From 854cb6571e100b4259ca70861a226a0d8a14c2c1 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Mon, 15 Feb 2016 14:22:04 +0000
Subject: [PATCH] First attempt to add additional info to the vtu files as formatted xml. Pegs are still missing, however the vesicle is done
---
src/io.c | 229 ++++++++++++++++++++++++++++++++++++++++++---------------
1 files changed, 168 insertions(+), 61 deletions(-)
diff --git a/src/io.c b/src/io.c
index 17adda4..e7461d6 100644
--- a/src/io.c
+++ b/src/io.c
@@ -1,7 +1,6 @@
#include "general.h"
#include<stdio.h>
#include "io.h"
-#include <confuse.h>
#include "vertex.h"
#include "bond.h"
#include<string.h>
@@ -10,22 +9,23 @@
#include <dirent.h>
#include "initial_distribution.h"
#include "poly.h"
-
+#include "cell.h"
#include <getopt.h>
#include <sys/stat.h>
#include <sys/types.h>
#include <dirent.h>
#include <errno.h>
+#include <snapshot.h>
/** DUMP STATE TO DISK DRIVE **/
ts_bool dump_state(ts_vesicle *vesicle, ts_uint iteration){
/* save current state with wrong pointers. Will fix that later */
ts_uint i,j,k;
- FILE *fh=fopen("dump.bin","wb");
+ FILE *fh=fopen(command_line_args.dump_fullfilename,"wb");
/* dump vesicle */
- fwrite(vesicle, sizeof(ts_vesicle),1,fh);
+ fwrite(vesicle, sizeof(ts_vesicle)-sizeof(ts_double),1,fh);
/* dump vertex list */
fwrite(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
/* dump bond list */
@@ -169,8 +169,9 @@
poly_list->poly->bond
*/
- fwrite(vesicle->clist, sizeof(ts_cell_list),1, fh);
-
+// fwrite(vesicle->clist, sizeof(ts_cell_list),1, fh);
+/* write tape information on vesicle */
+// fwrite(vesicle->tape,sizeof(ts_tape),1,fh);
fwrite(&iteration, sizeof(ts_uint),1,fh);
fclose(fh);
return TS_SUCCESS;
@@ -180,10 +181,10 @@
/** RESTORE DUMP FROM DISK **/
ts_vesicle *restore_state(ts_uint *iteration){
ts_uint i,j,k;
- FILE *fh=fopen("dump.bin","rb");
+ FILE *fh=fopen(command_line_args.dump_fullfilename,"rb");
struct stat sb;
- if (stat("dump.bin", &sb) == -1) {
+ if (stat(command_line_args.dump_fullfilename, &sb) == -1) {
//dump file does not exist.
return NULL;
}
@@ -201,7 +202,7 @@
/* we restore all the data from the dump */
/* restore vesicle */
ts_vesicle *vesicle=(ts_vesicle *)calloc(1,sizeof(ts_vesicle));
- retval=fread(vesicle, sizeof(ts_vesicle),1,fh);
+ retval=fread(vesicle, sizeof(ts_vesicle)-sizeof(ts_double),1,fh);
// fprintf(stderr,"was here! %e\n",vesicle->dmax);
/* restore vertex list */
@@ -418,16 +419,12 @@
vesicle->filament_list->poly[i]->blist->bond[j]->vtx2=vesicle->filament_list->poly[i]->vlist->vtx[idx];
}
}
-
+ vesicle->tape=parsetape(command_line_args.tape_fullfilename);
// recreating space for cells //
- vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
- retval=fread(vesicle->clist, sizeof(ts_cell_list), 1,fh);
- vesicle->clist->cell=(ts_cell **)malloc(sizeof(ts_cell *)*vesicle->clist->ncmax[0]*vesicle->clist->ncmax[1]*vesicle->clist->ncmax[2]);
- for(i=0;i<vesicle->clist->ncmax[0]*vesicle->clist->ncmax[1]*vesicle->clist->ncmax[2];i++){
- vesicle->clist->cell[i]=(ts_cell *)calloc(1,sizeof(ts_cell));
- vesicle->clist->cell[i]->idx=i+1; // We enumerate cells! Probably never required!
- }
-
+ vesicle->clist=init_cell_list(vesicle->tape->ncxmax, vesicle->tape->ncymax, vesicle->tape->nczmax, vesicle->tape->stepsize);
+ vesicle->clist->max_occupancy=8;
+// vesicle->tape=(ts_tape *)malloc(sizeof(ts_tape));
+// retval=fread(vesicle->tape, sizeof(ts_tape),1,fh);
retval=fread(iteration,sizeof(ts_uint),1,fh);
if(retval);
fclose(fh);
@@ -440,9 +437,10 @@
int c, retval;
struct stat sb;
sprintf(command_line_args.path, "./"); //clear string;
- sprintf(command_line_args.output_fullfilename,"./output.pvd");
- sprintf(command_line_args.dump_fullfilename,"./dump.bin");
- sprintf(command_line_args.tape_fullfilename,"./tape");
+ sprintf(command_line_args.output_fullfilename,"output.pvd");
+ sprintf(command_line_args.dump_fullfilename,"dump.bin");
+ sprintf(command_line_args.tape_fullfilename,"tape");
+ sprintf(command_line_args.tape_templatefull,"./tape");
FILE *file;
while (1)
@@ -455,12 +453,15 @@
{"output-file", required_argument, 0, 'o'},
{"directory", required_argument, 0, 'd'},
{"dump-filename", required_argument,0, 'f'},
+ {"tape-options",required_argument,0,'c'},
+ {"tape-template", required_argument,0,0},
+ {"dump-from-vtk",required_argument,0,0},
{0, 0, 0, 0}
};
/* getopt_long stores the option index here. */
int option_index = 0;
- c = getopt_long (argc, argv, "d:f:o:t:",
+ c = getopt_long (argc, argv, "d:f:o:t:c:",
long_options, &option_index);
/* Detect the end of the options. */
@@ -473,31 +474,27 @@
/* If this option set a flag, do nothing else now. */
if (long_options[option_index].flag != 0)
break;
- printf ("option %s", long_options[option_index].name);
+/* printf ("option %s", long_options[option_index].name);
if (optarg)
- printf (" with arg %s", optarg);
- printf ("\n");
+ printf (" with arg %s", optarg);
+ printf ("\n"); */
+ //TODO: find a better way.
+ if(strcmp(long_options[option_index].name,"tape-template")==0){
+ strcpy(command_line_args.tape_templatefull,optarg);
+ }
+ if(strcmp(long_options[option_index].name,"dump-from-vtk")==0){
+ strcpy(command_line_args.dump_from_vtk,optarg);
+ }
break;
- case 't':
- //check if tape exists. If not, fail immediately.
- if (stat(optarg, &sb) == -1) {
- ts_fprintf(stderr,"Tape '%s' does not exist!\n",optarg);
- fatal("Please select correct tape",1);
- } else {
+ case 'c':
+ strcpy(command_line_args.tape_opts,optarg);
+ break;
+ case 't': //tape
strcpy(command_line_args.tape_fullfilename,optarg);
- }
break;
- case 'o':
- //set filename of master output file
- if ((file = fopen(optarg, "w")) == NULL) {
- fprintf(stderr,"Could not create output file!\n");
- fatal("Please specify correct output file",1);
-
- } else {
- fclose(file);
- }
+ case 'o': //set filename of master pvd output file
strcpy(command_line_args.output_fullfilename, optarg);
break;
@@ -522,14 +519,6 @@
break;
case 'f':
- //check if dump file specified exists. Defaults to dump.bin
- if ((file = fopen(optarg, "w")) == NULL) {
- fprintf(stderr,"Could not create dump file!\n");
- fatal("Please specify correct dump file",1);
-
- } else {
- fclose(file);
- }
strcpy(command_line_args.dump_fullfilename, optarg);
break;
@@ -545,10 +534,64 @@
}
}
+//Here we set correct values for full filenames!
+ char *buffer=(char *)malloc(10000*sizeof(char));
+ //correct the path and add trailing /
+ if(command_line_args.path[strlen(command_line_args.path)-1]!='/') strcat(command_line_args.path,"/");
+
+/* master pvd output file */
+ strcpy(buffer,command_line_args.path);
+ strcat(buffer,command_line_args.output_fullfilename);
+ if ((file = fopen(buffer, "w")) == NULL) {
+ fprintf(stderr,"Could not create output file %s!\n", buffer);
+ fatal("Please specify correct output file or check permissions of the file",1);
+ //there is a tape template. make a copy into desired directory
+
+ } else {
+ fclose(file);
+ strcpy(command_line_args.output_fullfilename,buffer);
+ }
+
+/* tape file */
+ strcpy(buffer,command_line_args.path);
+ strcat(buffer,command_line_args.tape_fullfilename);
+ if (stat(buffer, &sb) == -1) {
+
+ //tape does not exist. does tape template exist?
+ if(stat(command_line_args.tape_templatefull, &sb)==-1){
+ ts_fprintf(stderr,"Tape '%s' does not exist and no tape template was specified (or does not exist)!\n",buffer);
+ fatal("Please select correct tape or check permissions of the file",1);
+ } else {
+ //tape template found
+ fatal("Samo did not program template copy yet",1);
+ }
+ } else {
+ strcpy(command_line_args.tape_fullfilename,buffer);
+ }
+
+
+/* dump file */
+ strcpy(buffer,command_line_args.path);
+ strcat(buffer,command_line_args.dump_fullfilename);
+ //check if dump file exist first.
+ if (stat(buffer, &sb) == -1) {
+ //no dump file. check if we can create one.
+ if ((file = fopen(buffer, "w")) == NULL) {
+ fprintf(stderr,"Could not create dump file '%s'!\n",buffer);
+ fatal("Please specify correct dump file or check permissions of the file",1);
+ } else {
+ fclose(file);
+ //good, file is writeable. delete it for now.
+ remove(buffer);
+ }
+ }
+ strcpy(command_line_args.dump_fullfilename, buffer);
+
+
+ free(buffer);
return TS_SUCCESS;
}
-
@@ -720,7 +763,7 @@
}
fprintf(fh,"<?xml version=\"1.0\"?>\n<VTKFile type=\"Collection\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n<Collection>");
- DIR *dir = opendir(".");
+ DIR *dir = opendir(command_line_args.path);
if(dir){
struct dirent *ent;
tstep=0;
@@ -749,10 +792,13 @@
ts_bond_list *blist=vesicle->blist;
ts_vertex **vtx=vlist->vtx;
ts_uint i,j;
- char filename[255];
+ char filename[10000];
+ char just_name[255];
FILE *fh;
+ strcpy(filename,command_line_args.path);
+ sprintf(just_name,"timestep_%.6u.vtu",timestepno);
+ strcat(filename,just_name);
- sprintf(filename,"timestep_%.6u.vtu",timestepno);
fh=fopen(filename, "w");
if(fh==NULL){
err("Cannot open file %s for writing");
@@ -779,7 +825,9 @@
}
}
- fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n <UnstructuredGrid>\n");
+ fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n");
+ xml_trisurf_data(fh,vesicle);
+ fprintf(fh, " <UnstructuredGrid>\n");
fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+monono*polyno+fonono*filno, blist->n+monono*polyno+filno*(fonono-1));
fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">");
for(i=0;i<vlist->n;i++){
@@ -952,15 +1000,8 @@
ts_tape *parsetape(char *filename){
- // long int nshell=17,ncxmax=60, ncymax=60, nczmax=60, npoly=10, nmono=20, pswitch=0; // THIS IS DUE TO CONFUSE BUG!
ts_tape *tape=(ts_tape *)calloc(1,sizeof(ts_tape));
tape->multiprocessing=calloc(255,sizeof(char));
- /* long int brezveze0=1;
- long int brezveze1=1;
- long int brezveze2=1;
- ts_double xk0=25.0, dmax=1.67,stepsize=0.15,kspring=800.0,pressure=0.0;
- long int iter=1000, init=1000, mcsw=1000;
-*/
cfg_opt_t opts[] = {
CFG_SIMPLE_INT("nshell", &tape->nshell),
@@ -970,8 +1011,12 @@
CFG_SIMPLE_INT("nfono",&tape->nfono),
CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
+ CFG_SIMPLE_FLOAT("dmin_interspecies", &tape->dmin_interspecies),
CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
CFG_SIMPLE_INT("pswitch",&tape->pswitch),
+ CFG_SIMPLE_INT("constvolswitch",&tape->constvolswitch),
+ CFG_SIMPLE_INT("constareaswitch",&tape->constareaswitch),
+ CFG_SIMPLE_FLOAT("constvolprecision",&tape->constvolprecision),
CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
CFG_SIMPLE_FLOAT("xi",&tape->xi),
@@ -987,6 +1032,7 @@
CFG_SIMPLE_INT("smp_cores",&tape->brezveze0),
CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
+ CFG_SIMPLE_INT("spherical_harmonics_coefficients",&tape->shc),
CFG_END()
};
cfg_t *cfg;
@@ -1000,6 +1046,8 @@
fatal("Invalid tape!",100);
}
+ /* here we override all values read from tape with values from commandline*/
+ getcmdline_tape(cfg,command_line_args.tape_opts);
cfg_free(cfg);
@@ -1015,6 +1063,65 @@
}
+
+ts_bool getcmdline_tape(cfg_t *cfg, char *opts){
+
+ char *commands, *backup, *saveptr, *saveopptr, *command, *operator[2];
+ ts_uint i,j;
+ commands=(char *)malloc(10000*sizeof(char));
+ backup=commands; //since the pointer to commands will be lost, we acquire a pointer that will serve as backup.
+ strcpy(commands,opts);
+ for(i=0; ;i++, commands=NULL){
+ //breaks comma separated list of commands into specific commands.
+ command=strtok_r(commands,",",&saveptr);
+ if(command==NULL) break;
+// fprintf(stdout,"Command %d: %s\n",i,command);
+ //extracts name of command and value of command into operator[2] array.
+ for(j=0; j<2;j++,command=NULL){
+ operator[j]=strtok_r(command,"=",&saveopptr);
+ if(operator[j]==NULL) break;
+// fprintf(stdout," ---> Operator %d: %s\n",j,operator[j]);
+ }
+ //1. check: must have 2 operators.
+ if(j!=2) fatal("Error. Command line tape options are not formatted properly",1);
+
+ // cfg_setstr(cfg,operator[0],operator[1]);
+ cmdline_to_tape(cfg,operator[0],operator[1]);
+ //2. check: must be named properly.
+ //3. check: must be of right format (integer, double, string, ...)
+
+ }
+ free(backup);
+ return TS_SUCCESS;
+}
+
+
+ts_bool cmdline_to_tape(cfg_t *cfg, char *key, char *val){
+
+ cfg_opt_t *cfg_opt=cfg_getopt(cfg,key);
+ if(cfg_opt==NULL) fatal("Commandline tape option not recognised",1); //return TS_FAIL;
+ switch (cfg_opt->type){
+ case CFGT_INT:
+ cfg_setint(cfg,key,atol(val));
+ break;
+ case CFGT_FLOAT:
+ cfg_setfloat(cfg,key,atof(val));
+ break;
+/* case CFGT_BOOL:
+ cfg_setbool(cfg,operator[0],operator[1]);
+ break; */
+ case CFGT_STR:
+ cfg_setstr(cfg,key,val);
+ break;
+ default:
+ break;
+
+ }
+ return TS_SUCCESS;
+}
+
+
+
ts_bool read_geometry_file(char *fname, ts_vesicle *vesicle){
FILE *fh;
ts_uint i, nvtx,nedges,ntria;
--
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