fixed bug.

introduced possibility for poke bounding box in all dimensions.

processing/pre/seeds_fromPokes.py

@@ -23,10 +23,10 @@ parser.add_option('-N', '--points',
                   dest = 'N',
                   type = 'int', metavar = 'int',
                   help = 'number of poking locations [%default]')
-parser.add_option('-z', '--planes',
+parser.add_option('-b', '--box',
-                  dest = 'z',
+                  dest = 'box',
-                  type = 'float', nargs = 2, metavar='float float',
+                  type = 'float', nargs = 6, metavar = ' '.join(['float']*6),
-                  help = 'top and bottom z plane')
+                  help = 'bounding box as fraction in x, y, and z directions')
 parser.add_option('-x',
                   action = 'store_true',
                   dest   = 'x', 
@@ -42,13 +42,15 @@ parser.add_option('-p','--position',
 
 parser.set_defaults(x = False,
                     y = False,
-                    z = [0.0,1.0],
+                    box = [0.0,1.0,0.0,1.0,0.0,1.0],
                     N = 16,
                     position = 'pos',
                    )
 
 (options,filenames) = parser.parse_args()
 
+options.box = np.array(options.box).reshape(3,2)
+
 # --- loop over output files -------------------------------------------------------------------------
 
 if filenames == []: filenames = [None]
@@ -90,24 +92,26 @@ for name in filenames:
   newInfo = {
              'microstructures': 0,
             }
+  offset = (np.amin(options.box, axis=1)*info['grid']/info['size']).astype(int)
+  box = np.amax(options.box, axis=1) - np.amin(options.box, axis=1)
 
-  Nx = int(options.N/math.sqrt(options.N*info['size'][1]/info['size'][0]))
+  Nx = int(options.N/math.sqrt(options.N*info['size'][1]*box[1]/info['size'][0]/box[0]))
-  Ny = int(options.N/math.sqrt(options.N*info['size'][0]/info['size'][1]))
+  Ny = int(options.N/math.sqrt(options.N*info['size'][0]*box[0]/info['size'][1]/box[1]))
-  Nz = int((max(options.z)-min(options.z))/info['size'][2]*info['grid'][2])
+  Nz = int(box[2]*info['grid'][2])
-  offset = int(min(options.z)/info['size'][2]*info['grid'][2])                                      # offset due to lower z-plane
 
-  damask.util.croak('poking {} x {} x {}...'.format(Nx,Ny,Nz))
+  damask.util.croak('poking {} x {} x {} in box {} {} {}...'.format(Nx,Ny,Nz,*box))
 
   seeds = np.zeros((Nx*Ny*Nz,4),'d')
   grid = np.zeros(3,'i')
 
   n = 0
   for i in xrange(Nx):
-    grid[0] = round((i+0.5)*info['grid'][0]/Nx-0.5)
     for j in xrange(Ny):
-      grid[1] = round((j+0.5)*info['grid'][1]/Ny-0.5)
+      grid[0] = round((i+0.5)*box[0]*info['grid'][0]/Nx-0.5)+offset[0]
+      grid[1] = round((j+0.5)*box[1]*info['grid'][1]/Ny-0.5)+offset[1]
+      damask.util.croak('x,y coord on surface: {},{}...'.format(*grid[:2]))
       for k in xrange(Nz):
-        grid[2] = offset + k
+        grid[2] = k + offset[2]
         grid %= info['grid']
         seeds[n,0:3] = (0.5+grid)/info['grid']                                                     # normalize coordinates to box
         seeds[n,  3] = microstructure[grid[0],grid[1],grid[2]]
@@ -128,9 +132,9 @@ for name in filenames:
   table.info_append(extra_header+[
     scriptID + ' ' + ' '.join(sys.argv[1:]),
     "poking\ta {}\tb {}\tc {}".format(Nx,Ny,Nz),
-    "grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=info['grid']),
+    "grid\ta {}\tb {}\tc {}".format(*info['grid']),
-    "size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=info['size']),
+    "size\tx {}\ty {}\tz {}".format(*info['size']),
-    "origin\tx {origin[0]}\ty {origin[1]}\tz {origin[2]}".format(origin=info['origin']),
+    "origin\tx {}\ty {}\tz {}".format(*info['origin']),
     "homogenization\t{}".format(info['homogenization']),
     "microstructures\t{}".format(newInfo['microstructures']),
     ])