From 37791bf67add4094040a9b8706450695805bf88f Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Fri, 20 May 2016 18:35:21 +0000
Subject: [PATCH] Minimal changes to trisurf core to permit the trout rbc simulations with eliptical nucleus (optional parameters in tape R_nucleusX, R_nucleusY and R_nucleusZ) were added
---
src/io.c | 594 +++++++++++++++++++++++++++++++++++++++++++++++++++--------
1 files changed, 511 insertions(+), 83 deletions(-)
diff --git a/src/io.c b/src/io.c
index 547c51c..2461de5 100644
--- a/src/io.c
+++ b/src/io.c
@@ -1,7 +1,7 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
#include "general.h"
#include<stdio.h>
#include "io.h"
-#include <confuse.h>
#include "vertex.h"
#include "bond.h"
#include<string.h>
@@ -10,19 +10,23 @@
#include <dirent.h>
#include "initial_distribution.h"
#include "poly.h"
-
-
-
+#include "cell.h"
+#include <getopt.h>
+#include <sys/stat.h>
+#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_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 */
@@ -33,6 +37,8 @@
fwrite(vesicle->clist, sizeof(ts_cell_list),1,fh);
/* dump poly list */
fwrite(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
+ /* dump filament list */
+ fwrite(vesicle->filament_list, sizeof(ts_poly_list),1,fh);
/* level 1 complete */
/*dump vertices*/
@@ -115,6 +121,43 @@
}
}
+
+ /*dump filamentes grandes svinjas */
+ for(i=0;i<vesicle->filament_list->n;i++){
+ fwrite(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh);
+ fwrite(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
+ fwrite(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
+ }
+
+ /* dump filamentes vertex(monomer) list*/
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
+ fwrite(vesicle->filament_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
+ /* dump offset for neigh and bond */
+ for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
+ // off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
+ fwrite(&vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh);
+ }
+ for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no;k++){
+ //off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
+ fwrite(&vesicle->filament_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh);
+ }
+ }
+ }
+ /* dump poly bonds between monomers list*/
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
+ fwrite(vesicle->filament_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
+ /* dump vtx1 and vtx2 offsets */
+ //off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
+ fwrite(&vesicle->filament_list->poly[i]->blist->bond[j]->vtx1->idx,sizeof(ts_uint),1,fh);
+// off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
+ fwrite(&vesicle->filament_list->poly[i]->blist->bond[j]->vtx2->idx,sizeof(ts_uint),1,fh);
+ }
+ }
+
+
+
/* pointer offsets for fixing the restored pointers */
/* need pointers for
vlist->vtx
@@ -127,24 +170,40 @@
poly_list->poly->bond
*/
- fwrite(vesicle->clist, sizeof(ts_cell_list),1, fh);
-
+// fwrite(vesicle->clist, sizeof(ts_cell_list),1, fh);
+/* write tape information on vesicle */
+// fwrite(vesicle->tape,sizeof(ts_tape),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");
+ FILE *fh=fopen(command_line_args.dump_fullfilename,"rb");
+
+ struct stat sb;
+ if (stat(command_line_args.dump_fullfilename, &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;
/* 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 */
@@ -162,6 +221,9 @@
/* restore poly list */
vesicle->poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
retval=fread(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
+ /* restore filament list */
+ vesicle->filament_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
+ retval=fread(vesicle->filament_list, sizeof(ts_poly_list),1,fh);
/* level 1 complete */
/* prerequisity. Bonds must be malloced before vertexes are recreated */
@@ -304,18 +366,238 @@
}
}
-// 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!
- }
+ /*restore filaments */
+ vesicle->filament_list->poly = (ts_poly **)calloc(vesicle->filament_list->n,sizeof(ts_poly *));
+ for(i=0;i<vesicle->filament_list->n;i++){
+ vesicle->filament_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
+ retval=fread(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh);
+ vesicle->filament_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
+ retval=fread(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
+ vesicle->filament_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
+ retval=fread(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
+ /* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
+ vesicle->filament_list->poly[i]->vlist->vtx=(ts_vertex **)calloc(vesicle->filament_list->poly[i]->vlist->n,sizeof(ts_vertex *));
+ vesicle->filament_list->poly[i]->blist->bond=(ts_bond **)calloc(vesicle->filament_list->poly[i]->blist->n,sizeof(ts_bond *));
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
+ vesicle->filament_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
+ }
+ for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
+ vesicle->filament_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
+ }
+ }
+
+
+ /* restore poly vertex(monomer) list*/
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
+ retval=fread(vesicle->filament_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
+
+ /* restore neigh and bonds */
+ vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh=(ts_vertex **)calloc(vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no, sizeof(ts_vertex *));
+ for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->filament_list->poly[i]->vlist->vtx[idx];
+ }
+ vesicle->filament_list->poly[i]->vlist->vtx[j]->bond=(ts_bond **)calloc(vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no, sizeof(ts_bond *));
+ for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no;k++){
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->filament_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->filament_list->poly[i]->blist->bond[idx];
+ }
+
+ }
+ }
+
+ /* restore poly bonds between monomers list*/
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
+ // vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
+ retval=fread(vesicle->filament_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
+ /* restore vtx1 and vtx2 */
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->filament_list->poly[i]->blist->bond[j]->vtx1=vesicle->filament_list->poly[i]->vlist->vtx[idx];
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->filament_list->poly[i]->blist->bond[j]->vtx2=vesicle->filament_list->poly[i]->vlist->vtx[idx];
+ }
+ }
+ 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;
+// vesicle->tape=(ts_tape *)malloc(sizeof(ts_tape));
+// retval=fread(vesicle->tape, sizeof(ts_tape),1,fh);
+ 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;
+ 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");
+ sprintf(command_line_args.tape_templatefull,"./tape");
+ FILE *file;
+
+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'},
+ {"version", no_argument, 0, 'v'},
+ {"output-file", required_argument, 0, 'o'},
+ {"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. */
+ int option_index = 0;
+
+ c = getopt_long (argc, argv, "d:f:o:t:c:v",
+ 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"); */
+ //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 'v':
+ fprintf(stdout,"TRISURF-NG v. %s, compiled on: %s %s.\n", TS_VERSION, __DATE__, __TIME__);
+ fprintf(stdout,"Programming done by: Samo Penic and Miha Fosnaric\n");
+ fprintf(stdout,"Released under terms of GPLv3\n");
+ exit(0);
+
+ case 'c':
+ strcpy(command_line_args.tape_opts,optarg);
+ break;
+ case 't': //tape
+ strcpy(command_line_args.tape_fullfilename,optarg);
+ break;
+
+ case 'o': //set filename of master pvd output 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);
+ 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);
+ }
+ }
+ //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);
+ }
+ strcpy(command_line_args.path, optarg);
+ break;
+
+ case 'f':
+ strcpy(command_line_args.dump_fullfilename, optarg);
+ 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);
+ }
+ }
+
+//Here we set correct values for full filenames!
+ char *buffer=(char *)malloc(10000*sizeof(char));
+ //correct the path and add trailing /
+ if(command_line_args.path[strlen(command_line_args.path)-1]!='/') strcat(command_line_args.path,"/");
+
+/* master pvd output file */
+ strcpy(buffer,command_line_args.path);
+ strcat(buffer,command_line_args.output_fullfilename);
+ 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);
+ strcpy(command_line_args.output_fullfilename,buffer);
+ }
+
+/* tape file */
+ strcpy(buffer,command_line_args.path);
+ strcat(buffer,command_line_args.tape_fullfilename);
+ if (stat(buffer, &sb) == -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);
+ }
+
+
+/* dump file */
+ strcpy(buffer,command_line_args.path);
+ strcat(buffer,command_line_args.dump_fullfilename);
+ //check if dump file exist first.
+ if (stat(buffer, &sb) == -1) {
+ //no dump file. check if we can create one.
+ if ((file = fopen(buffer, "w")) == NULL) {
+ fprintf(stderr,"Could not create dump file '%s'!\n",buffer);
+ fatal("Please specify correct dump file or check permissions of the file",1);
+ } else {
+ fclose(file);
+ //good, file is writeable. delete it for now.
+ remove(buffer);
+ }
+ }
+ strcpy(command_line_args.dump_fullfilename, buffer);
+
+
+ free(buffer);
+ return TS_SUCCESS;
+
}
@@ -417,11 +699,11 @@
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");
@@ -488,7 +770,7 @@
}
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;
@@ -517,10 +799,13 @@
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");
@@ -529,8 +814,8 @@
/* Here comes header of the file */
//find number of extra vtxs and bonds of polymeres
- ts_uint monono=0, polyno=0, poly_idx=0;
- ts_bool poly=0;
+ ts_uint monono=0, polyno=0, poly_idx=0, filno=0, fonono=0;
+ ts_bool poly=0, fil=0;
if(vesicle->poly_list!=NULL){
if(vesicle->poly_list->poly[0]!=NULL){
polyno=vesicle->poly_list->n;
@@ -538,8 +823,19 @@
poly=1;
}
}
- fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n <UnstructuredGrid>\n");
- fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+monono*polyno, blist->n+monono*polyno);
+
+ if(vesicle->filament_list!=NULL){
+ if(vesicle->filament_list->poly[0]!=NULL){
+ filno=vesicle->filament_list->n;
+ fonono=vesicle->filament_list->poly[0]->vlist->n;
+ fil=1;
+ }
+ }
+
+ 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++){
fprintf(fh,"%u ",vtx[i]->idx);
@@ -553,16 +849,34 @@
}
}
}
+ //filaments
+ if(fil){
+ poly_idx=vlist->n+monono*polyno;
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
+ // fprintf(stderr,"was here\n");
+ fprintf(fh,"%u ", poly_idx);
+ }
+ }
+ }
fprintf(fh,"</DataArray>\n</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
for(i=0;i<vlist->n;i++){
- fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
+ fprintf(fh,"%.17e %.17e %.17e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
}
//polymeres
if(poly){
for(i=0;i<vesicle->poly_list->n;i++){
for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
- fprintf(fh,"%e %e %e\n", vesicle->poly_list->poly[i]->vlist->vtx[j]->x,vesicle->poly_list->poly[i]->vlist->vtx[j]->y, vesicle->poly_list->poly[i]->vlist->vtx[j]->z );
+ fprintf(fh,"%.17e %.17e %.17e\n", vesicle->poly_list->poly[i]->vlist->vtx[j]->x,vesicle->poly_list->poly[i]->vlist->vtx[j]->y, vesicle->poly_list->poly[i]->vlist->vtx[j]->z );
+ }
+ }
+ }
+ //filaments
+ if(fil){
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
+ fprintf(fh,"%.17e %.17e %.17e\n", vesicle->filament_list->poly[i]->vlist->vtx[j]->x,vesicle->filament_list->poly[i]->vlist->vtx[j]->y, vesicle->filament_list->poly[i]->vlist->vtx[j]->z );
}
}
}
@@ -585,14 +899,26 @@
}
+ //filaments
+ if(fil){
+ poly_idx=vlist->n+monono*polyno;
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
+ fprintf(fh,"%u %u\n", vesicle->filament_list->poly[i]->blist->bond[j]->vtx1->idx+vlist->n+monono*polyno+i*fonono,vesicle->filament_list->poly[i]->blist->bond[j]->vtx2->idx+vlist->n+monono*polyno+i*fonono);
+// fprintf(stderr,"was here\n");
+
+ }
+ }
+
+ }
fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
- for (i=2;i<(blist->n+monono*polyno)*2+1;i+=2){
+ for (i=2;i<(blist->n+monono*polyno+(fonono-1)*filno)*2+1;i+=2){
fprintf(fh,"%u ",i);
}
fprintf(fh,"\n");
fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
- for (i=0;i<blist->n+monono*polyno;i++){
+ for (i=0;i<blist->n+monono*polyno+fonono*filno;i++){
fprintf(fh,"3 ");
}
@@ -647,76 +973,178 @@
-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;
- long int brezveze1=1;
- long int brezveze2=1;
- ts_double xk0=25.0, dmax=1.67,stepsize=0.15,kspring=800.0;
- long int iter=1000, init=1000, mcsw=1000;
+ts_bool write_pov_file(ts_vesicle *vesicle, char *filename){
+ FILE *fh;
+ ts_uint i;
+
+ fh=fopen(filename, "w");
+ if(fh==NULL){
+ err("Cannot open file %s for writing");
+ return TS_FAIL;
+ }
+ for(i=0;i<vesicle->tlist->n;i++){
+
+ fprintf(fh,"\ttriangle {");
+ fprintf(fh,"\t<%e,%e,%e> <%e,%e,%e> <%e,%e,%e> }\n",
+ vesicle->tlist->tria[i]->vertex[0]->x,
+ vesicle->tlist->tria[i]->vertex[0]->y,
+ vesicle->tlist->tria[i]->vertex[0]->z,
+
+ vesicle->tlist->tria[i]->vertex[1]->x,
+ vesicle->tlist->tria[i]->vertex[1]->y,
+ vesicle->tlist->tria[i]->vertex[1]->z,
+
+ vesicle->tlist->tria[i]->vertex[2]->x,
+ vesicle->tlist->tria[i]->vertex[2]->y,
+ vesicle->tlist->tria[i]->vertex[2]->z
+ );
+ }
+
+ fclose(fh);
+ return TS_SUCCESS;
+}
+
+
+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));
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_INT("nfil",&tape->nfil),
+ CFG_SIMPLE_INT("nfono",&tape->nfono),
+ CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
+ CFG_SIMPLE_FLOAT("R_nucleusX",&tape->R_nucleusX),
+ CFG_SIMPLE_FLOAT("R_nucleusY",&tape->R_nucleusY),
+ CFG_SIMPLE_FLOAT("R_nucleusZ",&tape->R_nucleusZ),
+ CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
+ CFG_SIMPLE_FLOAT("dmin_interspecies", &tape->dmin_interspecies),
+ 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),
+ CFG_SIMPLE_FLOAT("xi",&tape->xi),
+ 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_SIMPLE_INT("spherical_harmonics_coefficients",&tape->shc),
CFG_END()
};
cfg_t *cfg;
ts_uint retval;
cfg = cfg_init(opts, 0);
- retval=cfg_parse(cfg, "tape");
+ retval=cfg_parse_buf(cfg, buffer);
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;
-
+ /* here we override all values read from tape with values from commandline*/
+ getcmdline_tape(cfg,command_line_args.tape_opts);
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;
+}
+
+
+
+ts_bool getcmdline_tape(cfg_t *cfg, char *opts){
+
+ char *commands, *backup, *saveptr, *saveopptr, *command, *operator[2];
+ ts_uint i,j;
+ commands=(char *)malloc(10000*sizeof(char));
+ backup=commands; //since the pointer to commands will be lost, we acquire a pointer that will serve as backup.
+ strcpy(commands,opts);
+ for(i=0; ;i++, commands=NULL){
+ //breaks comma separated list of commands into specific commands.
+ command=strtok_r(commands,",",&saveptr);
+ if(command==NULL) break;
+// fprintf(stdout,"Command %d: %s\n",i,command);
+ //extracts name of command and value of command into operator[2] array.
+ for(j=0; j<2;j++,command=NULL){
+ operator[j]=strtok_r(command,"=",&saveopptr);
+ if(operator[j]==NULL) break;
+// fprintf(stdout," ---> Operator %d: %s\n",j,operator[j]);
+ }
+ //1. check: must have 2 operators.
+ if(j!=2) fatal("Error. Command line tape options are not formatted properly",1);
+
+ // cfg_setstr(cfg,operator[0],operator[1]);
+ cmdline_to_tape(cfg,operator[0],operator[1]);
+ //2. check: must be named properly.
+ //3. check: must be of right format (integer, double, string, ...)
+
+ }
+ free(backup);
+ return TS_SUCCESS;
+}
+
+
+ts_bool cmdline_to_tape(cfg_t *cfg, char *key, char *val){
+
+ cfg_opt_t *cfg_opt=cfg_getopt(cfg,key);
+ if(cfg_opt==NULL) fatal("Commandline tape option not recognised",1); //return TS_FAIL;
+ switch (cfg_opt->type){
+ case CFGT_INT:
+ cfg_setint(cfg,key,atol(val));
+ break;
+ case CFGT_FLOAT:
+ cfg_setfloat(cfg,key,atof(val));
+ break;
+/* case CFGT_BOOL:
+ cfg_setbool(cfg,operator[0],operator[1]);
+ break; */
+ case CFGT_STR:
+ cfg_setstr(cfg,key,val);
+ break;
+ default:
+ break;
+
+ }
+ return TS_SUCCESS;
+}
+
+
ts_bool read_geometry_file(char *fname, ts_vesicle *vesicle){
FILE *fh;
--
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