[yt-svn] commit/yt: 4 new changesets

[commits-noreply at bitbucket.org]

4 new commits in yt:

https://bitbucket.org/yt_analysis/yt/commits/4da52ce743fd/
Changeset:   4da52ce743fd
User:        MatthewTurk
Date:        2017-11-14 16:40:11+00:00
Summary:     Adding geometry detection to GAMER frontend.
Affected #:  1 file

diff -r dca5e454d03e59c1f9ab4a52301e74dc12f245e7 -r 4da52ce743fd8b86857eeb7394a8d70493c8f938 yt/frontends/gamer/data_structures.py
--- a/yt/frontends/gamer/data_structures.py
+++ b/yt/frontends/gamer/data_structures.py
@@ -304,6 +304,12 @@
         # old data format (version < 2210) does not contain any information of code units
         self.parameters.setdefault('Opt__Unit', 0)
 
+        self.geometry = {1: "cartesian",
+                         2: ("cylindrical", ("r", "theta", "z")),
+                         3: ("spherical", ("r", "theta", "phi"))}[
+                             parameters.get("Coordinate", 1)]
+
+
     @classmethod
     def _is_valid(self, *args, **kwargs):
         try:


https://bitbucket.org/yt_analysis/yt/commits/870211f1fdb9/
Changeset:   870211f1fdb9
User:        MatthewTurk
Date:        2017-11-14 16:48:50+00:00
Summary:     Get domain edges and offsets and add them to the grids.
Affected #:  1 file

diff -r 4da52ce743fd8b86857eeb7394a8d70493c8f938 -r 870211f1fdb9dca56a55e6e0fe2a3f34175b9400 yt/frontends/gamer/data_structures.py
--- a/yt/frontends/gamer/data_structures.py
+++ b/yt/frontends/gamer/data_structures.py
@@ -101,6 +101,8 @@
                 = (grid_corner[ gid0:gid0 + num_grids_level ] + patch_scale)*convert2physical
 
             gid0 += num_grids_level
+        self.grid_left_edge += self.dataset.domain_left_edge
+        self.grid_right_edge += self.dataset.domain_left_edge
 
         # allocate all grid objects
         self.grids = np.empty(self.num_grids, dtype='object')
@@ -272,8 +274,10 @@
         # simulation time and domain
         self.current_time      = parameters['Time'][0]
         self.dimensionality    = 3  # always 3D
-        self.domain_left_edge  = np.array([0.,0.,0.], dtype='float64')
-        self.domain_right_edge = parameters['BoxSize'].astype('float64')
+        self.domain_left_edge  = parameters.get("BoxEdgeL",
+                np.array([0.,0.,0.])).astype("f8")
+        self.domain_right_edge  = parameters.get("BoxEdgeR",
+                parameters["BoxSize"]).astype("f8")
         self.domain_dimensions = parameters['NX0'].astype('int64')
 
         # periodicity


https://bitbucket.org/yt_analysis/yt/commits/30fa0a70f2ea/
Changeset:   30fa0a70f2ea
User:        MatthewTurk
Date:        2017-11-14 16:58:28+00:00
Summary:     Moving dict into definitions.py
Affected #:  2 files

diff -r 870211f1fdb9dca56a55e6e0fe2a3f34175b9400 -r 30fa0a70f2eab45eb35c11229f63d1c0834367da yt/frontends/gamer/data_structures.py
--- a/yt/frontends/gamer/data_structures.py
+++ b/yt/frontends/gamer/data_structures.py
@@ -30,6 +30,7 @@
 from yt.utilities.file_handler import \
     HDF5FileHandler
 from .fields import GAMERFieldInfo
+from .definitions import geometry_parameters
 from yt.testing import assert_equal
 
 
@@ -308,11 +309,7 @@
         # old data format (version < 2210) does not contain any information of code units
         self.parameters.setdefault('Opt__Unit', 0)
 
-        self.geometry = {1: "cartesian",
-                         2: ("cylindrical", ("r", "theta", "z")),
-                         3: ("spherical", ("r", "theta", "phi"))}[
-                             parameters.get("Coordinate", 1)]
-
+        self.geometry = geometry_parameters[parameters.get("Coordinate", 1)]
 
     @classmethod
     def _is_valid(self, *args, **kwargs):

diff -r 870211f1fdb9dca56a55e6e0fe2a3f34175b9400 -r 30fa0a70f2eab45eb35c11229f63d1c0834367da yt/frontends/gamer/definitions.py
--- a/yt/frontends/gamer/definitions.py
+++ b/yt/frontends/gamer/definitions.py
@@ -0,0 +1,3 @@
+geometry_parameters = {1: "cartesian",
+                       2: ("cylindrical", ("r", "theta", "z")),
+                       3: ("spherical", ("r", "theta", "phi"))}


https://bitbucket.org/yt_analysis/yt/commits/3445446d0f2a/
Changeset:   3445446d0f2a
User:        ngoldbaum
Date:        2018-01-19 17:14:03+00:00
Summary:     Merge pull request #1622 from MatthewTurk/gamer_noncart

Add non-cartesian dataset support to the GAMER frontend
Affected #:  2 files

diff -r 603ae9af03a73e3a843d94ba741bde062d98a1eb -r 3445446d0f2a9f93f040a619a4b4eab4f7c3c070 yt/frontends/gamer/data_structures.py
--- a/yt/frontends/gamer/data_structures.py
+++ b/yt/frontends/gamer/data_structures.py
@@ -30,6 +30,7 @@
 from yt.utilities.file_handler import \
     HDF5FileHandler
 from .fields import GAMERFieldInfo
+from .definitions import geometry_parameters
 from yt.testing import assert_equal
 
 
@@ -101,6 +102,8 @@
                 = (grid_corner[ gid0:gid0 + num_grids_level ] + patch_scale)*convert2physical
 
             gid0 += num_grids_level
+        self.grid_left_edge += self.dataset.domain_left_edge
+        self.grid_right_edge += self.dataset.domain_left_edge
 
         # allocate all grid objects
         self.grids = np.empty(self.num_grids, dtype='object')
@@ -272,8 +275,10 @@
         # simulation time and domain
         self.current_time      = parameters['Time'][0]
         self.dimensionality    = 3  # always 3D
-        self.domain_left_edge  = np.array([0.,0.,0.], dtype='float64')
-        self.domain_right_edge = parameters['BoxSize'].astype('float64')
+        self.domain_left_edge  = parameters.get("BoxEdgeL",
+                np.array([0.,0.,0.])).astype("f8")
+        self.domain_right_edge  = parameters.get("BoxEdgeR",
+                parameters["BoxSize"]).astype("f8")
         self.domain_dimensions = parameters['NX0'].astype('int64')
 
         # periodicity
@@ -304,6 +309,8 @@
         # old data format (version < 2210) does not contain any information of code units
         self.parameters.setdefault('Opt__Unit', 0)
 
+        self.geometry = geometry_parameters[parameters.get("Coordinate", 1)]
+
     @classmethod
     def _is_valid(self, *args, **kwargs):
         try:

diff -r 603ae9af03a73e3a843d94ba741bde062d98a1eb -r 3445446d0f2a9f93f040a619a4b4eab4f7c3c070 yt/frontends/gamer/definitions.py
--- a/yt/frontends/gamer/definitions.py
+++ b/yt/frontends/gamer/definitions.py
@@ -0,0 +1,3 @@
+geometry_parameters = {1: "cartesian",
+                       2: ("cylindrical", ("r", "theta", "z")),
+                       3: ("spherical", ("r", "theta", "phi"))}

Repository URL: https://bitbucket.org/yt_analysis/yt/

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