atom

Version 3.00 (27,3 MB) von Michael Holmboe
Atomistic Topology Operations in MATLAB (atom), is a MATLAB library for manipulation of (periodic) molecular systems
5.0
(7)
1,4K Downloads
Aktualisiert 2. Dez 2024
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Zitieren als

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.

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Erstellt mit R2022a
Kompatibel mit allen Versionen
Plattform-Kompatibilität
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Quellenangaben

Inspiriert von: molecule3D

Inspiriert: Import and plot Gromacs .xvg data files

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ATOM_scripts_lecture/CLAYFF_2004_3W_NaMMT/MMT_clayff/buildscripts

ATOM_scripts_lecture/CLAYFF_3W_NaMMT/MMT_clayff/buildscripts

ATOM_scripts_lecture/CLAYFF_3W_NaMMT_basic_workflow/MMT_clayff/buildscripts

LiveScripts

build_functions

custom_functions

examples/Basic_examples

examples/Build_a_2xlayer_clay_system

export_functions

external

forcefield_functions

general_functions

import_functions

neigh_functions

structures/minerals/Hexagonal_pyro_mmt

structures/minerals/Hexagonal_talc_laponite

structures/water

variables

LiveScripts

examples/Basic_examples

Versionen, die den GitHub-Standardzweig verwenden, können nicht heruntergeladen werden

Version Veröffentlicht Versionshinweise
3.00

See release notes for this release on GitHub: https://github.com/mholmboe/atom/releases/tag/v3.00
Starting from v3.0 of this MATLAB library/toolbox, support for general/tailored versions of the mineral forcefield called MINFF is supported, see the minff_atom function.
2.11

Some new functions.
2.10.1

Small updates.
2.10

A few updates that hopefully will speed up certain things.
2.07

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.
2.06

Updates to the rdf_atom, density_atom and xrd_atom functions, plus a new very basic import_atom_mol2 function.
2.05

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.
2.04

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.
2.03

Small updates.
2.02

Moved from GitHub
2.01

Small updates.
2.0

New functions for healing/fusing/protonating sites, reading pdb trajectories with changing number of atoms etc.
1.24.0.0

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.
1.23.0.0

Some new functions and better support for triclinic systems.
1.22.0.0

Updated the documentation
1.21.0.0

Updated some documentation.
1.11.0.0

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.
1.10.0.0

Updated these files:
import_atom_gro.m, import_atom_xyz.m, import_gro_traj.m, import_traj.m, import_xyz_traj.m, write_atom_xyz.m, write_gro_traj.m, write_xyz_traj.m
1.5.0.0

Added more functions
Change of title.
1.4.0.0

Added more functions
1.3.0.0

Added some more functions.
Changed tags.
1.2.0.0

Added some functions for writing .psf and Gromacs .itp files
Mostly updates to some functions. Also added lists of all functions by category.
1.1.0.0

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.
1.0.0.0

Changed title
Changed the description.
Changed the description
Changed the description
Added some more functions.
Added a picture!
Update some plotting functions. If you want to use VMD, set your VMD path in PATH2VMD().
Changed the description again..
Change description.
Um Probleme in diesem GitHub Add-On anzuzeigen oder zu melden, besuchen Sie das GitHub Repository.
Um Probleme in diesem GitHub Add-On anzuzeigen oder zu melden, besuchen Sie das GitHub Repository.