Molecular and Electronic Dynamics Using the OpenAtom Software
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1 Molecular and Electronic Dynamics Using the OpenAtom Software Sohrab Ismail-Beigi (Yale Applied Physics) Subhasish Mandal (Yale), Minjung Kim (Yale), Raghavendra Kanakagiri (UIUC), Kavitha Chandrasekar (UIUC), Eric Mikida (UIUC), Eric Bohm (UIUC), Prateek Jindal (UIUC), Laxmikant V. Kale (UIUC), Nikhil Jain (LLNL), Qi Li (IBM), Glenn J. Martyna (IBM)
2 What is OpenAtom Sohrab Ismail-Beigi Applied Physics & Materials Yale Sanjay Kalé Computer Science UIUC NSF SI2-SSI: Scalable, Extensible, and Open Framework for Ground and Excited State Properties of Complex Systems OpenAtom software package : DFT, GW Plane waves and pseudopotentials charm++ parallel infrastructure Glenn Martyna Physical Chemistry & Materials IBM
3 OpenAtom: what does it do? Massively parallel ab initio molecular dynamics (AIMD) Excited electronic states (Green function methods) Describes electrons quantum mechanically, i.e., bonding, explicitly using basic physics (no fudge parameters or fits) Uses general Fourier basis to represent electron waves Uses Charm-FFT library: 2D decomposed parallel FFT with spherical cutoff awareness For the experts: Plane waves, pseudopotentials, LDA or GGA Car-Parrinello and Born-Oppenheimer MD of electronic ground state GW self-energy for electronic excitations
4 What is OpenAtom? Overview We are studying metal organic frameworks (MOFS) o What is a MOF? o Why study hydrogen in MOFs? What we learned so far on MOFs Improving large scale GW calculations
5 Hydrogen storage for green energy Hydrogen as fuel o energy dense o clean burn o hard to store Need lightweight material that stores and releases a lot of H 2 Metal organic frameworks (MOFs) o Porous DOE target for a H o Large interior surface area 2 storage system not yet been reached: e.g., capacity of 40 g H 2 per L. o Stores plenty of H 2 o Complex material, details of process not known o Optimization of H 2 storage not great to date
6 Typical MOF structure
7 MOFs we study MOF-5 : Zn 4 O(1,4 benzenedicarboxylate) atoms in a simulation cell Can change Zn to other metals Questions to answer: How do H 2 bind / diffuse inside MOF? Temperature & loading dependence Molecular dynamics (MD) needed Simulate motion of MOF + H 2 to see what happens in real time Dynamics & thermodynamics Technical challenge: H 2 is very light Standard MD: point-like atoms move due to interatomic forces Hydrogen is quantum mechanical: not point-like but wavy
8 Difficulties: quantum nuclei Quantum nuclear module validated/tested in serial Quantum nuclear module validated/tested on small parallel calculations we can do locally Quantum nuclear for large MOF with many nodes and beads (quantum replicas) fails on BW at present (need to run ~1000 nodes for ~3 hours to reach failure) Some type of irreproducible parallel problem ~9 months of work and bug removal has narrowed it to a single module but not isolated yet General problem: how to validate/test parallel code when only possible on a computer as big as BW? How to know code is correct before BW allocation?
9 What is OpenAtom? Overview We are studying metal organic frameworks (MOFS) o What is a MOF? o Why study hydrogen in MOFs? What we learned so far on MOFs Improving large scale GW calculations
10 Preliminary results: MD itself
11 Preliminary results: diffusion Paths of H 2 molecules over simulation (a) Heatmap: mean H 2 positions in simulation cell (b) Diffusive paths followed by H 2 molecules over time mini-mof with 6 H 2 MOF with 43 H 2 z-axis (Å) z-axis (Å) x-axis (Å) x-axis (Å)
12 Preliminary results: diffusion Heatmap: mean H 2 positions in simulation cell
13 Preliminary results: diffusion Slope of black curve: 6!2 = (for long times t)! 8.5 ± *+,-. Seems to agree with available literature! 7 10 *0,-. J. Phys. Chem. C 2008, 112,
14 Preliminary results: diffusion D ( 10-8 m 2 /s ) Mini-MOF Full MOF 77 K K ratio
15 What is OpenAtom? Overview We are studying metal organic frameworks (MOFS) o What is a MOF? o Why study hydrogen in MOFs? What we learned so far on MOFs Improving large scale GW calculations
![DFT: problems with excitations Energy gaps (ev) Material LDA Expt. [1] Diamond 3.9 5.48 Si 0.5 1.](/docs-images/90/103915943/images/16-1.jpg "17 LiCl 6.0 9.4 [1] Landolt-Bornstien, vol. III; Baldini & Bosacchi, Phys. Stat. Solidi (1970).")
16 DFT: problems with excitations Energy gaps (ev) Material LDA Expt. [1] Diamond Si LiCl [1] Landolt-Bornstien, vol. III; Baldini & Bosacchi, Phys. Stat. Solidi (1970). Solar spectrum
17 GW : scaling
18 GW : scaling Scaling'on'Mira' 32'threads'per'node 1000 Scaling/on/BlueWaters/ 32/cores/per/node Time'(Sec) OpenAtom BerkeleyGW1.2 Time(Sec) OpenAtom BerkeleyGW Number'of'Nodes Number/of/Nodes
19 GW : scaling! "# = % " % # for all v,c ' +=! "#! "# ) for all f
20 Summary Study metal organic frameworks (MOFS) for H 2 storage Used OpenAtom on Blue Waters Preliminary non-quantum simulations o Seem reasonable o Must be mined for more physical insight o Next 3 months: finalize analysis of MD results GW part in OpenAtom: scaling greatly improved on BW ready for pubic release
Understanding hydrogen storage in metal organic frameworks from first principles
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