Code cleanup before moving into production mode.

git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOPanda/trunk@29 38c3d835-c875-442e-b0fe-21c19ce1d001

8 files changed, 310 insertions, 331 deletions

diff --git a/src/GHExtension.c b/src/GHExtension.c
deleted file mode 100644
index b3cdd1d..0000000
--- a/src/GHExtension.c
+++ /dev/null
@@ -1,159 +0,0 @@
- /*@@
-   @file      GHExtension.c
-   @date      01 Oct 1999
-   @author    Jonghyun Lee
-   @desc      IOPanda GH extension stuff
-   @enddesc 
-   @history
-   @endhistory
- @@*/
-
-/*#define DEBUG_IO*/
-
-#include <stdlib.h>
-#include <string.h>
-#include <stdio.h>
-
-#include "cctk.h"
-#include "cctk_Parameters.h"
-#include "CactusBase/IOUtil/src/ioGH.h"
-#include "ioPandaGH.h"
-
-void *IOPanda_SetupGH (tFleshConfig *config,
-                       int convergence_level,
-                       cGH *GH);
-int IOPanda_InitGH (cGH *GH);
-void Panda_Create(int, int);
-
-
- /*@@
-   @routine    IOPanda_SetupGH
-   @date       Fri 01 Oct 1999
-   @author     Jonghyun Lee
-   @desc
-               Allocates the IOPanda GH extension structure.
-   @enddesc
-   @calledby   CCTK scheduler at CCTK_INITIALIZE
-   @var        config
-   @vdesc      flesh configuration structure (unused)
-   @vtype      tFleshConfig *
-   @vio        in
-   @endvar
-   @var        convergence_level
-   @vdesc      convergence level (unused)
-   @vtype      int
-   @vio        in
-   @endvar
-   @var        GH
-   @vdesc      pointer to grid hierarchy
-   @vtype      cGH *
-   @vio        in
-   @endvar
-   @history
-
-   @endhistory
-@@*/
-void *IOPanda_SetupGH (tFleshConfig *config,
-                       int convergence_level,
-                       cGH *GH)
-{
-  int numvars;
-  pandaGH *newGH;
-
-
-  /* avoid warnings about unused arguments */
-  config = config;
-  convergence_level = convergence_level;
-  GH = GH;
-
-  numvars = CCTK_NumVars ();
-
-  newGH             = (pandaGH *) malloc (sizeof (pandaGH));
-  newGH->do_out3D   = (char *)    malloc (numvars * sizeof (char));
-  newGH->out3D_last = (int *)     malloc (numvars * sizeof (int));
-
-  return (newGH);
-}
-
-
- /*@@
-   @routine    IOPanda_InitGH
-   @date       Fri 01 Oct 1999
-   @author     Jonghyun Lee
-   @desc
-               The GH initialization routine for IOFlexIO.
-               Necessary output dirs are created.
-   @enddesc
-   @calledby   CCTK scheduler at CCTK_INITIALIZE
-   @var        GH
-   @vdesc      pointer to grid hierarchy
-   @vtype      cGH *
-   @vio        in
-   @endvar
-   @history
-
-   @endhistory
-@@*/
-int IOPanda_InitGH (cGH *GH)
-{
-  DECLARE_CCTK_PARAMETERS
-  int i;
-  ioGH *ioUtilGH;
-  pandaGH *myGH; 
-
-
-  /* get the handles for IOUtil and IOPanda extensions */
-  ioUtilGH = (ioGH *) GH->extensions [CCTK_GHExtensionHandle ("IO")];
-  myGH = (pandaGH *) GH->extensions [CCTK_GHExtensionHandle ("IOPanda")];
-  
-  /* How often to output */
-  myGH->out3D_every = out_every > 0 ? out_every : -1;
-  if (out3D_every > 0)
-  {
-    myGH->out3D_every = out3D_every;
-  }
-
-  /* Check whether "outdir3D" was set.
-     If so take this dir otherwise default to "IO::outdir" */
-  if (CCTK_ParameterQueryTimesSet ("outdir3D", CCTK_THORNSTRING) > 0)
-  {
-    myGH->outdir3D = strdup (outdir3D);
-  }
-  else
-  {
-    myGH->outdir3D = strdup (outdir);
-  }
-
-  /* Create the output directory */
-  if (CCTK_MyProc (GH) == 0)
-  {
-    FILE *fp;
-
-
-    i = CCTK_CreateDirectory (0755, myGH->outdir3D);
-    if (i < 0)
-    {
-      CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
-                  "IOPanda_InitGH: Problem creating IOPanda 3D output "
-                  "directory '%s'", myGH->outdir3D);
-    }
-    else if (i > 0)
-    {
-      CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING,
-                  "IOPanda_InitGH: IOPanda 3D output directory '%s' already "
-                  "exists", myGH->outdir3D);
-    }
-    fp = fopen ("FILEPREFIX", "w");
-    fprintf (fp, "%s", myGH->outdir3D);
-    fclose (fp);
-  }
-
-  for (i = 0; i < CCTK_NumVars (); i++)
-  {
-    myGH->out3D_last [i] = -1;
-  }
-
-  Panda_Create (ioUtilGH->ioproc_every, 1);
-
-  return (0);
-}
diff --git a/src/Output3D.c b/src/Output.c
index 860f96a..4bb6a86 100644
--- a/src/Output3D.c
+++ b/src/Output.c
@@ -1,8 +1,9 @@
  /*@@
-   @file      Output3D.c
+   @file      Output.c
    @date      01 Oct 1999
    @author    Jonghyun Lee
-   @desc      Functions to deal 3D output of GFs
+   @desc
+              Functions to deal with IOPanda output of grid variables
    @enddesc
    @version   $Id$
  @@*/
@@ -15,26 +16,18 @@
 #include "cctk_Parameters.h"
 #include "CactusBase/IOUtil/src/ioGH.h"
 #include "CactusPUGH/PUGH/src/include/pugh.h"
-#include "CactusExternal/FlexIO/src/IOProtos.h"
+
 #include "ioPandaGH.h"
 #include "Panda/c_interface.h"
 
 /* the rcs ID and its dummy funtion to use it */
 static const char *rcsid = "$Header$";
-CCTK_FILEVERSION(BetaThorns_IOPanda_Output3D_c)
-
+CCTK_FILEVERSION(BetaThorns_IOPanda_Output_c)
 
-/* function prototypes */
-int IOPanda_Output3DGH (const cGH *GH);
-int IOPanda_TriggerOutput3D (const cGH *GH, int vindex);
-int IOPanda_Output3DVarAs (const cGH *GH, const char *var, const char *alias);
-int IOPanda_TimeFor3D (const cGH *GH, int vindex);
-void IOPanda_getDumpData (const cGH *GH, int vindex, int timelevel, void **outme,
-                         int *free_outme, CCTK_INT4 *geom, int element_size);
-void PandaTimestep(ArrayInfo *);
-int PandaIsNewFile(char *);
-void Panda_WriteAttribute(const char *, const char *, int, int, const void *);
 
+/********************************************************************
+ ********************    Internal Routines   ************************
+ ********************************************************************/
 static int CheckOutputVar (int vindex);
 static void CheckSteerableParameters (pandaGH *myGH);
 static void SetOutputFlag (int vindex, const char *optstring, void *arg);
@@ -43,13 +36,18 @@ static void IOPanda_IEEEIOStructDump (const cGH *GH, const char *fname);
 static void IOPanda_AddCommonAttributes (const cGH *GH, int vindex, int timelevel, int global_size[3], char *fname);
 static void IOPanda_AddChunkAttributes (const cGH *GH, int vindex, CCTK_INT4 *geom, char *fname);
 
+
 /*@@
-   @routine    IOPanda_Output3DGH
+   @routine    IOPanda_OutputGH
    @date       Sat March 6 1999
    @author     Gabrielle Allen
    @desc
                Loops over all variables and outputs them if necessary
    @enddesc
+
+   @calls      IOPanda_TimeFor
+               IOPanda_Timestep
+
    @var        GH
    @vdesc      Pointer to CCTK GH
    @vtype      const cGH *
@@ -62,12 +60,12 @@ static void IOPanda_AddChunkAttributes (const cGH *GH, int vindex, CCTK_INT4 *ge
                (or 0 if it wasn't time to output yet)
    @endreturndesc
 @@*/
-int IOPanda_Output3DGH (const cGH *GH)
+int IOPanda_OutputGH (const cGH *GH)
 {
   int vindex, retval;
+  pandaGH *myGH;
   char *fullname;
   const char *name;
-  pandaGH *myGH;
   DECLARE_CCTK_PARAMETERS
 
 
@@ -76,7 +74,7 @@ int IOPanda_Output3DGH (const cGH *GH)
 
   CheckSteerableParameters (myGH);
 
-  if (myGH->out3D_every <= 0)
+  if (myGH->out_every <= 0)
   {
     return (0);
   }
@@ -84,23 +82,23 @@ int IOPanda_Output3DGH (const cGH *GH)
   /* Loop over all variables */
   for (vindex = retval = 0; vindex < CCTK_NumVars (); vindex++)
   {
-    if (IOPanda_TimeFor3D (GH, vindex))
+    if (IOPanda_TimeFor (GH, vindex))
     {
-      name     = CCTK_VarName (vindex);
+      name = CCTK_VarName (vindex);
 
       if (verbose)
       {
         fullname = CCTK_FullName (vindex);
-        CCTK_VInfo (CCTK_THORNSTRING, "IOPanda_Output3DGH: "
+        CCTK_VInfo (CCTK_THORNSTRING, "IOPanda_OutputGH: "
                     "(fullname, name) = (%s, %s)", fullname, name);
         free (fullname);
       }
 
-      /* Do the 3D output */
+      /* Do the output */
       if (IOPanda_Timestep (GH, vindex, name) == 0)
       {
-        /* Register variable as having 3D output this iteration */
-        myGH->out3D_last [vindex] = GH->cctk_iteration;
+        /* Register variable as having output this iteration */
+        myGH->out_last [vindex] = GH->cctk_iteration;
         retval++;
       }
     }
@@ -111,14 +109,15 @@ int IOPanda_Output3DGH (const cGH *GH)
 
 
 /*@@
-   @routine    IOPanda_Output3DVarAs
+   @routine    IOPanda_OutputVarAs
    @date       Sat March 6 1999
    @author     Gabrielle Allen
    @desc
-               Unconditional output of a variable
-               using the IOPanda 3D output method
+               Unconditional output of a variable using the IOPanda I/O method
    @enddesc
-   @calledby   IOPanda_Output3DGH
+
+   @calls      IOPanda_Timestep
+
    @var        GH
    @vdesc      Pointer to CCTK GH
    @vtype      const cGH *
@@ -141,24 +140,21 @@ int IOPanda_Output3DGH (const cGH *GH)
                return code of @seeroutine IOPanda_Timestep
    @endreturndesc
 @@*/
-int IOPanda_Output3DVarAs (const cGH *GH,
-                           const char *fullname,
-                           const char *alias)
+int IOPanda_OutputVarAs (const cGH *GH, const char *fullname, const char *alias)
 {
   int vindex, retval;
   DECLARE_CCTK_PARAMETERS
 
 
-  vindex = CCTK_VarIndex(fullname);
-
+  vindex = CCTK_VarIndex (fullname);
   if (verbose)
   {
-    CCTK_VInfo (CCTK_THORNSTRING, "IOPanda_Output3DVarAs: "
+    CCTK_VInfo (CCTK_THORNSTRING, "IOPanda_OutputVarAs: "
                 "(fullname, alias, index) = (%s, %s, %d)",
                 fullname, alias, vindex);
   }
 
-  /* Do the 3D output */
+  /* Do the output */
   retval = IOPanda_Timestep (GH, vindex, alias);
 
   return (retval);
@@ -166,14 +162,16 @@ int IOPanda_Output3DVarAs (const cGH *GH,
 
 
 /*@@
-   @routine    IOPanda_TimeFor3D
+   @routine    IOPanda_TimeFor
    @date       Sat March 6 1999
    @author     Gabrielle Allen
    @desc
                Decides if it is time to output a variable
-               using the IOPanda 3D output method
+               using the IOPanda output method
    @enddesc
-   @calledby   IOPanda_Output3DGH
+
+   @calls      CheckSteerableParameters
+
    @var        GH
    @vdesc      Pointer to CCTK GH
    @vtype      const cGH *
@@ -191,10 +189,10 @@ int IOPanda_Output3DVarAs (const cGH *GH,
                0 if not
    @endreturndesc
 @@*/
-int IOPanda_TimeFor3D (const cGH *GH,
-                       int vindex)
+int IOPanda_TimeFor (const cGH *GH, int vindex)
 {
   pandaGH *myGH;
+  char *fullname;
 
 
   /* Get the GH extension for IOPanda */
@@ -203,25 +201,23 @@ int IOPanda_TimeFor3D (const cGH *GH,
   CheckSteerableParameters (myGH);
 
   /* Check if any output was requested */
-  if (myGH->out3D_every <= 0)
+  if (myGH->out_every <= 0)
   {
     return (0);
   }
 
   /* Check this variable should be output */
-  if (! (myGH->do_out3D [vindex] && GH->cctk_iteration % myGH->out3D_every == 0))
+  if (! (myGH->do_out[vindex] && GH->cctk_iteration % myGH->out_every == 0))
   {
     return (0);
   }
 
   /* Check variable not already output this iteration */
-  if (myGH->out3D_last [vindex] == GH->cctk_iteration)
+  if (myGH->out_last [vindex] == GH->cctk_iteration)
   {
-    char *fullname = CCTK_FullName (vindex);
-
-
+    fullname = CCTK_FullName (vindex);
     CCTK_VWarn (5, __LINE__, __FILE__, CCTK_THORNSTRING,
-                "Already done IOPanda 3D output for variable '%s' in current "
+                "Already done IOPanda output for variable '%s' in current "
                 "iteration (probably via triggers)", fullname);
     free (fullname);
     return (0);
@@ -232,12 +228,15 @@ int IOPanda_TimeFor3D (const cGH *GH,
 
 
 /*@@
-   @routine    IOPanda_TriggerOutput3D
+   @routine    IOPanda_TriggerOutput
    @date       Sat March 6 1999
    @author     Gabrielle Allen
    @desc
-               Triggers the output a variable using the IOPanda 3D output method
+               Triggers the output a variable using the IOPanda output method
    @enddesc
+
+   @calls      IOPanda_Timestep
+
    @var        GH
    @vdesc      Pointer to CCTK GH
    @vtype      const cGH *
@@ -254,8 +253,7 @@ int IOPanda_TimeFor3D (const cGH *GH,
                return code of @seeroutine IOPanda_Timestep
    @endreturndesc
 @@*/
-int IOPanda_TriggerOutput3D (const cGH *GH,
-                             int vindex)
+int IOPanda_TriggerOutput (const cGH *GH, int vindex)
 {
   int retval;
   pandaGH *myGH;
@@ -270,59 +268,77 @@ int IOPanda_TriggerOutput3D (const cGH *GH,
 
   if (verbose)
   {
-    CCTK_VInfo (CCTK_THORNSTRING, "TriggerOutput3D: "
+    CCTK_VInfo (CCTK_THORNSTRING, "TriggerOutput: "
                 "name, index = %s, %d", varname, vindex);
   }
 
-  /* Do the 3D output */
+  /* Do the output */
   retval = IOPanda_Timestep (GH, vindex, varname);
 
   if (retval == 0)
   {
-    /* Register variable as having 3D output this iteration */
-    myGH->out3D_last [vindex] = GH->cctk_iteration;
+    /* Register variable as having output this iteration */
+    myGH->out_last [vindex] = GH->cctk_iteration;
   }
 
   return (retval);
 }
 
 
-/**************************** local functions ******************************/
-/* check if steerable parameters have changed */
+/********************************************************************
+ ********************    Internal Routines   ************************
+ ********************************************************************/
+/*@@
+   @routine    CheckSteerableParameters
+   @date       Mon Oct 10 2000
+   @author     Thomas Radke
+   @desc
+               Checks if IOPanda steerable parameters were changed
+               and does appropriate re-evaluation.
+   @enddesc
+
+   @calls      CCTK_TraverseString
+
+   @var        myGH
+   @vdesc      Pointer to IOPanda GH
+   @vtype      pandaGH *
+   @vio        in
+   @endvar
+@@*/
 static void CheckSteerableParameters (pandaGH *myGH)
 {
-  DECLARE_CCTK_PARAMETERS
   int times_set;
-  static int out3D_vars_lastset = -1;
+  static int out_vars_lastset = -1;
+  DECLARE_CCTK_PARAMETERS
 
 
-  /* How often to output */
-  myGH->out3D_every = out_every > 0 ? out_every : -1;
-  if (out3D_every > 0)
+  /* how often to output */
+  myGH->out_every = out_every;
+  if (myGH->out_every < 0)
   {
-    myGH->out3D_every = out3D_every;
+    myGH->out_every = *(const CCTK_INT *)
+                      CCTK_ParameterGet ("out_every",
+                                         CCTK_ImplementationThorn ("IO"), NULL);
   }
 
-  /* re-parse the 'out3D_vars' parameter if it was changed */
-  times_set = CCTK_ParameterQueryTimesSet ("out3D_vars", CCTK_THORNSTRING);
-  if (times_set != out3D_vars_lastset)
+  /* re-parse the 'out_vars' parameter if it was changed */
+  times_set = CCTK_ParameterQueryTimesSet ("out_vars", CCTK_THORNSTRING);
+  if (times_set != out_vars_lastset)
   {
-    memset (myGH->do_out3D, 0, CCTK_NumVars ());
-    CCTK_TraverseString (out3D_vars, SetOutputFlag, myGH->do_out3D,
+    memset (myGH->do_out, 0, CCTK_NumVars ());
+    CCTK_TraverseString (out_vars, SetOutputFlag, myGH->do_out,
                          CCTK_GROUP_OR_VAR);
 
-    /* Save the last setting of 'out3D_vars' parameter */
-    out3D_vars_lastset = times_set;
+    /* Save the last setting of 'out_vars' parameter */
+    out_vars_lastset = times_set;
   }
-
 }
 
 
 /* check if this variable can be output (static conditions) */
 static int CheckOutputVar (int vindex)
 {
-  char *errormsg;
-  char *fullname;
+  char *errormsg, *fullname;
 
 
   errormsg = NULL;
@@ -333,11 +349,11 @@ static int CheckOutputVar (int vindex)
             is created and nothing is written to, it crashes at re-opening. ***/
   if (CCTK_VarTypeI (vindex) == CCTK_VARIABLE_COMPLEX)
   {
-    errormsg = "IOPanda 3D output for complex variable '%s' not yet supported";
+    errormsg = "IOPanda output for complex variable '%s' not yet supported";
   }
   else if (CCTK_GroupTypeFromVarI (vindex) == CCTK_SCALAR)
   {
-    errormsg = "IOPanda 3D output for scalar variable '%s' not supported";
+    errormsg = "IOPanda output for scalar variable '%s' not supported";
   }
 
   if (errormsg)
@@ -354,18 +370,13 @@ static int CheckOutputVar (int vindex)
 
 /* callback for CCTK_TraverseString() to set the output flag
    for the given variable */
-static void SetOutputFlag (int vindex,
-                           const char *optstring,
-                           void *arg)
+static void SetOutputFlag (int vindex, const char *optstring, void *arg)
 {
   char *flags = (char *) arg;
 
 
   /* Check the variable type */
-  if (CheckOutputVar (vindex) == 0)
-  {
-    flags[vindex] = 1;
-  }
+  flags[vindex] = CheckOutputVar (vindex) == 0;
 
   if (optstring)
   {
@@ -385,6 +396,7 @@ static int IOPanda_Timestep (const cGH *GH, int vindex, const char *alias)
   ArrayInfo ainfo;
   ioGH *ioUtilGH;
   pGH *pughGH;
+  char *fullname;
   union
   {
     char *non_const_char;
@@ -393,17 +405,12 @@ static int IOPanda_Timestep (const cGH *GH, int vindex, const char *alias)
   DECLARE_CCTK_PARAMETERS
 
 
-  /* prevent compiler warning "cast discards `const' from pointer target type"*/
-  cast_to_const.const_char = alias;
-
   /* check if variable has storage assigned */
   if (! CCTK_QueryGroupStorageI (GH, CCTK_GroupIndexFromVarI (vindex)))
   {
-    char *fullname = CCTK_FullName (vindex);
-
-
+    fullname = CCTK_FullName (vindex);
     CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING,
-                "No IOPanda 3D output for '%s' (no storage)", fullname);
+                "No IOPanda output for '%s' (no storage)", fullname);
     free (fullname);
     return (-1);
   }
@@ -412,6 +419,8 @@ static int IOPanda_Timestep (const cGH *GH, int vindex, const char *alias)
   pughGH = PUGH_pGH (GH);
   ioUtilGH = (ioGH *) CCTK_GHExtension (GH, "IO");
 
+  /* prevent compiler warning "cast discards `const' from pointer target type"*/
+  cast_to_const.const_char = alias;
   ainfo.name_ = cast_to_const.non_const_char;
 
   ainfo.rank_ = 3;
@@ -549,7 +558,7 @@ static void IOPanda_AddCommonAttributes (const cGH *GH,
   d3_to_IO [0] = GH->cctk_delta_space [0] * ioUtilGH->downsample[0];
   d3_to_IO [1] = GH->cctk_delta_space [1] * ioUtilGH->downsample[1];
   d3_to_IO [2] = GH->cctk_delta_space [2] * ioUtilGH->downsample[2];
-  Panda_WriteAttribute (fname, "delta", FLOAT64, 3,d3_to_IO);
+  Panda_WriteAttribute (fname, "delta", FLOAT64, 3, d3_to_IO);
 
   if (ioUtilGH->downsample[0] > 1 ||
       ioUtilGH->downsample[1] > 1 ||
@@ -592,7 +601,9 @@ static void IOPanda_AddChunkAttributes (const cGH *GH,
 
   /* there is nothing to do for a serial run */
   if (CCTK_nProcs (GH) == 1)
+  {
     return;
+  }
 
   /* get the dimension of the variable */
   dim = CCTK_GroupDimI (CCTK_GroupIndexFromVarI (vindex));
diff --git a/src/Panda/c_interface.h b/src/Panda/c_interface.h
index 1b0786c..e142ab3 100644
--- a/src/Panda/c_interface.h
+++ b/src/Panda/c_interface.h
@@ -25,4 +25,11 @@ typedef struct ArrayInfo {
   struct ArrayInfo *next_;      /* next element */
 } ArrayInfo;
 
+/* prototypes for functions called in the Panda library */
+int Panda_Create (int ioproc_every, int is_part_time_mode);
+void Panda_Finalize (void);
+void PandaTimestep (ArrayInfo *);
+int PandaIsNewFile (char *);
+void Panda_WriteAttribute (const char *, const char *, int, int, const void *);
+
 #endif
diff --git a/src/Startup.c b/src/Startup.c
index d4cd4eb..04a5fe6 100644
--- a/src/Startup.c
+++ b/src/Startup.c
@@ -2,10 +2,10 @@
    @file      Startup.c
    @date      01 Oct 1999
    @author    Jonghyun Lee
-   @desc      Startup routines for IOPanda.
-   @enddesc 
-   @history
-   @endhistory
+   @desc
+              Startup routines for IOPanda.
+   @enddesc
+   @version   $Id$
  @@*/
 
 #include <stdio.h>
@@ -16,77 +16,180 @@
 #include "cctk_GHExtensions.h"
 #include "cctk_Parameters.h"
 #include "CactusBase/IOUtil/src/ioGH.h"
+#include "CactusBase/IOUtil/src/ioutil_Utils.h"
+#include "ioPandaGH.h"
 
-/* prototypes of functions to be registered */
-int IOPanda_Output3DGH (const cGH *GH);
-int IOPanda_TriggerOutput3D (const cGH *GH, int);
-int IOPanda_TimeFor3D (const cGH *GH, int);
-int IOPanda_Output3DVarAs (const cGH *GH, const char *var, const char *alias);
-void *IOPanda_SetupGH (tFleshConfig *config, int convergence_level, cGH *GH);
-int IOPanda_InitGH (cGH *GH);
-int IOPanda_RecoverGH (cGH *GH, const char *basename, int called_from);
+/* the rcs ID and its dummy function to use it */
+static const char *rcsid = "$Id$";
+CCTK_FILEVERSION(BetaThorns_IOPanda_Startup_c)
 
+
+/********************************************************************
+ ********************    External Routines   ************************
+ ********************************************************************/
 void IOPanda_Startup (void);
-void IOPanda_Finalize(void);
-void Panda_Finalize(void);
+void IOPanda_Finalize (void);
+
+
+/********************************************************************
+ ********************    Internal Routines   ************************
+ ********************************************************************/
+static void *SetupGH (tFleshConfig *config, int convergence_level, cGH *GH);
+
 
  /*@@
    @routine   IOPanda_Startup
    @date      Fri May 21 1999
    @author    Thomas Radke
-   @desc 
-   The startup registration routine for IOPanda.
-   Registers the GH extensions needed for IOPanda and
-   the registerable routines used for each method of IOPanda.
-   IOPanda does not overload any functions.
-   @enddesc 
-   @calls     
-   @calledby   
-   @history 
- 
-   @endhistory 
-
+   @desc
+              The startup registration routine for IOPanda.
+              Registers the GH extensions needed for IOPanda
+              along with its setup routine.
+   @enddesc
+   @calls     CCTK_RegisterGHExtension
+              CCTK_RegisterGHExtensionSetupGH
 @@*/
 void IOPanda_Startup (void)
 {
-  int IO_GHExtension;
-  int IOMethod;
-
-
-  if (CCTK_GHExtensionHandle ("IO") < 0)
+  /* check that thorn PUGH was activated */
+  if (CCTK_GHExtensionHandle ("PUGH") >= 0)
   {
-    CCTK_WARN (1, "Thorn IOUtil was not activated. "
-                  "No IOPanda IO methods will be enabled.");
-    return;
+    CCTK_RegisterGHExtensionSetupGH (CCTK_RegisterGHExtension ("IOPanda"),
+                                     SetupGH);
   }
-  if (CCTK_GHExtensionHandle ("PUGH") < 0)
+  else
   {
     CCTK_WARN (1, "Thorn PUGH was not activated. "
-                  "No IOPanda IO methods will be enabled.");
-    return;
+                  "No IOPanda I/O methods will be enabled.");
   }
+}
+
+
+ /*@@
+   @routine   IOPanda_Finalize
+   @date      Fri May 21 1999
+   @author    Thomas Radke
+   @desc
+              The termination routine for IOPanda.
+              Shuts down the Panda subsystem.
+   @enddesc
+@@*/
+void IOPanda_Finalize (void)
+{
+  Panda_Finalize ();
+}
 
-  IO_GHExtension = CCTK_RegisterGHExtension ("IOPanda");
-  CCTK_RegisterGHExtensionSetupGH (IO_GHExtension, IOPanda_SetupGH);
-  CCTK_RegisterGHExtensionInitGH (IO_GHExtension, IOPanda_InitGH);
 
-  /* Register the 3D IOPandaIO routines as output methods  */
-  IOMethod = CCTK_RegisterIOMethod ("IOPandaIO_3D");
-  CCTK_RegisterIOMethodOutputGH (IOMethod, IOPanda_Output3DGH);
-  CCTK_RegisterIOMethodOutputVarAs (IOMethod, IOPanda_Output3DVarAs);
-  CCTK_RegisterIOMethodTimeToOutput (IOMethod, IOPanda_TimeFor3D);
-  CCTK_RegisterIOMethodTriggerOutput (IOMethod, IOPanda_TriggerOutput3D);
+/********************************************************************
+ ********************    Internal Routines   ************************
+ ********************************************************************/
+ /*@@
+   @routine    SetupGH
+   @date       Fri 01 Oct 1999
+   @author     Jonghyun Lee
+   @desc
+               Allocates and sets up IOPanda's GH extension structure.
+   @enddesc
 
-#if 0
-  /* Register the IOPanda recovery routine to thorn IOUtil */
-  if (IOUtil_RegisterRecover ("IOPanda recovery", IOPanda_RecoverGH) < 0)
-    CCTK_WARN (1, "Failed to register IOPanda recovery routine");
-  Panda_Create(1, 1);
-#endif
+   @calls      CCTK_RegisterIOMethod
+               CCTK_RegisterIOMethodOutputGH
+               CCTK_RegisterIOMethodOutputVarAs
+               CCTK_RegisterIOMethodTimeToOutput
+               CCTK_RegisterIOMethodTriggerOutput
+               IOUtil_CreateDirectory
 
-}
+   @var        config
+   @vdesc      flesh configuration structure (unused)
+   @vtype      tFleshConfig *
+   @vio        in
+   @endvar
+   @var        convergence_level
+   @vdesc      convergence level (unused)
+   @vtype      int
+   @vio        in
+   @endvar
+   @var        GH
+   @vdesc      pointer to grid hierarchy
+   @vtype      cGH *
+   @vio        in
+   @endvar
 
-void IOPanda_Finalize(void)
+   @returntype void *
+   @returndesc
+               pointer to the allocated GH extension structure
+   @endreturndesc
+@@*/
+static void *SetupGH (tFleshConfig *config, int convergence_level, cGH *GH)
 {
-  Panda_Finalize();
+  int i, numvars;
+  FILE *fp;
+  pandaGH *myGH;
+  const ioGH *ioUtilGH;
+  DECLARE_CCTK_PARAMETERS
+
+
+  /* suppress compiler warnings about unused variables */
+  (void) (config + 0);
+  (void) (convergence_level + 0);
+
+
+  /* Register IOPanda's routines as a new I/O method */
+  i = CCTK_RegisterIOMethod ("IOPandaIO");
+  CCTK_RegisterIOMethodOutputGH (i, IOPanda_OutputGH);
+  CCTK_RegisterIOMethodOutputVarAs (i, IOPanda_OutputVarAs);
+  CCTK_RegisterIOMethodTimeToOutput (i, IOPanda_TimeFor);
+  CCTK_RegisterIOMethodTriggerOutput (i, IOPanda_TriggerOutput);
+
+  /* allocate a new GH extension structure */
+  myGH = (pandaGH *) malloc (sizeof (pandaGH));
+  numvars = CCTK_NumVars ();
+  myGH->do_out = (char *) malloc (numvars * sizeof (char));
+  myGH->out_last = (int *) malloc (numvars * sizeof (int));
+
+  for (i = 0; i < numvars; i++)
+  {
+    myGH->out_last[i] = -1;
+  }
+
+  /* get the handle for IOUtil extensions */
+  ioUtilGH = (const ioGH *) CCTK_GHExtension (GH, "IO");
+
+  /* Check whether "IOPanda::outdir" was set.
+     If so take this directory otherwise default to "IO::outdir" */
+  if (CCTK_ParameterQueryTimesSet ("outdir", CCTK_THORNSTRING) > 0)
+  {
+    myGH->outdir = strdup (outdir);
+  }
+  else
+  {
+    myGH->outdir = CCTK_ParameterValString ("outdir",
+                                            CCTK_ImplementationThorn ("IO"));
+  }
+
+  /* Create the output directory */
+  i = IOUtil_CreateDirectory (GH, myGH->outdir,
+                              ! CCTK_Equals (out3D_mode, "onefile"),
+                              ioUtilGH->ioproc);
+  if (i < 0)
+  {
+    CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
+                "Problem creating IOPanda output directory '%s'", myGH->outdir);
+  }
+  else if (i > 0 && CCTK_Equals (newverbose, "full"))
+  {
+    CCTK_VInfo (CCTK_THORNSTRING,
+                "IOPanda output directory '%s' already exists", myGH->outdir);
+  }
+
+  if (CCTK_MyProc (GH) == 0)
+  {
+    fp = fopen ("FILEPREFIX", "w");
+    fprintf (fp, "%s", myGH->outdir);
+    fclose (fp);
+  }
+
+  /* start the Panda subsystem */
+  Panda_Create (ioUtilGH->ioproc_every, 1);
+
+  return (myGH);
 }
diff --git a/src/DumpVar.c b/src/Write.c
index 5715d9e..9900d96 100644
--- a/src/DumpVar.c
+++ b/src/Write.c
@@ -1,5 +1,5 @@
 /*@@
-   @file      DumpVar.c
+   @file      Write.c
    @date      01 Oct 1999
    @author    Jonghyun Lee
    @desc      Do the actual writing of a 3D grid array.
diff --git a/src/ioPandaGH.h b/src/ioPandaGH.h
index b4c20a8..d066d37 100644
--- a/src/ioPandaGH.h
+++ b/src/ioPandaGH.h
@@ -2,28 +2,47 @@
    @header    ioPandaGH.h
    @date      01 Oct 1999
    @author    Jonghyun Lee
-   @desc      The extensions to the GH structure from IOPanda.
-   @history
-   @endhistory
+   @desc
+              The extensions to the GH structure from IOPanda.
+   @enddesc
+   @version   $Header$
  @@*/
 
-#include <string.h>
+#ifndef _IOPANDA_IOPANDAGH_H_
+#define _IOPANDA_IOPANDAGH_H_ 1
 
 #include "StoreNamedData.h"
 
 
-typedef struct IOPandaGH {
-
+typedef struct IOPandaGH
+{
   /* the number of times to output */
-  int  out3D_every;
+  int  out_every;
 
-  /* flags indicating output for var [i] */
-  char *do_out3D;
+  /* flags indicating output for variable[i] */
+  char *do_out;
 
   /* directory in which to output */
-  char *outdir3D;
-
-  /* the last iteration output for var [i] */
-  int  *out3D_last;
+  char *outdir;
 
+  /* the last iteration output for variable[i] */
+  int  *out_last;
 } pandaGH;
+
+
+#ifdef __cplusplus
+extern "C"
+{
+#endif
+
+/* prototypes of functions to be registered as IOPanda's IO method */
+int IOPanda_OutputGH (const cGH *GH);
+int IOPanda_TriggerOutput (const cGH *GH, int);
+int IOPanda_TimeFor (const cGH *GH, int);
+int IOPanda_OutputVarAs (const cGH *GH, const char *var, const char *alias);
+
+#ifdef __cplusplus
+} // extern "C"
+#endif
+
+#endif  /* _IOPANDA_IOPANDAGH_H_ */
diff --git a/src/make.code.defn b/src/make.code.defn
index 4ab0091..f16782d 100644
--- a/src/make.code.defn
+++ b/src/make.code.defn
@@ -1,6 +1,11 @@
-SRCS = 	Startup.c GHExtension.c Output3D.c DumpVar.c 
+# Main make.code.defn file for thorn IOPanda
+# $Header$
 
+# Source files in this directory
+SRCS = 	Startup.c Output.c DumpVar.c 
+
+# Other subdirectories
 SUBDIRS = Panda
 
-# all compilers should understand ANSI C
+# This avoids warnings when including the FlexIO headers
 CFLAGS += -DANSI
diff --git a/src/make.configuration.defn b/src/make.configuration.defn
index 75357f2..5457011 100644
--- a/src/make.configuration.defn
+++ b/src/make.configuration.defn
@@ -1,20 +1,13 @@
 # make.configuration.defn for IOPanda
+# $Header$
 
 # make sure that IOPanda was configured with PUGH and MPI
 
 ifeq ($(findstring CactusPUGH/PUGH,$(THORNS)),)
-.pseudo: MissingPUGHinIOPanda
-MissingPUGHinIOPanda:
-	@echo "IOPanda: requires PUGH"
-	@echo "IOPanda: Please add CactusPUGH/PUGH or remove IOPanda from Thornlist !"
-	exit 2
+  $(error "IOPanda requires PUGH. Please add CactusPUGH/PUGH or remove IOPanda from Thornlist !")
 endif
 
 MPI_CONFIGURED := $(shell grep -l CCTK_MPI $(CONFIG)/cctk_Extradefs.h)
 ifneq ("$(MPI_CONFIGURED)", "$(CONFIG)/cctk_Extradefs.h")
-.pseudo: MissingMPIinIOPanda
-MissingMPIinIOPanda:
-	@echo "IOPanda: requires MPI"
-	@echo "IOPanda: Please configure with MPI or remove IOPanda from Thornlist !"
-	exit 2
+  $(error "IOPanda requires MPI. Please configure with MPI or remove IOPanda from Thornlist !")
 endif