Merge branch 'master' into reconnection

CMakeLists.txt

@@ -66,7 +66,7 @@ if(ENABLE_MPI)
 	endif()
 endif()
 
-option(ENABLE_OPENMP "Enable OpenMP support." ON)
+option(ENABLE_OPENMP "Enable OpenMP support." OFF)
 if(ENABLE_OPENMP)
 	find_package(OpenMP COMPONENTS Fortran)
 	if(OpenMP_Fortran_FOUND)

python/amunpy/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r", encoding="utf-8") as fh:
 
 setuptools.setup(
     name="amunpy",
-    version="0.9.7",
+    version="0.9.8",
     author="Grzegorz Kowal",
     author_email="grzegorz@amuncode.org",
     description="Python Interface for the AMUN code's snapshots",

python/amunpy/src/amunpy/__init__.py

@@ -21,6 +21,6 @@ __all__ = [ 'AmunXML', 'AmunH5', 'WriteVTK', \
 
 __author__ = "Grzegorz Kowal"
 __copyright__ = "Copyright 2018-2022 Grzegorz Kowal <grzegorz@amuncode.org>"
-__version__ = "0.9.7"
+__version__ = "0.9.8"
 __maintainer__ = "Grzegorz Kowal"
 __email__ = "grzegorz@amuncode.org"

python/amunpy/src/amunpy/amun.py

@@ -177,14 +177,18 @@ class Amun:
         """
             Add derived variables.
         """
+        denflag = 'dens' in self.variables
+        preflag = 'pres' in self.variables
+        velflag = all(v in self.variables for v in ['velx','vely','velz'])
+        magflag = all(v in self.variables for v in ['magx','magy','magz'])
         self.variables['refinement level']                  = 'mlev'
-        if 'dens' in self.variables:
+        if denflag:
             self.variables['density']                       = 'dens'
             self.variables['logarithm of density']          = 'logd'
-        if 'pres' in self.variables or self.attributes['eos'] == 'iso':
+        if preflag or self.attributes['eos'] == 'iso':
             self.variables['pressure']                      = 'pres'
             self.variables['logarithm of pressure']         = 'logp'
-        if all(v in self.variables for v in ['velx','vely','velz']):
+        if velflag:
             self.variables['velocity']                      = 'vvec'
             self.variables['velocity magnitude']            = 'velo'
             self.variables['x-velocity']                    = 'velx'
@@ -196,7 +200,7 @@ class Amun:
             self.variables['z-vorticity']                   = 'vorz'
             self.variables['vorticity']                     = 'wvec'
             self.variables['vorticity magnitude']           = 'vort'
-        if all(v in self.variables for v in ['magx','magy','magz']):
+        if magflag:
             self.variables['magnetic field']                = 'bvec'
             self.variables['magnetic field magnitude']      = 'magn'
             self.variables['x-magnetic field']              = 'magx'
@@ -210,28 +214,25 @@ class Amun:
             self.variables['current density magnitude']     = 'curr'
         if 'bpsi' in self.variables:
             self.variables['magnetic divergence potential'] = 'bpsi'
-        if 'pres' in self.variables and 'adiabatic_index' in self.attributes:
+        if preflag and 'adiabatic_index' in self.attributes:
             self.variables['internal energy']               = 'eint'
-        if all(v in self.variables for v in ['dens', 'pres']):
+        if denflag and preflag:
             self.variables['temperature']                   = 'temp'
-        if self.attributes['eqsys'] in [ 'hd', 'mhd' ] \
-                        and all(v in self.variables for v in ['dens','velx','vely','velz']):
+        if self.attributes['eqsys'] in ['hd','mhd'] and denflag and velflag:
             self.variables['kinetic energy']                = 'ekin'
-        if self.attributes['eqsys'] in [ 'mhd', 'srmhd' ] \
-                        and all(v in self.variables for v in ['magx','magy','magz']):
+        if self.attributes['eqsys'] in ['mhd','srmhd'] and magflag:
             self.variables['magnetic energy']               = 'emag'
             self.variables['magnetic pressure']             = 'emag'
-        if all(v in self.variables for v in ['velx','vely','velz', 'magx','magy','magz']) in self.variables:
+        if velflag and magflag:
             self.variables['electric field']                = 'evec'
             self.variables['electric field magnitude']      = 'elec'
             self.variables['x-electric field']              = 'elex'
             self.variables['y-electric field']              = 'eley'
             self.variables['z-electric field']              = 'elez'
-        if self.attributes['eqsys'] in [ 'srhd', 'srmhd' ] \
-                        and all(v in self.variables for v in ['velx','vely','velz']):
+        if self.attributes['eqsys'] in ['srhd','srmhd'] and velflag:
             self.variables['Lorentz factor']                = 'lore'
 
-        delete_datasets = [ 'dens', 'pres', 'velx', 'vely', 'velz', 'magx','magy','magz', 'bpsi' ]
+        delete_datasets = ['dens','pres','velx','vely','velz','magx','magy','magz','bpsi']
         for v in delete_datasets:
             if v in self.variables:
                 del self.variables[v]

sources/boundaries.F90

@@ -316,7 +316,7 @@ module boundaries
 #ifdef MPI
     use blocks     , only : block_info, pointer_info
 #endif /* MPI */
-    use blocks     , only : ndims, nsides
+    use blocks     , only : nsides
     use coordinates, only : minlev, maxlev
     use coordinates, only : nh => ncells_half
     use coordinates, only : nb, ne, nbm, nbp, nem, nep
@@ -862,7 +862,6 @@ module boundaries
 !
   subroutine boundary_variables(t, dt, status)
 
-    use blocks     , only : ndims
     use coordinates, only : minlev, maxlev
 
     implicit none

sources/equations.F90

@@ -1391,7 +1391,11 @@ module equations
     use blocks     , only : block_data
     use coordinates, only : nn => bcells
     use helpers    , only : print_message
+#if NDIMS == 3
     use coordinates, only : ax, ay, az
+#else /* NDIMS == 3 */
+    use coordinates, only : ax, ay
+#endif /* NDIMS == 3 */
 
     implicit none