Corrected AM reaction rate, included option to choose CCDischarge or …

…CCCV, resolves #29
BattMoTeam · Mar 5, 2024 · e8ba95e · e8ba95e
1 parent a287ec5
commit e8ba95e
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Showing 18 changed files with 201 additions and 165 deletions.
diff --git a/flask_api/Dockerfile b/flask_api/Dockerfile
@@ -19,8 +19,9 @@ RUN jill install 1.10.0 --confirm
 # RUN julia --project=/app -e 'using Pkg; Pkg.precompile();'
 
 RUN julia -e 'using Pkg; Pkg.add(PackageSpec(;name = "PythonCall",version = "0.9.14"))'
-RUN julia -e 'using Pkg; Pkg.add(PackageSpec(;name = "JSON",version = "0.21.4"))'
 RUN julia -e 'using Pkg; Pkg.add(PackageSpec(;url="https://github.com/BattMoTeam/BattMo.jl.git", rev="cccv"))'
+RUN julia -e 'using Pkg; Pkg.add(PackageSpec(;name = "JSON",version = "0.21.4"))'
+
 #RUN julia -e 'using Pkg; Pkg.add(PackageSpec(;name = "BattMo",version = "0.1.6"))'
 #RUN julia -e 'using Pkg; Pkg.add("BattMo")'
 RUN julia -e 'using Pkg; Pkg.add(PackageSpec(;name = "Jutul",version = "0.2.23"))'

diff --git a/flask_api/api.py b/flask_api/api.py
@@ -35,9 +35,15 @@ def run_julia(q_in,q_out):
 
             # Define the Julia code to execute
             julia_code = f"runP2DBattery.runP2DBatt(\"{file_name}\")"
+
+            # try:
             log_messages, number_of_states, cell_voltage, cell_current, time_values, negative_electrode_grid, negative_electrode_grid_bc, electrolyte_grid, electrolyte_grid_bc, positive_electrode_grid, positive_electrode_grid_bc, negative_electrode_concentration, electrolyte_concentration, positive_electrode_concentration, negative_electrode_potential, electrolyte_potential, positive_electrode_potential = jl.seval(julia_code)
 
             print("The simulation has completed {} time steps.".format(number_of_states))
+            # except:
+            #     print("The simulation has failed.")
+            #     log_messages, number_of_states, cell_voltage, cell_current, time_values, negative_electrode_grid, negative_electrode_grid_bc, electrolyte_grid, electrolyte_grid_bc, positive_electrode_grid, positive_electrode_grid_bc, negative_electrode_concentration, electrolyte_concentration, positive_electrode_concentration, negative_electrode_potential, electrolyte_potential, positive_electrode_potential = ([0],[0],[0],[0],[0],[0],[0],[0],[0],[0],[0],[0],[0],[0],[0],[0],[0])
+            #     return log_messages, number_of_states, cell_voltage, cell_current, time_values, negative_electrode_grid, negative_electrode_grid_bc, electrolyte_grid, electrolyte_grid_bc, positive_electrode_grid, positive_electrode_grid_bc, negative_electrode_concentration, electrolyte_concentration, positive_electrode_concentration, negative_electrode_potential, electrolyte_potential, positive_electrode_potential
 
             # Converting data to python objects
             negative_electrode_concentration = [jl.Py(subarray).to_numpy() for subarray in negative_electrode_concentration],

diff --git a/streamlit/app_scripts/app_calculations.py b/streamlit/app_scripts/app_calculations.py
@@ -21,7 +21,7 @@ def validate_volume_fraction(vf_sum,category_display_name,_tab):
     for id, value in vf_sum.items():
         vf_summing += value
     if vf_summing != 1.0:
-        _tab.warning("The sum of the '%s' material volume fractions is not equal to 1." % (category_display_name))
+        _tab.warning("The sum of the '%s' material mass fractions is not equal to 1." % (category_display_name))
 
 @st.cache_data
 def calc_density_mix(vf, density):

diff --git a/streamlit/app_scripts/app_view.py b/streamlit/app_scripts/app_view.py
diff --git a/streamlit/app_scripts/match_json_LD.py b/streamlit/app_scripts/match_json_LD.py
@@ -17,6 +17,7 @@ def get_dict_from_has_quantitative(has_quantitative):
     for item in has_quantitative:
 
         if type(item) != str:
+
             item_value_type = item.get("value", {}).get("@type", None)
             if item_value_type == "emmo:Numerical":
                 new_dict[item.get("label")] = {
@@ -156,7 +157,7 @@ def get_batt_mo_dict_from_gui_dict(gui_dict):
         "NegativeElectrode": {
             "Coating":{
                 "thickness": json_ld.ne.properties.get("coating_thickness").get("value")*10**(-6),
-                "N": json_ld.ne.am.get("number_of_discrete_cells_electrode").get("value"),
+                "N": json_ld.ne.am.get("number_of_discrete_cells_particle_radius").get("value"),
                 "effectiveDensity": 1900, # calculated_values["effective_density"]["negative_electrode"],
                 "bruggemanCoefficient": json_ld.ne.properties.get("bruggeman_coefficient").get("value"),
                 "ActiveMaterial": {
@@ -217,7 +218,7 @@ def get_batt_mo_dict_from_gui_dict(gui_dict):
         "PositiveElectrode": {
             "Coating":{
                 "thickness": json_ld.pe.properties.get("coating_thickness").get("value")*10**(-6),
-                "N": json_ld.pe.am.get("number_of_discrete_cells_electrode").get("value"),
+                "N": json_ld.pe.am.get("number_of_discrete_cells_particle_radius").get("value"),
                 "effectiveDensity": 3500, #calculated_values["effective_density"]["positive_electrode"],
                 "bruggemanCoefficient": json_ld.pe.properties.get("bruggeman_coefficient").get("value"),
                 "ActiveMaterial": {
@@ -324,8 +325,8 @@ def get_batt_mo_dict_from_gui_dict(gui_dict):
         "Control": {
             "controlPolicy": json_ld.protocol.get("protocol_name"),
             "initialControl": json_ld.protocol.get("initial_step_type"),
-            #"numberOfCycles": json_ld.protocol.get("number_of_cycles").get("value"),
-            #"CRate": json_ld.protocol.get("c_rate").get("value"),
+            "numberOfCycles": json_ld.protocol.get("number_of_cycles").get("value"),
+            "CRate": json_ld.protocol.get("c_rate").get("value"),
             "DRate": json_ld.protocol.get("d_rate").get("value"),
             "lowerCutoffVoltage": json_ld.protocol.get("lower_cutoff_voltage").get("value"),
             "rampupTime" : 0.1,

diff --git a/streamlit/database/BattMo_gui.db b/streamlit/database/BattMo_gui.db
diff --git a/...ter_sets/experimental_data/negative_electrode/active_material/Graphite_SiOx_Chen2020.json b/...ter_sets/experimental_data/negative_electrode/active_material/Graphite_SiOx_Chen2020.json
@@ -9,7 +9,7 @@
        "density": 2260.0,
        "number_of_electrons_transferred": 1,
        "activation_energy_of_reaction": 35000.0,
-       "reaction_rate_constant": 6.48e-7,
+       "reaction_rate_constant": 6.716e-12,
        "maximum_lithium_stoichiometry": 0.9014,
        "minimum_lithium_stoichiometry": 0.0279,
        "open_circuit_potential": {

diff --git a/...sets/experimental_data/negative_electrode/active_material/battmo_json_ne_am_advanced.json b/...sets/experimental_data/negative_electrode/active_material/battmo_json_ne_am_advanced.json
@@ -8,7 +8,6 @@
       "activation_energy_of_diffusion": 5e3,
       "diffusion_pre_exponential_factor": 3.9e-14,
       "particle_radius": 1e-6,
-      "number_of_discrete_cells_electrode": 10,
       "number_of_discrete_cells_particle_radius": 10,
       "specific_heat_capacity": 632,
       "thermal_conductivity": 1.04

diff --git a/.../parameter_sets/experimental_data/positive_electrode/active_material/NMC811_Chen2020.json b/.../parameter_sets/experimental_data/positive_electrode/active_material/NMC811_Chen2020.json
@@ -9,7 +9,7 @@
        "density": 4950,
        "number_of_electrons_transferred": 1,
        "activation_energy_of_reaction":17800,
-       "reaction_rate_constant": 3.42e-6,
+       "reaction_rate_constant": 3.545e-11,
        "maximum_lithium_stoichiometry": 0.2661,
        "minimum_lithium_stoichiometry": 0.9084,
        "open_circuit_potential": {

diff --git a/...sets/experimental_data/positive_electrode/active_material/battmo_json_pe_am_advanced.json b/...sets/experimental_data/positive_electrode/active_material/battmo_json_pe_am_advanced.json
@@ -8,7 +8,6 @@
       "activation_energy_of_diffusion": 5e3,
       "diffusion_pre_exponential_factor": 1e-14,
       "particle_radius": 1e-6,
-      "number_of_discrete_cells_electrode": 10,
       "number_of_discrete_cells_particle_radius": 10,
       "specific_heat_capacity": 700,
       "thermal_conductivity": 2.1

diff --git a/streamlit/database/recources/parameter_sets/experimental_data/protocol/CCCV.json b/streamlit/database/recources/parameter_sets/experimental_data/protocol/CCCV.json
@@ -5,7 +5,6 @@
    "material": false,
    "Header": {},
    "Parameters": {
-      "protocol_name": "CCDischarge",
       "initial_step_type": "discharging",
       "number_of_cycles": 1,
       "d_rate": 1,

diff --git a/streamlit/database/recources/parameter_sets/experimental_data/protocol/CCDischarge.json b/streamlit/database/recources/parameter_sets/experimental_data/protocol/CCDischarge.json
@@ -0,0 +1,15 @@
+{
+    "Name": "CCDischarge",
+    "Category": "protocol",
+    "component": "protocol_properties",
+    "material": false,
+    "Header": {},
+    "Parameters": {
+       "initial_step_type": "discharging",
+       "d_rate": 1,
+       "lower_cutoff_voltage": 2.4,
+       "upper_cutoff_voltage": 4.1,
+       "d_idt_limit": 0.01,
+       "d_edt_limit": 0.01
+    }
+ }
diff --git a/streamlit/database/recources/parameter_sets/meta_data/active_material_full_template.json b/streamlit/database/recources/parameter_sets/meta_data/active_material_full_template.json
@@ -223,7 +223,7 @@
          "display_name": "Diffusion pre exponential factor"
       },
       "number_of_discrete_cells_electrode": {
-         "model_name": "p2d_p3d_p4d",
+         "model_name": "p3d_p4d",
          "par_class": "non_material",
          "difficulty": "advanced",
          "context_type": "emmo:NumberOfEntities",

diff --git a/streamlit/database/recources/parameter_sets/meta_data/protocol_full_template.json b/streamlit/database/recources/parameter_sets/meta_data/protocol_full_template.json
@@ -2,15 +2,6 @@
    "Type": "template",
    "Name": "protocol_full_template",
    "Parameters": {
-      "protocol_name": {
-         "model_name": "p2d_p3d_p4d",
-         "par_class": "non_material",
-         "difficulty": "advanced",
-         "description": "",
-         "is_shown_to_user": true,
-         "type": "str",
-         "display_name": "Protocol name"
-      },
       "initial_step_type": {
          "model_name": "p2d_p3d_p4d",
          "par_class": "non_material",
@@ -21,7 +12,7 @@
          "display_name": "Initial step type"
       },
       "number_of_cycles": {
-         "model_name": "p3d_p4d",
+         "model_name": "p2d_p3d_p4d",
          "par_class": "non_material",
          "difficulty": "basis",
          "context_type": "emmo:NumberOfEntities",
@@ -39,7 +30,7 @@
       "d_rate": {
          "model_name": "p2d_p3d_p4d",
          "par_class": "non_material",
-         "difficulty": "advanced",
+         "difficulty": "basis",
          "context_type_iri":"https://w3id.org/emmo/domain/electrochemistry#electrochemistry_25e20915_c35d_4bee_ad31_736235a79780",
          "max_value": 10,
          "min_value": 0.01,
@@ -52,9 +43,9 @@
          "display_name": "Crate"
       },
       "c_rate": {
-         "model_name": "p3d_p4d",
+         "model_name": "p2d_p3d_p4d",
          "par_class": "non_material",
-         "difficulty": "advanced",
+         "difficulty": "basis",
          "context_type_iri":"https://w3id.org/emmo/domain/electrochemistry#electrochemistry_e1fd84eb_acdb_4b2c_b90c_e899d552a3ee",
          "max_value": 10,
          "min_value": 0.01,

diff --git a/streamlit/input_files/battmo_formatted_input.json b/streamlit/input_files/battmo_formatted_input.json
@@ -21,7 +21,7 @@
                "density": 2260.0,
                "numberOfElectronsTransferred": 1,
                "activationEnergyOfReaction": 35000.0,
-               "reactionRateConstant": 6.48e-07,
+               "reactionRateConstant": 6.716e-12,
                "guestStoichiometry100": 0.9014,
                "guestStoichiometry0": 0.0279,
                "chargeTransferCoefficient": 0.5,
@@ -81,7 +81,7 @@
                "density": 4950.0,
                "numberOfElectronsTransferred": 1,
                "activationEnergyOfReaction": 17800.0,
-               "reactionRateConstant": 3.42e-06,
+               "reactionRateConstant": 3.545e-11,
                "guestStoichiometry100": 0.2661,
                "guestStoichiometry0": 0.9084,
                "chargeTransferCoefficient": 0.5,
@@ -167,8 +167,10 @@
    "initT": 298.15,
    "include_current_collectors": false,
    "Control": {
-      "controlPolicy": "CCDischarge",
+      "controlPolicy": "CCCV",
       "initialControl": "discharging",
+      "numberOfCycles": 1,
+      "CRate": 1.0,
       "DRate": 1.0,
       "lowerCutoffVoltage": 2.4,
       "rampupTime": 0.1,

diff --git a/streamlit/input_files/linked_data_input.json b/streamlit/input_files/linked_data_input.json
@@ -163,7 +163,7 @@
                         "@type": "None",
                         "value": {
                            "@type": "emmo:Numerical",
-                           "hasNumericalData": 6.48e-07
+                           "hasNumericalData": 6.716e-12
                         },
                         "unit": {
                            "label": "MolePerSquareMetrePerSecond",
@@ -287,19 +287,6 @@
                            "@type": "emmo:ReciprocalSecond"
                         }
                      },
-                     {
-                        "label": "number_of_discrete_cells_electrode",
-                        "@type": "https://w3id.org/emmo#EMMO_41efdf5d_0c9c_4ea0_bb65_f8236e663be5",
-                        "value": {
-                           "@type": "emmo:Numerical",
-                           "hasNumericalData": 10
-                        },
-                        "unit": {
-                           "label": "UnitOne",
-                           "symbol": "1",
-                           "@type": "emmo:UnitOne"
-                        }
-                     },
                      {
                         "label": "particle_radius",
                         "@type": "https://w3id.org/emmo#EMMO_32dcd601_47c7_4028_b7fa_5e972ae57f12",
@@ -671,7 +658,7 @@
                         "@type": "None",
                         "value": {
                            "@type": "emmo:Numerical",
-                           "hasNumericalData": 3.42e-06
+                           "hasNumericalData": 3.545e-11
                         },
                         "unit": {
                            "label": "MolePerSquareMetrePerSecond",
@@ -795,19 +782,6 @@
                            "@type": "emmo:ReciprocalSecond"
                         }
                      },
-                     {
-                        "label": "number_of_discrete_cells_electrode",
-                        "@type": "https://w3id.org/emmo#EMMO_41efdf5d_0c9c_4ea0_bb65_f8236e663be5",
-                        "value": {
-                           "@type": "emmo:Numerical",
-                           "hasNumericalData": 10
-                        },
-                        "unit": {
-                           "label": "UnitOne",
-                           "symbol": "1",
-                           "@type": "emmo:UnitOne"
-                        }
-                     },
                      {
                         "label": "particle_radius",
                         "@type": "https://w3id.org/emmo#EMMO_32dcd601_47c7_4028_b7fa_5e972ae57f12",
@@ -1472,11 +1446,16 @@
                }
             },
             {
-               "label": "protocol_name",
-               "@type": "None",
+               "label": "number_of_cycles",
+               "@type": "https://w3id.org/emmo#EMMO_41efdf5d_0c9c_4ea0_bb65_f8236e663be5",
                "value": {
-                  "@type": "emmo:String",
-                  "hasStringData": "CCDischarge"
+                  "@type": "emmo:Numerical",
+                  "hasNumericalData": 1
+               },
+               "unit": {
+                  "label": "UnitOne",
+                  "symbol": "1",
+                  "@type": "emmo:UnitOne"
                }
             },
             {
@@ -1492,6 +1471,26 @@
                   "@type": "emmo:UnitOne"
                }
             },
+            {
+               "label": "c_rate",
+               "@type": "https://w3id.org/emmo/domain/electrochemistry#electrochemistry_e1fd84eb_acdb_4b2c_b90c_e899d552a3ee",
+               "value": {
+                  "@type": "emmo:Numerical",
+                  "hasNumericalData": 1.0
+               },
+               "unit": {
+                  "label": "UnitOne",
+                  "symbol": "1",
+                  "@type": "emmo:UnitOne"
+               }
+            },
+            {
+               "label": "protocol_name",
+               "value": {
+                  "@type": "emmo:String",
+                  "hasStringData": "CCCV"
+               }
+            },
             {
                "label": "lower_cutoff_voltage",
                "@type": "https://w3id.org/emmo/domain/electrochemistry#electrochemistry_534dd59c_904c_45d9_8550_ae9d2eb6bbc9",

diff --git a/streamlit/output_files/battmo_results b/streamlit/output_files/battmo_results
diff --git a/streamlit/output_files/indicator_values.json b/streamlit/output_files/indicator_values.json
@@ -1,7 +1,7 @@
 {
    "Cell": {
       "cellMass": {
-         "value": 34.64493824,
+         "value": 34.66146224,
          "unit": "g"
       },
       "nominalCellCapacity": {
@@ -15,7 +15,7 @@
    },
    "NegativeElectrode": {
       "massLoading": {
-         "value": 14.9872,
+         "value": 15.0484,
          "unit": "mg(cm)\u207b\u00b2"
       },
       "thickness": {
@@ -27,7 +27,7 @@
          "unit": "1"
       },
       "specificCapacity": {
-         "value": 1116.0263763796381,
+         "value": 1120.5836528712066,
          "unit": "mAh"
       },
       "ActiveMaterial": {