Fix chromatography system settings

This commit fixes some model settings as well as the refinement unit ID
for the cyclic setting

src/test_cadet_core/2025_frandsen_et_al_continuousChrom.py

@@ -106,13 +106,13 @@ def json_to_csv(json_file, csv_file, subgroup_path, ignore_data):
     # ignore_data not required since desired columns can be picked in latex
     ignore_data = []#['$N_d$', 'Min. value', 'DoF', 'Bulk DoF']
 
-    json_file = str(output_path) + r"/convergence_acyclicSystem1_LRM_linBnd_1comp.json"  # Input JSON file
-    csv_file = str(output_path) + r"/convergence_acyclicSystem1_LRM_linBnd_1comp.csv"  # Output CSV file
+    json_file = str(output_path) + r"/convergence_acyclicSystem1_LRMP_linBnd_1comp.json"  # Input JSON file
+    csv_file = str(output_path) + r"/convergence_acyclicSystem1_LRMP_linBnd_1comp.csv"  # Output CSV file
     json_to_csv(json_file, csv_file, subgroup_path, ignore_data)
 
     subgroup_path = ['convergence', 'DG_P2', 'outlet']  # Path to the subgroup in the JSON file
-    json_file = str(output_path) + r"/convergence_cyclicSystem1_LRM_linBnd_1comp.json"  # Input JSON file
-    csv_file = str(output_path) + r"/convergence_cyclicSystem1_LRM_linBnd_1comp.csv"  # Output CSV file
+    json_file = str(output_path) + r"/convergence_cyclicSystem1_LRMP_linBnd_1comp.json"  # Input JSON file
+    csv_file = str(output_path) + r"/convergence_cyclicSystem1_LRMP_linBnd_1comp.csv"  # Output CSV file
     json_to_csv(json_file, csv_file, subgroup_path, ignore_data)
 
 

src/test_cadet_core/chrom_systems.py

@@ -58,10 +58,10 @@ def chromatography_systems_tests(n_jobs, database_path, small_test,
 
     if analytical_reference:
         ref = convergence.get_solution(
-            reference_data_path+'/ref_cyclicSystem1_LRM_linBnd_1comp.h5', unit='unit_'+unit_IDs[0])
+            reference_data_path+'/ref_cyclicSystem1_LRMP_linBnd_1comp.h5', unit='unit_'+unit_IDs[0])
         ref_files = [[ref]]
 
-    config_names = ['cyclicSystem1_LRM_linBnd_1comp']
+    config_names = ['cyclicSystem1_LRMP_linBnd_1comp']
 
     # %% run convergence analysis
 
@@ -81,7 +81,7 @@ def chromatography_systems_tests(n_jobs, database_path, small_test,
         idas_abstol=idas_abstol,
         n_jobs=n_jobs,
         rerun_sims=True,
-        system_refinement_IDs=['002', '003'],
+        system_refinement_IDs=['001', '002'],
         analytical_reference=analytical_reference
     )
 
@@ -114,13 +114,13 @@ def chromatography_systems_tests(n_jobs, database_path, small_test,
      # we compare the simulated outlet of unit 006 with the analytical
      # solution of the combined outlets of unit 004 and 005
         ref = convergence.get_solution(
-            reference_data_path+'/ref_acyclicSystem1_LRM_linBnd_1comp.h5', unit='unit_004')
+            reference_data_path+'/ref_acyclicSystem1_LRMP_linBnd_1comp.h5', unit='unit_004')
         ref = 0.5 * ref + 0.5 * convergence.get_solution(
-            reference_data_path+'/ref_acyclicSystem1_LRM_linBnd_1comp.h5', unit='unit_005')
+            reference_data_path+'/ref_acyclicSystem1_LRMP_linBnd_1comp.h5', unit='unit_005')
 
         ref_files = [[ref]]
 
-    config_names = ['acyclicSystem1_LRM_linBnd_1comp']
+    config_names = ['acyclicSystem1_LRMP_linBnd_1comp']
 
     # %% run convergence analysis
 

src/test_cadet_core/settings_columnSystems.py

@@ -50,7 +50,6 @@ def Cyclic_model1(nelem, polydeg, exactInt, analytical_reference=False):
     Cyclic_model.root.input.model.unit_001.par_porosity = 0.75
     Cyclic_model.root.input.model.unit_001.col_dispersion = 2e-7
     Cyclic_model.root.input.model.unit_001.col_length = 1.4e-2
-    # From Lubke2007, is not important
     Cyclic_model.root.input.model.unit_001.cross_section_area = 1
     Cyclic_model.root.input.model.unit_001.film_diffusion = 6.9e-6
     Cyclic_model.root.input.model.unit_001.par_radius = 45e-6
@@ -97,10 +96,10 @@ def Cyclic_model1(nelem, polydeg, exactInt, analytical_reference=False):
         Cyclic_model.root.input.model.unit_001)
 
     # Unit LRMP2
-    Cyclic_model.root.input.model.unit_003.adsorption.is_kinetic = False    # Kinetic binding
-    Cyclic_model.root.input.model.unit_003.adsorption.LIN_KA = [
+    Cyclic_model.root.input.model.unit_002.adsorption.is_kinetic = False    # Kinetic binding
+    Cyclic_model.root.input.model.unit_002.adsorption.LIN_KA = [
         35.5]  # m^3 / (mol * s)   (mobile phase)
-    Cyclic_model.root.input.model.unit_003.adsorption.LIN_KD = [
+    Cyclic_model.root.input.model.unit_002.adsorption.LIN_KD = [
         1]      # 1 / s (desorption)
 
     # To write out last output to check for steady state
@@ -206,7 +205,6 @@ def Acyclic_model1(nelem, polydeg, exactInt, analytical_reference=False):
     Acyclic_model.root.input.model.unit_002.par_porosity = 0.75
     Acyclic_model.root.input.model.unit_002.col_dispersion = 2e-7
     Acyclic_model.root.input.model.unit_002.col_length = 1.4e-2
-    # From Lubke2007, is not important
     Acyclic_model.root.input.model.unit_002.cross_section_area = 1
     Acyclic_model.root.input.model.unit_002.film_diffusion = 6.9e-6
     Acyclic_model.root.input.model.unit_002.par_radius = 45e-6
@@ -272,9 +270,9 @@ def Acyclic_model1(nelem, polydeg, exactInt, analytical_reference=False):
         1]      # 1 / s (desorption)
 
     # Unit LRMP6
-    Acyclic_model.root.input.model.unit_004.adsorption.LIN_KA = [
+    Acyclic_model.root.input.model.unit_005.adsorption.LIN_KA = [
         4.55]  # m^3 / (mol * s)   (mobile phase)
-    Acyclic_model.root.input.model.unit_004.adsorption.LIN_KD = [
+    Acyclic_model.root.input.model.unit_005.adsorption.LIN_KD = [
         0.12]      # 1 / s (desorption)
 
     # To write out last output to check for steady state
@@ -290,7 +288,7 @@ def Acyclic_model1(nelem, polydeg, exactInt, analytical_reference=False):
     Acyclic_model.root.input.model.unit_000.sec_000.const_coeff = [
         1]  # Inlet flowrate concentration
     Acyclic_model.root.input.model.unit_001.sec_000.const_coeff = [
-        0]  # Desorbent stream
+        1]  # Desorbent stream
 
     Acyclic_model.root.input.model.unit_000.sec_001.const_coeff = [
         0]  # Inlet flowrate concentration