From 7ec6fb63c690080d0624c7bf138d0fd84fe7664e Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Tue, 15 May 2018 16:11:14 +0000
Subject: [PATCH] First working version, not debugged and energy assigned to vesicles on timesteps
---
src/io.c | 166 +++++++++++++++++++++++++++++++++++++++++++++++++++----
1 files changed, 154 insertions(+), 12 deletions(-)
diff --git a/src/io.c b/src/io.c
index 7cb0d62..83bb26d 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>
@@ -423,7 +424,7 @@
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->clist->max_occupancy=16;
// 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);
@@ -612,11 +613,17 @@
fprintf(fd,"Flags:\n\n");
fprintf(fd,"--force-from-tape\t\t makes initial shape of the vesicle from tape. Ignores already existing binary dump and possible simulation results.\n");
fprintf(fd,"--restore-from-vtk\t\t VTK's file ending with '.vtu' are preferred way to make state snapshots for restoration. With this flag the restoration of the vesicle from vtk is possible. The simulation will continue if hidden '.status' file with last iteration done is present. Otherwise it will start simulation from timestep 0.\n");
- fprintf(fd,"--reset-iteration-count\t\t starts simulation from the beginning (using binary dump or tape).\n");
+ fprintf(fd,"--reset-iteration-count\t\t starts simulation from the beginning (using binary dump).\n");
fprintf(fd,"--tape (or -t)\t\t specifies tape filename. For --force-from-tape and restoring from binary dump. Defaults to 'tape'.\n");
fprintf(fd,"--version (or -v)\t\t Prints version information.\n");
fprintf(fd,"--output-file (or -o)\t\t Specifies filename of .PVD file. Defaults to 'output.pvd'\n");
- fprintf(fd,"--dump-filename (or -f)\t\t specifies filename for binary dump&restore. Defaults to 'dump.bin'\n\n");
+ fprintf(fd,"--dump-filename (or -f)\t\t specifies filename for binary dump&restore. Defaults to 'dump.bin'\n\n\n");
+ fprintf(fd,"Examples:\n\n");
+ fprintf(fd,"trisurf --force-from-tape\n");
+ fprintf(fd,"trisurf --reset-iteration-count\n");
+ fprintf(fd,"trisurf --restore-from-vtk filename.vtu\n");
+ fprintf(fd,"\n\n");
+
return TS_SUCCESS;
}
@@ -814,11 +821,12 @@
return TS_SUCCESS;
}
-ts_bool write_vertex_xml_file(ts_vesicle *vesicle, ts_uint timestepno){
+ts_bool write_vertex_xml_file(ts_vesicle *vesicle, ts_uint timestepno, ts_cluster_list *cstlist){
ts_vertex_list *vlist=vesicle->vlist;
ts_bond_list *blist=vesicle->blist;
ts_vertex **vtx=vlist->vtx;
ts_uint i,j;
+ ts_double senergy=0.0;
char filename[10000];
char just_name[255];
FILE *fh;
@@ -855,8 +863,8 @@
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\">");
+ fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+monono*polyno+fonono*filno, blist->n+monono*polyno+filno*(fonono-1)+vesicle->tlist->n);
+ fprintf(fh,"<PointData Scalars=\"vertices_idx\">\n<DataArray type=\"Int64\" Name=\"vertices_idx\" format=\"ascii\">");
for(i=0;i<vlist->n;i++){
fprintf(fh,"%u ",vtx[i]->idx);
}
@@ -880,7 +888,125 @@
}
}
- fprintf(fh,"</DataArray>\n</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
+ fprintf(fh,"</DataArray>\n");
+ if(cstlist!=NULL){
+ fprintf(fh,"<DataArray type=\"Int64\" Name=\"vertices_in_cluster\" format=\"ascii\">");
+ for(i=0;i<vlist->n;i++){
+ if(vtx[i]->cluster!=NULL){
+ fprintf(fh,"%u ",vtx[i]->cluster->nvtx);
+ } else {
+ fprintf(fh,"-1 ");
+ }
+ }
+ //polymeres
+ if(poly){
+ 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,"-1 ");
+ }
+ }
+ }
+ //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,"-1 ");
+ }
+ }
+ }
+
+ fprintf(fh,"</DataArray>\n");
+
+
+ }
+
+ //here comes additional data as needed. Currently only spontaneous curvature
+ fprintf(fh,"<DataArray type=\"Float64\" Name=\"spontaneous_curvature\" format=\"ascii\">");
+ for(i=0;i<vlist->n;i++){
+ fprintf(fh,"%.17e ",vtx[i]->c);
+ }
+ //polymeres
+ if(poly){
+ 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,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->c);
+ }
+ }
+ }
+ //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,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->c);
+ }
+ }
+ }
+ fprintf(fh,"</DataArray>\n");
+
+ //here comes additional data. Energy!
+ fprintf(fh,"<DataArray type=\"Float64\" Name=\"bending_energy\" format=\"ascii\">");
+ for(i=0;i<vlist->n;i++){
+ fprintf(fh,"%.17e ",vtx[i]->energy*vtx[i]->xk);
+ }
+ //polymeres
+ if(poly){
+ 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,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->energy* vesicle->poly_list->poly[i]->k);
+ }
+ }
+ }
+ //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,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->energy* vesicle->filament_list->poly[i]->k);
+ }
+ }
+ }
+ fprintf(fh,"</DataArray>\n");
+ if(vesicle->tape->stretchswitch==1){
+ fprintf(fh,"<DataArray type=\"Float64\" Name=\"stretching_energy\" format=\"ascii\">");
+ for(i=0;i<vlist->n;i++){
+ senergy=0.0;
+ for(j=0;j<vtx[i]->tristar_no;j++){
+ senergy+=vtx[i]->tristar[j]->energy;
+ }
+ fprintf(fh,"%.17e ",senergy);
+ }
+ //polymeres
+ if(poly){
+ 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,"%.17e ", 0.0);
+ }
+ }
+ }
+ //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,"%.17e ", 0.0);
+ }
+ }
+ }
+ fprintf(fh,"</DataArray>\n");
+ }
+
+
+ fprintf(fh,"</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,"%.17e %.17e %.17e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
}
@@ -931,17 +1057,24 @@
}
}
-
+ for(i=0;i<vesicle->tlist->n;i++){
+ fprintf(fh,"%u %u %u\n", vesicle->tlist->tria[i]->vertex[0]->idx, vesicle->tlist->tria[i]->vertex[1]->idx, vesicle->tlist->tria[i]->vertex[2]->idx);
+ }
fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
for (i=2;i<(blist->n+monono*polyno+(fonono-1)*filno)*2+1;i+=2){
fprintf(fh,"%u ",i);
}
+ for(j=i+1;j<i+3*(vesicle->tlist->n);j+=3){ //let's continue counting from where we left of
+ fprintf(fh,"%u ", j);
+ }
fprintf(fh,"\n");
fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
- for (i=0;i<blist->n+monono*polyno+fonono*filno;i++){
+ for (i=0;i<blist->n+monono*polyno+(fonono-1)*filno;i++){
fprintf(fh,"3 ");
}
-
+ for(i=0;i<vesicle->tlist->n;i++){
+ fprintf(fh,"5 ");
+ }
fprintf(fh,"</DataArray>\n</Cells>\n</Piece>\n</UnstructuredGrid>\n</VTKFile>\n");
fclose(fh);
return TS_SUCCESS;
@@ -1050,6 +1183,7 @@
CFG_SIMPLE_INT("nmono", &tape->nmono),
CFG_SIMPLE_INT("nfil",&tape->nfil),
CFG_SIMPLE_INT("nfono",&tape->nfono),
+ CFG_SIMPLE_INT("internal_poly",&tape->internal_poly),
CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
CFG_SIMPLE_FLOAT("R_nucleusX",&tape->R_nucleusX),
CFG_SIMPLE_FLOAT("R_nucleusY",&tape->R_nucleusY),
@@ -1061,6 +1195,8 @@
CFG_SIMPLE_INT("constvolswitch",&tape->constvolswitch),
CFG_SIMPLE_INT("constareaswitch",&tape->constareaswitch),
CFG_SIMPLE_FLOAT("constvolprecision",&tape->constvolprecision),
+ CFG_SIMPLE_INT("stretchswitch",&tape->stretchswitch),
+ CFG_SIMPLE_FLOAT("xkA0",&tape->xkA0),
CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
CFG_SIMPLE_FLOAT("xi",&tape->xi),
@@ -1071,12 +1207,16 @@
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_BOOL("quiet",(cfg_bool_t *)&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_SIMPLE_INT("number_of_vertices_with_c0", &tape->number_of_vertices_with_c0),
+ CFG_SIMPLE_FLOAT("c0",&tape->c0),
+ CFG_SIMPLE_FLOAT("w",&tape->w),
+ CFG_SIMPLE_FLOAT("F",&tape->F),
CFG_END()
};
cfg_t *cfg;
@@ -1111,6 +1251,8 @@
ts_bool getcmdline_tape(cfg_t *cfg, char *opts){
char *commands, *backup, *saveptr, *saveopptr, *command, *operator[2];
+ operator[0]=0;
+ operator[1]=0;
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.
--
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