Gygi Research Group at UC Davis
Welcome to the Electronic Structure Laboratory at the University of California
Our research focuses on the development of numerical
algorithms and high-performance software for electronic
structure computations and
First-Principles Molecular Dynamics (FPMD) simulations.
DOE creates the Midwest Center for Computational Materials
(MICCoM) at Argonne National Laboratory
will develop methods and
optimized codes to compute structural,
electronic properties, and transport coefficients from atomistic and
first principles simulations, integrating ab initio molecular dynamics
(MD) with classical and continuum codes. As a member of MICCoM, the UC Davis
Electronic Structure Laboratory will develop high-performance quantum
simulation algorithms and implementations of first-principles molecular
Coming up graduate course/Spring 2016
ECS289K Introduction to Quantum Simulations
News [2016-01-28] Qbox 1.63.2 is available, featuring the option to add an
applied electric field, enabling simulation in the presence of a finite
field and calculations of polarizabilities. See detailed release notes at
Version 1.63.2 includes Optimized Norm-Conserving Vanderbilt (ONCV)
pseudopotentials introduced in 1.62.3. See the
Qbox home page and the
Qbox source repository. The SG15 table of ONCV pseudopotentials is available
and a full description is given in:
M. Schlipf and F. Gygi, Comput. Phys. Comm. 196, 36-44 (2015).
High-Performance First-Principles Molecular Dynamics
In order to enable accurate numerical simulations of
atomic-scale properties of matter for applications in chemistry, physics
and materials science, we are developing scalable algorithms for
First-Principles Molecular Dynamics (FPMD). FPMD combines a quantum-mechanical
description of electronic structure with a classical description of
statistical properties. Our goal is to efficiently
use the power of the largest supercomputers available today to extend the range
of applications of FPMD. We develop advanced simulation features such as
on-the-fly computation of spectroscopic data and
coupling of FPMD simulations with efficient statistical sampling algorithms.
Code development is carried out using C++/MPI/OpenMP and targets platforms
such as Cray XE6, IBM BlueGene/Q, as well as computers based on the
Intel Multi-Integrated Core (MIC) architecture (ANL Aurora).
This project is supported by the US Department of Energy Office of Basic Energy
Sciences through grant DE-SC0008938 and is pursued in
collaboration with Prof. G. Galli
(UChicago), Dr. E. Schwegler (Quantum Simulations
Group, Lawrence Livermore National Laboratory), and other international
Algorithm research projects
We are developing specialized parallel algorithms
to accelerate the most time-consuming steps of electronic structure
computations. We explore the problem of data compression for
efficient storage of electronic wave function when solving the electronic
structure problem, and more generally the problem of generating
optimally localized electronic wave functions. This problem is related to
algorithms for simultaneous
approximate diagonalization of symmetric/hermitian matrices, used in
signal processing applications.
New: Version 1.63.2 is available.
We develop and support Qbox,
a C++/MPI implementation of
FPMD for massively parallel computers.
Qbox is available in source form under a GPL license. See the
Qbox home page.
Qbox latest features includes
an implementation of Optimized Norm-Conserving Vanderbilt (ONCV)
pseudopotentials and the option to include an applied electric field.
Qbox implements the plane-wave,
pseudopotential electronic structure
method and was designed for scalability on thousands of
processors. It has been ported to large parallel platforms,
including BlueGene/P, BlueGene/Q, Cray XT-5, Cray XE-6, and a variety of
Linux/Intel clusters. It is currently used in projects
involving simulations of liquids, semiconductor
nanostructures, and materials science. Qbox achieved a
performance of 207 TFlops on the BlueGene/L computer.
Large-Scale Electronic Structure Calculations of High-Z Metals on the
was awarded the 2006 ACM/IEEE Gordon Bell Prize for Peak Performance.
The design of Qbox is described in the following
project aims at developing a framework for the automatic verification
and validation of electronic structure programs. It allows users of
electronic structure codes to archive and compare results obtained with
various electronic structure programs (Abinit, Quantum Espresso, Qbox,
Exciting and Siesta). ESTEST is available at
A paper describing ESTEST has appeared in Computational Science and
Discovery, available at
A more recent paper
describing the distributed network features of ESTEST has appeared in
Computer Physics Communications, available at
Pseudopotential repository project
A pseudopotential repository is available at
http://fpmd.ucdavis.edu/potentials/index.htm. The repository
contains potentials generated using the method of Hamann, Schluter and
Chiang, modified by Vanderbilt, for LDA and PBE exchange-correlation
functionals. Potentials translated from the UPF format used in the
Quantum Espresso package are also included to facilitate validation
The SG15 collection of Optimized Norm-Conserving Vanderbilt (ONCV) potentials
is available at http://quantum-simulation.org.
We develop XML-based tools to facilitate web-based information
exchange for FPMD simulations. Web tools are built to interface to the
Qbox code and other post-processing tools, including visualization
programs. They conform to the FPMD XML Schema specification