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This commit is contained in:
Nils Berglund
2024-08-17 12:04:42 +02:00
committed by GitHub
parent f7be9f43fc
commit 623d353390
18 changed files with 3808 additions and 491 deletions
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68
global_ljones.c
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@@ -11,14 +11,16 @@
#define D_CIRCLES 20 /* several circles */
#define D_CIRCLES_IN_RECT 201 /* several circles in a rectangle */
#define NMAXCIRCLES 100000 /* total number of circles/polygons (must be at least NCX*NCY for square grid) */
#define NMAXCIRCLES 200000 /* total number of circles/polygons (must be at least NCX*NCY for square grid) */
#define MAXNEIGH 20 /* max number of neighbours kept in memory */
#define NMAXOBSTACLES 1000 /* max number of obstacles */
#define NMAXSEGMENTS 1000 /* max number of repelling segments */
#define NMAXGROUPS 50 /* max number of groups of segments */
#define NMAXCOLLISIONS 200000 /* max number of collisions */
#define NMAXPARTNERS 30 /* max number of partners in molecule */
#define NMAXPARTNERMOLECULES 10 /* max number of partners of a molecule */
#define NMAXPARTNERMOLECULES 30 /* max number of partners of a molecule */
#define NMAXPARTINCLUSTER 500 /* max number of particles in cluster */
#define NMAXBELTS 10 /* max number of conveyor belts */
#define C_SQUARE 0 /* square grid of circles */
#define C_HEX 1 /* hexagonal/triangular grid of circles */
@@ -76,6 +78,7 @@
#define S_DAM_BRICKS 17 /* dam made of several bricks */
#define S_HLINE_HOLE 18 /* horizontal line with a hole in the bottom */
#define S_HLINE_HOLE_SPOKES 181 /* horizontal line with a hole in the bottom and extra spokes */
#define S_HLINE_HOLE_SLOPED 182 /* slanted lines with a hole */
#define S_EXT_CIRCLE_RECT 19 /* particles outside a circle and a rectangle */
#define S_BIN_OPENING 20 /* bin containing particles opening at deactivation time */
#define S_BIN_LARGE 201 /* larger bin */
@@ -88,6 +91,10 @@
#define S_CYLINDER 27 /* walls at top and bottom, for cylindrical b.c. */
#define S_TREE 28 /* Christmas tree(s) */
#define S_CONE 29 /* cone */
#define S_CONVEYOR_BELT 30 /* conveyor belt */
#define S_TWO_CONVEYOR_BELTS 31 /* two angled conveyor belts */
#define S_PERIODIC_CONVEYORS 32 /* one wrapping belt, and one short horizontal belt */
#define S_TEST_CONVEYORS 321 /* test */
/* particle interaction */
@@ -108,6 +115,10 @@
#define I_COULOMB_IMAGINARY 14 /* Coulomb interaction with "imaginary charge" */
#define I_DNA_CHARGED 15 /* Coulomb-type interaction between end points of DNA nucleotides */
#define I_DNA_CHARGED_B 151 /* stronger Coulomb-type interaction between end points of DNA nucleotides */
#define I_SEGMENT 16 /* harmonic interaction between segments */
#define I_SEGMENT_CHARGED 161 /* harmonic interaction between segments and Coulomb interaction between ends*/
#define I_POLYGON 17 /* harmonic interaction between regular polygons */
#define I_POLYGON_ALIGN 171 /* harmonic interaction between polygons with an aligning torque */
/* Boundary conditions */
@@ -208,6 +219,9 @@
#define CHEM_DNA_BASE_SPLIT 254 /* aggregation/splitting of DNA molecules when base pairs don't match */
#define CHEM_DNA_ENZYME 255 /* aggregation/splitting of DNA molecules in presence of enzymes */
#define CHEM_DNA_ENZYME_REPAIR 256 /* aggregation/splitting of DNA molecules in presence of enzymes and additional repairing of bad connections */
#define CHEM_POLYGON_AGGREGATION 26 /* aggregation of polygons */
#define CHEM_POLYGON_CLUSTER 261 /* clustering of polygons into new clusters */
#define CHEM_POLYGON_ONECLUSTER 262 /* clustering of polygons, with only one cluster allowed */
/* Initial conditions for chemical reactions */
@@ -254,12 +268,16 @@
#define P_NUMBER 12 /* colors depend on particle number */
#define P_EMEAN 13 /* averaged kinetic energy (with exponential damping) */
#define P_LOG_EMEAN 131 /* log of averaged kinetic energy (with exponential damping) */
#define P_EMEAN_DENSITY 132 /* averaged kinetic energy divided by the cluster size */
#define P_DIRECT_EMEAN 14 /* averaged version of P_DIRECT_ENERGY */
#define P_NOPARTICLE 15 /* particles are not drawn (only the links between them) */
#define P_NPARTNERS 16 /* number of partners */
#define P_CHARGE 17 /* colors represent charge */
#define P_MOL_ANGLE 18 /* orientation of molecule defined by partners */
#define P_CLUSTER 19 /* colors depend on connected component */
#define P_CLUSTER_SIZE 20 /* colors depend on size of connected component */
#define P_CLUSTER_SELECTED 21 /* colors show which clusters are slected for growth */
#define P_COLLISION 22 /* colors depend on number of collision/reaction */
/* Rotation schedules */
@@ -275,6 +293,8 @@
#define POLY_STAR 0 /* star-shaped graph (central molecule attracts outer ones) */
#define POLY_ALL 1 /* all-to-all coupling */
#define POLY_STAR_CHARGED 11 /* star-shaped graph with charged molecules */
#define POLY_POLYGON 12 /* polygonal shape */
#define POLY_WATER 2 /* star-shaped with a 120° separation between anions */
#define POLY_SOAP 3 /* polymers with all-to-all coupling and polar end */
#define POLY_SOAP_B 4 /* polymers with pairwise coupling and polar end */
@@ -287,6 +307,9 @@
#define POLY_DNA_ALT 71 /* simplified model for DNA with different short ends */
#define POLY_DNA_DOUBLE 72 /* simplified model for DNA with double ends for rigidity */
#define POLY_DNA_FLEX 73 /* simplified model for DNA with less backbone rigidity (beta) */
#define POLY_KITE 8 /* kite for kites and darts quasicrystal */
#define POLY_DART 81 /* dart for kites and darts quasicrystal */
#define POLY_SEG_POLYGON 9 /* polygon of segments */
/* Background color schemes */
@@ -365,18 +388,42 @@ typedef struct
int partner[NMAXPARTNERS]; /* partner particles for option PAIR_PARTICLES */
short int npartners; /* number of partner particles */
double partner_eqd[NMAXPARTNERS]; /* equilibrium distances between partners */
double partner_eqa[NMAXPARTNERS]; /* equilibrium angle between partners */
int p0, p1; /* numbers of two first partners (for P_MOL_ANGLE color scheme) */
// short int mol_angle; /* for color scheme P_MOL_ANGLE */
int cluster; /* number of cluster */
int cluster_color; /* color of cluster */
int cluster_size; /* size of cluster */
int molecule; /* number of molecule */
short int tested, cactive; /* for cluster search */
short int coulomb; /* has value 1 if DNA-Coulomb interaction is attractive */
short int added; /* has value 1 if particle has been added */
short int reactive; /* has value 1 if particle can react */
short int paired; /* has value 1 if belongs to base-paired molecule */
short int flip; /* keeps track of which particles in a cluster are flipped by PI */
int partner_molecule; /* number of partner molecule */
int collision; /* number of collision */
} t_particle;
typedef struct
{
short int active; /* has value 1 if cluster is active */
short int thermostat; /* has value 1 if cluster is coupled to thermostat */
short int selected; /* has value 1 if cluster is selected to be able to grow */
double xg, yg; /* center of gravity */
double vx, vy; /* velocity of center of gravity */
double angle; /* orientation of cluster */
double omega; /* angular velocity of cluster */
double mass, mass_inv; /* mass of cluster and its inverse */
double inertia_moment, inertia_moment_inv; /* moment of inertia */
double fx, fy, torque; /* force and torque */
double energy, emean; /* energy and averaged energy */
double dirmean; /* time-averaged direction */
int nparticles; /* number of particles in cluster */
int particle[NMAXPARTINCLUSTER]; /* list of particles in cluster */
// int angle_ref; /* reference particle for orientation */
} t_cluster;
typedef struct
{
int number; /* total number of particles in cell */
@@ -433,6 +480,8 @@ typedef struct
double pressure; /* pressure acting on segement */
double avrg_pressure; /* time-averaged pressure */
short int inactivate; /* set to 1 for segment to become inactive at time SEGMENT_DEACTIVATION_TIME */
short int conveyor; /* set to 1 for segment to exert lateral force */
double conveyor_speed; /* speed of conveyor belt */
} t_segment;
typedef struct
@@ -468,13 +517,24 @@ typedef struct
typedef struct
{
int nparticles; /* number of particles */
int particle[NPARTNERS+1]; /* list of particles */
int particle[2*NPARTNERS+1]; /* list of particles */
int npartners; /* number of partner molecules */
int partner[NMAXPARTNERMOLECULES]; /* list of partner molecules */
int connection_type[NMAXPARTNERMOLECULES]; /* types of particles in connection */
short int added; /* has value 1 if molecule has been added */
} t_molecule;
typedef struct
{
double x1, y1, x2, y2; /* positions of extremities */
double width; /* width of belt */
double speed; /* speed of conveyor belt */
double position; /* position of belt (needed for display of rotating parts) */
double length; /* distance between (x1,x2) and (y1,y2) */
double angle; /* angle of (x1,x2) - (y1,y2) */
double tx, ty; /* coordinates of tangent vector */
} t_belt;
typedef struct
{
int nactive; /* number of active particles */
@@ -496,6 +556,6 @@ typedef struct
int frame_time = 0, ncircles, nobstacles, nsegments, ngroups = 1, counter = 0, nmolecules = 0;
int frame_time = 0, ncircles, nobstacles, nsegments, ngroups = 1, counter = 0, nmolecules = 0, nbelts = 0;
FILE *lj_log;