Merge pull request #68 from popelier-group/docs/ichor-summary

add supported file formats

.gitignore

@@ -38,3 +38,4 @@ test.*
 .pytest_cache
 output.txt
 docs/build
+Dockerfile

.pre-commit-config.yaml

@@ -31,7 +31,7 @@ repos:
         exclude: ^(examples/*)|(.github/ISSUE_TEMPLATE/*)|(docs/source/_static/*)|(docs/build)
     -   id: script-must-have-extension
     -   id: forbid-binary
-        exclude: ^(examples/*)|(example_files/*)|(docs/build)
+        exclude: ^(examples/*)|(example_files/*)|(docs/build)|(docs/source/extra_files/*)
 -   repo: https://github.com/Lucas-C/pre-commit-hooks
     rev: v1.5.5
     hooks:

docs/source/file_formats.rst

@@ -0,0 +1,139 @@
+Supported File Formats
+======================
+
+.. list-table:: **AIMALL**
+   :widths: 8 50 10
+   :header-rows: 1
+
+   * - File Type
+     - Description
+     - Role
+   * - .aim
+     - Contains information about the calculation e.g. settings and timings.
+     - Output
+   * - .int
+     - Result file from calculating a set of atomic properties.
+     - Output
+   * - .wfn
+     - AIM traditional wavefunction file.
+     - Input
+   * - .wfx
+     - AIM extended wavefunction file.
+     - Input
+
+.. list-table:: **AMBER**
+   :widths: 8 60 10
+   :header-rows: 1
+
+   * - File Type
+     - Description
+     - Role
+   * - .in
+     - Defines the simulation parameters for AMBER molecular dynamics.
+     - Input
+
+.. list-table:: **CP2K**
+   :widths: 8 60 10
+   :header-rows: 1
+
+   * - File Type
+     - Description
+     - Role
+   * - .inp
+     - Defines the simulation parameters for CP2K molecular dynamics.
+     - Input
+
+.. list-table:: **DL_Poly (DP) / DL_FFLUX (DF)**
+   :widths: 8 50 10
+   :header-rows: 1
+
+   * - File Type
+     - Description
+     - Role
+   * - CONFIG
+     - Contains the geometry information of the system.
+     - Input (DP, DF)
+   * - CONTROL
+     - Defines the control parameters used to run a simulation.
+     - Input (DP, DF)
+   * - FIELD
+     - The dump file of atomic coordinates, velocities and forces.
+     - Output (DP, DF)
+   * - HISTORY
+     - Contains information about the calculation e.g. settings and timings.
+     - Output (DP, DF)
+   * - IQA_ENERGIES
+     - Contains information about the calculation e.g. settings and timings.
+     - Output (DF)
+   * - IQA_FORCES
+     - Contains the IQA forces from FFLUX.
+     - Output (DF)
+
+.. list-table:: **Gaussian**
+   :widths: 8 50 10
+   :header-rows: 1
+
+   * - File Type
+     - Description
+     - Role
+   * - .gau, .gaussianoutput
+     - Contains coordinates (in Angstroms), forces and molecular multipole moments.
+     - Output
+   * - .gjf
+     - Defines input parameters, method, basis set etc. for Gaussian calculations.
+     - Input
+   * - .wfn
+     - AIM traditional wavefunction file.
+     - Input
+   * - .wfx
+     - AIM extended wavefunction file.
+     - Input
+
+.. list-table:: **MORFI**
+   :widths: 8 50 10
+   :header-rows: 1
+
+   * - File Type
+     - Description
+     - Role
+   * - .mout
+     - Output file for in-house code MORFI.
+     - Output
+     * - .pandora
+     - Input file for in-house code MORFI.
+     - Input
+
+.. list-table:: **ORCA**
+   :widths: 8 50 10
+   :header-rows: 1
+
+   * - File Type
+     - Description
+     - Role
+   * - .engrad
+     - Contains the energy and gradient calculated by ORCA.
+     - Output
+   * - .orcainput
+     - Contains input parameters, method, basis set, molecular structure etc.
+     - Input
+   * - .orcaoutput
+     - Contains information such as coordinates and molecular dipoles/quadrupoles.
+     - Input
+
+.. list-table:: **Other**
+   :widths: 8 50
+   :header-rows: 1
+
+   * - File Type
+     - Description
+   * - .model
+     - A model file from a machine learning program, such as FEREBUS.
+   * - .sh
+     - Job submission scripts for various programs such as Gaussian and AIMALL.
+   * - .xyz
+     - A file containing molecular dynamics trajectories.
+
+++++++++
+Workflow
+++++++++
+.. image:: /extra_files/WORKFLOW.png

docs/source/index.rst

@@ -40,6 +40,7 @@ Below are examples of how to use ``ichor``.
    ichor_core_examples_toc
    ichor_hpc_examples_toc
    ichor_cli_examples_toc
+   file_formats
 
 .. toctree::
    :maxdepth: 1