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Main changes: lennardjones, wave_billiard, rde
This commit is contained in:
Nils Berglund
GitHub
149
rde.c
149
rde.c
@@ -46,31 +46,27 @@
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/* General geometrical parameters */
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// #define WINWIDTH 1920 /* window width */
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#define WINWIDTH 1150 /* window width */
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#define WINWIDTH 1920 /* window width */
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#define WINHEIGHT 1150 /* window height */
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// #define NX 720 /* number of grid points on x axis */
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#define NX 432 /* number of grid points on x axis */
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#define NY 432 /* number of grid points on y axis */
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#define NX 870 /* number of grid points on x axis */
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#define NY 520 /* number of grid points on y axis */
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#define HRES 1 /* factor for high resolution plots */
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// #define XMIN -2.0
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// #define XMAX 2.0 /* x interval */
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#define XMIN -1.041666667
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#define XMAX 1.041666667 /* x interval */
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#define XMIN -2.0
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#define XMAX 2.0 /* x interval */
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#define YMIN -1.041666667
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#define YMAX 1.041666667 /* y interval for 9/16 aspect ratio */
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/* Choice of simulated equation */
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#define RDE_EQUATION 10 /* choice of reaction term, see list in global_3d.c */
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#define NFIELDS 2 /* number of fields in reaction-diffusion equation */
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#define NLAPLACIANS 2 /* number of fields for which to compute Laplacian */
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#define RDE_EQUATION 11 /* choice of reaction term, see list in global_3d.c */
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#define NFIELDS 3 /* number of fields in reaction-diffusion equation */
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#define NLAPLACIANS 0 /* number of fields for which to compute Laplacian */
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#define SPHERE 0 /* set to 1 to simulate equation on sphere */
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#define SPHERE 1 /* set to 1 to simulate equation on sphere */
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#define DPOLE 1 /* safety distance to poles */
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#define DSMOOTH 1 /* size of neighbourhood of poles that are smoothed */
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#define SMOOTHPOLE 0.00 /* smoothing coefficient at poles */
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#define SMOOTHPOLE 0.01 /* smoothing coefficient at poles */
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#define SMOOTHCOTPOLE 0.05 /* smoothing coefficient of cotangent at poles */
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#define PHISHIFT 0.0 /* shift of phi in 2D plot (in degrees) */
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#define SMOOTHBLOCKS 0 /* set to 1 to use blocks of points near the poles */
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@@ -145,8 +141,7 @@
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/* Physical parameters of wave equation */
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#define DT 0.000003
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// #define DT 0.00000025
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#define DT 0.000002
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#define VISCOSITY 0.02
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#define POISSON_STIFFNESS 1.0 /* stiffness of Poisson equation solver for incompressible Euler */
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@@ -167,11 +162,12 @@
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#define NU_KURAMOTO 0.0 /* viscosity in Kuramoto model */
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#define OMEGA_KURAMOTO 0.02 /* frequency in Kuramoto model */
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#define A_KS 0.15 /* coupling constant in Keller-Segel model */
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#define C_KS 3.0 /* coupling constant in Keller-Segel model */
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#define D_KSU 1.2 /* diffusion in Keller-Segel model */
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#define D_KSV 0.75 /* diffusion in Keller-Segel model */
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#define KS_RSCALE 0.001 /* scaling factor for reaction term of Keller-Segel model */
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#define KS_UMAX 10.0 /* max value for u component of Keller-Segel model */
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#define C_KS 3.5 /* coupling constant in Keller-Segel model */
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#define D_KSU 1.0 /* organism diffusion in Keller-Segel model */
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#define D_KSV 1.2 /* nutrient diffusion in Keller-Segel model */
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#define KS_RSCALE 0.07 /* scaling factor for reaction term of Keller-Segel model */
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#define KS_UMAX 100.0 /* max value for u component of Keller-Segel model */
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#define KS_CHIMAX_FACTOR 30.0 /* limiter on the value of chi/D_KSU */
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#define V_MAZE 0.4 /* potential in walls of maze */
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#define BZQ 0.0008 /* parameter in BZ equation */
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#define BZF 1.2 /* parameter in BZ equation */
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@@ -254,8 +250,8 @@
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/* Parameters for length and speed of simulation */
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#define NSTEPS 1800 /* number of frames of movie */
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#define NVID 100 /* number of iterations between images displayed on screen */
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#define NSTEPS 1400 /* number of frames of movie */
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#define NVID 12 /* number of iterations between images displayed on screen */
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#define ACCELERATION_FACTOR 1.0 /* factor by which to increase NVID in course of simulation */
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#define DT_ACCELERATION_FACTOR 1.0 /* factor by which to increase time step in course of simulation */
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#define MAX_DT 0.024 /* maximal value of integration step */
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@@ -274,14 +270,15 @@
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/* Visualisation */
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#define PLOT_3D 1 /* controls whether plot is 2D or 3D */
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#define PLOT_SPHERE 0 /* draws fields on a sphere */
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#define PLOT_SPHERE 1 /* draws fields on a sphere */
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#define SIMULATION_GRID 1 /* type of simulation grid, for certain equations */
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#define OPTIMIZE_GRID 1 /* set to 1 to optimize grid by evolving grid points */
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#define ROTATE_VIEW 1 /* set to 1 to rotate position of observer */
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#define ROTATE_ANGLE 360.0 /* total angle of rotation during simulation */
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#define SHADE_3D 1 /* set to 1 to change luminosity according to normal vector */
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#define SHADE_2D 0 /* set to 1 to change luminosity according to normal vector */
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#define VIEWPOINT_TRAJ 0 /* type of viewpoint trajectory */
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#define SHADE_2D 0 /* set to 1 to change luminosity according to normal vector */
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#define VIEWPOINT_TRAJ 1 /* type of viewpoint trajectory */
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#define MAX_LATITUDE 45.0 /* maximal latitude for viewpoint trajectory VP_ORBIT2 */
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#define DRAW_PERIODICISED 0 /* set to 1 to repeat wave periodically in x and y directions */
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@@ -340,7 +337,7 @@
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/* Color schemes, see list in global_pdes.c */
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#define COLOR_PALETTE 11 /* Color palette, see list in global_pdes.c */
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#define COLOR_PALETTE 15 /* Color palette, see list in global_pdes.c */
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#define COLOR_PALETTE_B 11 /* Color palette, see list in global_pdes.c */
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#define BLACK 1 /* black background */
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@@ -355,8 +352,8 @@
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#define SCALE 0 /* set to 1 to adjust color scheme to variance of field */
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#define SLOPE 1.0 /* sensitivity of color on wave amplitude */
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#define COLOR_RANGE 1.0 /* max range of color (default: 1.0) */
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#define VSHIFT_AMPLITUDE -2.7 /* additional shift for wave amplitude */
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#define VSCALE_AMPLITUDE 3.0 /* additional scaling factor for color scheme P_3D_AMPLITUDE */
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#define VSHIFT_AMPLITUDE -0.75 /* additional shift for wave amplitude */
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#define VSCALE_AMPLITUDE 1.5 /* additional scaling factor for color scheme P_3D_AMPLITUDE */
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#define ATTENUATION 0.0 /* exponential attenuation coefficient of contrast with time */
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#define CURL_SCALE 1.25 /* scaling factor for curl representation */
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#define RESCALE_COLOR_IN_CENTER 0 /* set to 1 to decrease color intentiy in the center (for wave escaping ring) */
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@@ -398,7 +395,7 @@
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#define MAZE_XSHIFT 0.0 /* horizontal shift of maze */
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#define MAZE_WIDTH 0.04 /* half width of maze walls */
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#define DRAW_COLOR_SCHEME 0 /* set to 1 to plot the color scheme */
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#define DRAW_COLOR_SCHEME 1 /* set to 1 to plot the color scheme */
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#define COLORBAR_RANGE 2.5 /* scale of color scheme bar */
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#define COLORBAR_RANGE_B 2.5 /* scale of color scheme bar for 2nd part */
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#define ROTATE_COLOR_SCHEME 0 /* set to 1 to draw color scheme horizontally */
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@@ -413,6 +410,7 @@
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#define MANDEL_IOR_SCALE -0.05 /* parameter controlling dependence of IoR on Mandelbrot escape speed */
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#define OMEGA 0.005 /* frequency of periodic excitation */
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#define OSCIL_YMAX 0.2 /* defines oscillation range */
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#define OSCIL_YMID -0.75 /* defines oscilling beam midpoint */
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#define COURANT 0.08 /* Courant number */
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#define COURANTB 0.03 /* Courant number in medium B */
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#define INITIAL_AMP 0.5 /* amplitude of initial condition */
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@@ -480,12 +478,12 @@ int reset_view = 0; /* switch to reset 3D view parameters (for option RO
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#define VENUS_NODATA_FACTOR 0.5 /* altitude to assign to DEM points without data (fraction of mean altitude) */
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#define Z_SCALING_FACTOR 0.75 /* overall scaling factor of z axis for REP_PROJ_3D representation */
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#define XY_SCALING_FACTOR 1.5 /* overall scaling factor for on-screen (x,y) coordinates after projection */
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#define XY_SCALING_FACTOR 1.9 /* overall scaling factor for on-screen (x,y) coordinates after projection */
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#define ZMAX_FACTOR 1.0 /* max value of z coordinate for REP_PROJ_3D representation */
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#define XSHIFT_3D -0.0 /* overall x shift for REP_PROJ_3D representation */
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#define YSHIFT_3D -0.5 /* overall y shift for REP_PROJ_3D representation */
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#define YSHIFT_3D -0.0 /* overall y shift for REP_PROJ_3D representation */
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#define BORDER_PADDING 0 /* distance from boundary at which to plot points, to avoid boundary effects due to gradient */
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#define DRAW_ARROW 0 /* set to 1 to draw arrow above sphere */
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#define DRAW_ARROW 1 /* set to 1 to draw arrow above sphere */
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#define ZMAX 3.0 /* maximal value of z coordinate */
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#define ZMIN -3.0 /* maximal value of z coordinate */
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@@ -493,7 +491,7 @@ int reset_view = 0; /* switch to reset 3D view parameters (for option RO
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#define RSCALE_B 1.00 /* experimental, additional radial scaling factor in ij_to_sphere */
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#define RSHIFT 0.0 /* shift in radial component */
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#define RMAX 4.0 /* max value of radial component */
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#define RMIN 0.5 /* min value of radial component */
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#define RMIN 0.0 /* min value of radial component */
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#define COS_VISIBLE -0.35 /* limit on cosine of normal to shown facets */
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/* For debugging purposes only */
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@@ -1251,10 +1249,11 @@ double gfield[2*NX*NY], t_rde rde[NX*NY], t_wave_sphere wsphere[NX*NY])
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{
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int i, j, k, iplus, iminus, jplus, jminus, ropening, w, n;
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double x, y, z, deltax, deltay, deltaz, rho, rhox, rhoy, pot, u, v, ux, uy, vx, vy, test = 0.0, dx, dy, xy[2], padding, a, eta, etax, etay, sum, phi0, chi;
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double *delta_phi[NLAPLACIANS], *nabla_phi, *nabla_psi, *nabla_omega, *delta_vorticity, *delta_pressure, *delta_p, *delta_u, *delta_v, *nabla_rho, *nabla_u, *nabla_v, *nabla_eta, *kuramoto_int, *keller_segel_drift, *keller_segel_div;
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double *delta_phi[NLAPLACIANS], *nabla_phi, *nabla_psi, *nabla_omega, *delta_vorticity, *delta_pressure, *delta_p, *delta_u, *delta_v, *nabla_rho, *nabla_u, *nabla_v, *nabla_eta, *kuramoto_int, *chi_u, *prod_gradients;
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// double u_bc[NY], v_bc[NY];
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static double invsqr3 = 0.577350269; /* 1/sqrt(3) */
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static int smooth = 0, y_channels, y_channels1, imin, imax, first = 1;
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int floor_chi, floor_u;
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if (first) /* for D_MAZE_CHANNELS boundary conditions in Euler equation */
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{
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@@ -1424,10 +1423,7 @@ double gfield[2*NX*NY], t_rde rde[NX*NY], t_wave_sphere wsphere[NX*NY])
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case (E_KELLER_SEGEL):
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{
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// keller_segel_drift = (double *)malloc(NX*NY*sizeof(double));
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// keller_segel_div = (double *)malloc(NX*NY*sizeof(double));
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nabla_psi = (double *)malloc(2*NX*NY*sizeof(double));
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// compute_gradient_euler_test(phi_in[1], nabla_psi, xy_in, wsphere);
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compute_gradient_euler_plane(phi_in[1], nabla_psi, rde, 0.0);
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/* multiply gradient by chi */
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#pragma omp parallel for private(i)
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@@ -1435,15 +1431,51 @@ double gfield[2*NX*NY], t_rde rde[NX*NY], t_wave_sphere wsphere[NX*NY])
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{
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x = phi_in[0][i];
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chi = C_KS*x*(1.0+x*x);
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// chi = C_KS*x/(1.0+x*x);
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nabla_psi[i] *= chi;
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nabla_psi[NX*NY + i] *= chi;
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}
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/* compute divergence */
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// compute_divergence(nabla_psi, keller_segel_div, xy_in, wsphere);
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compute_divergence_rde(nabla_psi, rde, xy_in, wsphere);
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break;
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}
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case (E_KELLER_SEGEL_SPHERE):
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{
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delta_u = (double *)malloc(NX*NY*sizeof(double));
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delta_v = (double *)malloc(NX*NY*sizeof(double));
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chi_u = (double *)malloc(NX*NY*sizeof(double));
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prod_gradients = (double *)malloc(NX*NY*sizeof(double));
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compute_laplacian_grid(phi_in[1], delta_u, wsphere, ngridpoints);
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compute_laplacian_grid(phi_in[2], delta_v, wsphere, ngridpoints);
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/* multiply gradient by chi */
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floor_chi = 0;
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#pragma omp parallel for private(i)
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for (i=0; i<ngridpoints; i++)
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{
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x = phi_in[1][i];
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chi_u[i] = C_KS*x*(1.0+x*x);
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// chi_u[i] = C_KS*x/(1.0+x*x);
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if (chi_u[i] > KS_CHIMAX_FACTOR*D_KSU)
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{
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// printf("chi_i[%i] = %.5lg\n", i, chi_u[i]);
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chi_u[i] = KS_CHIMAX_FACTOR*D_KSU;
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floor_chi++;
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}
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}
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if (floor_chi > 0)
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{
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nfloorchi++;
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// printf("Floored chi at %i points\n", floor_chi);
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}
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// printf("Floored chi %i times\n", nfloorchi);
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/* compute product of gradients */
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compute_grad_product_grid(phi_in[2], chi_u, prod_gradients, wsphere, ngridpoints);
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break;
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}
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default:
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{
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/* do nothing */
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@@ -1507,10 +1539,8 @@ double gfield[2*NX*NY], t_rde rde[NX*NY], t_wave_sphere wsphere[NX*NY])
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y = phi_in[1][i*NY+j];
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deltax = D_KSU*delta_phi[0][i*NY+j];
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deltay = D_KSV*delta_phi[1][i*NY+j];
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// phi_out[0][i*NY+j] = x + intstep*(deltax - keller_segel_div[i*NY+j] + KS_RSCALE*x*(1.0-x));
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phi_out[0][i*NY+j] = x + intstep*(deltax - rde[i*NY+j].divergence + KS_RSCALE*x*(1.0-x));
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if (phi_out[0][i*NY+j] > KS_UMAX) phi_out[0][i*NY+j] = KS_UMAX;
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// if (phi_out[0][i*NY+j] < -1.0) phi_out[0][i*NY+j] = -1.0;
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phi_out[1][i*NY+j] = y + intstep*(deltay + KS_RSCALE*(x - A_KS*y));
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break;
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@@ -1781,6 +1811,26 @@ double gfield[2*NX*NY], t_rde rde[NX*NY], t_wave_sphere wsphere[NX*NY])
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/* TEST */
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// for (i=0; i<NX*NY; i++) rde[i].theta = phi_out[0][i];
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}
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else if (RDE_EQUATION == E_KELLER_SEGEL_SPHERE)
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{
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floor_u = 0;
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#pragma omp parallel for private(i,x)
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for (i=0; i<ngridpoints; i++)
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{
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x = phi_in[1][i];
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phi_out[1][i] = x + intstep*(D_KSU*delta_u[i] - chi_u[i]*delta_v[i] - prod_gradients[i] + KS_RSCALE*x*(1.0-x));
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if (phi_out[1][i] > KS_UMAX)
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{
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phi_out[1][i] = KS_UMAX;
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floor_u = 1;
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}
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phi_out[2][i] = phi_in[2][i] + intstep*(D_KSV*delta_v[i] + KS_RSCALE*(x - A_KS*y));
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}
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if (floor_u) printf("u floored to KS_UMAX\n");
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/* convert field 1 on simulation grid to field 0 on longitude_latitude grid */
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convert_fields_from_grids(phi_out[1], phi_out[0], wsphere);
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}
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/* in-flow/out-flow b.c. for incompressible Euler equation */
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if (((RDE_EQUATION == E_EULER_INCOMP)||(RDE_EQUATION == E_EULER_COMP))&&(IN_OUT_FLOW_BC > 0))
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@@ -1846,11 +1896,17 @@ double gfield[2*NX*NY], t_rde rde[NX*NY], t_wave_sphere wsphere[NX*NY])
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}
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case (E_KELLER_SEGEL):
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{
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// free(keller_segel_drift);
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// free(keller_segel_div);
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free(nabla_psi);
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break;
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}
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case (E_KELLER_SEGEL_SPHERE):
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{
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free(delta_u);
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free(delta_v);
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free(chi_u);
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free(prod_gradients);
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break;
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}
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}
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if (COMPUTE_PRESSURE)
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@@ -2339,7 +2395,7 @@ void animation()
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// if (ADD_TRACERS) tracers = (double *)malloc(2*NSTEPS*N_TRACERS*sizeof(double));
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if (ADD_TRACERS) tracers = (double *)malloc(4*NSTEPS*N_TRACERS*sizeof(double));
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if (RDE_EQUATION == E_KURAMOTO_SPHERE)
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if ((RDE_EQUATION == E_KURAMOTO_SPHERE)||(RDE_EQUATION == E_KELLER_SEGEL_SPHERE))
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ngridpoints = initialize_simulation_grid_sphere(wsphere);
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dx = (XMAX-XMIN)/((double)NX);
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@@ -2418,7 +2474,7 @@ void animation()
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// init_linear_blob_sphere(0, 1.3*PI, 0.65*PI, 0.0, 0.0, 0.3, 0.1, 0.1, SWATER_MIN_HEIGHT, phi, xy_in, wsphere);
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init_random(0.4, 0.4, phi, xy_in, wsphere);
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init_random(0.5, 0.4, phi, xy_in, wsphere);
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// init_onefield_random(1, 0.2, 0.1, phi, xy_in, wsphere);
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// init_random_smoothed(0.0, 0.4, phi, xy_in, wsphere);
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@@ -2470,6 +2526,7 @@ void animation()
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for (i=0; i<=NSTEPS; i++)
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{
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printf("floored chi %i times\n", nfloorchi);
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nvid = NVID;
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if (CHANGE_VISCOSITY)
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{
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