From 0fb40c28545e8418469cf7d3600547dfe4083edb Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 08 Mar 2014 12:00:38 +0000
Subject: [PATCH] Merged with dump-state. Added some arg switches that need to be inished
---
src/io.c | 151 +++++++++++++++++++++++++++++++++++++++++++++-----
1 files changed, 136 insertions(+), 15 deletions(-)
diff --git a/src/io.c b/src/io.c
index 262e482..93fda4c 100644
--- a/src/io.c
+++ b/src/io.c
@@ -11,8 +11,11 @@
#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){
@@ -22,7 +25,7 @@
FILE *fh=fopen("dump.bin","wb");
/* dump vesicle */
- fwrite(vesicle, sizeof(vesicle),1,fh);
+ fwrite(vesicle, sizeof(ts_vesicle),1,fh);
/* dump vertex list */
fwrite(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
/* dump bond list */
@@ -127,6 +130,8 @@
poly_list->poly->bond
*/
+ fwrite(vesicle->clist, sizeof(ts_cell_list),1, fh);
+
fclose(fh);
return TS_SUCCESS;
}
@@ -142,7 +147,9 @@
/* we restore all the data from the dump */
/* restore vesicle */
ts_vesicle *vesicle=(ts_vesicle *)calloc(1,sizeof(ts_vesicle));
- retval=fread(vesicle, sizeof(vesicle),1,fh);
+ retval=fread(vesicle, sizeof(ts_vesicle),1,fh);
+// fprintf(stderr,"was here! %e\n",vesicle->dmax);
+
/* restore vertex list */
vesicle->vlist=(ts_vertex_list *)malloc(sizeof(ts_vertex_list));
retval=fread(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
@@ -170,11 +177,13 @@
for(i=0;i<vesicle->tlist->n;i++){
vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
}
-
- /*restore vertices*/
+/* prerequisity. Vertices must be malloced before vertexes are recreated */
vesicle->vlist->vtx=(ts_vertex **)calloc(vesicle->vlist->n,sizeof(ts_vertex *));
- for(i=0;i<vesicle->vlist->n;i++){
+ for(i=0;i<vesicle->vlist->n;i++){
vesicle->vlist->vtx[i]=(ts_vertex *)malloc(sizeof(ts_vertex));
+ }
+ /*restore vertices*/
+ for(i=0;i<vesicle->vlist->n;i++){
retval=fread(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
/*restore neigh, bond, tristar. Ignoring cell */
vesicle->vlist->vtx[i]->neigh=(ts_vertex **)calloc(vesicle->vlist->vtx[i]->neigh_no, sizeof(ts_vertex *));
@@ -298,13 +307,119 @@
}
}
-
-
+// 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!
+ }
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, &force_from_tape, 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;
+
+}
+
@@ -405,11 +520,11 @@
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");
@@ -636,12 +751,12 @@
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!
+ 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;
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;
@@ -651,7 +766,9 @@
CFG_SIMPLE_INT("nmono", &nmono),
CFG_SIMPLE_FLOAT("dmax", &dmax),
CFG_SIMPLE_FLOAT("xk0",&xk0),
- CFG_SIMPLE_FLOAT("k_spring",&kspring),
+ 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),
@@ -689,12 +806,16 @@
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);
--
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