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**Dr. Andreas Götz: Research**

(back to top) Workshops and Symposia
In March 2016 I organized a 4-day symposium at the spring 2016 ACS national meeting that brought together researchers that share a common interest in the computational modeling of catalytic processes. Presentations spanned all domains of catalysis including homogeneous and heterogeneous catalysis, biocatalysis, photocatalysis, and electrocatalysis. A wide range of modeling methods were discussed, including ab initio electronic structure theory, kinetics simulations (mean field, KMC), molecular dynamics, non-adiabatic dynamics and free energy perturbations. Co-organizers of the symposium were my collaborators Dion Vlachos from University of Delaware and Carine Michel and Philippe Sautet from the ENS Lyon in France.
This two day GPU computing event was organized by myself and Ross Walker (co-directors of the CUDA Teaching Center at SDSC) with help from Jon Saposhnik (NVIDIA). The symposium covered trends, tools and research discoveris using GPU accelerated computing in areas ranging from pharmaceutical research to geophysics (see the program). The workshop featured lectures on GPU programming using both CUDA and OpenAcc as well as hands-on exercises.
I am organizer and instructor of an AMBER workshop at East China Normal University (ECNU) in Shanghai. This five day workshop (22-26 August, 2011) aims to introduce researchers in the field of (bio)molecular simulations to the broad collection of computational tools implemented in the AMBER and AmberTools software packages for molecular dynamics simulations.
Together with Dr. Matt Kundrat from SCM I have organized and tutored an ADF workshop that was held on Thursday, 24 March 2011 at the San Diego Supercomputer Center. The workshop was geared both at begineers and expert users of ADF wishing to learn about the new features of the ADF2010.02 release.
(back to top) QUICK: Open-source GPU Accelerated Quantum ChemistryWork done at SDSC since September 2018
This work is supported by NSF award OAC-1835144.
QUICK (QUantum
Interaction Computational Kernel) is an open-source GPU
enabled We recently added an implementation for general density functional methods (LDA, GGA, and hybrid functionals) that uses an octree algorithm for efficient numerical quadrature of the exchange-correlation (xc) potential [1]. The code is parallelized with MPI for execution on CPUs and fully ported for execution on GPUs via CUDA. We employ the libxc library for xc functional evaluation, which we have ported to GPUs along the way. In follow-up work we have developed a multi-GPU capable implementation that distributes the workload of electron repulsion integral (ERI) and xc quadrature contributions to the Fock or Kohn-Sham operator matrix to multiple GPUs via MPI [2]. This works both for multiple GPUs in a single compute node or across many compute nodes in a GPU cluster. See the Figure below for performance of our code for single point energy plus gradient calculations on up to 16 V100 GPUs of the Expanse Supercomputer at SDSC. We can get B3LYP/6-31G** gradients for morphine in under 3 seconds and for the 642 atom protein crambin in under 10 minutes. We have also turned QUICK into a library with an API that facilitates use of QUICK as QM energy and force engine from other software packages. We have used this API to integrate QUICK as default QM engine for QM and QM/MM molecular dynamics simulations with Amber [3].
[1] M. Manathunga, Y. Miao, D. Mu, A. W. Götz, K. M. Merz, Jr.,
[2] M. Manathunga, C. Jin, V. W. D. Cruzeiro, Y. Miao, D. Mu, K. Arumugam, K. Keipert, H. M. Aktulga, K. M. Merz, Jr., A. W. Götz,
[3] V. W. D. Cruzeiro, M. Manathunga, K. M. Merz, Jr., A. W. Götz,
(back to top) GPU Accelerated Molecular Dynamics for Biomolecular SimulationsWork done at SDSC since June 2009
This work is partially supported by NSF award ACI-1835144.
[1] A. W. Götz, M. J. Williamson, D. Xu, D. Poole, S. Le Grand,
R. C. Walker,
[2] S. Le Grand, A. W. Götz, R. C. Walker,
[3] R. Salomon-Ferrer, A. W. Götz, D. Poole, S. Le Grand, R. C. Walker,
(back to top) QM/MM for Biomolecular SimulationsWork done at SDSC since June 2009
This work is partially supported by NSF award ACI-1835144 and NSF award CHE-1416571.
(back to top) CAICE (Center for Aerosol Impacts on Chemistry of
the Environment) - Atmospheric ChemistryWork done at SDSC since 2017
This work is supported by NSF award CHE-1801971.
(back to top) Cytochrome c oxidase - electronic structure, reactions, molecular dynamicsWork done at SDSC since 2012
This work is supported by NIH award R01 GM100934.
(back to top) Many-body potentials and machine learningWork done at SDSC since 2017
This work is supported by NSF award ACI-1642336.
(back to top) GAL17: a force field for water over platinum;
and multiscale simulations of catalysisWork done at SDSC since 2014
This work is supported by NSF award CHE-1416571.
(back to top) Subsystem Density Functional Theory
Postdoc in Amsterdam with Dr. L. Visscher (November 2006 - April 2009)
I have been and still continue to work on the extension of the frozen density embedding (FDE) method in density functional theory (DFT). The main research topics are analytical gradients for FDE and nuclear spin-spin coupling constants in the framework of FDE. The research work is done with Dr. L. Visscher at the chair of theoretical chemistry at the Vrije Universiteit Amsterdam which is headed by Prof. Dr. E.-J. Baerends. DFT is undoubtedly the most popular computational method for the investigation of the electronic structure of molecules. It allows to obtain accurate information on molecular properties at a moderate computational cost. Studies of molecules of interest for classic organic or inorganic chemistry are routine by now. It is the time to find new approaches to be able to study also more complex systems in fields of increasing importance such as life sciences and nanotechnology. The extension of FDE to a general subsystem DFT has a tremendous potential as an accurate (in principle exact) multi-scale modelling method. Such methods allow to focus the computational effort on those parts of the system which is of importance for the property of interest, while still taking into account the interaction with the remaining parts of the system. Proper implementations will allow to tackle the investigation of properties of chemical systems of unprecedented size and complexity. The implementation is done in the Amsterdam Density Functional (ADF) program package. (back to top) Optimized Effective Potential Method and Time-dependent Density Functional Theory
Postdoc in Erlangen with Prof. Dr. A. Görling (October 2005 - October 2006)
Conventional density functional theory (DFT) methods like those based on the local density approximation (LDA) or generalized gradient approximations (GGAs) employ approximate functionals for the exchange-correlation (XC) energy that are integrals of functions of the electron density and its gradient. GGA methods are widely and successfully employed routine methods to investigate electronic ground states and their properties in chemistry and solid state physics. Despite their success, these conventional DFT methods are not accurate enough for many questions of interest.
Based on our numerically stable OEP approach I have worked out algorithms and implemented these into the TD-DFT module of the quantum chemical program package TURBOMOLE. Research along these lines is further pursued in Prof. Dr. A. Görling's group.
[1] A. Heßelmann, A. W. Götz, F. Della Salla, A. Görling,
[2] A. Görling, A. Ipatov, A. W. Götz,
A. Heßelmann,
[3] A. Görling, (back to top) Density Fitting Approaches for Efficient Density Functional Calculations
PhD thesis, Erlangen, Germany (November 2001 - August 2005)
My PhD thesis in Theoretical Chemistry was accomplished at the University of Erlangen under the supervision of Prof. Dr. B. A. Heß (University of Bonn, deceased) and later under the supervision of Prof. Dr. A. Görling. I have been working on the LEDO-DFT [1] formalism and its implementation into the quantum chemical program package TURBOMOLE. LEDO-DFT speeds up density functional theory (DFT) calculations and thus enables simulations of larger molecules.
During my PhD I have implemented the calculation of analytical gradients [2] within the LEDO-DFT formalism [1]. Furthermore, I have worked out criteria for the optimization of auxiliary basis sets for the LEDO expansion and optimized auxiliary orbitals which allow for LEDO-DFT calculations with sufficient accuracy [3]. My PhD thesis can be downloaded in pdf format from the opus server of the University of Erlangen. diploma thesis, Erlangen, Germany (April 2001 - October 2001)
My diploma thesis was accomplished during the time from April to October 2001
under the supervision of
Prof. Dr. B. A. Heß
(University of Bonn, deceased) at
the University of Erlangen.
It is entitled My diploma thesis (available only in German) can be download here: ps / pdf
[1] C. Kollmar, B. A. Hess,
[2] A. W. Götz, C. Kollmar, B. A. Hess,
[3] A. W. Götz, C. Kollmar, B. A. Hess, (back to top) Renovating a Monastery in Northern Italy
(back to top)Work camp in Àcqui Terme, Italy (September 1995)
In September 1995, after finishing school and before university started, I participated in a workcamp organized by SCI (Service Civil International). It took place in a small village near Àcqui Terme which is close to the town of Asti in the Piemont region in northern Italy. The philosohpy of the workcamps organized by SCI is to bring together the working and/or creative power of people from different countries in order to realize a project of social welfare. In general the participants have to pay the trip to the workcamp by themselves, but board and lodging at the working place are for free. In my case the project of the work camp was to renovate the run-down accomodations of a small protestant church for future use as a cost-free excursion center for schools or other institutions or people in need. We have been a dozen people from Great Britain, the Netherlands, Germany and Italy. It was hard work, but also a lot of fun. The duration of the workcamp was two weeks, rather short. Nevertheless it was a unique and worthy experience. If you have time, I can just recommend to participate in a workcamp organized by SCI. (back to top) last modification: 2021/04/16 |