return 0;
}
+double temperature_calc(t_moldyn *moldyn) {
+
+ double double_ekin;
+ int i;
+ t_atom *atom;
+
+ atom=moldyn->atom;
+
+ 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);
+
+ return moldyn->t;
+}
+
+double get_temperature(t_moldyn *moldyn) {
+
+ return moldyn->t;
+}
+
int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
int i;
count=0;
for(i=0;i<moldyn->count;i++) {
if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
- e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+ e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
count+=1;
}
}
+ e*=0.5;
if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
else return 0; /* no atoms involved in scaling! */
return 0;
}
+double pressure_calc(t_moldyn *moldyn) {
+
+ int i;
+ t_atom *atom;
+ double p1,p2,p=0;
+
+ for(i=0;i<moldyn->count;i++) {
+
+
+ }
+
+ p1=(moldyn->count*K_BOLTZMANN*moldyn->t-ONE_THIRD*moldyn->vt1);
+ p1/=moldyn->volume;
+
+ p2=(moldyn->count*K_BOLTZMANN*moldyn->t-ONE_THIRD*moldyn->vt2);
+ p2/=moldyn->volume;
+
+ printf("compare pressures: %f %f\n",p1/ATM,p2/ATM);
+
+ return moldyn->p;
+}
+
+double get_pressure(t_moldyn *moldyn) {
+
+ return moldyn->p;
+
+}
+
int scale_volume(t_moldyn *moldyn) {
t_atom *atom;
return moldyn->ekin;
}
-double get_e_pot(t_moldyn *moldyn) {
-
- return moldyn->energy;
-}
-
double update_e_kin(t_moldyn *moldyn) {
return(get_e_kin(moldyn));
lc->cells=lc->nx*lc->ny*lc->nz;
lc->subcell=malloc(lc->cells*sizeof(t_list));
+ if(lc->cells<27)
+ printf("[moldyn] FATAL: less then 27 subcells!\n");
+
printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
for(i=0;i<lc->cells;i++)
scale_volume(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,update_e_kin(moldyn),
+ 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);
}
if(m) {
if(!(i%m)) {
int velocity_verlet(t_moldyn *moldyn) {
int i,count;
- double tau,tau_square;
+ double tau,tau_square,h;
t_3dvec delta;
t_atom *atom;
for(i=0;i<count;i++) {
/* new positions */
+ h=0.5/atom[i].mass;
v3_scale(&delta,&(atom[i].v),tau);
v3_add(&(atom[i].r),&(atom[i].r),&delta);
- v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
+ v3_scale(&delta,&(atom[i].f),h*tau_square);
v3_add(&(atom[i].r),&(atom[i].r),&delta);
check_per_bound(moldyn,&(atom[i].r));
- /* velocities */
- v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
+ /* velocities [actually v(t+tau/2)] */
+ v3_scale(&delta,&(atom[i].f),h*tau);
v3_add(&(atom[i].v),&(atom[i].v),&delta);
}
potential_force_calc(moldyn);
for(i=0;i<count;i++) {
- /* again velocities */
+ /* again velocities [actually v(t+tau)] */
v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
v3_add(&(atom[i].v),&(atom[i].v),&delta);
}
/*
*
- * potentials & corresponding forces
+ * potentials & corresponding forces & virial routine
*
*/
/* reset energy */
moldyn->energy=0.0;
+
+ moldyn->vt2=0.0;
/* get energy and force of every atom */
for(i=0;i<count;i++) {
virial->xy=0.0;
virial->xz=0.0;
virial->yz=0.0;
+ moldyn->vt1=0.0;
/* reset site energy */
itom[i].e=0.0;
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;
+}
+
+/*
+ * virial calculation
+ */
+
+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;
+
return 0;
}
t_ho_params *params;
t_3dvec force,distance;
- double d;
+ double d,f;
double sc,equi_dist;
params=moldyn->pot2b_params;
sc=params->spring_constant;
equi_dist=params->equilibrium_distance;
+ if(ai<aj) return 0;
+
v3_sub(&distance,&(aj->r),&(ai->r));
if(bc) check_per_bound(moldyn,&distance);
d=v3_norm(&distance);
if(d<=moldyn->cutoff) {
- /* energy is 1/2 (d-d0)^2, but we will add this twice ... */
- moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
+ moldyn->energy+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
/* f = -grad E; grad r_ij = -1 1/r_ij distance */
- v3_scale(&force,&distance,sc*(1.0-(equi_dist/d)));
+ f=sc*(1.0-equi_dist/d);
+ v3_scale(&force,&distance,f);
v3_add(&(ai->f),&(ai->f),&force);
+ virial_calc(ai,&force,&distance);
+ virial_calc(aj,&force,&distance); /* f and d signe switched */
+ v3_scale(&force,&distance,-f);
+ v3_add(&(aj->f),&(aj->f),&force);
}
return 0;
sig6=params->sigma6;
sig12=params->sigma12;
+ if(ai<aj) return 0;
+
v3_sub(&distance,&(aj->r),&(ai->r));
if(bc) check_per_bound(moldyn,&distance);
d=v3_absolute_square(&distance); /* 1/r^2 */
h2=d*d; /* 1/r^4 */
h2*=d; /* 1/r^6 */
h1=h2*h2; /* 1/r^12 */
- /* energy is eps*..., but we will add this twice ... */
- moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
+ moldyn->energy+=(eps*(sig12*h1-sig6*h2)-params->uc);
h2*=d; /* 1/r^8 */
h1*=d; /* 1/r^14 */
h2*=6*sig6;
h1*=12*sig12;
d=+h1-h2;
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_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;
zeta=exchange->zeta_ij;
if(zeta==0.0) {
moldyn->debug++; /* just for debugging ... */
- db=0.0;
b=chi;
v3_scale(&force,dist_ij,df_a*b*f_c);
}
v3_add(&(ai->f),&(ai->f),&force);
/* virial - plus sign, as dist_ij = - dist_ji - (really??) */
- ai->virial.xx+=force.x*dist_ij->x;
- ai->virial.yy+=force.y*dist_ij->y;
- ai->virial.zz+=force.z*dist_ij->z;
- ai->virial.xy+=force.x*dist_ij->y;
- ai->virial.xz+=force.x*dist_ij->z;
- ai->virial.yz+=force.y*dist_ij->z;
+// TEST ... with a minus instead
+ ai->virial.xx-=force.x*dist_ij->x;
+ ai->virial.yy-=force.y*dist_ij->y;
+ ai->virial.zz-=force.z*dist_ij->z;
+ ai->virial.xy-=force.x*dist_ij->y;
+ ai->virial.xz-=force.x*dist_ij->z;
+ ai->virial.yz-=force.y*dist_ij->z;
#ifdef DEBUG
if(ai==&(moldyn->atom[0])) {
projects / physik / posic.git / blobdiff