From 2c4278db6ead5c27e30a3000097ed898c968534e Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 09 Mar 2019 19:45:22 +0000
Subject: [PATCH] Added direct force plugin and fixes in stretching energy
---
src/main.c | 204 ++++++++++++++++++++++++++++++++++++++------------
1 files changed, 154 insertions(+), 50 deletions(-)
diff --git a/src/main.c b/src/main.c
index c402ebf..ecf9678 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"
@@ -10,68 +12,170 @@
#include "initial_distribution.h"
#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_bool retval;
-ts_uint i;
- ts_vertex_list *vlist=init_vertex_list(5);
-ts_vertex_list *vlist1;
-ts_bond_list *blist=init_bond_list();
-ts_triangle_list *tlist=init_triangle_list();
-ts_cell_list *clist=init_cell_list(3,3,3,0.3);
-ts_vesicle *vesicle;
+ 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");
+
+/* 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;
+ }
-retval=vtx_add_cneighbour(blist,vlist->vtx[1],vlist->vtx[0]);
-if(retval==TS_FAIL) printf("1. already a member or vertex is null!\n");
+ 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(command_line_args.tape_fullfilename);
+ vesicle=create_vesicle_from_tape(tape);
+ } else {
-retval=vtx_add_cneighbour(blist,vlist->vtx[0],vlist->vtx[1]);
-if(retval==TS_FAIL) printf("2. already a member or vertex is null!\n");
-
-retval=vtx_remove_neighbour(vlist->vtx[0],vlist->vtx[1]);
-vtx_add_neighbour(vlist->vtx[0],vlist->vtx[1]);
-
-vlist->vtx[0]->data->x=1.0;
-vlist->vtx[0]->data->x=1.1;
-vlist1=vertex_list_copy(vlist);
-bond_add(blist, vlist->vtx[1],vlist->vtx[0]);
-triangle_add(tlist,vlist->vtx[1],vlist->vtx[2],vlist->vtx[3]);
-
-triangle_add(tlist,vlist->vtx[1],vlist->vtx[2],vlist->vtx[3]);
-
-printf("Cell idx=1 has vertices=%u\n",clist->cell[0]->data->nvertex);
-cell_add_vertex(clist->cell[0], vlist->vtx[0]);
-printf("Cell idx=1 has vertices=%u\n",clist->cell[0]->data->nvertex);
-printf("Cell idx=1 has vertex[0] has x coordinate=%e\n",clist->cell[0]->data->vertex[0]->data->x);
-cell_list_cell_occupation_clear(clist);
-printf("Cell idx=1 has vertices=%u\n",clist->cell[0]->data->nvertex);
-cell_add_vertex(clist->cell[0], vlist->vtx[0]);
+ ts_fprintf(stdout,"**********************************************************************\n");
+ ts_fprintf(stdout,"**** Recreating vesicle from dump file and continuing simulation *****\n");
+ ts_fprintf(stdout,"**********************************************************************\n\n");
+ 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");
+ return 1;
+ }
+ // 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;
-triangle_list_free(tlist);
-bond_list_free(blist);
-vtx_list_free(vlist);
-cell_list_free(clist);
-vtx_list_free(vlist1);
-printf("Tests complete.\n");
-vesicle=initial_distribution_dipyramid(17,60,60,60,0.15);
+ /* spherical harmonics */
+ if(tape->shc>0){
+ vesicle->sphHarmonics=complex_sph_init(vesicle->vlist,tape->shc);
+ }
+ else {
+ vesicle->sphHarmonics=NULL;
+ }
-centermass(vesicle);
-cell_occupation(vesicle);
+ if(command_line_args.reset_iteration_count) start_iteration=tape->inititer;
+ else start_iteration++;
-for(i=0;i<100;i++){
-single_timestep(vesicle);
-write_vertex_xml_file(vesicle,i);
-}
-write_master_xml_file("test.pvd");
-write_dout_fcompat_file(vesicle,"dout");
-vesicle_free(vesicle);
+ 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;
+ }
-return 0; //program finished perfectly ok. We 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(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.
}
--
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