X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=f564075adece43f086ccd660cba312c4e6cd1ed3;hb=4871747c5c848e5881bea7949a41ceb589263841;hp=817a72788b45f2572258873aaa8ca64cace0397f;hpb=f3e4193447ac49a8953515910d4b4e6ce2c7608b;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 817a727..f564075 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) {
 
@@ -590,18 +591,9 @@ 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 +674,21 @@ 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;
 }	
@@ -1196,6 +1193,7 @@ 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 +1201,6 @@ 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,
@@ -1236,7 +1233,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 				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);
+				       sched->count,i,moldyn->p/ATM,moldyn->p/ATM);
 				fflush(stdout);
 			}
 		}
@@ -1580,7 +1577,7 @@ 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 */