Multiscale Modeling and Simulation

Materials and Process Simulation Center (MSC)

California Institute of Technology

 

 

 

 

 

 

 

 

Back
Up
Next

Projects

bulletO(n) and O(Log n) Constrained Molecular Dynamics
bulletNon-adiabatic Force Fields for Explicit Electron Molecular Dynamics

O(n) and O(Log n) Constrained Molecular Dynamics

Funding

Leveraged partially from different grants

Start date

(initial development started on September, 1996)

June 2006

Expires

on-going

   

Investigators

bullet

Andres Jaramillo-Botero

bullet

William A. Goddard, III

 

Past collaborators:
bullet

Tahir Cagin (now at Texas A&M)

bullet

Amir Fijany (JPL)

Abstract  

In the study of molecular systems using Molecular Dynamics (MD) simulations it is often desired to impose relative or absolute motion constraints on atoms or groups of atoms. This offers several different advantages depending on the type of constraint involved, i.e. absolute or relative, and on the type of generalized coordinates used to describe the equations of motion (EOM) of the system, i.e. Cartesian or internal. Indistinctively, both approaches involve the formulation of mixed systems of differential EOM and nonlinear algebraic equations of constraint.

Our approach involves the use of internal coordinates, even though this  increases the complexity of the solution to the EOM (mainly because we now have a highly coupled molecular system with highly non-linear, non inertial terms in velocity, a dense mass matrix operator and potential numerical conditioning of the formulation solution) hence requiring efficient algorithms to compute the algebraic differential solution in linear, or better, computation time, it offers several advantages over the conventional Cartesian constrained dynamics methods (the Figure to the left depicts an NVT@300K of a polymer chain that results in an order of magnitude increase in simulation time-step in comparison to conventional atomistic Cartesian MD). 

We have successfully demonstrated its use in large-scale, long-term dynamics of complex systems in polymer and protein science [see Publication list].  Current research involves addressing challenges in closed loop kinematics systems and correcting bad contact dynamics without time penalties.

 
Related Publications
bulletJaramillo-Botero, A. "Molecular Nanomanipulator Dynamic Design Criteria" In: Dekker Encyclopedia of Nanoscience and Nanotechnology. 1st Ed. New York : Marcel Dekker Publ., 2004.
bulletJaramillo-Botero, A., Matta, A., Correa, JF, Perea, W. Software platform for robot modeling and simulation, Vol. 3, No. 1, December 2004
bulletJaramillo-Botero, A. "Computational Nanotechnology in the Design of Nanoscale Molecular Positional Devices", NASA Jet Propulsion Laboratory Seminar (invited talk), Pasadena, California (US) November 23, 2004
bulletJaramillo-Botero, A. and Crespo, A. "A Unified Formulation For Massively Parallel Rigid Multibody Dynamics Of O(Log2 N) Computational Complexity", Journal of Parallel and Distributed Computing, Academic Press, Vol. 62, No. 6, June 1, 2002.
bulletJaramillo-Botero, A "Design Criteria for a 3 DOF positional nanomanipulator based on a Constrained Molecular Dynamics Model" In: Mathematics in Nanoscale Science and Engineering 2004 Reunion Conference (invited talk), 2004, University of California at Los Angeles, Lake Arowhead Conference, California (US) January 2004.
bulletMassively Parallel Algorithms for Long-term Simulations of Large-scale Molecular Systems, Universidad Politecnica de Valencia, Doctoral Thesis, (spanish) ISBN: 958-8162-60-2, 1998.
bulletFijany, A., Jaramillo-Botero, A., Cagin, T., and Goddard, W.A. III, A Fast Algorithm for Massively Parallel, Long Term Simulations of Complex Molecular Dynamics Systems, pp 505-515 (1998), in Parallel Computing: Fundamentals, Applications and New Directions, Eds. E. H. D'Hollander, G. R. Joubert, F. J. Peters and U. Trottenberg.
bulletFijany, A., Cagin, T., A., Jaramillo-Botero, and Goddard, W. A. III. Novel Algorithms for massively parallel, long term simulation of molecular dynamics systems, Advances in Engineering Software, 29, 441-450 (1998).
bulletFijany, A., T. Cagin, A. Jaramillo-Botero, S. Gulati, and W.A. Goddard,"Novel Algorithms for Massively Parallel, Long-Term, Simulation of Molecular Dynamics Systems," 4th NASA National Symposium on Large-Scale Analysis and Design on High-Performance Computers and Workstation, Williamsburg, VA, October 1997.
bulletFijany, A., T. Cagin, A. Jaramillo-Botero, and W.A. Goddard, "Massively Parallel Constraint Force Algorithm for MD Simulation of Polymers and Dendrimers," Presented at the 1997 American Physical Society (APS) Int. Conf. on Computational Physics (PC97), Santa Cruz, CA, Aug. 1997.
bulletFijany, A. A. Jaramillo -Botero, T. Cagin, and W.A. Goddard, "A Fast Algorithm for Massively Parallel, Long-Term, Simulation of Complex Molecular Dynamics Systems," Proceedings Parallel Computing 97 (PARCO 97), Bonn, Germany, September 1997.
bulletFijany, A., T. Cagin, A. Jaramillo -Botero, T. Coley, and W.A. Goddard, "A Massively Parallel Algorithm for Solution of Constrained Equations of Motion with Application to Large-Scale Long-Time Molecular Dynamics Simulations," Presented at the 2nd Parallel Computational Chemistry Symposium, American Chemistry Society (ACS), San Francisco, CA, April 1997.
bulletFijany, A., T. Cagin, A. Jaramillo -Botero, and W.A. Goddard,"A Massively Parallel Algorithm for Solution of Constrained Equations of Motion in Molecular Dynamics," Presented at the American Physical Society Meeting, Kansas City, MO, March 1997.
bulletRigid Multibody Molecular Dynamics: Strictly Parallel Computations, ISBN: 958-33-4988-7, TR-RAG-1996 - Robotics and Automation Group (RAG), 1996. online: http://ingenieria.puj.edu.co/centros/cap/proyectos/multicuerpos/html/Intro.html

 

Non-adiabatic force fields for explicit electron molecular dynamics

Funding Agencies

NNSA-DOE

Start date

June 2007

Expires

on-going

   

Investigators

bullet

Andres Jaramillo-Botero

bullet

William A. Goddard, III

bullet

Julius Su

 

Graduate students
bulletQi An (Materials Science)
bulletHai Xiao (Materials Science)
bulletPatrick Theofanis (Chemistry)

 

Abstract

Our research involves developing and using first principles based methods to examine the chemical processes of matter at extreme conditions that may have significant concentrations of molecules, atoms, ions, and electrons exposed to transient mechanical, thermal and electrical fields. In particular we want to understand the processes for heterogeneous systems and interfaces in systems with temperatures ranging from ~0.1-100ís eV [~103-106ísK] and densities up to 10 times standard value (often referred to as warm-dense-matter - WDM - see top-left figure). Studies of such systems have mainly been the province of physics and astrophysics. We want to bring in the chemistry to bridge the transition regimes from solid to liquid to plasma driven by extreme conditions, using a first-principles-based modeling and simulation methodology capable of accurately expressing the non-adiabatic energetics and dynamics of excited electronic states. For this, we have been developing the first-principles-based electron force field (eFF) methodology, which enables modeling of the simultaneous dynamics of electrons and nuclei (eMD) evolving nonadiabatically under transient extreme conditions.  In eFF the N-electron wavefunction is described as a product of one-electron Gaussian functions, whose size is a dynamical variable and whose position is not constrained to a nuclear center. This form allows for straightforward propagation of the wavefunction, with time, using a simple formulation. The nuclei are described as point charges.  The full Hamiltonian has then a standard description for electrostatic interactions between a set of delocalized point and Gaussian charges which include, nuclei-nuclei, electron-electron, and nuclei-electron.  In addition to the electrostatics, eFF introduces QM effects through an electron kinetic energy from the Gaussians and a spin-dependent Pauli repulsion potential term between Gaussians. 

Thus eFF is a simplified QM method rather than a conventional force field method, in which electron motions are averaged out into ground state nuclear motions (i.e a single electronic state) described by empirically parameterized interatomic potential functions. 

We have demonstrated the applicability of eFF to multiple problems, including: predicting the single shock Hugoniots for Hydrogen [Su and Goddard, 2007], Lithium [Kim, Su, and Goddard, 2010; Jaramillo-Botero, Su, An, and Goddard, 2010], Carbon [An, Su, Jaramillo-Botero, and Goddard, 2010], Beryllium, Auger dynamics [Su and Goddard, 2010], among others.  Bottom figure shows the shock wave kinematics, including mass velocities (Up) and shock wave velocities (Us) , and the corresponding single shock Hugoniot for lithium metal, obtained from a pEFF dynamics simulation.

Current effort focused on:

bullet

making it practical to perform simulations of the nonadiabatic dynamics of materials in extreme environments involving millions of nuclei and electrons, over multi-picosecond time-scales (for this we have developed pEFF [Jaramillo-Botero et al, submitted JCC, 2010], see lithium shock hypervelocity impact movie),

bullet

extend the scope of our current method (Z=1-6) to include higher p- and d-block elements of the periodic table (e.g. use of floating elliptical Gaussians to improve the representation of electrons with p-character),

bullet

Improve its efficiency and accuracy by supporting effective core pseudo potentials, electron correlation and dispersion

 

 
Related Publications
bulletCarbon Phases Under Extreme Conditions of Temperature and Pressure during Shock Compression, An, Q; Su, JT; Jaramillo-Botero, A; Zybin, S; Goddard, WA. In preparation 2010.
bulletLarge-scale, Long-term Non-adiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments, Jaramillo-Botero, A; Su, JT; An, Q; Goddard, WA. in print JCC, 2010.
bulletDiscovery of New Amorphous Lithium under High Temperature & High Pressure, Kim, H; Su, JT; Goddard, WA. Under review.
bulletThe dynamics of highly excited electronic systems: Applications of the electron force field, Su, JT; Goddard, WA, J. Chem. Phys. 131 (24): 244501 (2009)
bulletMechanisms of Auger-induced chemistry derived from wave packet dynamics, Su JT, Goddard WA, P Natl. Acad. Sci. USA 106 (4)1001-1005 (2009)
bulletExcited electron dynamics modeling of warm dense matter, Su JT, Goddard WA, Phys. Rev. Lett. 99 (18): Art. No. 185003 (2007)

Home | Research | Members | Archive | Opportunities | Related links | Search | Contact Information

 (C) Materials and Process Simulation Center, Caltech, 2007.
Contact: Andres Jaramillo-Botero [ajaramil at wag.caltech.edu].
Last updated: 04/04/12.