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/main.c | 81 ++++++++++++----------------------------
1 files changed, 25 insertions(+), 56 deletions(-)
diff --git a/src/main.c b/src/main.c
index 8cf3e92..47cf2a8 100644
--- a/src/main.c
+++ b/src/main.c
@@ -17,6 +17,8 @@
#include "shcomplex.h"
#include "dumpstate.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
@@ -24,10 +26,15 @@
*/
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 */
+ 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");
@@ -38,12 +45,23 @@
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,"**** 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;
-// tape=parsetape(command_line_args.tape_fullfilename);
- // vesicle=vtk2vesicle(command_line_args.dump_from_vtk,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");
@@ -56,59 +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);
}
-
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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