CarpetIOHDF5: support IO->alias option in reader

this allows the reader to read a dataset into a different variable than
which one was written. Eg. GRHydro::dens in PPAnalysis::dens.

16 files changed, 132 insertions, 4 deletions

diff --git a/Carpet/CarpetIOHDF5/src/Input.cc b/Carpet/CarpetIOHDF5/src/Input.cc
index bf182f506..21a855a01 100644
--- a/Carpet/CarpetIOHDF5/src/Input.cc
+++ b/Carpet/CarpetIOHDF5/src/Input.cc
@@ -5,6 +5,8 @@
 #include <sstream>
 #include <string>
 #include <vector>
+#include <map>
+#include <algorithm>
 
 #include "util_Table.h"
 #include "cctk.h"
@@ -534,6 +536,20 @@ int Recover (cGH* cctkGH, const char *basefilename, int called_from)
     }
   }
 
+  // construct list of aliases for variable names. This is a global list even
+  // though the user gives a per-variable list.
+  std::map<string, unsigned int> alias;
+#ifdef IOUTIL_IOGH_HAS_ALIAS
+  for (unsigned int vindex = 0; vindex < read_completely.size(); vindex++) {
+    if (ioUtilGH->alias && ioUtilGH->alias[vindex]) {
+      string key(ioUtilGH->alias[vindex]);
+      // the explicit cast avoids ambiguity in the overloaded function pointer
+      transform(key.begin(), key.end(), key.begin(), (int(*)(int))toupper);
+      alias[key] = vindex;
+    }
+  }
+#endif
+
   CarpetIOHDF5GH* myGH =
                   (CarpetIOHDF5GH*) CCTK_GHExtension (cctkGH, CCTK_THORNSTRING);
   // allocate list of recovery filenames
@@ -598,8 +614,9 @@ int Recover (cGH* cctkGH, const char *basefilename, int called_from)
       HDF5_ERROR (H5Pclose (fapl_id));
 
       // browse through all datasets contained in this file
+      void *args[2] = {&file, &alias};
       HDF5_ERROR (H5Giterate (file.indexfile >= 0 ? file.indexfile : file.file,
-                              "/", NULL, BrowseDatasets, &file));
+                              "/", NULL, BrowseDatasets, args));
     }
     assert (file.patches.size() > 0);
     if (myGH->recovery_filename_list and not myGH->recovery_filename_list[i]) {
@@ -1177,10 +1194,12 @@ static void ReadMetadata (fileset_t& fileset, hid_t file)
 // Browses through all the datasets in a checkpoint/data file
 // and stores this information in a list of patch_t objects
 //////////////////////////////////////////////////////////////////////////////
-static herr_t BrowseDatasets (hid_t group, const char *objectname, void *arg)
+static herr_t BrowseDatasets (hid_t group, const char *objectname, void *args)
 {
   int error_count = 0;
-  file_t *file = (file_t *) arg;
+  file_t *file = ((file_t **) args)[0];
+  std::map<string, unsigned int>& alias =
+    *((std::map<string, unsigned int>**)args)[1];
   patch_t patch;
   hid_t dataset, dataspace, attr, attrtype;
   H5G_stat_t object_info;
@@ -1216,7 +1235,13 @@ static herr_t BrowseDatasets (hid_t group, const char *objectname, void *arg)
   HDF5_ERROR (H5Aread (attr, attrtype, &varname[0]));
   HDF5_ERROR (H5Tclose (attrtype));
   HDF5_ERROR (H5Aclose (attr));
-  patch.vindex = CCTK_VarIndex (&varname[0]);
+  string key(&varname[0]);
+  transform(key.begin(), key.end(), key.begin(), (int(*)(int))toupper);
+  if (alias.count(key)) {
+    patch.vindex = alias[key];
+  } else {
+    patch.vindex = CCTK_VarIndex (&varname[0]);
+  }
   HDF5_ERROR (attr = H5Aopen_name (dataset, "carpet_mglevel"));
   HDF5_ERROR (H5Aread (attr, H5T_NATIVE_INT, &patch.mglevel));
   HDF5_ERROR (H5Aclose (attr));
diff --git a/Carpet/CarpetIOHDF5/test/alias_datasets.par b/Carpet/CarpetIOHDF5/test/alias_datasets.par
new file mode 100644
index 000000000..689703fe5
--- /dev/null
+++ b/Carpet/CarpetIOHDF5/test/alias_datasets.par
@@ -0,0 +1,61 @@
+# deactivate the IDScalarWaveMoL thorn
+# initial data is read from files using the filereader
+ActiveThorns = "Carpet CarpetLib CarpetRegrid CarpetInterp CarpetReduce LoopControl GSL Boundary CoordBase InitBase SymBase CartGrid3D Periodic LocalInterp NaNChecker Slab Time MoL WaveToyMoL IOUtil CarpetIOBasic CarpetIOScalar HDF5 CarpetIOHDF5"
+#ActiveThorns = "Carpet CarpetLib CarpetRegrid CarpetInterp CarpetReduce LoopControl GSL Boundary CoordBase InitBase SymBase CartGrid3D Periodic LocalInterp NaNChecker Slab Time MoL WaveToyMoL IOUtil CarpetIOBasic CarpetIOScalar HDF5 CarpetIOHDF5 IDScalarWaveMoL"
+
+
+Cactus::cctk_itlast = 0
+
+Driver::global_nx  = 24
+Driver::global_ny  = 5
+Driver::global_nz  = 5
+Driver::ghost_size = 2
+
+InitBase::initial_data_setup_method = "init_all_levels"
+
+Carpet::max_refinement_levels    = 3
+Carpet::prolongation_order_space = 3
+Carpet::prolongation_order_time  = 2
+
+CarpetRegrid::refinement_levels = 1
+CarpetRegrid::refined_regions   = "manual-gridpoint-list"
+CarpetRegrid::gridpoints        = "[[ ([28,4,4]:[68,12,12]:[2,2,2]) ]]"
+CarpetRegrid::outerbounds       = "[[ [[0,0],[1,1],[1,1]] ]]"
+
+NaNChecker::check_every     = 16
+NaNChecker::check_vars      = "wavetoymol::phi wavetoymol::psi"
+NaNChecker::action_if_found = "terminate"
+
+Grid::domain = full
+Grid::type   = byrange
+Grid::xmin   = -0.1
+Grid::ymin   = -0.15
+Grid::zmin   = -0.15
+Grid::xmax   = +1.05
+Grid::ymax   = +0.15
+Grid::zmax   = +0.15
+
+Periodic::periodic = "yes"
+
+Time::dtfac = 0.25
+
+MoL::ODE_Method = "ICN"
+
+IO::out_dir       = $parfile
+IO::out_fileinfo  = "none"
+IO::parfile_write = "no"
+IO::out_every     = 1
+IO::out_yline_x   = 0.5
+IO::out_zline_x   = 0.5
+ 
+IOBasic::outInfo_vars          = "WaveToyMoL::scalarevolve"
+IOScalar::outScalar_vars       = "WaveToyMoL::scalarevolve"
+IOScalar::outScalar_reductions = "average count maximum minimum  norm1 norm2 norm_inf"
+
+# filereader input files and directory
+IO::filereader_ID_files = "psi phi"
+# to generate use
+#IO::filereader_ID_dir   = "../../../../../arrangements/Carpet/CarpetIOHDF5/test/input_initial_data"
+IO::filereader_ID_dir   = "../../../arrangements/Carpet/CarpetIOHDF5/test/input_initial_data"
+IO::filereader_ID_vars  = "WaveToyMoL::psi{alias='WaveToyMoL::phi'}
+                           WaveToyMoL::phi{alias='WaveToyMoL::psi'}"
diff --git a/Carpet/CarpetIOHDF5/test/alias_datasets/phi.average.asc b/Carpet/CarpetIOHDF5/test/alias_datasets/phi.average.asc
new file mode 100644
index 000000000..057e09b85
--- /dev/null
+++ b/Carpet/CarpetIOHDF5/test/alias_datasets/phi.average.asc
@@ -0,0 +1,3 @@
+# Scalar ASCII output created by CarpetIOScalar
+#
+0 0 0.12249510216753
diff --git a/Carpet/CarpetIOHDF5/test/alias_datasets/phi.count.asc b/Carpet/CarpetIOHDF5/test/alias_datasets/phi.count.asc
new file mode 100644
index 000000000..5eda0a7d7
--- /dev/null
+++ b/Carpet/CarpetIOHDF5/test/alias_datasets/phi.count.asc
@@ -0,0 +1,3 @@
+# Scalar ASCII output created by CarpetIOScalar
+#
+0 0 368
diff --git a/Carpet/CarpetIOHDF5/test/alias_datasets/phi.maximum.asc b/Carpet/CarpetIOHDF5/test/alias_datasets/phi.maximum.asc
new file mode 100644
index 000000000..0c3f4aab4
--- /dev/null
+++ b/Carpet/CarpetIOHDF5/test/alias_datasets/phi.maximum.asc
@@ -0,0 +1,3 @@
+# Scalar ASCII output created by CarpetIOScalar
+#
+0 0 6.28318530717959
diff --git a/Carpet/CarpetIOHDF5/test/alias_datasets/phi.minimum.asc b/Carpet/CarpetIOHDF5/test/alias_datasets/phi.minimum.asc
new file mode 100644
index 000000000..c6ca2be94
--- /dev/null
+++ b/Carpet/CarpetIOHDF5/test/alias_datasets/phi.minimum.asc
@@ -0,0 +1,3 @@
+# Scalar ASCII output created by CarpetIOScalar
+#
+0 0 -6.28318530717959
diff --git a/Carpet/CarpetIOHDF5/test/alias_datasets/phi.norm1.asc b/Carpet/CarpetIOHDF5/test/alias_datasets/phi.norm1.asc
new file mode 100644
index 000000000..bc9e777c1
--- /dev/null
+++ b/Carpet/CarpetIOHDF5/test/alias_datasets/phi.norm1.asc
@@ -0,0 +1,3 @@
+# Scalar ASCII output created by CarpetIOScalar
+#
+0 0 3.65651912560683
diff --git a/Carpet/CarpetIOHDF5/test/alias_datasets/phi.norm2.asc b/Carpet/CarpetIOHDF5/test/alias_datasets/phi.norm2.asc
new file mode 100644
index 000000000..5fed12880
--- /dev/null
+++ b/Carpet/CarpetIOHDF5/test/alias_datasets/phi.norm2.asc
@@ -0,0 +1,3 @@
+# Scalar ASCII output created by CarpetIOScalar
+#
+0 0 4.20795667182769
diff --git a/Carpet/CarpetIOHDF5/test/alias_datasets/phi.norm_inf.asc b/Carpet/CarpetIOHDF5/test/alias_datasets/phi.norm_inf.asc
new file mode 100644
index 000000000..0c3f4aab4
--- /dev/null
+++ b/Carpet/CarpetIOHDF5/test/alias_datasets/phi.norm_inf.asc
@@ -0,0 +1,3 @@
+# Scalar ASCII output created by CarpetIOScalar
+#
+0 0 6.28318530717959
diff --git a/Carpet/CarpetIOHDF5/test/alias_datasets/psi.average.asc b/Carpet/CarpetIOHDF5/test/alias_datasets/psi.average.asc
new file mode 100644
index 000000000..ae3b0aac2
--- /dev/null
+++ b/Carpet/CarpetIOHDF5/test/alias_datasets/psi.average.asc
@@ -0,0 +1,3 @@
+# Scalar ASCII output created by CarpetIOScalar
+#
+0 0 0.123091011810009
diff --git a/Carpet/CarpetIOHDF5/test/alias_datasets/psi.count.asc b/Carpet/CarpetIOHDF5/test/alias_datasets/psi.count.asc
new file mode 100644
index 000000000..5eda0a7d7
--- /dev/null
+++ b/Carpet/CarpetIOHDF5/test/alias_datasets/psi.count.asc
@@ -0,0 +1,3 @@
+# Scalar ASCII output created by CarpetIOScalar
+#
+0 0 368
diff --git a/Carpet/CarpetIOHDF5/test/alias_datasets/psi.maximum.asc b/Carpet/CarpetIOHDF5/test/alias_datasets/psi.maximum.asc
new file mode 100644
index 000000000..d9860b263
--- /dev/null
+++ b/Carpet/CarpetIOHDF5/test/alias_datasets/psi.maximum.asc
@@ -0,0 +1,3 @@
+# Scalar ASCII output created by CarpetIOScalar
+#
+0 0 1
diff --git a/Carpet/CarpetIOHDF5/test/alias_datasets/psi.minimum.asc b/Carpet/CarpetIOHDF5/test/alias_datasets/psi.minimum.asc
new file mode 100644
index 000000000..c3bbf657e
--- /dev/null
+++ b/Carpet/CarpetIOHDF5/test/alias_datasets/psi.minimum.asc
@@ -0,0 +1,3 @@
+# Scalar ASCII output created by CarpetIOScalar
+#
+0 0 -1
diff --git a/Carpet/CarpetIOHDF5/test/alias_datasets/psi.norm1.asc b/Carpet/CarpetIOHDF5/test/alias_datasets/psi.norm1.asc
new file mode 100644
index 000000000..175184158
--- /dev/null
+++ b/Carpet/CarpetIOHDF5/test/alias_datasets/psi.norm1.asc
@@ -0,0 +1,3 @@
+# Scalar ASCII output created by CarpetIOScalar
+#
+0 0 0.672112882651314
diff --git a/Carpet/CarpetIOHDF5/test/alias_datasets/psi.norm2.asc b/Carpet/CarpetIOHDF5/test/alias_datasets/psi.norm2.asc
new file mode 100644
index 000000000..091b839ce
--- /dev/null
+++ b/Carpet/CarpetIOHDF5/test/alias_datasets/psi.norm2.asc
@@ -0,0 +1,3 @@
+# Scalar ASCII output created by CarpetIOScalar
+#
+0 0 0.742616320690188
diff --git a/Carpet/CarpetIOHDF5/test/alias_datasets/psi.norm_inf.asc b/Carpet/CarpetIOHDF5/test/alias_datasets/psi.norm_inf.asc
new file mode 100644
index 000000000..d9860b263
--- /dev/null
+++ b/Carpet/CarpetIOHDF5/test/alias_datasets/psi.norm_inf.asc
@@ -0,0 +1,3 @@
+# Scalar ASCII output created by CarpetIOScalar
+#
+0 0 1