Scientific Computing

SimulationTools Suite

Under Development

Comprehensive documentation for the eight pre-configured solver packages and mesh utilities available on our computational nodes.

Finite Element Library

deal.II

A C++ software library supporting the creation of finite element codes, equipped with adaptive mesh refinement and parallel processing grids.

Earth Engineering Application

Solving high-dimensional ground deformation stress fields and thermal heat vectors.

Execution Setup Sample

bash

1	// Sample deal.II compilation flag
2	cmake -DDEAL_II_WITH_MPI=ON -DDEAL_II_WITH_PETSC=ON .
3	make

PDE Solver Environment

FEniCS Project

An open-source computing platform for solving partial differential equations (PDEs) using finite elements, with high-level Python/C++ interfaces.

Earth Engineering Application

On-demand calculation of multi-physics soil compaction and chemical nutrient diffusions.

Execution Setup Sample

python

1	from fenics import *
2	# Solve Poisson equation on unit square mesh
3	mesh = UnitSquareMesh(32, 32)
4	V = FunctionSpace(mesh, 'P', 1)

3D Mesh Generator

Gmsh

A three-dimensional finite element mesh generator with built-in pre- and post-processing CAD engine models.

Earth Engineering Application

Generating complex tetrahedral volume meshes from digital elevation terrain models.

Execution Setup Sample

bash

1	// Gmsh command to generate a 3D volume mesh from a terrain geometry file
2	gmsh terrain_surface.geo -3 -o terrain_volume.msh

Computational Fluid Dynamics

OpenFOAM

A free, open-source CFD software package configured to solve fluid flows, chemical reactions, and turbulence.

Earth Engineering Application

Simulating watershed precipitation runoff and underground aquifer groundwater hydrology flows.

Execution Setup Sample

bash

1	# Run the OpenFOAM parallel pressure-linked fluid solver
2	mpirun -np 8 simpleFoam -parallel

Linear Algebra Solver Suite

PETSc

Portable, Extensible Toolkit for Scientific Computation. Provides scalable parallel algorithms for solving linear equations.

Earth Engineering Application

Solving large-scale linear equations generated by finite-difference and finite-element solvers.

Execution Setup Sample

bash

1	# Compile code linked against parallel PETSc solvers
2	make PETSC_DIR=/usr/lib/petsc PETSC_ARCH=arch-linux-c-opt

Micromagnetics (GPU)

MuMax3

GPU-accelerated micromagnetic simulation solver that integrates the LLG equation across structured finite-difference grids.

Earth Engineering Application

Calculating magnetic domain wall states and spin orientation dynamics.

Execution Setup Sample

bash

1	// Run MuMax3 script on a target GPU node
2	mumax3 simulation_profile.mx3

Micromagnetics (CPU)

OOMMF

Object Oriented Micromagnetic Framework. NIST's modular micromagnetics package built using C++ and Tcl/Tk interfaces.

Earth Engineering Application

Benchmarking micromagnetic material parameters on server nodes.

Execution Setup Sample

bash

1	# Launch the OOMMF batch solver thread
2	tclsh oommf.tcl boxsi -threads 4 simulation.mif

Scientific Plotting Engine

GNUPlot

Interactive command-line plotting tool for rendering scientific calculations, supporting both 2D and 3D data projections.

Earth Engineering Application

Generating real-time line charts, vector flows, and LST scatter graphics.

Execution Setup Sample

bash

1	# GNUPlot script to plot 3D topography coordinates
2	gnuplot -e "set terminal png; set output 'elevation.png'; splot 'dem_coordinates.txt'"