Tesi magistrale.bib

@article{al-saidiAssessmentVdWTSMethod2012,
  title = {An {{Assessment}} of the {{vdW-TS Method}} for {{Extended Systems}}},
  author = {Al-Saidi, W. A. and Voora, Vamsee K. and Jordan, Kenneth D.},
  date = {2012-04-10},
  journaltitle = {Journal of Chemical Theory and Computation},
  shortjournal = {J. Chem. Theory Comput.},
  volume = {8},
  number = {4},
  pages = {1503--1513},
  publisher = {American Chemical Society},
  issn = {1549-9618},
  doi = {10.1021/ct200618b},
  url = {https://doi.org/10.1021/ct200618b},
  urldate = {2024-06-05},
  abstract = {The Tkatchenko--Scheffler vdW-TS method [Phys. Rev. Lett.2009, 102, 073005] has been implemented in a plane-wave DFT code and used to characterize several dispersion-dominated systems, including layered materials, noble-gas solids, and molecular crystals. Full optimizations of the structures, including relaxation of the stresses on the unit cells, were carried out. Internal geometrical parameters, lattice constants, bulk moduli, and cohesive energies are reported and compared to experimental results.},
  file = {/home/mariano/Zotero/storage/KA2D2XH3/Al-Saidi et al. - 2012 - An Assessment of the vdW-TS Method for Extended Sy.pdf}
}

@article{alfeCrystalStructureThermodynamic,
  title = {Crystal Structure and Thermodynamic Stability of Ferropericlase at Planetary Interior Conditions},
  author = {Alf\`e, Dario and Della Pia, Flaviano},
  langid = {english},
  file = {/home/mariano/Zotero/storage/4KLI3QHG/Alfè e Pia - Crystal structure and thermodynamic stability of f.pdf}
}

@unpublished{alfeNotesStatisticalComputational2023,
  title = {Notes on {{Statistical}} and {{Computational Physics}}},
  author = {Alf\`e, Dario},
  date = {2023},
  langid = {english},
  file = {/home/mariano/Zotero/storage/TEK2WENU/Alfe - Notes on Statistical and Computational Physics.pdf}
}

@article{alfePHONProgramCalculate2009,
  title = {{{PHON}}: {{A}} Program to Calculate Phonons Using the Small Displacement Method},
  shorttitle = {{{PHON}}},
  author = {Alf\`e, Dario},
  date = {2009-12-01},
  journaltitle = {Computer Physics Communications},
  shortjournal = {Computer Physics Communications},
  series = {40 {{YEARS OF CPC}}: {{A}} Celebratory Issue Focused on Quality Software for High Performance, Grid and Novel Computing Architectures},
  volume = {180},
  number = {12},
  pages = {2622--2633},
  issn = {0010-4655},
  doi = {10.1016/j.cpc.2009.03.010},
  url = {https://www.sciencedirect.com/science/article/pii/S0010465509001064},
  urldate = {2023-09-09},
  abstract = {The program phon calculates force constant matrices and phonon frequencies in crystals. From the frequencies it also calculates various thermodynamic quantities, like the Helmholtz free energy, the entropy, the specific heat and the internal energy of the harmonic crystal. The procedure is based on the small displacement method, and can be used in combination with any program capable to calculate forces on the atoms of the crystal. In order to examine the usability of the method, I present here two examples: metallic Al and insulating MgO. The phonons of these two materials are calculated using density functional theory. The small displacement method results are compared with those obtained using the linear response method. In the case of Al the method provides accurate phonon frequencies everywhere in the Brillouin Zone (BZ). In the case of MgO the longitudinal branch of the optical phonons near the centre of the BZ is incorrectly described as degenerate with the two transverse branches, because the non-analytical part of the dynamical matrix is ignored here; however, thermodynamic properties like the Helmholtz free are essentially unaffected. Program summary Program title: PHON Catalogue identifier: AEDP\_v1\_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEDP\_v1\_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 19\,580 No. of bytes in distributed program, including test data, etc.: 612\,193 Distribution format: tar.gz Programming language: Fortran 90 Computer: Any Unix, Linux Operating system: Unix RAM: Depends on super-cell size, but usually negligible Classification: 7.8 External routines: Subprograms ZHEEV and DSYEV (Lapack); needs BLAS. A tutorial is provided with the distribution which requires the installation of the quantum-espresso package (http://www.quantum-espresso.org) Nature of problem: Stable crystals at low temperature can be well described by expanding the potential energy around the atomic equilibrium positions. The movements of the atoms around their equilibrium positions can then be described using harmonic theory, and is characterised by global vibrations called phonons, which can be identified by vectors in the Brillouin zone of the crystal, and there are 3 phonon branches for each atom in the primitive cell. The problem is to calculate the frequencies of these phonons for any arbitrary choice of q-vector in the Brillouin zone. Solution method: The small displacement method: each atom in the primitive cell is displaced by a small amount, and the forces induced on all the other atoms in the crystal are calculated and used to construct the force constant matrix. Supercells of {$\sim$}100 atoms are usually large enough to describe the force constant matrix up to the range where its elements have fallen to negligibly small values. The force constant matrix is then used to compute the dynamical matrix at any chosen q-vector in the Brillouin zone, and the diagonalisation of the dynamical matrix provides the squares of the phonon frequencies. The PHON code needs external programs to calculate these forces, and it can be used with any program capable of calculating forces in crystals. The most useful applications are obtained with codes based on density functional theory, but there is no restriction on what can be used. Running time: Negligible, typically a few seconds (or at most a few minutes) on a PC. It can take longer if very dense meshes of q-points are needed, for example, to compute very accurate phonon density of states.},
  keywords = {Direct method,Free energies,Harmonic approximation,Phonons,Small displacement},
  file = {/home/mariano/Zotero/storage/Z5D3EEUF/Alfè - 2009 - PHON A program to calculate phonons using the sma.pdf;/home/mariano/Zotero/storage/UUDU8NPZ/Alfè - 2009 - PHON A program to calculate phonons using the sma.html}
}

@article{andersenMolecularDynamicsSimulations1980,
  title = {Molecular Dynamics Simulations at Constant Pressure and/or Temperature},
  author = {Andersen, Hans C.},
  date = {1980-02-15},
  journaltitle = {The Journal of Chemical Physics},
  volume = {72},
  number = {4},
  pages = {2384--2393},
  issn = {0021-9606, 1089-7690},
  doi = {10.1063/1.439486},
  url = {https://pubs.aip.org/jcp/article/72/4/2384/218722/Molecular-dynamics-simulations-at-constant},
  urldate = {2024-07-12},
  abstract = {In the molecular dynamics simulation method for fluids, the equations of motion for a collection of particles in a fixed volume are solved numerically. The energy, volume, and number of particles are constant for a particular simulation, and it is assumed that time averages of properties of the simulated fluid are equal to microcanonical ensemble averages of the same properties. In some situations, it is desirable to perform simulations of a fluid for particular values of temperature and/or pressure or under conditions in which the energy and volume of the fluid can fluctuate. This paper proposes and discusses three methods for performing molecular dynamics simulations under conditions of constant temperature and/or pressure, rather than constant energy and volume. For these three methods, it is shown that time averages of properties of the simulated fluid are equal to averages over the isoenthalpic--isobaric, canonical, and isothermal--isobaric ensembles. Each method is a way of describing the dynamics of a certain number of particles in a volume element of a fluid while taking into account the influence of surrounding particles in changing the energy and/or density of the simulated volume element. The influence of the surroundings is taken into account without introducing unwanted surface effects. Examples of situations where these methods may be useful are discussed.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/LZX7M34A/Andersen - 1980 - Molecular dynamics simulations at constant pressure andor temperature.pdf}
}

@article{barnettBornOppenheimerMoleculardynamicsSimulations1993,
  title = {Born-{{Oppenheimer}} Molecular-Dynamics Simulations of Finite Systems: {{Structure}} and Dynamics of ( {{H}} 2 {{O}} ) 2},
  shorttitle = {Born-{{Oppenheimer}} Molecular-Dynamics Simulations of Finite Systems},
  author = {Barnett, Robert N. and Landman, Uzi},
  date = {1993-07-15},
  journaltitle = {Physical Review B},
  shortjournal = {Phys. Rev. B},
  volume = {48},
  number = {4},
  pages = {2081--2097},
  issn = {0163-1829, 1095-3795},
  doi = {10.1103/PhysRevB.48.2081},
  url = {https://link.aps.org/doi/10.1103/PhysRevB.48.2081},
  urldate = {2024-02-26},
  langid = {english},
  keywords = {dimer,H2O},
  file = {/home/mariano/Zotero/storage/4JY8RQCW/Barnett e Landman - 1993 - Born-Oppenheimer molecular-dynamics simulations of.pdf}
}

@article{baroneVibrationalZeropointEnergies2004,
  title = {Vibrational Zero-Point Energies and Thermodynamic Functions beyond the Harmonic Approximation},
  author = {Barone, Vincenzo},
  date = {2004-02-15},
  journaltitle = {The Journal of Chemical Physics},
  volume = {120},
  number = {7},
  pages = {3059--3065},
  issn = {0021-9606, 1089-7690},
  doi = {10.1063/1.1637580},
  url = {https://pubs.aip.org/jcp/article/120/7/3059/535809/Vibrational-zero-point-energies-and-thermodynamic},
  urldate = {2024-09-25},
  abstract = {This paper compares harmonic and anharmonic zero-point energies and thermodynamic functions for a number of molecules of small and medium size. Anharmonic corrections cannot be neglected for quantitative studies, but can be obtained quite effectively by a perturbative treatment including cubic force constants to the second order and semidiagonal quartic constants to the first order. Simple finite difference equations provide all the necessary terms by at most 6N-11 Hessian evaluations, where N is the number of atoms in the system. Accurate values are obtained by this method using the Becke three parameter Lee--Yang--Parr functional, medium size basis sets, and, when needed, proper treatment of internal rotations. The whole model has been completely automated in the Gaussian package.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/66IGK9FN/Barone - 2004 - Vibrational zero-point energies and thermodynamic functions beyond the harmonic approximation.pdf}
}

@online{batatiaDesignSpaceEquivariant2022,
  title = {The {{Design Space}} of {{E}}(3)-{{Equivariant Atom-Centered Interatomic Potentials}}},
  author = {Batatia, Ilyes and Batzner, Simon and Kov\'acs, D\'avid P\'eter and Musaelian, Albert and Simm, Gregor N. C. and Drautz, Ralf and Ortner, Christoph and Kozinsky, Boris and Cs\'anyi, G\'abor},
  date = {2022},
  doi = {10.48550/ARXIV.2205.06643},
  url = {https://arxiv.org/abs/2205.06643},
  urldate = {2024-06-02},
  abstract = {The rapid progress of machine learning interatomic potentials over the past couple of years produced a number of new architectures. Particularly notable among these are the Atomic Cluster Expansion (ACE), which unified many of the earlier ideas around atom density-based descriptors, and Neural Equivariant Interatomic Potentials (NequIP), a message passing neural network with equivariant features that showed state of the art accuracy. In this work, we construct a mathematical framework that unifies these models: ACE is generalised so that it can be recast as one layer of a multi-layer architecture. From another point of view, the linearised version of NequIP is understood as a particular sparsification of a much larger polynomial model. Our framework also provides a practical tool for systematically probing different choices in the unified design space. We demonstrate this by an ablation study of NequIP via a set of experiments looking at in- and out-of-domain accuracy and smooth extrapolation very far from the training data, and shed some light on which design choices are critical for achieving high accuracy. Finally, we present BOTNet (Body-Ordered-Tensor-Network), a much-simplified version of NequIP, which has an interpretable architecture and maintains accuracy on benchmark datasets.},
  pubstate = {prepublished},
  version = {2},
  keywords = {Chemical Physics (physics.chem-ph),FOS: Computer and information sciences,FOS: Physical sciences,Machine Learning (cs.LG),Machine Learning (stat.ML),Materials Science (cond-mat.mtrl-sci)}
}

@online{batatiaFoundationModelAtomistic2023,
  title = {A Foundation Model for Atomistic Materials Chemistry},
  author = {Batatia, Ilyes and Benner, Philipp and Chiang, Yuan and Elena, Alin M. and Kov\'acs, D\'avid P. and Riebesell, Janosh and Advincula, Xavier R. and Asta, Mark and Baldwin, William J. and Bernstein, Noam and Bhowmik, Arghya and Blau, Samuel M. and C\u arare, Vlad and Darby, James P. and De, Sandip and Della Pia, Flaviano and Deringer, Volker L. and Elijo\v sius, Rokas and El-Machachi, Zakariya and Fako, Edvin and Ferrari, Andrea C. and Genreith-Schriever, Annalena and George, Janine and Goodall, Rhys E. A. and Grey, Clare P. and Han, Shuang and Handley, Will and Heenen, Hendrik H. and Hermansson, Kersti and Holm, Christian and Jaafar, Jad and Hofmann, Stephan and Jakob, Konstantin S. and Jung, Hyunwook and Kapil, Venkat and Kaplan, Aaron D. and Karimitari, Nima and Kroupa, Namu and Kullgren, Jolla and Kuner, Matthew C. and Kuryla, Domantas and Liepuoniute, Guoda and Margraf, Johannes T. and Magd\u au, Ioan-Bogdan and Michaelides, Angelos and Moore, J. Harry and Naik, Aakash A. and Niblett, Samuel P. and Norwood, Sam Walton and O'Neill, Niamh and Ortner, Christoph and Persson, Kristin A. and Reuter, Karsten and Rosen, Andrew S. and Schaaf, Lars L. and Schran, Christoph and Sivonxay, Eric and Stenczel, Tam\'as K. and Svahn, Viktor and Sutton, Christopher and family=Oord, given=Cas, prefix=van der, useprefix=true and Varga-Umbrich, Eszter and Vegge, Tejs and Vondr\'ak, Martin and Wang, Yangshuai and Witt, William C. and Zills, Fabian and Cs\'anyi, G\'abor},
  date = {2023-12-29},
  eprint = {2401.00096},
  eprinttype = {arXiv},
  eprintclass = {cond-mat, physics:physics},
  url = {http://arxiv.org/abs/2401.00096},
  urldate = {2024-01-11},
  abstract = {Machine-learned force fields have transformed the atomistic modelling of materials by enabling simulations of ab initio quality on unprecedented time and length scales. However, they are currently limited by: (i) the significant computational and human effort that must go into development and validation of potentials for each particular system of interest; and (ii) a general lack of transferability from one chemical system to the next. Here, using the state-of-the-art MACE architecture we introduce a single general-purpose ML model, trained on a public database of 150k inorganic crystals, that is capable of running stable molecular dynamics on molecules and materials. We demonstrate the power of the MACE-MP-0 model -- and its qualitative and at times quantitative accuracy -- on a diverse set problems in the physical sciences, including the properties of solids, liquids, gases, and chemical reactions. The model can be applied out of the box and as a starting or "foundation model" for any atomistic system of interest and is thus a step towards democratising the revolution of ML force fields by lowering the barriers to entry.},
  langid = {english},
  pubstate = {prepublished},
  keywords = {Condensed Matter - Materials Science,Physics - Chemical Physics},
  file = {/home/mariano/Zotero/storage/W9BT2K54/Batatia et al. - 2023 - A foundation model for atomistic materials chemist.pdf}
}

@article{batatiaMACEHigherOrder2022,
  title = {{{MACE}}: {{Higher Order Equivariant Message Passing Neural Networks}} for {{Fast}} and {{Accurate Force Fields}}},
  author = {Batatia, Ilyes and Kov\'acs, D\'avid P\'eter and Simm, Gregor N C and Ortner, Christoph and Cs\'anyi, G\'abor},
  date = {2022},
  abstract = {Creating fast and accurate force fields is a long-standing challenge in computational chemistry and materials science. Recently, several equivariant message passing neural networks (MPNNs) have been shown to outperform models built using other approaches in terms of accuracy. However, most MPNNs suffer from high computational cost and poor scalability. We propose that these limitations arise because MPNNs only pass two-body messages leading to a direct relationship between the number of layers and the expressivity of the network. In this work, we introduce MACE, a new equivariant MPNN model that uses higher body order messages. In particular, we show that using four-body messages reduces the required number of message passing iterations to just two, resulting in a fast and highly parallelizable model, reaching or exceeding state-of-the-art accuracy on the rMD17, 3BPA, and AcAc benchmark tasks. We also demonstrate that using higher order messages leads to an improved steepness of the learning curves.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/EEWVCLJH/Batatia et al. - MACE Higher Order Equivariant Message Passing Neu.pdf}
}

@online{battagliaRelationalInductiveBiases2018,
  title = {Relational Inductive Biases, Deep Learning, and Graph Networks},
  author = {Battaglia, Peter W. and Hamrick, Jessica B. and Bapst, Victor and Sanchez-Gonzalez, Alvaro and Zambaldi, Vinicius and Malinowski, Mateusz and Tacchetti, Andrea and Raposo, David and Santoro, Adam and Faulkner, Ryan and Gulcehre, Caglar and Song, Francis and Ballard, Andrew and Gilmer, Justin and Dahl, George and Vaswani, Ashish and Allen, Kelsey and Nash, Charles and Langston, Victoria and Dyer, Chris and Heess, Nicolas and Wierstra, Daan and Kohli, Pushmeet and Botvinick, Matt and Vinyals, Oriol and Li, Yujia and Pascanu, Razvan},
  date = {2018-10-17},
  eprint = {1806.01261},
  eprinttype = {arXiv},
  eprintclass = {cs, stat},
  doi = {10.48550/arXiv.1806.01261},
  url = {http://arxiv.org/abs/1806.01261},
  urldate = {2024-07-13},
  abstract = {Artificial intelligence (AI) has undergone a renaissance recently, making major progress in key domains such as vision, language, control, and decision-making. This has been due, in part, to cheap data and cheap compute resources, which have fit the natural strengths of deep learning. However, many defining characteristics of human intelligence, which developed under much different pressures, remain out of reach for current approaches. In particular, generalizing beyond one's experiences--a hallmark of human intelligence from infancy--remains a formidable challenge for modern AI. The following is part position paper, part review, and part unification. We argue that combinatorial generalization must be a top priority for AI to achieve human-like abilities, and that structured representations and computations are key to realizing this objective. Just as biology uses nature and nurture cooperatively, we reject the false choice between "hand-engineering" and "end-to-end" learning, and instead advocate for an approach which benefits from their complementary strengths. We explore how using relational inductive biases within deep learning architectures can facilitate learning about entities, relations, and rules for composing them. We present a new building block for the AI toolkit with a strong relational inductive bias--the graph network--which generalizes and extends various approaches for neural networks that operate on graphs, and provides a straightforward interface for manipulating structured knowledge and producing structured behaviors. We discuss how graph networks can support relational reasoning and combinatorial generalization, laying the foundation for more sophisticated, interpretable, and flexible patterns of reasoning. As a companion to this paper, we have released an open-source software library for building graph networks, with demonstrations of how to use them in practice.},
  pubstate = {prepublished},
  keywords = {Computer Science - Artificial Intelligence,Computer Science - Machine Learning,Statistics - Machine Learning},
  file = {/home/mariano/Zotero/storage/CLISIB7Z/Battaglia et al. - 2018 - Relational inductive biases, deep learning, and graph networks.pdf;/home/mariano/Zotero/storage/G39V66TF/1806.html}
}

@article{behlerConstructingHighDimensional2015,
  title = {Constructing High-dimensional Neural Network Potentials: {{A}} Tutorial Review},
  shorttitle = {Constructing High-dimensional Neural Network Potentials},
  author = {Behler, J\"org},
  date = {2015-08-15},
  journaltitle = {International Journal of Quantum Chemistry},
  shortjournal = {Int J of Quantum Chemistry},
  volume = {115},
  number = {16},
  pages = {1032--1050},
  issn = {0020-7608, 1097-461X},
  doi = {10.1002/qua.24890},
  url = {https://onlinelibrary.wiley.com/doi/10.1002/qua.24890},
  urldate = {2024-07-10},
  abstract = {A lot of progress has been made in recent years in the development of atomistic potentials using machine learning (ML) techniques. In contrast to most conventional potentials, which are based on physical approximations and simplifications to derive an analytic functional relation between the atomic configuration and the potential-energy, ML potentials rely on simple but very flexible mathematical terms without a direct physical meaning. Instead, in case of ML potentials the topology of the potential-energy surface is ``learned'' by adjusting a number of parameters with the aim to reproduce a set of reference electronic structure data as accurately as possible. Due to this bias-free construction, they are applicable to a wide range of systems without changes in their functional form, and a very high accuracy close to the underlying first-principles data can be obtained. Neural network potentials (NNPs), which have first been proposed about two decades ago, are an important class of ML potentials. Although the first NNPs have been restricted to small molecules with only a few degrees of freedom, they are now applicable to high-dimensional systems containing thousands of atoms, which enables addressing a variety of problems in chemistry, physics, and materials science. In this tutorial review, the basic ideas of NNPs are presented with a special focus on developing NNPs for high-dimensional condensed systems. A recipe for the construction of these potentials is given and remaining limitations of the method are discussed. \copyright{} 2015 Wiley Periodicals, Inc.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/JUWHN73C/Behler - 2015 - Constructing high‐dimensional neural network potentials A tutorial review.pdf}
}

@article{behlerFourGenerationsHighDimensional2021,
  title = {Four {{Generations}} of {{High-Dimensional Neural Network Potentials}}},
  author = {Behler, J\"org},
  date = {2021-08-25},
  journaltitle = {Chemical Reviews},
  shortjournal = {Chem. Rev.},
  volume = {121},
  number = {16},
  pages = {10037--10072},
  issn = {0009-2665, 1520-6890},
  doi = {10.1021/acs.chemrev.0c00868},
  url = {https://pubs.acs.org/doi/10.1021/acs.chemrev.0c00868},
  urldate = {2024-07-10},
  abstract = {Since their introduction about 25 years ago, machine learning (ML) potentials have become an important tool in the field of atomistic simulations. After the initial decade, in which neural networks were successfully used to construct potentials for rather small molecular systems, the development of high-dimensional neural network potentials (HDNNPs) in 2007 opened the way for the application of ML potentials in simulations of large systems containing thousands of atoms. To date, many other types of ML potentials have been proposed continuously increasing the range of problems that can be studied. In this review, the methodology of the family of HDNNPs including new recent developments will be discussed using a classification scheme into four generations of potentials, which is also applicable to many other types of ML potentials. The first generation is formed by early neural network potentials designed for low-dimensional systems. High-dimensional neural network potentials established the second generation and are based on three key steps: first, the expression of the total energy as a sum of environmentdependent atomic energy contributions; second, the description of the atomic environments by atom-centered symmetry functions as descriptors fulfilling the requirements of rotational, translational, and permutation invariance; and third, the iterative construction of the reference electronic structure data sets by active learning. In third-generation HDNNPs, in addition, long-range interactions are included employing environment-dependent partial charges expressed by atomic neural networks. In fourth-generation HDNNPs, which are just emerging, in addition, nonlocal phenomena such as long-range charge transfer can be included. The applicability and remaining limitations of HDNNPs are discussed along with an outlook at possible future developments.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/AFLUPJCJ/Behler - 2021 - Four Generations of High-Dimensional Neural Network Potentials.pdf}
}

@article{benningtonPhononSofteningIce1999,
  title = {Phonon Softening in Ice {{Ih}}},
  author = {Bennington, Stephen M and Li, Jichen and Harris, Mark J and Keith Ross, D},
  date = {1999-03-01},
  journaltitle = {Physica B: Condensed Matter},
  shortjournal = {Physica B: Condensed Matter},
  volume = {263--264},
  pages = {396--399},
  issn = {0921-4526},
  doi = {10.1016/S0921-4526(98)01396-9},
  url = {https://www.sciencedirect.com/science/article/pii/S0921452698013969},
  urldate = {2024-01-22},
  abstract = {We present detailed phonon dispersion measurements along the (11.0) and (10.0) directions in a crystal of ice Ih, measured using neutron scattering. The softening of the TA and LA branches are measured as a function of temperature. We show that an instability in the TA-mode is responsible for the negative thermal expansion of ice below 50K.},
  keywords = {Disordered systems,Ice,Inelastic neutron scattering,Phonons},
  file = {/home/mariano/Zotero/storage/BPIYVHGH/Bennington et al. - 1999 - Phonon softening in ice Ih.pdf;/home/mariano/Zotero/storage/LWTMTS6Y/S0921452698013969.html}
}

@article{beranPredictingMolecularCrystal2016,
  title = {Predicting {{Molecular Crystal Properties}} from {{First Principles}}: {{Finite-Temperature Thermochemistry}} to {{NMR Crystallography}}},
  shorttitle = {Predicting {{Molecular Crystal Properties}} from {{First Principles}}},
  author = {Beran, Gregory J. O. and Hartman, Joshua D. and Heit, Yonaton N.},
  date = {2016-11-15},
  journaltitle = {Accounts of Chemical Research},
  shortjournal = {Acc. Chem. Res.},
  volume = {49},
  number = {11},
  pages = {2501--2508},
  publisher = {American Chemical Society},
  issn = {0001-4842},
  doi = {10.1021/acs.accounts.6b00404},
  url = {https://doi.org/10.1021/acs.accounts.6b00404},
  urldate = {2024-06-03},
  abstract = {ConspectusMolecular crystals occur widely in pharmaceuticals, foods, explosives, organic semiconductors, and many other applications. Thanks to substantial progress in electronic structure modeling of molecular crystals, attention is now shifting from basic crystal structure prediction and lattice energy modeling toward the accurate prediction of experimentally observable properties at finite temperatures and pressures. This Account discusses how fragment-based electronic structure methods can be used to model a variety of experimentally relevant molecular crystal properties. First, it describes the coupling of fragment electronic structure models with quasi-harmonic techniques for modeling the thermal expansion of molecular crystals, and what effects this expansion has on thermochemical and mechanical properties.Excellent agreement with experiment is demonstrated for the molar volume, sublimation enthalpy, entropy, and free energy, and the bulk modulus of phase I carbon dioxide when large basis second-order M\o ller--Plesset perturbation theory (MP2) or coupled cluster theories (CCSD(T)) are used. In addition, physical insight is offered into how neglect of thermal expansion affects these properties. Zero-point vibrational motion leads to an appreciable expansion in the molar volume; in carbon dioxide, it accounts for around 30\% of the overall volume expansion between the electronic structure energy minimum and the molar volume at the sublimation point. In addition, because thermal expansion typically weakens the intermolecular interactions, neglecting thermal expansion artificially stabilizes the solid and causes the sublimation enthalpy to be too large at higher temperatures. Thermal expansion also frequently weakens the lower-frequency lattice phonon modes; neglecting thermal expansion causes the entropy of sublimation to be overestimated. Interestingly, the sublimation free energy is less significantly affected by neglecting thermal expansion because the systematic errors in the enthalpy and entropy cancel somewhat.Second, because solid state nuclear magnetic resonance (NMR) plays an increasingly important role in molecular crystal studies, this Account discusses how fragment methods can be used to achieve higher-accuracy chemical shifts in molecular crystals. Whereas widely used plane wave density functional theory models are largely restricted to generalized gradient approximation (GGA) functionals like PBE in practice, fragment methods allow the routine use of hybrid density functionals with only modest increases in computational cost. In extensive molecular crystal benchmarks, hybrid functionals like PBE0 predict chemical shifts with 20--30\% higher accuracy than GGAs, particularly for 1H, 13C, and 15N nuclei. Due to their higher sensitivity to polarization effects, 17O chemical shifts prove slightly harder to predict with fragment methods. Nevertheless, the fragment model results are still competitive with those from GIPAW.The improved accuracy achievable with fragment approaches and hybrid density functionals increases discrimination between different potential assignments of individual shifts or crystal structures, which is critical in NMR crystallography applications. This higher accuracy and greater discrimination are highlighted in application to the solid state NMR of different acetaminophen and testosterone crystal forms.},
  file = {/home/mariano/Zotero/storage/7ERDP69U/Beran et al. - 2016 - Predicting Molecular Crystal Properties from First.pdf}
}

@article{bisboEfficientGlobalStructure2020,
  title = {Efficient {{Global Structure Optimization}} with a {{Machine-Learned Surrogate Model}}},
  author = {Bisbo, Malthe K. and Hammer, Bj\o rk},
  date = {2020-02-27},
  journaltitle = {Physical Review Letters},
  shortjournal = {Phys. Rev. Lett.},
  volume = {124},
  number = {8},
  pages = {086102},
  issn = {0031-9007, 1079-7114},
  doi = {10.1103/PhysRevLett.124.086102},
  url = {https://link.aps.org/doi/10.1103/PhysRevLett.124.086102},
  urldate = {2024-07-10},
  langid = {english},
  file = {/home/mariano/Zotero/storage/FC3FUIGQ/Bisbo e Hammer - 2020 - Efficient Global Structure Optimization with a Machine-Learned Surrogate Model.pdf}
}

@article{bjorneholmWaterInterfaces2016,
  title = {Water at {{Interfaces}}},
  author = {Bj\"orneholm, Olle and Hansen, Martin H. and Hodgson, Andrew and Liu, Li-Min and Limmer, David T. and Michaelides, Angelos and Pedevilla, Philipp and Rossmeisl, Jan and Shen, Huaze and Tocci, Gabriele and Tyrode, Eric and Walz, Marie-Madeleine and Werner, Josephina and Bluhm, Hendrik},
  date = {2016-07-13},
  journaltitle = {Chemical Reviews},
  shortjournal = {Chem. Rev.},
  volume = {116},
  number = {13},
  pages = {7698--7726},
  issn = {0009-2665, 1520-6890},
  doi = {10.1021/acs.chemrev.6b00045},
  url = {https://pubs.acs.org/doi/10.1021/acs.chemrev.6b00045},
  urldate = {2024-07-10},
  abstract = {The interfaces of neat water and aqueous solutions play a prominent role in many technological processes and in the environment. Examples of aqueous interfaces are ultrathin water films that cover most hydrophilic surfaces under ambient relative humidities, the liquid/solid interface which drives many electrochemical reactions, and the liquid/vapor interface, which governs the uptake and release of trace gases by the oceans and cloud droplets. In this article we review some of the recent experimental and theoretical advances in our knowledge of the properties of aqueous interfaces and discuss open questions and gaps in our understanding.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/36FP286I/Björneholm et al. - 2016 - Water at Interfaces.pdf}
}

@article{blagdenCrystalEngineeringActive2007,
  title = {Crystal Engineering of Active Pharmaceutical Ingredients to Improve Solubility and Dissolution Rates},
  author = {Blagden, N. and family=Matas, given=M., prefix=de, useprefix=true and Gavan, P. T. and York, P.},
  date = {2007-07-30},
  journaltitle = {Advanced Drug Delivery Reviews},
  shortjournal = {Advanced Drug Delivery Reviews},
  series = {Drug {{Solubility}}: {{How}} to {{Measure}} It, {{How}} to {{Improve}} It},
  volume = {59},
  number = {7},
  pages = {617--630},
  issn = {0169-409X},
  doi = {10.1016/j.addr.2007.05.011},
  url = {https://www.sciencedirect.com/science/article/pii/S0169409X07000828},
  urldate = {2024-06-05},
  abstract = {The increasing prevalence of poorly soluble drugs in development provides notable risk of new products demonstrating low and erratic bioavailabilty with consequences for safety and efficacy, particularly for drugs delivered by the oral route of administration. Although numerous strategies exist for enhancing the bioavailability of drugs with low aqueous solubility, the success of these approaches is not yet able to be guaranteed and is greatly dependent on the physical and chemical nature of the molecules being developed. Crystal engineering offers a number of routes to improved solubility and dissolution rate, which can be adopted through an in-depth knowledge of crystallisation processes and the molecular properties of active pharmaceutical ingredients. This article covers the concept and theory of crystal engineering and discusses the potential benefits, disadvantages and methods of preparation of co-crystals, metastable polymorphs, high-energy amorphous forms and ultrafine particles. Also considered within this review is the influence of crystallisation conditions on crystal habit and particle morphology with potential implications for dissolution and oral absorption.},
  keywords = {Co-crystals,Crystal engineering,Crystallisation,Dissolution rate,Polymorphism,Solubility,Supramolecular chemistry},
  file = {/home/mariano/Zotero/storage/9K6RWRE7/Blagden et al. - 2007 - Crystal engineering of active pharmaceutical ingre.pdf;/home/mariano/Zotero/storage/ASBB8AG6/S0169409X07000828.html}
}

@inproceedings{bornDynamicalTheoryCrystal1955,
  title = {Dynamical {{Theory}} of {{Crystal Lattices}}},
  booktitle = {American {{Journal}} of {{Physics}}},
  author = {Born, Max and Huang, Kun and Lax, M.},
  date = {1955-10-01},
  volume = {23},
  number = {7},
  pages = {474--474},
  issn = {0002-9505, 1943-2909},
  doi = {10.1119/1.1934059},
  url = {https://pubs.aip.org/ajp/article/23/7/474/1035768/Dynamical-Theory-of-Crystal-Lattices},
  urldate = {2024-04-04},
  abstract = {Although Born and Huang's classic work on the dynamics of crystal lattices was published over thirty years ago, the book remains the definitive treatment of the subject. It begins with a brief introduction to atomic forces, lattice vibrations and elasticity, and then breaks off into four sections. The first section deals with the general statistical mechanics of ideal lattices, leading to the electric polarizability and to the scattering of light. The second section deals with the properties of long lattice waves, the third with thermal properties, and the fourth with optical properties.},
  langid = {english}
}

@book{bransdenPhysicsAtomsMolecules1992,
  title = {Physics of Atoms and Molecules},
  author = {Bransden, Brian Harold and Joachain, Charles Jean},
  date = {1992},
  publisher = {Longman scientific \& technical copublished in the United States with J. Wiley \& sons},
  location = {Harlow (GB) New York},
  isbn = {978-0-470-20424-5 978-0-582-44401-0},
  langid = {english},
  file = {/home/mariano/Zotero/storage/H464VQ9Z/Bransden e Joachain - 1992 - Physics of atoms and molecules.djvu}
}

@article{buckinghamThermalExpansionSingleCrystal2018,
  title = {Thermal {{Expansion}} of {{Single-Crystal H2O}} and {{D2O Ice Ih}}},
  author = {Buckingham, David T. W. and Neumeier, J. J. and Masunaga, Sueli H. and Yu, Yi-Kuo},
  date = {2018-11-02},
  journaltitle = {Physical Review Letters},
  shortjournal = {Phys. Rev. Lett.},
  volume = {121},
  number = {18},
  pages = {185505},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevLett.121.185505},
  url = {https://link.aps.org/doi/10.1103/PhysRevLett.121.185505},
  urldate = {2024-01-22},
  abstract = {Thermal expansion of H2O and D2O ice Ih with relative resolution of 1 ppb is reported. A large transition in the thermal expansion coefficient at 101 K in H2O moves to 125 K in D2O, revealing one of the largest-known isotope effects. Rotational oscillatory modes that couple poorly to phonons, i.e., lattice solitons, may be responsible.},
  file = {/home/mariano/Zotero/storage/6CMAJ8XX/Buckingham et al. - 2018 - Thermal Expansion of Single-Crystal H2O and D2O Ic.pdf;/home/mariano/Zotero/storage/4CGLEQZX/PhysRevLett.121.html}
}

@article{carUnifiedApproachMolecular1985,
  title = {Unified {{Approach}} for {{Molecular Dynamics}} and {{Density-Functional Theory}}},
  author = {Car, R. and Parrinello, M.},
  date = {1985-11-25},
  journaltitle = {Physical Review Letters},
  shortjournal = {Phys. Rev. Lett.},
  volume = {55},
  number = {22},
  pages = {2471--2474},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevLett.55.2471},
  url = {https://link.aps.org/doi/10.1103/PhysRevLett.55.2471},
  urldate = {2024-02-25},
  abstract = {We present a unified scheme that, by combining molecular dynamics and density-functional theory, profoundly extends the range of both concepts. Our approach extends molecular dynamics beyond the usual pair-potential approximation, thereby making possible the simulation of both covalently bonded and metallic systems. In addition it permits the application of density-functional theory to much larger systems than previously feasible. The new technique is demonstrated by the calculation of some static and dynamic properties of crystalline silicon within a self-consistent pseudopotential framework.},
  keywords = {molecular dynamics},
  file = {/home/mariano/Zotero/storage/LRRYRL7P/Car e Parrinello - 1985 - Unified Approach for Molecular Dynamics and Densit.pdf}
}

@book{chaikinPrinciplesCondensedMatter1995,
  title = {Principles of Condensed Matter Physics},
  author = {Chaikin, Paul M. and Lubensky, T. C.},
  date = {1995},
  publisher = {Cambridge University Press},
  location = {Cambridge ; New York, NY, USA},
  isbn = {978-0-521-43224-5},
  langid = {english},
  pagetotal = {699},
  keywords = {Condensed matter},
  file = {/home/mariano/Zotero/storage/ZEASTIVI/Chaikin e Lubensky - 1995 - Principles of condensed matter physics.pdf}
}

@article{chengInitioThermodynamicsLiquid2019,
  title = {Ab Initio Thermodynamics of Liquid and Solid Water},
  author = {Cheng, Bingqing and Engel, Edgar A. and Behler, J\"org and Dellago, Christoph and Ceriotti, Michele},
  date = {2019-01-22},
  journaltitle = {Proceedings of the National Academy of Sciences},
  shortjournal = {Proc. Natl. Acad. Sci. U.S.A.},
  volume = {116},
  number = {4},
  eprint = {1811.08630},
  eprinttype = {arXiv},
  eprintclass = {cond-mat, physics:physics},
  pages = {1110--1115},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1815117116},
  url = {http://arxiv.org/abs/1811.08630},
  urldate = {2024-01-17},
  abstract = {Thermodynamic properties of liquid water as well as hexagonal (Ih) and cubic (Ic) ice are predicted based on density functional theory at the hybrid-functional level, rigorously taking into account quantum nuclear motion, anharmonic fluctuations and proton disorder. This is made possible by combining advanced free energy methods and state-of-the-art machine learning techniques. The ab initio description leads to structural properties in excellent agreement with experiments, and reliable estimates of the melting points of light and heavy water. We observe that nuclear quantum effects contribute a crucial 0.2 meV/H\$\_2\$O to the stability of ice Ih, making it more stable than ice Ic. Our computational approach is general and transferable, providing a comprehensive framework for quantitative predictions of ab initio thermodynamic properties using machine learning potentials as an intermediate step.},
  keywords = {Condensed Matter - Materials Science,Condensed Matter - Statistical Mechanics,Physics - Chemical Physics},
  file = {/home/mariano/Zotero/storage/G4PTHXUF/Cheng et al. - 2019 - Ab initio thermodynamics of liquid and solid water.pdf;/home/mariano/Zotero/storage/E8CAQ35I/1811.html}
}

@article{chenThermodynamicsWaterIce2024,
  title = {Thermodynamics of {{Water}} and {{Ice}} from a {{Fast}} and {{Scalable First-Principles Neuroevolution Potential}}},
  author = {Chen, Zekun and Berrens, Margaret L. and Chan, Kam-Tung and Fan, Zheyong and Donadio, Davide},
  date = {2024-01-11},
  journaltitle = {Journal of Chemical \& Engineering Data},
  shortjournal = {J. Chem. Eng. Data},
  volume = {69},
  number = {1},
  pages = {128--140},
  publisher = {American Chemical Society},
  issn = {0021-9568},
  doi = {10.1021/acs.jced.3c00561},
  url = {https://doi.org/10.1021/acs.jced.3c00561},
  urldate = {2024-01-22},
  abstract = {Machine learning potentials enable molecular dynamics simulations to exceed the size and time scales that can be accessed by first-principles methods like density functional theory, while still maintaining the accuracy of the underlying training data set. However, accurate machine learning potentials come with relatively high computational costs that limit their ability to predict properties requiring extensive sampling, large simulation cells, or long runs to converge. Here, we have developed and tested a neuroevolution-potential model for water trained to hybrid-dispersion-corrected density functional calculations. This model exhibits accuracy and transferability comparable to state-of-the-art machine learning potentials but at a much lower computational cost. As a result, it enabled us to compute well-converged thermodynamic averages and fluctuations. This allowed us to assess the ability of our model to reproduce several thermodynamic properties of water and ice as well as the anomalous behavior of water density, heat capacity, and compressibility. The efficient GPU acceleration of our model and its capability to reproduce water thermodynamics in good agreement with experiments make it suitable for simulating phase transitions and slow dynamic processes in aqueous systems.},
  file = {/home/mariano/Zotero/storage/RD2YZQWM/Chen et al. - 2024 - Thermodynamics of Water and Ice from a Fast and Sc.pdf}
}

@online{cheonDatasetRandomRelaxations2023,
  title = {Dataset of {{Random Relaxations}} for {{Crystal Structure Search}} of {{Li-Si System}}},
  author = {Cheon, Gowoon and Yang, Lusann and McCloskey, Kevin and Reed, Evan J. and Cubuk, Ekin D.},
  date = {2023-03-08},
  eprint = {2012.02920},
  eprinttype = {arXiv},
  eprintclass = {cond-mat, physics:physics},
  doi = {10.48550/arXiv.2012.02920},
  url = {http://arxiv.org/abs/2012.02920},
  urldate = {2024-09-16},
  abstract = {Crystal structure search is a long-standing challenge in materials design. We present a dataset of more than 100,000 structural relaxations of potential battery anode materials from randomized structures using density functional theory calculations. We illustrate the usage of the dataset by training graph neural networks to predict structural relaxations from randomly generated structures. Our models directly predict stresses in addition to forces, which allows them to accurately simulate relaxations of both ionic positions and lattice vectors. We show that models trained on the molecular dynamics simulations fail to simulate relaxations from random structures, while training on our data leads to up to two orders of magnitude decrease in error for the same task. Our model is able to find an experimentally verified structure of a stoichiometry held out from training. We find that randomly perturbing atomic positions during training improves both the accuracy and out of domain generalization of the models.},
  pubstate = {prepublished},
  keywords = {Computer Science - Machine Learning,Condensed Matter - Materials Science,Physics - Computational Physics},
  file = {/home/mariano/Zotero/storage/7NPLNX7N/Cheon et al. - 2023 - Dataset of Random Relaxations for Crystal Structure Search of Li-Si System.pdf;/home/mariano/Zotero/storage/UWYL3V4Q/2012.html}
}

@thesis{ciacchiDynamicGraphNeural2022,
  title = {Dynamic {{Graph Neural Networks Applications}} to {{Glassy Systems}}},
  author = {Ciacchi, Massimo},
  date = {2022},
  langid = {english},
  file = {/home/mariano/Zotero/storage/BFYLXI8R/LastName - Dynamic Graph Neural Networks Applications to Glassy Systems.pdf}
}

@article{curtissStudiesMolecularAssociation1979,
  title = {Studies of Molecular Association in {{H2O}} and {{D2O}} Vapors by Measurement of Thermal Conductivity},
  author = {Curtiss, L. A. and Frurip, D. J. and Blander, M.},
  date = {1979-09-15},
  journaltitle = {The Journal of Chemical Physics},
  volume = {71},
  number = {6},
  pages = {2703--2711},
  issn = {0021-9606, 1089-7690},
  doi = {10.1063/1.438628},
  url = {https://pubs.aip.org/jcp/article/71/6/2703/443153/Studies-of-molecular-association-in-H2O-and-D2O},
  urldate = {2024-03-27},
  abstract = {The thermal conductivities of H2O and D2O vapors were measured in a modified thick hot wire cell between 358 and 386 K at pressures ranging from 100 to 1000 Torr. Analysis of the data indicates that molecular association to form a dimeric species is the main source of enhancement of the thermal conductivity of both vapors. The enthalpy and entropy of association of the H2O dimer are -3.59 kcal\,mol-1 and -18.59 cal\,deg-1\,mol-1, respectively. The enthalpy and entropy of association of the D2O dimer are -3.66 kcal\,mol-1 and -18.67 cal\,deg-1\,mol-1, respectively. The measured enthalpy of association of the H2O dimer is in agreement with recently reported ab\hphantom{,}initio molecular orbital calculations on the H2O dimer. The entropies of association of the H2O and D2O dimers are calculated theoretically and are found to be in agreement with the measured values.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/R6P8Z3JV/Curtiss et al. - 1979 - Studies of molecular association in H2O and D2O va.pdf}
}

@book{daanfrenkelUnderstandingMolecularSimulation2002,
  title = {Understanding {{Molecular Simulation}}},
  author = {{Daan Frenkel} and {Berend Smit}},
  date = {2002},
  publisher = {Elsevier},
  doi = {10.1016/B978-0-12-267351-1.X5000-7},
  url = {https://linkinghub.elsevier.com/retrieve/pii/B9780122673511X50007},
  urldate = {2024-07-12},
  isbn = {978-0-12-267351-1},
  langid = {english},
  file = {/home/mariano/Zotero/storage/VFZI6ECM/2002 - Understanding Molecular Simulation.pdf}
}

@article{darbyTensorReducedAtomicDensity2023,
  title = {Tensor-{{Reduced Atomic Density Representations}}},
  author = {Darby, James P. and Kov\'acs, D\'avid P. and Batatia, Ilyes and Caro, Miguel A. and Hart, Gus L. W. and Ortner, Christoph and Cs\'anyi, G\'abor},
  date = {2023-07-13},
  journaltitle = {Physical Review Letters},
  shortjournal = {Phys. Rev. Lett.},
  volume = {131},
  number = {2},
  pages = {028001},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevLett.131.028001},
  url = {https://link.aps.org/doi/10.1103/PhysRevLett.131.028001},
  urldate = {2024-07-08},
  abstract = {Density-based representations of atomic environments that are invariant under Euclidean symmetries have become a widely used tool in the machine learning of interatomic potentials, broader data-driven atomistic modeling, and the visualization and analysis of material datasets. The standard mechanism used to incorporate chemical element information is to create separate densities for each element and form tensor products between them. This leads to a steep scaling in the size of the representation as the number of elements increases. Graph neural networks, which do not explicitly use density representations, escape this scaling by mapping the chemical element information into a fixed dimensional space in a learnable way. By exploiting symmetry, we recast this approach as tensor factorization of the standard neighbour-density-based descriptors and, using a new notation, identify connections to existing compression algorithms. In doing so, we form compact tensor-reduced representation of the local atomic environment whose size does not depend on the number of chemical elements, is systematically convergable, and therefore remains applicable to a wide range of data analysis and regression tasks.},
  file = {/home/mariano/Zotero/storage/63VYB4IF/Darby et al. - 2023 - Tensor-Reduced Atomic Density Representations.pdf;/home/mariano/Zotero/storage/2VDMR4R9/PhysRevLett.131.html}
}

@article{dellapiaDMCICE13AmbientHigh2022,
  title = {{{DMC-ICE13}} : {{Ambient}} and High Pressure Polymorphs of Ice from Diffusion {{Monte Carlo}} and Density Functional Theory},
  shorttitle = {{{DMC-ICE13}}},
  author = {Della Pia, Flaviano and Zen, Andrea and Alf\`e, Dario and Michaelides, Angelos},
  date = {2022-10-07},
  journaltitle = {The Journal of Chemical Physics},
  volume = {157},
  number = {13},
  pages = {134701},
  issn = {0021-9606, 1089-7690},
  doi = {10.1063/5.0102645},
  url = {https://pubs.aip.org/jcp/article/157/13/134701/2841942/DMC-ICE13-Ambient-and-high-pressure-polymorphs-of},
  urldate = {2024-01-26},
  abstract = {Ice is one of the most important and interesting molecular crystals, exhibiting a rich and evolving phase diagram. Recent discoveries mean that there are now 20 distinct polymorphs; a structural diversity that arises from a delicate interplay of hydrogen bonding and van der Waals dispersion forces. This wealth of structures provides a stern test of electronic structure theories, with Density Functional Theory (DFT) often not able to accurately characterize the relative energies of the various ice polymorphs. Thanks to recent advances that enable the accurate and efficient treatment of molecular crystals with Diffusion Monte Carlo (DMC), we present here the DMC-ICE13 dataset; a dataset of lattice energies of 13 ice polymorphs. This dataset encompasses the full structural complexity found in the ambient and high-pressure molecular ice polymorphs, and when experimental reference energies are available, our DMC results deliver sub-chemical accuracy. Using this dataset, we then perform an extensive benchmark of a broad range of DFT functionals. Of the functionals considered, revPBE-D3 and RSCAN reproduce reference absolute lattice energies with the smallest error, while optB86b-vdW and SCAN+rVV10 have the best performance on the relative lattice energies. Our results suggest that a single functional achieving reliable performance for all phases is still missing, and that care is needed in the selection of the most appropriate functional for the desired application. The insights obtained here may also be relevant to liquid water and other hydrogen-bonded and dispersion-bonded molecular crystals.},
  langid = {english},
  keywords = {molecular crystal},
  file = {/home/mariano/Zotero/storage/M5BGMC8Y/Della Pia et al. - 2022 - DMC-ICE13  Ambient and high pressure polymorphs o.pdf;/home/mariano/Zotero/storage/Y8ZDN7QC/Supporting Information.pdf}
}

@article{delrossoDensityPhononStates2021,
  title = {Density of {{Phonon States}} in {{Cubic Ice Ic}}},
  author = {family=Rosso, given=Leonardo, prefix=del, useprefix=true and Celli, Milva and Colognesi, Daniele and Rudi\'c, Svemir and English, Niall J. and Ulivi, Lorenzo},
  date = {2021-10-28},
  journaltitle = {The Journal of Physical Chemistry C},
  shortjournal = {J. Phys. Chem. C},
  volume = {125},
  number = {42},
  pages = {23533--23538},
  publisher = {American Chemical Society},
  issn = {1932-7447},
  doi = {10.1021/acs.jpcc.1c07647},
  url = {https://doi.org/10.1021/acs.jpcc.1c07647},
  urldate = {2024-03-14},
  abstract = {Despite the simplicity of water molecules, for more than a century, a lot of scientific effort has been made on exploring ice polymorphism, especially more elusive phases such as cubic ice Ic. In this work, measurement of the density of phonon states (DOPSs) of polycrystalline ice Ic, and of its deuterated counterpart, has been performed in a sample having an almost perfect crystallographic purity, obtained from the transformation of ice XVII, and with a remarkable accuracy. Results are compared with the new accurate measurements of DOPSs in ice Ih and with centroid molecular dynamics (CMD) simulations. The differences between the experimental DOPSs in these two forms of ice are subtle but quantitatively measurable. In addition, they are reproduced semiquantitatively by computational methods, demonstrating the effectiveness of this innovative simulation tool for calculating the dynamical properties of ice structures.},
  keywords = {Phonons},
  file = {/home/mariano/Zotero/storage/DP3VCBJZ/del Rosso et al. - 2021 - Density of Phonon States in Cubic Ice Ic.pdf}
}

@article{delrossoRefinedStructureMetastable2016,
  title = {Refined {{Structure}} of {{Metastable Ice XVII}} from {{Neutron Diffraction Measurements}}},
  author = {family=Rosso, given=Leonardo, prefix=del, useprefix=true and Grazzi, Francesco and Celli, Milva and Colognesi, Daniele and Garcia-Sakai, Victoria and Ulivi, Lorenzo},
  date = {2016-12-01},
  journaltitle = {The Journal of Physical Chemistry C},
  shortjournal = {J. Phys. Chem. C},
  volume = {120},
  number = {47},
  pages = {26955--26959},
  publisher = {American Chemical Society},
  issn = {1932-7447},
  doi = {10.1021/acs.jpcc.6b10569},
  url = {https://doi.org/10.1021/acs.jpcc.6b10569},
  urldate = {2024-02-08},
  abstract = {The structure of the recently identified metastable ice XVII, obtained by release of hydrogen from the C0-structure D2O-H2 compound (filled ice), has been accurately measured by neutron powder diffraction. The diffraction pattern is indexed with a hexagonal cell and can be refined with space group P6122 so as to obtain accurate values of the oxygen and deuterium positions. The values of the lattice constants at three temperatures between 25 and 100 K are reported, and their behavior is compared with that of ice Ih. Ice XVII is a microporous solid that, if exposed to H2 gas, may adsorb a substantial amount of it. Monitoring this effect at a constant temperature of 50 K, we have observed that the two lattice constants show opposite behavior, a increases and c decreases, with the volume showing a linear increase. At temperatures higher than 130 K, the metastability of this form of microporous ice is lost and the sample transforms into ice Ih.},
  file = {/home/mariano/Zotero/storage/USJMIRNX/del Rosso et al. - 2016 - Refined Structure of Metastable Ice XVII from Neut.pdf}
}

@article{dengCHGNetPretrainedUniversal2023,
  title = {{{CHGNet}} as a Pretrained Universal Neural Network Potential for Charge-Informed Atomistic Modelling},
  author = {Deng, Bowen and Zhong, Peichen and Jun, KyuJung and Riebesell, Janosh and Han, Kevin and Bartel, Christopher J. and Ceder, Gerbrand},
  date = {2023-09-14},
  journaltitle = {Nature Machine Intelligence},
  shortjournal = {Nat Mach Intell},
  volume = {5},
  number = {9},
  pages = {1031--1041},
  publisher = {{Springer Science and Business Media LLC}},
  issn = {2522-5839},
  doi = {10.1038/s42256-023-00716-3},
  url = {https://www.nature.com/articles/s42256-023-00716-3},
  urldate = {2024-09-16},
  abstract = {AbstractLarge-scale simulations with complex electron interactions remain one of the greatest challenges for atomistic modelling. Although classical force fields often fail to describe the coupling between electronic states and ionic rearrangements, the more accurate ab initio molecular dynamics suffers from computational complexity that prevents long-time and large-scale simulations, which are essential to study technologically relevant phenomena. Here we present the Crystal Hamiltonian Graph Neural Network (CHGNet), a graph neural network-based machine-learning interatomic potential (MLIP) that models the universal potential energy surface. CHGNet is pretrained on the energies, forces, stresses and magnetic moments from the Materials Project Trajectory Dataset, which consists of over 10\,years of density functional theory calculations of more than 1.5\,million inorganic structures. The explicit inclusion of magnetic moments enables CHGNet to learn and accurately represent the orbital occupancy of electrons, enhancing its capability to describe both atomic and electronic degrees of freedom. We demonstrate several applications of CHGNet in solid-state materials, including charge-informed molecular dynamics in LixMnO2, the finite temperature phase diagram for LixFePO4 and Li diffusion in garnet conductors. We highlight the significance of charge information for capturing appropriate chemistry and provide insights into ionic systems with additional electronic degrees of freedom that cannot be observed by previous MLIPs.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/CYDCRFAI/Deng et al. - 2023 - CHGNet as a pretrained universal neural network potential for charge-informed atomistic modelling.pdf}
}

@article{dolgonosRevisedValuesX232019,
  title = {Revised Values for the {{X23}} Benchmark Set of Molecular Crystals},
  author = {Dolgonos, Grygoriy A. and Hoja, Johannes and Boese, A. Daniel},
  date = {2019},
  journaltitle = {Physical Chemistry Chemical Physics},
  shortjournal = {Phys. Chem. Chem. Phys.},
  volume = {21},
  number = {44},
  pages = {24333--24344},
  issn = {1463-9076, 1463-9084},
  doi = {10.1039/C9CP04488D},
  url = {http://xlink.rsc.org/?DOI=C9CP04488D},
  urldate = {2023-09-20},
  abstract = {A revised reference value set for molecular crystals: X23b; new cell volumes and lattice energies including volumetric expansion due to zero-point energy and thermal effects.           ,                             We present revised reference values for cell volumes and lattice energies for the widely used X23 benchmark set of molecular crystals by including the effect of thermal expansion. For this purpose, thermally-expanded structures were calculated               via               the quasi-harmonic approximation utilizing three dispersion-inclusive density-functional approximations. Experimental unit-cell volumes were back-corrected for thermal and zero-point energy effects, allowing now a direct comparison with lattice relaxations based on electronic energies. For the derivation of reference lattice energies, we utilized harmonic vibrational contributions averaged over four density-functional approximations. In addition, the new reference values also take the change in electronic and vibrational energy due to thermal expansion into account. This is accomplished by either utilizing experimentally determined cell volumes and heat capacities, or by relying on the quasi-harmonic approximation. The new X23b reference values obtained this way will enable a more accurate benchmark for the performance of computational methods for molecular crystals.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/9929M94A/Dolgonos et al. - 2019 - Revised values for the X23 benchmark set of molecu.pdf}
}

@article{dussonAtomicClusterExpansion2022,
  title = {Atomic Cluster Expansion: {{Completeness}}, Efficiency and Stability},
  shorttitle = {Atomic Cluster Expansion},
  author = {Dusson, Genevi\`eve and Bachmayr, Markus and Cs\'anyi, G\'abor and Drautz, Ralf and Etter, Simon and Van Der Oord, Cas and Ortner, Christoph},
  date = {2022-04},
  journaltitle = {Journal of Computational Physics},
  shortjournal = {Journal of Computational Physics},
  volume = {454},
  pages = {110946},
  issn = {00219991},
  doi = {10.1016/j.jcp.2022.110946},
  url = {https://linkinghub.elsevier.com/retrieve/pii/S0021999122000080},
  urldate = {2024-07-12},
  langid = {english},
  file = {/home/mariano/Zotero/storage/NP5ANA3B/Dusson et al. - 2022 - Atomic cluster expansion Completeness, efficiency and stability.pdf}
}

@article{dykeStructureWaterDimer1977,
  title = {The Structure of Water Dimer from Molecular Beam Electric Resonance Spectroscopy},
  author = {Dyke, Thomas R. and Mack, Kenneth M. and Muenter, J. S.},
  date = {1977-01-15},
  journaltitle = {The Journal of Chemical Physics},
  volume = {66},
  number = {2},
  pages = {498--510},
  issn = {0021-9606, 1089-7690},
  doi = {10.1063/1.433969},
  url = {https://pubs.aip.org/jcp/article/66/2/498/773453/The-structure-of-water-dimer-from-molecular-beam},
  urldate = {2024-05-29},
  abstract = {Molecular beams of hydrogen bonded water dimer, generated in a supersonic nozzle, have been studied using electric resonance spectroscopy. Radiofrequency and microwave transitions have been observed in (H2\,16O)2, (D2\,16O)2, and (H2\,18O)2. Transitions arising from both pure rotation and rotation--tunneling occur. The pure rotational transitions have been fit to a rigid rotor model to obtain structural information. Information on the relative orientation of the two monomer units is also contained in the electric dipole moment component along the A inertial axis {$\mu$}a, which is obtained from Stark effect measurements. The resultant structure is that of a ''trans-linear'' complex with an oxygen--oxygen distance ROO of 2.98(1) \AA, the proton accepting water axis is 58(6) {$^\circ$} with respect to ROO, and the proton donating water axis at -51(6) {$^\circ$} with respect to ROO. This structure is consistent with a linear hydrogen bond and the proton acceptor tetrahedrally oriented to the hydrogen bond. The limits of uncertainty are wholly model dependent and are believed to cover variations from the zero-point vibrational structure observed to the equilibrium structure. {$\mu$}a shows strong dependence on J and K and is about 2.6 D. Centrifugal distortion constants have been interpreted in terms of the monomer--monomer stretching frequency and give {$\omega$}=150 cm-1.},
  langid = {english}
}

@book{eisenbergStructurePropertiesWater2005,
  title = {The {{Structure}} and {{Properties}} of {{Water}}},
  author = {Eisenberg, D. and Kauzmann, W.},
  date = {2005-10-20},
  publisher = {Oxford University Press},
  doi = {10.1093/acprof:oso/9780198570264.001.0001},
  url = {https://academic.oup.com/book/34782},
  urldate = {2024-03-27},
  abstract = {Abstract. This book has correlated many experimental observations and theoretical discussions from scientific literature on water. Topics covered include t},
  isbn = {978-0-19-171526-6},
  langid = {english},
  file = {/home/mariano/Zotero/storage/R6DTMVB6/The Structure and Properties of Water (D. Eisenberg, W. Kauzmann) (Z-Library).djvu;/home/mariano/Zotero/storage/V5AAYXN9/Eisenberg e Kauzmann - 2005 - The Structure and Properties of Water.pdf}
}

@incollection{eisenbergWaterMolecule2005,
  title = {The {{Water Molecule}}},
  booktitle = {The {{Structure}} and {{Properties}} of {{Water}}},
  author = {Eisenberg, D. and Kauzmann, W.},
  editor = {Eisenberg, D and Kauzmann, W},
  date = {2005-10-20},
  pages = {0},
  publisher = {Oxford University Press},
  doi = {10.1093/acprof:oso/9780198570264.003.0001},
  url = {https://doi.org/10.1093/acprof:oso/9780198570264.003.0001},
  urldate = {2024-03-27},
  abstract = {This chapter presents descriptions of an isolated water molecule based on experiment and theory. The description based on experiment involves measurements made on water vapour at sufficiently low pressures or high temperatures to ensure that interactions between molecules are largely absent. The description based on theory provides details such as the shape of the electronic charge cloud of water, and an indication of which parts of the charge contribute most heavily to the total polarity of the molecule. The separation of these interdependent descriptions is artificial, but it serves to emphasize which portion of our understanding of water is based on observation, and which is based on reasonably accurate models of the molecule.},
  isbn = {978-0-19-857026-4},
  file = {/home/mariano/Zotero/storage/DDPJ38VV/297485104.html}
}

@article{flubacherHeatCapacityIce1960,
  title = {Heat {{Capacity}} of {{Ice}} at {{Low Temperatures}}},
  author = {Flubacher, P. and Leadbetter, A. J. and Morrison, J. A.},
  date = {1960-12-01},
  journaltitle = {The Journal of Chemical Physics},
  volume = {33},
  number = {6},
  pages = {1751--1755},
  issn = {0021-9606, 1089-7690},
  doi = {10.1063/1.1731497},
  url = {https://pubs.aip.org/jcp/article/33/6/1751/77407/Heat-Capacity-of-Ice-at-Low-Temperatures},
  urldate = {2024-03-18},
  abstract = {The heat capacity of normal hexagonal ice has been measured over the temperature range 2{$^\circ$} to 27{$^\circ$}K with an estimated precision varying between \textpm 2\% at the lowest temperatures and \textpm 0.2\% at the higher temperatures. The results agree satisfactorily with those of earlier measurements in the region T\> 10{$^\circ$}K, and do not significantly affect the value of the residual entropy of ice calculated by Giauque and Stout [W. F. Giauque and J. W. Stout, J. Am. Chem. Soc. 58, 1144 (1936)]. Although the new results do not influence the existing thermodynamic description of ice, they provide information which is important in understanding its vibrational properties. In the first place, extrapolation of the results to T=0{$^\circ$}K yields a value of {$\Theta$}0, the Debye characteristic temperature corresponding to continuum behavior. This is found to agree satisfactorily with {$\Theta$} (elastic) estimated from the elastic constants of ice. In the second place, complete {$\Theta$}D(T) curves can be constructed, and an examination of these, computed for different sizes of vibrational unit, enables the gross features of the lattice frequency spectrum of ice to be determined. The conclusion reached is that the three components of the spectrum, due respectively to translational and rotational vibrations of the water molecule and to intramolecular vibrations, are well separated. The contribution of the librational modes to the thermodynamic properties can be approximated rather well by a single frequency of 620 cm---1.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/GUXPBDTV/Flubacher et al. - 1960 - Heat Capacity of Ice at Low Temperatures.pdf}
}

@incollection{galliFirstprinciplesMolecularDynamics1993,
  title = {First-Principles {{Molecular Dynamics}}},
  booktitle = {Computer {{Simulation}} in {{Chemical Physics}}},
  author = {Galli, G. and Pasquarello, A.},
  date = {1993},
  pages = {261--313},
  publisher = {Springer, Dordrecht},
  doi = {10.1007/978-94-011-1679-4_8},
  url = {https://springer.dosf.top/chapter/10.1007/978-94-011-1679-4_8},
  urldate = {2024-02-25},
  abstract = {We review the foundations and practical implementation of first-principles molecular dynamics and discuss some applications of the method to disordered systems and surfaces.},
  isbn = {978-94-011-1679-4},
  langid = {english},
  file = {/home/mariano/Zotero/storage/9F988CYE/Galli e Pasquarello - 1993 - First-principles Molecular Dynamics.pdf;/home/mariano/Zotero/storage/QJA9E742/Galli e Pasquarello - 1993 - First-principles Molecular Dynamics.pdf}
}

@article{garkulMolecularDynamicsAnalysis2022,
  title = {Molecular Dynamics Analysis of Elastic Properties and New Phase Formation during Amorphous Ices Transformations},
  author = {Garkul, Anastasiia and Stegailov, Vladimir},
  date = {2022-08-03},
  journaltitle = {Scientific Reports},
  shortjournal = {Sci Rep},
  volume = {12},
  number = {1},
  pages = {13325},
  publisher = {Nature Publishing Group},
  issn = {2045-2322},
  doi = {10.1038/s41598-022-17666-2},
  url = {https://www.nature.com/articles/s41598-022-17666-2},
  urldate = {2024-01-07},
  abstract = {Unlike conventional first-order phase transitions, the kinetics of amorphous-amorphous transitions has been much less studied. The ultrasonic experiments on the transformations between low-density and high-density amorphous ice induced by pressure or heating provided the pressure and temperature dependencies of elastic moduli. In this article, we make an attempt to build a microscopic picture of these experimentally studied transformations using the molecular dynamics method with the TIP4P/Ice water model. We study carefully the dependence of the results of elastic constants calculations on the deformation rates. The system size effects are considered as well. The comparison with the experimental data enriches our understanding of the transitions observed. Our modeling gives new information about the formation mechanisms of new phase clusters during the transition between low-density and high-density amorphous ices. We analyse the applicability of the term ``nucleation'' for these processes.},
  issue = {1},
  langid = {english},
  keywords = {Atomistic models,H2O,Phase transitions and critical phenomena},
  file = {/home/mariano/Zotero/storage/67ZXCUB7/Garkul e Stegailov - 2022 - Molecular dynamics analysis of elastic properties .pdf}
}

@article{geigerE3nnEuclideanNeural2022,
  title = {E3nn: {{Euclidean Neural Networks}}},
  shorttitle = {E3nn},
  author = {Geiger, Mario and Smidt, Tess},
  date = {2022},
  publisher = {arXiv},
  doi = {10.48550/ARXIV.2207.09453},
  url = {https://arxiv.org/abs/2207.09453},
  urldate = {2024-01-18},
  abstract = {We present e3nn, a generalized framework for creating E(3) equivariant trainable functions, also known as Euclidean neural networks. e3nn naturally operates on geometry and geometric tensors that describe systems in 3D and transform predictably under a change of coordinate system. The core of e3nn are equivariant operations such as the TensorProduct class or the spherical harmonics functions that can be composed to create more complex modules such as convolutions and attention mechanisms. These core operations of e3nn can be used to efficiently articulate Tensor Field Networks, 3D Steerable CNNs, Clebsch-Gordan Networks, SE(3) Transformers and other E(3) equivariant networks.},
  version = {1},
  keywords = {Artificial Intelligence (cs.AI),FOS: Computer and information sciences,Machine Learning (cs.LG),Neural and Evolutionary Computing (cs.NE)},
  file = {/home/mariano/Zotero/storage/C6DPW6CV/Geiger e Smidt - 2022 - e3nn Euclidean Neural Networks.pdf}
}

@article{gillanPerspectiveHowGood2016,
  title = {Perspective: {{How}} Good Is {{DFT}} for Water?},
  shorttitle = {Perspective},
  author = {Gillan, Michael J. and Alf\`e, Dario and Michaelides, Angelos},
  date = {2016-04-07},
  journaltitle = {The Journal of Chemical Physics},
  volume = {144},
  number = {13},
  pages = {130901},
  issn = {0021-9606, 1089-7690},
  doi = {10.1063/1.4944633},
  url = {https://pubs.aip.org/jcp/article/144/13/130901/152221/Perspective-How-good-is-DFT-for-water},
  urldate = {2024-01-14},
  abstract = {Kohn-Sham density functional theory (DFT) has become established as an indispensable tool for investigating aqueous systems of all kinds, including those important in chemistry, surface science, biology, and the earth sciences. Nevertheless, many widely used approximations for the exchange-correlation (XC) functional describe the properties of pure water systems with an accuracy that is not fully satisfactory. The explicit inclusion of dispersion interactions generally improves the description, but there remain large disagreements between the predictions of different dispersion-inclusive methods. We present here a review of DFT work on water clusters, ice structures, and liquid water, with the aim of elucidating how the strengths and weaknesses of different XC approximations manifest themselves across this variety of water systems. Our review highlights the crucial role of dispersion in describing the delicate balance between compact and extended structures of many different water systems, including the liquid. By referring to a wide range of published work, we argue that the correct description of exchange-overlap interactions is also extremely important, so that the choice of semi-local or hybrid functional employed in dispersion-inclusive methods is crucial. The origins and consequences of beyond-2-body errors of approximate XC functionals are noted, and we also discuss the substantial differences between different representations of dispersion. We propose a simple numerical scoring system that rates the performance of different XC functionals in describing water systems, and we suggest possible future developments.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/2TA6CEYF/Gillan et al. - 2016 - Perspective How good is DFT for water.pdf}
}

@inproceedings{gilmerNeuralMessagePassing2017,
  title = {Neural {{Message Passing}} for {{Quantum Chemistry}}},
  booktitle = {Proceedings of the 34th {{International Conference}} on {{Machine Learning}}},
  author = {Gilmer, Justin and Schoenholz, Samuel S. and Riley, Patrick F. and Vinyals, Oriol and Dahl, George E.},
  date = {2017-07-17},
  pages = {1263--1272},
  publisher = {PMLR},
  issn = {2640-3498},
  url = {https://proceedings.mlr.press/v70/gilmer17a.html},
  urldate = {2024-07-13},
  abstract = {Supervised learning on molecules has incredible potential to be useful in chemistry, drug discovery, and materials science. Luckily, several promising and closely related neural network models invariant to molecular symmetries have already been described in the literature. These models learn a message passing algorithm and aggregation procedure to compute a function of their entire input graph. At this point, the next step is to find a particularly effective variant of this general approach and apply it to chemical prediction benchmarks until we either solve them or reach the limits of the approach. In this paper, we reformulate existing models into a single common framework we call Message Passing Neural Networks (MPNNs) and explore additional novel variations within this framework. Using MPNNs we demonstrate state of the art results on an important molecular property prediction benchmark; these results are strong enough that we believe future work should focus on datasets with larger molecules or more accurate ground truth labels.},
  eventtitle = {International {{Conference}} on {{Machine Learning}}},
  langid = {english},
  file = {/home/mariano/Zotero/storage/BBSVCS7J/Gilmer et al. - 2017 - Neural Message Passing for Quantum Chemistry.pdf;/home/mariano/Zotero/storage/UQZ37AY2/Gilmer et al. - 2017 - Neural Message Passing for Quantum Chemistry.pdf}
}

@article{grevConcerningZeropointVibrational1991,
  title = {Concerning Zero-Point Vibrational Energy Corrections to Electronic Energies},
  author = {Grev, Roger S. and Janssen, Curtis L. and Schaefer, Henry F.},
  date = {1991-10-01},
  journaltitle = {The Journal of Chemical Physics},
  volume = {95},
  number = {7},
  pages = {5128--5132},
  issn = {0021-9606, 1089-7690},
  doi = {10.1063/1.461680},
  url = {https://pubs.aip.org/jcp/article/95/7/5128/98279/Concerning-zero-point-vibrational-energy},
  urldate = {2024-09-25},
  abstract = {For comparison with experimentally obtained thermochemical data, zero-point vibrational energies (ZPVEs) are required to convert total electronic energies obtained from ab\hphantom{,}initio quantum mechanical studies into 0 K enthalpies. The currently accepted practice is to employ self-consistent-field (SCF) harmonic frequencies that have been scaled to reproduce experimentally observed fundamental frequencies. This procedure introduces systematic errors that result from a recognizable flaw in the method, namely that the correct ZPVE, G(0), is not one half the sum of the fundamental vibrational frequencies. Until better methods for accurately determining ZPVEs are presented, we recommend using different scaling factors for the determination of ZPVEs than those used to compare theoretically determined harmonic frequencies to observed fundamentals.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/LHZVC999/Grev et al. - 1991 - Concerning zero-point vibrational energy corrections to electronic energies.pdf}
}

@article{grimmeConsistentAccurateInitio2010,
  title = {A Consistent and Accurate Ab Initio Parametrization of Density Functional Dispersion Correction ({{DFT-D}}) for the 94 Elements {{H-Pu}}},
  author = {Grimme, Stefan and Antony, Jens and Ehrlich, Stephan and Krieg, Helge},
  date = {2010-04-16},
  journaltitle = {The Journal of Chemical Physics},
  shortjournal = {The Journal of Chemical Physics},
  volume = {132},
  number = {15},
  pages = {154104},
  issn = {0021-9606},
  doi = {10.1063/1.3382344},
  url = {https://doi.org/10.1063/1.3382344},
  urldate = {2024-06-03},
  abstract = {The method of dispersion correction as an add-on to standard Kohn--Sham density functional theory (DFT-D) has been refined regarding higher accuracy, broader range of applicability, and less empiricism. The main new ingredients are atom-pairwise specific dispersion coefficients and cutoff radii that are both computed from first principles. The coefficients for new eighth-order dispersion terms are computed using established recursion relations. System (geometry) dependent information is used for the first time in a DFT-D type approach by employing the new concept of fractional coordination numbers (CN). They are used to interpolate between dispersion coefficients of atoms in different chemical environments. The method only requires adjustment of two global parameters for each density functional, is asymptotically exact for a gas of weakly interacting neutral atoms, and easily allows the computation of atomic forces. Three-body nonadditivity terms are considered. The method has been assessed on standard benchmark sets for inter- and intramolecular noncovalent interactions with a particular emphasis on a consistent description of light and heavy element systems. The mean absolute deviations for the S22 benchmark set of noncovalent interactions for 11 standard density functionals decrease by 15\%--40\% compared to the previous (already accurate) DFT-D version. Spectacular improvements are found for a tripeptide-folding model and all tested metallic systems. The rectification of the long-range behavior and the use of more accurate C6 coefficients also lead to a much better description of large (infinite) systems as shown for graphene sheets and the adsorption of benzene on an Ag(111) surface. For graphene it is found that the inclusion of three-body terms substantially (by about 10\%) weakens the interlayer binding. We propose the revised DFT-D method as a general tool for the computation of the dispersion energy in molecules and solids of any kind with DFT and related (low-cost) electronic structure methods for large systems.},
  file = {/home/mariano/Zotero/storage/HE8UZG7M/Grimme et al. - 2010 - A consistent and accurate ab initio parametrizatio.pdf}
}

@article{grimmeEffectDampingFunction2011,
  title = {Effect of the Damping Function in Dispersion Corrected Density Functional Theory},
  author = {Grimme, Stefan and Ehrlich, Stephan and Goerigk, Lars},
  date = {2011-05},
  journaltitle = {Journal of Computational Chemistry},
  shortjournal = {J Comput Chem},
  volume = {32},
  number = {7},
  pages = {1456--1465},
  issn = {0192-8651, 1096-987X},
  doi = {10.1002/jcc.21759},
  url = {https://onlinelibrary.wiley.com/doi/10.1002/jcc.21759},
  urldate = {2024-09-26},
  abstract = {It is shown by an extensive benchmark on molecular energy data that the mathematical form of the damping function in DFT-D methods has only a minor impact on the quality of the results. For 12 different functionals, a standard ``zero-damping'' formula and rational damping to finite values for small interatomic distances according to Becke and Johnson (BJ-damping) has been tested. The same (DFT-D3) scheme for the computation of the dispersion coefficients is used. The BJ-damping requires one fit parameter more for each functional (three instead of two) but has the advantage of avoiding repulsive interatomic forces at shorter distances. With BJ-damping better results for nonbonded distances and more clear effects of intramolecular dispersion in four representative molecular structures are found. For the noncovalentlybonded structures in the S22 set, both schemes lead to very similar intermolecular distances. For noncovalent interaction energies BJ-damping performs slightly better but both variants can be recommended in general. The exception to this is Hartree-Fock that can be recommended only in the BJ-variant and which is then close to the accuracy of corrected GGAs for non-covalent interactions. According to the thermodynamic benchmarks BJ-damping is more accurate especially for medium-range electron correlation problems and only small and practically insignificant double-counting effects are observed. It seems to provide a physically correct short-range behavior of correlation/dispersion even with unmodified standard functionals. In any case, the differences between the two methods are much smaller than the overall dispersion effect and often also smaller than the influence of the underlying density functional.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/883MKNBX/Grimme et al. - 2011 - Effect of the damping function in dispersion corrected density functional theory.pdf}
}

@article{guptaPhononsAnomalousThermal2018,
  title = {Phonons and Anomalous Thermal Expansion Behavior of {{H2O}} and {{D2O}} Ice {{Ih}}},
  author = {Gupta, M. K. and Mittal, R. and Singh, Baltej and Mishra, S. K. and Adroja, D. T. and Fortes, A. D. and Chaplot, S. L.},
  date = {2018-09-04},
  journaltitle = {Physical Review B},
  shortjournal = {Phys. Rev. B},
  volume = {98},
  number = {10},
  pages = {104301},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevB.98.104301},
  url = {https://link.aps.org/doi/10.1103/PhysRevB.98.104301},
  urldate = {2024-06-18},
  abstract = {In order to identify and quantitatively analyze the anharmonicity of phonons relevant to the anomalous thermal expansion in the I⁢ℎ phase of ice, we performed neutron inelastic scattering measurements to study the phonon spectrum as a function of pressure up to 1 kbar at 225 K in deuterated ice (D2⁢O), and as a function of temperature over 10--225 K at ambient pressure in both H2⁢O and D2⁢O ice. We also performed density functional theory calculations of the lattice dynamics. The anomalous expansion is quantitatively reproduced from the analysis of the neutron data as well as from the ab initio calculations. Further, the ab initio calculations are used to visualize the nature of anharmonic phonons across a large part of the Brillouin zone. We find that the negative thermal expansion below 60 K in the hexagonal plane is due to anharmonic librational motion of the hexagonal rings of the ice molecules, and that along the hexagonal axis originates from the transverse vibrations of the hexagonal layers.},
  file = {/home/mariano/Zotero/storage/THAKK845/Gupta et al. - 2018 - Phonons and anomalous thermal expansion behavior of H2O and D2O ice Ih.pdf;/home/mariano/Zotero/storage/2KIFT4HI/PhysRevB.98.html}
}

@article{hobzaReliableTheoreticalTreatment1999,
  title = {Reliable Theoretical Treatment of Molecular Clusters: {{Counterpoise-corrected}} Potential Energy Surface and Anharmonic Vibrational Frequencies of the Water Dimer},
  shorttitle = {Reliable Theoretical Treatment of Molecular Clusters},
  author = {Hobza, Pavel and Bludsk\'y, Ota and Suhai, S\'andor},
  date = {1999-01-01},
  journaltitle = {Physical Chemistry Chemical Physics},
  shortjournal = {Phys. Chem. Chem. Phys.},
  volume = {1},
  number = {13},
  pages = {3073--3078},
  publisher = {The Royal Society of Chemistry},
  issn = {1463-9084},
  doi = {10.1039/A902109D},
  url = {https://pubs.rsc.org/en/content/articlelanding/1999/cp/a902109d},
  urldate = {2024-05-29},
  abstract = {Structure, properties and energetics of the water dimer were determined by counterpoise (CP)-corrected gradient optimization which apriori eliminates the basis set superposition error (BSSE). Calculations were carried out at the MP2 level with various basis sets up to the aug-cc-pVQZ one. Besides harmonic vibrational frequencies twelve-dimensional anharmonic frequencies were also determined using the second-order perturbation treatment. Harmonic and anharmonic frequencies were based on CP-corrected Hessians. The equilibrium geometry of the dimer differs from that determined by a standard optimization and the difference becomes small only for the largest basis set (aug-cc-pVQZ). The best theoretical estimate of the intermolecular oxygen--oxygen distance (2.92 \AA ) is shorter than the experimental result of 2.95 \AA. An estimate of the complete basis set limit of the stabilization energy was obtained by extrapolating the stabilization energies as a function of the reciprocal size of the basis set; this value (21.05 kJ mol-1) is slightly smaller than other literature estimates. Adding the changes due to zero-point energy and temperature-dependent enthalpy terms (determined using anharmonic frequencies obtained from the CP-corrected Hessian) we obtain an estimate to the theoretical stabilization enthalpy at 375 K (12.76 kJ mol-1) which is by 0.8--1.3 kJ mol-1 smaller than the literature results. Our theoretical value supports the very low limit of the experimental value. Red shift of the O--H stretching frequency accompanying formation of the dimer was determined at various theoretical levels and best agreement with the experimental value was found for anharmonic frequencies calculated with CP-corrected Hessians.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/3WZVIJFM/Hobza et al. - 1999 - Reliable theoretical treatment of molecular cluste.pdf}
}

@article{hohenbergInhomogeneousElectronGas1964,
  title = {Inhomogeneous {{Electron Gas}}},
  author = {Hohenberg, P. and Kohn, W.},
  date = {1964-11-09},
  journaltitle = {Physical Review},
  shortjournal = {Phys. Rev.},
  volume = {136},
  pages = {B864-B871},
  issn = {0031-899X},
  doi = {10.1103/PhysRev.136.B864},
  url = {https://link.aps.org/doi/10.1103/PhysRev.136.B864},
  urldate = {2024-08-25},
  issue = {3B},
  langid = {english},
  file = {/home/mariano/Zotero/storage/PAKY9BRF/Hohenberg e Kohn - 1964 - Inhomogeneous Electron Gas.pdf;/home/mariano/Zotero/storage/IJAKCIYX/PhysRev.136.html}
}

@article{holzapfelCoherentThermodynamicModel2021,
  title = {Coherent Thermodynamic Model for Ice {{Ih}}---{{A}} Model Case for Complex Behavior},
  author = {Holzapfel, Wilfried B. and Klotz, Stefan},
  date = {2021-07-12},
  journaltitle = {The Journal of Chemical Physics},
  shortjournal = {The Journal of Chemical Physics},
  volume = {155},
  number = {2},
  pages = {024506},
  issn = {0021-9606},
  doi = {10.1063/5.0049215},
  url = {https://doi.org/10.1063/5.0049215},
  urldate = {2024-03-18},
  abstract = {New data on the variation of the thermal expansion of ice Ih with temperature at ambient pressure together with new evaluations of the bulk modulus and earlier data for the heat capacity provide the basis for a coherent thermodynamic modeling of the main thermophysical properties of ice Ih over its whole range of stability. The quasi-harmonic approximation with one Debye term and seven Einstein terms, together with explicit anharmonicity, represents the dominant contribution next to minor ``anomalies'' from hydrogen ordering and lattice defects. The model accurately fits the main features of all experimental data and provides a basis for the comparison with earlier determinations of the phonon density of states and the Gr\"uneisen parameters.},
  file = {/home/mariano/Zotero/storage/LYBZJXG9/Holzapfel e Klotz - 2021 - Coherent thermodynamic model for ice Ih—A model ca.pdf;/home/mariano/Zotero/storage/8PQ4TY4S/Coherent-thermodynamic-model-for-ice-Ih-A-model.html}
}

@article{israelachviliIntermolecularSurfaceForces,
  title = {Intermolecular and {{Surface Forces}}},
  author = {Israelachvili, Jacob N},
  langid = {english},
  file = {/home/mariano/Zotero/storage/7IMLL5LH/Israelachvili - Intermolecular and Surface Forces.pdf}
}

@article{kalesckyLocalVibrationalModes2012,
  title = {Local Vibrational Modes of the Water Dimer -- {{Comparison}} of Theory and Experiment},
  author = {Kalescky, R. and Zou, W. and Kraka, E. and Cremer, D.},
  date = {2012-12},
  journaltitle = {Chemical Physics Letters},
  shortjournal = {Chemical Physics Letters},
  volume = {554},
  pages = {243--247},
  issn = {00092614},
  doi = {10.1016/j.cplett.2012.10.047},
  url = {https://linkinghub.elsevier.com/retrieve/pii/S0009261412012146},
  urldate = {2024-06-29},
  abstract = {Local and normal vibrational modes of the water dimer are calculated at the CCSD(T)/CBS level of theory. The local H-bond stretching frequency is 528 cm 1 compared to a normal mode stretching frequency of just 143 cm 1. The adiabatic connection scheme between local and normal vibrational modes reveals that the lowering is due to mass coupling, a change in the anharmonicity, and coupling with the local HOH bending modes. The local mode stretching force constant is related to the strength of the H-bond whereas the normal mode stretching force constant and frequency lead to an erroneous underestimation of the Hbond strength.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/3IZ4C73B/Kalescky et al. - 2012 - Local vibrational modes of the water dimer – Comparison of theory and experiment.pdf}
}

@article{kapilCompleteDescriptionThermodynamic2022,
  title = {A Complete Description of Thermodynamic Stabilities of Molecular Crystals},
  author = {Kapil, Venkat and Engel, Edgar A.},
  date = {2022-02-08},
  journaltitle = {Proceedings of the National Academy of Sciences},
  volume = {119},
  number = {6},
  pages = {e2111769119},
  publisher = {Proceedings of the National Academy of Sciences},
  doi = {10.1073/pnas.2111769119},
  url = {https://www.pnas.org/doi/full/10.1073/pnas.2111769119},
  urldate = {2023-09-20},
  abstract = {Predictions of relative stabilities of (competing) molecular crystals are of great technological relevance, most notably for the pharmaceutical industry. However, they present a long-standing challenge for modeling, as often minuscule free energy differences are sensitively affected by the description of electronic structure, the statistical mechanics of the nuclei and the cell, and thermal expansion. The importance of these effects has been individually established, but rigorous free energy calculations for general molecular compounds, which simultaneously account for all effects, have hitherto not been computationally viable. Here we present an efficient ``end to end'' framework that seamlessly combines state-of-the art electronic structure calculations, machine-learning potentials, and advanced free energy methods to calculate ab initio Gibbs free energies for general organic molecular materials. The facile generation of machine-learning potentials for a diverse set of polymorphic compounds---benzene, glycine, and succinic acid---and predictions of thermodynamic stabilities in qualitative and quantitative agreement with experiments highlight that predictive thermodynamic studies of industrially relevant molecular materials are no longer a daunting task.},
  keywords = {ab initio thermodynamics,machine learning,polymorphism,statistical mechanics},
  file = {/home/mariano/Zotero/storage/UJM8NHDR/Kapil e Engel - 2022 - A complete description of thermodynamic stabilitie.pdf}
}

@article{karkiImprovingMechanicalProperties2009,
  title = {Improving {{Mechanical Properties}} of {{Crystalline Solids}} by {{Cocrystal Formation}}: {{New Compressible Forms}} of {{Paracetamol}}},
  shorttitle = {Improving {{Mechanical Properties}} of {{Crystalline Solids}} by {{Cocrystal Formation}}},
  author = {Karki, Shyam and Fri\v s\v ci\'c, Tomislav and F\'abi\'an, L\'aszl\'o and Laity, Peter R. and Day, Graeme M. and Jones, William},
  date = {2009},
  journaltitle = {Advanced Materials},
  volume = {21},
  number = {38-39},
  pages = {3905--3909},
  issn = {1521-4095},
  doi = {10.1002/adma.200900533},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/adma.200900533},
  urldate = {2024-06-05},
  abstract = {Poor mechanical properties of paracetamol are improved through the strategy of cocrystal formation. Mechanochemical screening by liquid-assisted grinding generated four cocrystals of paracetamol that readily form tablets by direct compression. Computational studies reveal the mechanical properties can be related to structural features, before all the formation of hydrogen-bonded layers.},
  keywords = {cocrystals,elastic properties,lattice energy calculations,mechanochemistry,pharmaceutical materials},
  file = {/home/mariano/Zotero/storage/SHTU9RAJ/Karki et al. - 2009 - Improving Mechanical Properties of Crystalline Sol.pdf;/home/mariano/Zotero/storage/PHU5FJ5Z/adma.html}
}

@article{kathmannUnderstandingSurfacePotential2011,
  title = {Understanding the {{Surface Potential}} of {{Water}}},
  author = {Kathmann, Shawn M. and Kuo, I-Feng William and Mundy, Christopher J. and Schenter, Gregory K.},
  date = {2011-04-21},
  journaltitle = {The Journal of Physical Chemistry B},
  shortjournal = {J. Phys. Chem. B},
  volume = {115},
  number = {15},
  pages = {4369--4377},
  publisher = {American Chemical Society},
  issn = {1520-6106},
  doi = {10.1021/jp1116036},
  url = {https://doi.org/10.1021/jp1116036},
  urldate = {2024-01-19},
  abstract = {We have resolved the inconsistency in quantifying the surface potential at the liquid-vapor interface when using explicit ab initio electronic charge density and effective atomic partial charge models of liquid water. This is related, in part, to the fact that the resulting electric potentials from partial-charge models and ab initio charge distributions are quite different except for those regions of space between the molecules. We show that the electrostatic surface potential from a quantum mechanical charge distribution compares well to high-energy electron diffraction and electron holography measurements, as opposed to the comparison with electrochemical measurements. We suggest that certain regions of space be excluded when comparing computed surface potentials with electrochemical measurements. This work describes a novel interpretation of ab initio computed surface potentials through high-energy electron holography measurements as useful benchmarks toward a better understanding of electrochemistry.},
  file = {/home/mariano/Zotero/storage/ABLHG3I4/Kathmann et al. - 2011 - Understanding the Surface Potential of Water.pdf}
}

@online{kaurDataefficientFinetuningFoundational2024,
  title = {Data-Efficient Fine-Tuning of Foundational Models for First-Principles Quality Sublimation Enthalpies},
  author = {Kaur, Harveen and Della Pia, Flaviano and Batatia, Ilyes and Advincula, Xavier R. and Shi, Benjamin X. and Lan, Jinggang and Cs\'anyi, G\'abor and Michaelides, Angelos and Kapil, Venkat},
  date = {2024-05-30},
  eprint = {2405.20217},
  eprinttype = {arXiv},
  eprintclass = {cond-mat, physics:physics},
  doi = {10.48550/arXiv.2405.20217},
  url = {http://arxiv.org/abs/2405.20217},
  urldate = {2024-06-11},
  abstract = {Calculating sublimation enthalpies of molecular crystal polymorphs is relevant to a wide range of technological applications. However, predicting these quantities at first-principles accuracy -- even with the aid of machine learning potentials -- is a challenge that requires sub-kJ/mol accuracy in the potential energy surface and finite-temperature sampling. We present an accurate and data-efficient protocol based on fine-tuning of the foundational MACE-MP-0 model and showcase its capabilities on sublimation enthalpies and physical properties of ice polymorphs. Our approach requires only a few tens of training structures to achieve sub-kJ/mol accuracy in the sublimation enthalpies and sub 1 \% error in densities for polymorphs at finite temperature and pressure. Exploiting this data efficiency, we explore simulations of hexagonal ice at the random phase approximation level of theory at experimental temperatures and pressures, calculating its physical properties, like pair correlation function and density, with good agreement with experiments. Our approach provides a way forward for predicting the stability of molecular crystals at finite thermodynamic conditions with the accuracy of correlated electronic structure theory.},
  pubstate = {prepublished},
  keywords = {Condensed Matter - Materials Science,Physics - Chemical Physics},
  file = {/home/mariano/Zotero/storage/39NDAIWK/Kaur et al. - 2024 - Data-efficient fine-tuning of foundational models for first-principles quality sublimation enthalpie.pdf;/home/mariano/Zotero/storage/ASREN8NU/2405.html}
}

@article{kjaergaardCalculationVibrationalTransition2008,
  title = {Calculation of {{Vibrational Transition Frequencies}} and {{Intensities}} in {{Water Dimer}}: {{Comparison}} of {{Different Vibrational Approaches}}},
  shorttitle = {Calculation of {{Vibrational Transition Frequencies}} and {{Intensities}} in {{Water Dimer}}},
  author = {Kjaergaard, Henrik G. and Garden, Anna L. and Chaban, Galina M. and Gerber, R. Benny and Matthews, Devin A. and Stanton, John F.},
  date = {2008-05-01},
  journaltitle = {The Journal of Physical Chemistry A},
  shortjournal = {J. Phys. Chem. A},
  volume = {112},
  number = {18},
  pages = {4324--4335},
  issn = {1089-5639, 1520-5215},
  doi = {10.1021/jp710066f},
  url = {https://pubs.acs.org/doi/10.1021/jp710066f},
  urldate = {2024-06-29},
  langid = {english},
  file = {/home/mariano/Zotero/storage/A369CA8U/Kjaergaard et al. - 2008 - Calculation of Vibrational Transition Frequencies and Intensities in Water Dimer Comparison of Diff.pdf}
}

@article{klopperComputationalDeterminationEquilibrium2000,
  title = {Computational Determination of Equilibrium Geometry and Dissociation Energy of the Water Dimer},
  author = {Klopper, W. and family=Rijdt, given=J. G. C. M. van Duijneveldt-van, prefix=de, useprefix=false and family=Duijneveldt, given=F. B., prefix=van, useprefix=false},
  date = {2000-01-01},
  journaltitle = {Physical Chemistry Chemical Physics},
  shortjournal = {Phys. Chem. Chem. Phys.},
  volume = {2},
  number = {10},
  pages = {2227--2234},
  publisher = {The Royal Society of Chemistry},
  issn = {1463-9084},
  doi = {10.1039/A910312K},
  url = {https://pubs.rsc.org/en/content/articlelanding/2000/cp/a910312k},
  urldate = {2024-05-29},
  abstract = {The equilibrium geometry and dissociation energy of the water dimer have been determined as accurately as technically possible. Various quantum chemical methods and high-quality basis sets have been applied---that is, at the level of a nearly complete basis---and both the intermolecular separation and the deformation of the donor and acceptor molecules have been optimized at the level of CCSD(T) theory (coupled-cluster theory with singles and doubles excitations plus a perturbation correction for connected triples). It is found at the CCSD(T) level that the monomer deformation in the dimer amounts to 86\% of the deformation computed at the MP2 level (second-order M\o ller-Plesset perturbation theory) and that the core/valence electron correlation effects at the CCSD(T) level amount to 80\% of the same effects at the MP2 level. The equilibrium O{$\cdot\cdot\cdot$}O distance is determined as Re=291.2\textpm 0.5 pm and the equilibrium dissociation energy as De=21.0\textpm 0.2 kJ mol-1, with respect to dissociation into two isolated water molecules at equilibrium. Accounting for zero-point vibrational energy, the theoretical prediction for the dissociation energy becomes D0=13.8\textpm 0.4 kJ mol-1, a result which is open to direct experimental verification.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/R3NJRAIN/Klopper et al. - 2000 - Computational determination of equilibrium geometr.pdf}
}

@article{koFourthgenerationHighdimensionalNeural2021,
  title = {A Fourth-Generation High-Dimensional Neural Network Potential with Accurate Electrostatics Including Non-Local Charge Transfer},
  author = {Ko, Tsz Wai and Finkler, Jonas A. and Goedecker, Stefan and Behler, J\"org},
  date = {2021-01-15},
  journaltitle = {Nature Communications},
  shortjournal = {Nat Commun},
  volume = {12},
  number = {1},
  pages = {398},
  issn = {2041-1723},
  doi = {10.1038/s41467-020-20427-2},
  url = {https://www.nature.com/articles/s41467-020-20427-2},
  urldate = {2024-07-10},
  abstract = {Abstract             Machine learning potentials have become an important tool for atomistic simulations in many fields, from chemistry via molecular biology to materials science. Most of the established methods, however, rely on local properties and are thus unable to take global changes in the electronic structure into account, which result from long-range charge transfer or different charge states. In this work we overcome this limitation by introducing a fourth-generation high-dimensional neural network potential that combines a charge equilibration scheme employing environment-dependent atomic electronegativities with accurate atomic energies. The method, which is able to correctly describe global charge distributions in arbitrary systems, yields much improved energies and substantially extends the applicability of modern machine learning potentials. This is demonstrated for a series of systems representing typical scenarios in chemistry and materials science that are incorrectly described by current methods, while the fourth-generation neural network potential is in excellent agreement with electronic structure calculations.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/Y6DT4H83/Ko et al. - 2021 - A fourth-generation high-dimensional neural network potential with accurate electrostatics including.pdf}
}

@article{kohnSelfConsistentEquationsIncluding1965,
  title = {Self-{{Consistent Equations Including Exchange}} and {{Correlation Effects}}},
  author = {Kohn, W. and Sham, L. J.},
  date = {1965-11-15},
  journaltitle = {Physical Review},
  shortjournal = {Phys. Rev.},
  volume = {140},
  pages = {A1133-A1138},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRev.140.A1133},
  url = {https://link.aps.org/doi/10.1103/PhysRev.140.A1133},
  urldate = {2023-06-11},
  abstract = {From a theory of Hohenberg and Kohn, approximation methods for treating an inhomogeneous system of interacting electrons are developed. These methods are exact for systems of slowly varying or high density. For the ground state, they lead to self-consistent equations analogous to the Hartree and Hartree-Fock equations, respectively. In these equations the exchange and correlation portions of the chemical potential of a uniform electron gas appear as additional effective potentials. (The exchange portion of our effective potential differs from that due to Slater by a factor of 23.) Electronic systems at finite temperatures and in magnetic fields are also treated by similar methods. An appendix deals with a further correction for systems with short-wavelength density oscillations.},
  issue = {4A},
  file = {/home/mariano/Zotero/storage/BTSWA5PW/Kohn e Sham - 1965 - Self-Consistent Equations Including Exchange and C.pdf;/home/mariano/Zotero/storage/5RP6RSWE/PhysRev.140.html}
}

@article{korthMindlessDFTBenchmarking2009,
  title = {``{{Mindless}}'' {{DFT Benchmarking}}},
  author = {Korth, Martin and Grimme, Stefan},
  date = {2009-04-14},
  journaltitle = {Journal of Chemical Theory and Computation},
  shortjournal = {J. Chem. Theory Comput.},
  volume = {5},
  number = {4},
  pages = {993--1003},
  issn = {1549-9618, 1549-9626},
  doi = {10.1021/ct800511q},
  url = {https://pubs.acs.org/doi/10.1021/ct800511q},
  urldate = {2024-09-26},
  abstract = {A diversity-oriented approach for the generation of thermochemical benchmark sets is presented. Test sets consisting of randomly generated ``artificial molecules'' (AMs) are proposed that rely on systematic constraints rather than uncontrolled chemical biases. In this way, the narrow structural space of chemical intuition is opened up and electronically difficult cases can be produced in an unforeseeable manner. For the calculation of chemically meaningful relative energies, AMs are systematically decomposed into small molecules (hydrides and diatomics). Two different example test sets containing eight-atom, single-reference, main group AMs with chemically very diverse and unusual structures are generated. Highly accurate all-electron, estimated CCSD(T)/complete basis set reference energies are also provided. They are used to benchmark the density functionals S-VWN, BP86, B-LYP, B97-D, PBE, TPSS, PBEh, BH-LYP, B3-PW91, B3-LYP, B2-PLYP, B2GP-PLYP, BMK, MPW1B95, M05, M05-2X, PW6B95, M06, M06-L, and M06-2X. In selected cases, an empirical dispersion correction (DFT-D) has been applied. Due to the composition of the sets, it is expected that a good performance indicates ``robustness'' in many different chemical applications. The results of a statistical analysis of the errors for the entire set with 165 entries (average reaction energy of 117 kcal/mol, dubbed as the MB08-165 set) perfectly fit to the ``Jacob's ladder'' metaphor for the ordering of density functionals according to their theoretical complexity. The mean absolute deviation (MAD) decreases very strongly from LDA (20 kcal/mol) to GGAs (MAD of about 10 kcal/mol) but then was less pronounced to hybrid-GGAs (MAD of about 6-8 kcal/mol). The best performance (MAD of 4.1-4.2 kcal/mol) is found for the (fifth-rung) double-hybrid functionals B2-PLYP-D and B2GP-PLYP-D, followed by the M06-2X meta-hybrid (MAD of 4.8 kcal/mol). The significance of the proposed approach for thermodynamic benchmarking is discussed and related to the observed performance ranking also regarding wave function based methods.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/H2CYUTT5/Korth e Grimme - 2009 - “Mindless” DFT Benchmarking.pdf}
}

@article{kovacsEvaluationMACEForce2023,
  title = {Evaluation of the {{MACE}} Force Field Architecture: {{From}} Medicinal Chemistry to Materials Science},
  shorttitle = {Evaluation of the {{MACE}} Force Field Architecture},
  author = {Kov\'acs, D\'avid P\'eter and Batatia, Ilyes and Arany, Eszter S\'ara and Cs\'anyi, G\'abor},
  date = {2023-07-31},
  journaltitle = {The Journal of Chemical Physics},
  shortjournal = {The Journal of Chemical Physics},
  volume = {159},
  number = {4},
  pages = {044118},
  issn = {0021-9606},
  doi = {10.1063/5.0155322},
  url = {https://doi.org/10.1063/5.0155322},
  urldate = {2024-07-08},
  abstract = {The MACE architecture represents the state of the art in the field of machine learning force fields for a variety of in-domain, extrapolation, and low-data regime tasks. In this paper, we further evaluate MACE by fitting models for published benchmark datasets. We show that MACE generally outperforms alternatives for a wide range of systems, from amorphous carbon, universal materials modeling, and general small molecule organic chemistry to large molecules and liquid water. We demonstrate the capabilities of the model on tasks ranging from constrained geometry optimization to molecular dynamics simulations and find excellent performance across all tested domains. We show that MACE is very data efficient and can reproduce experimental molecular vibrational spectra when trained on as few as 50 randomly selected reference configurations. We further demonstrate that the strictly local atom-centered model is sufficient for such tasks even in the case of large molecules and weakly interacting molecular assemblies.},
  file = {/home/mariano/Zotero/storage/9NC5R3UC/Kovács et al. - 2023 - Evaluation of the MACE force field architecture From medicinal chemistry to materials science.pdf;/home/mariano/Zotero/storage/BMHJZ2A8/Evaluation-of-the-MACE-force-field-architecture.html}
}

@article{kresseEfficiencyInitioTotal1996,
  title = {Efficiency of Ab-Initio Total Energy Calculations for Metals and Semiconductors Using a Plane-Wave Basis Set},
  author = {Kresse, G. and Furthm\"uller, J.},
  date = {1996-07-01},
  journaltitle = {Computational Materials Science},
  shortjournal = {Computational Materials Science},
  volume = {6},
  number = {1},
  pages = {15--50},
  issn = {0927-0256},
  doi = {10.1016/0927-0256(96)00008-0},
  url = {https://www.sciencedirect.com/science/article/pii/0927025696000080},
  urldate = {2024-09-17},
  abstract = {We present a detailed description and comparison of algorithms for performing ab-initio quantum-mechanical calculations using pseudopotentials and a plane-wave basis set. We will discuss: (a) partial occupancies within the framework of the linear tetrahedron method and the finite temperature density-functional theory, (b) iterative methods for the diagonalization of the Kohn-Sham Hamiltonian and a discussion of an efficient iterative method based on the ideas of Pulay's residual minimization, which is close to an order Natoms2 scaling even for relatively large systems, (c) efficient Broyden-like and Pulay-like mixing methods for the charge density including a new special `preconditioning' optimized for a plane-wave basis set, (d) conjugate gradient methods for minimizing the electronic free energy with respect to all degrees of freedom simultaneously. We have implemented these algorithms within a powerful package called VAMP (Vienna ab-initio molecular-dynamics package). The program and the techniques have been used successfully for a large number of different systems (liquid and amorphous semiconductors, liquid simple and transition metals, metallic and semi-conducting surfaces, phonons in simple metals, transition metals and semiconductors) and turned out to be very reliable.},
  file = {/home/mariano/Zotero/storage/WFT9G9SU/0927025696000080.html}
}

@article{kresseEfficientIterativeSchemes1996,
  title = {Efficient Iterative Schemes for Ab Initio Total-Energy Calculations Using a Plane-Wave Basis Set},
  author = {Kresse, G. and Furthm\"uller, J.},
  date = {1996-10-15},
  journaltitle = {Physical Review B},
  shortjournal = {Phys. Rev. B},
  volume = {54},
  number = {16},
  pages = {11169--11186},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevB.54.11169},
  url = {https://link.aps.org/doi/10.1103/PhysRevB.54.11169},
  urldate = {2024-09-17},
  abstract = {We present an efficient scheme for calculating the Kohn-Sham ground state of metallic systems using pseudopotentials and a plane-wave basis set. In the first part the application of Pulay's DIIS method (direct inversion in the iterative subspace) to the iterative diagonalization of large matrices will be discussed. Our approach is stable, reliable, and minimizes the number of order {$N$}3atoms operations. In the second part, we will discuss an efficient mixing scheme also based on Pulay's scheme. A special ``metric'' and a special ``preconditioning'' optimized for a plane-wave basis set will be introduced. Scaling of the method will be discussed in detail for non-self-consistent and self-consistent calculations. It will be shown that the number of iterations required to obtain a specific precision is almost independent of the system size. Altogether an order {$N$}2atoms scaling is found for systems containing up to 1000 electrons. If we take into account that the number of k points can be decreased linearly with the system size, the overall scaling can approach {$N$}atoms. We have implemented these algorithms within a powerful package called VASP (Vienna ab initio simulation package). The program and the techniques have been used successfully for a large number of different systems (liquid and amorphous semiconductors, liquid simple and transition metals, metallic and semiconducting surfaces, phonons in simple metals, transition metals, and semiconductors) and turned out to be very reliable. \copyright{} 1996 The American Physical Society., This article appears in the following collection:},
  file = {/home/mariano/Zotero/storage/HL57TWMC/PhysRevB.54.html}
}

@article{kresseInitioMolecularDynamics1993,
  title = {Ab Initio Molecular Dynamics for Liquid Metals},
  author = {Kresse, G. and Hafner, J.},
  date = {1993-01-01},
  journaltitle = {Physical Review B},
  shortjournal = {Phys. Rev. B},
  volume = {47},
  number = {1},
  pages = {558--561},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevB.47.558},
  url = {https://link.aps.org/doi/10.1103/PhysRevB.47.558},
  urldate = {2024-09-17},
  abstract = {We present ab initio quantum-mechanical molecular-dynamics calculations based on the calculation of the electronic ground state and of the Hellmann-Feynman forces in the local-density approximation at each molecular-dynamics step. This is possible using conjugate-gradient techniques for energy minimization, and predicting the wave functions for new ionic positions using subspace alignment. This approach avoids the instabilities inherent in quantum-mechanical molecular-dynamics calculations for metals based on the use of a fictitious Newtonian dynamics for the electronic degrees of freedom. This method gives perfect control of the adiabaticity and allows us to perform simulations over several picoseconds.},
  file = {/home/mariano/Zotero/storage/G23C6UL4/PhysRevB.47.html}
}

@article{kuhneStaticDynamicalProperties2009,
  title = {Static and {{Dynamical Properties}} of {{Liquid Water}} from {{First Principles}} by a {{Novel Car}}-{{Parrinello-like Approach}}},
  author = {K\"uhne, Thomas D. and Krack, Matthias and Parrinello, Michele},
  date = {2009-02-10},
  journaltitle = {Journal of Chemical Theory and Computation},
  shortjournal = {J. Chem. Theory Comput.},
  volume = {5},
  number = {2},
  pages = {235--241},
  issn = {1549-9618, 1549-9626},
  doi = {10.1021/ct800417q},
  url = {https://pubs.acs.org/doi/10.1021/ct800417q},
  urldate = {2024-05-09},
  abstract = {Using the recently developed Car-Parrinello-like approach to Born-Oppenheimer molecular dynamics (Ku\textasciidieresis{} hne, T. D.; et al. Phys. Rev. Lett. 2007, 98, 066401.), we assess the accuracy of ab initio molecular dynamics at the semilocal density functional level of theory to describe structural and dynamic properties of liquid water at ambient conditions. We have performed a series of large-scale simulations using a number of parameter-free exchange and correlation functionals, to minimize and investigate the influence of finite size effects as well as statistical errors. We find that finite size effects in structural properties are rather small and, given an extensive sampling, reproducible. On the other hand, the influence of finite size effects on dynamical properties are much larger than generally appreciated. So much so that the infinite size limit is practically out of reach. However, using a finite size scaling procedure, thanks to the greater effectiveness of our new method we can estimate both the thermodynamic value of the diffusion coefficient and the shear viscosity. The hydrogen bond network structure and its kinetics are consistent with the conventional view of tetrahedrally coordinated water.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/NABF58CQ/Kühne et al. - 2009 - Static and Dynamical Properties of Liquid Water fr.pdf}
}

@article{laasonenInitioLiquidWater1993,
  title = {``{{Ab}}\hphantom{,}Initio'' Liquid Water},
  author = {Laasonen, K. and Sprik, M. and Parrinello, M. and Car, R.},
  date = {1993-12-01},
  journaltitle = {The Journal of Chemical Physics},
  shortjournal = {The Journal of Chemical Physics},
  volume = {99},
  number = {11},
  pages = {9080--9089},
  issn = {0021-9606},
  doi = {10.1063/1.465574},
  url = {https://doi.org/10.1063/1.465574},
  urldate = {2024-01-19},
  abstract = {An ab\hphantom{,}initio molecular dynamics simulation of liquid water has been performed using density functional theory in the Kohn--Sham formulation and a plane wave basis set to determine the electronic structure and the forces at each time step. For an accurate description of the hydrogen bonding in the liquid, it was necessary to extend the exchange functional with a term that depends on the gradient of the electron density. A further important technical detail is that supersoft pseudopotentials were used to treat the valence orbitals of the oxygen atoms in a plane wave expansion. The structural and dynamical properties of the liquid were found to be in good agreement with experiment. The ab\hphantom{,}initio molecular dynamics also yields information on the electronic structure. The electronic feature of special interest is the lowest unoccupied molecular orbital (LUMO) of the liquid which is the state occupied by a thermalized excess electron in the conductive state. The main result of calculating the liquid LUMO is that it is a delocalized state distributed over interstitial space between the molecules with a significant admixture of the {$\sigma$}* orbitals of the individual water molecules.},
  file = {/home/mariano/Zotero/storage/ZJVCNL7D/Laasonen et al. - 1993 - ‘‘Ab initio’’ liquid water.pdf}
}

@article{larsenAtomicSimulationEnvironment2017,
  title = {The Atomic Simulation Environment---a {{Python}} Library for Working with Atoms},
  author = {Larsen, Ask Hjorth and Mortensen, Jens J\o rgen and Blomqvist, Jakob and Castelli, Ivano E. and Christensen, Rune and Du\l ak, Marcin and Friis, Jesper and Groves, Michael N. and Hammer, Bj\o rk and Hargus, Cory and Hermes, Eric D. and Jennings, Paul C. and Jensen, Peter Bjerre and Kermode, James and Kitchin, John R. and Kolsbjerg, Esben Leonhard and Kubal, Joseph and Kaasbjerg, Kristen and Lysgaard, Steen and Maronsson, J\'on Bergmann and Maxson, Tristan and Olsen, Thomas and Pastewka, Lars and Peterson, Andrew and Rostgaard, Carsten and Schi\o tz, Jakob and Sch\"utt, Ole and Strange, Mikkel and Thygesen, Kristian S. and Vegge, Tejs and Vilhelmsen, Lasse and Walter, Michael and Zeng, Zhenhua and Jacobsen, Karsten W.},
  date = {2017-06},
  journaltitle = {Journal of Physics: Condensed Matter},
  shortjournal = {J. Phys.: Condens. Matter},
  volume = {29},
  number = {27},
  pages = {273002},
  publisher = {IOP Publishing},
  issn = {0953-8984},
  doi = {10.1088/1361-648X/aa680e},
  url = {https://dx.doi.org/10.1088/1361-648X/aa680e},
  urldate = {2024-09-21},
  abstract = {The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple `for-loop' construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/XCW2CGG8/Larsen et al. - 2017 - The atomic simulation environment—a Python library for working with atoms.pdf}
}

@article{leadbetterThermodynamicVibrationalProperties1965,
  title = {The Thermodynamic and Vibrational Properties of {{H2O}} Ice and {{D2O}} Ice},
  author = {Leadbetter, A. J.},
  date = {1965-09-14},
  journaltitle = {Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences},
  shortjournal = {Proc. R. Soc. Lond. A},
  volume = {287},
  number = {1410},
  pages = {403--425},
  issn = {0080-4630, 2053-9169},
  doi = {10.1098/rspa.1965.0187},
  url = {https://royalsocietypublishing.org/doi/10.1098/rspa.1965.0187},
  urldate = {2024-03-18},
  abstract = {The thermodynamic properties of H2O ice and D2O ice have been analysed in terms of the effective harmonic spectrum of lattice vibrations. In this approximation the vibrations are treated as harmonic, but with frequencies which are both volume and temperature dependent. Analysis of the heat capacity then gives properties of the effective spectrum at 0 {$^\circ$}K, and the average temperature dependence of the spectrum at constant volume. It has been shown that the parts of the spectrum associated with translational and librational motion of the molecules are distinct, and their contributions to the thermodynamic properties may be separated.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/H9QGIB7I/Leadbetter - 1965 - The thermodynamic and vibrational properties of H2O ice and D2O ice.pdf}
}

@incollection{liComputationalModellingInitio2012,
  title = {Computational Modelling and Ab Initio Calculations in {{MAX}} Phases -- {{I}}},
  booktitle = {Advances in {{Science}} and {{Technology}} of {{Mn}}+{{1AXn Phases}}},
  author = {Li, C. and Wang, Z.},
  date = {2012},
  pages = {197--222},
  publisher = {Elsevier},
  doi = {10.1533/9780857096012.197},
  url = {https://linkinghub.elsevier.com/retrieve/pii/B9781845699918500096},
  urldate = {2024-04-04},
  abstract = {Computer simulation has become a very important tool in the field of scientific research since it is a bridge between theory and experiment. First principles or ab initio methods are being used widely and frequently in order to determine various properties of different materials. At present, various properties of Mn+1AXn compounds have been widely studied for potential use in technological applications. This chapter reviews progress in the use of first-principle calculations for predicting the structural, electrical, mechanical and optical properties of Mn+1AXn compounds. First, we briefly introduce first principles or ab initio methods based on density functional theory (DFT). Then, the question of how to calculate the properties of Mn+1AXn compounds is introduced, and these calculated results are also summarized. Moreover, the calculated results for the effect of pressure on the structural, electronic, mechanical and optical properties of Mn+1AXn are also discussed and summarized.},
  isbn = {978-1-84569-991-8},
  langid = {english},
  file = {/home/mariano/Zotero/storage/CC26SN8R/Li e Wang - 2012 - Computational modelling and ab initio calculations.pdf}
}

@article{liKohnShamEquationsRegularizer2021,
  title = {Kohn-{{Sham Equations}} as {{Regularizer}}: {{Building Prior Knowledge}} into {{Machine-Learned Physics}}},
  shorttitle = {Kohn-{{Sham Equations}} as {{Regularizer}}},
  author = {Li, Li and Hoyer, Stephan and Pederson, Ryan and Sun, Ruoxi and Cubuk, Ekin D. and Riley, Patrick and Burke, Kieron},
  date = {2021-01-20},
  journaltitle = {Physical Review Letters},
  shortjournal = {Phys. Rev. Lett.},
  volume = {126},
  number = {3},
  pages = {036401},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevLett.126.036401},
  url = {https://link.aps.org/doi/10.1103/PhysRevLett.126.036401},
  urldate = {2024-09-16},
  abstract = {Including prior knowledge is important for effective machine learning models in physics and is usually achieved by explicitly adding loss terms or constraints on model architectures. Prior knowledge embedded in the physics computation itself rarely draws attention. We show that solving the Kohn-Sham equations when training neural networks for the exchange-correlation functional provides an implicit regularization that greatly improves generalization. Two separations suffice for learning the entire one-dimensional H2 dissociation curve within chemical accuracy, including the strongly correlated region. Our models also generalize to unseen types of molecules and overcome self-interaction error.},
  file = {/home/mariano/Zotero/storage/H3NIC3WM/Li et al. - 2021 - Kohn-Sham Equations as Regularizer Building Prior Knowledge into Machine-Learned Physics.pdf;/home/mariano/Zotero/storage/TTHP6A9F/PhysRevLett.126.html}
}

@article{luoStructuralElasticProperties2008,
  title = {Structural and Elastic Properties of {{LaAlO3}} from First-Principles Calculations},
  author = {Luo, Xin and Wang, Biao},
  date = {2008-10-06},
  journaltitle = {Journal of Applied Physics},
  shortjournal = {Journal of Applied Physics},
  volume = {104},
  number = {7},
  pages = {073518},
  issn = {0021-8979},
  doi = {10.1063/1.2990068},
  url = {https://doi.org/10.1063/1.2990068},
  urldate = {2024-04-04},
  abstract = {Using the first-principles linearized augmented plane wave calculations within density functional theory, the stable structure, the phase transition, and elastic properties of the LaAlO3 are investigated. At low temperature, our calculation indicates that the rhombohedral R-3C phase is the most energetically stable structure among the three proposed structures: R-3C (No. 167), R-3M (No. 166), and R3C (No. 161). It is found that the LaAlO3 transforms from rhombohedral R-3C phase to cubic PM-3M phase with a volume change of 1\% when the applied hydrostatic pressure is 15.4 GPa, which is consistent with the experimental value. The elastic constants, shear modulus, bulk modulus, and Poisson's ratio of LaAlO3 are calculated and compared with corresponding experimental data. Our result shows that the rotation of the AlO6 octahedra in LaAlO3 has a large influence on the anisotropic elastic constants. From the calculated Debye temperature and elastic constants, the R-3C phase of LaAlO3 is predicted to be more thermostable and to exhibit higher fracture toughness than the high-pressured PM-3M phase.},
  file = {/home/mariano/Zotero/storage/WFALZSCU/Luo e Wang - 2008 - Structural and elastic properties of LaAlO3 from f.pdf;/home/mariano/Zotero/storage/DN3ZIPAS/Structural-and-elastic-properties-of-LaAlO3-from.html}
}

@article{martinsTemperaturePressureInducedProton2009,
  title = {Temperature- and {{Pressure-Induced Proton Transfer}} in the 1:1 {{Adduct Formed}} between {{Squaric Acid}} and 4,4{$\prime$}-{{Bipyridine}}},
  shorttitle = {Temperature- and {{Pressure-Induced Proton Transfer}} in the 1},
  author = {Martins, David M. S. and Middlemiss, Derek S. and Pulham, Colin R. and Wilson, Chick C. and Weller, Mark T. and Henry, Paul F. and Shankland, Norman and Shankland, Kenneth and Marshall, William G. and Ibberson, Richard M. and Knight, Kevin and Moggach, Stephen and Brunelli, Michela and Morrison, Carole A.},
  date = {2009-03-25},
  journaltitle = {Journal of the American Chemical Society},
  shortjournal = {J. Am. Chem. Soc.},
  volume = {131},
  number = {11},
  pages = {3884--3893},
  publisher = {American Chemical Society},
  issn = {0002-7863},
  doi = {10.1021/ja8082973},
  url = {https://doi.org/10.1021/ja8082973},
  urldate = {2024-06-05},
  abstract = {We have applied a combination of spectroscopic and diffraction methods to study the adduct formed between squaric acid and bypridine, which has been postulated to exhibit proton transfer associated with a single-crystal to single-crystal phase transition at ca. 450 K. A combination of X-ray single-crystal and very-high flux powder neutron diffraction data confirmed that a proton does transfer from the acid to the base in the high-temperature form. Powder X-ray diffraction measurements demonstrated that the transition was reversible but that a significant kinetic energy barrier must be overcome to revert to the original structure. Computational modeling is consistent with these results. Modeling also revealed that, while the proton transfer event would be strongly discouraged in the gas phase, it occurs in the solid state due to the increase in charge state of the molecular ions and their arrangement inside the lattice. The color change is attributed to a narrowing of the squaric acid to bipyridine charge-transfer energy gap. Finally, evidence for the possible existence of two further phases at high pressure is also presented.},
  file = {/home/mariano/Zotero/storage/X6JGVDEU/Martins et al. - 2009 - Temperature- and Pressure-Induced Proton Transfer .pdf}
}

@article{morroneNuclearQuantumEffects2008,
  title = {Nuclear {{Quantum Effects}} in {{Water}}},
  author = {Morrone, Joseph A. and Car, Roberto},
  date = {2008-07-01},
  journaltitle = {Physical Review Letters},
  shortjournal = {Phys. Rev. Lett.},
  volume = {101},
  number = {1},
  pages = {017801},
  issn = {0031-9007, 1079-7114},
  doi = {10.1103/PhysRevLett.101.017801},
  url = {https://link.aps.org/doi/10.1103/PhysRevLett.101.017801},
  urldate = {2024-06-30},
  langid = {english},
  file = {/home/mariano/Zotero/storage/JBS98XDE/Morrone e Car - 2008 - Nuclear Quantum Effects in Water.pdf}
}

@article{mukhopadhyayWaterDimerExperimental2015,
  title = {The Water Dimer {{I}}: {{Experimental}} Characterization},
  shorttitle = {The Water Dimer {{I}}},
  author = {Mukhopadhyay, Anamika and Cole, William T. S. and Saykally, Richard J.},
  date = {2015-07-16},
  journaltitle = {Chemical Physics Letters},
  shortjournal = {Chemical Physics Letters},
  volume = {633},
  pages = {13--26},
  issn = {0009-2614},
  doi = {10.1016/j.cplett.2015.04.016},
  url = {https://www.sciencedirect.com/science/article/pii/S0009261415002535},
  urldate = {2024-01-29},
  abstract = {As the archetype of water hydrogen bonding, the water dimer has been studied extensively by both theory and experiment for nearly seven decades. In this article, we present a detailed chronological review of the experimental dimer studies and the insights into the complex nature of water and hydrogen bonding gained from them. A subsequent letter will review the corresponding theoretical advances.},
  file = {/home/mariano/Zotero/storage/D3I9QUGN/Mukhopadhyay et al. - 2015 - The water dimer I Experimental characterization.pdf;/home/mariano/Zotero/storage/ATCH9V7N/S0009261415002535.html}
}

@article{mukhopadhyayWaterDimerII2018,
  title = {The Water Dimer {{II}}: {{Theoretical}} Investigations},
  shorttitle = {The Water Dimer {{II}}},
  author = {Mukhopadhyay, Anamika and Xantheas, Sotiris S. and Saykally, Richard J.},
  date = {2018-05-16},
  journaltitle = {Chemical Physics Letters},
  shortjournal = {Chemical Physics Letters},
  volume = {700},
  pages = {163--175},
  issn = {0009-2614},
  doi = {10.1016/j.cplett.2018.03.057},
  url = {https://www.sciencedirect.com/science/article/pii/S0009261418302409},
  urldate = {2024-01-29},
  abstract = {As the archetype of aqueous hydrogen bonding, the water dimer has been extensively studied by both theory and experiment for nearly seven decades. In this article, we present a detailed chronological review of the theoretical advances made using electronic structure methods to address the structure, hydrogen bonding and vibrational spectroscopy of the water dimer, as well as the role of its potential energy surface in the development of classical force fields to describe intermolecular interactions in clusters and the condensed phases of water.},
  file = {/home/mariano/Zotero/storage/FRKMQV63/Mukhopadhyay et al. - 2018 - The water dimer II Theoretical investigations.pdf;/home/mariano/Zotero/storage/4PJVP6AS/S0009261418302409.html}
}

@article{needsVariationalDiffusionQuantum2020,
  title = {Variational and Diffusion Quantum {{Monte Carlo}} Calculations with the {{CASINO}} Code},
  author = {Needs, R. J. and Towler, M. D. and Drummond, N. D. and L\'opez R\'ios, P. and Trail, J. R.},
  date = {2020-04-21},
  journaltitle = {The Journal of Chemical Physics},
  volume = {152},
  number = {15},
  pages = {154106},
  issn = {0021-9606, 1089-7690},
  doi = {10.1063/1.5144288},
  url = {https://pubs.aip.org/jcp/article/152/15/154106/1058781/Variational-and-diffusion-quantum-Monte-Carlo},
  urldate = {2024-02-09},
  abstract = {We present an overview of the variational and diffusion quantum Monte Carlo methods as implemented in the casino program. We particularly focus on developments made in the last decade, describing state-of-the-art quantum Monte Carlo algorithms and software and discussing their strengths and weaknesses. We review a range of recent applications of casino.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/FNGZMGKI/Needs et al. - 2020 - Variational and diffusion quantum Monte Carlo calc.pdf}
}

@article{neumeierElasticConstantsBulk2018,
  title = {Elastic {{Constants}}, {{Bulk Modulus}}, and {{Compressibility}} of {{H2O Ice I}} {\emph{h}} for the {{Temperature Range}} 50 {{K}}--273 {{K}}},
  author = {Neumeier, J. J.},
  date = {2018-09-01},
  journaltitle = {Journal of Physical and Chemical Reference Data},
  volume = {47},
  number = {3},
  pages = {033101},
  issn = {0047-2689, 1529-7845},
  doi = {10.1063/1.5030640},
  url = {https://pubs.aip.org/jpr/article/47/3/033101/242110/Elastic-Constants-Bulk-Modulus-and-Compressibility},
  urldate = {2024-06-08},
  abstract = {Published elastic constant data for H2O ice in the Ih phase are compiled and evaluated. Fits of the five elastic constants for 50 {$\leq$} T/K {$\leq$} 273 are conducted to yield a reliable and convenient source for elastic constant values. Various elastic properties can be calculated from the elastic constants obtained herein. The elastic constants are used to determine the adiabatic bulk modulus BS for the same temperature range with an estimated uncertainty of less than 1.3\%. Fitting those data yields an equation for BS that is extrapolated to provide values for 0 {$\leq$} T/K \< 50. The adiabatic compressibility KS, isothermal bulk modulus BT, and isothermal compressibility KT are calculated from BS. Comparisons are made to published data.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/HAB9Q4JW/Neumeier - 2018 - Elastic Constants, Bulk Modulus, and Compressibility of H2O Ice I h for the Temperature Range.pdf}
}

@article{otero-de-la-rozaBenchmarkNoncovalentInteractions2012,
  title = {A Benchmark for Non-Covalent Interactions in Solids},
  author = {Otero-de-la-Roza, A. and Johnson, Erin R.},
  date = {2012-08-01},
  journaltitle = {The Journal of Chemical Physics},
  shortjournal = {The Journal of Chemical Physics},
  volume = {137},
  number = {5},
  pages = {054103},
  issn = {0021-9606},
  doi = {10.1063/1.4738961},
  url = {https://doi.org/10.1063/1.4738961},
  urldate = {2023-09-20},
  abstract = {A benchmark for non-covalent interactions in solids (C21) based on the experimental sublimation enthalpies and geometries of 21 molecular crystals is presented. Thermal and zero-point effects are carefully accounted for and reference lattice energies and thermal pressures are provided, which allow dispersion-corrected density functionals to be assessed in a straightforward way. Other thermal corrections to the sublimation enthalpy (the 2RT term) are reexamined. We compare the recently implemented exchange-hole dipole moment (XDM) model with other approaches in the literature to find that XDM roughly doubles the accuracy of DFT-D2 and non-local functionals in computed lattice energies (4.8 kJ/mol mean absolute error) while, at the same time, predicting cell geometries within less than 2\% of the experimental result on average. The XDM model of dispersion interactions is confirmed as a very promising approach in solid-state applications.},
  file = {/home/mariano/Zotero/storage/8ZNNUZXY/Otero-de-la-Roza e Johnson - 2012 - A benchmark for non-covalent interactions in solid.pdf}
}

@book{parrDensityFunctionalTheoryAtoms1994,
  title = {Density-{{Functional Theory}} of {{Atoms}} and {{Molecules}}},
  author = {Parr, Robert G. and Weitao, Yang},
  date = {1994-05-26},
  eprint = {mGOpScSIwU4C},
  eprinttype = {googlebooks},
  publisher = {Oxford University Press},
  abstract = {This book is a rigorous, unified account of the fundamental principles of the density-functional theory of the electronic structure of matter and its applications to atoms and molecules. Containing a detailed discussion of the chemical potential and its derivatives, it provides an understanding of the concepts of electronegativity, hardness and softness, and chemical reactivity. Both the Hohenberg-Kohn-Sham and the Levy-Lieb derivations of the basic theorems are presented, and extensive references to the literature are included. Two introductory chapters and several appendices provide all the background material necessary beyond a knowledge of elementary quantum theory. The book is intended for physicists, chemists, and advanced students in chemistry.},
  isbn = {978-0-19-535773-8},
  langid = {english},
  pagetotal = {344},
  keywords = {Science / Chemistry / Physical & Theoretical,Science / Physics / Atomic & Molecular}
}

@article{parrinelloBreviariumMotuSimulato2022,
  title = {Breviarium de {{Motu Simulato Ad Atomos Pertinenti}}},
  author = {Parrinello, Michele},
  date = {2022-02},
  journaltitle = {Israel Journal of Chemistry},
  shortjournal = {Israel Journal of Chemistry},
  volume = {62},
  number = {1-2},
  pages = {e202100105},
  issn = {0021-2148, 1869-5868},
  doi = {10.1002/ijch.202100105},
  url = {https://onlinelibrary.wiley.com/doi/10.1002/ijch.202100105},
  urldate = {2024-02-24},
  abstract = {Abstract             In this paper I will present a personal recollection of the development of molecular-dynamics-based atomistic simulations in the last forty years. The paper is not meant as a historical account but rather a personal and certainly biased view of the ideas that have underpinned the author's research, allowing ever more complex systems to be studied in an ever more realistic way.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/P2Y7SED5/Parrinello - 2022 - Breviarium de Motu Simulato Ad Atomos Pertinenti.pdf}
}

@article{partridgeDeterminationAccurateIsotope1997,
  title = {The Determination of an Accurate Isotope Dependent Potential Energy Surface for Water from Extensive Ab Initio Calculations and Experimental Data},
  author = {Partridge, Harry and Schwenke, David W.},
  date = {1997-03-15},
  journaltitle = {The Journal of Chemical Physics},
  volume = {106},
  number = {11},
  pages = {4618--4639},
  issn = {0021-9606, 1089-7690},
  doi = {10.1063/1.473987},
  url = {https://pubs.aip.org/jcp/article/106/11/4618/181654/The-determination-of-an-accurate-isotope-dependent},
  urldate = {2024-02-08},
  abstract = {We report on the determination of a high quality ab initio potential energy surface (PES) and dipole moment function for water. This PES is empirically adjusted to improve the agreement between the computed line positions and those from the HITRAN 92 data base with J{$\leq$}5 for H216O. The changes in the PES are small, nonetheless including an estimate of core (oxygen 1s) electron correlation greatly improves the agreement with the experiment. Using this adjusted PES, we can match 30\,092 of the 30\,117 transitions in the HITRAN 96 data base for H216O with theoretical lines. The 10, 25, 50, 75, and 90 percentiles of the difference between the calculated and tabulated line positions are -0.11,\hphantom{,}-0.04,\hphantom{,}-0.01,\hphantom{,}0.02, and 0.07\hphantom{,}cm-1. Nonadiabatic effects are not explicitly included. About 3\% of the tabulated line positions appear to be incorrect. Similar agreement using this adjusted PES is obtained for the 17O and 18O isotopes. For HD16O, the agreement is not as good, with a root-mean-square error of 0.25 cm-1 for lines with J{$\leq$}5. This error is reduced to 0.02 cm-1 by including a small asymmetric correction to the PES, which is parameterized by simultaneously fitting to HD16O and D216O data. Scaling this correction by mass factors yields good results for T2O and HTO. The intensities summed over vibrational bands are usually in good agreement between the calculations and the tabulated results, but individual line strengths can differ greatly. A high-temperature list consisting of 307\,721\,352 lines is generated for H216O using our PES and dipole moment function.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/5WLUGBVD/Partridge e Schwenke - 1997 - The determination of an accurate isotope dependent.pdf}
}

@article{paulingStructureEntropyIce1935,
  title = {The {{Structure}} and {{Entropy}} of {{Ice}} and of {{Other Crystals}} with {{Some Randomness}} of {{Atomic Arrangement}}},
  author = {Pauling, Linus},
  date = {1935-12-01},
  journaltitle = {Journal of the American Chemical Society},
  shortjournal = {J. Am. Chem. Soc.},
  volume = {57},
  number = {12},
  pages = {2680--2684},
  publisher = {American Chemical Society},
  issn = {0002-7863},
  doi = {10.1021/ja01315a102},
  url = {https://doi.org/10.1021/ja01315a102},
  urldate = {2024-01-19},
  file = {/home/mariano/Zotero/storage/99PS49FV/Pauling - 1935 - The Structure and Entropy of Ice and of Other Crys.pdf}
}

@online{PhysicalChemistryWater2020,
  title = {Physical {{Chemistry}} of {{Water}}},
  date = {2020-10-20},
  url = {https://web.archive.org/web/20201020055601/https://msu.edu/course/css/850/snapshot.afs/teppen/physical_chemistry_of_water.htm},
  urldate = {2024-05-18},
  file = {/home/mariano/Zotero/storage/B2Z8WKY3/physical_chemistry_of_water.html}
}

@article{priceComputationalPredictionPharmaceutical2004,
  title = {The Computational Prediction of Pharmaceutical Crystal Structures and Polymorphism},
  author = {Price, Sarah L},
  date = {2004-02-23},
  journaltitle = {Advanced Drug Delivery Reviews},
  shortjournal = {Advanced Drug Delivery Reviews},
  series = {Pharmaceutical Solid Polymorphism in Drug Development and Regulation},
  volume = {56},
  number = {3},
  pages = {301--319},
  issn = {0169-409X},
  doi = {10.1016/j.addr.2003.10.006},
  url = {https://www.sciencedirect.com/science/article/pii/S0169409X03002199},
  urldate = {2024-06-05},
  abstract = {A computational method of predicting all the polymorphs of an organic molecule would be a valuable complement to polymorph screening in the developmental phase. Such a computational method is in its early stages of development, and the current methodologies, which are based on searches for the most stable lattice structure, are critically reviewed. This crude thermodynamic approach generally overestimates the propensity for polymorphism, at least for most of the molecules studied so far, showing the need to model kinetic effects as well as to refine the thermodynamic models. Although the ultimate goal of these studies is still far off, computational predictions of crystal structures have proved useful in aiding the characterisation of polymorphs from powder X-ray data, and in providing insights into the range of types of packing that may be adopted by a given molecule. Thus, computational studies already have the potential to be a valuable tool in pharmaceutical solid state science.},
  keywords = {Computational prediction,Crystal structure prediction,Force-fields,Lattice energy,Polymorphism},
  file = {/home/mariano/Zotero/storage/Z7WUR4X4/Price - 2004 - The computational prediction of pharmaceutical cry.pdf}
}

@article{rappoportWhichFunctionalShould,
  title = {Which Functional Should {{I}} Choose?},
  author = {Rappoport, Dmitrij and Crawford, Nathan R M and Furche, Filipp and Burke, Kieron},
  langid = {english},
  file = {/home/mariano/Zotero/storage/PLNL836Z/Rappoport et al. - Which functional should I choose.pdf}
}

@book{raschkaMachineLearningPyTorch2022,
  title = {Machine {{Learning}} with {{PyTorch}} and {{Scikit-Learn}}: {{Develop}} Machine Learning and Deep Learning Models with {{Python}}},
  shorttitle = {Machine {{Learning}} with {{PyTorch}} and {{Scikit-Learn}}},
  author = {Raschka, Sebastian and Liu, Yuxi and Mirjalili, Vahid and Dzhulgakov, Dmytro},
  date = {2022-02-25},
  edition = {1st edition},
  publisher = {Packt Publishing},
  abstract = {This book of the bestselling and widely acclaimed Python Machine Learning series is a comprehensive guide to machine and deep learning using PyTorch's simple to code framework.Purchase of the print or Kindle book includes a free eBook in PDF format.Key FeaturesLearn applied machine learning with a solid foundation in theoryClear, intuitive explanations take you deep into the theory and practice of Python machine learningFully updated and expanded to cover PyTorch, transformers, XGBoost, graph neural networks, and best practicesBook DescriptionMachine Learning with PyTorch and Scikit-Learn is a comprehensive guide to machine learning and deep learning with PyTorch. It acts as both a step-by-step tutorial and a reference you'll keep coming back to as you build your machine learning systems.Packed with clear explanations, visualizations, and examples, the book covers all the essential machine learning techniques in depth. While some books teach you only to follow instructions, with this machine learning book, we teach the principles allowing you to build models and applications for yourself.Why PyTorch?PyTorch is the Pythonic way to learn machine learning, making it easier to learn and simpler to code with. This book explains the essential parts of PyTorch and how to create models using popular libraries, such as PyTorch Lightning and PyTorch Geometric.You will also learn about generative adversarial networks (GANs) for generating new data and training intelligent agents with reinforcement learning. Finally, this new edition is expanded to cover the latest trends in deep learning, including graph neural networks and large-scale transformers used for natural language processing (NLP).This PyTorch book is your companion to machine learning with Python, whether you're a Python developer new to machine learning or want to deepen your knowledge of the latest developments.What you will learnExplore frameworks, models, and techniques for machines to 'learn' from dataUse scikit-learn for machine learning and PyTorch for deep learningTrain machine learning classifiers on images, text, and moreBuild and train neural networks, transformers, and boosting algorithmsDiscover best practices for evaluating and tuning modelsPredict continuous target outcomes using regression analysisDig deeper into textual and social media data using sentiment analysisWho this book is forIf you have a good grasp of Python basics and want to start learning about machine learning and deep learning, then this is the book for you. This is an essential resource written for developers and data scientists who want to create practical machine learning and deep learning applications using scikit-learn and PyTorch.Before you get started with this book, you'll need a good understanding of calculus, as well as linear algebra.Table of ContentsGiving Computers the Ability to Learn from DataTraining Simple Machine Learning Algorithms for ClassificationA Tour of Machine Learning Classifiers Using Scikit-LearnBuilding Good Training Datasets -- Data PreprocessingCompressing Data via Dimensionality ReductionLearning Best Practices for Model Evaluation and Hyperparameter TuningCombining Different Models for Ensemble LearningApplying Machine Learning to Sentiment AnalysisPredicting Continuous Target Variables with Regression AnalysisWorking with Unlabeled Data -- Clustering AnalysisImplementing a Multilayer Artificial Neural Network from Scratch(N.B. Please use the Look Inside option to see further chapters)},
  langid = {english},
  pagetotal = {770},
  file = {/home/mariano/Zotero/storage/ZLK64VEL/Raschka et al. - 2022 - Machine Learning with PyTorch and Scikit-Learn De.pdf}
}

@article{reddyMechanicalPropertiesMolecular2010,
  title = {Mechanical Properties of Molecular Crystals---Applications to Crystal Engineering},
  author = {Reddy, C. Malla and Rama Krishna, G. and Ghosh, Soumyajit},
  date = {2010},
  journaltitle = {CrystEngComm},
  shortjournal = {CrystEngComm},
  volume = {12},
  number = {8},
  pages = {2296},
  issn = {1466-8033},
  doi = {10.1039/c003466e},
  url = {https://xlink.rsc.org/?DOI=c003466e},
  urldate = {2024-06-05},
  langid = {english},
  file = {/home/mariano/Zotero/storage/VTPRMAV3/Reddy et al. - 2010 - Mechanical properties of molecular crystals—applic.pdf}
}

@article{reillyUnderstandingRoleVibrations2013,
  title = {Understanding the Role of Vibrations, Exact Exchange, and Many-Body van Der {{Waals}} Interactions in the Cohesive Properties of Molecular Crystals},
  author = {Reilly, Anthony M. and Tkatchenko, Alexandre},
  date = {2013-07-14},
  journaltitle = {The Journal of Chemical Physics},
  shortjournal = {J Chem Phys},
  volume = {139},
  number = {2},
  eprint = {23862957},
  eprinttype = {pmid},
  pages = {024705},
  issn = {1089-7690},
  doi = {10.1063/1.4812819},
  abstract = {The development and application of computational methods for studying molecular crystals, particularly density-functional theory (DFT), is a large and ever-growing field, driven by their numerous applications. Here we expand on our recent study of the importance of many-body van der Waals interactions in molecular crystals [A. M. Reilly and A. Tkatchenko, J. Phys. Chem. Lett. 4, 1028 (2013)], with a larger database of 23 molecular crystals. Particular attention has been paid to the role of the vibrational contributions that are required to compare experiment sublimation enthalpies with calculated lattice energies, employing both phonon calculations and experimental heat-capacity data to provide harmonic and anharmonic estimates of the vibrational contributions. Exact exchange, which is rarely considered in DFT studies of molecular crystals, is shown to have a significant contribution to lattice energies, systematically improving agreement between theory and experiment. When the vibrational and exact-exchange contributions are coupled with a many-body approach to dispersion, DFT yields a mean absolute error (3.92 kJ/mol) within the coveted "chemical accuracy" target (4.2 kJ/mol). The role of many-body dispersion for structures has also been investigated for a subset of the database, showing good performance compared to X-ray and neutron diffraction crystal structures. The results show that the approach employed here can reach the demanding accuracy of crystal-structure prediction and organic material design with minimal empiricism.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/2KVAMU4H/Reilly e Tkatchenko - 2013 - Understanding the role of vibrations, exact exchan.pdf}
}

@article{rossiAnharmonicQuantumFluctuations2016,
  title = {Anharmonic and {{Quantum Fluctuations}} in {{Molecular Crystals}}: {{A First-Principles Study}} of the {{Stability}} of {{Paracetamol}}},
  shorttitle = {Anharmonic and {{Quantum Fluctuations}} in {{Molecular Crystals}}},
  author = {Rossi, Mariana and Gasparotto, Piero and Ceriotti, Michele},
  date = {2016-09-08},
  journaltitle = {Physical Review Letters},
  shortjournal = {Phys. Rev. Lett.},
  volume = {117},
  number = {11},
  pages = {115702},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevLett.117.115702},
  url = {https://link.aps.org/doi/10.1103/PhysRevLett.117.115702},
  urldate = {2023-09-20},
  abstract = {Molecular crystals often exist in multiple competing polymorphs, showing significantly different physicochemical properties. Computational crystal structure prediction is key to interpret and guide the search for the most stable or useful form, a real challenge due to the combinatorial search space, and the complex interplay of subtle effects that work together to determine the relative stability of different structures. Here we take a comprehensive approach based on different flavors of thermodynamic integration in order to estimate all contributions to the free energies of these systems with density-functional theory, including the oft-neglected anharmonic contributions and nuclear quantum effects. We take the two main stable forms of paracetamol as a paradigmatic example. We find that anharmonic contributions, different descriptions of van der Waals interactions, and nuclear quantum effects all matter to quantitatively determine the stability of different phases. Our analysis highlights the many challenges inherent in the development of a quantitative and predictive framework to model molecular crystals. However, it also indicates which of the components of the free energy can benefit from a cancellation of errors that can redeem the predictive power of approximate models, and suggests simple steps that could be taken to improve the reliability of ab initio crystal structure prediction.},
  file = {/home/mariano/Zotero/storage/5QB379PL/Rossi et al. - 2016 - Anharmonic and Quantum Fluctuations in Molecular C.pdf;/home/mariano/Zotero/storage/Q293EFK5/Rossi et al. - 2016 - Anharmonic and Quantum Fluctuations in Molecular C.pdf;/home/mariano/Zotero/storage/Q74UHGYF/PhysRevLett.117.html}
}

@article{salzmannAdvancesExperimentalExploration2019,
  title = {Advances in the Experimental Exploration of Water's Phase Diagram},
  author = {Salzmann, Christoph G.},
  date = {2019-02-08},
  journaltitle = {The Journal of Chemical Physics},
  shortjournal = {The Journal of Chemical Physics},
  volume = {150},
  number = {6},
  pages = {060901},
  issn = {0021-9606},
  doi = {10.1063/1.5085163},
  url = {https://doi.org/10.1063/1.5085163},
  urldate = {2024-02-08},
  abstract = {Water's phase diagram displays enormous complexity with currently 17 experimentally confirmed polymorphs of ice and several more predicted computationally. For almost 120 years, it has been a stomping ground for scientific discovery, and ice research has often been a trailblazer for investigations into a wide range of materials-related phenomena. Here, the experimental progress of the last couple of years is reviewed, and open questions as well as future challenges are discussed. The specific topics include (i) the polytypism and stacking disorder of ice I, (ii) the mechanism of the pressure amorphization of ice I, (iii) the emptying of gas-filled clathrate hydrates to give new low-density ice polymorphs, (iv) the effects of acid/base doping on hydrogen-ordering phase transitions as well as (v) the formation of solid solutions between salts and the ice polymorphs, and the effect this has on the appearance of the phase diagram. In addition to continuing efforts to push the boundaries in terms of the extremes of pressure and temperature, the exploration of the ``chemical'' dimensions of ice research appears to now be a newly emerging trend. It is without question that ice research has entered a very exciting era.},
  file = {/home/mariano/Zotero/storage/GLAJCFIN/Salzmann - 2019 - Advances in the experimental exploration of water’.pdf;/home/mariano/Zotero/storage/76MF37E3/Advances-in-the-experimental-exploration-of-water.html}
}

@inproceedings{sanchez-gonzalezLearningSimulateComplex2020,
  title = {Learning to {{Simulate Complex Physics}} with {{Graph Networks}}},
  booktitle = {Proceedings of the 37th {{International Conference}} on {{Machine Learning}}},
  author = {Sanchez-Gonzalez, Alvaro and Godwin, Jonathan and Pfaff, Tobias and Ying, Rex and Leskovec, Jure and Battaglia, Peter},
  date = {2020-11-21},
  pages = {8459--8468},
  publisher = {PMLR},
  issn = {2640-3498},
  url = {https://proceedings.mlr.press/v119/sanchez-gonzalez20a.html},
  urldate = {2024-07-13},
  abstract = {Here we present a machine learning framework and model implementation that can learn to simulate a wide variety of challenging physical domains, involving fluids, rigid solids, and deformable materials interacting with one another. Our framework---which we term "Graph Network-based Simulators" (GNS)---represents the state of a physical system with particles, expressed as nodes in a graph, and computes dynamics via learned message-passing. Our results show that our model can generalize from single-timestep predictions with thousands of particles during training, to different initial conditions, thousands of timesteps, and at least an order of magnitude more particles at test time. Our model was robust to hyperparameter choices across various evaluation metrics: the main determinants of long-term performance were the number of message-passing steps, and mitigating the accumulation of error by corrupting the training data with noise. Our GNS framework advances the state-of-the-art in learned physical simulation, and holds promise for solving a wide range of complex forward and inverse problems.},
  eventtitle = {International {{Conference}} on {{Machine Learning}}},
  langid = {english},
  file = {/home/mariano/Zotero/storage/CWRFBTHB/Sanchez-Gonzalez et al. - 2020 - Learning to Simulate Complex Physics with Graph Networks.pdf;/home/mariano/Zotero/storage/R4I6GJPT/Sanchez-Gonzalez et al. - 2020 - Learning to Simulate Complex Physics with Graph Networks.pdf}
}

@article{sanchez-lengelingGentleIntroductionGraph2021,
  title = {A {{Gentle Introduction}} to {{Graph Neural Networks}}},
  author = {Sanchez-Lengeling, Benjamin and Reif, Emily and Pearce, Adam and Wiltschko, Alex},
  date = {2021-08-17},
  journaltitle = {Distill},
  shortjournal = {Distill},
  volume = {6},
  number = {8},
  pages = {10.23915/distill.00033},
  issn = {2476-0757},
  doi = {10.23915/distill.00033},
  url = {https://distill.pub/2021/gnn-intro},
  urldate = {2024-07-13},
  file = {/home/mariano/Zotero/storage/YS7LPTQX/gnn-intro.html}
}

@article{schranMachineLearningPotentials2021,
  title = {Machine Learning Potentials for Complex Aqueous Systems Made Simple},
  author = {Schran, Christoph and Thiemann, Fabian L. and Rowe, Patrick and M\"uller, Erich A. and Marsalek, Ondrej and Michaelides, Angelos},
  date = {2021-09-21},
  journaltitle = {Proceedings of the National Academy of Sciences},
  volume = {118},
  number = {38},
  pages = {e2110077118},
  publisher = {Proceedings of the National Academy of Sciences},
  doi = {10.1073/pnas.2110077118},
  url = {https://www.pnas.org/doi/full/10.1073/pnas.2110077118},
  urldate = {2024-07-10},
  abstract = {Simulation techniques based on accurate and efficient representations of potential energy surfaces are urgently needed for the understanding of complex systems such as solid--liquid interfaces. Here we present a machine learning framework that enables the efficient development and validation of models for complex aqueous systems. Instead of trying to deliver a globally optimal machine learning potential, we propose to develop models applicable to specific thermodynamic state points in a simple and user-friendly process. After an initial ab initio simulation, a machine learning potential is constructed with minimum human effort through a data-driven active learning protocol. Such models can afterward be applied in exhaustive simulations to provide reliable answers for the scientific question at hand or to systematically explore the thermal performance of ab initio methods. We showcase this methodology on a diverse set of aqueous systems comprising bulk water with different ions in solution, water on a titanium dioxide surface, and water confined in nanotubes and between molybdenum disulfide sheets. Highlighting the accuracy of our approach with respect to the underlying ab initio reference, the resulting models are evaluated in detail with an automated validation protocol that includes structural and dynamical properties and the precision of the force prediction of the models. Finally, we demonstrate the capabilities of our approach for the description of water on the rutile titanium dioxide (110) surface to analyze the structure and mobility of water on this surface. Such machine learning models provide a straightforward and uncomplicated but accurate extension of simulation time and length scales for complex systems.},
  file = {/home/mariano/Zotero/storage/WRP2QBNF/Schran et al. - 2021 - Machine learning potentials for complex aqueous systems made simple.pdf}
}

@article{schutzWaterDimerInteraction1997,
  title = {The Water Dimer Interaction Energy: {{Convergence}} to the Basis Set Limit at the Correlated Level},
  shorttitle = {The Water Dimer Interaction Energy},
  author = {Sch\"utz, Martin and Brdarski, Steve and Widmark, Per-Olof and Lindh, Roland and Karlstr\"om, Gunnar},
  date = {1997-09-22},
  journaltitle = {The Journal of Chemical Physics},
  volume = {107},
  number = {12},
  pages = {4597--4605},
  issn = {0021-9606, 1089-7690},
  doi = {10.1063/1.474820},
  url = {https://pubs.aip.org/jcp/article/107/12/4597/478974/The-water-dimer-interaction-energy-Convergence-to},
  urldate = {2024-03-06},
  abstract = {The water dimer interaction energy and its convergence to the basis set limit was investigated, with electron correlation effects treated at the level of second order Mo/ller-Plesset perturbation theory (MP2). ANO-type and large uncontracted basis sets were used, spreading over a wide range in size; the biggest set included 1046 functions with angular momentum up to (l=7). Core correlation effects were treated accurately by augmenting the original valence basis with extended sets of core polarization functions. The MP2 dimer interaction energy at the basis set limit was determined to -4.94\textpm 0.02 kcal/mol, with a contribution due to core correlation of -0.04 kcal/mol. Furthermore, based on some elementary considerations from intermolecular perturbation theory, a simple procedure was devised, which brings the counterpoise corrected interaction energies of moderate basis set calculations closer to the basis set limit. The interaction energies so obtained turned out be surprisingly stable with respect to extensions of the basis set.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/FTNUDW4M/Schütz et al. - 1997 - The water dimer interaction energy Convergence to.pdf}
}

@article{simGaussianDensityFunctional1992,
  title = {Gaussian Density Functional Calculations on Hydrogen-Bonded Systems},
  author = {Sim, Fiona and St. Amant, Alain and Papai, Imre and Salahub, Dennis R.},
  date = {1992-05},
  journaltitle = {Journal of the American Chemical Society},
  shortjournal = {J. Am. Chem. Soc.},
  volume = {114},
  number = {11},
  pages = {4391--4400},
  issn = {0002-7863, 1520-5126},
  doi = {10.1021/ja00037a055},
  url = {https://pubs.acs.org/doi/abs/10.1021/ja00037a055},
  urldate = {2024-04-14},
  abstract = {As a test of the applicability of the density functional theory to systems containing hydrogen bonds, linear combination of Gaussian type orbitals---local density calculations have been performed on two intermolecular and two intramolecular hydrogen-bonded systems. A comparison is made of results using the local density approximation (LDA) and those including nonlocal density gradient type corrections, using two different nonlocal functionals. The calculated minimum energy structures for the water dimer and the formamide-water complex are presented. The binding energies calculated for these systems, including a treatment of the basis set superposition error using the counterpoise method, are also presented. For the water dimer, the calculated harmonic frequencies and intensities are reported, and their shifts with respect to those of the water molecule are discussed. The minimum energy structures and calculated vibrational frequencies are reported for malonaldehyde and glyoxylic acid. Overall, the LDA is found to be seriously deficient. The nonlocal corrections provide encouraging improvement.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/WPLM3U5R/sim-et-al-2002-gaussian-density-functional-calculations-on-hydrogen-bonded-systems.pdf}
}

@article{skinnerBenchmarkOxygenoxygenPairdistribution2013,
  title = {Benchmark Oxygen-Oxygen Pair-Distribution Function of Ambient Water from x-Ray Diffraction Measurements with a Wide {{Q-range}}},
  author = {Skinner, Lawrie B. and Huang, Congcong and Schlesinger, Daniel and Pettersson, Lars G. M. and Nilsson, Anders and Benmore, Chris J.},
  date = {2013-02-20},
  journaltitle = {The Journal of Chemical Physics},
  shortjournal = {The Journal of Chemical Physics},
  volume = {138},
  number = {7},
  pages = {074506},
  issn = {0021-9606},
  doi = {10.1063/1.4790861},
  url = {https://doi.org/10.1063/1.4790861},
  urldate = {2024-01-20},
  abstract = {Four recent x-ray diffraction measurements of ambient liquid water are reviewed here. Each of these measurements represents a significant development of the x-ray diffraction technique applied to the study of liquid water. Sources of uncertainty from statistical noise, Q-range, Compton scattering, and self-scattering are discussed. The oxygen-hydrogen contribution to the measured x-ray scattering pattern was subtracted using literature data to yield an experimental determination, with error bars, of the oxygen-oxygen pair-distribution function, gOO(r), which essentially describes the distribution of molecular centers. The extended Q-range and low statistical noise of these measurements has significantly reduced truncation effects and related errors in the gOO(r) functions obtained. From these measurements and error analysis, the position and height of the nearest neighbor maximum in gOO(r) were found to be 2.80(1) \AA{} and 2.57(5) respectively. Numerical data for the coherent differential x-ray scattering cross-section IX(Q), the oxygen-oxygen structure factor SOO(Q), and the derived gOO(r) are provided as benchmarks for calibrating force-fields for water.},
  file = {/home/mariano/Zotero/storage/59BTVCD4/074506_1_supplements.zip;/home/mariano/Zotero/storage/JGBQJL3E/Skinner et al. - 2013 - Benchmark oxygen-oxygen pair-distribution function.pdf;/home/mariano/Zotero/storage/VG2Y6WYT/Benchmark-oxygen-oxygen-pair-distribution-function.html}
}

@article{soperRadialDistributionFunctions2000,
  title = {The Radial Distribution Functions of Water and Ice from 220 to 673 {{K}} and at Pressures up to 400 {{MPa}}},
  author = {Soper, A. K.},
  date = {2000-08-15},
  journaltitle = {Chemical Physics},
  shortjournal = {Chemical Physics},
  volume = {258},
  number = {2},
  pages = {121--137},
  issn = {0301-0104},
  doi = {10.1016/S0301-0104(00)00179-8},
  url = {https://www.sciencedirect.com/science/article/pii/S0301010400001798},
  urldate = {2024-01-11},
  abstract = {Neutron diffraction data for water and ice in the form of OO, OH and HH partial structure factors now exist over a temperature range 220--673 K, and at pressures up to {$\sim$}400 MPa. In order for these data to be useful for comparing with different computer simulations and theories of water, it is first necessary to Fourier transform them to the corresponding site--site radial distribution functions. The process of doing this is not straightforward because of the inherent systematic uncertainties in the data, which arise primarily in the case of neutron scattering, from the inelasticity or recoil effects that can distort the experimental data. In this paper, it is shown that the empirical potential structure refinement procedure, which attempts to fit a three-dimensional ensemble of water molecules to all three partial structure factors simultaneously, leads to improved reliability in the extracted radial distribution functions. There are still some uncertainties, primarily associated with the hardness of the repulsive core of the intermolecular potential, which current data are not precise enough to resolve. The derived empirical potentials show some variability associated with particular experiments. General trends can be discerned however which indicate polarisation effects may be significant when effective intermolecular potentials are used over a wide temperature and density range.},
  file = {/home/mariano/Zotero/storage/ZEDGANMD/Soper - 2000 - The radial distribution functions of water and ice.pdf;/home/mariano/Zotero/storage/TP5MAND9/S0301010400001798.html}
}

@article{sprikInitioMolecularDynamics1996,
  title = {Ab\hphantom{,}Initio Molecular Dynamics Simulation of Liquid Water: {{Comparison}} of Three Gradient-corrected Density Functionals},
  shorttitle = {Ab\hphantom{,}Initio Molecular Dynamics Simulation of Liquid Water},
  author = {Sprik, Michiel and Hutter, J\"urg and Parrinello, Michele},
  date = {1996-07-15},
  journaltitle = {The Journal of Chemical Physics},
  shortjournal = {The Journal of Chemical Physics},
  volume = {105},
  number = {3},
  pages = {1142--1152},
  issn = {0021-9606},
  doi = {10.1063/1.471957},
  url = {https://doi.org/10.1063/1.471957},
  urldate = {2024-01-19},
  abstract = {Three frequently used gradient-corrected density functionals (B, BP, and BLYP) are applied in an ab\hphantom{,}initio molecular dynamics simulation of liquid water in order to evaluate their performance for the description of condensed aqueous systems. A comparison of structural characteristics (radial distribution functions) and dynamical properties (vibrational spectra, orientational relaxation, and self-diffusion) leads to the conclusion that hydrogen bonding is too weak in the usual local density approximation corrected for exchange only according to Becke (B), whereas adding the gradient correction for correlation according to Perdew (BP) yields effective hydrogen bonds in the liquid that are too strong. The combination of B with the semilocal correlation functional according to Lee, Yang, and Parr (BLYP) yields the best agreement with experiment. The computational method, which is the basis for the determination of (adiabatic) electronic structure in the ab\hphantom{,}initio molecular dynamics simulation, has been validated by an extensive series of test calculations for the water dimer, which will also be presented here.},
  keywords = {H2O},
  file = {/home/mariano/Zotero/storage/3EC7NTNE/Sprik et al. - 1996 - Ab initio molecular dynamics simulation of liquid .pdf;/home/mariano/Zotero/storage/WSYEQ3YU/Ab-initio-molecular-dynamics-simulation-of-liquid.html}
}

@article{stillingerWaterRevisited1980,
  title = {Water {{Revisited}}},
  author = {Stillinger, Frank H.},
  date = {1980-07-25},
  journaltitle = {Science},
  volume = {209},
  number = {4455},
  pages = {451--457},
  publisher = {American Association for the Advancement of Science},
  doi = {10.1126/science.209.4455.451},
  url = {https://www.science.org/doi/10.1126/science.209.4455.451},
  urldate = {2024-01-19},
  abstract = {Liquid water consists of a macroscopically connected, random network of hydrogen bonds, with frequent strained and broken bonds, that is continually undergoing topological reformation. Anomalous properties of water arise from the competition between relatively bulky ways of connecting molecules into local patterns characterized by strong bonds and nearly tetrahedral angles and more compact arrangements characterized by more strain and bond breakage. However, these alternatives constitute virtually a continuum of architectural possibilities rather than a discrete pair of options. The singular behavior of supercooled water near --45{$^\circ$}C and the "hydrophobic" attraction between nonpolar entities are due to the same underlying phenomenon, namely, the clumping tendency of relatively strain-free convex cages or polyhedra.},
  file = {/home/mariano/Zotero/storage/XQYRT7JV/Stillinger - 1980 - Water Revisited.pdf}
}

@article{strasslePhononDispersionIce2004,
  title = {Phonon {{Dispersion}} of {{Ice}} under {{Pressure}}},
  author = {family=Str\"assle, given=Th., given-i={{Th}} and Saitta, A. M. and Klotz, S. and Braden, M.},
  date = {2004-11-23},
  journaltitle = {Physical Review Letters},
  shortjournal = {Phys. Rev. Lett.},
  volume = {93},
  number = {22},
  pages = {225901},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevLett.93.225901},
  url = {https://link.aps.org/doi/10.1103/PhysRevLett.93.225901},
  urldate = {2024-03-14},
  abstract = {We report measurements of the phonon dispersion of ice Ih under hydrostatic pressure up to 0.5 GPa, at 140 K, using inelastic neutron scattering. They reveal a pronounced softening of various low-energy modes, in particular, those of the transverse acoustic phonon branch in the [100] direction and polarization in the hexagonal plane. We demonstrate with the aid of a lattice dynamical model that these anomalous features in the phonon dispersion are at the origin of the negative thermal expansion (NTE) coefficient in ice below 60 K. Moreover, extrapolation to higher pressures shows that the mode frequencies responsible for the NTE approach zero at {$\sim$}2.5 GPa, which explains the known pressure-induced amorphization (PIA) in ice. These results give the first clear experimental evidence that PIA in ice is due to a lattice instability, i.e., mechanical melting.},
  keywords = {Phonons},
  file = {/home/mariano/Zotero/storage/RAAD4SH4/Strässle et al. - 2004 - Phonon Dispersion of Ice under Pressure.pdf;/home/mariano/Zotero/storage/XSAJ54NR/PhysRevLett.93.html}
}

@article{togoFirstprinciplesPhononCalculations2023,
  title = {First-Principles {{Phonon Calculations}} with {{Phonopy}} and {{Phono3py}}},
  author = {Togo, Atsushi},
  date = {2023-01-15},
  journaltitle = {Journal of the Physical Society of Japan},
  shortjournal = {J. Phys. Soc. Jpn.},
  volume = {92},
  number = {1},
  pages = {012001},
  issn = {0031-9015, 1347-4073},
  doi = {10.7566/JPSJ.92.012001},
  url = {https://journals.jps.jp/doi/10.7566/JPSJ.92.012001},
  urldate = {2024-08-26},
  langid = {english},
  file = {/home/mariano/Zotero/storage/7ZZTBDEW/Togo - 2023 - First-principles Phonon Calculations with Phonopy and Phono3py.pdf}
}

@article{toriyamaHowAnalyseDensity2022,
  title = {How to Analyse a Density of States},
  author = {Toriyama, Michael Y. and Ganose, Alex M. and Dylla, Maxwell and Anand, Shashwat and Park, Junsoo and Brod, Madison K. and Munro, Jason M. and Persson, Kristin A. and Jain, Anubhav and Snyder, G. Jeffrey},
  date = {2022-05-01},
  journaltitle = {Materials Today Electronics},
  shortjournal = {Materials Today Electronics},
  volume = {1},
  pages = {100002},
  issn = {2772-9494},
  doi = {10.1016/j.mtelec.2022.100002},
  url = {https://www.sciencedirect.com/science/article/pii/S277294942200002X},
  urldate = {2024-05-03},
  abstract = {The density of states of electrons is a simple, yet highly-informative, summary of the electronic structure of a material. Here, some remarkable features of the electronic structure that are perceptible from the density of states are concisely reviewed, notably the analytical E vs. k dispersion relation near the band edges, effective mass, Van Hove singularities, and the effective dimensionality of the electrons, all of which have a strong influence on physical properties of materials. We emphasize that appropriate parameters in electronic structure calculations are necessary to obtain even a sufficient-quality density of states exhibiting fine features of the electronic structure.},
  keywords = {Density of states,Electrical transport,Electronic properties,Electronic structure},
  file = {/home/mariano/Zotero/storage/GR8TBNWB/Toriyama et al. - 2022 - How to analyse a density of states.pdf;/home/mariano/Zotero/storage/G6M7HAWK/S277294942200002X.html}
}

@article{tuckermanInitioSimulationsWater1994,
  title = {Ab Initio Simulations of Water and Water Ions},
  author = {Tuckerman, M. E. and Laasonen, K. and Sprik, M. and Parrinello, M.},
  date = {1994-06},
  journaltitle = {Journal of Physics: Condensed Matter},
  shortjournal = {J. Phys.: Condens. Matter},
  volume = {6},
  pages = {A93},
  issn = {0953-8984},
  doi = {10.1088/0953-8984/6/23A/010},
  url = {https://dx.doi.org/10.1088/0953-8984/6/23A/010},
  urldate = {2024-01-19},
  abstract = {Ab initio studies of H+ and OH- in water reveal a variety of interesting structures. In the case of the OH-, an H9O5- structure is observed in which the four hydrogen bonds with the ligands lie in a plane that also contains the oxygen atom of the anion. In the case of H+, there is strong evidence for the existence of the H9O4+ structure originally postulated by Eigen and coworkers. Proton migration in this system is relatively fast and is observed to occur via the Grotthus mechanism.},
  issue = {23A},
  langid = {english},
  file = {/home/mariano/Zotero/storage/3QPCFPBW/Tuckerman et al. - 1994 - Ab initio simulations of water and water ions.pdf}
}

@article{verletComputerExperimentsClassical1967,
  title = {Computer "{{Experiments}}" on {{Classical Fluids}}. {{I}}. {{Thermodynamical Properties}} of {{Lennard-Jones Molecules}}},
  author = {Verlet, Loup},
  date = {1967-07-05},
  journaltitle = {Physical Review},
  shortjournal = {Phys. Rev.},
  volume = {159},
  number = {1},
  pages = {98--103},
  doi = {10.1103/PhysRev.159.98},
  url = {https://link.aps.org/doi/10.1103/PhysRev.159.98},
  urldate = {2023-09-10},
  abstract = {The equation of motion of a system of 864 particles interacting through a Lennard-Jones potential has been integrated for various values of the temperature and density, relative, generally, to a fluid state. The equilibrium properties have been calculated and are shown to agree very well with the corresponding properties of argon. It is concluded that, to a good approximation, the equilibrium state of argon can be described through a two-body potential.},
  file = {/home/mariano/Zotero/storage/SI9QBEE6/Verlet - 1967 - Computer Experiments on Classical Fluids. I. The.pdf;/home/mariano/Zotero/storage/ZXS35Z4K/Verlet - 1967 - Computer Experiments on Classical Fluids. I. The.html}
}

@article{wangMixedspaceApproachFirstprinciples2010,
  title = {A Mixed-Space Approach to First-Principles Calculations of Phonon Frequencies for Polar Materials},
  author = {Wang, Y and Wang, J J and Wang, W Y and Mei, Z G and Shang, S L and Chen, L Q and Liu, Z K},
  date = {2010-05-26},
  journaltitle = {Journal of Physics: Condensed Matter},
  shortjournal = {J. Phys.: Condens. Matter},
  volume = {22},
  number = {20},
  pages = {202201},
  issn = {0953-8984, 1361-648X},
  doi = {10.1088/0953-8984/22/20/202201},
  url = {https://iopscience.iop.org/article/10.1088/0953-8984/22/20/202201},
  urldate = {2024-01-22},
  abstract = {We propose a mixed-space approach using the accurate force constants calculated by the direct approach in real space and the dipole--dipole interactions calculated by linear response theory in reciprocal space, making the accurate prediction of phonon frequencies for polar materials possible using the direct approach as well as linear response theory. As examples, by using the present approach, we predict the first-principles phonon properties of the polar materials {$\alpha$}-Al2O3, MgO, c-SiC, and h-BN, which are in excellent agreement with available experimental data.},
  langid = {english},
  file = {/home/mariano/Zotero/storage/Z32HDFLD/Wang et al. - 2010 - A mixed-space approach to first-principles calcula.pdf}
}

@online{WaterDimerSmall,
  title = {Water Dimer and Small Clusters},
  url = {https://water.lsbu.ac.uk/water/water_dimer.html},
  urldate = {2024-06-29},
  file = {/home/mariano/Zotero/storage/6TX5G2DN/water_dimer.html}
}

@article{whalleyEnergiesPhasesIce1984,
  title = {Energies of the Phases of Ice at Zero Temperature and Pressure},
  author = {Whalley, E.},
  date = {1984-11-01},
  journaltitle = {The Journal of Chemical Physics},
  shortjournal = {The Journal of Chemical Physics},
  volume = {81},
  number = {9},
  pages = {4087--4092},
  issn = {0021-9606},
  doi = {10.1063/1.448153},
  url = {https://doi.org/10.1063/1.448153},
  urldate = {2024-06-03},
  abstract = {The energies of the high-pressure phases of ice at zero temperature and pressure, relative to the energy of ice I, have been evaluated from the equilibrium pressures of the various pairs of phases extrapolated to zero temperature. The values should be useful for evaluating interaction potentials between water molecules.},
  file = {/home/mariano/Zotero/storage/NY3YA3FB/Whalley - 1984 - Energies of the phases of ice at zero temperature .pdf}
}

@online{WikiArchit_ib_enIbisco,
  title = {Wiki:Archit\_ib\_en [Ibisco {{HPC Wiki}}]},
  url = {https://ibiscohpc-wiki.scope.unina.it/wiki:archit_ib_en},
  urldate = {2024-07-12},
  file = {/home/mariano/Zotero/storage/9RJCAE8V/wikiarchit_ib_en.html}
}

@article{zenFastAccurateQuantum2018,
  title = {Fast and Accurate Quantum {{Monte Carlo}} for Molecular Crystals},
  author = {Zen, Andrea and Brandenburg, Jan Gerit and Klime\v s, Ji\v r\'i and Tkatchenko, Alexandre and Alf\`e, Dario and Michaelides, Angelos},
  date = {2018-02-20},
  journaltitle = {Proceedings of the National Academy of Sciences},
  volume = {115},
  number = {8},
  pages = {1724--1729},
  publisher = {Proceedings of the National Academy of Sciences},
  doi = {10.1073/pnas.1715434115},
  url = {https://www.pnas.org/doi/10.1073/pnas.1715434115},
  urldate = {2023-09-20},
  abstract = {Computer simulation plays a central role in modern-day materials science. The utility of a given computational approach depends largely on the balance it provides between accuracy and computational cost. Molecular crystals are a class of materials of great technological importance which are challenging for even the most sophisticated ab initio electronic structure theories to accurately describe. This is partly because they are held together by a balance of weak intermolecular forces but also because the primitive cells of molecular crystals are often substantially larger than those of atomic solids. Here, we demonstrate that diffusion quantum Monte Carlo (DMC) delivers subchemical accuracy for a diverse set of molecular crystals at a surprisingly moderate computational cost. As such, we anticipate that DMC can play an important role in understanding and predicting the properties of a large number of molecular crystals, including those built from relatively large molecules which are far beyond reach of other high-accuracy methods.},
  keywords = {electronic structure,molecular crystal,quantum Monte Carlo},
  file = {/home/mariano/Zotero/storage/5F7AVNBJ/Zen et al. - 2018 - Fast and accurate quantum Monte Carlo for molecula.pdf;/home/mariano/Zotero/storage/YHZQJAXM/2018_PNAS_Zen_SI.pdf}
}

@article{zenOptimizedStructureVibrational2012,
  title = {Optimized {{Structure}} and {{Vibrational Properties}} by {{Error Affected Potential Energy Surfaces}}},
  author = {Zen, Andrea and Zhelyazov, Delyan and Guidoni, Leonardo},
  date = {2012-11-13},
  journaltitle = {Journal of Chemical Theory and Computation},
  shortjournal = {J. Chem. Theory Comput.},
  volume = {8},
  number = {11},
  pages = {4204--4215},
  issn = {1549-9618, 1549-9626},
  doi = {10.1021/ct300576n},
  url = {https://pubs.acs.org/doi/10.1021/ct300576n},
  urldate = {2024-01-26},
  abstract = {The precise theoretical determination of the geometrical parameters of molecules at the minima of their potential energy surface and of the corresponding vibrational properties are of fundamental importance for the interpretation of vibrational spectroscopy experiments. Quantum Monte Carlo techniques are correlated electronic structure methods promising for large molecules, which are intrinsically affected by stochastic errors on both energy and force calculations, making the mentioned calculations more challenging with respect to other more traditional quantum chemistry tools. To circumvent this drawback in the present work, we formulate the general problem of evaluating the molecular equilibrium structures, the harmonic frequencies, and the anharmonic coefficients of an error affected potential energy surface. The proposed approach, based on a multidimensional fitting procedure, is illustrated together with a critical evaluation of systematic and statistical errors. We observe that the use of forces instead of energies in the fitting procedure reduces the statistical uncertainty of the vibrational parameters by 1 order of magnitude. Preliminary results based on variational Monte Carlo calculations on the water molecule demonstrate the possibility to evaluate geometrical parameters and harmonic and anharmonic coefficients at this level of theory with an affordable computational cost and a small stochastic uncertainty ({$<$}0.07\% for geometries and {$<$}0.7\% for vibrational properties).},
  langid = {english},
  file = {/home/mariano/Zotero/storage/3K8MNDUW/Zen et al. - 2012 - Optimized Structure and Vibrational Properties by .pdf}
}