X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=881f0b698565fe7495ee151ecca63239d32e74cf;hb=c0ddf2bdd8067456f39f6b63fe2261624ebde6b7;hp=9db5cd9053fea64ce0cc5bd09cc667caa360bd4a;hpb=9f6af2cd82a72451741b68ca333f94c6c1d2eec5;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 9db5cd9..881f0b6 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -16,6 +16,7 @@
 #include <math.h>
 
 #include "moldyn.h"
+#include "report/report.h"
 
 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 
@@ -121,12 +122,15 @@ int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
 		moldyn->vis.dim.z=z;
 	}
 
+	moldyn->dv=0.000001*moldyn->volume;
+
 	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?"yes":"no");
+	printf("  delta volume (pressure calc): %f\n",moldyn->dv);
 
 	return 0;
 }
@@ -196,6 +200,14 @@ int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
 
 	return 0;
 }
+
+int moldyn_set_report(t_moldyn *moldyn,char *author,char *title) {
+
+	strncpy(moldyn->rauthor,author,63);
+	strncpy(moldyn->rtitle,title,63);
+
+	return 0;
+}
 	
 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 
@@ -244,6 +256,28 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 			}
 			printf("visual file (%d)\n",timer);
 			break;
+		case CREATE_REPORT:
+			snprintf(filename,127,"%s/report.tex",moldyn->vlsdir);
+			moldyn->rfd=open(filename,
+			                 O_WRONLY|O_CREAT|O_EXCL,
+			                 S_IRUSR|S_IWUSR);
+			if(moldyn->rfd<0) {
+				perror("[moldyn] report fd open");	
+				return moldyn->rfd;
+			}
+			snprintf(filename,127,"%s/plot.scr",moldyn->vlsdir);
+			moldyn->pfd=open(filename,
+			                 O_WRONLY|O_CREAT|O_EXCL,
+			                 S_IRUSR|S_IWUSR);
+			if(moldyn->pfd<0) {
+				perror("[moldyn] plot fd open");
+				return moldyn->pfd;
+			}
+			dprintf(moldyn->rfd,report_start,
+			        moldyn->rauthor,moldyn->rtitle);
+			dprintf(moldyn->pfd,plot_script);
+			close(moldyn->pfd);
+			break;
 		default:
 			printf("unknown log type: %02x\n",type);
 			return -1;
@@ -254,9 +288,23 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 
 int moldyn_log_shutdown(t_moldyn *moldyn) {
 
+	char sc[256];
+
 	printf("[moldyn] log shutdown\n");
 	if(moldyn->efd) close(moldyn->efd);
 	if(moldyn->mfd) close(moldyn->mfd);
+	if(moldyn->rfd) {
+		dprintf(moldyn->rfd,report_end);
+		close(moldyn->rfd);
+		snprintf(sc,255,"cd %s && gnuplot plot.scr",moldyn->vlsdir);
+		system(sc);
+		snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
+		system(sc);
+		snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
+		system(sc);
+		snprintf(sc,255,"cd %s && dvipdf report",moldyn->vlsdir);
+		system(sc);
+	}
 	if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
 
 	return 0;
@@ -279,6 +327,7 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	count=moldyn->count;
 
 	/* how many atoms do we expect */
+	if(type==CUBIC) new*=1;
 	if(type==FCC) new*=4;
 	if(type==DIAMOND) new*=8;
 
@@ -294,8 +343,14 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	v3_zero(&origin);
 
 	switch(type) {
+		case CUBIC:
+			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:
-			ret=fcc_init(a,b,c,lc,atom,&origin);
+			ret=fcc_init(a,b,c,lc,atom,NULL);
 			break;
 		case DIAMOND:
 			ret=diamond_init(a,b,c,lc,atom,&origin);
@@ -329,6 +384,44 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	return ret;
 }
 
+/* cubic init */
+int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+	int count;
+	t_3dvec r;
+	int i,j,k;
+	t_3dvec o;
+
+	count=0;
+	if(origin)
+		v3_copy(&o,origin);
+	else
+		v3_zero(&o);
+
+	r.x=o.x;
+	for(i=0;i<a;i++) {
+		r.y=o.y;
+		for(j=0;j<b;j++) {
+			r.z=o.z;
+			for(k=0;k<c;k++) {
+				v3_copy(&(atom[count].r),&r);
+				count+=1;
+				r.z+=lc;
+			}
+			r.y+=lc;
+		}
+		r.x+=lc;
+	}
+
+	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;
+}
+
 /* fcc lattice init */
 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 
@@ -501,17 +594,9 @@ int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 
 double temperature_calc(t_moldyn *moldyn) {
 
-	double double_ekin;
-	int i;
-	t_atom *atom;
-
-	atom=moldyn->atom;
+	/* assume up to date kinetic energy, which is 3/2 N k_B T */
 
-	for(i=0;i<moldyn->count;i++)
-		double_ekin+=atom[i].mass*v3_absolute_square(&(atom[i].v));
-
-	/* kinetic energy = 3/2 N k_B T */
-	moldyn->t=double_ekin/(3.0*K_BOLTZMANN*moldyn->count);
+	moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
 
 	return moldyn->t;
 }
@@ -577,27 +662,127 @@ int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 	return 0;
 }
 
+double ideal_gas_law_pressure(t_moldyn *moldyn) {
+
+	double p;
+
+	p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
+
+	return p;
+}
+
 double pressure_calc(t_moldyn *moldyn) {
 
 	int i;
-	t_atom *atom;
-	double p1,p2,p=0;
-	
+	double v;
+	t_virial *virial;
+
+	/*
+	 * P = 1/(3V) sum_i ( p_i^2 / 2m + f_i r_i )
+	 *
+	 * virial = f_i r_i
+	 */
+
+	v=0.0;
 	for(i=0;i<moldyn->count;i++) {
-		
+		virial=&(moldyn->atom[i].virial);
+		v+=(virial->xx+virial->yy+virial->zz);
+	}
+
+	/* assume up to date kinetic energy */
+	moldyn->p=2.0*moldyn->ekin+v;
+	moldyn->p/=(3.0*moldyn->volume);
+
+	return moldyn->p;
+}	
+
+double thermodynamic_pressure_calc(t_moldyn *moldyn) {
 
+	t_3dvec dim,*tp;
+	double u,p;
+	double scale;
+	t_atom *store;
+
+	tp=&(moldyn->tp);
+	store=malloc(moldyn->count*sizeof(t_atom));
+	if(store==NULL) {
+		printf("[moldyn] allocating store mem failed\n");
+		return -1;
 	}
 
-	p1=(moldyn->count*K_BOLTZMANN*moldyn->t-ONE_THIRD*moldyn->vt1);
-	p1/=moldyn->volume;
+	/* save unscaled potential energy + atom/dim configuration */
+	u=moldyn->energy;
+	memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
+	dim=moldyn->dim;
 
-	p2=(moldyn->count*K_BOLTZMANN*moldyn->t-ONE_THIRD*moldyn->vt2);
-	p2/=moldyn->volume;
+	/* derivative with respect to x direction */
+	scale=1.0+moldyn->dv/(moldyn->dim.y*moldyn->dim.z);
+	scale_dim(moldyn,scale,TRUE,0,0);
+	scale_atoms(moldyn,scale,TRUE,0,0);
+	link_cell_shutdown(moldyn);
+	link_cell_init(moldyn);
+	potential_force_calc(moldyn);
+	tp->x=(moldyn->energy-u)/moldyn->dv;
+	p=tp->x*tp->x;
 
-	printf("compare pressures: %f %f\n",p1/ATM,p2/ATM);
+	/* restore atomic configuration + dim */
+	memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
+	moldyn->dim=dim;
 
-	return moldyn->p;
-}	
+	/* derivative with respect to y direction */
+	scale=1.0+moldyn->dv/(moldyn->dim.x*moldyn->dim.z);
+	scale_dim(moldyn,scale,0,TRUE,0);
+	scale_atoms(moldyn,scale,0,TRUE,0);
+	link_cell_shutdown(moldyn);
+	link_cell_init(moldyn);
+	potential_force_calc(moldyn);
+	tp->y=(moldyn->energy-u)/moldyn->dv;
+	p+=tp->y*tp->y;
+
+	/* restore atomic configuration + dim */
+	memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
+	moldyn->dim=dim;
+
+	/* derivative with respect to z direction */
+	scale=1.0+moldyn->dv/(moldyn->dim.x*moldyn->dim.y);
+	scale_dim(moldyn,scale,0,0,TRUE);
+	scale_atoms(moldyn,scale,0,0,TRUE);
+	link_cell_shutdown(moldyn);
+	link_cell_init(moldyn);
+	potential_force_calc(moldyn);
+	tp->z=(moldyn->energy-u)/moldyn->dv;
+	p+=tp->z*tp->z;
+
+	/* restore atomic configuration + dim */
+	memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
+	moldyn->dim=dim;
+
+	printf("dU/dV komp addiert = %f %f %f\n",tp->x,tp->y,tp->z);
+
+	scale=1.0+pow(moldyn->dv/moldyn->volume,ONE_THIRD);
+
+printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
+	scale_dim(moldyn,scale,1,1,1);
+	scale_atoms(moldyn,scale,1,1,1);
+	link_cell_shutdown(moldyn);
+	link_cell_init(moldyn);
+	potential_force_calc(moldyn);
+printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
+
+	printf("dU/dV einfach = %f\n",((moldyn->energy-u)/moldyn->dv)/ATM);
+
+	/* restore atomic configuration + dim */
+	memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
+	moldyn->dim=dim;
+
+	/* restore energy */
+	moldyn->energy=u;
+
+	link_cell_shutdown(moldyn);
+	link_cell_init(moldyn);
+
+	return sqrt(p);
+}
 
 double get_pressure(t_moldyn *moldyn) {
 
@@ -605,6 +790,34 @@ double get_pressure(t_moldyn *moldyn) {
 
 }
 
+int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
+
+	t_3dvec *dim;
+
+	dim=&(moldyn->dim);
+
+	if(x) dim->x*=scale;
+	if(y) dim->y*=scale;
+	if(z) dim->z*=scale;
+
+	return 0;
+}
+
+int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
+
+	int i;
+	t_3dvec *r;
+
+	for(i=0;i<moldyn->count;i++) {
+		r=&(moldyn->atom[i].r);
+		if(x) r->x*=scale;
+		if(y) r->y*=scale;
+		if(z) r->z*=scale;
+	}
+
+	return 0;
+}
+
 int scale_volume(t_moldyn *moldyn) {
 
 	t_atom *atom;
@@ -918,6 +1131,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	int fd;
 	char dir[128];
 	double ds;
+	double energy_scale;
 
 	sched=&(moldyn->schedule);
 	atom=moldyn->atom;
@@ -935,8 +1149,13 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	moldyn->tau_square=moldyn->tau*moldyn->tau;
 	moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
 
+	/* energy scaling factor */
+	energy_scale=moldyn->count*EV;
+
+printf("debug: %f\n",moldyn->atom[0].f.x);
 	/* calculate initial forces */
 	potential_force_calc(moldyn);
+printf("debug: %f\n",moldyn->atom[0].f.x);
 
 	/* some stupid checks before we actually start calculating bullshit */
 	if(moldyn->cutoff>0.5*moldyn->dim.x)
@@ -979,22 +1198,19 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
 			scale_volume(moldyn);
 
+		update_e_kin(moldyn);
+		temperature_calc(moldyn);
+		pressure_calc(moldyn);
+		//thermodynamic_pressure_calc(moldyn);
+
 		/* check for log & visualization */
-//double ax;
-//double ao;
-//double av;
 		if(e) {
 			if(!(i%e))
-//ao=sqrt(0.1/M_SI);
-//ax=((0.28-0.25)*sqrt(3)*LC_SI/2)*cos(ao*i);
-//av=ao*(0.28-0.25)*sqrt(3)*LC_SI/2*sin(ao*i);
-				update_e_kin(moldyn);
 				dprintf(moldyn->efd,
 				        "%f %f %f %f\n",
-				        moldyn->time,moldyn->ekin,
-				        moldyn->energy,
-				        get_total_energy(moldyn));
-//moldyn->atom[0].r.x,ax,av*av*M_SI,0.1*ax*ax,av*av*M_SI+0.1*ax*ax);
+				        moldyn->time,moldyn->ekin/energy_scale,
+				        moldyn->energy/energy_scale,
+				        get_total_energy(moldyn)/energy_scale);
 		}
 		if(m) {
 			if(!(i%m)) {
@@ -1021,8 +1237,8 @@ int moldyn_integrate(t_moldyn *moldyn) {
 			if(!(i%v)) {
 				visual_atoms(&(moldyn->vis),moldyn->time,
 				             moldyn->atom,moldyn->count);
-				printf("\rsched: %d, steps: %d, debug: %d",
-				       sched->count,i,moldyn->debug);
+				printf("\rsched: %d, steps: %d, debug: %f",
+				       sched->count,i,moldyn->p/ATM);
 				fflush(stdout);
 			}
 		}
@@ -1115,27 +1331,29 @@ int potential_force_calc(t_moldyn *moldyn) {
 	/* reset energy */
 	moldyn->energy=0.0;
 
-	moldyn->vt2=0.0;
-	
-	/* get energy and force of every atom */
+	/* reset force, site energy and virial of every atom */
 	for(i=0;i<count;i++) {
 
 		/* reset force */
 		v3_zero(&(itom[i].f));
 
-		/* reset viral of atom i */
-		virial=&(itom[i].virial);
+		/* reset virial */
+		virial=(&(itom[i].virial));
 		virial->xx=0.0;
 		virial->yy=0.0;
 		virial->zz=0.0;
 		virial->xy=0.0;
 		virial->xz=0.0;
 		virial->yz=0.0;
-		moldyn->vt1=0.0;
-
+	
 		/* reset site energy */
 		itom[i].e=0.0;
 
+	}
+
+	/* get energy,force and virial of every atom */
+	for(i=0;i<count;i++) {
+
 		/* single particle potential/force */
 		if(itom[i].attr&ATOM_ATTR_1BP)
 			moldyn->func1b(moldyn,&(itom[i]));
@@ -1234,6 +1452,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 		}
 
 	}
+
 #ifdef DEBUG
 printf("\n\n");
 #endif
@@ -1241,14 +1460,6 @@ printf("\n\n");
 printf("\n\n");
 #endif
 
-	moldyn->vt2=0.0;
-	for(i=0;i<count;i++)
-		moldyn->vt2-=v3_scalar_product(&(itom[i].r),&(itom[i].f));
-
-//printf("compare: vt1: %f vt2: %f\n",moldyn->vt1,moldyn->vt2);
-
-//pressure_calc(moldyn);
-
 	return 0;
 }
 
@@ -1258,12 +1469,12 @@ printf("\n\n");
 
 inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
 
-	a->virial.xx-=f->x*d->x;
-	a->virial.yy-=f->y*d->y;
-	a->virial.zz-=f->z*d->z;
-	a->virial.xy-=f->x*d->y;
-	a->virial.xz-=f->x*d->z;
-	a->virial.yz-=f->y*d->z;
+	a->virial.xx+=f->x*d->x;
+	a->virial.yy+=f->y*d->y;
+	a->virial.zz+=f->z*d->z;
+	a->virial.xy+=f->x*d->y;
+	a->virial.xz+=f->x*d->z;
+	a->virial.yz+=f->y*d->z;
 
 	return 0;
 }
@@ -1371,11 +1582,10 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 		d*=eps;
 		v3_scale(&force,&distance,d);
 		v3_add(&(aj->f),&(aj->f),&force);
-		v3_scale(&force,&distance,-1.0*d); /* f = - grad E */
+		v3_scale(&force,&force,-1.0); /* f = - grad E */
 		v3_add(&(ai->f),&(ai->f),&force);
 		virial_calc(ai,&force,&distance);
 		virial_calc(aj,&force,&distance); /* f and d signe switched */
-		moldyn->vt1-=v3_scalar_product(&force,&distance);
 	}
 
 	return 0;