Add support for serial and parallel GDF read write.

.gitignore

@@ -0,0 +1,2 @@
+*.mod
+*.o

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "sac/src/fgdfio"]
+	path = sac/src/fgdfio
+	url = git://github.com/SWAT-Sheffield/fgdfio.git

sac/par/mhdmodes → sac/par/binout

@@ -1,18 +1,21 @@
-&testlist /
+&testlist 
+    teststr='readfileini'
+/
 
 &filelist
-	filenameini='/archive/mhdmodes_2D.ini'
+	filenameini='/archive/gdf_testing/mhdmodes_2D.ini'
 
 	typefileini='binary'
-	filename=   '/archive/mhdmodes_2D.log',
-     		    '/archive/mhdmodes_2D.out'
+	filename=   '/archive/gdf_testing/mhdmodes_2D.log',
+     		    '/archive/gdf_testing/mhdmodes_2D.out'
 	typefileout='binary'
-        fullgridout= T
+        fullgridout= F
         fullgridini= T
  /
 
 &savelist
-	dtsave=0.1,0.0001
+    dtsave = 1,0.1
+    itsave(1,2)=0
 
  /
 

sac/par/binoutmpi

@@ -0,0 +1,52 @@
+&testlist 
+    teststr='readfileini'
+/
+
+&filelist
+	filenameini='/archive/gdf_testing/mhdmodes_np0202.ini'
+
+	typefileini='binary'
+	filename=   '/archive/gdf_testing/mhdmodes_np0202.log',
+     		    '/archive/gdf_testing/mhdmodes_np0202.out'
+	typefileout='binary'
+        fullgridout= F
+        fullgridini= T
+ /
+
+&savelist
+    dtsave = 1,0.1
+    itsave(1,2)=0
+
+ /
+
+ &stoplist
+	tmax=0.2d0
+	itmax = 10000
+ /
+
+ &methodlist
+
+	wnames=		'h 	m1  	 m2	e	b1	b2	eb	rhob	bg1	bg2'
+	typefull=	6*'cd4',4*'nul'
+        typeadvance=    'onestep'
+	typefilter=	10*'nul'
+	dimsplit=	F
+	sourcesplit=	F
+	divBfix=	F
+	smallp= 	10.d0
+ /
+
+ &boundlist
+	typeB=	10*'fixed'
+		10*'fixed'
+		10*'fixed'
+		10*'fixed'
+		10*'fixed'
+		10*'fixed'
+
+ /
+
+ &paramlist
+	courantpar=0.2
+
+ /

sac/par/gdfini

@@ -0,0 +1,52 @@
+&testlist 
+    teststr='readfileini readfileini_gdf'
+/
+
+&filelist
+	filenameini='/archive/gdf_testing/mhdmodes_2D_00000000.gdf'
+
+	typefileini='gdf'
+	filename=   '/archive/gdf_testing/mhdmodes_2D.log',
+     		    '/archive/gdf_testing/mhdmodes_2D_ii_'
+	typefileout='gdf'
+        fullgridout= F
+        fullgridini= F
+ /
+
+&savelist
+    dtsave=1,0.1
+    itsave(1,2)=0
+
+ /
+
+ &stoplist
+	tmax=0.2d0
+	itmax = 10000
+ /
+
+ &methodlist
+
+	wnames=		'h 	m1  	 m2	e	b1	b2	eb	rhob	bg1	bg2'
+	typefull=	6*'cd4',4*'nul'
+        typeadvance=    'onestep'
+	typefilter=	10*'nul'
+	dimsplit=	F
+	sourcesplit=	F
+	divBfix=	F
+	smallp= 	10.d0
+ /
+
+ &boundlist
+	typeB=	10*'fixed'
+		10*'fixed'
+		10*'fixed'
+		10*'fixed'
+		10*'fixed'
+		10*'fixed'
+
+ /
+
+ &paramlist
+	courantpar=0.2
+
+ /

sac/par/gdfout

@@ -0,0 +1,52 @@
+&testlist 
+    teststr='readfileini'
+/
+
+&filelist
+	filenameini='/archive/gdf_testing/mhdmodes_2D.ini'
+
+	typefileini='binary'
+	filename=   '/archive/gdf_testing/mhdmodes_2D.log',
+     		    '/archive/gdf_testing/mhdmodes_2D_'
+	typefileout='gdf'
+        fullgridout= F
+        fullgridini= T
+ /
+
+&savelist
+    dtsave=1,0.1
+    itsave(1,2)=0
+
+ /
+
+ &stoplist
+	tmax=0.2d0
+	itmax = 10000
+ /
+
+ &methodlist
+
+	wnames=		'h m1 m2 e b1 b2 eb rhob bg1 bg2'
+	typefull=	6*'cd4',4*'nul'
+    typeadvance= 'onestep'
+	typefilter=	10*'nul'
+	dimsplit=	F
+	sourcesplit=	F
+	divBfix=	F
+	smallp= 	10.d0
+ /
+
+ &boundlist
+	typeB=	10*'fixed'
+		10*'fixed'
+		10*'fixed'
+		10*'fixed'
+		10*'fixed'
+		10*'fixed'
+
+ /
+
+ &paramlist
+	courantpar=0.2
+
+ /

sac/par/gdfoutmpi

@@ -0,0 +1,52 @@
+&testlist 
+    teststr=''
+/
+
+&filelist
+	filenameini='/archive/gdf_testing/mhdmodes_np0202.ini'
+
+	typefileini='binary'
+	filename=   '/archive/gdf_testing/mhdmodes_np0202.log',
+     		    '/archive/gdf_testing/mhdmodes_np0202_'
+	typefileout='gdf'
+        fullgridout= F
+        fullgridini= T
+ /
+
+&savelist
+    dtsave = 1,0.1
+    itsave(1,2)=0
+
+ /
+
+ &stoplist
+	tmax=0.2d0
+	itmax = 10000
+ /
+
+ &methodlist
+
+	wnames=		'h 	m1  	 m2	e	b1	b2	eb	rhob	bg1	bg2'
+	typefull=	6*'cd4',4*'nul'
+        typeadvance=    'onestep'
+	typefilter=	10*'nul'
+	dimsplit=	F
+	sourcesplit=	F
+	divBfix=	F
+	smallp= 	10.d0
+ /
+
+ &boundlist
+	typeB=	10*'fixed'
+		10*'fixed'
+		10*'fixed'
+		10*'fixed'
+		10*'fixed'
+		10*'fixed'
+
+ /
+
+ &paramlist
+	courantpar=0.2
+
+ /

sac/src/Makefile

@@ -1,8 +1,7 @@
 # This is a VERY striped down makefile for compiling sac with gfortran
-
-# Check to see if the ENV variables are defined for the compiler
+# This will become a SAC only f2py makefile hopefully 
 ifndef F90
-    F90=mpif90
+    F90=h5pfc
 endif
 ifndef F90FLG
     F90FLG=-std=f2008
@@ -23,20 +22,27 @@ F=.f90
 O=.o
 
 VACDIR=.
+GDFDIR=./fgdfio/lib
 
 ################# Definitions for source files #############################
 
-LIBS = vacdef$F
-INCLUDES = vacdef$F vacpar$F vacusrpar$F
+LIBS = vacdef$F sacgdf$F
+INCLUDES = vacdef$F vacpar$F vacusrpar$F sacgdf$F
+GDF_INCLUDES = $(GDFDIR)/gdf_types.F90 $(GDFDIR)/helpers_hdf5.F90 $(GDFDIR)/grid_data_format.F90 $(GDFDIR)/gdf_datasets.F90
 
 VAC_FOR = vac$F vacio$F vacgrid$F vacphys0$F vacphys$F vacusr$F
 VAC_OBJ = vac$O vacio$O vacgrid$O vacphys0$O vacphys$O vacusr$O
 
 # The VACCD, VACMC, VACFCT, VACTVDLF, VACTVD, VACIMPL, VACPOISSON, VACMPI 
 # modules are removed or added in the following two lines by "setvac". 
 # DO NOT TOUCH THESE TWO LINES:
-VACFOR = $(VAC_FOR) vaccd$F
-VACOBJ = $(VAC_OBJ) vaccd$O
+VACFOR = $(VAC_FOR) vaccd$F vacmpi$F
+VACOBJ = $(VAC_OBJ) vaccd$O vacmpi$O
+
+# The VACMPI module is removed or added the following two lines by "setvac".
+# DO NOT TOUCH THESE TWO LINES:
+VACINIFOR = vacini$F vacio$F vacphys0$F vacusr$F vacmpi$F
+VACINIOBJ = vacini$O vacio$O vacphys0$O vacusr$O vacmpi$O
 
 ROEOBJ = roetest$O vacphys0$O vacphys$O
 
@@ -47,10 +53,11 @@ PREPROC= $(VACPP_)
 .SUFFIXES:
 .SUFFIXES: .t $F  $O
 
-$(VACFOR) vacini$F vacdef$F vacpar$F vacusrpar$F        : $(PREPROC)
+$(VACFOR) vacini$F vacdef$F vacpar$F vacusrpar$F sacgdf$F       : $(PREPROC)
 roetest$F                           : $(PREPROC)
 
-$(VACOBJ) vacini$O vacall$O vaciniall$O vacsmall$O roetest$O    : $(INCLUDES)
+$(VACOBJ) vacini$O vacall$O vaciniall$O vacsmall$O roetest$O sacgdf$0   : $(INCLUDES)
+$(VACINIOBJ) vacini$O vacall$O vaciniall$O vacsmall$O roetest$O sacgdf$0   : $(INCLUDES)
 
 vacusrpar$F: vacusrpar.t
 	$(VACPP) $< $(PREFOR) > $@
@@ -62,6 +69,9 @@ vacpar$F: vacpar.t
 vacdef$F: vacdef.t
 	$(VACPP) $< $(PREFOR) > $@
 
+sacgdf$F: sacgdf.t
+	$(VACPP) $< $(PREFOR) > $@
+	$(FOR) -c sacgdf.f90
 
 # General precompilation rule
 .t$(F):
@@ -71,22 +81,27 @@ vacdef$F: vacdef.t
 $(F)$(O):
 	$(FOR) $(FORFLG) -c $<
 
-
-
 ########### Extra dependencies for some files with "INCLUDE:" statements
 vacphys$F: vacphys.t vacphys.mhd0.t vacphys.mhdres.t
 	$(VACPP) $< $(PREFOR) > $@
 
 vacgrid$F: vacgrid.t
 	$(VACPP) $< $(PREFOR) > $@
 
-vac :$(VACOBJ) $(LIBS_)
-	$(FOR) $(FORFLG) -o $(VACDIR)/vac $(VACOBJ) $(LIBS)
+gdf :
+	$(FOR) $(FORFLG) -c $(GDF_INCLUDES)
+
+# The "vacini" and "vac" targets use the default Fortran compiler
+vacini : gdf $(VACINIOBJ) $(LIBS_)
+	$(FOR) $(FORFLG) -o $(VACDIR)/vacini $(GDF_INCLUDES) $(VACINIOBJ) $(LIBS)
+
+vac : gdf $(VACOBJ) $(LIBS_)
+	$(FOR) $(FORFLG) -o $(VACDIR)/vac $(GDF_INCLUDES) $(VACOBJ) $(LIBS) 
 
 ###### Removing object files, precompiled Fortran files, and symbolic links
 
 clean   :
-	rm -f vac*$F roetest$F Vvac*$F vac*.d *$O *~
+	rm -f vac*$F sac*$F roetest$F Vvac*$F vac*.d *$O *~ *.mod
 
 cleanall: clean
 	rm -f vacphys.t vacphys0.t vacpar.t vacusrpar.t vacusr.t