From 698ae18f535c3e388b6ebcdca1582005a29ff2f2 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Mon, 29 Feb 2016 11:52:16 +0000
Subject: [PATCH] Tape is in the dump and successfully restored.
---
src/snapshot.c | 6 +-
src/initial_distribution.h | 2
src/io.c | 16 +++++++
src/initial_distribution.c | 12 ++++-
src/restore.h | 1
src/restore.c | 21 +++++++++-
src/io.h | 3 +
7 files changed, 49 insertions(+), 12 deletions(-)
diff --git a/src/initial_distribution.c b/src/initial_distribution.c
index 35d533d..3af821d 100644
--- a/src/initial_distribution.c
+++ b/src/initial_distribution.c
@@ -39,11 +39,17 @@
ts_vesicle *create_vesicle_from_tape(ts_tape *tape){
ts_vesicle *vesicle;
- ts_vertex *vtx;
vesicle=initial_distribution_dipyramid(tape->nshell,tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
- vesicle->tape=tape;
+ vesicle->tape=tape;
+ set_vesicle_values_from_tape(vesicle);
+ return vesicle;
+}
+
+ts_bool set_vesicle_values_from_tape(ts_vesicle *vesicle){
// Nucleus:
+ ts_vertex *vtx;
+ ts_tape *tape=vesicle->tape;
vesicle->R_nucleus=tape->R_nucleus*tape->R_nucleus;
vesicle->clist->dmin_interspecies = tape->dmin_interspecies*tape->dmin_interspecies;
@@ -101,7 +107,7 @@
else {
vesicle->sphHarmonics=NULL;
}
- return vesicle;
+ return TS_SUCCESS;
}
diff --git a/src/initial_distribution.h b/src/initial_distribution.h
index 20bbf18..39815d9 100644
--- a/src/initial_distribution.h
+++ b/src/initial_distribution.h
@@ -13,7 +13,7 @@
ts_vesicle *initial_distribution_dipyramid(ts_uint nshell, ts_uint ncmax1, ts_uint ncmax2, ts_uint ncmax3, ts_double stepsize);
ts_vesicle *create_vesicle_from_tape(ts_tape *tape);
-
+ts_bool set_vesicle_values_from_tape(ts_vesicle *vesicle);
/** Sets the initial position of the vertexes to dipyramid
*
* @param *vlist is a pointer to list of vertices
diff --git a/src/io.c b/src/io.c
index e7461d6..0a6cd57 100644
--- a/src/io.c
+++ b/src/io.c
@@ -1000,6 +1000,20 @@
ts_tape *parsetape(char *filename){
+ FILE *fd = fopen (filename, "r");
+ long length;
+ size_t size;
+ fseek (fd, 0, SEEK_END);
+ length = ftell (fd);
+ fseek (fd, 0, SEEK_SET);
+ size=fread (tapetxt, 1, length, fd);
+ fclose(fd);
+ if(size);
+ ts_tape *tape=parsetapebuffer(tapetxt);
+ return tape;
+}
+
+ts_tape *parsetapebuffer(char *buffer){
ts_tape *tape=(ts_tape *)calloc(1,sizeof(ts_tape));
tape->multiprocessing=calloc(255,sizeof(char));
@@ -1038,7 +1052,7 @@
cfg_t *cfg;
ts_uint retval;
cfg = cfg_init(opts, 0);
- retval=cfg_parse(cfg, filename);
+ retval=cfg_parse_buf(cfg, buffer);
if(retval==CFG_FILE_ERROR){
fatal("No tape file.",100);
}
diff --git a/src/io.h b/src/io.h
index 69de4e9..6c1e18a 100644
--- a/src/io.h
+++ b/src/io.h
@@ -7,7 +7,7 @@
static ts_bool restore=0;
static char tape[1024]; */
int force_from_tape;
-
+char tapetxt[128000]; //stores text file of the tape
typedef struct{
ts_int force_from_tape;
ts_int reset_iteration_count;
@@ -76,6 +76,7 @@
ts_bool write_pov_file(ts_vesicle *vesicle, char *filename);
ts_tape *parsetape(char *filename);
+ts_tape *parsetapebuffer(char *buffer);
ts_bool tape_free(ts_tape *tape);
ts_bool getcmdline_tape(cfg_t *cfg, char *opts);
ts_bool cmdline_to_tape(cfg_t *cfg, char *key, char *val);
diff --git a/src/restore.c b/src/restore.c
index aae6cb0..5db794e 100644
--- a/src/restore.c
+++ b/src/restore.c
@@ -14,12 +14,12 @@
#include "energy.h"
#include "poly.h"
#include "initial_distribution.h"
+#include "io.h"
ts_bool parseDump(char *dumpfname) {
xmlDocPtr doc;
xmlNodePtr cur, cur1,cur2;
ts_vesicle *vesicle=NULL;
-
doc = xmlParseFile(dumpfname);
if (doc == NULL ) {
@@ -38,6 +38,11 @@
cur = cur->xmlChildrenNode;
while (cur != NULL) {
+
+ if ((!xmlStrcmp(cur->name, (const xmlChar *)"tape"))){
+ setGlobalTapeTXTfromTapeTag(doc, cur);
+ }
+
if ((!xmlStrcmp(cur->name, (const xmlChar *)"trisurf"))){
vesicle=parseTrisurfTag(doc, cur);
}
@@ -84,6 +89,12 @@
return TS_SUCCESS;
}
+ts_bool setGlobalTapeTXTfromTapeTag(xmlDocPtr doc, xmlNodePtr cur){
+ xmlChar *tape = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
+ strcpy(tapetxt,(char *)tape);
+ xmlFree(tape);
+ return TS_SUCCESS;
+}
/* this is a parser of additional data in xml */
@@ -129,8 +140,10 @@
nvtx = xmlGetProp(cur, (xmlChar *)"nvtx");
npoly=xmlGetProp(cur, (xmlChar *)"npoly");
nfono=xmlGetProp(cur, (xmlChar *)"nfono");
- fprintf(stderr,"nvtx=%u\n",atoi((char *)nvtx));
- ts_vesicle *vesicle=init_vesicle(atoi((char *)nvtx),10,10,10,0.1);
+ ts_tape *tape=parsetapebuffer(tapetxt);
+ //fprintf(stderr,"nvtx=%u\n",atoi((char *)nvtx));
+ //TODO: check if nvtx is in agreement with nshell from tape
+ ts_vesicle *vesicle=init_vesicle(atoi((char *)nvtx),tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
//vesicle->poly_list=init_poly_list(atoi((char *)npoly),atoi((char *)nmono), vesicle->vlist, vesicle);
xmlFree(nvtx);
xmlFree(npoly);
@@ -155,6 +168,8 @@
}
+ vesicle->tape=tape;
+ set_vesicle_values_from_tape(vesicle);
return vesicle;
}
diff --git a/src/restore.h b/src/restore.h
index 16efff2..4c97a09 100644
--- a/src/restore.h
+++ b/src/restore.h
@@ -3,6 +3,7 @@
ts_bool parseDump(char *dumpfname);
ts_vesicle *parseTrisurfTag(xmlDocPtr doc, xmlNodePtr cur);
+ts_bool setGlobalTapeTXTfromTapeTag(xmlDocPtr doc, xmlNodePtr cur);
ts_bool parseTrisurfVtxn(ts_vertex_list *vlist, xmlDocPtr doc, xmlNodePtr cur);
ts_bool parseTrisurfTria(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur);
ts_bool parseTrisurfTriaNeigh(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur);
diff --git a/src/snapshot.c b/src/snapshot.c
index 12bb19a..177557d 100644
--- a/src/snapshot.c
+++ b/src/snapshot.c
@@ -7,7 +7,7 @@
#include<inttypes.h>
#include<config.h>
#include <time.h>
-
+#include "io.h"
/* a helper function that utilizes ts_string data structure and performs same as sprintf */
ts_uint ts_sprintf(ts_string *str, char *fmt, ...){
va_list ap;
@@ -56,7 +56,7 @@
fprintf(fh, "<dumpdate>%s</dumpdate>\n", c_time_string);
fprintf(fh, "<tape>\n");
-
+ fprintf(fh,"%s",tapetxt);
fprintf(fh, "</tape>\n");
if(vesicle->poly_list!=NULL){
npoly=vesicle->poly_list->n;
@@ -69,7 +69,7 @@
npoly=0;
nfono=0;
}
- fprintf(fh, "<trisurf nvtx=\"%u\" npoly=\"%u\" nfono=\"%u\">\n", vesicle->vlist->n, npoly, nfono);
+ fprintf(fh, "<trisurf nvtx=\"%u\" npoly=\"%u\" nfono=\"%u\" compressed=\"false\">\n", vesicle->vlist->n, npoly, nfono);
return TS_SUCCESS;
}
--
Gitblit v1.9.3