moldyn->p_ref=p_ref;
- printf("[moldyn] pressure [atm]: %f\n",moldyn->p_ref/ATM);
+ printf("[moldyn] pressure [bar]: %f\n",moldyn->p_ref/BAR);
return 0;
}
return 0;
}
-int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func) {
+int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func) {
- moldyn->func2b_post=func;
+ moldyn->func3b_j1=func;
return 0;
}
-int set_potential3b(t_moldyn *moldyn,pf_func3b func) {
+int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func) {
- moldyn->func3b=func;
+ moldyn->func3b_j2=func;
+
+ return 0;
+}
+
+int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func) {
+
+ moldyn->func3b_j3=func;
+
+ return 0;
+}
+
+int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func) {
+
+ moldyn->func3b_k1=func;
+
+ return 0;
+}
+
+int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func) {
+
+ moldyn->func3b_k2=func;
return 0;
}
return 0;
}
+int set_avg_skip(t_moldyn *moldyn,int skip) {
+
+ printf("[moldyn] skip %d steps before starting average calc\n",skip);
+ moldyn->avg_skip=skip;
+
+ return 0;
+}
+
int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
strncpy(moldyn->vlsdir,dir,127);
perror("[moldyn] report fd open");
return moldyn->rfd;
}
+ printf("report -> ");
if(moldyn->efd) {
snprintf(filename,127,"%s/e_plot.scr",
moldyn->vlsdir);
}
dprintf(moldyn->epfd,e_plot_script);
close(moldyn->epfd);
+ printf("energy ");
}
if(moldyn->pfd) {
snprintf(filename,127,"%s/pressure_plot.scr",
}
dprintf(moldyn->ppfd,pressure_plot_script);
close(moldyn->ppfd);
+ printf("pressure ");
}
if(moldyn->tfd) {
snprintf(filename,127,"%s/temperature_plot.scr",
}
dprintf(moldyn->tpfd,temperature_plot_script);
close(moldyn->tpfd);
+ printf("temperature ");
}
dprintf(moldyn->rfd,report_start,
moldyn->rauthor,moldyn->rtitle);
+ printf("\n");
break;
default:
printf("unknown log type: %02x\n",type);
if(moldyn->rfd) {
dprintf(moldyn->rfd,report_end);
close(moldyn->rfd);
- snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
+ snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
+ moldyn->vlsdir);
system(sc);
- snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
+ snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
+ moldyn->vlsdir);
system(sc);
- snprintf(sc,255,"cd %s && dvipdf report",moldyn->vlsdir);
+ snprintf(sc,255,"cd %s && dvipdf report >/dev/null 2>&1",
+ moldyn->vlsdir);
system(sc);
}
if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
*/
int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
- u8 attr,u8 brand,int a,int b,int c) {
+ u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin) {
int new,count;
int ret;
- t_3dvec origin;
+ t_3dvec orig;
void *ptr;
t_atom *atom;
atom=&(moldyn->atom[count]);
/* no atoms on the boundaries (only reason: it looks better!) */
- origin.x=0.5*lc;
- origin.y=0.5*lc;
- origin.z=0.5*lc;
+ if(!origin) {
+ orig.x=0.5*lc;
+ orig.y=0.5*lc;
+ orig.z=0.5*lc;
+ }
+ else {
+ orig.x=origin->x;
+ orig.y=origin->y;
+ orig.z=origin->z;
+ }
switch(type) {
case CUBIC:
set_nn_dist(moldyn,lc);
- ret=cubic_init(a,b,c,lc,atom,&origin);
+ ret=cubic_init(a,b,c,lc,atom,&orig);
break;
case FCC:
- v3_scale(&origin,&origin,0.5);
+ if(!origin)
+ v3_scale(&orig,&orig,0.5);
set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
- ret=fcc_init(a,b,c,lc,atom,&origin);
+ ret=fcc_init(a,b,c,lc,atom,&orig);
break;
case DIAMOND:
- v3_scale(&origin,&origin,0.25);
+ if(!origin)
+ v3_scale(&orig,&orig,0.25);
set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
- ret=diamond_init(a,b,c,lc,atom,&origin);
+ ret=diamond_init(a,b,c,lc,atom,&orig);
break;
default:
printf("unknown lattice type (%02x)\n",type);
check_per_bound(moldyn,&(atom[ret].r));
}
+ /* update total system mass */
+ total_mass_calc(moldyn);
+
return ret;
}
atom[count].tag=count;
atom[count].attr=attr;
+ /* update total system mass */
+ total_mass_calc(moldyn);
+
return 0;
}
return 0;
}
+double total_mass_calc(t_moldyn *moldyn) {
+
+ int i;
+
+ moldyn->mass=0.0;
+
+ for(i=0;i<moldyn->count;i++)
+ moldyn->mass+=moldyn->atom[i].mass;
+
+ return moldyn->mass;
+}
+
double temperature_calc(t_moldyn *moldyn) {
/* assume up to date kinetic energy, which is 3/2 N k_B T */
return p;
}
-double pressure_calc(t_moldyn *moldyn) {
+double virial_sum(t_moldyn *moldyn) {
int i;
double v;
t_virial *virial;
+ /* virial (sum over atom virials) */
+ v=0.0;
+ for(i=0;i<moldyn->count;i++) {
+ virial=&(moldyn->atom[i].virial);
+ v+=(virial->xx+virial->yy+virial->zz);
+ }
+ moldyn->virial=v;
+
+ /* global virial (absolute coordinates) */
+ virial=&(moldyn->gvir);
+ moldyn->gv=virial->xx+virial->yy+virial->zz;
+
+ return moldyn->virial;
+}
+
+double pressure_calc(t_moldyn *moldyn) {
+
/*
* PV = NkT + <W>
- * W = 1/3 sum_i f_i r_i
+ * with W = 1/3 sum_i f_i r_i (- skipped!)
* 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 virial & up to date kinetic energy */
- /* assume up to date kinetic energy */
- moldyn->p=2.0*moldyn->ekin+v;
+ /* pressure (atom virials) */
+ moldyn->p=2.0*moldyn->ekin+moldyn->virial;
moldyn->p/=(3.0*moldyn->volume);
+ /* pressure (absolute coordinates) */
+ moldyn->gp=2.0*moldyn->ekin+moldyn->gv;
+ moldyn->gp/=(3.0*moldyn->volume);
+
return moldyn->p;
-}
+}
+
+int average_and_fluctuation_calc(t_moldyn *moldyn) {
+
+ if(moldyn->total_steps<moldyn->avg_skip)
+ return 0;
+
+ int denom=moldyn->total_steps+1-moldyn->avg_skip;
+
+ /* assume up to date energies, temperature, pressure etc */
+
+ /* kinetic energy */
+ moldyn->k_sum+=moldyn->ekin;
+ moldyn->k2_sum+=(moldyn->ekin*moldyn->ekin);
+ moldyn->k_avg=moldyn->k_sum/denom;
+ moldyn->k2_avg=moldyn->k2_sum/denom;
+ moldyn->dk2_avg=moldyn->k2_avg-(moldyn->k_avg*moldyn->k_avg);
+
+ /* potential energy */
+ moldyn->v_sum+=moldyn->energy;
+ moldyn->v2_sum+=(moldyn->energy*moldyn->energy);
+ moldyn->v_avg=moldyn->v_sum/denom;
+ moldyn->v2_avg=moldyn->v2_sum/denom;
+ moldyn->dv2_avg=moldyn->v2_avg-(moldyn->v_avg*moldyn->v_avg);
+
+ /* temperature */
+ moldyn->t_sum+=moldyn->t;
+ moldyn->t_avg=moldyn->t_sum/denom;
+
+ /* virial */
+ moldyn->virial_sum+=moldyn->virial;
+ moldyn->virial_avg=moldyn->virial_sum/denom;
+ moldyn->gv_sum+=moldyn->gv;
+ moldyn->gv_avg=moldyn->gv_sum/denom;
+
+ /* pressure */
+ moldyn->p_sum+=moldyn->p;
+ moldyn->p_avg=moldyn->p_sum/denom;
+ moldyn->gp_sum+=moldyn->gp;
+ moldyn->gp_avg=moldyn->gp_sum/denom;
+
+ return 0;
+}
+
+int get_heat_capacity(t_moldyn *moldyn) {
+
+ double temp2,ighc;
+
+ /* averages needed for heat capacity calc */
+ if(moldyn->total_steps<moldyn->avg_skip)
+ return 0;
+
+ /* (temperature average)^2 */
+ temp2=moldyn->t_avg*moldyn->t_avg;
+ printf("[moldyn] specific heat capacity for T=%f K [J/(kg K)]\n",
+ moldyn->t_avg);
+
+ /* ideal gas contribution */
+ ighc=3.0*moldyn->count*K_BOLTZMANN/2.0;
+ printf(" ideal gas contribution: %f\n",
+ ighc/moldyn->mass*KILOGRAM/JOULE);
+
+ /* specific heat for nvt ensemble */
+ moldyn->c_v_nvt=moldyn->dv2_avg/(K_BOLTZMANN*temp2)+ighc;
+ moldyn->c_v_nvt/=moldyn->mass;
+
+ /* specific heat for nve ensemble */
+ moldyn->c_v_nve=ighc/(1.0-(moldyn->dv2_avg/(ighc*K_BOLTZMANN*temp2)));
+ moldyn->c_v_nve/=moldyn->mass;
+
+ printf(" NVE: %f\n",moldyn->c_v_nve*KILOGRAM/JOULE);
+ printf(" NVT: %f\n",moldyn->c_v_nvt*KILOGRAM/JOULE);
+printf(" --> <dV2> sim: %f experimental: %f\n",moldyn->dv2_avg,1.5*moldyn->count*K_B2*moldyn->t_avg*moldyn->t_avg*(1.0-1.5*moldyn->count*K_BOLTZMANN/(700*moldyn->mass*JOULE/KILOGRAM)));
+
+ return 0;
+}
double thermodynamic_pressure_calc(t_moldyn *moldyn) {
t_3dvec dim,*tp;
- double u,p;
- double scale,dv;
+ double u_up,u_down,dv;
+ double scale,p;
t_atom *store;
/*
*
* => p = - dU/dV
*
- * dV: dx,y,z = 0.001 x,y,z
*/
- scale=1.00001;
-printf("\n\nP-DEBUG:\n");
+ scale=0.00001;
+ dv=8*scale*scale*scale*moldyn->volume;
- tp=&(moldyn->tp);
store=malloc(moldyn->count*sizeof(t_atom));
if(store==NULL) {
printf("[moldyn] allocating store mem failed\n");
}
/* 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=0.00001*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;
-printf("e: %f eV de: %f eV dV: %f A^3\n",moldyn->energy/moldyn->count/EV,(moldyn->energy-u)/moldyn->count/EV,dv);
-
- /* 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=0.00001*moldyn->dim.y*moldyn->dim.x*moldyn->dim.z;
+ /* scale up dimension and atom positions */
+ scale_dim(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
+ scale_atoms(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
link_cell_shutdown(moldyn);
link_cell_init(moldyn,QUIET);
potential_force_calc(moldyn);
- tp->y=(moldyn->energy-u)/dv;
- p+=tp->y*tp->y;
+ u_up=moldyn->energy;
/* 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=0.00001*moldyn->dim.z*moldyn->dim.x*moldyn->dim.y;
+ /* scale down dimension and atom positions */
+ scale_dim(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
+ scale_atoms(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
link_cell_shutdown(moldyn);
link_cell_init(moldyn,QUIET);
potential_force_calc(moldyn);
- tp->z=(moldyn->energy-u)/dv;
- p+=tp->z*tp->z;
+ u_down=moldyn->energy;
+
+ /* calculate pressure */
+ p=-(u_up-u_down)/dv;
+printf("-------> %.10f %.10f %f\n",u_up/EV/moldyn->count,u_down/EV/moldyn->count,p/BAR);
/* restore atomic configuration + dim */
memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
moldyn->dim=dim;
/* restore energy */
- moldyn->energy=u;
+ potential_force_calc(moldyn);
link_cell_shutdown(moldyn);
link_cell_init(moldyn,QUIET);
- return sqrt(p);
+ return p;
}
double get_pressure(t_moldyn *moldyn) {
}
-int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
+int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
t_3dvec *dim;
dim=&(moldyn->dim);
+ if(dir==SCALE_UP)
+ scale=1.0+scale;
+
+ if(dir==SCALE_DOWN)
+ scale=1.0-scale;
+
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 scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
int i;
t_3dvec *r;
+ if(dir==SCALE_UP)
+ scale=1.0+scale;
+
+ if(dir==SCALE_DOWN)
+ scale=1.0-scale;
+
for(i=0;i<moldyn->count;i++) {
r=&(moldyn->atom[i].r);
if(x) r->x*=scale;
moldyn->debug=scale;
/* scale the atoms and dimensions */
- scale_atoms(moldyn,scale,TRUE,TRUE,TRUE);
- scale_dim(moldyn,scale,TRUE,TRUE,TRUE);
+ scale_atoms(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
+ scale_dim(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
/* visualize dimensions */
if(vdim->x!=0) {
}
-double get_e_kin(t_moldyn *moldyn) {
+double e_kin_calc(t_moldyn *moldyn) {
int i;
t_atom *atom;
return moldyn->ekin;
}
-double update_e_kin(t_moldyn *moldyn) {
-
- return(get_e_kin(moldyn));
-}
-
double get_total_energy(t_moldyn *moldyn) {
return(moldyn->ekin+moldyn->energy);
if(lc->cells<27)
printf("[moldyn] FATAL: less then 27 subcells!\n");
- if(vol) printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
+ 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]));
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(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
+ list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
&(atom[count]));
}
/* calculate initial forces */
potential_force_calc(moldyn);
+#ifdef DEBUG
+return 0;
+#endif
/* some stupid checks before we actually start calculating bullshit */
if(moldyn->cutoff>0.5*moldyn->dim.x)
/* zero absolute time */
moldyn->time=0.0;
+ moldyn->total_steps=0;
/* debugging, ignore */
moldyn->debug=0;
printf("[moldyn] integration start, go get a coffee ...\n");
/* executing the schedule */
- for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
+ sched->count=0;
+ while(sched->count<sched->total_sched) {
/* setting amount of runs and finite time step size */
moldyn->tau=sched->tau[sched->count];
moldyn->integrate(moldyn);
/* calculate kinetic energy, temperature and pressure */
- update_e_kin(moldyn);
+ e_kin_calc(moldyn);
temperature_calc(moldyn);
+ virial_sum(moldyn);
pressure_calc(moldyn);
- //tp=thermodynamic_pressure_calc(moldyn);
+ average_and_fluctuation_calc(moldyn);
/* p/t scaling */
if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
if(p) {
if(!(i%p)) {
dprintf(moldyn->pfd,
- "%f %f\n",moldyn->time,moldyn->p/ATM);
+ "%f %f %f %f %f\n",moldyn->time,
+ moldyn->p/BAR,moldyn->p_avg/BAR,
+ moldyn->gp/BAR,moldyn->gp_avg/BAR);
}
}
if(t) {
if(!(i%t)) {
dprintf(moldyn->tfd,
- "%f %f\n",moldyn->time,moldyn->t);
+ "%f %f %f\n",
+ moldyn->time,moldyn->t,moldyn->t_avg);
}
}
if(s) {
/* display progress */
if(!(i%10)) {
- printf("\rsched: %d, steps: %d, T: %f, P: %f V: %f",
- sched->count,i,
- moldyn->t,moldyn->p/ATM,moldyn->volume);
- fflush(stdout);
+ printf("\rsched:%d, steps:%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f",
+ sched->count,i,
+ moldyn->t,moldyn->t_avg,
+ moldyn->p_avg/BAR,moldyn->p/BAR,
+ moldyn->volume);
+ fflush(stdout);
}
/* increase absolute time */
moldyn->time+=moldyn->tau;
+ moldyn->total_steps+=1;
}
/* check for hooks */
- if(sched->hook)
+ if(sched->hook) {
+ printf("\n ## schedule hook %d/%d start ##\n",
+ sched->count+1,sched->total_sched-1);
sched->hook(moldyn,sched->hook_params);
+ printf(" ## schedule hook end ##\n");
+ }
- /* get a new info line */
- printf("\n");
+ /* increase the schedule counter */
+ sched->count+=1;
}
/* reset energy */
moldyn->energy=0.0;
+ /* reset global virial */
+ memset(&(moldyn->gvir),0,sizeof(t_virial));
+
/* reset force, site energy and virial of every atom */
for(i=0;i<count;i++) {
}
- /* get energy,force and virial of every atom */
+ /* get energy, force and virial of every atom */
+
+ /* first (and only) loop over atoms i */
for(i=0;i<count;i++) {
/* single particle potential/force */
if(itom[i].attr&ATOM_ATTR_1BP)
- moldyn->func1b(moldyn,&(itom[i]));
+ if(moldyn->func1b)
+ moldyn->func1b(moldyn,&(itom[i]));
if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
continue;
dnlc=lc->dnlc;
+ /* first loop over atoms j */
+ if(moldyn->func2b) {
+ for(j=0;j<27;j++) {
+
+ this=&(neighbour_i[j]);
+ list_reset_f(this);
+
+ if(this->start==NULL)
+ continue;
+
+ bc_ij=(j<dnlc)?0:1;
+
+ do {
+ jtom=this->current->data;
+
+ if(jtom==&(itom[i]))
+ continue;
+
+ if((jtom->attr&ATOM_ATTR_2BP)&
+ (itom[i].attr&ATOM_ATTR_2BP)) {
+ moldyn->func2b(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
+ }
+ } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+
+ }
+ }
+
+ /* 3 body potential/force */
+
+ if(!(itom[i].attr&ATOM_ATTR_3BP))
+ continue;
+
+ /* copy the neighbour lists */
+ memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
+
+ /* second loop over atoms j */
for(j=0;j<27;j++) {
this=&(neighbour_i[j]);
if(jtom==&(itom[i]))
continue;
- if((jtom->attr&ATOM_ATTR_2BP)&
- (itom[i].attr&ATOM_ATTR_2BP)) {
- moldyn->func2b(moldyn,
- &(itom[i]),
- jtom,
- bc_ij);
- }
+ if(!(jtom->attr&ATOM_ATTR_3BP))
+ continue;
+
+ /* reset 3bp run */
+ moldyn->run3bp=1;
- /* 3 body potential/force */
+ if(moldyn->func3b_j1)
+ moldyn->func3b_j1(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
- if(!(itom[i].attr&ATOM_ATTR_3BP)||
- !(jtom->attr&ATOM_ATTR_3BP))
+ /* in first j loop, 3bp run can be skipped */
+ if(!(moldyn->run3bp))
continue;
+
+ /* first loop over atoms k */
+ if(moldyn->func3b_k1) {
+
+ for(k=0;k<27;k++) {
+
+ that=&(neighbour_i2[k]);
+ list_reset_f(that);
+
+ if(that->start==NULL)
+ continue;
- /* copy the neighbour lists */
- memcpy(neighbour_i2,neighbour_i,
- 27*sizeof(t_list));
+ bc_ik=(k<dnlc)?0:1;
+
+ do {
+
+ ktom=that->current->data;
+
+ if(!(ktom->attr&ATOM_ATTR_3BP))
+ continue;
+
+ if(ktom==jtom)
+ continue;
+
+ if(ktom==&(itom[i]))
+ continue;
+
+ moldyn->func3b_k1(moldyn,
+ &(itom[i]),
+ jtom,
+ ktom,
+ bc_ik|bc_ij);
+
+ } while(list_next_f(that)!=\
+ L_NO_NEXT_ELEMENT);
+
+ }
+
+ }
+
+ if(moldyn->func3b_j2)
+ moldyn->func3b_j2(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
+
+ /* second loop over atoms k */
+ if(moldyn->func3b_k2) {
- /* get neighbours of i */
for(k=0;k<27;k++) {
that=&(neighbour_i2[k]);
if(ktom==&(itom[i]))
continue;
- moldyn->func3b(moldyn,
- &(itom[i]),
- jtom,
- ktom,
- bc_ik|bc_ij);
+ moldyn->func3b_k2(moldyn,
+ &(itom[i]),
+ jtom,
+ ktom,
+ bc_ik|bc_ij);
} while(list_next_f(that)!=\
L_NO_NEXT_ELEMENT);
}
+
+ }
/* 2bp post function */
- if(moldyn->func2b_post) {
- moldyn->func2b_post(moldyn,
- &(itom[i]),
- jtom,bc_ij);
+ if(moldyn->func3b_j3) {
+ moldyn->func3b_j3(moldyn,
+ &(itom[i]),
+ jtom,bc_ij);
}
} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
}
+
+#ifdef DEBUG
+ //printf("\n\n");
+#endif
+#ifdef VDEBUG
+ printf("\n\n");
+#endif
}
#ifdef DEBUG
-printf("\n\n");
-#endif
-#ifdef VDEBUG
-printf("\n\n");
+ printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
#endif
+ /* calculate global virial */
+ for(i=0;i<count;i++) {
+ moldyn->gvir.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
+ moldyn->gvir.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
+ moldyn->gvir.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
+ moldyn->gvir.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
+ moldyn->gvir.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
+ moldyn->gvir.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
+ }
+
return 0;
}
}
/*
- * periodic boundayr checking
+ * periodic boundary checking
*/
//inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
return 0;
}
+
+/*
+ * post processing functions
+ */
+
+int get_line(int fd,char *line,int max) {
+
+ int count,ret;
+
+ count=0;
+
+ while(1) {
+ if(count==max) return count;
+ ret=read(fd,line+count,1);
+ if(ret<=0) return ret;
+ if(line[count]=='\n') {
+ line[count]='\0';
+ return count+1;
+ }
+ count+=1;
+ }
+}
+
projects / physik / posic.git / blobdiff