From c0d703a09da108f218b687beeec671f71b7a44c9 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 08 Mar 2014 18:25:50 +0000
Subject: [PATCH] Merge branch 'trisurf-polyel'
---
src/io.c | 203 +++++++++++++++++++++++++++++++++++++-------------
1 files changed, 149 insertions(+), 54 deletions(-)
diff --git a/src/io.c b/src/io.c
index 547c51c..d4a9cc4 100644
--- a/src/io.c
+++ b/src/io.c
@@ -11,11 +11,14 @@
#include "initial_distribution.h"
#include "poly.h"
-
-
+#include <getopt.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <dirent.h>
+#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;
@@ -128,14 +131,15 @@
*/
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");
ts_uint retval;
@@ -313,10 +317,112 @@
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;
}
+
+
+
+ts_bool parse_args(int argc, char **argv){
+ int c, retval;
+ DIR *dir;
+ path[0]=0;
+while (1)
+ {
+ static struct option long_options[] =
+ {
+ {"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'},
+ {0, 0, 0, 0}
+ };
+ /* getopt_long stores the option index here. */
+ int option_index = 0;
+
+ c = getopt_long (argc, argv, "d:fot",
+ long_options, &option_index);
+
+ /* Detect the end of the options. */
+ if (c == -1)
+ break;
+
+ switch (c)
+ {
+ case 0:
+ /* 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);
+ if (optarg)
+ printf (" with arg %s", optarg);
+ printf ("\n");
+ break;
+
+ case 't':
+ //check if tape exists. If not, fail immediately.
+ puts ("option -t\n");
+ break;
+
+ case 'o':
+ //set filename of master output file
+ printf ("option -o with value `%s'\n", 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. */
+ retval=mkdir(optarg, 0700);
+ if(retval){
+ 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);
+ }
+ ts_fprintf(stdout,"\n*** Using output directory: %s\n\n", optarg);
+// sprintf(path,"%s", optarg);
+ strcpy(path, optarg);
+ // ts_fprintf(stdout,"ok!\n");
+
+ break;
+
+ case 'f':
+ //check if dump file specified exists. Defaults to dump.bin
+ break;
+
+ case '?':
+ /* getopt_long already printed an error message. */
+
+ ts_fprintf(stderr,"\n\nhere comes the help.\n\n");
+ fatal("Ooops, read help first",1);
+ break;
+
+ default:
+ exit (1);
+ }
+ }
+
+ return TS_SUCCESS;
+
+}
+
@@ -417,11 +523,11 @@
fprintf(fh," %.17E\t%.17E\t%.17E\t%.17E\t%.17E\t%u\n",
vlist->vtx[i]->xk,vlist->vtx[i]->c,vlist->vtx[i]->energy,
vlist->vtx[i]->energy_h, vlist->vtx[i]->curvature, 0);
- for(j=0;j<vlist->vtx[i]->neigh_no;j++){
+ for(j=0;j<vlist->vtx[i]->bond_no;j++){
fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual);
}
fprintf(fh,"\n");
- for(j=0;j<vlist->vtx[i]->neigh_no;j++){
+ for(j=0;j<vlist->vtx[i]->bond_no;j++){
fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
}
fprintf(fh,"\n");
@@ -647,74 +753,63 @@
-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; // 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;
+ 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_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;
- vesicle->stepsize=stepsize;
- vesicle->clist->ncmax[0]=ncxmax;
- vesicle->clist->ncmax[1]=ncymax;
- vesicle->clist->ncmax[2]=nczmax;
- vesicle->clist->max_occupancy=8;
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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