Added direct force plugin and fixes in stretching energy

Samo Penic

2019-03-09 2c4278db6ead5c27e30a3000097ed898c968534e

 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"
@@ -11,32 +13,100 @@
#include "frame.h"
#include "timestep.h"
#include "poly.h"

#include "sh.h"
#include "shcomplex.h"
#include "dumpstate.h"
#include "restore.h"
#include "plugins.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
  * @returns returns 0 on success, any other number on fail.
*/

#include <string.h>
int main(int argv, char *argc[]){
   ts_char *plugin0 = (ts_char *)calloc(255,sizeof(ts_char));
   ts_char *plugin1 = (ts_char *)calloc(255,sizeof(ts_char));
   ts_char *plugin2 = (ts_char *)calloc(255,sizeof(ts_char));
   ts_char *plugin3 = (ts_char *)calloc(255,sizeof(ts_char));
   ts_char *plugin4 = (ts_char *)calloc(255,sizeof(ts_char));
   ts_char *plugin5 = (ts_char *)calloc(255,sizeof(ts_char));
   ts_char *plugin6 = (ts_char *)calloc(255,sizeof(ts_char));
   ts_char *plugin7 = (ts_char *)calloc(255,sizeof(ts_char));
   strcpy(plugin0,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/demoplugin.so");
   strcpy(plugin1,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/vmdefaulthardconstraints.so");
   strcpy(plugin2,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/plane_confinement.so");
   strcpy(plugin3,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/pressure.so");
   strcpy(plugin4,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/constant_volume.so");
   strcpy(plugin5,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/constant_area.so");
   strcpy(plugin6,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/stretching_energy.so");
   strcpy(plugin7,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/direct_force_on_c0.so");
   ts_char **plugins=(ts_char **)calloc(8,sizeof(ts_char *));
   plugins[0]=plugin0;
   plugins[1]=plugin1;
   plugins[2]=plugin2;
   plugins[3]=plugin3;
   plugins[4]=plugin4;
   plugins[5]=plugin5;
   plugins[6]=plugin6;
   plugins[7]=plugin7;
   ts_plugin_list *plist=init_plugin_list(plugins,8);
   //printf("%s", plist->chain->at_start->next->plugin->filename);
   //ts_fprintf(stdout, "TRISURF in PRVI PLUGIN %s\n", plist->plugin[0]->details->name);
   ts_vesicle *vesicle;
   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){
	
/* Entry point for plugin function at_start() */
   ts_plugin_chain *ptr=plist->chain->at_start;
   while(ptr!=NULL){
      ptr->plugin->function->at_start(argv,argc);
      ptr=ptr->next;
   }

    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);
      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");
    }
   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");
@@ -45,22 +115,66 @@
      // 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;

      if(command_line_args.reset_iteration_count) start_iteration=tape->inititer-1;


        /* 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);

      }
      }
   }

   vesicle->plist=plist;
/* Entry point for plugin after_vesicle_init() function */
   vesicle->plist->pointer=vesicle->plist->chain->after_vesicle_init;
   while(vesicle->plist->pointer!=NULL){
      vesicle=vesicle->plist->pointer->plugin->function->after_vesicle_init(vesicle);
      vesicle->plist->pointer=vesicle->plist->pointer->next;
   }

   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");
/* Entry point for plugin cleanup() function */
   ptr=plist->chain->cleanup;
   while(ptr!=NULL){
      ptr->plugin->function->cleanup();
      ptr=ptr->next;
   }


   vesicle_free(vesicle);
   tape_free(tape);
   return 0; //program finished perfectly ok. We return 0.