Center for Scientific Software Infrastructure

Software

Faculty and researchers affiliated with the Center for Scientific Software Infrastructure have open source software to address a variety of research questions. The list below contains links to descriptions and downloads for these software packages. To submit software for listing here, please fill out this form.

SOFTWARE CATALOG

Title	Related Field(s)	Description	Author(s)
ALPScore	Physics	Applications and Libraries for Physics Simulations Core libraries (ALPSCore) provides a set of well-tested, robust and standardized components for numerical simulations of condensed matter systems, in particular systems with strongly correlated electrons.	E. Gull et al.
CRIMSON	Physics, Multiphysics	An integrated software for image-based modeling of hemodynamics. Based on best-in-class open source standards, it features components for image data visualization and segmentation, analytical representations of the geometry, advanced boundary condition specification, Python scripting, and a massively parallel stabilized fluid-structure interaction solver.	C. A. Figueroa, C. Arthurs, M. Marcan, R. Khlebnikov, K. Lau et al.
DFT-FE	Materials Science, Physics	DFT-FE is a massively parallel real-space code written in C++ for first principles based materials modelling using Kohn-Sham density functional theory (DFT). It is based on adaptive finite-element discretization that handles all-electron and pseudopotential calculations in the same framework, accommodates arbitrary boundary conditions, and incorporates scalable and efficient solvers for the solution of the Kohn-Sham equations.Documentation	V. Gavini, P. Motamarri, S. Das, K. Ghosh, S. Rudraraju et al.
FGR	Chemistry, Multiphysics, Physics	This repo contains the codes of equilibrium Fermi’s Golden Rule charge transfer rate constants (E-FGR) and nonequilibrium Fermi’s Golden Rule charge transfer rates (NE-FGR) for spin-boson systems with Condon and non-Condon diabatic couplings. The linearized semiclassical (LSC) approximation was applied in the derivation of the theory. It is worth-mentioning that a hierarchy of approximations from LSC to the classic Marcus theory is proposed and benchmarked. The new strategies allow one to calculate charge transfer rates and rate constants directly from molecular dynamics simulations and can be extended to large-scales complex light-harvesting systems.	X. Sun & E. Geva
freud	Chemistry, Materials Science, Multiphysics, Physics	The freud library provides users the ability to analyze molecular dynamics and Monte Carlo simulation trajectories for advanced metrics such as the radial distribution function and various order parameters. Its modules work with and return NumPy arrays, and are able to process both 2D and 3D data. Features in freud include computing the radial distribution function, local density, hexagonal order parameter and local bond order parameters, potentials of mean force and torque (PMFTs), Voronoi tessellations, and more.This is an Open Source, BSD-3 Clause License. Documentation	B. Dice, V. Ramasubramani, M. Spelling, E. Harper, J. Anderson et al.
Futility	Physics, Multiphysics, Software infrastructure	FORTRAN Utilities for Scientific Computing. Provides unit testing and design by contract features. Exception handler, interfaces to MPI, Trilinos, PETSc, HDF5, BLAS, and other libraries. Random number generators, mesh transfer operators, VTK export, basic computational geometry and intersection routines, and searching and sorting algorithms.	B. Kochunas
Growing String Method	Chemistry	Fast and reliable method to find transition states and reaction paths for molecular and surface reactions.Documentation	M. Jafari, P. Zimmerman, C. Aldaz
gsd	Materials Science, Multiphysics, Physics	GSD (General Simulation Data) is a file format specification and a library to read and write it. The package also contains a python module that reads and writes hoomd schema gsd files with an easy to use syntax.Documentation	J. Anderson & S. Glotzer
HOOMD-blue	Materials Science, Multiphysics, Physics	HOOMD-blue is a general-purpose particle simulation toolkit. It scales from a single CPU core to thousands of GPUs.Documentation HOOMD-blue is open source with more than 60 contributors. See https://hoomd-blue.readthedocs.io/en/stable/credits.html for full credits.	J. Anderson, J. Glaser, S. Glotzer et al.
mechanoChem	Solid mechanics and chemistry	The mechanoChem code is an isogeometric analysis based code used to solve the partial differential equations describing solid mechanics (including gradient elasticity) and chemistry (including the Cahn-Hilliard phase field model). Developed by the Computational Physics Group at the University of Michigan [http://www.umich.edu/~compphys/index.html]. The mechanoChem code is built on the PetIGA [https://bitbucket.org/dalcinl/petiga/] and PETSc [https://www.mcs.anl.gov/petsc/] libraries, and it uses the automatic differentiation capabilities of the Sacado package from the Trilinos library [https://trilinos.org/packages/sacado/]. Documentation	G. Teichert, S. Rudraraju, K. Sagiyama et al.