From 19c1fd84d1fd75e9bfd55feb670fda87a2e02086 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Fri, 08 Feb 2019 08:32:29 +0000
Subject: [PATCH] Merge branch 'master' of ssh://git.penic.eu:29418/trisurf-ng
---
src/main.c | 75 ++++++++++++++++++++++++++++++++++---
1 files changed, 69 insertions(+), 6 deletions(-)
diff --git a/src/main.c b/src/main.c
index 9bb3430..3f91f43 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"
@@ -12,7 +14,11 @@
#include "timestep.h"
#include "poly.h"
#include "sh.h"
+#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
@@ -24,20 +30,54 @@
ts_tape *tape;
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");
- if(command_line_args.force_from_tape){
+// vesicle = parseDump("timestep_000000.vtu");
+// run_simulation(vesicle, vesicle->tape->mcsweeps, vesicle->tape->inititer, vesicle->tape->iterations, 1);
+
+ 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");
+/* 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");
ts_fprintf(stdout,"**** Generating initial geometry from tape *****\n");
ts_fprintf(stdout,"************************************************\n\n");
- tape=parsetape("tape");
+ tape=parsetape(command_line_args.tape_fullfilename);
vesicle=create_vesicle_from_tape(tape);
} else {
ts_fprintf(stdout,"**********************************************************************\n");
ts_fprintf(stdout,"**** Recreating vesicle from dump file and continuing simulation *****\n");
ts_fprintf(stdout,"**********************************************************************\n\n");
- tape=parsetape("tape");
+ 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");
@@ -50,10 +90,15 @@
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=sph_init(vesicle->vlist,tape->shc);
+ vesicle->sphHarmonics=complex_sph_init(vesicle->vlist,tape->shc);
}
else {
vesicle->sphHarmonics=NULL;
@@ -66,10 +111,28 @@
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);
+
+ }
+ }
+ }
+ //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("test.pvd");
+ write_master_xml_file(command_line_args.output_fullfilename);
write_dout_fcompat_file(vesicle,"dout");
vesicle_free(vesicle);
tape_free(tape);
--
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