Interactive physics simulation engine
Project description
Mechanica
Mechanica is an interactive particle based physics, chemistry and biology simulation environment, with a heavy emphasis towards enabling users to model and simulate complex sub-cellular and cellular biological physics problems. Mechanica is part of the Tellurium http://tellurium.analogmachine.org project.
Mechanica is designed first and foremost to enable users to work interactively with simulations – so they can build, and run a simulation in real-time, and interact with that simulation whilst it’s running. The goal is to create an SolidWorks type environment where users can create and explore virtual models of soft condensed matter physics, with a emphasis towards biological physics.
Mechanica is a native compiled C++ shared library with a native and extensive Python API, that’s designed to used from an ipython console (or via scripts of course).
History
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
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