+ /* zero total momentum */
+ v3_scale(&p_total,&p_total,1.0/moldyn->count);
+ for(i=0;i<moldyn->count;i++) {
+ v3_scale(&delta,&p_total,1.0/atom[i].mass);
+ v3_sub(&(atom[i].v),&(atom[i].v),&delta);
+ }
+
+ /* velocity scaling */
+ scale_velocity(moldyn,equi_init);
+
+ return 0;
+}
+
+double temperature_calc(t_moldyn *moldyn) {
+
+ /* assume up to date kinetic energy, which is 3/2 N k_B T */
+
+ moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
+ moldyn->t_sum+=moldyn->t;
+ moldyn->mean_t=moldyn->t_sum/moldyn->total_steps;
+
+ return moldyn->t;
+}
+
+double get_temperature(t_moldyn *moldyn) {
+
+ return moldyn->t;
+}
+
+int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
+
+ int i;
+ double e,scale;
+ t_atom *atom;
+ int count;
+
+ atom=moldyn->atom;
+
+ /*
+ * - velocity scaling (E = 3/2 N k T), E: kinetic energy
+ */
+
+ /* get kinetic energy / temperature & count involved atoms */
+ e=0.0;
+ count=0;
+ for(i=0;i<moldyn->count;i++) {
+ if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
+ 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! */
+
+ /* (temporary) hack for e,t = 0 */
+ if(e==0.0) {
+ moldyn->t=0.0;
+ if(moldyn->t_ref!=0.0) {
+ thermal_init(moldyn,equi_init);
+ return 0;
+ }
+ else
+ return 0; /* no scaling needed */
+ }
+
+
+ /* get scaling factor */
+ scale=moldyn->t_ref/moldyn->t;
+ if(equi_init&TRUE)
+ scale*=2.0;
+ else
+ if(moldyn->pt_scale&T_SCALE_BERENDSEN)
+ scale=1.0+(scale-1.0)/moldyn->t_tc;
+ scale=sqrt(scale);
+
+ /* velocity scaling */
+ for(i=0;i<moldyn->count;i++) {
+ if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
+ v3_scale(&(atom[i].v),&(atom[i].v),scale);
+ }
+
+ 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;
+ double v;
+ t_virial *virial;
+
+ /*
+ * PV = NkT + <W>
+ * W = 1/3 sum_i f_i r_i
+ * virial = sum_i f_i r_i
+ *
+ * => P = (2 Ekin + virial) / (3V)
+ */
+
+ 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);
+ moldyn->p_sum+=moldyn->p;
+ moldyn->mean_p=moldyn->p_sum/moldyn->total_steps;
+
+ /* pressure from 'absolute coordinates' virial */
+ virial=&(moldyn->virial);
+ v=virial->xx+virial->yy+virial->zz;
+ moldyn->gp=2.0*moldyn->ekin+v;
+ moldyn->gp/=(3.0*moldyn->volume);
+ moldyn->gp_sum+=moldyn->gp;
+ moldyn->mean_gp=moldyn->gp_sum/moldyn->total_steps;
+
+ return moldyn->p;
+}
+
+double thermodynamic_pressure_calc(t_moldyn *moldyn) {
+
+ t_3dvec dim,*tp;
+ double u,p;
+ double scale,dv;
+ t_atom *store;
+
+ /*
+ * dU = - p dV
+ *
+ * => p = - dU/dV
+ *
+ * dV: dx,y,z = 0.001 x,y,z
+ */
+
+ scale=1.00000000000001;
+printf("\n\nP-DEBUG:\n");
+
+ tp=&(moldyn->tp);
+ store=malloc(moldyn->count*sizeof(t_atom));
+ if(store==NULL) {
+ printf("[moldyn] allocating store mem failed\n");
+ return -1;
+ }
+
+ /* save unscaled potential energy + atom/dim configuration */
+ u=moldyn->energy;
+ memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
+ dim=moldyn->dim;
+
+ /* derivative with respect to x direction */
+ scale_dim(moldyn,scale,TRUE,0,0);
+ scale_atoms(moldyn,scale,TRUE,0,0);
+ dv=0.00000000000001*moldyn->dim.x*moldyn->dim.y*moldyn->dim.z;
+ link_cell_shutdown(moldyn);
+ link_cell_init(moldyn,QUIET);
+ potential_force_calc(moldyn);
+ tp->x=(moldyn->energy-u)/dv;
+ p=tp->x*tp->x;
+
+ /* restore atomic configuration + dim */
+ memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
+ moldyn->dim=dim;
+
+ /* derivative with respect to y direction */
+ scale_dim(moldyn,scale,0,TRUE,0);
+ scale_atoms(moldyn,scale,0,TRUE,0);
+ dv=0.00000000000001*moldyn->dim.y*moldyn->dim.x*moldyn->dim.z;
+ link_cell_shutdown(moldyn);
+ link_cell_init(moldyn,QUIET);
+ potential_force_calc(moldyn);
+ tp->y=(moldyn->energy-u)/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_dim(moldyn,scale,0,0,TRUE);
+ scale_atoms(moldyn,scale,0,0,TRUE);
+ dv=0.00000000000001*moldyn->dim.z*moldyn->dim.x*moldyn->dim.y;
+ link_cell_shutdown(moldyn);
+ link_cell_init(moldyn,QUIET);
+ potential_force_calc(moldyn);
+ tp->z=(moldyn->energy-u)/dv;
+ p+=tp->z*tp->z;
+
+ /* 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,QUIET);
+
+ return sqrt(p);
+}
+
+double get_pressure(t_moldyn *moldyn) {
+
+ return moldyn->p;
+
+}