From 3006183b769f2e126b1a96e6bf697c2b7f657df7 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sun, 26 Apr 2020 17:35:26 +0000
Subject: [PATCH] Code for incremental adding of inclusions done

---
 src/timestep.c |  213 ++++++++++++++++++++++++++++++++++++++++++++++------
 1 files changed, 186 insertions(+), 27 deletions(-)

diff --git a/src/timestep.c b/src/timestep.c
index c25c1fb..fe0ca24 100644
--- a/src/timestep.c
+++ b/src/timestep.c
@@ -1,3 +1,4 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
 #include<stdlib.h>
 #include<stdio.h>
 #include<math.h>
@@ -7,58 +8,216 @@
 #include "vertexmove.h"
 #include "bondflip.h"
 #include "frame.h"
-#include "vertex.h"
 #include "io.h"
-ts_bool run_simulation(ts_vesicle *vesicle, ts_uint mcsweeps, ts_uint inititer, ts_uint iterations){
-	ts_uint i, j;
+#include "stats.h"
+#include "sh.h"
+#include "shcomplex.h"
+#include "vesicle.h"
+#include<gsl/gsl_complex.h>
+#include<gsl/gsl_complex_math.h>
+#include<string.h>
+#include <sys/stat.h>
+#include "initial_distribution.h"
 
+ts_bool run_simulation(ts_vesicle *vesicle, ts_uint mcsweeps, ts_uint inititer, ts_uint iterations, ts_uint start_iteration){
+	ts_uint i, j,k; //,l,m;
+	ts_double kc1=0,kc2=0,kc3=0,kc4=0;
+	ts_double l1,l2,l3,vmsr,bfsr, vmsrt, bfsrt;
+	ts_ulong epochtime;
+	ts_double max_z,min_z;
+	FILE *fd3=NULL;
+ 	char filename[10000];
+	//struct stat st;
+	strcpy(filename,command_line_args.path);
+	strcat(filename,"statistics.csv");
+	//int result = stat(filename, &st);
+	FILE *fd;
+	if(start_iteration==0)
+		fd=fopen(filename,"w");
+	else
+		fd=fopen(filename,"a");
+	if(fd==NULL){
+		fatal("Cannot open statistics.csv file for writing",1);
+	}
+	if(start_iteration==0)
+		fprintf(fd, "Epoch OuterLoop VertexMoveSucessRate BondFlipSuccessRate Volume Area lamdba1 lambda2 lambda3 Kc(2-9) Kc(6-9) Kc(2-end) Kc(3-6)\n");
+
+/*	 if(vesicle->sphHarmonics!=NULL){
+        strcpy(filename,command_line_args.path);
+        strcat(filename,"ulm2.csv"); 
+//	int result = stat(filename, &st);
+	if(start_iteration==0)
+		fd2=fopen(filename,"w");
+	else
+		fd2=fopen(filename,"a");
+	if(fd2==NULL){
+		fatal("Cannot open ulm2.csv file for writing",1);
+	} 
+
+	if(start_iteration==0) //file does not exist
+		fprintf(fd2, "Timestep u_00^2 u_10^2 u_11^2 u_20^2 ...\n");	
+	}
+*/
+
+/* RANDOM SEED SET BY CURRENT TIME */
+	epochtime=get_epoch();			
+	srand48(epochtime);
 	centermass(vesicle);
 	cell_occupation(vesicle);
-	ts_fprintf(stdout, "Starting simulation (first %d x %d MC sweeps will not be recorded on disk)\n", inititer, mcsweeps);
-	for(i=0;i<inititer+iterations;i++){
-		for(j=0;j<mcsweeps;j++){
-			single_timestep(vesicle);
+	vesicle_volume(vesicle); //needed for constant volume at this moment
+	vesicle_area(vesicle); //needed for constant area at this moment
+	if(V0<0.000001) 
+		V0=vesicle->volume; 
+	ts_fprintf(stdout,"Setting volume V0=%.17f\n",V0);
+	if(A0<0.000001)
+		A0=vesicle->area;
+	ts_fprintf(stdout,"Setting area A0=%.17f\n",A0);
+	epsvol=4.0*sqrt(2.0*M_PI)/pow(3.0,3.0/4.0)*V0/pow(vesicle->tlist->n,3.0/2.0);
+//	printf("epsvol=%e\n",epsvol);
+	epsarea=A0/(ts_double)vesicle->tlist->n;
+	
+	int delta_number_c0=ceil((float)vesicle->tape->number_of_vertices_with_c0/(float)(iterations-1));
+	ts_fprintf(stdout, "Adding additional %d inclusions every %d iterations (%d times, total=%d).\n",delta_number_c0, mcsweeps, (vesicle->tape->number_of_vertices_with_c0)/delta_number_c0,(vesicle->tape->number_of_vertices_with_c0/delta_number_c0)*delta_number_c0); 
+
+	if(start_iteration<inititer) ts_fprintf(stdout, "Starting simulation (first %d x %d MC sweeps will not be recorded on disk)\n", inititer, mcsweeps);
+	for(i=start_iteration;i<inititer+iterations;i++){
+		vmsr=0.0;
+		bfsr=0.0;
+
+	//plane confinement
+	if(vesicle->tape->plane_confinement_switch){
+		min_z=1e10;
+		max_z=-1e10;
+		for(k=0;k<vesicle->vlist->n;k++){
+			if(vesicle->vlist->vtx[k]->z > max_z) max_z=vesicle->vlist->vtx[k]->z;
+			if(vesicle->vlist->vtx[k]->z < min_z) min_z=vesicle->vlist->vtx[k]->z;
 		}
+		vesicle->confinement_plane.force_switch=0;
+		if(max_z>=vesicle->tape->plane_d/2.0){
+			ts_fprintf(stdout, "Max vertex out of bounds (z>=%e). Plane set to max_z = %e.\n",vesicle->tape->plane_d/2.0,max_z);
+			vesicle->confinement_plane.z_max = max_z;
+			vesicle->confinement_plane.force_switch=1;
+		} else {
+			vesicle->confinement_plane.z_max=vesicle->tape->plane_d/2.0;
+		}
+		if(min_z<=-vesicle->tape->plane_d/2.0){
+			ts_fprintf(stdout, "Min vertex out of bounds (z<=%e). Plane set to min_z = %e.\n",-vesicle->tape->plane_d/2.0,min_z);
+			vesicle->confinement_plane.z_min = min_z;
+			vesicle->confinement_plane.force_switch=1;
+		} else {
+			vesicle->confinement_plane.z_min=-vesicle->tape->plane_d/2.0;
+		}
+		ts_fprintf(stdout,"Vesicle confinement by plane set to (zmin, zmax)=(%e,%e).\n",vesicle->confinement_plane.z_min,vesicle->confinement_plane.z_max);
+		if(vesicle->confinement_plane.force_switch) ts_fprintf(stdout,"Squeezing with force %e.\n",vesicle->tape->plane_F);
+	}
+
+	//end plane confinement
+
+/*    vesicle_volume(vesicle);
+    fprintf(stderr,"Volume before TS=%1.16e\n", vesicle->volume); */
+
+		if(i*delta_number_c0<vesicle->tape->number_of_vertices_with_c0){
+			fprintf(stdout, "Adding %d inclusions.\n", delta_number_c0);
+			add_vertices_with_c0(vesicle, delta_number_c0, vesicle->tape->c0, vesicle->tape->w);
+		}
+		for(j=0;j<mcsweeps;j++){
+			single_timestep(vesicle, &vmsrt, &bfsrt);
+			vmsr+=vmsrt;
+			bfsr+=bfsrt;
+		}
+/*
+    vesicle_volume(vesicle);
+    fprintf(stderr,"Volume after TS=%1.16e\n", vesicle->volume); */
+		vmsr/=(ts_double)mcsweeps;
+		bfsr/=(ts_double)mcsweeps;
 		centermass(vesicle);
 		cell_occupation(vesicle);
-		if(i>inititer){
-			write_vertex_xml_file(vesicle,i-inititer);
+/* BINARY DUMPS ARE OBSOLETE. SHOULD WORK AS OF MAR 2020, BUT NO LONGER MAINTAINED */
+//            	dump_state(vesicle,i);
+			vesicle_volume(vesicle); //calculates just volume. 
+            		vesicle_area(vesicle); //calculates area.
+		if(vesicle->tape->constvolswitch==0){
+			V0=vesicle->volume;
 		}
+		if(vesicle->tape->constareaswitch==0){
+			A0=vesicle->area;
+		}
+		if(i>=inititer){
+			write_vertex_xml_file(vesicle,i-inititer,NULL);
+			write_master_xml_file(command_line_args.output_fullfilename);
+			epochtime=get_epoch();			
+			gyration_eigen(vesicle, &l1, &l2, &l3);
+			//r0=getR0(vesicle);
+
+			fprintf(fd, "%lu %u %e %e %1.16e %1.16e %1.16e %1.16e %1.16e %1.16e %1.16e %1.16e %1.16e\n",epochtime,i,vmsr,bfsr,vesicle->volume, vesicle->area,l1,l2,l3,kc1, kc2, kc3,kc4);
+
+		    fflush(fd);	
+		//	sprintf(filename,"timestep-%05d.pov",i-inititer);
+		//	write_pov_file(vesicle,filename);
+		} //end if(inititer....)
+		fd3=fopen(".status","w"); //write status file when everything is written to disk.
+		if(fd3==NULL){
+			fatal("Cannot open .status file for writing",1);
+		}
+		fprintf(fd3,"%d",i);
+		fclose(fd3);
+		ts_fprintf(stdout,"Done %d out of %d iterations (x %d MC sweeps).\n",i+1,inititer+iterations,mcsweeps);
 	}
+	fclose(fd);
+//	if(fd2!=NULL) fclose(fd2);
 	return TS_SUCCESS;
 }
 
-ts_bool single_timestep(ts_vesicle *vesicle){
+ts_bool single_timestep(ts_vesicle *vesicle,ts_double *vmsr, ts_double *bfsr){
+//    vesicle_volume(vesicle);
+//    fprintf(stderr,"Volume before TS=%1.16e\n", vesicle->volume);
     ts_bool retval;
     ts_double rnvec[3];
-    ts_uint i;// b;
+    ts_uint i,j, b;
+    ts_uint vmsrcnt=0;
     for(i=0;i<vesicle->vlist->n;i++){
         rnvec[0]=drand48();
         rnvec[1]=drand48();
         rnvec[2]=drand48();
-	vertex_taint(vesicle->vlist->vtx[i],1);
-//		ts_fprintf(stdout, "Vertex %d should be tainted, level=%d.\n", i, vesicle->vlist->vtx[i]->locked);
-	if(vertex_tainted(vesicle->vlist->vtx[i],1,1)){
-		ts_fprintf(stdout, "Vertex %d tainted, level=%d. Waiting....\n", i, vesicle->vlist->vtx[i]->locked);
-		while(vertex_tainted(vesicle->vlist->vtx[i],1,1));
-	}
         retval=single_verticle_timestep(vesicle,vesicle->vlist->vtx[i],rnvec);
-	vertex_untaint(vesicle->vlist->vtx[i],1);
-//		ts_fprintf(stdout, "Vertex %d should be untainted, level=%d.\n", i, vesicle->vlist->vtx[i]->locked);
+	if(retval==TS_SUCCESS) vmsrcnt++;        
     }
 
-//	ts_int cnt=0;
-/*
-    for(i=0;i<vesicle->vlist->n;i++){
+	ts_int bfsrcnt=0;
+    for(i=0;i<3*vesicle->vlist->n;i++){
 	b=rand() % vesicle->blist->n;
         //find a bond and return a pointer to a bond...
         //call single_bondflip_timestep...
         retval=single_bondflip_timestep(vesicle,vesicle->blist->bond[b],rnvec);
-//	if(retval==TS_SUCCESS) cnt++;        
-    } 
-//	printf("Bondflip success rate in one sweep: %d/%d=%e\n", cnt,vesicle->blist->n,(double)cnt/(double)vesicle->blist->n);
-*/
-	if(retval);
+       //     b++; retval=TS_FAIL;
+	if(retval==TS_SUCCESS) bfsrcnt++;        
+    }
+
+	for(i=0;i<vesicle->poly_list->n;i++){
+		for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
+			rnvec[0]=drand48();
+			rnvec[1]=drand48();
+			rnvec[2]=drand48();
+			retval=single_poly_vertex_move(vesicle,vesicle->poly_list->poly[i],vesicle->poly_list->poly[i]->vlist->vtx[j],rnvec);	
+		}
+	}
+
+
+	for(i=0;i<vesicle->filament_list->n;i++){
+		for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
+			rnvec[0]=drand48();
+			rnvec[1]=drand48();
+			rnvec[2]=drand48();
+			retval=single_filament_vertex_move(vesicle,vesicle->filament_list->poly[i],vesicle->filament_list->poly[i]->vlist->vtx[j],rnvec);	
+		}
+	}
+ 
+
+//	printf("Bondflip success rate in one sweep: %d/%d=%e\n", cnt,3*vesicle->blist->n,(double)cnt/(double)vesicle->blist->n/3.0);
+	*vmsr=(ts_double)vmsrcnt/(ts_double)vesicle->vlist->n;
+	*bfsr=(ts_double)bfsrcnt/(ts_double)vesicle->vlist->n/3.0;
+//    vesicle_volume(vesicle);
+//    fprintf(stderr,"Volume after TS=%1.16e\n", vesicle->volume);
     return TS_SUCCESS;
 }
 

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