From: hackbard <hackbard>
Date: Thu, 30 Nov 2006 10:46:08 +0000 (+0000)
Subject: vel scaling fixed/changed
X-Git-Url: https://hackdaworld.org/gitweb/?a=commitdiff_plain;h=180ff86ae35ca0ea6ee857e92e56120e65315d17;p=physik%2Fposic.git

vel scaling fixed/changed
---

diff --git a/moldyn.c b/moldyn.c
index de7bbbf..d52fcd3 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -93,6 +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)
@@ -221,6 +228,7 @@ 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) {
 		moldyn->atom[count-1].element=element;
@@ -311,15 +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;
@@ -328,17 +336,14 @@ int scale_velocity(t_moldyn *moldyn) {
 	 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 	 */
 
-	if(moldyn->t==0.0) {
-		printf("[moldyn] no velocity scaling for T = 0 K\n");
-		return -1;
-	}
-
 	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;
 }
@@ -594,9 +599,9 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	t_3dvec p;
 	t_moldyn_schedule *schedule;
 	t_atom *atom;
-
 	int fd;
 	char fb[128];
+	double ds;
 
 	schedule=&(moldyn->schedule);
 	atom=moldyn->atom;
@@ -617,6 +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;
 
@@ -758,7 +774,6 @@ int potential_force_calc(t_moldyn *moldyn) {
 	moldyn->energy=0.0;
 
 	for(i=0;i<count;i++) {
-printf("BAR %d %d\n",i,count);
 	
 		/* reset force */
 		v3_zero(&(atom[i].f));
diff --git a/moldyn.h b/moldyn.h
index a2855a7..63dd14f 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -81,8 +81,9 @@ typedef struct s_moldyn {
 
 	double cutoff;		/* cutoff radius */
 	double cutoff_square;	/* square of the cutoff radius */
+	double nnd;		/* nearest neighbour distance (optional) */
 
-	t_linkcell lc;		/* linked cell method */
+	t_linkcell lc;		/* linked cell list interface */
 
 	double t;		/* temperature */
 
@@ -122,9 +123,12 @@ typedef struct s_moldyn {
 #define MOLDYN_STAT_PBY			0x10	/* y */
 #define MOLDYN_STAT_PBZ			0x20	/* and z direction */
 
-#define MOLDYN_1BP			0x00
-#define MOLDYN_2BP			0x01
-#define MOLDYN_3BP			0x02
+#define MOLDYN_1BP			0x00	/* care about single */
+#define MOLDYN_2BP			0x01	/* 2 body */
+#define MOLDYN_3BP			0x02	/* and 3 body particle pots */
+
+#define VSCALE_INIT_EQUI		0x00	/* initial, eq positions */
+#define VSCALE_BERENDSEN		0x01	/* berendsen control */
 
 
 /*
@@ -281,6 +285,7 @@ int set_int_alg(t_moldyn *moldyn,u8 algo);
 int set_cutoff(t_moldyn *moldyn,double cutoff);
 int set_temperature(t_moldyn *moldyn,double t);
 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize);
+int set_nn_dist(t_moldyn *moldyn,double dist);
 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
 int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params);
 int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params);
@@ -296,7 +301,7 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
 int destroy_atoms(t_moldyn *moldyn);
 
 int thermal_init(t_moldyn *moldyn);
-int scale_velocity(t_moldyn *moldyn);
+int scale_velocity(t_moldyn *moldyn,u8 type);
 
 double get_e_kin(t_moldyn *moldyn);
 double get_e_pot(t_moldyn *moldyn);
diff --git a/sic.c b/sic.c
index 649d1e9..7c40a7e 100644
--- a/sic.c
+++ b/sic.c
@@ -61,11 +61,11 @@ int main(int argc,char **argv) {
 
 	/* cutoff radius */
 	printf("[sic] setting cutoff radius\n");
-	set_cutoff(&md,5*LC_SI);
+	set_cutoff(&md,1*LC_SI);
 
 	/* set (initial) dimensions of simulation volume */
 	printf("[sic] setting dimensions\n");
-	set_dim(&md,10*LC_SI,10*LC_SI,10*LC_SI,TRUE);
+	set_dim(&md,4*LC_SI,4*LC_SI,4*LC_SI,TRUE);
 
 	/* set periodic boundary conditions in all directions */
 	printf("[sic] setting periodic boundary conditions\n");
@@ -80,11 +80,14 @@ int main(int argc,char **argv) {
 	//add_atom(&md,SI,M_SI,0,ATOM_ATTR_2BP,&r,&v);
 	//r.x=-r.x;
 	//add_atom(&md,SI,M_SI,0,ATOM_ATTR_2BP,&r,&v);
-	create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,ATOM_ATTR_2BP,0,10,10,10);
+	create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,ATOM_ATTR_2BP,0,4,4,4);
+
+	/* setting a nearest neighbour distance for the moldyn checks */
+	set_nn_dist(&md,sqrt(3.0)*LC_SI/4.0); /* diamond ! */
 
 	/* set temperature */
 	printf("[sic] setting temperature\n");
-	set_temperature(&md,0.0);
+	set_temperature(&md,273.0);
 	
 	/* initial thermal fluctuations of particles */
 	printf("[sic] thermal init\n");
@@ -92,12 +95,12 @@ int main(int argc,char **argv) {
 
 	/* create the simulation schedule */
 	printf("[sic] adding schedule\n");
-	moldyn_add_schedule(&md,100,1.0e-15);
+	moldyn_add_schedule(&md,10000,1.0e-15);
 
 	/* activate logging */
 	printf("[sic] activate logging\n");
-	moldyn_set_log(&md,LOG_TOTAL_ENERGY,"saves/test-energy",1);
-	moldyn_set_log(&md,VISUAL_STEP,"saves/test-visual",1);
+	moldyn_set_log(&md,LOG_TOTAL_ENERGY,"saves/test-energy",100);
+	moldyn_set_log(&md,VISUAL_STEP,"saves/test-visual",100);
 
 	/*
 	 * let's do the actual md algorithm now