MEDYAN  3.1
Software for simulating active matter dynamics
common.h
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1 
2 //------------------------------------------------------------------
3 // **MEDYAN** - Simulation Package for the Mechanochemical
4 // Dynamics of Active Networks, v3.1
5 //
6 // Copyright (2015-2016) Papoian Lab, University of Maryland
7 //
8 // ALL RIGHTS RESERVED
9 //
10 // See the MEDYAN web page for more information:
11 // http://www.medyan.org
12 //------------------------------------------------------------------
13 
14 #ifndef MEDYAN_common_h
15 #define MEDYAN_common_h
16 
17 #include <iostream>
18 #include <vector>
19 #include <boost/signals2/shared_connection_block.hpp>
20 
21 #include "utility.h"
22 
24 typedef unsigned int species_copy_t;
25 const species_copy_t max_ulim = 1000000;
26 
28 extern double global_time;
29 
30 inline double tau() {return global_time;}
31 inline void resetglobaltime() {global_time=0.0;}
33 const double kT = 4.1; //in pN * nm
34 
36 using namespace std;
37 
39 typedef boost::signals2::shared_connection_block ConnectionBlock;
40 
42 #define MAX_FILAMENT_TYPES 10
43 
45 
48 #define SPECIESFILAMENT 0
49 #define SPECIESPLUSEND 1
50 #define SPECIESMINUSEND 2
51 
52 #define SPECIESBOUND 0
53 #define SPECIESLINKER 1
54 #define SPECIESMOTOR 2
55 #define SPECIESBRANCHER 3
56 
57 
59 
63 #define POLYREACTANTS 2
64 #define POLYPRODUCTS 2
65 
67 #define DEPOLYREACTANTS 2
68 #define DEPOLYPRODUCTS 2
69 
71 #define LMBINDINGREACTANTS 3
72 #define LMBINDINGPRODUCTS 2
73 
75 #define LMUNBINDINGREACTANTS 2
76 #define LMUNBINDINGPRODUCTS 3
77 
79 #define MWALKINGREACTANTS 2
80 #define MWALKINGPRODUCTS 2
81 
83 #define NUCLEATIONREACTANTS 2
84 #define NUCLEATIONPRODUCTS 3
85 
87 #define DESTRUCTIONREACTANTS 2
88 #define DESTRUCTIONPRODUCTS 2
89 
91 #define AGINGREACTANTS 1
92 #define AGINGPRODUCTS 1
93 
95 #define SEVERINGREACTANTS 1
96 #define SEVERINGPRODUCTS 0
97 
99 #define BRANCHINGREACTANTS 3
100 #define BRANCHINGPRODUCTS 2
101 
103 #define BUNBINDINGREACTANTS 1
104 #define BUNBINDINGPRODUCTS 2
105 
106 
107 #endif
unsigned int species_copy_t
Species constants.
Definition: common.h:24
const species_copy_t max_ulim
Definition: common.h:25
STL namespace.
boost::signals2::shared_connection_block ConnectionBlock
Boost typedef.
Definition: common.h:39
void resetglobaltime()
Definition: common.h:31
const double kT
Some constants.
Definition: common.h:33
double global_time
Global time.
Definition: common.cpp:16
double tau()
Definition: common.h:30