vel-perplex.sh is a shell script to execute BUILD, VERTEX, WERAMI functions of [Perple_X (Connolly 2005, Connolly 2009](https://www.perplex.ethz.ch/) automatically.
The format of the directory set-up to be followed as shown here for easier workflow according to the script. Any changes here needs to be reflected on the script as well.
Here, 1-Project-Vel is the main directory and datafiles & comp-input are the sub-directories and vel-perplex.sh is the main script.
Na2O
MgO
Al2O3
SiO2
K2O
CaO
FeO
3.21 8.73 15.48 48.3 1.21 9.52 8.87
Here the directory name for the composition files are to be followed as per the thermodynamic datfile.
For example, hp represent the directory that contains the compositions to be calculated for Holland & Powell thermodynamic datafile, similarly stx for Stixrude & Lithgow-Bertelloni etc. The script is made such that it checks with the first part of the thermodynamic datafile name input by the user (the part before the year in thermodynamic datafile name). The script will run only if it matches.
The names of composition and the directories are case sensitive. The script is set up such that it takes the names till the line before it finds a line starting with a numeric character which are the proportion of the components.
To run the script make it an executable and then
./vel-perplex.sh
# Prompt the user for the project name
read -p "Enter a name for the project (this name shall contain short info about themodynamic datafile and the composition): " project_name
echo "Your project is ${project_name}.dat"
echo -e "\n"
# Set a default value for the thermodynamic data file if the user presses enter
echo "Default Thermodynamic data file is hp633ver.dat"
echo "Some available examples of thermodynamic data files are: " #hp02ver.dat, hp633ver.dat, stx21ver.dat and stx24ver.dat
ls datafiles/hp*
ls datafiles/stx*
read -p "Enter the thermodynamic data file name (press Enter for default): " thermo_datafile
thermo_datafile=${thermo_datafile:-hp633ver.dat}
# Check if the thermodynamic data file exists in the /datafiles directory
if [ ! -f "$datafiles_dir/$thermo_datafile" ]; then
echo "Error: Thermodynamic data file $thermo_datafile not found in $datafiles_dir."
exit 1
fi
echo "Thermodynamic data file is $thermo_datafile"
echo -e "\n"
# Set a default value for the computational option file if the user presses enter
echo "Default Computational option file is perplex_option.dat"
echo "Some available examples of computational option files are: " #hp02ver.dat, hp633ver.dat, stx21ver.dat and stx24ver.dat
ls datafiles/perplex_option*
read -p "Enter the Computational option file name (press Enter for default): " optn_file
optn_file=${optn_file:-perplex_option.dat}
# Check if the computational option file exists in the /datafiles directory
if [ ! -f "$datafiles_dir/$optn_file" ]; then
echo "Error: Computational option file $optn_file not found in $datafiles_dir."
exit 1
fi
echo "Computational option file is $optn_file"
echo -e "\n"
# Set a default value for the solution model file if the user presses enter
echo "Default Solution model file is solution_model.dat"
echo "Available Solution model files are: " #solution_model.dat, stx21_solution_model.dat and stx24_solution_model.dat
ls datafiles/*solution*
read -p "Enter the solution model file name (press Enter for default): " soln_mod
soln_mod=${soln_mod:-solution_model.dat}
# Check if the solution model file exists in the /datafiles directory
if [ ! -f "$datafiles_dir/$soln_mod" ]; then
echo "Error: Solution model file $soln_mod not found in $datafiles_dir."
exit 1
fi
echo "Solution Model is $soln_mod"
echo -e "\n"
#Composition Name
#echo "Currently available Compositions are:"
#ls comp-input/
#read -p "Enter a name of the Composition: " composition_name
# Check if the solution model file exists in the /datafiles directory
#composition_file="$comp_files/$composition_name"
#!/bin/bash
# Ask the user whether they want Crust or Mantle
read -p "Do you want to calculate for Crust or Mantle? " layer_type
# Set the comp_files directory based on the user's choice
if [ "$layer_type" == "Crust" ]; then
comp_files="comp-input/Crust"
elif [ "$layer_type" == "Mantle" ]; then
comp_files="comp-input/Mantle"
else
echo "Invalid choice! Please select either Crust or Mantle."
exit 1
fi
# Extract the prefix from the thermo_datafile
#thermo_datafile="hp02ver.dat" # Example; replace with actual input
prefix=$(echo "$thermo_datafile" | sed -E 's/[0-9]+.*//')
# Now, display available compositions based on the extracted prefix and layer
echo "Currently available Compositions for the selected thermodynamics data file are:"
ls "$comp_files/$prefix"
# Ask for the composition name
read -p "Enter a name of the Composition: " composition_name
# Construct the path to the composition file
composition_file="$comp_files/$prefix/$composition_name"
# Check if the composition file exists
if [ -f "$composition_file" ]; then
echo "Composition file found: $composition_file"
else
echo "Composition file not found: $composition_file"
fi
# Initialize arrays for components and mass amounts
components=()
mass_amounts=""
# Check if the composition file exists
if [[ -f "$composition_file" ]]; then
# Read the components (all lines except the last one)
while IFS= read -r line; do
# Add line to components array until the last line
components+=("$line") # Add each line to the components array
done < <(head -n -1 "$composition_file") # Read all but the last line
# Read the mass amounts from the last line
read -r mass_amounts < <(tail -n 1 "$composition_file")
# Check if mass amounts are not empty
if [[ -z "$mass_amounts" ]]; then
echo "Error: No mass amounts found in $composition_file."
exit 1
fi
else
echo "Error: Composition file $composition_file not found in $comp_files."
exit 1
fi
echo "Composition is $composition_name"
The directories are arranged based on the script design. *Any changes in directory path/file path needs to be reflected here.
{
echo "$project_name" # Project name
echo "$datafiles_dir/$thermo_datafile" # Thermodynamic data file
echo "$datafiles_dir/$optn_file" # Computational option file
echo "n" # Transform components (Y/N)
echo "2" # Computational mode (2d grid)
echo "n" # Calculations with saturated fluids (Y/N)
echo "n" # Calculations with saturated components (Y/N)
echo "n" # Use chemical potentials, activities, fugacities (Y/N)
# Loop through the components array and echo each component
for component in "${components[@]}"; do
echo "$component" # Thermodynamic components
done
echo "" # End of thermodynamic components selection
echo "n" # Make P dependent on T (Y/N)
echo "2" # Select x-axis variable (2 for T(K))
echo "273" # Minimum T(K)
echo "2000" # Maximum T(K)
echo "15" # Minimum P(bar)
echo "150000" # Maximum P(bar)
echo "y" # Specify component amounts by mass (Y/N)
echo "$mass_amounts" # Mass amounts for components
echo "y" # Output a print file (Y/N)
echo "y" # Exclude pure/endmember phases (Y/N)
echo "n" # Do you want to be prompted for phases (Y/N)?
echo "ne" # Enter names, left justified, 1 per line, press <enter> to finish:
echo "ab" # Enter names, left justified, 1 per line, press <enter> to finish:
echo "san" # Enter names, left justified, 1 per line, press <enter> to finish:
echo "lc" # Enter names, left justified, 1 per line, press <enter> to finish:
echo "sil8L" # Enter names, left justified, 1 per line, press <enter> to finish:
echo "qjL" # Enter names, left justified, 1 per line, press <enter> to finish:
echo "qHL" # Enter names, left justified, 1 per line, press <enter> to finish:
echo "q8L" # Enter names, left justified, 1 per line, press <enter> to finish:
echo "crst" # Enter names, left justified, 1 per line, press <enter> to finish:
echo "trd" # Enter names, left justified, 1 per line, press <enter> to finish:
echo "qL" # Enter names, left justified, 1 per line, press <enter> to finish:
echo "q" # Enter names, left justified, 1 per line, press <enter> to finish:
echo "kjdTH" # Enter names, left justified, 1 per line, press <enter> to finish:
echo "kjdh" # Enter names, left justified, 1 per line, press <enter> to finish:
echo "qTHL" # Enter names, left justified, 1 per line, press <enter> to finish:
echo "qWL" # Enter names, left justified, 1 per line, press <enter> to finish:
echo "anL" # Enter names, left justified, 1 per line, press <enter> to finish:
echo ""
echo "y" # Include solution models (Y/N)
echo "$datafiles_dir/$soln_mod" # Solution model file
echo "O(HP)" # Solution Model Phases
echo "Sp(HP)" # Solution Model Phases
echo "Gt(HP)" # Solution Model Phases
echo "Opx(HP)" # Solution Model Phases
#echo "Cpx(HP)" # Solution Model Phases
echo "Pl(h)" # Solution Model Phases
echo "Wad" # Solution Model Phases
#echo "San(TH)" # Solution Model Phases
#echo "C2_c(jca)" # Solution Model Phases
#echo "GlTrTsPg" # Solution Model Phases
#echo "B" # Solution Model Phases
#echo "Chl(HP)" # Solution Model Phases
#echo "KN-Phen" # Solution Model Phases
#echo "T" # Solution Model Phases
#echo "A-phase" # Solution Model Phases
#echo "Atg" # Solution Model Phases
echo "" # End of solution model selection
echo "${project_name}" # Calculation title (same as project name)
} > "$input_file"
All input parameters are based on wrok preferences. Suggestion: Run the build manually before executing the code. The input prompts changes based on the requiremnts of the job
input_file="werami_input.txt" # For all the input and their functions check https://www.perplex.ethz.ch/perplex_66_seismic_velocity.html#top
{
echo "$project_name" # Project name
echo "2" # Operational mode: properties on a 2d grid
echo "38" # Select a property: multiple property output
echo "1" # Properties of the system
echo "n" # Include fluid in computation of aggregate (or modal) properties (y/n)?
echo "2" # Property: Density (kg/m3)
echo "13" # Property: P-wave velocity (Vp, km/s)
echo "14" # Property: S-wave velocity (Vs, km/s)
echo "3" # Property: Specific heat capacity (J/K/m3)
echo "19" # Property: Heat Capacity (J/K/kg)
echo "27" # Property: P-wave velocity T derivative (km/s/K)
echo "28" # Property: S-wave velocity T derivative (km/s/K)
echo "32" # Property: P-wave velocity P derivative (km/s/bar)
echo "33" # Property: S-wave velocity P derivative (km/s/bar)
echo "0" # End property selection
echo "n" # Change default variable range: No
echo "4" # Grid resolution: 313 x 313 nodes
echo "y" # Continue with operation
echo "0" # End werami
} > "$input_file"
All input parameters are based on wrok preferences. Suggestion: Run the build manually before executing the code. The input prompts changes based on the requiremnts of the job
The script is designed such a way all the outputs will be visble in a directory creadted during execution named after the project name as per user input and all the .tab files containig the metadata and the various physical properties based varying with Pressure and Temperature is also placed onto another directory called output-files
# Extract the composition data (lines 29-34)
comp_data=$(sed -n '29,35p' "${project_name}.dat" | awk '{print $1, $3}')
# Extract T and P ranges (lines 65-66)
t_p_range=$(sed -n '81,82p' "${project_name}.dat" | awk '{print $1, $2}')
# Format composition data (columns 1 and 3)
comp_elements=$(echo "$comp_data" | awk '{printf "%s\t", $1}') # Elements separated by tab
comp_amounts=$(echo "$comp_data" | awk '{printf "%.2f\t", $2}') # Amounts with two decimal places
# Format T(K) and P(bar) range
T_min=$(echo "$t_p_range" | awk 'NR==2 {print $2}')
T_max=$(echo "$t_p_range" | awk 'NR==1 {print $2}')
P_min=$(echo "$t_p_range" | awk 'NR==2 {print $1}')
P_max=$(echo "$t_p_range" | awk 'NR==1 {print $1}')
# Get the current date
current_date=$(date)
Here make changes as per the first project file (.dat) file created after running the build. The temperature and pressure ranges need to be extracted from whci line it is on the project file.