Trisurf Monte Carlo simulator
Samo Penic
2016-07-05 8c91d2bcad7df7c647f1379483673183329ddfe8
commit | author | age
7f6076 1 /* vim: set ts=4 sts=4 sw=4 noet : */
d7639a 2 #include<stdio.h>
SP 3 #include<math.h>
2b14da 4 #include<stdlib.h>
d7639a 5 #include "general.h"
SP 6 #include "vertex.h"
a10dd5 7 #include "bond.h"
a2a676 8 #include "triangle.h"
bb77ca 9 #include "cell.h"
7958e9 10 #include "vesicle.h"
a6b1b5 11 #include "io.h"
7958e9 12 #include "initial_distribution.h"
dac2e5 13 #include "frame.h"
aec47d 14 #include "timestep.h"
8db569 15 #include "poly.h"
dc77e8 16 #include "sh.h"
459ff9 17 #include "shcomplex.h"
ee84bd 18 #include "dumpstate.h"
8c1bb1 19 #include "restore.h"
6e42ef 20
SP 21 #include <fcntl.h>
d7639a 22 /** Entrance function to the program
SP 23   * @param argv is a number of parameters used in program call (including the program name
24   * @param argc is a pointer to strings (character arrays) which holds the arguments
25   * @returns returns 0 on success, any other number on fail.
26 */
27
28 int main(int argv, char *argc[]){
1ab449 29     ts_vesicle *vesicle;
SP 30     ts_tape *tape;
8a6614 31     ts_uint start_iteration=0;
152052 32     force_from_tape=0;
fab2ad 33     /* Area and volume for constant area and constant volume are initialized to be zero */
SP 34     A0=0;
35     V0=0;
6e42ef 36     /* create lock file */
SP 37     createPidFile("ts_trisurf",".lock",0);
8a6614 38     parse_args(argv,argc); // sets global variable command_line_args (defined in io.h)
7f6076 39     ts_fprintf(stdout,"TRISURF-NG v. %s, compiled on: %s %s.\n", TS_VERSION, __DATE__, __TIME__);
SP 40     ts_fprintf(stdout,"Programming done by: Samo Penic and Miha Fosnaric\n");
41     ts_fprintf(stdout,"Released under terms of GPLv3\n");
8a6614 42     ts_fprintf(stdout,"Starting program...\n\n");
ab798b 43 //    vesicle = parseDump("timestep_000000.vtu");
SP 44 //        run_simulation(vesicle, vesicle->tape->mcsweeps, vesicle->tape->inititer, vesicle->tape->iterations, 1);
45
ee84bd 46     if(command_line_args.dump_from_vtk[0]!=0){
SP 47         ts_fprintf(stdout,"************************************************\n");
57f830 48         ts_fprintf(stdout,"**** Restoring vesicle from VTK points list ****\n");
ee84bd 49         ts_fprintf(stdout,"************************************************\n\n");
ab798b 50         vesicle = parseDump(command_line_args.dump_from_vtk);
SP 51         tape = vesicle->tape;
bb2074 52         int arguments_no;
3d0247 53         FILE *fd=fopen(".status","r");
SP 54         if(fd!=NULL){
bb2074 55             arguments_no=fscanf(fd,"%u", &start_iteration);
SP 56             if(arguments_no==0){
57                 ts_fprintf(stdout,"No information of start iteration in .status file");
58                 }
3d0247 59             fclose(fd);
SP 60             start_iteration++;
61         }
bb2074 62         else
SP 63             ts_fprintf(stdout,"No .status file. The iteration count will start from 0");
57f830 64 /* Here you should read new tape file, reassign some values in vertex from the tape and assign read tape to vesicle->tape */
ab798b 65 //        tape=parsetape(command_line_args.tape_fullfilename);
SP 66   //      vesicle=vtk2vesicle(command_line_args.dump_from_vtk,tape);
ee84bd 67     }
SP 68     else if(command_line_args.force_from_tape){
8a6614 69         ts_fprintf(stdout,"************************************************\n");
SP 70         ts_fprintf(stdout,"**** Generating initial geometry from tape *****\n");
71         ts_fprintf(stdout,"************************************************\n\n");
267db5 72         tape=parsetape(command_line_args.tape_fullfilename);
8a6614 73         vesicle=create_vesicle_from_tape(tape);
SP 74     } else {
083e03 75
8a6614 76         ts_fprintf(stdout,"**********************************************************************\n");
SP 77         ts_fprintf(stdout,"**** Recreating vesicle from dump file and continuing simulation *****\n");
78         ts_fprintf(stdout,"**********************************************************************\n\n");
267db5 79         tape=parsetape(command_line_args.tape_fullfilename);
8a6614 80         vesicle=restore_state(&start_iteration);
3f5c83 81         if(vesicle==NULL){
SP 82             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");
83             return 1;
84         }
152052 85         // nove vrednosti iz tapea...
d9cb01 86         vesicle->bending_rigidity=tape->xk0;
M 87         vtx_set_global_values(vesicle);
bc9583 88         vesicle->pswitch =tape->pswitch;
152052 89         vesicle->pressure=tape->pressure;
2dcc65 90         vesicle->dmax=tape->dmax*tape->dmax;
bcf455 91         poly_assign_filament_xi(vesicle,tape);
2b14da 92         free(vesicle->tape);
9166cb 93         vesicle->tape=tape;
ea1cce 94         vesicle->clist->dmin_interspecies = tape->dmin_interspecies*tape->dmin_interspecies;
47a7ac 95
SP 96
97
632960 98         /* spherical harmonics */
SP 99         if(tape->shc>0){
459ff9 100             vesicle->sphHarmonics=complex_sph_init(vesicle->vlist,tape->shc);
632960 101         }
SP 102         else {
103             vesicle->sphHarmonics=NULL;
104         }
d9cb01 105
144784 106         if(command_line_args.reset_iteration_count) start_iteration=tape->inititer;
8a6614 107         else start_iteration++;
083e03 108
8a6614 109         if(start_iteration>=tape->iterations){
SP 110             ts_fprintf(stdout, "Simulation already completed. if you want to rerun it try with --force-from-tape or --reset-iteration-count\n\n");
111             return 0;
112         }
a752b5 113
SP 114     /* if requested in tape, we can have smaller number of polymeres attached to membrane than the number of polymeres in dump file */
115         if(vesicle->tape->npoly != vesicle->poly_list->n){
116
117         ts_fprintf(stdout,"(INFO) the number of polymeres attached to membrane in tape is different than a number of polymeres in dump file!\n");
118         if(vesicle->tape->npoly > vesicle->poly_list->n){
119             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);
120             fatal("Terminating due to increase of number of polymeres",1);
121         } else {
122             remove_random_polymeres(vesicle->poly_list, vesicle->poly_list->n - vesicle->tape->npoly);
123             ts_fprintf(stdout,"(INFO)\n(INFO) The new number of polymeres from tape is %d.\n\n",vesicle->poly_list->n);
124
125         }
126         }
8a6614 127     }
bac004 128             //printf("nucleus coords: %.17e %.17e %.17e\n",vesicle->nucleus_center[0], vesicle->nucleus_center[1], vesicle->nucleus_center[2]);
8a6614 129
38ed80 130             //write_vertex_xml_file(vesicle,1000);
8a6614 131     run_simulation(vesicle, tape->mcsweeps, tape->inititer, tape->iterations, start_iteration);
267db5 132     write_master_xml_file(command_line_args.output_fullfilename);
8a6614 133     write_dout_fcompat_file(vesicle,"dout");
SP 134     vesicle_free(vesicle);
135     tape_free(tape);
136     return 0; //program finished perfectly ok. We return 0.
d7639a 137