

 @article{pyscf,
    author = {Sun, Qiming and Zhang, Xing and Banerjee, Samragni and Bao, Peng and Barbry, Marc and Blunt, Nick S. and Bogdanov, Nikolay A. and Booth, George H. and Chen, Jia and Cui, Zhi-Hao and Eriksen, Janus J. and Gao, Yang and Guo, Sheng and Hermann, Jan and Hermes, Matthew R. and Koh, Kevin and Koval, Peter and Lehtola, Susi and Li, Zhendong and Liu, Junzi and Mardirossian, Narbe and McClain, James D. and Motta, Mario and Mussard, Bastien and Pham, Hung Q. and Pulkin, Artem and Purwanto, Wirawan and Robinson, Paul J. and Ronca, Enrico and Sayfutyarova, Elvira R. and Scheurer, Maximilian and Schurkus, Henry F. and Smith, James E. T. and Sun, Chong and Sun, Shi-Ning and Upadhyay, Shiv and Wagner, Lucas K. and Wang, Xiao and White, Alec and Whitfield, James Daniel and Williamson, Mark J. and Wouters, Sebastian and Yang, Jun and Yu, Jason M. and Zhu, Tianyu and Berkelbach, Timothy C. and Sharma, Sandeep and Sokolov, Alexander Yu. and Chan, Garnet Kin-Lic},
    title = "{Recent developments in the PySCF program package}",
    journal = {The Journal of Chemical Physics},
    volume = {153},
    number = {2},
    pages = {024109},
    year = {2020},
    month = {07},
    abstract = "{PySCF is a Python-based general-purpose electronic structure platform that supports first-principles simulations of molecules and solids as well as accelerates the development of new methodology and complex computational workflows. This paper explains the design and philosophy behind PySCF that enables it to meet these twin objectives. With several case studies, we show how users can easily implement their own methods using PySCF as a development environment. We then summarize the capabilities of PySCF for molecular and solid-state simulations. Finally, we describe the growing ecosystem of projects that use PySCF across the domains of quantum chemistry, materials science, machine learning, and quantum information science.}",
    issn = {0021-9606},
    doi = {10.1063/5.0006074},
    url = {https://doi.org/10.1063/5.0006074},
    eprint = {https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/5.0006074/16722275/024109\_1\_online.pdf},
}


@article{Lee2019,
author = {Lee, Changyeon and Lee, Seungjin and Kim, Geon-U and Lee, Wonho and Kim, Bumjoon J.},
title = {Recent Advances, Design Guidelines, and Prospects of All-Polymer Solar Cells},
journal = {Chemical Reviews},
volume = {119},
number = {13},
pages = {8028-8086},
year = {2019},
doi = {10.1021/acs.chemrev.9b00044},
    note ={PMID: 31181904},
URL = {https://doi.org/10.1021/acs.chemrev.9b00044},
eprint = {https://doi.org/10.1021/acs.chemrev.9b00044}
}

@article{Svaneborg2023,
    author = {Svaneborg, Carsten and Everaers, Ralf},
    title = "{Multiscale equilibration of highly entangled isotropic model polymer melts}",
    journal = {The Journal of Chemical Physics},
    volume = {158},
    number = {5},
    pages = {054903},
    year = {2023},
    month = {02},
    abstract = "{We present a computationally efficient multiscale method for preparing equilibrated, isotropic long-chain model polymer melts. As an application, we generate Kremer–Grest melts of 1000 chains with 200 entanglements and 25 000–2000 beads/chain, which cover the experimentally relevant bending rigidities up to and beyond the limit of the isotropic–nematic transition. In the first step, we employ Monte Carlo simulations of a lattice model to equilibrate the large-scale chain structure above the tube scale while ensuring a spatially homogeneous density distribution. We then use theoretical insight from a constrained mode tube model to introduce the bead degrees of freedom together with random walk conformational statistics all the way down to the Kuhn scale of the chains. This is followed by a sequence of simulations with carefully parameterized force-capped bead–spring models, which slowly introduce the local bead packing while reproducing the larger-scale chain statistics of the target Kremer–Grest system at all levels of force-capping. Finally, we can switch to the full Kremer–Grest model without perturbing the structure. The resulting chain statistics is in excellent agreement with literature results on all length scales accessible in brute-force simulations of shorter chains.}",
    issn = {0021-9606},
    doi = {10.1063/5.0123431},
    url = {https://doi.org/10.1063/5.0123431},
    eprint = {https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/5.0123431/16706372/054903\_1\_online.pdf},
}


@article{Rudzinski_2021,
  doi = {10.1088/1361-648X/abe6e1},
  url = {https://dx.doi.org/10.1088/1361-648X/abe6e1},
  year = {2021},
  month = {may},
  publisher = {IOP Publishing},
  volume = {33},
  number = {22},
  pages = {224001},
  author = {Joseph F Rudzinski and Sebastian Kloth and Svenja Wörner and Tamisra Pal and Kurt Kremer and Tristan Bereau and Michael Vogel},
  title = {Dynamical properties across different coarse-grained models for ionic liquids},
  journal = {Journal of Physics: Condensed Matter}
}




@Inbook{engl2000regularization,
  title={Regularization of Inverse Problems},
  author={Engl, Heinz W. and Ramlau, Ronny},
  editor={Engquist, Bj{\"o}rn},
  bookTitle={Encyclopedia of Applied and Computational Mathematics},
  year={2015},
  publisher={Springer Berlin Heidelberg},
  address={Berlin, Heidelberg},
  pages={1233--1241},
  isbn={978-3-540-70529-1},
  doi={10.1007/978-3-540-70529-1_52},
  url={https://doi.org/10.1007/978-3-540-70529-1_52}
}


@article{turbomole,
    author = {Balasubramani, Sree Ganesh and Chen, Guo P. and Coriani, Sonia and Diedenhofen, Michael and Frank, Marius S. and Franzke, Yannick J. and Furche, Filipp and Grotjahn, Robin and Harding, Michael E. and Hättig, Christof and Hellweg, Arnim and Helmich-Paris, Benjamin and Holzer, Christof and Huniar, Uwe and Kaupp, Martin and Marefat Khah, Alireza and Karbalaei Khani, Sarah and Müller, Thomas and Mack, Fabian and Nguyen, Brian D. and Parker, Shane M. and Perlt, Eva and Rappoport, Dmitrij and Reiter, Kevin and Roy, Saswata and Rückert, Matthias and Schmitz, Gunnar and Sierka, Marek and Tapavicza, Enrico and Tew, David P. and van Wüllen, Christoph and Voora, Vamsee K. and Weigend, Florian and Wodyński, Artur and Yu, Jason M.},
    title = "{TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations}",
    journal = {The Journal of Chemical Physics},
    volume = {152},
    number = {18},
    pages = {184107},
    year = {2020},
    month = {05},
    abstract = "{TURBOMOLE is a collaborative, multi-national software development project aiming to provide highly efficient and stable computational tools for quantum chemical simulations of molecules, clusters, periodic systems, and solutions. The TURBOMOLE software suite is optimized for widely available, inexpensive, and resource-efficient hardware such as multi-core workstations and small computer clusters. TURBOMOLE specializes in electronic structure methods with outstanding accuracy–cost ratio, such as density functional theory including local hybrids and the random phase approximation (RPA), GW-Bethe–Salpeter methods, second-order Møller–Plesset theory, and explicitly correlated coupled-cluster methods. TURBOMOLE is based on Gaussian basis sets and has been pivotal for the development of many fast and low-scaling algorithms in the past three decades, such as integral-direct methods, fast multipole methods, the resolution-of-the-identity approximation, imaginary frequency integration, Laplace transform, and pair natural orbital methods. This review focuses on recent additions to TURBOMOLE’s functionality, including excited-state methods, RPA and Green’s function methods, relativistic approaches, high-order molecular properties, solvation effects, and periodic systems. A variety of illustrative applications along with accuracy and timing data are discussed. Moreover, available interfaces to users as well as other software are summarized. TURBOMOLE’s current licensing, distribution, and support model are discussed, and an overview of TURBOMOLE’s development workflow is provided. Challenges such as communication and outreach, software infrastructure, and funding are highlighted.}",
    issn = {0021-9606},
    doi = {10.1063/5.0004635},
    url = {https://doi.org/10.1063/5.0004635},
    eprint = {https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/5.0004635/16685296/184107\_1\_online.pdf},
}





@Article{ADF2001,
  Title                    = {Chemistry with ADF},
  Author                   = {te Velde, G. and Bickelhaupt, F. M. and Baerends, E. J. and Fonseca Guerra, C. and van Gisbergen, S. J. A. and Snijders, J. G. and Ziegler, T.},
  Journal                  = {J. Comput. Chem.},
  Year                     = {2001},
  Number                   = {9},
  Pages                    = {931--967},
  Volume                   = {22},
  Doi                      = {10.1002/jcc.1056},
  ISSN                     = {1096-987X},
  Publisher                = {John Wiley \& Sons, Inc.},
  Url                      = {http://dx.doi.org/10.1002/jcc.1056}
}

@article{molgw,
title = {molgw 1: Many-body perturbation theory software for atoms, molecules, and clusters},
journal = {Computer Physics Communications},
volume = {208},
pages = {149-161},
year = {2016},
issn = {0010-4655},
doi = {10.1016/j.cpc.2016.06.019},
url = {https://www.sciencedirect.com/science/article/pii/S0010465516301990},
author = {Fabien Bruneval and Tonatiuh Rangel and Samia M. Hamed and Meiyue Shao and Chao Yang and Jeffrey B. Neaton},
keywords = {Electronic structure of molecules, Many-body perturbation theory,  approximation, Bethe–Salpeter equation},
abstract = {We summarize the molgw code that implements density-functional theory and many-body perturbation theory in a Gaussian basis set. The code is dedicated to the calculation of the many-body self-energy within the GW approximation and the solution of the Bethe–Salpeter equation. These two types of calculations allow the user to evaluate physical quantities that can be compared to spectroscopic experiments. Quasiparticle energies, obtained through the calculation of the GW self-energy, can be compared to photoemission or transport experiments, and neutral excitation energies and oscillator strengths, obtained via solution of the Bethe–Salpeter equation, are measurable by optical absorption. The implementation choices outlined here have aimed at the accuracy and robustness of calculated quantities with respect to measurements. Furthermore, the algorithms implemented in molgw allow users to consider molecules or clusters containing up to 100 atoms with rather accurate basis sets, and to choose whether or not to apply the resolution-of-the-identity approximation. Finally, we demonstrate the parallelization efficacy of the molgw code over several hundreds of processors. Program title: MOLGW Catalogue identifier: AFAW_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AFAW_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU GPL v3 No. of lines in distributed program, including test data, etc.: 167871 No. of bytes in distributed program, including test data, etc.: 1309269 Distribution format: tar.gz Programming language: Fortran 2003 with a few C subroutines, Python scripts. Classification: 7.3, 16.6, 16.10. External routines: libint [2], libxc [3], SCALAPACK [4] (optional) Nature of problem: Prediction of the electronic structure of atoms, molecules, clusters with a particular interest in their spectroscopic features, such as quasiparticle energies and optical spectra. Solution method: Using the GW approximation to many-body perturbation theory, MOLGW calculates total-energies, quasiparticle energies, and optical excitations. Additional comments: Python3 is required to run the test suite provided. Running time: From 30 s to a few hours References: [1]http://www.gnu.org/copyleft/gpl.txt[2]https://github.com/evaleev/libint[3]http://www.tddft.org/programs/octopus/wiki/index.php/Libxc[4]http://www.netlib.org/scalapack}
}




@article{manby2012simple,
  title={A Simple, Exact Density-Functional-Theory Embedding Scheme},
  author={Manby, F. R. and Stella, M. and Goodpaster, J. D. and Miller, T. F.},
  journal={J. Chem. Theory Comput.},
  year={2012},
  volume={8},
  pages={2564--2568},
  doi={10.1021/ct300544e}
}

@inbook{intelMKL,
	author="Wang, Endong and Zhang, Qing and Shen, Bo and Zhang, Guangyong and Lu, Xiaowei and Wu, Qing and Wang, Yajuan",
	title="Intel Math Kernel Library",
	bookTitle="High-Performance Computing on the Intel® Xeon Phi{\texttrademark}: How to Fully Exploit MIC Architectures",
	year="2014",
	publisher="Springer International Publishing",
	address="Cham",
	pages="167--188",
	isbn="978-3-319-06486-4",
	doi="10.1007/978-3-319-06486-4_7",
	url="https://doi.org/10.1007/978-3-319-06486-4_7"
}

@article{Shaw2017,
author = {Shaw, Robert A. and Hill, J. Grant},
doi = {10.1063/1.4986887},
issn = {0021-9606},
journal = {The Journal of Chemical Physics},
month = {aug},
number = {7},
pages = {074108},
title = {{Prescreening and efficiency in the evaluation of integrals over ab initio effective core potentials}},
url = {http://aip.scitation.org/doi/10.1063/1.4986887},
volume = {147},
year = {2017}
}

@Misc{Libint2,
  author = "E.~F.~Valeev",
  title = "Libint: A library for the evaluation of molecular integrals of many-body operators over Gaussian functions",
  howpublished = "http://libint.valeyev.net/",
  doi = {10.5281/zenodo.10780719},
  note = "version 2.9.0",
  year =         2024
}

@article{Lehtola2018,
    title = {{Recent developments in LIBXC — A comprehensive library of functionals for density functional theory}},
    year = {2018},
    journal = {SoftwareX},
    author = {Lehtola, Susi and Steigemann, Conrad and Oliveira, Micael J.T. and Marques, Miguel A.L.},
    month = {1},
    pages = {1--5},
    volume = {7},
    publisher = {Elsevier},
    url = {https://www.sciencedirect.com/science/article/pii/S2352711017300602?via%3Dihub},
    doi = {10.1016/j.softx.2017.11.002},
    issn = {23527110},
    keywords = {Density functional theory, Exchange–correlation, Generalized gradient approximations, Local density approximations, meta-GGA approximations}
}

@misc{eigenweb,
    title = {{Eigen v3}},
    year = {2010},
    author = {Guennebaud, Gaël and Jacob, Benoît and {others}},
    howpublished = {http://eigen.tuxfamily.org}
}

@article{stone_distributed_2005,
  title = {Distributed {{Multipole Analysis}}: {{Stability}} for {{Large Basis Sets}}},
  shorttitle = {Distributed {{Multipole Analysis}}},
  author = {Stone, Anthony J.},
  year = {2005},
  month = nov,
  journal = {Journal of Chemical Theory and Computation},
  volume = {1},
  number = {6},
  pages = {1128--1132},
  issn = {1549-9618},
  doi = {10.1021/ct050190+},
  urldate = {2021-05-04},
  abstract = {The distributed multipole analysis procedure, for describing a molecular charge distribution in terms of multipole moments on the individual atoms (or other sites) of the molecule, is not stable with respect to a change of basis set, and indeed, the calculated moments change substantially and unpredictably when the basis set is improved, even though the resulting electrostatic potential changes very little. A revised procedure is proposed, which uses grid-based quadrature for partitioning the contributions to the charge density from diffuse basis functions. The resulting procedure is very stable, and the calculated multipole moments converge rapidly to stable values as the size of the basis is increased.}
}

@article{neeseORCAProgramSystem2012,
  title = {The {{ORCA}} Program System},
  author = {Neese, Frank},
  year = {2012},
  journal = {WIREs Computational Molecular Science},
  volume = {2},
  number = {1},
  pages = {73--78},
  issn = {1759-0884},
  doi = {10.1002/wcms.81},
  urldate = {2022-01-05},
  abstract = {ORCA is a general-purpose quantum chemistry program package that features virtually all modern electronic structure methods (density functional theory, many-body perturbation and coupled cluster theories, and multireference and semiempirical methods). It is designed with the aim of generality, extendibility, efficiency, and user friendliness. Its main field of application is larger molecules, transition metal complexes, and their spectroscopic properties. ORCA uses standard Gaussian basis functions and is fully parallelized. The article provides an overview of its current possibilities and documents its efficiency. {\copyright} 2011 John Wiley \& Sons, Ltd. This article is categorized under: Software {$>$} Quantum Chemistry},
  langid = {english},
  file = {/Users/bbaumeie/Zotero/storage/HW8TH5XZ/Neese - 2012 - The ORCA program system.pdf;/Users/bbaumeie/Zotero/storage/NWEZNM5Z/wcms.html}
}

@article{lyubartsev_calculation_1995,
	title = {Calculation of effective interaction potentials from radial distribution functions: {A} reverse {Monte} {Carlo} approach},
	volume = {52},
	issn = {1063-651X, 1095-3787},
	shorttitle = {Calculation of effective interaction potentials from radial distribution functions},
	url = {https://link.aps.org/doi/10.1103/PhysRevE.52.3730},
	doi = {10.1103/PhysRevE.52.3730},
	language = {en},
	number = {4},
	urldate = {2017-08-15},
	journal = {Physical Review E},
	author = {Lyubartsev, Alexander P. and Laaksonen, Aatto},
	month = oct,
	year = {1995},
	pages = {3730--3737}
}
@article{rosenberger_comparison_2016,
	title = {Comparison of iterative inverse coarse-graining methods},
	volume = {225},
	issn = {1951-6355, 1951-6401},
	url = {http://link.springer.com/10.1140/epjst/e2016-60120-1},
	doi = {10.1140/epjst/e2016-60120-1},
	language = {en},
	number = {8-9},
	urldate = {2017-08-15},
	journal = {The European Physical Journal Special Topics},
	author = {Rosenberger, David and Hanke, Martin and van der Vegt, Nico F.A.},
	month = oct,
	year = {2016},
	pages = {1323--1345}
}
@article{murtola_coarse-grained_2007,
	title = {Coarse-grained model for phospholipid/cholesterol bilayer employing inverse {Monte} {Carlo} with thermodynamic constraints},
	volume = {126},
	issn = {0021-9606, 1089-7690},
	url = {http://aip.scitation.org/doi/10.1063/1.2646614},
	doi = {10.1063/1.2646614},
	language = {en},
	number = {7},
	urldate = {2017-08-15},
	journal = {The Journal of Chemical Physics},
	author = {Murtola, Teemu and Falck, Emma and Karttunen, Mikko and Vattulainen, Ilpo},
	month = feb,
	year = {2007},
	pages = {075101}
}
@article{lyubartsev_systematic_2010,
	title = {Systematic coarse-graining of molecular models by the {Newton} inversion method},
	volume = {144},
	issn = {1359-6640, 1364-5498},
	url = {http://xlink.rsc.org/?DOI=B901511F},
	doi = {10.1039/B901511F},
	language = {en},
	urldate = {2024-02-20},
	journal = {Faraday Discuss.},
	author = {Lyubartsev, Alexander P. and Mirzoev, Alexander and Chen, LiJun and Laaksonen, Aatto},
	year = {2010},
	pages = {43--56},
	file = {Eingereichte Version:/Users/davidrosenberger/Zotero/storage/ZXJ4DZPK/Lyubartsev et al. - 2010 - Systematic coarse-graining of molecular models by .pdf:application/pdf},
}

@article{toth_iterative_2003,
	title = {An iterative scheme to derive pair potentials from structure factors and its application to liquid mercury},
	volume = {118},
	issn = {0021-9606, 1089-7690},
	url = {https://pubs.aip.org/jcp/article/118/9/3949/535605/An-iterative-scheme-to-derive-pair-potentials-from},
	doi = {10.1063/1.1543142},
	language = {en},
	number = {9},
	urldate = {2024-02-20},
	journal = {The Journal of Chemical Physics},
	author = {Tóth, Gergely},
	month = mar,
	year = {2003},
}
@article{bernhardt_stability_2023,
	title = {Stability, Speed, and Constraints for Structural Coarse-Graining in {VOTCA}},
	volume = {19},
	issn = {1549-9618, 1549-9626},
	url = {https://pubs.acs.org/doi/10.1021/acs.jctc.2c00665},
	doi = {10.1021/acs.jctc.2c00665},
	pages = {580--595},
	number = {2},
	journaltitle = {Journal of Chemical Theory and Computation},
	shortjournal = {J. Chem. Theory Comput.},
	author = {Bernhardt, Marvin P. and Hanke, Martin and Van Der Vegt, Nico F.A.},
	urldate = {2024-02-27},
	date = {2023-01-24},
	langid = {english},
}

@article{bernhardt_iterative_2021,
	title = {Iterative integral equation methods for structural coarse-graining},
	volume = {154},
	issn = {0021-9606},
	url = {https://aip.scitation.org/doi/10.1063/5.0038633},
	doi = {10.1063/5.0038633},
	pages = {084118},
	number = {8},
	journaltitle = {The Journal of Chemical Physics},
	shortjournal = {J. Chem. Phys.},
	author = {Bernhardt, Marvin P. and Hanke, Martin and van der Vegt, Nico F. A.},
	urldate = {2022-08-30},
	date = {2021-02-28},
	note = {tex.ids= {bernhardtIterativeIntegralEquation}
publisher: American Institute of Physics},
}

@article{delbaryGeneralizedNewtonIteration2020,
	title = {A generalized Newton iteration for computing the solution of the inverse Henderson problem},
	volume = {28},
	issn = {1741-5977},
	url = {https://doi.org/10.1080/17415977.2019.1710504},
	doi = {10.1080/17415977.2019.1710504},
	pages = {1166--1190},
	number = {8},
	journaltitle = {Inverse Problems in Science and Engineering},
	shortjournal = {Inverse Probl. Sci. Eng.},
	author = {Delbary, Fabrice and Hanke, Martin and Ivanizki, Dmitry},
	urldate = {2020-10-29},
	date = {2020-08-02},
	note = {\_eprint: https://doi.org/10.1080/17415977.2019.1710504
tex.ids: {delbaryGeneralizedNewtonIteration}2020
publisher: Taylor \& Francis},
	keywords = {65Z05, 82B21, Coarse-graining, Inverse Monte Carlo, Iterative Boltzmann Inversion, effective potential, radial distribution function},
}

@misc{pybind11,
   author = {Wenzel Jakob and Jason Rhinelander and Dean Moldovan},
   year = {2017},
   note = {https://github.com/pybind/pybind11},
   title = {pybind11 -- Seamless operability between C++11 and Python},
   doi = {10.5281/zenodo.5807779}
}

@article{ase,
  author={Ask Hjorth Larsen and Jens Jørgen Mortensen and Jakob Blomqvist and Ivano E Castelli and Rune Christensen and Marcin
Dułak and Jesper Friis and Michael N Groves and Bjørk Hammer and Cory Hargus and Eric D Hermes and Paul C Jennings and Peter
Bjerre Jensen and James Kermode and John R Kitchin and Esben Leonhard Kolsbjerg and Joseph Kubal and Kristen
Kaasbjerg and Steen Lysgaard and Jón Bergmann Maronsson and Tristan Maxson and Thomas Olsen and Lars Pastewka and Andrew
Peterson and Carsten Rostgaard and Jakob Schiøtz and Ole Schütt and Mikkel Strange and Kristian S Thygesen and Tejs
Vegge and Lasse Vilhelmsen and Michael Walter and Zhenhua Zeng and Karsten W Jacobsen},
  title={The atomic simulation environment—a Python library for working with atoms},
  journal={Journal of Physics: Condensed Matter},
  volume={29},
  number={27},
  pages={273002},
  url={http://stacks.iop.org/0953-8984/29/i=27/a=273002},
  doi={10.1088/1361-648X/aa680e},
  year={2017},
  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.}
}

@article{debuyl2014h5md,
	title = {H5MD: A structured, efficient, and portable file format for molecular data},
	journal = {Computer Physics Communications},
	volume = {185},
	number = {6},
	pages = {1546-1553},
	year = {2014},
	issn = {0010-4655},
	doi = {10.1016/j.cpc.2014.01.018},
	url = {https://www.sciencedirect.com/science/article/pii/S0010465514000447},
	author = {Pierre {de Buyl} and Peter H. Colberg and Felix Höfling},
	keywords = {Molecular simulation, HDF5},
}

@inbook{hdf5,
	author="Koranne, Sandeep",
	title="Hierarchical Data Format 5 : HDF5",
	bookTitle="Handbook of Open Source Tools",
	year="2011",
	publisher="Springer US",
	address="Boston, MA",
	pages="191--200",
	isbn="978-1-4419-7719-9",
	doi="10.1007/978-1-4419-7719-9_10",
	url="https://doi.org/10.1007/978-1-4419-7719-9_10"
}

@article{bocs,
	author = {Dunn, Nicholas J. H. and Lebold, Kathryn M. and DeLyser, Michael R. and Rudzinski, Joseph F. and Noid, W.G.},
	title = {BOCS: Bottom-up Open-source Coarse-graining Software},
	journal = {The Journal of Physical Chemistry B},
	volume = {122},
	number = {13},
	pages = {3363-3377},
	year = {2018},
	doi = {10.1021/acs.jpcb.7b09993},
	note ={PMID: 29227668},
	URL = { https://doi.org/10.1021/acs.jpcb.7b09993 },
	eprint = { https://doi.org/10.1021/acs.jpcb.7b09993 }
}

@article{deepcg,
    author = {Zhang, Linfeng and Han, Jiequn and Wang, Han and Car, Roberto and E, Weinan},
    title = "{DeePCG: Constructing coarse-grained models via deep neural networks}",
    journal = {The Journal of Chemical Physics},
    volume = {149},
    number = {3},
    pages = {034101},
    year = {2018},
    month = {07},
    issn = {0021-9606},
    doi = {10.1063/1.5027645},
    url = {https://doi.org/10.1063/1.5027645},
    eprint = {https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/1.5027645/15545672/034101\_1\_online.pdf},
}

@article{ibisco,
	author = {Karimi-Varzaneh, Hossein Ali and Qian, Hu-Jun and Chen, Xiaoyu and Carbone, Paola and Müller-Plathe, Florian},
	title = {IBIsCO: A molecular dynamics simulation package for coarse-grained simulation},
	journal = {Journal of Computational Chemistry},
	volume = {32},
	number = {7},
	pages = {1475-1487},
	keywords = {molecular dynamics simulation package, coarse-graining simulation, iterative Boltzmann inversion method},
	doi = {10.1002/jcc.21717},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.21717},
	eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.21717},
	year = {2011}
}

@article{magic,
	author = {Mirzoev, Alexander and Lyubartsev, Alexander P.},
	title = {MagiC: Software Package for Multiscale Modeling},
	journal = {Journal of Chemical Theory and Computation},
	volume = {9},
	number = {3},
	pages = {1512-1520},
	year = {2013},
	doi = {10.1021/ct301019v},
	note ={PMID: 26587613},
	URL = { https://doi.org/10.1021/ct301019v },
	eprint = { https://doi.org/10.1021/ct301019v }
}

@article{openmscg,
	author = {Peng, Yuxing and Pak, Alexander J. and Durumeric, Aleksander E. P. and Sahrmann, Patrick G. and Mani, Sriramvignesh and Jin, Jaehyeok and Loose, Timothy D. and Beiter, Jeriann and Voth, Gregory A.},
	title = {OpenMSCG: A Software Tool for Bottom-Up Coarse-Graining},
	journal = {The Journal of Physical Chemistry B},
	volume = {127},
	number = {40},
	pages = {8537-8550},
	year = {2023},
	doi = {10.1021/acs.jpcb.3c04473},
	note ={PMID: 37791670},
	URL = { https://doi.org/10.1021/acs.jpcb.3c04473 },
	eprint = { https://doi.org/10.1021/acs.jpcb.3c04473 }
}


@software{mpip-votca,
	title = {MPI-P Fork of VOTCA},
        author = {Andrienko, Denis and Scherer, Christoph and Stanisic, Luka and {others}},
        version = {2023.1},
        date = {2023-12-07},
	url = {https://gitlab.mpcdf.mpg.de/votca/votca}
}

@article{mlpot,
	author = {Scherer, Christoph and Scheid, René and Andrienko, Denis and Bereau, Tristan},
	title = {Kernel-Based Machine Learning for Efficient Simulations of Molecular Liquids},
	journal = {Journal of Chemical Theory and Computation},
	volume = {16},
	number = {5},
	pages = {3194-3204},
	year = {2020},
	doi = {10.1021/acs.jctc.9b01256},
	note ={PMID: 32282206},
	URL = { https://doi.org/10.1021/acs.jctc.9b01256 },
	eprint = { https://doi.org/10.1021/acs.jctc.9b01256 }
}

@article{kokkos,
  author={Trott, Christian R. and Lebrun-Grandié, Damien and Arndt, Daniel and Ciesko, Jan and Dang, Vinh and Ellingwood, Nathan and Gayatri, Rahulkumar and Harvey, Evan and Hollman, Daisy S. and Ibanez, Dan and Liber, Nevin and Madsen, Jonathan and Miles, Jeff and Poliakoff, David and Powell, Amy and Rajamanickam, Sivasankaran and Simberg, Mikael and Sunderland, Dan and Turcksin, Bruno and Wilke, Jeremiah},
  journal={IEEE Transactions on Parallel and Distributed Systems},
  title={Kokkos 3: Programming Model Extensions for the Exascale Era},
  year={2022},
  volume={33},
  number={4},
  pages={805-817},
  doi={10.1109/TPDS.2021.3097283}
}

@article{cabana,
	doi = {10.21105/joss.04115},
	url = {https://doi.org/10.21105/joss.04115},
	year = {2022},
	publisher = {The Open Journal},
	volume = {7},
	number = {72},
	pages = {4115},
	author = {Stuart Slattery and Samuel Temple Reeve and Christoph Junghans and Damien Lebrun-Grandié and Robert Bird and Guangye Chen and Shane Fogerty and Yuxing Qiu and Stephan Schulz and Aaron Scheinberg and Austin Isner and Kwitae Chong and Stan Moore and Timothy Germann and James Belak and Susan Mniszewski},
	title = {Cabana: A Performance Portable Library for Particle-Based Simulations}, journal = {Journal of Open Source Software}
}

@article{LAMMPS,
  author = "A. P. Thompson and H. M. Aktulga and R. Berger and 
     D. S. Bolintineanu and W. M. Brown and P. S. Crozier and
     P. J. in 't Veld and A. Kohlmeyer and S. G. Moore and T. D. Nguyen and
     R. Shan and M. J. Stevens and J. Tranchida and C. Trott and S. J. Plimpton",
  title = "{LAMMPS} - a flexible simulation tool for
     particle-based materials modeling at the 
     atomic, meso, and continuum scales",
  journal = "Comp. Phys. Comm.",
  volume =  "271",
  pages =   "108171",
  year =    "2022",
  doi = "10.1016/j.cpc.2021.108171"
} 

@article{GUZMAN201966,
title = {ESPResSo++ 2.0: Advanced methods for multiscale molecular simulation},
journal = {Computer Physics Communications},
volume = {238},
pages = {66-76},
year = {2019},
issn = {0010-4655},
doi = {10.1016/j.cpc.2018.12.017},
url = {https://www.sciencedirect.com/science/article/pii/S0010465518304399},
author = {Horacio V. Guzman and Nikita Tretyakov and Hideki Kobayashi and Aoife C. Fogarty and Karsten Kreis and Jakub Krajniak and Christoph Junghans and Kurt Kremer and Torsten Stuehn},
}


@article{weik2019espresso,
  title={ESPResSo 4.0--an extensible software package for simulating soft matter systems},
  author={Weik, Florian and Weeber, Rudolf and Szuttor, Kai and Breitsprecher, Konrad and de Graaf, Joost and Kuron, Michael and Landsgesell, Jonas and Menke, Henri and Sean, David and Holm, Christian},
  journal={The European Physical Journal Special Topics},
  volume={227},
  pages={1789--1816},
  year={2019},
  publisher={Springer},
  doi={10.1140/epjst/e2019-800186-9}
}
