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This commit is contained in:
Nils Berglund
2024-08-17 12:04:42 +02:00
committed by GitHub
parent f7be9f43fc
commit 623d353390
18 changed files with 3808 additions and 491 deletions
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471
lennardjones.c
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@@ -36,8 +36,8 @@
#include <omp.h>
#include <time.h>
#define MOVIE 1 /* set to 1 to generate movie */
#define DOUBLE_MOVIE 0 /* set to 1 to produce movies for wave height and energy simultaneously */
#define MOVIE 0 /* set to 1 to generate movie */
#define DOUBLE_MOVIE 1 /* set to 1 to produce movies for wave height and energy simultaneously */
#define SAVE_MEMORY 1 /* set to 1 to save memory while saving frames */
#define NO_EXTRA_BUFFER_SWAP 1 /* some OS require one less buffer swap when recording images */
@@ -58,10 +58,10 @@
#define YMIN -1.125
#define YMAX 1.125 /* y interval for 9/16 aspect ratio */
#define INITXMIN -1.95
#define INITXMAX 1.95 /* x interval for initial condition */
#define INITYMIN -1.1
#define INITYMAX 1.1 /* y interval for initial condition */
#define INITXMIN -1.8
#define INITXMAX 1.8 /* x interval for initial condition */
#define INITYMIN 0.9
#define INITYMAX 2.2 /* y interval for initial condition */
#define THERMOXMIN -1.25
#define THERMOXMAX 1.25 /* x interval for initial condition */
@@ -78,7 +78,7 @@
#define BCXMIN -2.0
#define BCXMAX 2.0 /* x interval for boundary condition */
#define BCYMIN -1.125
#define BCYMAX 1.125 /* y interval for boundary condition */
#define BCYMAX 2.4 /* y interval for boundary condition */
#define OBSXMIN -2.0
#define OBSXMAX 2.0 /* x interval for motion of obstacle */
@@ -91,14 +91,16 @@
#define ADD_FIXED_OBSTACLES 0 /* set to 1 do add fixed circular obstacles */
#define OBSTACLE_PATTERN 71 /* pattern of obstacles, see list in global_ljones.c */
#define ADD_FIXED_SEGMENTS 0 /* set to 1 to add fixed segments as obstacles */
#define SEGMENT_PATTERN 29 /* pattern of repelling segments, see list in global_ljones.c */
#define ADD_FIXED_SEGMENTS 1 /* set to 1 to add fixed segments as obstacles */
#define SEGMENT_PATTERN 182 /* 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 */
#define NOZZLE_SHAPE_B 6 /* shape of nozzle for second rocket, see list in global_ljones.c */
#define BELT_SPEED1 20.0 /* speed of first conveyor belt */
#define BELT_SPEED2 -10.0 /* speed of second conveyor belt */
#define TWO_TYPES 1 /* set to 1 to have two types of particles */
#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 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 */
@@ -106,31 +108,31 @@
#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_B 12 /* particle interaction for second type of particle, see list in global_ljones.c */
#define SPIN_INTER_FREQUENCY 2.0 /* angular frequency of spin-spin interaction */
#define SPIN_INTER_FREQUENCY_B 2.0 /* angular frequency of spin-spin interaction for second particle type */
#define MOL_ANGLE_FACTOR 1.0 /* rotation angle for P_MOL_ANGLE color scheme */
#define INTERACTION 171 /* 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 6.0 /* angular frequency of spin-spin interaction */
#define SPIN_INTER_FREQUENCY_B 6.0 /* angular frequency of spin-spin interaction for second particle type */
#define MOL_ANGLE_FACTOR 6.0 /* rotation angle for P_MOL_ANGLE color scheme */
#define P_PERCOL 0.25 /* probability of having a circle in C_RAND_PERCOL arrangement */
#define NPOISSON 100 /* number of points for Poisson C_RAND_POISSON arrangement */
#define PDISC_DISTANCE 9.6 /* minimal distance in Poisson disc process, controls density of particles */
#define PDISC_DISTANCE 2.5 /* minimal distance in Poisson disc process, controls density of particles */
#define PDISC_CANDIDATES 100 /* number of candidates in construction of Poisson disc process */
#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 0.0087 /* parameter controlling radius of particles */
#define MU_B 0.012 /* parameter controlling radius of particles of second type */
#define NPOLY 40 /* number of sides of polygon */
#define APOLY 0.0 /* angle by which to turn polygon, in units of Pi/2 */
#define MU 0.025 /* parameter controlling radius of particles */
#define MU_B 0.03 /* parameter controlling radius of particles of second type */
#define NPOLY 6 /* number of sides of polygon */
#define APOLY 0.075 /* angle by which to turn polygon, in units of Pi/2 */
#define AWEDGE 0.5 /* opening angle of wedge, in units of Pi/2 */
#define MDEPTH 4 /* depth of computation of Menger gasket */
#define MRATIO 3 /* ratio defining Menger gasket */
#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 40 /* number of grid point for grid of disks */
#define NGRIDY 20 /* number of grid point for grid of disks */
#define NGRIDX 36 /* number of grid point for grid of disks */
#define NGRIDY 36 /* 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 */
@@ -146,11 +148,10 @@
/* Parameters for length and speed of simulation */
#define NSTEPS 2500 /* number of frames of movie */
// #define NSTEPS 200 /* number of frames of movie */
#define NVID 50 /* number of iterations between images displayed on screen */
#define NSTEPS 2700 /* number of frames of movie */
#define NVID 200 /* number of iterations between images displayed on screen */
#define NSEG 25 /* number of segments of boundary of circles */
#define INITIAL_TIME 5 /* time after which to start saving frames */
#define INITIAL_TIME 200 /* time after which to start saving frames */
#define OBSTACLE_INITIAL_TIME 0 /* time after which to start moving obstacle */
#define BOUNDARY_WIDTH 1 /* width of particle boundary */
#define LINK_WIDTH 2 /* width of links between particles */
@@ -161,45 +162,49 @@
#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 250 /* number of still frames at end of movie */
#define END_FRAMES 100 /* number of still frames at end of movie */
/* Boundary conditions, see list in global_ljones.c */
#define BOUNDARY_COND 3
#define BOUNDARY_COND 1
/* Plot type, see list in global_ljones.c */
#define PLOT 5
#define PLOT_B 13 /* plot type for second movie */
#define PLOT 11
#define PLOT_B 14 /* plot type for second movie */
/* Background color depending on particle properties */
#define COLOR_BACKGROUND 1 /* set to 1 to color background */
#define COLOR_BACKGROUND 0 /* set to 1 to color background */
#define BG_COLOR 2 /* type of background coloring, see list in global_ljones.c */
#define BG_COLOR_B 0 /* type of background coloring, see list in global_ljones.c */
#define DRAW_BONDS 1 /* set to 1 to draw bonds between neighbours */
#define DRAW_BONDS 0 /* set to 1 to draw bonds between neighbours */
#define COLOR_BONDS 1 /* set to 1 to color bonds according to length */
#define FILL_TRIANGLES 0 /* set to 1 to fill triangles between neighbours */
#define DRAW_CLUSTER_LINKS 0 /* set to 1 to draw links between particles in cluster */
#define ALTITUDE_LINES 0 /* set to 1 to add horizontal lines to show altitude */
#define COLOR_SEG_GROUPS 0 /* set to 1 to collor segment groups differently */
#define N_PARTICLE_COLORS 200 /* number of colors for P_NUMBER color scheme */
#define INITIAL_POS_TYPE 0 /* type of initial position dependence */
#define ERATIO 0.995 /* ratio for time-averaging in P_EMEAN color scheme */
#define DRATIO 0.995 /* ratio for time-averaging in P_DIRECT_EMEAN color scheme */
#define DRATIO 0.999 /* ratio for time-averaging in P_DIRECT_EMEAN color scheme */
/* Color schemes */
#define COLOR_PALETTE 10 /* Color palette, see list in global_ljones.c */
#define COLOR_PALETTE_EKIN 10 /* Color palette for kinetic energy */
#define COLOR_PALETTE_ANGLE 10 /* Color palette for angle representation */
#define COLOR_PALETTE_DIRECTION 0 /* Color palette for direction representation */
#define COLOR_PALETTE_ANGLE 0 /* Color palette for angle representation */
#define COLOR_PALETTE_DIRECTION 17 /* Color palette for direction representation */
#define COLOR_PALETTE_INITIAL_POS 10 /* Color palette for initial position representation */
#define COLOR_PALETTE_DIFFNEIGH 10 /* Color palette for different neighbours representation */
#define COLOR_PALETTE_PRESSURE 11 /* Color palette for different neighbours representation */
#define COLOR_PALETTE_CHARGE 18 /* Color palette for charge representation */
#define COLOR_PALETTE_CLUSTER 11 /* Color palette for cluster representation */
#define COLOR_PALETTE_CLUSTER 14 /* Color palette for cluster representation */
#define COLOR_PALETTE_CLUSTER_SIZE 13 /* Color palette for cluster size representation */
#define COLOR_PALETTE_CLUSTER_SELECTED 11 /* Color palette for selected cluster representation */
#define COLOR_HUE_CLUSTER_SELECTED 90.0 /* Color hue for selected cluster */
#define COLOR_HUE_CLUSTER_NOT_SELECTED 220.0 /* Color hue for selected cluster */
#define BLACK 1 /* background */
@@ -234,12 +239,11 @@
#define ENERGY_HUE_MAX 50.0 /* color of saturated particle */
#define PARTICLE_HUE_MIN 359.0 /* color of original particle */
#define PARTICLE_HUE_MAX 0.0 /* color of saturated particle */
// #define PARTICLE_EMAX 50000.0 /* energy of particle with hottest color */
#define PARTICLE_EMIN 10.0 /* energy of particle with coolest color */
#define PARTICLE_EMAX 20000.0 /* energy of particle with hottest color */
#define HUE_TYPE0 300.0 /* hue of particles of type 0 */
#define HUE_TYPE1 00.0 /* hue of particles of type 1 */
#define HUE_TYPE2 340.0 /* hue of particles of type 2 */
#define PARTICLE_EMAX 100.0 /* energy of particle with hottest color */
#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_TYPE5 60.0 /* hue of particles of type 5 */
@@ -249,39 +253,40 @@
#define RANDOM_RADIUS 0 /* set to 1 for random circle radius */
#define DT_PARTICLE 3.0e-6 /* time step for particle displacement */
#define KREPEL 15.0 /* constant in repelling force between particles */
#define EQUILIBRIUM_DIST 5.0 /* Lennard-Jones equilibrium distance */
#define EQUILIBRIUM_DIST_B 5.0 /* Lennard-Jones equilibrium distance for second type of particle */
#define KREPEL 50.0 /* constant in repelling force between particles */
#define EQUILIBRIUM_DIST 2.3 /* Lennard-Jones equilibrium distance */
#define EQUILIBRIUM_DIST_B 2.5 /* Lennard-Jones equilibrium distance for second type of particle */
#define REPEL_RADIUS 25.0 /* radius in which repelling force acts (in units of particle radius) */
#define DAMPING 500.0 /* damping coefficient of particles */
#define INITIAL_DAMPING 5000.0 /* damping coefficient of particles during initial phase */
#define DAMPING_ROT 1.0e6 /* damping coefficient for rotation of particles */
#define INITIAL_DAMPING 1000.0 /* damping coefficient of particles during initial phase */
#define DAMPING_ROT 1000.0 /* damping coefficient for rotation of particles */
#define PARTICLE_MASS 2.0 /* mass of particle of radius MU */
#define PARTICLE_MASS_B 16.0 /* mass of particle of radius MU_B */
#define PARTICLE_INERTIA_MOMENT 0.2 /* moment of inertia of particle */
#define PARTICLE_INERTIA_MOMENT_B 0.02 /* moment of inertia of second type of particle */
#define PARTICLE_MASS_B 2.0 /* mass of particle of radius MU_B */
#define PARTICLE_INERTIA_MOMENT 0.5 /* moment of inertia of particle */
#define PARTICLE_INERTIA_MOMENT_B 0.5 /* moment of inertia of second type of particle */
#define V_INITIAL 50.0 /* initial velocity range */
#define OMEGA_INITIAL 10.0 /* initial angular velocity range */
#define OMEGA_INITIAL 50.0 /* 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 V_INITIAL_TYPE 0 /* type of initial speed distribution (see VI_ in global_ljones.c) */
#define THERMOSTAT 1 /* set to 1 to switch on thermostat */
#define THERMOSTAT 0 /* 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 0.00007 /* initial inverse temperature */
#define BETA 0.004 /* 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 2.0e11 /* harmonic potential of obstacles */
#define NBH_DIST_FACTOR 5.0 /* radius in which to count neighbours */
#define GRAVITY 0.0 /* gravity acting on all particles */
#define KSPRING_OBSTACLE 1.0e9 /* harmonic potential of obstacles */
#define NBH_DIST_FACTOR 4.0 /* radius in which to count neighbours */
#define GRAVITY 4000.0 /* 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 */
#define GRAVITY_SCHEDULE 1 /* type of gravity schedule, see list in global_ljones.c */
#define GRAVITY_FACTOR 10.0 /* factor by which to increase gravity */
#define GRAVITY_INITIAL_TIME 200 /* time at start of simulation with constant gravity */
#define GRAVITY_INITIAL_TIME 250 /* time at start of simulation with constant gravity */
#define GRAVITY_RESTORE_TIME 500 /* time at end of simulation with gravity restored to initial value */
#define KSPRING_VICSEK 0.2 /* spring constant for I_VICSEK_SPEED interaction */
#define VICSEK_REPULSION 10.0 /* repulsion between particles in Vicsek model */
@@ -291,9 +296,8 @@
#define ADD_BFIELD 0 /* set to 1 to add a magnetic field */
#define BFIELD 2.666666667 /* value of magnetic field */
#define CHARGE 1.0 /* charge of particles of first type */
#define CHARGE_B -1.5 /* charge of particles of second type */
#define CHARGE_B 1.0 /* charge of particles of second type */
#define INCREASE_E 0 /* set to 1 to increase electric field */
// #define EFIELD_FACTOR 2500000.0 /* factor by which to increase electric field */
#define EFIELD_FACTOR 5000000.0 /* factor by which to increase electric field */
#define INCREASE_B 0 /* set to 1 to increase magnetic field */
#define BFIELD_FACTOR 20000.0 /* factor by which to increase magnetic field */
@@ -301,25 +305,24 @@
#define OBSTACLE_CHARGE 3.0 /* charge of obstacles */
#define KCOULOMB_OBSTACLE 1000.0 /* Coulomb force constant for charged obstacles */
#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 -100.0 /* force constant in angular dynamics */
#define KTORQUE_BOUNDARY 1.0e6 /* constant in torque from the boundary */
#define KTORQUE 5.0e3 /* force constant in angular dynamics */
#define KTORQUE_BOUNDARY 5.0e5 /* constant in torque from the boundary */
#define KTORQUE_B 10.0 /* force constant in angular dynamics */
#define KTORQUE_DIFF -150.0 /* force constant in angular dynamics for different particles */
#define KTORQUE_DIFF 500.0 /* force constant in angular dynamics for different particles */
#define DRAW_SPIN 0 /* set to 1 to draw spin vectors of particles */
#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 DRAW_CROSS 0 /* set to 1 to draw cross on particles of second type */
#define DRAW_MINUS 0 /* 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 QUADRUPOLE_RATIO 0.6 /* anisotropy in quadrupole potential */
#define INCREASE_BETA 1 /* set to 1 to increase BETA during simulation */
#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 10.0 /* factor by which to change BETA during simulation */
// #define BETA_FACTOR 0.08 /* factor by which to change BETA during simulation */
#define BETA_FACTOR 0.06 /* 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 NO_OSCILLATION 0 /* set to 1 to have exponential BETA change only */
@@ -380,7 +383,7 @@
#define SMOOTH_ROTATION 1 /* set to 1 to update segments at each time step (rather than at each movie frame) */
#define ROTATION_SCHEDULE 0 /* time-dependence of rotation angle, see ROT_* in global_ljones.c */
#define PERIOD_ROTATE_BOUNDARY 1000 /* period of rotating boundary */
#define ROTATE_INITIAL_TIME 300 /* initial time without rotation */
#define ROTATE_INITIAL_TIME 150 /* initial time without rotation */
#define ROTATE_FINAL_TIME 300 /* final time without rotation */
#define ROTATE_CHANGE_TIME 0.5 /* relative duration of acceleration/deceleration phases */
#define OMEGAMAX -2.0*PI /* maximal rotation speed */
@@ -388,7 +391,7 @@
#define MOVE_BOUNDARY 0 /* set to 1 to move repelling segments, due to force from particles */
#define SEGMENTS_MASS 40.0 /* mass of collection of segments */
#define DEACTIVATE_SEGMENT 1 /* set to 1 to deactivate last segment after a certain time */
#define SEGMENT_DEACTIVATION_TIME 20 /* time at which to deactivate last segment */
#define SEGMENT_DEACTIVATION_TIME 200 /* time at which to deactivate last segment */
#define RELEASE_ROCKET_AT_DEACTIVATION 0 /* set to 1 to limit segments velocity before segment release */
#define SEGMENTS_X0 1.5 /* initial position of segments */
#define SEGMENTS_Y0 0.0 /* initial position of segments */
@@ -405,6 +408,7 @@
#define SEGMENT_GROUP_DAMPING 0.0 /* damping of segment groups */
#define GROUP_REPULSION 0 /* set to 1 for groups of segments to repel each other */
#define KSPRING_GROUPS 5.0e11 /* harmonic potential between segment groups */
#define KSPRING_BELT 1.0e4 /* spring constant from belt */
#define GROUP_WIDTH 0.05 /* interaction width of groups */
#define GROUP_G_REPEL 0 /* set to 1 to add repulsion between centers of mass of groups */
#define GROUP_G_REPEL_RADIUS 1.2 /* radius within which centers of mass of groups repel each other */
@@ -418,20 +422,29 @@
#define PRINT_ENTROPY 0 /* set to 1 to compute entropy */
#define REACTION_DIFFUSION 0 /* set to 1 to simulate a chemical reaction (particles may change type) */
#define RD_REACTION 256 /* type of reaction, see list in global_ljones.c */
#define RD_TYPES 6 /* number of types in reaction-diffusion equation */
#define RD_INITIAL_COND 10 /* initial condition of particles */
#define REACTION_DIST 4.0 /* maximal distance for reaction to occur */
#define RD_REACTION 262 /* type of reaction, see list in global_ljones.c */
#define RD_TYPES 1 /* number of types in reaction-diffusion equation */
#define RD_INITIAL_COND 0 /* initial condition of particles */
#define REACTION_DIST 1.2 /* maximal distance for reaction to occur */
#define REACTION_PROB 1.0 /* probability controlling reaction term */
#define DISSOCIATION_PROB 0.0 /* probability controlling dissociation reaction */
#define KILLING_PROB 0.0015 /* probability of enzymes being killed */
#define KILLING_PROB 0.0015 /* probability of enzymes being killed */
#define DELTAMAX 0.1 /* max orientation difference for pairing polygons */
#define CENTER_COLLIDED_PARTICLES 0 /* set to 1 to recenter particles upon reaction (may interfere with thermostat) */
#define EXOTHERMIC 0 /* set to 1 to make reaction exo/endothermic */
#define DELTA_EKIN 2000.0 /* change of kinetic energy in reaction */
#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 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 6 /* maximal number of partners for CHEM_AGGREGATION reaction */
#define AGREG_DECOUPLE 12 /* minimal number of partners to decouple from thermostat */
#define CLUSTER_PARTICLES 0 /* set to 1 for particles to form rigid clusters */
#define CLUSTER_MAXSIZE 1000 /* max size of clusters */
#define SMALL_CLUSTER_MAXSIZE 10 /* size limitation on smaller cluster */
#define SMALL_NP_MAXSIZE 2 /* limitation on number of partners of particle in smaller cluster */
#define NOTSELECTED_CLUSTER_MAXSIZE 0 /* limit on size of clusters that can merge with non-selected cluster */
#define REPAIR_CLUSTERS 0 /* set to 1 to repair alignment in clusters */
#define REPAIR_MIN_DIST 0.75 /* relative distance below which overlapping polygons are inactivated */
#define CHANGE_RADIUS 0 /* set to 1 to change particle radius during simulation */
#define MU_RATIO 0.666666667 /* ratio by which to increase radius */
@@ -458,35 +471,36 @@
#define PROP_MIN 0.1 /* min proportion of type 1 particles */
#define PROP_MAX 0.9 /* max proportion of type 1 particles */
#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 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 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 KSPRING_PAIRS 5.0e10 /* 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 NPARTNERS 4 /* number of partners of particles - for DNA, set NPARTNERS_DNA */
#define NPARTNERS_DNA 8 /* number of partners of particles, case of DNA, should be at least 8 */
#define NARMS 5 /* number of "arms" for certain paring types */
#define PAIRING_TYPE 9 /* 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 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 PAIR_DRATIO 1.1 /* 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 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 */
#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 2 /* number of partners of particles */
#define NPARTNERS_B 5 /* 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 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 CHARGE_D 1.0 /* charge of partner particle */
#define NXMAZE 12 /* width of maze */
#define NYMAZE 12 /* height of maze */
@@ -500,8 +514,8 @@
#define FLOOR_OMEGA 0 /* set to 1 to limit particle momentum to PMAX */
#define PMAX 1000.0 /* maximal force */
#define HASHX 80 /* size of hashgrid in x direction */
#define HASHY 40 /* size of hashgrid in y direction */
#define HASHX 100 /* size of hashgrid in x direction */
#define HASHY 88 /* 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 */
@@ -515,11 +529,12 @@
#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))
#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_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)||(PLOT == P_EMEAN_DENSITY)||(PLOT_B == P_EMEAN_DENSITY))
#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)||(RD_REACTION == CHEM_AGGREGATION_CHARGE)||(RD_REACTION == CHEM_AGGREGATION_NNEIGH))))
#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))))
#define COMPUTE_PAIR_TORQUE (KTORQUE_PAIR_ANGLE != 0.0)
#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)))
double xshift = 0.0; /* x shift of shown window */
double xspeed = 0.0; /* x speed of obstacle */
@@ -960,6 +975,8 @@ double evolve_particles(t_particle particle[NMAXCIRCLES], t_hashgrid hashgrid[HA
if (initial_phase) damping = INITIAL_DAMPING;
else damping = DAMPING;
// printf("Evolving particles\n");
#pragma omp parallel for private(j,xi,totalenergy,a,move)
for (j=0; j<ncircles; j++) if (particle[j].active)
{
@@ -979,7 +996,9 @@ double evolve_particles(t_particle particle[NMAXCIRCLES], t_hashgrid hashgrid[HA
if (COMPUTE_DIRMEAN)
{
direction = argument(particle[j].vx, particle[j].vy);
// printf("direction = %.3lg\t", direction);
dmean = particle[j].dirmean;
// printf("dirmean = %.3lg\n", particle[j].dirmean);
if (dmean < direction - PI) dmean += DPI;
else if (dmean > direction + PI) dmean -= DPI;
particle[j].dirmean = DRATIO*dmean + (1.0-DRATIO)*direction;
@@ -1092,6 +1111,135 @@ double evolve_particles(t_particle particle[NMAXCIRCLES], t_hashgrid hashgrid[HA
return(totalenergy);
}
double evolve_clusters(t_particle particle[NMAXCIRCLES], t_cluster cluster[NMAXCIRCLES],
t_hashgrid hashgrid[HASHX*HASHY],
double cqx[NMAXCIRCLES], double cqy[NMAXCIRCLES], double cqangle[NMAXCIRCLES],
double cpx[NMAXCIRCLES], double cpy[NMAXCIRCLES], double cpangle[NMAXCIRCLES],
double beta, int *nactive, int *nsuccess, int *nmove, int *ncoupled, int initial_phase, int verbose)
{
double a, totalenergy = 0.0, damping, direction, dmean, newx, newy, newangle, deltax, deltay, deltaangle;
static double b = 0.25*SIGMA*SIGMA*DT_PARTICLE/MU_XI, xi = 0.0;
int j, move, ncoup;
if (initial_phase) damping = INITIAL_DAMPING;
else damping = DAMPING;
#pragma omp parallel for private(j,xi,totalenergy,a,move)
for (j=0; j<ncircles; j++) if (cluster[j].active)
{
cluster[j].vx = cpx[j] + 0.5*DT_PARTICLE*cluster[j].fx;
cluster[j].vy = cpy[j] + 0.5*DT_PARTICLE*cluster[j].fy;
cluster[j].omega = cpangle[j] + 0.5*DT_PARTICLE*cluster[j].torque;
cpx[j] = cluster[j].vx + 0.5*DT_PARTICLE*cluster[j].fx;
cpy[j] = cluster[j].vy + 0.5*DT_PARTICLE*cluster[j].fy;
cpangle[j] = cluster[j].omega + 0.5*DT_PARTICLE*cluster[j].torque;
cluster[j].energy = (cpx[j]*cpx[j] + cpy[j]*cpy[j])*cluster[j].mass_inv;
if (COMPUTE_EMEAN)
cluster[j].emean = ERATIO*cluster[j].emean + (1.0-ERATIO)*cluster[j].energy;
if (COMPUTE_DIRMEAN)
{
direction = argument(cluster[j].vx, cluster[j].vy);
dmean = cluster[j].dirmean;
if (dmean < direction - PI) dmean += DPI;
else if (dmean > direction + PI) dmean -= DPI;
cluster[j].dirmean = DRATIO*dmean + (1.0-DRATIO)*direction;
if (cluster[j].dirmean < 0.0) cluster[j].dirmean += DPI;
else if (cluster[j].dirmean > DPI) cluster[j].dirmean -= DPI;
}
if ((COUPLE_ANGLE_TO_THERMOSTAT)&&(cluster[j].thermostat))
cluster[j].energy += cpangle[j]*cpangle[j]*cluster[j].inertia_moment_inv;
cqx[j] = cluster[j].xg + 0.5*DT_PARTICLE*cpx[j]*cluster[j].mass_inv;
cqy[j] = cluster[j].yg + 0.5*DT_PARTICLE*cpy[j]*cluster[j].mass_inv;
cqangle[j] = cluster[j].angle + 0.5*DT_PARTICLE*cpangle[j]*cluster[j].inertia_moment_inv;
if ((THERMOSTAT_ON)&&(cluster[j].thermostat))
{
cpx[j] *= exp(- 0.5*DT_PARTICLE*xi);
cpy[j] *= exp(- 0.5*DT_PARTICLE*xi);
}
if ((COUPLE_ANGLE_TO_THERMOSTAT)&&(cluster[j].thermostat))
cpangle[j] *= exp(- 0.5*DT_PARTICLE*xi);
}
/* compute kinetic energy */
// *nactive = 0;
ncoup = 1;
for (j=0; j<ncircles; j++)
if ((cluster[j].active)&&(cluster[j].thermostat))
{
totalenergy += cluster[j].energy;
ncoup++;
// *nactive++;
}
totalenergy *= DIMENSION_FACTOR; /* normalize energy to take number of degrees of freedom into account */
if (THERMOSTAT_ON)
{
/* TODO - fix nactive vs ncoupled */
// a = DT_PARTICLE*(totalenergy - (double)*nactive/beta)/MU_XI;
a = DT_PARTICLE*(totalenergy - (double)ncoup/beta)/MU_XI;
a += SIGMA*sqrt(DT_PARTICLE)*gaussian();
xi = (xi + a - b*xi)/(1.0 + b);
}
move = 0;
for (j=0; j<ncircles; j++) if (cluster[j].active)
{
if ((THERMOSTAT_ON)&&(cluster[j].thermostat))
{
cpx[j] *= exp(- 0.5*DT_PARTICLE*xi);
cpy[j] *= exp(- 0.5*DT_PARTICLE*xi);
if (!COUPLE_ANGLE_TO_THERMOSTAT) cpangle[j] *= exp(- DT_PARTICLE*DAMPING_ROT);
}
else
{
cpx[j] *= exp(- DT_PARTICLE*damping);
cpy[j] *= exp(- DT_PARTICLE*damping);
cpangle[j] *= exp(- DT_PARTICLE*DAMPING_ROT);
// printf("Damping cluster angular velocity\n");
}
if ((THERMOSTAT_ON)&&(COUPLE_ANGLE_TO_THERMOSTAT)&&(cluster[j].thermostat))
cpangle[j] *= exp(- 0.5*DT_PARTICLE*xi);
newx = cqx[j] + 0.5*DT_PARTICLE*cpx[j]*cluster[j].mass_inv;
newy = cqy[j] + 0.5*DT_PARTICLE*cpy[j]*cluster[j].mass_inv;
newangle = cqangle[j] + 0.5*DT_PARTICLE*cpangle[j]*cluster[j].inertia_moment_inv;
deltax = newx - cluster[j].xg;
deltay = newy - cluster[j].yg;
deltaangle = newangle - cluster[j].angle;
// translate_cluster(j, cluster, particle, deltax, deltay, 0);
// rotate_cluster(j, cluster, particle, deltaangle);
translate_and_rotate_cluster(j, cluster, particle, deltax, deltay, deltaangle);
// cluster[j].vx = cpx[j] + 0.5*DT_PARTICLE*cluster[j].fx;
// cluster[j].vy = cpy[j] + 0.5*DT_PARTICLE*cluster[j].fy;
// cluster[j].omega = cpangle[j] + 0.5*DT_PARTICLE*cluster[j].torque;
/* FIXME: adapt to clusters */
// else if (!NO_WRAP_BC)
// {
// move += wrap_particle(&particle[j], &px[j], &py[j]);
// }
// if (move > 0)
// {
// compute_relative_positions(particle, hashgrid);
// update_hashgrid(particle, hashgrid, 0); /* REDUNDANT ? */
// }
}
// sleep(1);
*ncoupled = ncoup;
return(totalenergy);
}
void evolve_lid(double fboundary)
{
@@ -1394,16 +1542,18 @@ 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;
angle, theta, sum, alpha;
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,
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;
group, gshift, n_total_active = 0, ncollisions = 0, ncoupled = 1, np, belt;
int *particle_numbers;
static int imin, imax;
static short int first = 1;
t_particle *particle;
t_cluster *cluster;
t_obstacle *obstacle;
t_segment *segment;
t_group_segments *segment_group;
@@ -1413,6 +1563,7 @@ void animation()
t_hashgrid *hashgrid;
t_molecule *molecule;
t_lj_parameters params;
t_belt *conveyor_belt;
char message[100];
ratioc = 1.0 - ratio;
@@ -1426,14 +1577,19 @@ void animation()
params.gravity = GRAVITY;
params.radius = MU;
particle = (t_particle *)malloc(NMAXCIRCLES*sizeof(t_particle)); /* particles */
particle = (t_particle *)malloc(NMAXCIRCLES*sizeof(t_particle)); /* particles */
if (CLUSTER_PARTICLES)
cluster = (t_cluster *)malloc(NMAXCIRCLES*sizeof(t_cluster)); /* particle clusters */
if (ADD_FIXED_OBSTACLES) obstacle = (t_obstacle *)malloc(NMAXOBSTACLES*sizeof(t_obstacle)); /* circular obstacles */
if (ADD_FIXED_SEGMENTS)
{
segment = (t_segment *)malloc(NMAXSEGMENTS*sizeof(t_segment)); /* linear obstacles */
segment_group = (t_group_segments *)malloc(NMAXGROUPS*sizeof(t_group_segments));
conveyor_belt = (t_belt *)malloc(NMAXBELTS*sizeof(t_belt));
}
if (TRACER_PARTICLE)
trajectory = (t_tracer *)malloc(TRAJECTORY_LENGTH*N_TRACER_PARTICLES*sizeof(t_tracer));
@@ -1450,6 +1606,16 @@ void animation()
pangle = (double *)malloc(NMAXCIRCLES*sizeof(double));
pressure = (double *)malloc(N_PRESSURES*sizeof(double));
if (CLUSTER_PARTICLES)
{
cqx = (double *)malloc(NMAXCIRCLES*sizeof(double));
cqy = (double *)malloc(NMAXCIRCLES*sizeof(double));
cpx = (double *)malloc(NMAXCIRCLES*sizeof(double));
cpy = (double *)malloc(NMAXCIRCLES*sizeof(double));
cqangle = (double *)malloc(NMAXCIRCLES*sizeof(double));
cpangle = (double *)malloc(NMAXCIRCLES*sizeof(double));
}
if (REACTION_DIFFUSION)
{
collisions = (t_collision *)malloc(2*NMAXCOLLISIONS*sizeof(t_collision));
@@ -1465,7 +1631,7 @@ void animation()
lj_log = fopen("lj_logfile.txt", "w");
if (ADD_FIXED_OBSTACLES) init_obstacle_config(obstacle);
if (ADD_FIXED_SEGMENTS) init_segment_config(segment);
if (ADD_FIXED_SEGMENTS) init_segment_config(segment, conveyor_belt);
if ((MOVE_SEGMENT_GROUPS)&&(ADD_FIXED_SEGMENTS))
{
@@ -1503,6 +1669,8 @@ void animation()
params.nactive = initialize_configuration(particle, hashgrid, obstacle, px, py, pangle, tracer_n, segment, molecule);
printf("%i active particles\n", params.nactive);
if (CLUSTER_PARTICLES) init_cluster_config(particle, cluster);
// xi = 0.0;
@@ -1510,7 +1678,7 @@ void animation()
// {
// printf("Particle %i at (%.3f, %.3f) of energy %.3f\n", i, particle[i].xc, particle[i].yc, particle[i].energy);
// }
sleep(1);
// sleep(1);
update_hashgrid(particle, hashgrid, 1);
printf("Updated hashgrid\n");
@@ -1695,6 +1863,29 @@ void animation()
}
}
}
/* TEST: average angles for clustered polygons */
// if ((REACTION_DIFFUSION)&&(RD_REACTION == CHEM_POLYGON_AGGREGATION))
// {
// np = particle[j].npartners;
// alpha = DPI/(double)NPOLY;
// if (np >= 2)
// {
// angle = particle[j].angle;
// while (angle > alpha) angle -= alpha;
// sum = angle;
// for (p=0; p<np; p++)
// {
// angle = particle[particle[j].partner[p]].angle;
// while (angle > alpha) angle -= alpha;
// sum += angle;
// }
// sum *= 1.0/(double)(np+1);
// particle[j].angle = sum;
// for (p=0; p<np; p++)
// particle[particle[j].partner[p]].angle = sum;
// }
//
// }
/* add gravity */
if (INCREASE_GRAVITY)
@@ -1742,10 +1933,29 @@ void animation()
}
}
/* timestep of thermostat algorithm */
totalenergy = evolve_particles(particle, hashgrid, qx, qy, qangle, px, py, pangle, params.beta, &params.nactive, &nsuccess, &nmove, &ncoupled, i < INITIAL_TIME);
/* compute force and torque on clusters */
if (CLUSTER_PARTICLES) compute_cluster_force(cluster, particle);
/* timestep of thermostat algorithm */
if (CLUSTER_PARTICLES)
{
totalenergy = evolve_clusters(particle, cluster, hashgrid, cqx, cqy, cqangle, cpx, cpy, cpangle, params.beta, &params.nactive, &nsuccess, &nmove, &ncoupled, i < INITIAL_TIME, n == 0);
/* FIXME: update particle data */
for (j=0; j<ncircles; j++)
particle[j].emean = cluster[particle[j].cluster].emean;
}
else
totalenergy = evolve_particles(particle, hashgrid, qx, qy, qangle, px, py, pangle, params.beta, &params.nactive, &nsuccess, &nmove, &ncoupled, i < INITIAL_TIME);
/* TEST */
/* repair clusters */
if ((CLUSTER_PARTICLES)&&(REPAIR_CLUSTERS)) for (cl=0; cl<ncircles; cl++)
if ((cluster[cl].active)&&(cluster[cl].nparticles >= 2))
repair_cluster(cl, particle, cluster, 1000/NVID, 1);
/* evolution of lid coordinate */
if (BOUNDARY_COND == BC_RECTANGLE_LID) evolve_lid(params.fboundary);
if (BOUNDARY_COND == BC_RECTANGLE_WALL)
@@ -1755,11 +1965,24 @@ void animation()
}
if ((MOVE_BOUNDARY)&&(i > OBSTACLE_INITIAL_TIME)) evolve_segments(segment, i);
if (ADD_CONVEYOR_FORCE) for (belt = 0; belt < nbelts; belt++)
conveyor_belt[belt].position += conveyor_belt[belt].speed*DT_PARTICLE;
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);
} /* end of for (n=0; n<NVID; n++) */
/* TEST */
// for (j=0; j<ncircles; j++)
// {
// if (particle[j].active)
// printf("Particle %i: (x,y) = (%.3lg, %.3lg), F = (%.3lg, %.3lg)\n", j, particle[j].xc, particle[j].yc, particle[j].fx, particle[j].fy);
// if (cluster[j].active)
// printf("Cluster %i: (x,y) = (%.3lg, %.3lg), F = (%.3lg, %.3lg)\n", j, cluster[j].xg, cluster[j].yg, cluster[j].fx, cluster[j].fy);
// }
// sleep(1);
if ((i>INITIAL_TIME)&&(SAVE_TIME_SERIES))
{
n_total_active = 0;
@@ -1881,7 +2104,7 @@ void animation()
/* case of reaction-diffusion equation */
if ((i > INITIAL_TIME)&&(REACTION_DIFFUSION))
{
ncollisions = update_types(particle, molecule, collisions, ncollisions, particle_numbers, i - INITIAL_TIME - 1, &delta_energy);
ncollisions = update_types(particle, molecule, cluster, 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)
@@ -1904,8 +2127,8 @@ void animation()
}
if (TRACER_PARTICLE) draw_trajectory(trajectory, traj_position, traj_length);
draw_particles(particle, PLOT, params.beta, collisions, ncollisions, BG_COLOR, hashgrid, params);
draw_container(params.xmincontainer, params.xmaxcontainer, obstacle, segment, wall);
draw_particles(particle, cluster, PLOT, params.beta, collisions, ncollisions, BG_COLOR, hashgrid, params);
draw_container(params.xmincontainer, params.xmaxcontainer, obstacle, segment, conveyor_belt, wall);
/* add a particle */
if ((ADD_PARTICLES)&&(i > ADD_TIME)&&((i - INITIAL_TIME - ADD_TIME)%ADD_PERIOD == 1)&&(i < NSTEPS - FINAL_NOADD_PERIOD))
@@ -1956,8 +2179,8 @@ void animation()
count_particle_number(particle, particle_numbers, i - INITIAL_TIME);
draw_frame(i, PLOT, BG_COLOR, ncollisions, traj_position, traj_length,
wall, pressure, pleft, pright, particle_numbers, 1, params, particle,
collisions, hashgrid, trajectory, obstacle, segment, group_speeds, segment_group);
wall, pressure, pleft, pright, particle_numbers, 1, params, particle, cluster,
collisions, hashgrid, trajectory, obstacle, segment, group_speeds, segment_group, conveyor_belt);
if (!((NO_EXTRA_BUFFER_SWAP)&&(MOVIE))) glutSwapBuffers();
@@ -1988,8 +2211,8 @@ void animation()
if ((i >= INITIAL_TIME)&&(DOUBLE_MOVIE))
{
draw_frame(i, PLOT_B, BG_COLOR_B, ncollisions, traj_position, traj_length,
wall, pressure, pleft, pright, particle_numbers, 0, params, particle,
collisions, hashgrid, trajectory, obstacle, segment, group_speeds, segment_group);
wall, pressure, pleft, pright, particle_numbers, 0, params, particle, cluster,
collisions, hashgrid, trajectory, obstacle, segment, group_speeds, segment_group, conveyor_belt);
glutSwapBuffers();
save_frame_lj_counter(NSTEPS + MID_FRAMES + 1 + counter);
counter++;
@@ -2029,8 +2252,8 @@ void animation()
{
blank();
draw_frame(NSTEPS, PLOT, BG_COLOR, ncollisions, traj_position, traj_length,
wall, pressure, pleft, pright, particle_numbers, 0, params, particle,
collisions, hashgrid, trajectory, obstacle, segment, group_speeds, segment_group);
wall, pressure, pleft, pright, particle_numbers, 0, params, particle, cluster,
collisions, hashgrid, trajectory, obstacle, segment, group_speeds, segment_group, conveyor_belt);
}
if (DOUBLE_MOVIE) for (i=0; i<MID_FRAMES; i++)
{
@@ -2041,8 +2264,8 @@ void animation()
if (DOUBLE_MOVIE)
{
draw_frame(NSTEPS, PLOT_B, BG_COLOR_B, ncollisions, traj_position, traj_length,
wall, pressure, pleft, pright, particle_numbers, 0, params, particle,
collisions, hashgrid, trajectory, obstacle, segment, group_speeds, segment_group);
wall, pressure, pleft, pright, particle_numbers, 0, params, particle, cluster,
collisions, hashgrid, trajectory, obstacle, segment, group_speeds, segment_group, conveyor_belt);
if (!((NO_EXTRA_BUFFER_SWAP)&&(MOVIE))) glutSwapBuffers();
}
if ((TIME_LAPSE)&&(!DOUBLE_MOVIE))
@@ -2064,6 +2287,8 @@ void animation()
// printf("1\n");
free(particle);
if (CLUSTER_PARTICLES) free(cluster);
// printf("2\n");
if (ADD_FIXED_OBSTACLES) free(obstacle);
// printf("3\n");
@@ -2071,6 +2296,7 @@ void animation()
{
free(segment);
free(segment_group);
free(conveyor_belt);
}
// printf("4\n");
if (MOVE_SEGMENT_GROUPS) free(group_speeds);
@@ -2095,6 +2321,17 @@ void animation()
// printf("14\n");
free(pangle);
// printf("15\n");
if (CLUSTER_PARTICLES)
{
free(cqx);
free(cqy);
free(cpx);
free(cpy);
free(cqangle);
free(cpangle);
}
free(pressure);
// printf("16\n");
if (REACTION_DIFFUSION) free(collisions);