From 842378276ab4c4a8dabd02324bb24b8da39c4384 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Fri, 18 Oct 2019 10:28:34 +0000
Subject: [PATCH] Done and implemented compression. It doesn't segfaults at the moment
---
src/main.c | 114 ++++++++++++++++++++++++++++++---------------------------
1 files changed, 60 insertions(+), 54 deletions(-)
diff --git a/src/main.c b/src/main.c
index c402ebf..92df3d8 100644
--- a/src/main.c
+++ b/src/main.c
@@ -1,5 +1,7 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
#include<stdio.h>
#include<math.h>
+#include<stdlib.h>
#include "general.h"
#include "vertex.h"
#include "bond.h"
@@ -10,7 +12,12 @@
#include "initial_distribution.h"
#include "frame.h"
#include "timestep.h"
+#include "poly.h"
+#include "sh.h"
+#include "shcomplex.h"
+#include "restore.h"
+#include <fcntl.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
@@ -18,60 +25,59 @@
*/
int main(int argv, char *argc[]){
-ts_bool retval;
-ts_uint i;
- ts_vertex_list *vlist=init_vertex_list(5);
-ts_vertex_list *vlist1;
-ts_bond_list *blist=init_bond_list();
-ts_triangle_list *tlist=init_triangle_list();
-ts_cell_list *clist=init_cell_list(3,3,3,0.3);
-ts_vesicle *vesicle;
+ 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 */
+ A0=0;
+ V0=0;
+ /* create lock file */
+ createPidFile("ts_trisurf",".lock",0);
+ parse_args(argv,argc); // sets global variable command_line_args (defined in io.h)
+ ts_fprintf(stdout,"TRISURF-NG v. %s, compiled on: %s %s.\n", TS_VERSION, __DATE__, __TIME__);
+ ts_fprintf(stdout,"Programming done by: Samo Penic and Miha Fosnaric\n");
+ ts_fprintf(stdout,"Released under terms of GPLv3\n");
+ ts_fprintf(stdout,"Starting program...\n\n");
+// vesicle = parseDump("timestep_000000.vtu");
+// run_simulation(vesicle, vesicle->tape->mcsweeps, vesicle->tape->inititer, vesicle->tape->iterations, 1);
-retval=vtx_add_cneighbour(blist,vlist->vtx[1],vlist->vtx[0]);
-if(retval==TS_FAIL) printf("1. already a member or vertex is null!\n");
+ if(command_line_args.dump_from_vtk[0]!=0){
+ ts_fprintf(stdout,"************************************************\n");
+ ts_fprintf(stdout,"**** Restoring vesicle from VTK points list ****\n");
+ ts_fprintf(stdout,"************************************************\n\n");
+ vesicle = parseDump(command_line_args.dump_from_vtk);
+// write_vertex_xml_file(vesicle,9999); // here you can test if restoration and rewritting results in the same dump file. Only the date od creation of dump file must differ.
+ tape = vesicle->tape;
+ int arguments_no;
+ FILE *fd=fopen(".status","r");
+ if(fd!=NULL){
+ arguments_no=fscanf(fd,"%u", &start_iteration);
+ if(arguments_no==0){
+ ts_fprintf(stdout,"No information of start iteration in .status file\n");
+ }
+ fclose(fd);
+ start_iteration++;
+ }
+ else
+ ts_fprintf(stdout,"No .status file. The iteration count will start from 0\n");
+ }
+ else if(command_line_args.force_from_tape){
+ ts_fprintf(stdout,"************************************************\n");
+ ts_fprintf(stdout,"**** Generating initial geometry from tape *****\n");
+ ts_fprintf(stdout,"************************************************\n\n");
+ tape=parsetape(command_line_args.tape_fullfilename);
+ vesicle=create_vesicle_from_tape(tape);
+ } else {
-retval=vtx_add_cneighbour(blist,vlist->vtx[0],vlist->vtx[1]);
-if(retval==TS_FAIL) printf("2. already a member or vertex is null!\n");
-
-retval=vtx_remove_neighbour(vlist->vtx[0],vlist->vtx[1]);
-vtx_add_neighbour(vlist->vtx[0],vlist->vtx[1]);
-
-vlist->vtx[0]->data->x=1.0;
-vlist->vtx[0]->data->x=1.1;
-vlist1=vertex_list_copy(vlist);
-bond_add(blist, vlist->vtx[1],vlist->vtx[0]);
-triangle_add(tlist,vlist->vtx[1],vlist->vtx[2],vlist->vtx[3]);
-
-triangle_add(tlist,vlist->vtx[1],vlist->vtx[2],vlist->vtx[3]);
-
-printf("Cell idx=1 has vertices=%u\n",clist->cell[0]->data->nvertex);
-cell_add_vertex(clist->cell[0], vlist->vtx[0]);
-printf("Cell idx=1 has vertices=%u\n",clist->cell[0]->data->nvertex);
-printf("Cell idx=1 has vertex[0] has x coordinate=%e\n",clist->cell[0]->data->vertex[0]->data->x);
-cell_list_cell_occupation_clear(clist);
-printf("Cell idx=1 has vertices=%u\n",clist->cell[0]->data->nvertex);
-cell_add_vertex(clist->cell[0], vlist->vtx[0]);
-
-
-triangle_list_free(tlist);
-bond_list_free(blist);
-vtx_list_free(vlist);
-cell_list_free(clist);
-
-vtx_list_free(vlist1);
-printf("Tests complete.\n");
-vesicle=initial_distribution_dipyramid(17,60,60,60,0.15);
-
-centermass(vesicle);
-cell_occupation(vesicle);
-
-for(i=0;i<100;i++){
-single_timestep(vesicle);
-write_vertex_xml_file(vesicle,i);
-}
-write_master_xml_file("test.pvd");
-write_dout_fcompat_file(vesicle,"dout");
-vesicle_free(vesicle);
-
-return 0; //program finished perfectly ok. We return 0.
+ ts_fprintf(stdout,"**********************************************************************\n");
+ ts_fprintf(stdout,"**** Recreating vesicle from dump file and continuing simulation *****\n");
+ ts_fprintf(stdout,"**********************************************************************\n\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);
+ }
+ run_simulation(vesicle, tape->mcsweeps, tape->inititer, tape->iterations, start_iteration);
+ vesicle_free(vesicle);
+ tape_free(tape);
+ return 0; //program finished perfectly ok. We return 0.
}
--
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