Major changes to PUGH as the dearly loved pGF is removed, and a grid function

is lowered to being simply a special case of a grid array, pGA. Grid arrays
can all have different sizes, which means that now the size of a GA is moved
from the GH to a structure on the GA, along with a lot of other connectivity
and additional information which was formerly on the GH.

If you need to care about these changes, take a look at the files in
src/include/pGH.h and src/include/pGA.h, to see the new structures
(I'll leave the old files pGF.h and SetupPGF.c around for a while to compare with).
Also, look at a PUGH dependent file which has already been converted, such
as CactusPUGHIO/IOASCII/src/Write1D.c.



Warning:

This commit breaks the development versions of IOHDF5 and IsoSurfacer, these
will be fixed real quick.


git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGH/PUGH/trunk@182 b61c5cb5-eaca-4651-9a7a-d64986f99364

3 files changed, 27 insertions, 72 deletions

diff --git a/src/include/pGH.h b/src/include/pGH.h
index c27fa35..2794f8f 100644
--- a/src/include/pGH.h
+++ b/src/include/pGH.h
@@ -1,28 +1,10 @@
  /*@@
    @header    pGH.h
    @date      Fri Feb 21 10:12:58 1997
-   @author    
+   @author    Tom Goodale, Paul Walker
    @desc 
-   The Pugh Grid Hierarchy structure. There isn't much point in having
-   a GridHierarchy without GridFunctions, so you'd better see
-   @seefile pGF.h also.
+   The Pugh Grid Hierarchy structure. 
    @enddesc 
-   @history
-   @hauthor Gabrielle Allen
-   @hdate Sep 10 @hdesc Added the iteration number on a GH
-   @endhistory
-   @history
-   @hauthor Gabrielle Allen @hdate 26 Sep 1998
-   @desc Changed IO parameter names, removed GH->out3D_mode, added t_iopars
-        structure
-   @hauthor Gabrielle Allen @hdate 17 Oct 1998
-   @desc Added more IO parameters to IO structure
-        structure
-   @hauthor Gabrielle Allen @hdate 3 Nov 1998
-   @desc Added forceSync
-   @hauthor Thomas Radke @hdate 30 Mar 1999
-   @desc Added sync_verbose and comm_time
-   @endhistory
    @version $Header$
  @@*/
 
@@ -43,58 +25,29 @@ typedef struct PGH
   /* Size of the processor group */
   int       nprocs;             /* Number of processors */
   int       myproc;             /* My processor */
-  int      *nproc;              /* Processor topology */
+  /*int      *nproc;*/              /* Processor topology */
   int       commmodel;          /* Comm model is PUGH_ALLOCATEDBUFFERS */ 
                                 /* or PUGH_DERIVEDTYPES. Currently unused */
   
   /* Size of the problems */
   int       nvariables;         /* Number of Grid variables */
   void   ***variables;          /* Pointers to them */
-  int      *nsize;              /* Physical size of the Problem */
-  int      *nghostzones;        /* Width of ghost zone */
 
   /* What time level we're on */
   int       timelevel;
 
-  /* Processor group layouts */
-  CCTK_REAL maxskew;            /* Maximum point skew */
+  int      *perme;               /* Periodic in each direction? */
   int       periodic;           /* Is the system periodic? */
-  int     **lb;                 /* Lower bound (nprocs X 3) for each proc */
-  int     **ub;                 /* Upper bound (same sizes) */
-  int      *lnsize;             /* Size on this processor */
-  int       npoints;            /* LOCAL number of points on this proc. */
-  int      *rnpoints;           /* Number of points on each proc */
-  int     **rnsize;             /* [#points on a proc][in each dir] */
-  int     **neighbors;          /* Neighbours (proc num) on each side */
-                                /* [nprocs x 2 * dim] */
-  int       stagger;            /* Is staggering turned on? */
 
   int       forceSync;          /* force synchronisation of GFs with storage */
 
-  /* Ghosts and overlaps. */
-  int      *ownership[PUGH_NSTAGGER][2];        
-                                /* The box owned in each direction. */
-                                /* [stagger][min/max][dir] */
-                                
-  int     **ghosts[PUGH_NSTAGGER][2];   
-                                /* The ghost zones on each face. */
-                                /* [stagger][min/max][face][dir] */
-                                
-  int     **overlap[PUGH_NSTAGGER][2];  
-                                /* The overlap region owned on each face. */
-                                /* [stagger][min/max][face][ijk] */
-                                 
 
   /* Coordinate information */
-  CCTK_REAL cx0, cy0, cz0;      /* Origin of our system */
   CCTK_REAL dx0, dy0, dz0, dt0; /* Delta of our system */
   CCTK_REAL lx0, ly0, lz0;      /* Processor-Local coordinate origins */
-  CCTK_REAL phys_time;          /* physical time */
+  /*  CCTK_REAL phys_time;      */    /* physical time */
   int       GHiteration;        /* iteration number on processor */
 
-  
-  
-
   /* Indentification for a pGH */
   int       level;              /* level in Berger-Oliger stack */
   int       mglevel;            /* level in multigrid stack */
@@ -104,7 +57,6 @@ typedef struct PGH
   int       active;             /* 1 -> GH active */
                                 /* 0 -> GH is skipped for conv.test */
                                 /* is used in NanCheckGH.c */
-  int       sync_verbose;       /* verbose output during synchronization */
 
   /* FIXME */
   double    comm_time;          /* time spent in communication */
@@ -127,19 +79,17 @@ typedef struct PGH
   pGExtras **GFExtras;          /* [dim] stagger ? */
   pConnectivity **Connectivity; /* [dim] */
 
-  /* #include "pGH_Extensions.h" */
-
   /* FIXME :  should be a dynamically allocated string.
    * If you change this, please change the line in pugh_SetupGH.
    */
   char identity_string[20];
 } pGH;
 
+/*
 #define XDP   1
 #define XDM   0
 #define YDP   3
 #define YDM   2
 #define ZDP   5
 #define ZDM   4
-
-
+*/
diff --git a/src/include/pGV.h b/src/include/pGV.h
index 4cae517..a69f10d 100644
--- a/src/include/pGV.h
+++ b/src/include/pGV.h
@@ -16,6 +16,8 @@ extern "C"
 {
 #endif
 
+#define DATINDEX(GH,i,j,k) ((i) + GH->lnsize[0]*((j)+GH->lnsize[1]*(k)))
+
 typedef enum {pgv_none, pgv_scalar, pgv_array, pgv_gf} pgv_type;
 
 typedef struct PConnectivity
@@ -23,7 +25,7 @@ typedef struct PConnectivity
   int dim;
   int *nprocs;
   int **neighbours;
-  int periodic;         /* Is the system periodic? */
+  int *perme;         /* Is the system periodic? */
 } pConnectivity;
 
 typedef struct PGS
diff --git a/src/include/pugh.h b/src/include/pugh.h
index 41869c6..af42aef 100644
--- a/src/include/pugh.h
+++ b/src/include/pugh.h
@@ -63,10 +63,12 @@
 
 #define PUGH_MPI_INT4 (sizeof (int) == 8 ? MPI_SHORT : MPI_INT)
 
+#define HEREINPUGH printf("I'm in %s at line %d\n",__FILE__,__LINE__);
+
 #include "pugh_constants.h"
 
 #include "pGV.h"
-#include "pGF.h"
+/*#include "pGF.h"*/
 #include "pGH.h"
 
 #ifdef MPI
@@ -91,34 +93,35 @@ extern "C"
 #endif
 
 
-int PUGH_SetupGroup
-  (
-   pGH *newGH, 
-   int *nsize,
-   int *nghostsize,
-   int  gtype, 
-   int  vtype, 
-   int  dim, 
-   int  n_variables,
-   int  staggertype,
-   int  n_timelevels
-  );
+int PUGH_SetupGroup(pGH *newGH, 
+		    int *nsize,
+		    int *nghostsize,
+		    int  gtype, 
+		    int  vtype, 
+		    int  dim, 
+		    int  n_variables,
+		    int  staggertype,
+		    int  n_timelevels);
 
 pGH *PUGH_SetupPGH(void *callerid, 
                    int dim, 
                    int *nsize, 
                    int *nghostzones,
 		   int staggertype,
-		   int periodic);
+		   int *perme);
 
 int pugh_GFSize(int dim, 
                 int *nsize);
 
 int pugh_GFGhostsize(int dim,
                      int *ghostsize);
+int pugh_GFPeriodic(int dim,
+		    int *perme);
 
 pGH *pugh_pGH(cGH *GH);
 
+int PUGH_Evolve(tFleshConfig *config);           
+
 int GetSliceSizes(int np,
                   int grid_points,
                   char *slicesS,