Handson workshop Chemistry Materials with the Amsterdam Modeling

Hands-on workshop Chemistry & Materials with the Amsterdam Modeling Suite Seoul, 29 May 2019 Fedor Goumans, goumans@scm. com SCM support: support@scm. com T&J support: comj@tnjtech. co. kr

Program • Introduction o • Getting started with the GUI o • o Setting up calculations ADF, BAND, DFTB, QE, COSMO-RS Visualizing results (p. DOS, UV/VIS, properties, …. ) The AMS driver & engine features o • Building molecules, importing structures, bulk, surfaces Electronic structure methods o • SCM & AMS, the compute engines Finding transition states, MD, molecule gun Afternoon: Reax. FF o o Acceleration methods Building training data & fitting parameters AMS hands-on workshop T&J Tech, 29 May 2019 © SCM 2

Background: SCM, ADF & AMS ADF = first DFT code for chemistry (1970 s) Baerends@VU (>’ 73), Ziegler@Calgary(+) (>’ 75) • • SCM: Spin-off company 1995 • 20 people (10 senior Ph. D’s) + 3 EU fellows • Many academic collaborators / EU networks o o • articles &patents in materials science with “density functional theory”, Nat. Mat. 4619 ~140 authors New functionality SCM: development, debug, port, optimize, docs & support Papers with “DFT and Chemistry” AMS hands-on workshop T&J Tech, 29 May 2019 © SCM 3

The SCM team in Amsterdam ? ? ? Software Engineer AMS hands-on workshop T&J Tech, 29 May 2019 © SCM 4

Amsterdam Modeling Suite • ADF: powerful molecular DFT o o • BAND: periodic DFT o • Spectroscopy: NMR, EPR, VCD, UV, XAS Advanced solvation / environments (2 D) Materials, spectroscopy, analysis Interface with and binaries for QE DFTB & MOPAC fast electronic structure • • Reax. FF: Reactive MD o • Dynamics of large complicated systems COSMO-RS: fluid thermodynamics o VLE, LLE, log. P, solubility • Integrated GUI: use out of the box • Scripting: workflows & automation AMS hands-on workshop T&J Tech, 29 May 2019 © SCM 5

ADF: Molecular DFT Strong & unique points • All-electron Slaters, H-Og • Relativity: ZORA (SR, SOC) • Spectroscopy o o • Bonding analysis: o o o • NMR calculations locate 13 C di-Rh carbene EPR, NMR, IR (VCD), UVVIS, XAS Phosphorescence Fragment-based approach ETS-NOCV, QTAIM, MO diagrams, NCI, . . Transfer integrals (charge mobility) Environments o Subsystem DFT (FDE), DIM/QM, QM/MM catalyst intermediate, Science, 342, 351 (2013) AMS hands-on workshop T&J Tech, 29 May 2019 © SCM 6

BAND vs. Plane Wave codes (QE) • Atom centered basis functions, STO or NAO o o o o • True 2 D surfaces, 1 D polymers o o o • Compare cluster with periodic No pseudopotentials, all elements Core spectroscopy (core holes) Easy orbital analysis: p. DOS, COOP, EDA Fast for empty (1 D, 2 D, porous) xc: SCAN, MN 15 -L, HSE 06, GLLB-sc, D 3(BJ), DFT-1/2 Self-consistent NEGF § Gate & bias potential § Spin transport o COOP in perovskites (tutorial) Goesten & Hoffmann JACS (2018) Het. catalysis: polarization, COSMO, SM 12 2 D electronics (homogeneous E field) Nanotubes Integrated Graphical Interface: o periodic energy decomposition analysis (tutorial) L. Pecher and R. Tonner WIREs CMS, (2018) Easy set up & analysis Switch: ADF, BAND & Quantum Espresso Polarizing 2 D semiconductor (tutorial) N. Zibouche et al. PCCP (2014) AMS hands-on workshop T&J Tech, 29 May 2019 © SCM 7

DFTB: ‘fast DFT’ for molecules & periodic Approximated DFT • Nearest neighbor & minimal basis • Tabulated elec & rep. parameters: o Grimme GFN-x. TB (Z = 1 -86) o Quasi. Na. No & DFTB. org Capabilities & Features • UV/VIS (fast!) • MOs • (Band structures, DOS) Through AMS • Geometries, frequencies, phonons • Stress tensors (optimize under p) • Advanced MD, PES scans • GCMC, molecule gun Also: MOPAC library AMS hands-on workshop T&J Tech, 29 May 2019 © SCM 8

Reax. FF – reactive molecular dynamics Li battery discharge: J. Electrochem. Soc. 161, E 3009 (2014); PCCP, 17, 3383 (2015), tutorial Crystallization Ti. O 2 nano-particles in water Nano Lett. 14, 1836 -1842 (2014) Hydrogen embrittlement of steels Phys. Chem. Phys. 18 761 (2016) Pd-catalysed CO oxidation GCMC+Reax. FF J. Chem. Phys. , 139 044109 (2013) AMS hands-on workshop T&J Tech, 29 May 2019 © SCM 9

Reax. FF tools in Amsterdam Modeling Suite Chem. Tra. Yzer: Automated rates & pathways New: Analyze surface reactions T-NEMD, local T: heat transport fb. MC, CVHD, PRD? : speed up kinetics Molecule gun: depositing molecules on surfaces e. Reax. FF: include e- CMA-ES Reax. FF force field (re)parameterization bond boost build polymers GCMC: speed up thermo AMS hands-on workshop T&J Tech, 29 May 2019 © SCM 10

COSMO-RS/SAC: thermodynamic properties of fluids Quantum Chemistry & QSPR for quick property predictions COntinuum Solvation MOdel + RS (Klamt), SAC (Sandler) chemical potential => activity coefficients => instantaneous properties • Solvation & excess energies, p. Ka • Solubilities, LLE, VLE, boiling points • Optimize mixtures: solubility, LLE • Polymers: Flory-Huggins X AMS hands-on workshop T&J Tech, 29 May 2019 © SCM 11

AMSdriver, PLAMS & GUI AMS hands-on workshop T&J Tech, 29 May 2019 © SCM 12

The AMS driver: decouple from Engine • • • Frequencies (+ analysis) & phonons Stress & elastic tensors Scan (multiple) coords, any periodicity Geometries, TS, IRC Advanced Molecular Dynamics (Grand Canonical) Monte Carlo AMS hands-on workshop T&J Tech, 29 May 2019 © SCM 13

1 GUI: build, run & analyze AMS hands-on workshop T&J Tech, 29 May 2019 © SCM 14

PLAMS: python scripting Links all modules + various tools → workflows & screening → (custom) post-processing → rapid prototyping AMS hands-on workshop T&J Tech, 29 May 2019 © SCM 15