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| − | =Implementation in C++=
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| − | The code is written in C++ for speed. We attempt to use an somewhat object-based approach, but a good many of the member variables are declared as static global to allow their access across threads. | + | The flowchart below shows a detailed view of the how the program works. |
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| − | Here is a breakdown of the main classes and functions in the program. There are numerous other functions but this is the core of the program:
| + | [[file:Overview_complex.png|800px|Figure 2: Comet program flow (detailed)]] |
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| − | * Main()
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| − | ** Spawns threads: <code>collisiondetectionthread</code> , <code>linkforcesthread</code> and <code>applyforcesthread</code> depending on the <code>USETHREAD_COLLISION</code> , <code>USETHREAD_LINKFORCES</code> and <code>USETHREAD_APPLYFORCES</code> parameters.
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| − | ** Parses the <code>comet_params.ini</code> file to read parameters. All of the parameters are implemented as globals (should fix at some point)
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| − | ** Creates the main <code>theactin</code> and <code>nuc_object</code> objects.
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| − | ** Runs through the main iteration loop, calling <code>theactin.iterate()</code> and saving snapshots every so often.
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| − | * Actin class
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| − | ** There is only one actin object, <code>theactin</code> , which constitutes the network, i.e.~contains the nodes and the functions that deal with them.
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| − | ** The <code>iterate()</code> function does one iteration pass, calling:
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| − | ***<code>nucleator_node_interactions()</code> displaces any nodes out of the nucleator object along a normal to the nucleator surface
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| − | ***<code>nucleate()</code> adds new harbinger nodes to the surface of the nucleator
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| − | ***<code>crosslinknewnodes()</code> crosslinks harbingers once they are ready
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| − | ***<code>sortnodesbygridpoint()</code> orders nodes by gridpoint. The {\it only} reason for this is for the division of labor when using threads: We do repulsion by gridpoint to save re-calculating nearby nodes if there are multiple nodes on one gridpoint, and we do not want to divide nodes on one gridpoint across multiple threads.
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| − | ***<code>collisiondetection()</code> detects whether nodes are within <code>NODE_REPULSIVE_RANGE</code> of one another and adds the repulsive force to <code>rep_force_vec[]</code> .
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| − | ***<code>linkforces()</code> Calculates the forces between nodes due to links and puts into <code>link_force_vec[]</code> . If a link goes above a certain threshold force, marks it as broken and removes next time (again to prevent thread problems---since a link is removed both ways and we can't guarantee that both nodes are being processed by same thread)
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| − | ***<code>applyforces()</code> updates the positions of all the nodes. Sums over the threads for <code>rep_force_vec[]</code> , <code>link_force_vec[]</code> and <code>repulsion_displacement_vec[]</code> .
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| − | ***Numerous other functions for things like saving bmps, vrml etc.
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| − | **Nucleator class
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| − | *** There is only one nucleator object at the moment, <code>nuc_object</code> , which is closely linked to the actin object
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| − | *** The nucleator is either a sphere, a capsule (i.e.~a sphere with a cylindrical segment stuck in the middle) or ellipsoid
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| − | *** <code>addnodes()</code> adds harbingers to the surface of the nucleator. The probablility of addition of nodes is normalized by surface area and is symmetric if <code>ASYMMETRIC_NUCLEATION</code> is zero, or asymmetric if 1 or 2 (stepped or linear bias)
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| − | *** <code>definenucleatorgrid()</code> sets a list of gridpoints to check in case of nodes entering the nucleator. Called once at the beginning.
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| − | *** <code>iswithinnucleator()</code> returns true if the node is within the nucleator
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| − | *** <code>collision()</code> moves a node out of the nucleator along a normal vector
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| − | ** Nodes class
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| − | *** Nodes exist only as members of the actin object
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| − | *** <code>nodegrid</code> is a 3 dimensional C++ vector of node pointers. Each nodegrid entry starts a circularly linked list of nodes representing the nodes within that gridpoint voxel.
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| − | *** The actin class contains a vector of nodes. Each node has an associated <code>nodenum</code> , <code>x</code> <code>y</code> and <code>z</code> position, <code>nextnode</code> and <code>prevnode</code> node pointers for the nodegrid linked list, <code>rep_force_vec[]</code> , <code>link_force_vec[]</code> and <code>repulsion_displacement_vec[]</code> as described above, the grid position of the node, <code>harbinger</code> and <code>polymer</code> flags and a <code>listoflinks</code> i.e. a vector of link object which attach this node to other nodes.
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| − | *** <code>polymerize()</code> Creates a node as a harbinger. Adds its pointer to the gridpoint linked list.
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| − | *** <code>depolymerize()</code> Removes a node, deletes all links and removes from grid.
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| − | *** <code>setgridcoords()</code> Calculates new grid co-ordinates based on x,y,z position
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| − | *** <code>addtogrid()</code> adds the node to the current gridpoint
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| − | *** <code>removefromgrid()</code> removes node from the grid
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| − | *** <code>updategrid()</code> checks to see if node has moved gridpoints, and updates grid is needs to
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| − | *** <code>removelink()</code> removes the specified node from the list of links
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| − | ** Links class
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| − | *** Links exist only as members of the node objects
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| − | *** Each link has an associated <code>linkednodeptr</code> which points to the target node that the link is to and a <code>broken</code> flag which is read by <code>actin::linkforces()</code> and tells it to delete the link if it broke.
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| − | *** <code>orig_dist</code> and <code>orig_distsqr</code> store the original distance of the link (and the square of that in a misguided attempt to avoid taking square roots.)
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| − | *** <code>breakcount</code> stores the number of consecutive iterations the link force has been above <code>LINK_BREAKAGE_FORCE</code> and is used to increase the probability of breakage
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| − | *** <code>getlinkforces()</code> returns the force acting on the link. Also sets the <code>broken</code> flag and increments <code>breakcount</code> if appropriate
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