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 memset(moldyn,0,sizeof(t_moldyn));
24 rand_init(&(moldyn->random),NULL,1);
25 moldyn->random.status|=RAND_STAT_VERBOSE;
30 int moldyn_shutdown(t_moldyn *moldyn) {
32 printf("[moldyn] shutdown\n");
33 moldyn_log_shutdown(moldyn);
34 link_cell_shutdown(moldyn);
35 rand_close(&(moldyn->random));
41 int set_int_alg(t_moldyn *moldyn,u8 algo) {
44 case MOLDYN_INTEGRATE_VERLET:
45 moldyn->integrate=velocity_verlet;
48 printf("unknown integration algorithm: %02x\n",algo);
55 int set_cutoff(t_moldyn *moldyn,double cutoff) {
57 moldyn->cutoff=cutoff;
62 int set_temperature(t_moldyn *moldyn,double t_ref) {
69 int set_pressure(t_moldyn *moldyn,double p_ref) {
76 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
78 moldyn->pt_scale=(ptype|ttype);
85 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
99 printf("[moldyn] dimensions in A and A^3 respectively:\n");
100 printf(" x: %f\n",moldyn->dim.x);
101 printf(" y: %f\n",moldyn->dim.y);
102 printf(" z: %f\n",moldyn->dim.z);
103 printf(" volume: %f\n",moldyn->volume);
104 printf(" visualize simulation box: %s\n",visualize?"on":"off");
109 int set_nn_dist(t_moldyn *moldyn,double dist) {
116 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
119 moldyn->status|=MOLDYN_STAT_PBX;
122 moldyn->status|=MOLDYN_STAT_PBY;
125 moldyn->status|=MOLDYN_STAT_PBZ;
130 int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
133 moldyn->pot1b_params=params;
138 int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
141 moldyn->pot2b_params=params;
146 int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) {
148 moldyn->func2b_post=func;
149 moldyn->pot2b_params=params;
154 int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
157 moldyn->pot3b_params=params;
162 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
164 strncpy(moldyn->vlsdir,dir,127);
169 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
175 case LOG_TOTAL_ENERGY:
176 moldyn->ewrite=timer;
177 snprintf(filename,127,"%s/energy",moldyn->vlsdir);
178 moldyn->efd=open(filename,
179 O_WRONLY|O_CREAT|O_EXCL,
182 perror("[moldyn] energy log fd open");
185 dprintf(moldyn->efd,"# total energy log file\n");
187 case LOG_TOTAL_MOMENTUM:
188 moldyn->mwrite=timer;
189 snprintf(filename,127,"%s/momentum",moldyn->vlsdir);
190 moldyn->mfd=open(filename,
191 O_WRONLY|O_CREAT|O_EXCL,
194 perror("[moldyn] momentum log fd open");
197 dprintf(moldyn->efd,"# total momentum log file\n");
200 moldyn->swrite=timer;
203 moldyn->vwrite=timer;
204 ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
206 printf("[moldyn] visual init failure\n");
211 printf("[moldyn] unknown log mechanism: %02x\n",type);
218 int moldyn_log_shutdown(t_moldyn *moldyn) {
220 printf("[moldyn] log shutdown\n");
221 if(moldyn->efd) close(moldyn->efd);
222 if(moldyn->mfd) close(moldyn->mfd);
223 if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
229 * creating lattice functions
232 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
233 u8 attr,u8 brand,int a,int b,int c) {
244 /* how many atoms do we expect */
245 if(type==FCC) new*=4;
246 if(type==DIAMOND) new*=8;
248 /* allocate space for atoms */
249 ptr=realloc(moldyn->atom,(count+new)*sizeof(t_atom));
251 perror("[moldyn] realloc (create lattice)");
255 atom=&(moldyn->atom[count]);
261 ret=fcc_init(a,b,c,lc,atom,&origin);
264 ret=diamond_init(a,b,c,lc,atom,&origin);
267 printf("unknown lattice type (%02x)\n",type);
273 printf("[moldyn] creating lattice failed\n");
274 printf(" amount of atoms\n");
275 printf(" - expected: %d\n",new);
276 printf(" - created: %d\n",ret);
281 printf("[moldyn] created lattice with %d atoms\n",new);
283 for(ret=0;ret<new;ret++) {
284 atom[ret].element=element;
287 atom[ret].brand=brand;
288 atom[ret].tag=count+ret;
289 check_per_bound(moldyn,&(atom[ret].r));
295 /* fcc lattice init */
296 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
309 if(origin) v3_copy(&o,origin);
312 /* construct the basis */
315 if(i!=j) help[j]=0.5*lc;
318 v3_set(&basis[i],help);
324 /* fill up the room */
331 v3_copy(&(atom[count].r),&r);
332 atom[count].element=1;
335 v3_add(&n,&r,&basis[i]);
339 v3_copy(&(atom[count].r),&n);
350 /* coordinate transformation */
356 v3_sub(&(atom[i].r),&(atom[i].r),&n);
361 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
366 count=fcc_init(a,b,c,lc,atom,origin);
372 if(origin) v3_add(&o,&o,origin);
374 count+=fcc_init(a,b,c,lc,&atom[count],&o);
379 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
380 t_3dvec *r,t_3dvec *v) {
387 count=(moldyn->count)++;
389 ptr=realloc(atom,(count+1)*sizeof(t_atom));
391 perror("[moldyn] realloc (add atom)");
399 atom[count].element=element;
400 atom[count].mass=mass;
401 atom[count].brand=brand;
402 atom[count].tag=count;
403 atom[count].attr=attr;
408 int destroy_atoms(t_moldyn *moldyn) {
410 if(moldyn->atom) free(moldyn->atom);
415 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
418 * - gaussian distribution of velocities
419 * - zero total momentum
420 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
425 t_3dvec p_total,delta;
430 random=&(moldyn->random);
432 /* gaussian distribution of velocities */
434 for(i=0;i<moldyn->count;i++) {
435 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
437 v=sigma*rand_get_gauss(random);
439 p_total.x+=atom[i].mass*v;
441 v=sigma*rand_get_gauss(random);
443 p_total.y+=atom[i].mass*v;
445 v=sigma*rand_get_gauss(random);
447 p_total.z+=atom[i].mass*v;
450 /* zero total momentum */
451 v3_scale(&p_total,&p_total,1.0/moldyn->count);
452 for(i=0;i<moldyn->count;i++) {
453 v3_scale(&delta,&p_total,1.0/atom[i].mass);
454 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
457 /* velocity scaling */
458 scale_velocity(moldyn,equi_init);
463 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
473 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
476 /* get kinetic energy / temperature & count involved atoms */
479 for(i=0;i<moldyn->count;i++) {
480 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
481 e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
485 if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
486 else return 0; /* no atoms involved in scaling! */
488 /* (temporary) hack for e,t = 0 */
491 if(moldyn->t_ref!=0.0) {
492 thermal_init(moldyn,equi_init);
496 return 0; /* no scaling needed */
500 /* get scaling factor */
501 scale=moldyn->t_ref/moldyn->t;
505 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
506 scale=1.0+(scale-1.0)/moldyn->t_tc;
509 /* velocity scaling */
510 for(i=0;i<moldyn->count;i++) {
511 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
512 v3_scale(&(atom[i].v),&(atom[i].v),scale);
518 int scale_volume(t_moldyn *moldyn) {
529 vdim=&(moldyn->vis.dim);
532 memset(&virial,0,sizeof(t_virial));
534 for(i=0;i<moldyn->count;i++) {
535 virial.xx+=atom[i].virial.xx;
536 virial.yy+=atom[i].virial.yy;
537 virial.zz+=atom[i].virial.zz;
538 virial.xy+=atom[i].virial.xy;
539 virial.xz+=atom[i].virial.xz;
540 virial.yz+=atom[i].virial.yz;
543 /* just a guess so far ... */
544 v=virial.xx+virial.yy+virial.zz;
547 /* get pressure from virial */
548 moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t+ONE_THIRD*v;
549 moldyn->p/=moldyn->volume;
550 printf("%f | %f\n",moldyn->p/(ATM),moldyn->p_ref/ATM);
553 if(moldyn->pt_scale&P_SCALE_BERENDSEN)
554 scale=3*sqrt(1-(moldyn->p_ref-moldyn->p)/moldyn->p_tc);
556 /* should actually never be used */
557 scale=pow(moldyn->p/moldyn->p_ref,1.0/3.0);
559 printf("scale = %f\n",scale);
564 if(vdim->x) vdim->x=dim->x;
565 if(vdim->y) vdim->y=dim->y;
566 if(vdim->z) vdim->z=dim->z;
567 moldyn->volume*=(scale*scale*scale);
569 /* check whether we need a new linkcell init */
570 if((dim->x/moldyn->cutoff!=lc->nx)||
571 (dim->y/moldyn->cutoff!=lc->ny)||
572 (dim->z/moldyn->cutoff!=lc->nx)) {
573 link_cell_shutdown(moldyn);
574 link_cell_init(moldyn);
581 double get_e_kin(t_moldyn *moldyn) {
589 for(i=0;i<moldyn->count;i++)
590 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
595 double get_e_pot(t_moldyn *moldyn) {
597 return moldyn->energy;
600 double update_e_kin(t_moldyn *moldyn) {
602 return(get_e_kin(moldyn));
605 double get_total_energy(t_moldyn *moldyn) {
607 return(moldyn->ekin+moldyn->energy);
610 t_3dvec get_total_p(t_moldyn *moldyn) {
619 for(i=0;i<moldyn->count;i++) {
620 v3_scale(&p,&(atom[i].v),atom[i].mass);
621 v3_add(&p_total,&p_total,&p);
627 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
631 /* nn_dist is the nearest neighbour distance */
633 tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
642 /* linked list / cell method */
644 int link_cell_init(t_moldyn *moldyn) {
651 /* partitioning the md cell */
652 lc->nx=moldyn->dim.x/moldyn->cutoff;
653 lc->x=moldyn->dim.x/lc->nx;
654 lc->ny=moldyn->dim.y/moldyn->cutoff;
655 lc->y=moldyn->dim.y/lc->ny;
656 lc->nz=moldyn->dim.z/moldyn->cutoff;
657 lc->z=moldyn->dim.z/lc->nz;
659 lc->cells=lc->nx*lc->ny*lc->nz;
660 lc->subcell=malloc(lc->cells*sizeof(t_list));
662 printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
664 for(i=0;i<lc->cells;i++)
665 list_init_f(&(lc->subcell[i]));
667 link_cell_update(moldyn);
672 int link_cell_update(t_moldyn *moldyn) {
690 for(i=0;i<lc->cells;i++)
691 list_destroy_f(&(lc->subcell[i]));
693 for(count=0;count<moldyn->count;count++) {
694 i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
695 j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
696 k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
697 list_add_immediate_f(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
704 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
722 cell[0]=lc->subcell[i+j*nx+k*a];
723 for(ci=-1;ci<=1;ci++) {
730 for(cj=-1;cj<=1;cj++) {
737 for(ck=-1;ck<=1;ck++) {
744 if(!(ci|cj|ck)) continue;
746 cell[--count2]=lc->subcell[x+y*nx+z*a];
749 cell[count1++]=lc->subcell[x+y*nx+z*a];
760 int link_cell_shutdown(t_moldyn *moldyn) {
767 for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
768 list_destroy_f(&(moldyn->lc.subcell[i]));
775 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
779 t_moldyn_schedule *schedule;
781 schedule=&(moldyn->schedule);
782 count=++(schedule->total_sched);
784 ptr=realloc(schedule->runs,count*sizeof(int));
786 perror("[moldyn] realloc (runs)");
790 schedule->runs[count-1]=runs;
792 ptr=realloc(schedule->tau,count*sizeof(double));
794 perror("[moldyn] realloc (tau)");
798 schedule->tau[count-1]=tau;
803 int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
805 moldyn->schedule.hook=hook;
806 moldyn->schedule.hook_params=hook_params;
813 * 'integration of newtons equation' - algorithms
817 /* start the integration */
819 int moldyn_integrate(t_moldyn *moldyn) {
822 unsigned int e,m,s,v;
824 t_moldyn_schedule *sched;
830 sched=&(moldyn->schedule);
833 /* initialize linked cell method */
834 link_cell_init(moldyn);
836 /* logging & visualization */
842 /* sqaure of some variables */
843 moldyn->tau_square=moldyn->tau*moldyn->tau;
844 moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
846 /* calculate initial forces */
847 potential_force_calc(moldyn);
849 /* some stupid checks before we actually start calculating bullshit */
850 if(moldyn->cutoff>0.5*moldyn->dim.x)
851 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
852 if(moldyn->cutoff>0.5*moldyn->dim.y)
853 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
854 if(moldyn->cutoff>0.5*moldyn->dim.z)
855 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
856 ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
857 if(ds>0.05*moldyn->nnd)
858 printf("[moldyn] warning: forces too high / tau too small!\n");
860 /* zero absolute time */
863 /* debugging, ignore */
866 /* executing the schedule */
867 for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
869 /* setting amount of runs and finite time step size */
870 moldyn->tau=sched->tau[sched->count];
871 moldyn->tau_square=moldyn->tau*moldyn->tau;
872 moldyn->time_steps=sched->runs[sched->count];
874 /* integration according to schedule */
876 for(i=0;i<moldyn->time_steps;i++) {
878 /* integration step */
879 moldyn->integrate(moldyn);
882 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
883 scale_velocity(moldyn,FALSE);
884 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
885 scale_volume(moldyn);
887 /* check for log & visualization */
892 moldyn->time,update_e_kin(moldyn),
894 get_total_energy(moldyn));
898 p=get_total_p(moldyn);
900 "%f %f\n",moldyn->time,v3_norm(&p));
905 snprintf(dir,128,"%s/s-%07.f.save",
906 moldyn->vlsdir,moldyn->time);
907 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
908 if(fd<0) perror("[moldyn] save fd open");
910 write(fd,moldyn,sizeof(t_moldyn));
911 write(fd,moldyn->atom,
912 moldyn->count*sizeof(t_atom));
919 visual_atoms(&(moldyn->vis),moldyn->time,
920 moldyn->atom,moldyn->count);
921 printf("\rsched: %d, steps: %d, debug: %d",
922 sched->count,i,moldyn->debug);
927 /* increase absolute time */
928 moldyn->time+=moldyn->tau;
932 /* check for hooks */
934 sched->hook(moldyn,sched->hook_params);
936 /* get a new info line */
944 /* velocity verlet */
946 int velocity_verlet(t_moldyn *moldyn) {
949 double tau,tau_square;
956 tau_square=moldyn->tau_square;
958 for(i=0;i<count;i++) {
960 v3_scale(&delta,&(atom[i].v),tau);
961 v3_add(&(atom[i].r),&(atom[i].r),&delta);
962 v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
963 v3_add(&(atom[i].r),&(atom[i].r),&delta);
964 check_per_bound(moldyn,&(atom[i].r));
967 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
968 v3_add(&(atom[i].v),&(atom[i].v),&delta);
971 /* neighbour list update */
972 link_cell_update(moldyn);
974 /* forces depending on chosen potential */
975 potential_force_calc(moldyn);
977 for(i=0;i<count;i++) {
978 /* again velocities */
979 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
980 v3_add(&(atom[i].v),&(atom[i].v),&delta);
989 * potentials & corresponding forces
993 /* generic potential and force calculation */
995 int potential_force_calc(t_moldyn *moldyn) {
998 t_atom *itom,*jtom,*ktom;
1001 t_list neighbour_i[27];
1002 t_list neighbour_i2[27];
1007 count=moldyn->count;
1014 /* get energy and force of every atom */
1015 for(i=0;i<count;i++) {
1018 v3_zero(&(itom[i].f));
1020 /* reset viral of atom i */
1021 virial=&(itom[i].virial);
1029 /* reset site energy */
1032 /* single particle potential/force */
1033 if(itom[i].attr&ATOM_ATTR_1BP)
1034 moldyn->func1b(moldyn,&(itom[i]));
1036 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
1039 /* 2 body pair potential/force */
1041 link_cell_neighbour_index(moldyn,
1042 (itom[i].r.x+moldyn->dim.x/2)/lc->x,
1043 (itom[i].r.y+moldyn->dim.y/2)/lc->y,
1044 (itom[i].r.z+moldyn->dim.z/2)/lc->z,
1051 this=&(neighbour_i[j]);
1054 if(this->start==NULL)
1060 jtom=this->current->data;
1062 if(jtom==&(itom[i]))
1065 if((jtom->attr&ATOM_ATTR_2BP)&
1066 (itom[i].attr&ATOM_ATTR_2BP)) {
1067 moldyn->func2b(moldyn,
1073 /* 3 body potential/force */
1075 if(!(itom[i].attr&ATOM_ATTR_3BP)||
1076 !(jtom->attr&ATOM_ATTR_3BP))
1079 /* copy the neighbour lists */
1080 memcpy(neighbour_i2,neighbour_i,
1083 /* get neighbours of i */
1086 that=&(neighbour_i2[k]);
1089 if(that->start==NULL)
1096 ktom=that->current->data;
1098 if(!(ktom->attr&ATOM_ATTR_3BP))
1104 if(ktom==&(itom[i]))
1107 moldyn->func3b(moldyn,
1113 } while(list_next_f(that)!=\
1118 /* 2bp post function */
1119 if(moldyn->func2b_post) {
1120 moldyn->func2b_post(moldyn,
1125 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1141 * periodic boundayr checking
1144 inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1155 if(moldyn->status&MOLDYN_STAT_PBX) {
1156 if(a->x>=x) a->x-=dim->x;
1157 else if(-a->x>x) a->x+=dim->x;
1159 if(moldyn->status&MOLDYN_STAT_PBY) {
1160 if(a->y>=y) a->y-=dim->y;
1161 else if(-a->y>y) a->y+=dim->y;
1163 if(moldyn->status&MOLDYN_STAT_PBZ) {
1164 if(a->z>=z) a->z-=dim->z;
1165 else if(-a->z>z) a->z+=dim->z;
1173 * example potentials
1176 /* harmonic oscillator potential and force */
1178 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1180 t_ho_params *params;
1181 t_3dvec force,distance;
1183 double sc,equi_dist;
1185 params=moldyn->pot2b_params;
1186 sc=params->spring_constant;
1187 equi_dist=params->equilibrium_distance;
1189 v3_sub(&distance,&(aj->r),&(ai->r));
1191 if(bc) check_per_bound(moldyn,&distance);
1192 d=v3_norm(&distance);
1193 if(d<=moldyn->cutoff) {
1194 /* energy is 1/2 (d-d0)^2, but we will add this twice ... */
1195 moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
1196 /* f = -grad E; grad r_ij = -1 1/r_ij distance */
1197 v3_scale(&force,&distance,sc*(1.0-(equi_dist/d)));
1198 v3_add(&(ai->f),&(ai->f),&force);
1204 /* lennard jones potential & force for one sort of atoms */
1206 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1208 t_lj_params *params;
1209 t_3dvec force,distance;
1211 double eps,sig6,sig12;
1213 params=moldyn->pot2b_params;
1214 eps=params->epsilon4;
1215 sig6=params->sigma6;
1216 sig12=params->sigma12;
1218 v3_sub(&distance,&(aj->r),&(ai->r));
1219 if(bc) check_per_bound(moldyn,&distance);
1220 d=v3_absolute_square(&distance); /* 1/r^2 */
1221 if(d<=moldyn->cutoff_square) {
1222 d=1.0/d; /* 1/r^2 */
1225 h1=h2*h2; /* 1/r^12 */
1226 /* energy is eps*..., but we will add this twice ... */
1227 moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
1234 v3_scale(&force,&distance,-1.0*d); /* f = - grad E */
1235 v3_add(&(ai->f),&(ai->f),&force);
1242 * tersoff potential & force for 2 sorts of atoms
1245 /* create mixed terms from parameters and set them */
1246 int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
1248 printf("[moldyn] tersoff parameter completion\n");
1249 p->S2[0]=p->S[0]*p->S[0];
1250 p->S2[1]=p->S[1]*p->S[1];
1251 p->Smixed=sqrt(p->S[0]*p->S[1]);
1252 p->S2mixed=p->Smixed*p->Smixed;
1253 p->Rmixed=sqrt(p->R[0]*p->R[1]);
1254 p->Amixed=sqrt(p->A[0]*p->A[1]);
1255 p->Bmixed=sqrt(p->B[0]*p->B[1]);
1256 p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
1257 p->mu_m=0.5*(p->mu[0]+p->mu[1]);
1259 printf("[moldyn] tersoff mult parameter info:\n");
1260 printf(" S (A) | %f | %f | %f\n",p->S[0],p->S[1],p->Smixed);
1261 printf(" R (A) | %f | %f | %f\n",p->R[0],p->R[1],p->Rmixed);
1262 printf(" A (eV) | %f | %f | %f\n",p->A[0]/EV,p->A[1]/EV,p->Amixed/EV);
1263 printf(" B (eV) | %f | %f | %f\n",p->B[0]/EV,p->B[1]/EV,p->Bmixed/EV);
1264 printf(" lambda | %f | %f | %f\n",p->lambda[0],p->lambda[1],
1266 printf(" mu | %f | %f | %f\n",p->mu[0],p->mu[1],p->mu_m);
1267 printf(" beta | %.10f | %.10f\n",p->beta[0],p->beta[1]);
1268 printf(" n | %f | %f\n",p->n[0],p->n[1]);
1269 printf(" c | %f | %f\n",p->c[0],p->c[1]);
1270 printf(" d | %f | %f\n",p->d[0],p->d[1]);
1271 printf(" h | %f | %f\n",p->h[0],p->h[1]);
1272 printf(" chi | %f \n",p->chi);
1277 /* tersoff 1 body part */
1278 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
1281 t_tersoff_mult_params *params;
1282 t_tersoff_exchange *exchange;
1285 params=moldyn->pot1b_params;
1286 exchange=&(params->exchange);
1289 * simple: point constant parameters only depending on atom i to
1290 * their right values
1293 exchange->beta_i=&(params->beta[brand]);
1294 exchange->n_i=&(params->n[brand]);
1295 exchange->c_i=&(params->c[brand]);
1296 exchange->d_i=&(params->d[brand]);
1297 exchange->h_i=&(params->h[brand]);
1299 exchange->betaini=pow(*(exchange->beta_i),*(exchange->n_i));
1300 exchange->ci2=params->c[brand]*params->c[brand];
1301 exchange->di2=params->d[brand]*params->d[brand];
1302 exchange->ci2di2=exchange->ci2/exchange->di2;
1307 /* tersoff 2 body part */
1308 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1310 t_tersoff_mult_params *params;
1311 t_tersoff_exchange *exchange;
1312 t_3dvec dist_ij,force;
1314 double A,B,R,S,S2,lambda,mu;
1321 params=moldyn->pot2b_params;
1323 exchange=&(params->exchange);
1325 /* clear 3bp and 2bp post run */
1327 exchange->run2bp_post=0;
1329 /* reset S > r > R mark */
1330 exchange->d_ij_between_rs=0;
1333 * calc of 2bp contribution of V_ij and dV_ij/ji
1335 * for Vij and dV_ij we need:
1339 * for dV_ji we need:
1340 * - f_c_ji = f_c_ij, df_c_ji = df_c_ij
1341 * - f_r_ji = f_r_ij; df_r_ji = df_r_ij
1346 if(brand==ai->brand) {
1348 S2=params->S2[brand];
1352 lambda=params->lambda[brand];
1353 mu=params->mu[brand];
1362 lambda=params->lambda_m;
1364 params->exchange.chi=params->chi;
1368 v3_sub(&dist_ij,&(aj->r),&(ai->r));
1369 if(bc) check_per_bound(moldyn,&dist_ij);
1370 d_ij2=v3_absolute_square(&dist_ij);
1372 /* if d_ij2 > S2 => no force & potential energy contribution */
1376 /* now we will need the distance */
1377 //d_ij=v3_norm(&dist_ij);
1380 /* save for use in 3bp */
1381 exchange->d_ij=d_ij;
1382 exchange->d_ij2=d_ij2;
1383 exchange->dist_ij=dist_ij;
1385 /* more constants */
1386 exchange->beta_j=&(params->beta[brand]);
1387 exchange->n_j=&(params->n[brand]);
1388 exchange->c_j=&(params->c[brand]);
1389 exchange->d_j=&(params->d[brand]);
1390 exchange->h_j=&(params->h[brand]);
1391 if(brand==ai->brand) {
1392 exchange->betajnj=exchange->betaini;
1393 exchange->cj2=exchange->ci2;
1394 exchange->dj2=exchange->di2;
1395 exchange->cj2dj2=exchange->ci2di2;
1398 exchange->betajnj=pow(*(exchange->beta_j),*(exchange->n_j));
1399 exchange->cj2=params->c[brand]*params->c[brand];
1400 exchange->dj2=params->d[brand]*params->d[brand];
1401 exchange->cj2dj2=exchange->cj2/exchange->dj2;
1404 /* f_r_ij = f_r_ji, df_r_ij = df_r_ji */
1405 f_r=A*exp(-lambda*d_ij);
1406 df_r=lambda*f_r/d_ij;
1408 /* f_a, df_a calc (again, same for ij and ji) | save for later use! */
1409 exchange->f_a=-B*exp(-mu*d_ij);
1410 exchange->df_a=mu*exchange->f_a/d_ij;
1412 /* f_c, df_c calc (again, same for ij and ji) */
1414 /* f_c = 1, df_c = 0 */
1417 /* two body contribution (ij, ji) */
1418 v3_scale(&force,&dist_ij,-df_r);
1422 arg=M_PI*(d_ij-R)/s_r;
1423 f_c=0.5+0.5*cos(arg);
1424 df_c=0.5*sin(arg)*(M_PI/(s_r*d_ij));
1425 /* two body contribution (ij, ji) */
1426 v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
1427 /* tell 3bp that S > r > R */
1428 exchange->d_ij_between_rs=1;
1431 /* add forces of 2bp (ij, ji) contribution
1432 * dVij = dVji and we sum up both: no 1/2) */
1433 v3_add(&(ai->f),&(ai->f),&force);
1436 ai->virial.xx-=force.x*dist_ij.x;
1437 ai->virial.yy-=force.y*dist_ij.y;
1438 ai->virial.zz-=force.z*dist_ij.z;
1439 ai->virial.xy-=force.x*dist_ij.y;
1440 ai->virial.xz-=force.x*dist_ij.z;
1441 ai->virial.yz-=force.y*dist_ij.z;
1444 if(ai==&(moldyn->atom[0])) {
1445 printf("dVij, dVji (2bp) contrib:\n");
1446 printf("%f | %f\n",force.x,ai->f.x);
1447 printf("%f | %f\n",force.y,ai->f.y);
1448 printf("%f | %f\n",force.z,ai->f.z);
1452 if(ai==&(moldyn->atom[0])) {
1453 printf("dVij, dVji (2bp) contrib:\n");
1454 printf("%f | %f\n",force.x*dist_ij.x,ai->virial.xx);
1455 printf("%f | %f\n",force.y*dist_ij.y,ai->virial.yy);
1456 printf("%f | %f\n",force.z*dist_ij.z,ai->virial.zz);
1460 /* energy 2bp contribution (ij, ji) is 0.5 f_r f_c ... */
1461 moldyn->energy+=(0.5*f_r*f_c);
1463 /* save for use in 3bp */
1465 exchange->df_c=df_c;
1467 /* enable the run of 3bp function and 2bp post processing */
1469 exchange->run2bp_post=1;
1471 /* reset 3bp sums */
1472 exchange->zeta_ij=0.0;
1473 exchange->zeta_ji=0.0;
1474 v3_zero(&(exchange->dzeta_ij));
1475 v3_zero(&(exchange->dzeta_ji));
1480 /* tersoff 2 body post part */
1482 int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1485 * here we have to allow for the 3bp sums
1488 * - zeta_ij, dzeta_ij
1489 * - zeta_ji, dzeta_ji
1491 * to compute the 3bp contribution to:
1497 t_tersoff_mult_params *params;
1498 t_tersoff_exchange *exchange;
1503 double f_c,df_c,f_a,df_a;
1504 double chi,ni,betaini,nj,betajnj;
1507 params=moldyn->pot2b_params;
1508 exchange=&(params->exchange);
1510 /* we do not run if f_c_ij was detected to be 0! */
1511 if(!(exchange->run2bp_post))
1515 df_c=exchange->df_c;
1517 df_a=exchange->df_a;
1518 betaini=exchange->betaini;
1519 betajnj=exchange->betajnj;
1520 ni=*(exchange->n_i);
1521 nj=*(exchange->n_j);
1523 dist_ij=&(exchange->dist_ij);
1526 zeta=exchange->zeta_ij;
1528 moldyn->debug++; /* just for debugging ... */
1531 v3_scale(&force,dist_ij,df_a*b*f_c);
1534 tmp=betaini*pow(zeta,ni-1.0); /* beta^n * zeta^n-1 */
1535 b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
1536 db=chi*pow(b,-1.0/(2*ni)-1); /* x(...)^(-1/2n - 1) */
1538 db*=-0.5*tmp; /* db_ij */
1539 v3_scale(&force,&(exchange->dzeta_ij),f_a*db);
1540 v3_scale(&temp,dist_ij,df_a*b);
1541 v3_add(&force,&force,&temp);
1542 v3_scale(&force,&force,f_c);
1544 v3_scale(&temp,dist_ij,df_c*b*f_a);
1545 v3_add(&force,&force,&temp);
1546 v3_scale(&force,&force,-0.5);
1549 v3_add(&(ai->f),&(ai->f),&force);
1552 ai->virial.xx-=force.x*dist_ij->x;
1553 ai->virial.yy-=force.y*dist_ij->y;
1554 ai->virial.zz-=force.z*dist_ij->z;
1555 ai->virial.xy-=force.x*dist_ij->y;
1556 ai->virial.xz-=force.x*dist_ij->z;
1557 ai->virial.yz-=force.y*dist_ij->z;
1560 if(ai==&(moldyn->atom[0])) {
1561 printf("dVij (3bp) contrib:\n");
1562 printf("%f | %f\n",force.x,ai->f.x);
1563 printf("%f | %f\n",force.y,ai->f.y);
1564 printf("%f | %f\n",force.z,ai->f.z);
1568 if(ai==&(moldyn->atom[0])) {
1569 printf("dVij (3bp) contrib:\n");
1570 printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
1571 printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
1572 printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
1576 /* add energy of 3bp sum */
1577 moldyn->energy+=(0.5*f_c*b*f_a);
1580 zeta=exchange->zeta_ji;
1584 v3_scale(&force,dist_ij,df_a*b*f_c);
1587 tmp=betajnj*pow(zeta,nj-1.0); /* beta^n * zeta^n-1 */
1588 b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
1589 db=chi*pow(b,-1.0/(2*nj)-1); /* x(...)^(-1/2n - 1) */
1591 db*=-0.5*tmp; /* db_ij */
1592 v3_scale(&force,&(exchange->dzeta_ji),f_a*db);
1593 v3_scale(&temp,dist_ij,df_a*b);
1594 v3_add(&force,&force,&temp);
1595 v3_scale(&force,&force,f_c);
1597 v3_scale(&temp,dist_ij,df_c*b*f_a);
1598 v3_add(&force,&force,&temp);
1599 v3_scale(&force,&force,-0.5);
1602 v3_add(&(ai->f),&(ai->f),&force);
1604 /* virial - plus sign, as dist_ij = - dist_ji - (really??) */
1605 ai->virial.xx+=force.x*dist_ij->x;
1606 ai->virial.yy+=force.y*dist_ij->y;
1607 ai->virial.zz+=force.z*dist_ij->z;
1608 ai->virial.xy+=force.x*dist_ij->y;
1609 ai->virial.xz+=force.x*dist_ij->z;
1610 ai->virial.yz+=force.y*dist_ij->z;
1613 if(ai==&(moldyn->atom[0])) {
1614 printf("dVji (3bp) contrib:\n");
1615 printf("%f | %f\n",force.x,ai->f.x);
1616 printf("%f | %f\n",force.y,ai->f.y);
1617 printf("%f | %f\n",force.z,ai->f.z);
1621 if(ai==&(moldyn->atom[0])) {
1622 printf("dVji (3bp) contrib:\n");
1623 printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
1624 printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
1625 printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
1632 /* tersoff 3 body part */
1634 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
1636 t_tersoff_mult_params *params;
1637 t_tersoff_exchange *exchange;
1638 t_3dvec dist_ij,dist_ik,dist_jk;
1639 t_3dvec temp1,temp2;
1643 double d_ij,d_ik,d_jk,d_ij2,d_ik2,d_jk2;
1646 double f_c_ik,df_c_ik,arg;
1650 double cos_theta,d_costheta1,d_costheta2;
1651 double h_cos,d2_h_cos2;
1652 double frac,g,zeta,chi;
1656 params=moldyn->pot3b_params;
1657 exchange=&(params->exchange);
1659 if(!(exchange->run3bp))
1663 * calc of 3bp contribution of V_ij and dV_ij/ji/jk &
1664 * 2bp contribution of dV_jk
1666 * for Vij and dV_ij we still need:
1667 * - b_ij, db_ij (zeta_ij)
1668 * - f_c_ik, df_c_ik, constants_i, cos_theta_ijk, d_costheta_ijk
1670 * for dV_ji we still need:
1671 * - b_ji, db_ji (zeta_ji)
1672 * - f_c_jk, d_c_jk, constants_j, cos_theta_jik, d_costheta_jik
1674 * for dV_jk we need:
1678 * - f_c_ji, df_c_ji, constants_j, cos_theta_jki, d_costheta_jki
1686 /* dist_ij, d_ij - this is < S_ij ! */
1687 dist_ij=exchange->dist_ij;
1688 d_ij=exchange->d_ij;
1689 d_ij2=exchange->d_ij2;
1691 /* f_c_ij, df_c_ij (same for ji) */
1693 df_c=exchange->df_c;
1696 * calculate unknown values now ...
1699 /* V_ij and dV_ij stuff (in b_ij there is f_c_ik) */
1702 v3_sub(&dist_ik,&(ak->r),&(ai->r));
1703 if(bc) check_per_bound(moldyn,&dist_ik);
1704 d_ik2=v3_absolute_square(&dist_ik);
1708 if(brand==ak->brand) {
1711 S2=params->S2[brand];
1719 /* zeta_ij/dzeta_ij contribution only for d_ik < S */
1722 /* now we need d_ik */
1725 /* get constants_i from exchange data */
1732 c2d2=exchange->ci2di2;
1734 /* cosine of theta_ijk by scalaproduct */
1735 rr=v3_scalar_product(&dist_ij,&dist_ik);
1741 d_costheta1=cos_theta/d_ij2-tmp;
1742 d_costheta2=cos_theta/d_ik2-tmp;
1744 /* some usefull values */
1745 h_cos=(h-cos_theta);
1746 d2_h_cos2=d2+(h_cos*h_cos);
1747 frac=c2/(d2_h_cos2);
1752 /* d_costheta_ij and dg(cos_theta) - needed in any case! */
1753 v3_scale(&temp1,&dist_ij,d_costheta1);
1754 v3_scale(&temp2,&dist_ik,d_costheta2);
1755 v3_add(&temp1,&temp1,&temp2);
1756 v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
1758 /* f_c_ik & df_c_ik + {d,}zeta contribution */
1759 dzeta=&(exchange->dzeta_ij);
1763 // => df_c_ik=0.0; of course we do not set this!
1766 exchange->zeta_ij+=g;
1769 v3_add(dzeta,dzeta,&temp1);
1774 arg=M_PI*(d_ik-R)/s_r;
1775 f_c_ik=0.5+0.5*cos(arg);
1776 df_c_ik=0.5*sin(arg)*(M_PI/(s_r*d_ik));
1779 exchange->zeta_ij+=f_c_ik*g;
1782 v3_scale(&temp1,&temp1,f_c_ik);
1783 v3_scale(&temp2,&dist_ik,g*df_c_ik);
1784 v3_add(&temp1,&temp1,&temp2);
1785 v3_add(dzeta,dzeta,&temp1);
1789 /* dV_ji stuff (in b_ji there is f_c_jk) + dV_jk stuff! */
1792 v3_sub(&dist_jk,&(ak->r),&(aj->r));
1793 if(bc) check_per_bound(moldyn,&dist_jk);
1794 d_jk2=v3_absolute_square(&dist_jk);
1798 if(brand==ak->brand) {
1801 S2=params->S2[brand];
1803 mu=params->mu[brand];
1815 /* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */
1818 /* now we need d_ik */
1821 /* constants_j from exchange data */
1828 c2d2=exchange->cj2dj2;
1830 /* cosine of theta_jik by scalaproduct */
1831 rr=-v3_scalar_product(&dist_ij,&dist_jk); /* -1, as ij -> ji */
1837 d_costheta2=cos_theta/d_ij2;
1839 /* some usefull values */
1840 h_cos=(h-cos_theta);
1841 d2_h_cos2=d2+(h_cos*h_cos);
1842 frac=c2/(d2_h_cos2);
1847 /* d_costheta_jik and dg(cos_theta) - needed in any case! */
1848 v3_scale(&temp1,&dist_jk,d_costheta1);
1849 v3_scale(&temp2,&dist_ij,-d_costheta2); /* ji -> ij => -1 */
1850 //v3_add(&temp1,&temp1,&temp2);
1851 v3_sub(&temp1,&temp1,&temp2); /* there is a minus! */
1852 v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
1854 /* store dg in temp2 and use it for dVjk later */
1855 v3_copy(&temp2,&temp1);
1857 /* f_c_jk + {d,}zeta contribution (df_c_jk = 0) */
1858 dzeta=&(exchange->dzeta_ji);
1864 exchange->zeta_ji+=g;
1867 v3_add(dzeta,dzeta,&temp1);
1872 arg=M_PI*(d_jk-R)/s_r;
1873 f_c_jk=0.5+0.5*cos(arg);
1876 exchange->zeta_ji+=f_c_jk*g;
1879 v3_scale(&temp1,&temp1,f_c_jk);
1880 v3_add(dzeta,dzeta,&temp1);
1883 /* dV_jk stuff | add force contribution on atom i immediately */
1884 if(exchange->d_ij_between_rs) {
1886 v3_scale(&temp1,&temp2,f_c);
1887 v3_scale(&temp2,&dist_ij,df_c*g);
1888 v3_add(&temp2,&temp2,&temp1); /* -> dzeta_jk in temp2 */
1892 // dzeta_jk is simply dg, which is stored in temp2
1894 /* betajnj * zeta_jk ^ nj-1 */
1895 tmp=exchange->betajnj*pow(zeta,(n-1.0));
1896 tmp=-chi/2.0*pow((1+tmp*zeta),(-1.0/(2.0*n)-1))*tmp;
1897 v3_scale(&temp2,&temp2,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
1898 v3_add(&(ai->f),&(ai->f),&temp2); /* -1 skipped in f_a calc ^ */
1899 /* scaled with 0.5 ^ */
1902 ai->virial.xx-=temp2.x*dist_jk.x;
1903 ai->virial.yy-=temp2.y*dist_jk.y;
1904 ai->virial.zz-=temp2.z*dist_jk.z;
1905 ai->virial.xy-=temp2.x*dist_jk.y;
1906 ai->virial.xz-=temp2.x*dist_jk.z;
1907 ai->virial.yz-=temp2.y*dist_jk.z;
1910 if(ai==&(moldyn->atom[0])) {
1911 printf("dVjk (3bp) contrib:\n");
1912 printf("%f | %f\n",temp2.x,ai->f.x);
1913 printf("%f | %f\n",temp2.y,ai->f.y);
1914 printf("%f | %f\n",temp2.z,ai->f.z);
1918 if(ai==&(moldyn->atom[0])) {
1919 printf("dVjk (3bp) contrib:\n");
1920 printf("%f | %f\n",temp2.x*dist_jk.x,ai->virial.xx);
1921 printf("%f | %f\n",temp2.y*dist_jk.y,ai->virial.yy);
1922 printf("%f | %f\n",temp2.z*dist_jk.z,ai->virial.zz);
1933 * debugging / critical check functions
1936 int moldyn_bc_check(t_moldyn *moldyn) {
1949 for(i=0;i<moldyn->count;i++) {
1950 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
1951 printf("FATAL: atom %d: x: %.20f (%.20f)\n",
1952 i,atom[i].r.x,dim->x/2);
1953 printf("diagnostic:\n");
1954 printf("-----------\natom.r.x:\n");
1956 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
1959 ((byte)&(1<<k))?1:0,
1962 printf("---------------\nx=dim.x/2:\n");
1964 memcpy(&byte,(u8 *)(&x)+j,1);
1967 ((byte)&(1<<k))?1:0,
1970 if(atom[i].r.x==x) printf("the same!\n");
1971 else printf("different!\n");
1973 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
1974 printf("FATAL: atom %d: y: %.20f (%.20f)\n",
1975 i,atom[i].r.y,dim->y/2);
1976 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
1977 printf("FATAL: atom %d: z: %.20f (%.20f)\n",
1978 i,atom[i].r.z,dim->z/2);