diff --git a/README.rst b/README.rst index f9fba942..a0435a3a 100644 --- a/README.rst +++ b/README.rst @@ -16,7 +16,7 @@ What is gprMax? gprMax is currently released under the `GNU General Public License v3 or higher `_. -gprMax is written in `Python 3 `_ and includes performance-critical parts written in `Cython(OpenMP) `_. +gprMax is written in `Python `_ 3 and includes performance-critical parts written in `Cython `_ with `OpenMP `_. Using gprMax? Cite us --------------------- @@ -77,7 +77,7 @@ You can watch `screencasts that demonstrate the installation and update processe 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. -* `Install Miniconda (Python 3.5 version) `_ (`Miniconda installation instructions `_) +* `Download and install Miniconda `_. Choose the Python 3.6 version for your platform (see the `Quick Install page `_ for help installing Miniconda) * Open a Terminal (Linux/macOS) or Command Prompt (Windows) and run the following commands: .. code-block:: none @@ -98,13 +98,13 @@ If you prefer to install Python and the required Python packages manually, i.e. Linux ^^^^^ -* gcc (https://gcc.gnu.org) should be already installed, so no action is required. +* `gcc `_ should be already installed, so no action is required. macOS ^^^^^ -* Installations of Xcode on macOS come with the LLVM (clang) compiler, but it does not currently support OpenMP, so you must install gcc (https://gcc.gnu.org). This is easily done by installing the Homebrew package manager (http://brew.sh) and running: +* Installations of Xcode on macOS come with the LLVM (clang) compiler, but it does not currently support OpenMP, so you must install `gcc `_. This is easily done by installing the `Homebrew package manager `_ and running: .. code-block:: none @@ -113,9 +113,9 @@ macOS Microsoft Windows ^^^^^^^^^^^^^^^^^ -* Download and install Build Tools for Visual Studio 2017 directly from https://www.visualstudio.com/thank-you-downloading-visual-studio/?sku=BuildTools&rel=15. Use the default installation options. +* Download and install `Build Tools for Visual Studio 2017 `_ directly. Use the default installation options. -You can also download Build Tools for Visual Studio 2017 by going to https://www.visualstudio.com/downloads/, and the section Other Tools and Frameworks -> Build Tools for Visual Studio 2017. +You can download the Build Tools for Visual Studio 2017 by visiting the `Visual Studio downloads page <>`_ and going to the section Other Tools and Frameworks -> Build Tools for Visual Studio 2017. 3. Build and install gprMax --------------------------- @@ -157,7 +157,7 @@ When the simulation is complete you can plot the A-scan using: (gprMax)$ python -m tools.plot_Ascan user_models/cylinder_Ascan_2D.out -Your results should like those from the A-scan from a metal cylinder example in introductory/basic 2D models section (http://docs.gprmax.com/en/latest/examples_simple_2D.html#view-the-results). +Your results should like those from the A-scan from a metal cylinder example in `introductory/basic 2D models section `_ When you are finished using gprMax, the conda environment can be deactivated using :code:`source deactivate` (Linux/macOS) or :code:`deactivate` (Windows). @@ -169,7 +169,7 @@ Argument name Type Description ====================== ======= =========== ``-n`` integer number of times to run the input file. This option can be used to run a series of models, e.g. to create a B-scan with 60 traces: ``(gprMax)$ python -m gprMax user_models/cylinder_Bscan_2D.in -n 60`` ``-restart`` integer model number to start/restart simulation from. It would typically be used to restart a series of models from a specific model number, with the ``-n`` argument, e.g. to restart from A-scan 45 when creating a B-scan with 60 traces: ``(gprMax)$ python -m gprMax user_models/cylinder_Bscan_2D.in -n 15 -restart 45`` -``-task`` integer task identifier (model number) when running simulation as a job array on Open Grid Scheduler/Grid Engine (http://gridscheduler.sourceforge.net/index.html)'). For further details see the Parallel performance section (http://docs.gprmax.com/en/latest/openmp_mpi.html) +``-task`` integer task identifier (model number) when running simulation as a job array on `Open Grid Scheduler/Grid Engine `_). For further details see the `Parallel performance section `_ ``-mpi`` integer number of Message Passing Interface (MPI) tasks, i.e. master + workers, for MPI task farm. This option is most usefully combined with ``-n`` to allow individual models to be farmed out using a MPI task farm, e.g. to create a B-scan with 60 traces and use MPI to farm out each trace: ``(gprMax)$ python -m gprMax user_models/cylinder_Bscan_2D.in -n 60 -mpi 61``. For further details see the Parallel performance section (http://docs.gprmax.com/en/latest/openmp_mpi.html) ``-benchmark`` flag switch on benchmarking mode. This can be used to benchmark the threading (parallel) performance of gprMax on different hardware. For further details see the benchmarking section (http://docs.gprmax.com/en/latest/benchmarking.html) ``--geometry-only`` flag build a model and produce any geometry views but do not run the simulation, e.g. to check the geometry of a model is correct: ``(gprMax)$ python -m gprMax user_models/heterogeneous_soil.in --geometry-only``