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: %f\n",moldyn->t_ref);
81 int set_pressure(t_moldyn *moldyn,double p_ref) {
85 printf("[moldyn] pressure: %f\n",moldyn->p_ref);
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]);
350 ret=cubic_init(a,b,c,lc,atom,&origin);
353 ret=fcc_init(a,b,c,lc,atom,NULL);
356 ret=diamond_init(a,b,c,lc,atom,&origin);
359 printf("unknown lattice type (%02x)\n",type);
365 printf("[moldyn] creating lattice failed\n");
366 printf(" amount of atoms\n");
367 printf(" - expected: %d\n",new);
368 printf(" - created: %d\n",ret);
373 printf("[moldyn] created lattice with %d atoms\n",new);
375 for(ret=0;ret<new;ret++) {
376 atom[ret].element=element;
379 atom[ret].brand=brand;
380 atom[ret].tag=count+ret;
381 check_per_bound(moldyn,&(atom[ret].r));
388 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
407 v3_copy(&(atom[count].r),&r);
416 for(i=0;i<count;i++) {
417 atom[i].r.x-=(a*lc)/2.0;
418 atom[i].r.y-=(b*lc)/2.0;
419 atom[i].r.z-=(c*lc)/2.0;
425 /* fcc lattice init */
426 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
439 if(origin) v3_copy(&o,origin);
442 /* construct the basis */
445 if(i!=j) help[j]=0.5*lc;
448 v3_set(&basis[i],help);
454 /* fill up the room */
461 v3_copy(&(atom[count].r),&r);
462 atom[count].element=1;
465 v3_add(&n,&r,&basis[i]);
469 v3_copy(&(atom[count].r),&n);
480 /* coordinate transformation */
486 v3_sub(&(atom[i].r),&(atom[i].r),&n);
491 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
496 count=fcc_init(a,b,c,lc,atom,origin);
502 if(origin) v3_add(&o,&o,origin);
504 count+=fcc_init(a,b,c,lc,&atom[count],&o);
509 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
510 t_3dvec *r,t_3dvec *v) {
517 count=(moldyn->count)++;
519 ptr=realloc(atom,(count+1)*sizeof(t_atom));
521 perror("[moldyn] realloc (add atom)");
529 atom[count].element=element;
530 atom[count].mass=mass;
531 atom[count].brand=brand;
532 atom[count].tag=count;
533 atom[count].attr=attr;
538 int destroy_atoms(t_moldyn *moldyn) {
540 if(moldyn->atom) free(moldyn->atom);
545 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
548 * - gaussian distribution of velocities
549 * - zero total momentum
550 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
555 t_3dvec p_total,delta;
560 random=&(moldyn->random);
562 printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
564 /* gaussian distribution of velocities */
566 for(i=0;i<moldyn->count;i++) {
567 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
569 v=sigma*rand_get_gauss(random);
571 p_total.x+=atom[i].mass*v;
573 v=sigma*rand_get_gauss(random);
575 p_total.y+=atom[i].mass*v;
577 v=sigma*rand_get_gauss(random);
579 p_total.z+=atom[i].mass*v;
582 /* zero total momentum */
583 v3_scale(&p_total,&p_total,1.0/moldyn->count);
584 for(i=0;i<moldyn->count;i++) {
585 v3_scale(&delta,&p_total,1.0/atom[i].mass);
586 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
589 /* velocity scaling */
590 scale_velocity(moldyn,equi_init);
595 double temperature_calc(t_moldyn *moldyn) {
597 /* assume up to date kinetic energy, which is 3/2 N k_B T */
599 moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
604 double get_temperature(t_moldyn *moldyn) {
609 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
619 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
622 /* get kinetic energy / temperature & count involved atoms */
625 for(i=0;i<moldyn->count;i++) {
626 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
627 e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
632 if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
633 else return 0; /* no atoms involved in scaling! */
635 /* (temporary) hack for e,t = 0 */
638 if(moldyn->t_ref!=0.0) {
639 thermal_init(moldyn,equi_init);
643 return 0; /* no scaling needed */
647 /* get scaling factor */
648 scale=moldyn->t_ref/moldyn->t;
652 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
653 scale=1.0+(scale-1.0)/moldyn->t_tc;
656 /* velocity scaling */
657 for(i=0;i<moldyn->count;i++) {
658 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
659 v3_scale(&(atom[i].v),&(atom[i].v),scale);
665 double ideal_gas_law_pressure(t_moldyn *moldyn) {
669 p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
674 double pressure_calc(t_moldyn *moldyn) {
681 * P = 1/(3V) sum_i ( p_i^2 / 2m + f_i r_i )
687 for(i=0;i<moldyn->count;i++) {
688 virial=&(moldyn->atom[i].virial);
689 v+=(virial->xx+virial->yy+virial->zz);
692 /* assume up to date kinetic energy */
693 moldyn->p=2.0*moldyn->ekin+v;
694 moldyn->p/=(3.0*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 printf("debug: %f\n",moldyn->atom[0].f.x);
1156 /* calculate initial forces */
1157 potential_force_calc(moldyn);
1158 printf("debug: %f\n",moldyn->atom[0].f.x);
1160 /* some stupid checks before we actually start calculating bullshit */
1161 if(moldyn->cutoff>0.5*moldyn->dim.x)
1162 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
1163 if(moldyn->cutoff>0.5*moldyn->dim.y)
1164 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
1165 if(moldyn->cutoff>0.5*moldyn->dim.z)
1166 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
1167 ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
1168 if(ds>0.05*moldyn->nnd)
1169 printf("[moldyn] warning: forces too high / tau too small!\n");
1171 /* zero absolute time */
1174 /* debugging, ignore */
1177 /* tell the world */
1178 printf("[moldyn] integration start, go get a coffee ...\n");
1180 /* executing the schedule */
1181 for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
1183 /* setting amount of runs and finite time step size */
1184 moldyn->tau=sched->tau[sched->count];
1185 moldyn->tau_square=moldyn->tau*moldyn->tau;
1186 moldyn->time_steps=sched->runs[sched->count];
1188 /* integration according to schedule */
1190 for(i=0;i<moldyn->time_steps;i++) {
1192 /* integration step */
1193 moldyn->integrate(moldyn);
1196 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
1197 scale_velocity(moldyn,FALSE);
1198 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
1199 scale_volume(moldyn);
1201 update_e_kin(moldyn);
1202 temperature_calc(moldyn);
1203 pressure_calc(moldyn);
1204 //thermodynamic_pressure_calc(moldyn);
1206 /* check for log & visualization */
1209 dprintf(moldyn->efd,
1211 moldyn->time,moldyn->ekin/energy_scale,
1212 moldyn->energy/energy_scale,
1213 get_total_energy(moldyn)/energy_scale);
1217 p=get_total_p(moldyn);
1218 dprintf(moldyn->mfd,
1219 "%f %f\n",moldyn->time,v3_norm(&p));
1224 snprintf(dir,128,"%s/s-%07.f.save",
1225 moldyn->vlsdir,moldyn->time);
1226 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
1227 if(fd<0) perror("[moldyn] save fd open");
1229 write(fd,moldyn,sizeof(t_moldyn));
1230 write(fd,moldyn->atom,
1231 moldyn->count*sizeof(t_atom));
1238 visual_atoms(&(moldyn->vis),moldyn->time,
1239 moldyn->atom,moldyn->count);
1240 printf("\rsched: %d, steps: %d, debug: %f",
1241 sched->count,i,moldyn->p/ATM);
1246 /* increase absolute time */
1247 moldyn->time+=moldyn->tau;
1251 /* check for hooks */
1253 sched->hook(moldyn,sched->hook_params);
1255 /* get a new info line */
1263 /* velocity verlet */
1265 int velocity_verlet(t_moldyn *moldyn) {
1268 double tau,tau_square,h;
1273 count=moldyn->count;
1275 tau_square=moldyn->tau_square;
1277 for(i=0;i<count;i++) {
1280 v3_scale(&delta,&(atom[i].v),tau);
1281 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1282 v3_scale(&delta,&(atom[i].f),h*tau_square);
1283 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1284 check_per_bound(moldyn,&(atom[i].r));
1286 /* velocities [actually v(t+tau/2)] */
1287 v3_scale(&delta,&(atom[i].f),h*tau);
1288 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1291 /* neighbour list update */
1292 link_cell_update(moldyn);
1294 /* forces depending on chosen potential */
1295 potential_force_calc(moldyn);
1297 for(i=0;i<count;i++) {
1298 /* again velocities [actually v(t+tau)] */
1299 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
1300 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1309 * potentials & corresponding forces & virial routine
1313 /* generic potential and force calculation */
1315 int potential_force_calc(t_moldyn *moldyn) {
1318 t_atom *itom,*jtom,*ktom;
1321 t_list neighbour_i[27];
1322 t_list neighbour_i2[27];
1327 count=moldyn->count;
1334 /* reset force, site energy and virial of every atom */
1335 for(i=0;i<count;i++) {
1338 v3_zero(&(itom[i].f));
1341 virial=(&(itom[i].virial));
1349 /* reset site energy */
1354 /* get energy,force and virial of every atom */
1355 for(i=0;i<count;i++) {
1357 /* single particle potential/force */
1358 if(itom[i].attr&ATOM_ATTR_1BP)
1359 moldyn->func1b(moldyn,&(itom[i]));
1361 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
1364 /* 2 body pair potential/force */
1366 link_cell_neighbour_index(moldyn,
1367 (itom[i].r.x+moldyn->dim.x/2)/lc->x,
1368 (itom[i].r.y+moldyn->dim.y/2)/lc->y,
1369 (itom[i].r.z+moldyn->dim.z/2)/lc->z,
1376 this=&(neighbour_i[j]);
1379 if(this->start==NULL)
1385 jtom=this->current->data;
1387 if(jtom==&(itom[i]))
1390 if((jtom->attr&ATOM_ATTR_2BP)&
1391 (itom[i].attr&ATOM_ATTR_2BP)) {
1392 moldyn->func2b(moldyn,
1398 /* 3 body potential/force */
1400 if(!(itom[i].attr&ATOM_ATTR_3BP)||
1401 !(jtom->attr&ATOM_ATTR_3BP))
1404 /* copy the neighbour lists */
1405 memcpy(neighbour_i2,neighbour_i,
1408 /* get neighbours of i */
1411 that=&(neighbour_i2[k]);
1414 if(that->start==NULL)
1421 ktom=that->current->data;
1423 if(!(ktom->attr&ATOM_ATTR_3BP))
1429 if(ktom==&(itom[i]))
1432 moldyn->func3b(moldyn,
1438 } while(list_next_f(that)!=\
1443 /* 2bp post function */
1444 if(moldyn->func2b_post) {
1445 moldyn->func2b_post(moldyn,
1450 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1467 * virial calculation
1470 inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1472 a->virial.xx+=f->x*d->x;
1473 a->virial.yy+=f->y*d->y;
1474 a->virial.zz+=f->z*d->z;
1475 a->virial.xy+=f->x*d->y;
1476 a->virial.xz+=f->x*d->z;
1477 a->virial.yz+=f->y*d->z;
1483 * periodic boundayr checking
1486 inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1497 if(moldyn->status&MOLDYN_STAT_PBX) {
1498 if(a->x>=x) a->x-=dim->x;
1499 else if(-a->x>x) a->x+=dim->x;
1501 if(moldyn->status&MOLDYN_STAT_PBY) {
1502 if(a->y>=y) a->y-=dim->y;
1503 else if(-a->y>y) a->y+=dim->y;
1505 if(moldyn->status&MOLDYN_STAT_PBZ) {
1506 if(a->z>=z) a->z-=dim->z;
1507 else if(-a->z>z) a->z+=dim->z;
1515 * example potentials
1518 /* harmonic oscillator potential and force */
1520 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1522 t_ho_params *params;
1523 t_3dvec force,distance;
1525 double sc,equi_dist;
1527 params=moldyn->pot2b_params;
1528 sc=params->spring_constant;
1529 equi_dist=params->equilibrium_distance;
1533 v3_sub(&distance,&(aj->r),&(ai->r));
1535 if(bc) check_per_bound(moldyn,&distance);
1536 d=v3_norm(&distance);
1537 if(d<=moldyn->cutoff) {
1538 moldyn->energy+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
1539 /* f = -grad E; grad r_ij = -1 1/r_ij distance */
1540 f=sc*(1.0-equi_dist/d);
1541 v3_scale(&force,&distance,f);
1542 v3_add(&(ai->f),&(ai->f),&force);
1543 virial_calc(ai,&force,&distance);
1544 virial_calc(aj,&force,&distance); /* f and d signe switched */
1545 v3_scale(&force,&distance,-f);
1546 v3_add(&(aj->f),&(aj->f),&force);
1552 /* lennard jones potential & force for one sort of atoms */
1554 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1556 t_lj_params *params;
1557 t_3dvec force,distance;
1559 double eps,sig6,sig12;
1561 params=moldyn->pot2b_params;
1562 eps=params->epsilon4;
1563 sig6=params->sigma6;
1564 sig12=params->sigma12;
1568 v3_sub(&distance,&(aj->r),&(ai->r));
1569 if(bc) check_per_bound(moldyn,&distance);
1570 d=v3_absolute_square(&distance); /* 1/r^2 */
1571 if(d<=moldyn->cutoff_square) {
1572 d=1.0/d; /* 1/r^2 */
1575 h1=h2*h2; /* 1/r^12 */
1576 moldyn->energy+=(eps*(sig12*h1-sig6*h2)-params->uc);
1583 v3_scale(&force,&distance,d);
1584 v3_add(&(aj->f),&(aj->f),&force);
1585 v3_scale(&force,&force,-1.0); /* f = - grad E */
1586 v3_add(&(ai->f),&(ai->f),&force);
1587 virial_calc(ai,&force,&distance);
1588 virial_calc(aj,&force,&distance); /* f and d signe switched */
1595 * tersoff potential & force for 2 sorts of atoms
1598 /* create mixed terms from parameters and set them */
1599 int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
1601 printf("[moldyn] tersoff parameter completion\n");
1602 p->S2[0]=p->S[0]*p->S[0];
1603 p->S2[1]=p->S[1]*p->S[1];
1604 p->Smixed=sqrt(p->S[0]*p->S[1]);
1605 p->S2mixed=p->Smixed*p->Smixed;
1606 p->Rmixed=sqrt(p->R[0]*p->R[1]);
1607 p->Amixed=sqrt(p->A[0]*p->A[1]);
1608 p->Bmixed=sqrt(p->B[0]*p->B[1]);
1609 p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
1610 p->mu_m=0.5*(p->mu[0]+p->mu[1]);
1612 printf("[moldyn] tersoff mult parameter info:\n");
1613 printf(" S (A) | %f | %f | %f\n",p->S[0],p->S[1],p->Smixed);
1614 printf(" R (A) | %f | %f | %f\n",p->R[0],p->R[1],p->Rmixed);
1615 printf(" A (eV) | %f | %f | %f\n",p->A[0]/EV,p->A[1]/EV,p->Amixed/EV);
1616 printf(" B (eV) | %f | %f | %f\n",p->B[0]/EV,p->B[1]/EV,p->Bmixed/EV);
1617 printf(" lambda | %f | %f | %f\n",p->lambda[0],p->lambda[1],
1619 printf(" mu | %f | %f | %f\n",p->mu[0],p->mu[1],p->mu_m);
1620 printf(" beta | %.10f | %.10f\n",p->beta[0],p->beta[1]);
1621 printf(" n | %f | %f\n",p->n[0],p->n[1]);
1622 printf(" c | %f | %f\n",p->c[0],p->c[1]);
1623 printf(" d | %f | %f\n",p->d[0],p->d[1]);
1624 printf(" h | %f | %f\n",p->h[0],p->h[1]);
1625 printf(" chi | %f \n",p->chi);
1630 /* tersoff 1 body part */
1631 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
1634 t_tersoff_mult_params *params;
1635 t_tersoff_exchange *exchange;
1638 params=moldyn->pot1b_params;
1639 exchange=&(params->exchange);
1642 * simple: point constant parameters only depending on atom i to
1643 * their right values
1646 exchange->beta_i=&(params->beta[brand]);
1647 exchange->n_i=&(params->n[brand]);
1648 exchange->c_i=&(params->c[brand]);
1649 exchange->d_i=&(params->d[brand]);
1650 exchange->h_i=&(params->h[brand]);
1652 exchange->betaini=pow(*(exchange->beta_i),*(exchange->n_i));
1653 exchange->ci2=params->c[brand]*params->c[brand];
1654 exchange->di2=params->d[brand]*params->d[brand];
1655 exchange->ci2di2=exchange->ci2/exchange->di2;
1660 /* tersoff 2 body part */
1661 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1663 t_tersoff_mult_params *params;
1664 t_tersoff_exchange *exchange;
1665 t_3dvec dist_ij,force;
1667 double A,B,R,S,S2,lambda,mu;
1674 params=moldyn->pot2b_params;
1676 exchange=&(params->exchange);
1678 /* clear 3bp and 2bp post run */
1680 exchange->run2bp_post=0;
1682 /* reset S > r > R mark */
1683 exchange->d_ij_between_rs=0;
1686 * calc of 2bp contribution of V_ij and dV_ij/ji
1688 * for Vij and dV_ij we need:
1692 * for dV_ji we need:
1693 * - f_c_ji = f_c_ij, df_c_ji = df_c_ij
1694 * - f_r_ji = f_r_ij; df_r_ji = df_r_ij
1699 if(brand==ai->brand) {
1701 S2=params->S2[brand];
1705 lambda=params->lambda[brand];
1706 mu=params->mu[brand];
1715 lambda=params->lambda_m;
1717 params->exchange.chi=params->chi;
1721 v3_sub(&dist_ij,&(aj->r),&(ai->r));
1722 if(bc) check_per_bound(moldyn,&dist_ij);
1723 d_ij2=v3_absolute_square(&dist_ij);
1725 /* if d_ij2 > S2 => no force & potential energy contribution */
1729 /* now we will need the distance */
1730 //d_ij=v3_norm(&dist_ij);
1733 /* save for use in 3bp */
1734 exchange->d_ij=d_ij;
1735 exchange->d_ij2=d_ij2;
1736 exchange->dist_ij=dist_ij;
1738 /* more constants */
1739 exchange->beta_j=&(params->beta[brand]);
1740 exchange->n_j=&(params->n[brand]);
1741 exchange->c_j=&(params->c[brand]);
1742 exchange->d_j=&(params->d[brand]);
1743 exchange->h_j=&(params->h[brand]);
1744 if(brand==ai->brand) {
1745 exchange->betajnj=exchange->betaini;
1746 exchange->cj2=exchange->ci2;
1747 exchange->dj2=exchange->di2;
1748 exchange->cj2dj2=exchange->ci2di2;
1751 exchange->betajnj=pow(*(exchange->beta_j),*(exchange->n_j));
1752 exchange->cj2=params->c[brand]*params->c[brand];
1753 exchange->dj2=params->d[brand]*params->d[brand];
1754 exchange->cj2dj2=exchange->cj2/exchange->dj2;
1757 /* f_r_ij = f_r_ji, df_r_ij = df_r_ji */
1758 f_r=A*exp(-lambda*d_ij);
1759 df_r=lambda*f_r/d_ij;
1761 /* f_a, df_a calc (again, same for ij and ji) | save for later use! */
1762 exchange->f_a=-B*exp(-mu*d_ij);
1763 exchange->df_a=mu*exchange->f_a/d_ij;
1765 /* f_c, df_c calc (again, same for ij and ji) */
1767 /* f_c = 1, df_c = 0 */
1770 /* two body contribution (ij, ji) */
1771 v3_scale(&force,&dist_ij,-df_r);
1775 arg=M_PI*(d_ij-R)/s_r;
1776 f_c=0.5+0.5*cos(arg);
1777 df_c=0.5*sin(arg)*(M_PI/(s_r*d_ij));
1778 /* two body contribution (ij, ji) */
1779 v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
1780 /* tell 3bp that S > r > R */
1781 exchange->d_ij_between_rs=1;
1784 /* add forces of 2bp (ij, ji) contribution
1785 * dVij = dVji and we sum up both: no 1/2) */
1786 v3_add(&(ai->f),&(ai->f),&force);
1789 ai->virial.xx-=force.x*dist_ij.x;
1790 ai->virial.yy-=force.y*dist_ij.y;
1791 ai->virial.zz-=force.z*dist_ij.z;
1792 ai->virial.xy-=force.x*dist_ij.y;
1793 ai->virial.xz-=force.x*dist_ij.z;
1794 ai->virial.yz-=force.y*dist_ij.z;
1797 if(ai==&(moldyn->atom[0])) {
1798 printf("dVij, dVji (2bp) contrib:\n");
1799 printf("%f | %f\n",force.x,ai->f.x);
1800 printf("%f | %f\n",force.y,ai->f.y);
1801 printf("%f | %f\n",force.z,ai->f.z);
1805 if(ai==&(moldyn->atom[0])) {
1806 printf("dVij, dVji (2bp) contrib:\n");
1807 printf("%f | %f\n",force.x*dist_ij.x,ai->virial.xx);
1808 printf("%f | %f\n",force.y*dist_ij.y,ai->virial.yy);
1809 printf("%f | %f\n",force.z*dist_ij.z,ai->virial.zz);
1813 /* energy 2bp contribution (ij, ji) is 0.5 f_r f_c ... */
1814 moldyn->energy+=(0.5*f_r*f_c);
1816 /* save for use in 3bp */
1818 exchange->df_c=df_c;
1820 /* enable the run of 3bp function and 2bp post processing */
1822 exchange->run2bp_post=1;
1824 /* reset 3bp sums */
1825 exchange->zeta_ij=0.0;
1826 exchange->zeta_ji=0.0;
1827 v3_zero(&(exchange->dzeta_ij));
1828 v3_zero(&(exchange->dzeta_ji));
1833 /* tersoff 2 body post part */
1835 int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1838 * here we have to allow for the 3bp sums
1841 * - zeta_ij, dzeta_ij
1842 * - zeta_ji, dzeta_ji
1844 * to compute the 3bp contribution to:
1850 t_tersoff_mult_params *params;
1851 t_tersoff_exchange *exchange;
1856 double f_c,df_c,f_a,df_a;
1857 double chi,ni,betaini,nj,betajnj;
1860 params=moldyn->pot2b_params;
1861 exchange=&(params->exchange);
1863 /* we do not run if f_c_ij was detected to be 0! */
1864 if(!(exchange->run2bp_post))
1868 df_c=exchange->df_c;
1870 df_a=exchange->df_a;
1871 betaini=exchange->betaini;
1872 betajnj=exchange->betajnj;
1873 ni=*(exchange->n_i);
1874 nj=*(exchange->n_j);
1876 dist_ij=&(exchange->dist_ij);
1879 zeta=exchange->zeta_ij;
1881 moldyn->debug++; /* just for debugging ... */
1883 v3_scale(&force,dist_ij,df_a*b*f_c);
1886 tmp=betaini*pow(zeta,ni-1.0); /* beta^n * zeta^n-1 */
1887 b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
1888 db=chi*pow(b,-1.0/(2*ni)-1); /* x(...)^(-1/2n - 1) */
1890 db*=-0.5*tmp; /* db_ij */
1891 v3_scale(&force,&(exchange->dzeta_ij),f_a*db);
1892 v3_scale(&temp,dist_ij,df_a*b);
1893 v3_add(&force,&force,&temp);
1894 v3_scale(&force,&force,f_c);
1896 v3_scale(&temp,dist_ij,df_c*b*f_a);
1897 v3_add(&force,&force,&temp);
1898 v3_scale(&force,&force,-0.5);
1901 v3_add(&(ai->f),&(ai->f),&force);
1904 ai->virial.xx-=force.x*dist_ij->x;
1905 ai->virial.yy-=force.y*dist_ij->y;
1906 ai->virial.zz-=force.z*dist_ij->z;
1907 ai->virial.xy-=force.x*dist_ij->y;
1908 ai->virial.xz-=force.x*dist_ij->z;
1909 ai->virial.yz-=force.y*dist_ij->z;
1912 if(ai==&(moldyn->atom[0])) {
1913 printf("dVij (3bp) contrib:\n");
1914 printf("%f | %f\n",force.x,ai->f.x);
1915 printf("%f | %f\n",force.y,ai->f.y);
1916 printf("%f | %f\n",force.z,ai->f.z);
1920 if(ai==&(moldyn->atom[0])) {
1921 printf("dVij (3bp) contrib:\n");
1922 printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
1923 printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
1924 printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
1928 /* add energy of 3bp sum */
1929 moldyn->energy+=(0.5*f_c*b*f_a);
1932 zeta=exchange->zeta_ji;
1936 v3_scale(&force,dist_ij,df_a*b*f_c);
1939 tmp=betajnj*pow(zeta,nj-1.0); /* beta^n * zeta^n-1 */
1940 b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
1941 db=chi*pow(b,-1.0/(2*nj)-1); /* x(...)^(-1/2n - 1) */
1943 db*=-0.5*tmp; /* db_ij */
1944 v3_scale(&force,&(exchange->dzeta_ji),f_a*db);
1945 v3_scale(&temp,dist_ij,df_a*b);
1946 v3_add(&force,&force,&temp);
1947 v3_scale(&force,&force,f_c);
1949 v3_scale(&temp,dist_ij,df_c*b*f_a);
1950 v3_add(&force,&force,&temp);
1951 v3_scale(&force,&force,-0.5);
1954 v3_add(&(ai->f),&(ai->f),&force);
1956 /* virial - plus sign, as dist_ij = - dist_ji - (really??) */
1957 // TEST ... with a minus instead
1958 ai->virial.xx-=force.x*dist_ij->x;
1959 ai->virial.yy-=force.y*dist_ij->y;
1960 ai->virial.zz-=force.z*dist_ij->z;
1961 ai->virial.xy-=force.x*dist_ij->y;
1962 ai->virial.xz-=force.x*dist_ij->z;
1963 ai->virial.yz-=force.y*dist_ij->z;
1966 if(ai==&(moldyn->atom[0])) {
1967 printf("dVji (3bp) contrib:\n");
1968 printf("%f | %f\n",force.x,ai->f.x);
1969 printf("%f | %f\n",force.y,ai->f.y);
1970 printf("%f | %f\n",force.z,ai->f.z);
1974 if(ai==&(moldyn->atom[0])) {
1975 printf("dVji (3bp) contrib:\n");
1976 printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
1977 printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
1978 printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
1985 /* tersoff 3 body part */
1987 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
1989 t_tersoff_mult_params *params;
1990 t_tersoff_exchange *exchange;
1991 t_3dvec dist_ij,dist_ik,dist_jk;
1992 t_3dvec temp1,temp2;
1996 double d_ij,d_ik,d_jk,d_ij2,d_ik2,d_jk2;
1999 double f_c_ik,df_c_ik,arg;
2003 double cos_theta,d_costheta1,d_costheta2;
2004 double h_cos,d2_h_cos2;
2005 double frac,g,zeta,chi;
2009 params=moldyn->pot3b_params;
2010 exchange=&(params->exchange);
2012 if(!(exchange->run3bp))
2016 * calc of 3bp contribution of V_ij and dV_ij/ji/jk &
2017 * 2bp contribution of dV_jk
2019 * for Vij and dV_ij we still need:
2020 * - b_ij, db_ij (zeta_ij)
2021 * - f_c_ik, df_c_ik, constants_i, cos_theta_ijk, d_costheta_ijk
2023 * for dV_ji we still need:
2024 * - b_ji, db_ji (zeta_ji)
2025 * - f_c_jk, d_c_jk, constants_j, cos_theta_jik, d_costheta_jik
2027 * for dV_jk we need:
2031 * - f_c_ji, df_c_ji, constants_j, cos_theta_jki, d_costheta_jki
2039 /* dist_ij, d_ij - this is < S_ij ! */
2040 dist_ij=exchange->dist_ij;
2041 d_ij=exchange->d_ij;
2042 d_ij2=exchange->d_ij2;
2044 /* f_c_ij, df_c_ij (same for ji) */
2046 df_c=exchange->df_c;
2049 * calculate unknown values now ...
2052 /* V_ij and dV_ij stuff (in b_ij there is f_c_ik) */
2055 v3_sub(&dist_ik,&(ak->r),&(ai->r));
2056 if(bc) check_per_bound(moldyn,&dist_ik);
2057 d_ik2=v3_absolute_square(&dist_ik);
2061 if(brand==ak->brand) {
2064 S2=params->S2[brand];
2072 /* zeta_ij/dzeta_ij contribution only for d_ik < S */
2075 /* now we need d_ik */
2078 /* get constants_i from exchange data */
2085 c2d2=exchange->ci2di2;
2087 /* cosine of theta_ijk by scalaproduct */
2088 rr=v3_scalar_product(&dist_ij,&dist_ik);
2094 d_costheta1=cos_theta/d_ij2-tmp;
2095 d_costheta2=cos_theta/d_ik2-tmp;
2097 /* some usefull values */
2098 h_cos=(h-cos_theta);
2099 d2_h_cos2=d2+(h_cos*h_cos);
2100 frac=c2/(d2_h_cos2);
2105 /* d_costheta_ij and dg(cos_theta) - needed in any case! */
2106 v3_scale(&temp1,&dist_ij,d_costheta1);
2107 v3_scale(&temp2,&dist_ik,d_costheta2);
2108 v3_add(&temp1,&temp1,&temp2);
2109 v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
2111 /* f_c_ik & df_c_ik + {d,}zeta contribution */
2112 dzeta=&(exchange->dzeta_ij);
2116 // => df_c_ik=0.0; of course we do not set this!
2119 exchange->zeta_ij+=g;
2122 v3_add(dzeta,dzeta,&temp1);
2127 arg=M_PI*(d_ik-R)/s_r;
2128 f_c_ik=0.5+0.5*cos(arg);
2129 df_c_ik=0.5*sin(arg)*(M_PI/(s_r*d_ik));
2132 exchange->zeta_ij+=f_c_ik*g;
2135 v3_scale(&temp1,&temp1,f_c_ik);
2136 v3_scale(&temp2,&dist_ik,g*df_c_ik);
2137 v3_add(&temp1,&temp1,&temp2);
2138 v3_add(dzeta,dzeta,&temp1);
2142 /* dV_ji stuff (in b_ji there is f_c_jk) + dV_jk stuff! */
2145 v3_sub(&dist_jk,&(ak->r),&(aj->r));
2146 if(bc) check_per_bound(moldyn,&dist_jk);
2147 d_jk2=v3_absolute_square(&dist_jk);
2151 if(brand==ak->brand) {
2154 S2=params->S2[brand];
2156 mu=params->mu[brand];
2168 /* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */
2171 /* now we need d_ik */
2174 /* constants_j from exchange data */
2181 c2d2=exchange->cj2dj2;
2183 /* cosine of theta_jik by scalaproduct */
2184 rr=-v3_scalar_product(&dist_ij,&dist_jk); /* -1, as ij -> ji */
2190 d_costheta2=cos_theta/d_ij2;
2192 /* some usefull values */
2193 h_cos=(h-cos_theta);
2194 d2_h_cos2=d2+(h_cos*h_cos);
2195 frac=c2/(d2_h_cos2);
2200 /* d_costheta_jik and dg(cos_theta) - needed in any case! */
2201 v3_scale(&temp1,&dist_jk,d_costheta1);
2202 v3_scale(&temp2,&dist_ij,-d_costheta2); /* ji -> ij => -1 */
2203 //v3_add(&temp1,&temp1,&temp2);
2204 v3_sub(&temp1,&temp1,&temp2); /* there is a minus! */
2205 v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
2207 /* store dg in temp2 and use it for dVjk later */
2208 v3_copy(&temp2,&temp1);
2210 /* f_c_jk + {d,}zeta contribution (df_c_jk = 0) */
2211 dzeta=&(exchange->dzeta_ji);
2217 exchange->zeta_ji+=g;
2220 v3_add(dzeta,dzeta,&temp1);
2225 arg=M_PI*(d_jk-R)/s_r;
2226 f_c_jk=0.5+0.5*cos(arg);
2229 exchange->zeta_ji+=f_c_jk*g;
2232 v3_scale(&temp1,&temp1,f_c_jk);
2233 v3_add(dzeta,dzeta,&temp1);
2236 /* dV_jk stuff | add force contribution on atom i immediately */
2237 if(exchange->d_ij_between_rs) {
2239 v3_scale(&temp1,&temp2,f_c);
2240 v3_scale(&temp2,&dist_ij,df_c*g);
2241 v3_add(&temp2,&temp2,&temp1); /* -> dzeta_jk in temp2 */
2245 // dzeta_jk is simply dg, which is stored in temp2
2247 /* betajnj * zeta_jk ^ nj-1 */
2248 tmp=exchange->betajnj*pow(zeta,(n-1.0));
2249 tmp=-chi/2.0*pow((1+tmp*zeta),(-1.0/(2.0*n)-1))*tmp;
2250 v3_scale(&temp2,&temp2,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
2251 v3_add(&(ai->f),&(ai->f),&temp2); /* -1 skipped in f_a calc ^ */
2252 /* scaled with 0.5 ^ */
2255 ai->virial.xx-=temp2.x*dist_jk.x;
2256 ai->virial.yy-=temp2.y*dist_jk.y;
2257 ai->virial.zz-=temp2.z*dist_jk.z;
2258 ai->virial.xy-=temp2.x*dist_jk.y;
2259 ai->virial.xz-=temp2.x*dist_jk.z;
2260 ai->virial.yz-=temp2.y*dist_jk.z;
2263 if(ai==&(moldyn->atom[0])) {
2264 printf("dVjk (3bp) contrib:\n");
2265 printf("%f | %f\n",temp2.x,ai->f.x);
2266 printf("%f | %f\n",temp2.y,ai->f.y);
2267 printf("%f | %f\n",temp2.z,ai->f.z);
2271 if(ai==&(moldyn->atom[0])) {
2272 printf("dVjk (3bp) contrib:\n");
2273 printf("%f | %f\n",temp2.x*dist_jk.x,ai->virial.xx);
2274 printf("%f | %f\n",temp2.y*dist_jk.y,ai->virial.yy);
2275 printf("%f | %f\n",temp2.z*dist_jk.z,ai->virial.zz);
2286 * debugging / critical check functions
2289 int moldyn_bc_check(t_moldyn *moldyn) {
2302 for(i=0;i<moldyn->count;i++) {
2303 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
2304 printf("FATAL: atom %d: x: %.20f (%.20f)\n",
2305 i,atom[i].r.x,dim->x/2);
2306 printf("diagnostic:\n");
2307 printf("-----------\natom.r.x:\n");
2309 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
2312 ((byte)&(1<<k))?1:0,
2315 printf("---------------\nx=dim.x/2:\n");
2317 memcpy(&byte,(u8 *)(&x)+j,1);
2320 ((byte)&(1<<k))?1:0,
2323 if(atom[i].r.x==x) printf("the same!\n");
2324 else printf("different!\n");
2326 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
2327 printf("FATAL: atom %d: y: %.20f (%.20f)\n",
2328 i,atom[i].r.y,dim->y/2);
2329 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
2330 printf("FATAL: atom %d: z: %.20f (%.20f)\n",
2331 i,atom[i].r.z,dim->z/2);