From bd826de2f539f2e48c8c01d2d7f9f34c7e97104a Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Fri, 13 May 2016 07:43:27 +0000
Subject: [PATCH] Fix in trisurf output, inhibiting print of successful reconstruction. Multiple fixes and improvements in python module. Added symlinking of tapes into the running directories and dumping tapes from snapshots into tape files.
---
src/io.c | 73 ++++++++++++++++++++++++++++--------
1 files changed, 56 insertions(+), 17 deletions(-)
diff --git a/src/io.c b/src/io.c
index d8c1009..51ef836 100644
--- a/src/io.c
+++ b/src/io.c
@@ -1,3 +1,4 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
#include "general.h"
#include<stdio.h>
#include "io.h"
@@ -15,16 +16,17 @@
#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 */
@@ -180,10 +182,10 @@
/** 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 +203,7 @@
/* 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 */
@@ -418,7 +420,7 @@
vesicle->filament_list->poly[i]->blist->bond[j]->vtx2=vesicle->filament_list->poly[i]->vlist->vtx[idx];
}
}
- vesicle->tape=parsetape("tape");
+ vesicle->tape=parsetape(command_line_args.tape_fullfilename);
// recreating space for cells //
vesicle->clist=init_cell_list(vesicle->tape->ncxmax, vesicle->tape->ncymax, vesicle->tape->nczmax, vesicle->tape->stepsize);
vesicle->clist->max_occupancy=8;
@@ -439,6 +441,7 @@
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)
@@ -452,6 +455,8 @@
{"directory", required_argument, 0, 'd'},
{"dump-filename", required_argument,0, 'f'},
{"tape-options",required_argument,0,'c'},
+ {"tape-template", required_argument,0,0},
+ {"restore-from-vtk",required_argument,0,0},
{0, 0, 0, 0}
};
/* getopt_long stores the option index here. */
@@ -470,10 +475,17 @@
/* 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,"restore-from-vtk")==0){
+ strcpy(command_line_args.dump_from_vtk,optarg);
+ }
break;
case 'c':
@@ -534,6 +546,7 @@
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);
@@ -544,8 +557,15 @@
strcpy(buffer,command_line_args.path);
strcat(buffer,command_line_args.tape_fullfilename);
if (stat(buffer, &sb) == -1) {
- ts_fprintf(stderr,"Tape '%s' does not exist!\n",buffer);
- fatal("Please select correct tape or check permissions of the file",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);
}
@@ -573,7 +593,6 @@
return TS_SUCCESS;
}
-
@@ -745,7 +764,7 @@
}
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;
@@ -774,10 +793,13 @@
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");
@@ -804,7 +826,9 @@
}
}
- 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++){
@@ -977,6 +1001,20 @@
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));
@@ -992,6 +1030,7 @@
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),
@@ -1014,7 +1053,7 @@
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);
}
--
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