Merge pull request #420 from equinor/CCS-411_B

CCS-411: Replace occurrences of Pflotran with Cirrus

Author: FredrikNevjenNR

README.md

@@ -1,6 +1,6 @@
 # ccs-scripts
 
-:scroll: **ccs-scripts** gathers a collection of post-processing scripts dedicated to CCS outputs from Eclipse and Pflotran.
+:scroll: **ccs-scripts** gathers a collection of post-processing scripts dedicated to CCS outputs from Eclipse and Cirrus.
 
 >Note: These scripts are beeing tested and frequently updated, new releases will be available occasionally :recycle:
 

docs/scripts/co2_plume_area.rst

@@ -7,7 +7,7 @@ CO2_PLUME_AREA
    :func: get_parser
    :prog: plume_area
 
-Calculates the area of the CO\ :sub:`2` plume for each formation and time step, for both SGAS and AMFG (Pflotran) / YMF2 (Eclipse).
+Calculates the area of the CO\ :sub:`2` plume for each formation and time step, for both SGAS and AMFG (Cirrus) / YMF2 (Eclipse).
 
 Output is a table on CSV format.
 

docs/scripts/co2_plume_extent.rst

@@ -10,7 +10,7 @@ CO2_PLUME_EXTENT
 Calculates the maximum lateral distance of the CO\ :sub:`2` plume from a given location,
 for instance an injection point. It is also possible to instead calculate the distance
 to a point or a line (north-south or east-west). The distances are calculated for each
-time step, for both SGAS and AMFG (Pflotran) / YMF2 (Eclipse). It is possible to
+time step, for both SGAS and AMFG (Cirrus) / YMF2 (Eclipse). It is possible to
 use an YAML-file to set up multiple calculations.
 
 Output is a table on CSV format. Multiple calculations specified in the YAML-file

src/ccs_scripts/co2_containment/co2_calculation.py

@@ -28,7 +28,7 @@
 
 DEFAULT_CO2_MOLAR_MASS = 44.0
 DEFAULT_WATER_MOLAR_MASS = 18.0
-PROPERTIES_NEEDED_PFLOTRAN = ["SGAS", "DGAS", "DWAT"]
+PROPERTIES_NEEDED_CIRRUS = ["SGAS", "DGAS", "DWAT"]
 PROPERTIES_NEEDED_ECLIPSE = ["SGAS", "BGAS", "BWAT", "XMF2", "YMF2"]
 
 RELEVANT_PROPERTIES = [
@@ -747,7 +747,7 @@ def _set_calc_type_from_input_string(calc_type_input: str) -> CalculationType:
     return CalculationType[calc_type_input]
 
 
-def _pflotran_co2mass(
+def _cirrus_co2mass(
     source_data,
     scenario: Scenario,
     pore_volume_prop: str,
@@ -757,7 +757,7 @@ def _pflotran_co2mass(
     oil_molar_mass: Optional[float] = None,
 ) -> Dict[str, List[np.ndarray]]:
     """
-    Calculates CO2 mass based on the existing properties in PFlotran
+    Calculates CO2 mass based on the existing properties in Cirrus
 
     Args:
       source_data (SourceData): Data with the information of the necessary properties
@@ -918,7 +918,7 @@ def _compositional_co2mass(
     soil = source_data.SOIL
     eff_vols = source_data.RPORV if pore_volume_prop == "RPORV" else source_data.PORV
     conv_fact = co2_molar_mass
-    if co2_position is not None and source != "PFlotran COMP":
+    if co2_position is not None and source != "Cirrus COMP":
         xmf_co2 = getattr(source_data, f"XMF{co2_position}")
         ymf_co2 = getattr(source_data, f"YMF{co2_position}")
     else:
@@ -945,7 +945,7 @@ def _compositional_co2mass(
         else:
             zmf_co2 = (
                 getattr(source_data, f"ZMF{co2_position}")
-                if co2_position is not None and source != "PFlotran COMP"
+                if co2_position is not None and source != "Cirrus COMP"
                 else source_data.ZMF2
             )
             phase_moles[date].extend([boil[date] * soil[date] * eff_vols[date]])
@@ -970,7 +970,7 @@ def _compositional_co2mass(
     return co2_mass
 
 
-def _pflotran_co2_molar_volume(
+def _cirrus_co2_molar_volume(
     source_data,
     scenario: Scenario,
     water_density: np.ndarray,
@@ -982,7 +982,7 @@ def _pflotran_co2_molar_volume(
     oil_molar_mass: Optional[float] = None,
 ) -> Dict:
     """
-    Calculates CO2 molar volume (mol/m3) based on the existing properties in PFlotran
+    Calculates CO2 molar volume (mol/m3) based on the existing properties in Cirrus
 
     Args:
       source_data (SourceData): Data with the information of the necessary properties
@@ -1322,17 +1322,17 @@ def _calculate_co2_data_from_source_data(
     gas_molar_mass = None
     oil_molar_mass = None
     comp_molar_masses = None
-    if source == "PFlotran COMP":
+    if source == "Cirrus COMP":
         if cirrus_info_file is None:
-            error_text = "Source: PFlotran COMP"
+            error_text = "Source: Cirrus EOS COMP"
             error_text += f"\nScenario: {scenario.name}."
             error_text += (
                 "\nTo compute mass or actual volume in this scenario "
                 "path to cirrus INFO file must be provided."
             )
             raise ValueError(format_error(error_text))
         comp_molar_masses = _extract_comp_molar_masses(cirrus_info_file)
-    elif source == "PFlotran":
+    elif source == "Cirrus":
         gas_molar_mass, oil_molar_mass = _extract_molar_masses(
             scenario, cirrus_info_file
         )
@@ -1393,21 +1393,21 @@ def _find_pore_volume_prop(active_props: List[str]) -> str:
 def _find_source_and_scenario(
     residual_trapping: bool, active_props: List[str]
 ) -> Tuple[str, Scenario]:
-    props_needed_pflotran = PROPERTIES_NEEDED_PFLOTRAN.copy()
+    props_needed_cirrus = PROPERTIES_NEEDED_CIRRUS.copy()
     props_needed_eclipse = PROPERTIES_NEEDED_ECLIPSE.copy()
     if residual_trapping:
-        props_needed_pflotran.append("SGSTRAND")
+        props_needed_cirrus.append("SGSTRAND")
         props_needed_eclipse.append("SGTRH")
-    if is_subset(props_needed_pflotran, active_props):
-        source = "PFlotran"
+    if is_subset(props_needed_cirrus, active_props):
+        source = "Cirrus"
         if is_subset(["AMFS", "YMFO"], active_props):
             scenario = Scenario.DEPLETED_OIL_GAS_FIELD
         elif is_subset(["AMFS"], active_props):
             scenario = Scenario.DEPLETED_GAS_FIELD
         elif is_subset(["AMFG", "YMFG"], active_props):
             scenario = Scenario.AQUIFER
         elif is_subset(["XMF2"], active_props):
-            source = "PFlotran COMP"
+            source = "Cirrus COMP"
             if _n_components(active_props) <= 3:
                 scenario = Scenario.AQUIFER
             elif is_subset(["SOIL"], active_props):
@@ -1429,7 +1429,7 @@ def _find_source_and_scenario(
             scenario = Scenario.DEPLETED_GAS_FIELD
     else:
         _raise_missing_props_error(
-            active_props, props_needed_pflotran, props_needed_eclipse
+            active_props, props_needed_cirrus, props_needed_eclipse
         )
     return source, scenario
 
@@ -1447,8 +1447,8 @@ def _calc_co2_amount(
     oil_molar_mass: Optional[float],
     comp_molar_masses: Optional[Dict[str, Tuple[int, float]]],
 ) -> Co2Data:
-    if source == "PFlotran":
-        co2_mass_cell = _pflotran_co2mass(
+    if source == "Cirrus":
+        co2_mass_cell = _cirrus_co2mass(
             source_data,
             scenario,
             pore_volume_prop,
@@ -1459,7 +1459,7 @@ def _calc_co2_amount(
         )
     else:
         co2_position = None
-        if source == "PFlotran COMP" and comp_molar_masses is not None:
+        if source == "Cirrus COMP" and comp_molar_masses is not None:
             bwat, bgas, boil = _convert_phase_density_from_mass_to_mole(
                 source_data,
                 comp_molar_masses,
@@ -1576,7 +1576,7 @@ def _calculate_molar_vols_co2(
     gas_molar_mass: Optional[float],
     oil_molar_mass: Optional[float],
 ):
-    if source == "PFlotran":
+    if source == "Cirrus":
         y_prop = source_data.AMFG if scenario == Scenario.AQUIFER else source_data.AMFS
         y = y_prop[source_data.DATES[0]]
         where_min_amf_co2 = np.where(y < THRESHOLD_DISSOLVED)[0]
@@ -1629,7 +1629,7 @@ def _calculate_molar_vols_co2(
                     for x in enumerate(doil)
                 ]
             )
-        molar_vols_co2 = _pflotran_co2_molar_volume(
+        molar_vols_co2 = _cirrus_co2_molar_volume(
             source_data,
             scenario,
             water_density,
@@ -1721,13 +1721,13 @@ def _calc_co2_amount_cell_volume(
 
 def _raise_missing_props_error(
     active_props: List[str],
-    props_needed_pflotran: List[str],
+    props_needed_cirrus: List[str],
     props_needed_eclipse: List[str],
 ):
-    if any(prop in props_needed_pflotran for prop in active_props):
-        missing_props = [x for x in props_needed_pflotran if x not in active_props]
+    if any(prop in props_needed_cirrus for prop in active_props):
+        missing_props = [x for x in props_needed_cirrus if x not in active_props]
         error_text = "Lacking some required properties to compute CO2 mass/volume."
-        error_text += "\nAssumed source: PFlotran"
+        error_text += "\nAssumed source: Cirrus"
         error_text += "\nMissing properties: "
         error_text += ", ".join(missing_props)
         raise ValueError(format_error(error_text))
@@ -1740,8 +1740,8 @@ def _raise_missing_props_error(
         raise ValueError(format_error(error_text))
     error_text = "Lacking all required properties to compute CO2 mass/volume."
     error_text += "\nNeed either:"
-    error_text += f"\n  PFlotran: \
-        {', '.join(props_needed_pflotran)}"
+    error_text += f"\n  Cirrus: \
+        {', '.join(props_needed_cirrus)}"
     error_text += f"\n  Eclipse : \
         {', '.join(props_needed_eclipse)}"
     raise ValueError(format_error(error_text))

src/ccs_scripts/hook_implementations/forward_model_steps.py

@@ -376,7 +376,7 @@ def documentation() -> ForwardModelStepDocumentation:
 
 _DESC_CO2_PLUME_AREA = """
 Calculates the area of the CO2 plume for each formation and time step, for both
-SGAS and AMFG (Pflotran) / YMF2 (Eclipse).
+SGAS and AMFG (Cirrus) / YMF2 (Eclipse).
 
 Output is a table on CSV format.
 """
@@ -386,7 +386,7 @@ def documentation() -> ForwardModelStepDocumentation:
 Calculates the maximum lateral distance of the CO2 plume from a given location,
 for instance an injection point. It is also possible to instead calculate the
 distance to a point or a line (north-south or east-west). The distances are
-calculated for each time step, for both SGAS and AMFG (Pflotran) / XMF2
+calculated for each time step, for both SGAS and AMFG (Cirrus) / XMF2
 (Eclipse).
 
 Output is a table on CSV format. Multiple calculations specified in the