Sketches at the frontiers of computational chemistry

A presentation given to the LIF group, includes an introduction to Wailord.

Transcript

1. SKETCHES AT THE FRONTIERS OF COMPUTATIONAL CHEMISTRY ROHIT GOSWAMI Created: 2020-11-19 Thu 05:54 1
2. HELLO GROUP! Find me here: Who? Rohit Goswami MInstP AMIChemE AMIE Doctoral Researcher, University of Iceland, Faculty of Physical Sciences https://rgoswami.me 2
3. BASIC CONCEPTS 3
4. SCALING CONCERNS A horse in motion is too quick to see each moving foot The foot still moves! Sampling is intimately linked to the event considered A measure of rarity 4
5. Objects ∞ ways of cataloging these Classical Objects Quantum Objects Optical Effects (relativity) MODELING CATEGORIES Celestial Bodies Homogenous Bodies People Proteins and Macromolecules Atoms and molecules Electrons and Nucleons F = (mv) d dt HΨ = ι dΨ dt L = L₀ 1 − v² c² − − − − − − √ 5
6. Reasonable Assumptions SEPARATION OF CONCERNS The motion of Halley’s comet does not affect a boulder System size de nition The spinning of the Earth does not invalidate cartesian trajectories for small objects on earth Magnitude can split objects Nucleons are larger than electrons 6
7. POTENTIAL ENERGY SURFACES Electrons move on a potential energy surface de ned by the slower nuclei Adiabatic assumption One electron surfaces Born-Oppenheimer assumption Electrons and nuclei are independent 7
8. Quantum Chemistry Approaches Considers electrons separately Is energy optimal in a sense …. many things happen Quickly becomes unfeasible for larger quantities Density Functional Theory Considers only the density of electrons TWIN APPROACHES TO CHEMICAL SYSTEMS [kohnNobelLectureElectronic1999a] 8
9. RESEARCH PROBLEM? Are the predictions of each method signi cantly different? 9
10. WHAT? A random effects model, since the elements will have correlated results , = ϵⱼ + [n(r)] − ∫ (r)n(r)dv − ∫ E dft ∑ j E xc v xc 1 2 n(r)n(r') |r − r'| = ⟨i|h|i⟩ + [ii|jj] − [ij|ji] E HF ∑ i 1 2 ∑ ij = μ + αᵢ + bⱼ + ϵᵢⱼ y model b ∼ N(0, σ ) ² B ϵ ∼ N(0, σ²) 10
11. METHOD Add a grad student! 11
12. INTRODUCING WAILORD Inherits from ORCA 12
13. Removes the human element Validation of inputs and outputs is automated Integrates with SLURM by jobscript generation Flexible and provides graphing utilities and units Lets us focus on the questions SOME FEATURES linDat = waio.orca.genEBASet(Path("bui linDat["deviation"] = esr.magnitude - linDat["perc_error"] = ( linDat.deviation / linDat.angle.ap ) 13
14. BIKESHEDDING AND ELEGANCE Taking a CS hammer to a QC nail grammar_xyz = Grammar( r""" meta = natoms ws coord_block ws? natoms = number coord_block = (aline ws)+ aline = (atype ws cline) atype = ~"[a-zA-Z]" / ~"[0-9]" cline = (float ws float ws float) float = pm number "." number pm = ~"[+-]?" number = ~"\\d+" ws = ~"\\s*" """ ) 11 C -0.180226841 0.360945118 C -0.180226841 1.559292118 C -0.180226841 1.503191118 N -0.180226841 0.360945118 C -0.180226841 -0.781300882 C -0.180226841 -0.837401882 H -0.180226841 0.360945118 H -0.180226841 2.517950118 H -0.180226841 2.421289118 H -0.180226841 -1.699398882 H -0.180226841 -1.796059882 14
15. WATER AND ANOMALIES 15
16. Rare phase transitions Many phases Topological analysis SCME elegantly deals with long range electrostatics Needs SOAP or other ML for shorter ranges Needs to be upscaled OVERVIEW 16
17. CATALYSIS AND MACHINE LEARNING 17
18. Saddle points on potential energy surfaces indicate transition states Finding these is computationally intensive Important for catalysis Slow implementation in MATLAB Being reworked in C++ with SURFSara, NL Part of REAXPRO SCALING GPR-NEB 18
19. FUTURE DIRECTIONS 19
20. Unfortunately very hush- hush at the moment MAGMAL 20
21. PERSONAL GOALS Strengthen the foundations of QC Bring modern comp sci. and stats to bear Better administration of garpur Plus some functional programming paradigms for users! ………… 21
22. ACKNOWLEDGEMENTS Advisor Prof. Hannes Jonsson Committee Dr. Elvar Örn Jónsson, Prof. Egill Skúlason Also Family, Lab members, Everyone here 22
23. THE END 23
24. BIBLIOGRAPHY Kohn, Nobel Lecture: Electronic Structure of Matter\textemdash Wave Functions and Density Functionals, Reviews of Modern Physics, 71(5), 1253-1266 . . . [kohnNobelLectureElectronic1999a] link doi 24
25. THANKS! 25