cleaning scripts

new_prob.sh

 #!/bin/bash
 gyacomo_dir=$(pwd)
+echo "Setup of a new problem in /simulations"
 
 # Check if an argument is provided
 if [ $# -ne 1 ]; then
-    echo "- using 2D Z-pinch parameter"
-    echo "  (you can ask for a cyclone base case by adding "CBC" after the call of the script)"
+echo "- 2D Z-pinch parameter"
+echo "  (add "CBC" for a cyclone base case)"
     inputfile=$gyacomo_dir/scripts/parameter_files/parameters_Zpinch.in
 else
     # Check the value of the argument
-    if [ "$1" = "help" ]; then
-        echo "This script setup a new simulation directory in /simulation"
-        echo "The basic setup is a small 2D z-pinch simulation."
-        echo "You can ask a cyclone base case (more expensive) by typing sh new_prob.sh CBC"
-        exit 1
-    elif [ "$1" = "CBC" ]; then
-        echo "- using CBC parameter"
+if [ "$1" = "CBC" ]; then
+        echo "- CBC parameter"
         inputfile=$gyacomo_dir/scripts/parameter_files/parameters_CBC.in
     elif [ "$1" = "ZBC" ]; then
-        echo "- using Zpinch parameter"
+        echo "- 2D Z-pinch parameter"
         inputfile=$gyacomo_dir/scripts/parameter_files/parameters_Zpinch.in
     else
-        echo "ERROR STOP unknown entry"
-        echo "(usage: sh new_prob.sh [CBC or ZBC (opt)])"
+        echo "- ERROR STOP unknown entry"
+        echo "  (usage: sh new_prob.sh [CBC or ZBC (opt)] [folder_name (opt)])"
         exit 1
     fi
 fi
-echo "Setup of a new problem in the simulations directory..."
 
 mkdir -p $gyacomo_dir/simulations
 cd $gyacomo_dir/simulations
@@ -45,7 +40,7 @@ get_next_problem_folder() {
 # Function to display usage information
 usage() {
     echo "- usage: $0 [base_case_type] [folder_name]"
-    echo "If folder_name is not provided, default is the next available 'problem_xx'"
+    echo "  If folder_name is not provided, default is the next available 'problem_xx'"
     exit 1
 }
 
@@ -59,7 +54,7 @@ folder_name="${2:-$(get_next_problem_folder)}"
 
 # Check if the executable exists
 if [ ! -x $gyacomo_dir/bin/gyacomo23_dp ]; then
-    echo "Error: Executable 'bin/gyacomo23_dp' not found or not executable. Please compile the code first."
+    echo "- Error: Executable 'bin/gyacomo23_dp' not found or not executable. Please compile the code first."
     exit 1
 fi
 
@@ -70,7 +65,7 @@ mkdir -p "$folder_name"
 cp $inputfile "$folder_name/params.in"
 
 # Copy the marconi job submission example
-cp $gyacomo_dir/scripts/parameter_files/submit_marconi_example.cmd "$folder_name/submit_marconi.cmd"
+cp $gyacomo_dir/scripts/shell_scripts/submit_marconi_example.cmd "$folder_name/submit_marconi.cmd"
 
 # Copy tutorial file
 cp $gyacomo_dir/scripts/tutorials/tutorial.md "$folder_name/."
@@ -82,6 +77,11 @@ ln -s $gyacomo_dir/bin/gyacomo23_dp "$folder_name/gyacomo.exe"
 ln -s $gyacomo_dir/scripts/python_utilities/minimal_analysis.py "$folder_name/."
 ln -s $gyacomo_dir/scripts/python_utilities/movie.py "$folder_name/."
 
-echo "- folder 'simulations/$folder_name' created with symbolic link to the executable."
-echo "- check the tutorial file in there!"
-echo "...done"
+echo "- simulations/$folder_name created"
+echo "  (check the tutorial file in there)"
+
\ No newline at end of file
+echo "You can now run Gyacomo with"
+echo "  cd simulations/$folder_name"
+echo "  mpirun -np 4 ./gyacomo.exe 1 4 1"
+echo "Then use the example analysis script"
+echo "  python3 minimal_analysis.py"
\ No newline at end of file

scripts/tutorials/spcpc_installation_auto.sh

@@ -17,7 +17,7 @@ echo '=============================================='
 
 # 1. Prelude
 # 1.1 - First, we clone the repository.
-echo "1. Clone the directory "
+echo "1/6 Clone the directory "
 git clone https://gitlab.epfl.ch/ahoffman/gyacomo.git &> gyacomo_clone.out
 cd gyacomo
 
@@ -44,12 +44,12 @@ mkdir lib
 # Each of these libraries must be installed in the `/lib` folder (here `/gyacomo/lib`).
 
 echo "      repository cloned"
-echo ______________________________________________
+echo "______________________________________________"
 
 #############################################
 ### 2. Futils installation
 # 2.1 - We navigate to our `lib` folder and clone first the `futils` library.
-echo "2. Installing Futils"
+echo "2/6 Installing Futils"
 cd lib
 echo "      clone repository"
 git clone https://c4science.ch/diffusion/FUTILS/futils.git &> futils_clone.out
@@ -79,11 +79,11 @@ make install &> futils_make_install.out
 # 2.7 - We can test now the installation and linkage of futils by typing `make` in `/gyacomo`. The compilation should pass the previously observed error and halt now with an error at the call of `fftw` routines in `src.fourier_mod.F90`.
 cd ../../
 echo "      Futils installed"
-echo ______________________________________________
+echo "______________________________________________"
 
 #############################################
 ### 3. FFTW3 installation
-echo "3. Installing FFTW3"
+echo "3/6 Installing FFTW3"
 echo "      download source"
 # 3.1 - We download the `fftw` zip directory, unzip it, and navigate to the directory.
 wget http://www.fftw.org/fftw-3.3.10.tar.gz &> wget_fftw3.out
@@ -118,12 +118,12 @@ cd ../
 
 # 3.8 - We test the installation and linkage by typing `make` in `/gyacomo`. The compilation should halt with an error at the call of `FM` routines in the `src/coeff_mod.F90` file.
 echo "      FFTW3 installed"
-echo ______________________________________________
+echo "______________________________________________"
 
 
 #############################################
 ## 4. FM installation
-echo "4. Installing FM"
+echo "4/6 Installing FM"
 
 # 4.1 - Navigate back to the main `lib` directory (e.g., `/gyacomo/lib/`) and download the zipped folder.
 echo "      download source"
@@ -168,24 +168,24 @@ mv *.mod mod
 
 cd ../
 echo "      FM installed"
-echo ______________________________________________
+echo "______________________________________________"
 
 #############################################
 # 5 compilation of GYACOMO
 cd ../
-echo "5. Compilation of GYACOMO"
+echo "5/6 Compilation of GYACOMO"
 make 2>&1 | tee make.out
-echo ______________________________________________
+echo "______________________________________________"
 
 #############################################
 # 6. setup of a testcase
-echo "6. Test case setup"
+echo "6/6 Test case setup"
 make new_prob
 echo "-- GYACOMO is ready --"
 echo "you can test running it using:"
 echo "cd gyacomo/simulations/problem_01"
 echo "mpirun -np 4 ./gyacomo.exe 1 4 1"
-echo ______________________________________________
+echo "______________________________________________"
 
 #############################################
 # 7. Epilogue