Status¶

Mechancia is very early in the development cycle, as such, it’s EXTREMLY feature-incomplete, unstable, and will almost certainly crash.

However, as such, this is YOUR chance to try it out, and let us know what kind of features you’d like to see.

History¶

Version Alpha 1.0.18.1¶

generalized passive, consumer and producer fluxes
better OpenGL info reporting, gl_info(), egl_info()
enable boundary conditions on chemical speices, bug fix parsing init conditions
use species boundary value to enable source / sinks
source / sinks in example

Version Alpha 1.0.17.1¶

multi-threaded rendering fixes

Version Alpha 1.0.16.2¶

Logging, standardized all logging output, python api for setting log level.
fix kinetic energy reporting
synchronize gl contexts between GLFW and Magnum for multi-thread rendering

Version Alpha 1.0.16.2¶

initialize Mechanica either via m.init, m.Simulator, or m.simulator.init

Version Alpha 1.0.16.1¶

finally, completly expunged pybind11! pybind11 is finally GONE!
context managment methods for multi-threaded headless rendering.
universe.reset() method, clears objects
set window title to script name
add ‘positions()’, ‘velocities()’ and ‘forces()’ methods to particle list.
universe.particles() is now a method, and returns a proper list

Version Alpha 1.0.15.5¶

bug fix with boundary condition constants

Version Alpha 1.0.15.5¶

bug fix with force calculation when distance too short: pic random separation vector of with minimal distance. Seems to work…
better diagnostic messages
added normal to boundary vectors

Version Alpha 1.0.15.4¶

generalized boundary conditions
add potentials to boundary conditions
velocity, free-slip, no-slip and periodic boundary conditions
render updates, back face culling
headless rendering, rendering without X11 using GLES on Linux
generalized power potential
much improved error handling, much more consistency
particle list fixes
Rigid Body Dynamics ! (only cuboids currently supported, but still rigid bodies)
add potentials to rigid bodies
python api rigid body updates
rendering updates, more consistency, simplify
rigid body particle interactions
friction force
more expunging pybind, soon, soon we will be rid of pybind.
bond dissociation_energy (break strength)
lattice initializer
add bonds to lattice initliazer
performance logging
updates to dissapative particle dynamics forces
enable adding DPD force to boundaries.
generlized single body force (external force)
fluid dynamics examples
visco-elastic materials, with bond breaking
single-body time-dependent force definitions in python

Version Alpha 1.0.15.2¶

initial dissapative particle dynamics
doc constant force, dpd

Version Alpha 1.0.15.1¶

Version Alpha 0.0.14.1¶

added convenience methods to get spherical and cartesian coords from lists
updated example models
update docs
added plot function in examples to plot polar angle velocity.
code cleanup

Version Alpha 0.0.14¶

All new FLUX / DIFFUSION / TRANSPORT, We’ve not got Transport-Dissipative-Dynamics working!!!
secrete methods on particle to perform atomic secrete
bug fixes in neighbor list, make sure neighbor don’t contain the particle
bug fixes in harmonic potential
new overlapped sphere potential
new potential plotting method, lots of nice improvements
new examples
update become to copy over species values
lattice initializers
add decay to flux
detect hardware concurrency
bug fix in Windows release-mode CPUID crash
multi-threaded integration
all new C++ thread pool, working on getting rid of OpenMP / pthreads
event system bug fixes
documentation updates

Version Alpha 0.0.13¶

preliminary SBML species per object support
SBML parsing, create state vector per object
cpuinfo to determine instruction set support
neighbor list bug fixes
improve and simplify events
on_keypress event
colormap support per SBML species

Version Alpha 0.0.12¶

free-slip boundary conditions
rendering updates
energy minimizer in initial condition generator
updates to init condition code
initial vertex model support

Version Alpha 0.0.11¶

new linear potential
triagulated surface mesh generation for spheres, triangulate sphere surfaces with particles and bonds, returns the set.
banded spherical mesh generation
bug fixes in making particle list from python list
points works with spherical geometry
internal refactoring and updates
Dynamic Bonds! can dynamically create and destory bonds
lots of changes to deal with variable bond numbers
rendering updates for dyanmic bonds
particle init refactor
added metrics (pressure, center of mass, etc…) to particle lists
add properties and methods to Python bond API
bond energy calcs avail in python
bond_str and repr
automatically delete delete bond if particle is deleted

Version Alpha 0.0.10-dev1¶

bug fixes in bond pairwise search
improved particle __repr__, __str__
new style visible attribute to style to toggle visibility on any rendered object
make show() work in command line mode
internal changes for more consistent use of handles vs direct pointers
bind_pairwise to search a particle list for pairs, and bind them with a bond.
new points and random_points to generate position distributions
spherical plot updates
new distance method on particles
implmement become – now allow dynamic type change
big fixes in simulation start right away instead of wait for event
basic bond rendering (still lines, will upgrade to cylinders in future
render large particles with higher resolution
new particle list composite structure, all particles returned to python in this new list type. fast low overhead list.
major performance improvment, large object cutoff optimization
numpy array conversion bug fix
neighbor list for particles in range
enumerate all particles of type with ‘items()’
new c++ <-> python type conversions, getting rid of pybind.
better error handling, check space cells are compatible with periodic boundary conditions.
add start, stop, show, etc. methods to top-level as convenience.
fix ipython interaction with show, default is universe not running when showing
enable single stepping and visualization with ipython
enable start and stop with keyboard space bar.
pressure tensor calculations, add to different objects.
new Universe.center property
better error handling in Universe.bind
clean up of importing numpy
expose periodic boundary conditions to python.
periodic on individual axis.
new metrics calculations, including center of mass, radius of gyration, centroid, moment of inertia
new spherical coords method
frozen particles
add harmonic term to generalized Lennard-Jones ‘glj’ potential

Version Alpha 0.0.9-dev4¶

tweaks in example models
more options (periodic, max distance) in simulator ctor
add flags to potentials
persistence time in random force
frozen option for particles
make glj also have harmonic potential
in force eval, if distance is less than min, set eval force to value at min position.
accept bound python methods for events

Version Alpha 0.0.9¶

all new cluster dynamics to create sub-cellular element models
cluster splitting
splitting via cleavage plane
splitting via cleavage axis
other splitting options
new potential system to deal with cluster and non-cluster interactions
revamped generalized Lennard-Jones (glj) potential
new ‘shifted’ potential takes into account particle radius
updated potential plotting
more examples
fixed major integrator bug

Version Alpha 0.0.8¶

explicit Bond and Angle objects
new example apps
new square well potential to model constrained particles
bug fixes in potential
thread count in Simulator init

Version Alpha 0.0.7¶

lots of changes related to running in Spyder.
force windows of background process to forground
detect if running in IPython connsole – use different message loop
fix re-entrancy bugs in ipython message loop.
Spyder on Windows tested.

Version Alpha 0.0.6¶

lots of changes to simulation running / showing windows / closing windows, etc..
documentation updates

Version Alpha 0.0.5 Dev 1¶

Add documentation to event handlers, and example programs
fix bugs in creating event events
add version info to build system and make available as API.

Version Alpha 0.0.4 Dev 1¶

All new particle rendering based on instanced meshes. Rendering quality is dramatically improved. Now in a position to do all sorts of discrete elements like ellipsoids, bonds, rigid particles, etc…
Implement NOMStyle objects. This is essentially the CSS model, but for 3D applications. Each object has a ‘style’ property that’s a collection of all sorts of style attributes. The renderer looks at the current object, and chain of parent objects to find style attributes. Basically the CSS approach.
More demo applications.
Memory bugs resolved.

Version Alpha 0.0.3 Dev 1¶

Windows Build!
lots of portability updates
some memleak fixes

Version Alpha 0.0.2 Dev 5¶

lots of new documentation
reorganize utility stuff to utily file
add performance timing info to particle engine
add examples (multi-size particles, random force, epiboly, events with creation, destruction, mitosis, …)
new dynamics options, include both Newtonian (Velocity-Verlet) and over-damped.
new defaults to set space cell size, better threading
New explicit bond object
add creation time / age to particle
particle fission (mitosis) method (simple)
clean up potential flags
harmonic potential
new reactive potential to trigger (partial implementation)
random points function to create points for geometric regions
prime number generator
Fixed major bug in cell pair force calculation (was in wrong direction)
major bug fix in not making sure potential distance does not go past end of interpolation segments.
new random force
new soft-sphere interaction potential
add radius to particle type def
update renderer to draw different sized particles
add number of space cells to simulator constructor
configurable dynamics (Newtonian, Over-damped), more to come particle delete functionality, and fix particle events
examples bind events to destroy, creation and mitosis methods
new event model

Version Alpha 0.0.1 Dev 3¶

Refactoring of Particle python meta-types, simpler and cleaner
Upgrade to GLFW 3.3
New single body generalized force system
Berendsen thermostat as first example single body generalized forces
Per-type thermostat
Arc-ball user interaction
Simplify and eliminate redundancy between C++ and Python apps.

Version Alpha 0.0.1 Dev 2¶

First public release

Features to be implemented¶

Linux binaries
mouse interction – rotate, zoom simulation
Documentation
Event system to hook up simulation events to user objects
strike: User definable visualization style
Nosé–Hoover thermostat
Destroying particles
Collision reactions (when particles collide, they react, and can create and destroy particles)
Particle mitois
strike: attach chemical cargo to particles
strike: inter-particle flux of chemical cargo
reaction-kinetics network at each particle
strike: Windows binaries
Movable boundary conditions
strike: reflective boundary conditions (only have periodic now)
mouse object picking
strike: Python API for bonded interactions (bonds, angles, dihedrals, impropers)
strike: pre-made DPD potentials (conservative, friction, thermostat)
strike: `With addition of particle chemical cargo, fluxes and above potentials, we will

have complete transport-dissapative-particle-dynamics simulation. And reactions gives us reactive TDPD.`
strike: `Visualization:

We will attach a ‘style’ attribute to the particle type that will let users define how they’re presented in the renderer. This will have attributes such as color, size, etc… We want to let users attach transfer functions here, that will read particle attributes, such as local chemical concentration and map this to a color. To get decent performance, we’ll have to compile user specified functions into pixel shader and run them on the GPU.`
strike: `Multi-process rendering. Jupyter notebooks now uses a two process model, so

it’s probematic to create a window in a background process. We want to enable the simulator render to an off-screen buffer, and render to this buffer. Then copy the buffer to the foreground process and display it here.`

Known Bugs¶

strike: In ipython, closing the window does not work correctly
strike: energy is not conserved – bug in integrator.
only a subset of features are implmented

Features for next release¶

Python API for vertex model (polygons, cells)