Running
=======

This page describes how to run SolvHybrid and extract the results.

Classical Run
-------------

The GitLab repository provides example input files in the
``examples_to_run/`` directory. These reproduce a full **surface** and **bulk**
TI run (corresponding to compute TI1 and TI2 from the reference paper).

The clean initial directory structure should look like::

   ├── ambersub.j         # Example SLURM submission script
   │                      # (can be either a header or a full script)
   ├── cleanup.sh         # Optional script to remove intermediate files
   ├── Input
   │   ├── CONTCAR_ads    # Adsorbed system structure (ASE-compatible)  
   │   ├── CONTCAR_mol    # Isolated molecule structure (ASE-compatible)
   │   ├── CONTCAR_surf   # Clean surface structure (ASE-compatible)  
   │   ├── OUTCAR_ads     # VASP OUTCAR with Hirshfeld charges (adsorbed system)
   │   ├── OUTCAR_mol     # VASP OUTCAR with Hirshfeld charges (molecule)     
   │   └── OUTCAR_surf    # VASP OUTCAR with Hirshfeld charges (surface)
   ├── solv_input.inp     # Input file for SolvHybrid
   └── tmpl               # Templates for sander input files (min, heat, equi, SP)

In the ``solv_input.inp`` file you specify parameters for both TI workflows and
how to launch them (e.g. dry run vs. full run).  
We recommend consulting the :ref:`input file manual <global>` for detailed
parameter explanations.

Run preparation
---------------

Once the input files are prepared, the Python environment activated, the
``PATH`` set to include ``solvhybrid/``, and Amber (or AmberTools) installed,
launch a run with:

.. code-block:: bash

   solvhybrid.py -i solv_input.inp

This generates a ``solvhybrid.log`` file showing the progress of the workflow.

Depending on the chosen run type, different directories will be created to hold
the prepared structures (solvated molecule, solvated surface, solvated adsorbed
system, etc.) from the DFT structure given in input (in vacuum). For example, for the adsorbed system::

   ├── adsorbed
   │   ├── solvent
   │   └── vacuum

Thermodynamic Integration (example with TI_surface)::

   ├── TI_surface
   │   ├── TI_computation            # Actual TI calculations     
   │   │   ├── GALsoft               # One stage of TI1
   │   │   │   ├── 0.005             # One λ-window directory
   │   │   ├── GALunsoft
   │   │   ├── decharge
   │   │   ├── recharge
   │   │   └── vdw_bonded
   │   ├── base_files                # Reference files for non-soft TI stages
   │   └── base_files_soft           # Reference files for soft TI stages (if soft=True)

Single-point jobs::

   ├── SP
   │   ├── adsorbate
   │   ├── molecule
   │   └── surface

Run analysis
------------

After simulations finish, compute adsorption free energies with:

.. code-block:: bash

   solvhybrid.py -a

.. warning::
   This will overwrite any existing ``solvhybrid.log`` file in the current directory.

This step collects:

* ΔG from TI_surface and TI_bulk (if available)
* DFT single-point energies
* MM single-point energies  

and computes:

.. math::

   \Delta G_{\mathrm{ads}}^{\mathrm{solv}}
   \;=\;
   E_{\mathrm{ads}}^{\mathrm{DFT(vac)}} \;-\;
   E_{\mathrm{ads}}^{\mathrm{MM(vac)}} \;+\;
   \Delta G_{\mathrm{bulk\,(TI2)}} \;-\;
   \Delta G_{\mathrm{surface\,(TI1)}}

and writes the results to ``analyse.dat``.

Workflow outputs
----------------

* **TI_surface/**, **TI_bulk/** – Thermodynamic Integration runs  
* **SP/** – single-point MM and DFT energies  
* **adsorbed/**, **surface/**, **molecule/** – prepared systems  
* **tleap/** – tleap logs and intermediate files  
* **solvhybrid.log** – workflow log file