CarpetIOF5: More development

darcs-hash:20050514115336-891bb-a65eca247e30c35b99c6d5a6c98b759489372276.gz

22 files changed, 403 insertions, 220 deletions

diff --git a/CarpetDev/CarpetIOF5/param.ccl b/CarpetDev/CarpetIOF5/param.ccl
index c05d61922..1fae1f165 100644
--- a/CarpetDev/CarpetIOF5/param.ccl
+++ b/CarpetDev/CarpetIOF5/param.ccl
@@ -58,4 +58,4 @@ REAL out_dt "How often to do CarpetIOF5 output (overrides IO::out_dt)" STEERABLE
 REAL dt_fudge "Fudge factor for time comparisons" STEERABLE=always
 {
   0:* :: ""
-} 1.0e-8
+} 1.0e-12
diff --git a/CarpetDev/CarpetIOF5/schedule.ccl b/CarpetDev/CarpetIOF5/schedule.ccl
index c729ccccc..91f484a74 100644
--- a/CarpetDev/CarpetIOF5/schedule.ccl
+++ b/CarpetDev/CarpetIOF5/schedule.ccl
@@ -1,5 +1,7 @@
 # Schedule definitions for thorn CarpetIOF5
 
+STORAGE: next_output_iteration next_output_time this_iteration
+
 SCHEDULE CarpetIOF5_Startup AT startup AFTER IOUtil_Startup
 {
   LANG: C
diff --git a/CarpetDev/CarpetIOF5/src/IOF5.cc b/CarpetDev/CarpetIOF5/src/IOF5.cc
index 830d986a3..79cff030a 100644
--- a/CarpetDev/CarpetIOF5/src/IOF5.cc
+++ b/CarpetDev/CarpetIOF5/src/IOF5.cc
@@ -2,6 +2,7 @@
 #include <cassert>
 #include <cstdlib>
 #include <sstream>
+#include <string>
 #include <vector>
 
 #include "cctk.h"
@@ -43,9 +44,9 @@ namespace CarpetIOF5 {
   CarpetIOF5_Startup ();
   
   static void *
-  SetupGH (tFleshConfig * fleshconfig,
-           int convlevel,
-           cGH * cctkGH);
+  Setup (tFleshConfig * const fleshconfig,
+         int const convlevel,
+         cGH * const cctkGH);
   
   
   
@@ -83,6 +84,12 @@ namespace CarpetIOF5 {
                      int variable);
   
   static void
+  write_global (cGH const * cctkGH,
+                F5::simulation_t & simulation,
+                int group,
+                int variable);
+
+  static void
   write_one_reflevel (cGH const * cctkGH,
                       F5::simulation_t & simulation,
                       int group,
@@ -104,37 +111,24 @@ namespace CarpetIOF5 {
   
   
   
-  extern "C" int
+  int
   CarpetIOF5_Startup ()
   {
-    int const ierr
-      = CCTK_RegisterBanner ("AMR HDF5 I/O provided by CarpetIOF5");
-    assert (! ierr);
-    
-    extending_t::create();
-    
-    return 0;                   // no error
+    CCTK_INFO ("Startup");
+    return extending_t::create (Setup);
   }
   
   
   
   void *
-  SetupGH (tFleshConfig * const fleshconfig,
-           int const convlevel,
-           cGH * const cctkGH)
+  Setup (tFleshConfig * const fleshconfig,
+         int const convlevel,
+         cGH * const cctkGH)
   {
-    int ierr;
-    int const io_method = CCTK_RegisterIOMethod ("IOF5");
-    ierr = CCTK_RegisterIOMethodOutputGH (io_method, OutputGH);
-    assert (! ierr);
-    ierr = CCTK_RegisterIOMethodOutputVarAs (io_method, OutputVarAs);
-    assert (! ierr);
-    ierr = CCTK_RegisterIOMethodTimeToOutput (io_method, TimeToOutput);
-    assert (! ierr);
-    ierr = CCTK_RegisterIOMethodTriggerOutput (io_method, TriggerOutput);
-    assert (! ierr);
-    
-    return extending_t::setup (fleshconfig, convlevel, cctkGH);
+    assert (fleshconfig != 0);
+    CCTK_INFO ("Setup");
+    return extending_t::setup
+      (cctkGH, OutputGH, TimeToOutput, TriggerOutput, OutputVarAs);
   }
   
   
@@ -146,6 +140,8 @@ namespace CarpetIOF5 {
     
     assert (cctkGH != 0);
     
+    CCTK_INFO ("OutputGH");
+    
     int ierr;
     
     vector<bool> want_variables (CCTK_NumVars());
@@ -194,13 +190,19 @@ namespace CarpetIOF5 {
   TimeToOutput (cGH const * const cctkGH,
                 int const variable)
   {
+    DECLARE_CCTK_ARGUMENTS;
     DECLARE_CCTK_PARAMETERS;
     
     assert (cctkGH != 0);
     assert (variable >= 0 and variable < CCTK_NumVars());
     
     assert (Carpet::is_level_mode());
-    extending_t extending (cctkGH);
+    
+    {
+      char * const fullname = CCTK_FullName(variable);
+      CCTK_VInfo (CCTK_THORNSTRING, "TimeToOutput \"%s\"", fullname);
+      free (fullname);
+    }
     
     bool should_output;
     
@@ -219,9 +221,6 @@ namespace CarpetIOF5 {
     }
     else if (CCTK_EQUALS (my_out_criterion, "iteration"))
     {
-      int const last_output_iteration
-        = (extending.get_last_output_iteration
-           (Carpet::mglevel, Carpet::reflevel, variable));
       int const my_out_every = out_every == -2 ? IO_out_every : out_every;
       switch (my_out_every)
       {
@@ -232,30 +231,55 @@ namespace CarpetIOF5 {
         should_output = false;
         break;
       default:
-        should_output
-          = cctkGH->cctk_iteration >= last_output_iteration + my_out_every;
+        if (* this_iteration == cctk_iteration)
+        {
+          // we already decided to output this iteration
+          should_output = true;
+        }
+        else if (cctk_iteration >= * next_output_iteration)
+        {
+          // it is time for the next output
+          should_output = true;
+          * this_iteration = cctk_iteration;
+          * next_output_iteration = cctk_iteration + my_out_every;
+        }
+        else
+        {
+          should_output = false;
+        }
         break;
       }
     }
     else if (CCTK_EQUALS (my_out_criterion, "time"))
     {
-      CCTK_REAL const last_output_time
-        = (extending.get_last_output_time
-           (Carpet::mglevel, Carpet::reflevel, variable));
-      CCTK_REAL const my_out_dt
-        = abs (out_dt - (-2)) <= dt_fudge ? IO_out_dt : out_dt;
+      CCTK_REAL const my_out_dt = out_dt == -2 ? IO_out_dt : out_dt;
       if (out_dt == 0)
       {
         should_output = true;
       }
-      else if (abs (out_dt - (-1)) <= dt_fudge)
+      else if (out_dt == -1)
       {
         should_output = false;
       }
       else
       {
-        should_output
-          = cctkGH->cctk_time - dt_fudge >= last_output_time + my_out_dt;
+        if (* this_iteration == cctk_iteration)
+        {
+          // we already decided to output this iteration
+          should_output = true;
+        }
+        else if (cctk_time / cctk_delta_time
+                 >= * next_output_time / cctk_delta_time - dt_fudge)
+        {
+          // it is time for the next output
+          should_output = true;
+          * this_iteration = cctk_iteration;
+          * next_output_time = cctk_time + my_out_dt;
+        }
+        else
+        {
+          should_output = false;
+        }
       }
     }
     else
@@ -264,6 +288,27 @@ namespace CarpetIOF5 {
       should_output = false;
     }
     
+    if (should_output)
+    {
+      extending_t extending (cctkGH);
+      int const last_output_iteration
+        = (extending.get_last_output_iteration
+           (Carpet::mglevel, Carpet::reflevel, variable));
+      assert (last_output_iteration <= cctk_iteration);
+      if (last_output_iteration == cctk_iteration)
+      {
+        // Skipping output for variable, because this variable has
+        // already been output during the current iteration --
+        // probably via a trigger during the analysis stage
+        should_output = false;
+      }
+      else
+      {
+        extending.set_last_output_iteration
+          (Carpet::mglevel, Carpet::reflevel, variable, cctk_iteration);
+      }
+    }
+    
     return should_output;
   }
   
@@ -278,6 +323,12 @@ namespace CarpetIOF5 {
     assert (cctkGH != 0);
     assert (variable >= 0 and variable < CCTK_NumVars());
     
+    {
+      char * const fullname = CCTK_FullName(variable);
+      CCTK_VInfo (CCTK_THORNSTRING, "TriggerOutput \"%s\"", fullname);
+      free (fullname);
+    }
+    
     char * fullname = CCTK_FullName (variable);
     assert (fullname);
     
@@ -285,13 +336,6 @@ namespace CarpetIOF5 {
     
     free (fullname);
     
-    assert (Carpet::is_level_mode());
-    extending_t extending (cctkGH);
-    extending.set_last_output_iteration
-      (Carpet::mglevel, Carpet::reflevel, variable, cctkGH->cctk_iteration);
-    extending.set_last_output_time
-      (Carpet::mglevel, Carpet::reflevel, variable, cctkGH->cctk_time);
-    
     return ierr;
   }
   
@@ -308,6 +352,9 @@ namespace CarpetIOF5 {
     assert (varname != 0);
     assert (alias != 0);
     
+    CCTK_VInfo (CCTK_THORNSTRING, "OutputVarAs \"%s\" \"%s\"",
+                varname, alias);
+    
     int const variable = CCTK_VarIndex (varname);
     if (variable < 0)
     {
@@ -325,49 +372,30 @@ namespace CarpetIOF5 {
     
     extending_t extending (cctkGH);
     
-    std::ostringstream filenamebuf;
+    ostringstream filenamebuf;
     bool const use_IO_out_dir = strcmp (out_dir, "") == 0;
     filenamebuf << (use_IO_out_dir ? IO_out_dir : out_dir)
                 << "/"
                 << alias
                 << out_extension;
-    char const * const filename = filenamebuf.str().c_str();
+    string const filename = filenamebuf.str();
     
     bool const did_truncate = extending.get_did_truncate (filename);
     bool const do_truncate
       = ! did_truncate and IO_TruncateOutputFiles (cctkGH);
     extending.set_did_truncate (filename);
     
-    F5::file_t file (cctkGH, filenamebuf.str().c_str(), do_truncate);
+    F5::file_t file (cctkGH, filename, do_truncate);
     
     F5::timestep_t timestep (file, cctkGH->cctk_time);
     
     if (Carpet::is_meta_mode())
     {
-      int const grouptype = CCTK_GroupTypeI (group);
-      assert (grouptype >= 0);
-      switch (grouptype)
+      for (Carpet::mglevel_iterator mglevel_iter (cctkGH);
+           ! mglevel_iter.done();
+           mglevel_iter.step())
       {
-      case CCTK_GF:
-        {
-          for (Carpet::mglevel_iterator mglevel_iter (cctkGH);
-               ! mglevel_iter.done();
-               mglevel_iter.step())
-          {
-            write_one_mglevel (cctkGH, timestep, group, variable);
-          }
-        }
-        break;
-      case CCTK_ARRAY:
-      case CCTK_SCALAR:
-        {
-          Carpet::enter_global_mode (cctkGH, 0);
-          write_one_mglevel (cctkGH, timestep, group, variable);
-          Carpet::leave_global_mode (cctkGH);
-        }
-        break;
-      default:
-        assert (0);
+        write_one_mglevel (cctkGH, timestep, group, variable);
       }
     }
     else
@@ -386,17 +414,31 @@ namespace CarpetIOF5 {
                      int const group,
                      int const variable)
   {
-    std::ostringstream namebuf;
-    namebuf << "convlevel " << cctkGH->cctk_convlevel;
-    F5::simulation_t simulation (timestep, namebuf.str().c_str());
-    
-    if (grouptype == CCTK_GF and Carpet::is_global_mode())
+    CCTK_VInfo (CCTK_THORNSTRING,
+                "OutputVarAs/write_one_mglevel mglevel=%d", Carpet::mglevel);
+    
+    ostringstream namebuf;
+    namebuf << "convlevel=" << cctkGH->cctk_convlevel;
+    string const namestr = namebuf.str();
+    char const * const name = namestr.c_str();
+    F5::simulation_t simulation (timestep, name);
+    
+    int const grouptype = CCTK_GroupTypeI (group);
+    assert (grouptype >= 0);
+    switch (grouptype)
     {
-      int const grouptype = CCTK_GroupTypeI (group);
-      assert (grouptype >= 0);
-      switch (grouptype)
+    case CCTK_ARRAY:
+    case CCTK_SCALAR:
+      {
+        if (Carpet::do_global_mode)
+        {
+          write_global (cctkGH, simulation, group, variable);
+        }
+      }
+      break;
+    case CCTK_GF:
       {
-      case CCTK_GF:
+        if (Carpet::is_global_mode())
         {
           for (Carpet::reflevel_iterator reflevel_iter (cctkGH);
                ! reflevel_iter.done();
@@ -405,23 +447,58 @@ namespace CarpetIOF5 {
             write_one_reflevel (cctkGH, simulation, group, variable);
           }
         }
-        break;
-      case CCTK_ARRAY:
-      case CCTK_SCALAR:
+        else
         {
-          Carpet::enter_level_mode (cctkGH, 0);
-          write_one_reflevel (cctkGH, timestep, group, variable);
-          Carpet::leave_level_mode (cctkGH);
+          write_one_reflevel (cctkGH, simulation, group, variable);
         }
-        break;
-      default:
-        assert (0);
       }
+      break;
+    default:
+      assert (0);
     }
-    else
+  }
+  
+  
+  
+  void
+  write_global (cGH const * const cctkGH,
+                F5::simulation_t & simulation,
+                int const group,
+                int const variable)
+  {
+    CCTK_INFO ("OutputVarAs/write_global");
+    
+    F5::unigrid_topology_t topology (simulation);
+    
+    int const grouptype = CCTK_GroupTypeI (group);
+    assert (grouptype >= 0);
+    assert (grouptype == CCTK_SCALAR or grouptype == CCTK_ARRAY);
+    
+    vect<CCTK_REAL, dim> level_origin, level_delta;
+    for (int d=0; d<dim; ++d)
     {
-      write_one_reflevel (cctkGH, simulation, group, variable);
+      level_origin[d] = 0.0;
+      level_delta[d]  = 1.0;
     }
+    F5::Cartesian_coordinate_system_t coordinate_system
+      (topology, level_origin, level_delta);
+    
+    F5::physical_quantity_t physical_quantity (coordinate_system, group);
+    
+    F5::tensor_component_t tensor_component (physical_quantity, variable);
+    
+    int const myproc = CCTK_MyProc (cctkGH);
+    dh * const dd = Carpet::arrdata.at(group).at(0).dd;
+    bbox<int, dim> const & region
+      = dd->boxes.at(Carpet::mglevel).at(0).at(myproc).exterior;
+    
+    F5::data_region_t data_region (tensor_component, region);
+    
+    void const * const varptr = CCTK_VarDataPtrI (cctkGH, 0, variable);
+    assert (varptr != 0);
+    int const vartype = CCTK_VarTypeI (variable);
+    assert (vartype >= 0);
+    data_region.write (varptr, vartype);
   }
   
   
@@ -432,6 +509,14 @@ namespace CarpetIOF5 {
                       int const group,
                       int const variable)
   {
+    CCTK_VInfo (CCTK_THORNSTRING,
+                "OutputVarAs/write_one_reflevel reflevel=%d",
+                Carpet::reflevel);
+    
+    int const grouptype = CCTK_GroupTypeI (group);
+    assert (grouptype >= 0);
+    assert (grouptype == CCTK_GF);
+    
     F5::mesh_refinement_topology_t topology
       (simulation, Carpet::reflevel, Carpet::maxreflevels,
        Carpet::spacereflevelfact, Carpet::maxspacereflevelfact);
@@ -452,9 +537,6 @@ namespace CarpetIOF5 {
     
     if (Carpet::is_level_mode())
     {
-      int const grouptype = CCTK_GroupTypeI (group);
-      assert (grouptype >= 0);
-      
       for (Carpet::map_iterator map_iter (cctkGH, grouptype);
            ! map_iter.done();
            map_iter.step())
@@ -475,6 +557,9 @@ namespace CarpetIOF5 {
                  F5::tensor_component_t & tensor_component,
                  int const group)
   {
+    CCTK_VInfo (CCTK_THORNSTRING,
+                "OutputVarAs/write_one_map map=%d", Carpet::map);
+    
     if (Carpet::is_singlemap_mode())
     {
       int const grouptype = CCTK_GroupTypeI (group);
@@ -499,21 +584,27 @@ namespace CarpetIOF5 {
   write_one_component (cGH const * const cctkGH,
                        F5::tensor_component_t & tensor_component)
   {
-    int const variable = tensor_component.get_variable();
-    int const group = tensor_component.get_physical_quantity().get_group();
-    
-    dh * const dd = Carpet::arrdata.at(group).at(Carpet::map).dd;
-    bbox<int, dim> const & region
-      = (dd->boxes.at(Carpet::mglevel).at(Carpet::reflevel)
-         .at(Carpet::component).exterior);
+    CCTK_VInfo (CCTK_THORNSTRING,
+                "OutputVarAs/write_one_component component=%d",
+                Carpet::component);
     
-    F5::data_region_t data_region (tensor_component, region);
-    
-    void const * const varptr = CCTK_VarDataPtrI (cctkGH, 0, variable);
-    assert (varptr != 0);
-    int const vartype = CCTK_VarTypeI (variable);
-    assert (vartype >= 0);
-    data_region.write (varptr, vartype);
+    gh * const hh = Carpet::vhh.at(Carpet::map);
+    if (hh->is_local (Carpet::reflevel, Carpet::component))
+    {
+      dh * const dd = Carpet::vdd.at(Carpet::map);
+      bbox<int, dim> const & region
+        = (dd->boxes.at(Carpet::mglevel).at(Carpet::reflevel)
+           .at(Carpet::component).exterior);
+      
+      F5::data_region_t data_region (tensor_component, region);
+      
+      int const variable = tensor_component.get_variable();
+      void const * const varptr = CCTK_VarDataPtrI (cctkGH, 0, variable);
+      assert (varptr != 0);
+      int const vartype = CCTK_VarTypeI (variable);
+      assert (vartype >= 0);
+      data_region.write (varptr, vartype);
+    }
   }
   
   
diff --git a/CarpetDev/CarpetIOF5/src/README b/CarpetDev/CarpetIOF5/src/README
new file mode 100644
index 000000000..5795c9892
--- /dev/null
+++ b/CarpetDev/CarpetIOF5/src/README
@@ -0,0 +1,10 @@
+An F5 file contains the following hierarchy:
+
+        file
+        timestep
+        simulation
+        topology
+        coordinate_system
+        physical_quantity
+        tensor_component
+        data_region
diff --git a/CarpetDev/CarpetIOF5/src/coordinate_system.cc b/CarpetDev/CarpetIOF5/src/coordinate_system.cc
index a96ebd94b..3e0aa8fd8 100644
--- a/CarpetDev/CarpetIOF5/src/coordinate_system.cc
+++ b/CarpetDev/CarpetIOF5/src/coordinate_system.cc
@@ -1,4 +1,5 @@
 #include <sstream>
+#include <string>
 
 #include <hdf5.h>
 
@@ -112,9 +113,11 @@ namespace CarpetIOF5 {
     {
       assert (all (m_level_delta > 0));
       
-      std::ostringstream buf;
-      buf << "Cartesian 3D, x0=" << m_level_origin << ", dx=" << m_level_delta;
-      char const * const name = buf.str().c_str();
+      ostringstream namebuf;
+      namebuf << "Cartesian 3D, x0=" << m_level_origin
+              << ", dx=" << m_level_delta;
+      string const namestr = namebuf.str();
+      char const * const name = namestr.c_str();
       
       m_hdf5_coordinate_system
         = open_or_create_group (m_topology.get_hdf5_topology(), name);
diff --git a/CarpetDev/CarpetIOF5/src/coordinate_system.hh b/CarpetDev/CarpetIOF5/src/coordinate_system.hh
index 740a8a86a..06c93603e 100644
--- a/CarpetDev/CarpetIOF5/src/coordinate_system.hh
+++ b/CarpetDev/CarpetIOF5/src/coordinate_system.hh
@@ -18,6 +18,10 @@ namespace CarpetIOF5 {
     
     class coordinate_system_t {
       
+      coordinate_system_t ();
+      coordinate_system_t (coordinate_system_t const &);
+      coordinate_system_t operator= (coordinate_system_t const &);
+      
     protected:
       
       topology_t & m_topology;
@@ -52,6 +56,11 @@ namespace CarpetIOF5 {
       vect<CCTK_REAL, dim> m_level_origin;
       vect<CCTK_REAL, dim> m_level_delta;
       
+      Cartesian_coordinate_system_t ();
+      Cartesian_coordinate_system_t (Cartesian_coordinate_system_t const &);
+      Cartesian_coordinate_system_t
+      operator= (Cartesian_coordinate_system_t const &);
+      
     public:
       
       Cartesian_coordinate_system_t (topology_t & topology,
diff --git a/CarpetDev/CarpetIOF5/src/data_region.cc b/CarpetDev/CarpetIOF5/src/data_region.cc
index 6f713911e..d19700cc3 100644
--- a/CarpetDev/CarpetIOF5/src/data_region.cc
+++ b/CarpetDev/CarpetIOF5/src/data_region.cc
@@ -1,6 +1,7 @@
 #include <cassert>
 #include <cstdlib>
 #include <sstream>
+#include <string>
 
 #include "cctk.h"
 
@@ -25,9 +26,10 @@ namespace CarpetIOF5 {
     {
       assert (! region.empty());
       
-      ostringstream buf;
-      buf << "Region " << m_region;
-      char const * const name = buf.str().c_str();
+      ostringstream namebuf;
+      namebuf << "region=" << m_region;
+      string const namestr = namebuf.str();
+      char const * const name = namestr.c_str();
       assert (name != 0);
       
       int const vartype = CCTK_VarTypeI (m_tensor_component.get_variable());
@@ -44,8 +46,8 @@ namespace CarpetIOF5 {
       assert (m_dataspace >= 0);
 
       m_dataset
-        = H5Dcreate (m_dataspace, name, hdf5_datatype,
-                     m_dataspace, m_properties);
+        = H5Dcreate (m_tensor_component.get_hdf5_tensor_component(), name,
+                     hdf5_datatype, m_dataspace, m_properties);
       assert (m_dataset >= 0);
       
       write_or_check_attribute
diff --git a/CarpetDev/CarpetIOF5/src/data_region.hh b/CarpetDev/CarpetIOF5/src/data_region.hh
index 3f08e7c3a..9b354166a 100644
--- a/CarpetDev/CarpetIOF5/src/data_region.hh
+++ b/CarpetDev/CarpetIOF5/src/data_region.hh
@@ -24,6 +24,10 @@ namespace CarpetIOF5 {
       hid_t m_dataset;
       hid_t m_dataspace;
       
+      data_region_t ();
+      data_region_t (data_region_t const &);
+      data_region_t operator= (data_region_t const &);
+      
     public:
       
       data_region_t (tensor_component_t & tensor_component,
diff --git a/CarpetDev/CarpetIOF5/src/extending.cc b/CarpetDev/CarpetIOF5/src/extending.cc
index ab07491ab..4ec9a4e8b 100644
--- a/CarpetDev/CarpetIOF5/src/extending.cc
+++ b/CarpetDev/CarpetIOF5/src/extending.cc
@@ -1,5 +1,6 @@
 #include <cassert>
 #include <cstring>
+#include <iostream>
 
 #include "cctk.h"
 
@@ -12,22 +13,42 @@ namespace CarpetIOF5 {
   char const * const extending_t::
   extension_name = "CarpetIOF5";
   
-  void extending_t::
-  create ()
+  int extending_t::
+  create (void * (* const Setup) (tFleshConfig * config,
+                                  int convlevel,
+                                  cGH * cctkGH))
   {
     int const handle = CCTK_RegisterGHExtension (extension_name);
     assert (handle >= 0);
-    int const ierr = CCTK_RegisterGHExtensionSetupGH (handle, setup);
-    assert (! ierr);
+    int const iflag = CCTK_RegisterGHExtensionSetupGH (handle, Setup);
+    assert (iflag);
+    return 0;                   // no error
   }
   
   void * extending_t::
-  setup (tFleshConfig * const fleshconfig,
-         int const convlevel,
-         cGH * const cctkGH)
+  setup (cGH * const cctkGH,
+         int (* const OutputGH) (cGH const * cctkGH),
+         int (* const TimeToOutput) (cGH const * cctkGH,
+                                     int variable),
+         int (* const TriggerOutput) (cGH const * cctkGH,
+                                      int variable),
+         int (* const OutputVarAs) (cGH const * cctkGH,
+                                    char const * varname,
+                                    char const * alias))
   {
-    assert (fleshconfig != 0);
     assert (cctkGH != 0);
+    
+    int ierr;
+    int const io_method = CCTK_RegisterIOMethod (extension_name);
+    ierr = CCTK_RegisterIOMethodOutputGH (io_method, OutputGH);
+    assert (! ierr);
+    ierr = CCTK_RegisterIOMethodTimeToOutput (io_method, TimeToOutput);
+    assert (! ierr);
+    ierr = CCTK_RegisterIOMethodTriggerOutput (io_method, TriggerOutput);
+    assert (! ierr);
+    ierr = CCTK_RegisterIOMethodOutputVarAs (io_method, OutputVarAs);
+    assert (! ierr);
+    
     return new extension_t;
   }
   
@@ -41,26 +62,24 @@ namespace CarpetIOF5 {
   }
   
   bool extending_t::
-  get_did_truncate (char const * const name)
+  get_did_truncate (string const name)
     const
   {
-    assert (name != 0);
     return (m_extension->did_truncate.find (name)
             != m_extension->did_truncate.end());
   }
   
   void extending_t::
-  set_did_truncate (char const * const name)
+  set_did_truncate (string const name)
   {
-    assert (name != 0);
-    m_extension->did_truncate.insert (strdup (name));
+    m_extension->did_truncate.insert (name);
   }
   
   int extending_t::
   get_last_output_iteration (int const ml, int const rl, int const vi)
     const
   {
-    resize_last_output (ml, rl, vi, m_extension->last_output_iteration);
+    resize_last_output_iteration (ml, rl, vi);
     return m_extension->last_output_iteration.at(ml).at(rl).at(vi);
   }
   
@@ -68,54 +87,28 @@ namespace CarpetIOF5 {
   set_last_output_iteration (int const ml, int const rl, int const vi,
                              int const iteration)
   {
-    resize_last_output (ml, rl, vi, m_extension->last_output_iteration);
+    resize_last_output_iteration (ml, rl, vi);
     m_extension->last_output_iteration.at(ml).at(rl).at(vi) = iteration;
   }
   
-  CCTK_REAL extending_t::
-  get_last_output_time (int const ml, int const rl, int const vi)
-    const
-  {
-    resize_last_output (ml, rl, vi, m_extension->last_output_time);
-    return m_extension->last_output_time.at(ml).at(rl).at(vi);
-  }
-  
-  void extending_t::
-  set_last_output_time (int const ml, int const rl, int const vi,
-                        CCTK_REAL const time)
-  {
-    resize_last_output (ml, rl, vi, m_extension->last_output_time);
-    m_extension->last_output_time.at(ml).at(rl).at(vi) = time;
-  }
-  
-  template<typename T>
   void extending_t::
-  resize_last_output (int ml, int rl, int vi,
-                      vector<vector<vector<T> > > & array)
+  resize_last_output_iteration (int ml, int rl, int vi)
+    const
   {
     assert (ml >= 0);
-    if (ml >= array.size())
+    if (ml >= m_extension->last_output_iteration.size())
     {
-      array.resize (ml+1);
+      m_extension->last_output_iteration.resize (ml+1);
     }
     assert (rl >= 0);
-    if (rl >= array.at(ml).size())
+    if (rl >= m_extension->last_output_iteration.at(ml).size())
     {
-      array.at(ml).resize (rl+1);
+      m_extension->last_output_iteration.at(ml).resize (rl+1);
     }
-    if (vi >= array.at(ml).at(rl).size())
+    if (vi >= m_extension->last_output_iteration.at(ml).at(rl).size())
     {
-      array.at(ml).at(rl).resize (vi+1, -1);
+      m_extension->last_output_iteration.at(ml).at(rl).resize (vi+1, -1);
     }
   }
   
-  template
-  void extending_t::
-  resize_last_output (int ml, int rl, int vi,
-                      vector<vector<vector<int> > > & array);
-  template
-  void extending_t::
-  resize_last_output (int ml, int rl, int vi,
-                      vector<vector<vector<CCTK_REAL> > > & array);
-  
 } // namespace CarpetIOF5
diff --git a/CarpetDev/CarpetIOF5/src/extending.hh b/CarpetDev/CarpetIOF5/src/extending.hh
index 55d0d186e..4f9bc9cc1 100644
--- a/CarpetDev/CarpetIOF5/src/extending.hh
+++ b/CarpetDev/CarpetIOF5/src/extending.hh
@@ -2,6 +2,7 @@
 #define EXTENDING_HH
 
 #include <set>
+#include <string>
 #include <vector>
 
 #include "cctk.h"
@@ -11,6 +12,7 @@
 namespace CarpetIOF5 {
   
   using std::set;
+  using std::string;
   using std::vector;
   
   
@@ -20,32 +22,39 @@ namespace CarpetIOF5 {
     static char const * const extension_name;
     
     struct extension_t {
-      set<char const *> did_truncate;
+      set<string> did_truncate;
       // [mglevel][reflevel][variable];
       vector<vector<vector<int> > > last_output_iteration;
-      vector<vector<vector<CCTK_REAL> > > last_output_time;
     };
     
     extension_t * m_extension;
     
   public:
     
-    static void
-    create ();
+    static int
+    create (void * (* Setup) (tFleshConfig * config,
+                              int convlevel,
+                              cGH * cctkGH));
     
     static void *
-    setup (tFleshConfig * config,
-           int convlevel,
-           cGH * cctkGH);
+    setup (cGH * cctkGH,
+           int (* OutputGH) (cGH const * cctkGH),
+           int (* TimeToOutput) (cGH const * cctkGH,
+                                 int variable),
+           int (* TriggerOutput) (cGH const * cctkGH,
+                                  int variable),
+           int (* OutputVarAs) (cGH const * cctkGH,
+                                char const * varname,
+                                char const * alias));
     
     extending_t (cGH const * cctkGH);
     
     bool
-    get_did_truncate (char const * name)
+    get_did_truncate (string name)
       const;
     
     void
-    set_did_truncate (char const * name);
+    set_did_truncate (string name);
     
     int
     get_last_output_iteration (int ml, int rl, int vi)
@@ -54,19 +63,11 @@ namespace CarpetIOF5 {
     void
     set_last_output_iteration (int ml, int rl, int vi, int iteration);
     
-    CCTK_REAL
-    get_last_output_time (int ml, int rl, int vi)
-      const;
-    
-    void
-    set_last_output_time (int ml, int rl, int vi, CCTK_REAL time);
-    
   private:
     
-    template<typename T>
-    static void
-    resize_last_output (int ml, int rl, int vi,
-                        vector<vector<vector<T> > > & array);
+    void
+    resize_last_output_iteration (int ml, int rl, int vi)
+      const;
     
   };
   
diff --git a/CarpetDev/CarpetIOF5/src/file.cc b/CarpetDev/CarpetIOF5/src/file.cc
index 0582e2071..07366f072 100644
--- a/CarpetDev/CarpetIOF5/src/file.cc
+++ b/CarpetDev/CarpetIOF5/src/file.cc
@@ -1,4 +1,5 @@
 #include <cassert>
+#include <string>
 
 #include <hdf5.h>
 
@@ -14,26 +15,29 @@ namespace CarpetIOF5 {
     
     file_t::
     file_t (cGH const * const cctkGH,
-            char const * const filename,
+            string const filename,
             bool const do_truncate)
       : m_cctkGH (cctkGH),
         m_filename (filename)
     {
       assert (cctkGH);
-      assert (filename);
       
-      htri_t is_hdf5 = H5Fis_hdf5 (filename);
-      assert (is_hdf5 >= 0);
+      char const * const filenameptr = filename.c_str();
+      
+      htri_t is_hdf5;
+      H5E_BEGIN_TRY {
+        is_hdf5 = H5Fis_hdf5 (filenameptr);
+      } H5E_END_TRY;
       bool const file_exists = is_hdf5 > 0;
       
       if (do_truncate or ! file_exists)
       {
         m_hdf5_file
-          = H5Fcreate (filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+          = H5Fcreate (filenameptr, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
       }
       else
       {
-        m_hdf5_file = H5Fopen (filename, H5F_ACC_RDWR, H5P_DEFAULT);
+        m_hdf5_file = H5Fopen (filenameptr, H5F_ACC_RDWR, H5P_DEFAULT);
       }
       
       assert (invariant());
@@ -73,7 +77,6 @@ namespace CarpetIOF5 {
       const
     {
       return (m_cctkGH != 0
-              and m_filename != 0
               and m_hdf5_file >= 0);
     }
     
diff --git a/CarpetDev/CarpetIOF5/src/file.hh b/CarpetDev/CarpetIOF5/src/file.hh
index 042dc9148..b5ac2d696 100644
--- a/CarpetDev/CarpetIOF5/src/file.hh
+++ b/CarpetDev/CarpetIOF5/src/file.hh
@@ -1,6 +1,8 @@
 #ifndef FILE_HH
 #define FILE_HH
 
+#include <string>
+
 #include <hdf5.h>
 
 #include "cctk.h"
@@ -11,20 +13,28 @@
 
 namespace CarpetIOF5 {
   
+  using std::string;
+  
+  
+  
   namespace F5 {
     
     class file_t {
       
       cGH const * const m_cctkGH;
       
-      char const * const m_filename;
+      string const m_filename;
       
       hid_t m_hdf5_file;
       
+      file_t ();
+      file_t (file_t const &);
+      file_t operator= (file_t const &);
+      
     public:
       
       file_t (cGH const * cctkGH,
-              char const * filename,
+              string filename,
               bool do_truncate);
       
       virtual
diff --git a/CarpetDev/CarpetIOF5/src/physical_quantity.hh b/CarpetDev/CarpetIOF5/src/physical_quantity.hh
index 0c3982061..56f768799 100644
--- a/CarpetDev/CarpetIOF5/src/physical_quantity.hh
+++ b/CarpetDev/CarpetIOF5/src/physical_quantity.hh
@@ -19,6 +19,10 @@ namespace CarpetIOF5 {
       
       hid_t m_hdf5_physical_quantity;
       
+      physical_quantity_t ();
+      physical_quantity_t (physical_quantity_t const &);
+      physical_quantity_t operator= (physical_quantity_t const &);
+      
     public:
       
       physical_quantity_t (coordinate_system_t & coordinate_system,
diff --git a/CarpetDev/CarpetIOF5/src/simulation.cc b/CarpetDev/CarpetIOF5/src/simulation.cc
index 22fe58d57..eaf83fb1c 100644
--- a/CarpetDev/CarpetIOF5/src/simulation.cc
+++ b/CarpetDev/CarpetIOF5/src/simulation.cc
@@ -1,6 +1,4 @@
 #include <cassert>
-#include <string>
-#include <sstream>
 
 #include <hdf5.h>
 
@@ -22,12 +20,9 @@ namespace CarpetIOF5 {
     simulation_t::
     simulation_t (timestep_t & timestep,
                   char const * const name)
-      : m_timestep (timestep)
+      : m_timestep (timestep),
+        m_name (name)
     {
-      ostringstream buf;
-      buf << name;
-      m_name = buf.str();
-      
       m_hdf5_simulation
         = open_or_create_group (m_timestep.get_hdf5_timestep(),
                                 m_name.c_str());
diff --git a/CarpetDev/CarpetIOF5/src/simulation.hh b/CarpetDev/CarpetIOF5/src/simulation.hh
index baf02b725..7aed7ca11 100644
--- a/CarpetDev/CarpetIOF5/src/simulation.hh
+++ b/CarpetDev/CarpetIOF5/src/simulation.hh
@@ -22,10 +22,14 @@ namespace CarpetIOF5 {
       
       timestep_t & m_timestep;
       
-      string m_name;
+      string const m_name;
       
       hid_t m_hdf5_simulation;
       
+      simulation_t ();
+      simulation_t (simulation_t const &);
+      simulation_t operator= (simulation_t const &);
+      
     public:
       
       simulation_t (timestep_t & timestep,
diff --git a/CarpetDev/CarpetIOF5/src/tensor_component.cc b/CarpetDev/CarpetIOF5/src/tensor_component.cc
index 0741e3265..a9ea0e20c 100644
--- a/CarpetDev/CarpetIOF5/src/tensor_component.cc
+++ b/CarpetDev/CarpetIOF5/src/tensor_component.cc
@@ -20,7 +20,7 @@ namespace CarpetIOF5 {
     {
       assert (variable >= 0 and variable < CCTK_NumVars());
       
-      char * const name = CCTK_FullName (variable);
+      char const * const name = CCTK_VarName (variable);
       assert (name != 0);
       
       m_hdf5_tensor_component
@@ -29,8 +29,6 @@ namespace CarpetIOF5 {
                                 name);
       assert (m_hdf5_tensor_component >= 0);
       
-      free (name);
-      
       assert (invariant());
     }
     
diff --git a/CarpetDev/CarpetIOF5/src/tensor_component.hh b/CarpetDev/CarpetIOF5/src/tensor_component.hh
index cbdb2383f..8377983a7 100644
--- a/CarpetDev/CarpetIOF5/src/tensor_component.hh
+++ b/CarpetDev/CarpetIOF5/src/tensor_component.hh
@@ -19,6 +19,10 @@ namespace CarpetIOF5 {
       
       hid_t m_hdf5_tensor_component;
       
+      tensor_component_t ();
+      tensor_component_t (tensor_component_t const &);
+      tensor_component_t operator= (tensor_component_t const &);
+      
     public:
       
       tensor_component_t (physical_quantity_t & physical_quantity,
diff --git a/CarpetDev/CarpetIOF5/src/timestep.hh b/CarpetDev/CarpetIOF5/src/timestep.hh
index 715759c6d..203cb6683 100644
--- a/CarpetDev/CarpetIOF5/src/timestep.hh
+++ b/CarpetDev/CarpetIOF5/src/timestep.hh
@@ -27,6 +27,10 @@ namespace CarpetIOF5 {
       
       hid_t m_hdf5_timestep;
       
+      timestep_t ();
+      timestep_t (timestep_t const &);
+      timestep_t operator= (timestep_t const &);
+      
     public:
       
       timestep_t (file_t & file,
diff --git a/CarpetDev/CarpetIOF5/src/topology.cc b/CarpetDev/CarpetIOF5/src/topology.cc
index 337e1ca0b..b45f580d6 100644
--- a/CarpetDev/CarpetIOF5/src/topology.cc
+++ b/CarpetDev/CarpetIOF5/src/topology.cc
@@ -108,9 +108,10 @@ namespace CarpetIOF5 {
       assert (all (level_refinement_factor > 0));
       assert (all (level_refinement_factor <= max_refinement_factor));
       
-      ostringstream buf;
-      buf << "Vertices level " << refinement_level;
-      char const * const name = buf.str().c_str();
+      ostringstream namebuf;
+      namebuf << "Vertices level=" << refinement_level;
+      string const namestr = namebuf.str();
+      char const * const name = namestr.c_str();
       
       m_hdf5_topology
         = open_or_create_group (m_simulation.get_hdf5_simulation(), name);
@@ -133,7 +134,7 @@ namespace CarpetIOF5 {
       assert (all (coarse_delta > 0));
       assert (all (level_offset_denominator > 0));
       
-      CCTK_REAL const one = 1;
+      vect<CCTK_REAL, dim> const one = 1;
       level_delta = coarse_delta / m_level_refinement_factor;
       level_origin
         = (coarse_origin
diff --git a/CarpetDev/CarpetIOF5/src/topology.hh b/CarpetDev/CarpetIOF5/src/topology.hh
index 8f9399f51..81534f945 100644
--- a/CarpetDev/CarpetIOF5/src/topology.hh
+++ b/CarpetDev/CarpetIOF5/src/topology.hh
@@ -18,6 +18,10 @@ namespace CarpetIOF5 {
     
     class topology_t {
       
+      topology_t ();
+      topology_t (topology_t const &);
+      topology_t operator= (topology_t const &);
+      
     protected:
       
       simulation_t & m_simulation;
@@ -50,6 +54,10 @@ namespace CarpetIOF5 {
     
     class unigrid_topology_t : public topology_t {
       
+      unigrid_topology_t ();
+      unigrid_topology_t (unigrid_topology_t const &);
+      unigrid_topology_t operator= (unigrid_topology_t const &);
+      
     public:
       
       // Create unigrid topology
@@ -72,6 +80,11 @@ namespace CarpetIOF5 {
       vect<int, dim> const m_level_refinement_factor;
       vect<int, dim> const m_max_refinement_factor;
       
+      mesh_refinement_topology_t ();
+      mesh_refinement_topology_t (mesh_refinement_topology_t const &);
+      mesh_refinement_topology_t
+      operator= (mesh_refinement_topology_t const &);
+      
     public:
       
       mesh_refinement_topology_t (simulation_t & simulation,
diff --git a/CarpetDev/CarpetIOF5/src/utils.cc b/CarpetDev/CarpetIOF5/src/utils.cc
index 4102e36c5..ad0943ac6 100644
--- a/CarpetDev/CarpetIOF5/src/utils.cc
+++ b/CarpetDev/CarpetIOF5/src/utils.cc
@@ -70,26 +70,32 @@ namespace CarpetIOF5 {
       return H5T_NATIVE_LDOUBLE;
     }
     
+#ifdef HAVE_CCTK_COMPLEX8
     hid_t
     hdf5_datatype_from_dummy (CCTK_COMPLEX8 const & dummy)
     {
       CCTK_REAL4 real;
       return hdf5_complex_datatype_from_dummy (dummy, real);
     }
+#endif
     
+#ifdef HAVE_CCTK_COMPLEX16
     hid_t
     hdf5_datatype_from_dummy (CCTK_COMPLEX16 const & dummy)
     {
       CCTK_REAL8 real;
       return hdf5_complex_datatype_from_dummy (dummy, real);
     }
+#endif
     
+#ifdef HAVE_CCTK_COMPLEX32
     hid_t
     hdf5_datatype_from_dummy (CCTK_COMPLEX32 const & dummy)
     {
       CCTK_REAL16 real;
       return hdf5_complex_datatype_from_dummy (dummy, real);
     }
+#endif
     
     template<typename T, typename R>
     hid_t
@@ -102,12 +108,12 @@ namespace CarpetIOF5 {
       {
         initialised = true;
         
-        hsize_t const dim = 2;
+        hsize_t const cdim = 2;
         int const perm = 0;
         
         hdf_complex_datatype
           = H5Tarray_create (hdf5_datatype_from_dummy (real),
-                             1, & dim, & perm);
+                             1, & cdim, & perm);
         assert (hdf_complex_datatype >= 0);
       }
       
@@ -130,18 +136,38 @@ namespace CarpetIOF5 {
           break
       CASE (CCTK_VARIABLE_BYTE     , CCTK_BYTE     );
       CASE (CCTK_VARIABLE_INT      , CCTK_INT      );
+#ifdef HAVE_CCTK_INT1
       CASE (CCTK_VARIABLE_INT1     , CCTK_INT1     );
+#endif
+#ifdef HAVE_CCTK_INT1
       CASE (CCTK_VARIABLE_INT2     , CCTK_INT2     );
+#endif
+#ifdef HAVE_CCTK_INT2
       CASE (CCTK_VARIABLE_INT4     , CCTK_INT4     );
+#endif
+#ifdef HAVE_CCTK_INT4
       CASE (CCTK_VARIABLE_INT8     , CCTK_INT8     );
+#endif
       CASE (CCTK_VARIABLE_REAL     , CCTK_REAL     );
+#ifdef HAVE_CCTK_REAL4
       CASE (CCTK_VARIABLE_REAL4    , CCTK_REAL4    );
+#endif
+#ifdef HAVE_CCTK_REAL8
       CASE (CCTK_VARIABLE_REAL8    , CCTK_REAL8    );
+#endif
+#ifdef HAVE_CCTK_REAL16
       CASE (CCTK_VARIABLE_REAL16   , CCTK_REAL16   );
+#endif
       CASE (CCTK_VARIABLE_COMPLEX  , CCTK_COMPLEX  );
+#ifdef HAVE_CCTK_COMPLEX8
       CASE (CCTK_VARIABLE_COMPLEX8 , CCTK_COMPLEX8 );
+#endif
+#ifdef HAVE_CCTK_COMPLEX16
       CASE (CCTK_VARIABLE_COMPLEX16, CCTK_COMPLEX16);
+#endif
+#ifdef HAVE_CCTK_COMPLEX32
       CASE (CCTK_VARIABLE_COMPLEX32, CCTK_COMPLEX32);
+#endif
 #undef CASE
       case CCTK_VARIABLE_CHAR     : return H5I_INVALID_HID;
       case CCTK_VARIABLE_STRING   : return H5I_INVALID_HID;
@@ -206,8 +232,8 @@ namespace CarpetIOF5 {
       if (attribute < 0)
       {
         // The attribute does not yet exist; create it
-        hsize_t const dim = num_values;
-        hid_t const dataspace = H5Screate_simple (1, & dim, & dim);
+        hsize_t const adim = num_values;
+        hid_t const dataspace = H5Screate_simple (1, & adim, & adim);
         assert (dataspace >= 0);
         attribute = H5Acreate (where, name, datatype, dataspace, H5P_DEFAULT);
         assert (attribute >= 0);
@@ -228,11 +254,11 @@ namespace CarpetIOF5 {
         assert (is_simple > 0);
         int const ndims = H5Sget_simple_extent_ndims (dataspace);
         assert (ndims == 1);
-        hsize_t dim;
+        hsize_t adim;
         herr_t herr;
-        herr = H5Sget_simple_extent_dims (dataspace, & dim, 0);
-        assert (dim == num_values);
-        vector<T> buf (dim);
+        herr = H5Sget_simple_extent_dims (dataspace, & adim, 0);
+        assert (adim == num_values);
+        vector<T> buf (adim);
         herr = H5Aread (attribute, datatype, & buf.front());
         assert (! herr);
         herr = H5Sclose (dataspace);
diff --git a/CarpetDev/CarpetIOF5/src/utils.hh b/CarpetDev/CarpetIOF5/src/utils.hh
index 910328aae..0c7869b68 100644
--- a/CarpetDev/CarpetIOF5/src/utils.hh
+++ b/CarpetDev/CarpetIOF5/src/utils.hh
@@ -29,12 +29,18 @@ namespace CarpetIOF5 {
     hdf5_datatype_from_dummy (double const & dummy);
     hid_t
     hdf5_datatype_from_dummy (long double const & dummy);
+#ifdef HAVE_CCTK_COMPLEX8
     hid_t
     hdf5_datatype_from_dummy (CCTK_COMPLEX8 const & dummy);
+#endif
+#ifdef HAVE_CCTK_COMPLEX16
     hid_t
     hdf5_datatype_from_dummy (CCTK_COMPLEX16 const & dummy);
+#endif
+#ifdef HAVE_CCTK_COMPLEX32
     hid_t
     hdf5_datatype_from_dummy (CCTK_COMPLEX32 const & dummy);
+#endif
     
     template<typename T, typename R>
     hid_t