName);
/* --- Close inputdata file --- */
if (( H5Gclose(ncid_mpi) ) < 0) HERR(routineName);
if (( H5Fclose(ncid) ) < 0) HERR(routineName);
return;
}
/* ------- begin -------------------------- writeMPI_p.c ----- */
void writeMPI_p(int task) {
/* Writes output on indata file, MPI group, one task at once */
const char routineName[] = "writeMPI_p";
hsize_t offset[] = {0, 0, 0, 0};
hsize_t count[] = {1, 1, 1, 1};
hsize_t dims[4];
hid_t file_dspace, mem_dspace;
dims[0] = 1;
if (( mem_dspace = H5Screate_simple(1, dims, NULL) ) < 0) HERR(routineName);
offset[0] = mpi.ix;
offset[1] = mpi.iy;
if (( file_dspace = H5Dget_space(io.in_mpi_tm) ) < 0) HERR(routineName);
if (( H5Sselect_hyperslab(file_dspace, H5S_SELECT_SET, offset,
NULL, count, NULL) ) < 0) HERR(routineName);
if (( H5Dwrite(io.in_mpi_tm, H5T_NATIVE_INT, mem_dspace, file_dspace,
H5P_DEFAULT, &mpi.rank) ) < 0) HERR(routineName);
if (( H5Dwrite(io.in_mpi_tn, H5T_NATIVE_INT, mem_dspace, file_dspace,
H5P_DEFAULT, &task) ) < 0) HERR(routineName);
if (( H5Dwrite(io.in_mpi_it, H5T_NATIVE_INT, mem_dspace, file_dspace,
H5P_DEFAULT, &mpi.niter[0]) ) < 0) HERR(routineName);
if (( H5Dwrite(io.in_mpi_conv, H5T_NATIVE_INT, mem_dspace, file_dspace,
H5P_DEFAULT, &mpi.convergence[0]) ) < 0) HERR(routineName);
if (( H5Dwrite(io.in_mpi_zc, H5T_NATIVE_INT, mem_dspace, file_dspace,
H5P_DEFAULT, &mpi.zcut_hist[0]) ) < 0) HERR(routineName);
if (( H5Dwrite(io.in_mpi_dm, H5T_NATIVE_DOUBLE, mem_dspace, file_dspace,
H5P_DEFAULT, &mpi.dpopsmax[0]) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
if (( H5Sclose(mem_dspace) ) < 0) HERR(routineName);
dims[0] = mpi.niter[0];
if (( mem_dspace = H5Screate_simple(1, dims, NULL) ) < 0) HERR(routineName);
offset[0] = mpi.ix;
offset[1] = mpi.iy;
count[2] = mpi.niter[0];
if (( file_dspace = H5Dget_space(io.in_mpi_dmh) ) < 0) HERR(routineName);
if (( H5Sselect_hyperslab(file_dspace, H5S_SELECT_SET, offset,
NULL, count, NULL) ) < 0) HERR(routineName);
if (( H5Dwrite(io.in_mpi_dmh, H5T_NATIVE_DOUBLE, mem_dspace, file_dspace,
H5P_DEFAULT, mpi.dpopsmax_hist[0]) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
if (( H5Sclose(mem_dspace) ) < 0) HERR(routineName);
return;
}
/* ------- begin -------------------------- writeMPI_all.c --- */
void writeMPI_all(void) {
/* Writes output on indata file, MPI group, all tasks at once */
const char routineName[] = "writeMPI_all";
int task;
hsize_t offset[] = {0, 0, 0, 0};
hsize_t count[] = {1, 1, 1, 1};
hsize_t dims[4];
hid_t file_dspace, mem_dspace;
/* Write single values of Ntasks, one value at a time */
dims[0] = 1;
if (( mem_dspace = H5Screate_simple(1, dims, NULL) ) < 0)
HERR(routineName);
for (task = 0; task < mpi.Ntasks; task++) {
offset[0] = mpi.taskmap[task + mpi.my_start][0];
offset[1] = mpi.taskmap[task + mpi.my_start][1];
if (( file_dspace = H5Dget_space(io.in_mpi_it) ) < 0) HERR(routineName);
if (( H5Sselect_hyperslab(file_dspace, H5S_SELECT_SET, offset,
NULL, count, NULL) ) < 0) HERR(routineName);
if (( H5Dwrite(io.in_mpi_it, H5T_NATIVE_INT, mem_dspace, file_dspace,
H5P_DEFAULT, &mpi.niter[task]) ) < 0) HERR(routineName);
if (( H5Dwrite(io.in_mpi_conv, H5T_NATIVE_INT, mem_dspace, file_dspace,
H5P_DEFAULT, &mpi.convergence[task]) ) < 0) HERR(routineName);
if (( H5Dwrite(io.in_mpi_zc, H5T_NATIVE_INT, mem_dspace, file_dspace,
H5P_DEFAULT, &mpi.zcut_hist[task]) ) < 0) HERR(routineName);
if (( H5Dwrite(io.in_mpi_dm, H5T_NATIVE_DOUBLE, mem_dspace, file_dspace,
H5P_DEFAULT, &mpi.dpopsmax[task]) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
}
if (( H5Sclose(mem_dspace) ) < 0) HERR(routineName);
/* Write array with multiple values */
for (task = 0; task < mpi.Ntasks; task++) {
dims[0] = mpi.niter[task];
if (( mem_dspace = H5Screate_simple(1, dims, NULL) ) < 0)
HERR(routineName);
offset[0] = mpi.taskmap[task + mpi.my_start][0];
offset[1] = mpi.taskmap[task + mpi.my_start][1];
count[2] = mpi.niter[task];
if (( file_dspace = H5Dget_space(io.in_mpi_dmh) ) < 0) HERR(routineName);
if (( H5Sselect_hyperslab(file_dspace, H5S_SELECT_SET, offset,
NULL, count, NULL) ) < 0) HERR(routineName);
if (( H5Dwrite(io.in_mpi_dmh, H5T_NATIVE_DOUBLE, mem_dspace, file_dspace,
H5P_DEFAULT, mpi.dpopsmax_hist[task]) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
if (( H5Sclose(mem_dspace) ) < 0) HERR(routineName);
}
return;
}
/* ------- begin -------------------------- init_hdf5_indata.c --- */
void init_hdf5_indata_new(void)
/* Creates the netCDF file for the input data */
{
const char routineName[] = "init_hdf5_indata_new";
int i, PRD_angle_dep;
double *eweight, *eabund, *x, *y;
/* This value is harcoded for efficiency.
Maximum number of iterations ever needed */
int NMaxIter = 1500;
hid_t plist, ncid, file_dspace, ncid_input, ncid_atmos, ncid_mpi;
hsize_t dims[4];
bool_t XRD;
char startJ[MAX_LINE_SIZE], StokesMode[MAX_LINE_SIZE], angleSet[MAX_LINE_SIZE];
/* Create the file */
if (( plist = H5Pcreate(H5P_FILE_ACCESS )) < 0) HERR(routineName);
if (( H5Pset_fapl_mpio(plist, mpi.comm, mpi.info) ) < 0) HERR(routineName);
if (( ncid = H5Fcreate(INPUTDATA_FILE, H5F_ACC_TRUNC, H5P_DEFAULT,
plist) ) < 0) HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
/* Create groups */
if (( ncid_input = H5Gcreate(ncid, "/input", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( ncid_atmos = H5Gcreate(ncid, "/atmos", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( ncid_mpi = H5Gcreate(ncid, "/mpi", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT) ) < 0) HERR(routineName);
/* --- Definitions for the root group --- */
/* dimensions as attributes */
if (( H5LTset_attribute_int(ncid, "/", "nx", &mpi.nx, 1) ) < 0)
HERR(routineName);
if (( H5LTset_attribute_int(ncid, "/", "ny", &mpi.ny, 1) ) < 0)
HERR(routineName);
if (( H5LTset_attribute_int(ncid, "/", "nz", (int *) &infile.nz, 1 )) < 0)
HERR(routineName);
/* attributes */
if (( H5LTset_attribute_string(ncid, "/", "atmosID", atmos.ID)) < 0)
HERR(routineName);
if (( H5LTset_attribute_string(ncid, "/", "rev_id", mpi.rev_id) ) < 0)
HERR(routineName);
/* --- Definitions for the INPUT group --- */
/* attributes */
if ( atmos.NPRDactive > 0)
PRD_angle_dep = input.PRD_angle_dep;
else
PRD_angle_dep=0;
XRD = (input.XRD && atmos.NPRDactive > 0);
if (( H5LTset_attribute_uchar(ncid_input, ".", "Magneto_optical",
(unsigned char *) &input.magneto_optical, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_uchar(ncid_input, ".", "PRD_angle_dep",
(unsigned char *) &PRD_angle_dep, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_uchar(ncid_input, ".", "XRD",
(unsigned char *) &XRD, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_uchar(ncid_input, ".", "Background_polarization",
(unsigned char *) &input.backgr_pol, 1)) < 0) HERR(routineName);
switch (input.startJ) {
case UNKNOWN:
strcpy(startJ, "Unknown");
break;
case LTE_POPULATIONS:
strcpy(startJ, "LTE_POPULATIONS");
break;
case ZERO_RADIATION:
strcpy(startJ, "ZERO_RADIATION");
break;
case OLD_POPULATIONS:
strcpy(startJ, "OLD_POPULATIONS");
break;
case ESCAPE_PROBABILITY:
strcpy(startJ, "ESCAPE_PROBABILITY");
break;
case NEW_J:
strcpy(startJ, "NEW_J");
break;
case OLD_J:
strcpy(startJ, "OLD_J");
break;
}
if (( H5LTset_attribute_string(ncid_input, ".", "Start_J", startJ)) < 0)
HERR(routineName);
switch (input.StokesMode) {
case NO_STOKES:
strcpy(StokesMode, "NO_STOKES");
break;
case FIELD_FREE:
strcpy(StokesMode, "FIELD_FREE");
break;
case POLARIZATION_FREE:
strcpy(StokesMode, "POLARIZATION_FREE");
break;
case FULL_STOKES:
strcpy(StokesMode, "FULL_STOKES");
break;
}
if (( H5LTset_attribute_string(ncid_input, ".", "Stokes_mode",
StokesMode) ) < 0) HERR(routineName);
switch (atmos.angleSet.set) {
case SET_VERTICAL:
strcpy(angleSet, "SET_VERTICAL");
break;
case SET_GL:
strcpy(angleSet, "SET_GL");
break;
case SET_A2:
strcpy(angleSet, "SET_A2");
break;
case SET_A4:
strcpy(angleSet, "SET_A4");
break;
case SET_A6:
strcpy(angleSet, "SET_A6");
break;
case SET_A8:
strcpy(angleSet, "SET_A8");
break;
case SET_B4:
strcpy(angleSet, "SET_B4");
break;
case SET_B6:
strcpy(angleSet, "SET_B6");
break;
case SET_B8:
strcpy(angleSet, "SET_B8");
break;
case NO_SET:
strcpy(angleSet, "NO_SET");
break;
}
if (( H5LTset_attribute_string(ncid_input, ".", "Angle_set",
angleSet) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_input, ".", "Atmos_file",
input.atmos_input) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_input, ".", "Abundances_file",
input.abund_input) ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_input, ".", "Kurucz_PF_data",
input.pfData) ) < 0) HERR(routineName);
if (( H5LTset_attribute_double(ncid_input, ".", "Iteration_limit",
&input.iterLimit, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_double(ncid_input, ".", "PRD_Iteration_limit",
&input.PRDiterLimit, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "N_max_iter",
&input.NmaxIter, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "Ng_delay",
&input.Ngdelay, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "Ng_order",
&input.Ngorder, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "Ng_period",
&input.Ngperiod, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "PRD_N_max_iter",
&input.PRD_NmaxIter, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "PRD_Ng_delay",
&input.PRD_Ngdelay, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "PRD_Ng_order",
&input.PRD_Ngorder, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_input, ".", "PRD_Ng_period",
&input.PRD_Ngperiod, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_double(ncid_input, ".", "Metallicity",
&input.metallicity, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_double(ncid_input, ".", "Lambda_reference",
&atmos.lambda_ref, 1) ) < 0) HERR(routineName);
/* --- Definitions for the ATMOS group --- */
/* dimensions */
if (( H5LTset_attribute_int(ncid_atmos, ".", "nhydr",
&atmos.H->Nlevel, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_atmos, ".", "nelements",
&atmos.Nelem, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_atmos, ".", "nrays",
&geometry.Nrays, 1) ) < 0) HERR(routineName);
/* variables*/
dims[0] = mpi.nx;
dims[1] = mpi.ny;
dims[2] = infile.nz;
if (( file_dspace = H5Screate_simple(3, dims, NULL) ) < 0) HERR(routineName);
if (( plist = H5Pcreate(H5P_DATASET_CREATE) ) < 0) HERR(routineName);
if (( H5Pset_fill_value(plist, H5T_NATIVE_FLOAT, &FILLVALUE) ) < 0)
HERR(routineName);
if (( H5Pset_alloc_time(plist, H5D_ALLOC_TIME_EARLY) ) < 0) HERR(routineName);
if (( H5Pset_fill_time(plist, H5D_FILL_TIME_ALLOC) ) < 0) HERR(routineName);
if (( io.in_atmos_T = H5Dcreate(ncid_atmos, "temperature", H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_atmos_vz = H5Dcreate(ncid_atmos, "velocity_z", H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_atmos_z = H5Dcreate(ncid_atmos, "height", H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
/* --- Write some data that does not depend on xi, yi, ATMOS group --- */
/* arrays of number of elements */
eweight = (double *) malloc(atmos.Nelem * sizeof(double));
eabund = (double *) malloc(atmos.Nelem * sizeof(double));
for (i=0; i < atmos.Nelem; i++) {
eweight[i] = atmos.elements[i].weight;
eabund[i] = atmos.elements[i].abund;
}
dims[0] = atmos.Nelem;
if (( H5LTmake_dataset(ncid_atmos, "element_weight", 1, dims,
H5T_NATIVE_DOUBLE, eweight) ) < 0) HERR(routineName);
if (( H5LTmake_dataset(ncid_atmos, "element_abundance", 1, dims,
H5T_NATIVE_DOUBLE, eabund) ) < 0) HERR(routineName);
/* Not writing element_id for now
dims[1] = strlen;
if (( H5LTmake_dataset(ncid_atmos, "element_id", 2, dims,
H5T_C_S1, eID) ) < 0) HERR(routineName);
*/
free(eweight);
free(eabund);
dims[0] = geometry.Nrays;
if (( H5LTmake_dataset(ncid_atmos, "muz", 1, dims,
H5T_NATIVE_DOUBLE, geometry.muz) ) < 0) HERR(routineName);
if (( H5LTmake_dataset(ncid_atmos, "wmu", 1, dims,
H5T_NATIVE_DOUBLE, geometry.wmu) ) < 0) HERR(routineName);
x = (double *) malloc(mpi.nx * sizeof(double));
y = (double *) malloc(mpi.ny * sizeof(double));
for (i=0; i < mpi.nx; i++) x[i] = infile.x[mpi.xnum[i]];
for (i=0; i < mpi.ny; i++) y[i] = infile.y[mpi.ynum[i]];
dims[0] = mpi.nx;
if (( H5LTmake_dataset(ncid_atmos, "x", 1, dims,
H5T_NATIVE_DOUBLE, x) ) < 0) HERR(routineName);
dims[0] = mpi.ny;
if (( H5LTmake_dataset(ncid_atmos, "y", 1, dims,
H5T_NATIVE_DOUBLE, y) ) < 0) HERR(routineName);
free(x);
free(y);
/* attributes */
if (( H5LTset_attribute_uchar(ncid_atmos, ".", "moving",
(unsigned char *) &atmos.moving, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_uchar(ncid_atmos, ".", "stokes",
(unsigned char *) &atmos.Stokes, 1)) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "temperature", "units",
"K") ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "velocity_z", "units",
"m s^-1") ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "height", "units",
"m") ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "element_weight", "units",
"atomic_mass_units") ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "x", "units",
"m") ) < 0) HERR(routineName);
if (( H5LTset_attribute_string(ncid_atmos, "y", "units",
"m") ) < 0) HERR(routineName);
/* --- Definitions for the MPI group --- */
/* dimensions */
if (( H5LTset_attribute_int(ncid_mpi, ".", "nprocesses",
&mpi.size, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "niterations",
&NMaxIter, 1) ) < 0) HERR(routineName);
/* variables*/
dims[0] = mpi.nx;
if (( H5LTmake_dataset(ncid_mpi, XNUM_NAME, 1, dims,
H5T_NATIVE_INT, mpi.xnum) ) < 0) HERR(routineName);
dims[0] = mpi.ny;
if (( H5LTmake_dataset(ncid_mpi, YNUM_NAME, 1, dims,
H5T_NATIVE_INT, mpi.ynum) ) < 0) HERR(routineName);
dims[0] = mpi.nx;
dims[1] = mpi.ny;
if (( file_dspace = H5Screate_simple(2, dims, NULL) ) < 0) HERR(routineName);
if (( plist = H5Pcreate(H5P_DATASET_CREATE) ) < 0) HERR(routineName);
if (( H5Pset_fill_value(plist, H5T_NATIVE_FLOAT, &FILLVALUE) ) < 0)
HERR(routineName);
if (( H5Pset_alloc_time(plist, H5D_ALLOC_TIME_EARLY) ) < 0) HERR(routineName);
if (( H5Pset_fill_time(plist, H5D_FILL_TIME_ALLOC) ) < 0) HERR(routineName);
if (( io.in_mpi_tm = H5Dcreate(ncid_mpi, TASK_MAP, H5T_NATIVE_LONG,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_mpi_tn = H5Dcreate(ncid_mpi, TASK_NUMBER, H5T_NATIVE_LONG,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_mpi_it = H5Dcreate(ncid_mpi, ITER_NAME, H5T_NATIVE_LONG,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_mpi_conv = H5Dcreate(ncid_mpi, CONV_NAME, H5T_NATIVE_LONG,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_mpi_dm = H5Dcreate(ncid_mpi, DM_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( io.in_mpi_zc = H5Dcreate(ncid_mpi, ZC_NAME, H5T_NATIVE_INT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
dims[0] = mpi.nx;
dims[1] = mpi.ny;
dims[2] = NMaxIter;
if (( file_dspace = H5Screate_simple(3, dims, NULL) ) < 0) HERR(routineName);
if (( plist = H5Pcreate(H5P_DATASET_CREATE) ) < 0) HERR(routineName);
if (( H5Pset_fill_value(plist, H5T_NATIVE_FLOAT, &FILLVALUE) ) < 0)
HERR(routineName);
if (( H5Pset_alloc_time(plist, H5D_ALLOC_TIME_EARLY) ) < 0) HERR(routineName);
if (( H5Pset_fill_time(plist, H5D_FILL_TIME_ALLOC) ) < 0) HERR(routineName);
if (( io.in_mpi_dmh = H5Dcreate(ncid_mpi, DMH_NAME, H5T_NATIVE_FLOAT,
file_dspace, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0) HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
/* attributes */
if (( H5LTset_attribute_int(ncid_mpi, ".", "x_start",
&input.p15d_x0, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "x_end",
&input.p15d_x1, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "x_step",
&input.p15d_xst, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "y_start",
&input.p15d_y0, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "y_end",
&input.p15d_y1, 1) ) < 0) HERR(routineName);
if (( H5LTset_attribute_int(ncid_mpi, ".", "y_step",
&input.p15d_yst, 1) ) < 0) HERR(routineName);
/* Tiago: most of the arrays involving Ntasks or rank as index are not
currently being written. They should eventually be migrated into
arrays of [ix, iy] and be written for each task. This is to
avoid causing problems with pool mode, where these quantities are
not known from the start.
*/
/* Flush ensures file is created in case of crash */
if (( H5Fflush(ncid, H5F_SCOPE_LOCAL) ) < 0) HERR(routineName);
/* --- Copy stuff to the IO data struct --- */
io.in_ncid = ncid;
io.in_input_ncid = ncid_input;
io.in_atmos_ncid = ncid_atmos;
io.in_mpi_ncid = ncid_mpi;
return;
}
/* ------- begin -------------------------- close_hdf5_indata.c --- */
void close_hdf5_indata(void)
/* Closes the indata netCDF file */
{
const char routineName[] = "close_hdf5_indata";
/* Close all datasets */
if (( H5Dclose(io.in_atmos_T) ) < 0) HERR(routineName);
if (( H5Dclose(io.in_atmos_vz) ) < 0) HERR(routineName);
if (( H5Dclose(io.in_atmos_z) ) < 0) HERR(routineName);
if (( H5Dclose(io.in_mpi_tm) ) < 0) HERR(routineName);
if (( H5Dclose(io.in_mpi_tn) ) < 0) HERR(routineName);
if (( H5Dclose(io.in_mpi_it) ) < 0) HERR(routineName);
if (( H5Dclose(io.in_mpi_conv) ) < 0) HERR(routineName);
if (( H5Dclose(io.in_mpi_dm) ) < 0) HERR(routineName);
if (( H5Dclose(io.in_mpi_dmh) ) < 0) HERR(routineName);
if (( H5Dclose(io.in_mpi_zc) ) < 0) HERR(routineName);
/* Close all groups */
if (( H5Gclose(io.in_input_ncid) ) < 0) HERR(routineName);
if (( H5Gclose(io.in_atmos_ncid) ) < 0) HERR(routineName);
if (( H5Gclose(io.in_mpi_ncid) ) < 0) HERR(routineName);
/* Close file */
if (( H5Fclose(io.in_ncid) ) < 0) HERR(routineName);
return;
}
/* ------- begin -------------------------- init_hdf5_indata_old.c --- */
void init_hdf5_indata_existing(void)
/* Opens an existing NetCDF input data file, loads structures and ids */
{
const char routineName[] = "init_hdf5_indata_existing";
int ncid;
size_t attr_size;
hid_t plist;
char *atmosID;
H5T_class_t type_class;
/* Open the file with parallel MPI-IO access */
if (( plist = H5Pcreate(H5P_FILE_ACCESS )) < 0) HERR(routineName);
if (( H5Pset_fapl_mpio(plist, mpi.comm, mpi.info) ) < 0) HERR(routineName);
if (( ncid = H5Fopen(INPUTDATA_FILE, H5F_ACC_RDWR, plist) ) < 0)
HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
io.in_ncid = ncid;
/* --- Consistency checks --- */
/* Check that atmosID is the same */
if (( H5LTget_attribute_info(ncid, "/", "atmosID", NULL, &type_class,
&attr_size) ) < 0) HERR(routineName);
atmosID = (char *) malloc(attr_size + 1);
if (( H5LTget_attribute_string(ncid, "/", "atmosID", atmosID) ) < 0)
HERR(routineName);
if (!strstr(atmosID, atmos.ID)) {
sprintf(messageStr,
"Indata file was calculated for different atmosphere (%s) than current",
atmosID);
Error(WARNING, routineName, messageStr);
}
free(atmosID);
/* Get group IDs */
if (( io.in_input_ncid = H5Gopen(ncid, "input", H5P_DEFAULT) ) < 0)
HERR(routineName);
if (( io.in_atmos_ncid = H5Gopen(ncid, "atmos", H5P_DEFAULT) ) < 0)
HERR(routineName);
if (( io.in_mpi_ncid = H5Gopen(ncid, "mpi", H5P_DEFAULT) ) < 0)
HERR(routineName);
/* --- Open datasets collectively ---*/
if (( io.in_atmos_T = H5Dopen(io.in_atmos_ncid, "temperature",
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.in_atmos_vz = H5Dopen(io.in_atmos_ncid, "velocity_z",
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.in_atmos_z = H5Dopen(io.in_atmos_ncid, "height",
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.in_mpi_tm = H5Dopen(io.in_mpi_ncid, TASK_MAP,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.in_mpi_tn = H5Dopen(io.in_mpi_ncid, TASK_NUMBER,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.in_mpi_it = H5Dopen(io.in_mpi_ncid, ITER_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.in_mpi_conv = H5Dopen(io.in_mpi_ncid, CONV_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.in_mpi_dm = H5Dopen(io.in_mpi_ncid, DM_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.in_mpi_dmh = H5Dopen(io.in_mpi_ncid, DMH_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.in_mpi_zc = H5Dopen(io.in_mpi_ncid, ZC_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
return;
}
