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Main changes: lennardjones, wave_billiard, rde
This commit is contained in:
Nils Berglund
2025-11-02 19:13:40 +01:00
committed by GitHub
parent cade2054f3
commit ab63c4d200
22 changed files with 4706 additions and 1179 deletions
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lennardjones.c
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@@ -53,15 +53,15 @@
#define WINWIDTH 1760 /* window width */
#define WINHEIGHT 990 /* window height */
#define XMIN -2.0
#define XMAX 2.0 /* x interval */
#define YMIN -1.125
#define YMAX 1.125 /* y interval for 9/16 aspect ratio */
#define XMIN 0.0
#define XMAX 6.283185307 /* x interval */
#define YMIN 0.0
#define YMAX 3.141592654 /* y interval for 9/16 aspect ratio */
#define INITXMIN -0.1
#define INITXMAX 0.1 /* x interval for initial condition */
#define INITYMIN -0.1
#define INITYMAX 0.1 /* y interval for initial condition */
#define INITXMIN 0.025
#define INITXMAX 6.255 /* x interval for initial condition */
#define INITYMIN 0.4
#define INITYMAX 2.74 /* y interval for initial condition */
#define THERMOXMIN -1.25
#define THERMOXMAX 1.25 /* x interval for initial condition */
@@ -72,13 +72,13 @@
#define ADDXMAX 1.9 /* x interval for adding particles */
#define ADDYMIN 1.2
#define ADDYMAX 1.3 /* y interval for adding particles */
#define ADDRMIN 4.75
#define ADDRMAX 6.0 /* r interval for adding particles */
#define ADDRMIN 2.0
#define ADDRMAX 2.1 /* r interval for adding particles */
#define BCXMIN -2.0
#define BCXMAX 2.0 /* x interval for boundary condition */
#define BCYMIN -1.125
#define BCYMAX 1.325 /* y interval for boundary condition */
#define BCXMIN 0.0
#define BCXMAX 6.283185307 /* x interval for boundary condition */
#define BCYMIN 0.05
#define BCYMAX 3.091592654 /* y interval for boundary condition */
#define OBSXMIN -2.0
#define OBSXMAX 2.0 /* x interval for motion of obstacle */
@@ -108,7 +108,7 @@
#define COUPLE_MINLENGTH 0.5 /* length at which bonds decouple */
#define ADD_FIXED_SEGMENTS 0 /* set to 1 to add fixed segments as obstacles */
#define SEGMENT_PATTERN 15 /* pattern of repelling segments, see list in global_ljones.c */
#define SEGMENT_PATTERN 100 /* pattern of repelling segments, see list in global_ljones.c */
#define ROCKET_SHAPE 3 /* shape of rocket combustion chamber, see list in global_ljones.c */
#define ROCKET_SHAPE_B 3 /* shape of second rocket */
#define NOZZLE_SHAPE 6 /* shape of nozzle, see list in global_ljones.c */
@@ -119,14 +119,14 @@
#define OBSTACLE_OMEGA 300.0 /* obstacle rotation speed */
#define TWO_TYPES 0 /* set to 1 to have two types of particles */
#define TYPE_PROPORTION 0.5 /* proportion of particles of first type */
#define TYPE_PROPORTION 0.75 /* proportion of particles of first type */
#define TWOTYPE_CONFIG 0 /* choice of types, see TTC_ list in global_ljones.c */
#define SYMMETRIZE_FORCE 1 /* set to 1 to symmetrize two-particle interaction, only needed if particles are not all the same */
#define SYMMETRIZE_FORCE 0 /* set to 1 to symmetrize two-particle interaction, only needed if particles are not all the same */
#define CENTER_PX 0 /* set to 1 to center horizontal momentum */
#define CENTER_PY 0 /* set to 1 to center vertical momentum */
#define CENTER_PANGLE 0 /* set to 1 to center angular momentum */
#define INTERACTION 12 /* particle interaction, see list in global_ljones.c */
#define INTERACTION 1 /* particle interaction, see list in global_ljones.c */
#define INTERACTION_B 1 /* particle interaction for second type of particle, see list in global_ljones.c */
#define SPIN_INTER_FREQUENCY 4.0 /* angular frequency of spin-spin interaction */
#define SPIN_INTER_FREQUENCY_B 4.0 /* angular frequency of spin-spin interaction for second particle type */
@@ -139,9 +139,10 @@
#define RANDOM_POLY_ANGLE 0 /* set to 1 to randomize angle of polygons */
#define LAMBDA 0.2 /* parameter controlling the dimensions of domain */
#define MU 0.016 /* parameter controlling radius of particles */
#define MU_B 0.012 /* parameter controlling radius of particles of second type */
#define MU_ADD 0.016 /* parameter controlling radius of added particles */
#define MU 0.022 /* parameter controlling radius of particles */
#define MU_B 0.022 /* parameter controlling radius of particles of second type */
#define MU_ADD 0.022 /* parameter controlling radius of added particles */
#define MU_ADD_B 0.022 /* parameter controlling radius of added particles */
#define NPOLY 3 /* number of sides of polygon */
#define APOLY 0.0 /* angle by which to turn polygon, in units of Pi/2 */
#define AWEDGE 0.5 /* opening angle of wedge, in units of Pi/2 */
@@ -150,8 +151,8 @@
#define MANDELLEVEL 1000 /* iteration level for Mandelbrot set */
#define MANDELLIMIT 10.0 /* limit value for approximation of Mandelbrot set */
#define FOCI 1 /* set to 1 to draw focal points of ellipse */
#define NGRIDX 1 /* number of grid point for grid of disks */
#define NGRIDY 1 /* number of grid point for grid of disks */
#define NGRIDX 40 /* number of grid point for grid of disks */
#define NGRIDY 20 /* number of grid point for grid of disks */
#define EHRENFEST_RADIUS 0.9 /* radius of container for Ehrenfest urn configuration */
#define EHRENFEST_WIDTH 0.035 /* width of tube for Ehrenfest urn configuration */
#define TWO_CIRCLES_RADIUS_RATIO 0.8 /* ratio of radii for S_TWO_CIRCLES_EXT segment configuration */
@@ -167,8 +168,8 @@
/* Parameters for length and speed of simulation */
#define NSTEPS 4800 /* number of frames of movie */
#define NVID 100 /* number of iterations between images displayed on screen */
#define NSTEPS 2300 /* number of frames of movie */
#define NVID 100 /* number of iterations between images displayed on screen */
#define NSEG 25 /* number of segments of boundary of circles */
#define INITIAL_TIME 0 /* time after which to start saving frames */
#define OBSTACLE_INITIAL_TIME 0 /* time after which to start moving obstacle */
@@ -181,22 +182,22 @@
#define SLEEP1 1 /* initial sleeping time */
#define SLEEP2 1 /* final sleeping time */
#define MID_FRAMES 100 /* number of still frames between parts of two-part movie */
#define END_FRAMES 100 /* number of still frames at end of movie */
#define END_FRAMES 200 /* number of still frames at end of movie */
/* Boundary conditions, see list in global_ljones.c */
#define BOUNDARY_COND 1
#define BOUNDARY_COND 30
/* Plot type, see list in global_ljones.c */
#define PLOT 13
#define PLOT_B 17 /* plot type for second movie */
#define PLOT 5
#define PLOT_B 13 /* plot type for second movie */
/* Background color depending on particle properties */
#define COLOR_BACKGROUND 0 /* set to 1 to color background */
#define BG_COLOR 6 /* type of background coloring, see list in global_ljones.c */
#define BG_COLOR_B 9 /* type of background coloring, see list in global_ljones.c */
#define BG_COLOR 10 /* type of background coloring, see list in global_ljones.c */
#define BG_COLOR_B 3 /* type of background coloring, see list in global_ljones.c */
#define OBSTACLE_COLOR 0 /* type of obstacle, see OC_ in global_ljones.c */
#define DRAW_BONDS 0 /* set to 1 to draw bonds between neighbours */
@@ -249,8 +250,8 @@
#define HUEAMP -50.0 /* amplitude of variation of hue for color scheme C_HUE */
#define COLOR_HUESHIFT 1.0 /* shift in color hue (for some cyclic palettes) */
#define PRINT_PARAMETERS 1 /* set to 1 to print certain parameters */
#define PRINT_TEMPERATURE 0 /* set to 1 to print current temperature */
#define PRINT_PARAMETERS 0 /* set to 1 to print certain parameters */
#define PRINT_TEMPERATURE 1 /* set to 1 to print current temperature */
#define PRINT_ANGLE 0 /* set to 1 to print obstacle orientation */
#define PRINT_OMEGA 0 /* set to 1 to print angular speed */
#define PRINT_PARTICLE_SPEEDS 0 /* set to 1 to print average speeds/momenta of particles */
@@ -267,7 +268,9 @@
#define PARTICLE_HUE_MIN 359.0 /* color of original particle */
#define PARTICLE_HUE_MAX 0.0 /* color of saturated particle */
#define PARTICLE_EMIN 0.0 /* energy of particle with coolest color */
#define PARTICLE_EMAX 50000.0 /* energy of particle with hottest color */
#define PARTICLE_EMAX 2000.0 /* energy of particle with hottest color */
#define PARTICLE_DMIN 200.0 /* energy of particle with largest local density */
#define PARTICLE_DMAX 500.0 /* energy of particle with largest local density */
#define SEGMENT_HUE_MIN 275.0 /* color of original segment */
#define SEGMENT_HUE_MAX 30.0 /* color of saturated segment */
#define OBSTACLE_EMAX 1000000.0 /* energy of obstacle with hottest color */
@@ -275,12 +278,14 @@
#define HUE_TYPE0 320.0 /* hue of particles of type 0 */
#define HUE_TYPE1 60.0 /* hue of particles of type 1 */
#define HUE_TYPE2 320.0 /* hue of particles of type 2 */
#define HUE_TYPE3 260.0 /* hue of particles of type 3 */
#define HUE_TYPE4 200.0 /* hue of particles of type 4 */
#define HUE_TYPE3 140.0 /* hue of particles of type 3 */
#define HUE_TYPE4 200.0 /* hue of particles of type 4 */
#define HUE_TYPE5 60.0 /* hue of particles of type 5 */
#define HUE_TYPE6 130.0 /* hue of particles of type 6 */
#define HUE_TYPE7 150.0 /* hue of particles of type 7 */
#define BG_FORCE_SLOPE 1.0e-6 /* contant in BG_FORCE backgound color scheme*/
#define HUE_TYPE7 200.0 /* hue of particles of type 7 */
#define BG_LOG_EKIN_SHIFT 1.0 /* constant in BG_LOG_EKIN background color scheme */
#define BG_FORCE_SLOPE 1.0e-6 /* constant in BG_FORCE backgound color scheme */
#define BG_CHARGE_SLOPE 0.75 /* constant in BG_CHARGE backgound color scheme (default: 0.5) */
#define PARTICLE_LMAX 1.5e4 /* angular momentum particle with brightest color */
#define RANDOM_RADIUS 0 /* set to 1 for random particle radius */
@@ -290,39 +295,42 @@
#define ADAPT_DAMPING_TO_RADIUS 0.0 /* set to positive value to for friction prop to power of radius */
#define ADAPT_DAMPING_FACTOR 0.0 /* factor by which damping is adapted to radius */
#define DT_PARTICLE 1.0e-6 /* time step for particle displacement */
#define KREPEL 20.0 /* constant in repelling force between particles */
#define EQUILIBRIUM_DIST 4.0 /* Lennard-Jones equilibrium distance */
#define EQUILIBRIUM_DIST_B 4.0 /* Lennard-Jones equilibrium distance for second type of particle */
#define KREPEL 50.0 /* constant in repelling force between particles */
#define EQUILIBRIUM_DIST 3.5 /* Lennard-Jones equilibrium distance */
#define EQUILIBRIUM_DIST_B 3.5 /* Lennard-Jones equilibrium distance for second type of particle */
#define SEGMENT_FORCE_EQR 1.0 /* equilibrium distance factor for force from segments (default 1.5) */
#define REPEL_RADIUS 25.0 /* radius in which repelling force acts (in units of particle radius) */
#define DAMPING 50.0 /* damping coefficient of particles */
#define DAMPING 0.0 /* damping coefficient of particles */
#define INITIAL_DAMPING 1000.0 /* damping coefficient of particles during initial phase */
#define DAMPING_ROT 5.0 /* damping coefficient for rotation of particles */
#define DAMPING_ROT 0.0 /* damping coefficient for rotation of particles */
#define DAMPING_PAIRS 0.0 /* damping between paired particles */
#define PARTICLE_MASS 2.0 /* mass of particle of radius MU */
#define PARTICLE_MASS 1.0 /* mass of particle of radius MU */
#define PARTICLE_MASS_B 1.0 /* mass of particle of radius MU_B */
#define PARTICLE_ADD_MASS 2.0 /* mass of added particles */
#define PARTICLE_ADD_MASS 1.0 /* mass of added particles */
#define PARTICLE_ADD_MASS_B 1.0 /* mass of added particles */
#define PARTICLE_INERTIA_MOMENT 0.1 /* moment of inertia of particle */
#define PARTICLE_INERTIA_MOMENT_B 0.1 /* moment of inertia of second type of particle */
#define V_INITIAL 100.0 /* initial velocity range */
#define V_INITIAL_ADD 100.0 /* initial velocity range for added particles */
#define V_INITIAL 25.0 /* initial velocity range */
#define V_INITIAL_ADD 0.0 /* initial velocity range for added particles */
#define OMEGA_INITIAL 100.0 /* initial angular velocity range */
#define VICSEK_VMIN 1.0 /* minimal speed of particles in Vicsek model */
#define VICSEK_VMAX 40.0 /* minimal speed of particles in Vicsek model */
#define COULOMB_LJ_FACTOR 1.0 /* relative intensity of LJ interaction in I_COULOMB_LJ interaction (default: 0.01) */
#define KCOULOMB_FACTOR 50.0 /* relative intensity of Coulomb interaction in I_COULOMB_LJ (default: 100.0) */
#define OBSTACLE_DAMPING 0.0 /* damping of oscillating obstacles */
#define V_INITIAL_TYPE 0 /* type of initial speed distribution (see VI_ in global_ljones.c) */
#define THERMOSTAT 0 /* set to 1 to switch on thermostat */
#define THERMOSTAT 1 /* set to 1 to switch on thermostat */
#define VARY_THERMOSTAT 0 /* set to 1 for time-dependent thermostat schedule */
#define SIGMA 5.0 /* noise intensity in thermostat */
#define BETA 0.004 /* initial inverse temperature */
#define BETA 0.0002 /* initial inverse temperature */
#define MU_XI 0.005 /* friction constant in thermostat */
#define KSPRING_BOUNDARY 2.0e11 /* confining harmonic potential outside simulation region */
#define KSPRING_OBSTACLE 5.0e11 /* harmonic potential of obstacles */
#define NBH_DIST_FACTOR 4.0 /* radius in which to count neighbours */
#define GRAVITY 10000.0 /* gravity acting on all particles */
#define NBH_DIST_FACTOR 6.0 /* radius in which to count neighbours */
#define BOND_DIST_FACTOR 6.0 /* radius in which to draw bonds */
#define GRAVITY 0.0 /* gravity acting on all particles */
#define GRAVITY_X 0.0 /* horizontal gravity acting on all particles */
#define CIRCULAR_GRAVITY 0 /* set to 1 to have gravity directed to center */
#define INCREASE_GRAVITY 0 /* set to 1 to increase gravity during the simulation */
@@ -338,9 +346,10 @@
#define EFIELD_Y 0.0 /* value of electric field */
#define ADD_BFIELD 0 /* set to 1 to add a magnetic field */
#define BFIELD 20000.0 /* value of magnetic field */
#define CHARGE 1.0 /* charge of particles of first type */
#define CHARGE_B -1.0 /* charge of particles of second type */
#define CHARGE_ADD 1.0 /* charge of added particles */
#define CHARGE 0.0 /* charge of particles of first type */
#define CHARGE_B 0.0 /* charge of particles of second type */
#define CHARGE_ADD 0.0 /* charge of added particles */
#define CHARGE_ADD_B 0.0 /* charge of added particles */
#define INCREASE_E 0 /* set to 1 to increase electric field */
#define OSCILLATE_E 0 /* set to 1 for oscillating electric field */
#define E_PERIOD 1000 /* period of oscillating electric field */
@@ -367,10 +376,10 @@
#define WIND_FORCE 1.35e6 /* force of wind */
#define WIND_YMIN -0.6 /* min altitude of region with wind */
#define ROTATION 0 /* set to 1 to include rotation of particles */
#define ROTATION 1 /* set to 1 to include rotation of particles */
#define COUPLE_ANGLE_TO_THERMOSTAT 0 /* set to 1 to couple angular degrees of freedom to thermostat */
#define DIMENSION_FACTOR 1.0 /* scaling factor taking into account number of degrees of freedom */
#define KTORQUE 1.0e5 /* force constant in angular dynamics */
#define DIMENSION_FACTOR 0.25 /* scaling factor taking into account number of degrees of freedom */
#define KTORQUE 2.0e3 /* force constant in angular dynamics */
#define KTORQUE_BOUNDARY 1.0e5 /* constant in torque from the boundary */
#define KTORQUE_B 10.0 /* force constant in angular dynamics */
#define KTORQUE_DIFF 500.0 /* force constant in angular dynamics for different particles */
@@ -378,19 +387,20 @@
#define DRAW_SPIN_B 0 /* set to 1 to draw spin vectors of particles */
#define DRAW_CROSS 1 /* set to 1 to draw cross on particles of second type */
#define DRAW_MINUS 1 /* set to 1 to draw cross on particles of negative charge */
#define SPIN_RANGE 10.0 /* range of spin-spin interaction */
#define SPIN_RANGE_B 10.0 /* range of spin-spin interaction for second type of particle */
#define SPIN_RANGE 5.0 /* range of spin-spin interaction */
#define SPIN_RANGE_B 5.0 /* range of spin-spin interaction for second type of particle */
#define QUADRUPOLE_RATIO 0.6 /* anisotropy in quadrupole potential */
#define INCREASE_BETA 0 /* set to 1 to increase BETA during simulation */
#define BETA_SCHEDULE 3 /* type of temperature schedule, see TS_* in global_ljones */
#define BETA_FACTOR 0.06 /* factor by which to change BETA during simulation */
#define BETA_SCHEDULE 5 /* type of temperature schedule, see TS_* in global_ljones */
#define BETA_FACTOR 50.0 /* factor by which to change BETA during simulation */
#define TS_SLOPE 8.5 /* controls speed of change of BETA for TS_TANH schedule (default 1.0) */
#define N_TOSCILLATIONS 1.0 /* number of temperature oscillations in BETA schedule */
#define N_TOSCILLATIONS 1.5 /* number of temperature oscillations in BETA schedule */
#define NO_OSCILLATION 0 /* set to 1 to have exponential BETA change only */
#define MIDDLE_CONSTANT_PHASE 0 /* final phase in which temperature is constant */
#define FINAL_DECREASE_PHASE 0 /* final phase in which temperature decreases */
#define FINAL_CONSTANT_PHASE -1 /* final phase in which temperature is constant */
#define INITIAL_CONSTANT_PHASE 500 /* initial phase in which temperature is constant */
#define MIDDLE_CONSTANT_PHASE 0 /* middle phase in which temperature is constant */
#define FINAL_DECREASE_PHASE 1 /* final phase in which temperature decreases */
#define FINAL_CONSTANT_PHASE 200 /* final phase in which temperature is constant */
#define DECREASE_CONTAINER_SIZE 0 /* set to 1 to decrease size of container */
#define SMOOTH_CONTAINER_DECREASE 1 /* set to 1 to decrease size smoothly at each simulation step */
@@ -427,23 +437,25 @@
#define MASS_PART_BOTTOM 10000.0 /* mass of particles at bottom */
#define NPART_BOTTOM 100 /* number of particles at the bottom */
#define ADD_PARTICLES 1 /* set to 1 to add particles */
#define ADD_REGION 0 /* shape of add regions, cf ADD_* in global_ljones */
#define ADD_PARTICLES 0 /* set to 1 to add particles */
#define ADD_REGION 1 /* shape of add regions, cf ADD_* in global_ljones */
#define ADD_TIME 0 /* time at which to add first particle */
#define ADD_PERIOD 25 /* time interval between adding further particles */
#define ADD_PERIOD 6 /* time interval between adding further particles */
#define ADD_TYPE 1 /* type of added particles */
#define N_ADD_PARTICLES 1 /* number of particles to add */
#define FINAL_NOADD_PERIOD 1000 /* final period where no particles are added */
#define SAFETY_FACTOR 4.0 /* no particles are added at distance less than MU*SAFETY_FACTOR of other particles */
#define FINAL_NOADD_PERIOD 1800 /* final period where no particles are added */
#define SAFETY_FACTOR 10.0 /* no particles are added at distance less than MU*SAFETY_FACTOR of other particles */
#define ADD_ALTERNATE_CHARGE 1 /* set to 1 to randomly select sign of added charge */
#define TIME_DEPENDENT_ADD_CHARGE 0 /* set to 1 to have added charge depend on time */
#define ALTERNATE_CHARGE_PROPORTION 0.5 /* proportion of particles of opposite charge */
#define TRACER_PARTICLE 1 /* set to 1 to have a tracer particle */
#define N_TRACER_PARTICLES 500 /* number of tracer particles */
#define N_TRACER_PARTICLES 3000 /* number of tracer particles */
#define TRACER_STEPS 5 /* number of tracer steps recorded between images */
#define TRAJECTORY_LENGTH 5200 /* length of recorded trajectory */
#define TRAJECTORY_DRAW_LENGTH 1000 /* length of drawn trajectory */
#define TRACER_LUM_FACTOR 25.0 /* controls luminosity decrease of trajectories with time */
#define TRACER_PARTICLE_MASS 2.0 /* relative mass of tracer particle */
#define TRAJECTORY_LENGTH 7000 /* length of recorded trajectory */
#define TRAJECTORY_DRAW_LENGTH 250 /* length of drawn trajectory */
#define TRACER_LUM_FACTOR 100.0 /* controls luminosity decrease of trajectories with time */
#define TRACER_PARTICLE_MASS 1.0 /* relative mass of tracer particle */
#define TRAJECTORY_WIDTH 2 /* width of tracer particle trajectory */
#define TRACK_PARTICLE 0 /* set to 1 to track a given particle */
@@ -494,26 +506,28 @@
#define POSITION_DEP_X -0.625 /* threshold value for position-dependent type */
#define PRINT_ENTROPY 0 /* set to 1 to compute entropy */
#define SPECIAL_IC 0 /* set to 1 for choosing specaial initial condition RD_INITIAL_COND */
#define REACTION_DIFFUSION 0 /* set to 1 to simulate a chemical reaction (particles may change type) */
#define REACTION_MAX_TIME 100 /* time after which no reactions take place */
#define RD_REACTION 231 /* type of reaction, see list in global_ljones.c */
#define RD_TYPES 2 /* number of types in reaction-diffusion equation */
#define RD_INITIAL_COND 51 /* initial condition of particles */
#define REACTION_DIST 1.8 /* maximal distance for reaction to occur */
#define REACTION_PROB 1.0 /* probability controlling reaction term */
#define SPECIAL_IC 1 /* set to 1 for choosing specaial initial condition RD_INITIAL_COND */
#define REACTION_DIFFUSION 1 /* set to 1 to simulate a chemical reaction (particles may change type) */
#define REACTION_MAX_TIME 100000 /* time after which no reactions take place */
#define RD_REACTION 11 /* type of reaction, see list in global_ljones.c */
#define RD_TYPES 5 /* number of types in reaction-diffusion equation */
#define RD_PLOT_TYPES 4 /* number of types shown in graph */
#define RD_INITIAL_COND 5 /* initial condition of particles */
#define REACTION_DIST 2.0 /* maximal distance for reaction to occur */
#define REACTION_PROB 0.5 /* probability controlling reaction term */
#define DISSOCIATION_PROB 0.0 /* probability controlling dissociation reaction */
#define KILLING_PROB 0.0015 /* probability of enzymes being killed */
#define DELTAMAX 0.1 /* max orientation difference for pairing polygons */
#define CENTER_COLLIDED_PARTICLES 1 /* set to 1 to recenter particles upon reaction (may interfere with thermostat) */
#define EXOTHERMIC 1 /* set to 1 to make reaction exo/endothermic */
#define DELTA_EKIN -2.0e10 /* change of kinetic energy in reaction */
#define DELTA_EKIN -2.0e3 /* change of kinetic energy in reaction */
#define CORRECT_EQUILIBRIUM_POSITION 1 /* set to 1 to nudge particle dist towards eq dist */
#define COLLISION_TIME 25 /* time during which collisions are shown */
#define COLLISION_RADIUS 2.0 /* radius of discs showing collisions, in units of MU */
#define DELTAVMAX 200.0 /* maximal deltav allowed for pairing molecules */
#define AGREGMAX 1 /* maximal number of partners for CHEM_AGGREGATION reaction */
#define AGREGMAX 4 /* maximal number of partners for CHEM_AGGREGATION reaction */
#define AGREG_DECOUPLE 12 /* minimal number of partners to decouple from thermostat */
#define NEUTRALIZE_REACTING_PARTICLES 0 /* set to 1 for reacting particles to become neutral */
#define CLUSTER_PARTICLES 0 /* set to 1 for particles to form rigid clusters */
#define CLUSTER_MAXSIZE 2 /* max size of clusters */
#define SMALL_CLUSTER_MAXSIZE 2 /* size limitation on smaller cluster */
@@ -526,7 +540,7 @@
#define MU_RATIO 0.666666667 /* ratio by which to increase radius */
#define PRINT_PARTICLE_NUMBER 0 /* set to 1 to print total number of particles */
#define PLOT_PARTICLE_NUMBER 0 /* set to 1 to make of plot of particle number over time */
#define PLOT_PARTICLE_NUMBER 1 /* set to 1 to make of plot of particle number over time */
#define PARTICLE_NB_PLOT_FACTOR 1.0 /* expected final number of particles over initial number */
#define PRINT_LEFT 0 /* set to 1 to print certain parameters at the top left instead of right */
#define PLOT_SPEEDS 0 /* set to 1 to add a plot of obstacle speeds (e.g. for rockets) */
@@ -545,10 +559,12 @@
#define WALL_TIME 0 /* time during which to keep wall */
#define CHANGE_TYPES 0 /* set to 1 to change type proportion in course of simulation */
#define PROP_MIN 0.1 /* min proportion of type 1 particles */
#define PROP_MAX 0.9 /* max proportion of type 1 particles */
#define PROP_MIN 0.0 /* min proportion of type 1 particles */
#define PROP_MAX 1.0 /* max proportion of type 1 particles */
#define PROP_TINITIAL 250 /* initial time without change */
#define PROP_TFINAL 250 /* final time without change */
#define PAIR_PARTICLES 1 /* set to 1 to form particles pairs */
#define PAIR_PARTICLES 0 /* set to 1 to form particles pairs */
#define RANDOMIZE_ANGLE 0 /* set to 1 for random orientation */
#define DEACIVATE_CLOSE_PAIRS 0 /* set to 1 to test for closeness to other particles */
#define PAIR_SAFETY_FACTOR 1.2 /* distance to deactivate divided by sum of radii */
@@ -564,7 +580,7 @@
#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 0.035 /* radius of partner particle */
#define PARTICLE_MASS_C 2.0 /* mass or partner particle */
#define PARTICLE_MASS_C 1.0 /* mass or partner particle */
#define CHARGE_C 1.0 /* charge of partner particle */
#define CLUSTER_COLOR_FACTOR 40 /* factor for initialization of cluster colors */
#define ALTERNATE_POLY_CHARGE 1 /* set to 1 for alternating charges in molecule */
@@ -576,7 +592,7 @@
#define NARMS_B 1 /* number of "arms" for certain paring types */
#define PAIRING_TYPE_B 81 /* type of pairing, see POLY_ in global_ljones.c */
#define MU_D 0.035 /* radius of partner particle */
#define PARTICLE_MASS_D 2.0 /* mass or partner particle */
#define PARTICLE_MASS_D 1.0 /* mass or partner particle */
#define CHARGE_D 1.0 /* charge of partner particle */
#define NXMAZE 16 /* width of maze */
@@ -587,12 +603,12 @@
#define MAZE_WIDTH 0.015 /* width of maze walls */
#define FLOOR_FORCE 1 /* set to 1 to limit force on particle to FMAX */
#define FMAX 1.0e9 /* maximal force */
#define FMAX 1.0e8 /* maximal force */
#define FLOOR_OMEGA 0 /* set to 1 to limit particle momentum to PMAX */
#define PMAX 1000.0 /* maximal force */
#define HASHX 40 /* size of hashgrid in x direction */
#define HASHY 20 /* size of hashgrid in y direction */
#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 HASHGRID_PADDING 0.1 /* padding of hashgrid outside simulation window */
@@ -603,6 +619,29 @@
#define LIMIT_ENERGY 0 /* set to 1 to limit energy, when there is no thermostat */
/* constants related to evolution on a sphere */
#define SPHERE 1 /* set to 1 to compute evolution in spherical geometry */
#define SIN_THETA_REG 0.05 /* regularization of sin(theta) for motion on sphere */
#define POLAR_PADDING 0.1 /* region around poles that belong to the same hashcell */
#define DRAW_SPHERE 1 /* set to 1 to draw 3D sphere */
#define NX_SPHERE 3000
#define NY_SPHERE 1500 /* number of points on sphere */
#define Z_SCALING_FACTOR 0.75 /* overall scaling factor of z axis for REP_PROJ_3D representation */
#define XY_SCALING_FACTOR 1.9 /* overall scaling factor for on-screen (x,y) coordinates after projection */
#define ZMAX_FACTOR 1.0 /* max value of z coordinate for REP_PROJ_3D representation */
#define XSHIFT_3D -0.0 /* overall x shift for REP_PROJ_3D representation */
#define YSHIFT_3D -0.0 /* overall y shift for REP_PROJ_3D representation */
#define COS_VISIBLE -0.35 /* limit on cosine of normal to shown facets */
#define ROTATE_VIEW 1 /* set to 1 to rotate position of observer */
#define ROTATE_ANGLE 360.0 /* total angle of rotation during simulation */
#define VIEWPOINT_TRAJ 1 /* type of viewpoint trajectory */
#define MAX_LATITUDE 45.0 /* maximal latitude for viewpoint trajectory VP_ORBIT2 */
double light[3] = {0.40824829, -0.816496581, 0.40824829}; /* vector of "light" direction for P_3D_ANGLE color scheme */
double observer[3] = {3.0, -3.0, -2.5}; /* location of observer for REP_PROJ_3D representation */
#define NO_WRAP_BC ((BOUNDARY_COND != BC_PERIODIC)&&(BOUNDARY_COND != BC_PERIODIC_CIRCLE)&&(BOUNDARY_COND != BC_PERIODIC_TRIANGLE)&&(BOUNDARY_COND != BC_KLEIN)&&(BOUNDARY_COND != BC_PERIODIC_FUNNEL)&&(BOUNDARY_COND != BC_BOY)&&(BOUNDARY_COND != BC_GENUS_TWO))
#define PERIODIC_BC ((BOUNDARY_COND == BC_PERIODIC)||(BOUNDARY_COND == BC_PERIODIC_CIRCLE)||(BOUNDARY_COND == BC_PERIODIC_FUNNEL)||(BOUNDARY_COND == BC_PERIODIC_TRIANGLE))
#define TWO_OBSTACLES ((SEGMENT_PATTERN == S_TWO_CIRCLES_EXT)||(SEGMENT_PATTERN == S_TWO_ROCKETS))
@@ -633,12 +672,14 @@ double vysegments[2] = {SEGMENTS_VY0, SEGMENTS_VY0}; /* vy coordinate of s
int thermostat_on = 1; /* thermostat switch used when VARY_THERMOSTAT is on */
double cosangle[NSEG+1];
double sinangle[NSEG+1]; /* precomputed trig functions of angles to draw circles faster */
short int reset_view = 0; /* for moving observer in 3D plot */
#define THERMOSTAT_ON ((THERMOSTAT)&&((!VARY_THERMOSTAT)||(thermostat_on)))
#include "global_ljones.c"
#include "sub_maze.c"
#include "sub_hashgrid.c"
#include "sub_lj_sphere.c"
#include "sub_lj.c"
FILE *lj_time_series, *lj_final_position;
@@ -688,16 +729,17 @@ double bfield_schedule(int i)
double temperature_schedule(int i)
{
static double bexponent, omega, bexp2, factor2, logf, ac, bc;
static int first = 1, t1, t2, t3;
static int first = 1, t1, t2, t3, t4;
double beta, t;
if (first)
{
t1 = NSTEPS - MIDDLE_CONSTANT_PHASE - FINAL_DECREASE_PHASE - FINAL_CONSTANT_PHASE;
t2 = NSTEPS - FINAL_DECREASE_PHASE - FINAL_CONSTANT_PHASE;
t3 = NSTEPS - FINAL_CONSTANT_PHASE;
bexponent = log(BETA_FACTOR)/(double)(t1);
omega = N_TOSCILLATIONS*DPI/(double)(t1);
t1 =INITIAL_CONSTANT_PHASE;
t2 = NSTEPS - MIDDLE_CONSTANT_PHASE - FINAL_DECREASE_PHASE - FINAL_CONSTANT_PHASE;
t3 = NSTEPS - FINAL_DECREASE_PHASE - FINAL_CONSTANT_PHASE;
t4 = NSTEPS - FINAL_CONSTANT_PHASE;
bexponent = log(BETA_FACTOR)/(double)(t2-t1);
omega = N_TOSCILLATIONS*DPI/(double)(t2-t1);
logf = log(BETA_FACTOR);
switch (BETA_SCHEDULE)
@@ -709,7 +751,7 @@ double temperature_schedule(int i)
}
case (TS_CYCLING):
{
factor2 = BETA_FACTOR*2.0/(1.0 + cos(N_TOSCILLATIONS*DPI));
factor2 = BETA_FACTOR*2.0/(1.0 + 1.0e-10 + cos(N_TOSCILLATIONS*DPI));
break;
}
case (TS_PERIODIC):
@@ -751,75 +793,78 @@ double temperature_schedule(int i)
factor2 = 1.0/BETA_FACTOR - 1.0;
break;
}
}
}
bexp2 = -log(factor2)/(double)(FINAL_DECREASE_PHASE);
first = 0;
printf("bexp2 = %.3lg\n", bexp2);
printf("factor2 = %.3lg\n", factor2);
// exit(0);
// printf("t1 = %i, factor2 = %.3lg\n", t1, factor2);
}
if (i < INITIAL_TIME) beta = BETA;
else if (i < INITIAL_TIME + t1)
//
if (i < INITIAL_TIME + t1) beta = BETA;
else if (i < INITIAL_TIME + t2)
{
switch (BETA_SCHEDULE)
{
case (TS_EXPONENTIAL):
{
beta = BETA*exp(bexponent*(double)(i - INITIAL_TIME));
beta = BETA*exp(bexponent*(double)(i - INITIAL_TIME - t1));
break;
}
case (TS_CYCLING):
{
beta = BETA*exp(bexponent*(double)(i - INITIAL_TIME));
beta = beta*2.0/(1.0 + cos(omega*(double)(i - INITIAL_TIME)));
beta = BETA*exp(bexponent*(double)(i - INITIAL_TIME - t1));
beta = beta*2.0/(1.0 + 1.0e-10 + cos(omega*(double)(i - INITIAL_TIME - t1)));
break;
}
case (TS_PERIODIC):
{
beta = BETA*exp(logf*sin(omega*(double)(i - INITIAL_TIME)));
beta = BETA*exp(logf*sin(omega*(double)(i - INITIAL_TIME - t1)));
break;
}
case (TS_LINEAR):
{
beta = BETA/(1.0 + (1.0/BETA_FACTOR - 1.0)*(double)(i - INITIAL_TIME)/(double)(t1));
beta = BETA/(1.0 + (1.0/BETA_FACTOR - 1.0)*(double)(i - INITIAL_TIME - t1)/(double)(t2-t1));
// printf("i = %i, beta = %.3lg\n", i, beta);
break;
}
case (TS_COSINE):
{
beta = ac/(1.0 + bc*cos(omega*(double)(i - INITIAL_TIME)));
beta = ac/(1.0 + bc*cos(omega*(double)(i - INITIAL_TIME - t1)));
printf("i = %i, beta = %.3lg\n", i, beta);
break;
}
case (TS_EXPCOS):
{
beta = BETA*exp(bc*(-1.0 + cos(omega*(double)(i - INITIAL_TIME))));
beta = BETA*exp(bc*(-1.0 + cos(omega*(double)(i - INITIAL_TIME - t1))));
// printf("i = %i, beta = %.3lg\n", i, beta);
break;
}
case (TS_ASYM_EXPCOS):
{
t = (double)(i - INITIAL_TIME)/(double)(t1);
t = (double)(i - INITIAL_TIME - t1)/(double)(t2 - t1);
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)));
beta = BETA/(1.0 + factor2*atan(2.0*(double)(i - INITIAL_TIME - t1)/(double)(t2 - t1)));
break;
}
case (TS_TANH):
{
beta = BETA/(1.0 + factor2*tanh(TS_SLOPE*(double)(i - INITIAL_TIME)/(double)(t1)));
beta = BETA/(1.0 + factor2*tanh(TS_SLOPE*(double)(i - INITIAL_TIME - t1)/(double)(t2 - t1)));
break;
}
}
}
else if (i < INITIAL_TIME + t2) beta = BETA*factor2;
else if (i < INITIAL_TIME + t3)
{
beta = BETA*exp(bexp2*(double)(i - INITIAL_TIME - t3));
}
else beta = BETA;
// else if ((i < INITIAL_TIME + t3)&&(t3 > t2)) beta = BETA*factor2;
// else if ((i < INITIAL_TIME + t4)&&(t4 > t3))
// beta = BETA*exp(bexp2*(double)(i - INITIAL_TIME - t3) + 1.0e-10);
else beta = BETA*1.0e10;
// else beta = BETA;
printf("beta = %.3lg\n", beta);
return(beta);
}
@@ -1035,6 +1080,7 @@ double evolve_particles(t_particle particle[NMAXCIRCLES], t_obstacle obstacle[NM
double beta, int *nactive, int *nsuccess, int *nmove, int *ncoupled, int initial_phase)
{
double a, totalenergy = 0.0, damping, damping1, damping_rot1, direction, dmean, dratio;
double ctheta, stheta, stheta_reg, ffx, ffy;
static double b = 0.25*SIGMA*SIGMA*DT_PARTICLE/MU_XI, xi = 0.0;
int j, move, ncoup;
@@ -1047,15 +1093,40 @@ double evolve_particles(t_particle particle[NMAXCIRCLES], t_obstacle obstacle[NM
for (j=0; j<ncircles; j++) if (particle[j].active)
{
// printf("Particle %i\n", j);
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;
if (SPHERE) /* add inertial terms for equation on a sphere */
{
ctheta = cos(particle[j].yc);
stheta = sin(particle[j].yc);
stheta_reg = stheta + SIN_THETA_REG;
ffx = -2.0*ctheta*px[j]*py[j];
ffy = stheta*ctheta*px[j]*px[j];
particle[j].vx = px[j] + 0.5*DT_PARTICLE*(particle[j].fx + ffx)/stheta_reg;
particle[j].vy = py[j] + 0.5*DT_PARTICLE*(particle[j].fy + ffy);
particle[j].omega = pangle[j] + 0.5*DT_PARTICLE*particle[j].torque;
// particle[j].omega = pangle[j] + 0.5*DT_PARTICLE*particle[j].torque/stheta_reg;
/* TODO: check/fix angular evolution */
ffx = -2.0*ctheta*particle[j].vx*particle[j].vy;
ffy = stheta*ctheta*particle[j].vx*particle[j].vx;
px[j] = particle[j].vx + 0.5*DT_PARTICLE*(particle[j].fx + ffx)/stheta_reg;
py[j] = particle[j].vy + 0.5*DT_PARTICLE*(particle[j].fy + ffy);
pangle[j] = particle[j].omega + 0.5*DT_PARTICLE*particle[j].torque;
// pangle[j] = particle[j].omega + 0.5*DT_PARTICLE*particle[j].torque/stheta_reg;
particle[j].energy = (stheta*stheta*px[j]*px[j] + py[j]*py[j])*particle[j].mass_inv;
}
else
{
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;
particle[j].energy = (px[j]*px[j] + py[j]*py[j])*particle[j].mass_inv;
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;
particle[j].energy = (px[j]*px[j] + py[j]*py[j])*particle[j].mass_inv;
}
if (COMPUTE_EMEAN)
particle[j].emean = ERATIO*particle[j].emean + (1.0-ERATIO)*particle[j].energy;
@@ -1170,7 +1241,7 @@ double evolve_particles(t_particle particle[NMAXCIRCLES], t_obstacle obstacle[NM
if (particle[j].yc > BCYMAX) particle[j].yc += BCYMIN - BCYMAX;
else if (particle[j].yc < BCYMIN) particle[j].yc += BCYMAX - BCYMIN;
}
else if (!NO_WRAP_BC)
else if ((!NO_WRAP_BC)||(BOUNDARY_COND == BC_SPHERE))
{
move += wrap_particle(&particle[j], &px[j], &py[j]);
}
@@ -1757,6 +1828,7 @@ void animation()
t_belt *conveyor_belt;
t_otriangle *otriangle;
t_ofacet *ofacet;
t_lj_sphere *wsphere;
char message[100];
ratioc = 1.0 - ratio;
@@ -1772,6 +1844,13 @@ void animation()
particle = (t_particle *)malloc(NMAXCIRCLES*sizeof(t_particle)); /* particles */
/* sphere data */
if (DRAW_SPHERE)
{
wsphere = (t_lj_sphere *)malloc(NX_SPHERE*NY_SPHERE*sizeof(t_lj_sphere));
init_lj_sphere(wsphere);
}
if (CLUSTER_PARTICLES)
cluster = (t_cluster *)malloc(NMAXCIRCLES*sizeof(t_cluster)); /* particle clusters */
@@ -1920,6 +1999,12 @@ void animation()
printf("Termostat: %i\n", thermostat_on);
}
if (ROTATE_VIEW)
{
viewpoint_schedule(i - INITIAL_TIME);
reset_view = 1;
}
/* deactivate some segments */
if ((ADD_FIXED_SEGMENTS)&&(DEACTIVATE_SEGMENT)&&(i == INITIAL_TIME + SEGMENT_DEACTIVATION_TIME + 1))
@@ -2411,7 +2496,9 @@ void animation()
/* case of varying type proportion */
if (CHANGE_TYPES)
{
t = (double)i/(double)NSTEPS;
if (i < PROP_TINITIAL) t = 0.0;
else if (i > NSTEPS - PROP_TFINAL) t = 1.0;
else t = (double)(i - PROP_TINITIAL)/(double)(NSTEPS - PROP_TINITIAL - PROP_TFINAL);
params.prop = PROP_MIN*(1.0-t) + PROP_MAX*t;
change_type_proportion(particle, params.prop);
}
@@ -2427,11 +2514,12 @@ 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, tracer_n);
nadd_particle = add_particles(particle, px, py, nadd_particle, 7, molecule, tracer_n, i);
}
else for (k=0; k<N_ADD_PARTICLES; k++)
nadd_particle = add_particles(particle, px, py, nadd_particle, 3, molecule, tracer_n);
nadd_particle = add_particles(particle, px, py, nadd_particle, ADD_TYPE, molecule, tracer_n, i);
// params.nactive = nadd_particle;
if (PAIR_PARTICLES) init_molecule_data(particle, molecule);
params.nactive = 0;
for (j=0; j<ncircles; j++) if (particle[j].active)
{
@@ -2480,7 +2568,7 @@ void animation()
draw_frame(i, PLOT, BG_COLOR, ncollisions, traj_position, traj_length,
wall, pressure, pleft, pright, currents, particle_numbers, 1, params, particle, cluster,
collisions, hashgrid, trajectory, obstacle, segment, group_speeds, segment_group, conveyor_belt, tracer_n, otriangle, ofacet);
collisions, hashgrid, trajectory, obstacle, segment, group_speeds, segment_group, conveyor_belt, tracer_n, otriangle, ofacet, wsphere);
if (!((NO_EXTRA_BUFFER_SWAP)&&(MOVIE))) glutSwapBuffers();
@@ -2512,7 +2600,7 @@ void animation()
{
draw_frame(i, PLOT_B, BG_COLOR_B, ncollisions, traj_position, traj_length,
wall, pressure, pleft, pright, currents, particle_numbers, 0, params, particle, cluster,
collisions, hashgrid, trajectory, obstacle, segment, group_speeds, segment_group, conveyor_belt, tracer_n, otriangle, ofacet);
collisions, hashgrid, trajectory, obstacle, segment, group_speeds, segment_group, conveyor_belt, tracer_n, otriangle, ofacet, wsphere);
glutSwapBuffers();
save_frame_lj_counter(NSTEPS + MID_FRAMES + 1 + counter);
counter++;
@@ -2553,7 +2641,7 @@ void animation()
blank();
draw_frame(NSTEPS, PLOT, BG_COLOR, ncollisions, traj_position, traj_length,
wall, pressure, pleft, pright, currents, particle_numbers, 0, params, particle, cluster,
collisions, hashgrid, trajectory, obstacle, segment, group_speeds, segment_group, conveyor_belt, tracer_n, otriangle, ofacet);
collisions, hashgrid, trajectory, obstacle, segment, group_speeds, segment_group, conveyor_belt, tracer_n, otriangle, ofacet, wsphere);
}
if (DOUBLE_MOVIE) for (i=0; i<MID_FRAMES; i++)
{
@@ -2565,7 +2653,7 @@ void animation()
{
draw_frame(NSTEPS, PLOT_B, BG_COLOR_B, ncollisions, traj_position, traj_length,
wall, pressure, pleft, pright, currents, particle_numbers, 0, params, particle, cluster,
collisions, hashgrid, trajectory, obstacle, segment, group_speeds, segment_group, conveyor_belt, tracer_n, otriangle, ofacet);
collisions, hashgrid, trajectory, obstacle, segment, group_speeds, segment_group, conveyor_belt, tracer_n, otriangle, ofacet, wsphere);
if (!((NO_EXTRA_BUFFER_SWAP)&&(MOVIE))) glutSwapBuffers();
}
if ((TIME_LAPSE)&&(!DOUBLE_MOVIE))
@@ -2651,6 +2739,8 @@ void animation()
fclose(lj_final_position);
}
if (DRAW_SPHERE) free(wsphere);
fclose(lj_log);
}
@@ -2691,7 +2781,8 @@ int main(int argc, char** argv)
glutInitWindowSize(WINWIDTH,WINHEIGHT);
glutCreateWindow("Particles with Lennard-Jones interaction in a planar domain");
init();
if (DRAW_SPHERE) init_3d();
else init();
glutDisplayFunc(display);