toughanimator 0.1.11__tar.gz → 0.1.13__tar.gz

{toughanimator-0.1.11 → toughanimator-0.1.13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: toughanimator
-Version: 0.1.11
+Version: 0.1.13
 Summary: A tool for visualizing TOUGH simulation outputs.
 Home-page: https://github.com/scarletref/toughanimator
 Author: scarletref

{toughanimator-0.1.11 → toughanimator-0.1.13}/setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name='toughanimator',  # Package name on PyPI
-    version='0.1.11',
+    version='0.1.13',
     description='A tool for visualizing TOUGH simulation outputs.',
     long_description=open('README.md').read(),
     long_description_content_type='text/markdown',

{toughanimator-0.1.11 → toughanimator-0.1.13}/toughanimator/run.py

@@ -11,7 +11,8 @@ case_name = "3D five spot MINC"
 test_case_dir = os.path.join(os.path.dirname(os.path.dirname(__file__)), dir_name) 
 
 case_dir = os.path.join(test_case_dir, case_name)
-case_dir = r"D:\Projects\tough-processing\uwc\tough_case\uwc_polygonal_20251231\PetraSim"
+case_dir = r"D:\Projects\202601\0 Base_res_k"
+#case_dir = r"D:\Projects\202601\260123_UWC_homo"
 #case_dir = r"D:\Projects\202511\ta-post\0 Base_res_k"
 #case_dir = r"D:\Projects\202504\polygonal\poly_test"
 #case_dir = r"D:\Projects\202507\tough系列output\tough output format\TR_MINC_exe"
@@ -19,10 +20,10 @@ case_dir = r"D:\Projects\tough-processing\uwc\tough_case\uwc_polygonal_20251231\
 #case_dir = r"D:\Projects\202511\case_TRv4\uwc"
 #case_dir = r"D:\Projects\202501\toughanimator\test_cases\2DCCS 100yrs_RC"
 reader = ta.vis_reader(case_dir)
-reader.write_eleme_conne()
-reader.write_geometry()
+#reader.write_eleme_conne()
+#reader.write_geometry()
 #reader.write_incon()
 #reader.write_result()
-#reader.write_all()
+reader.write_all()
 
 

{toughanimator-0.1.11 → toughanimator-0.1.13}/toughanimator/tough_classes.py

@@ -9,7 +9,6 @@ import pandas as pd
 from vtkmodules.all import *
 import pathlib
 import json
-import chardet
 
 from enum import Enum
 
@@ -71,7 +70,7 @@ class VisVariable:
         }
 
 class VisSetting:
-    def __init__(self, input_file_paths, out_file_paths, vis_dir, corners_file="unkown", out_format_type=OutType.Unknown, tough_version = ToughVersion.Unknown, vis_types=[VisType.ParaView, VisType.Tecplot], mesh_type=MeshType.RegularGrid, debug=False, eos="ECO2N", minc=False, selected_variables_scalar = [], selected_variables_vector = [], ngv=False):
+    def __init__(self, input_file_paths, out_file_paths, vis_dir, corners_file="unkown", out_format_type=OutType.Unknown, tough_version = ToughVersion.Unknown, vis_types=[VisType.ParaView, VisType.Tecplot], mesh_type=MeshType.RegularGrid, debug=False, eos="ECO2N", minc=False, selected_variables_scalar = [], selected_variables_vector = [], ngv=False, trap=False):
         self.mesh_type = mesh_type
         self.out_format_type = out_format_type
         self.vis_types = vis_types
@@ -90,6 +89,7 @@ class VisSetting:
         self.selected_variables_scalar = selected_variables_scalar
         self.selected_variables_vector = selected_variables_vector
         self.ngv = ngv
+        self.trap = trap
 
 
     def setBounds(self, x_bounds, y_bounds, z_bounds):
@@ -107,7 +107,7 @@ class vis_reader:
         self.rock_dict = []
         if os.path.isdir(case_dir):
             config_path = os.path.join(case_dir, "config.json")
-            if os.path.exists(config_path):
+            if os.path.isfile(config_path):
                 with open(config_path,  "r", encoding="latin-1") as config_file:
                     config = json.load(config_file)
             
@@ -168,7 +168,8 @@ class vis_reader:
             selected_variables_scalar = config['selected_variables_scalar'] if 'selected_variables_scalar' in config else [],
             selected_variables_vector = config['selected_variables_vector'] if 'selected_variables_vector' in config else [],
             #ngv= config['NGV'] if 'NGV' in config else False
-            ngv = next((v for k, v in config.items() if k.lower() == "ngv"),False)
+            ngv = next((v for k, v in config.items() if k.lower() == "ngv"),False),
+            trap= next((v for k, v in config.items() if k.lower() == "trap"),False)
         )
 
         # check if the project is using MINC
@@ -407,10 +408,15 @@ class vis_reader:
                             
                             #skip 1 lines
                             f.readline()
-                            third_line = f.readline()
-                            new_line = f'{first_line}{third_line}'
-                            self.rocks_buffer.write(new_line)
                             f.readline()
+                            forth_line = f.readline() # read forth line
+                            if len(forth_line) < 30:
+                                # create a line with fixed lenth dafault value
+                                values = [8, 0, 0.03]
+                                forth_line = "".join(f"{v:10.3f}" for v in values)
+                            new_line = f'{first_line}{forth_line}' # merge first and forth line
+                            self.rocks_buffer.write(new_line)
+                            
 
 
         if has_rocks == False:
@@ -852,8 +858,8 @@ class vis_reader:
         extension = os.path.splitext(self.main_geometry)[1]
         vtr_path = os.path.join(self.setting.vis_dir, 'paraview', f'time_step_{vis_time_step.time_step}{extension}')
         self.time_steps_list[time_index].vtu_file_name = vtr_path
-        scalar_vtr = self.__read_vtk_file(vtr_path)   
-        vtr = scalar_vtr
+        vtr = self.__read_vtk_file(vtr_path)   
+
 
         post_variable_list = []
         # p
@@ -890,7 +896,8 @@ class vis_reader:
 
         
         # add toughreact variables
-        if self.setting.tough_version == ToughVersion.TOUGHReact or self.setting.tough_version == ToughVersion.TOUGH3:
+        #if self.setting.tough_version == ToughVersion.TOUGHReact or self.setting.tough_version == ToughVersion.TOUGH3:
+        if self.setting.trap:
             trapHCO2_array = vtkDoubleArray()
             trapHCO2_array.SetName('trapHCO2')
 
@@ -903,49 +910,94 @@ class vis_reader:
             trapMCO2_array = vtkDoubleArray()
             trapMCO2_array.SetName('trapMCO2')
 
+
+            
+            # 1. Saturation of gas
+            sat_gas_array = None
+            sat_gas_names = ["SatGas", "SAT_G", "SG"]
+            for sat_gas_name in sat_gas_names:
+                if vtr.GetCellData().GetArray(sat_gas_name) is not None:
+                    sat_gas_array = vtr.GetCellData().GetArray(sat_gas_name)
+            if sat_gas_array is None:
+                print(f'    ⚠️  Can\'t find gas saturation array (SatGas/SAT_G/SG). Skipping trap calculations.')
+                return
+            
+            # 2. Porosity
+            porosity_array = None
+            porosity_names = ["Porosity", "POR"] # if not found, try Rock_dict # TODO:異質性考慮
+            for porosity_name in porosity_names:
+                if vtr.GetCellData().GetArray(porosity_name) is not None:
+                    porosity_array = vtr.GetCellData().GetArray(porosity_name)
+            if porosity_array is None:
+                porosity_array = vtr.GetCellData().GetArray("rock_por")
+                if porosity_array is None:
+                    print(f'    ⚠️  Can\'t find porosity array (Porosity/POR). Skipping trap calculations.')
+                    return
+
+            # 3. Gas density
+            dgas_kg_m3_array = None
+            dgas_names = ["DGas_kg/m3", "DEN_G", "DG (kg/m^3)"]
+            for dgas_name in dgas_names:
+                if vtr.GetCellData().GetArray(dgas_name) is not None:
+                    dgas_kg_m3_array = vtr.GetCellData().GetArray(dgas_name)
+            if dgas_kg_m3_array is None:
+                print(f'    ⚠️  Can\'t find gas density array (DGas_kg/m3/DEN_G). Skipping trap calculations.')
+                return
+            
+            # 4. Liquid saturation (if not, 1-SG)
+            sat_liq_array = None
+            sat_liq_names = ["SatLiq", "SAT_L"]
+            for sat_liq_name in sat_liq_names:
+                if vtr.GetCellData().GetArray(sat_liq_name) is not None:
+                    sat_liq_array = vtr.GetCellData().GetArray(sat_liq_name)
+            if sat_liq_array is None:
+                if sat_gas_array is not None:
+                    sat_liq_array = vtkDoubleArray()
+                    for index in range(0, vtr.GetNumberOfCells()):
+                        sat_liq_value = 1 - sat_gas_array.GetValue(index)
+                        sat_liq_array.InsertNextValue(sat_liq_value)
+                else:
+                    print(f'    ⚠️  Can\'t find liquid saturation array (SatLiq/SAT_L). Skipping trap calculations.')
+                    return
+
+            # 5. CO2 concentration in liquid
+            xco2_liq_array = None
+            xco2_liq_names = ["XCO2Liq", "X_CO2 _L", "XCO2aq"]
+            for xco2_liq_name in xco2_liq_names: 
+                if vtr.GetCellData().GetArray(xco2_liq_name) is not None:
+                    xco2_liq_array = vtr.GetCellData().GetArray(xco2_liq_name)
+            if xco2_liq_array is None:
+                print(f'    ⚠️  Can\'t find XCO2 in liquid array (XCO2Liq/X_CO2_L). Skipping trap calculations.')
+                return
+
+            # 6. residual gas saturation
+            sgr_array = None
+            if vtr.GetCellData().GetArray("sgr") is not None: # rock line4 3rd value default = 0.03  user guide:resitual of gas
+                sgr_array = vtr.GetCellData().GetArray("sgr")
+            if sgr_array is None:
+                print(f'    ⚠️  Can\'t find residual gas saturation array (sgr). Skipping trap calculations.')
+                return
+            
+            # 7. VOLX
+            volx_array = None
+            if vtr.GetCellData().GetArray("VOLX") is not None:
+                volx_array = vtr.GetCellData().GetArray("VOLX")
+            else:
+                print(f'    ⚠️  Can\'t find cell volume array (VOLX). Skipping trap calculations.')
+                return
+
             for index in range(0, vtr.GetNumberOfCells()):
                 trapHCO2 = 0
                 trapRCO2 = 0
                 trapDCO2 = 0
                 trapMCO2 = 0   
-                VOLX = 0
-                if vtr.GetCellData().GetArray("VOLX") is not None:
-                    VOLX = vtr.GetCellData().GetArray("VOLX").GetValue(index)
-
-                SatGas = 0
-                if vtr.GetCellData().GetArray("SatGas") is not None:
-                    SatGas = vtr.GetCellData().GetArray("SatGas").GetValue(index)
-                elif vtr.GetCellData().GetArray("SAT_G") is not None:
-                    SatGas = vtr.GetCellData().GetArray("SAT_G").GetValue(index)
-
-                Porosity = 0
-                if vtr.GetCellData().GetArray("Porosity") is not None:
-                    Porosity = vtr.GetCellData().GetArray("Porosity").GetValue(index)
-                elif vtr.GetCellData().GetArray("POR") is not None:
-                    Porosity = vtr.GetCellData().GetArray("POR").GetValue(index)
-                
-                DGas_kg_m3 = 0
-                if vtr.GetCellData().GetArray("DGas_kg/m3") is not None:
-                    DGas_kg_m3 = vtr.GetCellData().GetArray("DGas_kg/m3").GetValue(index)
-                elif vtr.GetCellData().GetArray("DEN_G") is not None:
-                    DGas_kg_m3 = vtr.GetCellData().GetArray("DEN_G").GetValue(index)
-
-                SatLiq = 0
-                if vtr.GetCellData().GetArray("SatLiq") is not None: 
-                    SatLiq = vtr.GetCellData().GetArray("SatLiq").GetValue(index)
-                elif vtr.GetCellData().GetArray("SAT_L") is not None:
-                    SatLiq = vtr.GetCellData().GetArray("SAT_L").GetValue(index)
-                
-                XCO2Liq = 0
-                if vtr.GetCellData().GetArray("XCO2Liq") is not None:
-                    XCO2Liq = vtr.GetCellData().GetArray("XCO2Liq").GetValue(index)
-                elif vtr.GetCellData().GetArray("X_CO2_L") is not None:
-                    XCO2Liq = vtr.GetCellData().GetArray("X_CO2_L").GetValue(index)
-
-                sgr = 0
-                if vtr.GetCellData().GetArray("sgr") is not None:
-                    sgr = vtr.GetCellData().GetArray("sgr").GetValue(index)
-
+                VOLX = volx_array.GetValue(index)
+                SatGas = sat_gas_array.GetValue(index)
+                Porosity = porosity_array.GetValue(index)
+                DGas_kg_m3 = dgas_kg_m3_array.GetValue(index)
+                SatLiq = sat_liq_array.GetValue(index)
+                XCO2Liq = xco2_liq_array.GetValue(index)
+                sgr = sgr_array.GetValue(index)
 
                 trapHCO2 =(SatGas-sgr)*VOLX*Porosity*DGas_kg_m3* (SatGas>sgr)
                 trapRCO2 = 0.05 * VOLX * Porosity * DGas_kg_m3* (SatGas > sgr)+ SatGas * VOLX * Porosity * DGas_kg_m3*(SatGas <= sgr)
@@ -1587,12 +1639,12 @@ class vis_reader:
         '''
         compute permeability
         '''
-        rock_colspecs = [(0, 5), (30, 40), (40, 50), (50, 60), (100, 110)]  # define column widths
-        rock_names = ['MAT', 'PER_1', 'PER_2', 'PER_3', 'SGR']
+        rock_colspecs = [(0, 5), (20, 30), (30, 40), (40, 50), (50, 60), (100, 110)]  # define column widths
+        rock_names = ['MAT', 'POR', 'PER_1', 'PER_2', 'PER_3', 'SGR']
         self.rocks_buffer.seek(0)
         rocks_df = pd.read_fwf(self.rocks_buffer, colspecs=rock_colspecs, header=None,
                               names=rock_names,
-                              dtype={'MAT':str, 'PER_1':str, 'PER_2':str, 'PER_3':str, 'SGR':str})
+                              dtype={'MAT':str, 'POR':str, 'PER_1':str, 'PER_2':str, 'PER_3':str, 'SGR':str})
         
         #sgr_dict = {}
         self.rock_dict = None
@@ -1604,6 +1656,7 @@ class vis_reader:
                 rock_dict.append({
                     'id': i,
                     'rock_name': rocks_df['MAT'][i],
+                    'por':self.__parse_float(rocks_df['POR'][i]),
                     'per_1':self.__parse_float(rocks_df['PER_1'][i]),
                     'per_2':self.__parse_float(rocks_df['PER_2'][i]),
                     'per_3':self.__parse_float(rocks_df['PER_3'][i]),
@@ -1616,22 +1669,31 @@ class vis_reader:
 
             sgr_array = vtkDoubleArray()
             sgr_array.SetName('sgr')
+
+            porosity_array = vtkDoubleArray()
+            porosity_array.SetName('rock_por')
+
             for i in range(0, len(elem_df.values)):
                 value = 0
-
+                sgr = 0
+                porosity = 0
                 mat = matArray.GetValue(i)
                 if self.__isInt(mat):  
                     mat_id = int(mat)
                     value = pmxArray.GetValue(i) * rock_dict[mat_id-1]['per_1']
                     sgr = rock_dict[mat_id-1]['sgr']
+                    porosity = rock_dict[mat_id-1]['por']
                 else:
                     rock_item = [rock for rock in rock_dict if rock['rock_name'] == mat]
                     #if mat in rock_dict:
                     value = pmxArray.GetValue(i) * rock_item[0]['per_1']
                     sgr = rock_item[0]['sgr']
+                    porosity = rock_item[0]['por']
+                
                 
                 per_array.InsertNextValue(value)
                 sgr_array.InsertNextValue(sgr)
+                porosity_array.InsertNextValue(porosity)
             self.rock_dict = rock_dict
 
 
@@ -1674,6 +1736,10 @@ class vis_reader:
         elem_conne_vtu.GetPointData().AddArray(volxArray)
         elem_conne_vtu.GetPointData().AddArray(matArray)
         elem_conne_vtu.GetPointData().AddArray(matIDArray)
+        if self.rock_dict is not None:
+            elem_conne_vtu.GetPointData().AddArray(per_array)
+            elem_conne_vtu.GetPointData().AddArray(sgr_array)
+            elem_conne_vtu.GetPointData().AddArray(porosity_array)
 
         elem_conne_vtu.SetCells(4, line_cell_array)
         elem_conne_vtu.GetCellData().AddArray(d1_array)
@@ -1712,8 +1778,9 @@ class vis_reader:
         matIDArray = elem_conne_vtu.GetPointData().GetArray('Material_ID')
         pmxArray = elem_conne_vtu.GetPointData().GetArray('PMX')
         if self.rock_dict is not None:
-            per_array = elem_conne_vtu.GetCellData().GetArray('Permeability')
-            sgr_array = elem_conne_vtu.GetCellData().GetArray('sgr')
+            per_array = elem_conne_vtu.GetPointData().GetArray('Permeability')
+            sgr_array = elem_conne_vtu.GetPointData().GetArray('sgr')
+            porosity_array = elem_conne_vtu.GetPointData().GetArray('rock_por')
         
 
 
@@ -1755,7 +1822,7 @@ class vis_reader:
 
 
         if all(xyz_elem) and range_ratio < 1000:
-            if os.path.exists(self.setting.corners_file):
+            if os.path.isfile(self.setting.corners_file):
                 self.setting.mesh_type = MeshType.StructuredGridOrth
             else:
                 self.setting.mesh_type = MeshType.RegularGrid
@@ -1763,7 +1830,7 @@ class vis_reader:
         else:
             is_parallel = self.__checkParallel(elem_conne_vtu)
             # check if polygonal mesh
-            if os.path.exists(self.setting.corners_file):
+            if os.path.isfile(self.setting.corners_file):
 
                 if is_parallel:
                     self.setting.mesh_type = MeshType.StructuredGridFree
@@ -1776,7 +1843,7 @@ class vis_reader:
         print(f'    Mesh type: {self.setting.mesh_type.name}')
 
         # Read corners file to dataframe
-        if os.path.exists(self.setting.corners_file):
+        if os.path.isfile(self.setting.corners_file):
             corners_buffer = io.StringIO()
             csv_headers = []
             line_number = -1
@@ -1935,6 +2002,7 @@ class vis_reader:
             if self.rock_dict is not None:
                 rGrid.GetCellData().AddArray(per_array)
                 rGrid.GetCellData().AddArray(sgr_array)
+                rGrid.GetCellData().AddArray(porosity_array)
             rGrid.GetCellData().AddArray(pmxArray)
 
             self.main_geometry = os.path.join(
@@ -1974,6 +2042,7 @@ class vis_reader:
             if self.rock_dict is not None:
                 vts.GetCellData().AddArray(per_array)
                 vts.GetCellData().AddArray(sgr_array)
+                vts.GetCellData().AddArray(porosity_array)
             self.main_geometry = os.path.join(self.setting.vis_dir, "main_geometry.vts")
             self.__write_vtk_file(vts, self.main_geometry)
             
@@ -2021,6 +2090,7 @@ class vis_reader:
             if self.rock_dict is not None:
                 auto_corner_vtu.GetCellData().AddArray(per_array)
                 auto_corner_vtu.GetCellData().AddArray(sgr_array)
+                auto_corner_vtu.GetCellData().AddArray(porosity_array)
             auto_corner_vtu.GetCellData().AddArray(matIDArray)
             self.main_geometry = os.path.join(self.setting.vis_dir, "main_geometry.vtu")
             self.__write_vtk_file(auto_corner_vtu, self.main_geometry)
@@ -2361,6 +2431,7 @@ class vis_reader:
             if self.rock_dict is not None:
                 main_geometray.GetCellData().AddArray(per_array)
                 main_geometray.GetCellData().AddArray(sgr_array)
+                main_geometray.GetCellData().AddArray(porosity_array)
 
             main_geometray.GetCellData().AddArray(matIDArray)
             main_geometray.GetCellData().AddArray(horizon_id_array)

{toughanimator-0.1.11 → toughanimator-0.1.13}/toughanimator.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: toughanimator
-Version: 0.1.11
+Version: 0.1.13
 Summary: A tool for visualizing TOUGH simulation outputs.
 Home-page: https://github.com/scarletref/toughanimator
 Author: scarletref