diff --git a/testcases/ExB_shear_atomic_tests/fort_00.90 b/testcases/ExB_shear_atomic_tests/fort_00.90
deleted file mode 100644
index 9bc39d2e7957e65f46b5fab2b99bfe10b0bcafd7..0000000000000000000000000000000000000000
--- a/testcases/ExB_shear_atomic_tests/fort_00.90
+++ /dev/null
@@ -1,100 +0,0 @@
-&BASIC
- nrun = 100000000
- dt = 0.00075
- tmax = 2.0
- maxruntime = 356400
- job2load = -1
-/
-&GRID
- pmax = 0
- jmax = 0
- Nx = 186
- Lx = 100
- Ny = 186
- Ly = 100
- Nz = 1
- SG = .false.
- Nexc = 1
-/
-&GEOMETRY
- geom = 'zpinch'!'miller'
- q0 = 1.0
- shear = 0.0
- eps = 0.0
- kappa = 1
- s_kappa = 0
- delta = 0
- s_delta = 0
- zeta = 0
- s_zeta = 0
- parallel_bc = 'dirichlet'
- shift_y = 0
- Npol = 1
- PB_PHASE= .false.
-/
-&DIAGNOSTICS
- dtsave_0d = 0.01
- dtsave_1d = -1
- dtsave_2d = -1
- dtsave_3d = 0.01
- dtsave_5d = 100
- write_doubleprecision = .true.
- write_gamma = .true.
- write_hf = .true.
- write_phi = .true.
- write_Na00 = .true.
- write_Napj = .true.
- write_dens = .true.
- write_temp = .true.
-/
-&MODEL
-LINEARITY = 'nonlinear'
-RM_LD_T_EQ= .false.
- Na = 1
- mu_x = 1
- mu_y = 1
- N_HD = 4
- mu_z = 0
- HYP_V = 'hypcoll'
- mu_p = 0
- mu_j = 0
- nu = 1
- k_gB = 0
- k_cB = 0
- lambdaD = 0
- beta = 0.0
- ExBrate = 0.0
- ikxZF = 2
- ZFamp = 400
- ADIAB_E = .true.
- ADIAB_I = .false.
- tau_i = 1
- MHD_PD = .false.
-/
-&CLOSURE
- hierarchy_closure='truncation'
- dmax =-1
- nonlinear_closure='truncation'
- nmax =0
-/
-&SPECIES
- name_ = 'ions'
- tau_ = 1
- sigma_ = 1
- q_ = 1
- K_N_ = 0
- K_T_ = 0
-/
-&COLLISION
- collision_model = 'DG'
- GK_CO = .false.
- INTERSPECIES = .true.
- mat_file = '/home/ahoffman/gyacomo/iCa/null'
- collision_kcut = 1
-/
-&INITIAL
- INIT_OPT = 'ricci'
-/
-&TIME_INTEGRATION
- numerical_scheme = 'RK4'
-/
diff --git a/testcases/ExB_shear_atomic_tests/fort_01.90 b/testcases/ExB_shear_atomic_tests/fort_01.90
deleted file mode 100644
index 2aa6249f0ade57f2e74e98b317b2a05928776589..0000000000000000000000000000000000000000
--- a/testcases/ExB_shear_atomic_tests/fort_01.90
+++ /dev/null
@@ -1,98 +0,0 @@
-&BASIC
- nrun = 100000000
- dt = 0.00075
- tmax = 0.5
- maxruntime = 356400
- job2load = -1
-/
-&GRID
- pmax = 0
- jmax = 0
- Nx = 186
- Lx = 100
- Ny = 186
- Ly = 100
- Nz = 1
- SG = .false.
- Nexc = 1
-/
-&GEOMETRY
- geom = 'zpinch'!'miller'
- q0 = 1.0
- shear = 0.0
- eps = 0.0
- kappa = 1
- s_kappa = 0
- delta = 0
- s_delta = 0
- zeta = 0
- s_zeta = 0
- parallel_bc = 'dirichlet'
- shift_y = 0
- Npol = 1
- PB_PHASE= .false.
-/
-&DIAGNOSTICS
- dtsave_0d = 0.01
- dtsave_1d = -1
- dtsave_2d = -1
- dtsave_3d = 0.01
- dtsave_5d = 100
- write_doubleprecision = .true.
- write_gamma = .true.
- write_hf = .true.
- write_phi = .true.
- write_Na00 = .true.
- write_Napj = .true.
- write_dens = .true.
- write_temp = .true.
-/
-&MODEL
-LINEARITY = 'linear'
-RM_LD_T_EQ= .false.
- Na = 1
- mu_x = 1
- mu_y = 1
- N_HD = 4
- mu_z = 0
- HYP_V = 'hypcoll'
- mu_p = 0
- mu_j = 0
- nu = 1
- k_gB = 0
- k_cB = 0
- lambdaD = 0
- beta = 0.0
- ExBrate = 5.0
- ADIAB_E = .true.
- ADIAB_I = .false.
- tau_i = 1
- MHD_PD = .false.
-/
-&CLOSURE
- hierarchy_closure='truncation'
- dmax =-1
- nonlinear_closure='truncation'
- nmax =0
-/
-&SPECIES
- name_ = 'ions'
- tau_ = 1
- sigma_ = 1
- q_ = 1
- K_N_ = 0
- K_T_ = 0
-/
-&COLLISION
- collision_model = 'DG'
- GK_CO = .false.
- INTERSPECIES = .true.
- mat_file = '/home/ahoffman/gyacomo/iCa/null'
- collision_kcut = 1
-/
-&INITIAL
- INIT_OPT = 'ricci'
-/
-&TIME_INTEGRATION
- numerical_scheme = 'RK4'
-/
diff --git a/testcases/ExB_shear_atomic_tests/fort_02.90 b/testcases/ExB_shear_atomic_tests/fort_02.90
deleted file mode 100644
index f4070b569b8ceaaabe65442cedd09727c4df5de4..0000000000000000000000000000000000000000
--- a/testcases/ExB_shear_atomic_tests/fort_02.90
+++ /dev/null
@@ -1,102 +0,0 @@
-&BASIC
- nrun = 100000000
- dt = 0.001
- tmax = 2.0
- maxruntime = 356400
- job2load = -1
-/
-&GRID
- pmax = 0
- jmax = 0
- Nx = 96
- Lx = 100
- Ny = 64
- Ly = 100
- Nz = 1
- SG = .false.
- Nexc = 1
-/
-&GEOMETRY
- geom = 'zpinch'!'miller'
- q0 = 1.0
- shear = 0.0
- eps = 0.0
- kappa = 1
- s_kappa = 0
- delta = 0
- s_delta = 0
- zeta = 0
- s_zeta = 0
- parallel_bc = 'dirichlet'
- shift_y = 0
- Npol = 1
- PB_PHASE= .false.
-/
-&DIAGNOSTICS
- dtsave_0d = 0.05
- dtsave_1d = -1
- dtsave_2d = -1
- dtsave_3d = 0.02
- dtsave_5d = 100
- write_doubleprecision = .true.
- write_gamma = .true.
- write_hf = .true.
- write_phi = .true.
- write_Na00 = .true.
- write_Napj = .true.
- write_dens = .true.
- write_temp = .true.
-/
-&MODEL
-LINEARITY = 'nonlinear'
-RM_LD_T_EQ= .false.
- Na = 1
- mu_x = 0
- mu_y = 0
- N_HD = 4
- mu_z = 0
- HYP_V = 'hypcoll'
- mu_p = 0
- mu_j = 0
- nu = 0
- k_gB = 0
- k_cB = 0
- lambdaD = 0
- beta = 0.0
- ExBrate = 0.0
- ExB_NL_CORRECTION = .false.
- ADIAB_E = .true.
- ADIAB_I = .false.
- tau_i = 1
- MHD_PD = .false.
-/
-&CLOSURE
- hierarchy_closure='truncation'
- dmax =-1
- nonlinear_closure='truncation'
- nmax =-1
-/
-&SPECIES
- name_ = 'ions'
- tau_ = 1
- sigma_ = 1
- q_ = 1
- K_N_ = 0
- K_T_ = 0
-/
-&COLLISION
- collision_model = 'DG'
- GK_CO = .false.
- INTERSPECIES = .true.
- mat_file = '/home/ahoffman/gyacomo/iCa/null'
- collision_kcut = 1
-/
-&INITIAL
- INIT_OPT = 'mom00_single_mode'
- init_amp = 1000
- ikx_init = 3
- iky_init = 3
-/
-&TIME_INTEGRATION
- numerical_scheme = 'RK4'
-/
diff --git a/testcases/ExB_shear_atomic_tests/fort_03.90 b/testcases/ExB_shear_atomic_tests/fort_03.90
deleted file mode 100644
index a8ac8dedc213b9ff63f4ad8c737a96a8ee88b29b..0000000000000000000000000000000000000000
--- a/testcases/ExB_shear_atomic_tests/fort_03.90
+++ /dev/null
@@ -1,105 +0,0 @@
-&BASIC
- nrun = 100000000
- dt = 0.001
- tmax = 1.0
- maxruntime = 356400
- job2load = -1
-/
-&GRID
- pmax = 0
- jmax = 0
- Nx = 96
- Lx = 120
- Ny = 32
- Ly = 80
- Nz = 1
- SG = .false.
- Nexc = 1
-/
-&GEOMETRY
- geom = 'zpinch'!'miller'
- q0 = 1.0
- shear = 0.0
- eps = 0.0
- kappa = 1
- s_kappa = 0
- delta = 0
- s_delta = 0
- zeta = 0
- s_zeta = 0
- parallel_bc = 'dirichlet'
- shift_y = 0
- Npol = 1
- PB_PHASE= .false.
-/
-&DIAGNOSTICS
- dtsave_0d = 0.05
- dtsave_1d = -1
- dtsave_2d = -1
- dtsave_3d = 0.02
- dtsave_5d = 100
- write_doubleprecision = .true.
- write_gamma = .true.
- write_hf = .true.
- write_phi = .true.
- write_Na00 = .true.
- write_Napj = .true.
- write_dens = .true.
- write_temp = .true.
-/
-&MODEL
-LINEARITY = 'nonlinear'
-RM_LD_T_EQ= .false.
- Na = 1
- mu_x = 0
- mu_y = 0
- N_HD = 4
- mu_z = 0
- HYP_V = 'hypcoll'
- mu_p = 0
- mu_j = 0
- nu = 0
- k_gB = 0
- k_cB = 0
- lambdaD = 0
- beta = 0.0
- ExBrate = 2.0
- ExB_NL_CORRECTION = .false.
- ADIAB_E = .true.
- ADIAB_I = .false.
- tau_i = 1
- MHD_PD = .false.
-/
-&CLOSURE
- hierarchy_closure='truncation'
- dmax =-1
- nonlinear_closure='truncation'
- nmax =-1
-/
-&SPECIES
- name_ = 'ions'
- tau_ = 1
- sigma_ = 1
- q_ = 1
- K_N_ = 0
- K_T_ = 0
-/
-&COLLISION
- collision_model = 'DG'
- GK_CO = .false.
- INTERSPECIES = .true.
- mat_file = '/home/ahoffman/gyacomo/iCa/null'
- collision_kcut = 1
-/
-&INITIAL
- INIT_OPT = 'mom00_modes'
- Nmodes = 1
-/
-&MODE
- I_ = 2
- J_ = 2
- amp_ = 1000
-/
-&TIME_INTEGRATION
- numerical_scheme = 'RK4'
-/
diff --git a/testcases/ExB_shear_atomic_tests/fort_04.90 b/testcases/ExB_shear_atomic_tests/fort_04.90
deleted file mode 100644
index efc03cda2d6195a59467de910e98384bf2a06167..0000000000000000000000000000000000000000
--- a/testcases/ExB_shear_atomic_tests/fort_04.90
+++ /dev/null
@@ -1,105 +0,0 @@
-&BASIC
- nrun = 100000000
- dt = 0.001
- tmax = 1.0
- maxruntime = 356400
- job2load = -1
-/
-&GRID
- pmax = 0
- jmax = 0
- Nx = 32
- Lx = 120
- Ny = 16
- Ly = 80
- Nz = 1
- SG = .false.
- Nexc = 1
-/
-&GEOMETRY
- geom = 'zpinch'!'miller'
- q0 = 1.0
- shear = 0.0
- eps = 0.0
- kappa = 1
- s_kappa = 0
- delta = 0
- s_delta = 0
- zeta = 0
- s_zeta = 0
- parallel_bc = 'dirichlet'
- shift_y = 0
- Npol = 1
- PB_PHASE= .false.
-/
-&DIAGNOSTICS
- dtsave_0d = 0.05
- dtsave_1d = -1
- dtsave_2d = -1
- dtsave_3d = 0.02
- dtsave_5d = 100
- write_doubleprecision = .true.
- write_gamma = .true.
- write_hf = .true.
- write_phi = .true.
- write_Na00 = .true.
- write_Napj = .true.
- write_dens = .true.
- write_temp = .true.
-/
-&MODEL
-LINEARITY = 'nonlinear'
-RM_LD_T_EQ= .false.
- Na = 1
- mu_x = 0
- mu_y = 0
- N_HD = 4
- mu_z = 0
- HYP_V = 'hypcoll'
- mu_p = 0
- mu_j = 0
- nu = 0
- k_gB = 0
- k_cB = 0
- lambdaD = 0
- beta = 0.0
- ExBrate = 2.0
- ExB_NL_CORRECTION = .true.
- ADIAB_E = .true.
- ADIAB_I = .false.
- tau_i = 1
- MHD_PD = .false.
-/
-&CLOSURE
- hierarchy_closure='truncation'
- dmax =-1
- nonlinear_closure='truncation'
- nmax =-1
-/
-&SPECIES
- name_ = 'ions'
- tau_ = 1
- sigma_ = 1
- q_ = 1
- K_N_ = 0
- K_T_ = 0
-/
-&COLLISION
- collision_model = 'DG'
- GK_CO = .false.
- INTERSPECIES = .true.
- mat_file = '/home/ahoffman/gyacomo/iCa/null'
- collision_kcut = 1
-/
-&INITIAL
- INIT_OPT = 'mom00_modes'
- Nmodes = 1
-/
-&MODE
- I_ = 2
- J_ = 2
- amp_ = 1000
-/
-&TIME_INTEGRATION
- numerical_scheme = 'RK4'
-/
diff --git a/testcases/ExB_shear_atomic_tests/fort_05.90 b/testcases/ExB_shear_atomic_tests/fort_05.90
deleted file mode 100644
index 5ca30d2f48108ce7f12212fef11ff951df57a474..0000000000000000000000000000000000000000
--- a/testcases/ExB_shear_atomic_tests/fort_05.90
+++ /dev/null
@@ -1,110 +0,0 @@
-&BASIC
- nrun = 100000000
- dt = 0.2
- tmax = 300
- maxruntime = 356400
- job2load = -1
-/
-&GRID
- pmax = 0
- jmax = 0
- Nx = 54
- Lx = 1257
- Ny = 32
- Ly = 628
- Nz = 1
- SG = .false.
- Nexc = 1
-/
-&GEOMETRY
- geom = 'zpinch'!'miller'
- q0 = 1.0
- shear = 0.0
- eps = 0.0
- kappa = 1
- s_kappa = 0
- delta = 0
- s_delta = 0
- zeta = 0
- s_zeta = 0
- parallel_bc = 'dirichlet'
- shift_y = 0
- Npol = 1
- PB_PHASE= .false.
-/
-&DIAGNOSTICS
- dtsave_0d = 0.5
- dtsave_1d = -1
- dtsave_2d = -1
- dtsave_3d = 1
- dtsave_5d = 100
- write_doubleprecision = .true.
- write_gamma = .true.
- write_hf = .true.
- write_phi = .true.
- write_Na00 = .true.
- write_Napj = .true.
- write_dens = .true.
- write_temp = .true.
-/
-&MODEL
-LINEARITY = 'nonlinear'
-RM_LD_T_EQ= .false.
- Na = 1
- mu_x = 0
- mu_y = 0
- N_HD = 4
- mu_z = 0
- HYP_V = 'hypcoll'
- mu_p = 0
- mu_j = 0
- nu = 0
- k_gB = 0
- k_cB = 0
- lambdaD = 0
- beta = 0.0
- ExBrate = 0.0016
- ExB_NL_CORRECTION = .f.
- ADIAB_E = .true.
- ADIAB_I = .false.
- tau_i = 1
- MHD_PD = .false.
-/
-&CLOSURE
- hierarchy_closure='truncation'
- dmax =-1
- nonlinear_closure='truncation'
- nmax =-1
-/
-&SPECIES
- name_ = 'ions'
- tau_ = 1
- sigma_ = 1
- q_ = 1
- K_N_ = 0
- K_T_ = 0
-/
-&COLLISION
- collision_model = 'DG'
- GK_CO = .false.
- INTERSPECIES = .true.
- mat_file = '/home/ahoffman/gyacomo/iCa/null'
- collision_kcut = 1
-/
-&INITIAL
- INIT_OPT = 'mom00_modes'
- Nmodes = 2
-/
-&MODE
- I_ = -12
- J_ = 3
- amp_ = 1
-/
-&MODE
- I_ = 14
- J_ = 5
- amp_ = 1
-/
-&TIME_INTEGRATION
- numerical_scheme = 'RK4'
-/
diff --git a/testcases/ExB_shear_atomic_tests/fort_06.90 b/testcases/ExB_shear_atomic_tests/fort_06.90
deleted file mode 100644
index c0ea7e22d4b66b7313667bfebcf5e4b36e5aa29b..0000000000000000000000000000000000000000
--- a/testcases/ExB_shear_atomic_tests/fort_06.90
+++ /dev/null
@@ -1,110 +0,0 @@
-&BASIC
- nrun = 100000000
- dt = 0.2
- tmax = 300
- maxruntime = 356400
- job2load = -1
-/
-&GRID
- pmax = 0
- jmax = 0
- Nx = 54
- Lx = 1257
- Ny = 32
- Ly = 628
- Nz = 1
- SG = .false.
- Nexc = 1
-/
-&GEOMETRY
- geom = 'zpinch'!'miller'
- q0 = 1.0
- shear = 0.0
- eps = 0.0
- kappa = 1
- s_kappa = 0
- delta = 0
- s_delta = 0
- zeta = 0
- s_zeta = 0
- parallel_bc = 'dirichlet'
- shift_y = 0
- Npol = 1
- PB_PHASE= .false.
-/
-&DIAGNOSTICS
- dtsave_0d = 0.5
- dtsave_1d = -1
- dtsave_2d = -1
- dtsave_3d = 1
- dtsave_5d = 100
- write_doubleprecision = .true.
- write_gamma = .true.
- write_hf = .true.
- write_phi = .true.
- write_Na00 = .true.
- write_Napj = .true.
- write_dens = .true.
- write_temp = .true.
-/
-&MODEL
-LINEARITY = 'nonlinear'
-RM_LD_T_EQ= .false.
- Na = 1
- mu_x = 0
- mu_y = 0
- N_HD = 4
- mu_z = 0
- HYP_V = 'hypcoll'
- mu_p = 0
- mu_j = 0
- nu = 0
- k_gB = 0
- k_cB = 0
- lambdaD = 0
- beta = 0.0
- ExBrate = 0.0016
- ExB_NL_CORRECTION = .t.
- ADIAB_E = .true.
- ADIAB_I = .false.
- tau_i = 1
- MHD_PD = .false.
-/
-&CLOSURE
- hierarchy_closure='truncation'
- dmax =-1
- nonlinear_closure='truncation'
- nmax =-1
-/
-&SPECIES
- name_ = 'ions'
- tau_ = 1
- sigma_ = 1
- q_ = 1
- K_N_ = 0
- K_T_ = 0
-/
-&COLLISION
- collision_model = 'DG'
- GK_CO = .false.
- INTERSPECIES = .true.
- mat_file = '/home/ahoffman/gyacomo/iCa/null'
- collision_kcut = 1
-/
-&INITIAL
- INIT_OPT = 'mom00_modes'
- Nmodes = 2
-/
-&MODE
- I_ = -12
- J_ = 3
- amp_ = 1
-/
-&MODE
- I_ = 14
- J_ = 5
- amp_ = 1
-/
-&TIME_INTEGRATION
- numerical_scheme = 'RK4'
-/
diff --git a/testcases/ExB_shear_atomic_tests/fort_07.90 b/testcases/ExB_shear_atomic_tests/fort_07.90
deleted file mode 100644
index 7675a5e8eca6ea3b03eb3a8532c37fac78b9ac82..0000000000000000000000000000000000000000
--- a/testcases/ExB_shear_atomic_tests/fort_07.90
+++ /dev/null
@@ -1,113 +0,0 @@
-&BASIC
- nrun = 1!00000000
- dt = 100
- tmax = 300
- maxruntime = 356400
- job2load = -1
-/
-&GRID
- pmax = 0
- jmax = 0
- Nx = 128
- Lx = 120!1257
- Ny = 64
- Ly = 70!628
- Nz = 1
- SG = .false.
- Nexc = 1
-/
-&GEOMETRY
- geom = 'zpinch'!'miller'
- q0 = 1.0
- shear = 0.0
- eps = 0.0
- kappa = 1
- s_kappa = 0
- delta = 0
- s_delta = 0
- zeta = 0
- s_zeta = 0
- parallel_bc = 'dirichlet'
- shift_y = 0
- Npol = 1
- PB_PHASE= .false.
-/
-&DIAGNOSTICS
- dtsave_0d = 0.5
- dtsave_1d = -1
- dtsave_2d = -1
- dtsave_3d = 0.5
- dtsave_5d = 100
- write_doubleprecision = .true.
- write_gamma = .true.
- write_hf = .true.
- write_phi = .true.
- write_Na00 = .true.
- write_Napj = .true.
- write_dens = .true.
- write_temp = .true.
-/
-&MODEL
-LINEARITY = 'nonlinear'
-RM_LD_T_EQ= .false.
- Na = 1
- mu_x = 0
- mu_y = 0
- N_HD = 4
- mu_z = 0
- HYP_V = 'hypcoll'
- mu_p = 0
- mu_j = 0
- nu = 0
- k_gB = 0
- k_cB = 0
- lambdaD = 0
- beta = 0.0
- ExBrate = 0.00
- ExB_NL_CORRECTION = .f.
- ADIAB_E = .t.
- ADIAB_I = .false.
- tau_i = 1
- MHD_PD = .false.
-/
-&CLOSURE
- hierarchy_closure='truncation'
- dmax =-1
- nonlinear_closure='truncation'
- nmax =-1
-/
-&SPECIES
- name_ = 'ions'
- tau_ = 1
- sigma_ = 1
- q_ = 1
- K_N_ = 0
- K_T_ = 0
-/
-&SPECIES
- name_ = 'electrons'
- tau_ = 1
- sigma_ = 0.0233
- q_ = -1
- K_N_ = 0
- K_T_ = 0
-/
-&COLLISION
- collision_model = 'DG'
- GK_CO = .false.
- INTERSPECIES = .true.
- mat_file = '/home/ahoffman/gyacomo/iCa/null'
- collision_kcut = 1
-/
-&INITIAL
- INIT_OPT = 'mom00_modes'
- Nmodes = 1
-/
-&MODE
- I_ = -4
- J_ = 4
- amp_ = 100
-/
-&TIME_INTEGRATION
- numerical_scheme = 'EE'
-/
diff --git a/testcases/ExB_shear_demo/2D_Z_pinch/background_Er/fort_01.90 b/testcases/ExB_shear_demo/2D_Z_pinch/background_Er/fort_01.90
index ed6756860ba2caff661e5992d3000c7811335c7f..d26c420e20af9b3c968a6e05dcf8ca3a2f627029 100644
--- a/testcases/ExB_shear_demo/2D_Z_pinch/background_Er/fort_01.90
+++ b/testcases/ExB_shear_demo/2D_Z_pinch/background_Er/fort_01.90
@@ -50,6 +50,7 @@
ADIAB_E = .f.
tau_i = 1.0
ExBrate = 0.5
+ ikxZF = 1
/
&CLOSURE
hierarchy_closure='truncation'
diff --git a/testcases/ExB_shear_demo/2D_Z_pinch/fort_01.90 b/testcases/ExB_shear_demo/2D_Z_pinch/fort_01.90
new file mode 100644
index 0000000000000000000000000000000000000000..5899fc021b571093f2888bc11c17d898f07800cf
--- /dev/null
+++ b/testcases/ExB_shear_demo/2D_Z_pinch/fort_01.90
@@ -0,0 +1,91 @@
+&BASIC
+ nrun = 1e6
+ dt = 0.05
+ tmax = 200
+ maxruntime = 72000
+ job2load = 0
+/
+&GRID
+ pmax = 2
+ jmax = 1
+ Nx = 128
+ Lx = 200
+ Ny = 48
+ Ly = 60
+ Nz = 1
+ SG = .f.
+ Nexc = 1
+/
+&GEOMETRY
+ geom = 'z-pinch'
+/
+&DIAGNOSTICS
+ dtsave_0d = 1
+ dtsave_1d = -1
+ dtsave_2d = 0.5
+ dtsave_3d = 0.5
+ dtsave_5d = 100
+ write_doubleprecision = .f.
+ write_gamma = .t.
+ write_hf = .t.
+ write_phi = .t.
+ write_Na00 = .t.
+ write_Napj = .t.
+ write_dens = .t.
+ write_fvel = .t.
+ write_temp = .t.
+/
+&MODEL
+ LINEARITY = 'nonlinear'
+ Na = 2 ! number of species
+ mu_x = 1.0
+ mu_y = 1.0
+ N_HD = 4
+ mu_z = 0.0
+ HYP_V = 'hypcoll'
+ mu_p = 0.0
+ mu_j = 0.0
+ nu = 0.1
+ beta = 0.0
+ ADIAB_E = .f.
+ tau_i = 1.0
+ ExBrate = 0
+/
+&CLOSURE
+ hierarchy_closure='truncation'
+ !hierarchy_closure='max_degree'
+ dmax = 2
+ nonlinear_closure='anti_laguerre_aliasing' !(truncation,full_sum,anti_laguerre_aliasing)
+ nmax = -1
+/
+&SPECIES
+ ! ions
+ name_ = 'ions'
+ tau_ = 1.0
+ sigma_= 1.0
+ q_ = 1.0
+ k_N_ = 2.0
+ k_T_ = 0.4
+/
+&SPECIES
+ ! electrons
+ name_ = 'electrons'
+ tau_ = 1.0
+ sigma_= 0.023338
+ q_ =-1.0
+ k_N_ = 2.0
+ k_T_ = 0.4
+/
+&COLLISION
+ collision_model = 'DG' !DG/SG/PA/LD (dougherty, sugama, pitch angle, landau)
+ GK_CO = .t.
+/
+&INITIAL
+ INIT_OPT = 'phi' !(phi,blob)
+ init_background = 0.0
+ init_noiselvl = 0.005
+ iseed = 42
+/
+&TIME_INTEGRATION
+ numerical_scheme = 'RK4'
+/
diff --git a/testcases/cyclone_example/fort.90 b/testcases/cyclone_example/fort.90
deleted file mode 100644
index cd59e47f8a2d402ad68f7176827736709a4646e3..0000000000000000000000000000000000000000
--- a/testcases/cyclone_example/fort.90
+++ /dev/null
@@ -1,96 +0,0 @@
-&BASIC
- nrun = 99999999
- dt = 0.01
- tmax = 1
- maxruntime = 72000
- job2load = -1
-/
-&GRID
- pmax = 2
- jmax = 1
- Nx = 64
- Lx = 120
- Ny = 48
- Ly = 120
- Nz = 16
- SG = .f.
- Nexc = 0
-/
-&GEOMETRY
- geom = 's-alpha'
- !geom = 'miller'
- q0 = 1.4
- shear = 0.8
- eps = 0.18
- kappa = 1.0
- s_kappa= 0.0
- delta = 0.0
- s_delta= 0.0
- zeta = 0.0
- s_zeta = 0.0
- parallel_bc = 'dirichlet'
- shift_y= 0.0
-/
-&DIAGNOSTICS
- dtsave_0d = 1
- dtsave_1d = -1
- dtsave_2d = -1
- dtsave_3d = 1
- dtsave_5d = 20
- write_doubleprecision = .f.
- write_gamma = .t.
- write_hf = .t.
- write_phi = .t.
- write_Na00 = .t.
- write_Napj = .t.
- write_dens = .t.
- write_fvel = .t.
- write_temp = .t.
-/
-&MODEL
- LINEARITY = 'nonlinear'
- Na = 1 ! number of species
- mu_x = 0.0
- mu_y = 0.0
- N_HD = 4
- mu_z = 1.0
- HYP_V = 'hypcoll'
- mu_p = 0.0
- mu_j = 0.0
- nu = 0.05
- beta = 0.0
- ADIAB_E = .t.
-/
-&CLOSURE
- hierarchy_closure='truncation'
- dmax = -1
- nonlinear_closure='truncation'
- nmax = 0
-/
-&SPECIES
- ! ions
- name_ = 'ions'
- tau_ = 1.0
- sigma_= 1.0
- q_ = 1.0
- k_N_ = 2.22
- k_T_ = 6.96
-/
-
-&COLLISION
- collision_model = 'DG' !DG/SG/PA/LD (dougherty, sugama, pitch angle, landau)
- GK_CO = .f.
- INTERSPECIES = .true.
- mat_file = 'gk_sugama_P_20_J_10_N_150_kpm_8.0.h5'
-/
-&INITIAL
- INIT_OPT = 'blob'
- ACT_ON_MODES = 'donothing'
- init_background = 0.0
- init_noiselvl = 0.005
- iseed = 42
-/
-&TIME_INTEGRATION
- !numerical_scheme = 'RK4'
- numerical_scheme = 'SSP_RK3'
-/
diff --git a/testcases/cyclone_example/fort_00.90 b/testcases/cyclone_example/fort_00.90
index efb2eeef82f35524268bb17d9b0a81c5623bba70..ce02b619f0d1394c95dc6ecde45bdf99934531b2 100644
--- a/testcases/cyclone_example/fort_00.90
+++ b/testcases/cyclone_example/fort_00.90
@@ -1,12 +1,12 @@
&BASIC
nrun = 99999999
dt = 0.01
- tmax = 50
+ tmax = 5
maxruntime = 72000
job2load = -1
/
&GRID
- pmax = 2
+ pmax = 4
jmax = 1
Nx = 64
Lx = 120
@@ -32,7 +32,7 @@
shift_y= 0.0
/
&DIAGNOSTICS
- dtsave_0d = 1
+ dtsave_0d = 0.1
dtsave_1d = -1
dtsave_2d = -1
dtsave_3d = 1
@@ -91,6 +91,6 @@
iseed = 42
/
&TIME_INTEGRATION
- !numerical_scheme = 'RK4'
- numerical_scheme = 'SSP_RK3'
+ numerical_scheme = 'RK4'
+ !numerical_scheme = 'SSP_RK3'
/
diff --git a/testcases/cyclone_example/fort_01.90 b/testcases/cyclone_example/fort_01.90
deleted file mode 100644
index 8b79aedbc5b91a761504c1ee9ebd59d742dcd422..0000000000000000000000000000000000000000
--- a/testcases/cyclone_example/fort_01.90
+++ /dev/null
@@ -1,96 +0,0 @@
-&BASIC
- nrun = 1!99999999
- dt = 0.01
- tmax = 2
- maxruntime = 72000
- job2load = 0
-/
-&GRID
- pmax = 2
- jmax = 1
- Nx = 64
- Lx = 120
- Ny = 48
- Ly = 120
- Nz = 16
- SG = .f.
- Nexc = 0
-/
-&GEOMETRY
- geom = 's-alpha'
- !geom = 'miller'
- q0 = 1.4
- shear = 0.8
- eps = 0.18
- kappa = 1.0
- s_kappa= 0.0
- delta = 0.0
- s_delta= 0.0
- zeta = 0.0
- s_zeta = 0.0
- parallel_bc = 'dirichlet'
- shift_y= 0.0
-/
-&DIAGNOSTICS
- dtsave_0d = 1
- dtsave_1d = -1
- dtsave_2d = -1
- dtsave_3d = 1
- dtsave_5d = 20
- write_doubleprecision = .f.
- write_gamma = .t.
- write_hf = .t.
- write_phi = .t.
- write_Na00 = .t.
- write_Napj = .t.
- write_dens = .t.
- write_fvel = .t.
- write_temp = .t.
-/
-&MODEL
- LINEARITY = 'nonlinear'
- Na = 1 ! number of species
- mu_x = 0.0
- mu_y = 0.0
- N_HD = 4
- mu_z = 1.0
- HYP_V = 'hypcoll'
- mu_p = 0.0
- mu_j = 0.0
- nu = 0.05
- beta = 0.0
- ADIAB_E = .t.
-/
-&CLOSURE
- hierarchy_closure='truncation'
- dmax = -1
- nonlinear_closure='truncation'
- nmax = 0
-/
-&SPECIES
- ! ions
- name_ = 'ions'
- tau_ = 1.0
- sigma_= 1.0
- q_ = 1.0
- k_N_ = 2.22
- k_T_ = 6.96
-/
-
-&COLLISION
- collision_model = 'DG' !DG/SG/PA/LD (dougherty, sugama, pitch angle, landau)
- GK_CO = .f.
- INTERSPECIES = .true.
- mat_file = 'gk_sugama_P_20_J_10_N_150_kpm_8.0.h5'
-/
-&INITIAL
- INIT_OPT = 'blob'
- ACT_ON_MODES = 'donothing'
- init_background = 0.0
- init_noiselvl = 0.005
- iseed = 42
-/
-&TIME_INTEGRATION
- !numerical_scheme = 'RK4'
- numerical_scheme = 'SSP_RK3'
-/
diff --git a/testcases/zpinch_example/plot_transport.py b/testcases/zpinch_example/plot_transport.py
new file mode 100644
index 0000000000000000000000000000000000000000..87b58c62b9297d58b40a2ebf1b074df597e9931d
--- /dev/null
+++ b/testcases/zpinch_example/plot_transport.py
@@ -0,0 +1,75 @@
+import sys
+import h5py
+import numpy as np
+import matplotlib.pyplot as plt
+
+def load_transport_data(file_path):
+ with h5py.File(file_path, 'r') as file:
+ # Check if the group exists
+ group_path = "/data/var0d"
+ if group_path not in file:
+ print(f"Group '{group_path}' not found in the HDF5 file.")
+ return None
+
+ group = file[group_path]
+ array_data = {key: np.array(group[key]) for key in group.keys()}
+
+ return array_data
+
+def plot_time_traces(time, data, key):
+ plt.plot(time, data, label=key)
+ plt.xlabel('Time')
+ plt.ylabel('Value')
+ plt.legend()
+ plt.show()
+
+def read_namelist_from_h5(file_path, namelist_path):
+ with h5py.File(file_path, 'r') as h5_file:
+ # Check if the namelist path exists
+ if namelist_path not in h5_file:
+ print(f"Namelist path '{namelist_path}' not found in the HDF5 file.")
+ return None
+
+ namelist_group = h5_file[namelist_path]
+
+ # Create a dictionary to store the namelist parameters
+ namelist_params = {}
+
+ # Iterate through items in the group
+ for key, value in namelist_group.items():
+ # Check if the item is a dataset (parameter)
+ if isinstance(value, h5py.Dataset):
+ namelist_params[key] = value[()] # Add the parameter to the dictionary
+
+ return namelist_params
+
+# Check for the correct number of command-line arguments
+if len(sys.argv) != 2:
+ print("Usage: python script.py <file_path>")
+ sys.exit(1)
+
+# Get file path from command-line arguments
+file_path = sys.argv[1]
+
+namelist_params = read_namelist_from_h5(file_path, "/files/STDIN.00")
+
+# Print the namelist parameters
+if namelist_params is not None:
+ print("Namelist Parameters:")
+ for key, value in namelist_params.items():
+ print(f"{key}: {value}")
+
+# Load all data in the group /data/var0d
+loaded_data = load_transport_data(file_path)
+time = loaded_data['time']
+del loaded_data['time']
+del loaded_data['cstep']
+
+# Plot it
+if loaded_data is not None:
+ # Print all arrays in the loaded group
+ print(f"Arrays loaded from '{file_path}' in group '/data/var0d':")
+ for key, value in loaded_data.items():
+ half_length = len(value) // 2
+ trace = value[:half_length]
+ plot_time_traces(time,trace,key)