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SOFTWARE
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.
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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.
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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.
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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.
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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.
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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)
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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.
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Loop counting in undirected
graphs (ANSI C and Python)
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Image feature extraction and
automated classification, using Fuzzy theory and ANNs (ANSI C)
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Feature extraction methods from
digital time-dependent signals using ANNs (Matlab)
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Quaternions and spatial
transformation operators library (ANSI C)
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