LaGriT Save

LaGriT: Los Alamos Grid Toolbox

LANL Software: LA-CC-15-069 No. C15097

:warning: Warning: There is a known issue with newer compilers that cause Poisson routines to fail. These routines are heavily used in DFNWorks. We have tested and found Clang 14 & 15 to work sucessfully, as well as GNU 9.4 and 11.4 on Ubuntu. A working poisson Docker container is available.

Los Alamos Grid Toolbox (LaGriT) is a library of user callable tools that provide mesh generation, mesh optimization and dynamic mesh maintenance in two and three dimensions. LaGriT is used for a variety of geology and geophysics modeling applications including porous flow and transport model construction, finite element modeling of stress/strain in crustal fault systems, seismology, discrete fracture networks, asteroids and hydrothermal systems.

The general capabilities of LaGriT can also be used outside of earth science applications and applied to nearly any system that requires a grid/mesh and initial and boundary conditions, setting of material properties and other model setup functions. It can also be use as a tool to pre- and post-process and analyze vertex and mesh based data.

PyLaGriT is a Python interface for LaGriT that allows LaGriT functionality to be accessed interactively and in batch mode from Python. This allows the meshing capabilities of LaGriT to be combined with the numeric and scientific functionality of Python. PyLaGriT allows interactive and automated querying of mesh properties, enhanced looping functionality, and user defined error checking based on LaGriT output.

Quick Start

Docker Container

The easiest way to get started with LaGriT is through Docker:

$ docker pull ees16/lagrit:latest
$ docker run -it -v $(pwd):/docker_user/work ees16/lagrit:latest

After the container launches, navigate to:

$ cd bin
$ ./lagrit

Building LaGriT

Dependencies

• CMake is used to generate the build system.
• C, C++, and compatible Fortran compilers. MacOS may need command line tools updated.
• OPTIONAL Exodus libraries installed in TPLs, requires bash and wget.

Note: There is an issue with Poisson Disk Commands using any Brew installed compilers and Gnu 10-12. Works on Clang 14-15 and Gnu 9.4.

Download LaGriT

Download the Https repo by running:

git clone https://github.com/lanl/LaGriT.git
cd LaGriT/

Note for developers, you will need the SSH version to enable Git version control to this repository.

Detailed Instructions for Building LaGriT with cmake and exodus

The simplest way to build LaGriT uses cmake with auto dectection and no options. Type the following (you can name the build directory anything you want).

mkdir build/ && cd build/
cmake .. && make

The cmake command creates the configuration and build files for lagrit and will look similar to this:

-- ==========================================
-- ============Configuring LaGriT============
-- ===================v3.3.3=================
-- Compile LaGriT as a static binary = ON
-- Compile LaGriT with ExodusII = OFF
LaGriT Compiling without ExodusII support.

-- Configuring done
-- Generating done

The make command will compile the libraries and build lagrit. Use make VERBOSE=1 to view compile progress. The lagrit executable is installed in the build/ directory.

• Type ./lagrit to make sure the executable is working.
• On the LaGriT command line type test which will execute a set of LaGriT commands.
• Type finish to exit.

The result will look like:

nnodes:              27                                                         
nelements:            8                                                         
xic(1:3):  1.00 1.25 1.50                                                       
imt(1:3):     1    1    1                                                       
epsilonl:   1.9229627E-13                                                       
     Released Mesh Object: test_hex                                             
lagrit test done.                                                               
 
 Enter a command
finish                                                                          
LaGriT successfully completed             

Testing LaGriT

To test LaGriT, start from top and simply run:

$ python test/runtests.py

Test output can be found in the test/lagrit-tests.log file.

Additional options are available by running:

$ python test/runtests.py --help

(Optional) Build LaGriT with ExodusII

The only LaGriT command used with ExodusII libs is dump/exodus and associated face set and node set commands. To include these commands you will need to install Seacas-Exodus.

Use the install-exodus.sh or MAC_install-exodus.sh to Install Exodus and associated libraries. You can run the file or use the file as a guide to copy and paste commands for installation. The script provides the flags needed by LaGriT and will install seacas in the directory TPLs.

For full and current Exodus Installation instructions, go to: Seacas ExodusII

Install, configure, and build ExodusII with script (use MAC_install-exodus.sh for mac machines):

$ ./install-exodus.sh

Configure and build LaGriT using ExodusII libs:

mkdir build/ && cd build/
cmake .. -DLAGRIT_BUILD_EXODUS=ON
make

Detailed Instructions for Building LaGriT with cmake and exodus

CMake Build Options

You can make changes in the CMakeLists.txt file, but your build directory must be empty for globals to take effect. These options are available on the command line and will update cmake global variables.

To use cmake options, use -D as shown in this example:

mkdir dir_name/ && cd dir_name/
cmake .. -DCMAKE_BUILD_TYPE=Debug -DLAGRIT_BUILD_EXODUS=ON
make

• -D CMAKE_BUILD_TYPE
  • Sets the build type. Choose between Debug and Release.
• -D LAGRIT_BUILD_EXODUS=ON
  • Builds LaGriT with ExodusII if installed.
• -D CMAKE_INSTALL_PREFIX
  • Sets where to install LaGriT when running make install. Defaults to /usr/local/.
• -D LaGriT_BUILD_STATIC
  • Builds LaGriT as a static binary (default; ON) or as a shared library (.so, .dylib, .dll)

Supporting Documentation

• LaGriT Documentation
• PyLaGriT documentation
• lagrit.lanl.gov: Web Page
• Contribution Agreement for External Collaborators
• Copyright License
• Code Development with cmake
• Installation for old LaGriT V2

LaGriT Mesh Images at https://meshing.lanl.gov/proj/screenshots/GRID_GALLERY.html