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Isak's proposal for stretching energy calculation, take 1

Samo Penic

2018-06-21 620ba72765eda244ca3f3806b8ad709929e74b3c

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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>
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;
3d0247	27	FILE fd1,fd2=NULL,*fd3=NULL;
267db5	28	char filename[10000];
ac9826	29	//struct stat st;
SP	30	strcpy(filename,command_line_args.path);
	31	strcat(filename,"statistics.csv");
	32	//int result = stat(filename, &st);
	33	FILE *fd;
	34	if(start_iteration==0)
	35	fd=fopen(filename,"w");
	36	else
	37	fd=fopen(filename,"a");
37d14a	38	if(fd==NULL){
SP	39	fatal("Cannot open statistics.csv file for writing",1);
	40	}
ac9826	41	if(start_iteration==0)
SP	42	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	43
M	44	if(vesicle->sphHarmonics!=NULL){
267db5	45	strcpy(filename,command_line_args.path);
SP	46	strcat(filename,"ulm2.csv");
ac9826	47	// int result = stat(filename, &st);
SP	48	if(start_iteration==0)
267db5	49	fd2=fopen(filename,"w");
ac9826	50	else
SP	51	fd2=fopen(filename,"a");
819a09	52	if(fd2==NULL){
S	53	fatal("Cannot open ulm2.csv file for writing",1);
	54	}
	55	if(start_iteration==0) //file does not exist
	56	fprintf(fd2, "Timestep u_00^2 u_10^2 u_11^2 u_20^2 ...\n");
5a3862	57	}
M	58
c60a49	59	/* RANDOM SEED SET BY CURRENT TIME */
M	60	epochtime=get_epoch();
	61	srand48(epochtime);
d7a113	62	centermass(vesicle);
SP	63	cell_occupation(vesicle);
fe5069	64	vesicle_volume(vesicle); //needed for constant volume at this moment
620ba7	65	vesicle_area(vesicle); //needed for constant area and stretching energy at this moment
49981c	66	if(V0<0.000001)
SP	67	V0=vesicle->volume;
	68	ts_fprintf(stdout,"Setting volume V0=%.17f\n",V0);
	69	if(A0<0.000001)
	70	A0=vesicle->area;
819a09	71	ts_fprintf(stdout,"Setting area A0=%.17f\n",A0);
a54977	72	epsvol=4.0sqrt(2.0M_PI)/pow(3.0,3.0/4.0)*V0/pow(vesicle->tlist->n,3.0/2.0);
c0ae90	73	epsarea=A0/(ts_double)vesicle->tlist->n;
a54977	74	// fprintf(stderr, "DVol=%1.16f (%1.16f), V0=%1.16f\n", epsvol,0.003e-2*V0,V0);
626811	75	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	76	for(i=start_iteration;i<inititer+iterations;i++){
37d14a	77	vmsr=0.0;
SP	78	bfsr=0.0;
3de289	79	/* vesicle_volume(vesicle);
SP	80	fprintf(stderr,"Volume before TS=%1.16e\n", vesicle->volume); */
d7a113	81	for(j=0;j<mcsweeps;j++){
37d14a	82	single_timestep(vesicle, &vmsrt, &bfsrt);
SP	83	vmsr+=vmsrt;
	84	bfsr+=bfsrt;
d7a113	85	}
3de289	86	/*
SP	87	vesicle_volume(vesicle);
	88	fprintf(stderr,"Volume after TS=%1.16e\n", vesicle->volume); */
37d14a	89	vmsr/=(ts_double)mcsweeps;
SP	90	bfsr/=(ts_double)mcsweeps;
d7a113	91	centermass(vesicle);
SP	92	cell_occupation(vesicle);
1ab449	93	dump_state(vesicle,i);
58230a	94	if(i>=inititer){
0a2c81	95	write_vertex_xml_file(vesicle,i-inititer,NULL);
267db5	96	write_master_xml_file(command_line_args.output_fullfilename);
37d14a	97	epochtime=get_epoch();
SP	98	gyration_eigen(vesicle, &l1, &l2, &l3);
c0ae90	99	vesicle_volume(vesicle); //calculates just volume.
SP	100	vesicle_area(vesicle); //calculates area.
dc77e8	101	r0=getR0(vesicle);
632960	102	if(vesicle->sphHarmonics!=NULL){
SP	103	preparationSh(vesicle,r0);
459ff9	104	//calculateYlmi(vesicle);
SP	105	calculateUlmComplex(vesicle);
	106	storeUlmComplex2(vesicle);
632960	107	saveAvgUlm2(vesicle);
22cdfd	108	kc1=calculateKc(vesicle, 2,9);
SP	109	kc2=calculateKc(vesicle, 6,9);
	110	kc3=calculateKc(vesicle, 2,vesicle->sphHarmonics->l);
1665aa	111	kc4=calculateKc(vesicle, 3,6);
267db5	112	strcpy(filename,command_line_args.path);
SP	113	strcat(filename,"state.dat");
	114	fd1=fopen(filename,"w");
5bb6bb	115	fprintf(fd1,"%e %e\n",vesicle->volume, getR0(vesicle));
M	116	for(k=0;k<vesicle->vlist->n;k++){
	117	fprintf(fd1,"%e %e %e %e %e\n",
	118	vesicle->vlist->vtx[k]->x,
	119	vesicle->vlist->vtx[k]->y,
	120	vesicle->vlist->vtx[k]->z,
	121	vesicle->vlist->vtx[k]->solAngle,
	122	vesicle->vlist->vtx[k]->relR
	123	);
	124	}
	125	fclose(fd1);
5a3862	126
M	127	fprintf(fd2,"%u ", i);
	128	for(l=0;l<vesicle->sphHarmonics->l;l++){
	129	for(m=l;m<2*l+1;m++){
	130	fprintf(fd2,"%e ", gsl_complex_abs2(vesicle->sphHarmonics->ulmComplex[l][m]) );
	131	}
	132	}
	133	fprintf(fd2,"\n");
	134
	135	fflush(fd2);
	136
632960	137	}
dc77e8	138
c0ae90	139	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	140
632960	141	fflush(fd);
144784	142	// sprintf(filename,"timestep-%05d.pov",i-inititer);
fe24d2	143	// write_pov_file(vesicle,filename);
49981c	144	} //end if(inititer....)
SP	145	fd3=fopen(".status","w"); //write status file when everything is written to disk.
	146	if(fd3==NULL){
	147	fatal("Cannot open .status file for writing",1);
d7a113	148	}
49981c	149	fprintf(fd3,"%d",i);
SP	150	fclose(fd3);
	151	ts_fprintf(stdout,"Done %d out of %d iterations (x %d MC sweeps).\n",i+1,inititer+iterations,mcsweeps);
d7a113	152	}
37d14a	153	fclose(fd);
5a3862	154	if(fd2!=NULL) fclose(fd2);
d7a113	155	return TS_SUCCESS;
SP	156	}
d7639a	157
37d14a	158	ts_bool single_timestep(ts_vesicle vesicle,ts_double vmsr, ts_double *bfsr){
3de289	159	// vesicle_volume(vesicle);
SP	160	// fprintf(stderr,"Volume before TS=%1.16e\n", vesicle->volume);
d7639a	161	ts_bool retval;
SP	162	ts_double rnvec[3];
fe5069	163	ts_uint i,j, b;
37d14a	164	ts_uint vmsrcnt=0;
aec47d	165	for(i=0;i<vesicle->vlist->n;i++){
d7639a	166	rnvec[0]=drand48();
SP	167	rnvec[1]=drand48();
	168	rnvec[2]=drand48();
aec47d	169	retval=single_verticle_timestep(vesicle,vesicle->vlist->vtx[i],rnvec);
37d14a	170	if(retval==TS_SUCCESS) vmsrcnt++;
d7639a	171	}
SP	172
37d14a	173	ts_int bfsrcnt=0;
fedf2b	174	for(i=0;i<3*vesicle->vlist->n;i++){
fe5069	175	b=rand() % vesicle->blist->n;
d7639a	176	//find a bond and return a pointer to a bond...
SP	177	//call single_bondflip_timestep...
fe5069	178	retval=single_bondflip_timestep(vesicle,vesicle->blist->bond[b],rnvec);
3de289	179	// b++; retval=TS_FAIL;
37d14a	180	if(retval==TS_SUCCESS) bfsrcnt++;
fedf2b	181	}
M	182
	183	for(i=0;i<vesicle->poly_list->n;i++){
58230a	184	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
M	185	rnvec[0]=drand48();
	186	rnvec[1]=drand48();
	187	rnvec[2]=drand48();
	188	retval=single_poly_vertex_move(vesicle,vesicle->poly_list->poly[i],vesicle->poly_list->poly[i]->vlist->vtx[j],rnvec);
	189	}
fedf2b	190	}
M	191
58230a	192
M	193	for(i=0;i<vesicle->filament_list->n;i++){
	194	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	195	rnvec[0]=drand48();
	196	rnvec[1]=drand48();
	197	rnvec[2]=drand48();
	198	retval=single_filament_vertex_move(vesicle,vesicle->filament_list->poly[i],vesicle->filament_list->poly[i]->vlist->vtx[j],rnvec);
	199	}
fedf2b	200	}
M	201
58230a	202
fedf2b	203	// 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	204	*vmsr=(ts_double)vmsrcnt/(ts_double)vesicle->vlist->n;
SP	205	*bfsr=(ts_double)bfsrcnt/(ts_double)vesicle->vlist->n/3.0;
3de289	206	// vesicle_volume(vesicle);
SP	207	// fprintf(stderr,"Volume after TS=%1.16e\n", vesicle->volume);
d7639a	208	return TS_SUCCESS;
SP	209	}
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