From 41637ae4c538b5f11b41dacf6f941479e7a5ff00 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Fri, 06 Jun 2014 09:48:41 +0000
Subject: [PATCH] CV bug fix. Changes in constant volume: verifying the neightbour distances and removed preliminary contraints check. Seems to work now.
---
src/io.c | 278 ++++++++++++++++++++++++++++++++++++++++++++++++------
1 files changed, 244 insertions(+), 34 deletions(-)
diff --git a/src/io.c b/src/io.c
index d4a9cc4..3fecef5 100644
--- a/src/io.c
+++ b/src/io.c
@@ -36,6 +36,8 @@
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*/
@@ -118,6 +120,43 @@
}
}
+
+ /*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
@@ -131,7 +170,8 @@
*/
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;
@@ -142,6 +182,20 @@
ts_vesicle *restore_state(ts_uint *iteration){
ts_uint i,j,k;
FILE *fh=fopen("dump.bin","rb");
+
+ struct stat sb;
+ if (stat("dump.bin", &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;
@@ -166,6 +220,9 @@
/* 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 */
@@ -308,6 +365,61 @@
}
}
+ /*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];
+ }
+ }
+
// recreating space for cells //
vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
retval=fread(vesicle->clist, sizeof(ts_cell_list), 1,fh);
@@ -317,6 +429,9 @@
vesicle->clist->cell[i]->idx=i+1; // We enumerate cells! Probably never required!
}
+//recreating stored tape information//
+ 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);
@@ -326,9 +441,14 @@
ts_bool parse_args(int argc, char **argv){
- int c, retval;
- DIR *dir;
- path[0]=0;
+ 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");
+ FILE *file;
+
while (1)
{
static struct option long_options[] =
@@ -338,13 +458,13 @@
{"tape", no_argument, 0, 't'},
{"output-file", required_argument, 0, 'o'},
{"directory", required_argument, 0, 'd'},
- {"dump-file", required_argument,0, 'f'},
+ {"dump-filename", 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",
+ c = getopt_long (argc, argv, "d:f:o:t:",
long_options, &option_index);
/* Detect the end of the options. */
@@ -365,46 +485,56 @@
case 't':
//check if tape exists. If not, fail immediately.
- puts ("option -t\n");
+ if (stat(optarg, &sb) == -1) {
+ ts_fprintf(stderr,"Tape '%s' does not exist!\n",optarg);
+ fatal("Please select correct tape",1);
+ } else {
+ strcpy(command_line_args.tape_fullfilename,optarg);
+ }
break;
case 'o':
//set filename of master output file
- printf ("option -o with value `%s'\n", optarg);
- break;
+ if ((file = fopen(optarg, "w")) == NULL) {
+ fprintf(stderr,"Could not create output file!\n");
+ fatal("Please specify correct output file",1);
+
+ } else {
+ fclose(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);
- dir = opendir(optarg);
- if (dir)
- {
- /* Directory exists. */
- closedir(dir);
- }
- else if (ENOENT == errno)
- {
- /* Directory does not exist. */
+ 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);
+ 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);
+ //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);
}
- ts_fprintf(stdout,"\n*** Using output directory: %s\n\n", optarg);
-// sprintf(path,"%s", optarg);
- strcpy(path, optarg);
- // ts_fprintf(stdout,"ok!\n");
-
+ strcpy(command_line_args.path, optarg);
break;
case 'f':
//check if dump file specified exists. Defaults to dump.bin
+ if ((file = fopen(optarg, "w")) == NULL) {
+ fprintf(stderr,"Could not create dump file!\n");
+ fatal("Please specify correct dump file",1);
+
+ } else {
+ fclose(file);
+ }
+ strcpy(command_line_args.dump_fullfilename, optarg);
break;
case '?':
@@ -635,8 +765,8 @@
/* 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;
@@ -644,8 +774,17 @@
poly=1;
}
}
+
+ 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 <UnstructuredGrid>\n");
- fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+monono*polyno, blist->n+monono*polyno);
+ 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);
@@ -655,6 +794,16 @@
poly_idx=vlist->n;
for(i=0;i<vesicle->poly_list->n;i++){
for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
+ fprintf(fh,"%u ", poly_idx);
+ }
+ }
+ }
+ //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);
}
}
@@ -669,6 +818,14 @@
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 );
+ }
+ }
+ }
+ //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,"%e %e %e\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 );
}
}
}
@@ -691,14 +848,26 @@
}
+ //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 ");
}
@@ -753,6 +922,39 @@
+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){
// 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));
@@ -768,11 +970,18 @@
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_INT("nfil",&tape->nfil),
+ CFG_SIMPLE_INT("nfono",&tape->nfono),
+ CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
+ 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_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),
@@ -785,6 +994,7 @@
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;
--
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