X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=881f0b698565fe7495ee151ecca63239d32e74cf;hb=c0ddf2bdd8067456f39f6b63fe2261624ebde6b7;hp=817a72788b45f2572258873aaa8ca64cace0397f;hpb=f3e4193447ac49a8953515910d4b4e6ce2c7608b;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 817a727..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) {
 
@@ -343,7 +344,10 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 
 	switch(type) {
 		case CUBIC:
-			ret=cubic_init(a,b,c,lc,atom,NULL);
+			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,NULL);
@@ -398,8 +402,8 @@ int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 	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++) {
-				r.z=o.z;
 				v3_copy(&(atom[count].r),&r);
 				count+=1;
 				r.z+=lc;
@@ -590,18 +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;
-
-	double_ekin=0;
-	for(i=0;i<moldyn->count;i++)
-		double_ekin+=atom[i].mass*v3_absolute_square(&(atom[i].v));
+	/* assume up to date kinetic energy, which is 3/2 N k_B T */
 
-	/* 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;
 }
@@ -682,16 +677,21 @@ double pressure_calc(t_moldyn *moldyn) {
 	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);
 	}
-	v*=ONE_THIRD;
-printf("kieck mal: %f %f %f\n",v,moldyn->count*K_BOLTZMANN*moldyn->t,v/moldyn->count);
 
-	moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t+v;
-	moldyn->p/=moldyn->volume;
+	/* assume up to date kinetic energy */
+	moldyn->p=2.0*moldyn->ekin+v;
+	moldyn->p/=(3.0*moldyn->volume);
 
 	return moldyn->p;
 }	
@@ -1152,8 +1152,10 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	/* 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)
@@ -1196,6 +1198,7 @@ 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);
@@ -1203,7 +1206,6 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		/* check for log & visualization */
 		if(e) {
 			if(!(i%e))
-				update_e_kin(moldyn);
 				dprintf(moldyn->efd,
 				        "%f %f %f %f\n",
 				        moldyn->time,moldyn->ekin/energy_scale,
@@ -1235,8 +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: %f | %f",
-				       sched->count,i,moldyn->p/ATM,moldyn->debug/ATM);
+				printf("\rsched: %d, steps: %d, debug: %f",
+				       sched->count,i,moldyn->p/ATM);
 				fflush(stdout);
 			}
 		}
@@ -1580,7 +1582,7 @@ 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 */