From 662a033d9199aa12d1b43e667edf3a6775655fc8 Mon Sep 17 00:00:00 2001
From: Philip Eisenlohr <eisenlohr@egr.msu.edu>
Date: Thu, 19 Nov 2020 14:26:15 -0500
Subject: [PATCH] adapted to VTR geom files

---
 PRIVATE                               | 2 +-
 processing/pre/geom_grainGrowth.py    | 8 ++++----
 processing/pre/mentat_pbcOnBoxMesh.py | 3 +--
 processing/pre/mentat_spectralBox.py  | 6 +++---
 python/damask/_geom.py                | 5 ++---
 5 files changed, 11 insertions(+), 13 deletions(-)

diff --git a/PRIVATE b/PRIVATE
index 2d00aa541..d04e6753e 160000
--- a/PRIVATE
+++ b/PRIVATE
@@ -1 +1 @@
-Subproject commit 2d00aa541f071dbfc200f32e358d324995a061f5
+Subproject commit d04e6753e7e6cea9089ee1d1602c55a715f73d45
diff --git a/processing/pre/geom_grainGrowth.py b/processing/pre/geom_grainGrowth.py
index 249cb07f5..5c751d662 100755
--- a/processing/pre/geom_grainGrowth.py
+++ b/processing/pre/geom_grainGrowth.py
@@ -15,8 +15,8 @@ scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
 
-getInterfaceEnergy = lambda A,B: np.float32((A*B != 0)*(A != B)*1.0)                               # 1.0 if A & B are distinct & nonzero, 0.0 otherwise
-struc = ndimage.generate_binary_structure(3,1)                                                     # 3D von Neumann neighborhood
+getInterfaceEnergy = lambda A,B: np.float32((A != B)*1.0)                                           # 1.0 if A & B are distinct, 0.0 otherwise
+struc = ndimage.generate_binary_structure(3,1)                                                      # 3D von Neumann neighborhood
 
 
 #--------------------------------------------------------------------------------------------------
@@ -62,7 +62,7 @@ if filenames == []: filenames = [None]
 for name in filenames:
   damask.util.report(scriptName,name)
 
-  geom = damask.Geom.load_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+  geom = damask.Geom.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
 
   grid_original = geom.grid
   damask.util.croak(geom)
@@ -174,4 +174,4 @@ for name in filenames:
               origin    = geom.origin,
               comments  = geom.comments + [scriptID + ' ' + ' '.join(sys.argv[1:])],
              )\
-        .save_ASCII(sys.stdout if name is None else name)
+        .save(sys.stdout if name is None else name)
diff --git a/processing/pre/mentat_pbcOnBoxMesh.py b/processing/pre/mentat_pbcOnBoxMesh.py
index e03a4e5c5..4a4f3d642 100755
--- a/processing/pre/mentat_pbcOnBoxMesh.py
+++ b/processing/pre/mentat_pbcOnBoxMesh.py
@@ -11,8 +11,6 @@ import numpy as np
 
 import damask
 
-sys.path.append(str(damask.solver.Marc().library_path))
-
 scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
@@ -235,6 +233,7 @@ if remote and filenames != []:
 if filenames == []: filenames = [None]
 
 if remote:
+  sys.path.append(str(damask.solver.Marc().library_path))
   import py_mentat
 
   damask.util.report(scriptName, 'waiting to connect...')
diff --git a/processing/pre/mentat_spectralBox.py b/processing/pre/mentat_spectralBox.py
index 57c2644c2..d182a6d54 100755
--- a/processing/pre/mentat_spectralBox.py
+++ b/processing/pre/mentat_spectralBox.py
@@ -9,7 +9,6 @@ import damask
 
 scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
-sys.path.append(str(damask.solver.Marc().library_path))
 
 #-------------------------------------------------------------------------------------------------
 def outMentat(cmd,locals):
@@ -185,9 +184,10 @@ parser.set_defaults(port = None,
 
 if options.port is not None:
     try:
+        sys.path.append(str(damask.solver.Marc().library_path))
         import py_mentat
     except ImportError:
-        parser.error('no valid Mentat release found.')
+        parser.error('no valid Mentat release found')
 
 # --- loop over input files ------------------------------------------------------------------------
 
@@ -196,7 +196,7 @@ if filenames == []: filenames = [None]
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    geom = damask.Geom.load_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    geom = damask.Geom.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
     material = geom.material.flatten(order='F')
 
     cmds = [\
diff --git a/python/damask/_geom.py b/python/damask/_geom.py
index 5b545fa41..b4806a008 100644
--- a/python/damask/_geom.py
+++ b/python/damask/_geom.py
@@ -213,9 +213,8 @@ class Geom:
         if not keyword.startswith('head') or header_length < 3:
             raise TypeError('Header length information missing or invalid')
 
-        content = f.readlines()
-
         comments = []
+        content = f.readlines()
         for i,line in enumerate(content[:header_length]):
             items = line.split('#')[0].lower().strip().split()
             key = items[0] if items else ''
@@ -510,7 +509,7 @@ class Geom:
 
         Parameters
         ----------
-        fname : str or or pathlib.Path
+        fname : str or pathlib.Path
             Filename to write. Valid extension is .vtr, it will be appended if not given.
         compress : bool, optional
             Compress with zlib algorithm. Defaults to True.