bugfix: fixed size of the readable portion of chunk['data'] (now it works also when no ghost cells are present)

.gitignore

@@ -0,0 +1 @@
+*__pycache__

bash/ucftar_pack

@@ -106,7 +106,8 @@ if [ ! -s ${din}/${fproc} ]; then
 fi
 if [ ! -s ${din}/${fpart} ]; then
   (>&2 echo "[Error] File not found or empty: ${din}/${fpart}")
-  exit 1
+  # exit 1
+  fpart=
 fi
 
 # Check if all velocity fields exist and are not empty

python/ibmppp/__init__.py

@@ -0,0 +1 @@
+from .ibmppp import *

python/ibmppp/ibmppp.py

@@ -291,19 +291,19 @@ class ibmppp:
         # Also determine file which contains the desired field as well as the
         # dataset ID
         if key[0]=='u':
-          filebase = self.__dir_base+'uvwp.'
+          filebase = self.__dir_base+'/uvwp.'
           dset = 1
         elif key[0]=='v':
-          filebase = self.__dir_base+'uvwp.'
+          filebase = self.__dir_base+'/uvwp.'
           dset = 2
         elif key[0]=='w':
-          filebase = self.__dir_base+'uvwp.'
+          filebase = self.__dir_base+'/uvwp.'
           dset = 3
         elif key[0]=='p':
-          filebase = self.__dir_base+'uvwp.'
+          filebase = self.__dir_base+'/uvwp.'
           dset = 4
         elif key[0]=='s':
-          filebase = self.__dir_base+'scal.'
+          filebase = self.__dir_base+'/scal.'
           dset = int(key[1])
           if dset!=1:
             self.fields[key] = None
@@ -348,10 +348,14 @@ class ibmppp:
               if kb1!=chunk['kbeg'] or ke1!=chunk['kbeg']+chunk['nzl']-1:
                   raise ValueError('Loaded chunk does not correspond to processor grid (kbeg={}, nzl={} vs kbeg={},nzl={}'.format(kb1,ke1-kb1+1,chunk['kbeg'],chunk['nzl']))
               ngh1 = chunk['ighost']
+              ibeg = [i + ngh1 for i in [0,0,0]]
+              iend = [i-ngh1 for i in chunk['data'].shape]
               # No need to care about ghost cells here, we communicate them later
               self.field[key][ib1-ib+self.__nghx:ie1-ib+self.__nghx+1,
                               jb1-jb+self.__nghy:je1-jb+self.__nghy+1,
-                              kb1-kb+self.__nghz:ke1-kb+self.__nghz+1] = chunk['data'][ngh1:-ngh1,ngh1:-ngh1,ngh1:-ngh1]
+                              kb1-kb+self.__nghz:ke1-kb+self.__nghz+1] = chunk['data'][ibeg[0]:iend[0],\
+                                                                                       ibeg[1]:iend[1],\
+                                                                                       ibeg[2]:iend[2]]
         # Exchange ghost cells and set boundary conditions
         self.exchangeGhostCells(key)
         self.imposeBoundaryConditions(key)

python/ucf/__init__.py

@@ -0,0 +1 @@
+from .ucf import *