Adds tests including molecules

templates/D_mols/header/default.py

@@ -0,0 +1,15 @@
+# This is the test header file
+# It is copied into the start of every test case
+# created from this subdirectory. It is the 
+# best place to include lines common to
+# all test cases, such as rate paths etc.
+
+from uedge import *
+from uedge.hdf5 import hdf5_restore
+
+try:
+    bbb.oldseec = 0
+    bbb.jhswitch = 0
+except:
+    pass
+

templates/D_mols/inputs/atoms/default.py

@@ -0,0 +1,6 @@
+bbb.isupwo[1] = 0
+bbb.ineudif = 2
+com.ngsp=1
+com.nhsp=2
+bbb.ziin[1]=0
+bbb.travis[1] = 0.	#shouldn't be used for neutrals - but to be sure

templates/D_mols/inputs/atoms/tg_mol_atoms.py

@@ -0,0 +1,22 @@
+bbb.isupwo[1] = 0
+bbb.ineudif = 2
+com.ngsp=1
+com.nhsp=2
+bbb.ziin[1]=0
+bbb.travis[1] = 0.	#shouldn't be used for neutrals - but to be sure
+
+
+bbb.istgon[0] = 1   # Turn on D0 temperature equation
+bbb.cftiexclg = 0.  # Remove the Tg part in the Ti equation
+bbb.cfdiss = 1.0
+bbb.istgcore[0] = 2 #..albedo
+bbb.istgpfc[0] = 4#2  #..zml flow change to 4 later
+bbb.istgwc[0] = 4#2   #..flow
+bbb.istglb[0] = 4
+bbb.istgrb[0] = 4
+bbb.recyce = 0.3
+bbb.recycm = -0.9
+bbb.cfnidhgy = 1.0
+bbb.cfnidhg2 = 1.0
+bbb.cfnidhdis = 1.0 #..consider drift heating for dissociation
+bbb.cfnidhmol = 1.0 #..ignore molecular v in dissociation drift heating

templates/D_mols/inputs/atoms/tg_mol_atoms_drift.py

@@ -0,0 +1,22 @@
+bbb.isupwo[1] = 0
+bbb.ineudif = 2
+com.ngsp=1
+com.nhsp=2
+bbb.ziin[1]=0
+bbb.travis[1] = 0.	#shouldn't be used for neutrals - but to be sure
+
+
+bbb.istgon[0] = 1   # Turn on D0 temperature equation
+bbb.cftiexclg = 0.  # Remove the Tg part in the Ti equation
+bbb.cfdiss = 1.0
+bbb.istgcore[0] = 2 #..albedo
+bbb.istgpfc[0] = 4#2  #..zml flow change to 4 later
+bbb.istgwc[0] = 4#2   #..flow
+bbb.istglb[0] = 4
+bbb.istgrb[0] = 4
+bbb.recyce = 0.3
+bbb.recycm = -0.9
+bbb.cfnidhgy = 1.0
+bbb.cfnidhg2 = 1.0
+bbb.cfnidhdis = 1.0 #..consider drift heating for dissociation
+bbb.cfnidhmol = 1.0 #..ignore molecular v in dissociation drift heating

templates/D_mols/inputs/boundary/core/density/default.py

@@ -0,0 +1,2 @@
+bbb.isnicore[0] = 1 	#use fixed-density BC on core
+bbb.ncore[0] = 2.e19	#hydrogen ion density on core

templates/D_mols/inputs/boundary/core/energy/default.py

@@ -0,0 +1,3 @@
+bbb.iflcore = 0		#flag=0, fixed Te,i;=1, fixed power on core
+bbb.tcoree = 100.	#core Te 
+bbb.tcorei = 100.	#core Ti

templates/D_mols/inputs/boundary/plates/particle/default.py

@@ -0,0 +1,4 @@
+bbb.recycp[0] = 0.9		#hydrogen recycling grd.coeff at plates
+#.. target pumping for atoms
+bbb.albedorb[0,0] = 0.25
+bbb.albedolb[0,0] = 0.25

templates/D_mols/inputs/boundary/walls/energy/default.py

@@ -0,0 +1,4 @@
+bbb.istewc = 1 		#=1 sets constant wall te
+bbb.tedge = 2.		#fixed wall,pf Te,i if istewcon=1, etc
+bbb.istepfc = 3		#=3 sets scale length bbb.lyte
+bbb.lyte = 0.03		#radial scale-length for Te on PF boundary

templates/D_mols/inputs/boundary/walls/particle/default.py

@@ -0,0 +1,40 @@
+bbb.matwso[0] = 1		#recycle on main-chamber wall
+bbb.isnwcono = 1		#if=1, set bbb.ni[,,com.ny+1]=bbb.nwallo
+bbb.isnwconi = 1		#if=1, set PF wall bbb.ni=bbb.nwalli
+bbb.allocate()		#bbb.allocate() space of bbb.nwallo,i
+bbb.nwallo = 1.e18
+bbb.nwalli = 1.e18
+
+
+# gas pumping
+bbb.nwsor = 2  #.. number of sources (sinks).  defalut: =1
+  #.. PRF
+bbb.igasi[0] = 0.   #.. pumping. default =0.
+bbb.xgasi[0] = 0.   #.. position from inner. default =0.
+bbb.wgasi[0] = 100. #.. width. default =100.(m)
+bbb.igspsori[0] = 1 #.. species. default =1
+bbb.albdsi[0] = 0.25 #.. pumping flux = (1.-albdsi)*1/4*n*sqrt(8T/pi/me)
+  #.. wall
+bbb.igaso[0] = 0.   #.. default =0.
+bbb.xgaso[0] = 0.   #.. position from inner. default =0.
+bbb.wgaso[0] = 100. #.. width. default =100.(m)
+bbb.igspsoro[0] = 1 #.. species. default =1
+bbb.albdso[0] = 0.25 #.. pumping flux = (1.-albdsi)*1/4*n*sqrt(8T/pi/me)
+
+#..new pumping for atoms
+  #.. PRF
+bbb.igasi[1] = 0.   #.. pumping. default =0.
+bbb.xgasi[1] = 0.   #.. position from inner. default =0.
+bbb.wgasi[1] = 100. #.. width. default =100.(m)
+bbb.igspsori[1] = 2 #.. species. default =1
+bbb.albdsi[1] = 0.9999 #.. pumping flux = (1.-albdsi)*1/4*n*sqrt(8T/pi/me)
+  #.. wall
+bbb.igaso[1] = 0.   #.. default =0.
+bbb.xgaso[1] = 0.   #.. position from inner. default =0.
+bbb.wgaso[1] = 100. #.. width. default =100.(m)
+bbb.igspsoro[1] = 2 #.. species. default =1
+bbb.albdso[1] = 0.9999 #.. pumping flux = (1.-albdsi)*1/4*n*sqrt(8T/pi/me)
+  #.. recycling
+bbb.matwsi[1] = 1   #.. default =0
+#bbb.recycw[0] = 0.9    #.. wall recycling coef. for igsp=1 (for PRF and wall)
+bbb.matwso[1] = 1   #.. coefficient is recycw

templates/D_mols/inputs/boundary/walls/recycling/default.py

@@ -0,0 +1 @@
+bbb.recycw[0:2] = [0.25, 0.95]

templates/D_mols/inputs/drifts/tg_mol_atoms_drift.py

@@ -0,0 +1,50 @@
+
+# Drifts and currents
+bbb.isphion = 1
+bbb.b0 = 1.0                    # =1 for normal direction of B-field
+bbb.rsigpl=1.e-8                #anomalous cross-field conductivity
+bbb.cfjhf=1.            #turn-on heat flow from current [bbb.fqp]
+bbb.cfjve = 1.          #makes bbb.vex = vix - bbb.cfjve*bbb.fqx
+bbb.cfjpy = 0.          #diamag. cur. in flx.y-direction
+bbb.cfjp2 = 0.          #diamag. cur. in 2-direction
+bbb.cfsigm = 1.0
+#
+bbb.newbcl=1
+bbb.newbcr=1
+bbb.isfdiax =1.         #Factor to turn on (ExB+diamag.) contrib. to sheath
+#
+bbb.cfyef = 1.0         #ExB drift in flx.y-dir.
+bbb.cf2ef = 1.0         #ExB drift in 2-dir.
+bbb.cfydd = 0.          #Diamag. drift in flx.y-dir. [always=0]
+bbb.cf2dd = 0.          #Diamag. drift in 2-dir. [always=0]
+bbb.cfrd = 0.           #Resistive drift in flx.y and 2 dirs.
+bbb.cfbgt = 0.          #Diamag. energy drift [always=0]
+bbb.cfybf = 1.0              #turns on bbb.vycb - radial grad_B drift
+bbb.cf2bf = 1.0              #turns on bbb.v2cb - perp grad_B drift [nearly pol]
+bbb.cfqybf = 1.0             #turns on bbb.vycb contrib to radial current
+bbb.cfq2bf = 1.0             #turns on bbb.v2cb contrib to perp["2"] current
+#..modified
+bbb.cfqybbo=1.     #turn off Grad B current on boundary
+bbb.cfqydbo=0.     #use full diagmagetic current on boundary to force j_r=0
+
+bbb.cfniybbo=1.   # use to avoid artificial source at core boundary
+bbb.cfniydbo=0.   # use to avoid artificial source at core boundary
+bbb.cfeeybbo=1.   # ditto
+bbb.cfeeydbo=0.   # ditto
+#bbb.cfeixdbo=1.   # turn on BXgrad(T) drift in plate BC
+#bbb.cfeexdbo=1.   # turn on diamagnetic drift in plate BC
+bbb.cfeixdbo=0.
+bbb.cfeexdbo=0.
+bbb.cftef=1.0     #turns on v2ce for toroidal velocity
+bbb.cftdd=1.0     #turns on v2dd (diamag vel) for toloidal velocity
+bbb.cfqym=1.0     #turns on inertial correction to fqy current
+#
+bbb.isnewpot = 1
+bbb.rnewpot = 1.
+#bbb.iphibcc = 0         #set bbb.phi[,1] uniform poloidally
+bbb.iphibcc=3     # =3 gives ey=eycore on core bdry
+bbb.iphibcwi=0    # set ey=0 on inner wall if =0
+                  # phi(PF)=phintewi*te(ix,0) on PF wall if =1
+bbb.iphibcwo=0    # same for outer wall
+bbb.isutcore=2    # =1, set dut/dy=0 on iy=0 (if iphibcc=0)
+                # =0, toroidal angular momentum=lzcore on iy=0 (iphibcc=0)

templates/D_mols/inputs/drifts/tg_mol_drift.py

@@ -0,0 +1,50 @@
+
+# Drifts and currents
+bbb.isphion = 1
+bbb.b0 = 1.0                    # =1 for normal direction of B-field
+bbb.rsigpl=1.e-8                #anomalous cross-field conductivity
+bbb.cfjhf=1.            #turn-on heat flow from current [bbb.fqp]
+bbb.cfjve = 1.          #makes bbb.vex = vix - bbb.cfjve*bbb.fqx
+bbb.cfjpy = 0.          #diamag. cur. in flx.y-direction
+bbb.cfjp2 = 0.          #diamag. cur. in 2-direction
+bbb.cfsigm = 1.0
+#
+bbb.newbcl=1
+bbb.newbcr=1
+bbb.isfdiax =1.         #Factor to turn on (ExB+diamag.) contrib. to sheath
+#
+bbb.cfyef = 1.0         #ExB drift in flx.y-dir.
+bbb.cf2ef = 1.0         #ExB drift in 2-dir.
+bbb.cfydd = 0.          #Diamag. drift in flx.y-dir. [always=0]
+bbb.cf2dd = 0.          #Diamag. drift in 2-dir. [always=0]
+bbb.cfrd = 0.           #Resistive drift in flx.y and 2 dirs.
+bbb.cfbgt = 0.          #Diamag. energy drift [always=0]
+bbb.cfybf = 1.0              #turns on bbb.vycb - radial grad_B drift
+bbb.cf2bf = 1.0              #turns on bbb.v2cb - perp grad_B drift [nearly pol]
+bbb.cfqybf = 1.0             #turns on bbb.vycb contrib to radial current
+bbb.cfq2bf = 1.0             #turns on bbb.v2cb contrib to perp["2"] current
+#..modified
+bbb.cfqybbo=1.     #turn off Grad B current on boundary
+bbb.cfqydbo=0.     #use full diagmagetic current on boundary to force j_r=0
+
+bbb.cfniybbo=1.   # use to avoid artificial source at core boundary
+bbb.cfniydbo=0.   # use to avoid artificial source at core boundary
+bbb.cfeeybbo=1.   # ditto
+bbb.cfeeydbo=0.   # ditto
+#bbb.cfeixdbo=1.   # turn on BXgrad(T) drift in plate BC
+#bbb.cfeexdbo=1.   # turn on diamagnetic drift in plate BC
+bbb.cfeixdbo=0.
+bbb.cfeexdbo=0.
+bbb.cftef=1.0     #turns on v2ce for toroidal velocity
+bbb.cftdd=1.0     #turns on v2dd (diamag vel) for toloidal velocity
+bbb.cfqym=1.0     #turns on inertial correction to fqy current
+#
+bbb.isnewpot = 1
+bbb.rnewpot = 1.
+#bbb.iphibcc = 0         #set bbb.phi[,1] uniform poloidally
+bbb.iphibcc=3     # =3 gives ey=eycore on core bdry
+bbb.iphibcwi=0    # set ey=0 on inner wall if =0
+                  # phi(PF)=phintewi*te(ix,0) on PF wall if =1
+bbb.iphibcwo=0    # same for outer wall
+bbb.isutcore=2    # =1, set dut/dy=0 on iy=0 (if iphibcc=0)
+                # =0, toroidal angular momentum=lzcore on iy=0 (iphibcc=0)

templates/D_mols/inputs/equations/default.py

@@ -0,0 +1,17 @@
+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
+
+
+# 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

@@ -0,0 +1,9 @@
+bbb.flalfe = 0.21	#electron parallel thermal conduct. grd.coeff
+bbb.flalfi = 0.21	#ion parallel thermal conduct. grd.coeff
+bbb.flalfv = 1.		#ion parallel viscosity grd.coeff
+bbb.flalfgx = 1.	#neut. density poloidal diffusion
+bbb.flalfgy = 1.	#neut. density radial diffusion
+bbb.flalfvgx = 1.	#neut. momentum poloidal viscosity
+bbb.flalfvgy = 1.	#neut. momentum radial viscosity
+bbb.flalftgx = 1.	#neut. particle poloidal heat diffusion 
+bbb.flalftgy = 1.	#neut. particle radial heat diffusion

templates/D_mols/inputs/mols/default.py

@@ -0,0 +1,5 @@
+bbb.ishymol = 1
+com.ngsp = 2
+com.nhgsp = 2
+bbb.isngon[1] = 1
+bbb.istgcon[1] = -1

templates/D_mols/inputs/mols/tg_mol.py

@@ -0,0 +1,11 @@
+bbb.ishymol = 1
+com.ngsp = 2
+com.nhgsp = 2
+bbb.isngon[1] = 1
+bbb.istgcon[1] = -1
+bbb.istgcore[1] = 2
+bbb.istgpfc[1] = 0
+bbb.istgwc[1] = 0
+bbb.istglb[1] = 0
+bbb.istgrb[1] = 0
+bbb.tgwall[1] = 0.2

templates/D_mols/inputs/mols/tg_mol_atoms.py

@@ -0,0 +1,11 @@
+bbb.ishymol = 1
+com.ngsp = 2
+com.nhgsp = 2
+bbb.isngon[1] = 1
+bbb.istgcon[1] = -1
+bbb.istgcore[1] = 2
+bbb.istgpfc[1] = 0
+bbb.istgwc[1] = 0
+bbb.istglb[1] = 0
+bbb.istgrb[1] = 0
+bbb.tgwall[1] = 0.2

templates/D_mols/inputs/mols/tg_mol_atoms_drift.py

@@ -0,0 +1,11 @@
+bbb.ishymol = 1
+com.ngsp = 2
+com.nhgsp = 2
+bbb.isngon[1] = 1
+bbb.istgcon[1] = -1
+bbb.istgcore[1] = 2
+bbb.istgpfc[1] = 0
+bbb.istgwc[1] = 0
+bbb.istglb[1] = 0
+bbb.istgrb[1] = 0
+bbb.tgwall[1] = 0.2

templates/D_mols/inputs/mols/tg_mol_drift.py

@@ -0,0 +1,11 @@
+bbb.ishymol = 1
+com.ngsp = 2
+com.nhgsp = 2
+bbb.isngon[1] = 1
+bbb.istgcon[1] = -1
+bbb.istgcore[1] = 2
+bbb.istgpfc[1] = 0
+bbb.istgwc[1] = 0
+bbb.istglb[1] = 0
+bbb.istgrb[1] = 0
+bbb.tgwall[1] = 0.2

templates/D_mols/inputs/mols/tg_mol_istgcore0.py

@@ -0,0 +1,11 @@
+bbb.ishymol = 1
+com.ngsp = 2
+com.nhgsp = 2
+bbb.isngon[1] = 1
+bbb.istgcon[1] = -1
+bbb.istgcore[1] = 0
+bbb.istgpfc[1] = 0
+bbb.istgwc[1] = 0
+bbb.istglb[1] = 0
+bbb.istgrb[1] = 0
+bbb.tgwall[1] = 0.2

templates/D_mols/inputs/mols/tg_mol_istgcore1.py

@@ -0,0 +1,11 @@
+bbb.ishymol = 1
+com.ngsp = 2
+com.nhgsp = 2
+bbb.isngon[1] = 1
+bbb.istgcon[1] = -1
+bbb.istgcore[1] = 1
+bbb.istgpfc[1] = 0
+bbb.istgwc[1] = 0
+bbb.istglb[1] = 0
+bbb.istgrb[1] = 0
+bbb.tgwall[1] = 0.2

templates/D_mols/inputs/mols/tg_mol_istgcore3.py

@@ -0,0 +1,11 @@
+bbb.ishymol = 1
+com.ngsp = 2
+com.nhgsp = 2
+bbb.isngon[1] = 1
+bbb.istgcon[1] = -1
+bbb.istgcore[1] = 3
+bbb.istgpfc[1] = 0
+bbb.istgwc[1] = 0
+bbb.istglb[1] = 0
+bbb.istgrb[1] = 0
+bbb.tgwall[1] = 0.2

templates/D_mols/inputs/mols/tg_mol_istglb1.py

@@ -0,0 +1,11 @@
+bbb.ishymol = 1
+com.ngsp = 2
+com.nhgsp = 2
+bbb.isngon[1] = 1
+bbb.istgcon[1] = -1
+bbb.istgcore[1] = 2
+bbb.istgpfc[1] = 0
+bbb.istgwc[1] = 0
+bbb.istglb[1] = 1
+bbb.istgrb[1] = 0
+bbb.tgwall[1] = 0.2

templates/D_mols/inputs/mols/tg_mol_istglb3.py

@@ -0,0 +1,11 @@
+bbb.ishymol = 1
+com.ngsp = 2
+com.nhgsp = 2
+bbb.isngon[1] = 1
+bbb.istgcon[1] = -1
+bbb.istgcore[1] = 2
+bbb.istgpfc[1] = 0
+bbb.istgwc[1] = 0
+bbb.istglb[1] = 3
+bbb.istgrb[1] = 0
+bbb.tgwall[1] = 0.2