From 0dd5baa7166ab9abd7ef2d6b374e72beab03ef2a Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Tue, 11 Dec 2018 10:58:51 +0000
Subject: [PATCH] First test successful
---
src/timestep.c | 217 ++++++++++++++++++++++++++++++++++++++++++++++++------
1 files changed, 193 insertions(+), 24 deletions(-)
diff --git a/src/timestep.c b/src/timestep.c
index 4ac20be..6430597 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>
@@ -8,65 +9,233 @@
#include "bondflip.h"
#include "frame.h"
#include "io.h"
+#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>
-ts_bool run_simulation(ts_vesicle *vesicle, ts_uint mcsweeps, ts_uint inititer, ts_uint iterations){
- ts_uint i, j;
+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 r0,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 *fd1,*fd2=NULL,*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);
+ epsarea=A0/(ts_double)vesicle->tlist->n;
+
+ 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); */
+ 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);
- ts_fprintf(stdout,"Done %d out of %d iterations (x %d MC sweeps).\n",i+1,inititer+iterations,mcsweeps);
dump_state(vesicle,i);
- if(i>inititer){
- write_vertex_xml_file(vesicle,i-inititer);
+ 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);
+ vesicle_volume(vesicle); //calculates just volume.
+ vesicle_area(vesicle); //calculates area.
+ r0=getR0(vesicle);
+ if(vesicle->sphHarmonics!=NULL){
+ preparationSh(vesicle,r0);
+ //calculateYlmi(vesicle);
+ calculateUlmComplex(vesicle);
+ storeUlmComplex2(vesicle);
+ saveAvgUlm2(vesicle);
+ kc1=calculateKc(vesicle, 2,9);
+ kc2=calculateKc(vesicle, 6,9);
+ kc3=calculateKc(vesicle, 2,vesicle->sphHarmonics->l);
+ kc4=calculateKc(vesicle, 3,6);
+ strcpy(filename,command_line_args.path);
+ strcat(filename,"state.dat");
+ fd1=fopen(filename,"w");
+ fprintf(fd1,"%e %e\n",vesicle->volume, getR0(vesicle));
+ for(k=0;k<vesicle->vlist->n;k++){
+ fprintf(fd1,"%e %e %e %e %e\n",
+ vesicle->vlist->vtx[k]->x,
+ vesicle->vlist->vtx[k]->y,
+ vesicle->vlist->vtx[k]->z,
+ vesicle->vlist->vtx[k]->solAngle,
+ vesicle->vlist->vtx[k]->relR
+ );
+ }
+ fclose(fd1);
+
+ fprintf(fd2,"%u ", i);
+ for(l=0;l<vesicle->sphHarmonics->l;l++){
+ for(m=l;m<2*l+1;m++){
+ fprintf(fd2,"%e ", gsl_complex_abs2(vesicle->sphHarmonics->ulmComplex[l][m]) );
+ }
+ }
+ fprintf(fd2,"\n");
+
+ fflush(fd2);
+
+ }
+
+ 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,j,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();
retval=single_verticle_timestep(vesicle,vesicle->vlist->vtx[i],rnvec);
+ if(retval==TS_SUCCESS) vmsrcnt++;
}
-// ts_int cnt=0;
+ ts_int bfsrcnt=0;
for(i=0;i<3*vesicle->vlist->n;i++){
-//why is rnvec needed in bondflip?
-/* rnvec[0]=drand48();
- rnvec[1]=drand48();
- rnvec[2]=drand48();
-*/
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++;
+ // 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(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);
- if(retval);
+ *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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