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Nils Berglund
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314
lennardjones.c
314
lennardjones.c
@@ -36,8 +36,8 @@
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#include <omp.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 MOVIE 1 /* set to 1 to generate movie */
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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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@@ -50,8 +50,6 @@
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/* General geometrical parameters */
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// #define WINWIDTH 1440 /* window width */
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// #define WINHEIGHT 810 /* window height */
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#define WINWIDTH 1760 /* window width */
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#define WINHEIGHT 990 /* window height */
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@@ -60,20 +58,20 @@
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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 -1.9
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#define INITXMAX 2.1 /* x interval for initial condition */
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#define INITYMIN -1.0
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#define INITYMAX 1.0 /* y interval for initial condition */
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#define INITXMIN -1.95
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#define INITXMAX 1.95 /* x interval for initial condition */
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#define INITYMIN -1.1
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#define INITYMAX 1.1 /* 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 -1.95
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#define ADDXMAX 1.95 /* x interval for adding particles */
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#define ADDYMIN 1.4
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#define ADDYMAX 3.7 /* y interval for adding particles */
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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 ADDRMIN 4.75
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#define ADDRMAX 6.0 /* r interval for adding particles */
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@@ -85,13 +83,13 @@
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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 1 /* pattern of circles, see list in global_ljones.c */
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#define CIRCLE_PATTERN 8 /* 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 1 /* pattern of circles for additional 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 6 /* pattern of obstacles, see list in global_ljones.c */
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#define OBSTACLE_PATTERN 71 /* pattern of obstacles, see list in global_ljones.c */
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#define ADD_FIXED_SEGMENTS 0 /* set to 1 to add fixed segments as obstacles */
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#define SEGMENT_PATTERN 29 /* pattern of repelling segments, see list in global_ljones.c */
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@@ -108,23 +106,21 @@
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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 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 INTERACTION 12 /* particle interaction, see list in global_ljones.c */
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#define INTERACTION_B 12 /* particle interaction for second type of particle, see list in global_ljones.c */
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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 SPIN_INTER_FREQUENCY 2.0 /* angular frequency of spin-spin interaction */
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#define SPIN_INTER_FREQUENCY_B 2.0 /* angular frequency of spin-spin interaction for second particle type */
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#define MOL_ANGLE_FACTOR 1.0 /* 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 9.0 /* minimal distance in Poisson disc process, controls density of particles */
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#define PDISC_DISTANCE 9.6 /* 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 0.75 /* parameter controlling the dimensions of domain */
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#define MU 0.009 /* parameter controlling radius of particles */
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#define MU_B 0.009 /* parameter controlling radius of particles of second type */
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#define LAMBDA 0.2 /* parameter controlling the dimensions of domain */
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#define MU 0.0087 /* parameter controlling radius of particles */
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#define MU_B 0.012 /* parameter controlling radius of particles of second type */
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#define NPOLY 40 /* number of sides of polygon */
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#define APOLY 0.0 /* 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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@@ -133,8 +129,8 @@
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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 20 /* number of grid point for grid of disks */
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#define NGRIDY 10 /* number of grid point for grid of disks */
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#define NGRIDX 40 /* number of grid point for grid of disks */
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#define NGRIDY 20 /* 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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@@ -150,11 +146,11 @@
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/* Parameters for length and speed of simulation */
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#define NSTEPS 1600 /* number of frames of movie */
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// #define NSTEPS 7275 /* number of frames of movie */
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#define NVID 65 /* number of iterations between images displayed on screen */
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#define NSTEPS 2500 /* number of frames of movie */
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// #define NSTEPS 200 /* number of frames of movie */
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#define NVID 50 /* 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 0 /* time after which to start saving frames */
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#define INITIAL_TIME 5 /* 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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@@ -164,7 +160,7 @@
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#define PSLEEP 1 /* sleep time during pause */
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#define SLEEP1 1 /* initial sleeping time */
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#define SLEEP2 1 /* final sleeping time */
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#define MID_FRAMES 20 /* number of still frames between parts of two-part movie */
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#define MID_FRAMES 100 /* number of still frames between parts of two-part movie */
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// #define END_FRAMES 250 /* number of still frames at end of movie */
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#define END_FRAMES 100 /* number of still frames at end of movie */
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@@ -174,15 +170,14 @@
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/* Plot type, see list in global_ljones.c */
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#define PLOT 19
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// #define PLOT_B 1 /* plot type for second movie */
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#define PLOT_B 18 /* plot type for second movie */
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#define PLOT 5
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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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#define COLOR_BACKGROUND 0 /* set to 1 to color background */
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#define BG_COLOR 0 /* type of background coloring, see list in global_ljones.c */
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#define BG_COLOR_B 2 /* type of background coloring, see list in global_ljones.c */
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#define COLOR_BACKGROUND 1 /* set to 1 to color background */
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#define BG_COLOR 2 /* type of background coloring, see list in global_ljones.c */
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#define BG_COLOR_B 0 /* type of background coloring, see list in global_ljones.c */
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#define DRAW_BONDS 1 /* set to 1 to draw bonds between neighbours */
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#define COLOR_BONDS 1 /* set to 1 to color bonds according to length */
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@@ -198,13 +193,13 @@
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#define COLOR_PALETTE 10 /* Color palette, see list in global_ljones.c */
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#define COLOR_PALETTE_EKIN 10 /* Color palette for kinetic energy */
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#define COLOR_PALETTE_ANGLE 0 /* Color palette for angle representation */
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#define COLOR_PALETTE_ANGLE 10 /* Color palette for angle representation */
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#define COLOR_PALETTE_DIRECTION 0 /* Color palette for direction representation */
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#define COLOR_PALETTE_INITIAL_POS 10 /* Color palette for initial position representation */
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#define COLOR_PALETTE_DIFFNEIGH 10 /* Color palette for different neighbours representation */
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#define COLOR_PALETTE_PRESSURE 11 /* Color palette for different neighbours representation */
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#define COLOR_PALETTE_CHARGE 18 /* Color palette for charge representation */
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#define COLOR_PALETTE_CLUSTER 0 /* Color palette for cluster representation */
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#define COLOR_PALETTE_CLUSTER 11 /* Color palette for cluster representation */
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#define BLACK 1 /* background */
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@@ -240,25 +235,29 @@
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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_EMAX 50000.0 /* energy of particle with hottest color */
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#define PARTICLE_EMIN 10.0 /* energy of particle with coolest color */
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#define PARTICLE_EMAX 50000.0 /* energy of particle with hottest color */
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#define HUE_TYPE0 280.0 /* hue of particles of type 0 */
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#define HUE_TYPE1 280.0 /* hue of particles of type 1 */
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#define HUE_TYPE2 70.0 /* hue of particles of type 2 */
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#define HUE_TYPE3 60.0 /* hue of particles of type 3 */
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#define PARTICLE_EMIN 10.0 /* energy of particle with coolest color */
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#define PARTICLE_EMAX 20000.0 /* energy of particle with hottest color */
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#define HUE_TYPE0 300.0 /* hue of particles of type 0 */
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#define HUE_TYPE1 00.0 /* hue of particles of type 1 */
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#define HUE_TYPE2 340.0 /* hue of particles of type 2 */
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#define HUE_TYPE3 260.0 /* hue of particles of type 3 */
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#define HUE_TYPE4 200.0 /* hue of particles of type 4 */
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#define HUE_TYPE5 60.0 /* hue of particles of type 5 */
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#define HUE_TYPE6 130.0 /* hue of particles of type 6 */
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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 DT_PARTICLE 3.0e-6 /* time step for particle displacement */
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#define KREPEL 150.0 /* constant in repelling force between particles */
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#define KREPEL 15.0 /* constant in repelling force between particles */
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#define EQUILIBRIUM_DIST 5.0 /* Lennard-Jones equilibrium distance */
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#define EQUILIBRIUM_DIST_B 5.0 /* Lennard-Jones equilibrium distance for second type of particle */
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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 20.0 /* damping coefficient of particles */
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#define DAMPING 500.0 /* damping coefficient of particles */
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#define INITIAL_DAMPING 5000.0 /* damping coefficient of particles during initial phase */
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#define DAMPING_ROT 100.0 /* dampint coefficient for rotation of particles */
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#define PARTICLE_MASS 1.0 /* 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 DAMPING_ROT 1.0e6 /* 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 16.0 /* mass of particle of radius MU_B */
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#define PARTICLE_INERTIA_MOMENT 0.2 /* moment of inertia of particle */
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#define PARTICLE_INERTIA_MOMENT_B 0.02 /* moment of inertia of second type of particle */
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#define V_INITIAL 50.0 /* initial velocity range */
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@@ -271,11 +270,11 @@
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#define THERMOSTAT 1 /* set to 1 to switch on thermostat */
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#define VARY_THERMOSTAT 0 /* set to 1 for time-dependent thermostat schedule */
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#define SIGMA 5.0 /* noise intensity in thermostat */
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#define BETA 0.0005 /* initial inverse temperature */
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#define BETA 0.00007 /* initial inverse temperature */
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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 2.0e11 /* harmonic potential of obstacles */
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#define NBH_DIST_FACTOR 5.0 /* radius in which to count neighbours */
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#define NBH_DIST_FACTOR 5.0 /* radius in which to count neighbours */
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#define GRAVITY 0.0 /* 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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@@ -288,39 +287,40 @@
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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 50000.0 /* value of electric field */
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#define EFIELD 100000.0 /* 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 CHARGE -0.0 /* charge of particles of first type */
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#define CHARGE_B 0.0 /* charge of particles of second type */
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#define CHARGE 1.0 /* charge of particles of first type */
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#define CHARGE_B -1.5 /* 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 2500000.0 /* factor by which 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 CHARGE_OBSTACLES 1 /* set to 1 for obstacles to be charged */
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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 ROTATION 0 /* set to 1 to include rotation of particles */
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#define COUPLE_ANGLE_TO_THERMOSTAT 1 /* set to 1 to couple angular degrees of freedom to thermostat */
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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 50.0 /* force constant in angular dynamics */
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#define KTORQUE -100.0 /* force constant in angular dynamics */
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#define KTORQUE_BOUNDARY 1.0e6 /* 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 150.0 /* force constant in angular dynamics for different particles */
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#define KTORQUE_DIFF -150.0 /* 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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#define DRAW_SPIN_B 0 /* set to 1 to draw spin vectors of particles */
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#define DRAW_CROSS 1 /* set to 1 to draw cross on particles of second type */
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#define DRAW_MINUS 1 /* set to 1 to draw cross on particles of negative charge */
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#define SPIN_RANGE 10.0 /* range of spin-spin interaction */
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#define SPIN_RANGE_B 5.0 /* range of spin-spin interaction for second type of particle */
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#define SPIN_RANGE_B 10.0 /* range of spin-spin interaction for second type of particle */
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#define QUADRUPOLE_RATIO 0.6 /* anisotropy in quadrupole potential */
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#define INCREASE_BETA 0 /* set to 1 to increase BETA during simulation */
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#define BETA_SCHEDULE 0 /* type of temperature schedule, see TS_* in global_ljones */
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// #define BETA_FACTOR 0.000001 /* factor by which to change BETA during simulation */
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#define BETA_FACTOR 1000.0 /* factor by which to change BETA during simulation */
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#define INCREASE_BETA 1 /* set to 1 to increase BETA during simulation */
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#define BETA_SCHEDULE 3 /* type of temperature schedule, see TS_* in global_ljones */
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#define BETA_FACTOR 10.0 /* factor by which to change BETA during simulation */
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// #define BETA_FACTOR 0.08 /* factor by which to change BETA during simulation */
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#define TS_SLOPE 8.5 /* controls speed of change of BETA for TS_TANH schedule (default 1.0) */
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#define N_TOSCILLATIONS 1.0 /* number of temperature oscillations in BETA schedule */
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#define NO_OSCILLATION 0 /* set to 1 to have exponential BETA change only */
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#define MIDDLE_CONSTANT_PHASE 0 /* final phase in which temperature is constant */
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@@ -356,7 +356,7 @@
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#define PARTIAL_THERMO_RFIN 1.3 /* final radius of region without coupling */
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#define INCREASE_KREPEL 0 /* set to 1 to increase KREPEL during simulation */
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#define KREPEL_FACTOR 1000.0 /* factor by which to change KREPEL during simulation */
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#define KREPEL_FACTOR 100.0 /* factor by which to change KREPEL during simulation */
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#define PART_AT_BOTTOM 0 /* set to 1 to include "seed" particles at bottom */
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#define MASS_PART_BOTTOM 10000.0 /* mass of particles at bottom */
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@@ -364,10 +364,10 @@
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#define ADD_PARTICLES 0 /* 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 0 /* time at which to add first particle */
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#define ADD_PERIOD 5 /* time interval between adding further particles */
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#define N_ADD_PARTICLES 5 /* number of particles to add */
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#define FINAL_NOADD_PERIOD 0 /* final period where no particles are added */
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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 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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@@ -417,20 +417,21 @@
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#define POSITION_DEP_X -0.625 /* threshold value for position-dependent type */
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#define PRINT_ENTROPY 0 /* set to 1 to compute entropy */
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#define REACTION_DIFFUSION 1 /* set to 1 to simulate a chemical reaction (particles may change type) */
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#define RD_REACTION 23 /* type of reaction, see list in global_ljones.c */
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#define RD_TYPES 2 /* number of types in reaction-diffusion equation */
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#define RD_INITIAL_COND 99 /* initial condition of particles */
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#define REACTION_DIST 3.5 /* maximal distance for reaction to occur */
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#define REACTION_DIFFUSION 0 /* set to 1 to simulate a chemical reaction (particles may change type) */
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#define RD_REACTION 256 /* type of reaction, see list in global_ljones.c */
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#define RD_TYPES 6 /* number of types in reaction-diffusion equation */
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#define RD_INITIAL_COND 10 /* initial condition of particles */
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#define REACTION_DIST 4.0 /* maximal distance for reaction to occur */
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#define REACTION_PROB 1.0 /* probability controlling reaction term */
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#define DISSOCIATION_PROB 0.0001 /* probability controlling dissociation reaction */
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#define DISSOCIATION_PROB 0.0 /* probability controlling dissociation reaction */
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#define KILLING_PROB 0.0015 /* probability of enzymes being killed */
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#define CENTER_COLLIDED_PARTICLES 0 /* set to 1 to recenter particles upon reaction (may interfere with thermostat) */
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#define EXOTHERMIC 0 /* set to 1 to make reaction exo/endothermic */
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#define DELTA_EKIN 2000.0 /* change of kinetic energy in reaction */
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#define COLLISION_TIME 25 /* time during which collisions are shown */
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#define DELTAVMAX 150.0 /* maximal deltav allowed for pairing molecules */
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#define AGREGMAX 6 /* maximal number of partners for CHEM_AGGREGATION reaction */
|
||||
#define AGREG_DECOUPLE 10 /* minimal number of partners to decouple from thermostat */
|
||||
#define COLLISION_TIME 25 /* time during which collisions are shown */
|
||||
#define DELTAVMAX 1000.0 /* maximal deltav allowed for pairing molecules */
|
||||
#define AGREGMAX 11 /* maximal number of partners for CHEM_AGGREGATION reaction */
|
||||
#define AGREG_DECOUPLE 12 /* minimal number of partners to decouple from thermostat */
|
||||
|
||||
#define CHANGE_RADIUS 0 /* set to 1 to change particle radius during simulation */
|
||||
#define MU_RATIO 0.666666667 /* ratio by which to increase radius */
|
||||
@@ -458,29 +459,34 @@
|
||||
#define PROP_MAX 0.9 /* max proportion of type 1 particles */
|
||||
|
||||
#define PAIR_PARTICLES 1 /* set to 1 to form particles pairs */
|
||||
#define RANDOMIZE_ANGLE 1 /* set to 1 for random orientation */
|
||||
#define DEACIVATE_CLOSE_PAIRS 0 /* set to 1 to test for closeness to other particles */
|
||||
#define RANDOMIZE_ANGLE 0 /* set to 1 for random orientation */
|
||||
#define DEACIVATE_CLOSE_PAIRS 1 /* set to 1 to test for closeness to other particles */
|
||||
#define PAIR_SAFETY_FACTOR 1.2 /* distance to deactivate divided by sum of radii */
|
||||
#define KSPRING_PAIRS 2.0e10 /* spring constant for pair interaction */
|
||||
#define NPARTNERS 16 /* number of partners of particles */
|
||||
#define NARMS 4 /* number of "arms" for certain paring types */
|
||||
#define PAIRING_TYPE 61 /* type of pairing, see POLY_ in global_ljones.c */
|
||||
#define THIRD_TYPE_PROPORTION 1.0 /* proportion of third type pairings, for certain pairing types */
|
||||
|
||||
#define KSPRING_PAIRS 1.0e10 /* spring constant for pair interaction */
|
||||
#define KTORQUE_PAIRS 1.0e10 /* constant for angular coupling in pair interaction */
|
||||
#define KTORQUE_PAIR_ANGLE 0.0 /* constant for coupling between orientation in pairs */
|
||||
#define NPARTNERS 8 /* number of partners of particles */
|
||||
#define NARMS 1 /* number of "arms" for certain paring types */
|
||||
#define PAIRING_TYPE 42 /* type of pairing, see POLY_ in global_ljones.c */
|
||||
#define PARTNER_ANGLE 104.45 /* angle (in degrees) between ions for POLY_WATER case */
|
||||
#define PAIR_DRATIO 1.0 /* ratio between equilibrium distance and radius (default: 1.0) */
|
||||
#define MU_C 0.014 /* radius of partner particle */
|
||||
#define PARTICLE_MASS_C 2.0 /* mass or partner particle */
|
||||
#define CHARGE_C 1.5 /* charge of partner particle */
|
||||
#define PAIR_DRATIO 0.9 /* ratio between equilibrium distance and radius (default: 1.0) */
|
||||
#define MU_C 0.0125 /* radius of partner particle */
|
||||
#define PARTICLE_MASS_C 8.0 /* mass or partner particle */
|
||||
#define CHARGE_C -1.0 /* charge of partner particle */
|
||||
#define CLUSTER_COLOR_FACTOR 400 /* factor for initialization of cluster colors */
|
||||
#define ALTERNATE_POLY_CHARGE 1 /* set to 1 for alternating charges in molecule */
|
||||
#define SECONDARY_PAIRING 0 /* set to 1 to pair with secondary partners, experimental */
|
||||
#define DNA_RIGIDITY 0.5 /* controls rigidity for POLY_DNA_DOUBLE pairs, default = 1 */
|
||||
|
||||
#define PAIR_TYPEB_PARTICLES 1 /* set to 1 to pair particle of type 1 */
|
||||
#define NPARTNERS_B 16 /* number of partners of particles */
|
||||
#define NARMS_B 4 /* number of "arms" for certain paring types */
|
||||
#define PAIRING_TYPE_B 61 /* type of pairing, see POLY_ in global_ljones.c */
|
||||
#define MU_D 0.014 /* radius of partner particle */
|
||||
#define PARTICLE_MASS_D 2.0 /* mass or partner particle */
|
||||
#define CHARGE_D -1.5 /* charge of partner particle */
|
||||
// #define PARTNER_ANGLE_B 104.45 /* angle (in degrees) between anions for POLY_WATER case */
|
||||
#define NPARTNERS_B 2 /* number of partners of particles */
|
||||
#define NARMS_B 1 /* number of "arms" for certain paring types */
|
||||
#define PAIRING_TYPE_B 2 /* type of pairing, see POLY_ in global_ljones.c */
|
||||
#define MU_D 0.008 /* radius of partner particle */
|
||||
#define PARTICLE_MASS_D 1.0 /* mass or partner particle */
|
||||
#define CHARGE_D 0.75 /* charge of partner particle */
|
||||
|
||||
#define NXMAZE 12 /* width of maze */
|
||||
#define NYMAZE 12 /* height of maze */
|
||||
@@ -494,9 +500,9 @@
|
||||
#define FLOOR_OMEGA 0 /* set to 1 to limit particle momentum to PMAX */
|
||||
#define PMAX 1000.0 /* maximal force */
|
||||
|
||||
#define HASHX 60 /* size of hashgrid in x direction */
|
||||
#define HASHY 30 /* size of hashgrid in y direction */
|
||||
#define HASHMAX 100 /* maximal number of particles per hashgrid cell */
|
||||
#define HASHX 80 /* size of hashgrid in x direction */
|
||||
#define HASHY 40 /* size of hashgrid in y direction */
|
||||
#define HASHMAX 100 /* maximal number of particles per hashgrid cell */
|
||||
#define HASHGRID_PADDING 0.1 /* padding of hashgrid outside simulation window */
|
||||
|
||||
#define DRAW_COLOR_SCHEME 0 /* set to 1 to plot the color scheme */
|
||||
@@ -512,7 +518,8 @@
|
||||
#define COMPUTE_EMEAN ((PLOT == P_EMEAN)||(PLOT_B == P_EMEAN)||(PLOT == P_LOG_EMEAN)||(PLOT_B == P_LOG_EMEAN)||(PLOT == P_DIRECT_EMEAN)||(PLOT_B == P_DIRECT_EMEAN))
|
||||
#define COMPUTE_DIRMEAN ((PLOT == P_DIRECT_EMEAN)||(PLOT_B == P_DIRECT_EMEAN))
|
||||
#define COUNT_PARTNER_TYPE ((RD_REACTION == CHEM_H2O_H_OH)||(RD_REACTION == CHEM_2H2O_H3O_OH))
|
||||
#define PAIR_FORCE ((PAIR_PARTICLES)||((REACTION_DIFFUSION)&&(RD_REACTION == CHEM_AGGREGATION)))
|
||||
#define PAIR_FORCE ((PAIR_PARTICLES)||((REACTION_DIFFUSION)&&((RD_REACTION == CHEM_AGGREGATION)||(RD_REACTION == CHEM_AGGREGATION_CHARGE)||(RD_REACTION == CHEM_AGGREGATION_NNEIGH))))
|
||||
#define COMPUTE_PAIR_TORQUE (KTORQUE_PAIR_ANGLE != 0.0)
|
||||
|
||||
double xshift = 0.0; /* x shift of shown window */
|
||||
double xspeed = 0.0; /* x speed of obstacle */
|
||||
@@ -654,6 +661,16 @@ double temperature_schedule(int i)
|
||||
bc = -0.5*log(BETA_FACTOR);
|
||||
break;
|
||||
}
|
||||
case (TS_ATAN):
|
||||
{
|
||||
factor2 = (1.0/BETA_FACTOR - 1.0)*2.0/PI;
|
||||
break;
|
||||
}
|
||||
case (TS_TANH):
|
||||
{
|
||||
factor2 = 1.0/BETA_FACTOR - 1.0;
|
||||
break;
|
||||
}
|
||||
}
|
||||
bexp2 = -log(factor2)/(double)(FINAL_DECREASE_PHASE);
|
||||
first = 0;
|
||||
@@ -705,6 +722,16 @@ double temperature_schedule(int i)
|
||||
beta = BETA*exp(bc*(-1.0 + cos(N_TOSCILLATIONS*DPI*(t - 0.5*t*(1.0-t)))));
|
||||
break;
|
||||
}
|
||||
case (TS_ATAN):
|
||||
{
|
||||
beta = BETA/(1.0 + factor2*atan(2.0*(double)(i - INITIAL_TIME)/(double)(t1)));
|
||||
break;
|
||||
}
|
||||
case (TS_TANH):
|
||||
{
|
||||
beta = BETA/(1.0 + factor2*tanh(TS_SLOPE*(double)(i - INITIAL_TIME)/(double)(t1)));
|
||||
break;
|
||||
}
|
||||
}
|
||||
}
|
||||
else if (i < INITIAL_TIME + t2) beta = BETA*factor2;
|
||||
@@ -1010,6 +1037,7 @@ double evolve_particles(t_particle particle[NMAXCIRCLES], t_hashgrid hashgrid[HA
|
||||
px[j] *= exp(- DT_PARTICLE*damping);
|
||||
py[j] *= exp(- DT_PARTICLE*damping);
|
||||
pangle[j] *= exp(- DT_PARTICLE*DAMPING_ROT);
|
||||
// printf("Damping particle angular velocity\n");
|
||||
}
|
||||
if ((THERMOSTAT_ON)&&(COUPLE_ANGLE_TO_THERMOSTAT)&&(particle[j].thermostat))
|
||||
pangle[j] *= exp(- 0.5*DT_PARTICLE*xi);
|
||||
@@ -1365,7 +1393,8 @@ void evolve_segment_groups(t_segment segment[NMAXSEGMENTS], int time, t_group_se
|
||||
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;
|
||||
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;
|
||||
double *qx, *qy, *px, *py, *qangle, *pangle, *pressure, *obstacle_speeds;
|
||||
int i, j, k, n, m, s, ij[2], i0, iplus, iminus, j0, jplus, jminus, p, q, p1, q1, p2, q2, total_neighbours = 0,
|
||||
min_nb, max_nb, close, wrapx = 0, wrapy = 0, nadd_particle = 0, nmove = 0, nsuccess = 0,
|
||||
@@ -1382,6 +1411,7 @@ void animation()
|
||||
t_group_data *group_speeds;
|
||||
t_collision *collisions;
|
||||
t_hashgrid *hashgrid;
|
||||
t_molecule *molecule;
|
||||
t_lj_parameters params;
|
||||
char message[100];
|
||||
|
||||
@@ -1407,6 +1437,9 @@ void animation()
|
||||
if (TRACER_PARTICLE)
|
||||
trajectory = (t_tracer *)malloc(TRAJECTORY_LENGTH*N_TRACER_PARTICLES*sizeof(t_tracer));
|
||||
|
||||
if (PAIR_PARTICLES)
|
||||
molecule = (t_molecule *)malloc(NMAXCIRCLES*sizeof(t_molecule)); /* molecules */
|
||||
|
||||
hashgrid = (t_hashgrid *)malloc(HASHX*HASHY*sizeof(t_hashgrid)); /* hashgrid */
|
||||
|
||||
qx = (double *)malloc(NMAXCIRCLES*sizeof(double));
|
||||
@@ -1429,6 +1462,8 @@ void animation()
|
||||
lj_final_position = fopen("lj_final_position.dat", "w");
|
||||
}
|
||||
|
||||
lj_log = fopen("lj_logfile.txt", "w");
|
||||
|
||||
if (ADD_FIXED_OBSTACLES) init_obstacle_config(obstacle);
|
||||
if (ADD_FIXED_SEGMENTS) init_segment_config(segment);
|
||||
|
||||
@@ -1445,7 +1480,11 @@ void animation()
|
||||
init_particle_config(particle);
|
||||
|
||||
/* add some particles, beta */
|
||||
if (ADD_INITIAL_PARTICLES) add_particle_config(particle, -0.6, 1.6, -1.0, 1.0, MU_B);
|
||||
if (ADD_INITIAL_PARTICLES)
|
||||
{
|
||||
add_particle_config(particle, INITXMIN - 0.5, INITXMAX + 0.5, INITYMAX + 0.1, YMAX-0.1, NGRIDX*5/4, 3, 0, MU);
|
||||
add_particle_config(particle, INITXMIN - 0.5, INITXMAX + 0.5, YMIN + 0.1, INITYMIN-0.1, NGRIDX*5/4, 3, 0, MU);
|
||||
}
|
||||
|
||||
init_hashgrid(hashgrid);
|
||||
|
||||
@@ -1461,7 +1500,7 @@ void animation()
|
||||
|
||||
printf("Initializing configuration\n");
|
||||
|
||||
params.nactive = initialize_configuration(particle, hashgrid, obstacle, px, py, pangle, tracer_n, segment);
|
||||
params.nactive = initialize_configuration(particle, hashgrid, obstacle, px, py, pangle, tracer_n, segment, molecule);
|
||||
|
||||
printf("%i active particles\n", params.nactive);
|
||||
|
||||
@@ -1486,8 +1525,12 @@ void animation()
|
||||
|
||||
for (i=0; i<=INITIAL_TIME + NSTEPS; i++)
|
||||
{
|
||||
printf("Computing frame %d\n",i);
|
||||
/* TEST */
|
||||
// if (i >= 2000) exit(0);
|
||||
|
||||
frame_time++;
|
||||
printf("Computing frame %d\n",i);
|
||||
|
||||
if (INCREASE_KREPEL) params.krepel = repel_schedule(i);
|
||||
if (INCREASE_BETA) params.beta = temperature_schedule(i);
|
||||
if (INCREASE_E) params.efield = efield_schedule(i);
|
||||
@@ -1615,10 +1658,44 @@ void animation()
|
||||
if (speed > VICSEK_VMAX) speed = 0.5*(speed + VICSEK_VMAX);
|
||||
px[j] = speed*cos(particle[j].angle);
|
||||
py[j] = speed*sin(particle[j].angle);
|
||||
|
||||
|
||||
}
|
||||
|
||||
/* TEST - adjust angles */
|
||||
if ((REACTION_DIFFUSION)&&(RD_REACTION == CHEM_AGGREGATION_NNEIGH))
|
||||
{
|
||||
// if (particle[j].npartners >= 1)
|
||||
// {
|
||||
// angle = 0.0;
|
||||
// theta = 0.99;
|
||||
// for (p=0; p<particle[j].npartners; p++)
|
||||
// angle += particle[particle[j].partner[p]].angle;
|
||||
// angle *= 1.0/(double)particle[j].npartners;
|
||||
// // particle[j].angle = theta*particle[j].angle - (1.0 - theta)*angle;
|
||||
// for (p=0; p<particle[j].npartners; p++)
|
||||
// {
|
||||
// k = particle[j].partner[p];
|
||||
// particle[k].angle = theta*particle[k].angle + (1.0 - theta)*angle;
|
||||
// }
|
||||
// }
|
||||
if (particle[j].npartners >= 1)
|
||||
{
|
||||
x = 0.0;
|
||||
y = 0.0;
|
||||
for (p=0; p<particle[j].npartners; p++)
|
||||
{
|
||||
x += particle[particle[j].partner[p]].xc;
|
||||
y += particle[particle[j].partner[p]].yc;
|
||||
}
|
||||
angle = argument(x, y);
|
||||
particle[i].angle = angle;
|
||||
for (p=0; p<particle[j].npartners; p++)
|
||||
{
|
||||
k = particle[j].partner[p];
|
||||
particle[k].angle = -angle;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* add gravity */
|
||||
if (INCREASE_GRAVITY)
|
||||
{
|
||||
@@ -1804,7 +1881,7 @@ void animation()
|
||||
/* case of reaction-diffusion equation */
|
||||
if ((i > INITIAL_TIME)&&(REACTION_DIFFUSION))
|
||||
{
|
||||
ncollisions = update_types(particle, collisions, ncollisions, particle_numbers, i - INITIAL_TIME - 1, &delta_energy);
|
||||
ncollisions = update_types(particle, molecule, collisions, ncollisions, particle_numbers, i - INITIAL_TIME - 1, &delta_energy);
|
||||
if (EXOTHERMIC) params.beta *= 1.0/(1.0 + delta_energy/totalenergy);
|
||||
params.nactive = 0;
|
||||
for (j=0; j<ncircles; j++) if (particle[j].active)
|
||||
@@ -1833,8 +1910,14 @@ void animation()
|
||||
/* add a particle */
|
||||
if ((ADD_PARTICLES)&&(i > ADD_TIME)&&((i - INITIAL_TIME - ADD_TIME)%ADD_PERIOD == 1)&&(i < NSTEPS - FINAL_NOADD_PERIOD))
|
||||
{
|
||||
for (k=0; k<N_ADD_PARTICLES; k++)
|
||||
nadd_particle = add_particles(particle, px, py, nadd_particle, params);
|
||||
/* add enzymes */
|
||||
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);
|
||||
}
|
||||
else for (k=0; k<N_ADD_PARTICLES; k++)
|
||||
nadd_particle = add_particles(particle, px, py, nadd_particle, 0, molecule);
|
||||
// params.nactive = nadd_particle;
|
||||
params.nactive = 0;
|
||||
for (j=0; j<ncircles; j++) if (particle[j].active) params.nactive++;
|
||||
@@ -1923,6 +2006,8 @@ void animation()
|
||||
}
|
||||
}
|
||||
|
||||
fclose(lj_log);
|
||||
lj_log = fopen("lj_logfile.txt", "a");
|
||||
}
|
||||
|
||||
if (SAVE_TIME_SERIES)
|
||||
@@ -1947,7 +2032,7 @@ void animation()
|
||||
wall, pressure, pleft, pright, particle_numbers, 0, params, particle,
|
||||
collisions, hashgrid, trajectory, obstacle, segment, group_speeds, segment_group);
|
||||
}
|
||||
for (i=0; i<MID_FRAMES; i++)
|
||||
if (DOUBLE_MOVIE) for (i=0; i<MID_FRAMES; i++)
|
||||
{
|
||||
save_frame_lj();
|
||||
if (!NO_EXTRA_BUFFER_SWAP) glutSwapBuffers();
|
||||
@@ -1962,10 +2047,13 @@ void animation()
|
||||
}
|
||||
if ((TIME_LAPSE)&&(!DOUBLE_MOVIE))
|
||||
{
|
||||
for (i=0; i<MID_FRAMES; i++) save_frame_lj();
|
||||
for (i=0; i<END_FRAMES; i++)
|
||||
save_frame_lj_counter(NSTEPS + MID_FRAMES + NSTEPS/TIME_LAPSE_FACTOR + i);
|
||||
}
|
||||
else for (i=0; i<END_FRAMES; i++) save_frame_lj_counter(NSTEPS + MID_FRAMES + 1 + counter + i);
|
||||
else if (DOUBLE_MOVIE)
|
||||
for (i=0; i<END_FRAMES; i++) save_frame_lj_counter(NSTEPS + MID_FRAMES + 1 + counter + i);
|
||||
else for (i=0; i<END_FRAMES; i++) save_frame_lj_counter(NSTEPS + 1 + counter + i);
|
||||
|
||||
s = system("mv lj*.tif tif_ljones/");
|
||||
}
|
||||
@@ -2011,11 +2099,15 @@ void animation()
|
||||
// printf("16\n");
|
||||
if (REACTION_DIFFUSION) free(collisions);
|
||||
|
||||
if (PAIR_PARTICLES) free(molecule);
|
||||
|
||||
if (SAVE_TIME_SERIES)
|
||||
{
|
||||
fclose(lj_time_series);
|
||||
fclose(lj_final_position);
|
||||
}
|
||||
|
||||
fclose(lj_log);
|
||||
}
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user