Creates dedicated test branch for tg-molcrm branch

.github/workflows/run_testsuite.yml

@@ -26,7 +26,7 @@ jobs:
     - name: Checkout develop branch
       uses: actions/checkout@v4
       with:
-        ref: develop
+        ref: tg_rewrite_H2CRM-compatible_boundary_modularization
         repository: LLNL/UEDGE 
     - name: Build UEDGE
       run: |

pytests/fulltests/orthogonal_unittest/test_ortho_default.py

@@ -162,6 +162,7 @@ def write_data(self):
         from uedge import bbb
         from uedge.hdf5 import hdf5_restore
         from copy import deepcopy
+        from numpy import ndarray
         # Helper function accessing UEDGE data using variable
         def getdata(var):
             from Forthon import package, packageobject

pytests/unittests/D_mols/nonog_mols/default/input.py

@@ -13,6 +13,16 @@
 except:
     pass
 
+setni = True
+setup = True
+setphi = True
+setphiofft = True
+setng = True
+setupg = True
+setti = True
+sette = True
+settg = True
+
 bbb.mhdgeo = 1 		#use MHD equilibrium
 bbb.gengrid=0		#read mesh from gridue file
 com.geometry = "snull"
@@ -100,24 +110,34 @@
 bbb.recycw[0:2] = [0.25, 0.95]
 
 # templates/D_mols/inputs/equations/default.py
-bbb.isnion = 1
-bbb.isupon = 1
-bbb.isteon = 1
-bbb.istion = 1
-bbb.isphion = 1
-bbb.isphiofft = 0
-bbb.istgon = 0
-bbb.isngon = 0
-bbb.isngon[0] = 0
-bbb.isupgon = 0
-bbb.isupgon[0] = 1
+if setni:
+    bbb.isnion = 1
+if setup:
+    bbb.isupon = 1
+if sette:
+    bbb.isteon = 1
+if setti:
+    bbb.istion = 1
+if setphi:
+    bbb.isphion = 1
+if setphiofft:
+    bbb.isphiofft = 0
+if settg:
+    bbb.istgon = 0
+if setng:
+    bbb.isngon = 0
+    bbb.isngon[0] = 0
+if setupg:
+    bbb.isupgon = 0
+    bbb.isupgon[0] = 1
 
 
 # Catch-all for turning off potential equaiton in slab geometry
 if bbb.mhdgeo == -1:
 	bbb.isphion = 0
 	bbb.isphiofft = 1
 
+
 # templates/D_mols/inputs/fluxlimits/default.py
 bbb.flalfe = 0.21	#electron parallel thermal conduct. grd.coeff
 bbb.flalfi = 0.21	#ion parallel thermal conduct. grd.coeff

pytests/unittests/D_mols/nonog_mols/tg_mol/input.py

@@ -13,6 +13,16 @@
 except:
     pass
 
+setni = True
+setup = True
+setphi = True
+setphiofft = True
+setng = True
+setupg = True
+setti = True
+sette = True
+settg = True
+
 bbb.mhdgeo = 1 		#use MHD equilibrium
 bbb.gengrid=0		#read mesh from gridue file
 com.geometry = "snull"
@@ -100,24 +110,34 @@
 bbb.recycw[0:2] = [0.25, 0.95]
 
 # templates/D_mols/inputs/equations/default.py
-bbb.isnion = 1
-bbb.isupon = 1
-bbb.isteon = 1
-bbb.istion = 1
-bbb.isphion = 1
-bbb.isphiofft = 0
-bbb.istgon = 0
-bbb.isngon = 0
-bbb.isngon[0] = 0
-bbb.isupgon = 0
-bbb.isupgon[0] = 1
+if setni:
+    bbb.isnion = 1
+if setup:
+    bbb.isupon = 1
+if sette:
+    bbb.isteon = 1
+if setti:
+    bbb.istion = 1
+if setphi:
+    bbb.isphion = 1
+if setphiofft:
+    bbb.isphiofft = 0
+if settg:
+    bbb.istgon = 0
+if setng:
+    bbb.isngon = 0
+    bbb.isngon[0] = 0
+if setupg:
+    bbb.isupgon = 0
+    bbb.isupgon[0] = 1
 
 
 # Catch-all for turning off potential equaiton in slab geometry
 if bbb.mhdgeo == -1:
 	bbb.isphion = 0
 	bbb.isphiofft = 1
 
+
 # templates/D_mols/inputs/fluxlimits/default.py
 bbb.flalfe = 0.21	#electron parallel thermal conduct. grd.coeff
 bbb.flalfi = 0.21	#ion parallel thermal conduct. grd.coeff
@@ -133,6 +153,7 @@
 bbb.ishymol = 1
 com.ngsp = 2
 com.nhgsp = 2
+setng=False
 bbb.isngon[1] = 1
 bbb.istgcon[1] = -1
 bbb.istgcore[1] = 2
@@ -142,6 +163,7 @@
 bbb.istgrb[1] = 0
 bbb.tgwall[1] = 0.2
 
+
 # templates/D_mols/inputs/radialtransport/default.py
 bbb.difni[1] = 1.	#D for radial hydrogen diffusion
 bbb.kye = 1.		#chi_e for radial elec energy diffusion

pytests/unittests/D_mols/nonog_mols/tg_mol_atoms/input.py

@@ -13,6 +13,16 @@
 except:
     pass
 
+setni = True
+setup = True
+setphi = True
+setphiofft = True
+setng = True
+setupg = True
+setti = True
+sette = True
+settg = True
+
 bbb.mhdgeo = 1 		#use MHD equilibrium
 bbb.gengrid=0		#read mesh from gridue file
 com.geometry = "snull"
@@ -33,6 +43,8 @@
 bbb.travis[1] = 0.	#shouldn't be used for neutrals - but to be sure
 
 
+settg = False
+bbb.istgon = 0      # Reset Tg equation
 bbb.istgon[0] = 1   # Turn on D0 temperature equation
 bbb.cftiexclg = 0.  # Remove the Tg part in the Ti equation
 bbb.cfdiss = 1.0
@@ -117,24 +129,34 @@
 bbb.recycw[0:2] = [0.25, 0.95]
 
 # templates/D_mols/inputs/equations/default.py
-bbb.isnion = 1
-bbb.isupon = 1
-bbb.isteon = 1
-bbb.istion = 1
-bbb.isphion = 1
-bbb.isphiofft = 0
-bbb.istgon = 0
-bbb.isngon = 0
-bbb.isngon[0] = 0
-bbb.isupgon = 0
-bbb.isupgon[0] = 1
+if setni:
+    bbb.isnion = 1
+if setup:
+    bbb.isupon = 1
+if sette:
+    bbb.isteon = 1
+if setti:
+    bbb.istion = 1
+if setphi:
+    bbb.isphion = 1
+if setphiofft:
+    bbb.isphiofft = 0
+if settg:
+    bbb.istgon = 0
+if setng:
+    bbb.isngon = 0
+    bbb.isngon[0] = 0
+if setupg:
+    bbb.isupgon = 0
+    bbb.isupgon[0] = 1
 
 
 # Catch-all for turning off potential equaiton in slab geometry
 if bbb.mhdgeo == -1:
 	bbb.isphion = 0
 	bbb.isphiofft = 1
 
+
 # templates/D_mols/inputs/fluxlimits/default.py
 bbb.flalfe = 0.21	#electron parallel thermal conduct. grd.coeff
 bbb.flalfi = 0.21	#ion parallel thermal conduct. grd.coeff
@@ -150,6 +172,7 @@
 bbb.ishymol = 1
 com.ngsp = 2
 com.nhgsp = 2
+setng=False
 bbb.isngon[1] = 1
 bbb.istgcon[1] = -1
 bbb.istgcore[1] = 2
@@ -159,6 +182,7 @@
 bbb.istgrb[1] = 0
 bbb.tgwall[1] = 0.2
 
+
 # templates/D_mols/inputs/radialtransport/default.py
 bbb.difni[1] = 1.	#D for radial hydrogen diffusion
 bbb.kye = 1.		#chi_e for radial elec energy diffusion

pytests/unittests/D_mols/nonog_mols/tg_mol_atoms_drift/input.py

@@ -13,6 +13,16 @@
 except:
     pass
 
+setni = True
+setup = True
+setphi = True
+setphiofft = True
+setng = True
+setupg = True
+setti = True
+sette = True
+settg = True
+
 bbb.mhdgeo = 1 		#use MHD equilibrium
 bbb.gengrid=0		#read mesh from gridue file
 com.geometry = "snull"
@@ -33,6 +43,8 @@
 bbb.travis[1] = 0.	#shouldn't be used for neutrals - but to be sure
 
 
+settg = False
+bbb.istgon = 0      # Reset Tg equation
 bbb.istgon[0] = 1   # Turn on D0 temperature equation
 bbb.cftiexclg = 0.  # Remove the Tg part in the Ti equation
 bbb.cfdiss = 1.0
@@ -170,24 +182,34 @@
 
 
 # templates/D_mols/inputs/equations/default.py
-bbb.isnion = 1
-bbb.isupon = 1
-bbb.isteon = 1
-bbb.istion = 1
-bbb.isphion = 1
-bbb.isphiofft = 0
-bbb.istgon = 0
-bbb.isngon = 0
-bbb.isngon[0] = 0
-bbb.isupgon = 0
-bbb.isupgon[0] = 1
+if setni:
+    bbb.isnion = 1
+if setup:
+    bbb.isupon = 1
+if sette:
+    bbb.isteon = 1
+if setti:
+    bbb.istion = 1
+if setphi:
+    bbb.isphion = 1
+if setphiofft:
+    bbb.isphiofft = 0
+if settg:
+    bbb.istgon = 0
+if setng:
+    bbb.isngon = 0
+    bbb.isngon[0] = 0
+if setupg:
+    bbb.isupgon = 0
+    bbb.isupgon[0] = 1
 
 
 # Catch-all for turning off potential equaiton in slab geometry
 if bbb.mhdgeo == -1:
 	bbb.isphion = 0
 	bbb.isphiofft = 1
 
+
 # templates/D_mols/inputs/fluxlimits/default.py
 bbb.flalfe = 0.21	#electron parallel thermal conduct. grd.coeff
 bbb.flalfi = 0.21	#ion parallel thermal conduct. grd.coeff
@@ -203,6 +225,7 @@
 bbb.ishymol = 1
 com.ngsp = 2
 com.nhgsp = 2
+setng=False
 bbb.isngon[1] = 1
 bbb.istgcon[1] = -1
 bbb.istgcore[1] = 2
@@ -212,6 +235,7 @@
 bbb.istgrb[1] = 0
 bbb.tgwall[1] = 0.2
 
+
 # templates/D_mols/inputs/radialtransport/default.py
 bbb.difni[1] = 1.	#D for radial hydrogen diffusion
 bbb.kye = 1.		#chi_e for radial elec energy diffusion