trisurf-ng.git - Gitblit

Use nucleus displaced centre in vertex move

Samo Penic

2016-05-31 5c3143e7b7d0979d6eed07b6dfbe9f214159bdbb

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7f6076	1	/* vim: set ts=4 sts=4 sw=4 noet : */
d7639a	2	#include<stdlib.h>
SP	3	#include<stdio.h>
aec47d	4	#include<math.h>
SP	5	//#include "io.h"
	6	#include "general.h"
	7	#include "timestep.h"
	8	#include "vertexmove.h"
30ee9c	9	#include "bondflip.h"
d7a113	10	#include "frame.h"
SP	11	#include "io.h"
37d14a	12	#include "stats.h"
dc77e8	13	#include "sh.h"
459ff9	14	#include "shcomplex.h"
dc77e8	15	#include "vesicle.h"
5a3862	16	#include<gsl/gsl_complex.h>
M	17	#include<gsl/gsl_complex_math.h>
267db5	18	#include<string.h>
fedf2b	19
626811	20	ts_bool run_simulation(ts_vesicle *vesicle, ts_uint mcsweeps, ts_uint inititer, ts_uint iterations, ts_uint start_iteration){
5a3862	21	ts_uint i, j,k,l,m;
cfab63	22	ts_double r0,kc1=0,kc2=0,kc3=0,kc4=0;
c0ae90	23	ts_double l1,l2,l3,vmsr,bfsr, vmsrt, bfsrt;
37d14a	24	ts_ulong epochtime;
3d0247	25	FILE fd1,fd2=NULL,*fd3=NULL;
267db5	26	char filename[10000];
SP	27	strcpy(filename,command_line_args.path);
	28	strcat(filename,"statistics.csv");
	29	FILE *fd=fopen(filename,"w");
37d14a	30	if(fd==NULL){
SP	31	fatal("Cannot open statistics.csv file for writing",1);
	32	}
1665aa	33	fprintf(fd, "Epoch OuterLoop VertexMoveSucessRate BondFlipSuccessRate Volume Area lamdba1 lambda2 lambda3 Kc(2-9) Kc(6-9) Kc(2-end) Kc(3-6)\n");
5a3862	34
M	35	if(vesicle->sphHarmonics!=NULL){
267db5	36	strcpy(filename,command_line_args.path);
SP	37	strcat(filename,"ulm2.csv");
	38	fd2=fopen(filename,"w");
5a3862	39	if(fd2==NULL){
M	40	fatal("Cannot open ulm2.csv file for writing",1);
	41	}
	42	fprintf(fd2, "Timestep u_00^2 u_10^2 u_11^2 u_20^2 ...\n");
	43
	44	}
	45
c60a49	46	/* RANDOM SEED SET BY CURRENT TIME */
M	47	epochtime=get_epoch();
	48	srand48(epochtime);
5a3862	49
d7a113	50	centermass(vesicle);
SP	51	cell_occupation(vesicle);
fe5069	52	vesicle_volume(vesicle); //needed for constant volume at this moment
c0ae90	53	vesicle_area(vesicle); //needed for constant area at this moment
1121fa	54	V0=vesicle->volume;
c0ae90	55	A0=vesicle->area;
a54977	56	epsvol=4.0sqrt(2.0M_PI)/pow(3.0,3.0/4.0)*V0/pow(vesicle->tlist->n,3.0/2.0);
c0ae90	57	epsarea=A0/(ts_double)vesicle->tlist->n;
a54977	58	// fprintf(stderr, "DVol=%1.16f (%1.16f), V0=%1.16f\n", epsvol,0.003e-2*V0,V0);
626811	59	if(start_iteration<inititer) ts_fprintf(stdout, "Starting simulation (first %d x %d MC sweeps will not be recorded on disk)\n", inititer, mcsweeps);
SP	60	for(i=start_iteration;i<inititer+iterations;i++){
37d14a	61	vmsr=0.0;
SP	62	bfsr=0.0;
3de289	63	/* vesicle_volume(vesicle);
SP	64	fprintf(stderr,"Volume before TS=%1.16e\n", vesicle->volume); */
d7a113	65	for(j=0;j<mcsweeps;j++){
37d14a	66	single_timestep(vesicle, &vmsrt, &bfsrt);
SP	67	vmsr+=vmsrt;
	68	bfsr+=bfsrt;
d7a113	69	}
3de289	70	/*
SP	71	vesicle_volume(vesicle);
	72	fprintf(stderr,"Volume after TS=%1.16e\n", vesicle->volume); */
37d14a	73	vmsr/=(ts_double)mcsweeps;
SP	74	bfsr/=(ts_double)mcsweeps;
d7a113	75	centermass(vesicle);
SP	76	cell_occupation(vesicle);
f8e6ba	77	ts_fprintf(stdout,"Done %d out of %d iterations (x %d MC sweeps).\n",i+1,inititer+iterations,mcsweeps);
1ab449	78	dump_state(vesicle,i);
3d0247	79	fd3=fopen(".status","w");
SP	80	if(fd3==NULL){
	81	fatal("Cannot open .status file for writing",1);
	82	}
	83	fprintf(fd3,"%d",i);
	84	fclose(fd3);
58230a	85	if(i>=inititer){
d7a113	86	write_vertex_xml_file(vesicle,i-inititer);
267db5	87	write_master_xml_file(command_line_args.output_fullfilename);
37d14a	88	epochtime=get_epoch();
SP	89	gyration_eigen(vesicle, &l1, &l2, &l3);
c0ae90	90	vesicle_volume(vesicle); //calculates just volume.
SP	91	vesicle_area(vesicle); //calculates area.
dc77e8	92	r0=getR0(vesicle);
632960	93	if(vesicle->sphHarmonics!=NULL){
SP	94	preparationSh(vesicle,r0);
459ff9	95	//calculateYlmi(vesicle);
SP	96	calculateUlmComplex(vesicle);
	97	storeUlmComplex2(vesicle);
632960	98	saveAvgUlm2(vesicle);
22cdfd	99	kc1=calculateKc(vesicle, 2,9);
SP	100	kc2=calculateKc(vesicle, 6,9);
	101	kc3=calculateKc(vesicle, 2,vesicle->sphHarmonics->l);
1665aa	102	kc4=calculateKc(vesicle, 3,6);
267db5	103	strcpy(filename,command_line_args.path);
SP	104	strcat(filename,"state.dat");
	105	fd1=fopen(filename,"w");
5bb6bb	106	fprintf(fd1,"%e %e\n",vesicle->volume, getR0(vesicle));
M	107	for(k=0;k<vesicle->vlist->n;k++){
	108	fprintf(fd1,"%e %e %e %e %e\n",
	109	vesicle->vlist->vtx[k]->x,
	110	vesicle->vlist->vtx[k]->y,
	111	vesicle->vlist->vtx[k]->z,
	112	vesicle->vlist->vtx[k]->solAngle,
	113	vesicle->vlist->vtx[k]->relR
	114	);
	115	}
	116	fclose(fd1);
5a3862	117
M	118	fprintf(fd2,"%u ", i);
	119	for(l=0;l<vesicle->sphHarmonics->l;l++){
	120	for(m=l;m<2*l+1;m++){
	121	fprintf(fd2,"%e ", gsl_complex_abs2(vesicle->sphHarmonics->ulmComplex[l][m]) );
	122	}
	123	}
	124	fprintf(fd2,"\n");
	125
	126	fflush(fd2);
	127
632960	128	}
dc77e8	129
c0ae90	130	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);
5a3862	131
632960	132	fflush(fd);
144784	133	// sprintf(filename,"timestep-%05d.pov",i-inititer);
fe24d2	134	// write_pov_file(vesicle,filename);
d7a113	135	}
SP	136	}
37d14a	137	fclose(fd);
5a3862	138	if(fd2!=NULL) fclose(fd2);
d7a113	139	return TS_SUCCESS;
SP	140	}
d7639a	141
37d14a	142	ts_bool single_timestep(ts_vesicle vesicle,ts_double vmsr, ts_double *bfsr){
3de289	143	// vesicle_volume(vesicle);
SP	144	// fprintf(stderr,"Volume before TS=%1.16e\n", vesicle->volume);
d7639a	145	ts_bool retval;
SP	146	ts_double rnvec[3];
fe5069	147	ts_uint i,j, b;
37d14a	148	ts_uint vmsrcnt=0;
aec47d	149	for(i=0;i<vesicle->vlist->n;i++){
d7639a	150	rnvec[0]=drand48();
SP	151	rnvec[1]=drand48();
	152	rnvec[2]=drand48();
aec47d	153	retval=single_verticle_timestep(vesicle,vesicle->vlist->vtx[i],rnvec);
37d14a	154	if(retval==TS_SUCCESS) vmsrcnt++;
d7639a	155	}
SP	156
37d14a	157	ts_int bfsrcnt=0;
fedf2b	158	for(i=0;i<3*vesicle->vlist->n;i++){
fe5069	159	b=rand() % vesicle->blist->n;
d7639a	160	//find a bond and return a pointer to a bond...
SP	161	//call single_bondflip_timestep...
fe5069	162	retval=single_bondflip_timestep(vesicle,vesicle->blist->bond[b],rnvec);
3de289	163	// b++; retval=TS_FAIL;
37d14a	164	if(retval==TS_SUCCESS) bfsrcnt++;
fedf2b	165	}
M	166
	167	for(i=0;i<vesicle->poly_list->n;i++){
58230a	168	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
M	169	rnvec[0]=drand48();
	170	rnvec[1]=drand48();
	171	rnvec[2]=drand48();
	172	retval=single_poly_vertex_move(vesicle,vesicle->poly_list->poly[i],vesicle->poly_list->poly[i]->vlist->vtx[j],rnvec);
	173	}
fedf2b	174	}
M	175
58230a	176
M	177	for(i=0;i<vesicle->filament_list->n;i++){
	178	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	179	rnvec[0]=drand48();
	180	rnvec[1]=drand48();
	181	rnvec[2]=drand48();
	182	retval=single_filament_vertex_move(vesicle,vesicle->filament_list->poly[i],vesicle->filament_list->poly[i]->vlist->vtx[j],rnvec);
	183	}
fedf2b	184	}
M	185
58230a	186
fedf2b	187	// printf("Bondflip success rate in one sweep: %d/%d=%e\n", cnt,3*vesicle->blist->n,(double)cnt/(double)vesicle->blist->n/3.0);
37d14a	188	*vmsr=(ts_double)vmsrcnt/(ts_double)vesicle->vlist->n;
SP	189	*bfsr=(ts_double)bfsrcnt/(ts_double)vesicle->vlist->n/3.0;
3de289	190	// vesicle_volume(vesicle);
SP	191	// fprintf(stderr,"Volume after TS=%1.16e\n", vesicle->volume);
d7639a	192	return TS_SUCCESS;
SP	193	}
	194
	195
	196