From: hackbard <hackbard>
Date: Wed, 31 Jan 2007 16:35:26 +0000 (+0000)
Subject: create_lattice fixes, still virial probs ...
X-Git-Url: https://hackdaworld.org/gitweb/?a=commitdiff_plain;h=cb177e7c208a85b45d77b09fcada23b62d0248b5;p=physik%2Fposic.git

create_lattice fixes, still virial probs ...
---

diff --git a/moldyn.c b/moldyn.c
index 0d5027c..f6c3c81 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -339,22 +339,24 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	}
 	moldyn->atom=ptr;
 	atom=&(moldyn->atom[count]);
-		
-	v3_zero(&origin);
+
+	/* no atoms on the boundaries (only reason: it looks better!) */
+	origin.x=0.5*lc;
+	origin.y=0.5*lc;
+	origin.z=0.5*lc;
 
 	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:
+			v3_scale(&origin,&origin,0.5);
 			set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
-			ret=fcc_init(a,b,c,lc,atom,NULL);
+			ret=fcc_init(a,b,c,lc,atom,&origin);
 			break;
 		case DIAMOND:
+			v3_scale(&origin,&origin,0.25);
 			set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
 			ret=diamond_init(a,b,c,lc,atom,&origin);
 			break;
@@ -429,65 +431,55 @@ int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 
 	int count;
-	int i,j;
+	int i,j,k,l;
 	t_3dvec o,r,n;
 	t_3dvec basis[3];
-	double help[3];
-	double x,y,z;
-
-	x=a*lc;
-	y=b*lc;
-	z=c*lc;
 
-	if(origin) v3_copy(&o,origin);
-	else v3_zero(&o);
+	count=0;
+	if(origin)
+		v3_copy(&o,origin);
+	else
+		v3_zero(&o);
 
 	/* construct the basis */
-	for(i=0;i<3;i++) {
-		for(j=0;j<3;j++) {
-			if(i!=j) help[j]=0.5*lc;
-			else help[j]=.0;
-		}
-		v3_set(&basis[i],help);
-	}
+	memset(basis,0,3*sizeof(t_3dvec));
+	basis[0].x=0.5*lc;
+	basis[0].y=0.5*lc;
+	basis[1].x=0.5*lc;
+	basis[1].z=0.5*lc;
+	basis[2].y=0.5*lc;
+	basis[2].z=0.5*lc;
 
-	v3_zero(&r);
-	count=0;
-	
 	/* fill up the room */
 	r.x=o.x;
-	while(r.x<x) {
+	for(i=0;i<a;i++) {
 		r.y=o.y;
-		while(r.y<y) {
+		for(j=0;j<b;j++) {
 			r.z=o.z;
-			while(r.z<z) {
+			for(k=0;k<c;k++) {
+				/* first atom */
 				v3_copy(&(atom[count].r),&r);
-				atom[count].element=1;
 				count+=1;
-				for(i=0;i<3;i++) {
-					v3_add(&n,&r,&basis[i]);
-					if((n.x<x+o.x)&&
-					   (n.y<y+o.y)&&
-					   (n.z<z+o.z)) {
-						v3_copy(&(atom[count].r),&n);
-						count+=1;
-					}
+				r.z+=lc;
+				/* the three face centered atoms */
+				for(l=0;l<3;l++) {
+					v3_add(&n,&r,&basis[l]);
+					v3_copy(&(atom[count].r),&n);
+					count+=1;
 				}
-				r.z+=lc;	
 			}
 			r.y+=lc;
 		}
 		r.x+=lc;
 	}
-
+				
 	/* coordinate transformation */
-	help[0]=x/2.0;
-	help[1]=y/2.0;
-	help[2]=z/2.0;
-	v3_set(&n,help);
-	for(i=0;i<count;i++)
-		v3_sub(&(atom[i].r),&(atom[i].r),&n);
-		
+	for(i=0;i<count;i++) {
+		atom[i].r.x-=(a*lc)/2.0;
+		atom[i].r.y-=(b*lc)/2.0;
+		atom[i].r.z-=(c*lc)/2.0;
+	}
+
 	return count;
 }
 
@@ -1575,6 +1567,7 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 		v3_scale(&force,&force,-1.0); /* f = - grad E */
 		v3_add(&(ai->f),&(ai->f),&force);
 		virial_calc(ai,&force,&distance);
+if(force.x*distance.x<=0) printf("virial xx: %.15f -> %f %f %f\n",force.x*distance.x,distance.x,distance.y,distance.z);
 		virial_calc(aj,&force,&distance); /* f and d signe switched */
 	}
 
diff --git a/moldyn.h b/moldyn.h
index f2ccdb5..3c53a86 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -334,7 +334,8 @@ typedef struct s_tersoff_mult_params {
 #define M_SI			28.08553			/* amu */
 
 //#define LJ_SIGMA_SI		((0.25*sqrt(3.0)*LC_SI)/1.122462)	/* A */
-#define LJ_SIGMA_SI		(LC_SI/1.122462)			/* A */
+//#define LJ_SIGMA_SI		(LC_SI/1.122462)			/* A */
+#define LJ_SIGMA_SI		(0.5*sqrt(2.0)*LC_SI/1.122462)			/* A */
 #define LJ_EPSILON_SI		(2.1678*EV)				/* NA */
 
 #define TM_R_SI			(2.7e-10*METER)			/* A */
diff --git a/report/report.h b/report/report.h
index 3868515..e46ff2a 100644
--- a/report/report.h
+++ b/report/report.h
@@ -53,7 +53,7 @@ set ytic auto \n\
 set title 'Energy per atom vs. time' \n\
 set xlabel 'Time [fs]' \n\
 set ylabel 'Energy per atom [eV]' \n\
-set terminal postscript eps enhanced color dashed lw 1 'Helvetica' 14 \n\
+set terminal postscript eps enhanced color solid lw 1 'Helvetica' 14 \n\
 set output 'energy.eps' \n\
 plot \"energy\" using 1:2 title 'Kinetic energy' with lines , \"energy\" using 1:3 title 'Potential energy' with lines , \"energy\" using 1:4 title 'Total energy' with lines\
 ";
diff --git a/sic.c b/sic.c
index 2a2c7bc..f97ffe8 100644
--- a/sic.c
+++ b/sic.c
@@ -121,8 +121,8 @@ int main(int argc,char **argv) {
 	set_pbc(&md,TRUE,TRUE,TRUE);
 
 	/* create the lattice / place atoms */
-	create_lattice(&md,CUBIC,LC_SI,SI,M_SI,
-	//create_lattice(&md,FCC,LC_SI,SI,M_SI,
+	//create_lattice(&md,CUBIC,LC_SI,SI,M_SI,
+	create_lattice(&md,FCC,LC_SI,SI,M_SI,
 	//create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
 	//               ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 	               ATOM_ATTR_2BP|ATOM_ATTR_HB,
@@ -151,8 +151,8 @@ int main(int argc,char **argv) {
 	set_pressure(&md,ATM);
 
 	/* set p/t scaling */
-	set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
-	                 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,0.001,0,0);
 	
@@ -160,7 +160,7 @@ int main(int argc,char **argv) {
 	thermal_init(&md,TRUE);
 
 	/* create the simulation schedule */
-	moldyn_add_schedule(&md,100001,1.0);
+	moldyn_add_schedule(&md,101,1.0);
 	//moldyn_add_schedule(&md,501,1.0);
 	//moldyn_add_schedule(&md,501,1.0);
 
@@ -171,7 +171,7 @@ int main(int argc,char **argv) {
 	moldyn_set_log_dir(&md,argv[1]);
 	moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
 	moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
-	moldyn_set_log(&md,VISUAL_STEP,1000);
+	moldyn_set_log(&md,VISUAL_STEP,1);
 	moldyn_set_log(&md,CREATE_REPORT,0);
 
 	/*
diff --git a/visual/visual.c b/visual/visual.c
index d6ce369..573ac4f 100644
--- a/visual/visual.c
+++ b/visual/visual.c
@@ -87,8 +87,7 @@ 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\n");
-	//dprintf(v->fd,"spacefill 100\n");
+	dprintf(v->fd,"spacefill 200\n");
 	dprintf(v->fd,"rotate x 100\n");
 	dprintf(v->fd,"rotate y 10\n");
 	dprintf(v->fd,"set ambient 20\n");