+ 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;
+
+}
+
+int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
+
+ t_3dvec *dim;
+
+ dim=&(moldyn->dim);
+
+ if(x) dim->x*=scale;
+ if(y) dim->y*=scale;
+ if(z) dim->z*=scale;
+
+ return 0;
+}
+
+int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
+
+ int i;
+ t_3dvec *r;
+
+ for(i=0;i<moldyn->count;i++) {
+ r=&(moldyn->atom[i].r);
+ if(x) r->x*=scale;
+ if(y) r->y*=scale;
+ if(z) r->z*=scale;
+ }
+
+ return 0;
+}
+
+int scale_volume(t_moldyn *moldyn) {
+
+ t_3dvec *dim,*vdim;
+ double scale;
+ t_linkcell *lc;
+
+ vdim=&(moldyn->vis.dim);
+ dim=&(moldyn->dim);
+ lc=&(moldyn->lc);
+
+ /* scaling factor */
+ if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
+ scale=1.0-(moldyn->p_ref-moldyn->p)/moldyn->p_tc;
+ scale=pow(scale,ONE_THIRD);
+ }
+ else {
+ scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
+ }
+moldyn->debug=scale;
+
+ /* scale the atoms and dimensions */
+ scale_atoms(moldyn,scale,TRUE,TRUE,TRUE);
+ scale_dim(moldyn,scale,TRUE,TRUE,TRUE);
+
+ /* visualize dimensions */
+ if(vdim->x!=0) {
+ vdim->x=dim->x;
+ vdim->y=dim->y;
+ vdim->z=dim->z;
+ }
+
+ /* recalculate scaled volume */
+ moldyn->volume=dim->x*dim->y*dim->z;
+
+ /* adjust/reinit linkcell */
+ if(((int)(dim->x/moldyn->cutoff)!=lc->nx)||
+ ((int)(dim->y/moldyn->cutoff)!=lc->ny)||
+ ((int)(dim->z/moldyn->cutoff)!=lc->nx)) {
+ link_cell_shutdown(moldyn);
+ link_cell_init(moldyn,QUIET);
+ } else {
+ lc->x*=scale;
+ lc->y*=scale;
+ lc->z*=scale;
+ }
+
+ return 0;
+
+}
+
+double e_kin_calc(t_moldyn *moldyn) {
+
+ int i;
+ t_atom *atom;
+
+ atom=moldyn->atom;
+ moldyn->ekin=0.0;
+
+ for(i=0;i<moldyn->count;i++)
+ moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+
+ return moldyn->ekin;
+}
+
+double get_total_energy(t_moldyn *moldyn) {
+
+ return(moldyn->ekin+moldyn->energy);
+}
+
+t_3dvec get_total_p(t_moldyn *moldyn) {
+
+ t_3dvec p,p_total;
+ int i;
+ t_atom *atom;
+
+ atom=moldyn->atom;
+
+ v3_zero(&p_total);
+ for(i=0;i<moldyn->count;i++) {
+ v3_scale(&p,&(atom[i].v),atom[i].mass);
+ v3_add(&p_total,&p_total,&p);
+ }
+
+ return p_total;
+}
+
+double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
+
+ double tau;
+
+ /* nn_dist is the nearest neighbour distance */
+
+ tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
+
+ return tau;
+}
+
+/*
+ * numerical tricks
+ */
+
+/* linked list / cell method */
+
+int link_cell_init(t_moldyn *moldyn,u8 vol) {
+
+ t_linkcell *lc;
+ int i;
+
+ lc=&(moldyn->lc);
+
+ /* partitioning the md cell */
+ lc->nx=moldyn->dim.x/moldyn->cutoff;
+ lc->x=moldyn->dim.x/lc->nx;
+ lc->ny=moldyn->dim.y/moldyn->cutoff;
+ lc->y=moldyn->dim.y/lc->ny;
+ lc->nz=moldyn->dim.z/moldyn->cutoff;
+ lc->z=moldyn->dim.z/lc->nz;
+
+ 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");
+
+ if(vol) {
+ printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
+ printf(" x: %d x %f A\n",lc->nx,lc->x);
+ printf(" y: %d x %f A\n",lc->ny,lc->y);
+ printf(" z: %d x %f A\n",lc->nz,lc->z);
+ }
+
+ for(i=0;i<lc->cells;i++)
+ list_init_f(&(lc->subcell[i]));
+
+ link_cell_update(moldyn);
+
+ return 0;
+}
+
+int link_cell_update(t_moldyn *moldyn) {
+
+ int count,i,j,k;
+ int nx,ny;
+ t_atom *atom;
+ t_linkcell *lc;
+ double x,y,z;
+
+ atom=moldyn->atom;
+ lc=&(moldyn->lc);
+
+ nx=lc->nx;
+ ny=lc->ny;
+
+ x=moldyn->dim.x/2;
+ y=moldyn->dim.y/2;
+ z=moldyn->dim.z/2;
+
+ for(i=0;i<lc->cells;i++)
+ list_destroy_f(&(lc->subcell[i]));
+
+ for(count=0;count<moldyn->count;count++) {
+ i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
+ j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
+ k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
+ list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
+ &(atom[count]));
+ }
+
+ return 0;
+}
+
+int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
+
+ t_linkcell *lc;
+ int a;
+ int count1,count2;
+ int ci,cj,ck;
+ int nx,ny,nz;
+ int x,y,z;
+ u8 bx,by,bz;
+
+ lc=&(moldyn->lc);
+ nx=lc->nx;
+ ny=lc->ny;
+ nz=lc->nz;
+ count1=1;
+ count2=27;
+ a=nx*ny;
+
+ cell[0]=lc->subcell[i+j*nx+k*a];
+ for(ci=-1;ci<=1;ci++) {
+ bx=0;
+ x=i+ci;
+ if((x<0)||(x>=nx)) {
+ x=(x+nx)%nx;
+ bx=1;
+ }
+ for(cj=-1;cj<=1;cj++) {
+ by=0;
+ y=j+cj;
+ if((y<0)||(y>=ny)) {
+ y=(y+ny)%ny;
+ by=1;
+ }
+ for(ck=-1;ck<=1;ck++) {
+ bz=0;
+ z=k+ck;
+ if((z<0)||(z>=nz)) {
+ z=(z+nz)%nz;
+ bz=1;
+ }
+ if(!(ci|cj|ck)) continue;
+ if(bx|by|bz) {
+ cell[--count2]=lc->subcell[x+y*nx+z*a];
+ }
+ else {
+ cell[count1++]=lc->subcell[x+y*nx+z*a];
+ }
+ }
+ }
+ }
+
+ lc->dnlc=count1;
+
+ return count1;
+}
+
+int link_cell_shutdown(t_moldyn *moldyn) {
+
+ int i;
+ t_linkcell *lc;
+
+ lc=&(moldyn->lc);
+
+ for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
+ list_destroy_f(&(moldyn->lc.subcell[i]));
+
+ free(lc->subcell);
+
+ return 0;
+}
+
+int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
+
+ int count;
+ void *ptr;
+ t_moldyn_schedule *schedule;
+
+ schedule=&(moldyn->schedule);
+ count=++(schedule->total_sched);
+
+ ptr=realloc(schedule->runs,count*sizeof(int));
+ if(!ptr) {
+ perror("[moldyn] realloc (runs)");
+ return -1;
+ }
+ schedule->runs=ptr;
+ schedule->runs[count-1]=runs;
+
+ ptr=realloc(schedule->tau,count*sizeof(double));
+ if(!ptr) {
+ perror("[moldyn] realloc (tau)");
+ return -1;
+ }
+ schedule->tau=ptr;
+ schedule->tau[count-1]=tau;
+
+ printf("[moldyn] schedule added:\n");
+ printf(" number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
+
+
+ return 0;
+}
+
+int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
+
+ moldyn->schedule.hook=hook;
+ moldyn->schedule.hook_params=hook_params;
+
+ return 0;
+}
+
+/*
+ *
+ * 'integration of newtons equation' - algorithms
+ *
+ */
+
+/* start the integration */
+
+int moldyn_integrate(t_moldyn *moldyn) {
+
+ int i;
+ unsigned int e,m,s,v,p,t;
+ t_3dvec momentum;
+ t_moldyn_schedule *sched;
+ t_atom *atom;
+ int fd;
+ char dir[128];
+ double ds;
+ double energy_scale;
+ //double tp;
+
+ sched=&(moldyn->schedule);
+ atom=moldyn->atom;
+
+ /* initialize linked cell method */
+ link_cell_init(moldyn,VERBOSE);
+
+ /* logging & visualization */
+ e=moldyn->ewrite;
+ m=moldyn->mwrite;
+ s=moldyn->swrite;
+ v=moldyn->vwrite;
+ p=moldyn->pwrite;
+ t=moldyn->twrite;
+
+ /* sqaure of some variables */
+ moldyn->tau_square=moldyn->tau*moldyn->tau;
+ moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
+
+ /* energy scaling factor */
+ energy_scale=moldyn->count*EV;
+
+ /* calculate initial forces */
+ potential_force_calc(moldyn);
+
+ /* some stupid checks before we actually start calculating bullshit */
+ if(moldyn->cutoff>0.5*moldyn->dim.x)
+ printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
+ if(moldyn->cutoff>0.5*moldyn->dim.y)
+ printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
+ if(moldyn->cutoff>0.5*moldyn->dim.z)
+ printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
+ ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
+ if(ds>0.05*moldyn->nnd)
+ printf("[moldyn] warning: forces too high / tau too small!\n");
+
+ /* zero absolute time */
+ moldyn->time=0.0;
+ moldyn->total_steps=0;
+
+ /* debugging, ignore */
+ moldyn->debug=0;
+
+ /* tell the world */
+ printf("[moldyn] integration start, go get a coffee ...\n");
+
+ /* executing the schedule */
+ for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
+
+ /* setting amount of runs and finite time step size */
+ moldyn->tau=sched->tau[sched->count];
+ moldyn->tau_square=moldyn->tau*moldyn->tau;
+ moldyn->time_steps=sched->runs[sched->count];
+
+ /* integration according to schedule */
+
+ for(i=0;i<moldyn->time_steps;i++) {
+
+ /* integration step */
+ moldyn->integrate(moldyn);
+
+ /* calculate kinetic energy, temperature and pressure */
+ e_kin_calc(moldyn);
+ temperature_calc(moldyn);
+ pressure_calc(moldyn);
+ //tp=thermodynamic_pressure_calc(moldyn);
+//printf("thermodynamic p: %f %f %f - %f\n",moldyn->tp.x/BAR,moldyn->tp.y/BAR,moldyn->tp.z/BAR,tp/BAR);
+
+ /* p/t scaling */
+ if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
+ scale_velocity(moldyn,FALSE);
+ if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
+ scale_volume(moldyn);
+
+ /* check for log & visualization */
+ if(e) {
+ if(!(i%e))
+ dprintf(moldyn->efd,
+ "%f %f %f %f\n",
+ moldyn->time,moldyn->ekin/energy_scale,
+ moldyn->energy/energy_scale,
+ get_total_energy(moldyn)/energy_scale);
+ }
+ if(m) {
+ if(!(i%m)) {
+ momentum=get_total_p(moldyn);
+ dprintf(moldyn->mfd,
+ "%f %f %f %f %f\n",moldyn->time,
+ momentum.x,momentum.y,momentum.z,
+ v3_norm(&momentum));
+ }
+ }
+ if(p) {
+ if(!(i%p)) {
+ dprintf(moldyn->pfd,
+ "%f %f %f %f %f\n",moldyn->time,
+ moldyn->p/BAR,moldyn->mean_p/BAR,
+ moldyn->gp/BAR,moldyn->mean_gp/BAR);
+ }
+ }
+ if(t) {
+ if(!(i%t)) {
+ dprintf(moldyn->tfd,
+ "%f %f %f\n",
+ moldyn->time,moldyn->t,moldyn->mean_t);
+ }
+ }
+ if(s) {
+ if(!(i%s)) {
+ snprintf(dir,128,"%s/s-%07.f.save",
+ moldyn->vlsdir,moldyn->time);
+ fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
+ if(fd<0) perror("[moldyn] save fd open");
+ else {
+ write(fd,moldyn,sizeof(t_moldyn));
+ write(fd,moldyn->atom,
+ moldyn->count*sizeof(t_atom));
+ }
+ close(fd);
+ }
+ }
+ if(v) {
+ if(!(i%v)) {
+ visual_atoms(&(moldyn->vis),moldyn->time,
+ moldyn->atom,moldyn->count);
+ }
+ }
+
+ /* display progress */
+ if(!(i%10)) {
+ printf("\rsched: %d, steps: %d, T: %f, P: %f %f V: %f",
+ sched->count,i,
+ moldyn->mean_t,
+ moldyn->mean_p/BAR,
+ moldyn->mean_gp/BAR,
+ moldyn->volume);
+ fflush(stdout);
+ }
+
+ /* increase absolute time */
+ moldyn->time+=moldyn->tau;
+ moldyn->total_steps+=1;
+
+ }
+
+ /* check for hooks */
+ if(sched->hook)
+ sched->hook(moldyn,sched->hook_params);
+
+ /* get a new info line */
+ printf("\n");
+
+ }
+
+ return 0;
+}
+
+/* velocity verlet */
+
+int velocity_verlet(t_moldyn *moldyn) {
+
+ int i,count;
+ double tau,tau_square,h;
+ t_3dvec delta;
+ t_atom *atom;