X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=d52fcd3868c2481e70cbc804b5a9cdf92542708d;hb=180ff86ae35ca0ea6ee857e92e56120e65315d17;hp=509a45da344a3f374567d8a727638763e68ed392;hpb=d888d2a17d4afa924939eb0d6528b2b73213d4f3;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 509a45d..d52fcd3 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -41,8 +41,9 @@ int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 
 int moldyn_shutdown(t_moldyn *moldyn) {
 
-	link_cell_shutdown(moldyn);
+	printf("[moldyn] shutdown\n");
 	moldyn_log_shutdown(moldyn);
+	link_cell_shutdown(moldyn);
 	rand_close(&(moldyn->random));
 	free(moldyn->atom);
 
@@ -92,6 +93,13 @@ int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
 	return 0;
 }
 
+int set_nn_dist(t_moldyn *moldyn,double dist) {
+
+	moldyn->nnd=dist;
+
+	return 0;
+}
+
 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 
 	if(x)
@@ -156,7 +164,7 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
 			strncpy(moldyn->sfb,fb,63);
 			break;
 		case VISUAL_STEP:
-			moldyn->mwrite=timer;
+			moldyn->vwrite=timer;
 			strncpy(moldyn->vfb,fb,63);
 			visual_init(&(moldyn->vis),fb);
 			break;
@@ -170,9 +178,10 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
 
 int moldyn_log_shutdown(t_moldyn *moldyn) {
 
+	printf("[moldyn] log shutdown\n");
 	if(moldyn->efd) close(moldyn->efd);
 	if(moldyn->mfd) close(moldyn->mfd);
-	if(moldyn->visual) visual_tini(moldyn->visual);
+	if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
 
 	return 0;
 }
@@ -183,17 +192,15 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	int count;
 	int ret;
 	t_3dvec origin;
-	t_atom *atom;
 
 	count=a*b*c;
-	atom=moldyn->atom;
 
 	if(type==FCC) count*=4;
 
 	if(type==DIAMOND) count*=8;
 
-	atom=malloc(count*sizeof(t_atom));
-	if(atom==NULL) {
+	moldyn->atom=malloc(count*sizeof(t_atom));
+	if(moldyn->atom==NULL) {
 		perror("malloc (atoms)");
 		return -1;
 	}
@@ -202,10 +209,10 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 
 	switch(type) {
 		case FCC:
-			ret=fcc_init(a,b,c,lc,atom,&origin);
+			ret=fcc_init(a,b,c,lc,moldyn->atom,&origin);
 			break;
 		case DIAMOND:
-			ret=diamond_init(a,b,c,lc,atom,&origin);
+			ret=diamond_init(a,b,c,lc,moldyn->atom,&origin);
 			break;
 		default:
 			printf("unknown lattice type (%02x)\n",type);
@@ -221,12 +228,13 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	}
 
 	moldyn->count=count;
+	printf("[moldyn] created lattice with %d atoms\n",count);
 
 	while(count) {
-		atom[count-1].element=element;
-		atom[count-1].mass=mass;
-		atom[count-1].attr=attr;
-		atom[count-1].bnum=bnum;
+		moldyn->atom[count-1].element=element;
+		moldyn->atom[count-1].mass=mass;
+		moldyn->atom[count-1].attr=attr;
+		moldyn->atom[count-1].bnum=bnum;
 		count-=1;
 	}
 
@@ -234,7 +242,7 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 }
 
 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
-             t_3dvec r,t_3dvec v) {
+             t_3dvec *r,t_3dvec *v) {
 
 	t_atom *atom;
 	void *ptr;
@@ -248,13 +256,15 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
 		perror("[moldyn] realloc (add atom)");
 		return -1;
 	}
-	
-	atom=ptr;
-	atom->r=r;
-	atom->v=v;
-	atom->element=element;
-	atom->bnum=bnum;
-	atom->attr=attr;
+	moldyn->atom=ptr;
+
+	atom=moldyn->atom;
+	atom[count-1].r=*r;
+	atom[count-1].v=*v;
+	atom[count-1].element=element;
+	atom[count-1].mass=mass;
+	atom[count-1].bnum=bnum;
+	atom[count-1].attr=attr;
 
 	return 0;
 }
@@ -309,15 +319,15 @@ int thermal_init(t_moldyn *moldyn) {
 	}
 
 	/* velocity scaling */
-	scale_velocity(moldyn);
+	scale_velocity(moldyn,VSCALE_INIT_EQUI);
 
 	return 0;
 }
 
-int scale_velocity(t_moldyn *moldyn) {
+int scale_velocity(t_moldyn *moldyn,u8 type) {
 
 	int i;
-	double e,c;
+	double e,scale;
 	t_atom *atom;
 
 	atom=moldyn->atom;
@@ -325,12 +335,15 @@ int scale_velocity(t_moldyn *moldyn) {
 	/*
 	 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 	 */
+
 	e=0.0;
 	for(i=0;i<moldyn->count;i++)
 		e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
-	c=sqrt((2.0*e)/(3.0*moldyn->count*K_BOLTZMANN*moldyn->t));
+	scale=(1.5*moldyn->count*K_BOLTZMANN*moldyn->t)/e;
+	if(type&VSCALE_INIT_EQUI) scale*=2.0; /* equipartition theorem */
+	scale=sqrt(scale);
 	for(i=0;i<moldyn->count;i++)
-		v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
+		v3_scale(&(atom[i].v),&(atom[i].v),scale);
 
 	return 0;
 }
@@ -381,15 +394,19 @@ t_3dvec get_total_p(t_moldyn *moldyn) {
 	return p_total;
 }
 
-double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
+double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
 
 	double tau;
 
-	tau=0.05*nn_dist/(sqrt(3.0*K_BOLTZMANN*t/moldyn->atom[0].mass));
-	tau*=1.0E-9;
-	if(tau<moldyn->tau)
-		printf("[moldyn] warning: time step  (%f > %.15f)\n",
-		       moldyn->tau,tau);
+	/* nn_dist is the nearest neighbour distance */
+
+	if(moldyn->t==5.0) {
+		printf("[moldyn] i do not estimate timesteps below %f K!\n",
+		       MOLDYN_CRITICAL_EST_TEMP);
+		return 23.42;
+	}
+
+	tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
 
 	return tau;	
 }
@@ -404,6 +421,9 @@ int link_cell_init(t_moldyn *moldyn) {
 
 	t_linkcell *lc;
 	int i;
+	int fd;
+
+	fd=open("/dev/null",O_WRONLY);
 
 	lc=&(moldyn->lc);
 
@@ -418,10 +438,11 @@ int link_cell_init(t_moldyn *moldyn) {
 	lc->cells=lc->nx*lc->ny*lc->nz;
 	lc->subcell=malloc(lc->cells*sizeof(t_list));
 
-	printf("initializing linked cells (%d)\n",lc->cells);
+	printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 
 	for(i=0;i<lc->cells;i++)
-		list_init(&(lc->subcell[i]),1);
+		//list_init(&(lc->subcell[i]),1);
+		list_init(&(lc->subcell[i]),fd);
 
  	link_cell_update(moldyn);
 	
@@ -541,6 +562,7 @@ int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
 		perror("[moldyn] realloc (runs)");
 		return -1;
 	}
+	moldyn->schedule.runs=ptr;
 	moldyn->schedule.runs[count-1]=runs;
 
 	ptr=realloc(schedule->tau,count*sizeof(double));
@@ -548,6 +570,7 @@ int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
 		perror("[moldyn] realloc (tau)");
 		return -1;
 	}
+	moldyn->schedule.tau=ptr;
 	moldyn->schedule.tau[count-1]=tau;
 
 	return 0;
@@ -575,11 +598,13 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	unsigned int e,m,s,v;
 	t_3dvec p;
 	t_moldyn_schedule *schedule;
-
+	t_atom *atom;
 	int fd;
 	char fb[128];
+	double ds;
 
 	schedule=&(moldyn->schedule);
+	atom=moldyn->atom;
 
 	/* initialize linked cell method */
 	link_cell_init(moldyn);
@@ -597,6 +622,17 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	/* calculate initial forces */
 	potential_force_calc(moldyn);
 
+	/* do some checks before we actually start calculating bullshit */
+	if(moldyn->cutoff>0.5*moldyn->dim.x)
+		printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
+	if(moldyn->cutoff>0.5*moldyn->dim.y)
+		printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
+	if(moldyn->cutoff>0.5*moldyn->dim.z)
+		printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
+	ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
+	if(ds>0.05*moldyn->nnd)
+		printf("[moldyn] warning: forces too high / tau too small!\n");
+
 	/* zero absolute time */
 	moldyn->time=0.0;
 
@@ -650,12 +686,13 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		}
 		if(v) {
 			if(!(i%v)) {
-				visual_atoms(moldyn->visual,i*moldyn->tau,
+				visual_atoms(&(moldyn->vis),moldyn->time,
 				             moldyn->atom,moldyn->count);
-				printf("\rsteps: %d",i);
+				printf("\rsched: %d, steps: %d",sched,i);
 				fflush(stdout);
 			}
 		}
+
 	}
 
 		/* check for hooks */
@@ -687,7 +724,7 @@ int velocity_verlet(t_moldyn *moldyn) {
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
 		v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
-		v3_per_bound(&(atom[i].r),&(moldyn->dim));
+		check_per_bound(moldyn,&(atom[i].r));
 
 		/* velocities */
 		v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
@@ -695,15 +732,11 @@ int velocity_verlet(t_moldyn *moldyn) {
 	}
 
 	/* neighbour list update */
-printf("list update ...\n");
 	link_cell_update(moldyn);
-printf("done\n");
 
 	/* forces depending on chosen potential */
-printf("calc potential/force ...\n");
 	potential_force_calc(moldyn);
 	//moldyn->potential_force_function(moldyn);
-printf("done\n");
 
 	for(i=0;i<count;i++) {
 		/* again velocities */
@@ -751,7 +784,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 		/* 2 body pair potential/force */
 		if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
-		
+	
 			link_cell_neighbour_index(moldyn,
 				(atom[i].r.x+moldyn->dim.x/2)/lc->x,
 				(atom[i].r.y+moldyn->dim.y/2)/lc->y,
@@ -885,7 +918,6 @@ int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
 	v3_sub(&distance,&(ai->r),&(aj->r));
 	
-	v3_per_bound(&distance,&(moldyn->dim));
 	if(bc) check_per_bound(moldyn,&distance);
 	d=v3_norm(&distance);
 	if(d<=moldyn->cutoff) {
@@ -929,7 +961,7 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 		d=+h1-h2;
 		d*=eps;
 		v3_scale(&force,&distance,d);
-		v3_add(&(ai->f),&(aj->f),&force);
+		v3_add(&(ai->f),&(ai->f),&force);
 	}
 
 	return 0;