Fixed documentation

README.md

@@ -1,11 +1,12 @@
-![QMC=Chem logo](https://github.com/trex-coe/qmcchem2/raw/master/docs/QmcChemLogo.png)
+![QMC=Chem logo](https://github.com/trex-coe/qmcchem2/raw/master/docs/source/_static/QmcChemLogo.png)
 
 This repository contains version 2 of QMC=Chem.
 Version 1 is available on [GitLab](https://gitlab.com/scemama/qmcchem).
 QMC=Chem is a quantum Monte Carlo program meant to be used after
 preparing a trial wave function with the
 [Quantum Package](https://github.com/quantumpackage/qp2) code.
 
+The documentation is available on [ReadTheDocs](https://qmcchem2.readthedocs.io/en/latest/index.html).
 
 Requirements
 ------------

docs/source/faq.rst

@@ -40,7 +40,7 @@ while working with QMC=Chem, along with solutions and advice for each scenario.
 
    **Solution**: If I/O is a bottleneck, consider increasing the block time so that computing a block takes at least twice as long as communicating results. This adjustment can help balance computation and I/O operations, improving overall efficiency.
 
-5. **Slow `qmcchem result` Command**
+5. **Slow ``qmcchem result`` Command**
 
    **Issue**: The ``qmcchem result`` command takes a long time to execute.
 

docs/source/index.rst

@@ -29,5 +29,3 @@ in computational chemistry simulations.
    refs
 
 
-
-#

docs/source/installation.rst

@@ -50,19 +50,19 @@ To compile QMC=Chem, execute the following commands:
     ./autogen.sh
     ./configure && make
 
-After compilation, it's necessary to set up the environment for QMC=Chem. The environment variables are specified in the `qmcchemrc` file:
+After compilation, it's necessary to set up the environment for QMC=Chem. The environment variables are specified in the ``qmcchemrc`` file:
 
 .. code-block:: bash
 
     source qmcchemrc
 
-Set the `QMCCHEM_NIC` environment variable to the appropriate network interface, typically `ib0` on HPC systems.
-If needed, set `QMCCHEM_IO=b` to store the results in binary format to accelerate post-processing.
+Set the ``QMCCHEM_NIC`` environment variable to the appropriate network interface, typically ``ib0`` on HPC systems.
+If needed, set ``QMCCHEM_IO=b`` to store the results in binary format to accelerate post-processing.
 
 Tuning for HPC Systems
 ----------------------
 
-For optimal performance, the Intel compiler is recommended. If using gfortran version 12 or higher, add the `-fallow-argument-mismatch` option.
+For optimal performance, the Intel compiler is recommended. If using gfortran version 12 or higher, add the ``-fallow-argument-mismatch`` option.
 
 Example configurations:
 
@@ -81,7 +81,7 @@ Example configurations:
 File Preparation
 ----------------
 
-To prepare files for QMC=Chem, the `save_for_qmcchem` plugin must be installed in Quantum Package:
+To prepare files for QMC=Chem, the ``save_for_qmcchem`` plugin must be installed in Quantum Package:
 
 .. code-block:: bash
 

docs/source/usage.rst

@@ -13,7 +13,7 @@ Preparing the System with Quantum Package
 
 1. **Create the EZFIO Database**
 
-   Begin by creating an `xyz` file with the nuclear coordinates of the system. For a water molecule:
+   Begin by creating an ``xyz`` file with the nuclear coordinates of the system. For a water molecule:
 
    .. code-block:: bash
 
@@ -63,7 +63,7 @@ Performing FN-DMC Calculation with QMC=Chem
 
 2. **Understanding the ``qmcchem`` Command**
 
-   The `qmcchem` command is central to operations in QMC=Chem. Running it without arguments displays a help message:
+   The ``qmcchem`` command is central to operations in QMC=Chem. Running it without arguments displays a help message:
 
    .. code-block:: none