2 * moldyn.c - molecular dynamics library main file
4 * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
12 #include <sys/types.h>
20 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
22 printf("[moldyn] init\n");
24 memset(moldyn,0,sizeof(t_moldyn));
26 rand_init(&(moldyn->random),NULL,1);
27 moldyn->random.status|=RAND_STAT_VERBOSE;
32 int moldyn_shutdown(t_moldyn *moldyn) {
34 printf("[moldyn] shutdown\n");
36 moldyn_log_shutdown(moldyn);
37 link_cell_shutdown(moldyn);
38 rand_close(&(moldyn->random));
44 int set_int_alg(t_moldyn *moldyn,u8 algo) {
46 printf("[moldyn] integration algorithm: ");
49 case MOLDYN_INTEGRATE_VERLET:
50 moldyn->integrate=velocity_verlet;
51 printf("velocity verlet\n");
54 printf("unknown integration algorithm: %02x\n",algo);
62 int set_cutoff(t_moldyn *moldyn,double cutoff) {
64 moldyn->cutoff=cutoff;
66 printf("[moldyn] cutoff [A]: %f\n",moldyn->cutoff);
71 int set_temperature(t_moldyn *moldyn,double t_ref) {
75 printf("[moldyn] temperature: %f\n",moldyn->t_ref);
80 int set_pressure(t_moldyn *moldyn,double p_ref) {
84 printf("[moldyn] pressure: %f\n",moldyn->p_ref);
89 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
91 moldyn->pt_scale=(ptype|ttype);
95 printf("[moldyn] p/t scaling:\n");
97 printf(" p: %s",ptype?"yes":"no ");
99 printf(" | type: %02x | factor: %f",ptype,ptc);
102 printf(" t: %s",ttype?"yes":"no ");
104 printf(" | type: %02x | factor: %f",ttype,ttc);
110 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
116 moldyn->volume=x*y*z;
124 moldyn->dv=0.000001*moldyn->volume;
126 printf("[moldyn] dimensions in A and A^3 respectively:\n");
127 printf(" x: %f\n",moldyn->dim.x);
128 printf(" y: %f\n",moldyn->dim.y);
129 printf(" z: %f\n",moldyn->dim.z);
130 printf(" volume: %f\n",moldyn->volume);
131 printf(" visualize simulation box: %s\n",visualize?"yes":"no");
132 printf(" delta volume (pressure calc): %f\n",moldyn->dv);
137 int set_nn_dist(t_moldyn *moldyn,double dist) {
144 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
146 printf("[moldyn] periodic boundary conditions:\n");
149 moldyn->status|=MOLDYN_STAT_PBX;
152 moldyn->status|=MOLDYN_STAT_PBY;
155 moldyn->status|=MOLDYN_STAT_PBZ;
157 printf(" x: %s\n",x?"yes":"no");
158 printf(" y: %s\n",y?"yes":"no");
159 printf(" z: %s\n",z?"yes":"no");
164 int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
167 moldyn->pot1b_params=params;
172 int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
175 moldyn->pot2b_params=params;
180 int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) {
182 moldyn->func2b_post=func;
183 moldyn->pot2b_params=params;
188 int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
191 moldyn->pot3b_params=params;
196 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
198 strncpy(moldyn->vlsdir,dir,127);
203 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title) {
205 strncpy(moldyn->rauthor,author,63);
206 strncpy(moldyn->rtitle,title,63);
211 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
216 printf("[moldyn] set log: ");
219 case LOG_TOTAL_ENERGY:
220 moldyn->ewrite=timer;
221 snprintf(filename,127,"%s/energy",moldyn->vlsdir);
222 moldyn->efd=open(filename,
223 O_WRONLY|O_CREAT|O_EXCL,
226 perror("[moldyn] energy log fd open");
229 dprintf(moldyn->efd,"# total energy log file\n");
230 printf("total energy (%d)\n",timer);
232 case LOG_TOTAL_MOMENTUM:
233 moldyn->mwrite=timer;
234 snprintf(filename,127,"%s/momentum",moldyn->vlsdir);
235 moldyn->mfd=open(filename,
236 O_WRONLY|O_CREAT|O_EXCL,
239 perror("[moldyn] momentum log fd open");
242 dprintf(moldyn->efd,"# total momentum log file\n");
243 printf("total momentum (%d)\n",timer);
246 moldyn->swrite=timer;
247 printf("save file (%d)\n",timer);
250 moldyn->vwrite=timer;
251 ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
253 printf("[moldyn] visual init failure\n");
256 printf("visual file (%d)\n",timer);
259 snprintf(filename,127,"%s/report.tex",moldyn->vlsdir);
260 moldyn->rfd=open(filename,
261 O_WRONLY|O_CREAT|O_EXCL,
264 perror("[moldyn] report fd open");
267 snprintf(filename,127,"%s/plot.scr",moldyn->vlsdir);
268 moldyn->pfd=open(filename,
269 O_WRONLY|O_CREAT|O_EXCL,
272 perror("[moldyn] plot fd open");
275 dprintf(moldyn->rfd,report_start,
276 moldyn->rauthor,moldyn->rtitle);
277 dprintf(moldyn->pfd,plot_script);
281 printf("unknown log type: %02x\n",type);
288 int moldyn_log_shutdown(t_moldyn *moldyn) {
292 printf("[moldyn] log shutdown\n");
293 if(moldyn->efd) close(moldyn->efd);
294 if(moldyn->mfd) close(moldyn->mfd);
296 dprintf(moldyn->rfd,report_end);
298 snprintf(sc,255,"cd %s && gnuplot plot.scr",moldyn->vlsdir);
300 snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
302 snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
304 snprintf(sc,255,"cd %s && dvipdf report",moldyn->vlsdir);
307 if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
313 * creating lattice functions
316 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
317 u8 attr,u8 brand,int a,int b,int c) {
328 /* how many atoms do we expect */
329 if(type==CUBIC) new*=1;
330 if(type==FCC) new*=4;
331 if(type==DIAMOND) new*=8;
333 /* allocate space for atoms */
334 ptr=realloc(moldyn->atom,(count+new)*sizeof(t_atom));
336 perror("[moldyn] realloc (create lattice)");
340 atom=&(moldyn->atom[count]);
346 ret=cubic_init(a,b,c,lc,atom,NULL);
349 ret=fcc_init(a,b,c,lc,atom,NULL);
352 ret=diamond_init(a,b,c,lc,atom,&origin);
355 printf("unknown lattice type (%02x)\n",type);
361 printf("[moldyn] creating lattice failed\n");
362 printf(" amount of atoms\n");
363 printf(" - expected: %d\n",new);
364 printf(" - created: %d\n",ret);
369 printf("[moldyn] created lattice with %d atoms\n",new);
371 for(ret=0;ret<new;ret++) {
372 atom[ret].element=element;
375 atom[ret].brand=brand;
376 atom[ret].tag=count+ret;
377 check_per_bound(moldyn,&(atom[ret].r));
384 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
403 v3_copy(&(atom[count].r),&r);
412 for(i=0;i<count;i++) {
413 atom[i].r.x-=(a*lc)/2.0;
414 atom[i].r.y-=(b*lc)/2.0;
415 atom[i].r.z-=(c*lc)/2.0;
421 /* fcc lattice init */
422 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
435 if(origin) v3_copy(&o,origin);
438 /* construct the basis */
441 if(i!=j) help[j]=0.5*lc;
444 v3_set(&basis[i],help);
450 /* fill up the room */
457 v3_copy(&(atom[count].r),&r);
458 atom[count].element=1;
461 v3_add(&n,&r,&basis[i]);
465 v3_copy(&(atom[count].r),&n);
476 /* coordinate transformation */
482 v3_sub(&(atom[i].r),&(atom[i].r),&n);
487 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
492 count=fcc_init(a,b,c,lc,atom,origin);
498 if(origin) v3_add(&o,&o,origin);
500 count+=fcc_init(a,b,c,lc,&atom[count],&o);
505 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
506 t_3dvec *r,t_3dvec *v) {
513 count=(moldyn->count)++;
515 ptr=realloc(atom,(count+1)*sizeof(t_atom));
517 perror("[moldyn] realloc (add atom)");
525 atom[count].element=element;
526 atom[count].mass=mass;
527 atom[count].brand=brand;
528 atom[count].tag=count;
529 atom[count].attr=attr;
534 int destroy_atoms(t_moldyn *moldyn) {
536 if(moldyn->atom) free(moldyn->atom);
541 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
544 * - gaussian distribution of velocities
545 * - zero total momentum
546 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
551 t_3dvec p_total,delta;
556 random=&(moldyn->random);
558 printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
560 /* gaussian distribution of velocities */
562 for(i=0;i<moldyn->count;i++) {
563 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
565 v=sigma*rand_get_gauss(random);
567 p_total.x+=atom[i].mass*v;
569 v=sigma*rand_get_gauss(random);
571 p_total.y+=atom[i].mass*v;
573 v=sigma*rand_get_gauss(random);
575 p_total.z+=atom[i].mass*v;
578 /* zero total momentum */
579 v3_scale(&p_total,&p_total,1.0/moldyn->count);
580 for(i=0;i<moldyn->count;i++) {
581 v3_scale(&delta,&p_total,1.0/atom[i].mass);
582 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
585 /* velocity scaling */
586 scale_velocity(moldyn,equi_init);
591 double temperature_calc(t_moldyn *moldyn) {
600 for(i=0;i<moldyn->count;i++)
601 double_ekin+=atom[i].mass*v3_absolute_square(&(atom[i].v));
603 /* kinetic energy = 3/2 N k_B T */
604 moldyn->t=double_ekin/(3.0*K_BOLTZMANN*moldyn->count);
609 double get_temperature(t_moldyn *moldyn) {
614 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
624 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
627 /* get kinetic energy / temperature & count involved atoms */
630 for(i=0;i<moldyn->count;i++) {
631 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
632 e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
637 if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
638 else return 0; /* no atoms involved in scaling! */
640 /* (temporary) hack for e,t = 0 */
643 if(moldyn->t_ref!=0.0) {
644 thermal_init(moldyn,equi_init);
648 return 0; /* no scaling needed */
652 /* get scaling factor */
653 scale=moldyn->t_ref/moldyn->t;
657 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
658 scale=1.0+(scale-1.0)/moldyn->t_tc;
661 /* velocity scaling */
662 for(i=0;i<moldyn->count;i++) {
663 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
664 v3_scale(&(atom[i].v),&(atom[i].v),scale);
670 double ideal_gas_law_pressure(t_moldyn *moldyn) {
674 p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
679 double pressure_calc(t_moldyn *moldyn) {
686 for(i=0;i<moldyn->count;i++) {
687 virial=&(moldyn->atom[i].virial);
688 v+=(virial->xx+virial->yy+virial->zz);
691 printf("kieck mal: %f %f %f\n",v,moldyn->count*K_BOLTZMANN*moldyn->t,v/moldyn->count);
693 moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t+v;
694 moldyn->p/=moldyn->volume;
699 double thermodynamic_pressure_calc(t_moldyn *moldyn) {
707 store=malloc(moldyn->count*sizeof(t_atom));
709 printf("[moldyn] allocating store mem failed\n");
713 /* save unscaled potential energy + atom/dim configuration */
715 memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
718 /* derivative with respect to x direction */
719 scale=1.0+moldyn->dv/(moldyn->dim.y*moldyn->dim.z);
720 scale_dim(moldyn,scale,TRUE,0,0);
721 scale_atoms(moldyn,scale,TRUE,0,0);
722 link_cell_shutdown(moldyn);
723 link_cell_init(moldyn);
724 potential_force_calc(moldyn);
725 tp->x=(moldyn->energy-u)/moldyn->dv;
728 /* restore atomic configuration + dim */
729 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
732 /* derivative with respect to y direction */
733 scale=1.0+moldyn->dv/(moldyn->dim.x*moldyn->dim.z);
734 scale_dim(moldyn,scale,0,TRUE,0);
735 scale_atoms(moldyn,scale,0,TRUE,0);
736 link_cell_shutdown(moldyn);
737 link_cell_init(moldyn);
738 potential_force_calc(moldyn);
739 tp->y=(moldyn->energy-u)/moldyn->dv;
742 /* restore atomic configuration + dim */
743 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
746 /* derivative with respect to z direction */
747 scale=1.0+moldyn->dv/(moldyn->dim.x*moldyn->dim.y);
748 scale_dim(moldyn,scale,0,0,TRUE);
749 scale_atoms(moldyn,scale,0,0,TRUE);
750 link_cell_shutdown(moldyn);
751 link_cell_init(moldyn);
752 potential_force_calc(moldyn);
753 tp->z=(moldyn->energy-u)/moldyn->dv;
756 /* restore atomic configuration + dim */
757 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
760 printf("dU/dV komp addiert = %f %f %f\n",tp->x,tp->y,tp->z);
762 scale=1.0+pow(moldyn->dv/moldyn->volume,ONE_THIRD);
764 printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
765 scale_dim(moldyn,scale,1,1,1);
766 scale_atoms(moldyn,scale,1,1,1);
767 link_cell_shutdown(moldyn);
768 link_cell_init(moldyn);
769 potential_force_calc(moldyn);
770 printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
772 printf("dU/dV einfach = %f\n",((moldyn->energy-u)/moldyn->dv)/ATM);
774 /* restore atomic configuration + dim */
775 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
781 link_cell_shutdown(moldyn);
782 link_cell_init(moldyn);
787 double get_pressure(t_moldyn *moldyn) {
793 int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
806 int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
811 for(i=0;i<moldyn->count;i++) {
812 r=&(moldyn->atom[i].r);
821 int scale_volume(t_moldyn *moldyn) {
832 vdim=&(moldyn->vis.dim);
835 memset(&virial,0,sizeof(t_virial));
837 for(i=0;i<moldyn->count;i++) {
838 virial.xx+=atom[i].virial.xx;
839 virial.yy+=atom[i].virial.yy;
840 virial.zz+=atom[i].virial.zz;
841 virial.xy+=atom[i].virial.xy;
842 virial.xz+=atom[i].virial.xz;
843 virial.yz+=atom[i].virial.yz;
846 /* just a guess so far ... */
847 v=virial.xx+virial.yy+virial.zz;
850 /* get pressure from virial */
851 moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t+ONE_THIRD*v;
852 moldyn->p/=moldyn->volume;
853 printf("%f | %f\n",moldyn->p/(ATM),moldyn->p_ref/ATM);
856 if(moldyn->pt_scale&P_SCALE_BERENDSEN)
857 scale=3*sqrt(1-(moldyn->p_ref-moldyn->p)/moldyn->p_tc);
859 /* should actually never be used */
860 scale=pow(moldyn->p/moldyn->p_ref,1.0/3.0);
862 printf("scale = %f\n",scale);
867 if(vdim->x) vdim->x=dim->x;
868 if(vdim->y) vdim->y=dim->y;
869 if(vdim->z) vdim->z=dim->z;
870 moldyn->volume*=(scale*scale*scale);
872 /* check whether we need a new linkcell init */
873 if((dim->x/moldyn->cutoff!=lc->nx)||
874 (dim->y/moldyn->cutoff!=lc->ny)||
875 (dim->z/moldyn->cutoff!=lc->nx)) {
876 link_cell_shutdown(moldyn);
877 link_cell_init(moldyn);
884 double get_e_kin(t_moldyn *moldyn) {
892 for(i=0;i<moldyn->count;i++)
893 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
898 double update_e_kin(t_moldyn *moldyn) {
900 return(get_e_kin(moldyn));
903 double get_total_energy(t_moldyn *moldyn) {
905 return(moldyn->ekin+moldyn->energy);
908 t_3dvec get_total_p(t_moldyn *moldyn) {
917 for(i=0;i<moldyn->count;i++) {
918 v3_scale(&p,&(atom[i].v),atom[i].mass);
919 v3_add(&p_total,&p_total,&p);
925 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
929 /* nn_dist is the nearest neighbour distance */
931 tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
940 /* linked list / cell method */
942 int link_cell_init(t_moldyn *moldyn) {
949 /* partitioning the md cell */
950 lc->nx=moldyn->dim.x/moldyn->cutoff;
951 lc->x=moldyn->dim.x/lc->nx;
952 lc->ny=moldyn->dim.y/moldyn->cutoff;
953 lc->y=moldyn->dim.y/lc->ny;
954 lc->nz=moldyn->dim.z/moldyn->cutoff;
955 lc->z=moldyn->dim.z/lc->nz;
957 lc->cells=lc->nx*lc->ny*lc->nz;
958 lc->subcell=malloc(lc->cells*sizeof(t_list));
961 printf("[moldyn] FATAL: less then 27 subcells!\n");
963 printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
965 for(i=0;i<lc->cells;i++)
966 list_init_f(&(lc->subcell[i]));
968 link_cell_update(moldyn);
973 int link_cell_update(t_moldyn *moldyn) {
991 for(i=0;i<lc->cells;i++)
992 list_destroy_f(&(lc->subcell[i]));
994 for(count=0;count<moldyn->count;count++) {
995 i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
996 j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
997 k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
998 list_add_immediate_f(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
1005 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
1023 cell[0]=lc->subcell[i+j*nx+k*a];
1024 for(ci=-1;ci<=1;ci++) {
1027 if((x<0)||(x>=nx)) {
1031 for(cj=-1;cj<=1;cj++) {
1034 if((y<0)||(y>=ny)) {
1038 for(ck=-1;ck<=1;ck++) {
1041 if((z<0)||(z>=nz)) {
1045 if(!(ci|cj|ck)) continue;
1047 cell[--count2]=lc->subcell[x+y*nx+z*a];
1050 cell[count1++]=lc->subcell[x+y*nx+z*a];
1061 int link_cell_shutdown(t_moldyn *moldyn) {
1068 for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
1069 list_destroy_f(&(moldyn->lc.subcell[i]));
1076 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
1080 t_moldyn_schedule *schedule;
1082 schedule=&(moldyn->schedule);
1083 count=++(schedule->total_sched);
1085 ptr=realloc(schedule->runs,count*sizeof(int));
1087 perror("[moldyn] realloc (runs)");
1091 schedule->runs[count-1]=runs;
1093 ptr=realloc(schedule->tau,count*sizeof(double));
1095 perror("[moldyn] realloc (tau)");
1099 schedule->tau[count-1]=tau;
1101 printf("[moldyn] schedule added:\n");
1102 printf(" number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
1108 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
1110 moldyn->schedule.hook=hook;
1111 moldyn->schedule.hook_params=hook_params;
1118 * 'integration of newtons equation' - algorithms
1122 /* start the integration */
1124 int moldyn_integrate(t_moldyn *moldyn) {
1127 unsigned int e,m,s,v;
1129 t_moldyn_schedule *sched;
1134 double energy_scale;
1136 sched=&(moldyn->schedule);
1139 /* initialize linked cell method */
1140 link_cell_init(moldyn);
1142 /* logging & visualization */
1148 /* sqaure of some variables */
1149 moldyn->tau_square=moldyn->tau*moldyn->tau;
1150 moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
1152 /* energy scaling factor */
1153 energy_scale=moldyn->count*EV;
1155 /* calculate initial forces */
1156 potential_force_calc(moldyn);
1158 /* some stupid checks before we actually start calculating bullshit */
1159 if(moldyn->cutoff>0.5*moldyn->dim.x)
1160 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
1161 if(moldyn->cutoff>0.5*moldyn->dim.y)
1162 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
1163 if(moldyn->cutoff>0.5*moldyn->dim.z)
1164 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
1165 ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
1166 if(ds>0.05*moldyn->nnd)
1167 printf("[moldyn] warning: forces too high / tau too small!\n");
1169 /* zero absolute time */
1172 /* debugging, ignore */
1175 /* tell the world */
1176 printf("[moldyn] integration start, go get a coffee ...\n");
1178 /* executing the schedule */
1179 for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
1181 /* setting amount of runs and finite time step size */
1182 moldyn->tau=sched->tau[sched->count];
1183 moldyn->tau_square=moldyn->tau*moldyn->tau;
1184 moldyn->time_steps=sched->runs[sched->count];
1186 /* integration according to schedule */
1188 for(i=0;i<moldyn->time_steps;i++) {
1190 /* integration step */
1191 moldyn->integrate(moldyn);
1194 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
1195 scale_velocity(moldyn,FALSE);
1196 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
1197 scale_volume(moldyn);
1199 temperature_calc(moldyn);
1200 pressure_calc(moldyn);
1201 //thermodynamic_pressure_calc(moldyn);
1203 /* check for log & visualization */
1206 update_e_kin(moldyn);
1207 dprintf(moldyn->efd,
1209 moldyn->time,moldyn->ekin/energy_scale,
1210 moldyn->energy/energy_scale,
1211 get_total_energy(moldyn)/energy_scale);
1215 p=get_total_p(moldyn);
1216 dprintf(moldyn->mfd,
1217 "%f %f\n",moldyn->time,v3_norm(&p));
1222 snprintf(dir,128,"%s/s-%07.f.save",
1223 moldyn->vlsdir,moldyn->time);
1224 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
1225 if(fd<0) perror("[moldyn] save fd open");
1227 write(fd,moldyn,sizeof(t_moldyn));
1228 write(fd,moldyn->atom,
1229 moldyn->count*sizeof(t_atom));
1236 visual_atoms(&(moldyn->vis),moldyn->time,
1237 moldyn->atom,moldyn->count);
1238 printf("\rsched: %d, steps: %d, debug: %f | %f",
1239 sched->count,i,moldyn->p/ATM,moldyn->debug/ATM);
1244 /* increase absolute time */
1245 moldyn->time+=moldyn->tau;
1249 /* check for hooks */
1251 sched->hook(moldyn,sched->hook_params);
1253 /* get a new info line */
1261 /* velocity verlet */
1263 int velocity_verlet(t_moldyn *moldyn) {
1266 double tau,tau_square,h;
1271 count=moldyn->count;
1273 tau_square=moldyn->tau_square;
1275 for(i=0;i<count;i++) {
1278 v3_scale(&delta,&(atom[i].v),tau);
1279 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1280 v3_scale(&delta,&(atom[i].f),h*tau_square);
1281 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1282 check_per_bound(moldyn,&(atom[i].r));
1284 /* velocities [actually v(t+tau/2)] */
1285 v3_scale(&delta,&(atom[i].f),h*tau);
1286 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1289 /* neighbour list update */
1290 link_cell_update(moldyn);
1292 /* forces depending on chosen potential */
1293 potential_force_calc(moldyn);
1295 for(i=0;i<count;i++) {
1296 /* again velocities [actually v(t+tau)] */
1297 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
1298 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1307 * potentials & corresponding forces & virial routine
1311 /* generic potential and force calculation */
1313 int potential_force_calc(t_moldyn *moldyn) {
1316 t_atom *itom,*jtom,*ktom;
1319 t_list neighbour_i[27];
1320 t_list neighbour_i2[27];
1325 count=moldyn->count;
1332 /* reset force, site energy and virial of every atom */
1333 for(i=0;i<count;i++) {
1336 v3_zero(&(itom[i].f));
1339 virial=(&(itom[i].virial));
1347 /* reset site energy */
1352 /* get energy,force and virial of every atom */
1353 for(i=0;i<count;i++) {
1355 /* single particle potential/force */
1356 if(itom[i].attr&ATOM_ATTR_1BP)
1357 moldyn->func1b(moldyn,&(itom[i]));
1359 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
1362 /* 2 body pair potential/force */
1364 link_cell_neighbour_index(moldyn,
1365 (itom[i].r.x+moldyn->dim.x/2)/lc->x,
1366 (itom[i].r.y+moldyn->dim.y/2)/lc->y,
1367 (itom[i].r.z+moldyn->dim.z/2)/lc->z,
1374 this=&(neighbour_i[j]);
1377 if(this->start==NULL)
1383 jtom=this->current->data;
1385 if(jtom==&(itom[i]))
1388 if((jtom->attr&ATOM_ATTR_2BP)&
1389 (itom[i].attr&ATOM_ATTR_2BP)) {
1390 moldyn->func2b(moldyn,
1396 /* 3 body potential/force */
1398 if(!(itom[i].attr&ATOM_ATTR_3BP)||
1399 !(jtom->attr&ATOM_ATTR_3BP))
1402 /* copy the neighbour lists */
1403 memcpy(neighbour_i2,neighbour_i,
1406 /* get neighbours of i */
1409 that=&(neighbour_i2[k]);
1412 if(that->start==NULL)
1419 ktom=that->current->data;
1421 if(!(ktom->attr&ATOM_ATTR_3BP))
1427 if(ktom==&(itom[i]))
1430 moldyn->func3b(moldyn,
1436 } while(list_next_f(that)!=\
1441 /* 2bp post function */
1442 if(moldyn->func2b_post) {
1443 moldyn->func2b_post(moldyn,
1448 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1465 * virial calculation
1468 inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1470 a->virial.xx+=f->x*d->x;
1471 a->virial.yy+=f->y*d->y;
1472 a->virial.zz+=f->z*d->z;
1473 a->virial.xy+=f->x*d->y;
1474 a->virial.xz+=f->x*d->z;
1475 a->virial.yz+=f->y*d->z;
1481 * periodic boundayr checking
1484 inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1495 if(moldyn->status&MOLDYN_STAT_PBX) {
1496 if(a->x>=x) a->x-=dim->x;
1497 else if(-a->x>x) a->x+=dim->x;
1499 if(moldyn->status&MOLDYN_STAT_PBY) {
1500 if(a->y>=y) a->y-=dim->y;
1501 else if(-a->y>y) a->y+=dim->y;
1503 if(moldyn->status&MOLDYN_STAT_PBZ) {
1504 if(a->z>=z) a->z-=dim->z;
1505 else if(-a->z>z) a->z+=dim->z;
1513 * example potentials
1516 /* harmonic oscillator potential and force */
1518 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1520 t_ho_params *params;
1521 t_3dvec force,distance;
1523 double sc,equi_dist;
1525 params=moldyn->pot2b_params;
1526 sc=params->spring_constant;
1527 equi_dist=params->equilibrium_distance;
1531 v3_sub(&distance,&(aj->r),&(ai->r));
1533 if(bc) check_per_bound(moldyn,&distance);
1534 d=v3_norm(&distance);
1535 if(d<=moldyn->cutoff) {
1536 moldyn->energy+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
1537 /* f = -grad E; grad r_ij = -1 1/r_ij distance */
1538 f=sc*(1.0-equi_dist/d);
1539 v3_scale(&force,&distance,f);
1540 v3_add(&(ai->f),&(ai->f),&force);
1541 virial_calc(ai,&force,&distance);
1542 virial_calc(aj,&force,&distance); /* f and d signe switched */
1543 v3_scale(&force,&distance,-f);
1544 v3_add(&(aj->f),&(aj->f),&force);
1550 /* lennard jones potential & force for one sort of atoms */
1552 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1554 t_lj_params *params;
1555 t_3dvec force,distance;
1557 double eps,sig6,sig12;
1559 params=moldyn->pot2b_params;
1560 eps=params->epsilon4;
1561 sig6=params->sigma6;
1562 sig12=params->sigma12;
1566 v3_sub(&distance,&(aj->r),&(ai->r));
1567 if(bc) check_per_bound(moldyn,&distance);
1568 d=v3_absolute_square(&distance); /* 1/r^2 */
1569 if(d<=moldyn->cutoff_square) {
1570 d=1.0/d; /* 1/r^2 */
1573 h1=h2*h2; /* 1/r^12 */
1574 moldyn->energy+=(eps*(sig12*h1-sig6*h2)-params->uc);
1581 v3_scale(&force,&distance,d);
1582 v3_add(&(aj->f),&(aj->f),&force);
1583 v3_scale(&force,&distance,-1.0*d); /* f = - grad E */
1584 v3_add(&(ai->f),&(ai->f),&force);
1585 virial_calc(ai,&force,&distance);
1586 virial_calc(aj,&force,&distance); /* f and d signe switched */
1593 * tersoff potential & force for 2 sorts of atoms
1596 /* create mixed terms from parameters and set them */
1597 int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
1599 printf("[moldyn] tersoff parameter completion\n");
1600 p->S2[0]=p->S[0]*p->S[0];
1601 p->S2[1]=p->S[1]*p->S[1];
1602 p->Smixed=sqrt(p->S[0]*p->S[1]);
1603 p->S2mixed=p->Smixed*p->Smixed;
1604 p->Rmixed=sqrt(p->R[0]*p->R[1]);
1605 p->Amixed=sqrt(p->A[0]*p->A[1]);
1606 p->Bmixed=sqrt(p->B[0]*p->B[1]);
1607 p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
1608 p->mu_m=0.5*(p->mu[0]+p->mu[1]);
1610 printf("[moldyn] tersoff mult parameter info:\n");
1611 printf(" S (A) | %f | %f | %f\n",p->S[0],p->S[1],p->Smixed);
1612 printf(" R (A) | %f | %f | %f\n",p->R[0],p->R[1],p->Rmixed);
1613 printf(" A (eV) | %f | %f | %f\n",p->A[0]/EV,p->A[1]/EV,p->Amixed/EV);
1614 printf(" B (eV) | %f | %f | %f\n",p->B[0]/EV,p->B[1]/EV,p->Bmixed/EV);
1615 printf(" lambda | %f | %f | %f\n",p->lambda[0],p->lambda[1],
1617 printf(" mu | %f | %f | %f\n",p->mu[0],p->mu[1],p->mu_m);
1618 printf(" beta | %.10f | %.10f\n",p->beta[0],p->beta[1]);
1619 printf(" n | %f | %f\n",p->n[0],p->n[1]);
1620 printf(" c | %f | %f\n",p->c[0],p->c[1]);
1621 printf(" d | %f | %f\n",p->d[0],p->d[1]);
1622 printf(" h | %f | %f\n",p->h[0],p->h[1]);
1623 printf(" chi | %f \n",p->chi);
1628 /* tersoff 1 body part */
1629 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
1632 t_tersoff_mult_params *params;
1633 t_tersoff_exchange *exchange;
1636 params=moldyn->pot1b_params;
1637 exchange=&(params->exchange);
1640 * simple: point constant parameters only depending on atom i to
1641 * their right values
1644 exchange->beta_i=&(params->beta[brand]);
1645 exchange->n_i=&(params->n[brand]);
1646 exchange->c_i=&(params->c[brand]);
1647 exchange->d_i=&(params->d[brand]);
1648 exchange->h_i=&(params->h[brand]);
1650 exchange->betaini=pow(*(exchange->beta_i),*(exchange->n_i));
1651 exchange->ci2=params->c[brand]*params->c[brand];
1652 exchange->di2=params->d[brand]*params->d[brand];
1653 exchange->ci2di2=exchange->ci2/exchange->di2;
1658 /* tersoff 2 body part */
1659 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1661 t_tersoff_mult_params *params;
1662 t_tersoff_exchange *exchange;
1663 t_3dvec dist_ij,force;
1665 double A,B,R,S,S2,lambda,mu;
1672 params=moldyn->pot2b_params;
1674 exchange=&(params->exchange);
1676 /* clear 3bp and 2bp post run */
1678 exchange->run2bp_post=0;
1680 /* reset S > r > R mark */
1681 exchange->d_ij_between_rs=0;
1684 * calc of 2bp contribution of V_ij and dV_ij/ji
1686 * for Vij and dV_ij we need:
1690 * for dV_ji we need:
1691 * - f_c_ji = f_c_ij, df_c_ji = df_c_ij
1692 * - f_r_ji = f_r_ij; df_r_ji = df_r_ij
1697 if(brand==ai->brand) {
1699 S2=params->S2[brand];
1703 lambda=params->lambda[brand];
1704 mu=params->mu[brand];
1713 lambda=params->lambda_m;
1715 params->exchange.chi=params->chi;
1719 v3_sub(&dist_ij,&(aj->r),&(ai->r));
1720 if(bc) check_per_bound(moldyn,&dist_ij);
1721 d_ij2=v3_absolute_square(&dist_ij);
1723 /* if d_ij2 > S2 => no force & potential energy contribution */
1727 /* now we will need the distance */
1728 //d_ij=v3_norm(&dist_ij);
1731 /* save for use in 3bp */
1732 exchange->d_ij=d_ij;
1733 exchange->d_ij2=d_ij2;
1734 exchange->dist_ij=dist_ij;
1736 /* more constants */
1737 exchange->beta_j=&(params->beta[brand]);
1738 exchange->n_j=&(params->n[brand]);
1739 exchange->c_j=&(params->c[brand]);
1740 exchange->d_j=&(params->d[brand]);
1741 exchange->h_j=&(params->h[brand]);
1742 if(brand==ai->brand) {
1743 exchange->betajnj=exchange->betaini;
1744 exchange->cj2=exchange->ci2;
1745 exchange->dj2=exchange->di2;
1746 exchange->cj2dj2=exchange->ci2di2;
1749 exchange->betajnj=pow(*(exchange->beta_j),*(exchange->n_j));
1750 exchange->cj2=params->c[brand]*params->c[brand];
1751 exchange->dj2=params->d[brand]*params->d[brand];
1752 exchange->cj2dj2=exchange->cj2/exchange->dj2;
1755 /* f_r_ij = f_r_ji, df_r_ij = df_r_ji */
1756 f_r=A*exp(-lambda*d_ij);
1757 df_r=lambda*f_r/d_ij;
1759 /* f_a, df_a calc (again, same for ij and ji) | save for later use! */
1760 exchange->f_a=-B*exp(-mu*d_ij);
1761 exchange->df_a=mu*exchange->f_a/d_ij;
1763 /* f_c, df_c calc (again, same for ij and ji) */
1765 /* f_c = 1, df_c = 0 */
1768 /* two body contribution (ij, ji) */
1769 v3_scale(&force,&dist_ij,-df_r);
1773 arg=M_PI*(d_ij-R)/s_r;
1774 f_c=0.5+0.5*cos(arg);
1775 df_c=0.5*sin(arg)*(M_PI/(s_r*d_ij));
1776 /* two body contribution (ij, ji) */
1777 v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
1778 /* tell 3bp that S > r > R */
1779 exchange->d_ij_between_rs=1;
1782 /* add forces of 2bp (ij, ji) contribution
1783 * dVij = dVji and we sum up both: no 1/2) */
1784 v3_add(&(ai->f),&(ai->f),&force);
1787 ai->virial.xx-=force.x*dist_ij.x;
1788 ai->virial.yy-=force.y*dist_ij.y;
1789 ai->virial.zz-=force.z*dist_ij.z;
1790 ai->virial.xy-=force.x*dist_ij.y;
1791 ai->virial.xz-=force.x*dist_ij.z;
1792 ai->virial.yz-=force.y*dist_ij.z;
1795 if(ai==&(moldyn->atom[0])) {
1796 printf("dVij, dVji (2bp) contrib:\n");
1797 printf("%f | %f\n",force.x,ai->f.x);
1798 printf("%f | %f\n",force.y,ai->f.y);
1799 printf("%f | %f\n",force.z,ai->f.z);
1803 if(ai==&(moldyn->atom[0])) {
1804 printf("dVij, dVji (2bp) contrib:\n");
1805 printf("%f | %f\n",force.x*dist_ij.x,ai->virial.xx);
1806 printf("%f | %f\n",force.y*dist_ij.y,ai->virial.yy);
1807 printf("%f | %f\n",force.z*dist_ij.z,ai->virial.zz);
1811 /* energy 2bp contribution (ij, ji) is 0.5 f_r f_c ... */
1812 moldyn->energy+=(0.5*f_r*f_c);
1814 /* save for use in 3bp */
1816 exchange->df_c=df_c;
1818 /* enable the run of 3bp function and 2bp post processing */
1820 exchange->run2bp_post=1;
1822 /* reset 3bp sums */
1823 exchange->zeta_ij=0.0;
1824 exchange->zeta_ji=0.0;
1825 v3_zero(&(exchange->dzeta_ij));
1826 v3_zero(&(exchange->dzeta_ji));
1831 /* tersoff 2 body post part */
1833 int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1836 * here we have to allow for the 3bp sums
1839 * - zeta_ij, dzeta_ij
1840 * - zeta_ji, dzeta_ji
1842 * to compute the 3bp contribution to:
1848 t_tersoff_mult_params *params;
1849 t_tersoff_exchange *exchange;
1854 double f_c,df_c,f_a,df_a;
1855 double chi,ni,betaini,nj,betajnj;
1858 params=moldyn->pot2b_params;
1859 exchange=&(params->exchange);
1861 /* we do not run if f_c_ij was detected to be 0! */
1862 if(!(exchange->run2bp_post))
1866 df_c=exchange->df_c;
1868 df_a=exchange->df_a;
1869 betaini=exchange->betaini;
1870 betajnj=exchange->betajnj;
1871 ni=*(exchange->n_i);
1872 nj=*(exchange->n_j);
1874 dist_ij=&(exchange->dist_ij);
1877 zeta=exchange->zeta_ij;
1879 moldyn->debug++; /* just for debugging ... */
1881 v3_scale(&force,dist_ij,df_a*b*f_c);
1884 tmp=betaini*pow(zeta,ni-1.0); /* beta^n * zeta^n-1 */
1885 b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
1886 db=chi*pow(b,-1.0/(2*ni)-1); /* x(...)^(-1/2n - 1) */
1888 db*=-0.5*tmp; /* db_ij */
1889 v3_scale(&force,&(exchange->dzeta_ij),f_a*db);
1890 v3_scale(&temp,dist_ij,df_a*b);
1891 v3_add(&force,&force,&temp);
1892 v3_scale(&force,&force,f_c);
1894 v3_scale(&temp,dist_ij,df_c*b*f_a);
1895 v3_add(&force,&force,&temp);
1896 v3_scale(&force,&force,-0.5);
1899 v3_add(&(ai->f),&(ai->f),&force);
1902 ai->virial.xx-=force.x*dist_ij->x;
1903 ai->virial.yy-=force.y*dist_ij->y;
1904 ai->virial.zz-=force.z*dist_ij->z;
1905 ai->virial.xy-=force.x*dist_ij->y;
1906 ai->virial.xz-=force.x*dist_ij->z;
1907 ai->virial.yz-=force.y*dist_ij->z;
1910 if(ai==&(moldyn->atom[0])) {
1911 printf("dVij (3bp) contrib:\n");
1912 printf("%f | %f\n",force.x,ai->f.x);
1913 printf("%f | %f\n",force.y,ai->f.y);
1914 printf("%f | %f\n",force.z,ai->f.z);
1918 if(ai==&(moldyn->atom[0])) {
1919 printf("dVij (3bp) contrib:\n");
1920 printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
1921 printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
1922 printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
1926 /* add energy of 3bp sum */
1927 moldyn->energy+=(0.5*f_c*b*f_a);
1930 zeta=exchange->zeta_ji;
1934 v3_scale(&force,dist_ij,df_a*b*f_c);
1937 tmp=betajnj*pow(zeta,nj-1.0); /* beta^n * zeta^n-1 */
1938 b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
1939 db=chi*pow(b,-1.0/(2*nj)-1); /* x(...)^(-1/2n - 1) */
1941 db*=-0.5*tmp; /* db_ij */
1942 v3_scale(&force,&(exchange->dzeta_ji),f_a*db);
1943 v3_scale(&temp,dist_ij,df_a*b);
1944 v3_add(&force,&force,&temp);
1945 v3_scale(&force,&force,f_c);
1947 v3_scale(&temp,dist_ij,df_c*b*f_a);
1948 v3_add(&force,&force,&temp);
1949 v3_scale(&force,&force,-0.5);
1952 v3_add(&(ai->f),&(ai->f),&force);
1954 /* virial - plus sign, as dist_ij = - dist_ji - (really??) */
1955 // TEST ... with a minus instead
1956 ai->virial.xx-=force.x*dist_ij->x;
1957 ai->virial.yy-=force.y*dist_ij->y;
1958 ai->virial.zz-=force.z*dist_ij->z;
1959 ai->virial.xy-=force.x*dist_ij->y;
1960 ai->virial.xz-=force.x*dist_ij->z;
1961 ai->virial.yz-=force.y*dist_ij->z;
1964 if(ai==&(moldyn->atom[0])) {
1965 printf("dVji (3bp) contrib:\n");
1966 printf("%f | %f\n",force.x,ai->f.x);
1967 printf("%f | %f\n",force.y,ai->f.y);
1968 printf("%f | %f\n",force.z,ai->f.z);
1972 if(ai==&(moldyn->atom[0])) {
1973 printf("dVji (3bp) contrib:\n");
1974 printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
1975 printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
1976 printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
1983 /* tersoff 3 body part */
1985 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
1987 t_tersoff_mult_params *params;
1988 t_tersoff_exchange *exchange;
1989 t_3dvec dist_ij,dist_ik,dist_jk;
1990 t_3dvec temp1,temp2;
1994 double d_ij,d_ik,d_jk,d_ij2,d_ik2,d_jk2;
1997 double f_c_ik,df_c_ik,arg;
2001 double cos_theta,d_costheta1,d_costheta2;
2002 double h_cos,d2_h_cos2;
2003 double frac,g,zeta,chi;
2007 params=moldyn->pot3b_params;
2008 exchange=&(params->exchange);
2010 if(!(exchange->run3bp))
2014 * calc of 3bp contribution of V_ij and dV_ij/ji/jk &
2015 * 2bp contribution of dV_jk
2017 * for Vij and dV_ij we still need:
2018 * - b_ij, db_ij (zeta_ij)
2019 * - f_c_ik, df_c_ik, constants_i, cos_theta_ijk, d_costheta_ijk
2021 * for dV_ji we still need:
2022 * - b_ji, db_ji (zeta_ji)
2023 * - f_c_jk, d_c_jk, constants_j, cos_theta_jik, d_costheta_jik
2025 * for dV_jk we need:
2029 * - f_c_ji, df_c_ji, constants_j, cos_theta_jki, d_costheta_jki
2037 /* dist_ij, d_ij - this is < S_ij ! */
2038 dist_ij=exchange->dist_ij;
2039 d_ij=exchange->d_ij;
2040 d_ij2=exchange->d_ij2;
2042 /* f_c_ij, df_c_ij (same for ji) */
2044 df_c=exchange->df_c;
2047 * calculate unknown values now ...
2050 /* V_ij and dV_ij stuff (in b_ij there is f_c_ik) */
2053 v3_sub(&dist_ik,&(ak->r),&(ai->r));
2054 if(bc) check_per_bound(moldyn,&dist_ik);
2055 d_ik2=v3_absolute_square(&dist_ik);
2059 if(brand==ak->brand) {
2062 S2=params->S2[brand];
2070 /* zeta_ij/dzeta_ij contribution only for d_ik < S */
2073 /* now we need d_ik */
2076 /* get constants_i from exchange data */
2083 c2d2=exchange->ci2di2;
2085 /* cosine of theta_ijk by scalaproduct */
2086 rr=v3_scalar_product(&dist_ij,&dist_ik);
2092 d_costheta1=cos_theta/d_ij2-tmp;
2093 d_costheta2=cos_theta/d_ik2-tmp;
2095 /* some usefull values */
2096 h_cos=(h-cos_theta);
2097 d2_h_cos2=d2+(h_cos*h_cos);
2098 frac=c2/(d2_h_cos2);
2103 /* d_costheta_ij and dg(cos_theta) - needed in any case! */
2104 v3_scale(&temp1,&dist_ij,d_costheta1);
2105 v3_scale(&temp2,&dist_ik,d_costheta2);
2106 v3_add(&temp1,&temp1,&temp2);
2107 v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
2109 /* f_c_ik & df_c_ik + {d,}zeta contribution */
2110 dzeta=&(exchange->dzeta_ij);
2114 // => df_c_ik=0.0; of course we do not set this!
2117 exchange->zeta_ij+=g;
2120 v3_add(dzeta,dzeta,&temp1);
2125 arg=M_PI*(d_ik-R)/s_r;
2126 f_c_ik=0.5+0.5*cos(arg);
2127 df_c_ik=0.5*sin(arg)*(M_PI/(s_r*d_ik));
2130 exchange->zeta_ij+=f_c_ik*g;
2133 v3_scale(&temp1,&temp1,f_c_ik);
2134 v3_scale(&temp2,&dist_ik,g*df_c_ik);
2135 v3_add(&temp1,&temp1,&temp2);
2136 v3_add(dzeta,dzeta,&temp1);
2140 /* dV_ji stuff (in b_ji there is f_c_jk) + dV_jk stuff! */
2143 v3_sub(&dist_jk,&(ak->r),&(aj->r));
2144 if(bc) check_per_bound(moldyn,&dist_jk);
2145 d_jk2=v3_absolute_square(&dist_jk);
2149 if(brand==ak->brand) {
2152 S2=params->S2[brand];
2154 mu=params->mu[brand];
2166 /* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */
2169 /* now we need d_ik */
2172 /* constants_j from exchange data */
2179 c2d2=exchange->cj2dj2;
2181 /* cosine of theta_jik by scalaproduct */
2182 rr=-v3_scalar_product(&dist_ij,&dist_jk); /* -1, as ij -> ji */
2188 d_costheta2=cos_theta/d_ij2;
2190 /* some usefull values */
2191 h_cos=(h-cos_theta);
2192 d2_h_cos2=d2+(h_cos*h_cos);
2193 frac=c2/(d2_h_cos2);
2198 /* d_costheta_jik and dg(cos_theta) - needed in any case! */
2199 v3_scale(&temp1,&dist_jk,d_costheta1);
2200 v3_scale(&temp2,&dist_ij,-d_costheta2); /* ji -> ij => -1 */
2201 //v3_add(&temp1,&temp1,&temp2);
2202 v3_sub(&temp1,&temp1,&temp2); /* there is a minus! */
2203 v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
2205 /* store dg in temp2 and use it for dVjk later */
2206 v3_copy(&temp2,&temp1);
2208 /* f_c_jk + {d,}zeta contribution (df_c_jk = 0) */
2209 dzeta=&(exchange->dzeta_ji);
2215 exchange->zeta_ji+=g;
2218 v3_add(dzeta,dzeta,&temp1);
2223 arg=M_PI*(d_jk-R)/s_r;
2224 f_c_jk=0.5+0.5*cos(arg);
2227 exchange->zeta_ji+=f_c_jk*g;
2230 v3_scale(&temp1,&temp1,f_c_jk);
2231 v3_add(dzeta,dzeta,&temp1);
2234 /* dV_jk stuff | add force contribution on atom i immediately */
2235 if(exchange->d_ij_between_rs) {
2237 v3_scale(&temp1,&temp2,f_c);
2238 v3_scale(&temp2,&dist_ij,df_c*g);
2239 v3_add(&temp2,&temp2,&temp1); /* -> dzeta_jk in temp2 */
2243 // dzeta_jk is simply dg, which is stored in temp2
2245 /* betajnj * zeta_jk ^ nj-1 */
2246 tmp=exchange->betajnj*pow(zeta,(n-1.0));
2247 tmp=-chi/2.0*pow((1+tmp*zeta),(-1.0/(2.0*n)-1))*tmp;
2248 v3_scale(&temp2,&temp2,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
2249 v3_add(&(ai->f),&(ai->f),&temp2); /* -1 skipped in f_a calc ^ */
2250 /* scaled with 0.5 ^ */
2253 ai->virial.xx-=temp2.x*dist_jk.x;
2254 ai->virial.yy-=temp2.y*dist_jk.y;
2255 ai->virial.zz-=temp2.z*dist_jk.z;
2256 ai->virial.xy-=temp2.x*dist_jk.y;
2257 ai->virial.xz-=temp2.x*dist_jk.z;
2258 ai->virial.yz-=temp2.y*dist_jk.z;
2261 if(ai==&(moldyn->atom[0])) {
2262 printf("dVjk (3bp) contrib:\n");
2263 printf("%f | %f\n",temp2.x,ai->f.x);
2264 printf("%f | %f\n",temp2.y,ai->f.y);
2265 printf("%f | %f\n",temp2.z,ai->f.z);
2269 if(ai==&(moldyn->atom[0])) {
2270 printf("dVjk (3bp) contrib:\n");
2271 printf("%f | %f\n",temp2.x*dist_jk.x,ai->virial.xx);
2272 printf("%f | %f\n",temp2.y*dist_jk.y,ai->virial.yy);
2273 printf("%f | %f\n",temp2.z*dist_jk.z,ai->virial.zz);
2284 * debugging / critical check functions
2287 int moldyn_bc_check(t_moldyn *moldyn) {
2300 for(i=0;i<moldyn->count;i++) {
2301 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
2302 printf("FATAL: atom %d: x: %.20f (%.20f)\n",
2303 i,atom[i].r.x,dim->x/2);
2304 printf("diagnostic:\n");
2305 printf("-----------\natom.r.x:\n");
2307 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
2310 ((byte)&(1<<k))?1:0,
2313 printf("---------------\nx=dim.x/2:\n");
2315 memcpy(&byte,(u8 *)(&x)+j,1);
2318 ((byte)&(1<<k))?1:0,
2321 if(atom[i].r.x==x) printf("the same!\n");
2322 else printf("different!\n");
2324 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
2325 printf("FATAL: atom %d: y: %.20f (%.20f)\n",
2326 i,atom[i].r.y,dim->y/2);
2327 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
2328 printf("FATAL: atom %d: z: %.20f (%.20f)\n",
2329 i,atom[i].r.z,dim->z/2);