Updated the instructions for compilation using cmake

compilation_instructions.md

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+## SPEC complition instructions
+
+Guide for installing SPEC including the python wrappers, relies on usign cmake
+
+### Compilation
+
+Get the repository and install the necessary compilers and libraries
+```
+git clone [email protected]:PrincetonUniversity/SPEC.git 
+conda create -n "spec_wrapper" python=3.11
+conda activate spec_wrapper
+conda install gcc_linux-64 gxx_linux-64 gfortran_linux-64
+conda install hdf5 openblas libopenblas fftw scalapack openmpi cmake ninja
+conda install h5py matplotlib f90nml scipy scikit-build mpi4py ipython
+pip install f90wrap
+```
+
+Link to the correct `f2py`
+```
+ln -s ~/anaconda3/envs/spec_wrapper/bin/f2py ~/anaconda3/envs/spec_wrapper/bin/f2py3
+```
+
+If necessary, unset HDF5 and FFTW environmental variables
+```
+unset HDF5, HDF5_ROOT, HDF5_HOME, FFTW, FFTW_DIR
+```
+
+Finally, install SPEC and the wrapper (logs will be in `compile.log`)
+```
+pip install -v . 2>&1 | tee compile.log
+```
+
+Install the `py_spec` python library
+```
+cd Utilities/pythontools/
+pip install -e .
+```
+
+
+### Testing your SPEC installation
+
+First, verify that the stand-alone executable is usable.
+A few test cases are provided in `InputFiles/TestCases`.
+
+Create a new directory for SPEC runs and change into it
+
+```bash
+mkdir ~/SPEC_runs
+cd ~/SPEC_runs
+```
+
+Copy a demo input file into the current working directory:
+
+```bash
+cp ~/SPEC/InputFiles/TestCases/G3V01L0Fi.001.sp .
+```
+
+Call SPEC with an input file (`*.sp`) as argument on the command line:
+
+```bash
+xspec G3V01L0Fi.001.sp
+```
+
+You should see the screen output of the SPEC run.
+Among the last lines should be something similar to this:
+
+```
+ending :       0.88 : myid=  0 ; completion ; time=      0.88s =     0.01m =   0.00h =  0.00d ; date= 2022/02/17 ; time= 17:35:33 ; ext = G1V02L0Fi.001                                               
+ending :            : 
+xspech :            :
+xspech :       0.88 : myid=  0 : time=    0.01m =   0.00h =  0.00d ;
+```
+
+This indicates that the stand-alone executable is usable.
+
+Next, the python wrapper is tested.
+
+1. Check that the SPEC version can be found:
+
+    ```bash
+    python -c "from spec import spec_f90wrapped as spec; print('SPEC version: {:}'.format(spec.constants.version))"
+    ```
+
+    This should print a message like "SPEC version: 3.1" on the screen.
+
+2. Check that the Python wrapper can be used as a stand-alone code:
+
+    ```bash
+    OMP_NUM_THREADS=1 python ~/SPEC/Utilities/python_wrapper/spec/core.py G3V01L0Fi.001.sp
+    ```
+
+    This should conclude with the message `SPEC called from python finished!`.
+
+3. Run the optimization example code:
+
+    ```bash
+    OMP_NUM_THREADS=1 python ~/SPEC/Utilities/python_wrapper/examples/example.py
+    ```
+
+    This should run a basic optimization problem,
+    where the SPEC inputs are controlled via `scipy.optimize`.
+
+4. Run the interactive re-convergence example code:
+
+    ```bash
+    OMP_NUM_THREADS=1 python ~/SPEC/Utilities/python_wrapper/examples/example_2.py
+    ```
+
+    This should compute a SPEC equilibrium, then change the central pressure,
+    re-converge SPEC, etc. for a set of five values of the central pressure
+    in a two-volume classical Stellarator case.
+    After the pressure scan with re-convergence,
+    a plot of the MHD energy vs. the central pressure is shown.