Open Source Software

Ames Laboratory offers open source software and an Ombuds Program to help address questions or concerns that may arise.

The software listed below was produced under U.S. Government contract DE-AC02-07CH11358 for The Ames Laboratory, which is operated by Iowa State University for the U.S. Department of Energy. The U.S. Government has rights to use, reproduce, and distribute this software. NEITHER THE GOVERNMENT NOR IOWA STATE UNIVERSITY MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LIABILITY FOR THE USE OF THIS SOFTWARE. If software is modified to produce derivative works, such modified software should be clearly marked, so as not to confuse it with the version available from Ames Laboratory.

As the software listed on this page may be released under various Open Source Software licenses, additional terms and conditions may apply.  Open Source software includes the following:

CyDime

As the rate, sophistication, and potential damage of cyber attacks continue to grow, the latency of human-speed analysis and response is becoming increasingly costly. Intelligent response to detected attacks and other malicious activity requires both knowledge of the characteristics of the attack as well as how resources involved in the attack related to the mission of the organization. Cyber Dynamic Impact Modeling Engine (Cydime) fills this need by estimating a key component of intrusion detection and response automation: the relationship type and strength between the target organization and the potential attacker.

Source Code

CyGutz

A versatile Gutzwiller solver to optimize the single Slater determinant and local many-body degrees of freedom simultaneously within the Gutzwiller approximation or equivalently Slave-boson approach

Source Code

C2-NEB

A nudged-elastic band (NEB) method is modified with concamitant two climbing images (C2-NEB) to find a transition state (TS) in complex potential energy landscape, using either quantum electronic-structure or classical atomic potential methods.

Source Code

GAMESS

GAMESS, or General Atomic and Molecular Electronic Structure System, is a general purpose electronic structure code for computational chemistry. Its primary focus is on ab initio quantum chemistry calculations. The software can also do density functional theory calculations and other semi-empirical calculations (Austin Model 1, Parameterization Model 3), quantum mechanics/molecular mechanics (QM/MM) calculations, and can handle solvent effects.GAMESS has several fragmentation methods that can scale to as many as 260,000 cores, so users can apply GAMESS to very large molecular species.

Source Code

HOOMD-blue

Stands for Highly Optimized Object-oriented Many-particles Dynamics--Blue Edition. It performs general purpose particle dynamics simulations on a single workstation, taking advantage of NVIDIA GPUs to attain a level of performance equivalent to many processor cores on a fast cluster. The HOOMD-blue development effort is led by the Glotzer group at the University of Michigan, and Ames Laboratory researchers have contributed to the effort.

Source Code

HostDesigner

HostDesigner is a computer-aided molecular design code that enables the general application of de novo structure-based methods to problems in chemistry and material science. Its purpose is to identify organic molecules with 3D structures that match user-input specifications. To accomplish this, the code connects chemical fragments to build millions of potential molecules, evaluates the resulting structures based on geometric constraints, and outputs a rank-ordered list of candidates. Example applications include the design of metal ion sequestering agents for use in separations processes, molecules that form self-assembled nanoscale containers, and molecular building blocks for metal-organic frameworks. Download includes User's Manual, HostDesigner 4.0 source code (in Fortran), data files, example input, HDViewer executables for MacOS, Linux, and Windows, and mengine source code (in C).

Source Code

ParFit

ParFit is a flexible and extendable framework and a library of classes for fitting force-field parameters to data from high-level ab-initio calculations on the basis of deterministic and stochastic algorithms. The code is written in Python with object-oriented constructs and is using the highly versatile Python libraries numpy, scipy, matplotlib and pyevolve. Currently the code is fitting MM3 and Merck force-field parameters but could be easily extended to other force-field types.

Source Code

ThermoPhonon

This software permits ease of determination of atomic "force constraints" needed for investigation of harmonic vibrational (i.e., phonon) effects in computational materials discovery efforts - typically falling under basic research and development. ThermoPhonon code provides a unique capability to use atomic displacements at a fixed temperature for calculating the temperature-specific phonon spectrum.

Source Code

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