As part of my research activities, I've developed numerous codes over the years, mainly associated to computational science and engineering problems.  I'll be making a sub-set of these available for download (i.e. ones not involving disclosure of any proprietary rights), once I get around to packing them for distribution, some as binaries and others as copyrighted sources only for non-commercial use. 

If you have an interest in any of the password protected programs below, please send me an e-mail message including your contact info, affiliation, a brief mention to your interest in the particular tool, and the application at hand.  I will then be happy to provide you with a password to retrieve the corresponding tool/s from our servers.

Molecular Mechanics/Dynamics Modeling and Simulation.

  • GARFfield: Genetic Algorithm based Reactive Force Field optimizer [Jaramillo-Botero et al, 2014, JCTC].  Is a hybrid genetic algorithm/conjugate-gradient force field optimization framework.  It is used to optimize existing or new force fields from first-principles quantum mechanics training sets. Currently supported force fields include ReaxFF, eFF effective core pseudopotentials, Morse (atomistic and coarse grain), and COMB (partially). GARFfield uses a modified LAMMPS library as the current MM/MD engine.  Limited distribution. 

  • pEFF: parallel Electron Force Field [Jaramillo-Botero et al, 2010, JCC].  A parallel implementation of eFF [Su et al, 2007] for LAMMPS to handle large-scale, long-term nuclei+electron mechanics and dynamics.  It allows SPE, minimization, and dynamics NVE, NVT and NPT ensembles on million+ particle systems, as well as additional extensions to the original eFF.  Available within the official LAMMPS distribution.

  • CMDF: Computational Materials Design Facility.  CMDF is a single-image materials and process modeling and simulation framework, integrated from different tools and engines, intended to allow hierarchical traversal between different length and time scales (first-principles quantum-mechanic <-> continuum mechanics), and between disparate paradigms (i.e. alternate methods) per scale. Its goal is to enable de novo design of new or optimized materials with improved performance and to enable first-principles predictive science in chemistry, physics and biology. CMDF uses the Python programming language to control the computational flow between disparate processing cores written in compiled languages (C/C++/Fortran) that carry out physicochemical calculations for multiscale/multiparadigm under a unified data model.  Not distributed openly. 

  • COMODYN: COnstrained MOlecular DYNamics. A complete library for clustering and solving the rigid-body equations of motion, in internal coordinates, for molecular systems with implicit kinematics constraints.

  • CFFA: Contrained Floating-base Force Algorithm for solving the forward dynamics of free-floating multibody systems [O(n) serial and O(log n) MPI-parallel versions] (ANSI C)

  • Systematic clustering of atomistic structures (from xyz or bgf formats) including ring topologies, using kinematics criteria, and vibrational mode analysis (ANSI C)


Robotics Modeling and Simulation frameworks.


Others, including general utilities and scripts.

  • Loop counting in undirected graphs (ANSI C and Python)

  • Image feature extraction and automated classification, using Fuzzy theory and ANNs (ANSI C)

  • Feature extraction methods from digital time-dependent signals using ANNs (Matlab)

  • Quaternions and spatial transformation operators library (ANSI C)




This page was last updated 3/15/2012 12:21:00 PM

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