Merge pull request #35 from vsnever/feature/element_lookup

Fixes and improvements in SOLPSSimulation, SOLPSMesh and related functions

CHANGELOG.md

@@ -1,6 +1,23 @@
 Project Changelog
 =================
 
+Release 1.2.0 (19 Sept 2020)
+----------------------------
+
+* Added support for Raysect 0.7.
+* Replaced unsafe SOLPSFunction3D and SOLPSVectorFunction3D with safe SOLPSFunction2D and SOLPSVectorFunction2D (use AxisymmetricMapper(SOLPSFunction2D) and VectorAxisymmetricMapper(SOLPSVectorFunction2D) for 3D).
+* Added correct initialisation of properties in SOLPSMesh and SOLPSSimulation.
+* Added new attributes to SOLPSMesh for basis vectors, cell connection areas, indices of neighbouring cells and new methods to_poloidal() and to_cartesian() for converting vectors defined on a grid from/to (poloidal, radial)/(R, Z).
+* Fixed incorrect calculation of cell basis vectors.
+* Inverted the indexing of data arrays and made all arrays row-major.
+* Added electron_velocities and neutral_listproperties to SOLPSSimulation.
+* Added 2D and 3D interpolators for plasma parameters to SOLPSSimulation.
+* Added parsing of additional quantities in load_solps_from_mdsplus(), load_solps_from_raw_output() and load_solps_from_balance().
+* Added support for B2 stand-alone simulations.
+* Added support for arbitrary plasma chemical composition.
+* Fixed incorrect calculation of velocities.
+* Other small fixes and improvements.
+
 Release 1.1.0 (30 July 2020)
 ----------------------------
 

cherab/solps/__init__.py

@@ -17,7 +17,7 @@
 # See the Licence for the specific language governing permissions and limitations
 # under the Licence.
 
-from .solps_3d_functions import SOLPSFunction3D, SOLPSVectorFunction3D
+from .solps_2d_functions import SOLPSFunction2D, SOLPSVectorFunction2D
 from .mesh_geometry import SOLPSMesh
 from .solps_plasma import SOLPSSimulation
 from .formats import load_solps_from_raw_output, load_solps_from_mdsplus, load_solps_from_balance

cherab/solps/b2/parse_b2_block_file.py

@@ -47,16 +47,16 @@ def _make_solps_data_object(_data):
 
         # Multiple 2D data field (e.g. na)
         if number > nxyg:
-            _data = np.array(_data).reshape((nxg, nyg, int(number / nxyg)), order='F')
+            _data = np.array(_data).reshape((number // nxyg, nyg, nxg))
             if debug:
-                print('Mesh data field {} with dimensions:  {:d} x {:d} x {:d}'.format(name, nxg, nyg, int(number/nxyg)))
+                print('Mesh data field {} with dimensions:  {:d} x {:d} x {:d}'.format(name, number // nxyg, nyg, nxg))
             return MESH_DATA, _data
 
         # 2D data field (e.g. ne)
         elif number == nxyg:
-            _data = np.array(_data).reshape((nxg, nyg), order='F')
+            _data = np.array(_data).reshape((nyg, nxg))
             if debug:
-                print('Mesh data field {} with dimensions:  {:d} x {:d}'.format(name, nxg, nyg))
+                print('Mesh data field {} with dimensions:  {:d} x {:d}'.format(name, nyg, nxg))
             return MESH_DATA, _data
 
         # Additional information field (e.g. zamin)

cherab/solps/eirene/eirene.py

@@ -16,8 +16,6 @@
 # See the Licence for the specific language governing permissions and limitations
 # under the Licence.
 
-import numpy as np
-
 
 # Code based on script by Felix Reimold (2016)
 class Eirene:
@@ -91,7 +89,7 @@ def __init__(self, nx, ny, na, nm, ni, ns, species_labels, version=None,
     @property
     def nx(self):
         """
-        Number of grid cells in the x direction
+        Number of grid cells in the poloidal direction
 
         :rtype: int
         """
@@ -100,7 +98,7 @@ def nx(self):
     @property
     def ny(self):
         """
-        Number of grid cells in the y direction
+        Number of grid cells in the radial direction
 
         :rtype: int
         """
@@ -395,7 +393,7 @@ def elosm(self):
 
     @elosm.setter
     def elosm(self, value):
-        self._check_dimensions(value, 1)
+        self._check_dimensions(value, self._nm)
         self._elosm = value
 
     @property
@@ -409,7 +407,7 @@ def edism(self):
 
     @edism.setter
     def edism(self, value):
-        self._check_dimensions(value, 1)
+        self._check_dimensions(value, self._nm)
         self._edism = value
 
     @property
@@ -426,13 +424,13 @@ def eradt(self, value):
         self._check_dimensions(value, 1)
         self._eradt = value
 
-    def _check_dimensions(self, data, dim2):
+    def _check_dimensions(self, data, dim0):
         """
         Checks compatibility of the data array dimension with the species number and grid size.
-        :param dim2: size of the 2nd dimenion
+        :param dim0: size of the 1st dimenion
         :return:
         """
 
-        if not data.shape == (self._nx, self._ny, dim2):
+        if not data.shape == (dim0, self._ny, self._nx):
             raise ValueError("Array with shape {0} obtained, but {1} expected".format(data.shape,
-                                                                                      (self._nx, self._ny, dim2)))
+                                                                                      (dim0, self._ny, self._nx)))

cherab/solps/eirene/parser/fort44.py

@@ -48,7 +48,7 @@ def load_fort44_file(file_path, debug=False):
 
         # Look up file parsing function and call it to obtain for44 block and update data dictionary
     parser = assign_fort44_parser(data["version"])
-    return parser(file_path)
+    return parser(file_path, debug)
 
 
 def assign_fort44_parser(file_version):

cherab/solps/eirene/parser/fort44_2013.py

@@ -98,8 +98,8 @@ def load_fort44_2013(file_path, debug=False):
         eirene.emism = read_block44(file_handle, 1, nx, ny)  # Molecular Halpha Emission
 
         # Radiated power (elosm, edism, eradt)
-        eirene.elosm = read_block44(file_handle, 1, nx, ny)  # Power loss due to molecules (including dissociation)
-        eirene.edism = read_block44(file_handle, 1, nx, ny)  # Power loss due to molecule dissociation
+        eirene.elosm = read_block44(file_handle, nm, nx, ny)  # Power loss due to molecules (including dissociation)
+        eirene.edism = read_block44(file_handle, nm, nx, ny)  # Power loss due to molecule dissociation
         eirene.eradt = read_block44(file_handle, 1, nx, ny)  # Neutral radiated power
 
     return eirene

cherab/solps/eirene/parser/fort44_2017.py

@@ -105,7 +105,7 @@ def load_fort44_2017(file_path, debug=False):
         _ = read_block44(file_handle, eirene.nm, eirene.nx, eirene.ny)  # Molecule particle source
 
         # Radiated power (elosm, edism, eradt)
-        eirene.edism = read_block44(file_handle, 1, eirene.nx, eirene.ny)  # Power loss due to molecule dissociation
+        eirene.edism = read_block44(file_handle, eirene.nm, eirene.nx, eirene.ny)  # Power loss due to molecule dissociation
 
         # Consume lines until eradt is reached
         while True:

cherab/solps/eirene/parser/utility.py

@@ -25,9 +25,9 @@ def read_block44(file_handle, ns, nx, ny):
     :param file_handle: A python core file handle object as a result of a
       call to open('./fort.44').
     :param int ns: total number of species
-    :param int nx: number of grid x cells
-    :param int ny: number of grid y cells
-    :return: ndarray of data with shape [nx, ny, ns]
+    :param int nx: number of grid poloidal cells
+    :param int ny: number of grid radial cells
+    :return: ndarray of data with shape [ns, ny, nx]
     """
     data = []
     npoints = ns * nx * ny
@@ -37,5 +37,5 @@ def read_block44(file_handle, ns, nx, ny):
             # This is a comment line. Ignore
             continue
         data.extend(line)
-    data = np.asarray(data, dtype=float).reshape((nx, ny, ns), order='F')
+    data = np.asarray(data, dtype=float).reshape((ns, ny, nx))
     return data