pyMolDyn: Identification, structure, and properties of cavities/vacancies in condensed matter and molecules

pyMolDyn is an interactive viewer of atomic systems defined in a unit cell and is particularly useful for crystalline and amorphous materials. It identifies and visualizes cavities (vacancies, voids) in simulation cells corresponding to all seven 3D Bravais lattices, makes no assumptions about cavit...

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Vydané v:	Journal of computational chemistry Ročník 38; číslo 6; s. 389 - 394
Hlavní autori:	Heimbach, Ingo, Rhiem, Florian, Beule, Fabian, Knodt, David, Heinen, Josef, Jones, Robert O.
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	United States Wiley Subscription Services, Inc 05.03.2017
Predmet:	Amorphous materials and surface area Anisotropy Asphericity Atomic structure cavity shape Chemical bonds Computer simulation Condensed matter physics Crystal structure Crystals Distribution functions Exports High resolution Holes Interactive systems Lattice vacancies Lattices marching cubes Marching cubes algorithms Mathematical analysis Molecular structure Molecules Python Routines split and merge Unit cell Visualization Voids volume volume and surface area marching cubes split and merge cavity shape Python
ISSN:	0192-8651, 1096-987X, 1096-987X
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Abstract	pyMolDyn is an interactive viewer of atomic systems defined in a unit cell and is particularly useful for crystalline and amorphous materials. It identifies and visualizes cavities (vacancies, voids) in simulation cells corresponding to all seven 3D Bravais lattices, makes no assumptions about cavity shapes, allows for atoms of different size, and locates the cavity centers (the centers of the largest spheres not including an atom center). We define three types of cavity and develop a method based on the split and merge algorithm to calculate all three. The visualization of the cavities uses the marching cubes algorithm. The program allows one to calculate and export pair distribution functions (between atoms and/or cavities), as well as bonding and dihedral angles, cavity volumes and surface areas, and measures of cavity shapes, including asphericity, acylindricity, and relative shape anisotropy. The open source Python program is based on GR framework and GR3 routines and can be used to generate high resolution graphics and videos. © 2016 Wiley Periodicals, Inc. Empty regions (vacancies, cavities, voids) of, for example, a disordered or crystalline material or a molecule, can influence or even dominate its properties. It is, however, difficult to determine—or even define—such empty regions. pyMolDyn is a Python program that calculates and visualizes such regions (for several definitions) and determines important properties, including the cavity centers, volumes, and surface areas, as well as several shape parameters.
AbstractList	pyMolDyn is an interactive viewer of atomic systems defined in a unit cell and is particularly useful for crystalline and amorphous materials. It identifies and visualizes cavities (vacancies, voids) in simulation cells corresponding to all seven 3D Bravais lattices, makes no assumptions about cavity shapes, allows for atoms of different size, and locates the cavity centers (the centers of the largest spheres not including an atom center). We define three types of cavity and develop a method based on the split and merge algorithm to calculate all three. The visualization of the cavities uses the marching cubes algorithm. The program allows one to calculate and export pair distribution functions (between atoms and/or cavities), as well as bonding and dihedral angles, cavity volumes and surface areas, and measures of cavity shapes, including asphericity, acylindricity, and relative shape anisotropy. The open source Python program is based on GR framework and GR3 routines and can be used to generate high resolution graphics and videos. pyMolDyn is an interactive viewer of atomic systems defined in a unit cell and is particularly useful for crystalline and amorphous materials. It identifies and visualizes cavities (vacancies, voids) in simulation cells corresponding to all seven 3D Bravais lattices, makes no assumptions about cavity shapes, allows for atoms of different size, and locates the cavity centers (the centers of the largest spheres not including an atom center). We define three types of cavity and develop a method based on the split and merge algorithm to calculate all three. The visualization of the cavities uses the marching cubes algorithm. The program allows one to calculate and export pair distribution functions (between atoms and/or cavities), as well as bonding and dihedral angles, cavity volumes and surface areas, and measures of cavity shapes, including asphericity, acylindricity, and relative shape anisotropy. The open source Python program is based on GR framework and GR3 routines and can be used to generate high resolution graphics and videos. © 2016 Wiley Periodicals, Inc.pyMolDyn is an interactive viewer of atomic systems defined in a unit cell and is particularly useful for crystalline and amorphous materials. It identifies and visualizes cavities (vacancies, voids) in simulation cells corresponding to all seven 3D Bravais lattices, makes no assumptions about cavity shapes, allows for atoms of different size, and locates the cavity centers (the centers of the largest spheres not including an atom center). We define three types of cavity and develop a method based on the split and merge algorithm to calculate all three. The visualization of the cavities uses the marching cubes algorithm. The program allows one to calculate and export pair distribution functions (between atoms and/or cavities), as well as bonding and dihedral angles, cavity volumes and surface areas, and measures of cavity shapes, including asphericity, acylindricity, and relative shape anisotropy. The open source Python program is based on GR framework and GR3 routines and can be used to generate high resolution graphics and videos. © 2016 Wiley Periodicals, Inc. pyMolDyn is an interactive viewer of atomic systems defined in a unit cell and is particularly useful for crystalline and amorphous materials. It identifies and visualizes cavities (vacancies, voids) in simulation cells corresponding to all seven 3D Bravais lattices, makes no assumptions about cavity shapes, allows for atoms of different size, and locates the cavity centers (the centers of the largest spheres not including an atom center). We define three types of cavity and develop a method based on the split and merge algorithm to calculate all three. The visualization of the cavities uses the marching cubes algorithm. The program allows one to calculate and export pair distribution functions (between atoms and/or cavities), as well as bonding and dihedral angles, cavity volumes and surface areas, and measures of cavity shapes, including asphericity, acylindricity, and relative shape anisotropy. The open source Python program is based on GR framework and GR3 routines and can be used to generate high resolution graphics and videos. © 2016 Wiley Periodicals, Inc. pyMolDyn is an interactive viewer of atomic systems defined in a unit cell and is particularly useful for crystalline and amorphous materials. It identifies and visualizes cavities (vacancies, voids) in simulation cells corresponding to all seven 3D Bravais lattices, makes no assumptions about cavity shapes, allows for atoms of different size, and locates the cavity centers (the centers of the largest spheres not including an atom center). We define three types of cavity and develop a method based on the split and merge algorithm to calculate all three. The visualization of the cavities uses the marching cubes algorithm. The program allows one to calculate and export pair distribution functions (between atoms and/or cavities), as well as bonding and dihedral angles, cavity volumes and surface areas, and measures of cavity shapes, including asphericity, acylindricity, and relative shape anisotropy. The open source Python program is based on GR framework and GR3 routines and can be used to generate high resolution graphics and videos. © 2016 Wiley Periodicals, Inc. pyMolDyn is an interactive viewer of atomic systems defined in a unit cell and is particularly useful for crystalline and amorphous materials. It identifies and visualizes cavities (vacancies, voids) in simulation cells corresponding to all seven 3D Bravais lattices, makes no assumptions about cavity shapes, allows for atoms of different size, and locates the cavity centers (the centers of the largest spheres not including an atom center). We define three types of cavity and develop a method based on the split and merge algorithm to calculate all three. The visualization of the cavities uses the marching cubes algorithm. The program allows one to calculate and export pair distribution functions (between atoms and/or cavities), as well as bonding and dihedral angles, cavity volumes and surface areas, and measures of cavity shapes, including asphericity, acylindricity, and relative shape anisotropy. The open source Python program is based on GR framework and GR3 routines and can be used to generate high resolution graphics and videos. © 2016 Wiley Periodicals, Inc. Empty regions (vacancies, cavities, voids) of, for example, a disordered or crystalline material or a molecule, can influence or even dominate its properties. It is, however, difficult to determine—or even define—such empty regions. pyMolDyn is a Python program that calculates and visualizes such regions (for several definitions) and determines important properties, including the cavity centers, volumes, and surface areas, as well as several shape parameters.
Author	Knodt, David Heinen, Josef Jones, Robert O. Heimbach, Ingo Beule, Fabian Rhiem, Florian
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Cites_doi	10.1088/0022-3719/21/19/018 10.1145/37402.37422 10.1103/PhysRevB.62.3181 10.1002/pssb.201200393 10.1103/PhysRevB.90.184109 10.1016/j.cpc.2015.06.011 10.1021/jp309363h 10.1021/jp2050788 10.1002/jcc.20484 10.1137/1114019 10.1103/PhysRevB.81.014201 10.1515/crll.1908.134.198 10.1098/rspa.1964.0147 10.1002/polb.1992.090300501 10.1088/0953-8984/20/46/465103 10.2172/946741 10.1039/b801115j 10.1088/0953-8984/27/48/485304 10.1016/j.cag.2006.07.021 10.1021/ma00148a028 10.1038/nmat2931 10.1080/13642818508244487 10.1515/crll.1850.40.209 10.1145/321941.321956 10.1098/rspa.1970.0189 10.1103/PhysRevB.76.235201 10.1103/PhysRevB.84.094124
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SubjectTerms	Amorphous materials and surface area Anisotropy Asphericity Atomic structure cavity shape Chemical bonds Computer simulation Condensed matter physics Crystal structure Crystals Distribution functions Exports High resolution Holes Interactive systems Lattice vacancies Lattices marching cubes Marching cubes algorithms Mathematical analysis Molecular structure Molecules Python Routines split and merge Unit cell Visualization Voids volume
Title	pyMolDyn: Identification, structure, and properties of cavities/vacancies in condensed matter and molecules
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