[yt-svn] commit/yt: 2 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Wed Aug 9 14:13:29 PDT 2017
2 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/3b025d8ce8a9/
Changeset: 3b025d8ce8a9
User: atmyers
Date: 2017-08-08 23:07:26+00:00
Summary: handle raw fields for WarpX datasets with mesh refinement.
Affected #: 2 files
diff -r c72d9bee3e75791d6882a9763119016b88c22ff8 -r 3b025d8ce8a9b7276152e5707ed89ec5b6b44224 yt/frontends/boxlib/data_structures.py
--- a/yt/frontends/boxlib/data_structures.py
+++ b/yt/frontends/boxlib/data_structures.py
@@ -1353,32 +1353,44 @@
def _read_header(raw_file, field):
- header_file = raw_file + field + "_H"
- with open(header_file, "r") as f:
+ level_files = glob.glob(raw_file + 'Level_*')
+ level_files.sort()
+
+ all_boxes = []
+ all_file_names = []
+ all_offsets = []
+
+ for level_file in level_files:
+ header_file = level_file + "/" + field + "_H"
+ with open(header_file, "r") as f:
- # skip the first five lines
- for _ in range(5):
- f.readline()
+ # skip the first five lines
+ for _ in range(5):
+ f.readline()
- # read boxes
- boxes = []
- for line in f:
- clean_line = line.strip().split()
- if clean_line == [')']:
- break
- lo_corner, hi_corner, node_type = _line_to_numpy_arrays(clean_line)
- boxes.append((lo_corner, hi_corner, node_type))
+ # read boxes
+ boxes = []
+ for line in f:
+ clean_line = line.strip().split()
+ if clean_line == [')']:
+ break
+ lo_corner, hi_corner, node_type = _line_to_numpy_arrays(clean_line)
+ boxes.append((lo_corner, hi_corner, node_type))
- # read the file and offset position for the corresponding box
- file_names = []
- offsets = []
- for line in f:
- if line.startswith("FabOnDisk:"):
- clean_line = line.strip().split()
- file_names.append(clean_line[1])
- offsets.append(int(clean_line[2]))
+ # read the file and offset position for the corresponding box
+ file_names = []
+ offsets = []
+ for line in f:
+ if line.startswith("FabOnDisk:"):
+ clean_line = line.strip().split()
+ file_names.append(clean_line[1])
+ offsets.append(int(clean_line[2]))
- return boxes, file_names, offsets
+ all_boxes += boxes
+ all_file_names += file_names
+ all_offsets += offsets
+
+ return all_boxes, all_file_names, all_offsets
class WarpXHeader(object):
@@ -1448,9 +1460,9 @@
super(WarpXHierarchy, self)._detect_output_fields()
# now detect the optional, non-cell-centered fields
- self.raw_file = self.ds.output_dir + "/raw_fields/Level_0/"
+ self.raw_file = self.ds.output_dir + "/raw_fields/"
self.ds.fluid_types += ("raw",)
- self.raw_fields = _read_raw_field_names(self.raw_file)
+ self.raw_fields = _read_raw_field_names(self.raw_file + 'Level_0/')
self.field_list += [('raw', f) for f in self.raw_fields]
self.raw_field_map = {}
self.ds.nodal_flags = {}
diff -r c72d9bee3e75791d6882a9763119016b88c22ff8 -r 3b025d8ce8a9b7276152e5707ed89ec5b6b44224 yt/frontends/boxlib/io.py
--- a/yt/frontends/boxlib/io.py
+++ b/yt/frontends/boxlib/io.py
@@ -76,7 +76,8 @@
fn_list = self.ds.index.raw_field_map[field_name][1]
offset_list = self.ds.index.raw_field_map[field_name][2]
- filename = base_dir + fn_list[grid.id]
+ lev = grid.Level
+ filename = base_dir + "Level_%d/" % lev + fn_list[grid.id]
offset = offset_list[grid.id]
box = box_list[grid.id]
https://bitbucket.org/yt_analysis/yt/commits/00f7ca8d4411/
Changeset: 00f7ca8d4411
User: ngoldbaum
Date: 2017-08-09 21:13:17+00:00
Summary: Merge pull request #1531 from atmyers/master
Handle raw fields for WarpX datasets with mesh refinement.
Affected #: 2 files
diff -r 68d50c94be9a88927df18b72b202167dd4a3696d -r 00f7ca8d4411a53c9b98afa929adf6040666bbfe yt/frontends/boxlib/data_structures.py
--- a/yt/frontends/boxlib/data_structures.py
+++ b/yt/frontends/boxlib/data_structures.py
@@ -1353,32 +1353,44 @@
def _read_header(raw_file, field):
- header_file = raw_file + field + "_H"
- with open(header_file, "r") as f:
+ level_files = glob.glob(raw_file + 'Level_*')
+ level_files.sort()
+
+ all_boxes = []
+ all_file_names = []
+ all_offsets = []
+
+ for level_file in level_files:
+ header_file = level_file + "/" + field + "_H"
+ with open(header_file, "r") as f:
- # skip the first five lines
- for _ in range(5):
- f.readline()
+ # skip the first five lines
+ for _ in range(5):
+ f.readline()
- # read boxes
- boxes = []
- for line in f:
- clean_line = line.strip().split()
- if clean_line == [')']:
- break
- lo_corner, hi_corner, node_type = _line_to_numpy_arrays(clean_line)
- boxes.append((lo_corner, hi_corner, node_type))
+ # read boxes
+ boxes = []
+ for line in f:
+ clean_line = line.strip().split()
+ if clean_line == [')']:
+ break
+ lo_corner, hi_corner, node_type = _line_to_numpy_arrays(clean_line)
+ boxes.append((lo_corner, hi_corner, node_type))
- # read the file and offset position for the corresponding box
- file_names = []
- offsets = []
- for line in f:
- if line.startswith("FabOnDisk:"):
- clean_line = line.strip().split()
- file_names.append(clean_line[1])
- offsets.append(int(clean_line[2]))
+ # read the file and offset position for the corresponding box
+ file_names = []
+ offsets = []
+ for line in f:
+ if line.startswith("FabOnDisk:"):
+ clean_line = line.strip().split()
+ file_names.append(clean_line[1])
+ offsets.append(int(clean_line[2]))
- return boxes, file_names, offsets
+ all_boxes += boxes
+ all_file_names += file_names
+ all_offsets += offsets
+
+ return all_boxes, all_file_names, all_offsets
class WarpXHeader(object):
@@ -1448,9 +1460,9 @@
super(WarpXHierarchy, self)._detect_output_fields()
# now detect the optional, non-cell-centered fields
- self.raw_file = self.ds.output_dir + "/raw_fields/Level_0/"
+ self.raw_file = self.ds.output_dir + "/raw_fields/"
self.ds.fluid_types += ("raw",)
- self.raw_fields = _read_raw_field_names(self.raw_file)
+ self.raw_fields = _read_raw_field_names(self.raw_file + 'Level_0/')
self.field_list += [('raw', f) for f in self.raw_fields]
self.raw_field_map = {}
self.ds.nodal_flags = {}
diff -r 68d50c94be9a88927df18b72b202167dd4a3696d -r 00f7ca8d4411a53c9b98afa929adf6040666bbfe yt/frontends/boxlib/io.py
--- a/yt/frontends/boxlib/io.py
+++ b/yt/frontends/boxlib/io.py
@@ -76,7 +76,8 @@
fn_list = self.ds.index.raw_field_map[field_name][1]
offset_list = self.ds.index.raw_field_map[field_name][2]
- filename = base_dir + fn_list[grid.id]
+ lev = grid.Level
+ filename = base_dir + "Level_%d/" % lev + fn_list[grid.id]
offset = offset_list[grid.id]
box = box_list[grid.id]
Repository URL: https://bitbucket.org/yt_analysis/yt/
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