nur foo ...

[physik/posic.git] / moldyn.c

diff --git a/moldyn.c b/moldyn.c
index 817a727..881f0b6 100644 (file)
--- 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 */