[BUGFIX] Well1 position in SPE11C

.gitignore

@@ -184,4 +184,5 @@ playground
 # Tests
 tests/configs/check_format.py
 tests/configs/is_notebook.py
-**/tests/configs/*/
+**/tests/configs/*/
+**/tests/decks/*/

src/pyopmspe11/core/pyopmspe11.py

@@ -16,9 +16,8 @@ def pyopmspe11():
     """Main function for the pyopmspe11 executable"""
     cmdargs = load_parser()
     file = cmdargs["input"].strip()  # Name of the input file
-    dic = {"fol": cmdargs["output"].strip()}  # Name for the output folder
+    dic = {"fol": os.path.abspath(cmdargs["output"])}  # Name for the output folder
     dic["generate"] = cmdargs["generate"].strip()  # What data to write
-    dic["exe"] = os.getcwd()  # Path to the folder of the input.txt file
     dic["mode"] = cmdargs["mode"].strip()  # Parts of the workflow to run
     dic["pat"] = os.path.dirname(__file__)[:-5]  # Path to the pyopmspe11 folder
     dic["compare"] = cmdargs["compare"].strip()  # Make common figures for comparison
@@ -43,12 +42,12 @@ def pyopmspe11():
     process_input(dic, file)
 
     # Make the output folders
-    if not os.path.exists(f"{dic['exe']}/{dic['fol']}"):
-        os.system(f"mkdir {dic['exe']}/{dic['fol']}")
+    if not os.path.exists(f"{dic['fol']}"):
+        os.system(f"mkdir {dic['fol']}")
     for fil in ["deck", "flow" if dic["mode"] != "deck" else ""]:
-        if not os.path.exists(f"{dic['exe']}/{dic['fol']}/{fil}"):
-            os.system(f"mkdir {dic['exe']}/{dic['fol']}/{fil}")
-    os.chdir(f"{dic['exe']}/{dic['fol']}")
+        if not os.path.exists(f"{dic['fol']}/{fil}"):
+            os.system(f"mkdir {dic['fol']}/{fil}")
+    os.chdir(f"{dic['fol']}")
 
     if dic["mode"] == "all" or "deck" in dic["mode"]:
         # Check the generated deck, flow version, and chosen co2store implementation
@@ -58,7 +57,7 @@ def pyopmspe11():
         # For corner-point grids, get the cell centers by executing flow
         if dic["grid"] == "corner-point":
             initial(dic)
-            os.chdir(f"{dic['exe']}/{dic['fol']}/deck")
+            os.chdir(f"{dic['fol']}/deck")
             simulations(dic, "INITIAL", "flow", True)
             print(
                 "Files used to generate the corner-point grid (INITIAL.* files).\n"
@@ -70,21 +69,21 @@ def pyopmspe11():
         positions(dic)
         # Write used opm related files
         opm_files(dic)
-        print(f"The deck files have been written to {dic['exe']}/{dic['fol']}/deck.")
+        print(f"The deck files have been written to {dic['fol']}/deck.")
     if dic["mode"] == "all" or "flow" in dic["mode"]:
         # Run the simulations
-        simulations(dic, dic["fol"].upper(), "flow", False)
+        simulations(dic, dic["fol"].split("/")[-1].upper(), "flow", False)
 
     if dic["mode"] == "all" or "data" in dic["mode"]:
         # Write the data
-        if not os.path.exists(f"{dic['exe']}/{dic['fol']}/data"):
-            os.system(f"mkdir {dic['exe']}/{dic['fol']}/data")
+        if not os.path.exists(f"{dic['fol']}/data"):
+            os.system(f"mkdir {dic['fol']}/data")
         data(dic)
 
     if dic["mode"] == "all" or "plot" in dic["mode"]:
         # Make some useful plots after the studies
-        if not os.path.exists(f"{dic['exe']}/{dic['fol']}/figures"):
-            os.system(f"mkdir {dic['exe']}/{dic['fol']}/figures")
+        if not os.path.exists(f"{dic['fol']}/figures"):
+            os.system(f"mkdir {dic['fol']}/figures")
         plotting(dic)
 
 

src/pyopmspe11/templates/common/saturation_functions.mako

@@ -57,7 +57,7 @@ def safu_evaluation():
     % endfor
 
     with open(
-        "${dic['exe']}/${dic['fol']}/deck/TABLES.INC",
+        "${dic['fol']}/deck/TABLES.INC",
         "w",
         encoding="utf8",
     ) as file:

src/pyopmspe11/utils/mapproperties.py

@@ -121,13 +121,13 @@ def structured_handling_spe11a(dic):
     sensors(dic)
     wells(dic)
     with open(
-        f"{dic['exe']}/{dic['fol']}/deck/centers.txt",
+        f"{dic['fol']}/deck/centers.txt",
         "w",
         encoding="utf8",
     ) as file:
         file.write("\n".join(centers))
     with open(
-        f"{dic['exe']}/{dic['fol']}/deck/corners.txt",
+        f"{dic['fol']}/deck/corners.txt",
         "w",
         encoding="utf8",
     ) as file:
@@ -251,13 +251,13 @@ def structured_handling_spe11bc(dic):
     sensors(dic)
     wells(dic)
     with open(
-        f"{dic['exe']}/{dic['fol']}/deck/centers.txt",
+        f"{dic['fol']}/deck/centers.txt",
         "w",
         encoding="utf8",
     ) as file:
         file.write("\n".join(centers))
     with open(
-        f"{dic['exe']}/{dic['fol']}/deck/corners.txt",
+        f"{dic['fol']}/deck/corners.txt",
         "w",
         encoding="utf8",
     ) as file:
@@ -406,13 +406,13 @@ def corner_point_handling_spe11a(dic):
     dic["wellijk"][0] = [well1ijk[0] + 1, 1, well1ijk[2] + 1]
     dic["wellijk"][1] = [well2ijk[0] + 1, 1, well2ijk[2] + 1]
     with open(
-        f"{dic['exe']}/{dic['fol']}/deck/centers.txt",
+        f"{dic['fol']}/deck/centers.txt",
         "w",
         encoding="utf8",
     ) as file:
         file.write("\n".join(centers))
     with open(
-        f"{dic['exe']}/{dic['fol']}/deck/corners.txt",
+        f"{dic['fol']}/deck/corners.txt",
         "w",
         encoding="utf8",
     ) as file:
@@ -580,13 +580,13 @@ def corner_point_handling_spe11bc(dic):
     dic["well2"] = pd.Series(well2).argmin()
     locate_wells_sensors(dic)
     with open(
-        f"{dic['exe']}/{dic['fol']}/deck/centers.txt",
+        f"{dic['fol']}/deck/centers.txt",
         "w",
         encoding="utf8",
     ) as file:
         file.write("\n".join(centers))
     with open(
-        f"{dic['exe']}/{dic['fol']}/deck/corners.txt",
+        f"{dic['fol']}/deck/corners.txt",
         "w",
         encoding="utf8",
     ) as file:
@@ -637,16 +637,9 @@ def locate_wells_sensors(dic):
             get_cell_info(dic, well1ijk[0] + k * dic["noCells"][0])
             z_centers.append(dic["xyz"][2])
         for j in range(dic["wellijk"][0][1], dic["wellijkf"][0][1] + 1):
-            midpoints = z_centers - map_z(dic, j - 1)
+            midpoints = z_centers - map_z(dic, j - 1) - dic["maxelevation"]
             dic["wellkh"].append(
-                pd.Series(
-                    abs(
-                        dic["wellCoord"][0][2]
-                        - map_z(dic, dic["wellijk"][0][1] - 1)
-                        - midpoints
-                    )
-                ).argmin()
-                + 1
+                pd.Series(abs(dic["wellCoord"][0][2] - midpoints)).argmin() + 1
             )
     dic["fipnum"][
         dic["sensorijk"][0][0]
@@ -741,8 +734,8 @@ def positions(dic):
         dic[f"{names}"] = []
     if dic["grid"] == "corner-point":
         if dic["use"] == "opm":
-            dic["gridf"] = OpmGrid(f"{dic['exe']}/{dic['fol']}/flow/INITIAL.EGRID")
-            dic["initf"] = OpmFile(f"{dic['exe']}/{dic['fol']}/flow/INITIAL.INIT")
+            dic["gridf"] = OpmGrid(f"{dic['fol']}/flow/INITIAL.EGRID")
+            dic["initf"] = OpmFile(f"{dic['fol']}/flow/INITIAL.INIT")
             dic["no_cells"] = (
                 dic["gridf"].dimension[0]
                 * dic["gridf"].dimension[1]
@@ -753,8 +746,8 @@ def positions(dic):
             dic["d_z"] = np.array([0.0] * dic["no_cells"])
             dic["d_z"][dic["actind"]] = list(dic["initf"]["DZ"])
         else:
-            dic["gridf"] = Grid(f"{dic['exe']}/{dic['fol']}/flow/INITIAL.EGRID")
-            dic["initf"] = ResdataFile(f"{dic['exe']}/{dic['fol']}/flow/INITIAL.INIT")
+            dic["gridf"] = Grid(f"{dic['fol']}/flow/INITIAL.EGRID")
+            dic["initf"] = ResdataFile(f"{dic['fol']}/flow/INITIAL.INIT")
             dic["actnum"] = list(dic["gridf"].export_actnum())
             dic["no_cells"] = dic["gridf"].nx * dic["gridf"].ny * dic["gridf"].nz
             dic["actind"] = list(i for i, act in enumerate(dic["actnum"]) if act == 1)
@@ -769,9 +762,7 @@ def positions(dic):
             structured_handling_spe11a(dic)
         else:
             structured_handling_spe11bc(dic)
-    np.savetxt(
-        f"{dic['exe']}/{dic['fol']}/deck/ycenters.txt", dic["ymy_center"], fmt="%.8E"
-    )
+    np.savetxt(f"{dic['fol']}/deck/ycenters.txt", dic["ymy_center"], fmt="%.8E")
 
 
 def sensors(dic):
@@ -847,16 +838,9 @@ def wells(dic):
     if dic["spe11"] == "spe11c":
         dic["wellkh"] = []
         for j in range(dic["wellijk"][0][1], dic["wellijkf"][0][1] + 1):
-            midpoints = dic["zmz_center"] - map_z(dic, j - 1)
+            midpoints = dic["zmz_center"] - map_z(dic, j - 1) - dic["maxelevation"]
             dic["wellkh"].append(
-                pd.Series(
-                    abs(
-                        dic["wellCoord"][0][2]
-                        - map_z(dic, dic["wellijk"][0][1] - 1)
-                        - midpoints
-                    )
-                ).argmin()
-                + 1
+                pd.Series(abs(dic["wellCoord"][0][2] - midpoints)).argmin() + 1
             )
 
 

src/pyopmspe11/utils/runs.py

@@ -28,8 +28,8 @@ def simulations(dic, deck, folder, dryrun):
         flow = dic["only_flow"]
         flag = "--enable-dry-run=1"
     os.system(
-        f"{flow} --output-dir={dic['exe']}/{dic['fol']}/{folder} "
-        f"{dic['exe']}/{dic['fol']}/deck/{deck}.DATA {flag} & wait\n"
+        f"{flow} --output-dir={dic['fol']}/{folder} "
+        f"{dic['fol']}/deck/{deck}.DATA {flag} & wait\n"
     )
 
 
@@ -44,7 +44,6 @@ def plotting(dic):
         None
 
     """
-    os.chdir(f"{dic['exe']}")
     plot_exe = [
         "python3",
         f"{dic['pat']}/visualization/plotting.py",
@@ -72,7 +71,6 @@ def data(dic):
         None
 
     """
-    os.chdir(f"{dic['exe']}")
     data_exe = [
         "python3",
         f"{dic['pat']}/visualization/data.py",

src/pyopmspe11/utils/writefile.py

@@ -25,17 +25,15 @@ def initial(dic):
     mytemplate = Template(filename=f"{dic['pat']}/templates/common/grid_initial.mako")
     filledtemplate = mytemplate.render(**var)
     with open(
-        f"{dic['exe']}/{dic['fol']}/deck/GRID.INC",
+        f"{dic['fol']}/deck/GRID.INC",
         "w",
         encoding="utf8",
     ) as file:
         file.write(filledtemplate)
     mytemplate = Template(filename=f"{dic['pat']}/templates/common/deck_initial.mako")
     var = {"dic": dic}
     filledtemplate = mytemplate.render(**var)
-    with open(
-        f"{dic['exe']}/{dic['fol']}/deck/INITIAL.DATA", "w", encoding="utf8"
-    ) as file:
+    with open(f"{dic['fol']}/deck/INITIAL.DATA", "w", encoding="utf8") as file:
         file.write(filledtemplate)
 
 
@@ -87,7 +85,7 @@ def write_keywords(dic):
         dic[f"{names}"].insert(0, "-- Copyright (C) 2023 NORCE")
         dic[f"{names}"].append("/")
         with open(
-            f"{dic['exe']}/{dic['fol']}/deck/{names.upper()}.INC",
+            f"{dic['fol']}/deck/{names.upper()}.INC",
             "w",
             encoding="utf8",
         ) as file:
@@ -111,7 +109,7 @@ def added_pv(dic, git):
     dic["porv"].insert(0, "-- Copyright (C) 2023 NORCE")
     dic["porv"].append("/")
     with open(
-        f"{dic['exe']}/{dic['fol']}/deck/PVBOUNDARIES.INC",
+        f"{dic['fol']}/deck/PVBOUNDARIES.INC",
         "w",
         encoding="utf8",
     ) as file:
@@ -134,7 +132,7 @@ def opm_files(dic):
     var = {"dic": dic}
     filledtemplate = mytemplate.render(**var)
     with open(
-        f"{dic['exe']}/{dic['fol']}/deck/{dic['fol'].upper()}.DATA",
+        f"{dic['fol']}/deck/{dic['fol'].split('/')[-1].upper()}.DATA",
         "w",
         encoding="utf8",
     ) as file:
@@ -150,7 +148,7 @@ def opm_files(dic):
             )
         filledtemplate = mytemplate.render(**var)
         with open(
-            f"{dic['exe']}/{dic['fol']}/deck/GRID.INC",
+            f"{dic['fol']}/deck/GRID.INC",
             "w",
             encoding="utf8",
         ) as file:
@@ -160,19 +158,19 @@ def opm_files(dic):
     )
     filledtemplate = mytemplate.render(**var)
     with open(
-        f"{dic['exe']}/{dic['fol']}/deck/saturation_functions.py",
+        f"{dic['fol']}/deck/saturation_functions.py",
         "w",
         encoding="utf8",
     ) as file:
         file.write(filledtemplate)
-    os.system(f"chmod u+x {dic['exe']}/{dic['fol']}/deck/saturation_functions.py")
+    os.system(f"chmod u+x {dic['fol']}/deck/saturation_functions.py")
     prosc = subprocess.run(
-        ["python3", f"{dic['exe']}/{dic['fol']}/deck/saturation_functions.py"],
+        ["python3", f"{dic['fol']}/deck/saturation_functions.py"],
         check=True,
     )
     if prosc.returncode != 0:
         raise ValueError(f"Invalid result: { prosc.returncode }")
-    os.system(f"rm -rf {dic['exe']}/{dic['fol']}/deck/saturation_functions.py")
+    os.system(f"rm -rf {dic['fol']}/deck/saturation_functions.py")
     inj_t = 0.0
     skip_unrst = 0
     ini_count = 0
@@ -186,7 +184,7 @@ def opm_files(dic):
             for _ in range(int(inj[0] / inj[1])):
                 times.append(f"{inj[1] + float(times[-1])}")
     with open(
-        f"{dic['exe']}/{dic['fol']}/deck/dt.txt",
+        f"{dic['fol']}/deck/dt.txt",
         "w",
         encoding="utf8",
     ) as file:

src/pyopmspe11/visualization/data.py

@@ -6,7 +6,6 @@
 Script to write the benchmark data
 """
 
-import os
 import argparse
 import warnings
 import csv
@@ -96,13 +95,12 @@ def main():
     dig = {"path": cmdargs["path"].strip()}
     dig["case"] = cmdargs["deck"].strip()
     dig["mode"] = cmdargs["generate"].strip()
-    dig["exe"] = os.getcwd()
-    dig["where"] = f"{dig['exe']}/{dig['path']}/data"
+    dig["where"] = f"{dig['path']}/data"
     dig["use"] = cmdargs["use"].strip()
     dig["nxyz"] = np.genfromtxt(
         StringIO(cmdargs["resolution"]), delimiter=",", dtype=int
     )
-    dig["sim"] = "./" + dig["path"] + "/flow/" + f"{dig['path'].upper()}"
+    dig["sim"] = dig["path"] + "/flow/" + f"{dig['path'].split('/')[-1].upper()}"
     if dig["case"] == "spe11a":
         dig["dense_t"] = (
             np.genfromtxt(StringIO(cmdargs["time"]), delimiter=",", dtype=float) * 3600
@@ -293,7 +291,9 @@ def performance(dig):
         0, dig["times"][-1], round(dig["times"][-1] / dig["sparse_t"]) + 1
     )
     with open(
-        f"{dig['path']}/flow/{dig['path'].upper()}.INFOSTEP", "r", encoding="utf8"
+        f"{dig['path']}/flow/{dig['path'].split('/')[-1].upper()}.INFOSTEP",
+        "r",
+        encoding="utf8",
     ) as file:
         for j, row in enumerate(csv.reader(file)):
             if j > 0:
@@ -1148,7 +1148,9 @@ def static_map_to_report_grid_performance_spatial(dig, dil):
     """
     dil["latest_dts"], infotimes, tsteps = [], [], []
     with open(
-        f"{dig['path']}/flow/{dig['path'].upper()}.INFOSTEP", "r", encoding="utf8"
+        f"{dig['path']}/flow/{dig['path'].split('/')[-1].upper()}.INFOSTEP",
+        "r",
+        encoding="utf8",
     ) as file:
         for j, row in enumerate(csv.reader(file)):
             if j > 0: