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| | | /* vim: set ts=4 sts=4 sw=4 noet : */ |
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| | | #include<stdio.h> |
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| | | #include<math.h> |
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| | | #include<stdlib.h> |
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| | | #include "general.h" |
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| | | #include "vertex.h" |
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| | | //#include "io.h" |
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| | | //#include "initial_timestep.h" |
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| | | #include "bond.h" |
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| | | #include "triangle.h" |
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| | | #include "cell.h" |
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| | | #include "vesicle.h" |
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| | | #include "io.h" |
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| | | #include "initial_distribution.h" |
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| | | #include "frame.h" |
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| | | #include "timestep.h" |
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| | | #include "poly.h" |
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| | | #include "sh.h" |
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| | | #include "shcomplex.h" |
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| | | #include "dumpstate.h" |
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| | | #include "restore.h" |
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| | | #include "plugins.h" |
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| | | #include <fcntl.h> |
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| | | /** Entrance function to the program |
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| | | * @param argv is a number of parameters used in program call (including the program name |
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| | | * @param argc is a pointer to strings (character arrays) which holds the arguments |
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| | | * @returns returns 0 on success, any other number on fail. |
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| | | */ |
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| | | |
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| | | #include <string.h> |
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| | | int main(int argv, char *argc[]){ |
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| | | ts_bool retval; |
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| | | ts_vertex_list *vlist=init_vertex_list(5); |
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| | | ts_char *plugin0 = (ts_char *)calloc(255,sizeof(ts_char)); |
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| | | ts_char *plugin1 = (ts_char *)calloc(255,sizeof(ts_char)); |
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| | | ts_char *plugin2 = (ts_char *)calloc(255,sizeof(ts_char)); |
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| | | ts_char *plugin3 = (ts_char *)calloc(255,sizeof(ts_char)); |
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| | | ts_char *plugin4 = (ts_char *)calloc(255,sizeof(ts_char)); |
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| | | ts_char *plugin5 = (ts_char *)calloc(255,sizeof(ts_char)); |
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| | | ts_char *plugin6 = (ts_char *)calloc(255,sizeof(ts_char)); |
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| | | ts_char *plugin7 = (ts_char *)calloc(255,sizeof(ts_char)); |
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| | | strcpy(plugin0,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/demoplugin.so"); |
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| | | strcpy(plugin1,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/vmdefaulthardconstraints.so"); |
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| | | strcpy(plugin2,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/plane_confinement.so"); |
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| | | strcpy(plugin3,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/pressure.so"); |
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| | | strcpy(plugin4,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/constant_volume.so"); |
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| | | strcpy(plugin5,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/constant_area.so"); |
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| | | strcpy(plugin6,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/stretching_energy.so"); |
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| | | strcpy(plugin7,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/direct_force_on_c0.so"); |
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| | | ts_char **plugins=(ts_char **)calloc(8,sizeof(ts_char *)); |
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| | | plugins[0]=plugin0; |
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| | | plugins[1]=plugin1; |
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| | | plugins[2]=plugin2; |
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| | | plugins[3]=plugin3; |
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| | | plugins[4]=plugin4; |
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| | | plugins[5]=plugin5; |
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| | | plugins[6]=plugin6; |
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| | | plugins[7]=plugin7; |
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| | | ts_plugin_list *plist=init_plugin_list(plugins,8); |
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| | | //printf("%s", plist->chain->at_start->next->plugin->filename); |
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| | | //ts_fprintf(stdout, "TRISURF in PRVI PLUGIN %s\n", plist->plugin[0]->details->name); |
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| | | ts_vesicle *vesicle; |
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| | | ts_tape *tape; |
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| | | ts_uint start_iteration=0; |
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| | | force_from_tape=0; |
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| | | /* Area and volume for constant area and constant volume are initialized to be zero */ |
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| | | A0=0; |
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| | | V0=0; |
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| | | /* create lock file */ |
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| | | createPidFile("ts_trisurf",".lock",0); |
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| | | parse_args(argv,argc); // sets global variable command_line_args (defined in io.h) |
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| | | ts_fprintf(stdout,"TRISURF-NG v. %s, compiled on: %s %s.\n", TS_VERSION, __DATE__, __TIME__); |
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| | | ts_fprintf(stdout,"Programming done by: Samo Penic and Miha Fosnaric\n"); |
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| | | ts_fprintf(stdout,"Released under terms of GPLv3\n"); |
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| | | ts_fprintf(stdout,"Starting program...\n\n"); |
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| | | |
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| | | /* Entry point for plugin function at_start() */ |
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| | | ts_plugin_chain *ptr=plist->chain->at_start; |
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| | | while(ptr!=NULL){ |
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| | | ptr->plugin->function->at_start(argv,argc); |
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| | | ptr=ptr->next; |
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| | | } |
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| | | |
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| | | if(command_line_args.dump_from_vtk[0]!=0){ |
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| | | ts_fprintf(stdout,"************************************************\n"); |
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| | | ts_fprintf(stdout,"**** Restoring vesicle from VTK points list ****\n"); |
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| | | ts_fprintf(stdout,"************************************************\n\n"); |
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| | | vesicle = parseDump(command_line_args.dump_from_vtk); |
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| | | tape = vesicle->tape; |
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| | | int arguments_no; |
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| | | FILE *fd=fopen(".status","r"); |
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| | | if(fd!=NULL){ |
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| | | arguments_no=fscanf(fd,"%u", &start_iteration); |
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| | | if(arguments_no==0){ |
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| | | ts_fprintf(stdout,"No information of start iteration in .status file\n"); |
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| | | } |
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| | | fclose(fd); |
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| | | start_iteration++; |
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| | | } |
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| | | else |
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| | | ts_fprintf(stdout,"No .status file. The iteration count will start from 0\n"); |
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| | | } |
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| | | else if(command_line_args.force_from_tape){ |
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| | | ts_fprintf(stdout,"************************************************\n"); |
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| | | ts_fprintf(stdout,"**** Generating initial geometry from tape *****\n"); |
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| | | ts_fprintf(stdout,"************************************************\n\n"); |
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| | | tape=parsetape(command_line_args.tape_fullfilename); |
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| | | vesicle=create_vesicle_from_tape(tape); |
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| | | } else { |
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| | | |
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| | | ts_fprintf(stdout,"**********************************************************************\n"); |
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| | | ts_fprintf(stdout,"**** Recreating vesicle from dump file and continuing simulation *****\n"); |
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| | | ts_fprintf(stdout,"**********************************************************************\n\n"); |
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| | | tape=parsetape(command_line_args.tape_fullfilename); |
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| | | vesicle=restore_state(&start_iteration); |
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| | | if(vesicle==NULL){ |
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| | | 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"); |
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| | | return 1; |
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| | | } |
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| | | // nove vrednosti iz tapea... |
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| | | vesicle->bending_rigidity=tape->xk0; |
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| | | vtx_set_global_values(vesicle); |
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| | | vesicle->pswitch =tape->pswitch; |
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| | | vesicle->pressure=tape->pressure; |
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| | | vesicle->dmax=tape->dmax*tape->dmax; |
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| | | poly_assign_filament_xi(vesicle,tape); |
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| | | free(vesicle->tape); |
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| | | vesicle->tape=tape; |
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| | | vesicle->clist->dmin_interspecies = tape->dmin_interspecies*tape->dmin_interspecies; |
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| | | |
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| | | |
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| | | retval=vtx_add_neighbour(VTX(vlist,1),VTX(vlist,0)); |
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| | | if(retval==TS_FAIL) printf("1. already a member or vertex is null!\n"); |
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| | | retval=vtx_add_neighbour(VTX(vlist,0),VTX(vlist,1)); |
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| | | if(retval==TS_FAIL) printf("2. already a member or vertex is null!\n"); |
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| | | |
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| | | vtx_list_free(vlist); |
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| | | printf("Done.\n"); |
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| | | return 0; //program finished perfectly ok. We return 0. |
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| | | /* spherical harmonics */ |
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| | | if(tape->shc>0){ |
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| | | vesicle->sphHarmonics=complex_sph_init(vesicle->vlist,tape->shc); |
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| | | } |
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| | | else { |
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| | | vesicle->sphHarmonics=NULL; |
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| | | } |
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| | | |
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| | | if(command_line_args.reset_iteration_count) start_iteration=tape->inititer; |
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| | | else start_iteration++; |
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| | | |
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| | | if(start_iteration>=tape->iterations){ |
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| | | ts_fprintf(stdout, "Simulation already completed. if you want to rerun it try with --force-from-tape or --reset-iteration-count\n\n"); |
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| | | return 0; |
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| | | } |
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| | | |
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| | | /* if requested in tape, we can have smaller number of polymeres attached to membrane than the number of polymeres in dump file */ |
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| | | if(vesicle->tape->npoly != vesicle->poly_list->n){ |
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| | | |
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| | | ts_fprintf(stdout,"(INFO) the number of polymeres attached to membrane in tape is different than a number of polymeres in dump file!\n"); |
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| | | if(vesicle->tape->npoly > vesicle->poly_list->n){ |
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| | | 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); |
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| | | fatal("Terminating due to increase of number of polymeres",1); |
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| | | } else { |
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| | | remove_random_polymeres(vesicle->poly_list, vesicle->poly_list->n - vesicle->tape->npoly); |
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| | | ts_fprintf(stdout,"(INFO)\n(INFO) The new number of polymeres from tape is %d.\n\n",vesicle->poly_list->n); |
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| | | |
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| | | } |
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| | | } |
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| | | } |
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| | | |
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| | | vesicle->plist=plist; |
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| | | /* Entry point for plugin after_vesicle_init() function */ |
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| | | vesicle->plist->pointer=vesicle->plist->chain->after_vesicle_init; |
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| | | while(vesicle->plist->pointer!=NULL){ |
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| | | vesicle=vesicle->plist->pointer->plugin->function->after_vesicle_init(vesicle); |
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| | | vesicle->plist->pointer=vesicle->plist->pointer->next; |
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| | | } |
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| | | |
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| | | run_simulation(vesicle, tape->mcsweeps, tape->inititer, tape->iterations, start_iteration); |
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| | | write_master_xml_file(command_line_args.output_fullfilename); |
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| | | write_dout_fcompat_file(vesicle,"dout"); |
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| | | /* Entry point for plugin cleanup() function */ |
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| | | ptr=plist->chain->cleanup; |
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| | | while(ptr!=NULL){ |
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| | | ptr->plugin->function->cleanup(); |
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| | | ptr=ptr->next; |
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| | | } |
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| | | |
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| | | vesicle_free(vesicle); |
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| | | tape_free(tape); |
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| | | return 0; //program finished perfectly ok. We return 0. |
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| | | } |
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