2 * moldyn.c - molecular dynamics library main file
4 * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
12 #include <sys/types.h>
19 #include "report/report.h"
21 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
23 printf("[moldyn] init\n");
25 memset(moldyn,0,sizeof(t_moldyn));
27 rand_init(&(moldyn->random),NULL,1);
28 moldyn->random.status|=RAND_STAT_VERBOSE;
33 int moldyn_shutdown(t_moldyn *moldyn) {
35 printf("[moldyn] shutdown\n");
37 moldyn_log_shutdown(moldyn);
38 link_cell_shutdown(moldyn);
39 rand_close(&(moldyn->random));
45 int set_int_alg(t_moldyn *moldyn,u8 algo) {
47 printf("[moldyn] integration algorithm: ");
50 case MOLDYN_INTEGRATE_VERLET:
51 moldyn->integrate=velocity_verlet;
52 printf("velocity verlet\n");
55 printf("unknown integration algorithm: %02x\n",algo);
63 int set_cutoff(t_moldyn *moldyn,double cutoff) {
65 moldyn->cutoff=cutoff;
67 printf("[moldyn] cutoff [A]: %f\n",moldyn->cutoff);
72 int set_temperature(t_moldyn *moldyn,double t_ref) {
76 printf("[moldyn] temperature [K]: %f\n",moldyn->t_ref);
81 int set_pressure(t_moldyn *moldyn,double p_ref) {
85 printf("[moldyn] pressure [atm]: %f\n",moldyn->p_ref/ATM);
90 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
92 moldyn->pt_scale=(ptype|ttype);
96 printf("[moldyn] p/t scaling:\n");
98 printf(" p: %s",ptype?"yes":"no ");
100 printf(" | type: %02x | factor: %f",ptype,ptc);
103 printf(" t: %s",ttype?"yes":"no ");
105 printf(" | type: %02x | factor: %f",ttype,ttc);
111 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
117 moldyn->volume=x*y*z;
125 moldyn->dv=0.000001*moldyn->volume;
127 printf("[moldyn] dimensions in A and A^3 respectively:\n");
128 printf(" x: %f\n",moldyn->dim.x);
129 printf(" y: %f\n",moldyn->dim.y);
130 printf(" z: %f\n",moldyn->dim.z);
131 printf(" volume: %f\n",moldyn->volume);
132 printf(" visualize simulation box: %s\n",visualize?"yes":"no");
133 printf(" delta volume (pressure calc): %f\n",moldyn->dv);
138 int set_nn_dist(t_moldyn *moldyn,double dist) {
145 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
147 printf("[moldyn] periodic boundary conditions:\n");
150 moldyn->status|=MOLDYN_STAT_PBX;
153 moldyn->status|=MOLDYN_STAT_PBY;
156 moldyn->status|=MOLDYN_STAT_PBZ;
158 printf(" x: %s\n",x?"yes":"no");
159 printf(" y: %s\n",y?"yes":"no");
160 printf(" z: %s\n",z?"yes":"no");
165 int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
168 moldyn->pot1b_params=params;
173 int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
176 moldyn->pot2b_params=params;
181 int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) {
183 moldyn->func2b_post=func;
184 moldyn->pot2b_params=params;
189 int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
192 moldyn->pot3b_params=params;
197 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
199 strncpy(moldyn->vlsdir,dir,127);
204 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title) {
206 strncpy(moldyn->rauthor,author,63);
207 strncpy(moldyn->rtitle,title,63);
212 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
217 printf("[moldyn] set log: ");
220 case LOG_TOTAL_ENERGY:
221 moldyn->ewrite=timer;
222 snprintf(filename,127,"%s/energy",moldyn->vlsdir);
223 moldyn->efd=open(filename,
224 O_WRONLY|O_CREAT|O_EXCL,
227 perror("[moldyn] energy log fd open");
230 dprintf(moldyn->efd,"# total energy log file\n");
231 printf("total energy (%d)\n",timer);
233 case LOG_TOTAL_MOMENTUM:
234 moldyn->mwrite=timer;
235 snprintf(filename,127,"%s/momentum",moldyn->vlsdir);
236 moldyn->mfd=open(filename,
237 O_WRONLY|O_CREAT|O_EXCL,
240 perror("[moldyn] momentum log fd open");
243 dprintf(moldyn->efd,"# total momentum log file\n");
244 printf("total momentum (%d)\n",timer);
247 moldyn->swrite=timer;
248 printf("save file (%d)\n",timer);
251 moldyn->vwrite=timer;
252 ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
254 printf("[moldyn] visual init failure\n");
257 printf("visual file (%d)\n",timer);
260 snprintf(filename,127,"%s/report.tex",moldyn->vlsdir);
261 moldyn->rfd=open(filename,
262 O_WRONLY|O_CREAT|O_EXCL,
265 perror("[moldyn] report fd open");
268 snprintf(filename,127,"%s/plot.scr",moldyn->vlsdir);
269 moldyn->pfd=open(filename,
270 O_WRONLY|O_CREAT|O_EXCL,
273 perror("[moldyn] plot fd open");
276 dprintf(moldyn->rfd,report_start,
277 moldyn->rauthor,moldyn->rtitle);
278 dprintf(moldyn->pfd,plot_script);
282 printf("unknown log type: %02x\n",type);
289 int moldyn_log_shutdown(t_moldyn *moldyn) {
293 printf("[moldyn] log shutdown\n");
294 if(moldyn->efd) close(moldyn->efd);
295 if(moldyn->mfd) close(moldyn->mfd);
297 dprintf(moldyn->rfd,report_end);
299 snprintf(sc,255,"cd %s && gnuplot plot.scr",moldyn->vlsdir);
301 snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
303 snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
305 snprintf(sc,255,"cd %s && dvipdf report",moldyn->vlsdir);
308 if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
314 * creating lattice functions
317 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
318 u8 attr,u8 brand,int a,int b,int c) {
329 /* how many atoms do we expect */
330 if(type==CUBIC) new*=1;
331 if(type==FCC) new*=4;
332 if(type==DIAMOND) new*=8;
334 /* allocate space for atoms */
335 ptr=realloc(moldyn->atom,(count+new)*sizeof(t_atom));
337 perror("[moldyn] realloc (create lattice)");
341 atom=&(moldyn->atom[count]);
343 /* no atoms on the boundaries (only reason: it looks better!) */
350 set_nn_dist(moldyn,lc);
351 ret=cubic_init(a,b,c,lc,atom,&origin);
354 v3_scale(&origin,&origin,0.5);
355 set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
356 ret=fcc_init(a,b,c,lc,atom,&origin);
359 v3_scale(&origin,&origin,0.25);
360 set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
361 ret=diamond_init(a,b,c,lc,atom,&origin);
364 printf("unknown lattice type (%02x)\n",type);
370 printf("[moldyn] creating lattice failed\n");
371 printf(" amount of atoms\n");
372 printf(" - expected: %d\n",new);
373 printf(" - created: %d\n",ret);
378 printf("[moldyn] created lattice with %d atoms\n",new);
380 for(ret=0;ret<new;ret++) {
381 atom[ret].element=element;
384 atom[ret].brand=brand;
385 atom[ret].tag=count+ret;
386 check_per_bound(moldyn,&(atom[ret].r));
393 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
412 v3_copy(&(atom[count].r),&r);
421 for(i=0;i<count;i++) {
422 atom[i].r.x-=(a*lc)/2.0;
423 atom[i].r.y-=(b*lc)/2.0;
424 atom[i].r.z-=(c*lc)/2.0;
430 /* fcc lattice init */
431 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
444 /* construct the basis */
445 memset(basis,0,3*sizeof(t_3dvec));
453 /* fill up the room */
461 v3_copy(&(atom[count].r),&r);
464 /* the three face centered atoms */
466 v3_add(&n,&r,&basis[l]);
467 v3_copy(&(atom[count].r),&n);
476 /* coordinate transformation */
477 for(i=0;i<count;i++) {
478 atom[i].r.x-=(a*lc)/2.0;
479 atom[i].r.y-=(b*lc)/2.0;
480 atom[i].r.z-=(c*lc)/2.0;
486 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
491 count=fcc_init(a,b,c,lc,atom,origin);
497 if(origin) v3_add(&o,&o,origin);
499 count+=fcc_init(a,b,c,lc,&atom[count],&o);
504 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
505 t_3dvec *r,t_3dvec *v) {
512 count=(moldyn->count)++;
514 ptr=realloc(atom,(count+1)*sizeof(t_atom));
516 perror("[moldyn] realloc (add atom)");
524 atom[count].element=element;
525 atom[count].mass=mass;
526 atom[count].brand=brand;
527 atom[count].tag=count;
528 atom[count].attr=attr;
533 int destroy_atoms(t_moldyn *moldyn) {
535 if(moldyn->atom) free(moldyn->atom);
540 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
543 * - gaussian distribution of velocities
544 * - zero total momentum
545 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
550 t_3dvec p_total,delta;
555 random=&(moldyn->random);
557 printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
559 /* gaussian distribution of velocities */
561 for(i=0;i<moldyn->count;i++) {
562 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
564 v=sigma*rand_get_gauss(random);
566 p_total.x+=atom[i].mass*v;
568 v=sigma*rand_get_gauss(random);
570 p_total.y+=atom[i].mass*v;
572 v=sigma*rand_get_gauss(random);
574 p_total.z+=atom[i].mass*v;
577 /* zero total momentum */
578 v3_scale(&p_total,&p_total,1.0/moldyn->count);
579 for(i=0;i<moldyn->count;i++) {
580 v3_scale(&delta,&p_total,1.0/atom[i].mass);
581 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
584 /* velocity scaling */
585 scale_velocity(moldyn,equi_init);
590 double temperature_calc(t_moldyn *moldyn) {
592 /* assume up to date kinetic energy, which is 3/2 N k_B T */
594 moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
599 double get_temperature(t_moldyn *moldyn) {
604 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
614 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
617 /* get kinetic energy / temperature & count involved atoms */
620 for(i=0;i<moldyn->count;i++) {
621 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
622 e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
627 if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
628 else return 0; /* no atoms involved in scaling! */
630 /* (temporary) hack for e,t = 0 */
633 if(moldyn->t_ref!=0.0) {
634 thermal_init(moldyn,equi_init);
638 return 0; /* no scaling needed */
642 /* get scaling factor */
643 scale=moldyn->t_ref/moldyn->t;
647 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
648 scale=1.0+(scale-1.0)/moldyn->t_tc;
651 /* velocity scaling */
652 for(i=0;i<moldyn->count;i++) {
653 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
654 v3_scale(&(atom[i].v),&(atom[i].v),scale);
660 double ideal_gas_law_pressure(t_moldyn *moldyn) {
664 p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
669 double pressure_calc(t_moldyn *moldyn) {
676 * P = 1/(3V) sum_i ( p_i^2 / 2m + f_i r_i )
682 for(i=0;i<moldyn->count;i++) {
683 virial=&(moldyn->atom[i].virial);
684 v+=(virial->xx+virial->yy+virial->zz);
687 /* assume up to date kinetic energy */
688 moldyn->p=2.0*moldyn->ekin+v;
689 moldyn->p/=(3.0*moldyn->volume);
694 double thermodynamic_pressure_calc(t_moldyn *moldyn) {
702 store=malloc(moldyn->count*sizeof(t_atom));
704 printf("[moldyn] allocating store mem failed\n");
708 /* save unscaled potential energy + atom/dim configuration */
710 memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
713 /* derivative with respect to x direction */
714 scale=1.0+moldyn->dv/(moldyn->dim.y*moldyn->dim.z);
715 scale_dim(moldyn,scale,TRUE,0,0);
716 scale_atoms(moldyn,scale,TRUE,0,0);
717 link_cell_shutdown(moldyn);
718 link_cell_init(moldyn,QUIET);
719 potential_force_calc(moldyn);
720 tp->x=(moldyn->energy-u)/moldyn->dv;
723 /* restore atomic configuration + dim */
724 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
727 /* derivative with respect to y direction */
728 scale=1.0+moldyn->dv/(moldyn->dim.x*moldyn->dim.z);
729 scale_dim(moldyn,scale,0,TRUE,0);
730 scale_atoms(moldyn,scale,0,TRUE,0);
731 link_cell_shutdown(moldyn);
732 link_cell_init(moldyn,QUIET);
733 potential_force_calc(moldyn);
734 tp->y=(moldyn->energy-u)/moldyn->dv;
737 /* restore atomic configuration + dim */
738 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
741 /* derivative with respect to z direction */
742 scale=1.0+moldyn->dv/(moldyn->dim.x*moldyn->dim.y);
743 scale_dim(moldyn,scale,0,0,TRUE);
744 scale_atoms(moldyn,scale,0,0,TRUE);
745 link_cell_shutdown(moldyn);
746 link_cell_init(moldyn,QUIET);
747 potential_force_calc(moldyn);
748 tp->z=(moldyn->energy-u)/moldyn->dv;
751 /* restore atomic configuration + dim */
752 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
755 printf("dU/dV komp addiert = %f %f %f\n",tp->x,tp->y,tp->z);
757 scale=1.0+pow(moldyn->dv/moldyn->volume,ONE_THIRD);
759 printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
760 scale_dim(moldyn,scale,1,1,1);
761 scale_atoms(moldyn,scale,1,1,1);
762 link_cell_shutdown(moldyn);
763 link_cell_init(moldyn,QUIET);
764 potential_force_calc(moldyn);
765 printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
767 printf("dU/dV einfach = %f\n",((moldyn->energy-u)/moldyn->dv)/ATM);
769 /* restore atomic configuration + dim */
770 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
776 link_cell_shutdown(moldyn);
777 link_cell_init(moldyn,QUIET);
782 double get_pressure(t_moldyn *moldyn) {
788 int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
801 int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
806 for(i=0;i<moldyn->count;i++) {
807 r=&(moldyn->atom[i].r);
816 int scale_volume(t_moldyn *moldyn) {
822 vdim=&(moldyn->vis.dim);
827 if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
828 scale=1.0-(moldyn->p_ref-moldyn->p)/moldyn->p_tc;
829 scale=pow(scale,ONE_THIRD);
832 scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
836 /* scale the atoms and dimensions */
837 scale_atoms(moldyn,scale,TRUE,TRUE,TRUE);
838 scale_dim(moldyn,scale,TRUE,TRUE,TRUE);
840 /* visualize dimensions */
847 /* recalculate scaled volume */
848 moldyn->volume=dim->x*dim->y*dim->z;
850 /* adjust/reinit linkcell */
851 if(((int)(dim->x/moldyn->cutoff)!=lc->nx)||
852 ((int)(dim->y/moldyn->cutoff)!=lc->ny)||
853 ((int)(dim->z/moldyn->cutoff)!=lc->nx)) {
854 link_cell_shutdown(moldyn);
855 link_cell_init(moldyn,QUIET);
866 double get_e_kin(t_moldyn *moldyn) {
874 for(i=0;i<moldyn->count;i++)
875 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
880 double update_e_kin(t_moldyn *moldyn) {
882 return(get_e_kin(moldyn));
885 double get_total_energy(t_moldyn *moldyn) {
887 return(moldyn->ekin+moldyn->energy);
890 t_3dvec get_total_p(t_moldyn *moldyn) {
899 for(i=0;i<moldyn->count;i++) {
900 v3_scale(&p,&(atom[i].v),atom[i].mass);
901 v3_add(&p_total,&p_total,&p);
907 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
911 /* nn_dist is the nearest neighbour distance */
913 tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
922 /* linked list / cell method */
924 int link_cell_init(t_moldyn *moldyn,u8 vol) {
931 /* partitioning the md cell */
932 lc->nx=moldyn->dim.x/moldyn->cutoff;
933 lc->x=moldyn->dim.x/lc->nx;
934 lc->ny=moldyn->dim.y/moldyn->cutoff;
935 lc->y=moldyn->dim.y/lc->ny;
936 lc->nz=moldyn->dim.z/moldyn->cutoff;
937 lc->z=moldyn->dim.z/lc->nz;
939 lc->cells=lc->nx*lc->ny*lc->nz;
940 lc->subcell=malloc(lc->cells*sizeof(t_list));
943 printf("[moldyn] FATAL: less then 27 subcells!\n");
945 if(vol) printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
947 for(i=0;i<lc->cells;i++)
948 list_init_f(&(lc->subcell[i]));
950 link_cell_update(moldyn);
955 int link_cell_update(t_moldyn *moldyn) {
973 for(i=0;i<lc->cells;i++)
974 list_destroy_f(&(lc->subcell[i]));
976 for(count=0;count<moldyn->count;count++) {
977 i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
978 j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
979 k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
980 list_add_immediate_f(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
987 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
1005 cell[0]=lc->subcell[i+j*nx+k*a];
1006 for(ci=-1;ci<=1;ci++) {
1009 if((x<0)||(x>=nx)) {
1013 for(cj=-1;cj<=1;cj++) {
1016 if((y<0)||(y>=ny)) {
1020 for(ck=-1;ck<=1;ck++) {
1023 if((z<0)||(z>=nz)) {
1027 if(!(ci|cj|ck)) continue;
1029 cell[--count2]=lc->subcell[x+y*nx+z*a];
1032 cell[count1++]=lc->subcell[x+y*nx+z*a];
1043 int link_cell_shutdown(t_moldyn *moldyn) {
1050 for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
1051 list_destroy_f(&(moldyn->lc.subcell[i]));
1058 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
1062 t_moldyn_schedule *schedule;
1064 schedule=&(moldyn->schedule);
1065 count=++(schedule->total_sched);
1067 ptr=realloc(schedule->runs,count*sizeof(int));
1069 perror("[moldyn] realloc (runs)");
1073 schedule->runs[count-1]=runs;
1075 ptr=realloc(schedule->tau,count*sizeof(double));
1077 perror("[moldyn] realloc (tau)");
1081 schedule->tau[count-1]=tau;
1083 printf("[moldyn] schedule added:\n");
1084 printf(" number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
1090 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
1092 moldyn->schedule.hook=hook;
1093 moldyn->schedule.hook_params=hook_params;
1100 * 'integration of newtons equation' - algorithms
1104 /* start the integration */
1106 int moldyn_integrate(t_moldyn *moldyn) {
1109 unsigned int e,m,s,v;
1111 t_moldyn_schedule *sched;
1116 double energy_scale;
1118 sched=&(moldyn->schedule);
1121 /* initialize linked cell method */
1122 link_cell_init(moldyn,VERBOSE);
1124 /* logging & visualization */
1130 /* sqaure of some variables */
1131 moldyn->tau_square=moldyn->tau*moldyn->tau;
1132 moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
1134 /* energy scaling factor */
1135 energy_scale=moldyn->count*EV;
1137 /* calculate initial forces */
1138 potential_force_calc(moldyn);
1140 /* some stupid checks before we actually start calculating bullshit */
1141 if(moldyn->cutoff>0.5*moldyn->dim.x)
1142 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
1143 if(moldyn->cutoff>0.5*moldyn->dim.y)
1144 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
1145 if(moldyn->cutoff>0.5*moldyn->dim.z)
1146 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
1147 ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
1148 if(ds>0.05*moldyn->nnd)
1149 printf("[moldyn] warning: forces too high / tau too small!\n");
1151 /* zero absolute time */
1154 /* debugging, ignore */
1157 /* tell the world */
1158 printf("[moldyn] integration start, go get a coffee ...\n");
1160 /* executing the schedule */
1161 for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
1163 /* setting amount of runs and finite time step size */
1164 moldyn->tau=sched->tau[sched->count];
1165 moldyn->tau_square=moldyn->tau*moldyn->tau;
1166 moldyn->time_steps=sched->runs[sched->count];
1168 /* integration according to schedule */
1170 for(i=0;i<moldyn->time_steps;i++) {
1172 /* integration step */
1173 moldyn->integrate(moldyn);
1175 /* calculate kinetic energy, temperature and pressure */
1176 update_e_kin(moldyn);
1177 temperature_calc(moldyn);
1178 pressure_calc(moldyn);
1179 //thermodynamic_pressure_calc(moldyn);
1182 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
1183 scale_velocity(moldyn,FALSE);
1184 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
1185 scale_volume(moldyn);
1187 /* check for log & visualization */
1190 dprintf(moldyn->efd,
1192 moldyn->time,moldyn->ekin/energy_scale,
1193 moldyn->energy/energy_scale,
1194 get_total_energy(moldyn)/energy_scale);
1198 p=get_total_p(moldyn);
1199 dprintf(moldyn->mfd,
1200 "%f %f\n",moldyn->time,v3_norm(&p));
1205 snprintf(dir,128,"%s/s-%07.f.save",
1206 moldyn->vlsdir,moldyn->time);
1207 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
1208 if(fd<0) perror("[moldyn] save fd open");
1210 write(fd,moldyn,sizeof(t_moldyn));
1211 write(fd,moldyn->atom,
1212 moldyn->count*sizeof(t_atom));
1219 visual_atoms(&(moldyn->vis),moldyn->time,
1220 moldyn->atom,moldyn->count);
1221 printf("\rsched: %d, steps: %d, T: %f, P: %f V: %f",
1223 moldyn->t,moldyn->p/ATM,moldyn->volume);
1228 /* increase absolute time */
1229 moldyn->time+=moldyn->tau;
1233 /* check for hooks */
1235 sched->hook(moldyn,sched->hook_params);
1237 /* get a new info line */
1245 /* velocity verlet */
1247 int velocity_verlet(t_moldyn *moldyn) {
1250 double tau,tau_square,h;
1255 count=moldyn->count;
1257 tau_square=moldyn->tau_square;
1259 for(i=0;i<count;i++) {
1262 v3_scale(&delta,&(atom[i].v),tau);
1263 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1264 v3_scale(&delta,&(atom[i].f),h*tau_square);
1265 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1266 check_per_bound(moldyn,&(atom[i].r));
1268 /* velocities [actually v(t+tau/2)] */
1269 v3_scale(&delta,&(atom[i].f),h*tau);
1270 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1273 /* neighbour list update */
1274 link_cell_update(moldyn);
1276 /* forces depending on chosen potential */
1277 potential_force_calc(moldyn);
1279 for(i=0;i<count;i++) {
1280 /* again velocities [actually v(t+tau)] */
1281 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
1282 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1291 * potentials & corresponding forces & virial routine
1295 /* generic potential and force calculation */
1297 int potential_force_calc(t_moldyn *moldyn) {
1300 t_atom *itom,*jtom,*ktom;
1303 t_list neighbour_i[27];
1304 t_list neighbour_i2[27];
1309 count=moldyn->count;
1316 /* reset force, site energy and virial of every atom */
1317 for(i=0;i<count;i++) {
1320 v3_zero(&(itom[i].f));
1323 virial=(&(itom[i].virial));
1331 /* reset site energy */
1336 /* get energy,force and virial of every atom */
1337 for(i=0;i<count;i++) {
1339 /* single particle potential/force */
1340 if(itom[i].attr&ATOM_ATTR_1BP)
1341 moldyn->func1b(moldyn,&(itom[i]));
1343 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
1346 /* 2 body pair potential/force */
1348 link_cell_neighbour_index(moldyn,
1349 (itom[i].r.x+moldyn->dim.x/2)/lc->x,
1350 (itom[i].r.y+moldyn->dim.y/2)/lc->y,
1351 (itom[i].r.z+moldyn->dim.z/2)/lc->z,
1358 this=&(neighbour_i[j]);
1361 if(this->start==NULL)
1367 jtom=this->current->data;
1369 if(jtom==&(itom[i]))
1372 if((jtom->attr&ATOM_ATTR_2BP)&
1373 (itom[i].attr&ATOM_ATTR_2BP)) {
1374 moldyn->func2b(moldyn,
1380 /* 3 body potential/force */
1382 if(!(itom[i].attr&ATOM_ATTR_3BP)||
1383 !(jtom->attr&ATOM_ATTR_3BP))
1386 /* copy the neighbour lists */
1387 memcpy(neighbour_i2,neighbour_i,
1390 /* get neighbours of i */
1393 that=&(neighbour_i2[k]);
1396 if(that->start==NULL)
1403 ktom=that->current->data;
1405 if(!(ktom->attr&ATOM_ATTR_3BP))
1411 if(ktom==&(itom[i]))
1414 moldyn->func3b(moldyn,
1420 } while(list_next_f(that)!=\
1425 /* 2bp post function */
1426 if(moldyn->func2b_post) {
1427 moldyn->func2b_post(moldyn,
1432 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1449 * virial calculation
1452 inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1454 a->virial.xx+=f->x*d->x;
1455 a->virial.yy+=f->y*d->y;
1456 a->virial.zz+=f->z*d->z;
1457 a->virial.xy+=f->x*d->y;
1458 a->virial.xz+=f->x*d->z;
1459 a->virial.yz+=f->y*d->z;
1465 * periodic boundayr checking
1468 inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1479 if(moldyn->status&MOLDYN_STAT_PBX) {
1480 if(a->x>=x) a->x-=dim->x;
1481 else if(-a->x>x) a->x+=dim->x;
1483 if(moldyn->status&MOLDYN_STAT_PBY) {
1484 if(a->y>=y) a->y-=dim->y;
1485 else if(-a->y>y) a->y+=dim->y;
1487 if(moldyn->status&MOLDYN_STAT_PBZ) {
1488 if(a->z>=z) a->z-=dim->z;
1489 else if(-a->z>z) a->z+=dim->z;
1497 * example potentials
1500 /* harmonic oscillator potential and force */
1502 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1504 t_ho_params *params;
1505 t_3dvec force,distance;
1507 double sc,equi_dist;
1509 params=moldyn->pot2b_params;
1510 sc=params->spring_constant;
1511 equi_dist=params->equilibrium_distance;
1515 v3_sub(&distance,&(aj->r),&(ai->r));
1517 if(bc) check_per_bound(moldyn,&distance);
1518 d=v3_norm(&distance);
1519 if(d<=moldyn->cutoff) {
1520 moldyn->energy+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
1521 /* f = -grad E; grad r_ij = -1 1/r_ij distance */
1522 f=sc*(1.0-equi_dist/d);
1523 v3_scale(&force,&distance,f);
1524 v3_add(&(ai->f),&(ai->f),&force);
1525 virial_calc(ai,&force,&distance);
1526 virial_calc(aj,&force,&distance); /* f and d signe switched */
1527 v3_scale(&force,&distance,-f);
1528 v3_add(&(aj->f),&(aj->f),&force);
1534 /* lennard jones potential & force for one sort of atoms */
1536 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1538 t_lj_params *params;
1539 t_3dvec force,distance;
1541 double eps,sig6,sig12;
1543 params=moldyn->pot2b_params;
1544 eps=params->epsilon4;
1545 sig6=params->sigma6;
1546 sig12=params->sigma12;
1550 v3_sub(&distance,&(aj->r),&(ai->r));
1551 if(bc) check_per_bound(moldyn,&distance);
1552 d=v3_absolute_square(&distance); /* 1/r^2 */
1553 if(d<=moldyn->cutoff_square) {
1554 d=1.0/d; /* 1/r^2 */
1557 h1=h2*h2; /* 1/r^12 */
1558 moldyn->energy+=(eps*(sig12*h1-sig6*h2)-params->uc);
1565 v3_scale(&force,&distance,d);
1566 v3_add(&(aj->f),&(aj->f),&force);
1567 v3_scale(&force,&force,-1.0); /* f = - grad E */
1568 v3_add(&(ai->f),&(ai->f),&force);
1569 virial_calc(ai,&force,&distance);
1570 if(force.x*distance.x<=0) printf("virial xx: %.15f -> %f %f %f\n",force.x*distance.x,distance.x,distance.y,distance.z);
1571 virial_calc(aj,&force,&distance); /* f and d signe switched */
1578 * tersoff potential & force for 2 sorts of atoms
1581 /* create mixed terms from parameters and set them */
1582 int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
1584 printf("[moldyn] tersoff parameter completion\n");
1585 p->S2[0]=p->S[0]*p->S[0];
1586 p->S2[1]=p->S[1]*p->S[1];
1587 p->Smixed=sqrt(p->S[0]*p->S[1]);
1588 p->S2mixed=p->Smixed*p->Smixed;
1589 p->Rmixed=sqrt(p->R[0]*p->R[1]);
1590 p->Amixed=sqrt(p->A[0]*p->A[1]);
1591 p->Bmixed=sqrt(p->B[0]*p->B[1]);
1592 p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
1593 p->mu_m=0.5*(p->mu[0]+p->mu[1]);
1595 printf("[moldyn] tersoff mult parameter info:\n");
1596 printf(" S (A) | %f | %f | %f\n",p->S[0],p->S[1],p->Smixed);
1597 printf(" R (A) | %f | %f | %f\n",p->R[0],p->R[1],p->Rmixed);
1598 printf(" A (eV) | %f | %f | %f\n",p->A[0]/EV,p->A[1]/EV,p->Amixed/EV);
1599 printf(" B (eV) | %f | %f | %f\n",p->B[0]/EV,p->B[1]/EV,p->Bmixed/EV);
1600 printf(" lambda | %f | %f | %f\n",p->lambda[0],p->lambda[1],
1602 printf(" mu | %f | %f | %f\n",p->mu[0],p->mu[1],p->mu_m);
1603 printf(" beta | %.10f | %.10f\n",p->beta[0],p->beta[1]);
1604 printf(" n | %f | %f\n",p->n[0],p->n[1]);
1605 printf(" c | %f | %f\n",p->c[0],p->c[1]);
1606 printf(" d | %f | %f\n",p->d[0],p->d[1]);
1607 printf(" h | %f | %f\n",p->h[0],p->h[1]);
1608 printf(" chi | %f \n",p->chi);
1613 /* tersoff 1 body part */
1614 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
1617 t_tersoff_mult_params *params;
1618 t_tersoff_exchange *exchange;
1621 params=moldyn->pot1b_params;
1622 exchange=&(params->exchange);
1625 * simple: point constant parameters only depending on atom i to
1626 * their right values
1629 exchange->beta_i=&(params->beta[brand]);
1630 exchange->n_i=&(params->n[brand]);
1631 exchange->c_i=&(params->c[brand]);
1632 exchange->d_i=&(params->d[brand]);
1633 exchange->h_i=&(params->h[brand]);
1635 exchange->betaini=pow(*(exchange->beta_i),*(exchange->n_i));
1636 exchange->ci2=params->c[brand]*params->c[brand];
1637 exchange->di2=params->d[brand]*params->d[brand];
1638 exchange->ci2di2=exchange->ci2/exchange->di2;
1643 /* tersoff 2 body part */
1644 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1646 t_tersoff_mult_params *params;
1647 t_tersoff_exchange *exchange;
1648 t_3dvec dist_ij,force;
1650 double A,B,R,S,S2,lambda,mu;
1657 params=moldyn->pot2b_params;
1659 exchange=&(params->exchange);
1661 /* clear 3bp and 2bp post run */
1663 exchange->run2bp_post=0;
1665 /* reset S > r > R mark */
1666 exchange->d_ij_between_rs=0;
1669 * calc of 2bp contribution of V_ij and dV_ij/ji
1671 * for Vij and dV_ij we need:
1675 * for dV_ji we need:
1676 * - f_c_ji = f_c_ij, df_c_ji = df_c_ij
1677 * - f_r_ji = f_r_ij; df_r_ji = df_r_ij
1682 if(brand==ai->brand) {
1684 S2=params->S2[brand];
1688 lambda=params->lambda[brand];
1689 mu=params->mu[brand];
1698 lambda=params->lambda_m;
1700 params->exchange.chi=params->chi;
1704 v3_sub(&dist_ij,&(aj->r),&(ai->r));
1705 if(bc) check_per_bound(moldyn,&dist_ij);
1706 d_ij2=v3_absolute_square(&dist_ij);
1708 /* if d_ij2 > S2 => no force & potential energy contribution */
1712 /* now we will need the distance */
1713 //d_ij=v3_norm(&dist_ij);
1716 /* save for use in 3bp */
1717 exchange->d_ij=d_ij;
1718 exchange->d_ij2=d_ij2;
1719 exchange->dist_ij=dist_ij;
1721 /* more constants */
1722 exchange->beta_j=&(params->beta[brand]);
1723 exchange->n_j=&(params->n[brand]);
1724 exchange->c_j=&(params->c[brand]);
1725 exchange->d_j=&(params->d[brand]);
1726 exchange->h_j=&(params->h[brand]);
1727 if(brand==ai->brand) {
1728 exchange->betajnj=exchange->betaini;
1729 exchange->cj2=exchange->ci2;
1730 exchange->dj2=exchange->di2;
1731 exchange->cj2dj2=exchange->ci2di2;
1734 exchange->betajnj=pow(*(exchange->beta_j),*(exchange->n_j));
1735 exchange->cj2=params->c[brand]*params->c[brand];
1736 exchange->dj2=params->d[brand]*params->d[brand];
1737 exchange->cj2dj2=exchange->cj2/exchange->dj2;
1740 /* f_r_ij = f_r_ji, df_r_ij = df_r_ji */
1741 f_r=A*exp(-lambda*d_ij);
1742 df_r=lambda*f_r/d_ij;
1744 /* f_a, df_a calc (again, same for ij and ji) | save for later use! */
1745 exchange->f_a=-B*exp(-mu*d_ij);
1746 exchange->df_a=mu*exchange->f_a/d_ij;
1748 /* f_c, df_c calc (again, same for ij and ji) */
1750 /* f_c = 1, df_c = 0 */
1753 /* two body contribution (ij, ji) */
1754 v3_scale(&force,&dist_ij,-df_r);
1758 arg=M_PI*(d_ij-R)/s_r;
1759 f_c=0.5+0.5*cos(arg);
1760 df_c=0.5*sin(arg)*(M_PI/(s_r*d_ij));
1761 /* two body contribution (ij, ji) */
1762 v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
1763 /* tell 3bp that S > r > R */
1764 exchange->d_ij_between_rs=1;
1767 /* add forces of 2bp (ij, ji) contribution
1768 * dVij = dVji and we sum up both: no 1/2) */
1769 v3_add(&(ai->f),&(ai->f),&force);
1772 ai->virial.xx-=force.x*dist_ij.x;
1773 ai->virial.yy-=force.y*dist_ij.y;
1774 ai->virial.zz-=force.z*dist_ij.z;
1775 ai->virial.xy-=force.x*dist_ij.y;
1776 ai->virial.xz-=force.x*dist_ij.z;
1777 ai->virial.yz-=force.y*dist_ij.z;
1780 if(ai==&(moldyn->atom[0])) {
1781 printf("dVij, dVji (2bp) contrib:\n");
1782 printf("%f | %f\n",force.x,ai->f.x);
1783 printf("%f | %f\n",force.y,ai->f.y);
1784 printf("%f | %f\n",force.z,ai->f.z);
1788 if(ai==&(moldyn->atom[0])) {
1789 printf("dVij, dVji (2bp) contrib:\n");
1790 printf("%f | %f\n",force.x*dist_ij.x,ai->virial.xx);
1791 printf("%f | %f\n",force.y*dist_ij.y,ai->virial.yy);
1792 printf("%f | %f\n",force.z*dist_ij.z,ai->virial.zz);
1796 /* energy 2bp contribution (ij, ji) is 0.5 f_r f_c ... */
1797 moldyn->energy+=(0.5*f_r*f_c);
1799 /* save for use in 3bp */
1801 exchange->df_c=df_c;
1803 /* enable the run of 3bp function and 2bp post processing */
1805 exchange->run2bp_post=1;
1807 /* reset 3bp sums */
1808 exchange->zeta_ij=0.0;
1809 exchange->zeta_ji=0.0;
1810 v3_zero(&(exchange->dzeta_ij));
1811 v3_zero(&(exchange->dzeta_ji));
1816 /* tersoff 2 body post part */
1818 int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1821 * here we have to allow for the 3bp sums
1824 * - zeta_ij, dzeta_ij
1825 * - zeta_ji, dzeta_ji
1827 * to compute the 3bp contribution to:
1833 t_tersoff_mult_params *params;
1834 t_tersoff_exchange *exchange;
1839 double f_c,df_c,f_a,df_a;
1840 double chi,ni,betaini,nj,betajnj;
1843 params=moldyn->pot2b_params;
1844 exchange=&(params->exchange);
1846 /* we do not run if f_c_ij was detected to be 0! */
1847 if(!(exchange->run2bp_post))
1851 df_c=exchange->df_c;
1853 df_a=exchange->df_a;
1854 betaini=exchange->betaini;
1855 betajnj=exchange->betajnj;
1856 ni=*(exchange->n_i);
1857 nj=*(exchange->n_j);
1859 dist_ij=&(exchange->dist_ij);
1862 zeta=exchange->zeta_ij;
1864 moldyn->debug++; /* just for debugging ... */
1866 v3_scale(&force,dist_ij,df_a*b*f_c);
1869 tmp=betaini*pow(zeta,ni-1.0); /* beta^n * zeta^n-1 */
1870 b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
1871 db=chi*pow(b,-1.0/(2*ni)-1); /* x(...)^(-1/2n - 1) */
1873 db*=-0.5*tmp; /* db_ij */
1874 v3_scale(&force,&(exchange->dzeta_ij),f_a*db);
1875 v3_scale(&temp,dist_ij,df_a*b);
1876 v3_add(&force,&force,&temp);
1877 v3_scale(&force,&force,f_c);
1879 v3_scale(&temp,dist_ij,df_c*b*f_a);
1880 v3_add(&force,&force,&temp);
1881 v3_scale(&force,&force,-0.5);
1884 v3_add(&(ai->f),&(ai->f),&force);
1887 ai->virial.xx-=force.x*dist_ij->x;
1888 ai->virial.yy-=force.y*dist_ij->y;
1889 ai->virial.zz-=force.z*dist_ij->z;
1890 ai->virial.xy-=force.x*dist_ij->y;
1891 ai->virial.xz-=force.x*dist_ij->z;
1892 ai->virial.yz-=force.y*dist_ij->z;
1895 if(ai==&(moldyn->atom[0])) {
1896 printf("dVij (3bp) contrib:\n");
1897 printf("%f | %f\n",force.x,ai->f.x);
1898 printf("%f | %f\n",force.y,ai->f.y);
1899 printf("%f | %f\n",force.z,ai->f.z);
1903 if(ai==&(moldyn->atom[0])) {
1904 printf("dVij (3bp) contrib:\n");
1905 printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
1906 printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
1907 printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
1911 /* add energy of 3bp sum */
1912 moldyn->energy+=(0.5*f_c*b*f_a);
1915 zeta=exchange->zeta_ji;
1919 v3_scale(&force,dist_ij,df_a*b*f_c);
1922 tmp=betajnj*pow(zeta,nj-1.0); /* beta^n * zeta^n-1 */
1923 b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
1924 db=chi*pow(b,-1.0/(2*nj)-1); /* x(...)^(-1/2n - 1) */
1926 db*=-0.5*tmp; /* db_ij */
1927 v3_scale(&force,&(exchange->dzeta_ji),f_a*db);
1928 v3_scale(&temp,dist_ij,df_a*b);
1929 v3_add(&force,&force,&temp);
1930 v3_scale(&force,&force,f_c);
1932 v3_scale(&temp,dist_ij,df_c*b*f_a);
1933 v3_add(&force,&force,&temp);
1934 v3_scale(&force,&force,-0.5);
1937 v3_add(&(ai->f),&(ai->f),&force);
1939 /* virial - plus sign, as dist_ij = - dist_ji - (really??) */
1940 // TEST ... with a minus instead
1941 ai->virial.xx-=force.x*dist_ij->x;
1942 ai->virial.yy-=force.y*dist_ij->y;
1943 ai->virial.zz-=force.z*dist_ij->z;
1944 ai->virial.xy-=force.x*dist_ij->y;
1945 ai->virial.xz-=force.x*dist_ij->z;
1946 ai->virial.yz-=force.y*dist_ij->z;
1949 if(ai==&(moldyn->atom[0])) {
1950 printf("dVji (3bp) contrib:\n");
1951 printf("%f | %f\n",force.x,ai->f.x);
1952 printf("%f | %f\n",force.y,ai->f.y);
1953 printf("%f | %f\n",force.z,ai->f.z);
1957 if(ai==&(moldyn->atom[0])) {
1958 printf("dVji (3bp) contrib:\n");
1959 printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
1960 printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
1961 printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
1968 /* tersoff 3 body part */
1970 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
1972 t_tersoff_mult_params *params;
1973 t_tersoff_exchange *exchange;
1974 t_3dvec dist_ij,dist_ik,dist_jk;
1975 t_3dvec temp1,temp2;
1979 double d_ij,d_ik,d_jk,d_ij2,d_ik2,d_jk2;
1982 double f_c_ik,df_c_ik,arg;
1986 double cos_theta,d_costheta1,d_costheta2;
1987 double h_cos,d2_h_cos2;
1988 double frac,g,zeta,chi;
1992 params=moldyn->pot3b_params;
1993 exchange=&(params->exchange);
1995 if(!(exchange->run3bp))
1999 * calc of 3bp contribution of V_ij and dV_ij/ji/jk &
2000 * 2bp contribution of dV_jk
2002 * for Vij and dV_ij we still need:
2003 * - b_ij, db_ij (zeta_ij)
2004 * - f_c_ik, df_c_ik, constants_i, cos_theta_ijk, d_costheta_ijk
2006 * for dV_ji we still need:
2007 * - b_ji, db_ji (zeta_ji)
2008 * - f_c_jk, d_c_jk, constants_j, cos_theta_jik, d_costheta_jik
2010 * for dV_jk we need:
2014 * - f_c_ji, df_c_ji, constants_j, cos_theta_jki, d_costheta_jki
2022 /* dist_ij, d_ij - this is < S_ij ! */
2023 dist_ij=exchange->dist_ij;
2024 d_ij=exchange->d_ij;
2025 d_ij2=exchange->d_ij2;
2027 /* f_c_ij, df_c_ij (same for ji) */
2029 df_c=exchange->df_c;
2032 * calculate unknown values now ...
2035 /* V_ij and dV_ij stuff (in b_ij there is f_c_ik) */
2038 v3_sub(&dist_ik,&(ak->r),&(ai->r));
2039 if(bc) check_per_bound(moldyn,&dist_ik);
2040 d_ik2=v3_absolute_square(&dist_ik);
2044 if(brand==ak->brand) {
2047 S2=params->S2[brand];
2055 /* zeta_ij/dzeta_ij contribution only for d_ik < S */
2058 /* now we need d_ik */
2061 /* get constants_i from exchange data */
2068 c2d2=exchange->ci2di2;
2070 /* cosine of theta_ijk by scalaproduct */
2071 rr=v3_scalar_product(&dist_ij,&dist_ik);
2077 d_costheta1=cos_theta/d_ij2-tmp;
2078 d_costheta2=cos_theta/d_ik2-tmp;
2080 /* some usefull values */
2081 h_cos=(h-cos_theta);
2082 d2_h_cos2=d2+(h_cos*h_cos);
2083 frac=c2/(d2_h_cos2);
2088 /* d_costheta_ij and dg(cos_theta) - needed in any case! */
2089 v3_scale(&temp1,&dist_ij,d_costheta1);
2090 v3_scale(&temp2,&dist_ik,d_costheta2);
2091 v3_add(&temp1,&temp1,&temp2);
2092 v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
2094 /* f_c_ik & df_c_ik + {d,}zeta contribution */
2095 dzeta=&(exchange->dzeta_ij);
2099 // => df_c_ik=0.0; of course we do not set this!
2102 exchange->zeta_ij+=g;
2105 v3_add(dzeta,dzeta,&temp1);
2110 arg=M_PI*(d_ik-R)/s_r;
2111 f_c_ik=0.5+0.5*cos(arg);
2112 df_c_ik=0.5*sin(arg)*(M_PI/(s_r*d_ik));
2115 exchange->zeta_ij+=f_c_ik*g;
2118 v3_scale(&temp1,&temp1,f_c_ik);
2119 v3_scale(&temp2,&dist_ik,g*df_c_ik);
2120 v3_add(&temp1,&temp1,&temp2);
2121 v3_add(dzeta,dzeta,&temp1);
2125 /* dV_ji stuff (in b_ji there is f_c_jk) + dV_jk stuff! */
2128 v3_sub(&dist_jk,&(ak->r),&(aj->r));
2129 if(bc) check_per_bound(moldyn,&dist_jk);
2130 d_jk2=v3_absolute_square(&dist_jk);
2134 if(brand==ak->brand) {
2137 S2=params->S2[brand];
2139 mu=params->mu[brand];
2151 /* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */
2154 /* now we need d_ik */
2157 /* constants_j from exchange data */
2164 c2d2=exchange->cj2dj2;
2166 /* cosine of theta_jik by scalaproduct */
2167 rr=-v3_scalar_product(&dist_ij,&dist_jk); /* -1, as ij -> ji */
2173 d_costheta2=cos_theta/d_ij2;
2175 /* some usefull values */
2176 h_cos=(h-cos_theta);
2177 d2_h_cos2=d2+(h_cos*h_cos);
2178 frac=c2/(d2_h_cos2);
2183 /* d_costheta_jik and dg(cos_theta) - needed in any case! */
2184 v3_scale(&temp1,&dist_jk,d_costheta1);
2185 v3_scale(&temp2,&dist_ij,-d_costheta2); /* ji -> ij => -1 */
2186 //v3_add(&temp1,&temp1,&temp2);
2187 v3_sub(&temp1,&temp1,&temp2); /* there is a minus! */
2188 v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
2190 /* store dg in temp2 and use it for dVjk later */
2191 v3_copy(&temp2,&temp1);
2193 /* f_c_jk + {d,}zeta contribution (df_c_jk = 0) */
2194 dzeta=&(exchange->dzeta_ji);
2200 exchange->zeta_ji+=g;
2203 v3_add(dzeta,dzeta,&temp1);
2208 arg=M_PI*(d_jk-R)/s_r;
2209 f_c_jk=0.5+0.5*cos(arg);
2212 exchange->zeta_ji+=f_c_jk*g;
2215 v3_scale(&temp1,&temp1,f_c_jk);
2216 v3_add(dzeta,dzeta,&temp1);
2219 /* dV_jk stuff | add force contribution on atom i immediately */
2220 if(exchange->d_ij_between_rs) {
2222 v3_scale(&temp1,&temp2,f_c);
2223 v3_scale(&temp2,&dist_ij,df_c*g);
2224 v3_add(&temp2,&temp2,&temp1); /* -> dzeta_jk in temp2 */
2228 // dzeta_jk is simply dg, which is stored in temp2
2230 /* betajnj * zeta_jk ^ nj-1 */
2231 tmp=exchange->betajnj*pow(zeta,(n-1.0));
2232 tmp=-chi/2.0*pow((1+tmp*zeta),(-1.0/(2.0*n)-1))*tmp;
2233 v3_scale(&temp2,&temp2,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
2234 v3_add(&(ai->f),&(ai->f),&temp2); /* -1 skipped in f_a calc ^ */
2235 /* scaled with 0.5 ^ */
2238 ai->virial.xx-=temp2.x*dist_jk.x;
2239 ai->virial.yy-=temp2.y*dist_jk.y;
2240 ai->virial.zz-=temp2.z*dist_jk.z;
2241 ai->virial.xy-=temp2.x*dist_jk.y;
2242 ai->virial.xz-=temp2.x*dist_jk.z;
2243 ai->virial.yz-=temp2.y*dist_jk.z;
2246 if(ai==&(moldyn->atom[0])) {
2247 printf("dVjk (3bp) contrib:\n");
2248 printf("%f | %f\n",temp2.x,ai->f.x);
2249 printf("%f | %f\n",temp2.y,ai->f.y);
2250 printf("%f | %f\n",temp2.z,ai->f.z);
2254 if(ai==&(moldyn->atom[0])) {
2255 printf("dVjk (3bp) contrib:\n");
2256 printf("%f | %f\n",temp2.x*dist_jk.x,ai->virial.xx);
2257 printf("%f | %f\n",temp2.y*dist_jk.y,ai->virial.yy);
2258 printf("%f | %f\n",temp2.z*dist_jk.z,ai->virial.zz);
2269 * debugging / critical check functions
2272 int moldyn_bc_check(t_moldyn *moldyn) {
2285 for(i=0;i<moldyn->count;i++) {
2286 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
2287 printf("FATAL: atom %d: x: %.20f (%.20f)\n",
2288 i,atom[i].r.x,dim->x/2);
2289 printf("diagnostic:\n");
2290 printf("-----------\natom.r.x:\n");
2292 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
2295 ((byte)&(1<<k))?1:0,
2298 printf("---------------\nx=dim.x/2:\n");
2300 memcpy(&byte,(u8 *)(&x)+j,1);
2303 ((byte)&(1<<k))?1:0,
2306 if(atom[i].r.x==x) printf("the same!\n");
2307 else printf("different!\n");
2309 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
2310 printf("FATAL: atom %d: y: %.20f (%.20f)\n",
2311 i,atom[i].r.y,dim->y/2);
2312 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
2313 printf("FATAL: atom %d: z: %.20f (%.20f)\n",
2314 i,atom[i].r.z,dim->z/2);