From 6c274defd904dedd6cb89c002f5eeced6c079d47 Mon Sep 17 00:00:00 2001 From: Samo Penic <samo.penic@gmail.com> Date: Tue, 11 Dec 2018 11:42:22 +0000 Subject: [PATCH] Added stretching variables --- src/io.c | 116 +++++++++++++++++++++++++++++++++++++++++++++++++++++++--- 1 files changed, 110 insertions(+), 6 deletions(-) diff --git a/src/io.c b/src/io.c index 47ca73b..c6a35cb 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); @@ -820,7 +821,7 @@ 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; @@ -862,7 +863,7 @@ 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)+vesicle->tlist->n); - 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\">"); for(i=0;i<vlist->n;i++){ fprintf(fh,"%u ",vtx[i]->idx); } @@ -887,7 +888,92 @@ } 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"); + fprintf(fh,"</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n"); @@ -1067,6 +1153,7 @@ 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), @@ -1088,18 +1175,33 @@ 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), +/* Variables related to plane confinement */ + CFG_INT("plane_confinement_switch", 0, CFGF_NONE), + CFG_FLOAT("plane_d", 15, CFGF_NONE), + CFG_FLOAT("plane_F", 1000, CFGF_NONE), +/* Variables related to stretching */ + CFG_FLOAT("stretchswitch", 0, CFGF_NONE), + CFG_FLOAT("xkA0",0,CFGF_NONE), CFG_END() }; cfg_t *cfg; ts_uint retval; cfg = cfg_init(opts, 0); retval=cfg_parse_buf(cfg, buffer); + tape->plane_confinement_switch=cfg_getint(cfg,"plane_confinement_switch"); + tape->plane_d=cfg_getfloat(cfg,"plane_d"); + tape->plane_F=cfg_getfloat(cfg,"plane_F"); + if(retval==CFG_FILE_ERROR){ fatal("No tape file.",100); } @@ -1128,6 +1230,8 @@ 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. -- Gitblit v1.9.3