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Windows/Mac/Linux builds now available

Windows/Linux builds are now available via the AppVeyor/Travis CI build system. They are published via the GitHub releases page.

First DynamO workshop: 23^rd January 2015

The first workshop on how to install and use DynamO has been opened for registration. This is hosted at the STFC Daresbury Laboratory and will cover the following topics:

• Introduction to event-driven simulation and discrete potentials.
• Installation and structure of the DynamO software.
• Equilibrium simulation of simple discrete fluids using DynamO
  • Simulation of single and multi-component hard-sphere, square-well, and stepped Lennard-Jones fluids.
  • Determination of the radial distribution function, pressure, and transport properties (viscosity, thermal conductivity/diffusivity, self/mutual diffusion coefficient).
• Non-equilibrium simulation of simple discrete fluids: Compression/packing, Lees-Edwards boundary conditions, Thermostats, and heated walls.
• Polymeric fluids, linear/ring/star polymers.
• Simple off-lattice models for protein folding: Square-well homopolymer, HP model

Workshop details and registration

Slides and workshop materials

• Introduction to DynamO and EDPD
• Tutorial session 1: slides and handout
• Tutorial session 2: slides and handout
• Tutorial session 3: slides and handout
• Tutorial session 4: slides and handout
• dynavis controls cheat-sheet
• Example scripts

Please note, movies and animations in the slides require Acroread 9.4.1 on Linux, or 9+ on Windows to play.

Dynamo 1.6.0 Released

DynamO 1.6.0 has been released. The major change for this release is the switch to the CMake build system. This should make compiling on other systems significantly simpler. The compilation tutorial has been rewritten and now includes instructions for RedHat systems as well as Ubuntu.

Updated: Tutorial 4 and 5 released

Two new tutorials are now available which introduce thermostats, general data processing, compression, and multiple Species/Interactions. Tutorial 4 also includes an introduction to the dynatransport tool for calculating transport properties.

Dynamo 1.5.0 Released

DynamO 1.5.0 has finally been released. A range of issues have been fixed (thanks to everyone who took the time to raise issues). This version contains many major improvements, including:

• Documentation
  There is now a complete reference for the output plugins and the file format. This covers almost every feature of DynamO, but the tutorials are still being written.
• Better XML error reports
  If there are errors in the configuration file, you should get a much friendlier message pointing out the location in the file where the error occurred.
• More automation/Simpler configuration files
  Many core features/settings required to run a system are now automatically set up (e.g. you don't have to specify a neighbourlist, one will be automatically set up).
• Visualiser improvements
  The visualiser is now capable of rendering bonds, and a range of other standard molecular features. Shadows have also been re-enabled following a rewrite.
• Better testing frameworks
  There is a more complete testing system which should help prevent regressions in future updates.

There are also a number of other minor bug fixes and improvements. The full changelog is available here.

Dynamo 1.4.0 Released

DynamO 1.4.0 has finally been released. This version contains many major improvements, including:

• Automatic full checking of configuration for invalid states on load
  As soon as the simulator has finished loading the configuration, it now verifies that no particles are in an invalid state before starting the simulation. If any particles are "overlapping" or the capture map has become invalid, these errors will be reported to the user on load. As these errors are the main source of difficulty, these changes should make DynamO much easier to use.
• Fully stabilised event-detection algorithms
  In this version of DynamO, all interactions have been reimplemented using the stable EDPD approach, as detailed in this preprint. This greatly enhances the stability of the simulator and even allows it to recover from some types of poorly initialised systems.
• Ubuntu Packages
  Users using a recent ubuntu version (12.04+) will no-longer have to compile their own copy of DynamO, as prebuilt packages are now available at the following PPA:
  DynamO Stable PPA
  More information on these packages (and how to use them) is available in the download section of the site.
• New Features
  A few new interactions, such as assymetric particle shapes, full wall support including compression and polydisperse particles, and constraint forces in gravity have been implemented. The features gallery has been updated with some example simulations using these features.
• Changed File Format
  Unfortunately, the file format has had to change to acommodate some new features and so configurations made using DynamO v1.3 will not load in v1.4. Although this is inconvenient for some users, at the same time many cleanups were also implemented to ensure the file format was as logical as possible and to maximise the flexibility/compatibility of the format so that future upgrades will not be so disruptive.
• Rewritten Tutorials
  As the file format has changed, all of the tutorials have been rewritten to reflect the changes to the way ranges are specified. This is part of a documentation push which will take place in the new year.

There are also a number of other minor bug fixes and improvements. Some of which are detailed in the Github Issue Tracker.

Daily Ubuntu Packages Available

As part of the push to DynamO 1.4.0, a Ubuntu PPA repository has been set up which automatically builds DynamO from the latest development code every day.

This makes it significantly easier to get started with DynamO, as you no longer have to compile the code yourself! To find out more, check out the Downloads section of the site, or click the button below.

Dynamo 1.3.2 Released

Another interim 1.3 version of DynamO is now released. There are no major bugs fixed in this release, aside from an almost negligble bias in the reported mean free time.

However, there are some usability fixes for the visualiser and a great increase in the quantity of properties reported in the simulation output file. In particular, the transport property correlators have been completely rewritten.

Please update to either the dynamo-1-3-2 or the master branch in the git repository.

Dynamo 1.3.1 Released

A bugfix release of DynamO is needed as there were some fairly major bugs reported and fixed recently. Please update as soon as possible to either the dynamo-1-3-1 or the master branch in the git repository.

The three significant bugs fixed are as follows:

• Issue 5 (major): Errors in the calculation of Cv and internal energy on replica exchanged systems.
• Issue 1 (major): Sheared systems with rectangular simulation domains fail to detect all events, leading to overlaps.
• Issue 8 (minor): Rendered glyph sizes are incorrect in polydisperse systems.

Dynamo 1.3 Released

The latest stable version of DynamO is now available. Thanks to a large increase in the number of people using the code and lots of feedback, there have been many stability fixes and general improvements to the code base. The project now has its own website, fully redesigned with improved documentation to encourage further collaboration with the community.

The major new features of this release are:

• New tutorials have been written to make DynamO easier to learn, and are hosted on the new DynamO site at dynamomd.org (and .com and .co.uk).
• 2D systems are now officially supported/maintained in DynamO.
• Up to 50% faster in polydisperse systems.
• It is now significantly easier to generate initial configurations of dense, complex systems such as polymers.
• The file format has been cleaned up to remove confusion about the dynamics and liouvillean tags (the useless Dynamics wrapper tag has been removed, and the Liouvillean tag has been renamed Dynamics to make it easier for new users to understand).
  Configuration files created using version 1.2 will not work with version 1.3, you will have to regenerate them.
• Updated to boost 1.49.0, (you will need to do a make distclean and make for this to take effect).
• Removed the requirement for the gzip library, and switched to a dynamic/shared version of the bzip2 library (fixes build problems on Gentoo and Suse).

According to the git log there have been 15707 lines of code inserted and 23107 lines of code deleted, so another big change between versions. You can compare the changes on GitHub, but it may take some time to display them.

This version continues the efforts to shrink and simplify the code to make it more accessible to new developers. There are also many bug fixes and usability improvements, all supported systems should now work out of the box. A full changelog is posted below:

Bug fixes/Improvements

• DynamO: Found the neighbourlists were not being correctly reinitialised, causing slowdowns and possible hangs in compressing systems (huge speed boost in compression).
• DynamO: Multi-core parallel tempering is now actually in parallel. Until now the code actually has been executing in serial.
• DynamO: Fixed a rare bug in compressing systems, where neighbourlists would be incorrectly sized after a compression.
• DynamO: Changed the default settings of the histogram reweighting program so that the results are accurate by default! Previously, the results coming out of dynahist_rw could be quite innaccurate unless "--min-err=1e-16" was set.
• DynamO: The uniform_01 distribution had its own copy of the random number generator. It is unlikely that this affected any results, but it is not good practice.
• DynamO: The Green-Kubo Mutual diffusion correlator now works (instead of just outputting NaN/inf).
• Coil: Fix light placement relative to camera.
• Coil: Fixed the bilateral blur filter.
• Coil: Fixed many bugs which only appear when resizing the display.

New features

• Coil: Added a fullscreen mode, toggled with the f key.
• Coil: Objects can now be dragged, for example, the lights can be repositioned using the mouse.
• DynamO: Packing of systems into systems is now easy to perform.
• DynamO: An estimate of the remaining time left for the simulation is now outputted on the screen.
• DynamO: Up to 50% faster in polydisperse systems thanks to a new cache friendly nblist implementation.
• DynamO: SLLOD dynamics have been removed, they are unmaintained and unused. Shearing systems are still available through Lees-Edwards boundary conditions, just not in transformed co-ordinates.
• DynamO: All particle positions are now shuffled for mixture systems in dynamod to enable faster equilibration.
• DynamO: Removed all deprecated Clone functions for copying of classes in the code.
• DynamO: Alter the functions in dynamics that add/get/set objects and take/return a pointer to return shared_ptr's (search for uses of shared_ptr's get() function).
• DynamO: Change the loadClass XML functions to return shared_ptr's.
• DynamO: Improved the sizing of systems when dropping random polymers (dynamod -m2).
• DynamO: 2D systems are now officially supported/maintained in DynamO.
• DynamO/Coil: Remove the requirement to pass the frequency to the visualiser, it guesses at one MFT for each particle.
• DynamO/Coil: Visualisation no longer requires an OpenCL compatible graphics card! However, you do still need an OpenCL library installed.
• Coil: Moved to a combined deferred/forward rendering pipline which greatly improves rendering performance and flexibility.
• Coil: Added High-Dynamic-Range (HDR) lighting and gamma correction.
• Coil: With HDR, Bloom effects can now be enabled to simulate over-exposure.
• Coil: Sphere glyphs used to render particles are ray-traced! This allows the rendering of millions of perfectly spherical particles.
• Coil: Cleaned up the stereo (3D) vision mode, so it's possible for 3D TV's to use it as well as red-cyan glasses.
• Coil: There is now a separate Volume rendering visualisation executable to allow direct visualisation of volume data.
• Coil: Volume rendering now uses pre-integrated transfer functions for greatly improved render quality.
• Coil: Added new camera controls for positioning and aligning the camera along with a new camera control modes.
• Coil: Now requires and complies with the OpenGL 3.3 Core profile.
• Coil: Fixed segfaults occurring when adding a window crashes the main render thread.
• Coil: Fixed a rare segfault caused by a miscalculation of the glade file data size stored in memory.
• Coil: The snapshot button now captures using the same file counter as the record button.
• Coil: Added some sharpen and hi-pass filters to the screen space effects.
• Coil: Now it is easy to use multiple light sources in the render scene.
• Magnet: Upgraded all shaders to GLSL 330.

The next version of DynamO will focus on new features, such as compression with walls, assymetric particle shapes, and automatic continuous to discrete potential mapping.

New DynamO site launched

The DynamO site has been redesigned and separated from marcusbannerman.co.uk to make it easier to find all of the information relating to DynamO. The launch of the website is to coincide with the release of DynamO 1.3.

DynamO now has its own web domains, including dynamomd.org, dynamomd.com, and dynamomd.co.uk.

Page last modified: Monday 16th December 2024

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