From: hackbard <hackbard>
Date: Wed, 22 Nov 2006 15:23:42 +0000 (+0000)
Subject: nearly finished tersoff 2 body part and new api
X-Git-Url: https://hackdaworld.org/gitweb/?a=commitdiff_plain;h=020789bbba5881e2abf58c362d0ce733696de3b3;p=physik%2Fposic.git

nearly finished tersoff 2 body part and new api
---

diff --git a/moldyn.c b/moldyn.c
index d74b391..9f88211 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -232,7 +232,7 @@ int moldyn_shutdown(t_moldyn *moldyn) {
 	return 0;
 }
 
-int create_lattice(unsigned char type,int element,double mass,double lc,
+int create_lattice(u8 type,int element,double mass,double lc,
                    int a,int b,int c,t_atom **atom) {
 
 	int count;
@@ -487,7 +487,7 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 	int ci,cj,ck;
 	int nx,ny,nz;
 	int x,y,z;
-	unsigned char bx,by,bz;
+	u8 bx,by,bz;
 
 	lc=&(moldyn->lc);
 	nx=lc->nx;
@@ -702,7 +702,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 	t_list neighbour[27];
 	t_list *this;
 	double u;
-	unsigned char bc,bc3;
+	u8 bc,bc3;
 	int countn,dnlc;
 
 	count=moldyn->count;
@@ -804,304 +804,174 @@ int potential_force_calc(t_moldyn *moldyn) {
 	return 0;
 }
 
+/*
+ * periodic boundayr checking
+ */
+
+int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
+	
+	double x,y,z;
+
+	x=0.5*dim->x;
+	y=0.5*dim->y;
+	z=0.5*dim->z;
+
+	if(moldyn->MOLDYN_ATTR_PBX)
+		if(a->x>=x) a->x-=dim->x;
+		else if(-a->x>x) a->x+=dim->x;
+	if(moldyn->MOLDYN_ATTR_PBY)
+		if(a->y>=y) a->y-=dim->y;
+		else if(-a->y>y) a->y+=dim->y;
+	if(moldyn->MOLDYN_ATTR_PBZ)
+		if(a->z>=z) a->z-=dim->z;
+		else if(-a->z>z) a->z+=dim->z;
+
+	return 0;
+}
+        
+
 /*
  * example potentials
  */
 
 /* harmonic oscillator potential and force */
 
-int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,unsigned char bc)) {
+int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc)) {
 
 	t_ho_params *params;
-	t_atom *atom,*btom;
-	t_linkcell *lc;
-	t_list *this,neighbour[27];
-	int i,j,c;
-	int count;
 	t_3dvec force,distance;
-	double d,u;
+	double d;
 	double sc,equi_dist;
-	int ni,nj,nk;
 
-	params=moldyn->pot_params;
-	atom=moldyn->atom;
-	lc=&(moldyn->lc);
+	params=moldyn->pot2b_params;
 	sc=params->spring_constant;
 	equi_dist=params->equilibrium_distance;
-	count=moldyn->count;
-
-	/* reset energy counter */
-	u=0.0;
 
-	for(i=0;i<count;i++) {
-		/* reset force */
-		v3_zero(&(atom[i].f));
-
-		/* determine cell + neighbours */
-		ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
-		nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
-		nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
-		c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
-
-		/*
-		 * processing cell of atom i
-		 * => no need to check for empty list (1 element at minimum)
-		 */
-		this=&(neighbour[0]);
-		list_reset(this);
-		do {
-			btom=this->current->data;
-			if(btom==&(atom[i]))
-				continue;
-			v3_sub(&distance,&(atom[i].r),&(btom->r));
-			d=v3_norm(&distance);
-			if(d<=moldyn->cutoff) {
-				u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
-				v3_scale(&force,&distance,
-				         -sc*(1.0-(equi_dist/d)));
-				v3_add(&(atom[i].f),&(atom[i].f),&force);
-			}
-		} while(list_next(this)!=L_NO_NEXT_ELEMENT);
-
-		/*
-		 * direct neighbour cells
-		 * => no boundary condition check necessary
-		 */
-		for(j=1;j<c;j++) {
-			this=&(neighbour[j]);
-			list_reset(this); /* there might not be a single atom */
-			if(this->start!=NULL) {
-
-			do {
-				btom=this->current->data;
-				v3_sub(&distance,&(atom[i].r),&(btom->r));
-				d=v3_norm(&distance);
-				if(d<=moldyn->cutoff) {
-					u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
-					v3_scale(&force,&distance,
-					         -sc*(1.0-(equi_dist/d)));
-					v3_add(&(atom[i].f),&(atom[i].f),
-					       &force);
-				}
-			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
-
-			}
-		}
-
-		/*
-		 * indirect neighbour cells
-		 * => check boundary conditions
-		 */
-		for(j=c;j<27;j++) {
-			this=&(neighbour[j]);
-			list_reset(this); /* check boundary conditions */
-			if(this->start!=NULL) {
-
-			do {
-				btom=this->current->data;
-				v3_sub(&distance,&(atom[i].r),&(btom->r));
-				v3_per_bound(&distance,&(moldyn->dim));
-				d=v3_norm(&distance);
-				if(d<=moldyn->cutoff) {
-					u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
-					v3_scale(&force,&distance,
-					         -sc*(1.0-(equi_dist/d)));
-					v3_add(&(atom[i].f),&(atom[i].f),
-					       &force);
-				}
-			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
-
-			}
-		}
+	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) {
+		/* energy is 1/2 (d-d0)^2, but we will add this twice ... */
+		moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
+		v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
+		v3_add(&(ai->f),&(ai->f),&force);
 	}
 
-	moldyn->energy=0.5*u;
-
 	return 0;
 }
 
 /* lennard jones potential & force for one sort of atoms */
  
-int lennard_jones(t_moldyn *moldyn) {
+int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
 	t_lj_params *params;
-	t_atom *atom,*btom;
-	t_linkcell *lc;
-	t_list *this,neighbour[27];
-	int i,j,c;
-	int count;
 	t_3dvec force,distance;
 	double d,h1,h2,u;
 	double eps,sig6,sig12;
-	int ni,nj,nk;
 
 	params=moldyn->pot_params;
-	atom=moldyn->atom;
-	lc=&(moldyn->lc);
-	count=moldyn->count;
 	eps=params->epsilon4;
 	sig6=params->sigma6;
 	sig12=params->sigma12;
 
-	/* reset energy counter */
-	u=0.0;
+	v3_sub(&distance,&(ai->r),&(aj->r));
+	if(bc) check_per_bound(moldyn,&distance);
+	d=v3_absolute_square(&distance);	/* 1/r^2 */
+	if(d<=moldyn->cutoff_square) {
+		d=1.0/d;			/* 1/r^2 */
+		h2=d*d; 			/* 1/r^4 */
+		h2*=d;	 			/* 1/r^6 */
+		h1=h2*h2; 			/* 1/r^12 */
+		/* energy is eps*..., but we will add this twice ... */
+		moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
+		h2*=d;				/* 1/r^8 */
+		h1*=d;				/* 1/r^14 */
+		h2*=6*sig6;
+		h1*=12*sig12;
+		d=+h1-h2;
+		d*=eps;
+		v3_scale(&force,&distance,d);
+		v3_add(&(ai->f),&(aj->f),&force);
+	}
 
-	for(i=0;i<count;i++) {
-		/* reset force */
-		v3_zero(&(atom[i].f));
+	return 0;
+}
 
-		/* determine cell + neighbours */
-		ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
-		nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
-		nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
-		c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
-
-		/* processing cell of atom i */
-		this=&(neighbour[0]);
-		list_reset(this); /* list has 1 element at minimum */
-		do {
-			btom=this->current->data;
-			if(btom==&(atom[i]))
-				continue;
-			v3_sub(&distance,&(atom[i].r),&(btom->r));
-			d=v3_absolute_square(&distance);	/* 1/r^2 */
-			if(d<=moldyn->cutoff_square) {
-				d=1.0/d;	/* 1/r^2 */
-				h2=d*d; 	/* 1/r^4 */
-				h2*=d;	 	/* 1/r^6 */
-				h1=h2*h2; 	/* 1/r^12 */
-				u+=eps*(sig12*h1-sig6*h2);
-				h2*=d;		/* 1/r^8 */
-				h1*=d;		/* 1/r^14 */
-				h2*=6*sig6;
-				h1*=12*sig12;
-				d=+h1-h2;
-				d*=eps;
-				v3_scale(&force,&distance,d);
-				v3_add(&(atom[i].f),&(atom[i].f),&force);
-			}
-		} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+/*
+ * tersoff potential & force for 2 sorts of atoms
+ */
 
-		/* neighbours not doing boundary condition overflow */
-		for(j=1;j<c;j++) {
-			this=&(neighbour[j]);
-			list_reset(this); /* there might not be a single atom */
-			if(this->start!=NULL) {
+/* tersoff 2 body part */
 
-			do {
-				btom=this->current->data;
-				v3_sub(&distance,&(atom[i].r),&(btom->r));
-				d=v3_absolute_square(&distance); /* r^2 */
-				if(d<=moldyn->cutoff_square) {
-					d=1.0/d;	/* 1/r^2 */
-					h2=d*d; 	/* 1/r^4 */
-					h2*=d;	 	/* 1/r^6 */
-					h1=h2*h2; 	/* 1/r^12 */
-					u+=eps*(sig12*h1-sig6*h2);
-					h2*=d;		/* 1/r^8 */
-					h1*=d;		/* 1/r^14 */
-					h2*=6*sig6;
-					h1*=12*sig12;
-					d=+h1-h2;
-					d*=eps;
-					v3_scale(&force,&distance,d);
-					v3_add(&(atom[i].f),&(atom[i].f),
-					       &force);
-				}
-			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
-				
-			}
-		}
+int tersoff_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
-		/* neighbours due to boundary conditions */
-		for(j=c;j<27;j++) {
-			this=&(neighbour[j]);
-			list_reset(this); /* check boundary conditions */
-			if(this->start!=NULL) {
+	t_tersoff_params *params;
+	t_3dvec dist_ij;
+	double d_ij;
 
-			do {
-				btom=this->current->data;
-				v3_sub(&distance,&(atom[i].r),&(btom->r));
-				v3_per_bound(&distance,&(moldyn->dim));
-				d=v3_absolute_square(&distance); /* r^2 */
-				if(d<=moldyn->cutoff_square) {
-					d=1.0/d;	/* 1/r^2 */
-					h2=d*d; 	/* 1/r^4 */
-					h2*=d; 		/* 1/r^6 */
-					h1=h2*h2; 	/* 1/r^12 */
-					u+=eps*(sig12*h1-sig6*h2);
-					h2*=d;		/* 1/r^8 */
-					h1*=d;		/* 1/r^14 */
-					h2*=6*sig6;
-					h1*=12*sig12;
-					d=+h1-h2;
-					d*=eps;
-					v3_scale(&force,&distance,d);
-					v3_add(&(atom[i].f),&(atom[i].f),
-					       &force);
-				}
-			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+	params=moldyn->pot_params;
+	
+	/*
+	 * we need: f_c, df_c, f_r, df_r
+	 *
+	 * therefore we need: R, S
+	 */
 
-			}
+	v3_sub(&dist_ij,&(ai->r),&(aj->r));
+
+	if(bc) check_per_bound(moldyn,&dist_ij);
+
+	if(ai->bnum==aj->bnum) {
+		S=params->S[ai->bnum];
+		R=params->R[ai->bnum];
+	}
+	else {
+		S=params->Smixed;
+		R=params->Rmixed;
+	}
+
+	d_ij=v3_norm(&dist_ij);
+
+	if(d_ij<=S) {
+		f_r=A*exp(-lamda*d_ij);
+		df_r=-lambda*f_r/d_ij;
+		if(d_ij<R) {
+			/* f_c = 1, df_c = 0 */
+			v3_scale(&force,&dist_ij,df_r);
+		}
+		else {
+			s_r=S-R;
+			arg=PI*(d_ij-R)/s_r;
+			f_c=0.5+0.5*cos(arg);
+			df_c=-0.5*sin(arg)*(PI/(s_r*d_ij));
+			scale=df_c*f_r+df_r*f_c;
+			v3_scale(&force,&dist_ij,scale);
+			v3_add(&(ai->f),&(ai->f),&force);
 		}
+		moldyn->energy+=(f_r*f_c);
 	}
 
-	moldyn->energy=0.5*u;
-	
 	return 0;
 }
 
-/* tersoff potential & force for 2 sorts of atoms */
+/* tersoff 3 body part */
 
-int tersoff(t_moldyn *moldyn) {
+int tersoff(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc,u8 bck) {
 
 	t_tersoff_params *params;
-	t_atom *atom,*btom,*ktom;
-	t_linkcell *lc;
-	t_list *this,*thisk,neighbour[27],neighbourk[27];
-	int i,j,k,c,ck;
-	int count;
-	double u;
-	int ni,nj,nk;
-	int ki,kj,kk;
-	
+	t_3dvec dist_ij;
+	double d_ij;
 
 	params=moldyn->pot_params;
-	atom=moldyn->atom;
-	lc=&(moldyn->lc);
-	count=moldyn->count;
 	
-	/* reset energy counter */
-	u=0.0;
-
-	for(i=0;i<count;i++) {
-		/* reset force */
-		v3_zero(&(atom[i].f));
-
-		/* determin cell neighbours */
-		ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
-		nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
-		nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
-		c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
-
-		/*
-		 * processing cell of atom i
-		 * => no need to check for empty list (1 element at minimum)
-		 */
-		this=&(neighbour[0]);
-		list_reset(this);
-		do {
-			btom=this->current->data;
-			if(btom==&(atom[i]))
-				continue;
-
-			/* 2 body stuff */
-
-			/* we need: f_c, df_c, f_r, df_r */
+	/* 2 body part of the tersoff potential */
 
-			v3_sub(&dist_ij,btom,&(atom[i]));
-			d_ij=v3_norm(&dist_ij);
-			if(d_ij<=S) {
+	v3_sub(&dist_ij,&(ai->r),&(aj->r));
+	if(bc) check_per_bound(moldyn,&dist_ij);
+	d_ij=v3_norm(&dist_ij);
+		if(d_ij<=S) {
 
 				/* determine the tersoff parameters */
 				if(atom[i].element!=btom->element) {
diff --git a/moldyn.h b/moldyn.h
index 66f774e..d98b428 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -25,7 +25,8 @@ typedef struct s_atom {
 	t_3dvec f;		/* force */
 	int element;		/* number of element in pse */
 	double mass;		/* atom mass */
-	unsigned char attr;	/* attributes */
+	u8 bnum;		/* brand number */
+	u8 attr;		/* attributes */
 } t_atom;
 
 #define ATOM_ATTR_FP	0x01	/* fixed position (bulk material) */
@@ -58,12 +59,14 @@ typedef struct s_moldyn {
 
 	t_3dvec dim;		/* dimensions of the simulation volume */
 
-	/* potential force function pointer and parameters */
+	/* potential force function and parameter pointers */
 	int (*pf_func1b)(struct s_moldyn *,t_atom *);
+	void *pot1b_params;
 	int (*pf_func2b)(struct s_moldyn *,t_atom *,t_atom *);
+	void *pot2b_params;
 	int (*pf_func3b)(struct s_moldyn *,t_atom *,t_atom *,t_atom *);
+	void *pot3b_params;
 	//int (*potential_force_function)(struct s_moldyn *moldyn);
-	void *pot_params;	/* parameters describing the potential */ 
 
 	double cutoff;		/* cutoff radius */
 	double cutoff_square;	/* square of the cutoff radius */
@@ -81,7 +84,7 @@ typedef struct s_moldyn {
 	double energy;		/* energy */
 
 	t_visual vis;		/* visualization/log/save interface structure */
-	unsigned char lvstat;	/* log & vis properties */
+	u8 lvstat;	/* log & vis properties */
 	unsigned int ewrite;	/* how often to log energy */
 	char efb[64];		/* energy log filename */
 	int efd;		/* fd for energy log */
@@ -93,7 +96,7 @@ typedef struct s_moldyn {
 	void *visual;		/* pointer (hack!) */
 	unsigned int swrite;	/* how often to create a save file */
 
-	unsigned char status;	/* general moldyn properties */
+	u8 status;	/* general moldyn properties */
 
 	t_random random;	/* random interface */
 } t_moldyn;
@@ -120,6 +123,11 @@ typedef struct s_lj_params {
 } t_lj_params;
 
 typedef struct s_tersoff_params {
+	double S[2];		/* tersoff cutoff radii */
+	double R[2];		/* tersoff cutoff radii */
+	double Smixed		/* mixed S radius */
+	double Rmixed		/* mixed R radius */
+
 	double l_1,l_2;
 	double m_1,m_2;
 	double a_1,a_2;
@@ -171,7 +179,7 @@ int moldyn_log_init(t_moldyn *moldyn);
 int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
 int moldyn_shutdown(t_moldyn *moldyn);
 
-int create_lattice(unsigned char type,int element,double mass,double lc,
+int create_lattice(u8 type,int element,double mass,double lc,
                    int a,int b,int c,t_atom **atom);
 int destroy_lattice(t_atom *atom);
 int thermal_init(t_moldyn *moldyn);