mirror of
https://bitbucket.org/cosmicvoids/vide_public.git
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Imported Healpix, cfitsio, cosmotool. Added cmake tool to build dependencies (cfitsio, hdf5, netcdf, boost, healpix, gsl, ..). Adjusted CMakeLists.txt
This commit is contained in:
Guilhem Lavaux
parent
4bfb62f177
commit
51f6798f88
241 changed files with 243806 additions and 0 deletions
474
external/cosmotool/src/h5_readFlash.cpp
vendored
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474
external/cosmotool/src/h5_readFlash.cpp
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@ -0,0 +1,474 @@
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/* This file contains the functions that read the data from the HDF5 file
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* The functions accept the PARAMESH data through arguments.
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*/
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#include "h5_readFlash.hpp"
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using namespace H5;
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/* indices of attributes in fof_particle_type */
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int iptag_out = 0;
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int ipx_out = 0;
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int ipy_out = 1;
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int ipz_out = 2;
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int ipvx_out = 3;
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int ipvy_out = 4;
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int ipvz_out = 5;
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/* xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx */
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/* n*_runtime_parameters should be set by the caller to
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the maximum number of runtime parameters to read.
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*/
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void h5_read_runtime_parameters
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(H5File* file, /* file handle */
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double* LBox, // box size
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int* numPart,
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double *hubble,
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double *omegam,
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double *omegalambda) // number of particles
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{
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int MAX_PARM = 200;
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int nreal_runtime_parameters, nint_runtime_parameters, nstr_runtime_parameters;
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char real_runtime_parameter_names[MAX_PARM][RUNTIME_PARAMETER_STRING_SIZE];
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char int_runtime_parameter_names[MAX_PARM][RUNTIME_PARAMETER_STRING_SIZE];
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char str_runtime_parameter_names[MAX_PARM][RUNTIME_PARAMETER_STRING_SIZE];
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double real_runtime_parameter_values[MAX_PARM];
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int int_runtime_parameter_values[MAX_PARM];
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char str_runtime_parameter_values[MAX_PARM][RUNTIME_PARAMETER_STRING_SIZE];
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int rank;
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hsize_t dimens_1d, maxdimens_1d;
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real_runtime_params_t *real_rt_parms;
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int_runtime_params_t *int_rt_parms;
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str_runtime_params_t *str_rt_parms;
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log_runtime_params_t *log_rt_parms;
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double omegarad;
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int i;
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nint_runtime_parameters = MAX_PARM;
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nreal_runtime_parameters = MAX_PARM;
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/* integer runtime parameters */
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int_rt_parms = (int_runtime_params_t *) malloc(nint_runtime_parameters * sizeof(int_runtime_params_t));
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rank = 1;
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DataSet dataset = file->openDataSet("integer runtime parameters");
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IntType int_rt_type = dataset.getIntType();
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//int_rt_type = H5Dget_type(dataset);
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DataSpace dataspace = dataset.getSpace();
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//dataspace = H5Dget_space(dataset);
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int ndims = dataspace.getSimpleExtentDims(&dimens_1d, NULL);
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//H5Sget_simple_extent_dims(dataspace, &dimens_1d, &maxdimens_1d);
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/* don't read in more than we can handle */
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if (nint_runtime_parameters < dimens_1d) {
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dimens_1d = nint_runtime_parameters;
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} else {
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nint_runtime_parameters = dimens_1d;
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}
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DataSpace memspace(rank, &dimens_1d);
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//memspace = H5Screate_simple(rank, &dimens_1d, NULL);
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dataset.read(int_rt_parms, int_rt_type, memspace, dataspace,
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H5P_DEFAULT);
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//status = H5Dread(dataset, int_rt_type, memspace, dataspace,
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// H5P_DEFAULT, int_rt_parms);
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for (i = 0; i < nint_runtime_parameters; i++) {
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strncpy(int_runtime_parameter_names[i], int_rt_parms[i].name, RUNTIME_PARAMETER_STRING_SIZE);
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int_runtime_parameter_values[i] = int_rt_parms[i].value;
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}
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free(int_rt_parms);
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memspace.close();
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dataspace.close();
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dataset.close();
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//H5Sclose(dataspace);
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//H5Dclose(dataset);
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/* done with int runtime parameters */
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/* reals */
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real_rt_parms = (real_runtime_params_t *) malloc(nreal_runtime_parameters * sizeof(real_runtime_params_t));
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rank = 1;
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dataset = file->openDataSet("real runtime parameters");
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//dataset = H5Dopen(*file_identifier, "real runtime parameters");
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dataspace = dataset.getSpace();
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FloatType real_rt_type = dataset.getFloatType();
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ndims = dataspace.getSimpleExtentDims(&dimens_1d, NULL);
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//dataspace = H5Dget_space(dataset);
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//real_rt_type = H5Dget_type(dataset);
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//H5Sget_simple_extent_dims(dataspace, &dimens_1d, &maxdimens_1d);
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/* don't read in more than we can handle */
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if (nreal_runtime_parameters < dimens_1d) {
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dimens_1d = nreal_runtime_parameters;
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} else {
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nreal_runtime_parameters = dimens_1d;
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}
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memspace = DataSpace(rank, &dimens_1d);
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//memspace = H5Screate_simple(rank, &dimens_1d, NULL);
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dataset.read(real_rt_parms, real_rt_type, memspace, dataspace,
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H5P_DEFAULT);
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//status = H5Dread(dataset, real_rt_type, memspace, dataspace,
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// H5P_DEFAULT, real_rt_parms);
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for (i = 0; i < nreal_runtime_parameters; i++) {
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strncpy(real_runtime_parameter_names[i], real_rt_parms[i].name, RUNTIME_PARAMETER_STRING_SIZE);
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real_runtime_parameter_values[i] = real_rt_parms[i].value;
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}
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free(real_rt_parms);
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memspace.close();
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dataspace.close();
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dataset.close();
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//H5Sclose(dataspace);
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//H5Dclose(dataset);
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/* done with reals */
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// grab the data we want
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for (i = 0; i < nreal_runtime_parameters; i++) {
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if (strncmp(real_runtime_parameter_names[i],"xmax",4) == 0 ) {
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*LBox = real_runtime_parameter_values[i];
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}
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if (strncmp(real_runtime_parameter_names[i],"hubbleconstant", 14) == 0 ) {
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*hubble = real_runtime_parameter_values[i];
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}
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if (strncmp(real_runtime_parameter_names[i],"omegamatter", 11) == 0 ) {
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*omegam = real_runtime_parameter_values[i];
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}
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if (strncmp(real_runtime_parameter_names[i],"omegaradiation", 11) == 0 ) {
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omegarad = real_runtime_parameter_values[i];
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}
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if (strncmp(real_runtime_parameter_names[i],"cosmologicalconstant", 20) == 0 ) {
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*omegalambda = real_runtime_parameter_values[i];
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}
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}
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for (i = 0; i < nint_runtime_parameters; i++) {
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if (strncmp(int_runtime_parameter_names[i],"pt_numx",7) == 0 ) {
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*numPart = int_runtime_parameter_values[i];
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*numPart = *numPart * *numPart * *numPart;
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}
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}
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}
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/* xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx*/
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void h5_read_flash3_particles (H5File* file,
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int* totalparticles,
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int* localnp,
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int* particle_offset,
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float *pos1,
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float *pos2,
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float *pos3,
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float *vel1,
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float *vel2,
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float *vel3,
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int *id)
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{
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herr_t status;
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hsize_t dimens_1d, maxdims_1d;
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hsize_t start_1d, stride_1d, count_1d;
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int rank;
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int numProps, i, p;
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int numPartBuffer = 5000, sizePartBuffer, sizePart;
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int pstack, poffset, pcount;
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int iptag, ipx, ipy, ipz, ipvx, ipvy, ipvz;
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char *propName;
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double *partBuffer;
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char part_names[50][OUTPUT_PROP_LENGTH];
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int string_size;
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// char part_names[NPART_PROPS][OUTPUT_PROP_LENGTH];
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hsize_t dimens_2d[2], maxdimens_2d[2];
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hsize_t start_2d[2], count_2d[2], stride_2d[2];
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/* skip this routine if no particles to read */
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if ((*localnp) == 0) {
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return;
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}
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/* first determine how many particle properties are
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present in the input data file, and determine which of these
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are the properties we are interested in */
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DataSet dataset = file->openDataSet("particle names");
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DataSpace dataspace = dataset.getSpace();
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//dataset = H5Dopen(*file_identifier, "particle names");
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//dataspace = H5Dget_space(dataset);
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int ndims = dataspace.getSimpleExtentDims(dimens_2d, NULL);
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//H5Sget_simple_extent_dims(dataspace, dimens_2d, maxdimens_2d);
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//total number of particle properties
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numProps = dimens_2d[0];
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string_size = OUTPUT_PROP_LENGTH;
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StrType string_type = H5Tcopy(H5T_C_S1);
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string_type.setSize(string_size);
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//status = H5Tset_size(string_type, string_size);
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rank = 2;
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start_2d[0] = 0;
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start_2d[1] = 0;
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stride_2d[0] = 1;
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stride_2d[1] = 1;
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count_2d[0] = dimens_2d[0];
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count_2d[1] = dimens_2d[1];
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dataspace.selectHyperslab(H5S_SELECT_SET, count_2d, start_2d);
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//status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, start_2d,
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// stride_2d, count_2d, NULL);
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DataSpace memspace(rank, dimens_2d);
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//memspace = H5Screate_simple(rank, dimens_2d, NULL);
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dataset.read(part_names, string_type, H5S_ALL, H5S_ALL, H5P_DEFAULT);
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//status = H5Dread(dataset, string_type, H5S_ALL, H5S_ALL,
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// H5P_DEFAULT, part_names);
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string_type.close();
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memspace.close();
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dataspace.close();
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dataset.close();
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//H5Tclose(string_type);
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//H5Sclose(memspace);
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//H5Sclose(dataspace);
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//H5Dclose(dataset);
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for (i=0;i<numProps;i++) {
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if (strncmp(part_names[i], "tag", 3) == 0) { iptag = i+1; }
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if (strncmp(part_names[i], "posx", 4) == 0) { ipx = i+1; }
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if (strncmp(part_names[i], "posy", 4) == 0) { ipy = i+1; }
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if (strncmp(part_names[i], "posz", 4) == 0) { ipz = i+1; }
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if (strncmp(part_names[i], "velx", 4) == 0) { ipvx = i+1; }
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if (strncmp(part_names[i], "vely", 4) == 0) { ipvy = i+1; }
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if (strncmp(part_names[i], "velz", 4) == 0) { ipvz = i+1; }
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}
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if ((iptag < 0) || (ipx < 0) || (ipy < 0) || (ipz < 0) || (ipvx < 0) ||
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(ipvy < 0) || (ipvz < 0) ) {
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printf("One or more required particle attributes not found in file!\n");
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return;
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}
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//printf("iptag = %d, ipx = %d, ipy = %d, ipz = %d\n", iptag, ipx, ipy, ipz);
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//printf("ipvx = %d, ipvy = %d, ipvz = %d\n", ipvx, ipvy, ipvz);
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//read particles
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dataset = file->openDataSet("tracer particles");
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//dataset = H5Dopen(*file_identifier, "tracer particles");
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FloatType datatype = dataset.getFloatType();
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//datatype = H5Dget_type(dataset);
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/* establish read-in particle buffer */
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sizePart = numProps*(sizeof(double));
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sizePartBuffer = numPartBuffer * sizePart;
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partBuffer = (double *)malloc(sizePartBuffer);
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dataspace = dataset.getSpace();
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ndims = dataspace.getSimpleExtentDims(dimens_2d, NULL);
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//dataspace = H5Dget_space(dataset);
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//H5Sget_simple_extent_dims(dataspace, dimens_2d, maxdimens_2d);
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/*insert particle properties (numPartBuffer) particles at a time*/
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pstack = (*localnp);
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poffset = 0;
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if (pstack > numPartBuffer) {
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pcount = numPartBuffer;
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}
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else {
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pcount = pstack;
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}
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while ( pstack > 0) {
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rank = 2;
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maxdimens_2d[0] = (hsize_t) (*totalparticles);
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maxdimens_2d[1] = (hsize_t) (numProps);
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start_2d[0] = (hsize_t) (*particle_offset + poffset);
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start_2d[1] = (hsize_t) 0;
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stride_2d[0] = 1;
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stride_2d[1] = 1;
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count_2d[0] = (hsize_t) (pcount);
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count_2d[1] = (hsize_t) (numProps);
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dimens_2d[0] = (pcount);
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dimens_2d[1] = (numProps);
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dataspace.selectHyperslab(H5S_SELECT_SET, count_2d, start_2d);
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//status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, start_2d,
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// stride_2d, count_2d, NULL);
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memspace = DataSpace(rank, dimens_2d);
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//memspace = H5Screate_simple(rank, dimens_2d, maxdimens_2d);
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/* read data from the dataset */
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dataset.read(partBuffer, datatype, memspace, dataspace, H5P_DEFAULT);
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//status = H5Dread(dataset, datatype, memspace, dataspace, H5P_DEFAULT, partBuffer);
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/* convert buffer into particle struct */
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if (id) {
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for(p=0; p < (pcount); p++) {
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id[p+poffset] = (int) *(partBuffer+iptag-1+p*numProps);
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} }
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if (pos1 && pos2 && pos3) {
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for(p=0; p < (pcount); p++) {
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pos1[p+poffset] = (float) *(partBuffer+ipx-1+p*numProps);
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pos2[p+poffset] = (float) *(partBuffer+ipy-1+p*numProps);
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pos3[p+poffset] = (float) *(partBuffer+ipz-1+p*numProps);
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}
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}
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if (vel1 && vel2 && vel3) {
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for(p=0; p < (pcount); p++) {
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vel1[p+poffset] = (float) *(partBuffer+ipvx-1+p*numProps);
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vel2[p+poffset] = (float) *(partBuffer+ipvy-1+p*numProps);
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vel3[p+poffset] = (float) *(partBuffer+ipvz-1+p*numProps);
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}
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}
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memspace.close();
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//status = H5Sclose(memspace);
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/* advance buffer */
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pstack = pstack - pcount;
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poffset = poffset + pcount;
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if (pstack > numPartBuffer) {
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pcount = numPartBuffer;
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}
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else {
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pcount = pstack;
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}
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} /* end while */
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datatype.close();
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dataspace.close();
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dataset.close();
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//status = H5Tclose(datatype);
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//status = H5Sclose(dataspace);
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//status = H5Dclose(dataset);
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}
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/*xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx*/
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void h5_read_flash3_header_info(H5File* file,
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double* time, /* simulation time */
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double* redshift) /* redshift of checkpoint */
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{
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herr_t status;
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int file_version;
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hid_t sp_type, si_type;
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hsize_t dimens_1d, maxdimens_1d;
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hid_t string_type;
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real_list_t *real_list;
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int* num_real, num_int;
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int MAX_SCALARS = 100;
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char real_names[MAX_SCALARS][MAX_STRING_LENGTH];
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double real_values[MAX_SCALARS];
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char int_names[MAX_SCALARS][MAX_STRING_LENGTH];
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int int_values[MAX_SCALARS];
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int i;
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H5std_string DATASET_NAME;
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string_type = H5Tcopy(H5T_C_S1);
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H5Tset_size(string_type, MAX_STRING_LENGTH);
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DataSet dataset = file->openDataSet("real scalars");
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DataSpace dataspace = dataset.getSpace();
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/* read extent of 'dataspace' (i.e. # of name/value pairs) into 'dimens_1d' */
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int ndims = dataspace.getSimpleExtentDims(&dimens_1d, NULL);
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if (dimens_1d > MAX_SCALARS) {
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printf("Error: reading more than MAX_SCALARS runtime parameters in checkpoint file!\n");
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}
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/* malloc a pointer to a list of real_list_t's */
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real_list = (real_list_t *) malloc(dimens_1d * sizeof(real_list_t));
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// create a new simple dataspace of 1 dimension and size of 'dimens_1d'
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DataSpace memspace(1, &dimens_1d);
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|
||||
// create an empty vessel sized to hold one real_list_t's worth of data
|
||||
CompType real_list_type( sizeof(real_list_t) );
|
||||
|
||||
// subdivide the empty vessel into its component sections (name and value)
|
||||
real_list_type.insertMember(
|
||||
"name",
|
||||
HOFFSET(real_list_t, name),
|
||||
string_type);
|
||||
|
||||
real_list_type.insertMember(
|
||||
"value",
|
||||
HOFFSET(real_list_t, value),
|
||||
PredType::NATIVE_DOUBLE);
|
||||
|
||||
// read the data into 'real_list'
|
||||
dataset.read( real_list, real_list_type, memspace, dataspace,
|
||||
H5P_DEFAULT);
|
||||
|
||||
|
||||
if (status < 0) {
|
||||
printf("Error readingruntime parameterss from data file\n");
|
||||
}
|
||||
|
||||
for (i = 0; i < dimens_1d; i++) {
|
||||
strncpy(real_names[i], real_list[i].name, MAX_STRING_LENGTH);
|
||||
real_values[i] = real_list[i].value;
|
||||
|
||||
if (strncmp(real_names[i],"time",4) == 0 ) {
|
||||
*time = real_values[i];
|
||||
}
|
||||
if (strncmp(real_names[i],"redshift",8) == 0 ) {
|
||||
*redshift = real_values[i];
|
||||
}
|
||||
}
|
||||
|
||||
free(real_list);
|
||||
real_list_type.close();
|
||||
memspace.close();
|
||||
dataspace.close();
|
||||
dataset.close();
|
||||
}
|
||||
Loading…
Add table
Add a link
Reference in a new issue