
Jan-Erik
Shared posts
[ASAP] Automation of Active Space Selection for Multireference Methods via Machine Learning on Chemical Bond Dissociation
[ASAP] Tapping on the Black Box: How Is the Scoring Power of a Machine-Learning Scoring Function Dependent on the Training Set?

[ASAP] Tautobase: An Open Tautomer Database

[ASAP] ChemStor: Using Formal Methods To Guarantee Safe Storage and Disposal of Chemicals

[ASAP] Automating the Development of High-Dimensional Reactive Potential Energy Surfaces with the robosurfer Program System

[ASAP] A Robust and Unified Solution for Choosing the Phases of Adiabatic States as a Function of Geometry: Extending Parallel Transport Concepts to the Cases of Trivial and Near-Trivial Crossings

Questaal: A package of electronic structure methods based on the linear muffin-tin orbital technique
Publication date: April 2020
Source: Computer Physics Communications, Volume 249
Author(s): Dimitar Pashov, Swagata Acharya, Walter R.L. Lambrecht, Jerome Jackson, Kirill D. Belashchenko, Athanasios Chantis, Francois Jamet, Mark van Schilfgaarde
PyProcar: A Python library for electronic structure pre/post-processing
Publication date: June 2020
Source: Computer Physics Communications, Volume 251
Author(s): Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz, Aldo H. Romero
Quantics: A general purpose package for Quantum molecular dynamics simulations
Publication date: March 2020
Source: Computer Physics Communications, Volume 248
Author(s): G.A. Worth
Simulation vs Understanding A Tension, in Quantum Chemistry and Beyond. Part C. Toward Consilience
In the last part of our essay, we outline a future of consilience, with a role both for fact‐seekers, and for searchers for understanding. We begin by looking at the surroundings of theory and simulation, their environment in fact shaped by experiment, especially in Chemistry. Experimenters ask questions both conceptual and numerical, and so bring the communities together. Two case studies show what brings the theoretician joy in this playground, and two more detailed ones make it in detail clear that computation/simulation is anyway deeply intertwined with theory‐building in what we do. From a definition of science we try to foresee how simulation and theory will interact in the AI‐dominated future ‐‐ Chemistry’s streak of creation provides in that conjoined future a link to Art, and a passage to a renewed vision of the sacred in science.
Simulation vs Understanding A Tension, in Quantum Chemistry and Beyond. PART B The March of Simulation, for Better or Worse
In the second part of this essay, we leave philosophy, simply describing Roald’s being trashed by simulation. This leads us to a general sketch of artificial intelligence (AI), Searle’s Chinese room, and Strevens’ account of what a go‐playing program knows. Back to our terrain ‐‐ we ask “Quantum Chemistry, † ca. 2020?” Then move to examples of Big Data, machine learning and neural networks in action, first in chemistry and then affecting social matters. trivial to scary. We argue that moral decisions are hardly to be left to a computer. And that causes are so much deeper than correlations.
Simulation vs. Understanding: A Tension, in Quantum Chemistry and Beyond. Part A. Stage Setting
There is a wave breaking over us —a wave of simulation and artificial intelligence. In three reflective Essays we make a case for true understanding, for scientific story‐telling, as well as a role for pleasure and the emotions within science in general and quantum chemistry in particular.
Abstract
We begin our tripartite Essay with a triangle of understanding, theory and simulation. Sketching the intimate tie between explanation and teaching, we also point to the emotional impact of understanding. As we trace the development of theory in chemistry, Dirac's characterization of what is known and what is needed for theoretical chemistry comes up, as does the role of prediction, and Thom's phrase “To predict is not to explain.” We give a typology of models, and then describe, no doubt inadequately, machine learning and neural networks. In the second part, we leave philosophy, beginning by describing Roald's being beaten by simulation. This leads us to artificial intelligence (AI), Searle's Chinese room, and Strevens’ account of what a go‐playing program knows. Back to our terrain—we ask “Quantum Chemistry, † ca. 2020?” Then move to examples of AI affecting social matters, ranging from trivial to scary. We argue that moral decisions are hardly to be left to a computer. At this point, we try to pull the reader up, giving the opposing view of an optimistic, limitless future a voice. But we don't do justice to that view—how could we? We return to questioning the ascetic dimension of scientists, their romance with black boxes. Onward: In the 3rd part of this Essay, we work our way up from pessimism. We trace (another triangle!) the special interests of experimentalists, who want the theory we love, and reliable numbers as well. We detail in our own science instances where theory gave us real joy. Two more examples‐on magnetic coupling in inorganic diradicals, and the way to think about alkali metal halides, show us the way to integrate simulation with theory. Back and forth is how it should be—between painfully‐obtained, intriguing numbers, begging for interpretation, in turn requiring new concepts, new models, new theoretically grounded tools of computation. Through such iterations understanding is formed. As our tripartite Essay ends, we outline a future of consilience, with a role both for fact‐seekers, and searchers for understanding. Chemistry's streak of creation provides in that conjoined future a passage to art and to perceiving, as we argue we must, the sacred in science.
[ASAP] New Basis Set Exchange: An Open, Up-to-Date Resource for the Molecular Sciences Community

Oxygen reduction reaction on TiO2 rutile (1 1 0) surface in the presence of bridging hydroxyl groups
Publication date: 15 November 2019
Source: Computational and Theoretical Chemistry, Volume 1168
Author(s): Ádám Ganyecz, Pál D. Mezei, Mihály Kállay
Abstract
The goal of this study is to provide insight into the mechanism of the oxygen reduction reaction on the TiO2 rutile (1 1 0) surface in the presence of bridging hydroxyl groups. Considering the Langmuir–Hinshelwood and Eley–Rideal mechanisms, each possible intermediate was identified using density functional theory and a cluster model along with the energy barriers of the reduction steps and the OO bond breaking. Our results show that the initial step, the O2 adsorption on the surface, is favored compared to the pure surface. At higher potentials, the oxygen reduction reaction was found to go through the formation of HO2, which can easily convert to two terminal hydroxyl groups. The rate-limiting step is the desorption of the first H2O with 0.58 eV energy requirement at zero applied potential, while at 1.23 V the reduction of the adsorbed OH to form H2O is the bottleneck with a barrier height of 1.71 eV.
Graphical abstract

KinBot: Automated stationary point search on potential energy surfaces
Publication date: March 2020
Source: Computer Physics Communications, Volume 248
Author(s): Ruben Van de Vijver, Judit Zádor
[ASAP] OpenMolcas: From Source Code to Insight
A Python Multiscale Thermochemistry Toolbox (pMuTT) for thermochemical and kinetic parameter estimation
Publication date: February 2020
Source: Computer Physics Communications, Volume 247
Author(s): Jonathan Lym, Gerhard R. Wittreich, Dionisios G. Vlachos
Abstract
Estimating the thermochemical properties of systems is important in many fields such as material science and catalysis. The Python multiscale thermochemistry toolbox (pMuTT) is a Python software library developed to streamline the conversion of ab-initio data to thermochemical properties using statistical mechanics, to perform thermodynamic analysis, and to create input files for kinetic modeling software. Its open-source implementation in Python leverages existing scientific codes, encourages users to write scripts for their needs, and allows the code to be expanded easily. The core classes developed include a statistical mechanical model in which energy modes can be included or excluded to suit the application, empirical models for rapid thermodynamic property estimation, and a reaction model to calculate kinetic parameters or changes in thermodynamic properties. In addition, pMuTT supports other features, such as Brønsted–Evans–Polanyi (BEP) relationships, coverage effects, and ab-initio phase diagrams.
Program summary
Program title: pMuTT
Program files doi: http://dx.doi.org/10.17632/b7f7d28ynd.1
Licensing provisions: MIT license (MIT)
Programming language: Python
External routines: ASE, NumPy, Pandas, SciPy, Matplotlib, Pygal, PyMongo, dnspython
Nature of problem: Conversion of ab-initio properties to thermochemical properties and rate constants is time consuming and error-prone.
Solution method: Python package with a modular approach to statistical thermodynamics and rate constant estimation.
[ASAP] Tios: The Internet of Simulations. Turning Molecular Dynamics into a Data Streaming Web Application
[ASAP] QMflows: A Tool Kit for Interoperable Parallel Workflows in Quantum Chemistry
[ASAP] Single-State Single-Reference and Multistate Multireference Zeroth-Order Hamiltonians in MS-CASPT2 and Conical Intersections
[ASAP] Quantum Package 2.0: An Open-Source Determinant-Driven Suite of Programs
[ASAP] MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry
SLABCC: Total energy correction code for charged periodic slab models
Publication date: Available online 6 March 2019
Source: Computer Physics Communications
Author(s): Meisam Farzalipour Tabriz, Bálint Aradi, Thomas Frauenheim, Peter Deák
Abstract
The surface of solids or their interface with the gas phase is often modeled by a slab, periodic in two dimensions and repeated artificially in the third. When studying charged systems, a compensating background charge is required to avoid the divergence of the Coulomb energy. However, the interactions between the periodic images of the localized charge and between the localized charge and its neutralizing background can cause significant errors in the total energy. We have implemented the correction scheme proposed by Komsa and Pasquarello (2013), which estimates the error in the total energy by modeling the distribution of the localized extra charge with Gaussian functions at different sites, and comparing its energy in the periodic and in the isolated case. The program is user-friendly and robust, it is automated for simple cases while keeping the flexibility for the advanced users to handle non-trivial ones.
Program Summary
Program title: SLABCC
Program Files doi: http://dx.doi.org/10.17632/42zd5p8gxc.1
Licensing provisions: BSD 2-Clause
Programming language: C++
Nature of problem: The error in the total energy of charged slab models under 3D periodic boundary condition
Solution method: Reading the total charge density and total local potential including the ionic, and Hartree potential for the neutral and charged system and approximating the extra charge with several Gaussians embedded in a dielectric medium. Calculating the difference in the energy of the model between the isolated and periodic cases, and using it as correction of the total energy in the original system. Current version works with the Vienna Ab initio Simulation Package (VASP) file format.
[ASAP] AUTOSURF: A Freely Available Program To Construct Potential Energy Surfaces
i-PI 2.0: A universal force engine for advanced molecular simulations
Publication date: March 2019
Source: Computer Physics Communications, Volume 236
Author(s): Venkat Kapil, Mariana Rossi, Ondrej Marsalek, Riccardo Petraglia, Yair Litman, Thomas Spura, Bingqing Cheng, Alice Cuzzocrea, Robert H. Meißner, David M. Wilkins, Benjamin A. Helfrecht, Przemysław Juda, Sébastien P. Bienvenue, Wei Fang, Jan Kessler, Igor Poltavsky, Steven Vandenbrande, Jelle Wieme, Clemence Corminboeuf, Thomas D. Kühne
Abstract
Progress in the atomic-scale modeling of matter over the past decade has been tremendous. This progress has been brought about by improvements in methods for evaluating interatomic forces that work by either solving the electronic structure problem explicitly, or by computing accurate approximations of the solution and by the development of techniques that use the Born–Oppenheimer (BO) forces to move the atoms on the BO potential energy surface. As a consequence of these developments it is now possible to identify stable or metastable states, to sample configurations consistent with the appropriate thermodynamic ensemble, and to estimate the kinetics of reactions and phase transitions. All too often, however, progress is slowed down by the bottleneck associated with implementing new optimization algorithms and/or sampling techniques into the many existing electronic-structure and empirical-potential codes. To address this problem, we are thus releasing a new version of the i-PI software. This piece of software is an easily extensible framework for implementing advanced atomistic simulation techniques using interatomic potentials and forces calculated by an external driver code. While the original version of the code (Ceriotti et al., 2014) was developed with a focus on path integral molecular dynamics techniques, this second release of i-PI not only includes several new advanced path integral methods, but also offers other classes of algorithms. In other words, i-PI is moving towards becoming a universal force engine that is both modular and tightly coupled to the driver codes that evaluate the potential energy surface and its derivatives.
Program summary
Program Title: i-PI
Program Files doi: http://dx.doi.org/10.17632/x792grbm9g.1
Licensing provisions: GPLv3, MIT
Programming language: Python
External routines/libraries: NumPy
Nature of problem: Lowering the implementation barrier to bring state-of-the-art sampling and atomistic modeling techniques to ab initio and empirical potentials programs.
Solution method: Advanced sampling methods, including path-integral molecular dynamics techniques, are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic coordinates from the Python interface, and to return the forces and energy that are used to integrate the equations of motion, optimize atomic geometries, etc.
Restrictions: This code does not compute interatomic potentials, although the distribution includes sample driver codes that can be used to test different techniques using a few simple model force fields.
[ASAP] The Use of Cluster Expansions To Predict the Structures and Properties of Surfaces and Nanostructured Materials
Thousand-atom ab initio calculations of excited states at organic/organic interfaces: toward first-principles investigations of charge photogeneration
DOI: 10.1039/C8CP05574B, Paper
Electron and hole wave functions of low-lying and hybridized interfacial charge-transfer states across the pentacene/C60 interface.
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[ASAP] Grain Boundary Facilitates Photocatalytic Reaction in Rutile TiO2 Despite Fast Charge Recombination: A Time-Domain ab Initio Analysis
Reimagining of Schrödinger’s cat breaks quantum mechanics — and stumps physicists
Reimagining of Schrödinger’s cat breaks quantum mechanics — and stumps physicists
Reimagining of Schrödinger’s cat breaks quantum mechanics — and stumps physicists, Published online: 18 September 2018; doi:10.1038/d41586-018-06749-8
In a multi-‘cat’ experiment, the textbook interpretation of quantum theory seems to lead to contradictory pictures of reality, physicists claim.








