atom
Atomistic Topology Operations in MATLAB (atom), is a MATLAB library for manipulation of (periodic) molecular systems
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Cite As
Holmboe, Michael. “Atom: A MATLAB PACKAGE FOR MANIPULATION OF MOLECULAR SYSTEMS.” Clays and Clay Minerals, Springer Science and Business Media LLC, Jan. 2020, doi:10.1007/s42860-019-00043-y.
General Information
- Version 3.0.0 (27.3 MB)
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View License on GitHub
MATLAB Release Compatibility
- Compatible with any release
Platform Compatibility
- Windows
- macOS
- Linux
| Version | Published | Release Notes | Action |
|---|---|---|---|
| 3.0.0 | See release notes for this release on GitHub: https://github.com/mholmboe/atom/releases/tag/v3.00 |
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| 2.11.0 | Some new functions. |
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| 2.10.1 | Small updates. |
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| 2.10.0 | A few updates that hopefully will speed up certain things. |
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| 2.7.0 | New bond_angle_dihedral_atom() function! A function that can find the indexes (see Dihedral_index) and calculate the dihedral angle between atoms that share two angles! Also some new features to the show_atom() plotting function. |
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| 2.6.0 | Updates to the rdf_atom, density_atom and xrd_atom functions, plus a new very basic import_atom_mol2 function. |
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| 2.5.0 | Various small updates, especially to the forcefield functions. Also, a new plotting function called show_atom(). Its a bit slow but puts on a good show! Try also the rewritten xrd_atom() function that can generate a simple X-ray profiles. |
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| 2.4.0 | New cool density_atom function that can plot density profiles and if charges are present also can plot charge density profiles, electric field profiles and the electrostatic profile. |
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| 2.3.0 | Small updates. |
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| 2.2.0 | Moved from GitHub |
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| 2.0.0 | New functions for healing/fusing/protonating sites, reading pdb trajectories with changing number of atoms etc. |
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| 1.24.0 | Some small updates plus one new function called xrd_atom which generates a simplistic XRD pattern from a .pdb | .gro file or an existing atom struct with is Box_dim taken as the unit cell. |
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| 1.23.0 | Some new functions and better support for triclinic systems. |
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| 1.22.0 | Updated the documentation |
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| 1.21.0 | Updated some documentation. |
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| 1.11.0 | Updated several functions, better supports trajectory import/export for instance. Try also the new solvate_atom function, solvates with spc, spce, tip3p, tip4p, tip5p water models at any given density. |
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| 1.10.0 | Updated these files:
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| 1.5.0 | Change of title. |
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| 1.4.0 | Added more functions |
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| 1.3.0 | Changed tags. |
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| 1.1.0 | Improved documentation and some new LiveScripts demonstrating some of the atom struct functions. I have also added a small tutorial on how to use the scripts to construct a hydrated organoclay system. |
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| 1.0.0 | Added some more functions. |
