1 files changed, 60 insertions, 83 deletions

diff --git a/src/Output3D.c b/src/Output3D.c
index ea97b62..c7ef26a 100644
--- a/src/Output3D.c
+++ b/src/Output3D.c
@@ -9,24 +9,17 @@
  @@*/
 
 #include <stdio.h>
-#include <assert.h>
 #include <stdlib.h>
 #include <string.h>
 
 #include "cctk.h"
 #include "cctk_Parameters.h"
-#include "cctk_DefineThorn.h"
-#include "ioPandaGH.h"
-#include "Panda/c_interface.h"
 #include "CactusBase/IOUtil/src/ioGH.h"
-#ifdef CACTUSPUGH_PUGH
 #include "CactusPUGH/PUGH/src/include/pugh.h"
-#endif
-#ifdef SGI
-#include <time.h>
-#endif
-
 #include "external/IEEEIO/src/IOProtos.h"
+#include "ioPandaGH.h"
+#include "Panda/c_interface.h"
+
 
 int IOPanda_Output3DVarAs (cGH *GH, const char *var, const char *alias);
 int IOPanda_TimeFor3D (cGH *GH, int index);
@@ -43,10 +36,9 @@ void IOPanda_IEEEIOStructDump (cGH *GH, char *fname);
    @enddesc
    @calls    CCTK_GHExtensionHandle
              CCTK_NumVars
-             CCTK_ImplementationFromVar
              CCTK_VarName
              IOPanda_TimeFor3D
-             IOPanda_Output3DVarAs
+             IOPanda_Timestep
    @calledby
    @history
 
@@ -63,41 +55,30 @@ int IOPanda_Output3DGH (cGH *GH)
 {
   int i;
   pandaGH *myGH;
-  char *implementation;
-  char *name;
-  char *fullname;
   DECLARE_CCTK_PARAMETERS
 
   /* Get the GH extension for IOPanda */
   myGH = (pandaGH *) GH->extensions [CCTK_GHExtensionHandle ("IOPanda")];
 
-  if (myGH->IO_3Devery <= 0)
-    return;
+  if (myGH->out3D_every <= 0)
+    return (0);
 
   /* Loop over all variables */
   for (i = 0; i < CCTK_NumVars (); i++) {
     if (IOPanda_TimeFor3D (GH, i)) {
-      implementation = CCTK_ImpFromVarI (i);
-      name           = CCTK_VarName (i);
-      fullname       = (char *) malloc (strlen (implementation) +
-                                        strlen (name) + 3);
-      assert (fullname);
-      sprintf (fullname, "%s::%s", implementation, name);
-
       if (verbose) {
+        char *fullname = CCTK_FullName (i);
+
         printf ("IOPanda Output3DGH : \n");
-        printf ("  fullname/name = %s/%s\n", fullname, name);
+        printf ("  index/fullname = %d/%s\n", i, fullname);
+        free (fullname);
       }
 
-      IOPanda_Output3DVarAs (GH, fullname, name);
-
-      free (fullname);
+      /* Do the 3D output */
+      IOPanda_Timestep (GH, i, CCTK_VarName (i));
 
-      /* Register another 3D output for this GF */
-      myGH->IO_3Dnum [i]++;
-
-      /* Register GF as having 3D output this iteration */
-      myGH->IO_3Dlast [i] = GH->cctk_iteration;
+      /* Register variable as having 3D output this iteration */
+      myGH->out3D_last [i] = GH->cctk_iteration;
     }
   }
 
@@ -144,18 +125,12 @@ int IOPanda_Output3DVarAs (cGH *GH, const char *fullname, const char *alias)
 {
   DECLARE_CCTK_PARAMETERS
   int index;
-  pandaGH *myGH;
 
   index = CCTK_VarIndex(fullname);
 
-  /* Get the GH extension for IOPanda */
-  myGH = (pandaGH *) GH->extensions [CCTK_GHExtensionHandle ("IOPanda")];
-
   if (verbose) {
     printf ("\nIn IOPanda Output3DVarAs\n-------------------\n");
-    printf ("  Fullname = -%s-\n", fullname);
-    printf ("  Alias = -%s-\n", alias);
-    printf ("  Index = %d\n", index);
+    printf ("  index/fullname/alias = %d/%s/%s\n", index, fullname, alias);
   }
 
   /* Do the 3D output */
@@ -173,11 +148,6 @@ int IOPanda_Output3DVarAs (cGH *GH, const char *fullname, const char *alias)
    Decides if it is time to output a variable using the IOPanda 3D output
    method
    @enddesc
-   @calls    CCTK_GHExtensionHandle
-             CCTK_GroupTypeFromVarI
-             CCTK_WARN
-             CCTK_QueryGroupStorageI
-             CCTK_GroupNameFromVarI
    @calledby IOPanda_Output3DGH
    @history
 
@@ -203,28 +173,18 @@ int IOPanda_TimeFor3D (cGH *GH, int index)
   /* Get the GH extension for IOPanda */
   myGH = (pandaGH *) GH->extensions [CCTK_GHExtensionHandle ("IOPanda")];
 
-  /* Check this GF should be output */
-  if (! (myGH->IO_3Dnum [index] != 0 &&
-         GH->cctk_iteration % myGH->IO_3Devery == 0))
+  /* Check this variable should be output */
+  if (! (myGH->do_out3D [index] && GH->cctk_iteration % myGH->out3D_every == 0))
     return (0);
 
-  /* Check GF not already output this iteration */
-  if (myGH->IO_3Dlast [index] == GH->cctk_iteration) {
-      CCTK_WARN (2, "Already done 3D output in IOPanda");
-      return (0);
-  }
-
-  /* Check GF has storage */
-  if (! CCTK_QueryGroupStorageI (GH,
-            CCTK_GroupIndexFromVarI(index))) {
-    char *fullname = CCTK_FullName (index);
-    char *msg = (char *) malloc (80 + strlen (fullname));
+  /* Check variable not already output this iteration */
+  if (myGH->out3D_last [index] == GH->cctk_iteration) {
+      char *fullname = CCTK_FullName (index);
 
-    sprintf (msg, "No IOPandaIO 3D output for '%s' (no storage)", fullname);
-    CCTK_WARN (2, msg);
-    free (fullname);
-    free (msg);
-    return (0);
+      CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING,
+                  "Already done IOPanda 3D output for '%s'", fullname);
+      free (fullname);
+      return (0);
   }
 
   return (1);
@@ -264,7 +224,7 @@ int IOPanda_TriggerOutput3D (cGH *GH, int index)
 {
   DECLARE_CCTK_PARAMETERS
   pandaGH *myGH;
-  char *varname;
+  const char *varname;
 
   varname = CCTK_VarName (index);
 
@@ -273,23 +233,19 @@ int IOPanda_TriggerOutput3D (cGH *GH, int index)
 
   if (verbose) {
     printf("\nIn IOPanda TriggerOutput3D\n---------------------\n");
-    printf("  Index = %d\n", index);
-    printf("  Variable = -%s-\n", varname);
+    printf("  index/name = %d/%s\n", index, varname);
   }
 
   /* Do the 3D output */
   IOPanda_Timestep (GH, index, varname);
 
-  /* Register another 3D output for this GF */
-  myGH->IO_3Dnum [index]++;
-
-  /* Register GF as having 3D output this iteration */
-  myGH->IO_3Dlast [index] = GH->cctk_iteration;
+  /* Register variable as having 3D output this iteration */
+  myGH->out3D_last [index] = GH->cctk_iteration;
 
   return (0);
 }
 
-void IOPanda_Timestep(cGH *GH, int index, const char *alias)
+void IOPanda_Timestep (cGH *GH, int index, const char *alias)
 {
   DECLARE_CCTK_PARAMETERS
   void *data;
@@ -307,8 +263,19 @@ void IOPanda_Timestep(cGH *GH, int index, const char *alias)
     return;
   } 
   
+  /* check if variable has storage assigned */
+  if (! CCTK_QueryGroupStorageI (GH, CCTK_GroupIndexFromVarI (index))) {
+    char *fullname = CCTK_FullName (index);
+
+    CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING,
+                "No IOPanda 3D output for '%s' (no storage)", fullname);
+    free (fullname);
+    return;
+  }
+
+  /* get the handles for PUGH and IOUtil GH extensions */
+  pughGH = PUGH_pGH (GH);
   ioUtilGH = (ioGH *) GH->extensions [CCTK_GHExtensionHandle ("IO")];
-  pughGH = (pGH *) GH->extensions [CCTK_GHExtensionHandle ("PUGH")];
   
   ainfo.name_ = (char *)alias;
   
@@ -342,8 +309,11 @@ void IOPanda_Timestep(cGH *GH, int index, const char *alias)
     }
   }
   
+  /* FIXME: rank */
   ainfo.mem_rank_ = 3;
-  tmp2[0] = pughGH->nprocz; tmp2[1] = pughGH->nprocy; tmp2[2] = pughGH->nprocx;
+  tmp2[0] = pughGH->Connectivity [2]->nprocs [2];
+  tmp2[1] = pughGH->Connectivity [2]->nprocs [1];
+  tmp2[2] = pughGH->Connectivity [2]->nprocs [0];
   ainfo.mem_layout_ = tmp2;
   dist1[0] = dist1[1] = dist1[2] = BLOCK;
   ainfo.mem_dist_ = dist1;
@@ -361,12 +331,18 @@ void IOPanda_Timestep(cGH *GH, int index, const char *alias)
   IOPanda_getDumpData(GH, index, timelevel, &data, &free_flag, bnd, 
 		      ainfo.esize_);
   ainfo.data_ = (char *)data;
-  ainfo.stencil_width_ = pughGH->nghostzones;
 
+  /*** FIXME: asymmetric ghostzones */
+  ainfo.stencil_width_ = GH->cctk_nghostzones [0];
 
   PandaTimestep(&ainfo);
+  if (free_flag)
+    free (data);
+
   IOPanda_AddCommonAttributes(GH, index, timelevel, ainfo.size_, ainfo.name_);
-  if (PandaIsNewFile(ainfo.name_)) IOPanda_IEEEIOStructDump(GH, ainfo.name_);
+
+  if (PandaIsNewFile(ainfo.name_))
+    IOPanda_IEEEIOStructDump(GH, ainfo.name_);
 }
 
 void IOPanda_AddCommonAttributes (cGH *GH, int index, int timelevel,
@@ -425,14 +401,15 @@ void IOPanda_AddCommonAttributes (cGH *GH, int index, int timelevel,
   Panda_WriteAttribute (fname, "min_ext",FLOAT64,3,d3_to_IO);
   Panda_WriteAttribute (fname, "max_ext",FLOAT64, 3,d3_to_IO+3);
 
-  d3_to_IO [0] = GH->cctk_delta_space [0] * ioUtilGH->downsample_x;
-  d3_to_IO [1] = GH->cctk_delta_space [1] * ioUtilGH->downsample_y;
-  d3_to_IO [2] = GH->cctk_delta_space [2] * ioUtilGH->downsample_z;
+  /* FIXME: dimension */
+  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);
 
-  if (ioUtilGH->downsample_x > 1 ||
-      ioUtilGH->downsample_y > 1 ||
-      ioUtilGH->downsample_z > 1) {
+  if (ioUtilGH->downsample[0] > 1 ||
+      ioUtilGH->downsample[1] > 1 ||
+      ioUtilGH->downsample[2] > 1) {
     d3_to_IO [0] = GH->cctk_delta_space [0];
     d3_to_IO [1] = GH->cctk_delta_space [1];
     d3_to_IO [2] = GH->cctk_delta_space [2];