add perplex-burnman-aspect workflow

Author: bobmyhill

.gitignore

@@ -7,4 +7,5 @@
 *.tmp
 *.pyc
 /contrib/perplex/perplex-installer
-/contrib/perplex/iron_olivine_lo_res
+/contrib/perplex/iron_olivine_lo_res
+/contrib/perplex/ASPECT_1D_isentrope_properties.txt

contrib/perplex/Readme.md

@@ -1,7 +1,9 @@
 # Perple_X P-T Table Generation
 
-This repository contains scripts and resources to download, install, and use **Perple_X** to generate and read a low-resolution thermodynamic table for an iron-olivine system. It can be used as a template to
-create and read your own tables.
+This repository contains scripts and resources to download, install, and use **Perple_X** to generate and read a low-resolution thermodynamic table for an iron-olivine system. It also contains a script to
+create a smoothed 1D adiabatic profile for use in ASPECT (https://github.com/geodynamics/aspect/).
+
+These scripts can be used as a template to create, read and process your own tables.
 
 ## Contents
 
@@ -12,10 +14,18 @@ create and read your own tables.
   A Python script to generate a low-resolution thermodynamic table using Perple_X. This script calls Perple_X programs and configures the run for a simplified system.
 
 - **read_lo_res_table.py**  
-  A Python script to read and parse the generated low-resolution table (e.g., from `table.txt`) for further analysis or plotting.
+  A Python script to read and parse the generated low-resolution table for further
+  analysis and plotting.
+
+- **generate_aspect_compatible_1D_adiabat_table.py**
+  A Python script to generate a smoothed table of properties along a 1D isentrope using
+  a generated table.
 
 - **perplex_utils.py**  
-  A python file containing useful Perple_X-related functions.
+  A python file containing useful Perple_X-related functions. The start of the file defines
+  some database dictionaries for the Holland and Powell (2018),
+  and Stixrude and Lithgow-Bertelloni (2021, 2024) datasets which can be passed to the other
+  functions or used as a basis for your own dictionaries.
 
 ## Getting Started
 
@@ -41,9 +51,18 @@ create and read your own tables.
    python read_lo_res_table.py
    ```
 
-   This script parses the output table for further use (e.g., plotting or machine learning workflows).
+   This script parses the output table for further use (e.g., evaluating properties or plotting).
+
+4. **Create ASPECT compatible Table:**
+
+   ```bash
+   python generate_aspect_compatible_1D_adiabat_table.py
+   ```
+
+   This script creates an ASPECT-compatible table.
 
 ## Notes
 
-- The resolution and thermodynamic scope in this example are intentionally simplified.
+- The resolution and thermodynamic scope in this example are intentionally simplified. You will
+  need to change the scripts if you want to increase the resolution. 
 - Make sure to review Perple_X license and citation guidelines when using in published work.

contrib/perplex/create_lo_res_table.py

@@ -9,68 +9,71 @@
 from perplex_utils import run_vertex, run_pssect
 from perplex_utils import create_perplex_table
 
-project_name = "iron_olivine_lo_res"
-database = databases["stx24"]
-composition = burnman.Composition(
-    {"MgO": 1.8, "FeO": 0.2, "SiO2": 1.0, "Fe": 0.1}, "molar"
-)
-pressure_range = [1.0e5, 10.0e9]
-temperature_range = [200.0, 3000.0]
-n_pressures = 11
-n_temperatures = 11
-outfile = "iron_olivine_lo_res_table.dat"
+if __name__ == "__main__":
+    project_name = "iron_olivine_lo_res"
+    database = databases["stx24"]
+    composition = burnman.Composition(
+        {"MgO": 1.8, "FeO": 0.2, "SiO2": 1.0, "Fe": 0.1}, "molar"
+    )
+    pressure_range = [1.0e5, 10.0e9]
+    temperature_range = [200.0, 3000.0]
+    n_pressures = 11
+    n_temperatures = 11
+    outfile = "iron_olivine_lo_res_table.dat"
 
-perplex_dir = os.path.join(os.getcwd(), "perplex-installer/Perple_X")
-perplex_bindir = os.path.join(os.getcwd(), "perplex-installer/Perple_X/bin")
+    perplex_dir = os.path.join(os.getcwd(), "perplex-installer/Perple_X")
+    perplex_bindir = os.path.join(os.getcwd(), "perplex-installer/Perple_X/bin")
 
-try:
-    shutil.rmtree(project_name)
-    print(f"Deleted old project directory ({project_name}).")
-except FileNotFoundError:
-    pass
+    try:
+        shutil.rmtree(project_name)
+        print(f"Deleted old project directory ({project_name}).")
+    except FileNotFoundError:
+        pass
 
-os.mkdir(project_name)
-os.chdir(project_name)
-print(f"Now working in newly created directory ({os.getcwd().split("/")[-1]}).")
+    os.mkdir(project_name)
+    os.chdir(project_name)
+    print(f"Now working in newly created directory ({project_name}).")
 
-print("Creating local copies of requested thermodynamic data files...")
-endmember_file = os.path.join(perplex_dir, "datafiles", database["data_file"])
-solution_file = os.path.join(perplex_dir, "datafiles", database["solution_model_file"])
-shutil.copyfile(endmember_file, os.path.join(os.getcwd(), database["data_file"]))
-shutil.copyfile(
-    solution_file, os.path.join(os.getcwd(), database["solution_model_file"])
-)
-perplex_option_file = "burnman_perplex_options.dat"
+    print("Creating local copies of requested thermodynamic data files...")
+    endmember_file = os.path.join(perplex_dir, "datafiles", database["data_file"])
+    solution_file = os.path.join(
+        perplex_dir, "datafiles", database["solution_model_file"]
+    )
+    shutil.copyfile(endmember_file, os.path.join(os.getcwd(), database["data_file"]))
+    shutil.copyfile(
+        solution_file, os.path.join(os.getcwd(), database["solution_model_file"])
+    )
+    perplex_option_file = "burnman_perplex_options.dat"
 
-with open(perplex_option_file, "w") as f:
-    f.write("sample_on_grid            F")
+    with open(perplex_option_file, "w") as f:
+        f.write("sample_on_grid            F")
 
-print("Making build file...")
-make_build_file(
-    perplex_bindir,
-    project_name,
-    database,
-    perplex_option_file,
-    composition,
-    pressure_range,
-    temperature_range,
-    verbose=False,
-)
+    print("Making build file...")
+    make_build_file(
+        perplex_bindir,
+        project_name,
+        database,
+        perplex_option_file,
+        composition,
+        pressure_range,
+        temperature_range,
+        verbose=False,
+    )
 
-print("Running vertex...")
-run_vertex(perplex_bindir, project_name, verbose=False)
+    print("Running vertex...")
+    run_vertex(perplex_bindir, project_name, verbose=False)
 
-print("Running pssect...")
-run_pssect(perplex_bindir, project_name, convert_to_pdf=False, verbose=False)
+    print("Running pssect...")
+    run_pssect(perplex_bindir, project_name, convert_to_pdf=False, verbose=False)
 
-print("Creating BurnMan-readable table...")
-create_perplex_table(
-    perplex_bindir,
-    project_name,
-    outfile,
-    n_pressures,
-    n_temperatures,
-    pressure_range,
-    temperature_range,
-)
-print("Processing complete.")
+    print("Creating BurnMan-readable table...")
+    create_perplex_table(
+        perplex_bindir,
+        project_name,
+        outfile,
+        n_pressures,
+        n_temperatures,
+        pressure_range,
+        temperature_range,
+    )
+    print("Processing complete.")

contrib/perplex/download_and_install_perplex.sh

@@ -1,9 +1,12 @@
 #!/bin/bash
 
 if [ -d perplex-installer ]; then
-    rm -rf perplex-installer
+    cd perplex-installer
+    git pull --recurse-submodules origin main
+    cd ..
+else
+    git clone --recurse-submodules https://github.com/bobmyhill/perplex-installer.git
+    cd perplex-installer
+    ./install_perplex.sh
+    cd ..
 fi
-git clone --recursive [email protected]:bobmyhill/perplex-installer.git
-cd perplex-installer
-./install_perplex.sh
-cd ..