Releases: ovilab/atomify
2.2-alpha
This version is a pre-release of the new 2.2 version.
Update: Fixed so it supports OSX 10.9 and newer. Thanks Vibeke :D
Stable 2.1.2
Stable 2.1.0
Updated LAMMPS to 11Aug17 stable release
Catch variable command errors as other errors are being caught (Issue #346)
Using OpenGL in figures for improved performance
Added --clearcache argument
Added statistics sampler to measure Atomify usage
Added ctrl +/ctrl - to increase/decrease font size. (Issue #339)
Added export to text/Python/Matlab for compute and variable plots
Added plotting controls to varibles
Added modifyable atom types file. (Issue #356)
Right column is prettier with documentation and number formatting
Periodic imgs work with hidden atoms (Issue #351)
Can resize list of files panel
Added cpuRemain and timestepsPerSecond to simulation summary
Added more packages to default lammps installation
Updated to Quick Controls 2.2
Added support for running regular LAMMPS from atomify terminal
Bugfixes, some features
Added openMP in configure on supported platforms (including macOS using homebrew).
Added working slice modifier.
Readding fix atomify after clear command.
Updated LAMMPS to 24Jul17.
Improved Rendering tab.
Removed .jpg as screenshot alternative (now defaulting to .png).
Added close button on RightBar text about Atomify.
Fixed shortcut text multiple places.
Added reax examples.
Updated and improved other examples.
Translate guides so positive direction can be identified.
Added lost_atoms detection in fix_atomify.
Not showing empty message overlay when stopped is clicked.
Attenuation calculation follows global scale.
Bugfixes
Updated LAMMPS version to 19May17.
Added extra moltemplate lammps files.
Prevent stealing of alt+8 and alt+9 (square brackets).
Added global scale so positions can be scaled.
Added better plotting control.
Fixed a problem where plots could crash atomify.
Fixed so bonds can have floating point distances.
Fixed erroneous "File has been updated on disk" message after saving.
Added more default atom colors and radii (up to atomic number 74).
Added user-reaxc to default packages.
Added menu item for guide / outline.
Added full screen to menu.
Fixed bug in some examples.
First stable release
Updated LAMMPS to 4 May 2017
Editor detects changes in open files
Fixed simulation speed integer problem
Pretty good release
v2.0.6 --version uses printf()
2.0.5
Atomify 2.0.3
v2.0.3 2.0.3
Atomify LAMMPS 2.0.2
Atomify 2.0 is released. Our engine is now running on top of the LAMMPS molecular dynamics simulator, hence the name Atomify LAMMPS. The editor makes it easy to run and visualize LAMMPS scripts.
Installation on Ubuntu
Currently only available for Ubuntu 16.04.
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Enable the xenial-proposed repository through System Settings > Software & Updates > Developer Options
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Close and reload
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Open a terminal and install the following packages:
sudo apt install snap-confine ubuntu-core-launcher
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Disable xenial-proposed if you don't want other (possibly unstable) Ubuntu packages to be installed on your next system update.
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Install atomify-lammps from terminal by running (or download the snap below)
sudo snap install atomify-lammps
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Run atomify-lammps from terminal with
atomify-lammps
A window with Atomify LAMMPS should appear, allowing you to run your LAMMPS scripts in the editor to the left. You may test with the following script:
#/atom 1 1.8 #E74C3C
#/atom 2 1.8 #3498DB
variable L equal 16.0
variable thickness equal 6.0
units lj
atom_style atomic
atom_modify map hash
lattice fcc 0.8442
variable left equal 0.5*$L-0.5*${thickness}
variable right equal 0.5*$L+0.5*${thickness}
variable Lhalf equal 0.5*$L
region system block 0 $L 0 $L 0 $L
region boxinside block 0 $L ${left} ${right} 0 $L
region boxoutside block 0 $L ${left} ${right} 0 $L side out
region lol sphere 0.0 ${Lhalf} ${Lhalf} 15.0
create_box 3 system
create_atoms 1 region boxinside
create_atoms 2 region boxoutside
mass * 1.0
velocity all create 3.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
run 100