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Nils Berglund
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216
lennardjones.c
216
lennardjones.c
@@ -34,10 +34,10 @@
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#include <sys/types.h>
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#include <tiffio.h> /* Sam Leffler's libtiff library. */
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#include <omp.h>
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#include <time.h>
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#include <time.h>
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#define MOVIE 0 /* set to 1 to generate movie */
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#define DOUBLE_MOVIE 1 /* set to 1 to produce movies for wave height and energy simultaneously */
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#define DOUBLE_MOVIE 0 /* set to 1 to produce movies for wave height and energy simultaneously */
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#define SAVE_MEMORY 1 /* set to 1 to save memory while saving frames */
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#define NO_EXTRA_BUFFER_SWAP 1 /* some OS require one less buffer swap when recording images */
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@@ -58,47 +58,50 @@
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#define YMIN -1.125
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#define YMAX 1.125 /* y interval for 9/16 aspect ratio */
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#define INITXMIN -1.8
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#define INITXMAX 1.8 /* x interval for initial condition */
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#define INITYMIN 0.9
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#define INITYMAX 2.2 /* y interval for initial condition */
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#define INITXMIN -2.1
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#define INITXMAX -2.0 /* x interval for initial condition */
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#define INITYMIN -0.7
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#define INITYMAX -0.6 /* y interval for initial condition */
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#define THERMOXMIN -1.25
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#define THERMOXMAX 1.25 /* x interval for initial condition */
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#define THERMOYMIN 0.0
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#define THERMOYMAX 0.75 /* y interval for initial condition */
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#define ADDXMIN -1.5
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#define ADDXMAX 1.5 /* x interval for adding particles */
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#define ADDYMIN -1.0
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#define ADDYMAX 1.0 /* y interval for adding particles */
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#define ADDXMIN -2.1
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#define ADDXMAX -2.0 /* x interval for adding particles */
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#define ADDYMIN -0.6
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#define ADDYMAX -0.5 /* y interval for adding particles */
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#define ADDRMIN 4.75
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#define ADDRMAX 6.0 /* r interval for adding particles */
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#define BCXMIN -2.0
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#define BCXMIN -2.2
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#define BCXMAX 2.0 /* x interval for boundary condition */
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#define BCYMIN -1.125
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#define BCYMAX 2.4 /* y interval for boundary condition */
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#define BCYMAX 1.4 /* y interval for boundary condition */
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#define OBSXMIN -2.0
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#define OBSXMAX 2.0 /* x interval for motion of obstacle */
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#define CIRCLE_PATTERN 8 /* pattern of circles, see list in global_ljones.c */
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#define CIRCLE_PATTERN 1 /* pattern of circles, see list in global_ljones.c */
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#define ADD_INITIAL_PARTICLES 0 /* set to 1 to add a second type of particles */
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#define CIRCLE_PATTERN_B 0 /* pattern of circles for additional particles */
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#define ADD_FIXED_OBSTACLES 0 /* set to 1 do add fixed circular obstacles */
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#define OBSTACLE_PATTERN 71 /* pattern of obstacles, see list in global_ljones.c */
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#define OBSTACLE_PATTERN 82 /* pattern of obstacles, see list in global_ljones.c */
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#define RATTLE_OBSTACLES 1 /* set to 1 to rattle obstacles (for pattern O_SIEVE_B) */
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#define ADD_FIXED_SEGMENTS 1 /* set to 1 to add fixed segments as obstacles */
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#define SEGMENT_PATTERN 182 /* pattern of repelling segments, see list in global_ljones.c */
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#define SEGMENT_PATTERN 361 /* pattern of repelling segments, see list in global_ljones.c */
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#define ROCKET_SHAPE 3 /* shape of rocket combustion chamber, see list in global_ljones.c */
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#define ROCKET_SHAPE_B 3 /* shape of second rocket */
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#define NOZZLE_SHAPE 6 /* shape of nozzle, see list in global_ljones.c */
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#define NOZZLE_SHAPE_B 6 /* shape of nozzle for second rocket, see list in global_ljones.c */
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#define BELT_SPEED1 20.0 /* speed of first conveyor belt */
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#define BELT_SPEED2 -10.0 /* speed of second conveyor belt */
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#define BELT_SPEED1 10.0 /* speed of first conveyor belt */
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#define BELT_SPEED2 15.0 /* speed of second conveyor belt */
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#define BELT_SPEED3 6.0 /* speed of second conveyor belt */
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#define OBSTACLE_OMEGA 300.0 /* obstacle rotation speed */
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#define TWO_TYPES 0 /* set to 1 to have two types of particles */
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#define TYPE_PROPORTION 0.5 /* proportion of particles of first type */
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@@ -108,22 +111,22 @@
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#define CENTER_PY 0 /* set to 1 to center vertical momentum */
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#define CENTER_PANGLE 0 /* set to 1 to center angular momentum */
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#define INTERACTION 171 /* particle interaction, see list in global_ljones.c */
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#define INTERACTION 1 /* particle interaction, see list in global_ljones.c */
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#define INTERACTION_B 1 /* particle interaction for second type of particle, see list in global_ljones.c */
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#define SPIN_INTER_FREQUENCY 6.0 /* angular frequency of spin-spin interaction */
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#define SPIN_INTER_FREQUENCY_B 6.0 /* angular frequency of spin-spin interaction for second particle type */
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#define MOL_ANGLE_FACTOR 6.0 /* rotation angle for P_MOL_ANGLE color scheme */
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#define SPIN_INTER_FREQUENCY 4.0 /* angular frequency of spin-spin interaction */
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#define SPIN_INTER_FREQUENCY_B 4.0 /* angular frequency of spin-spin interaction for second particle type */
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#define MOL_ANGLE_FACTOR 4.0 /* rotation angle for P_MOL_ANGLE color scheme */
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#define P_PERCOL 0.25 /* probability of having a circle in C_RAND_PERCOL arrangement */
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#define NPOISSON 100 /* number of points for Poisson C_RAND_POISSON arrangement */
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#define PDISC_DISTANCE 2.5 /* minimal distance in Poisson disc process, controls density of particles */
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#define PDISC_DISTANCE 1.0 /* minimal distance in Poisson disc process, controls density of particles */
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#define PDISC_CANDIDATES 100 /* number of candidates in construction of Poisson disc process */
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#define RANDOM_POLY_ANGLE 0 /* set to 1 to randomize angle of polygons */
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#define LAMBDA 0.2 /* parameter controlling the dimensions of domain */
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#define MU 0.025 /* parameter controlling radius of particles */
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#define MU 0.02 /* parameter controlling radius of particles */
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#define MU_B 0.03 /* parameter controlling radius of particles of second type */
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#define NPOLY 6 /* number of sides of polygon */
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#define NPOLY 3 /* number of sides of polygon */
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#define APOLY 0.075 /* angle by which to turn polygon, in units of Pi/2 */
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#define AWEDGE 0.5 /* opening angle of wedge, in units of Pi/2 */
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#define MDEPTH 4 /* depth of computation of Menger gasket */
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@@ -131,8 +134,8 @@
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#define MANDELLEVEL 1000 /* iteration level for Mandelbrot set */
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#define MANDELLIMIT 10.0 /* limit value for approximation of Mandelbrot set */
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#define FOCI 1 /* set to 1 to draw focal points of ellipse */
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#define NGRIDX 36 /* number of grid point for grid of disks */
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#define NGRIDY 36 /* number of grid point for grid of disks */
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#define NGRIDX 1 /* number of grid point for grid of disks */
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#define NGRIDY 1 /* number of grid point for grid of disks */
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#define EHRENFEST_RADIUS 0.9 /* radius of container for Ehrenfest urn configuration */
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#define EHRENFEST_WIDTH 0.035 /* width of tube for Ehrenfest urn configuration */
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#define TWO_CIRCLES_RADIUS_RATIO 0.8 /* ratio of radii for S_TWO_CIRCLES_EXT segment configuration */
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@@ -148,10 +151,10 @@
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/* Parameters for length and speed of simulation */
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#define NSTEPS 2700 /* number of frames of movie */
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#define NVID 200 /* number of iterations between images displayed on screen */
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#define NSTEPS 4800 /* number of frames of movie */
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#define NVID 120 /* number of iterations between images displayed on screen */
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#define NSEG 25 /* number of segments of boundary of circles */
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#define INITIAL_TIME 200 /* time after which to start saving frames */
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#define INITIAL_TIME 0 /* time after which to start saving frames */
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#define OBSTACLE_INITIAL_TIME 0 /* time after which to start moving obstacle */
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#define BOUNDARY_WIDTH 1 /* width of particle boundary */
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#define LINK_WIDTH 2 /* width of links between particles */
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@@ -170,8 +173,8 @@
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/* Plot type, see list in global_ljones.c */
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#define PLOT 11
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#define PLOT_B 14 /* plot type for second movie */
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#define PLOT 23
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#define PLOT_B 13 /* plot type for second movie */
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/* Background color depending on particle properties */
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@@ -185,7 +188,7 @@
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#define DRAW_CLUSTER_LINKS 0 /* set to 1 to draw links between particles in cluster */
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#define ALTITUDE_LINES 0 /* set to 1 to add horizontal lines to show altitude */
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#define COLOR_SEG_GROUPS 0 /* set to 1 to collor segment groups differently */
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#define N_PARTICLE_COLORS 200 /* number of colors for P_NUMBER color scheme */
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#define N_PARTICLE_COLORS 300 /* number of colors for P_NUMBER color scheme */
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#define INITIAL_POS_TYPE 0 /* type of initial position dependence */
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#define ERATIO 0.995 /* ratio for time-averaging in P_EMEAN color scheme */
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#define DRATIO 0.999 /* ratio for time-averaging in P_DIRECT_EMEAN color scheme */
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@@ -240,7 +243,7 @@
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#define PARTICLE_HUE_MIN 359.0 /* color of original particle */
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#define PARTICLE_HUE_MAX 0.0 /* color of saturated particle */
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#define PARTICLE_EMIN 10.0 /* energy of particle with coolest color */
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#define PARTICLE_EMAX 100.0 /* energy of particle with hottest color */
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#define PARTICLE_EMAX 2000.0 /* energy of particle with hottest color */
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#define HUE_TYPE0 320.0 /* hue of particles of type 0 */
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#define HUE_TYPE1 60.0 /* hue of particles of type 1 */
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#define HUE_TYPE2 320.0 /* hue of particles of type 2 */
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@@ -251,21 +254,27 @@
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#define HUE_TYPE7 150.0 /* hue of particles of type 7 */
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#define BG_FORCE_SLOPE 7.5e-8 /* contant in BG_FORCE backgound color scheme*/
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#define RANDOM_RADIUS 0 /* set to 1 for random circle radius */
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#define RANDOM_RADIUS 1 /* set to 1 for random particle radius */
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#define RANDOM_RADIUS_MIN 0.25 /* min of random particle radius (default 0.75) */
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#define RANDOM_RADIUS_RANGE 1.5 /* range of random particle radius (default 0.5) */
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#define ADAPT_MASS_TO_RADIUS 0 /* set to positive value to for mass prop to power of radius */
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#define ADAPT_DAMPING_TO_RADIUS 0.5 /* set to positive value to for friction prop to power of radius */
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#define ADAPT_DAMPING_FACTOR 0.5 /* factor by which damping is adapted to radius */
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#define DT_PARTICLE 3.0e-6 /* time step for particle displacement */
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#define KREPEL 50.0 /* constant in repelling force between particles */
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#define EQUILIBRIUM_DIST 2.3 /* Lennard-Jones equilibrium distance */
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#define EQUILIBRIUM_DIST 2.5 /* Lennard-Jones equilibrium distance */
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#define EQUILIBRIUM_DIST_B 2.5 /* Lennard-Jones equilibrium distance for second type of particle */
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#define SEGMENT_FORCE_EQR 1.0 /* equilibrium distance factor for force from segments (default 1.5) */
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#define REPEL_RADIUS 25.0 /* radius in which repelling force acts (in units of particle radius) */
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#define DAMPING 500.0 /* damping coefficient of particles */
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#define DAMPING 150.0 /* damping coefficient of particles */
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#define INITIAL_DAMPING 1000.0 /* damping coefficient of particles during initial phase */
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#define DAMPING_ROT 1000.0 /* damping coefficient for rotation of particles */
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#define DAMPING_ROT 5.0 /* damping coefficient for rotation of particles */
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#define PARTICLE_MASS 2.0 /* mass of particle of radius MU */
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#define PARTICLE_MASS_B 2.0 /* mass of particle of radius MU_B */
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#define PARTICLE_INERTIA_MOMENT 0.5 /* moment of inertia of particle */
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#define PARTICLE_INERTIA_MOMENT_B 0.5 /* moment of inertia of second type of particle */
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#define V_INITIAL 50.0 /* initial velocity range */
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#define OMEGA_INITIAL 50.0 /* initial angular velocity range */
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#define V_INITIAL 800.0 /* initial velocity range */
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#define OMEGA_INITIAL 100.0 /* initial angular velocity range */
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#define VICSEK_VMIN 1.0 /* minimal speed of particles in Vicsek model */
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#define VICSEK_VMAX 40.0 /* minimal speed of particles in Vicsek model */
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#define COULOMB_LJ_FACTOR 1.0 /* relative intensity of LJ interaction in I_COULOMB_LJ interaction (default: 0.01) */
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@@ -279,8 +288,8 @@
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#define MU_XI 0.005 /* friction constant in thermostat */
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#define KSPRING_BOUNDARY 2.0e11 /* confining harmonic potential outside simulation region */
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#define KSPRING_OBSTACLE 1.0e9 /* harmonic potential of obstacles */
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#define NBH_DIST_FACTOR 4.0 /* radius in which to count neighbours */
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#define GRAVITY 4000.0 /* gravity acting on all particles */
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#define NBH_DIST_FACTOR 4.0 /* radius in which to count neighbours */
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#define GRAVITY 5000.0 /* gravity acting on all particles */
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#define GRAVITY_X 0.0 /* horizontal gravity acting on all particles */
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#define CIRCULAR_GRAVITY 0 /* set to 1 to have gravity directed to center */
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#define INCREASE_GRAVITY 0 /* set to 1 to increase gravity during the simulation */
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@@ -292,24 +301,29 @@
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#define VICSEK_REPULSION 10.0 /* repulsion between particles in Vicsek model */
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#define ADD_EFIELD 0 /* set to 1 to add an electric field */
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#define EFIELD 100000.0 /* value of electric field */
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#define EFIELD 30000.0 /* value of electric field */
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#define ADD_BFIELD 0 /* set to 1 to add a magnetic field */
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#define BFIELD 2.666666667 /* value of magnetic field */
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#define BFIELD 225.0 /* value of magnetic field */
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#define CHARGE 1.0 /* charge of particles of first type */
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#define CHARGE_B 1.0 /* charge of particles of second type */
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#define INCREASE_E 0 /* set to 1 to increase electric field */
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#define EFIELD_FACTOR 5000000.0 /* factor by which to increase electric field */
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#define INCREASE_B 0 /* set to 1 to increase magnetic field */
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#define BFIELD_FACTOR 20000.0 /* factor by which to increase magnetic field */
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#define BFIELD_FACTOR 1.0 /* factor by which to increase magnetic field */
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#define CHARGE_OBSTACLES 0 /* set to 1 for obstacles to be charged */
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#define OBSTACLE_CHARGE 3.0 /* charge of obstacles */
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#define KCOULOMB_OBSTACLE 1000.0 /* Coulomb force constant for charged obstacles */
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#define BFIELD_REGION 1 /* space-dependent magnetic field (0 for constant) */
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#define ADD_WIND 1 /* set to 1 to add a "wind" friction force */
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#define WIND_FORCE 1.35e6 /* force of wind */
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#define WIND_YMIN -0.6 /* min altitude of region with wind */
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#define ROTATION 1 /* set to 1 to include rotation of particles */
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#define COUPLE_ANGLE_TO_THERMOSTAT 0 /* set to 1 to couple angular degrees of freedom to thermostat */
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#define DIMENSION_FACTOR 1.0 /* scaling factor taking into account number of degrees of freedom */
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#define KTORQUE 5.0e3 /* force constant in angular dynamics */
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#define KTORQUE_BOUNDARY 5.0e5 /* constant in torque from the boundary */
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#define KTORQUE 1.0e5 /* force constant in angular dynamics */
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#define KTORQUE_BOUNDARY 1.0e5 /* constant in torque from the boundary */
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#define KTORQUE_B 10.0 /* force constant in angular dynamics */
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#define KTORQUE_DIFF 500.0 /* force constant in angular dynamics for different particles */
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#define DRAW_SPIN 0 /* set to 1 to draw spin vectors of particles */
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@@ -341,7 +355,7 @@
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#define CENTER_VIEW_ON_OBSTACLE 0 /* set to 1 to center display on moving obstacle */
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#define RESAMPLE_Y 0 /* set to 1 to resample y coordinate of moved particles (for shock waves) */
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#define NTRIALS 2000 /* number of trials when resampling */
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#define OBSTACLE_RADIUS 0.015 /* radius of obstacle for circle boundary conditions */
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#define OBSTACLE_RADIUS 0.018 /* radius of obstacle for circle boundary conditions */
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#define FUNNEL_WIDTH 0.25 /* funnel width for funnel boundary conditions */
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#define OBSTACLE_XMIN 0.0 /* initial position of obstacle */
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#define OBSTACLE_XMAX 3.0 /* final position of obstacle */
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@@ -365,19 +379,20 @@
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#define MASS_PART_BOTTOM 10000.0 /* mass of particles at bottom */
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#define NPART_BOTTOM 100 /* number of particles at the bottom */
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#define ADD_PARTICLES 0 /* set to 1 to add particles */
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#define ADD_PARTICLES 1 /* set to 1 to add particles */
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#define ADD_REGION 0 /* shape of add regions, cf ADD_* in global_ljones */
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#define ADD_TIME 50 /* time at which to add first particle */
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#define ADD_PERIOD 2 /* time interval between adding further particles */
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#define N_ADD_PARTICLES 8 /* number of particles to add */
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#define FINAL_NOADD_PERIOD 4700 /* final period where no particles are added */
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#define ADD_TIME 0 /* time at which to add first particle */
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#define ADD_PERIOD 15 /* time interval between adding further particles */
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#define N_ADD_PARTICLES 1 /* number of particles to add */
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#define FINAL_NOADD_PERIOD 500 /* final period where no particles are added */
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#define SAFETY_FACTOR 4.0 /* no particles are added at distance less than MU*SAFETY_FACTOR of other particles */
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#define TRACER_PARTICLE 0 /* set to 1 to have a tracer particle */
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#define N_TRACER_PARTICLES 3 /* number of tracer particles */
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#define TRAJECTORY_LENGTH 8000 /* length of recorded trajectory */
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#define TRACER_PARTICLE_MASS 4.0 /* relative mass of tracer particle */
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#define TRAJECTORY_WIDTH 3 /* width of tracer particle trajectory */
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#define TRACER_PARTICLE 1 /* set to 1 to have a tracer particle */
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#define N_TRACER_PARTICLES 500 /* number of tracer particles */
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#define TRAJECTORY_LENGTH 4800 /* length of recorded trajectory */
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#define TRACER_LUM_FACTOR 5.0 /* controls luminosity decrease of trajectories with time */
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#define TRACER_PARTICLE_MASS 4.0 /* relative mass of tracer particle */
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#define TRAJECTORY_WIDTH 3 /* width of tracer particle trajectory */
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#define ROTATE_BOUNDARY 0 /* set to 1 to rotate the repelling segments */
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#define SMOOTH_ROTATION 1 /* set to 1 to update segments at each time step (rather than at each movie frame) */
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@@ -463,7 +478,7 @@
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#define LID_WIDTH 0.1 /* width of lid for BC_RECTANGLE_LID b.c. */
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#define WALL_MASS 2000.0 /* mass of wall for BC_RECTANGLE_WALL b.c. */
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#define WALL_FRICTION 0.0 /* friction on wall for BC_RECTANGLE_WALL b.c. */
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#define WALL_WIDTH 0.025 /* width of wall for BC_RECTANGLE_WALL b.c. */
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#define WALL_WIDTH 0.015 /* width of wall for BC_RECTANGLE_WALL b.c. */
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#define WALL_VMAX 100.0 /* max speed of wall */
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#define WALL_TIME 0 /* time during which to keep wall */
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@@ -514,8 +529,8 @@
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#define FLOOR_OMEGA 0 /* set to 1 to limit particle momentum to PMAX */
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#define PMAX 1000.0 /* maximal force */
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#define HASHX 100 /* size of hashgrid in x direction */
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#define HASHY 88 /* size of hashgrid in y direction */
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#define HASHX 40 /* size of hashgrid in x direction */
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#define HASHY 20 /* size of hashgrid in y direction */
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#define HASHMAX 100 /* maximal number of particles per hashgrid cell */
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#define HASHGRID_PADDING 0.1 /* padding of hashgrid outside simulation window */
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@@ -534,7 +549,10 @@
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#define COUNT_PARTNER_TYPE ((RD_REACTION == CHEM_H2O_H_OH)||(RD_REACTION == CHEM_2H2O_H3O_OH))
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#define PAIR_FORCE ((PAIR_PARTICLES)||((REACTION_DIFFUSION)&&((RD_REACTION == CHEM_AGGREGATION)||(RD_REACTION == CHEM_AGGREGATION_CHARGE)||(RD_REACTION == CHEM_AGGREGATION_NNEIGH)||(RD_REACTION == CHEM_POLYGON_AGGREGATION))))
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#define COMPUTE_PAIR_TORQUE (KTORQUE_PAIR_ANGLE != 0.0)
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#define ADD_CONVEYOR_FORCE ((ADD_FIXED_SEGMENTS)&&((SEGMENT_PATTERN == S_CONVEYOR_BELT)||(SEGMENT_PATTERN == S_TWO_CONVEYOR_BELTS)||(SEGMENT_PATTERN == S_PERIODIC_CONVEYORS)||(SEGMENT_PATTERN == S_TEST_CONVEYORS)))
|
||||
#define ADD_CONVEYOR_FORCE ((ADD_FIXED_SEGMENTS)&&((SEGMENT_PATTERN == S_CONVEYOR_BELT)||(SEGMENT_PATTERN == S_TWO_CONVEYOR_BELTS)||(SEGMENT_PATTERN == S_PERIODIC_CONVEYORS)||(SEGMENT_PATTERN == S_TEST_CONVEYORS)||(SEGMENT_PATTERN == S_CONVEYOR_SHOVELS)||(SEGMENT_PATTERN == S_CONVEYOR_MIXED)||(SEGMENT_PATTERN == S_CONVEYOR_SIEVE)||(SEGMENT_PATTERN == S_CONVEYOR_SIEVE_B)||(SEGMENT_PATTERN == S_CONVEYOR_SIEVE_LONG)))
|
||||
#define MOVE_CONVEYOR_BELT ((ADD_FIXED_SEGMENTS)&&((SEGMENT_PATTERN == S_CONVEYOR_SHOVELS)||(SEGMENT_PATTERN == S_CONVEYOR_MIXED)||(SEGMENT_PATTERN == S_CONVEYOR_SIEVE_LONG)))
|
||||
#define ROTATE_OBSTACLES ((ADD_FIXED_OBSTACLES)&&((OBSTACLE_PATTERN == O_SIEVE)||(OBSTACLE_PATTERN == O_SIEVE_B)||(OBSTACLE_PATTERN == O_SIEVE_LONG)))
|
||||
#define POLYGON_INTERACTION ((INTERACTION == I_POLYGON)||(INTERACTION == I_POLYGON_ALIGN))
|
||||
|
||||
double xshift = 0.0; /* x shift of shown window */
|
||||
double xspeed = 0.0; /* x speed of obstacle */
|
||||
@@ -968,7 +986,7 @@ double evolve_particles(t_particle particle[NMAXCIRCLES], t_hashgrid hashgrid[HA
|
||||
double px[NMAXCIRCLES], double py[NMAXCIRCLES], double pangle[NMAXCIRCLES],
|
||||
double beta, int *nactive, int *nsuccess, int *nmove, int *ncoupled, int initial_phase)
|
||||
{
|
||||
double a, totalenergy = 0.0, damping, direction, dmean;
|
||||
double a, totalenergy = 0.0, damping, damping1, damping_rot1, direction, dmean, dratio;
|
||||
static double b = 0.25*SIGMA*SIGMA*DT_PARTICLE/MU_XI, xi = 0.0;
|
||||
int j, move, ncoup;
|
||||
|
||||
@@ -983,7 +1001,7 @@ double evolve_particles(t_particle particle[NMAXCIRCLES], t_hashgrid hashgrid[HA
|
||||
particle[j].vx = px[j] + 0.5*DT_PARTICLE*particle[j].fx;
|
||||
particle[j].vy = py[j] + 0.5*DT_PARTICLE*particle[j].fy;
|
||||
particle[j].omega = pangle[j] + 0.5*DT_PARTICLE*particle[j].torque;
|
||||
|
||||
|
||||
px[j] = particle[j].vx + 0.5*DT_PARTICLE*particle[j].fx;
|
||||
py[j] = particle[j].vy + 0.5*DT_PARTICLE*particle[j].fy;
|
||||
pangle[j] = particle[j].omega + 0.5*DT_PARTICLE*particle[j].torque;
|
||||
@@ -1043,19 +1061,26 @@ double evolve_particles(t_particle particle[NMAXCIRCLES], t_hashgrid hashgrid[HA
|
||||
}
|
||||
|
||||
move = 0;
|
||||
damping1 = damping;
|
||||
damping_rot1 = DAMPING_ROT;
|
||||
for (j=0; j<ncircles; j++) if (particle[j].active)
|
||||
{
|
||||
if (ADAPT_DAMPING_TO_RADIUS > 0.0)
|
||||
{
|
||||
damping1 = damping*particle[j].damping;
|
||||
damping_rot1 = DAMPING_ROT*particle[j].damping;
|
||||
}
|
||||
if ((THERMOSTAT_ON)&&(particle[j].thermostat))
|
||||
{
|
||||
px[j] *= exp(- 0.5*DT_PARTICLE*xi);
|
||||
py[j] *= exp(- 0.5*DT_PARTICLE*xi);
|
||||
if (!COUPLE_ANGLE_TO_THERMOSTAT) pangle[j] *= exp(- DT_PARTICLE*DAMPING_ROT);
|
||||
if (!COUPLE_ANGLE_TO_THERMOSTAT) pangle[j] *= exp(- DT_PARTICLE*damping_rot1);
|
||||
}
|
||||
else
|
||||
{
|
||||
px[j] *= exp(- DT_PARTICLE*damping);
|
||||
py[j] *= exp(- DT_PARTICLE*damping);
|
||||
pangle[j] *= exp(- DT_PARTICLE*DAMPING_ROT);
|
||||
px[j] *= exp(- DT_PARTICLE*damping1);
|
||||
py[j] *= exp(- DT_PARTICLE*damping1);
|
||||
pangle[j] *= exp(- DT_PARTICLE*damping_rot1);
|
||||
// printf("Damping particle angular velocity\n");
|
||||
}
|
||||
if ((THERMOSTAT_ON)&&(COUPLE_ANGLE_TO_THERMOSTAT)&&(particle[j].thermostat))
|
||||
@@ -1542,13 +1567,13 @@ void animation()
|
||||
{
|
||||
double time, scale, diss, rgb[3], dissip, gradient[2], x, y, dx, dy, dt, xleft, xright,
|
||||
a, b, length, fx, fy, force[2], totalenergy = 0.0, pos[2], prop, vx, xi = 0.0, torque, torque_ij, pleft = 0.0, pright = 0.0, entropy[2], speed_ratio, xmin, xmax, ymin, ymax, delta_energy, speed, ratio = 1.0, ratioc, cum_etot = 0.0, emean = 0.0, radius_ratio, t,
|
||||
angle, theta, sum, alpha;
|
||||
angle, theta, sum, alpha, bfield;
|
||||
double *qx, *qy, *px, *py, *qangle, *pangle, *pressure, *obstacle_speeds;
|
||||
double *cqx, *cqy, *cpx, *cpy, *cqangle, *cpangle;
|
||||
int i, j, k, n, m, s, ij[2], i0, iplus, iminus, j0, jplus, jminus, p, q, p1, q1, p2, q2, total_neighbours = 0, cl,
|
||||
min_nb, max_nb, close, wrapx = 0, wrapy = 0, nadd_particle = 0, nmove = 0, nsuccess = 0,
|
||||
tracer_n[N_TRACER_PARTICLES], traj_position = 0, traj_length = 0, move = 0, old, m0, floor, nthermo, wall = 0,
|
||||
group, gshift, n_total_active = 0, ncollisions = 0, ncoupled = 1, np, belt;
|
||||
group, gshift, n_total_active = 0, ncollisions = 0, ncoupled = 1, np, belt, obs;
|
||||
int *particle_numbers;
|
||||
static int imin, imax;
|
||||
static short int first = 1;
|
||||
@@ -1702,7 +1727,9 @@ void animation()
|
||||
if (INCREASE_KREPEL) params.krepel = repel_schedule(i);
|
||||
if (INCREASE_BETA) params.beta = temperature_schedule(i);
|
||||
if (INCREASE_E) params.efield = efield_schedule(i);
|
||||
else params.efield = EFIELD;
|
||||
if (INCREASE_B) params.bfield = bfield_schedule(i);
|
||||
else params.bfield = BFIELD;
|
||||
if ((PARTIAL_THERMO_COUPLING)&&(PARTIAL_THERMO_REGION == TH_RING_EXPAND))
|
||||
params.thermo_radius = PARTIAL_THERMO_RIN + (double)i/(double)NSTEPS*(PARTIAL_THERMO_RFIN - PARTIAL_THERMO_RIN);
|
||||
if (DECREASE_CONTAINER_SIZE)
|
||||
@@ -1918,8 +1945,17 @@ void animation()
|
||||
/* add magnetic force */
|
||||
if (ADD_BFIELD)
|
||||
{
|
||||
particle[j].fx += params.bfield*particle[j].charge*particle[j].vy*particle[j].mass_inv;
|
||||
particle[j].fy -= params.bfield*particle[j].charge*particle[j].vx*particle[j].mass_inv;
|
||||
bfield = params.bfield;
|
||||
if (BFIELD_REGION != BF_CONST)
|
||||
bfield *= (double)partial_bfield(particle[j].xc, particle[j].yc);
|
||||
particle[j].fx += bfield*particle[j].charge*particle[j].vy*particle[j].mass_inv;
|
||||
particle[j].fy -= bfield*particle[j].charge*particle[j].vx*particle[j].mass_inv;
|
||||
}
|
||||
|
||||
/* add wind force */
|
||||
if ((ADD_WIND)&&(particle[j].yc > WIND_YMIN))
|
||||
{
|
||||
particle[j].fx += WIND_FORCE*particle[j].radius*particle[j].mass_inv;
|
||||
}
|
||||
|
||||
if (FLOOR_FORCE)
|
||||
@@ -1968,6 +2004,22 @@ void animation()
|
||||
if (ADD_CONVEYOR_FORCE) for (belt = 0; belt < nbelts; belt++)
|
||||
conveyor_belt[belt].position += conveyor_belt[belt].speed*DT_PARTICLE;
|
||||
|
||||
if (MOVE_CONVEYOR_BELT)
|
||||
update_conveyor_belts(segment, conveyor_belt);
|
||||
|
||||
if (ROTATE_OBSTACLES) for (obs = 0; obs < nobstacles; obs++)
|
||||
{
|
||||
/* TEST */
|
||||
obstacle[obs].omega = obstacle[obs].omega0*(1.0 + 0.5*cos(i*DPI/200.0));
|
||||
obstacle[obs].angle -= obstacle[obs].omega*DT_PARTICLE;
|
||||
if ((RATTLE_OBSTACLES)&&(obstacle[obs].oscillate))
|
||||
{
|
||||
theta = obstacle[obs].phase + DPI*(double)i/(double)obstacle[obs].period;
|
||||
obstacle[obs].xc = obstacle[obs].xc0 + obstacle[obs].amplitude*cos(theta);
|
||||
obstacle[obs].yc = obstacle[obs].yc0 + obstacle[obs].amplitude*sin(theta);
|
||||
}
|
||||
}
|
||||
|
||||
if ((MOVE_SEGMENT_GROUPS)&&(i > INITIAL_TIME + SEGMENT_DEACTIVATION_TIME)) evolve_segment_groups(segment, i, segment_group);
|
||||
|
||||
// if ((MOVE_SEGMENT_GROUPS)&&(i > OBSTACLE_INITIAL_TIME)) evolve_segment_groups(segment, i, segment_group);
|
||||
@@ -2049,7 +2101,7 @@ void animation()
|
||||
/* update tracer particle trajectory */
|
||||
if ((TRACER_PARTICLE)&&(i > INITIAL_TIME))
|
||||
{
|
||||
for (j=0; j<N_TRACER_PARTICLES; j++)
|
||||
for (j=0; j<n_tracers; j++)
|
||||
{
|
||||
trajectory[j*TRAJECTORY_LENGTH + traj_position].xc = particle[tracer_n[j]].xc;
|
||||
trajectory[j*TRAJECTORY_LENGTH + traj_position].yc = particle[tracer_n[j]].yc;
|
||||
@@ -2126,7 +2178,7 @@ void animation()
|
||||
change_type_proportion(particle, params.prop);
|
||||
}
|
||||
|
||||
if (TRACER_PARTICLE) draw_trajectory(trajectory, traj_position, traj_length);
|
||||
if (TRACER_PARTICLE) draw_trajectory(trajectory, traj_position, traj_length, particle, cluster, tracer_n, PLOT);
|
||||
draw_particles(particle, cluster, PLOT, params.beta, collisions, ncollisions, BG_COLOR, hashgrid, params);
|
||||
draw_container(params.xmincontainer, params.xmaxcontainer, obstacle, segment, conveyor_belt, wall);
|
||||
|
||||
@@ -2137,13 +2189,17 @@ void animation()
|
||||
if ((REACTION_DIFFUSION)&&((RD_REACTION == CHEM_DNA_ENZYME)||(RD_REACTION == CHEM_DNA_ENZYME_REPAIR)))
|
||||
{
|
||||
for (k=0; k<N_ADD_PARTICLES; k++)
|
||||
nadd_particle = add_particles(particle, px, py, nadd_particle, 7, molecule);
|
||||
nadd_particle = add_particles(particle, px, py, nadd_particle, 7, molecule, tracer_n);
|
||||
}
|
||||
else for (k=0; k<N_ADD_PARTICLES; k++)
|
||||
nadd_particle = add_particles(particle, px, py, nadd_particle, 0, molecule);
|
||||
nadd_particle = add_particles(particle, px, py, nadd_particle, 0, molecule, tracer_n);
|
||||
// params.nactive = nadd_particle;
|
||||
params.nactive = 0;
|
||||
for (j=0; j<ncircles; j++) if (particle[j].active) params.nactive++;
|
||||
for (j=0; j<ncircles; j++) if (particle[j].active)
|
||||
{
|
||||
params.nactive++;
|
||||
pangle[j] = particle[j].omega;
|
||||
}
|
||||
}
|
||||
|
||||
/* change particle radius */
|
||||
@@ -2180,7 +2236,7 @@ void animation()
|
||||
|
||||
draw_frame(i, PLOT, BG_COLOR, ncollisions, traj_position, traj_length,
|
||||
wall, pressure, pleft, pright, particle_numbers, 1, params, particle, cluster,
|
||||
collisions, hashgrid, trajectory, obstacle, segment, group_speeds, segment_group, conveyor_belt);
|
||||
collisions, hashgrid, trajectory, obstacle, segment, group_speeds, segment_group, conveyor_belt, tracer_n);
|
||||
|
||||
if (!((NO_EXTRA_BUFFER_SWAP)&&(MOVIE))) glutSwapBuffers();
|
||||
|
||||
@@ -2212,7 +2268,7 @@ void animation()
|
||||
{
|
||||
draw_frame(i, PLOT_B, BG_COLOR_B, ncollisions, traj_position, traj_length,
|
||||
wall, pressure, pleft, pright, particle_numbers, 0, params, particle, cluster,
|
||||
collisions, hashgrid, trajectory, obstacle, segment, group_speeds, segment_group, conveyor_belt);
|
||||
collisions, hashgrid, trajectory, obstacle, segment, group_speeds, segment_group, conveyor_belt, tracer_n);
|
||||
glutSwapBuffers();
|
||||
save_frame_lj_counter(NSTEPS + MID_FRAMES + 1 + counter);
|
||||
counter++;
|
||||
@@ -2253,7 +2309,7 @@ void animation()
|
||||
blank();
|
||||
draw_frame(NSTEPS, PLOT, BG_COLOR, ncollisions, traj_position, traj_length,
|
||||
wall, pressure, pleft, pright, particle_numbers, 0, params, particle, cluster,
|
||||
collisions, hashgrid, trajectory, obstacle, segment, group_speeds, segment_group, conveyor_belt);
|
||||
collisions, hashgrid, trajectory, obstacle, segment, group_speeds, segment_group, conveyor_belt, tracer_n);
|
||||
}
|
||||
if (DOUBLE_MOVIE) for (i=0; i<MID_FRAMES; i++)
|
||||
{
|
||||
@@ -2265,7 +2321,7 @@ void animation()
|
||||
{
|
||||
draw_frame(NSTEPS, PLOT_B, BG_COLOR_B, ncollisions, traj_position, traj_length,
|
||||
wall, pressure, pleft, pright, particle_numbers, 0, params, particle, cluster,
|
||||
collisions, hashgrid, trajectory, obstacle, segment, group_speeds, segment_group, conveyor_belt);
|
||||
collisions, hashgrid, trajectory, obstacle, segment, group_speeds, segment_group, conveyor_belt, tracer_n);
|
||||
if (!((NO_EXTRA_BUFFER_SWAP)&&(MOVIE))) glutSwapBuffers();
|
||||
}
|
||||
if ((TIME_LAPSE)&&(!DOUBLE_MOVIE))
|
||||
|
||||
Reference in New Issue
Block a user