[Commits] [svn:einsteintoolkit] incoming/PITTNullCode/SphericalHarmonicReconASCII/ (Rev. 57)
reisswig at tapir.caltech.edu
reisswig at tapir.caltech.edu
Mon Nov 7 18:03:20 CST 2011
User: reisswig
Date: 2011/11/07 06:03 PM
Modified:
/PITTNullCode/SphericalHarmonicReconASCII/
configuration.ccl, param.ccl
/PITTNullCode/SphericalHarmonicReconASCII/src/
sph_database.cc, sph_database.hh, startup.cc
Log:
Add capability of hdf5.
File Changes:
Directory: /PITTNullCode/SphericalHarmonicReconASCII/
=====================================================
File [modified]: configuration.ccl
Delta lines: +1 -1
===================================================================
--- PITTNullCode/SphericalHarmonicReconASCII/configuration.ccl 2011-09-04 20:16:09 UTC (rev 56)
+++ PITTNullCode/SphericalHarmonicReconASCII/configuration.ccl 2011-11-08 00:03:19 UTC (rev 57)
@@ -1 +1 @@
-REQUIRES
+REQUIRES HDF5
File [modified]: param.ccl
Delta lines: +3 -2
===================================================================
--- PITTNullCode/SphericalHarmonicReconASCII/param.ccl 2011-09-04 20:16:09 UTC (rev 56)
+++ PITTNullCode/SphericalHarmonicReconASCII/param.ccl 2011-11-08 00:03:19 UTC (rev 57)
@@ -5,8 +5,9 @@
KEYWORD format "Boundary data file format"
{
- ASCII :: "standard ASCII format: lm-modes and spheres are stored in a 2d array (gnuplot style) for a given timestep"
- DAT :: "all variables and lm-modes are stored in one row for a given timestep"
+ ASCII :: "standard ASCII format: lm-modes and spheres are stored in a 2d array (gnuplot style) for a given timestep"
+ DAT :: "optimized ASCII format: all variables and lm-modes are stored in one row for a given timestep"
+ SpEC-H5 :: "SpEC-HDF5 format: Data is stored in HDF5 files grouped according to SpEC output."
} "ASCII"
CCTK_INT sphere_number "the sphere number (if multiple spheres are present in one file) that corresponds to the worldtube radius NullSHRExtract::cr"
Directory: /PITTNullCode/SphericalHarmonicReconASCII/src/
=========================================================
File [modified]: sph_database.cc
Delta lines: +227 -0
===================================================================
--- PITTNullCode/SphericalHarmonicReconASCII/src/sph_database.cc 2011-09-04 20:16:09 UTC (rev 56)
+++ PITTNullCode/SphericalHarmonicReconASCII/src/sph_database.cc 2011-11-08 00:03:19 UTC (rev 57)
@@ -855,7 +855,234 @@
}
+
+
+
+
+
+
+
+
+
+
+
+
+
+//-------------------------------------------------------------------------------------------
+//
+//
+// SpEC-H5 format goes here...........
+//
+//
+//------------------------------------------------------------------------------------------
+
+
+
+
+const string SPH_db_SpEC_H5::time_attrib_name = "Time";
+const string SPH_db_SpEC_H5::step_basename = "Step";
+
+ // table of varibale names: this maps a column number to a group.
+ // The first entry per varibale is the main group, the second is a possible subgroup, e.g.
+ // /g/Step00001/xx
+ // for SpEC
+const string SPH_db_SpEC_H5::varname_table[30][2] =
+ { { "Lapse", "scalar"},
+ { "Shift", "x" }, { "Shift", "y" }, { "Shift", "z" },
+ { "g", "xx" }, { "g", "xy" }, { "g", "xz" },
+ { "g", "yy" }, { "g", "yz" },
+ { "g", "zz" },
+
+ { "DrLapse", "scalar"},
+ { "DrShift", "x" }, { "DrShift", "y" }, { "DrShift", "z" },
+ { "Drg", "xx" }, { "Drg", "xy" }, { "Drg", "xz" },
+ { "Drg", "yy" }, { "Drg", "yz" },
+ { "Drg", "zz" },
+
+ { "DtLapse", "scalar"},
+ { "DtShift", "x" }, { "DtShift", "y" }, { "DtShift", "z" },
+ { "Dtg", "xx" }, { "Dtg", "xy" }, { "Dtg", "xz" },
+ { "Dtg", "yy" }, { "Dtg", "yz" },
+ { "Dtg", "zz" } };
+
+
+SPH_db_SpEC_H5::SPH_db_SpEC_H5(const string& fname_,
+ const int cached_timesteps)
+ : SPH_database(cached_timesteps), _fname(fname_)
+{
+ // open file
+ file = H5Fopen(_fname.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
+
+ scan();
}
+
+SPH_db_SpEC_H5::~SPH_db_SpEC_H5()
+{
+ // close file
+ H5Fclose(file);
+}
+
+int SPH_db_SpEC_H5::remove_non_monotonic_steps(const int k)
+{
+ // go backwards from k and remove until we get monotonicity
+ const double time = steps[k].time;
+ const int size = steps.size();
+ int c = 1;
+ for (int i=k-1; i >= 0; --i) {
+ if (time > steps[i].time) {
+ break;
+ }
+ ++c;
+ }
+
+ steps.erase(steps.begin()+k-c, steps.begin()+k);
+ _times.erase(_times.begin()+k-c, _times.begin()+k);
+ _iterations.erase(_iterations.begin()+k-c, _iterations.begin()+k);
+
+ // return the number of steps that were removed
+ return size-steps.size();
+}
+
+
+void SPH_db_SpEC_H5::scan()
+{
+
+ // scan datasets
+ scan_HDF5();
+
+
+ // check continuity and delta_t of timesteps
+ if (_times.size() > 1)
+ {
+ cout << "SPH_db_SpEC_H5 " << _fname << ": t_0 = " << _times[0] << ", t_final = " << _times.back() << endl;
+ _delta_t = 0;
+ for (int i=1; i < _times.size(); ++i)
+ {
+ if (fabs(_times[i] - _times[i-1]) < 1e-8 || _times[i] < _times[i-1]) {
+ ostringstream str;
+ str << "Removing non-monotonic timesteps: time[" << i-1 << "] = " << _times[i-1] << ", time[" << i << "] = " << _times[i];
+ CCTK_WARN(1, str.str().c_str());
+ i -= remove_non_monotonic_steps(i);
+ continue;
+ }
+ if (fabs(_times[i] - _times[i-1] - _delta_t) >= 1e-8)
+ {
+ _delta_t = _times[i]-_times[i-1];
+ cout << "SPH_db_SpEC_H5 " << _fname << ": t = " << _times[i-1] << ", delta_t = " << _delta_t << endl;
+ }
+ }
+ // set _delta_t to correspond to initial delta_t
+ _delta_t = _times[1]-_times[0];
+ }
+
+}
+
+
+
+
+void SPH_db_SpEC_H5::read(const int timestep, const int varno,
+ vector<vector<vector<CCTK_COMPLEX> > >& coeff) const
+{
+ if (timestep >= steps.size()) {
+ CCTK_WARN(0, "Requested timestep not in worldtube data file. Stopping!");
+ }
+
+ hid_t dataset = H5Dopen(file, (varname_table[varno][0]+"/"+steps[timestep].name+"/"+varname_table[varno][1]).c_str());//, H5P_DEFAULT);
+ vector<double> buffer((_lmax+1)*(_lmax+1)*2);
+ H5Dread(dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &buffer.front());
+ H5Dclose(dataset);
+
+ int c = 0;
+ for (int l=0; l <= _lmax; ++l) {
+ for (int m=l; m >= -l; --m, ++c) {
+ //coeff[0][l][m+l] = CCTK_Cmplx(buffer[c], buffer[c + buffer.size()/2]);
+ coeff[0][l][m+l] = CCTK_Cmplx(buffer[2*c], buffer[2*c + 1]);
+ }
+ }
+}
+
+
+
+herr_t SPH_db_SpEC_H5::H5iter(hid_t loc_id, const char* name, const H5L_info_t* info, void* operator_data)
+{
+ SPH_db_SpEC_H5* SpEC_H5 = (SPH_db_SpEC_H5*) operator_data;
+
+ // Datasets are ignored! We only iterate over groups
+ switch (info->type) {
+ case H5O_TYPE_GROUP: {
+ const string gname = name;
+ // we have found a timstep group if the group contains the "step_basename" substring
+ if (gname.find(step_basename) != string::npos) {
+ // get time attribute
+ double time;
+ hid_t group = H5Gopen(loc_id, name);
+ hid_t attribute = H5Aopen(group, time_attrib_name.c_str(), H5P_DEFAULT);
+ H5Aread(attribute, H5T_NATIVE_DOUBLE, &time);
+ H5Aclose(attribute);
+ H5Gclose(group);
+
+ SpEC_H5->steps.push_back(timestep_t(name, time));
+ }
+ break;
+ }
+ case H5O_TYPE_DATASET:
+ // ignore datasets
+ return 0;
+ break;
+ default:
+ break;
+ }
+
+ return 0;
+}
+
+
+
+void SPH_db_SpEC_H5::scan_HDF5()
+{
+ // pick one variable and browse through entire file
+ // to find out how many (and what) cycles and times there are
+ // (assuming that all variables are present at the same timesteps)
+ herr_t status = H5Literate_by_name (file, varname_table[0][0].c_str(), H5_INDEX_NAME, H5_ITER_NATIVE, NULL, H5iter, this, H5P_DEFAULT);
+ // sort 'steps' vector
+ //sort(steps.begin(), steps.end());
+ _iterations.resize(steps.size());
+ _times.resize(steps.size());
+ for (int i=0; i < steps.size(); ++i) {
+ //cout << steps[i].name << " " << steps[i].time << endl;
+ _iterations[i] = i;
+ _times[i] = steps[i].time;
+ }
+
+ // get lmax from first variable and timestep
+ hid_t dataset = H5Dopen(file, (varname_table[0][0]+"/"+steps[0].name+"/"+varname_table[0][1]).c_str()); //, H5P_DEFAULT);
+ //cout << (varname_table[0][0]+"/"+steps[0].name+"/"+varname_table[0][1]) << endl;
+ hid_t dataspace = H5Dget_space(dataset);
+ hsize_t size = H5Sget_simple_extent_npoints(dataspace);
+ H5Sclose(dataspace);
+ H5Dclose(dataset);
+
+ _lmax = sqrt(size/2)-1;
+ _n_variables = 30;
+ _n_spheres = 1;
+
+ // cross-check that all expected variables are present
+
+
+ // display some info
+ cout << "SPH_db_SpEC_H5 " << _fname << ": n_spheres = " << _n_spheres << endl;
+ cout << "SPH_db_SpEC_H5 " << _fname << ": n_variables = " << _n_variables << endl;
+ cout << "SPH_db_SpEC_H5 " << _fname << ": lmax = " << _lmax << endl;
+ cout << "SPH_db_SpEC_H5 " << _fname << ": timesteps = " << _iterations.size() << endl;
+}
+
+
+
+
+
+
+
+}
File [modified]: sph_database.hh
Delta lines: +63 -0
===================================================================
--- PITTNullCode/SphericalHarmonicReconASCII/src/sph_database.hh 2011-09-04 20:16:09 UTC (rev 56)
+++ PITTNullCode/SphericalHarmonicReconASCII/src/sph_database.hh 2011-11-08 00:03:19 UTC (rev 57)
@@ -18,10 +18,14 @@
#include "mpi.h"
+#define H5_USE_16_API 1
+#include "hdf5.h"
#ifndef _SPH_database_
#define _SPH_database_
+
+
namespace SHR {
using namespace std;
@@ -276,7 +280,66 @@
+
/**
+ A SpEC-HDF5 database
+*/
+class SPH_db_SpEC_H5 : public SPH_database
+{
+ public :
+ SPH_db_SpEC_H5(const string& fname_,
+ const int cached_timesteps);
+
+ virtual ~SPH_db_SpEC_H5();
+
+ // scans the input file
+ virtual void scan();
+
+ // read all modes on all extraction spheres for a given timestep and variable number into array
+ virtual void read(const int timestep, const int varno,
+ vector<vector<vector<CCTK_COMPLEX> > >& coeff) const;
+
+ private :
+
+ int remove_non_monotonic_steps(const int k);
+ void scan_HDF5();
+ static herr_t H5iter(hid_t loc_id, const char* name, const H5L_info_t* info, void* operator_data);
+
+
+ string _fname;
+
+ // the hdf5 file handle
+ hid_t file;
+
+ static const string time_attrib_name;
+ static const string step_basename;
+
+ // table of varibale names: this maps a column number to a group.
+ // The first entry per varibale is the main group, the second is a possible subgroup, e.g.
+ // /g/Step00001/xx
+ // for SpEC
+ static const string varname_table[30][2];
+
+ struct timestep_t
+ {
+ string name;
+ double time;
+ timestep_t(const string& name_, const double time_)
+ : name(name_), time(time_)
+ {}
+ bool operator<(const timestep_t& rhs) const { return time < rhs.time; }
+ };
+
+ /// the cylces and names of the steps contained in the file
+ vector<timestep_t> steps;
+
+};
+
+
+
+
+
+/**
This class represents a set of spherical coefficients for one variable and over all extraction spheres.
It can read-in the coefficients from a database and reconstruct the angular dependence by
recomposing with the basis-functions, i.e. the sYlm.
File [modified]: startup.cc
Delta lines: +2 -0
===================================================================
--- PITTNullCode/SphericalHarmonicReconASCII/src/startup.cc 2011-09-04 20:16:09 UTC (rev 56)
+++ PITTNullCode/SphericalHarmonicReconASCII/src/startup.cc 2011-11-08 00:03:19 UTC (rev 57)
@@ -122,6 +122,8 @@
SHR::db[i] = new SHR::SPH_db_ASCII(pathname+fnames[i], cached_timesteps+1, column_time, column_iteration, column_radius);
if (CCTK_EQUALS(format, "DAT"))
SHR::db[i] = new SHR::SPH_db_DAT(pathname+fnames[i], cached_timesteps+1, lmaxInFile, column_time, column_iteration, column_radius, column_lmax, column_n_variables, column_data);
+ if (CCTK_EQUALS(format, "SpEC-H5"))
+ SHR::db[i] = new SHR::SPH_db_SpEC_H5(pathname+fnames[i], cached_timesteps+1);
// check if timestep-size found in file matches characteristic timestep!
if (fabs(SHR::db[i]->delta_t()-CCTK_DELTA_TIME) > 1e-8)
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