From 3f5c83bc26e98dd41e93fc9023a610cd0ec1d363 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Tue, 11 Mar 2014 08:52:58 +0000
Subject: [PATCH] Fixed bugs when dump file is missing. Prepared flags for setting filenames
---
src/io.c | 181 ++++++++++++++++++++++++--------------------
1 files changed, 98 insertions(+), 83 deletions(-)
diff --git a/src/io.c b/src/io.c
index 93fda4c..db4e64f 100644
--- a/src/io.c
+++ b/src/io.c
@@ -18,7 +18,7 @@
#include <errno.h>
/** DUMP STATE TO DISK DRIVE **/
-ts_bool dump_state(ts_vesicle *vesicle){
+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;
@@ -131,16 +131,31 @@
*/
fwrite(vesicle->clist, sizeof(ts_cell_list),1, fh);
-
+
+ fwrite(&iteration, sizeof(ts_uint),1,fh);
fclose(fh);
return TS_SUCCESS;
}
/** RESTORE DUMP FROM DISK **/
-ts_vesicle *restore_state(){
+ts_vesicle *restore_state(ts_uint *iteration){
ts_uint i,j,k;
FILE *fh=fopen("dump.bin","rb");
+
+ struct stat sb;
+ if (stat("dump.bin", &sb) == -1) {
+ //dump file does not exist.
+ return NULL;
+ }
+
+ //check if it is regular file
+ if((sb.st_mode & S_IFMT) != S_IFREG) {
+ //dump file is not a regular file.
+ ts_fprintf(stderr,"Dump file is not a regular file!\n");
+ return NULL;
+ }
+
ts_uint retval;
ts_uint idx;
@@ -316,6 +331,7 @@
vesicle->clist->cell[i]->idx=i+1; // We enumerate cells! Probably never required!
}
+ retval=fread(iteration,sizeof(ts_uint),1,fh);
if(retval);
fclose(fh);
return vesicle;
@@ -324,24 +340,30 @@
ts_bool parse_args(int argc, char **argv){
- int c, retval;
- DIR *dir;
- path[0]=0;
+ 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");
+ FILE *file;
+
while (1)
{
static struct option long_options[] =
{
- {"force-from-tape", no_argument, &force_from_tape, 1},
+ {"force-from-tape", no_argument, &(command_line_args.force_from_tape), 1},
+ {"reset-iteration-count", no_argument, &(command_line_args.reset_iteration_count), 1},
{"tape", no_argument, 0, 't'},
{"output-file", required_argument, 0, 'o'},
{"directory", required_argument, 0, 'd'},
- {"dump-file", required_argument,0, 'f'},
+ {"dump-filename", required_argument,0, 'f'},
{0, 0, 0, 0}
};
/* getopt_long stores the option index here. */
int option_index = 0;
- c = getopt_long (argc, argv, "d:fot",
+ c = getopt_long (argc, argv, "d:f:o:t:",
long_options, &option_index);
/* Detect the end of the options. */
@@ -362,46 +384,56 @@
case 't':
//check if tape exists. If not, fail immediately.
- puts ("option -t\n");
+ if (stat(optarg, &sb) == -1) {
+ ts_fprintf(stderr,"Tape '%s' does not exist!\n",optarg);
+ fatal("Please select correct tape",1);
+ } else {
+ strcpy(command_line_args.tape_fullfilename,optarg);
+ }
break;
case 'o':
//set filename of master output file
- printf ("option -o with value `%s'\n", optarg);
- break;
+ if ((file = fopen(optarg, "w")) == NULL) {
+ fprintf(stderr,"Could not create output file!\n");
+ fatal("Please specify correct output file",1);
+
+ } else {
+ fclose(file);
+ }
+ strcpy(command_line_args.output_fullfilename, optarg);
+ break;
case 'd':
//check if directory exists. If not create one. If creation is
//successful, set directory for output files.
//printf ("option -d with value `%s'\n", optarg);
- dir = opendir(optarg);
- if (dir)
- {
- /* Directory exists. */
- closedir(dir);
- }
- else if (ENOENT == errno)
- {
- /* Directory does not exist. */
+ if (stat(optarg, &sb) == -1) {
+ //directory does not exist
retval=mkdir(optarg, 0700);
if(retval){
- fatal("Could not create requested directory. Check if you have permissions",1);
+ fatal("Could not create requested directory. Check if you have permissions",1);
}
}
- else
- {
- /* opendir() failed for some other reason. */
- fatal("Could not check if directory exists. Reason unknown",1);
+ //check if is a proper directory
+ else if((sb.st_mode & S_IFMT) != S_IFDIR) {
+ //it is not a directory. fatal error.
+ ts_fprintf(stderr,"%s is not a directory!\n",optarg);
+ fatal("Cannot continue",1);
}
- ts_fprintf(stdout,"\n*** Using output directory: %s\n\n", optarg);
-// sprintf(path,"%s", optarg);
- strcpy(path, optarg);
- // ts_fprintf(stdout,"ok!\n");
-
+ strcpy(command_line_args.path, optarg);
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;
case '?':
@@ -750,80 +782,63 @@
-ts_vesicle *parsetape(ts_uint *mcsweeps, ts_uint *inititer, ts_uint *iterations){
- long int nshell=17,ncxmax=60, ncymax=60, nczmax=60, npoly=10, nmono=20, pswitch=0; // THIS IS DUE TO CONFUSE BUG!
- char *buf=malloc(255*sizeof(char));
- long int brezveze0=1;
+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", &nshell),
- CFG_SIMPLE_INT("npoly", &npoly),
- CFG_SIMPLE_INT("nmono", &nmono),
- CFG_SIMPLE_FLOAT("dmax", &dmax),
- CFG_SIMPLE_FLOAT("xk0",&xk0),
- CFG_SIMPLE_INT("pswitch",&pswitch),
- CFG_SIMPLE_FLOAT("pressure",&pressure),
- CFG_SIMPLE_FLOAT("k_spring",&kspring),
- CFG_SIMPLE_FLOAT("stepsize",&stepsize),
- CFG_SIMPLE_INT("nxmax", &ncxmax),
- CFG_SIMPLE_INT("nymax", &ncymax),
- CFG_SIMPLE_INT("nzmax", &nczmax),
- CFG_SIMPLE_INT("iterations",&iter),
- CFG_SIMPLE_INT("mcsweeps",&mcsw),
- CFG_SIMPLE_INT("inititer", &init),
- CFG_SIMPLE_BOOL("quiet",&quiet),
- CFG_SIMPLE_STR("multiprocessing",buf),
- CFG_SIMPLE_INT("smp_cores",&brezveze0),
- CFG_SIMPLE_INT("cluster_nodes",&brezveze1),
- CFG_SIMPLE_INT("distributed_processes",&brezveze2),
+ CFG_SIMPLE_INT("nshell", &tape->nshell),
+ CFG_SIMPLE_INT("npoly", &tape->npoly),
+ CFG_SIMPLE_INT("nmono", &tape->nmono),
+ CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
+ CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
+ CFG_SIMPLE_INT("pswitch",&tape->pswitch),
+ CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
+ CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
+ CFG_SIMPLE_FLOAT("stepsize",&tape->stepsize),
+ CFG_SIMPLE_INT("nxmax", &tape->ncxmax),
+ CFG_SIMPLE_INT("nymax", &tape->ncymax),
+ CFG_SIMPLE_INT("nzmax", &tape->nczmax),
+ CFG_SIMPLE_INT("iterations",&tape->iterations),
+ CFG_SIMPLE_INT("mcsweeps",&tape->mcsweeps),
+ CFG_SIMPLE_INT("inititer", &tape->inititer),
+ CFG_SIMPLE_BOOL("quiet",&tape->quiet),
+ CFG_SIMPLE_STR("multiprocessing",tape->multiprocessing),
+ CFG_SIMPLE_INT("smp_cores",&tape->brezveze0),
+ CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
+ CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
CFG_END()
};
cfg_t *cfg;
ts_uint retval;
cfg = cfg_init(opts, 0);
- retval=cfg_parse(cfg, "tape");
+ retval=cfg_parse(cfg, filename);
if(retval==CFG_FILE_ERROR){
fatal("No tape file.",100);
}
else if(retval==CFG_PARSE_ERROR){
fatal("Invalid tape!",100);
}
- ts_vesicle *vesicle;
- *iterations=iter;
- *inititer=init;
- *mcsweeps=mcsw;
- vesicle=initial_distribution_dipyramid(nshell,ncxmax,ncymax,nczmax,stepsize);
- vesicle->poly_list=init_poly_list(npoly,nmono, vesicle->vlist);
- vesicle->spring_constant=kspring;
- poly_assign_spring_const(vesicle);
-
- vesicle->nshell=nshell;
- vesicle->dmax=dmax*dmax;
- vesicle->bending_rigidity=xk0;
- vtx_set_global_values(vesicle); //copies xk0 to every vertex
-
-
- vesicle->stepsize=stepsize;
- vesicle->clist->ncmax[0]=ncxmax;
- vesicle->clist->ncmax[1]=ncymax;
- vesicle->clist->ncmax[2]=nczmax;
- vesicle->clist->max_occupancy=8;
- vesicle->pressure=pressure/vesicle->bending_rigidity; //all energy contributions need to be divided by bending_rigidity!
- vesicle->pswitch=pswitch;
cfg_free(cfg);
- free(buf);
- // fprintf(stderr,"NSHELL=%u\n",vesicle->nshell);
-
- return vesicle;
+ /* global variables are set automatically */
+ quiet=tape->quiet;
+ return tape;
+}
+ts_bool tape_free(ts_tape *tape){
+ free(tape->multiprocessing);
+ free(tape);
+ return TS_SUCCESS;
}
--
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