trisurf-ng.git - Gitblit

Samo Penic

2018-09-25 5eefcc281fda031d322599fd7094da4fc8450948

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;
5eefcc	27	ts_double max_z=0, min_z=0;
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;
5eefcc	75	if(vesicle->tape->plane_confinement_switch){
SP	76	min_z=1e10;
	77	max_z=-1e10;
	78	for(k=0;k<vesicle->vlist->n;k++){
	79	if(vesicle->vlist->vtx[k]->z > max_z) max_z=vesicle->vlist->vtx[k]->z;
	80	if(vesicle->vlist->vtx[k]->z < min_z) min_z=vesicle->vlist->vtx[k]->z;
	81	}
	82	if(max_z-min_z<=vesicle->tape->plane_d) {
	83	vesicle->confinement_plane.z_max=max_z;
	84	vesicle->confinement_plane.z_min=max_z-vesicle->tape->plane_d;
	85	} else {
	86	vesicle->confinement_plane.z_min=min_z;//-1e-5;
	87	vesicle->confinement_plane.z_max=max_z;//+1e-5;
	88	}
	89	}
267cf1	90
a54977	91	// fprintf(stderr, "DVol=%1.16f (%1.16f), V0=%1.16f\n", epsvol,0.003e-2*V0,V0);
626811	92	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	93	for(i=start_iteration;i<inititer+iterations;i++){
37d14a	94	vmsr=0.0;
SP	95	bfsr=0.0;
267cf1	96
SP	97	// plane confinement
	98	if(vesicle->tape->plane_confinement_switch){
	99	if(vesicle->confinement_plane.z_max-vesicle->confinement_plane.z_min<=vesicle->tape->plane_d){
5eefcc	100	ts_fprintf(stdout,"Force is off\n");
SP	101	} else {
	102	ts_fprintf(stdout,"Force is on\n");
	103
267cf1	104	min_z=1e10;
SP	105	max_z=-1e10;
	106	for(k=0;k<vesicle->vlist->n;k++){
	107	if(vesicle->vlist->vtx[k]->z > max_z) max_z=vesicle->vlist->vtx[k]->z;
	108	if(vesicle->vlist->vtx[k]->z < min_z) min_z=vesicle->vlist->vtx[k]->z;
	109	}
	110	if(max_z-min_z<=vesicle->tape->plane_d) {
	111	vesicle->confinement_plane.z_max=max_z;
	112	vesicle->confinement_plane.z_min=max_z-vesicle->tape->plane_d;
	113	} else {
5eefcc	114	vesicle->confinement_plane.z_min=min_z;//-1e-5;
SP	115	vesicle->confinement_plane.z_max=max_z;//+1e-5;
267cf1	116	}
5eefcc	117	}
SP	118	ts_fprintf(stdout,"Planes (zmin, zmax)=(%e,%e)\n",vesicle->confinement_plane.z_min,vesicle->confinement_plane.z_max);
267cf1	119	}
SP	120
3de289	121	/* vesicle_volume(vesicle);
SP	122	fprintf(stderr,"Volume before TS=%1.16e\n", vesicle->volume); */
d7a113	123	for(j=0;j<mcsweeps;j++){
37d14a	124	single_timestep(vesicle, &vmsrt, &bfsrt);
SP	125	vmsr+=vmsrt;
	126	bfsr+=bfsrt;
d7a113	127	}
3de289	128	/*
SP	129	vesicle_volume(vesicle);
	130	fprintf(stderr,"Volume after TS=%1.16e\n", vesicle->volume); */
37d14a	131	vmsr/=(ts_double)mcsweeps;
SP	132	bfsr/=(ts_double)mcsweeps;
d7a113	133	centermass(vesicle);
SP	134	cell_occupation(vesicle);
1ab449	135	dump_state(vesicle,i);
58230a	136	if(i>=inititer){
0a2c81	137	write_vertex_xml_file(vesicle,i-inititer,NULL);
267db5	138	write_master_xml_file(command_line_args.output_fullfilename);
37d14a	139	epochtime=get_epoch();
SP	140	gyration_eigen(vesicle, &l1, &l2, &l3);
c0ae90	141	vesicle_volume(vesicle); //calculates just volume.
SP	142	vesicle_area(vesicle); //calculates area.
dc77e8	143	r0=getR0(vesicle);
632960	144	if(vesicle->sphHarmonics!=NULL){
SP	145	preparationSh(vesicle,r0);
459ff9	146	//calculateYlmi(vesicle);
SP	147	calculateUlmComplex(vesicle);
	148	storeUlmComplex2(vesicle);
632960	149	saveAvgUlm2(vesicle);
22cdfd	150	kc1=calculateKc(vesicle, 2,9);
SP	151	kc2=calculateKc(vesicle, 6,9);
	152	kc3=calculateKc(vesicle, 2,vesicle->sphHarmonics->l);
1665aa	153	kc4=calculateKc(vesicle, 3,6);
267db5	154	strcpy(filename,command_line_args.path);
SP	155	strcat(filename,"state.dat");
	156	fd1=fopen(filename,"w");
5bb6bb	157	fprintf(fd1,"%e %e\n",vesicle->volume, getR0(vesicle));
M	158	for(k=0;k<vesicle->vlist->n;k++){
	159	fprintf(fd1,"%e %e %e %e %e\n",
	160	vesicle->vlist->vtx[k]->x,
	161	vesicle->vlist->vtx[k]->y,
	162	vesicle->vlist->vtx[k]->z,
	163	vesicle->vlist->vtx[k]->solAngle,
	164	vesicle->vlist->vtx[k]->relR
	165	);
	166	}
	167	fclose(fd1);
5a3862	168
M	169	fprintf(fd2,"%u ", i);
	170	for(l=0;l<vesicle->sphHarmonics->l;l++){
	171	for(m=l;m<2*l+1;m++){
	172	fprintf(fd2,"%e ", gsl_complex_abs2(vesicle->sphHarmonics->ulmComplex[l][m]) );
	173	}
	174	}
	175	fprintf(fd2,"\n");
	176
	177	fflush(fd2);
	178
632960	179	}
dc77e8	180
c0ae90	181	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	182
632960	183	fflush(fd);
144784	184	// sprintf(filename,"timestep-%05d.pov",i-inititer);
fe24d2	185	// write_pov_file(vesicle,filename);
49981c	186	} //end if(inititer....)
SP	187	fd3=fopen(".status","w"); //write status file when everything is written to disk.
	188	if(fd3==NULL){
	189	fatal("Cannot open .status file for writing",1);
d7a113	190	}
49981c	191	fprintf(fd3,"%d",i);
SP	192	fclose(fd3);
	193	ts_fprintf(stdout,"Done %d out of %d iterations (x %d MC sweeps).\n",i+1,inititer+iterations,mcsweeps);
d7a113	194	}
37d14a	195	fclose(fd);
5a3862	196	if(fd2!=NULL) fclose(fd2);
d7a113	197	return TS_SUCCESS;
SP	198	}
d7639a	199
37d14a	200	ts_bool single_timestep(ts_vesicle vesicle,ts_double vmsr, ts_double *bfsr){
3de289	201	// vesicle_volume(vesicle);
SP	202	// fprintf(stderr,"Volume before TS=%1.16e\n", vesicle->volume);
d7639a	203	ts_bool retval;
SP	204	ts_double rnvec[3];
fe5069	205	ts_uint i,j, b;
37d14a	206	ts_uint vmsrcnt=0;
aec47d	207	for(i=0;i<vesicle->vlist->n;i++){
d7639a	208	rnvec[0]=drand48();
SP	209	rnvec[1]=drand48();
	210	rnvec[2]=drand48();
aec47d	211	retval=single_verticle_timestep(vesicle,vesicle->vlist->vtx[i],rnvec);
37d14a	212	if(retval==TS_SUCCESS) vmsrcnt++;
d7639a	213	}
SP	214
37d14a	215	ts_int bfsrcnt=0;
fedf2b	216	for(i=0;i<3*vesicle->vlist->n;i++){
fe5069	217	b=rand() % vesicle->blist->n;
d7639a	218	//find a bond and return a pointer to a bond...
SP	219	//call single_bondflip_timestep...
fe5069	220	retval=single_bondflip_timestep(vesicle,vesicle->blist->bond[b],rnvec);
3de289	221	// b++; retval=TS_FAIL;
37d14a	222	if(retval==TS_SUCCESS) bfsrcnt++;
fedf2b	223	}
M	224
	225	for(i=0;i<vesicle->poly_list->n;i++){
58230a	226	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
M	227	rnvec[0]=drand48();
	228	rnvec[1]=drand48();
	229	rnvec[2]=drand48();
	230	retval=single_poly_vertex_move(vesicle,vesicle->poly_list->poly[i],vesicle->poly_list->poly[i]->vlist->vtx[j],rnvec);
	231	}
fedf2b	232	}
M	233
58230a	234
M	235	for(i=0;i<vesicle->filament_list->n;i++){
	236	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	237	rnvec[0]=drand48();
	238	rnvec[1]=drand48();
	239	rnvec[2]=drand48();
	240	retval=single_filament_vertex_move(vesicle,vesicle->filament_list->poly[i],vesicle->filament_list->poly[i]->vlist->vtx[j],rnvec);
	241	}
fedf2b	242	}
M	243
58230a	244
fedf2b	245	// 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	246	*vmsr=(ts_double)vmsrcnt/(ts_double)vesicle->vlist->n;
SP	247	*bfsr=(ts_double)bfsrcnt/(ts_double)vesicle->vlist->n/3.0;
3de289	248	// vesicle_volume(vesicle);
SP	249	// fprintf(stderr,"Volume after TS=%1.16e\n", vesicle->volume);
d7639a	250	return TS_SUCCESS;
SP	251	}
	252
	253
	254