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

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Presentation transcript:

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 Getting started with the GUI SCM & AMS, the compute engines Getting started with the GUI Building molecules, importing structures, bulk, surfaces Electronic structure methods Setting up calculations ADF, BAND, DFTB, QE, COSMO-RS Visualizing results (pDOS, UV/VIS, properties, …. ) The AMS driver & engine features Finding transition states, MD, molecule gun Afternoon: ReaxFF Acceleration methods Building training data & fitting parameters

Background: SCM, ADF & AMS ADF = first DFT code for chemistry (1970s) Baerends@VU (>’73), Ziegler@Calgary(+) (>’75) SCM: Spin-off company 1995 20 people (10 senior PhD’s) + 3 EU fellows Many academic collaborators / EU networks ~140 authors New functionality SCM: development, debug, port, optimize, docs & support articles &patents in materials science with “density functional theory”, Nat. Mat. 4619 Papers with “DFT and Chemistry”

The SCM team in Amsterdam ??? Software Engineer

Amsterdam Modeling Suite ADF: powerful molecular DFT Spectroscopy: NMR, EPR, VCD, UV, XAS Advanced solvation / environments BAND: periodic DFT (2D) Materials, spectroscopy, analysis Interface with and binaries for QE DFTB & MOPAC fast electronic structure ReaxFF: Reactive MD Dynamics of large complicated systems COSMO-RS: fluid thermodynamics VLE, LLE, logP, solubility Integrated GUI: use out of the box Scripting: workflows & automation

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

BAND vs. Plane Wave codes (QE) Atom centered basis functions, STO or NAO Compare cluster with periodic No pseudopotentials, all elements Core spectroscopy (core holes) Easy orbital analysis: pDOS, COOP, EDA Fast for empty (1D, 2D, porous) xc: SCAN, MN15-L, HSE06, GLLB-sc, D3(BJ), DFT-1/2 Self-consistent NEGF Gate & bias potential Spin transport True 2D surfaces, 1D polymers Het. catalysis: polarization, COSMO, SM12 2D electronics (homogeneous E field) Nanotubes Integrated Graphical Interface: Easy set up & analysis Switch: ADF, BAND & Quantum Espresso periodic energy decomposition analysis (tutorial) L. Pecher and R. Tonner WIREs CMS, (2018) COOP in perovskites (tutorial) Goesten & Hoffmann JACS (2018) Polarizing 2D semiconductor (tutorial) N. Zibouche et al. PCCP (2014)

DFTB: ‘fast DFT’ for molecules & periodic Approximated DFT Nearest neighbor & minimal basis Tabulated elec & rep. parameters: Grimme GFN-xTB (Z = 1-86) QuasiNaNo & 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

ReaxFF – reactive molecular dynamics Li battery discharge: J. Electrochem. Soc. 161, E3009 (2014); PCCP, 17, 3383 (2015), tutorial Hydrogen embrittlement of steels Phys. Chem. Chem. Phys. 18 761 (2016) Crystallization TiO2 nano-particles in water Nano Lett. 14, 1836-1842 (2014) Pd-catalysed CO oxidation GCMC+ReaxFF J. Chem. Phys., 139 044109 (2013)

ReaxFF tools in Amsterdam Modeling Suite ChemTraYzer: Automated rates & pathways New: Analyze surface reactions T-NEMD, local T: heat transport Molecule gun: depositing molecules on surfaces eReaxFF: include e- fbMC, CVHD, PRD?: speed up kinetics CMA-ES ReaxFF force field (re)parameterization GCMC: speed up thermo bond boost build polymers

Quantum Chemistry & QSPR for quick property predictions 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, pKa Solubilities, LLE, VLE, boiling points Optimize mixtures: solubility, LLE Polymers: Flory-Huggins X

AMSdriver, PLAMS & GUI

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

1 GUI: build, run & analyze

PLAMS: python scripting Links all modules + various tools → workflows & screening → (custom) post-processing → rapid prototyping