X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=c25fed3ae9d4c21587336bc2cf321d0bd96b5bbb;hb=785f05e0c0ddb57428dc71b0a3f7798673799871;hp=7ea5d5080ab1ab185fa46b2137894239e9233902;hpb=1d83ceb2ce2ff5150fd079f1066b7f583e38c8f4;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 7ea5d50..c25fed3 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -17,20 +17,8 @@
 
 #include "moldyn.h"
 
-#include "math/math.h"
-#include "init/init.h"
-#include "random/random.h"
-#include "visual/visual.h"
-#include "list/list.h"
-
-
 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 
-	//int ret;
-
-	//ret=moldyn_parse_argv(moldyn,argc,argv);
-	//if(ret<0) return ret;
-
 	memset(moldyn,0,sizeof(t_moldyn));
 
 	rand_init(&(moldyn->random),NULL,1);
@@ -78,6 +66,13 @@ int set_temperature(t_moldyn *moldyn,double t_ref) {
 	return 0;
 }
 
+int set_pressure(t_moldyn *moldyn,double p_ref) {
+
+	moldyn->p_ref=p_ref;
+
+	return 0;
+}
+
 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
 
 	moldyn->pt_scale=(ptype|ttype);
@@ -93,12 +88,21 @@ int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
 	moldyn->dim.y=y;
 	moldyn->dim.z=z;
 
+	moldyn->volume=x*y*z;
+
 	if(visualize) {
 		moldyn->vis.dim.x=x;
 		moldyn->vis.dim.y=y;
 		moldyn->vis.dim.z=z;
 	}
 
+	printf("[moldyn] dimensions in A and A^3 respectively:\n");
+	printf("  x: %f\n",moldyn->dim.x);
+	printf("  y: %f\n",moldyn->dim.y);
+	printf("  z: %f\n",moldyn->dim.z);
+	printf("  volume: %f\n",moldyn->volume);
+	printf("  visualize simulation box: %s\n",visualize?"on":"off");
+
 	return 0;
 }
 
@@ -221,6 +225,10 @@ int moldyn_log_shutdown(t_moldyn *moldyn) {
 	return 0;
 }
 
+/*
+ * creating lattice functions
+ */
+
 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
                    u8 attr,u8 bnum,int a,int b,int c) {
 
@@ -230,10 +238,11 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 
 	count=a*b*c;
 
+	/* how many atoms do we expect */
 	if(type==FCC) count*=4;
-
 	if(type==DIAMOND) count*=8;
 
+	/* allocate space for atoms */
 	moldyn->atom=malloc(count*sizeof(t_atom));
 	if(moldyn->atom==NULL) {
 		perror("malloc (atoms)");
@@ -256,9 +265,10 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 
 	/* debug */
 	if(ret!=count) {
-		printf("ok, there is something wrong ...\n");
-		printf("calculated -> %d atoms\n",count);
-		printf("created -> %d atoms\n",ret);
+		printf("[moldyn] creating lattice failed\n");
+		printf("  amount of atoms\n");
+		printf("  - expected: %d\n",count);
+		printf("  - created: %d\n",ret);
 		return -1;
 	}
 
@@ -274,10 +284,93 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 		check_per_bound(moldyn,&(moldyn->atom[count].r));
 	}
 
-
 	return ret;
 }
 
+/* fcc lattice init */
+int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+	int count;
+	int i,j;
+	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);
+
+	/* 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);
+	}
+
+	v3_zero(&r);
+	count=0;
+	
+	/* fill up the room */
+	r.x=o.x;
+	while(r.x<x) {
+		r.y=o.y;
+		while(r.y<y) {
+			r.z=o.z;
+			while(r.z<z) {
+				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;	
+			}
+			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);
+		
+	return count;
+}
+
+int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+	int count;
+	t_3dvec o;
+
+	count=fcc_init(a,b,c,lc,atom,origin);
+
+	o.x=0.25*lc;
+	o.y=0.25*lc;
+	o.z=0.25*lc;
+
+	if(origin) v3_add(&o,&o,origin);
+
+	count+=fcc_init(a,b,c,lc,&atom[count],&o);
+
+	return count;
+}
+
 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
              t_3dvec *r,t_3dvec *v) {
 
@@ -383,7 +476,7 @@ int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 			count+=1;
 		}
 	}
-	if(count!=0) moldyn->t=(2.0*e)/(3.0*count*K_BOLTZMANN);
+	if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
 	else return 0;	/* no atoms involved in scaling! */
 	
 	/* (temporary) hack for e,t = 0 */
@@ -416,6 +509,57 @@ int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 	return 0;
 }
 
+int scale_volume(t_moldyn *moldyn) {
+
+	t_atom *atom;
+	t_3dvec *dim,*vdim;
+	double virial,scale;
+	t_linkcell *lc;
+	int i;
+
+	atom=moldyn->atom;
+	dim=&(moldyn->dim);
+	vdim=&(moldyn->vis.dim);
+	lc=&(moldyn->lc);
+
+	for(i=0;i<moldyn->count;i++)
+		virial+=v3_norm(&(atom[i].virial));
+
+printf("%f\n",virial);
+	/* get pressure from virial */
+	moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t-ONE_THIRD*virial;
+	moldyn->p/=moldyn->volume;
+printf("%f\n",moldyn->p/(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)) {
+		link_cell_shutdown(moldyn);
+		link_cell_init(moldyn);
+	}
+
+	return 0;
+
+}
+
 double get_e_kin(t_moldyn *moldyn) {
 
 	int i;
@@ -483,9 +627,6 @@ int link_cell_init(t_moldyn *moldyn) {
 
 	t_linkcell *lc;
 	int i;
-	int fd;
-
-	fd=open("/dev/null",O_WRONLY);
 
 	lc=&(moldyn->lc);
 
@@ -503,8 +644,7 @@ int link_cell_init(t_moldyn *moldyn) {
 	printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 
 	for(i=0;i<lc->cells;i++)
-		//list_init(&(lc->subcell[i]),1);
-		list_init(&(lc->subcell[i]),fd);
+		list_init_f(&(lc->subcell[i]));
 
  	link_cell_update(moldyn);
 	
@@ -514,26 +654,30 @@ int link_cell_init(t_moldyn *moldyn) {
 int link_cell_update(t_moldyn *moldyn) {
 
 	int count,i,j,k;
-	int nx,ny,nz;
+	int nx,ny;
 	t_atom *atom;
 	t_linkcell *lc;
+	double x,y,z;
 
 	atom=moldyn->atom;
 	lc=&(moldyn->lc);
 
 	nx=lc->nx;
 	ny=lc->ny;
-	nz=lc->nz;
+
+	x=moldyn->dim.x/2;
+	y=moldyn->dim.y/2;
+	z=moldyn->dim.z/2;
 
 	for(i=0;i<lc->cells;i++)
-		list_destroy(&(moldyn->lc.subcell[i]));
+		list_destroy_f(&(lc->subcell[i]));
 	
 	for(count=0;count<moldyn->count;count++) {
-		i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
-		j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
-		k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
-		list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
-		                       &(atom[count]));
+		i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
+		j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
+		k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
+		list_add_immediate_f(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
+		                     &(atom[count]));
 	}
 
 	return 0;
@@ -603,7 +747,9 @@ int link_cell_shutdown(t_moldyn *moldyn) {
 	lc=&(moldyn->lc);
 
 	for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
-		list_shutdown(&(moldyn->lc.subcell[i]));
+		list_destroy_f(&(moldyn->lc.subcell[i]));
+
+	free(lc->subcell);
 
 	return 0;
 }
@@ -717,6 +863,8 @@ int moldyn_integrate(t_moldyn *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);
 
 		/* check for log & visualization */
 		if(e) {
@@ -833,7 +981,6 @@ int potential_force_calc(t_moldyn *moldyn) {
 	t_linkcell *lc;
 	t_list neighbour_i[27];
 	t_list neighbour_i2[27];
-	//t_list neighbour_j[27];
 	t_list *this,*that;
 	u8 bc_ij,bc_ik;
 	int dnlc;
@@ -844,13 +991,16 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 	/* reset energy */
 	moldyn->energy=0.0;
-
+	
 	/* get energy and force of every atom */
 	for(i=0;i<count;i++) {
 
 		/* reset force */
 		v3_zero(&(itom[i].f));
 
+		/* reset viral of atom i */
+		v3_zero(&(itom[i].virial));
+
 		/* single particle potential/force */
 		if(itom[i].attr&ATOM_ATTR_1BP)
 			moldyn->func1b(moldyn,&(itom[i]));
@@ -871,7 +1021,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 		for(j=0;j<27;j++) {
 
 			this=&(neighbour_i[j]);
-			list_reset(this);
+			list_reset_f(this);
 
 			if(this->start==NULL)
 				continue;
@@ -885,11 +1035,12 @@ int potential_force_calc(t_moldyn *moldyn) {
 					continue;
 
 				if((jtom->attr&ATOM_ATTR_2BP)&
-				   (itom[i].attr&ATOM_ATTR_2BP))
+				   (itom[i].attr&ATOM_ATTR_2BP)) {
 					moldyn->func2b(moldyn,
 					               &(itom[i]),
 					               jtom,
 					               bc_ij);
+				}
 
 				/* 3 body potential/force */
 
@@ -905,7 +1056,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 				for(k=0;k<27;k++) {
 
 					that=&(neighbour_i2[k]);
-					list_reset(that);
+					list_reset_f(that);
 					
 					if(that->start==NULL)
 						continue;
@@ -931,7 +1082,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 						               ktom,
 						               bc_ik|bc_ij);
 
-					} while(list_next(that)!=\
+					} while(list_next_f(that)!=\
 					        L_NO_NEXT_ELEMENT);
 
 				}
@@ -943,7 +1094,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 					                    jtom,bc_ij);
 				}
 					
-			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+			} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
 		
 		}
 
@@ -956,16 +1107,16 @@ int potential_force_calc(t_moldyn *moldyn) {
  * periodic boundayr checking
  */
 
-int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
+inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
 	
 	double x,y,z;
 	t_3dvec *dim;
 
 	dim=&(moldyn->dim);
 
-	x=0.5*dim->x;
-	y=0.5*dim->y;
-	z=0.5*dim->z;
+	x=dim->x/2;
+	y=dim->y/2;
+	z=dim->z/2;
 
 	if(moldyn->status&MOLDYN_STAT_PBX) {
 		if(a->x>=x) a->x-=dim->x;
@@ -1212,7 +1363,7 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
 	/* f_a, df_a calc (again, same for ij and ji) | save for later use! */
 	exchange->f_a=-B*exp(-mu*d_ij);
-	exchange->df_a=-mu*exchange->f_a/d_ij;
+	exchange->df_a=mu*exchange->f_a/d_ij;
 
 	/* f_c, df_c calc (again, same for ij and ji) */
 	if(d_ij<R) {
@@ -1226,7 +1377,8 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 		s_r=S-R;
 		arg=M_PI*(d_ij-R)/s_r;
 		f_c=0.5+0.5*cos(arg);
-		df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij));
+		//df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij));	/* MARK! */
+		df_c=0.5*sin(arg)*(M_PI/(s_r*d_ij));
 		/* two body contribution (ij, ji) */
 		v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
 		/* tell 3bp that S > r > R */
@@ -1354,7 +1506,7 @@ int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	v3_scale(&force,&force,-0.5);
 
 	/* add force */
-	v3_sub(&(ai->f),&(ai->f),&force);
+	v3_add(&(ai->f),&(ai->f),&force);
 
 	return 0;
 }
@@ -1497,7 +1649,8 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 			s_r=S-R;
 			arg=M_PI*(d_ik-R)/s_r;
 			f_c_ik=0.5+0.5*cos(arg);
-			df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik));
+			//df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik)); /* MARK */
+			df_c_ik=0.5*sin(arg)*(M_PI/(s_r*d_ik));
 
 			/* zeta_ij */
 			exchange->zeta_ij+=f_c_ik*g;
@@ -1547,13 +1700,13 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 		c2d2=exchange->cj2dj2;
 
 		/* cosine of theta_jik by scalaproduct */
-		rr=v3_scalar_product(&dist_ij,&dist_jk); /* times -1 */
+		rr=-v3_scalar_product(&dist_ij,&dist_jk); /* -1, as ij -> ji */
 		dd=d_ij*d_jk;
 		cos_theta=rr/dd;
 
 		/* d_costheta */
-		d_costheta1=1.0/(d_jk*d_ij);
-		d_costheta2=cos_theta/(d_ij*d_ij); /* in fact -cos(), but ^ */
+		d_costheta1=1.0/dd;
+		d_costheta2=cos_theta/(d_ij*d_ij);
 
 		/* some usefull values */
 		h_cos=(h-cos_theta);
@@ -1569,6 +1722,9 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 		v3_add(&temp1,&temp1,&temp2);
 		v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
 
+		/* store dg in temp2 and use it for dVjk later */
+		v3_copy(&temp2,&temp1);
+
 		/* f_c_jk + {d,}zeta contribution (df_c_jk = 0) */
 		dzeta=&(exchange->dzeta_ji);
 		if(d_jk<R) {
@@ -1590,7 +1746,7 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 			/* zeta_ji */
 			exchange->zeta_ji+=f_c_jk*g;
 
-			/* dzeta_ij */
+			/* dzeta_ji */
 			v3_scale(&temp1,&temp1,f_c_jk);
 			v3_add(dzeta,dzeta,&temp1);
 		}
@@ -1598,20 +1754,21 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 		/* dV_jk stuff | add force contribution on atom i immediately */
 		if(exchange->d_ij_between_rs) {
 			zeta=f_c*g;
-			v3_scale(&temp1,&temp1,f_c);
-			v3_scale(&temp2,&dist_ij,df_c);
-			v3_add(&temp1,&temp1,&temp2);
+			v3_scale(&temp1,&temp2,f_c);
+			v3_scale(&temp2,&dist_ij,df_c*g);
+			v3_add(&temp2,&temp2,&temp1); /* -> dzeta_jk in temp2 */
 		}
 		else {
 			zeta=g;
-			// dzeta_jk is simply dg, which is temp1
+			// dzeta_jk is simply dg, which is stored in temp2
 		}
 		/* betajnj * zeta_jk ^ nj-1 */
 		tmp=exchange->betajnj*pow(zeta,(n-1.0));
-		tmp=-chi/2.0*pow(1+tmp*zeta,-1.0/(2.0*n)-1)*tmp;
-		v3_scale(&temp1,&temp1,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
-		v3_add(&(ai->f),&(ai->f),&temp1); /* -1 skipped in f_a calc ^ */
+		tmp=-chi/2.0*pow((1+tmp*zeta),(-1.0/(2.0*n)-1))*tmp;
+		v3_scale(&temp2,&temp2,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
+		v3_add(&(ai->f),&(ai->f),&temp2); /* -1 skipped in f_a calc ^ */
 		                                  /* scaled with 0.5 ^ */
+
 	}
 
 	return 0;
@@ -1627,22 +1784,45 @@ int moldyn_bc_check(t_moldyn *moldyn) {
 	t_atom *atom;
 	t_3dvec *dim;
 	int i;
+double x;
+u8 byte;
+int j,k;
 
 	atom=moldyn->atom;
 	dim=&(moldyn->dim);
+x=dim->x/2;
 
 	for(i=0;i<moldyn->count;i++) {
-		if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2)
+		if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
 			printf("FATAL: atom %d: x: %.20f (%.20f)\n",
-			       i,atom[i].r.x*1e10,dim->x/2*1e10);
+			       i,atom[i].r.x,dim->x/2);
+			printf("diagnostic:\n");
+			printf("-----------\natom.r.x:\n");
+			for(j=0;j<8;j++) {
+				memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
+				for(k=0;k<8;k++)
+					printf("%d%c",
+					((byte)&(1<<k))?1:0,
+					(k==7)?'\n':'|');
+			}
+			printf("---------------\nx=dim.x/2:\n");
+			for(j=0;j<8;j++) {
+				memcpy(&byte,(u8 *)(&x)+j,1);
+				for(k=0;k<8;k++)
+					printf("%d%c",
+					((byte)&(1<<k))?1:0,
+					(k==7)?'\n':'|');
+			}
+			if(atom[i].r.x==x) printf("the same!\n");
+			else printf("different!\n");
+		}
 		if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
 			printf("FATAL: atom %d: y: %.20f (%.20f)\n",
-			       i,atom[i].r.y*1e10,dim->y/2*1e10);
+			       i,atom[i].r.y,dim->y/2);
 		if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
 			printf("FATAL: atom %d: z: %.20f (%.20f)\n",
-			       i,atom[i].r.z*1e10,dim->z/2*1e10);
+			       i,atom[i].r.z,dim->z/2);
 	}
 
 	return 0;
 }
-