58 research outputs found
ART Polymerization Networks
No full textThis repository contains the data underlying the results presented in:
"Accelerating Reaction Network Explorations with Automated Reaction Template Extraction and Application"
- Jan P. Unsleber, 2023, ChemRxi
qcserenity/serenity: Release 1.3.0
No full textRelease 1.3.0 (16.09.2020)
Functionalities
Added SystemSplittingTask and SystemAdditionTask to allow for modular system combining and splitting (Moritz Bensberg)
Added ElectronicStructureCopyTask to copy the orbitals between systems while taking care of displacement and rotation of the molecules (only implemented for spherical basis functions) (Moritz Bensberg)
Double hybrid functional support for FDE-type calculations (Moritz Bensberg)
Off-resonant Response Solver for TDDFT (standard and damped) (Niklas Niemeyer)
Response Properties from TDDFT (Niklas Niemeyer)
Dynamic Polarizabilities (and Linear-Absorption Cross Section)
Optical Rotation (and Electronic Circular Dichroism)
Added new functionals such as wB97, wB97X, wB97X-D, wB97X-V that became available with LibXC (Jan Unsleber)
Added x-only and lr-x gradients, enabling range-separated DFT gradient calculations (Jan Unsleber)
Continuum solvation (IEFPCM, CPCM) is now supported (Moritz Bensberg)
DLPNO-based methods are now available (DLPNO-(SCS-)MP2, DLPNO-CCSD(T0)) (Moritz Bensberg)
The direct orbital selection scheme for embedding calculations is now available (Moritz Bensberg)
DLPNO-MP2 can now be used for double hybrid functionals (Moritz Bensberg)
Core and valence orbitals can now be localized independently (Moritz Bensberg)
The CubeFileTask is now the PlotTask and can also plot 2D heat-maps (Anja Massolle)
Technical Features
Upgrade XCFun dependency to v2.0.2 (Jan Unsleber)
Added option to compile and use LibXC v5.0.0 (Jan Unsleber)
Both XCFun and LibXC can be present, default usage is an option at compile time.
Unittests require XCFun as default.
Upgrade Libint2 dependency to v2.7.0.beta6 (Jan Unsleber)
Allow linkage of parallel BLAS or Lapack to speed up Eigen3 (Jan Unsleber)
Remove ext/ folder style external projects in favor of CMake submodules (Jan Unsleber)
XCFun and LibECPint are now cloned from mirrors located publicly at https://github.com/qcserenity/xcfun and https://github.com/qcserenity/libecpint (Jan Unsleber)
Separate evaluation of Coulomb and exchange when using RI
Streamlining the keywords used in various embedding tasks by adding input-blocks (Moritz Bensberg)
Added print-levels to every task (Moritz Bensberg)
Energy output files are now encoded as plain ascii files (Moritz Bensberg)
Rework of some integral contraction routines (Niklas Niemeyer, Johannes Tölle)
Incremental Fock matrix build in the SCF (Johannes Tölle, Moritz Bensberg)
Bugfix for range-separate hybrids for Hoffmann and Huzinaga operator
Bugfix exact exchange evaluation TDDFT for non-hybrid Nadd-XC
Updated density-initial guess files (Patrick Eschenbach).
Various smaller technical bug
SUM Reaction Data: The Chemoton 2.0 Data Set
No full textThis repository contains the data underlying the results presented in Unsleber, J. P.; Grimmel, S. A.; Reiher, M. 2022, arXiv:2202.13011 [physics.chem-ph]
qcserenity/serenity: Release 1.2.0
No full textRelease 1.2.0 (13.07.2019)
Various small improvements and unit tests
TDDFT rework (Michael Boeckers, Johannes Toelle, Niklas Niemeyer)
Rework of the eigenvalue solver (Niklas Niemeyer)
Rework numerical integration (Johannes Toelle)
Sigma Vector rework and RI implementation (Johannes Toelle)
Coupled TDDFT calculation with root-following (Michael Boeckers)
Exact subsystem TDDFT with root-following (Johannes Toelle, Michael Boeckers)
Various orbital space selection tools (Johannes Toelle, Niklas Niemeyer)
LMO - TDDFT (Johannes Toelle)
Rotatory strengths, analytical electric (velocity-gauge) and magnetic dipole integrals, manually settable gauge-origin (Niklas Niemeyer)
Added unit tests and stability improvements (Johannes Toelle, Niklas Niemeyer)
Huzinaga/Hoffmann projection operator rework, Fermi-shifted Huzinaga operator (Moritz Bensberg)
Rework of task input structure (Moritz Bensberg)
Speed up basis function in real space evaluation using sparse matrices (Moritz Bensberg)
Added superposition of atomic potentials as initial guess option (Jan Unsleber
Accelerating Reaction Network Explorations with Automated Reaction Template Extraction and Application
No full textAutonomously exploring
chemical reaction networks with
first-principles
methods can generate vast data. Especially autonomous explorations
without tight constraints risk getting trapped in regions of reaction
networks that are not of interest. In many cases, these regions of
the networks are only exited once fully searched. Consequently, the
required human time for analysis and computer time for data generation
can make these investigations unfeasible. Here, we show how simple
reaction templates can facilitate the transfer of chemical knowledge
from expert input or existing data into new explorations. This process
significantly accelerates reaction network explorations and improves
cost-effectiveness. We discuss the definition of the reaction templates
and their generation based on molecular graphs. The resulting simple
filtering mechanism for autonomous reaction network investigations
is exemplified with a polymerization reaction
Strain-driven growth of GaAs(111) quantum dots with low fine structure splitting
No full textC.D.Y. acknowledges support from the Department of Energy Office of Science Graduate Fellowship Program (DOE SCGF), made possible in part by the American Recovery and Reinvestment Act of 2009, administered by ORISE-ORAU under Contract No. DE-AC05-06OR23100. Additional support was provided by the University of California Lab Fees Research Program (Grant No. 12-LR-238568).Symmetric quantum dots (QDs) on (111)-oriented surfaces are promising candidates for generating polarization-entangled photons due to their low excitonic fine structure splitting (FSS). However, (111) QDs are difficult to grow. The conventional use of compressive strain to drive QD self-assembly fails to form 3D nanostructures on (111) surfaces. Instead, we demonstrate that (111) QDs self-assemble under tensile strain by growing GaAs QDs on an InP(111)A substrate. Tensile GaAs self-assembly produces a low density of QDs with a symmetric triangular morphology. Coherent, tensile QDs are observed without dislocations, and the QDs luminescence at room temperature. Single QD measurements reveal low FSS with a median value of 7.6 μeV, due to the high symmetry of the (111) QDs. Tensile self-assembly thus offers a simple route to symmetric (111) QDs for entangled photon emitters.Peer reviewe
qcscine/art: Release 1.0.0
No full textInitial Features:
Four reaction template flavors (many features are only geared towards the first two):
'minimal' and 'minimal' with shape dressing
'minimal_shell' (the minimal template type with nearest neighbors added for each reactive atom)
'fragment' (all atom of one molecule have to form a single graph)
'fragment_shell' (all atom of one molecule have to form a single graph, neighbors are added)
Deduplication of reaction templates based on a template graph representation
A database to hold reaction templates
Automated template extraction from SCINE databases
Template application to new molecules
Incomplete atom mapping features for arbitrary molecule
Accelerating Reaction Network Explorations with Automated Reaction Template Extraction and Application
No full textAutonomously exploring chemical reaction networks with first-principles methods can generate vast data. Especially autonomous explorations without tight constraints risk getting trapped in regions of reaction networks that are not of interest. In many cases, these regions of the networks are only exited once fully searched. Consequently, the required human time for analysis and computer time for data generation can make these investigations unfeasible. Here, we show how simple reaction templates can facilitate the transfer of chemical knowledge from expert input or existing data into new explorations. This process significantly accelerates reaction network explorations and improves cost-effectiveness. We discuss the definition of the reaction templates and their generation based on molecular graphs. The resulting, simple filtering mechanism for autonomous reaction network investigations is exemplified with a polymerization reaction
Accelerating Reaction Network Explorations with Automated Reaction Template Extraction and Application
No full textISSN:1549-9596ISSN:0095-2338ISSN:1520-5142ISSN:0095-2338ISSN:1520-514
qcserenity/serenity: Release 1.4.0
No full textRelease 1.4.0 (21.10.2021) Functionalities General/Other Features
SCF convergence thresholds were changed! The new defaults are
energy convergence threshold: 5e-8 (old: 1e-8)
density convergence threshold: 1e-8 (old: 1e-8)
max(FP-PF) threshold: 5e-7 (old: 1e-7)
Add Broken-Symmetry calculations via KS-DFT and sDFT (Anja Massolle).
Add a task that orthogonalizes orbitals between subsystems (Anja Massolle).
The EnergyTask can now evaluate the non-additive kinetic energy contribution from orthogonalized subsystem orbitals (Anja Massolle).
Add ECP gradients (Jan Unsleber).
Add multi-state FDE Electron Transfer (FDE-ET) and FDE-diab (Patrick Eschenbach).
Add a task that allows reading of orbitals from other programs. Currently, only the ASCII format from turbomole and Serenity's own format are supported (Moritz Bensberg).
Add calculation of quasi-restricted orbitals (Moritz Bensberg).
Makes Serenity compatible with the MoViPac program (Moritz Bensberg).
Local Correlation
Add occupied orbital partitioning into an arbitrary number of subsystems by the generalized direct orbital selection procedure (Moritz Bensberg).
Add input simplification tasks for local correlation calculations (LocalCorrelationTask) and DFT-embedded local correlation calculations (DFTEmbeddedLocalCorrelationTask) (Moritz Bensberg).
Add a task for coupled-cluster-in-coupled-cluster embedding by adjusting the DLPNO-thresholds for each region [see JCTC 13, 3198-3207 (2017)] (Moritz Bensberg).
Added a task that allows the fully automatized calculations of relative energies form multi-level DLPNO-CC (DOSCCTask) (Moritz Bensberg).
Core orbitals may be specified in the orbital localization task either by an energy cut-off, by tabulated, element-specific numbers, or by explicitly giving a number of core orbitals (Moritz Bensberg).
Polarizable Continuum Model
Add a task to calculate the PCM energy contributions for a given subsystem density (Jan Unsleber, Moritz Bensberg).
Add CPCM gradients (Moritz Bensberg).
Add cavity creation energy calculation from scaled particle theory (Moritz Bensberg).
Changed the default for "minDistance" in the PCM-input block from 0.1 to 0.2.
Response Calculations
Restricted/unrestricted CC2/CIS(Dinf)/ADC(2) excitation energies and transition moments from the ground state (Niklas Niemeyer).
Spin-component and spin-opposite scaled CC2/CIS(Dinf)/ADC(2) (Niklas Niemeyer).
Quasi-linear and DIIS nonlinear eigenvalue solver (Niklas Niemeyer).
Natural auxiliary functions (NAFs) for GW/BSE/CC2/CIS(Dinf)/ADC(2) (Niklas Niemeyer).
Non-orthonormal eigenvalue subspace solver (Niklas Niemeyer).
Restart system of non-converged eigenpairs in the iterative eigenvalue solvers (Niklas Niemeyer).
Gauge-origin invariant optical rotation in the length gauge (Niklas Niemeyer).
Virtual orbital space selection [tested for GW/BSE/TDDFT/TDA/CIS/TDHF/CC2/CIS(Dinf)/ADC(2)/MP2] (Johannes Tölle).
Diabitazation procedures (multistate FXD, FED, FCD) (Johannes Tölle).
GW and BSE (with and without environmental screening) (Johannes Tölle).
Partial response-matrix construction (TDA, TDDFT) (Johannes Tölle, Niklas Niemeyer).
LibXC support for TDDFT/TDA-Kernel evaluation (Johannes Tölle).
Mixed exact-approximate embedding schemes for ground and excited states (Johannes Tölle).
Reimplementation of natural transition orbitals and support for coupled TDDFT (Johannes Tölle).
Grimme's simplified TDA and TDDFT (Niklas Niemeyer).
Sigmavector for Exchange contribution using RI, support for long-range exchange and coupled sTDDFT support (Niklas Niemeyer, Johannes Tölle).
Löwdin transition, hole, and particle charges for response calculations (Anton Rikus, Niklas Niemeyer).
Transition densities, hole densities, and particle densities can be plotted with the PlotTask (Anton Rikus).
Natural Response Orbitals can now be plotted (Anton Rikus).
Cholesky Decomposition Techniques
Added Cholesky decomposition techniques (full Cholesky decomposition, atomic Cholesky decomposition, atomic-compact Cholesky decomposition) for the evaluation of Coulomb and exchange contributions (Lars Hellmann).
Added atomic and atomic-compact Cholesky basis sets to be used in place of the auxiliary basis sets used in the RI formalism (Lars Hellmann).
Added atomic and atomic-compact Cholesky basis sets to fit integrals in the range-separation approach (Lars Hellmann).
Electric Fields
Numerical external electric fields can now be included through point charges arranged in circular capacitor plates around a molecule (Niklas Niemeyer, Patrick Eschenbach).
Analytical external electric fields and corresponding geometry gradients can now be included through dipole integrals and their derivatives. (Niklas Niemeyer, Patrick Eschenbach).
Finite-Field Task for (FDE-embedded) numerical and semi-numerical calculation of (hyper) polarizabilities (Niklas Niemeyer, Patrick Eschenbach).
Technical Features
Update Libecpint to v1.0.4.
Rework of Libint precision handling.
Output modifications for simplified handling with MoViPac.
The MultipoleMomentTask now accepts multiple systems and is able to print their total multipole moments.
The GradientTask may now print the gradient for all atoms in all systems in one table.
Removed outdated keyword "dispersion" from GradientTask, GeometryOptimizationTask and HessianTask.
All basis-set files have been updated to the latest version available on www.basissetexchange.org.
Errors in the def2-series RI MP2 basis sets have been fixed. The old versions were actually the MP2 fitting-basis sets of the def-series.
Rework of DLPNO-MP2/CCSD/CCSD(T). Now significantly faster, linear scaling, and caches integrals on disk.
Fixed an error where the tabulated probe radii for the PCM cavity construction where given in Bohr instead of angstrom.
The Schwarz-prescreening threshold is now by default tied to the basis set size. It is calculated as 1e-8/(3M), where M is the number of Cartesian basis functions.
The settings of other tasks may now be forwarded with the block-input system
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