trisurf-ng.git - Gitblit

Changes in code and README for easier compilation. May break something

Samo Penic

2023-01-24 a8e354c7fad70eb7fdfda62ec83faf1be6c4ed44

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"
06afc7	7	#include "globals.h"
aec47d	8	#include "timestep.h"
SP	9	#include "vertexmove.h"
30ee9c	10	#include "bondflip.h"
d7a113	11	#include "frame.h"
SP	12	#include "io.h"
37d14a	13	#include "stats.h"
dc77e8	14	#include "sh.h"
459ff9	15	#include "shcomplex.h"
dc77e8	16	#include "vesicle.h"
5a3862	17	#include<gsl/gsl_complex.h>
M	18	#include<gsl/gsl_complex_math.h>
267db5	19	#include<string.h>
ac9826	20	#include <sys/stat.h>
SP	21
fedf2b	22
626811	23	ts_bool run_simulation(ts_vesicle *vesicle, ts_uint mcsweeps, ts_uint inititer, ts_uint iterations, ts_uint start_iteration){
d5d78a	24	ts_uint i, j,k; //,l,m;
SP	25	ts_double kc1=0,kc2=0,kc3=0,kc4=0;
c0ae90	26	ts_double l1,l2,l3,vmsr,bfsr, vmsrt, bfsrt;
37d14a	27	ts_ulong epochtime;
0dd5ba	28	ts_double max_z,min_z;
d5d78a	29	FILE *fd3=NULL;
267db5	30	char filename[10000];
ac9826	31	//struct stat st;
SP	32	strcpy(filename,command_line_args.path);
	33	strcat(filename,"statistics.csv");
	34	//int result = stat(filename, &st);
	35	FILE *fd;
	36	if(start_iteration==0)
	37	fd=fopen(filename,"w");
	38	else
	39	fd=fopen(filename,"a");
37d14a	40	if(fd==NULL){
SP	41	fatal("Cannot open statistics.csv file for writing",1);
	42	}
ac9826	43	if(start_iteration==0)
SP	44	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	45
d5d78a	46	/* if(vesicle->sphHarmonics!=NULL){
267db5	47	strcpy(filename,command_line_args.path);
SP	48	strcat(filename,"ulm2.csv");
ac9826	49	// int result = stat(filename, &st);
SP	50	if(start_iteration==0)
267db5	51	fd2=fopen(filename,"w");
ac9826	52	else
SP	53	fd2=fopen(filename,"a");
819a09	54	if(fd2==NULL){
S	55	fatal("Cannot open ulm2.csv file for writing",1);
d5d78a	56	}
SP	57
819a09	58	if(start_iteration==0) //file does not exist
S	59	fprintf(fd2, "Timestep u_00^2 u_10^2 u_11^2 u_20^2 ...\n");
5a3862	60	}
d5d78a	61	*/
5a3862	62
c60a49	63	/* RANDOM SEED SET BY CURRENT TIME */
M	64	epochtime=get_epoch();
	65	srand48(epochtime);
d7a113	66	centermass(vesicle);
SP	67	cell_occupation(vesicle);
fe5069	68	vesicle_volume(vesicle); //needed for constant volume at this moment
88bdd7	69	vesicle_area(vesicle); //needed for constant area at this moment
49981c	70	if(V0<0.000001)
SP	71	V0=vesicle->volume;
	72	ts_fprintf(stdout,"Setting volume V0=%.17f\n",V0);
	73	if(A0<0.000001)
	74	A0=vesicle->area;
819a09	75	ts_fprintf(stdout,"Setting area A0=%.17f\n",A0);
a54977	76	epsvol=4.0sqrt(2.0M_PI)/pow(3.0,3.0/4.0)*V0/pow(vesicle->tlist->n,3.0/2.0);
d5d78a	77	// printf("epsvol=%e\n",epsvol);
88bdd7	78	epsarea=A0/(ts_double)vesicle->tlist->n;
SP	79
626811	80	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	81	for(i=start_iteration;i<inititer+iterations;i++){
37d14a	82	vmsr=0.0;
SP	83	bfsr=0.0;
0dd5ba	84
SP	85	//plane confinement
	86	if(vesicle->tape->plane_confinement_switch){
	87	min_z=1e10;
	88	max_z=-1e10;
	89	for(k=0;k<vesicle->vlist->n;k++){
	90	if(vesicle->vlist->vtx[k]->z > max_z) max_z=vesicle->vlist->vtx[k]->z;
	91	if(vesicle->vlist->vtx[k]->z < min_z) min_z=vesicle->vlist->vtx[k]->z;
	92	}
	93	vesicle->confinement_plane.force_switch=0;
	94	if(max_z>=vesicle->tape->plane_d/2.0){
	95	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);
	96	vesicle->confinement_plane.z_max = max_z;
	97	vesicle->confinement_plane.force_switch=1;
	98	} else {
	99	vesicle->confinement_plane.z_max=vesicle->tape->plane_d/2.0;
	100	}
	101	if(min_z<=-vesicle->tape->plane_d/2.0){
	102	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);
	103	vesicle->confinement_plane.z_min = min_z;
	104	vesicle->confinement_plane.force_switch=1;
	105	} else {
	106	vesicle->confinement_plane.z_min=-vesicle->tape->plane_d/2.0;
	107	}
	108	ts_fprintf(stdout,"Vesicle confinement by plane set to (zmin, zmax)=(%e,%e).\n",vesicle->confinement_plane.z_min,vesicle->confinement_plane.z_max);
	109	if(vesicle->confinement_plane.force_switch) ts_fprintf(stdout,"Squeezing with force %e.\n",vesicle->tape->plane_F);
	110	}
	111
	112	//end plane confinement
	113
3de289	114	/* vesicle_volume(vesicle);
SP	115	fprintf(stderr,"Volume before TS=%1.16e\n", vesicle->volume); */
d7a113	116	for(j=0;j<mcsweeps;j++){
37d14a	117	single_timestep(vesicle, &vmsrt, &bfsrt);
SP	118	vmsr+=vmsrt;
	119	bfsr+=bfsrt;
d7a113	120	}
3de289	121	/*
SP	122	vesicle_volume(vesicle);
	123	fprintf(stderr,"Volume after TS=%1.16e\n", vesicle->volume); */
37d14a	124	vmsr/=(ts_double)mcsweeps;
SP	125	bfsr/=(ts_double)mcsweeps;
d7a113	126	centermass(vesicle);
SP	127	cell_occupation(vesicle);
2a1e3d	128	/* BINARY DUMPS ARE OBSOLETE. SHOULD WORK AS OF MAR 2020, BUT NO LONGER MAINTAINED */
SP	129	// dump_state(vesicle,i);
d5d78a	130	vesicle_volume(vesicle); //calculates just volume.
SP	131	vesicle_area(vesicle); //calculates area.
	132	if(vesicle->tape->constvolswitch==0){
	133	V0=vesicle->volume;
	134	}
	135	if(vesicle->tape->constareaswitch==0){
	136	A0=vesicle->area;
	137	}
58230a	138	if(i>=inititer){
0a2c81	139	write_vertex_xml_file(vesicle,i-inititer,NULL);
267db5	140	write_master_xml_file(command_line_args.output_fullfilename);
37d14a	141	epochtime=get_epoch();
SP	142	gyration_eigen(vesicle, &l1, &l2, &l3);
d5d78a	143	//r0=getR0(vesicle);
SP	144	/* if(vesicle->sphHarmonics!=NULL){
632960	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);
d5d78a	154
267db5	155	strcpy(filename,command_line_args.path);
SP	156	strcat(filename,"state.dat");
	157	fd1=fopen(filename,"w");
5bb6bb	158	fprintf(fd1,"%e %e\n",vesicle->volume, getR0(vesicle));
M	159	for(k=0;k<vesicle->vlist->n;k++){
	160	fprintf(fd1,"%e %e %e %e %e\n",
	161	vesicle->vlist->vtx[k]->x,
	162	vesicle->vlist->vtx[k]->y,
	163	vesicle->vlist->vtx[k]->z,
	164	vesicle->vlist->vtx[k]->solAngle,
	165	vesicle->vlist->vtx[k]->relR
	166	);
	167	}
	168	fclose(fd1);
5a3862	169
M	170	fprintf(fd2,"%u ", i);
	171	for(l=0;l<vesicle->sphHarmonics->l;l++){
	172	for(m=l;m<2*l+1;m++){
	173	fprintf(fd2,"%e ", gsl_complex_abs2(vesicle->sphHarmonics->ulmComplex[l][m]) );
	174	}
	175	}
	176	fprintf(fd2,"\n");
	177
	178	fflush(fd2);
	179
d5d78a	180
632960	181	}
d5d78a	182	*/
dc77e8	183
c0ae90	184	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	185
632960	186	fflush(fd);
144784	187	// sprintf(filename,"timestep-%05d.pov",i-inititer);
fe24d2	188	// write_pov_file(vesicle,filename);
49981c	189	} //end if(inititer....)
SP	190	fd3=fopen(".status","w"); //write status file when everything is written to disk.
	191	if(fd3==NULL){
	192	fatal("Cannot open .status file for writing",1);
d7a113	193	}
49981c	194	fprintf(fd3,"%d",i);
SP	195	fclose(fd3);
	196	ts_fprintf(stdout,"Done %d out of %d iterations (x %d MC sweeps).\n",i+1,inititer+iterations,mcsweeps);
d7a113	197	}
37d14a	198	fclose(fd);
d5d78a	199	// if(fd2!=NULL) fclose(fd2);
d7a113	200	return TS_SUCCESS;
SP	201	}
d7639a	202
37d14a	203	ts_bool single_timestep(ts_vesicle vesicle,ts_double vmsr, ts_double *bfsr){
3de289	204	// vesicle_volume(vesicle);
SP	205	// fprintf(stderr,"Volume before TS=%1.16e\n", vesicle->volume);
d7639a	206	ts_bool retval;
SP	207	ts_double rnvec[3];
fe5069	208	ts_uint i,j, b;
37d14a	209	ts_uint vmsrcnt=0;
aec47d	210	for(i=0;i<vesicle->vlist->n;i++){
d7639a	211	rnvec[0]=drand48();
SP	212	rnvec[1]=drand48();
	213	rnvec[2]=drand48();
aec47d	214	retval=single_verticle_timestep(vesicle,vesicle->vlist->vtx[i],rnvec);
37d14a	215	if(retval==TS_SUCCESS) vmsrcnt++;
d7639a	216	}
SP	217
37d14a	218	ts_int bfsrcnt=0;
fedf2b	219	for(i=0;i<3*vesicle->vlist->n;i++){
fe5069	220	b=rand() % vesicle->blist->n;
d7639a	221	//find a bond and return a pointer to a bond...
SP	222	//call single_bondflip_timestep...
fe5069	223	retval=single_bondflip_timestep(vesicle,vesicle->blist->bond[b],rnvec);
3de289	224	// b++; retval=TS_FAIL;
37d14a	225	if(retval==TS_SUCCESS) bfsrcnt++;
fedf2b	226	}
M	227
	228	for(i=0;i<vesicle->poly_list->n;i++){
58230a	229	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
M	230	rnvec[0]=drand48();
	231	rnvec[1]=drand48();
	232	rnvec[2]=drand48();
	233	retval=single_poly_vertex_move(vesicle,vesicle->poly_list->poly[i],vesicle->poly_list->poly[i]->vlist->vtx[j],rnvec);
	234	}
fedf2b	235	}
M	236
58230a	237
M	238	for(i=0;i<vesicle->filament_list->n;i++){
	239	for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
	240	rnvec[0]=drand48();
	241	rnvec[1]=drand48();
	242	rnvec[2]=drand48();
	243	retval=single_filament_vertex_move(vesicle,vesicle->filament_list->poly[i],vesicle->filament_list->poly[i]->vlist->vtx[j],rnvec);
	244	}
fedf2b	245	}
M	246
58230a	247
fedf2b	248	// 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	249	*vmsr=(ts_double)vmsrcnt/(ts_double)vesicle->vlist->n;
SP	250	*bfsr=(ts_double)bfsrcnt/(ts_double)vesicle->vlist->n/3.0;
3de289	251	// vesicle_volume(vesicle);
SP	252	// fprintf(stderr,"Volume after TS=%1.16e\n", vesicle->volume);
d7639a	253	return TS_SUCCESS;
SP	254	}
	255
	256
	257