| 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" |
| eb7d7e | 20 | #include "plugins.h" |
| 6e42ef | 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 | */ | |
| eb7d7e | 27 | #include <string.h> |
| d7639a | 28 | int main(int argv, char *argc[]){ |
| eb7d7e | 29 | ts_char *plugin0 = (ts_char *)calloc(255,sizeof(ts_char)); |
| SP | 30 | strcpy(plugin0,"/home/samo/programiranje/trisurf-ng/src/first.so"); |
| 31 | ts_char **plugins=(ts_char **)calloc(1,sizeof(ts_char *)); | |
| 32 | *plugins=plugin0; | |
| 33 | ts_plugin_list *plist=init_plugin_list(plugins,1); | |
| 34 | ts_fprintf(stdout, "TRISURF in PRVI PLUGIN %s\n", plist->plugin[0]->details->name); | |
| 1ab449 | 35 | ts_vesicle *vesicle; |
| SP | 36 | ts_tape *tape; |
| 8a6614 | 37 | ts_uint start_iteration=0; |
| 152052 | 38 | force_from_tape=0; |
| fab2ad | 39 | /* Area and volume for constant area and constant volume are initialized to be zero */ |
| SP | 40 | A0=0; |
| 41 | V0=0; | |
| 6e42ef | 42 | /* create lock file */ |
| SP | 43 | createPidFile("ts_trisurf",".lock",0); |
| 8a6614 | 44 | parse_args(argv,argc); // sets global variable command_line_args (defined in io.h) |
| 7f6076 | 45 | ts_fprintf(stdout,"TRISURF-NG v. %s, compiled on: %s %s.\n", TS_VERSION, __DATE__, __TIME__); |
| SP | 46 | ts_fprintf(stdout,"Programming done by: Samo Penic and Miha Fosnaric\n"); |
| 47 | ts_fprintf(stdout,"Released under terms of GPLv3\n"); | |
| 8a6614 | 48 | ts_fprintf(stdout,"Starting program...\n\n"); |
| ab798b | 49 | // vesicle = parseDump("timestep_000000.vtu"); |
| SP | 50 | // run_simulation(vesicle, vesicle->tape->mcsweeps, vesicle->tape->inititer, vesicle->tape->iterations, 1); |
| 51 | ||
| ee84bd | 52 | if(command_line_args.dump_from_vtk[0]!=0){ |
| SP | 53 | ts_fprintf(stdout,"************************************************\n"); |
| 57f830 | 54 | ts_fprintf(stdout,"**** Restoring vesicle from VTK points list ****\n"); |
| ee84bd | 55 | ts_fprintf(stdout,"************************************************\n\n"); |
| ab798b | 56 | vesicle = parseDump(command_line_args.dump_from_vtk); |
| 3cd5f4 | 57 | // 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. |
| ab798b | 58 | tape = vesicle->tape; |
| bb2074 | 59 | int arguments_no; |
| 3d0247 | 60 | FILE *fd=fopen(".status","r"); |
| SP | 61 | if(fd!=NULL){ |
| bb2074 | 62 | arguments_no=fscanf(fd,"%u", &start_iteration); |
| SP | 63 | if(arguments_no==0){ |
| a17e91 | 64 | ts_fprintf(stdout,"No information of start iteration in .status file\n"); |
| bb2074 | 65 | } |
| 3d0247 | 66 | fclose(fd); |
| a17e91 | 67 | start_iteration++; |
| 3d0247 | 68 | } |
| bb2074 | 69 | else |
| a17e91 | 70 | ts_fprintf(stdout,"No .status file. The iteration count will start from 0\n"); |
| 57f830 | 71 | /* Here you should read new tape file, reassign some values in vertex from the tape and assign read tape to vesicle->tape */ |
| ab798b | 72 | // tape=parsetape(command_line_args.tape_fullfilename); |
| SP | 73 | // vesicle=vtk2vesicle(command_line_args.dump_from_vtk,tape); |
| ee84bd | 74 | } |
| SP | 75 | else if(command_line_args.force_from_tape){ |
| 8a6614 | 76 | ts_fprintf(stdout,"************************************************\n"); |
| SP | 77 | ts_fprintf(stdout,"**** Generating initial geometry from tape *****\n"); |
| 78 | ts_fprintf(stdout,"************************************************\n\n"); | |
| 267db5 | 79 | tape=parsetape(command_line_args.tape_fullfilename); |
| 8a6614 | 80 | vesicle=create_vesicle_from_tape(tape); |
| SP | 81 | } else { |
| 083e03 | 82 | |
| 8a6614 | 83 | ts_fprintf(stdout,"**********************************************************************\n"); |
| SP | 84 | ts_fprintf(stdout,"**** Recreating vesicle from dump file and continuing simulation *****\n"); |
| 85 | ts_fprintf(stdout,"**********************************************************************\n\n"); | |
| 267db5 | 86 | tape=parsetape(command_line_args.tape_fullfilename); |
| 8a6614 | 87 | vesicle=restore_state(&start_iteration); |
| 3f5c83 | 88 | if(vesicle==NULL){ |
| SP | 89 | 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"); |
| 90 | return 1; | |
| 91 | } | |
| 152052 | 92 | // nove vrednosti iz tapea... |
| d9cb01 | 93 | vesicle->bending_rigidity=tape->xk0; |
| M | 94 | vtx_set_global_values(vesicle); |
| bc9583 | 95 | vesicle->pswitch =tape->pswitch; |
| 152052 | 96 | vesicle->pressure=tape->pressure; |
| 2dcc65 | 97 | vesicle->dmax=tape->dmax*tape->dmax; |
| bcf455 | 98 | poly_assign_filament_xi(vesicle,tape); |
| 2b14da | 99 | free(vesicle->tape); |
| 9166cb | 100 | vesicle->tape=tape; |
| ea1cce | 101 | vesicle->clist->dmin_interspecies = tape->dmin_interspecies*tape->dmin_interspecies; |
| 47a7ac | 102 | |
| SP | 103 | |
| 104 | ||
| 632960 | 105 | /* spherical harmonics */ |
| SP | 106 | if(tape->shc>0){ |
| 459ff9 | 107 | vesicle->sphHarmonics=complex_sph_init(vesicle->vlist,tape->shc); |
| 632960 | 108 | } |
| SP | 109 | else { |
| 110 | vesicle->sphHarmonics=NULL; | |
| 111 | } | |
| d9cb01 | 112 | |
| 144784 | 113 | if(command_line_args.reset_iteration_count) start_iteration=tape->inititer; |
| 8a6614 | 114 | else start_iteration++; |
| 083e03 | 115 | |
| 8a6614 | 116 | if(start_iteration>=tape->iterations){ |
| SP | 117 | ts_fprintf(stdout, "Simulation already completed. if you want to rerun it try with --force-from-tape or --reset-iteration-count\n\n"); |
| 118 | return 0; | |
| 119 | } | |
| a752b5 | 120 | |
| SP | 121 | /* if requested in tape, we can have smaller number of polymeres attached to membrane than the number of polymeres in dump file */ |
| 122 | if(vesicle->tape->npoly != vesicle->poly_list->n){ | |
| 123 | ||
| 124 | ts_fprintf(stdout,"(INFO) the number of polymeres attached to membrane in tape is different than a number of polymeres in dump file!\n"); | |
| 125 | if(vesicle->tape->npoly > vesicle->poly_list->n){ | |
| 126 | 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); | |
| 127 | fatal("Terminating due to increase of number of polymeres",1); | |
| 128 | } else { | |
| 129 | remove_random_polymeres(vesicle->poly_list, vesicle->poly_list->n - vesicle->tape->npoly); | |
| 130 | ts_fprintf(stdout,"(INFO)\n(INFO) The new number of polymeres from tape is %d.\n\n",vesicle->poly_list->n); | |
| 131 | ||
| 132 | } | |
| 133 | } | |
| 8a6614 | 134 | } |
| bac004 | 135 | //printf("nucleus coords: %.17e %.17e %.17e\n",vesicle->nucleus_center[0], vesicle->nucleus_center[1], vesicle->nucleus_center[2]); |
| 90882f | 136 | // write_vertex_xml_file(vesicle,0); |
| SP | 137 | // exit(1); |
| 8a6614 | 138 | |
| 38ed80 | 139 | //write_vertex_xml_file(vesicle,1000); |
| 8a6614 | 140 | run_simulation(vesicle, tape->mcsweeps, tape->inititer, tape->iterations, start_iteration); |
| 267db5 | 141 | write_master_xml_file(command_line_args.output_fullfilename); |
| 8a6614 | 142 | write_dout_fcompat_file(vesicle,"dout"); |
| SP | 143 | vesicle_free(vesicle); |
| 144 | tape_free(tape); | |
| 145 | return 0; //program finished perfectly ok. We return 0. | |
| d7639a | 146 | } |
