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This commit is contained in:
Nils Berglund
2023-04-30 17:01:39 +02:00
committed by GitHub
parent b2d7f56e1c
commit b809ce9e55
14 changed files with 23373 additions and 5093 deletions
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148
lennardjones.c
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@@ -37,14 +37,14 @@
#include <time.h>
#define MOVIE 0 /* set to 1 to generate movie */
#define DOUBLE_MOVIE 0 /* set to 1 to produce movies for wave height and energy simultaneously */
#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 0 /* some OS require one less buffer swap when recording images */
#define NO_EXTRA_BUFFER_SWAP 1 /* some OS require one less buffer swap when recording images */
#define TIME_LAPSE 1 /* set to 1 to add a time-lapse movie at the end */
#define TIME_LAPSE 0 /* set to 1 to add a time-lapse movie at the end */
/* so far incompatible with double movie */
#define TIME_LAPSE_FACTOR 3 /* factor of time-lapse movie */
#define TIME_LAPSE_FIRST 1 /* set to 1 to show time-lapse version first */
#define TIME_LAPSE_FIRST 0 /* set to 1 to show time-lapse version first */
#define SAVE_TIME_SERIES 0 /* set to 1 to save time series of particle positions */
@@ -90,22 +90,22 @@
#define CENTER_PY 0 /* set to 1 to center vertical momentum */
#define CENTER_PANGLE 0 /* set to 1 to center angular momentum */
#define INTERACTION 1 /* particle interaction, see list in global_ljones.c */
#define INTERACTION 10 /* 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 5.0 /* angular frequency of spin-spin interaction */
#define SPIN_INTER_FREQUENCY 1.0 /* angular frequency of spin-spin interaction */
#define SPIN_INTER_FREQUENCY_B 2.0 /* angular frequency of spin-spin interaction for second particle type */
#define 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 4.2 /* minimal distance in Poisson disc process, controls density of particles */
#define PDISC_DISTANCE 1.3 /* 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 0.5 /* parameter controlling the dimensions of domain */
#define MU 0.008 /* parameter controlling radius of particles */
#define MU 0.035 /* parameter controlling radius of particles */
#define MU_B 0.012 /* parameter controlling radius of particles of second type */
#define NPOLY 25 /* number of sides of polygon */
#define APOLY 0.666666666 /* angle by which to turn polygon, in units of Pi/2 */
#define APOLY 0.0 /* angle by which to turn polygon, 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 */
@@ -125,11 +125,10 @@
/* Parameters for length and speed of simulation */
#define NSTEPS 5000 /* number of frames of movie */
// #define NSTEPS 3000 /* number of frames of movie */
#define NVID 175 /* number of iterations between images displayed on screen */
#define NSTEPS 3800 /* number of frames of movie */
#define NVID 50 /* number of iterations between images displayed on screen */
#define NSEG 250 /* number of segments of boundary */
#define INITIAL_TIME 20 /* time after which to start saving frames */
#define INITIAL_TIME 10 /* time after which to start saving frames */
#define OBSTACLE_INITIAL_TIME 200 /* time after which to start moving obstacle */
#define BOUNDARY_WIDTH 1 /* width of particle boundary */
#define LINK_WIDTH 2 /* width of links between particles */
@@ -144,22 +143,22 @@
/* Boundary conditions, see list in global_ljones.c */
#define BOUNDARY_COND 0
#define BOUNDARY_COND 3
/* Plot type, see list in global_ljones.c */
#define PLOT 5
#define PLOT_B 0 /* plot type for second movie */
#define PLOT 4
#define PLOT_B 6 /* plot type for second movie */
#define DRAW_BONDS 1 /* set to 1 to draw bonds between neighbours */
#define COLOR_BONDS 1 /* set to 1 to color bonds according to length */
#define FILL_TRIANGLES 1 /* set to 1 to fill triangles between neighbours */
#define FILL_TRIANGLES 0 /* set to 1 to fill triangles between neighbours */
#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 */
/* Color schemes */
#define COLOR_PALETTE 10 /* Color palette, see list in global_ljones.c */
#define COLOR_PALETTE 0 /* Color palette, see list in global_ljones.c */
#define BLACK 1 /* background */
@@ -193,27 +192,30 @@
#define RANDOM_RADIUS 0 /* set to 1 for random circle radius */
#define DT_PARTICLE 3.0e-6 /* time step for particle displacement */
#define KREPEL 12.0 /* constant in repelling force between particles */
#define KREPEL 0.1 /* constant in repelling force between particles */
#define EQUILIBRIUM_DIST 2.0 /* Lennard-Jones equilibrium distance */
#define EQUILIBRIUM_DIST_B 2.0 /* Lennard-Jones equilibrium distance for second type of particle */
#define REPEL_RADIUS 15.0 /* radius in which repelling force acts (in units of particle radius) */
#define DAMPING 200.0 /* damping coefficient of particles */
#define INITIAL_DAMPING 1000.0 /* damping coefficient of particles during initial phase */
#define PARTICLE_MASS 1.0 /* mass of particle of radius MU */
#define DAMPING 0.0 /* damping coefficient of particles */
#define INITIAL_DAMPING 50.0 /* damping coefficient of particles during initial phase */
#define DAMPING_ROT 100.0 /* dampint coefficient for rotation of particles */
#define PARTICLE_MASS 0.25 /* mass of particle of radius MU */
#define PARTICLE_MASS_B 0.5 /* mass of particle of radius MU */
#define PARTICLE_INERTIA_MOMENT 0.02 /* moment of inertia of particle */
#define PARTICLE_INERTIA_MOMENT 0.5 /* moment of inertia of particle */
#define PARTICLE_INERTIA_MOMENT_B 0.02 /* moment of inertia of second type of particle */
#define V_INITIAL 0.0 /* initial velocity range */
#define OMEGA_INITIAL 10.0 /* initial angular velocity range */
#define V_INITIAL 20.0 /* initial velocity range */
#define OMEGA_INITIAL 5.0 /* 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 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 0.002 /* initial inverse temperature */
#define MU_XI 0.01 /* friction constant in thermostat */
#define KSPRING_BOUNDARY 1.0e7 /* confining harmonic potential outside simulation region */
#define KSPRING_OBSTACLE 1.0e11 /* harmonic potential of obstacles */
#define NBH_DIST_FACTOR 10.0 /* radius in which to count neighbours */
#define NBH_DIST_FACTOR 3.0 /* radius in which to count neighbours */
#define GRAVITY 0.0 /* gravity acting on all particles */
#define GRAVITY_X 0.0 /* horizontal gravity acting on all particles */
#define INCREASE_GRAVITY 0 /* set to 1 to increase gravity during the simulation */
@@ -221,17 +223,19 @@
#define GRAVITY_FACTOR 100.0 /* factor by which to increase gravity */
#define GRAVITY_INITIAL_TIME 200 /* time at start of simulation with constant gravity */
#define GRAVITY_RESTORE_TIME 700 /* time at end of simulation with gravity restored to initial value */
#define KSPRING_VICSEK 0.2 /* spring constant for I_VICSEK_SPEED interaction */
#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 2.0e3 /* force constant in angular dynamics */
#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_BOUNDARY 1.0e6 /* constant in torque from the boundary */
#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 SPIN_RANGE 7.0 /* range of spin-spin interaction */
#define SPIN_RANGE 10.0 /* 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 */
@@ -326,7 +330,7 @@
#define POSITION_Y_DEPENDENCE 0 /* set to 1 for the separation between particles to be horizontal */
#define PRINT_ENTROPY 0 /* set to 1 to compute entropy */
#define REACTION_DIFFUSION 1 /* set to 1 to simulate a chemical reaction (particles may change type) */
#define REACTION_DIFFUSION 0 /* set to 1 to simulate a chemical reaction (particles may change type) */
#define RD_REACTION 15 /* type of reaction, see list in global_ljones.c */
#define RD_TYPES 5 /* number of types in reaction-diffusion equation */
#define RD_INITIAL_COND 2 /* initial condition of particles */
@@ -339,7 +343,7 @@
#define COLLISION_TIME 15 /* time during which collisions are shown */
#define PRINT_PARTICLE_NUMBER 0 /* set to 1 to print total number of particles */
#define PLOT_PARTICLE_NUMBER 1 /* set to 1 to make of plot of particle number over time */
#define PLOT_PARTICLE_NUMBER 0 /* set to 1 to make of plot of particle number over time */
#define PARTICLE_NB_PLOT_FACTOR 0.5 /* expected final number of particles over initial number */
#define PRINT_LEFT 1 /* 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) */
@@ -361,14 +365,15 @@
#define MAZE_MAX_NGBH 4 /* max number of neighbours of maze cell */
#define RAND_SHIFT 200 /* seed of random number generator */
#define MAZE_XSHIFT 0.0 /* horizontal shift of maze */
#define MAZE_WIDTH 0.01 /* width of maze walls */
#define FLOOR_FORCE 1 /* set to 1 to limit force on particle to FMAX */
#define FMAX 1.0e10 /* maximal force */
#define FLOOR_OMEGA 0 /* set to 1 to limit particle momentum to PMAX */
#define PMAX 1000.0 /* maximal force */
#define HASHX 100 /* size of hashgrid in x direction */
#define HASHY 50 /* 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 */
@@ -703,12 +708,13 @@ double evolve_particles(t_particle particle[NMAXCIRCLES], t_hashgrid hashgrid[HA
{
px[j] *= exp(- 0.5*DT_PARTICLE*xi);
py[j] *= exp(- 0.5*DT_PARTICLE*xi);
if (!COUPLE_ANGLE_TO_THERMOSTAT) pangle[j] *= exp(- DT_PARTICLE*DAMPING_ROT);
}
else
{
px[j] *= exp(- DT_PARTICLE*damping);
py[j] *= exp(- DT_PARTICLE*damping);
pangle[j] *= exp(- DT_PARTICLE*damping);
pangle[j] *= exp(- DT_PARTICLE*DAMPING_ROT);
}
if ((THERMOSTAT_ON)&&(COUPLE_ANGLE_TO_THERMOSTAT)&&(particle[j].thermostat))
pangle[j] *= exp(- 0.5*DT_PARTICLE*xi);
@@ -895,7 +901,15 @@ void evolve_segment_groups(t_segment segment[NMAXSEGMENTS], int time, t_group_se
double fx[NMAXGROUPS], fy[NMAXGROUPS], torque[NMAXGROUPS], dx[NMAXGROUPS], dy[NMAXGROUPS], dalpha[NMAXGROUPS];
double x, y, dx0, dy0, padding, proj, distance, f, xx[2], yy[2], xmean = 0.0, ymean = 0.0;
int i, j, k, group = 0;
static double maxdepth, saturation_depth;
static double maxdepth, saturation_depth, xmax;
static int first = 1;
if (first)
{
xmax = XMAX - TRACK_X_PADDING;
if ((PLOT_SPEEDS)||(PLOT_TRAJECTORIES)) xmax -= 1.8;
first = 0;
}
maxdepth = 0.5*GROUP_WIDTH;
saturation_depth = 0.1*GROUP_WIDTH;
@@ -1038,8 +1052,8 @@ void evolve_segment_groups(t_segment segment[NMAXSEGMENTS], int time, t_group_se
ymean = ymean/((double)(ngroups-1));
if (ymean > ytrack) ytrack = ymean;
if (xmean > XMAX - TRACK_X_PADDING)
xtrack = xmean - XMAX + TRACK_X_PADDING;
if (xmean > xmax)
xtrack = xmean - xmax;
else if (xmean < XMIN + TRACK_X_PADDING)
xtrack = xmean - XMIN - TRACK_X_PADDING;
}
@@ -1048,10 +1062,8 @@ 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, krepel = KREPEL, pos[2], prop, vx,
beta = BETA, xi = 0.0, xmincontainer = BCXMIN, xmaxcontainer = BCXMAX, torque, torque_ij,
fboundary = 0.0, pleft = 0.0, pright = 0.0, entropy[2], mean_energy, gravity = GRAVITY, speed_ratio, ymin, ymax, delta_energy;
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, krepel = KREPEL, pos[2], prop, vx, beta = BETA, xi = 0.0, xmincontainer = BCXMIN, xmaxcontainer = BCXMAX, torque, torque_ij, fboundary = 0.0, pleft = 0.0, pright = 0.0, entropy[2], mean_energy, gravity = GRAVITY, speed_ratio, ymin, ymax, delta_energy, speed, ratio = 1.0, ratioc;
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, nactive = 0, nadd_particle = 0, nmove = 0, nsuccess = 0,
@@ -1070,7 +1082,8 @@ void animation()
t_hashgrid *hashgrid;
char message[100];
ratioc = 1.0 - ratio;
particle = (t_particle *)malloc(NMAXCIRCLES*sizeof(t_particle)); /* particles */
if (ADD_FIXED_OBSTACLES) obstacle = (t_obstacle *)malloc(NMAXOBSTACLES*sizeof(t_obstacle)); /* circular obstacles */
if (ADD_FIXED_SEGMENTS)
@@ -1127,9 +1140,9 @@ void animation()
// printf("1\n");
printf("Initializing configuration\n");
nactive = initialize_configuration(particle, hashgrid, obstacle, px, py, pangle, tracer_n);
nactive = initialize_configuration(particle, hashgrid, obstacle, px, py, pangle, tracer_n, segment);
// xi = 0.0;
@@ -1140,8 +1153,9 @@ void animation()
sleep(1);
update_hashgrid(particle, hashgrid, 1);
printf("Updated hashgrid\n");
compute_relative_positions(particle, hashgrid);
printf("Computed relative positions\n");
blank();
// glColor3f(0.0, 0.0, 0.0);
@@ -1166,9 +1180,12 @@ void animation()
thermostat_on = thermostat_schedule(i);
printf("Termostat: %i\n", thermostat_on);
}
/* deactivate some segments */
if ((ADD_FIXED_SEGMENTS)&&(DEACTIVATE_SEGMENT)&&(i == INITIAL_TIME + SEGMENT_DEACTIVATION_TIME + 1))
for (j=0; j<nsegments; j++) if (segment[j].inactivate) segment[j].active = 0;
/* recolor particles in case if P_INITIAL_POS color code */
if ((i <= INITIAL_TIME-1)&&(i%10 == 0)&&((PLOT == P_INITIAL_POS)||(PLOT_B == P_INITIAL_POS)))
{
@@ -1184,7 +1201,7 @@ void animation()
particle[j].color_hue = 360.0*(particle[j].yc - ymin)/(ymax - ymin);
}
blank();
blank();
fboundary = 0.0;
pleft = 0.0;
@@ -1212,7 +1229,6 @@ void animation()
segment[j].torque = 0.0;
}
compute_relative_positions(particle, hashgrid);
update_hashgrid(particle, hashgrid, 0);
@@ -1225,10 +1241,27 @@ void animation()
/* compute force from other particles */
compute_particle_force(j, krepel, particle, hashgrid);
/* take care of boundary conditions */
fboundary += compute_boundary_force(j, particle, obstacle, segment, xmincontainer, xmaxcontainer, &pleft, &pright, pressure, wall);
/* align velocities in case of Vicsek models */
// if (VICSEK_INT)
if ((VICSEK_INT)&&(!particle[j].close_to_boundary))
{
speed = module2(particle[j].vx,particle[j].vy);
if ((VICSEK_VMIN > 0.0)&&(speed < VICSEK_VMIN)) speed = VICSEK_VMIN;
if (speed > VICSEK_VMAX) speed = 0.5*(speed + VICSEK_VMAX);
particle[j].vx = speed*cos(particle[j].angle);
particle[j].vy = speed*sin(particle[j].angle);
speed = module2(px[j],py[j]);
if ((VICSEK_VMIN > 0.0)&&(speed < VICSEK_VMIN)) speed = VICSEK_VMIN;
if (speed > VICSEK_VMAX) speed = 0.5*(speed + VICSEK_VMAX);
px[j] = speed*cos(particle[j].angle);
py[j] = speed*sin(particle[j].angle);
}
/* add gravity */
if (INCREASE_GRAVITY) particle[j].fy -= gravity/particle[j].mass_inv;
else
@@ -1260,7 +1293,9 @@ void animation()
}
if ((MOVE_BOUNDARY)&&(i > OBSTACLE_INITIAL_TIME)) evolve_segments(segment, i);
if ((MOVE_SEGMENT_GROUPS)&&(i > OBSTACLE_INITIAL_TIME)) evolve_segment_groups(segment, i, segment_group);
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++) */
if ((i>INITIAL_TIME)&&(SAVE_TIME_SERIES))
@@ -1305,7 +1340,7 @@ void animation()
// if ((PARTIAL_THERMO_COUPLING))
if ((PARTIAL_THERMO_COUPLING)&&(i>N_T_AVERAGE))
{
nthermo = partial_thermostat_coupling(particle, xshift + PARTIAL_THERMO_SHIFT);
nthermo = partial_thermostat_coupling(particle, xshift + PARTIAL_THERMO_SHIFT, segment);
printf("%i particles coupled to thermostat out of %i active\n", nthermo, nactive);
mean_energy = compute_mean_energy(particle);
}
@@ -1326,7 +1361,6 @@ void animation()
while (particle[j].angle < 0.0) particle[j].angle += DPI;
}
/* update tracer particle trajectory */
if ((TRACER_PARTICLE)&&(i > INITIAL_TIME))
{
@@ -1347,7 +1381,7 @@ void animation()
printf("Boundary force: %.3f\n", fboundary/(double)(ncircles*NVID));
if (RESAMPLE_Y) printf("%i succesful moves out of %i trials\n", nsuccess, nmove);
if (INCREASE_GRAVITY) printf("Gravity: %.3f\n", gravity);
total_neighbours = 0;
min_nb = 100;
max_nb = 0;
@@ -1509,6 +1543,7 @@ void animation()
{
if (DOUBLE_MOVIE)
{
blank();
if (TRACER_PARTICLE) draw_trajectory(trajectory, traj_position, traj_length);
draw_particles(particle, PLOT, beta, collisions, ncollisions);
draw_container(xmincontainer, xmaxcontainer, obstacle, segment, wall);
@@ -1528,9 +1563,14 @@ void animation()
else if (PRINT_PARTICLE_SPEEDS) print_particles_speeds(particle);
else if (PRINT_SEGMENTS_SPEEDS) print_segment_group_speeds(segment_group);
// print_segments_speeds(vxsegments, vysegments);
glutSwapBuffers();
// glutSwapBuffers();
}
for (i=0; i<MID_FRAMES; i++) save_frame_lj();
for (i=0; i<MID_FRAMES; i++)
{
save_frame_lj();
if (!NO_EXTRA_BUFFER_SWAP) glutSwapBuffers();
}
glutSwapBuffers();
if (DOUBLE_MOVIE)
{
if (TRACER_PARTICLE) draw_trajectory(trajectory, traj_position, traj_length);