From: hackbard <hackbard>
Date: Fri, 26 Jan 2007 15:36:19 +0000 (+0000)
Subject: pt scaling tests, though pressure estimation still a mess!
X-Git-Url: https://www.hackdaworld.org/gitweb/?p=physik%2Fposic.git;a=commitdiff_plain;h=91e4a00285261865ffce4b9553d153b562c80ee6

pt scaling tests, though pressure estimation still a mess!
---

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);
 			}
 		}
diff --git a/moldyn.h b/moldyn.h
index 0dbc1f9..f2ccdb5 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -313,6 +313,9 @@ typedef struct s_tersoff_mult_params {
 #define TRUE				1
 #define FALSE				0
 
+#define VERBOSE				1
+#define QUIET				0
+
 /*
  *
  * phsical values / constants
@@ -428,7 +431,7 @@ t_3dvec get_total_p(t_moldyn *moldyn);
 
 double estimate_time_step(t_moldyn *moldyn,double nn_dist);
 
-int link_cell_init(t_moldyn *moldyn);
+int link_cell_init(t_moldyn *moldyn,u8 vol);
 int link_cell_update(t_moldyn *moldyn);
 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
 int link_cell_shutdown(t_moldyn *moldyn);
diff --git a/sic.c b/sic.c
index 7e1249c..2a2c7bc 100644
--- a/sic.c
+++ b/sic.c
@@ -146,26 +146,15 @@ int main(int argc,char **argv) {
 	//           ATOM_ATTR_2BP|ATOM_ATTR_HB,
 	//           &r,&v);
 
-	/* setting a nearest neighbour distance for the moldyn checks */
-	//set_nn_dist(&md,0.25*sqrt(3.0)*LC_SI); /* diamond ! */
-	set_nn_dist(&md,LC_SI);
-
-	/* set temperature */
-	//set_temperature(&md,273.0+1410.0);
-	//set_temperature(&md,273.0+450.0);
-	//set_temperature(&md,273.0);
-	//set_temperature(&md,1.0);
-	//set_temperature(&md,0.0);
+	/* set temperature & pressure */
 	set_temperature(&md,atof(argv[2])+273.0);
-
-	/* set pressure */
 	set_pressure(&md,ATM);
 
 	/* set p/t scaling */
-	//set_pt_scale(&md,P_SCALE_BERENDSEN,100.0,
-	//                 T_SCALE_BERENDSEN,100.0);
+	set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
+	                 T_SCALE_BERENDSEN,100.0);
 	//set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
-	//set_pt_scale(&md,P_SCALE_BERENDSEN,100.0,0,0);
+	//set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
 	
 	/* initial thermal fluctuations of particles (in equilibrium) */
 	thermal_init(&md,TRUE);
diff --git a/visual/visual.c b/visual/visual.c
index a76c608..d6ce369 100644
--- a/visual/visual.c
+++ b/visual/visual.c
@@ -87,7 +87,8 @@ int visual_atoms(t_visual *v,double time,t_atom *atom,int n) {
 
 	/* script file update */
 	dprintf(v->fd,"load xyz %s\n",file);
-	dprintf(v->fd,"spacefill 100\n");
+	dprintf(v->fd,"spacefill\n");
+	//dprintf(v->fd,"spacefill 100\n");
 	dprintf(v->fd,"rotate x 100\n");
 	dprintf(v->fd,"rotate y 10\n");
 	dprintf(v->fd,"set ambient 20\n");