trisurf-ng.git - Gitblit

Samo Penic

2018-09-23 267cf14b1ced6fce480e4292131a987a1802e28a

commit \| author \| age
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>
ac9826	19	#include <sys/stat.h>
SP	20
fedf2b	21
626811	22	ts_bool run_simulation(ts_vesicle *vesicle, ts_uint mcsweeps, ts_uint inititer, ts_uint iterations, ts_uint start_iteration){
5a3862	23	ts_uint i, j,k,l,m;
cfab63	24	ts_double r0,kc1=0,kc2=0,kc3=0,kc4=0;
c0ae90	25	ts_double l1,l2,l3,vmsr,bfsr, vmsrt, bfsrt;
37d14a	26	ts_ulong epochtime;
267cf1	27	ts_double max_z, min_z;
3d0247	28	FILE fd1,fd2=NULL,*fd3=NULL;
267db5	29	char filename[10000];
ac9826	30	//struct stat st;
SP	31	strcpy(filename,command_line_args.path);
	32	strcat(filename,"statistics.csv");
	33	//int result = stat(filename, &st);
	34	FILE *fd;
	35	if(start_iteration==0)
	36	fd=fopen(filename,"w");
	37	else
	38	fd=fopen(filename,"a");
37d14a	39	if(fd==NULL){
SP	40	fatal("Cannot open statistics.csv file for writing",1);
	41	}
ac9826	42	if(start_iteration==0)
SP	43	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	44
M	45	if(vesicle->sphHarmonics!=NULL){
267db5	46	strcpy(filename,command_line_args.path);
SP	47	strcat(filename,"ulm2.csv");
ac9826	48	// int result = stat(filename, &st);
SP	49	if(start_iteration==0)
267db5	50	fd2=fopen(filename,"w");
ac9826	51	else
SP	52	fd2=fopen(filename,"a");
819a09	53	if(fd2==NULL){
S	54	fatal("Cannot open ulm2.csv file for writing",1);
	55	}
	56	if(start_iteration==0) //file does not exist
	57	fprintf(fd2, "Timestep u_00^2 u_10^2 u_11^2 u_20^2 ...\n");
5a3862	58	}
M	59
c60a49	60	/* RANDOM SEED SET BY CURRENT TIME */
M	61	epochtime=get_epoch();
	62	srand48(epochtime);
d7a113	63	centermass(vesicle);
SP	64	cell_occupation(vesicle);
fe5069	65	vesicle_volume(vesicle); //needed for constant volume at this moment
c0ae90	66	vesicle_area(vesicle); //needed for constant area at this moment
49981c	67	if(V0<0.000001)
SP	68	V0=vesicle->volume;
	69	ts_fprintf(stdout,"Setting volume V0=%.17f\n",V0);
	70	if(A0<0.000001)
	71	A0=vesicle->area;
819a09	72	ts_fprintf(stdout,"Setting area A0=%.17f\n",A0);
a54977	73	epsvol=4.0sqrt(2.0M_PI)/pow(3.0,3.0/4.0)*V0/pow(vesicle->tlist->n,3.0/2.0);
c0ae90	74	epsarea=A0/(ts_double)vesicle->tlist->n;
267cf1	75
SP	76
a54977	77	// fprintf(stderr, "DVol=%1.16f (%1.16f), V0=%1.16f\n", epsvol,0.003e-2*V0,V0);
626811	78	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	79	for(i=start_iteration;i<inititer+iterations;i++){
37d14a	80	vmsr=0.0;
SP	81	bfsr=0.0;
267cf1	82
SP	83	// plane confinement
	84	if(vesicle->tape->plane_confinement_switch){
	85	if(vesicle->confinement_plane.z_max-vesicle->confinement_plane.z_min<=vesicle->tape->plane_d){
	86	min_z=1e10;
	87	max_z=-1e10;
	88	for(k=0;k<vesicle->vlist->n;k++){
	89	if(vesicle->vlist->vtx[k]->z > max_z) max_z=vesicle->vlist->vtx[k]->z;
	90	if(vesicle->vlist->vtx[k]->z < min_z) min_z=vesicle->vlist->vtx[k]->z;
	91	}
	92	if(max_z-min_z<=vesicle->tape->plane_d) {
	93	vesicle->confinement_plane.z_max=max_z;
	94	vesicle->confinement_plane.z_min=max_z-vesicle->tape->plane_d;
	95	} else {
	96	vesicle->confinement_plane.z_min=min_z-1e-5;
	97	vesicle->confinement_plane.z_max=max_z+1e-5;
	98	}
	99	}
	100	}
	101
3de289	102	/* vesicle_volume(vesicle);
SP	103	fprintf(stderr,"Volume before TS=%1.16e\n", vesicle->volume); */
d7a113	104	for(j=0;j<mcsweeps;j++){
37d14a	105	single_timestep(vesicle, &vmsrt, &bfsrt);
SP	106	vmsr+=vmsrt;
	107	bfsr+=bfsrt;
d7a113	108	}
3de289	109	/*
SP	110	vesicle_volume(vesicle);
	111	fprintf(stderr,"Volume after TS=%1.16e\n", vesicle->volume); */
37d14a	112	vmsr/=(ts_double)mcsweeps;
SP	113	bfsr/=(ts_double)mcsweeps;
d7a113	114	centermass(vesicle);
SP	115	cell_occupation(vesicle);
1ab449	116	dump_state(vesicle,i);
58230a	117	if(i>=inititer){
0a2c81	118	write_vertex_xml_file(vesicle,i-inititer,NULL);
267db5	119	write_master_xml_file(command_line_args.output_fullfilename);
37d14a	120	epochtime=get_epoch();
SP	121	gyration_eigen(vesicle, &l1, &l2, &l3);
c0ae90	122	vesicle_volume(vesicle); //calculates just volume.
SP	123	vesicle_area(vesicle); //calculates area.
dc77e8	124	r0=getR0(vesicle);
632960	125	if(vesicle->sphHarmonics!=NULL){
SP	126	preparationSh(vesicle,r0);
459ff9	127	//calculateYlmi(vesicle);
SP	128	calculateUlmComplex(vesicle);
	129	storeUlmComplex2(vesicle);
632960	130	saveAvgUlm2(vesicle);
22cdfd	131	kc1=calculateKc(vesicle, 2,9);
SP	132	kc2=calculateKc(vesicle, 6,9);
	133	kc3=calculateKc(vesicle, 2,vesicle->sphHarmonics->l);
1665aa	134	kc4=calculateKc(vesicle, 3,6);
267db5	135	strcpy(filename,command_line_args.path);
SP	136	strcat(filename,"state.dat");
	137	fd1=fopen(filename,"w");
5bb6bb	138	fprintf(fd1,"%e %e\n",vesicle->volume, getR0(vesicle));
M	139	for(k=0;k<vesicle->vlist->n;k++){
	140	fprintf(fd1,"%e %e %e %e %e\n",
	141	vesicle->vlist->vtx[k]->x,
	142	vesicle->vlist->vtx[k]->y,
	143	vesicle->vlist->vtx[k]->z,
	144	vesicle->vlist->vtx[k]->solAngle,
	145	vesicle->vlist->vtx[k]->relR
	146	);
	147	}
	148	fclose(fd1);
5a3862	149
M	150	fprintf(fd2,"%u ", i);
	151	for(l=0;l<vesicle->sphHarmonics->l;l++){
	152	for(m=l;m<2*l+1;m++){
	153	fprintf(fd2,"%e ", gsl_complex_abs2(vesicle->sphHarmonics->ulmComplex[l][m]) );
	154	}
	155	}
	156	fprintf(fd2,"\n");
	157
	158	fflush(fd2);
	159
632960	160	}
dc77e8	161
c0ae90	162	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	163
632960	164	fflush(fd);
144784	165	// sprintf(filename,"timestep-%05d.pov",i-inititer);
fe24d2	166	// write_pov_file(vesicle,filename);
49981c	167	} //end if(inititer....)
SP	168	fd3=fopen(".status","w"); //write status file when everything is written to disk.
	169	if(fd3==NULL){
	170	fatal("Cannot open .status file for writing",1);
d7a113	171	}
49981c	172	fprintf(fd3,"%d",i);
SP	173	fclose(fd3);
	174	ts_fprintf(stdout,"Done %d out of %d iterations (x %d MC sweeps).\n",i+1,inititer+iterations,mcsweeps);
d7a113	175	}
37d14a	176	fclose(fd);
5a3862	177	if(fd2!=NULL) fclose(fd2);
d7a113	178	return TS_SUCCESS;
SP	179	}
d7639a	180
37d14a	181	ts_bool single_timestep(ts_vesicle vesicle,ts_double vmsr, ts_double *bfsr){
3de289	182	// vesicle_volume(vesicle);
SP	183	// fprintf(stderr,"Volume before TS=%1.16e\n", vesicle->volume);
d7639a	184	ts_bool retval;
SP	185	ts_double rnvec[3];
fe5069	186	ts_uint i,j, b;
37d14a	187	ts_uint vmsrcnt=0;
aec47d	188	for(i=0;i<vesicle->vlist->n;i++){
d7639a	189	rnvec[0]=drand48();
SP	190	rnvec[1]=drand48();
	191	rnvec[2]=drand48();
aec47d	192	retval=single_verticle_timestep(vesicle,vesicle->vlist->vtx[i],rnvec);
37d14a	193	if(retval==TS_SUCCESS) vmsrcnt++;
d7639a	194	}
SP	195
37d14a	196	ts_int bfsrcnt=0;
fedf2b	197	for(i=0;i<3*vesicle->vlist->n;i++){
fe5069	198	b=rand() % vesicle->blist->n;
d7639a	199	//find a bond and return a pointer to a bond...
SP	200	//call single_bondflip_timestep...
fe5069	201	retval=single_bondflip_timestep(vesicle,vesicle->blist->bond[b],rnvec);
3de289	202	// b++; retval=TS_FAIL;
37d14a	203	if(retval==TS_SUCCESS) bfsrcnt++;
fedf2b	204	}
M	205
	206	for(i=0;i<vesicle->poly_list->n;i++){
58230a	207	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
M	208	rnvec[0]=drand48();
	209	rnvec[1]=drand48();
	210	rnvec[2]=drand48();
	211	retval=single_poly_vertex_move(vesicle,vesicle->poly_list->poly[i],vesicle->poly_list->poly[i]->vlist->vtx[j],rnvec);
	212	}
fedf2b	213	}
M	214
58230a	215
M	216	for(i=0;i<vesicle->filament_list->n;i++){
	217	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	218	rnvec[0]=drand48();
	219	rnvec[1]=drand48();
	220	rnvec[2]=drand48();
	221	retval=single_filament_vertex_move(vesicle,vesicle->filament_list->poly[i],vesicle->filament_list->poly[i]->vlist->vtx[j],rnvec);
	222	}
fedf2b	223	}
M	224
58230a	225
fedf2b	226	// 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	227	*vmsr=(ts_double)vmsrcnt/(ts_double)vesicle->vlist->n;
SP	228	*bfsr=(ts_double)bfsrcnt/(ts_double)vesicle->vlist->n/3.0;
3de289	229	// vesicle_volume(vesicle);
SP	230	// fprintf(stderr,"Volume after TS=%1.16e\n", vesicle->volume);
d7639a	231	return TS_SUCCESS;
SP	232	}
	233
	234
	235