Dalton Project: A Python platform for molecular- and electronic-structure simulations of complex systems.

The Dalton Project provides a uniform platform access to the underlying full-fledged quantum chemistry codes Dalton and LSDalton as well as the PyFraME package for automatized fragmentation and parameterization of complex molecular environments. The platform is written in Python and defines a means for library communication and interaction. Intermediate data such as integrals are exposed to the platform and made accessible to the user in the form of NumPy arrays, and the resulting data are extracted, analyzed, and visualized. Complex computational protocols that may, for instance, arise due to a need for environment fragmentation and configuration-space sampling of biochemical systems are readily assisted by the platform. The platform is designed to host additional software libraries and will serve as a hub for future modular software development efforts in the distributed Dalton community.

[1]  Erik Rosendahl Kjellgren,et al.  Triplet excitation energies from multiconfigurational short-range density-functional theory response calculations. , 2019, The Journal of chemical physics.

[2]  Fernando Nogueira,et al.  Marine natural products from the deep Pacific as potential non-linear optical chromophores. , 2013, Physical Chemistry, Chemical Physics - PCCP.

[3]  Ville R. I. Kaila,et al.  Exploring the Light-Capturing Properties of Photosynthetic Chlorophyll Clusters Using Large-Scale Correlated Calculations. , 2016, Journal of chemical theory and computation.

[4]  Andreas W. Götz,et al.  PyADF — A scripting framework for multiscale quantum chemistry , 2011, J. Comput. Chem..

[5]  Andreas Savin,et al.  Density functionals for the Yukawa electron-electron interaction , 1995 .

[6]  Chandan Kumar,et al.  Accelerating Kohn‐Sham response theory using density fitting and the auxiliary‐density‐matrix method , 2018 .

[7]  D. L. Parnas,et al.  On the criteria to be used in decomposing systems into modules , 1972, Software Pioneers.

[8]  A. Savin,et al.  On degeneracy, near-degeneracy and density functional theory , 1996 .

[9]  Patrick Merlot,et al.  Charge-constrained auxiliary-density-matrix methods for the Hartree-Fock exchange contribution. , 2014, The Journal of chemical physics.

[10]  Jacob Kongsted,et al.  Damped Response Theory in Combination with Polarizable Environments: The Polarizable Embedding Complex Polarization Propagator Method. , 2014, Journal of chemical theory and computation.

[11]  Kasper Kristensen,et al.  LoFEx - A local framework for calculating excitation energies: Illustrations using RI-CC2 linear response theory. , 2016, The Journal of chemical physics.

[12]  Sonia Coriani,et al.  Molecular inner-shell photoabsorption/photoionization cross sections at core-valence-separated coupled cluster level: Theory and examples. , 2019, The Journal of chemical physics.

[13]  Ove Christiansen,et al.  A SECOND-ORDER DOUBLES CORRECTION TO EXCITATION ENERGIES IN THE RANDOM-PHASE APPROXIMATION , 1998 .

[14]  Erik D Hedegård,et al.  Investigation of Multiconfigurational Short-Range Density Functional Theory for Electronic Excitations in Organic Molecules. , 2016, Journal of chemical theory and computation.

[15]  Joost VandeVondele,et al.  Auxiliary Density Matrix Methods for Hartree-Fock Exchange Calculations. , 2010, Journal of chemical theory and computation.

[16]  Sonia Coriani,et al.  Erratum: "Communication: X-ray absorption spectra and core-ionization potentials within a core-valence separated coupled cluster framework" [J. Chem. Phys. 143, 181103 (2015)]. , 2016, The Journal of chemical physics.

[17]  Dan Jonsson,et al.  A general, recursive, and open‐ended response code , 2014, J. Comput. Chem..

[18]  Evgeny Epifanovsky,et al.  New and Efficient Equation-of-Motion Coupled-Cluster Framework for Core-Excited and Core-Ionized States. , 2018, Journal of chemical theory and computation.

[19]  Roland Lindh,et al.  Local properties of quantum chemical systems: the LoProp approach. , 2004, The Journal of chemical physics.

[20]  Thomas Kjærgaard,et al.  MP2 energy and density for large molecular systems with internal error control using the Divide-Expand-Consolidate scheme. , 2012, Physical chemistry chemical physics : PCCP.

[21]  Thomas Kjærgaard,et al.  The GPU‐enabled divide‐expand‐consolidate RI‐MP2 method (DEC‐RI‐MP2) , 2017, J. Comput. Chem..

[22]  Kasper Kristensen,et al.  Correlated natural transition orbital framework for low-scaling excitation energy calculations (CorNFLEx). , 2017, The Journal of chemical physics.

[23]  Tjerk P. Straatsma,et al.  Multilayer Divide-Expand-Consolidate Coupled-Cluster Method: Demonstrative Calculations of the Adsorption Energy of Carbon Dioxide in Mg-MOF-74 Metal-Organic Framework. , 2019, The journal of physical chemistry. A.

[24]  Thomas Kjærgaard,et al.  The Laplace transformed divide-expand-consolidate resolution of the identity second-order Møller-Plesset perturbation (DEC-LT-RIMP2) theory method. , 2017, The Journal of chemical physics.

[25]  Kenneth Ruud,et al.  Zero-point vibrational corrections to isotropic hyperfine coupling constants in polyatomic molecules. , 2011, Physical Chemistry, Chemical Physics - PCCP.

[26]  Patrick Norman,et al.  Resonant-convergent PCM response theory for the calculation of second harmonic generation in makaluvamines A-V: pyrroloiminoquinone marine natural products from poriferans of genus Zyzzya. , 2015, The journal of physical chemistry. A.

[27]  Pi A. B. Haase,et al.  Noniterative Doubles Corrections to the Random Phase and Higher Random Phase Approximations: Singlet and Triplet Excitation Energies , 2019, J. Comput. Chem..

[28]  Hui Cao,et al.  PCMSolver: an Open-Source Library for Solva(cid:2462)on Modeling , 2018 .

[29]  Jacob Kongsted,et al.  Excited states in large molecular systems through polarizable embedding. , 2016, Physical chemistry chemical physics : PCCP.

[30]  Prakash Chandra Jha,et al.  Time-dependent density functional theory for nonlinear properties of open-shell systems. , 2007, The Journal of chemical physics.

[31]  Julien Toulouse,et al.  On the universality of the long-/short-range separation in multiconfigurational density-functional theory. , 2007, The Journal of chemical physics.

[32]  K. V. Roberts,et al.  The publication of scientific fortran programs , 1969 .

[33]  Kenneth Ruud,et al.  Molecular quantum mechanical gradients within the polarizable embedding approach--application to the internal vibrational Stark shift of acetophenone. , 2015, The Journal of chemical physics.

[34]  Xiao Wang,et al.  Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability. , 2017, Journal of chemical theory and computation.

[35]  Andreas Dreuw,et al.  Simulating X-ray Spectroscopies and Calculating Core-Excited States of Molecules. , 2018, Chemical reviews.

[36]  Jacob Kongsted,et al.  Response properties of embedded molecules through the polarizable embedding model , 2018, International Journal of Quantum Chemistry.

[37]  Antonio Rizzo,et al.  A complex-polarization-propagator protocol for magneto-chiral axial dichroism and birefringence dispersion. , 2016, Physical chemistry chemical physics : PCCP.

[38]  S. Huzinaga,et al.  Theory of Separability of Many‐Electron Systems , 1971 .

[39]  Jacob Kongsted,et al.  Local electric fields and molecular properties in heterogeneous environments through polarizable embedding. , 2016, Physical chemistry chemical physics : PCCP.

[40]  Martin Head-Gordon,et al.  Scaled opposite-spin second order Møller-Plesset correlation energy: an economical electronic structure method. , 2004, The Journal of chemical physics.

[41]  Stefan Haacke,et al.  Absorption of schiff-base retinal chromophores in vacuo. , 2005, Journal of the American Chemical Society.

[42]  L. H. Andersen,et al.  S1 and S2 excited States of gas-phase Schiff-base retinal chromophores. , 2006, Physical review letters.

[43]  I. C. Walker,et al.  Core shell excitation of 2-propenal (acrolein) at the O 1s and C 1s edges: An experimental and ab initio study , 2003 .

[44]  Zilvinas Rinkevicius,et al.  Density functional theory for hyperfine coupling constants with the restricted-unrestricted approach. , 2004, The Journal of chemical physics.

[45]  Daniel Wüstner,et al.  Embedding beyond electrostatics-The role of wave function confinement. , 2016, The Journal of chemical physics.

[46]  Sonia Coriani,et al.  Spin adapted implementation of EOM-CCSD for triplet excited states: Probing intersystem crossings of acetylacetone at the carbon and oxygen K-edges. , 2019, Journal of Chemical Physics.

[47]  Marco Garavelli,et al.  Structure, spectroscopy, and spectral tuning of the gas-phase retinal chromophore: the beta-ionone "handle" and alkyl group effect. , 2005, The journal of physical chemistry. A.

[48]  Florent Réal,et al.  On the universality of the long-/short-range separation in multiconfigurational density-functional theory. II. Investigating f0 actinide species. , 2009, The Journal of chemical physics.

[49]  Thomas Kjærgaard,et al.  The molecular gradient using the divide-expand-consolidate resolution of the identity second-order Møller-Plesset perturbation theory: The DEC-RI-MP2 gradient. , 2016, The Journal of chemical physics.

[50]  Chandan Kumar,et al.  Nuclei-selected atomic-orbital response-theory formulation for the calculation of NMR shielding tensors using density-fitting. , 2016, The Journal of chemical physics.

[51]  S. Grimme.  Improved second-order Møller–Plesset perturbation theory by separate scaling of parallel- and antiparallel-spin pair correlation energies , 2003 .

[52]  Benjamin P Pritchard,et al.  New Basis Set Exchange: An Open, Up-to-Date Resource for the Molecular Sciences Community , 2019, J. Chem. Inf. Model..

[53]  Hui Li,et al.  Note: FixSol solvation model and FIXPVA2 tessellation scheme. , 2012, The Journal of chemical physics.

[54]  O. Christiansen,et al.  Coupled-cluster response theory for near-edge x-ray-absorption fine structure of atoms and molecules , 2012 .

[55]  Jacob Kongsted,et al.  Computational Approach for Studying Optical Properties of DNA Systems in Solution. , 2016, Journal of chemical theory and computation.

[56]  Markus Reiher,et al.  Density matrix renormalization group with efficient dynamical electron correlation through range separation. , 2015, The Journal of chemical physics.

[57]  Kenneth Ruud,et al.  Polarizable density embedding: a new QM/QM/MM-based computational strategy. , 2015, The journal of physical chemistry. A.

[58]  J. K. Pedersen,et al.  Description of correlation and relativistic effects in calculations of molecular properties , 2004 .

[59]  Trygve Helgaker,et al.  A unified scheme for the calculation of differentiated and undifferentiated molecular integrals over solid-harmonic Gaussians. , 2007, Physical chemistry chemical physics : PCCP.

[60]  Jeppe Olsen,et al.  Second‐order Mo/ller–Plesset perturbation theory as a configuration and orbital generator in multiconfiguration self‐consistent field calculations , 1988 .

[61]  Branislav Jansík,et al.  Linear scaling coupled cluster method with correlation energy based error control. , 2010, The Journal of chemical physics.

[62]  Poul Jørgensen,et al.  Trust Region Minimization of Orbital Localization Functions. , 2012, Journal of chemical theory and computation.

[63]  Trygve Helgaker,et al.  Translational and rotational symmetries of molecular geometrical derivatives , 1988 .

[64]  Christoph R. Jacob,et al.  Quantum-chemical embedding methods for treating local electronic excitations in complex chemical systems , 2012 .

[65]  Jacob Kongsted,et al.  Molecular Properties through Polarizable Embedding , 2011 .

[66]  Geng Dong,et al.  Exploration of H2 binding to the [NiFe]-hydrogenase active site with multiconfigurational density functional theory. , 2017, Physical chemistry chemical physics : PCCP.

[67]  Jacob Kongsted,et al.  Electronic Energy Transfer in Polarizable Heterogeneous Environments: A Systematic Investigation of Different Quantum Chemical Approaches. , 2015, Journal of chemical theory and computation.

[68]  Thomas Kjærgaard,et al.  Linear-Scaling Coupled Cluster with Perturbative Triple Excitations: The Divide-Expand-Consolidate CCSD(T) Model. , 2015, Journal of chemical theory and computation.

[69]  Trygve Helgaker,et al.  Density-functional theory calculations of optical rotatory dispersion in the nonresonant and resonant frequency regions. , 2004, The Journal of chemical physics.

[70]  Emmanuel Fromager,et al.  Self-consistent many-body perturbation theory in range-separated density-functional theory : A one-electron reduced-density-matrix-based formulation , 2008 .

[71]  Jacob Kongsted,et al.  The polarizable embedding coupled cluster method. , 2011, Journal of Chemical Physics.

[72]  Renzo Cimiraglia,et al.  Merging multireference perturbation and density-functional theories by means of range separation: Potential curves for Be 2 , Mg 2 , and Ca 2 , 2010 .

[73]  Frank Jensen,et al.  The same number of optimized parameters scheme for determining intermolecular interaction energies. , 2015, The Journal of chemical physics.

[74]  Thomas Kjærgaard,et al.  CC2 oscillator strengths within the local framework for calculating excitation energies (LoFEx). , 2016, The Journal of chemical physics.

[75]  Sonia Coriani,et al.  Photoionization cross section by Stieltjes imaging applied to coupled cluster Lanczos pseudo-spectra. , 2013, The Journal of chemical physics.

[76]  Thomas Kjærgaard,et al.  Efficient linear-scaling second-order Møller-Plesset perturbation theory: The divide-expand-consolidate RI-MP2 model. , 2016, The Journal of chemical physics.

[77]  Kurt V. Mikkelsen,et al.  On the importance of excited state dynamic response electron correlation in polarizable embedding methods , 2012, J. Comput. Chem..

[78]  Kenneth Ruud,et al.  The A and B terms of magnetic circular dichroism revisited. , 2008, The journal of physical chemistry. A.

[79]  Sandeep Sharma,et al.  PySCF: the Python‐based simulations of chemistry framework , 2018 .

[80]  Lucas Visscher,et al.  Molecular properties via a subsystem density functional theory formulation: a common framework for electronic embedding. , 2012, The Journal of chemical physics.

[81]  Paweł Sałek,et al.  Linear-scaling implementation of molecular response theory in self-consistent field electronic-structure theory. , 2007, The Journal of chemical physics.

[82]  Trygve Helgaker,et al.  An efficient density-functional-theory force evaluation for large molecular systems. , 2010, The Journal of chemical physics.

[83]  Kenneth Ruud,et al.  A density matrix-based quasienergy formulation of the Kohn-Sham density functional response theory using perturbation- and time-dependent basis sets. , 2008, The Journal of chemical physics.

[84]  Zilvinas Rinkevicius,et al.  Time-dependent density functional theory with the generalized restricted-unrestricted approach. , 2006, The Journal of chemical physics.

[85]  Luca Frediani,et al.  The Dalton quantum chemistry program system , 2013, Wiley interdisciplinary reviews. Computational molecular science.

[86]  Thomas Kjærgaard,et al.  Molecular gradient for second-order Møller-Plesset perturbation theory using the divide-expand-consolidate (DEC) scheme. , 2012, The Journal of chemical physics.

[87]  Daniel Wüstner,et al.  The Second-Order Polarization Propagator Approximation (SOPPA) method coupled to the polarizable continuum model , 2014 .

[88]  Thomas Kjærgaard,et al.  The explicitly correlated same number of optimized parameters (SNOOP-F12) scheme for calculating intermolecular interaction energies. , 2016, The Journal of chemical physics.

[89]  Erik D Hedegård,et al.  Excitation Spectra of Nucleobases with Multiconfigurational Density Functional Theory. , 2016, The journal of physical chemistry. A.

[90]  Joel Nothman,et al.  SciPy 1.0-Fundamental Algorithms for Scientific Computing in Python , 2019, ArXiv.

[91]  Kenneth Ruud,et al.  Benchmarking two-photon absorption cross sections: performance of CC2 and CAM-B3LYP. , 2015, Physical chemistry chemical physics : PCCP.

[92]  John D. Hunter,et al.  Matplotlib: A 2D Graphics Environment , 2007, Computing in Science & Engineering.

[93]  Sonia Coriani,et al.  Resonant Inelastic X-ray Scattering and Nonesonant X-ray Emission Spectra from Coupled-Cluster (Damped) Response Theory. , 2018, Journal of chemical theory and computation.

[94]  Jacob Kongsted,et al.  Polarizable embedding with a multiconfiguration short-range density functional theory linear response method. , 2015, The Journal of chemical physics.

[95]  Paweł Sałek,et al.  Restricted density functional theory of linear time-dependent properties in open-shell molecules , 2003 .

[96]  D. M. Bishop,et al.  Nonlinear response theory with relaxation: the first-order hyperpolarizability. , 2005, The Journal of chemical physics.

[97]  Patrick Norman,et al.  A perspective on nonresonant and resonant electronic response theory for time-dependent molecular properties. , 2011, Physical chemistry chemical physics : PCCP.

[98]  Kenneth Ruud,et al.  Arbitrary-Order Density Functional Response Theory from Automatic Differentiation. , 2010, Journal of chemical theory and computation.

[99]  Ardavan Saeedi,et al.  Variational Particle Approximations , 2014, J. Mach. Learn. Res..

[100]  Jacob Kongsted,et al.  A quantum-mechanical perspective on linear response theory within polarizable embedding. , 2017, The Journal of chemical physics.

[101]  Sonia Coriani,et al.  Communication: X-ray absorption spectra and core-ionization potentials within a core-valence separated coupled cluster framework. , 2015, The Journal of chemical physics.

[102]  Patrick Norman,et al.  Electronic circular dichroism spectra from the complex polarization propagator. , 2007, The Journal of chemical physics.

[103]  Cecilia Clementi,et al.  Perspective: Computational chemistry software and its advancement as illustrated through three grand challenge cases for molecular science. , 2018, The Journal of chemical physics.

[104]  Jacob Kongsted,et al.  The multi-configuration self-consistent field method within a polarizable embedded framework. , 2013, The Journal of chemical physics.

[105]  Jógvan Magnus Haugaard Olsen,et al.  Nuclear Magnetic Shielding Constants from Quantum Mechanical/Molecular Mechanical Calculations Using Polarizable Embedding: Role of the Embedding Potential. , 2014, Journal of Chemical Theory and Computation.

[106]  Stinne Høst,et al.  Local orbitals by minimizing powers of the orbital variance. , 2011, The Journal of chemical physics.

[107]  Julien Toulouse,et al.  Multiconfigurational short-range density-functional theory for open-shell systems. , 2017, The Journal of chemical physics.

[108]  Walter Thiel,et al.  Performance of SOPPA-based methods in the calculation of vertical excitation energies and oscillator strengths , 2015 .

[109]  Kenneth Ruud,et al.  GEN1INT: A unified procedure for the evaluation of one‐electron integrals over Gaussian basis functions and their geometric derivatives , 2011 .

[110]  Jacob Kongsted,et al.  Polarizable Density Embedding: A Solution to the Electron Spill-Out Problem in Multiscale Modeling. , 2017, The journal of physical chemistry letters.

[111]  Antonio Rizzo,et al.  Nuclear spin circular dichroism. , 2014, The Journal of chemical physics.

[112]  S. Grimme,et al.  Spin‐component‐scaled electron correlation methods , 2012 .

[113]  Kenneth Ruud,et al.  Complex polarization propagator calculations of magnetic circular dichroism spectra. , 2008, The Journal of chemical physics.

[114]  Paweł Sałek,et al.  Restricted density-functional linear response theory calculations of electronic g-tensors , 2003 .

[115]  Edsger W. Dijkstra,et al.  The structure of the “THE”-multiprogramming system , 1968, CACM.

[116]  Stefan Knecht,et al.  Assessment of charge-transfer excitations with time-dependent, range-separated density functional theory based on long-range MP2 and multiconfigurational self-consistent field wave functions. , 2013, The Journal of chemical physics.

[117]  John Z. H. Zhang,et al.  Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein-molecule interaction energy , 2003 .

[118]  Jacob Kongsted,et al.  Excited States in Solution through Polarizable Embedding , 2010 .

[119]  Donald F. Hornig,et al.  Molecular Vibrations. The Theory of Infrared and Raman Vibrational Spectra. , 1956 .

[120]  Lucas Visscher,et al.  Solvatochromic shifts from coupled-cluster theory embedded in density functional theory. , 2013, The Journal of chemical physics.

[121]  Thomas Fransson,et al.  Asymmetric-Lanczos-Chain-Driven Implementation of Electronic Resonance Convergent Coupled-Cluster Linear Response Theory. , 2012, Journal of chemical theory and computation.

[122]  Maximilian Scheurer,et al.  CPPE: An Open-Source C++ and Python Library for Polarizable Embedding. , 2019, Journal of chemical theory and computation.

[123]  Christoph R. Jacob,et al.  Subsystem density‐functional theory , 2014 .

[124]  Daniel G A Smith,et al.  Psi4NumPy: An Interactive Quantum Chemistry Programming Environment for Reference Implementations and Rapid Development. , 2018, Journal of chemical theory and computation.

[125]  T J Martinez,et al.  Probing ultrafast ππ*/nπ* internal conversion in organic chromophores via K-edge resonant absorption , 2016, Nature Communications.

[126]  Lucas Visscher,et al.  Calculation of local excitations in large systems by embedding wave-function theory in density-functional theory. , 2008, Physical chemistry chemical physics : PCCP.

[127]  Dmitry Liakh,et al.  A local framework for calculating coupled cluster singles and doubles excitation energies (LoFEx-CCSD) , 2017 .

[128]  V. Barone,et al.  A second-order perturbation theory route to vibrational averages and transition properties of molecules: general formulation and application to infrared and vibrational circular dichroism spectroscopies. , 2012, The Journal of chemical physics.

[129]  Henrik Koch,et al.  The multilevel CC3 coupled cluster model. , 2016, The Journal of chemical physics.

[130]  Maximilian Scheurer,et al.  VeloxChem: A Python‐driven density‐functional theory program for spectroscopy simulations in high‐performance computing environments , 2019, WIREs Computational Molecular Science.

[131]  Patrick Norman,et al.  A Polarization Propagator for Nonlinear X-ray Spectroscopies. , 2016, The journal of physical chemistry letters.

[132]  Stefan Knecht,et al.  Multi-configuration time-dependent density-functional theory based on range separation. , 2012, The Journal of chemical physics.

[133]  Mario A. Storti,et al.  MPI for Python: Performance improvements and MPI-2 extensions , 2008, J. Parallel Distributed Comput..

[134]  Olav Vahtras.  LoProp for Dalton , 2014 .

[135]  Patrick Norman,et al.  Resonant-convergent second-order nonlinear response functions at the levels of Hartree-Fock and Kohn-Sham density functional theory. , 2017, The Journal of chemical physics.

[136]  Vladimir V. Rybkin,et al.  Internal‐to‐Cartesian back transformation of molecular geometry steps using high‐order geometric derivatives , 2013, J. Comput. Chem..

[137]  Jacob Kongsted,et al.  Polarizable Density Embedding Coupled Cluster Method. , 2018, Journal of chemical theory and computation.

[138]  Zilvinas Rinkevicius,et al.  Density functional restricted-unrestricted approach for nonlinear properties: application to electron paramagnetic resonance parameters of square planar copper complexes. , 2008, The Journal of chemical physics.

[139]  Anna Kristina Schnack-Petersen,et al.  RPA(D) and HRPA(D): Two new models for calculations of NMR indirect nuclear spin–spin coupling constants , 2018, Journal of Computational Chemistry.