X-Git-Url: https://hackdaworld.org/gitweb/?p=physik%2Fposic.git;a=blobdiff_plain;f=moldyn.c;h=bd29afc9a3e6853bded38acae91dfafdf15a662a;hp=7698c24767b90de44a165602077a46714d86d476;hb=8524173a28f2c22a539ef1b0910a1136d9cb254b;hpb=a16579f010cb5d53b7bf44e854089019ab9b1df0

diff --git a/moldyn.c b/moldyn.c
index 7698c24..bd29afc 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -78,6 +78,14 @@ int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 	pthread_mutex_init(&emutex,NULL);
 #endif
 
+#ifdef CONSTRAINT_110_5832
+	printf("\n\n\nWARNING! WARNING! WARNING!\n\n\n");
+	printf("\n\n\n!! -- constraints enabled -- !!\n\n\n");
+#endif
+#ifdef CONSTRAINT_11X_5832
+	printf("\n\n\nWARNING! WARNING! WARNING!\n\n\n");
+	printf("\n\n\n!! -- constraints enabled -- !!\n\n\n");
+#endif
 	return 0;
 }
 
@@ -258,7 +266,7 @@ int set_potential(t_moldyn *moldyn,u8 type) {
 
 	switch(type) {
 		case MOLDYN_POTENTIAL_TM:
-			moldyn->func1b=tersoff_mult_1bp;
+			//moldyn->func1b=tersoff_mult_1bp;
 			moldyn->func3b_j1=tersoff_mult_3bp_j1;
 			moldyn->func3b_k1=tersoff_mult_3bp_k1;
 			moldyn->func3b_j2=tersoff_mult_3bp_j2;
@@ -516,7 +524,8 @@ int moldyn_log_shutdown(t_moldyn *moldyn) {
 
 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,
                    u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin,
-                   t_part_params *p_params,t_defect_params *d_params) {
+                   t_part_params *p_params,t_defect_params *d_params,
+                   t_offset_params *o_params) {
 
 	int new,count;
 	int ret;
@@ -588,6 +597,8 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,
 
 	switch(type) {
 		case CUBIC:
+			if(o_params->use)
+				v3_add(&orig,&orig,&(o_params->o));
 			set_nn_dist(moldyn,lc);
 			ret=cubic_init(a,b,c,lc,atom,&orig,p_params,d_params);
 			strcpy(name,"cubic");
@@ -595,6 +606,8 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,
 		case FCC:
 			if(!origin)
 				v3_scale(&orig,&orig,0.5);
+			if(o_params->use)
+				v3_add(&orig,&orig,&(o_params->o));
 			set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
 			ret=fcc_init(a,b,c,lc,atom,&orig,p_params,d_params);
 			strcpy(name,"fcc");
@@ -602,6 +615,8 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,
 		case DIAMOND:
 			if(!origin)
 				v3_scale(&orig,&orig,0.25);
+			if(o_params->use)
+				v3_add(&orig,&orig,&(o_params->o));
 			set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
 			ret=diamond_init(a,b,c,lc,atom,&orig,p_params,d_params);
 			strcpy(name,"diamond");
@@ -2071,11 +2086,11 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		temperature_calc(moldyn);
 		virial_sum(moldyn);
 		pressure_calc(moldyn);
-		/*
+#ifdef PDEBUG	
 		thermodynamic_pressure_calc(moldyn);
 		printf("\n\nDEBUG: numeric pressure calc: %f\n\n",
 		       moldyn->tp/BAR);
-		*/
+#endif
 
 		/* calculate fluctuations + averages */
 		average_and_fluctuation_calc(moldyn);
@@ -2182,15 +2197,20 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		}
 
 		/* display progress */
+#ifndef PDEBUG
 		if(!(i%10)) {
+#endif
 			/* get current time */
 			gettimeofday(&t2,NULL);
 
 printf("sched:%d, steps:%d/%d, T:%4.1f/%4.1f P:%4.1f/%4.1f V:%6.1f (%d)\n",
        sched->count,i,moldyn->total_steps,
        moldyn->t,moldyn->t_avg,
+#ifndef PDEBUG
        moldyn->p/BAR,moldyn->p_avg/BAR,
-       //moldyn->p/BAR,(moldyn->p-2.0*moldyn->ekin/(3.0*moldyn->volume))/BAR,
+#else
+       moldyn->p/BAR,(moldyn->p-2.0*moldyn->ekin/(3.0*moldyn->volume))/BAR,
+#endif
        moldyn->volume,
        (int)(t2.tv_sec-t1.tv_sec));
 
@@ -2198,7 +2218,9 @@ printf("sched:%d, steps:%d/%d, T:%4.1f/%4.1f P:%4.1f/%4.1f V:%6.1f (%d)\n",
 
 			/* copy over time */
 			t1=t2;
+#ifndef PDEBUG
 		}
+#endif
 
 		/* increase absolute time */
 		moldyn->time+=moldyn->tau;
@@ -2219,6 +2241,22 @@ printf("sched:%d, steps:%d/%d, T:%4.1f/%4.1f P:%4.1f/%4.1f V:%6.1f (%d)\n",
 
 	}
 
+	/* writing a final save file! */
+	if(s) {
+		snprintf(dir,128,"%s/s-final.save",moldyn->vlsdir);
+		fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT,S_IRUSR|S_IWUSR);
+		if(fd<0) perror("[moldyn] save fd open");
+		else {
+			write(fd,moldyn,sizeof(t_moldyn));
+			write(fd,moldyn->atom,
+			      moldyn->count*sizeof(t_atom));
+		}
+		close(fd);
+	}
+	/* writing a final visual file! */
+	if(a)
+		visual_atoms(moldyn);
+
 	return 0;
 }
 
@@ -2230,12 +2268,44 @@ int velocity_verlet(t_moldyn *moldyn) {
 	double tau,tau_square,h;
 	t_3dvec delta;
 	t_atom *atom;
+#ifdef CONSTRAINT_11X_5832
+	double xt,yt,zt;
+	double xtt,ytt,ztt;
+#endif
 
 	atom=moldyn->atom;
 	count=moldyn->count;
 	tau=moldyn->tau;
 	tau_square=moldyn->tau_square;
 
+#ifdef CONSTRAINT_110_5832
+	if(count==5833) {
+		atom[5832].f.x=0.5*(atom[5832].f.x-atom[5832].f.y);
+		atom[5832].f.y=-atom[5832].f.x;
+	}
+#endif
+#ifdef CONSTRAINT_11X_5832
+	if(count==5833) {
+		// second trafo
+		xt=atom[5832].f.x;
+		yt=atom[5832].f.y*cos(-0.16935129)-atom[5832].f.z*sin(-0.16935129);
+		zt=atom[5832].f.y*sin(-0.16935129)+atom[5832].f.z*cos(-0.16935129);
+		// first trafo
+		xtt=xt*cos(M_PI/4.0)-yt*sin(M_PI/4.0);
+		ytt=xt*sin(M_PI/4.0)+yt*sin(M_PI/4.0);
+		ztt=zt;
+		// apply constraints
+		ytt=0.0;
+		// first trafo backwards
+		xt=xtt*cos(M_PI/4.0)+ytt*sin(M_PI/4.0);
+		yt=-xtt*sin(M_PI/4.0)+ytt*sin(M_PI/4.0);
+		zt=ztt;
+		// second trafo backwards
+		atom[5832].f.x=xt;
+		atom[5832].f.y=yt*cos(-0.16935129)+zt*sin(-0.16935129);
+		atom[5832].f.z=-yt*sin(-0.16935129)+zt*cos(-0.16935129);
+	}
+#endif
 	for(i=0;i<count;i++) {
 		/* check whether fixed atom */
 		if(atom[i].attr&ATOM_ATTR_FP)
@@ -2243,9 +2313,70 @@ int velocity_verlet(t_moldyn *moldyn) {
 		/* new positions */
 		h=0.5/atom[i].mass;
 		v3_scale(&delta,&(atom[i].v),tau);
+#ifdef CONSTRAINT_110_5832
+		if(i==5832) {
+			delta.y=-delta.x;
+		}
+#endif
+#ifdef JHDVHJDV
+#ifdef CONSTRAINT_11X_5832
+	if(i==5833) {
+		// second trafo
+		xt=delta.x;
+		yt=delta.y*cos(-0.16935129)-delta.z*sin(-0.16935129);
+		zt=delta.y*sin(-0.16935129)+delta.z*cos(-0.16935129);
+		// first trafo
+		xtt=xt*cos(M_PI/4.0)-yt*sin(M_PI/4.0);
+		ytt=xt*sin(M_PI/4.0)+yt*sin(M_PI/4.0);
+		ztt=zt;
+		// apply constraints
+		ytt=0.0;
+		// first trafo backwards
+		xt=xtt*cos(M_PI/4.0)+ytt*sin(M_PI/4.0);
+		yt=-xtt*sin(M_PI/4.0)+ytt*sin(M_PI/4.0);
+		zt=ztt;
+		// second trafo backwards
+		delta.x=xt;
+		delta.y=yt*cos(-0.16935129)+zt*sin(-0.16935129);
+		delta.z=-yt*sin(-0.16935129)+zt*cos(-0.16935129);
+	}
+#endif
+#endif
+#ifndef QUENCH
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
+#endif
 		v3_scale(&delta,&(atom[i].f),h*tau_square);
+#ifdef CONSTRAINT_110_5832
+		if(i==5832) {
+			delta.y=-delta.x;
+		}
+#endif
+#ifdef GHDJHBSJBSD
+#ifdef CONSTRAINT_11X_5832
+	if(i==5833) {
+		// second trafo
+		xt=delta.x;
+		yt=delta.y*cos(-0.16935129)-delta.z*sin(-0.16935129);
+		zt=delta.y*sin(-0.16935129)+delta.z*cos(-0.16935129);
+		// first trafo
+		xtt=xt*cos(M_PI/4.0)-yt*sin(M_PI/4.0);
+		ytt=xt*sin(M_PI/4.0)+yt*sin(M_PI/4.0);
+		ztt=zt;
+		// apply constraints
+		ytt=0.0;
+		// first trafo backwards
+		xt=xtt*cos(M_PI/4.0)+ytt*sin(M_PI/4.0);
+		yt=-xtt*sin(M_PI/4.0)+ytt*sin(M_PI/4.0);
+		zt=ztt;
+		// second trafo backwards
+		delta.x=xt;
+		delta.y=yt*cos(-0.16935129)+zt*sin(-0.16935129);
+		delta.z=-yt*sin(-0.16935129)+zt*cos(-0.16935129);
+	}
+#endif
+#endif
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
+		//check_per_bound_and_care_for_pbc(moldyn,&(atom[i]));
 		check_per_bound(moldyn,&(atom[i].r));
 
 		/* velocities [actually v(t+tau/2)] */
@@ -2261,11 +2392,43 @@ int velocity_verlet(t_moldyn *moldyn) {
 
 	/* forces depending on chosen potential */
 #ifndef ALBE_FAST
-	potential_force_calc(moldyn);
+	// if albe, use albe force calc routine
+	//if(moldyn->func3b_j1==albe_mult_3bp_j1)
+	//	albe_potential_force_calc(moldyn);
+	//else
+		potential_force_calc(moldyn);
 #else
 	albe_potential_force_calc(moldyn);
 #endif
 
+#ifdef CONSTRAINT_110_5832
+	if(count==5833) {
+		atom[5832].f.x=0.5*(atom[5832].f.x-atom[5832].f.y);
+		atom[5832].f.y=-atom[5832].f.x;
+	}
+#endif
+#ifdef CONSTRAINT_11X_5832
+	if(count==5833) {
+		// second trafo
+		xt=atom[5832].f.x;
+		yt=atom[5832].f.y*cos(-0.16935129)-atom[5832].f.z*sin(-0.16935129);
+		zt=atom[5832].f.y*sin(-0.16935129)+atom[5832].f.z*cos(-0.16935129);
+		// first trafo
+		xtt=xt*cos(M_PI/4.0)-yt*sin(M_PI/4.0);
+		ytt=xt*sin(M_PI/4.0)+yt*sin(M_PI/4.0);
+		ztt=zt;
+		// apply constraints
+		ytt=0.0;
+		// first trafo backwards
+		xt=xtt*cos(M_PI/4.0)+ytt*sin(M_PI/4.0);
+		yt=-xtt*sin(M_PI/4.0)+ytt*sin(M_PI/4.0);
+		zt=ztt;
+		// second trafo backwards
+		atom[5832].f.x=xt;
+		atom[5832].f.y=yt*cos(-0.16935129)+zt*sin(-0.16935129);
+		atom[5832].f.z=-yt*sin(-0.16935129)+zt*cos(-0.16935129);
+	}
+#endif
 	for(i=0;i<count;i++) {
 		/* check whether fixed atom */
 		if(atom[i].attr&ATOM_ATTR_FP)
@@ -2713,6 +2876,51 @@ int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
 	return 0;
 }
         
+int check_per_bound_and_care_for_pbc(t_moldyn *moldyn,t_atom *a) {
+	
+	double x,y,z;
+	t_3dvec *dim;
+
+	dim=&(moldyn->dim);
+
+	x=dim->x/2;
+	y=dim->y/2;
+	z=dim->z/2;
+
+	if(moldyn->status&MOLDYN_STAT_PBX) {
+		if(a->r.x>=x) {
+			a->pbc[0]+=1;
+			a->r.x-=dim->x;
+		}
+		else if(-a->r.x>x) {
+			a->pbc[0]-=1;
+			a->r.x+=dim->x;
+		}
+	}
+	if(moldyn->status&MOLDYN_STAT_PBY) {
+		if(a->r.y>=y) {
+			a->pbc[1]+=1;
+			a->r.y-=dim->y;
+		}
+		else if(-a->r.y>y) {
+			a->pbc[1]-=1;
+			a->r.y+=dim->y;
+		}
+	}
+	if(moldyn->status&MOLDYN_STAT_PBZ) {
+		if(a->r.z>=z) {
+			a->pbc[2]+=1;
+			a->r.z-=dim->z;
+		}
+		else if(-a->r.z>z) {
+			a->pbc[2]-=1;
+			a->r.z+=dim->z;
+		}
+	}
+
+	return 0;
+}
+        
 /*
  * debugging / critical check functions
  */
@@ -2803,7 +3011,7 @@ int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
 	if(fsize!=sizeof(t_moldyn)+size) {
 		corr=fsize-sizeof(t_moldyn)-size;
 		printf("[moldyn] WARNING: lsf (illegal file size)\n");
-		printf("  moifying offset:\n");
+		printf("  modifying offset:\n");
 		printf("  - current pos: %d\n",sizeof(t_moldyn));
 		printf("  - atom size: %d\n",size);
 		printf("  - file size: %d\n",fsize);
@@ -3048,6 +3256,7 @@ int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc) {
 	int i;
 	t_atom *atom;
 	t_3dvec dist;
+	t_3dvec final_r;
 	double d2;
 	int a_cnt;
 	int b_cnt;
@@ -3061,8 +3270,12 @@ int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc) {
 
 	for(i=0;i<moldyn->count;i++) {
 
-		v3_sub(&dist,&(atom[i].r),&(atom[i].r_0));
-		check_per_bound(moldyn,&dist);
+		/* care for pb crossing */
+		final_r.x=atom[i].r.x+atom[i].pbc[0]*moldyn->dim.x;
+		final_r.y=atom[i].r.y+atom[i].pbc[1]*moldyn->dim.y;
+		final_r.z=atom[i].r.z+atom[i].pbc[2]*moldyn->dim.z;
+		/* calculate distance */
+		v3_sub(&dist,&final_r,&(atom[i].r_0));
 		d2=v3_absolute_square(&dist);
 
 		if(atom[i].brand) {
@@ -3084,6 +3297,57 @@ int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc) {
 	return 0;
 }
 
+int calculate_msd(t_moldyn *moldyn,double *msd) {
+
+	int i;
+	t_atom *atom;
+	t_3dvec dist;
+	t_3dvec final_r;
+	double d2;
+	int a_cnt;
+	int b_cnt;
+
+	atom=moldyn->atom;
+	msd[0]=0;
+	msd[1]=0;
+	msd[2]=0;
+	a_cnt=0;
+	b_cnt=0;
+
+	for(i=0;i<moldyn->count;i++) {
+
+		/* care for pb crossing */
+		if(atom[i].pbc[0]|atom[i].pbc[1]|atom[i].pbc[2]) {
+			printf("[moldyn] msd pb crossings for atom %d\n",i);
+			printf("  x: %d y: %d z: %d\n",
+			       atom[i].pbc[0],atom[i].pbc[1],atom[i].pbc[2]);
+		}
+		final_r.x=atom[i].r.x+atom[i].pbc[0]*moldyn->dim.x;
+		final_r.y=atom[i].r.y+atom[i].pbc[1]*moldyn->dim.y;
+		final_r.z=atom[i].r.z+atom[i].pbc[2]*moldyn->dim.z;
+		/* calculate distance */
+		v3_sub(&dist,&final_r,&(atom[i].r_0));
+		d2=v3_absolute_square(&dist);
+
+		if(atom[i].brand) {
+			b_cnt+=1;
+			msd[1]+=d2;
+		}
+		else {
+			a_cnt+=1;
+			msd[0]+=d2;
+		}
+
+		msd[2]+=d2;
+	}
+
+	msd[0]/=a_cnt;
+	msd[1]/=b_cnt;
+	msd[2]/=moldyn->count;
+		
+	return 0;
+}
+
 int bonding_analyze(t_moldyn *moldyn,double *cnt) {
 
 	return 0;