From 0634b97e436e480b203a22e1113c473d3ae4d281 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Tue, 06 Dec 2016 13:35:11 +0000
Subject: [PATCH] Merge branch 'nirgov' into HEAD
---
src/io.c | 150 +++++++++++++++++++++++++++++++++++++++++++++++--
1 files changed, 142 insertions(+), 8 deletions(-)
diff --git a/src/io.c b/src/io.c
index 2461de5..16ab2c8 100644
--- a/src/io.c
+++ b/src/io.c
@@ -531,8 +531,8 @@
case '?':
/* getopt_long already printed an error message. */
-
- ts_fprintf(stderr,"\n\nhere comes the help.\n\n");
+ print_help(stdout);
+//ts_fprintf(stderr,"\n\nhere comes the help.\n\n");
fatal("Ooops, read help first",1);
break;
@@ -598,6 +598,32 @@
free(buffer);
return TS_SUCCESS;
+}
+
+
+ts_bool print_help(FILE *fd){
+ fprintf(fd,"TRISURF-NG v. %s, compiled on: %s %s.\n", TS_VERSION, __DATE__, __TIME__);
+ fprintf(fd,"Programming done by: Samo Penic and Miha Fosnaric\n");
+ fprintf(fd,"Released under terms of GPLv3\n\n");
+
+ fprintf(fd, "Invoking trisurf-ng without any flags results in default operation. Program reads 'tape' file and 'dump.bin' binary representation of the vesicle from disk and continues the simulation where it was aborted (as specified in 'dump.bin').\n\n");
+ fprintf(fd,"If 'tape' has different values than binary dump, those are used (if possible -- some values in tape, such as nshell cannot be modified).\n\n\n");
+ fprintf(fd,"However, if dump.bin is not present, user is notified to specify --force-from-tape flag. The vesicle will be created from specifications in tape.\n\n\n");
+ 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).\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\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;
}
@@ -794,7 +820,7 @@
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;
@@ -835,8 +861,12 @@
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, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+monono*polyno+fonono*filno, blist->n+monono*polyno+filno*(fonono-1)+vesicle->tlist->n);
+<<<<<<< HEAD
fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">");
+=======
+ fprintf(fh,"<PointData Scalars=\"vertices_idx\">\n<DataArray type=\"Int64\" Name=\"vertices_idx\" format=\"ascii\">");
+>>>>>>> nirgov
for(i=0;i<vlist->n;i++){
fprintf(fh,"%u ",vtx[i]->idx);
}
@@ -860,7 +890,99 @@
}
}
- 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");
+<<<<<<< HEAD
+=======
+ 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");
+
+
+>>>>>>> nirgov
+
+ 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);
}
@@ -911,17 +1033,24 @@
}
}
-
+ 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;
@@ -1030,6 +1159,7 @@
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),
@@ -1057,6 +1187,10 @@
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;
--
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