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Nathan Mannall
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README.rst
158
README.rst
@@ -17,20 +17,30 @@ Getting Started
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What is gprMax?
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===============
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`gprMax <http://www.gprmax.com>`_ is an open source software that simulates electromagnetic wave propagation. It solves Maxwell's equations in 3D using the Finite-Difference Time-Domain (FDTD) method. gprMax was designed for modelling Ground Penetrating Radar (GPR) but can also be used to model electromagnetic wave propagation for many other applications.
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`gprMax <http://www.gprmax.com>`_ is an open source software that simulates electromagnetic wave
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propagation. It solves Maxwell's equations in 3D using the Finite-Difference Time-Domain (FDTD)
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method. gprMax was designed for modelling Ground Penetrating Radar (GPR) but can also be used to
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model electromagnetic wave propagation for many other applications.
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gprMax is currently released under the `GNU General Public License v3 or higher <http://www.gnu.org/copyleft/gpl.html>`_.
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gprMax is currently released under the `GNU General Public License v3 or higher
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<http://www.gnu.org/copyleft/gpl.html>`_.
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gprMax is principally written in `Python <https://www.python.org>`_ 3 with performance-critical parts written in `Cython <http://cython.org>`_. It includes accelerators for CPU using `OpenMP <http://www.openmp.org>`_, CPU/GPU using `OpenCL <https://www.khronos.org/api/opencl>`_, and GPU using `NVIDIA CUDA <https://developer.nvidia.com/cuda-zone>`_.
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gprMax is principally written in `Python <https://www.python.org>`_ 3 with performance-critical
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parts written in `Cython <http://cython.org>`_. It includes accelerators for CPU using `OpenMP
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<http://www.openmp.org>`_, CPU/GPU using `OpenCL <https://www.khronos.org/api/opencl>`_, and GPU
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using `NVIDIA CUDA <https://developer.nvidia.com/cuda-zone>`_.
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Using gprMax? Cite us
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---------------------
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If you use gprMax and publish your work we would be grateful if you could cite our work using:
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* Warren, C., Giannopoulos, A., & Giannakis I. (2016). gprMax: Open source software to simulate electromagnetic wave propagation for Ground Penetrating Radar, `Computer Physics Communications` (http://dx.doi.org/10.1016/j.cpc.2016.08.020)
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* Warren, C., Giannopoulos, A., & Giannakis I. (2016). gprMax: Open source software to simulate
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electromagnetic wave propagation for Ground Penetrating Radar, `Computer Physics Communications`
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(http://dx.doi.org/10.1016/j.cpc.2016.08.020)
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For further information on referencing gprMax visit the `Publications section of our website <http://www.gprmax.com/publications.shtml>`_.
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For further information on referencing gprMax visit the `Publications section of our website
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<http://www.gprmax.com/publications.shtml>`_.
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Package overview
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@@ -39,33 +49,54 @@ Package overview
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.. code-block:: bash
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gprMax/
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CITATION.cff
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conda_env.yml
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CREDITS
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docs/
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examples/
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gprMax/
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gprMax.toml
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LICENSE
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MANIFEST.in
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README.rst
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setup.py
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reframe_tests/
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testing/
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toolboxes/
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CITATION.cff
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CODE_OF_CONDUCT.md
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conda_env.yml
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CONTRIBUTING.md
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CREDITS
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LICENSE
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MANIFEST.in
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pyproject.toml
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README.rst
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requirements.txt
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setup.py
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* ``CITATION.cff`` is a plain text file with human- and machine-readable citation information for gprMax.
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* ``conda_env.yml`` is a configuration file for Anaconda (Miniconda) that sets up a Python environment with all the required Python packages for gprMax.
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* ``docs/`` contains source files for the User Guide. The User Guide is written using
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`reStructuredText <http://docutils.sourceforge.net/rst.html>`_ markup, and is built using
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`Sphinx <http://sphinx-doc.org>`_ and `Read the Docs <https://readthedocs.org>`_.
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* ``examples/`` is a sub-package where example input files and models are stored.
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* ``gprMax/`` is the main package. Within this package, the main module is ``gprMax.py``
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* ``reframe_tests/`` contains regression tests run using
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`ReFrame <https://reframe-hpc.readthedocs.io>`_. The regression checks are currently specific to
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the `ARCHER2 <https://www.archer2.ac.uk/>`_ system and additional work wil be required to make
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them portable between systems.
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* ``testing/`` is a sub-package which contains test modules and input files.
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* ``toolboxes/`` is a sub-package where useful modules contributed by users are stored.
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* ``CITATION.cff`` is a plain text file with human- and machine-readable citation information for
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gprMax.
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* ``conda_env.yml`` is a configuration file for Anaconda (Miniconda) that sets up a Python
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environment with all the required Python packages for gprMax.
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* ``CONTRIBUTING.md`` is guide on how to contribute to gprMax.
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* ``CREDITS`` contains a list of names of people who have contributed to the gprMax codebase.
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* ``docs`` contains source files for the User Guide. The User Guide is written using `reStructuredText <http://docutils.sourceforge.net/rst.html>`_ markup, and is built using `Sphinx <http://sphinx-doc.org>`_ and `Read the Docs <https://readthedocs.org>`_.
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* ``examples`` is a sub-package where example input files and models are stored.
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* ``gprMax`` is the main package. Within this package, the main module is ``gprMax.py``
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* ``gprMax.toml`` contains build system requirements.
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* ``LICENSE`` contains information on the `GNU General Public License v3 or higher <http://www.gnu.org/copyleft/gpl.html>`_.
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* ``MANIFEST.in`` consists of commands, one per line, instructing setuptools to add or remove files from the source distribution.
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* ``README.rst`` contains getting started information on installation, usage, and new features/changes.
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* ``setup.py`` is the centre of all activity in building, distributing, and installing gprMax, including building and compiling the Cython extension modules.
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* ``testing`` is a sub-package which contains test modules and input files.
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* ``toolboxes`` is a sub-package where useful modules contributed by users are stored.
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* ``LICENSE`` contains information on the
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`GNU General Public License v3 or higher <http://www.gnu.org/copyleft/gpl.html>`_.
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* ``MANIFEST.in`` consists of commands, one per line, instructing setuptools to add or remove files
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from the source distribution.
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* ``pyproject.toml`` contains build system requirements.
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* ``README.rst`` contains getting started information on installation, usage, and new
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features/changes.
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* ``requirements.txt`` is a configuration file for pip that sets up a Python environment with all
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the required Python packages for gprMax.
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* ``setup.py`` is the centre of all activity in building, distributing, and installing gprMax,
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including building and compiling the Cython extension modules.
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Installation
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============
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@@ -79,9 +110,17 @@ The following steps provide guidance on how to install gprMax:
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1. Install Python, the required Python packages, and get the gprMax source
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--------------------------------------------------------------------------
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We recommend using Miniconda to install Python and the required Python packages for gprMax in a self-contained Python environment. Miniconda is a mini version of Anaconda which is a completely free Python distribution (including for commercial use and redistribution). It includes more than 300 of the most popular Python packages for science, math, engineering, and data analysis.
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We recommend using Miniconda to install Python and the required Python packages for gprMax in a
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self-contained Python environment. Miniconda is a mini version of Anaconda which is a completely
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free Python distribution (including for commercial use and redistribution). It includes more than
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300 of the most popular Python packages for science, math, engineering, and data analysis.
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* `Download and install Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_. Choose the Python 3.x version for your platform. We recommend choosing the installation options to: install Miniconda only for your user account; add Miniconda to your PATH environment variable; and register Miniconda Python as your default Python. See the `Quick Install page <https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html>`_ for help installing Miniconda.
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* `Download and install Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_. Choose the
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Python 3.x version for your platform. We recommend choosing the installation options to: install
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Miniconda only for your user account; add Miniconda to your PATH environment variable; and
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register Miniconda Python as your default Python. See the `Quick Install page
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<https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html>`_ for help
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installing Miniconda.
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* Open a Terminal (Linux/macOS) or Command Prompt (Windows) and run the following commands:
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.. code-block:: bash
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@@ -92,11 +131,16 @@ We recommend using Miniconda to install Python and the required Python packages
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$ cd gprMax
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$ conda env create -f conda_env.yml
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This will make sure conda is up-to-date, install Git, get the latest gprMax source code from GitHub, and create an environment for gprMax with all the necessary Python packages.
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This will make sure conda is up-to-date, install Git, get the latest gprMax source code from GitHub,
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and create an environment for gprMax with all the necessary Python packages.
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If you prefer to install Python and the required Python packages manually, i.e. without using
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Anaconda/Miniconda, look in the ``conda_env.yml`` file for a list of the requirements.
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If you are using Arch Linux (https://www.archlinux.org/) you may need to also install ``wxPython``
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by adding it to the conda environment file (``conda_env.yml``).
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If you prefer to install Python and the required Python packages manually, i.e. without using Anaconda/Miniconda, look in the ``conda_env.yml`` file for a list of the requirements.
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If you are using Arch Linux (https://www.archlinux.org/) you may need to also install ``wxPython`` by adding it to the conda environment file (``conda_env.yml``).
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2. Install a C compiler which supports OpenMP
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---------------------------------------------
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@@ -110,7 +154,11 @@ Linux
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macOS
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^^^^^
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* Xcode (the IDE for macOS) comes with the LLVM (clang) compiler, but it does not currently support OpenMP, so you must install `gcc <https://gcc.gnu.org>`_. That said, it is still useful to have Xcode (with command line tools) installed. It can be downloaded from the App Store. Once Xcode is installed, download and install the `Homebrew package manager <http://brew.sh>`_ and then to install gcc, run:
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* Xcode (the IDE for macOS) comes with the LLVM (clang) compiler, but it does not currently support
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OpenMP, so you must install `gcc <https://gcc.gnu.org>`_. That said, it is still useful to have
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Xcode (with command line tools) installed. It can be downloaded from the App Store. Once Xcode is
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installed, download and install the `Homebrew package manager <http://brew.sh>`_ and then to
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install gcc, run:
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.. code-block:: bash
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@@ -119,17 +167,33 @@ macOS
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Microsoft Windows
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^^^^^^^^^^^^^^^^^
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* Download and install Microsoft `Build Tools for Visual Studio 2022 <https://aka.ms/vs/17/release/vs_BuildTools.exe>`_ (direct link). You can also find it on the `Microsoft Visual Studio downloads page <https://visualstudio.microsoft.com/downloads/>`_ by scrolling down to the 'All Downloads' section, clicking the disclosure triangle by 'Tools for Visual Studio 2022', then clicking the download button next to 'Build Tools for Visual Studio 2022'. When installing, choose the 'Desktop development with C++' Workload and select only 'MSVC v143' and 'Windows 10 SDK' or 'Windows 11 SDK options.
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* Set the Path and Environment Variables - this can be done by following the `instructions from Microsoft <https://docs.microsoft.com/en-us/cpp/build/building-on-the-command-line?view=msvc-160#developer_command_file_locations>`_, or manually by adding a form of :code:``C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.23.28105\bin\Hostx64\x64`` (this may vary according to your exact machine and installation) to your system Path environment variable.
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* Download and install Microsoft `Build Tools for Visual Studio 2022
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<https://aka.ms/vs/17/release/vs_BuildTools.exe>`_ (direct link). You can also find it on the
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`Microsoft Visual Studio downloads page <https://visualstudio.microsoft.com/downloads/>`_ by
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scrolling down to the 'All Downloads' section, clicking the disclosure triangle by 'Tools for
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Visual Studio 2022', then clicking the download button next to 'Build Tools for Visual Studio
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2022'. When installing, choose the 'Desktop development with C++' Workload and select only 'MSVC
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v143' and 'Windows 10 SDK' or 'Windows 11 SDK options.
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* Set the Path and Environment Variables - this can be done by following the `instructions from Microsoft
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<https://docs.microsoft.com/en-us/cpp/build/building-on-the-command-line?view=msvc-160#developer_command_file_locations>`_,
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or manually by adding a form of :code:``C:\Program Files
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(x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.23.28105\bin\Hostx64\x64`` (this
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may vary according to your exact machine and installation) to your system Path environment
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variable.
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Alternatively, if you are using Windows 10/11 you can install the `Windows Subsystem for Linux <https://docs.microsoft.com/en-gb/windows/wsl/about>`_ and then follow the Linux install instructions for gprMax. Note however that currently, WSL does not aim to support GUI desktops or applications, e.g. Gnome, KDE, etc....
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Alternatively, if you are using Windows 10/11 you can install the `Windows Subsystem for Linux
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<https://docs.microsoft.com/en-gb/windows/wsl/about>`_ and then follow the Linux install
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instructions for gprMax. Note however that currently, WSL does not aim to support GUI desktops or
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applications, e.g. Gnome, KDE, etc...
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3. Build and install gprMax
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---------------------------
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Once you have installed the aforementioned tools follow these steps to build and install gprMax:
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* Open a Terminal (Linux/macOS) or Command Prompt (Windows), **navigate into the directory above the gprMax package**, and if it is not already active, activate the gprMax conda environment :code:`conda activate gprMax`. Run the following commands:
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* Open a Terminal (Linux/macOS) or Command Prompt (Windows), **navigate into the directory above the
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gprMax package**, and if it is not already active, activate the gprMax conda environment
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:code:`conda activate gprMax`. Run the following commands:
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.. code-block:: bash
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@@ -140,9 +204,12 @@ Once you have installed the aforementioned tools follow these steps to build and
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Running gprMax
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==============
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gprMax is designed as a Python package, i.e. a namespace which can contain multiple packages and modules, much like a directory.
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gprMax is designed as a Python package, i.e. a namespace which can contain multiple packages and
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modules, much like a directory.
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Open a Terminal (Linux/macOS) or Command Prompt (Windows), navigate into the top-level gprMax directory, and if it is not already active, activate the gprMax conda environment :code:`conda activate gprMax`.
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Open a Terminal (Linux/macOS) or Command Prompt (Windows), navigate into the top-level gprMax
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directory, and if it is not already active, activate the gprMax conda environment
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:code:`conda activate gprMax`.
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Basic usage of gprMax is:
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@@ -162,9 +229,11 @@ When the simulation is complete you can plot the A-scan using:
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(gprMax)$ python -m toolboxes.Plotting.plot_Ascan examples/cylinder_Ascan_2D.h5
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Your results should be like those from the A-scan from the metal cylinder example in `introductory/basic 2D models section <http://docs.gprmax.com/en/latest/examples_simple_2D.html#view-the-results>`_
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Your results should be like those from the A-scan from the metal cylinder example in
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`introductory/basic 2D models section <http://docs.gprmax.com/en/latest/examples_simple_2D.html#view-the-results>`_
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When you are finished using gprMax, the conda environment can be deactivated using :code:`conda deactivate`.
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When you are finished using gprMax, the conda environment can be deactivated using
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:code:`conda deactivate`.
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Optional command line arguments
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-------------------------------
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@@ -188,7 +257,10 @@ Argument name Type Description
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Updating gprMax
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===============
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* The safest and simplest way to upgrade gprMax is to uninstall, clone the latest version, and re-install the software. Open a Terminal (Linux/macOS) or Command Prompt (Windows), navigate into the directory above the gprMax package, and if it is not already active, activate the gprMax conda environment :code:`conda activate gprMax`. Run the following command:
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* The safest and simplest way to upgrade gprMax is to uninstall, clone the latest version, and
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re-install the software. Open a Terminal (Linux/macOS) or Command Prompt (Windows), navigate into
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the directory above the gprMax package, and if it is not already active, activate the gprMax conda
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environment :code:`conda activate gprMax`. Run the following command:
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.. code-block:: bash
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@@ -196,13 +268,15 @@ Updating gprMax
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(gprMax)$ git clone https://github.com/gprMax/gprMax.git
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(gprMax)$ pip install -e gprMax
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This will uninstall gprMax, clone the most recent gprMax source code from GitHub, and then build and install the latest version of gprMax.
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This will uninstall gprMax, clone the most recent gprMax source code from GitHub, and then build and
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install the latest version of gprMax.
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Updating conda and Python packages
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----------------------------------
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Periodically you should update conda and the required Python packages. With the gprMax environment deactivated and from the top-level gprMax directory, run the following commands:
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Periodically you should update conda and the required Python packages. With the gprMax environment
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deactivated and from the top-level gprMax directory, run the following commands:
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.. code-block:: bash
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