From a00f10fd48a1de31c3ac923c2106969f84e831e0 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Mon, 09 Mar 2015 11:09:31 +0000
Subject: [PATCH] Documented energy.c
---
src/main.c | 101 ++++++++++++++++++++++++++++++++++++++++----------
1 files changed, 80 insertions(+), 21 deletions(-)
diff --git a/src/main.c b/src/main.c
index 44d90e2..c55d30a 100644
--- a/src/main.c
+++ b/src/main.c
@@ -1,5 +1,6 @@
#include<stdio.h>
#include<math.h>
+#include<stdlib.h>
#include "general.h"
#include "vertex.h"
#include "bond.h"
@@ -11,6 +12,9 @@
#include "frame.h"
#include "timestep.h"
#include "poly.h"
+#include "sh.h"
+#include "shcomplex.h"
+#include "dumpstate.h"
/** Entrance function to the program
* @param argv is a number of parameters used in program call (including the program name
@@ -22,27 +26,82 @@
ts_vesicle *vesicle;
ts_tape *tape;
ts_uint start_iteration=0;
- parse_args(argv,argc);
- ts_fprintf(stdout,"\nStarting program...\n\n");
-if(force_from_tape){
-ts_fprintf(stdout,"****************************************************\n");
-ts_fprintf(stdout,"**** Reinitializing initial geometry from tape *****\n");
-ts_fprintf(stdout,"****************************************************\n\n");
-tape=parsetape("tape");
-vesicle=create_vesicle_from_tape(tape);
-} else {
+ force_from_tape=0;
+ parse_args(argv,argc); // sets global variable command_line_args (defined in io.h)
+ ts_fprintf(stdout,"Starting program...\n\n");
-ts_fprintf(stdout,"**********************************************************************\n");
-ts_fprintf(stdout,"**** Recreating vesicle from dump file and continuing simulation *****\n");
-ts_fprintf(stdout,"**********************************************************************\n\n");
-tape=parsetape("tape");
-vesicle=restore_state(&start_iteration);
-}
+ if(command_line_args.dump_from_vtk[0]!=0){
+ ts_fprintf(stdout,"************************************************\n");
+ ts_fprintf(stdout,"***** Dumping vesicle from VTK points list *****\n");
+ ts_fprintf(stdout,"************************************************\n\n");
+ 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");
+ 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 {
-run_simulation(vesicle, tape->mcsweeps, tape->inititer, tape->iterations);
-write_master_xml_file("test.pvd");
-write_dout_fcompat_file(vesicle,"dout");
-vesicle_free(vesicle);
-tape_free(tape);
-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");
+ 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);
+
+ }
+ }
+ }
+
+ 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.
}
--
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