Cometparams.ini parameter file - Revision history

Markdayel at 23:48, 14 July 2009

2009-07-14T23:48:34Z

Markdayel at 23:45, 14 July 2009

2009-07-14T23:45:10Z

Markdayel: /* Node-node repulsion */

2009-04-28T17:44:27Z

‎Node-node repulsion

Markdayel: /* Node-node repulsion */

2009-04-27T20:17:23Z

‎Node-node repulsion

Markdayel: /* Drag */

2009-04-27T20:12:25Z

‎Drag

Markdayel: /* Node links */

2009-04-27T20:12:10Z

‎Node links

Markdayel: /* Node-node repulsion */

2009-04-27T20:11:32Z

‎Node-node repulsion

Markdayel: /* Nucleator Attachments */

2009-04-27T20:11:22Z

‎Nucleator Attachments

Markdayel: /* Nucleator Geometry */

2009-04-27T20:10:58Z

‎Nucleator Geometry

Markdayel: /* Run Time */

2009-04-27T20:10:33Z

‎Run Time

@@ Line 62: / Line 62: @@
   FORCE_SCALE_FACT      0.3 # (um.pN^-1.s^-1) how fast nodes move for a given force
-  VARY_INERT_W_RAD    false # (boolean) whether to vary nucleator inertia with radius
+  VARY_INERT_W_RAD    false # (boolean) whether to vary nucleator inertia (viscous drag) with radius
   NUCLEATOR_INERTIA      80 #  (unitless, or um^-1)  Scale factor for how much harder it is to move nucleator than nodes
   MofI                  0.5 # (rad.um^1.^pn) How hard it is to rotate the nucleator
-This section relates the forces to the actual movement of the nodes and nucleator.   FORCE_SCALE_FACT scales the movement of nodes (i.e. effectively inverse of node drag).  If you reduce this, you probably need to reduce DELTA_T as well. NUCLEATOR_INERTIA determines how hard it is to ''displace''  the nucleator and MofI determines how hard it is to rotate it.  If VARY_INERT_W_RAD is set, inertia will be scaled by the size of the nucleator.
+This section relates the forces to the actual movement of the nodes and nucleator.   FORCE_SCALE_FACT scales the movement of nodes (i.e. effectively inverse of node drag).  If you reduce this, you probably need to reduce DELTA_T as well. NUCLEATOR_INERTIA (viscous drag) determines how hard it is to ''displace''  the nucleator and MofI determines how hard it is to rotate it.  If VARY_INERT_W_RAD is set, inertia will be scaled by the size of the nucleator.

@@ Line 39: / Line 39: @@
 F_R = M_R \left( \left(\frac{d_R}{d}\right)^{P_R} - 1 \right), \quad 0<d<d_R
-</math></center> where <math>d</math> is the distance between nodes, <math> M_R </math> (NODE_REPULSIVE_MAG) is a magnitude scale factor, and <math> d_R </math> (NODE_REPULSIVE_RANGE) is maximum range of the repulsive force.
+</math></center> where <math>d</math> is the distance between nodes, <math> M_R </math> (NODE_REPULSIVE_MAG) is a magnitude scale factor, and   <math> d_R </math> (NODE_REPULSIVE_RANGE) is  a distance scale factor for the repulsive force (It tails off to zero by this point and is not calculated for node pairs further apart than this). The power factor <math> P_R </math> (NODE_REPULSIVE_POWER) is 2, so this is a simple inverse square repulsive force.
 The power factor <math> P_R </math> (NODE_REPULSIVE_POWER) is 2, so this is a simple inverse square repulsive force.
 ====Node links====

@@ Line 39: / Line 39: @@
 F_R = M_R \left( \left(\frac{d_R}{d}\right)^{P_R} - 1 \right), \quad 0<d<d_R
-</math></center> where <math>d</math> is the distance between nodes, <math> M_R </math> (NODE_REPULSIVE_MAG) is a magnitude scale factor, and <math> d_R </math> (NODE_REPULSIVE_MAG) is maximum range of the repulsive force.
+</math></center> where <math>d</math> is the distance between nodes, <math> M_R </math> (NODE_REPULSIVE_MAG) is a magnitude scale factor, and <math> d_R </math> (NODE_REPULSIVE_RANGE) is maximum range of the repulsive force.
 The power factor <math> P_R </math> (NODE_REPULSIVE_POWER) is 2, so this is a simple inverse square repulsive force.

@@ Line 30: / Line 30: @@
   NODE_REPULSIVE_RANGE  1.0  # (um) how far to calculate the node-node repulsion function
-  NODE_REPULSIVE_MAG    2.7  #  (pN)magnitude scale factor for repulsive force
+  NODE_REPULSIVE_MAG    2.7  # (pN) magnitude scale factor for repulsive force
   NODE_REPULSIVE_POWER  2.0  # (unitless) power of repulsion function (see equation) (always set to 2 for the moment)

@@ Line 62: / Line 62: @@
 ====Drag====
-  FORCE_SCALE_FACT        0.3 # (um.pN^-1.s^-1) how fast nodes move for a given force
+  FORCE_SCALE_FACT      0.3 # (um.pN^-1.s^-1) how fast nodes move for a given force
   VARY_INERT_W_RAD    false # (boolean) whether to vary nucleator inertia with radius
-  NUCLEATOR_INERTIA        80 #  (unitless, or um^-1)  Scale factor for how much harder it is to move nucleator than nodes
+  NUCLEATOR_INERTIA      80 #  (unitless, or um^-1)  Scale factor for how much harder it is to move nucleator than nodes
-  MofI                                 0.5 # (rad.um^1.^pn) How hard it is to rotate the nucleator
+  MofI                  0.5 # (rad.um^1.^pn) How hard it is to rotate the nucleator
 This section relates the forces to the actual movement of the nodes and nucleator.   FORCE_SCALE_FACT scales the movement of nodes (i.e. effectively inverse of node drag).  If you reduce this, you probably need to reduce DELTA_T as well. NUCLEATOR_INERTIA determines how hard it is to ''displace''  the nucleator and MofI determines how hard it is to rotate it.  If VARY_INERT_W_RAD is set, inertia will be scaled by the size of the nucleator.

@@ Line 43: / Line 43: @@
 ====Node links====
-  P_NUC                                    0.12  # (nodes.um^2.s^-1) Nucleation rate (probability of forming nodes)
+  P_NUC                  0.12 # (nodes.um^2.s^-1) Nucleation rate (probability of forming nodes)
-  XLINK_NODE_RANGE               1.0  # (um) maximum distance to link two nodes when they form
+  XLINK_NODE_RANGE       1.0  # (um) maximum distance to link two nodes when they form
-  MAX_LINKS_PER_NEW_NODE 10     # (links) cap the max number of links for a new node
+  MAX_LINKS_PER_NEW_NODE 10   # (links) cap the max number of links for a new node
-  LINK_BREAKAGE_FORCE        3.0  #  (pN) maximum node-node link force before it breaks
+  LINK_BREAKAGE_FORCE    3.0  #  (pN) maximum node-node link force before it breaks
-  LINK_FORCE                           3.0  # (pN) magnitude scale factor for link force
+  LINK_FORCE             3.0  # (pN) magnitude scale factor for link force
-  P_XLINK                               .700  # (unitless) Max probability (at d=0) of forming a crosslink to a neighboring node
+  P_XLINK               .700  # (unitless) Max probability (at d=0) of forming a crosslink to a neighboring node
-  VARY_P_XLINK                    true   # (boolean) whether to reduce probability of crosslinking linearly with distance
+  VARY_P_XLINK          true  # (boolean) whether to reduce probability of crosslinking linearly with distance
 P_NUC defines the rate of nucleation of new nodes per unit area per unit time. i.e. for one iteration, the number of new nodes added over the whole of the nucleator surface is P_NUC * DELTA_T * surf_area, where surf_area is in µm<math>^2</math>.  The nodes are added at random positions on the surface, with an even distribution unless the ASYMMETRIC_NUCLEATION variable is set.
@@ Line 58: / Line 58: @@
 Nodes are added to the surface and fixed there while their repulsive forces are ramped up linearly from 0 to full.  This allows time for nodes already at the surface move and make room for the new node before it is crosslinked.  The ramp-up occurs over CROSSLINKDELAY iterations. MAX_LINKS_PER_NEW_NODE limits the maximum number of crosslinks for each new node. LINK_FORCE is the spring constant, and when the
 extension forces reaches LINK_BREAKAGE_FORCE, the link breaks.  P_XLINK is the probability of forming a crosslink to a node within range (still restricted by the MAX_LINKS_PER_NEW_NODE limit).  The VARY_P_XLINK flag (normally on) also imposes a linear tail-off of this probability with distance.
 ====Drag====

@@ Line 20: / Line 20: @@
 ====Nucleator Attachments====
-  STICK_TO_NUCLEATOR          true   # (boolean) whether nodes stick to nucleator upon creation
+  STICK_TO_NUCLEATOR      true # (boolean) whether nodes stick to nucleator upon creation
-  RESTICK_TO_NUCLEATOR      true   # (boolean) whether nodes stick to nucleator upon contact
+  RESTICK_TO_NUCLEATOR    true # (boolean) whether nodes stick to nucleator upon contact
-  NUC_LINK_FORCE                    2.0    # (pN/um) nucleator-node link force scaling factor
+  NUC_LINK_FORCE          2.0  # (pN/um) nucleator-node link force scaling factor
-  NUC_LINK_BREAKAGE_DIST 0.237  # (um) maximum nucleator-node link length before it breaks
+  NUC_LINK_BREAKAGE_DIST 0.237 # (um) maximum nucleator-node link length before it breaks
 When nodes are created, STICK_TO_NUCLEATOR defines whether they stick to their point of creation on the nucleator surface.  Stuck nodes exert a force proportional to NUC_LINK_FORCE multiplied by the distance from the surface stuck point until they are extended beyond NUC_LINK_BREAKAGE_DIST when the link breaks.  If RESTICK_TO_NUCLEATOR is true, ''unstuck''  nodes will re-stick if they come into contact with the surface again.

@@ Line 11: / Line 11: @@
 ====Nucleator Geometry====
-  SHAPE                                SPHERE  # (SPHERE, ELLIPSOID or CAPSULE) Nuleator shape
+  SHAPE                   SPHERE  # (SPHERE, ELLIPSOID or CAPSULE) Nuleator shape
-  ELLIPSOID_STRETCHFACTOR 1.5  #  (unitless) Ratio of major to minor ellipse axes
+  ELLIPSOID_STRETCHFACTOR    1.5  # (unitless) Ratio of major to minor ellipse axes
-  RADIUS                                     2.5  # (um) Radius of sphere, minor axis of ellipse, radius of capsule
+  RADIUS                     2.5  # (um) Radius of sphere, minor axis of ellipse, radius of capsule
   CAPSULE_HALF_LINEAR        2.75 # (um) Half the length of the linear section for capsule

@@ Line 3: / Line 3: @@
 ====Run Time====
-  TOTAL_SIMULATION_TIME   5600.0     # (s)             how long  to run the simulation for (in simulation-time seconds)
+  TOTAL_SIMULATION_TIME 5600.0  # (s) how long  to run the simulation for (in simulation-time seconds)
-  TOT_FRAMES                            700          #  (frames) how many frames in this time
+  TOT_FRAMES             700    # (frames) how many frames in this time
-  DELTA_T                                       0.01   # (s)             iteration timestep
+  DELTA_T                  0.01 # (s) iteration timestep
 TOTAL_SIMULATION_TIME defines the run length in simulation time (uncalibrated, nominally seconds).  TOT_FRAMES defines the number of frames to be taken during the run, i.e. 700 frames would mean one frame every 800 iterations.   Frames are not time units, but simply represent equal-spaced points in time when data is saved, bitmaps calculated, etc.  DELTA_T defines the time step between iterations, i.e. for the given TOTAL_SIMULATION_TIME of 5600 and DELTA_T of 0.01, there will be a total of 560000 iterations.  Increasing DELTA_T makes the run faster, but risks errors.  Generally, a too-large DELTA_T will result in warnings that nodes are entering significant distances into the nucleator before being ejected, but also check that the network behavior is not being affected by artifacts of too large a DELTA_T by reducing DELTA_T by a factor of 2 or more to see if you get the same result)