diff --git a/.gitignore b/.gitignore index 03c9ef29..92268d25 100644 --- a/.gitignore +++ b/.gitignore @@ -38,3 +38,4 @@ test.* .pytest_cache output.txt docs/build +Dockerfile diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index da06bedf..7b2de338 100644 --- a/.pre-commit-config.yaml +++ b/.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: diff --git a/docs/source/extra_files/workflow.png b/docs/source/extra_files/workflow.png new file mode 100644 index 00000000..02d70f03 Binary files /dev/null and b/docs/source/extra_files/workflow.png differ diff --git a/docs/source/file_formats.rst b/docs/source/file_formats.rst new file mode 100644 index 00000000..60a57819 --- /dev/null +++ b/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 diff --git a/docs/source/index.rst b/docs/source/index.rst index 03dd3483..05beb6f1 100644 --- a/docs/source/index.rst +++ b/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