From 3c6e26add4550990dc81446b2aea00a6e4d2feeb Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Wed, 16 Oct 2019 09:02:16 +0000
Subject: [PATCH] Cleaning up io.c
---
src/Makefile.am | 10
src/main.c | 64 ---
/dev/null | 90 -----
src/timestep.c | 2
src/io.c | 703 -------------------------------------------
src/io.h | 50 --
6 files changed, 13 insertions(+), 906 deletions(-)
diff --git a/src/Makefile.am b/src/Makefile.am
index c7e3c88..3e55232 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,15 +1,15 @@
-bin_PROGRAMS = trisurf tsmeasure tspoststat
+bin_PROGRAMS = trisurf
trisurf_SOURCES = main.c
GITVERSION:=$(shell git --no-pager describe --tags --always --dirty)
AM_CFLAGS = -Wall -Werror -DTS_VERSION=\"$(GITVERSION)\" -fgnu89-inline -Wno-error=date-time
AM_CPPFLAGS = ${libxml2_CFLAGS} -fgnu89-inline
trisurf_LDADD = libtrisurf.la ${libcurl_LIBS} ${libxml2_LIBS}
-tsmeasure_SOURCES = tsmeasure.c
-tsmeasure_LDADD = libtrisurf.la ${libcurl_LIBS} ${libxml2_LIBS}
+#tsmeasure_SOURCES = tsmeasure.c
+#tsmeasure_LDADD = libtrisurf.la ${libcurl_LIBS} ${libxml2_LIBS}
-tspoststat_SOURCES = tspoststat.c
-tspoststat_LDADD = libtrisurf.la ${libcurl_LIBS} ${libxml2_LIBS}
+#tspoststat_SOURCES = tspoststat.c
+#tspoststat_LDADD = libtrisurf.la ${libcurl_LIBS} ${libxml2_LIBS}
#------------- LIBS ----------
diff --git a/src/io.c b/src/io.c
index 30bd4d6..482c0a5 100644
--- a/src/io.c
+++ b/src/io.c
@@ -1,4 +1,3 @@
-
/* vim: set ts=4 sts=4 sw=4 noet : */
#include "general.h"
#include<stdio.h>
@@ -18,421 +17,6 @@
#include <dirent.h>
#include <errno.h>
#include <snapshot.h>
-/** DUMP STATE TO DISK DRIVE **/
-
-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(command_line_args.dump_fullfilename,"wb");
-
- /* dump vesicle */
- 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 */
- fwrite(vesicle->blist, sizeof(ts_bond_list),1,fh);
- /* dump triangle list */
- fwrite(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
- /* dump cell list */
- 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*/
- for(i=0;i<vesicle->vlist->n;i++){
- fwrite(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
- /* dump pointer offsets for:
- neigh
- bond
- tria
- cell is ignored
- */
- for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
- fwrite(&vesicle->vlist->vtx[i]->neigh[j]->idx,sizeof(ts_uint),1,fh);
- }
- for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
- fwrite(&vesicle->vlist->vtx[i]->bond[j]->idx,sizeof(ts_uint),1,fh);
- }
- for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
- fwrite(&vesicle->vlist->vtx[i]->tristar[j]->idx,sizeof(ts_uint),1,fh);
- }
- }
-
- /*dump bonds*/
- for(i=0;i<vesicle->blist->n;i++){
- fwrite(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
- /* dump pointer offsets for vtx1 and vtx2 */
- //off=(ts_ulong)(vesicle->blist->bond[i]->vtx1-vesicle->vlist->vtx[0]);
- fwrite(&vesicle->blist->bond[i]->vtx1->idx,sizeof(ts_uint),1,fh);
- //off=(ts_ulong)(vesicle->blist->bond[i]->vtx2-vesicle->vlist->vtx[0]);
- fwrite(&vesicle->blist->bond[i]->vtx2->idx,sizeof(ts_uint),1,fh);
- }
-
- /*dump triangles*/
- for(i=0;i<vesicle->tlist->n;i++){
- fwrite(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
- /* dump pointer offsets for vertex */
- fwrite(&vesicle->tlist->tria[i]->vertex[0]->idx,sizeof(ts_uint),1,fh);
- fwrite(&vesicle->tlist->tria[i]->vertex[1]->idx,sizeof(ts_uint),1,fh);
- fwrite(&vesicle->tlist->tria[i]->vertex[2]->idx,sizeof(ts_uint),1,fh);
- /* dump pointer offsets for neigh */
- for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
- fwrite(&vesicle->tlist->tria[i]->neigh[j]->idx,sizeof(ts_uint),1,fh);
- }
- }
-
-
- /*dump polymeres */
- for(i=0;i<vesicle->poly_list->n;i++){
- fwrite(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
- fwrite(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
- fwrite(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
- }
-
- /* dump poly vertex(monomer) list*/
- for(i=0;i<vesicle->poly_list->n;i++){
- for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
- fwrite(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
- /* dump offset for neigh and bond */
- for(k=0;k<vesicle->poly_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->poly_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh);
- }
- for(k=0;k<vesicle->poly_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->poly_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh);
- }
- }
- // grafted vtx on vesicle data dump
- fwrite(&vesicle->poly_list->poly[i]->grafted_vtx->idx, sizeof(ts_uint),1,fh);
- }
- /* dump poly bonds between monomers list*/
- for(i=0;i<vesicle->poly_list->n;i++){
- for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
- fwrite(vesicle->poly_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->poly_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->poly_list->poly[i]->blist->bond[j]->vtx2->idx,sizeof(ts_uint),1,fh);
- }
- }
-
-
- /*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
- blist->bond
- tlist->tria
- clist->cell
- poly_list->poly
- and for each poly:
- poly_list->poly->vtx
- poly_list->poly->bond
-*/
-
-// 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_uint *iteration){
- ts_uint i,j,k;
- 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)-sizeof(ts_double),1,fh);
-// fprintf(stderr,"was here! %e\n",vesicle->dmax);
-
- /* restore vertex list */
- vesicle->vlist=(ts_vertex_list *)malloc(sizeof(ts_vertex_list));
- retval=fread(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
- /* restore bond list */
- vesicle->blist=(ts_bond_list *)malloc(sizeof(ts_bond_list));
- retval=fread(vesicle->blist, sizeof(ts_bond_list),1,fh);
- /* restore triangle list */
- vesicle->tlist=(ts_triangle_list *)malloc(sizeof(ts_triangle_list));
- retval=fread(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
- /* restore cell list */
- vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
- retval=fread(vesicle->clist, sizeof(ts_cell_list),1,fh);
- /* 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 */
- vesicle->blist->bond=(ts_bond **)calloc(vesicle->blist->n,sizeof(ts_bond *));
- for(i=0;i<vesicle->blist->n;i++){
- vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond));
- }
-/* prerequisity. Triangles must be malloced before vertexes are recreated */
- vesicle->tlist->tria=(ts_triangle **)calloc(vesicle->tlist->n,sizeof(ts_triangle *));
- for(i=0;i<vesicle->tlist->n;i++){
- vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
-}
-/* prerequisity. Vertices must be malloced before vertexes are recreated */
- vesicle->vlist->vtx=(ts_vertex **)calloc(vesicle->vlist->n,sizeof(ts_vertex *));
- for(i=0;i<vesicle->vlist->n;i++){
- vesicle->vlist->vtx[i]=(ts_vertex *)malloc(sizeof(ts_vertex));
- }
- /*restore vertices*/
- for(i=0;i<vesicle->vlist->n;i++){
- retval=fread(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
- /*restore neigh, bond, tristar. Ignoring cell */
- vesicle->vlist->vtx[i]->neigh=(ts_vertex **)calloc(vesicle->vlist->vtx[i]->neigh_no, sizeof(ts_vertex *));
- for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
- retval=fread(&idx,sizeof(ts_uint),1,fh);
- vesicle->vlist->vtx[i]->neigh[j]=vesicle->vlist->vtx[idx];
- }
- vesicle->vlist->vtx[i]->bond=(ts_bond **)calloc(vesicle->vlist->vtx[i]->bond_no, sizeof(ts_bond *));
- for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
- retval=fread(&idx,sizeof(ts_uint),1,fh);
-/* pointer can be assigned only when list of bonds is fully initialized in memory. Thus bondlist popularization must be done before vertex can reference to it */
- vesicle->vlist->vtx[i]->bond[j]=vesicle->blist->bond[idx];
- }
-
- vesicle->vlist->vtx[i]->tristar=(ts_triangle **)calloc(vesicle->vlist->vtx[i]->tristar_no, sizeof(ts_triangle *));
- for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
- retval=fread(&idx,sizeof(ts_uint),1,fh);
-/* same comment as above */
- vesicle->vlist->vtx[i]->tristar[j]=vesicle->tlist->tria[idx];
- }
-
- }
-
- /*restore bonds*/
- // vesicle->blist->bond=(ts_bond **)calloc(vesicle->blist->n,sizeof(ts_bond *)); // done before.
- for(i=0;i<vesicle->blist->n;i++){
- // vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond)); //done before.
- retval=fread(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
- /* restore vtx1 and vtx2 */
- retval=fread(&idx,sizeof(ts_uint),1,fh);
- vesicle->blist->bond[i]->vtx1=vesicle->vlist->vtx[idx];
- retval=fread(&idx,sizeof(ts_uint),1,fh);
- vesicle->blist->bond[i]->vtx2=vesicle->vlist->vtx[idx];
- }
-
- /*restore triangles*/
-// vesicle->tlist->tria=(ts_triangle **)calloc(vesicle->tlist->n,sizeof(ts_triangle *)); // done before
- for(i=0;i<vesicle->tlist->n;i++){
- // vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle)); // done before
- retval=fread(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
- /* restore pointers for vertices */
- retval=fread(&idx,sizeof(ts_uint),1,fh);
- vesicle->tlist->tria[i]->vertex[0]=vesicle->vlist->vtx[idx];
- retval=fread(&idx,sizeof(ts_uint),1,fh);
- vesicle->tlist->tria[i]->vertex[1]=vesicle->vlist->vtx[idx];
- retval=fread(&idx,sizeof(ts_uint),1,fh);
- vesicle->tlist->tria[i]->vertex[2]=vesicle->vlist->vtx[idx];
- /* restore pointers for neigh */
- vesicle->tlist->tria[i]->neigh=(ts_triangle **)malloc(vesicle->tlist->tria[i]->neigh_no*sizeof(ts_triangle *));
- for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
- retval=fread(&idx,sizeof(ts_uint),1,fh);
- vesicle->tlist->tria[i]->neigh[j]=vesicle->tlist->tria[idx];
- }
-
- }
-
- /*restore cells */
-/*TODO: do we need to recalculate cells here? */
-/* vesicle->clist->cell=(ts_cell **)malloc(vesicle->clist->cellno*sizeof(ts_cell *));
- for(i=0;i<vesicle->clist->cellno;i++){
- vesicle->clist->cell[i]=(ts_cell *)malloc(sizeof(ts_cell));
- retval=fread(vesicle->clist->cell[i],sizeof(ts_cell),1,fh);
- }
-*/
- /*restore polymeres */
- vesicle->poly_list->poly = (ts_poly **)calloc(vesicle->poly_list->n,sizeof(ts_poly *));
- for(i=0;i<vesicle->poly_list->n;i++){
- vesicle->poly_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
- retval=fread(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
- vesicle->poly_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
- retval=fread(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
- vesicle->poly_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
- retval=fread(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
- /* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
- vesicle->poly_list->poly[i]->vlist->vtx=(ts_vertex **)calloc(vesicle->poly_list->poly[i]->vlist->n,sizeof(ts_vertex *));
- vesicle->poly_list->poly[i]->blist->bond=(ts_bond **)calloc(vesicle->poly_list->poly[i]->blist->n,sizeof(ts_bond *));
- for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
- vesicle->poly_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
- }
- for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
- vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
- }
-
- }
-
-
- /* restore poly vertex(monomer) list*/
- for(i=0;i<vesicle->poly_list->n;i++){
- for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
- retval=fread(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
-
- /* restore neigh and bonds */
- vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh=(ts_vertex **)calloc(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no, sizeof(ts_vertex *));
- for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
- retval=fread(&idx,sizeof(ts_uint),1,fh);
- vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->poly_list->poly[i]->vlist->vtx[idx];
- }
- vesicle->poly_list->poly[i]->vlist->vtx[j]->bond=(ts_bond **)calloc(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no, sizeof(ts_bond *));
- for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
- retval=fread(&idx,sizeof(ts_uint),1,fh);
- vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->poly_list->poly[i]->blist->bond[idx];
- }
-
- }
- /* restore grafted vtx on vesicle and grafted_poly */
- retval=fread(&idx,sizeof(ts_uint),1,fh);
- vesicle->vlist->vtx[idx]->grafted_poly=vesicle->poly_list->poly[i];
- vesicle->poly_list->poly[i]->grafted_vtx=vesicle->vlist->vtx[idx];
- }
-
- /* restore poly bonds between monomers list*/
- for(i=0;i<vesicle->poly_list->n;i++){
- for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
- // vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
- retval=fread(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
- /* restore vtx1 and vtx2 */
- retval=fread(&idx,sizeof(ts_uint),1,fh);
- vesicle->poly_list->poly[i]->blist->bond[j]->vtx1=vesicle->poly_list->poly[i]->vlist->vtx[idx];
- retval=fread(&idx,sizeof(ts_uint),1,fh);
- vesicle->poly_list->poly[i]->blist->bond[j]->vtx2=vesicle->poly_list->poly[i]->vlist->vtx[idx];
- }
- }
-
- /*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=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);
- if(retval);
- fclose(fh);
- return vesicle;
-}
-
ts_bool parse_args(int argc, char **argv){
@@ -624,200 +208,6 @@
fprintf(fd,"trisurf --restore-from-vtk filename.vtu\n");
fprintf(fd,"\n\n");
- return TS_SUCCESS;
-}
-
-
-
-ts_bool print_vertex_list(ts_vertex_list *vlist){
- ts_uint i;
- printf("Number of vertices: %u\n",vlist->n);
- for(i=0;i<vlist->n;i++){
- printf("%u: %f %f %f\n",
-vlist->vtx[i]->idx,vlist->vtx[i]->x, vlist->vtx[i]->y, vlist->vtx[i]->z);
- }
- return TS_SUCCESS;
-}
-
-ts_bool print_vertex_neighbours(ts_vertex_list *vlist){
- ts_uint i,j;
- ts_vertex **vtx=vlist->vtx;
- printf("Vertex id(neigh no): (neighvertex coord) (neighvertex coord) ...\n");
- for(i=0;i<vlist->n;i++){
- printf("%u(%u): ",vtx[i]->idx,vtx[i]->neigh_no);
- for(j=0;j<vtx[i]->neigh_no;j++){
- printf("(%f,%f,%f)",vtx[i]->neigh[j]->x,
-vtx[i]->neigh[j]->y,vtx[i]->neigh[j]->z);
- }
- printf("\n");
- }
-
-return TS_SUCCESS;
-}
-
-ts_bool write_vertex_fcompat_file(ts_vertex_list *vlist,ts_char *filename){
- ts_vertex **vtx=vlist->vtx;
- ts_uint i;
- FILE *fh;
-
- fh=fopen(filename, "w");
- if(fh==NULL){
- err("Cannot open file %s for writing");
- return TS_FAIL;
- }
- for(i=0;i<vlist->n;i++)
- fprintf(fh," %E\t%E\t%E\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
-
- fclose(fh);
-return TS_SUCCESS;
-}
-
-
-ts_bool fprint_vertex_list(FILE *fh,ts_vertex_list *vlist){
- ts_uint i,j;
- for(i=0;i<vlist->n;i++){
- fprintf(fh," %.17E\t%.17E\t%.17E\t%u\n",vlist->vtx[i]->x,
- vlist->vtx[i]->y, vlist->vtx[i]->z,
- vlist->vtx[i]->neigh_no);
- for(j=0;j<vlist->vtx[i]->neigh_no;j++){
- fprintf(fh,"\t%u",(ts_uint)(vlist->vtx[i]->neigh[j]->idx));
- //-vlist->vtx+1));
- }
- fprintf(fh,"\n");
- }
- return TS_SUCCESS;
-}
-
-ts_bool fprint_tristar(FILE *fh, ts_vesicle *vesicle){
- ts_uint i,j;
- for(i=0;i<vesicle->vlist->n;i++){
- fprintf(fh,"\t%u",vesicle->vlist->vtx[i]->tristar_no);
- for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
- fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist->vtx[i]->tristar[j]->idx));//-vesicle->tlist->tria+1));
- }
- fprintf(fh,"\n");
- }
- return TS_SUCCESS;
-}
-
-ts_bool fprint_triangle_list(FILE *fh, ts_vesicle *vesicle){
- ts_triangle_list *tlist=vesicle->tlist;
- ts_uint i,j;
- for(i=0;i<tlist->n;i++){
- fprintf(fh,"\t%u",tlist->tria[i]->neigh_no);
- for(j=0;j<tlist->tria[i]->neigh_no;j++){
- fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->neigh[j]->idx));//-tlist->tria+1));
- }
- fprintf(fh,"\n");
- for(j=0;j<3;j++){
- fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->vertex[j]->idx));//-vesicle->vlist->vtx+1));
- }
- fprintf(fh,"\n");
- fprintf(fh,"%.17E\t%.17E\t%.17E\n",tlist->tria[i]->xnorm,
-tlist->tria[i]->ynorm,tlist->tria[i]->znorm);
- fprintf(fh,"0.00000000000000000\n0.00000000000000000\n");
- }
- return TS_SUCCESS;
-}
-
-ts_bool fprint_vertex_data(FILE *fh,ts_vertex_list *vlist){
- ts_uint i,j;
- for(i=0;i<vlist->n;i++){
- 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]->bond_no;j++){
- fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual);
- }
- fprintf(fh,"\n");
- for(j=0;j<vlist->vtx[i]->bond_no;j++){
- fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
- }
- fprintf(fh,"\n");
- }
- return TS_SUCCESS;
-}
-
-ts_bool fprint_bonds(FILE *fh,ts_vesicle *vesicle){
- ts_uint i;
- for(i=0;i<vesicle->blist->n;i++){
- fprintf(fh,"\t%u\t%u\n",(ts_uint)(vesicle->blist->bond[i]->vtx1->idx),
-//-vesicle->vlist->vtx+1),
- (ts_uint)(vesicle->blist->bond[i]->vtx2->idx));
- //-vesicle->vlist.vtx+1));
- }
- return TS_SUCCESS;
-}
-
-
-ts_bool write_dout_fcompat_file(ts_vesicle *vesicle, ts_char *filename){
- FILE *fh;
- fh=fopen(filename, "w");
- if(fh==NULL){
- err("Cannot open file %s for writing");
- return TS_FAIL;
- }
- fprintf(fh,"%.17E\n%.17E\n",vesicle->stepsize,vesicle->dmax);
- fprint_vertex_list(fh,vesicle->vlist);
- fprint_tristar(fh,vesicle);
- fprint_triangle_list(fh,vesicle);
- fprint_vertex_data(fh,vesicle->vlist);
- fprint_bonds(fh,vesicle);
- fclose(fh);
- return TS_SUCCESS;
-}
-
-ts_bool read_tape_fcompat_file(ts_vesicle *vesicle, ts_char *filename){
- FILE *fh;
- char line[255];
- fh=fopen(filename, "r");
- if(fh==NULL){
- err("Cannot open file for reading... Nonexistant file?");
- return TS_FAIL;
- }
- ts_uint retval=1;
- while(retval!=EOF){
- retval=fscanf(fh,"%s",line);
-
- fprintf(stderr,"%s",line);
- }
- fclose(fh);
- return TS_SUCCESS;
-}
-
-ts_bool write_master_xml_file(ts_char *filename){
- FILE *fh;
- ts_char *i,*j;
- ts_uint tstep;
- ts_char *number;
- fh=fopen(filename, "w");
- if(fh==NULL){
- err("Cannot open file %s for writing");
- return TS_FAIL;
- }
-
- fprintf(fh,"<?xml version=\"1.0\"?>\n<VTKFile type=\"Collection\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n<Collection>");
- DIR *dir = opendir(command_line_args.path);
- if(dir){
- struct dirent *ent;
- tstep=0;
- while((ent = readdir(dir)) != NULL)
- {
- i=rindex(ent->d_name,'.');
- if(i==NULL) continue;
- if(strcmp(i+1,"vtu")==0){
- j=rindex(ent->d_name,'_');
- if(j==NULL) continue;
- number=strndup(j+1,j-i);
- fprintf(fh,"<DataSet timestep=\"%u\" group=\"\" part=\"0\" file=\"%s\"/>\n",atoi(number),ent->d_name);
- tstep++;
- free(number);
- }
- }
- }
- free(dir);
- fprintf(fh,"</Collection>\n</VTKFile>\n");
- fclose(fh);
return TS_SUCCESS;
}
@@ -1069,51 +459,6 @@
}
-ts_bool write_vertex_vtk_file(ts_vesicle *vesicle,ts_char *filename, ts_char *text){
- ts_vertex_list *vlist=vesicle->vlist;
- ts_bond_list *blist=vesicle->blist;
- ts_vertex **vtx=vlist->vtx;
- ts_uint i;
- FILE *fh;
-
- fh=fopen(filename, "w");
- if(fh==NULL){
- err("Cannot open file %s for writing");
- return TS_FAIL;
- }
- /* Here comes header of the file */
-// fprintf(stderr,"NSHELL=%u\n",nshell);
- fprintf(fh, "# vtk DataFile Version 2.0\n");
- /* TODO: Do a sanity check on text. Max 255 char, must not me \n terminated */
- fprintf(fh, "%s\n", text);
- fprintf(fh,"ASCII\n");
- fprintf(fh,"DATASET UNSTRUCTURED_GRID\n");
- fprintf(fh,"POINTS %u double\n", vlist->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,"CELLS %u %u\n",blist->n,3*blist->n);
- for(i=0;i<blist->n;i++){
- fprintf(fh,"2 %u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
- }
- fprintf(fh,"CELL_TYPES %u\n",blist->n);
- for(i=0;i<blist->n;i++)
- fprintf(fh,"3\n");
-
- fprintf(fh,"POINT_DATA %u\n", vlist->n);
- fprintf(fh,"SCALARS scalars long 1\n");
- fprintf(fh,"LOOKUP_TABLE default\n");
-
- for(i=0;i<vlist->n;i++)
- fprintf(fh,"%u\n",vtx[i]->idx);
-
- fclose(fh);
- return TS_SUCCESS;
-}
-
-
-
ts_bool write_pov_file(ts_vesicle *vesicle, char *filename){
FILE *fh;
ts_uint i;
@@ -1302,53 +647,5 @@
break;
}
- return TS_SUCCESS;
-}
-
-
-
-ts_bool read_geometry_file(char *fname, ts_vesicle *vesicle){
- FILE *fh;
- ts_uint i, nvtx,nedges,ntria;
- ts_uint vtxi1,vtxi2;
- float x,y,z;
- ts_vertex_list *vlist;
- fh=fopen(fname, "r");
- if(fh==NULL){
- err("Cannot open file for reading... Nonexistant file?");
- return TS_FAIL;
- }
- ts_uint retval;
- retval=fscanf(fh,"%u %u %u",&nvtx, &nedges, &ntria);
- vesicle->vlist=init_vertex_list(nvtx);
- vlist=vesicle->vlist;
- for(i=0;i<nvtx;i++){
- // fscanf(fh,"%F %F %F",&vlist->vtx[i]->x,&vlist->vtx[i]->y,&vlist->vtx[i]->z);
- retval=fscanf(fh,"%F %F %F",&x,&y,&z);
- vlist->vtx[i]->x=x;
- vlist->vtx[i]->y=y;
- vlist->vtx[i]->z=z;
- }
- for(i=0;i<nedges;i++){
- retval=fscanf(fh,"%u %u",&vtxi1,&vtxi2);
- bond_add(vesicle->blist,vesicle->vlist->vtx[vtxi1-1],vesicle->vlist->vtx[vtxi2-1]);
- }
- //TODO: neighbours from bonds,
- //TODO: triangles from neigbours
-
-// Don't need to read triangles. Already have enough data
- /*
- for(i=0;i<ntria;i++){
- retval=fscanf(fh,"%u %u %u", &bi1, &bi2, &bi3);
- vtxi1=vesicle->blist->vertex1->idx;
- vtxi2=vesicle->blist->vertex1->idx;
-
- }
- */
- if(retval);
- fclose(fh);
-
-
-
return TS_SUCCESS;
}
diff --git a/src/io.h b/src/io.h
index 6ca8331..16bacfb 100644
--- a/src/io.h
+++ b/src/io.h
@@ -27,53 +27,13 @@
-/** @brief Prints the position of vertices for the whole list
- *
- * The function is meant more or less as a debug tool, but can be used in production
- * environment aswell.
- * the output is in form of idx: x y z
- * @param *vlist is a structure holding information on vertex list.
- * @returns TS_SUCCESS on successful execution, TS_FAIL otherwise.
-*/
-
-ts_bool print_vertex_list(ts_vertex_list *vlist);
-
-/** @brief Prints the neighbours of all the vertices
- *
- * The function is meant more or less as a debug tool, but can be used in production
- * environment aswell.
- * the output is in form of idx(number of neighbours): (x1,y1,z1) (x2,y2,z2) ...
- * @param *vlist is a structure holding information on vertex list.
- * @returns TS_SUCCESS on successful execution, TS_FAIL otherwise.
-*/
-ts_bool print_vertex_neighbours(ts_vertex_list *vlist);
-
-
-/** @brief Function outputs the vetex list file to comply to old fortran format
- *
- * @param *vlist is a list of vertices
- * @param *filename is a name of the output file to be created (note that if the file already
- * exists it will be overwritten.
- */
-ts_bool write_vertex_fcompat_file(ts_vertex_list *vlist,ts_char *filename);
-ts_bool fprint_vertex_list(FILE *fh,ts_vertex_list *vlist);
-ts_bool fprint_tristar(FILE *fh, ts_vesicle *vesicle);
-ts_bool fprint_triangle_list(FILE *fh, ts_vesicle *vesicle);
-ts_bool fprint_vertex_data(FILE *fh,ts_vertex_list *vlist);
-ts_bool fprint_bonds(FILE *fh,ts_vesicle *vesicle);
-ts_bool write_dout_fcompat_file(ts_vesicle *vesicle, ts_char *filename);
-ts_bool read_tape_fcompat_file(ts_vesicle *vesicle, ts_char *filename);
-
-
-/** @brief Outputs file in vtk format, compatible with paraview.
+/** @brief Outputs file in newer vtk xml format, compatible with paraview.
*
- * @param *vlist is a list of vertices
- * @param *filename is a name of the output file. If exists, it will be overwritten
- * @param *text is a description line (max. 255 characters) to be included in the file
+ * @param *vesicle is a list of vertices
+ * @param *timestepno is a timestep number. Output file will be timestep_XXXXXX.vtu
+ * @param *cstlist TO BE DOCUMENTED
*/
-ts_bool write_vertex_vtk_file(ts_vesicle *vesicle,ts_char *filename, ts_char *text);
ts_bool write_vertex_xml_file(ts_vesicle *vesicle, ts_uint timestepno, ts_cluster_list *cstlist);
-ts_bool write_master_xml_file(ts_char *filename);
ts_bool write_pov_file(ts_vesicle *vesicle, char *filename);
ts_tape *parsetape(char *filename);
@@ -82,6 +42,4 @@
ts_bool getcmdline_tape(cfg_t *cfg, char *opts);
ts_bool cmdline_to_tape(cfg_t *cfg, char *key, char *val);
ts_bool print_help(FILE *fd);
-ts_bool dump_state(ts_vesicle *vesicle, ts_uint iteration);
-ts_vesicle *restore_state(ts_uint *iteration);
#endif
diff --git a/src/main.c b/src/main.c
index 3f91f43..47cf2a8 100644
--- a/src/main.c
+++ b/src/main.c
@@ -26,8 +26,8 @@
*/
int main(int argv, char *argc[]){
- ts_vesicle *vesicle;
- ts_tape *tape;
+ ts_vesicle *vesicle=NULL;
+ ts_tape *tape=NULL;
ts_uint start_iteration=0;
force_from_tape=0;
/* Area and volume for constant area and constant volume are initialized to be zero */
@@ -62,9 +62,6 @@
}
else
ts_fprintf(stdout,"No .status file. The iteration count will start from 0\n");
-/* Here you should read new tape file, reassign some values in vertex from the tape and assign read tape to vesicle->tape */
-// tape=parsetape(command_line_args.tape_fullfilename);
- // vesicle=vtk2vesicle(command_line_args.dump_from_vtk,tape);
}
else if(command_line_args.force_from_tape){
ts_fprintf(stdout,"************************************************\n");
@@ -77,63 +74,10 @@
ts_fprintf(stdout,"**********************************************************************\n");
ts_fprintf(stdout,"**** Recreating vesicle from dump file and continuing simulation *****\n");
ts_fprintf(stdout,"**********************************************************************\n\n");
- tape=parsetape(command_line_args.tape_fullfilename);
- vesicle=restore_state(&start_iteration);
- if(vesicle==NULL){
- ts_fprintf(stderr, "Dump file does not exist or is not a regular file! Did you mean to invoke trisurf with --force-from-tape option?\n\n");
- return 1;
- }
- // nove vrednosti iz tapea...
- vesicle->bending_rigidity=tape->xk0;
- vtx_set_global_values(vesicle);
- vesicle->pswitch =tape->pswitch;
- vesicle->pressure=tape->pressure;
- vesicle->dmax=tape->dmax*tape->dmax;
- poly_assign_filament_xi(vesicle,tape);
- free(vesicle->tape);
- vesicle->tape=tape;
- vesicle->clist->dmin_interspecies = tape->dmin_interspecies*tape->dmin_interspecies;
-
-
-
- /* spherical harmonics */
- if(tape->shc>0){
- vesicle->sphHarmonics=complex_sph_init(vesicle->vlist,tape->shc);
- }
- else {
- vesicle->sphHarmonics=NULL;
- }
-
- if(command_line_args.reset_iteration_count) start_iteration=tape->inititer;
- else start_iteration++;
-
- if(start_iteration>=tape->iterations){
- ts_fprintf(stdout, "Simulation already completed. if you want to rerun it try with --force-from-tape or --reset-iteration-count\n\n");
- return 0;
- }
-
- /* if requested in tape, we can have smaller number of polymeres attached to membrane than the number of polymeres in dump file */
- if(vesicle->tape->npoly != vesicle->poly_list->n){
-
- ts_fprintf(stdout,"(INFO) the number of polymeres attached to membrane in tape is different than a number of polymeres in dump file!\n");
- if(vesicle->tape->npoly > vesicle->poly_list->n){
- ts_fprintf(stdout,"(INFO) It is possible to decrease the number of polymeres on the membrane, but it is not allowed to increase its number. The maximal allowed number in tape is %d The execution of program will terminate!\n",vesicle->poly_list->n);
- fatal("Terminating due to increase of number of polymeres",1);
- } else {
- remove_random_polymeres(vesicle->poly_list, vesicle->poly_list->n - vesicle->tape->npoly);
- ts_fprintf(stdout,"(INFO)\n(INFO) The new number of polymeres from tape is %d.\n\n",vesicle->poly_list->n);
-
- }
- }
+ ts_fprintf(stderr, "Dump file does not exist or is not a regular file! Did you mean to invoke trisurf with --force-from-tape or --restore-from-vtk option?\n\n");
+ fatal("Recreating vesicle from binary dump file not supported anymore. Sorry.",254);
}
- //printf("nucleus coords: %.17e %.17e %.17e\n",vesicle->nucleus_center[0], vesicle->nucleus_center[1], vesicle->nucleus_center[2]);
-// write_vertex_xml_file(vesicle,0);
-// exit(1);
-
- //write_vertex_xml_file(vesicle,1000);
run_simulation(vesicle, tape->mcsweeps, tape->inititer, tape->iterations, start_iteration);
- write_master_xml_file(command_line_args.output_fullfilename);
- write_dout_fcompat_file(vesicle,"dout");
vesicle_free(vesicle);
tape_free(tape);
return 0; //program finished perfectly ok. We return 0.
diff --git a/src/shdiscover.c b/src/shdiscover.c
deleted file mode 100644
index cf155ac..0000000
--- a/src/shdiscover.c
+++ /dev/null
@@ -1,82 +0,0 @@
-/* vim: set ts=4 sts=4 sw=4 noet : */
-#include "general.h"
-#include "vertex.h"
-#include "initial_distribution.h"
-#include "io.h"
-#include "vesicle.h"
-#include "sh.h"
-#include "frame.c"
-#include <math.h>
-#include <stdlib.h>
-int main(int argc, char *argv[]){
-
-ts_fprintf(stdout,"SHdiscover was called with %d coefficients!\n",argc-1);
-ts_uint n,i,j,l;
-ts_int m;
-ts_double fi,theta,r,Y;
-ts_vesicle *vesicle=initial_distribution_dipyramid(17,60,60,60,0.15);
-ts_vertex_list *vlist=vesicle->vlist;
-centermass(vesicle);
-ts_fprintf(stdout,"Vesicle has a CenterMass in %f,%f,%f\n",vesicle->cm[0],vesicle->cm[1], vesicle->cm[2]);
-
-n=vlist->n;
-
-ts_fprintf(stdout,"Tests\n");
-ts_fprintf(stdout,"P(0,0,0.5)=%f (%f)\n",plgndr(0,0,0.5),1.0);
-ts_fprintf(stdout,"P(1,0,0.5)=%f (%f)\n",plgndr(1,0,0.5),0.5);
-ts_fprintf(stdout,"P(2,0,0.5)=%f (%f)\n",plgndr(2,0,0.5),0.5*(3*0.5*0.5-1));
-ts_fprintf(stdout,"P(2,2,0.5)=%f (ni to:%f)\n",plgndr(2,2,0.5),0.5*(3*0.5*0.5-1));
-
-ts_fprintf(stdout,"Y(0,0,pi/6,pi/4)=%f (%f)\n",shY(0,0,M_PI/6,M_PI/4),sqrt(1/(4*M_PI)));
-ts_fprintf(stdout,"Y(1,0,pi/6,pi/4)=%f (%f)\n",shY(1,0,M_PI/6,M_PI/4),sqrt(3/(4*M_PI))*cos(M_PI/6));
-ts_fprintf(stdout,"Y(1,0,4*pi/6,6*pi/4)=%f (%f)\n",shY(1,0,4*M_PI/6,6*M_PI/4),sqrt(3/(4*M_PI))*cos(4*M_PI/6));
-ts_fprintf(stdout,"Y(1,1,pi/6,pi/4)=%f (%f)\n",shY(1,1,M_PI/6,M_PI/4),-sqrt(3/(8*M_PI))*sin(M_PI/6)*cos(M_PI/4));
-ts_fprintf(stdout,"Y(2,0,pi/6,pi/4)=%f (%f)\n",shY(2,0,M_PI/6,M_PI/4),sqrt(5/(4*M_PI))*(3.0/2.0*cos(M_PI/6)*cos(M_PI/6)-1.0/2.0));
-ts_fprintf(stdout,"Y(2,-2,pi/6,pi/4)=%f (0)\n",shY(2,-2,M_PI/6,M_PI/4));
-ts_fprintf(stdout,"Y(2,2,pi/6,pi/3)=%f (%f)\n",shY(2,2,M_PI/6,M_PI/3), sqrt(15.0/(32.0*M_PI))*sin(M_PI/6)*sin(M_PI/6)*cos(2*M_PI/3));
-
- for(j=1;j<argc;j++){
- l=(int)sqrt(j-1); /* determine l from dataline */
- m=j-1-l*(l+1); /* determine m from dataline */
- ts_fprintf(stdout,"l=%d, m=%d, u=%s\n",l,m,argv[j]);
- }
-
-/*we calculate new position of each vertex of vesicle */
-for(i=0;i<n;i++){
- fi=atan2(vlist->vtx[i]->y, vlist->vtx[i]->x);
-/* theta=atan2(
- sqrt(vlist->vtx[i]->data->x*vlist->vtx[i]->data->x +
- vlist->vtx[i]->data->y*vlist->vtx[i]->data->y),
- vlist->vtx[i]->data->z
- ); */
- theta=acos(
- vlist->vtx[i]->z /
- sqrt(vlist->vtx[i]->x*vlist->vtx[i]->x +
- vlist->vtx[i]->y*vlist->vtx[i]->y+
- vlist->vtx[i]->z*vlist->vtx[i]->z)
-
- );
-
-
-
- r=0.0;
- for(j=1;j<argc;j++){
- l=(int)sqrt(j-1); /* determine l from dataline */
- m=j-1-l*(l+1); /* determine m from dataline */
- Y=shY(l,m,theta,fi);
- r+=fabs(atof(argv[j])*Y);
- /*ts_fprintf(stdout,"l=%d, m=%d, u=%s\n",l,m,argv[j]);*/
- }
-
- vlist->vtx[i]->z=fabs(r)*cos(theta);
- vlist->vtx[i]->x=fabs(r)*sin(theta)*cos(fi);
- vlist->vtx[i]->y=fabs(r)*sin(theta)*sin(fi);
-}
-
-write_vertex_xml_file(vesicle,0);
-write_master_xml_file("test.pvd");
-
-
-vesicle_free(vesicle);
-return 0;
-}
diff --git a/src/spherical_trisurf.c b/src/spherical_trisurf.c
deleted file mode 100644
index 06a84f4..0000000
--- a/src/spherical_trisurf.c
+++ /dev/null
@@ -1,107 +0,0 @@
-/* vim: set ts=4 sts=4 sw=4 noet : */
-#include<stdio.h>
-#include<math.h>
-#include "general.h"
-#include "vertex.h"
-#include "bond.h"
-#include "triangle.h"
-#include "cell.h"
-#include "vesicle.h"
-#include "io.h"
-#include "initial_distribution.h"
-#include "frame.h"
-#include "timestep.h"
-#include "sh.h"
-
-/** Entrance function to the program
- * @param argv is a number of parameters used in program call (including the program name
- * @param argc is a pointer to strings (character arrays) which holds the arguments
- * @returns returns 0 on success, any other number on fail.
-*/
-ts_bool saveAvgUlm2(ts_vesicle *vesicle);
-int main(int argv, char *argc[]){
-ts_uint i,j,k;
-ts_vesicle *vesicle;
-ts_double r0;
-vesicle=initial_distribution_dipyramid(17,60,60,60,0.15);
-//parsetape(vesicle,&i);
-
-//similar to nmax in fortran code
-ts_uint nmax;
-
-//these four must come from parsetype!
-vesicle->dmax=1.67*1.67;
-vesicle->stepsize=0.15;
-vesicle->clist->max_occupancy=8;
-vesicle->bending_rigidity=25.0;
-//fprintf(stderr,"xk=%f",vesicle->bending_rigidity);
-
- centermass(vesicle);
-cell_occupation(vesicle);
-
-//test if the structure is internally organized into cells correctly
-ts_uint cind;
-for(i=0;i<vesicle->vlist->n;i++){
- cind=vertex_self_avoidance(vesicle, vesicle->vlist->vtx[i]);
-
- if(vesicle->clist->cell[cind]==vesicle->vlist->vtx[i]->cell){
- //fprintf(stdout,"(T) Idx match!\n");
- } else {
- fprintf(stderr,"(T) ***** Idx don't match!\n");
-
- }
-}
-//end test
-vesicle->sphHarmonics=sph_init(vesicle->vlist, 21);
-
-vesicle_volume(vesicle);
-r0=getR0(vesicle);
-
-preparationSh(vesicle,r0);
-calculateYlmi(vesicle);
-calculateUlm(vesicle);
-
-//preloop:
-ts_double vmsr, bfsr;
-for(i=0;i<1000;i++){
- cell_occupation(vesicle);
- for(j=0;j<1000;j++){
- single_timestep(vesicle, &vmsr, &bfsr);
- }
- centermass(vesicle);
- fprintf(stderr, "Preloop %d completed.\n",i+1);
-}
-
-nmax=1000;
-for(i=0;i<nmax;i++){
- for(j=0;j<200;j++){
- cell_occupation(vesicle);
- for(k=0;k<5;k++){
- single_timestep(vesicle, &vmsr, &bfsr);
- }
- centermass(vesicle);
- }
- vesicle_volume(vesicle);
- r0=getR0(vesicle);
-
- preparationSh(vesicle,r0);
- calculateYlmi(vesicle);
- calculateUlm(vesicle);
-
- storeUlm2(vesicle);
- saveAvgUlm2(vesicle);
-
- write_vertex_xml_file(vesicle,i);
- fprintf(stderr, "Loop %d out of %d completed.\n",i+1,nmax);
-
-}
-
-write_master_xml_file("test.pvd");
-write_dout_fcompat_file(vesicle,"dout");
-vesicle_free(vesicle);
-
-return 0; //program finished perfectly ok. We return 0.
-}
-
-
-
diff --git a/src/spherical_trisurf_ff.c b/src/spherical_trisurf_ff.c
deleted file mode 100644
index 8a0902f..0000000
--- a/src/spherical_trisurf_ff.c
+++ /dev/null
@@ -1,90 +0,0 @@
-/* vim: set ts=4 sts=4 sw=4 noet : */
-#include<stdio.h>
-#include<math.h>
-#include "general.h"
-#include "vertex.h"
-#include "bond.h"
-#include "triangle.h"
-#include "cell.h"
-#include "vesicle.h"
-#include "io.h"
-#include "initial_distribution.h"
-#include "frame.h"
-#include "timestep.h"
-#include "sh.h"
-
-/** Entrance function to the program
- * @param argv is a number of parameters used in program call (including the program name
- * @param argc is a pointer to strings (character arrays) which holds the arguments
- * @returns returns 0 on success, any other number on fail.
-*/
-ts_bool saveAvgUlm2(ts_vesicle *vesicle);
-int main(int argv, char *argc[]){
-ts_uint i,j;
-ts_vesicle *vesicle;
-ts_double r0;
-vesicle=initial_distribution_dipyramid(17,60,60,60,0.15);
-//parsetape(vesicle,&i);
-
-//these four must come from parsetype!
-vesicle->dmax=1.67*1.67;
-vesicle->stepsize=0.15;
-vesicle->clist->max_occupancy=8;
-vesicle->bending_rigidity=30.0*30.0;
-for(i=0;i<vesicle->vlist->n;i++){
- vesicle->vlist->vtx[i]->xk=vesicle->bending_rigidity;
-}
-//fprintf(stderr,"xk=%f",vesicle->bending_rigidity);
-
- centermass(vesicle);
-vesicle->sphHarmonics=sph_init(vesicle->vlist, 21);
-
-vesicle_volume(vesicle);
-r0=getR0(vesicle);
-
-preparationSh(vesicle,r0);
-calculateYlmi(vesicle);
-calculateUlm(vesicle);
-ts_double vmsr,bfsr;
-for(i=0;i<500;i++){
- cell_occupation(vesicle);
- for(j=0;j<1000;j++){
- single_timestep(vesicle,&vmsr,&bfsr);
- }
- centermass(vesicle);
- fprintf(stderr, "Preloop %d completed.\n",i+1);
-}
-
-vesicle->bending_rigidity=25.0;
-for(i=0;i<vesicle->vlist->n;i++){
- vesicle->vlist->vtx[i]->xk=vesicle->bending_rigidity;
-}
-
-
-for(i=0;i<10000;i++){
- cell_occupation(vesicle);
- for(j=0;j<1000;j++){
- single_timestep(vesicle,&vmsr,&bfsr);
- }
- centermass(vesicle);
- vesicle_volume(vesicle);
- r0=getR0(vesicle);
-
- preparationSh(vesicle,r0);
- calculateYlmi(vesicle);
- calculateUlm(vesicle);
-
- storeUlm2(vesicle);
- saveAvgUlm2(vesicle);
-
- write_vertex_xml_file(vesicle,i);
- fprintf(stderr, "Loop %d completed.\n",i+1);
-}
-write_master_xml_file("test.pvd");
-write_dout_fcompat_file(vesicle,"dout");
-vesicle_free(vesicle);
-
-return 0; //program finished perfectly ok. We return 0.
-}
-
-
diff --git a/src/timestep.c b/src/timestep.c
index 81101bf..2202982 100644
--- a/src/timestep.c
+++ b/src/timestep.c
@@ -124,7 +124,6 @@
bfsr/=(ts_double)mcsweeps;
centermass(vesicle);
cell_occupation(vesicle);
- dump_state(vesicle,i);
vesicle_volume(vesicle); //calculates just volume.
vesicle_area(vesicle); //calculates area.
if(vesicle->tape->constvolswitch==0){
@@ -135,7 +134,6 @@
}
if(i>=inititer){
write_vertex_xml_file(vesicle,i-inititer,NULL);
- write_master_xml_file(command_line_args.output_fullfilename);
epochtime=get_epoch();
gyration_eigen(vesicle, &l1, &l2, &l3);
//r0=getR0(vesicle);
--
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