Tips and tricks

From Gerris

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GfsView can read compressed GFS files directly. GfsView can read compressed GFS files directly.
- 
- 
- 
-== Writing generic or customized gerris output == 
- 
- 
-Since most of visualization package on the market (or as open-source) do not support quadtree/octree data format, to use benefits of third party visualization packages rather than GFSView we should convert Gerris results to a general unstructured data.  
- 
-The function "gfs_write_generic_output" is written for this purpose.  
- 
-This function could write output data in [http://www.tecplot.com/ Tecplot] or [http://www.cacr.caltech.edu/~slombey/asci/vtk/vtk_formats.simple.html VTK format]. We mean generic output because Tecplot format is almost a general unstructured data type and you could easily modify its (code or resulted file) for your own need. Alternatively you could contact me and I could do its for you (just describe your format). All data are written in ASCII format. 
- 
-VTK format could be visualized by powerful free package: [http://www.paraview.org/HTML/Index.html Paraview]. 
- 
-Tecplot format format could be visualized by commersial package 
-[http://www.tecplot.com/ Tecplot] 
- 
-Tecplot format is briefly as follows: 
- 
-1) Header (include list of field variables, number of vertexes, number of elements and elements type) 
- 
-2) Spatial coordinates plus filed variables related to listed variables in header 
- 
-3) Element connectivity 
- 
-[[Image:connectivity.jpg|thumb|200px|right]] 
- 
-For more details regarding to VTK format refer to VTK file format: [http://www.vtk.org/pdf/file-formats.pdf PDF] or [http://www.cacr.caltech.edu/~slombey/asci/vtk/vtk_formats.simple.html HTML] 
- 
- 
-=== Brief algorithm === 
- 
-1) Construct mesh connectivity 4/8 vertex per cell. 
- 
-2) Optimize connectivity by removing repeated vertexes, this considerably reduce data size and improve considerably speed of rendering (very important for 3d or large scale simulation). 
- 
-3) Interpolation of cell-wise data to vertexes. 
- 
-4) Writing results on a text file. 
- 
- 
-=== Function Prototype === 
- 
-Prototype of this function is as follows (6 input arguments): 
- 
-<source lang="c"> 
- void gfs_write_generic_output (gchar *type,  
- gint n_filed,  
- gchar **filed_name,  
- gint plot_depth,  
- GtsBBox * box,  
- GfsDomain * domain); 
-</source> 
- 
- 
-1. type: type of desired output, "VTK" or "TECPLOT" at the moment are supported. 
- 
-2. n_filed: number of filed data to be visualized, 0 mean just visualization of mesh. 
- 
-3. filed_name: string array, each item is correspond to each filed, you should include your desired field name, i.e., "U", "V", "W", "P" and desired tracer, e.g., "T", ..., also you could include "Vorticity" to compute and write vorticity field. If for any field, function can not find data pointer from name of variable (except for vorticity), this field is skiped. 
- 
-4. plot_depth: depth of cell which are desired to visualize, -1 mean visiting all levels. 
- 
-5. box: if box=NULL, all domain are considered for visualization, but user could define a box to visualize only portion of domain located in the box, to define box you should specify its two corner (by six coordinate, for 2d simulation define two z-value arbitrary). 
- 
-6. domain: simulation domain. 
- 
- 
-At the moment this function could be used to write data on-the-fly but it is easy to write a short code to convert "*.sim" data (result of Gerris) to described format. Maybe in future somebody write a tool to convert "*.sim" files to desired output, you could write its yourself, for this purpose follow instruction same as "gfs2oogl.c", to load simulation object from "*.sim" file). 
-  
- 
-=== How to Use === 
- 
- 
-To call this function on-the-fly it is sufficient to include this  
-file in "simulation.c" file, i.e. add statement  
- 
-<source lang="c"> 
- #include "generic_output.c" 
-</source> 
- 
-after include statements in the "simulation.c" file of your gerris and add its desired function call in time step loop of "simulation_run" function e.g. at a place like this (determined by "######") 
- 
-<source lang="c"> 
- 
- static void simulation_run (GfsSimulation * sim) 
- { 
- ... 
- ... 
- ... 
- 
- while (sim->time.t < sim->time.end && 
- sim->time.i < sim->time.iend) { 
- 
- ... 
- ... 
- ... 
- 
- sim->time.t = sim->tnext; 
- sim->time.i++; 
- 
- gts_range_add_value (&domain->timestep,  
- gfs_clock_elapsed(domain->timer) - tstart); 
- gts_range_update (&domain->timestep); 
- gts_range_add_value (&domain->size,  
- gfs_domain_size (domain, FTT_TRAVERSE_LEAFS, -1)); 
- gts_range_update (&domain->size); 
- 
- "######" 
- } 
- 
-</source> 
- 
-assume we like to run "heated.gfs" example  
- 
-use the following statements at the specified place (writing output file after each 100 time steps): 
- 
-<source lang="c"> 
- 
- { 
- gint n_field = 5, plot_depth = -1; 
- gchar *filed_name[5] = {"U", "V", "P", "T", "Vorticity"}; 
- GtsBBox *box= NULL;  
- 
- if(sim->time.i % 100 == 0)  
- gfs_write_generic_output ("TECPLOT", n_field, 
- filed_name,plot_depth,  
- box, domain); 
- 
- // or  
- 
- if(sim->time.i % 100 == 0)  
- gfs_write_generic_output ("VTK", n_field,  
- filed_name, plot_depth,  
- box, domain); 
- 
- } 
- 
-</source> 
-  
-or if you like to limit visulization within a box use this: 
- 
-<source lang="c"> 
- 
- { 
- gint n_field = 5, plot_depth = -1; 
- gchar *filed_name[5] = {"U", "V", "P", "T", "Vorticity"}; 
-  
- GtsBBox *box= gts_bbox_new (gts_bbox_class (), NULL,  
- -.5, -.5, -.5, 
- .5, .5, .5); 
-  
- if(sim->time.i % 100 == 0)  
- gfs_write_generic_output ("TECPLOT", n_field,  
- filed_name, plot_depth,  
- box, domain); 
- 
- // or  
- 
- if(sim->time.i % 100 == 0)  
- gfs_write_generic_output ("VTK", n_field,  
- filed_name, plot_depth,  
- box, domain); 
- 
- } 
- 
-</source> 
- 
-note that resulted files are names as: 
- 
- tecplot%i.plt or paraview%i.vtk 
- 
-where %i determine file number, it is automatically incremented after each output 
- 
-Note that you could write various type or a type with various proberties (e.g. writing both hole data and limited data by a box) simultaneously. For this for this purpose you just include suitable call of function in simulation loop. 
- 
-After modification of code, you should recompile your gerris code to activate this added feature. Of course it is better to include such data in input "*.gfs", i.e. treat its like an event, but prefarably this job should be performed by Gerris mantainer, if he detect that this feature is useful for a portion of Gerris users.  
-  
-(in the case of interest, you could announce your interest to this feature in GSF user mailing list). 
- 
- 
-=== Tecplot Snapshots === 
- 
- 
-[[Image:tecplot1.jpg|thumb|400px|left]] 
- 
- 
-[[Image:tecplot2.jpg|thumb|400px|left]] 
- 
-=== Paraview Snapshots === 
- 
- 
-[[Image:paraview1.jpg|thumb|300px|left]] 
- 
- 
-[[Image:paraview2.jpg|thumb|300px|left]] 
- 
- 
-[[Image:paraview3.jpg|thumb|600px|left]] 
- 
- 
- 
----- 
- 
-=== Source Code Listing === 
- 
-<source lang="c"> 
- 
-#include <stdlib.h> 
-#include <math.h> 
-#include <gmodule.h> 
-#include "config.h" 
-#include "gfsconfig.h" 
-#include "simulation.h" 
-#include "output.h" 
-#include "refine.h" 
-#include "solid.h" 
-#include "version.h" 
- 
- 
- 
-#define SQR(a) ((a)*(a)) 
- 
-#define my_alloc(pt, n, type, message) {\ 
- if(((pt) = (type *) calloc(n,sizeof(type)))==NULL) {\ 
- printf("\n\n Assertion: There is not sufficient memory to allocate: %s \n\n",message);\ 
- exit(1);\ 
- }\ 
- } 
- 
- 
-typedef struct { 
- gint node[(FTT_DIMENSION - 1)*4];  
-} Conectivity; 
- 
- 
-static gint tecplot_counter = 0; 
-static gint vtk_counter = 0; 
- 
-void gfs_write_generic_output (gchar *type, gint n_filed, gchar **filed_name, gint plot_depth, GtsBBox * box, GfsDomain * domain); 
- 
-/******************************************************************** 
- 
- count number of leaf cells and compute some spatial data 
- 
-********************************************************************/ 
- 
-void count_life_cells (FttCell * cell, gpointer * data) 
-{ 
- gint *ncells; 
- gdouble *scene_data, h, x_corner, y_corner, z_corner; 
- FttVector pos; 
- 
- g_return_if_fail (cell != NULL); 
- g_return_if_fail (data != NULL); 
- 
- ncells = data[0]; 
- scene_data = data[1]; 
- 
- h = ftt_cell_size (cell); 
- 
- scene_data[0] = MIN(h, scene_data[0]); 
- scene_data[1] = MAX(h, scene_data[1]); 
- 
- ftt_cell_pos (cell, &pos); 
- 
- h *= 0.5; 
- 
- x_corner = pos.x - h; 
- scene_data[3] = MIN(x_corner, scene_data[3]); 
- scene_data[6] = MAX(x_corner, scene_data[6]); 
- 
- y_corner = pos.y - h; 
- scene_data[4] = MIN(y_corner, scene_data[4]); 
- scene_data[7] = MAX(y_corner, scene_data[7]); 
- 
-#if FTT_3D 
- 
- z_corner = pos.z - h; 
- scene_data[5] = MIN(z_corner, scene_data[5]); 
- scene_data[8] = MAX(z_corner, scene_data[8]); 
- 
-#endif 
- 
- ++ *ncells; 
-} 
- 
-/******************************************************************** 
- 
- fill mesh coordinates 
- 
-********************************************************************/ 
- 
-void fill_mesh_coordinate (FttCell * cell, gpointer * data) 
-{ 
- gchar *type; 
- gint i, id, *cell_id; 
- FttVector pos, *coordinate; 
- gdouble h, *scene_data, *distance; 
- gdouble scale_y, scale_z, offset_x, offset_y, offset_z; 
-  
- g_return_if_fail (cell != NULL); 
- g_return_if_fail (data != NULL); 
- 
- cell_id = data[0]; 
- type = data[1]; 
- scene_data = data[2]; 
- coordinate = data[3]; 
- distance = data[4];  
- 
- /* scaling and offseting is performed to have only  
- same value of distance for exactly same points */ 
- offset_x = scene_data[3]; 
- offset_y = scene_data[4]; 
- offset_z = scene_data[5]; 
- 
- scale_y = scene_data[9]; 
- scale_z = scene_data[9] * scene_data[10]; 
- 
- id = *cell_id * (FTT_DIMENSION - 1)*4; 
- 
- h = 0.5 * ftt_cell_size (cell); 
- 
- ftt_cell_pos (cell, &pos); 
- 
-#if FTT_2D 
- 
- if(strcmp(type,"TECPLOT") == 0) { 
- coordinate[id+0].x = pos.x + h; coordinate[id+0].y = pos.y + h;  
- coordinate[id+1].x = pos.x - h; coordinate[id+1].y = pos.y + h; 
- coordinate[id+2].x = pos.x - h; coordinate[id+2].y = pos.y - h; 
- coordinate[id+3].x = pos.x + h; coordinate[id+3].y = pos.y - h; 
- } 
- 
- if(strcmp(type,"VTK") == 0) { 
- coordinate[id+0].x = pos.x - h; coordinate[id+0].y = pos.y - h;  
- coordinate[id+1].x = pos.x + h; coordinate[id+1].y = pos.y - h; 
- coordinate[id+2].x = pos.x - h; coordinate[id+2].y = pos.y + h; 
- coordinate[id+3].x = pos.x + h; coordinate[id+3].y = pos.y + h; 
- } 
- 
- for (i = 0; i < (FTT_DIMENSION - 1)*4; i++) 
- distance[id+i] = (coordinate[id+i].x - offset_x) +  
- (coordinate[id+i].y - offset_y) * ( scale_y + 1 ) ; 
- 
-#else /* 3D */ 
- 
- if(strcmp(type,"TECPLOT") == 0) { 
- coordinate[id+0].x = pos.x + h; coordinate[id+0].y = pos.y + h; coordinate[id+0].z = pos.z + h;  
- coordinate[id+1].x = pos.x - h; coordinate[id+1].y = pos.y + h; coordinate[id+1].z = pos.z + h;  
- coordinate[id+2].x = pos.x - h; coordinate[id+2].y = pos.y - h; coordinate[id+2].z = pos.z + h;  
- coordinate[id+3].x = pos.x + h; coordinate[id+3].y = pos.y - h; coordinate[id+3].z = pos.z + h;  
- coordinate[id+4].x = pos.x + h; coordinate[id+4].y = pos.y + h; coordinate[id+4].z = pos.z - h;  
- coordinate[id+5].x = pos.x - h; coordinate[id+5].y = pos.y + h; coordinate[id+5].z = pos.z - h;  
- coordinate[id+6].x = pos.x - h; coordinate[id+6].y = pos.y - h; coordinate[id+6].z = pos.z - h;  
- coordinate[id+7].x = pos.x + h; coordinate[id+7].y = pos.y - h; coordinate[id+7].z = pos.z - h; 
- } 
- 
- if(strcmp(type,"VTK") == 0) { 
- coordinate[id+0].x = pos.x - h; coordinate[id+0].y = pos.y - h; coordinate[id+0].z = pos.z - h;  
- coordinate[id+1].x = pos.x + h; coordinate[id+1].y = pos.y - h; coordinate[id+1].z = pos.z - h;  
- coordinate[id+2].x = pos.x - h; coordinate[id+2].y = pos.y + h; coordinate[id+2].z = pos.z - h;  
- coordinate[id+3].x = pos.x + h; coordinate[id+3].y = pos.y + h; coordinate[id+3].z = pos.z - h; 
- coordinate[id+4].x = pos.x - h; coordinate[id+4].y = pos.y - h; coordinate[id+4].z = pos.z + h;  
- coordinate[id+5].x = pos.x + h; coordinate[id+5].y = pos.y - h; coordinate[id+5].z = pos.z + h;  
- coordinate[id+6].x = pos.x - h; coordinate[id+6].y = pos.y + h; coordinate[id+6].z = pos.z + h;  
- coordinate[id+7].x = pos.x + h; coordinate[id+7].y = pos.y + h; coordinate[id+7].z = pos.z + h;  
- } 
-  
- for (i = 0; i < (FTT_DIMENSION - 1)*4; i++) 
- distance[id+i] = (coordinate[id+i].x - offset_x) +  
- (coordinate[id+i].y - offset_y) * ( scale_y + 1 ) +  
- (coordinate[id+i].z - offset_z) * ( scale_z + 1 ) ; 
- 
-#endif /* 3D */ 
-  
- ++ *cell_id; 
-} 
- 
-/******************************************************************** 
- 
- compute cell vorticity 
- 
-********************************************************************/ 
- 
-void compute_cell_vorticity (FttCell * cell, gpointer * data) { 
- 
- GfsVariable **velocity, *vorticity; 
- 
- g_return_if_fail (cell != NULL); 
- g_return_if_fail (data != NULL); 
- 
- velocity = data[0]; 
- vorticity = data[1]; 
- 
- GFS_VARIABLE (cell, vorticity->i) = gfs_vorticity (cell, velocity); 
- 
-} 
- 
-/******************************************************************** 
- 
- interpolate cell data to vertexes and compute interpolation weight 
- 
-********************************************************************/ 
- 
-void cell_to_vertex (FttCell * cell, gpointer * data) { 
- 
- static FttDirection d[(FTT_DIMENSION - 1)*4][FTT_DIMENSION] = { 
-#if FTT_2D 
- {FTT_RIGHT, FTT_TOP}, {FTT_LEFT, FTT_TOP}, {FTT_LEFT, FTT_BOTTOM}, {FTT_RIGHT, FTT_BOTTOM} 
-#else /* 3D */ 
- {FTT_RIGHT, FTT_TOP, FTT_FRONT}, {FTT_LEFT, FTT_TOP, FTT_FRONT},  
- {FTT_LEFT, FTT_BOTTOM, FTT_FRONT}, {FTT_RIGHT, FTT_BOTTOM, FTT_FRONT}, 
- {FTT_RIGHT, FTT_TOP, FTT_BACK}, {FTT_LEFT, FTT_TOP, FTT_BACK},  
- {FTT_LEFT, FTT_BOTTOM, FTT_BACK}, {FTT_RIGHT, FTT_BOTTOM, FTT_BACK}, 
-#endif /* 3D */ 
- }; 
- 
- gint i, j, k, n, *cell_id, *n_real_filed; 
- gdouble **field_data; 
- gint id_vertex_cell[(FTT_DIMENSION - 1)*4]; 
- 
- Conectivity *conectivity; 
- 
- GfsVariable *variable; 
- 
- g_return_if_fail (cell != NULL); 
- g_return_if_fail (data != NULL); 
-  
- cell_id = data[0]; 
- n_real_filed = data[1]; 
- conectivity = data[2];  
- field_data = data[4]; 
- k = 5; 
- 
- n = *n_real_filed; 
- 
- for (i = 0; i < (FTT_DIMENSION - 1)*4; i++)  
- id_vertex_cell[i] = conectivity[*cell_id].node[i]; 
- 
- for (j = 0; j < n; j++) { 
- variable = data[j+k]; 
- for (i = 0; i < (FTT_DIMENSION - 1)*4; i++) 
- field_data[j][id_vertex_cell[i]] = gfs_cell_corner_value (cell, d[i], variable, -1); 
- } 
-  
- ++ *cell_id; 
-} 
- 
-/**************************************************** 
-  
- quick sort of double array "a" with length "n"  
- and return integer permutation array "t"  
- 
-*****************************************************/ 
- 
-void my_fqsort (gint n, gdouble *a, gint *t) { 
- 
- static gint i, j, k, l, r, s, stackl[100], stackr[100], ww, flg1, flg2; 
- static gdouble w, x; 
- 
- --a; --t; 
- s = 1; stackl[1] = 1; stackr[1] = n; 
- 
-L10: l = stackl[s]; r = stackr[s--]; 
- 
-L20: i = l; j = r; k = ( l + r ) / 2; x = a[k]; 
- 
- /* repeat until i > j */ 
- flg1=1; 
- while (flg1) { 
- flg2=1; 
- while(flg2) 
- if (a[i]<x) ++i; /* search from lower end */  
- else flg2=0; 
- flg2=1; 
- while (flg2)  
- if (x<a[j]) --j; /* search from upper end */  
- else flg2=0; 
- 
- if (i<=j) { // swap positions i, j 
- w = a[i]; ww = t[i]; a[i] = a[j]; t[i++] = t[j]; a[j] = w; t[j--] = ww; 
- if (i>j) flg1=0; 
- } else flg1=0; 
- }; 
- 
- if ( j - l >= r - i ) { 
- if (l < j ) { 
- stackl[++s] = l; stackr[s] = j; 
- } 
- l = i; 
- } else { 
- if ( i < r ) { 
- stackl[++s]= i; stackr[s] = r; 
- } 
- r = j; 
- } 
- if (l < r) goto L20;  
- if ( s != 0 ) goto L10; 
- return; 
-} 
- 
-/**************************************************** 
- 
- quick sort of integer array "a" with length "n"  
- and return integer permutation array "t"  
- 
-****************************************************/ 
- 
-void my_iqsort (gint n, gint *a, gint *t) { 
- 
- static gint i, j, k, l, r, s, stackl[100], stackr[100], ww, flg1, flg2; 
- static gint w, x; 
- 
- --a; --t; 
- s = 1; stackl[1] = 1; stackr[1] = n; 
- 
-L10: l = stackl[s]; r = stackr[s--]; 
- 
-L20: i = l; j = r; k = ( l + r ) / 2; x = a[k]; 
- 
- /* repeat until i > j */ 
- flg1=1; 
- while (flg1) { 
- flg2=1; 
- while(flg2) 
- if (a[i]<x) ++i; /* search from lower end */  
- else flg2=0; 
- flg2=1; 
- while (flg2)  
- if (x<a[j]) --j; /* search from upper end */  
- else flg2=0; 
- 
- if (i<=j) { // swap positions i, j 
- w = a[i]; ww = t[i]; a[i] = a[j]; t[i++] = t[j]; a[j] = w; t[j--] = ww; 
- if (i>j) flg1=0; 
- } else flg1=0; 
- }; 
- 
- if ( j - l >= r - i ) { 
- if (l < j ) { 
- stackl[++s] = l; stackr[s] = j; 
- } 
- l = i; 
- } else { 
- if ( i < r ) { 
- stackl[++s]= i; stackr[s] = r; 
- } 
- r = j; 
- } 
- if (l < r) goto L20;  
- if ( s != 0 ) goto L10; 
- return; 
-} 
- 
-/******************************************************************** 
- 
- remove repeated vertex from conectivity and re-new conectivity 
- 
-********************************************************************/ 
- 
-void remove_repeated_vertex ( gint n_cells,  
- gint *n_vertex, 
- gdouble *scene_data, 
- gdouble *distance, 
- FttVector *coordinate, 
- Conectivity *conectivity 
- ) { 
- 
- gint i, j, n, n_vertexes_new, nv, *perm, *iperm, *label, *id_vertex; 
- gdouble small = 0.25 * scene_data[0]; 
- gchar *flg; 
- FttVector *new_coordinate; 
- 
- nv = 4*(FTT_DIMENSION - 1); 
- n = nv*n_cells; 
- 
- /* allocate array for permutation array and label of repeated vertexes */ 
- 
- my_alloc(perm, n, gint, "temporary permutation array"); 
- my_alloc(iperm, n, gint, "temporary ipermutation array"); 
- my_alloc(label, n, gint, "temporary label array"); 
- my_alloc(flg, n, gchar, "temporary flag array"); 
- 
- for (i=0; i<n; i++) { 
- perm [i] = label [i]= i; 
- flg [i] = 1; 
- } 
- 
- /*  
- quick sort algorithm, note that qsort of ANCI C is not suitable 
- for our purpose, since we need permutation array rather than sorted list  
- */ 
- 
- my_fqsort (n, distance, perm); 
- 
- n_vertexes_new = 1; 
- 
- for (i=0; i<(n-1); i++) { 
- 
- if( fabs( distance[i] - distance[i+1] ) < small ) { 
- 
- gint iv1 = perm[i]; 
- gint iv2 = perm[i+1]; 
- 
- if (  
- fabs( coordinate[iv1].x -  
- coordinate[iv2].x ) < small  
- && 
- fabs( coordinate[iv1].y -  
- coordinate[iv2].y ) < small 
-#if FTT_3D 
- && 
- fabs( coordinate[iv1].z -  
- coordinate[iv2].z ) < small 
-#endif 
- ) { 
- label[iv2] = label[iv1]; 
- flg[iv2] = 0; 
- } else ++n_vertexes_new; 
- } else ++n_vertexes_new; 
- } 
- 
- my_alloc(id_vertex, n_vertexes_new, gint, "temporary id vertex array"); 
- 
- n_vertexes_new = 0; 
- 
- for (i=0; i<n; i++) if( flg [i] > 0 ) { 
- perm [n_vertexes_new] = i; 
- id_vertex [n_vertexes_new++] = label[i]; 
- } 
- 
- my_iqsort (n_vertexes_new, id_vertex, perm); 
- 
- /* re-new conectivity */ 
- 
- for (i=0; i<n_vertexes_new; i++) iperm [perm[i]] = i; 
- 
- for (i=0; i<n_cells; i++) 
- for (j=0; j<nv; j++) 
- conectivity[i].node[j] = iperm [label[i*nv + j]]; 
-  
- g_free(label); 
- g_free(perm); 
- g_free(iperm); 
- g_free(id_vertex); 
- 
- my_alloc(new_coordinate, n_vertexes_new, FttVector, "temporary array for new_coordinate"); 
- 
- j=0; 
- for(i=0; i<n; i++) if(flg[i]>0) { 
- new_coordinate[j].x = coordinate[i].x; 
- new_coordinate[j].y = coordinate[i].y; 
-#if FTT_3D 
- new_coordinate[j].z = coordinate[i].z; 
-#endif 
- ++j; 
- } 
- 
- *n_vertex = n_vertexes_new; 
- 
- for(i=0; i<n_vertexes_new; i++) { 
- coordinate[i].x = new_coordinate[i].x; 
- coordinate[i].y = new_coordinate[i].y; 
-#if FTT_3D 
- coordinate[i].z = new_coordinate[i].z; 
-#endif 
- } 
- 
- g_free(flg); 
- g_free(new_coordinate); 
-} 
- 
-/******************************************************************** 
- 
- write a tecplot file 
- 
-*********************************************************************/ 
- 
-void gfs_write_generic_output (gchar *type, gint n_filed, gchar **filed_name, gint plot_depth, GtsBBox * box, GfsDomain * domain) 
-{ 
- gchar file_name[100], temp_string[60]; 
- FILE * fp; 
- gint n, n_cells, n_vertex, cell_id, i, j, k, n_real_filed, id_real_filed[20], vort, have_vel_vector[4]; 
- gdouble *distance, scene_data[20], *field_data[20]; 
- 
- GfsVariable *vorticity; 
- 
- Conectivity *conectivity; 
- FttVector *coordinate; 
-  
- gpointer data[20]; 
- 
- /* count number of leaf cells and some useful spatial data */ 
- 
- n_cells = 0; 
- 
- scene_data[0] = G_MAXDOUBLE; /* h_min */ 
- scene_data[1] = 0.0; /* h_max */ 
- 
- scene_data[3] = G_MAXDOUBLE; /* x_min */ 
- scene_data[4] = G_MAXDOUBLE; /* y_min */ 
- scene_data[5] = G_MAXDOUBLE; /* z_min */ 
- 
- scene_data[6] = G_MINDOUBLE; /* x_max */ 
- scene_data[7] = G_MINDOUBLE; /* y_max */ 
- scene_data[8] = G_MINDOUBLE; /* z_max */ 
- 
- data[0] = &n_cells;  
- data[1] = scene_data; 
- 
- if(box != NULL)  
- gfs_domain_cell_traverse_box (domain, box, FTT_PRE_ORDER, FTT_TRAVERSE_LEAFS, plot_depth, 
- (FttCellTraverseFunc) count_life_cells, data); 
- else  
- gfs_domain_cell_traverse (domain, FTT_PRE_ORDER, FTT_TRAVERSE_LEAFS, plot_depth, 
- (FttCellTraverseFunc) count_life_cells, data); 
- 
- scene_data[9] = scene_data[6] - scene_data[3]; /* lenght_x */ 
- scene_data[10] = scene_data[7] - scene_data[4]; /* lenght_y */ 
- scene_data[11] = scene_data[8] - scene_data[5]; /* lenght_z */ 
- 
- 
- /* allocate temporary memory to save mesh coordinates and its conectivity */ 
- 
- n = n_cells * 4*(FTT_DIMENSION - 1); 
- 
- my_alloc(conectivity, n_cells, Conectivity, "temporary mesh conectivity"); 
- my_alloc(coordinate, n, FttVector, "temporary mesh coordinates"); 
- my_alloc(distance, n, gdouble, "temporary distance of mesh nodes"); 
- 
- /* fill coordinates of leaf cells and their distance from a reference point */ 
- /* note that in this stage connectivity is priori known */ 
- 
- cell_id = 0; 
- 
- data[0] = &cell_id; 
- data[1] = type; 
- data[2] = scene_data; 
- data[3] = coordinate;  
- data[4] = distance; 
-  
- if(box != NULL)  
- gfs_domain_cell_traverse_box (domain, box, FTT_PRE_ORDER, FTT_TRAVERSE_LEAFS, plot_depth, 
- (FttCellTraverseFunc) fill_mesh_coordinate, data); 
- else  
- gfs_domain_cell_traverse (domain, FTT_PRE_ORDER, FTT_TRAVERSE_LEAFS, plot_depth, 
- (FttCellTraverseFunc) fill_mesh_coordinate, data); 
- 
- /*  
- removing repeated nodes from global connectivity  
- for this: we sort nodes based on the distance from 
- a refrence ponit and then detect repeated ones, remove  
- and renew connectivity. Note that to be compatible with formal  
- post-processors, like Tecplot, VTK, Ensight, we have to convert  
- cell-based data to vertex-based data and use weighted interpolation 
- of cell-wise data to compute data at vertexes. Also precence of  
- repeated vertexes decrease rendering speed of post-processor  
- */ 
- 
- remove_repeated_vertex ( n_cells, &n_vertex, scene_data, distance, coordinate, conectivity); 
- 
- /* allocate memory to store vertex interpolation of cell-wise data */ 
- k = 5;  
- vort = -1; 
- have_vel_vector[0] = 0; 
- n_real_filed = 0; 
- for(i=0; i<n_filed; i++) { 
- data[k+n_real_filed] = gfs_variable_from_name (domain->variables, filed_name[i]); 
- if(data[k+n_real_filed] == NULL) { 
- if(strcmp( filed_name[i], "Vorticity") == 0 ) vort = i; 
- } 
- else { 
- if(strcmp( filed_name[i], "U") == 0 ) {++have_vel_vector[0]; have_vel_vector[1] = i;} 
- if(strcmp( filed_name[i], "V") == 0 ) {++have_vel_vector[0]; have_vel_vector[2] = i;} 
- if(strcmp( filed_name[i], "W") == 0 ) {++have_vel_vector[0]; have_vel_vector[3] = i;} 
- 
- my_alloc(field_data[n_real_filed], n_vertex, gdouble, "temporary array to store vertex interpolated data"); 
- id_real_filed[n_real_filed++] = i; 
- } 
- } 
- 
- if(vort>0) { 
-  
- vorticity = gfs_temporary_variable (domain); 
- 
- data[0] = gfs_domain_velocity (domain); 
- data[1] = vorticity; 
- 
- if(box != NULL)  
- gfs_domain_cell_traverse_box (domain, box, FTT_PRE_ORDER, FTT_TRAVERSE_LEAFS, (plot_depth == -1 ? (-1):(plot_depth+1)),  
- (FttCellTraverseFunc) compute_cell_vorticity, data); 
- else  
- gfs_domain_cell_traverse (domain, FTT_PRE_ORDER, FTT_TRAVERSE_LEAFS, (plot_depth == -1 ? (-1):(plot_depth+1)), 
- (FttCellTraverseFunc) compute_cell_vorticity, data); 
- 
- data[k+n_real_filed] = vorticity; 
- 
- my_alloc(field_data[n_real_filed], n_vertex, gdouble, "temporary array to store vertex interpolated data"); 
- 
- id_real_filed[n_real_filed++] = vort; 
- } 
- 
- if(n_real_filed>0) { 
- for(j=0; j<n_real_filed; j++)  
- for(i=0; i<n_vertex; i++)  
- field_data[j][i] = 0.; 
- cell_id = 0; 
- 
- data[0] = &cell_id; 
- data[1] = &n_real_filed; 
- data[2] = conectivity;  
- data[4] = field_data; 
- 
- if(box != NULL)  
- gfs_domain_cell_traverse_box (domain, box, FTT_PRE_ORDER, FTT_TRAVERSE_LEAFS, plot_depth,  
- (FttCellTraverseFunc) cell_to_vertex, data); 
- else  
- gfs_domain_cell_traverse (domain, FTT_PRE_ORDER, FTT_TRAVERSE_LEAFS, plot_depth, 
- (FttCellTraverseFunc) cell_to_vertex, data); 
- 
- } 
- 
- 
- /* write data on a file */ 
- 
- /* --------------------------------------------------- 
- Tecplot output, it could be used as a general output 
- you could easily modify sort of data based on your 
- specific data format 
- ------------------------------------------------- */ 
- 
- if(strcmp(type,"TECPLOT") == 0) { 
- 
- int nn = (FTT_DIMENSION - 1)*4; 
- 
- /* name of output file */ 
- 
- ++ tecplot_counter; 
- 
- strcpy(file_name,"tecplot"); 
- sprintf(temp_string,"%i", tecplot_counter);  
- strcat(temp_string, ".plt"); 
- strcat(file_name,temp_string); 
- 
- fp = fopen (file_name, "w"); 
- 
- /* write header of vtk file */ 
- 
- fprintf (fp, " TITLE = 'Gerris Flow Solver Output' \n"); 
- 
-#if FTT_2D 
- fprintf (fp, " VARIABLES = 'X', 'Y'"); 
-#else /* 3D */ 
- fprintf (fp, " VARIABLES = 'X', 'Y', 'Z'"); 
-#endif 
- 
- for(j=0; j<n_real_filed; j++)  
- fprintf (fp, ", '%s' ",filed_name[id_real_filed[j]]); 
- fprintf (fp, " \n"); 
- 
-#if FTT_2D 
- fprintf (fp, " ZONE N=%i, E=%i, F=FEPOINT, ET=QUADRILATERAL \n", n_vertex, n_cells); 
-#else /* 3D */ 
- fprintf (fp, " ZONE N=%i, E=%i, F=FEPOINT, ET=BRICK \n", n_vertex, n_cells); 
-#endif 
- 
-  
- /* write vertex coordinates and related field data */ 
- 
- for(i=0; i<n_vertex; i++) { 
- 
-#if FTT_2D 
- fprintf (fp, " %f %f ", coordinate[i].x, coordinate[i].y); 
-#else /* 3D */ 
- fprintf (fp, " %f %f %f ", coordinate[i].x, coordinate[i].y, coordinate[i].z); 
-#endif 
- for(j=0; j<n_real_filed; j++)  
- fprintf (fp, " %f ",field_data[j][i]); 
- fprintf (fp, " \n"); 
- } 
- 
- /* write conectivity data */ 
- 
- for(i=0; i<n_cells; i++) { 
- for (j = 0; j < nn; j++) 
- fprintf (fp, " %i ", conectivity[i].node[j]+1); 
- fprintf (fp, " \n"); 
- } 
- fclose(fp); 
- fprintf (stderr, "\n %s file %i is dumped n_cells = %i \n", type, tecplot_counter, n_cells); 
- } 
- 
- 
- /* --------------------------------------------------- 
- VTK output, it could be imported and visualized by  
- free visualization package ParaView, due to  
- consistancy with various platform ASCII format is used 
- --------------------------------------------------- */ 
- 
- if(strcmp(type,"VTK") == 0) { 
- 
- int nn = (FTT_DIMENSION - 1)*4; 
- 
- /* name of output file */ 
-  
- ++ vtk_counter; 
-  
- strcpy(file_name,"paraview");  
- sprintf(temp_string,"%i", vtk_counter);  
- strcat(temp_string, ".vtk"); 
- strcat(file_name,temp_string); 
-  
- fp = fopen (file_name, "w"); 
- 
- 
- /* write header of vtk file */ 
- 
- fprintf (fp, "# vtk DataFile Version 2.0\n"); 
- fprintf (fp, "Unstructured Grid Example\n"); 
- fprintf (fp, "ASCII\n"); 
- fprintf (fp, "DATASET UNSTRUCTURED_GRID\n"); 
- fprintf (fp, "\n"); 
- 
- /* write spatial coordinates */ 
- 
- fprintf (fp, "POINTS %i float\n", n_vertex); 
-  
-#if FTT_2D 
- for(i=0; i<n_vertex; i++)  
- fprintf (fp, "%f %f 0 \n", coordinate[i].x, coordinate[i].y); 
-#else /* 3D */ 
- for(i=0; i<n_vertex; i++) 
- fprintf (fp, "%f %f %f\n", coordinate[i].x, coordinate[i].y, coordinate[i].z); 
-#endif 
- fprintf (fp, "\n"); 
- 
- /* write conectivity data */ 
- 
- fprintf (fp, "CELLS %i %i \n", n_cells, n_cells*(nn+1)); 
- 
- for(i=0; i<n_cells; i++) { 
- fprintf (fp, " %i ",nn); 
- for (j = 0; j < nn; j++) 
- fprintf (fp, " %i ", conectivity[i].node[j]); 
- fprintf (fp, " \n"); 
- } 
- fprintf (fp, "\n"); 
- 
- fprintf (fp, "CELL_TYPES %i \n",n_cells); 
- 
- for(i=0; i<n_cells; i++) 
-#if FTT_2D 
- fprintf (fp, "8 \n");  
-#else 
- fprintf (fp, "11 \n");  
-#endif 
- fprintf (fp, "\n"); 
- 
- /* write scaler fields */ 
- 
- if(n_real_filed>0) { 
- 
- fprintf (fp, "POINT_DATA %i\n",n_vertex); 
- fprintf (fp, "\n"); 
- 
- for(j=0; j<n_real_filed; j++) { 
-  
- fprintf (fp, "SCALARS %s float\n",filed_name[id_real_filed[j]]); 
- fprintf (fp, "LOOKUP_TABLE default \n"); 
- 
- for(i=0; i<n_vertex; i++)  
- fprintf(fp, "%f\n",field_data[j][i]); 
- fprintf (fp, "\n"); 
- } 
- } 
- 
- /* write velosity fields as a vector field,  
- if user include all velosity components */ 
- 
- if(have_vel_vector[0] == FTT_DIMENSION) { 
- 
- fprintf (fp, "VECTORS Velocity_vector float\n"); 
- 
-#if FTT_2D 
- for(i=0; i<n_vertex; i++) 
- fprintf (fp, "%f %f 0\n",field_data[have_vel_vector[1]][i], field_data[have_vel_vector[2]][i]); 
-#else 
- for(i=0; i<n_vertex; i++) 
- fprintf (fp, "%f %f %f\n",field_data[have_vel_vector[1]][i], field_data[have_vel_vector[2]][i], field_data[have_vel_vector[3]][i]); 
-#endif 
- } 
- fclose(fp);  
- fprintf (stderr, "\n %s file %i is dumped n_cells = %i \n", type, vtk_counter, n_cells); 
- } 
- 
- g_free(conectivity); 
- g_free(coordinate); 
- g_free(distance); 
- for(j=0; j<n_real_filed; j++) g_free(field_data[j]); 
-} 
- 
-</source> 

Revision as of 04:59, 5 February 2008

Emacs mode for Gerris files

Well, not really but something approaching. Add the following to your .emacs

(setq auto-mode-alist (cons '("\\.gfs\\'" . shell-script-mode) auto-mode-alist))

Generating several movies on-the-fly

While it is fairly simple to use the scripting mode of gfsview and unix pipes to generate a movie on the fly from a running simulation, how does one generate several movies simultaneously?

Using named unix fifos and the tee utility it is fairly easy too. For example if one has three gfsview files called wide.gfv, closeup.gfv and overview.gfv and want to generate the three corresponding movies wide.mpg, closeup.mpg and overview.mpg in one go, one could use the following script:

#!/bin/sh

movies="wide closeup overview"
rm -f $movies
mkfifo $movies

gerris3D mysimulation.gfs | tee $movies > /dev/null &
for movie in $movies; do
    gfsview-batch3D $movie.gfv < $movie | ppm2mpeg > $movie.mpg &
done
sleep 10
rm -f $movies

of course the simulation file mysimulation.gfs should contain lines looking like:

OutputSimulation { istep = 10 } stdout
EventScript { istep = 10 } { echo "Save stdout { width = 1024 height = 768 }" }

Compressing simulation files

When it is useful to save simulation results at regular intervals, the size of the files can be reduced by using on-the-fly compression. This can be done like this:

OutputSimulation { istep = 100 } sim-%ld.gfs
EventScript { istep = 100 } { gzip -f -q sim-*.gfs }

GfsView can read compressed GFS files directly.

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