X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=0d5027c57df699447bcdf61a2c2b516235c2fa0d;hb=91e4a00285261865ffce4b9553d153b562c80ee6;hp=881f0b698565fe7495ee151ecca63239d32e74cf;hpb=c0ddf2bdd8067456f39f6b63fe2261624ebde6b7;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 881f0b6..0d5027c 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -73,7 +73,7 @@ int set_temperature(t_moldyn *moldyn,double t_ref) {
 
 	moldyn->t_ref=t_ref;
 
-	printf("[moldyn] temperature: %f\n",moldyn->t_ref);
+	printf("[moldyn] temperature [K]: %f\n",moldyn->t_ref);
 
 	return 0;
 }
@@ -82,7 +82,7 @@ int set_pressure(t_moldyn *moldyn,double p_ref) {
 
 	moldyn->p_ref=p_ref;
 
-	printf("[moldyn] pressure: %f\n",moldyn->p_ref);
+	printf("[moldyn] pressure [atm]: %f\n",moldyn->p_ref/ATM);
 
 	return 0;
 }
@@ -344,15 +344,18 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 
 	switch(type) {
 		case CUBIC:
+			set_nn_dist(moldyn,lc);
 			origin.x=0.5*lc;
 			origin.y=0.5*lc;
 			origin.z=0.5*lc;
 			ret=cubic_init(a,b,c,lc,atom,&origin);
 			break;
 		case FCC:
+			set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
 			ret=fcc_init(a,b,c,lc,atom,NULL);
 			break;
 		case DIAMOND:
+			set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
 			ret=diamond_init(a,b,c,lc,atom,&origin);
 			break;
 		default:
@@ -720,7 +723,7 @@ double thermodynamic_pressure_calc(t_moldyn *moldyn) {
 	scale_dim(moldyn,scale,TRUE,0,0);
 	scale_atoms(moldyn,scale,TRUE,0,0);
 	link_cell_shutdown(moldyn);
-	link_cell_init(moldyn);
+	link_cell_init(moldyn,QUIET);
 	potential_force_calc(moldyn);
 	tp->x=(moldyn->energy-u)/moldyn->dv;
 	p=tp->x*tp->x;
@@ -734,7 +737,7 @@ double thermodynamic_pressure_calc(t_moldyn *moldyn) {
 	scale_dim(moldyn,scale,0,TRUE,0);
 	scale_atoms(moldyn,scale,0,TRUE,0);
 	link_cell_shutdown(moldyn);
-	link_cell_init(moldyn);
+	link_cell_init(moldyn,QUIET);
 	potential_force_calc(moldyn);
 	tp->y=(moldyn->energy-u)/moldyn->dv;
 	p+=tp->y*tp->y;
@@ -748,7 +751,7 @@ double thermodynamic_pressure_calc(t_moldyn *moldyn) {
 	scale_dim(moldyn,scale,0,0,TRUE);
 	scale_atoms(moldyn,scale,0,0,TRUE);
 	link_cell_shutdown(moldyn);
-	link_cell_init(moldyn);
+	link_cell_init(moldyn,QUIET);
 	potential_force_calc(moldyn);
 	tp->z=(moldyn->energy-u)/moldyn->dv;
 	p+=tp->z*tp->z;
@@ -765,7 +768,7 @@ printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
 	scale_dim(moldyn,scale,1,1,1);
 	scale_atoms(moldyn,scale,1,1,1);
 	link_cell_shutdown(moldyn);
-	link_cell_init(moldyn);
+	link_cell_init(moldyn,QUIET);
 	potential_force_calc(moldyn);
 printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
 
@@ -779,7 +782,7 @@ printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
 	moldyn->energy=u;
 
 	link_cell_shutdown(moldyn);
-	link_cell_init(moldyn);
+	link_cell_init(moldyn,QUIET);
 
 	return sqrt(p);
 }
@@ -820,61 +823,48 @@ int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
 
 int scale_volume(t_moldyn *moldyn) {
 
-	t_atom *atom;
 	t_3dvec *dim,*vdim;
-	double scale,v;
-	t_virial virial;
+	double scale;
 	t_linkcell *lc;
-	int i;
 
-	atom=moldyn->atom;
-	dim=&(moldyn->dim);
 	vdim=&(moldyn->vis.dim);
+	dim=&(moldyn->dim);
 	lc=&(moldyn->lc);
 
-	memset(&virial,0,sizeof(t_virial));
+	/* scaling factor */
+	if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
+		scale=1.0-(moldyn->p_ref-moldyn->p)/moldyn->p_tc;
+		scale=pow(scale,ONE_THIRD);
+	}
+	else {
+		scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
+	}
+moldyn->debug=scale;
 
-	for(i=0;i<moldyn->count;i++) {
-		virial.xx+=atom[i].virial.xx;
-		virial.yy+=atom[i].virial.yy;
-		virial.zz+=atom[i].virial.zz;
-		virial.xy+=atom[i].virial.xy;
-		virial.xz+=atom[i].virial.xz;
-		virial.yz+=atom[i].virial.yz;
+	/* scale the atoms and dimensions */
+	scale_atoms(moldyn,scale,TRUE,TRUE,TRUE);
+	scale_dim(moldyn,scale,TRUE,TRUE,TRUE);
+
+	/* visualize dimensions */
+	if(vdim->x!=0) {
+		vdim->x=dim->x;
+		vdim->y=dim->y;
+		vdim->z=dim->z;
 	}
 
-	/* just a guess so far ... */
-	v=virial.xx+virial.yy+virial.zz;
-
-printf("%f\n",v);
-	/* get pressure from virial */
-	moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t+ONE_THIRD*v;
-	moldyn->p/=moldyn->volume;
-printf("%f | %f\n",moldyn->p/(ATM),moldyn->p_ref/ATM);
-
-	/* scale factor */
-	if(moldyn->pt_scale&P_SCALE_BERENDSEN)
-		scale=3*sqrt(1-(moldyn->p_ref-moldyn->p)/moldyn->p_tc);
-	else 
-		/* should actually never be used */
-		scale=pow(moldyn->p/moldyn->p_ref,1.0/3.0);
-
-printf("scale = %f\n",scale);
-	/* actual scaling */
-	dim->x*=scale;
-	dim->y*=scale;
-	dim->z*=scale;
-	if(vdim->x) vdim->x=dim->x;
-	if(vdim->y) vdim->y=dim->y;
-	if(vdim->z) vdim->z=dim->z;
-	moldyn->volume*=(scale*scale*scale);
-
-	/* check whether we need a new linkcell init */
-	if((dim->x/moldyn->cutoff!=lc->nx)||
-	   (dim->y/moldyn->cutoff!=lc->ny)||
-	   (dim->z/moldyn->cutoff!=lc->nx)) {
+	/* recalculate scaled volume */
+	moldyn->volume=dim->x*dim->y*dim->z;
+
+	/* adjust/reinit linkcell */
+	if(((int)(dim->x/moldyn->cutoff)!=lc->nx)||
+	   ((int)(dim->y/moldyn->cutoff)!=lc->ny)||
+	   ((int)(dim->z/moldyn->cutoff)!=lc->nx)) {
 		link_cell_shutdown(moldyn);
-		link_cell_init(moldyn);
+		link_cell_init(moldyn,QUIET);
+	} else {
+		lc->x*=scale;
+		lc->y*=scale;
+		lc->z*=scale;
 	}
 
 	return 0;
@@ -939,7 +929,7 @@ double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
 
 /* linked list / cell method */
 
-int link_cell_init(t_moldyn *moldyn) {
+int link_cell_init(t_moldyn *moldyn,u8 vol) {
 
 	t_linkcell *lc;
 	int i;
@@ -960,7 +950,7 @@ int link_cell_init(t_moldyn *moldyn) {
 	if(lc->cells<27)
 		printf("[moldyn] FATAL: less then 27 subcells!\n");
 
-	printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
+	if(vol) printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 
 	for(i=0;i<lc->cells;i++)
 		list_init_f(&(lc->subcell[i]));
@@ -1137,7 +1127,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	atom=moldyn->atom;
 
 	/* initialize linked cell method */
-	link_cell_init(moldyn);
+	link_cell_init(moldyn,VERBOSE);
 
 	/* logging & visualization */
 	e=moldyn->ewrite;
@@ -1152,10 +1142,8 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	/* energy scaling factor */
 	energy_scale=moldyn->count*EV;
 
-printf("debug: %f\n",moldyn->atom[0].f.x);
 	/* calculate initial forces */
 	potential_force_calc(moldyn);
-printf("debug: %f\n",moldyn->atom[0].f.x);
 
 	/* some stupid checks before we actually start calculating bullshit */
 	if(moldyn->cutoff>0.5*moldyn->dim.x)
@@ -1192,17 +1180,18 @@ printf("debug: %f\n",moldyn->atom[0].f.x);
 		/* integration step */
 		moldyn->integrate(moldyn);
 
+		/* calculate kinetic energy, temperature and pressure */
+		update_e_kin(moldyn);
+		temperature_calc(moldyn);
+		pressure_calc(moldyn);
+		//thermodynamic_pressure_calc(moldyn);
+
 		/* p/t scaling */
 		if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
 			scale_velocity(moldyn,FALSE);
 		if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
 			scale_volume(moldyn);
 
-		update_e_kin(moldyn);
-		temperature_calc(moldyn);
-		pressure_calc(moldyn);
-		//thermodynamic_pressure_calc(moldyn);
-
 		/* check for log & visualization */
 		if(e) {
 			if(!(i%e))
@@ -1237,8 +1226,9 @@ printf("debug: %f\n",moldyn->atom[0].f.x);
 			if(!(i%v)) {
 				visual_atoms(&(moldyn->vis),moldyn->time,
 				             moldyn->atom,moldyn->count);
-				printf("\rsched: %d, steps: %d, debug: %f",
-				       sched->count,i,moldyn->p/ATM);
+				printf("\rsched: %d, steps: %d, T: %f, P: %f V: %f",
+				       sched->count,i,
+				       moldyn->t,moldyn->p/ATM,moldyn->volume);
 				fflush(stdout);
 			}
 		}