moldyn.c

   1 /*
   2  * moldyn.c - molecular dynamics library main file
   3  *
   4  * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
   5  *
   6  */
   7
   8 #define _GNU_SOURCE
   9 #include <stdio.h>
  10 #include <stdlib.h>
  11 #include <string.h>
  12 #include <sys/types.h>
  13 #include <sys/stat.h>
  14 #include <fcntl.h>
  15 #include <unistd.h>
  16 #include <math.h>
  17
  18 #include "moldyn.h"
  19
  20 #include "math/math.h"
  21 #include "init/init.h"
  22 #include "random/random.h"
  23 #include "visual/visual.h"
  24 #include "list/list.h"
  25
  26
  27 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
  28
  29         //int ret;
  30
  31         //ret=moldyn_parse_argv(moldyn,argc,argv);
  32         //if(ret<0) return ret;
  33
  34         memset(moldyn,0,sizeof(t_moldyn));
  35
  36         rand_init(&(moldyn->random),NULL,1);
  37         moldyn->random.status|=RAND_STAT_VERBOSE;
  38
  39         return 0;
  40 }
  41
  42 int moldyn_shutdown(t_moldyn *moldyn) {
  43
  44         link_cell_shutdown(moldyn);
  45         moldyn_log_shutdown(moldyn);
  46         rand_close(&(moldyn->random));
  47         free(moldyn->atom);
  48
  49         return 0;
  50 }
  51
  52 int set_int_alg(t_moldyn *moldyn,u8 algo) {
  53
  54         switch(alg) {
  55                 case 'MOLDYN_INTEGRATE_VERLET':
  56                         moldyn->integrate=velocity_verlet;
  57                         break;
  58                 default:
  59                         printf("unknown integration algorithm: %02x\",alg);
  60                         return -1;
  61         }
  62
  63         return 0;
  64 }
  65
  66 int set_cutoff(t_moldyn *moldyn,double cutoff) {
  67
  68         moldyn->cutoff=cutoff;
  69
  70         return 0;
  71 }
  72
  73 int set_temperature(t_moldyn *moldyn,double t) {
  74
  75         moldyn->t=t;
  76
  77         return 0;
  78 }
  79
  80 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
  81
  82         moldyn->dim.x=x;
  83         moldyn->dim.y=y;
  84         moldyn->dim.z=z;
  85
  86         if(visualize) {
  87                 moldyn->vis.dim.x=x;
  88                 moldyn->vis.dim.y=y;
  89                 moldyn->vis.dim.z=z;
  90         }
  91
  92         return 0;
  93 }
  94
  95 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
  96
  97         if(x)
  98                 moldyn->status|=MOLDYN_STAT_PBX;
  99
 100         if(y)
 101                 moldyn->status|=MOLDYN_STAT_PBY;
 102
 103         if(z)
 104                 moldyn->status|=MOLDYN_STAT_PBZ;
 105
 106         return 0;
 107 }
 108
 109 int set_potential(t_moldyn *moldyn,u8 type,(int *)(func),void *params) {
 110
 111         switch(type) {
 112                 case MOLDYN_1BP:
 113                         moldyn->pf_func1b=func;
 114                         moldyn->pot1b_params=params;
 115                         break;
 116                 case MOLDYN_2BP:
 117                         moldyn->pf_func2b=func;
 118                         moldyn->pot2b_params=params;
 119                         break;
 120                 case MOLDYN_3BP:
 121                         moldyn->pf_func3b=func;
 122                         moldyn->pot3b_params=params;
 123                         break;
 124                 default:
 125                         printf("unknown potential type: %02x\n",type);
 126                         return -1;
 127         }
 128
 129         return 0;
 130 }
 131
 132 int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
 133
 134         switch(type) {
 135                 case LOG_TOTAL_ENERGY:
 136                         moldyn->ewrite=timer;
 137                         moldyn->efd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
 138                         if(moldyn->efd<0) {
 139                                 perror("[moldyn] efd open");
 140                                 return moldyn->efd;
 141                         }
 142                         dprintf("# moldyn total energy log file\n");
 143                         break;
 144                 case LOG_TOTAL_MOMENTUM:
 145                         moldyn->mwrite=timer;
 146                         moldyn->mfd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
 147                         if(moldyn->mfd<0) {
 148                                 perror("[moldyn] mfd open");
 149                                 return moldyn->mfd;
 150                         }
 151                         dprintf("# moldyn total momentum log file\n");
 152                         break;
 153                 case SAVE_STEP:
 154                         moldyn->swrite=timer;
 155                         strncpy(moldyn->sfb,fb,63);
 156                         break;
 157                 case VISUAL_STEP:
 158                         moldyn->mwrite=timer;
 159                         strncpy(moldyn->vfb,fb,63);
 160                         visual_init(&(moldyn->vis),fb);
 161                         break;
 162                 default:
 163                         printf("unknown log mechanism: %02x\n",type);
 164                         return -1;
 165         }
 166
 167         return 0;
 168 }
 169
 170 int moldyn_log_shutdown(t_moldyn *moldyn) {
 171
 172         if(moldyn->efd) close(moldyn->efd);
 173         if(moldyn->mfd) close(moldyn->mfd);
 174         if(moldyn->visual) visual_tini(moldyn->visual);
 175
 176         return 0;
 177 }
 178
 179 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 180                    u8 attr,u8 bnum,int a,int b,int c) {
 181
 182         int count;
 183         int ret;
 184         t_3dvec origin;
 185         t_atom *atom;
 186
 187         count=a*b*c;
 188         atom=moldyn->atom;
 189
 190         if(type==FCC) count*=4;
 191
 192         if(type==DIAMOND) count*=8;
 193
 194         atom=malloc(count*sizeof(t_atom));
 195         if(atom==NULL) {
 196                 perror("malloc (atoms)");
 197                 return -1;
 198         }
 199
 200         v3_zero(&origin);
 201
 202         switch(type) {
 203                 case FCC:
 204                         ret=fcc_init(a,b,c,lc,atom,&origin);
 205                         break;
 206                 case DIAMOND:
 207                         ret=diamond_init(a,b,c,lc,atom,&origin);
 208                         break;
 209                 default:
 210                         printf("unknown lattice type (%02x)\n",type);
 211                         return -1;
 212         }
 213
 214         /* debug */
 215         if(ret!=count) {
 216                 printf("ok, there is something wrong ...\n");
 217                 printf("calculated -> %d atoms\n",count);
 218                 printf("created -> %d atoms\n",ret);
 219                 return -1;
 220         }
 221
 222         moldyn->count=count;
 223
 224         while(count) {
 225                 atom[count-1].element=element;
 226                 atom[count-1].mass=mass;
 227                 atom[count-1].attr=attr;
 228                 atom[count-1].bnum=bnum;
 229                 count-=1;
 230         }
 231
 232         return ret;
 233 }
 234
 235 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
 236              t_3dvec r,t_3dvec v) {
 237
 238         t_atom *atom;
 239         void *ptr;
 240         int count;
 241
 242         atom=moldyn->atom;
 243         count=++(moldyn->count);
 244
 245         ptr=realloc(atom,count*sizeof(t_atom));
 246         if(!ptr) {
 247                 perror("[moldyn] realloc (add atom)");
 248                 return -1;
 249         }
 250
 251         atom=ptr;
 252         atom->r=r;
 253         atom->v=v;
 254         atom->element=element;
 255         atom->bnum=bnum;
 256         atom->attr=attr;
 257
 258         return 0;
 259 }
 260
 261 int destroy_atoms(t_moldyn *moldyn) {
 262
 263         if(moldyn->atom) free(moldyn->atom);
 264
 265         return 0;
 266 }
 267
 268 int thermal_init(t_moldyn *moldyn) {
 269
 270         /*
 271          * - gaussian distribution of velocities
 272          * - zero total momentum
 273          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 274          */
 275
 276         int i;
 277         double v,sigma;
 278         t_3dvec p_total,delta;
 279         t_atom *atom;
 280         t_random *random;
 281
 282         atom=moldyn->atom;
 283         random=&(moldyn->random);
 284
 285         /* gaussian distribution of velocities */
 286         v3_zero(&p_total);
 287         for(i=0;i<moldyn->count;i++) {
 288                 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t/atom[i].mass);
 289                 /* x direction */
 290                 v=sigma*rand_get_gauss(random);
 291                 atom[i].v.x=v;
 292                 p_total.x+=atom[i].mass*v;
 293                 /* y direction */
 294                 v=sigma*rand_get_gauss(random);
 295                 atom[i].v.y=v;
 296                 p_total.y+=atom[i].mass*v;
 297                 /* z direction */
 298                 v=sigma*rand_get_gauss(random);
 299                 atom[i].v.z=v;
 300                 p_total.z+=atom[i].mass*v;
 301         }
 302
 303         /* zero total momentum */
 304         v3_scale(&p_total,&p_total,1.0/moldyn->count);
 305         for(i=0;i<moldyn->count;i++) {
 306                 v3_scale(&delta,&p_total,1.0/atom[i].mass);
 307                 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
 308         }
 309
 310         /* velocity scaling */
 311         scale_velocity(moldyn);
 312
 313         return 0;
 314 }
 315
 316 int scale_velocity(t_moldyn *moldyn) {
 317
 318         int i;
 319         double e,c;
 320         t_atom *atom;
 321
 322         atom=moldyn->atom;
 323
 324         /*
 325          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 326          */
 327         e=0.0;
 328         for(i=0;i<moldyn->count;i++)
 329                 e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 330         c=sqrt((2.0*e)/(3.0*moldyn->count*K_BOLTZMANN*moldyn->t));
 331         for(i=0;i<moldyn->count;i++)
 332                 v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
 333
 334         return 0;
 335 }
 336
 337 double get_e_kin(t_moldyn *moldyn) {
 338
 339         int i;
 340         t_atom *atom;
 341
 342         atom=moldyn->atom;
 343         moldyn->ekin=0.0;
 344
 345         for(i=0;i<moldyn->count;i++)
 346                 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 347
 348         return moldyn->ekin;
 349 }
 350
 351 double get_e_pot(t_moldyn *moldyn) {
 352
 353         return moldyn->energy;
 354 }
 355
 356 double get_total_energy(t_moldyn *moldyn) {
 357
 358         return(get_e_kin(moldyn)+get_e_pot(moldyn));
 359 }
 360
 361 t_3dvec get_total_p(t_moldyn *moldyn) {
 362
 363         t_3dvec p,p_total;
 364         int i;
 365         t_atom *atom;
 366
 367         atom=moldyn->atom;
 368
 369         v3_zero(&p_total);
 370         for(i=0;i<count;i++) {
 371                 v3_scale(&p,&(atom[i].v),atom[i].mass);
 372                 v3_add(&p_total,&p_total,&p);
 373         }
 374
 375         return p_total;
 376 }
 377
 378 double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
 379
 380         double tau;
 381
 382         tau=0.05*nn_dist/(sqrt(3.0*K_BOLTZMANN*t/moldyn->atom[0].mass));
 383         tau*=1.0E-9;
 384         if(tau<moldyn->tau)
 385                 printf("[moldyn] warning: time step  (%f > %.15f)\n",
 386                        moldyn->tau,tau);
 387
 388         return tau;
 389 }
 390
 391 /*
 392  * numerical tricks
 393  */
 394
 395 /* linked list / cell method */
 396
 397 int link_cell_init(t_moldyn *moldyn) {
 398
 399         t_linkcell *lc;
 400         int i;
 401
 402         lc=&(moldyn->lc);
 403
 404         /* list log fd */
 405         lc->listfd=open("/dev/null",O_WRONLY);
 406
 407         /* partitioning the md cell */
 408         lc->nx=moldyn->dim.x/moldyn->cutoff;
 409         lc->x=moldyn->dim.x/lc->nx;
 410         lc->ny=moldyn->dim.y/moldyn->cutoff;
 411         lc->y=moldyn->dim.y/lc->ny;
 412         lc->nz=moldyn->dim.z/moldyn->cutoff;
 413         lc->z=moldyn->dim.z/lc->nz;
 414
 415         lc->cells=lc->nx*lc->ny*lc->nz;
 416         lc->subcell=malloc(lc->cells*sizeof(t_list));
 417
 418         printf("initializing linked cells (%d)\n",lc->cells);
 419
 420         for(i=0;i<lc->cells;i++)
 421                 //list_init(&(lc->subcell[i]),1);
 422                 list_init(&(lc->subcell[i]));
 423
 424         link_cell_update(moldyn);
 425
 426         return 0;
 427 }
 428
 429 int link_cell_update(t_moldyn *moldyn) {
 430
 431         int count,i,j,k;
 432         int nx,ny,nz;
 433         t_atom *atom;
 434         t_linkcell *lc;
 435
 436         atom=moldyn->atom;
 437         lc=&(moldyn->lc);
 438
 439         nx=lc->nx;
 440         ny=lc->ny;
 441         nz=lc->nz;
 442
 443         for(i=0;i<lc->cells;i++)
 444                 list_destroy(&(moldyn->lc.subcell[i]));
 445
 446         for(count=0;count<moedyn->count;count++) {
 447                 i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
 448                 j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
 449                 k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
 450                 list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
 451                                        &(atom[count]));
 452         }
 453
 454         return 0;
 455 }
 456
 457 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 458
 459         t_linkcell *lc;
 460         int a;
 461         int count1,count2;
 462         int ci,cj,ck;
 463         int nx,ny,nz;
 464         int x,y,z;
 465         u8 bx,by,bz;
 466
 467         lc=&(moldyn->lc);
 468         nx=lc->nx;
 469         ny=lc->ny;
 470         nz=lc->nz;
 471         count1=1;
 472         count2=27;
 473         a=nx*ny;
 474
 475
 476         cell[0]=lc->subcell[i+j*nx+k*a];
 477         for(ci=-1;ci<=1;ci++) {
 478                 bx=0;
 479                 x=i+ci;
 480                 if((x<0)||(x>=nx)) {
 481                         x=(x+nx)%nx;
 482                         bx=1;
 483                 }
 484                 for(cj=-1;cj<=1;cj++) {
 485                         by=0;
 486                         y=j+cj;
 487                         if((y<0)||(y>=ny)) {
 488                                 y=(y+ny)%ny;
 489                                 by=1;
 490                         }
 491                         for(ck=-1;ck<=1;ck++) {
 492                                 bz=0;
 493                                 z=k+ck;
 494                                 if((z<0)||(z>=nz)) {
 495                                         z=(z+nz)%nz;
 496                                         bz=1;
 497                                 }
 498                                 if(!(ci|cj|ck)) continue;
 499                                 if(bx|by|bz) {
 500                                         cell[--count2]=lc->subcell[x+y*nx+z*a];
 501                                 }
 502                                 else {
 503                                         cell[count1++]=lc->subcell[x+y*nx+z*a];
 504                                 }
 505                         }
 506                 }
 507         }
 508
 509         lc->dnlc=count2;
 510         lc->countn=27;
 511
 512         return count2;
 513 }
 514
 515 int link_cell_shutdown(t_moldyn *moldyn) {
 516
 517         int i;
 518         t_linkcell *lc;
 519
 520         lc=&(moldyn->lc);
 521
 522         for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
 523                 list_shutdown(&(moldyn->lc.subcell[i]));
 524
 525         if(lc->listfd) close(lc->listfd);
 526
 527         return 0;
 528 }
 529
 530 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
 531
 532         int count;
 533         void *ptr;
 534         t_moldyn_schedule *schedule;
 535
 536         schedule=moldyn->schedule;
 537         count=++(schedule->content_count);
 538
 539         ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
 540         if(!ptr) {
 541                 perror("[moldyn] realloc (runs)");
 542                 return -1;
 543         }
 544         moldyn->schedule.runs[count-1]=runs;
 545
 546         ptr=realloc(schedule->tau,count*sizeof(double));
 547         if(!ptr) {
 548                 perror("[moldyn] realloc (tau)");
 549                 return -1;
 550         }
 551         moldyn->schedule.tau[count-1]=tau;
 552
 553         return 0;
 554 }
 555
 556 int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
 557
 558         moldyn->schedule.hook=hook;
 559         moldyn->schedule.hook_params=hook_params;
 560
 561         return 0;
 562 }
 563
 564 /*
 565  *
 566  * 'integration of newtons equation' - algorithms
 567  *
 568  */
 569
 570 /* start the integration */
 571
 572 int moldyn_integrate(t_moldyn *moldyn) {
 573
 574         int i,sched;
 575         unsigned int e,m,s,d,v;
 576         t_3dvec p;
 577
 578         int fd;
 579         char fb[128];
 580
 581         /* initialize linked cell method */
 582         link_cell_init(moldyn);
 583
 584         /* logging & visualization */
 585         e=moldyn->ewrite;
 586         m=moldyn->mwrite;
 587         s=moldyn->swrite;
 588         d=moldyn->dwrite;
 589         v=moldyn->vwrite;
 590
 591         if(!(moldyn->lvstat&MOLDYN_LVSTAT_INITIALIZED)) {
 592                 printf("[moldyn] warning, lv system not initialized\n");
 593                 return -1;
 594         }
 595
 596         /* sqaure of some variables */
 597         moldyn->tau_square=moldyn->tau*moldyn->tau;
 598         moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
 599
 600         /* calculate initial forces */
 601         moldyn->potential_force_function(moldyn);
 602
 603         for(sched=0;sched<moldyn->schedule.content_count;sched++) {
 604
 605                 /* setting amont of runs and finite time step size */
 606                 moldyn->tau=schedule->tau[sched];
 607                 moldyn->tau_square=moldyn->tau*moldyn->tau;
 608                 moldyn->timesteps=schedule->runs[sched];
 609
 610         /* integration according to schedule */
 611
 612         for(i=0;i<moldyn->time_steps;i++) {
 613
 614                 /* integration step */
 615                 moldyn->integrate(moldyn);
 616
 617                 /* check for log & visualization */
 618                 if(e) {
 619                         if(!(i%e))
 620                                 dprintf(moldyn->efd,
 621                                         "%.15f %.45f\n",i*moldyn->tau,
 622                                         get_total_energy(moldyn));
 623                 }
 624                 if(m) {
 625                         if(!(i%m)) {
 626                                 p=get_total_p(moldyn->atom,moldyn->count);
 627                                 dprintf(moldyn->mfd,
 628                                         "%.15f %.45f\n",i*moldyn->tau,
 629                                         v3_norm(&p));
 630                         }
 631                 }
 632                 if(s) {
 633                         if(!(i%s)) {
 634                                 snprintf(fb,128,"%s-%f-%.15f.save",moldyn->sfb,
 635                                          moldyn->t,i*moldyn->tau);
 636                                 fd=open(fb,O_WRONLY|O_TRUNC|O_CREAT);
 637                                 if(fd<0) perror("[moldyn] save fd open");
 638                                 else {
 639                                         write(fd,moldyn,sizeof(t_moldyn));
 640                                         write(fd,moldyn->atom,
 641                                               moldyn->count*sizeof(t_atom));
 642                                 }
 643                                 close(fd);
 644                         }
 645                 }
 646                 if(v) {
 647                         if(!(i%v)) {
 648                                 visual_atoms(moldyn->visual,i*moldyn->tau,
 649                                              moldyn->atom,moldyn->count);
 650                                 printf("\rsteps: %d",i);
 651                                 fflush(stdout);
 652                         }
 653                 }
 654         }
 655
 656                 /* check for hooks */
 657                 if(schedule->hook)
 658                         schedule->hook(moldyn,schedule->hook_params);
 659
 660         return 0;
 661 }
 662
 663 /* velocity verlet */
 664
 665 int velocity_verlet(t_moldyn *moldyn) {
 666
 667         int i,count;
 668         double tau,tau_square;
 669         t_3dvec delta;
 670         t_atom *atom;
 671
 672         atom=moldyn->atom;
 673         count=moldyn->count;
 674         tau=moldyn->tau;
 675         tau_square=moldyn->tau_square;
 676
 677         for(i=0;i<count;i++) {
 678                 /* new positions */
 679                 v3_scale(&delta,&(atom[i].v),tau);
 680                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 681                 v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
 682                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 683                 v3_per_bound(&(atom[i].r),&(moldyn->dim));
 684
 685                 /* velocities */
 686                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 687                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 688         }
 689
 690         /* neighbour list update */
 691 printf("list update ...\n");
 692         link_cell_update(moldyn);
 693 printf("done\n");
 694
 695         /* forces depending on chosen potential */
 696 printf("calc potential/force ...\n");
 697         potential_force_calc(moldyn);
 698         //moldyn->potential_force_function(moldyn);
 699 printf("done\n");
 700
 701         for(i=0;i<count;i++) {
 702                 /* again velocities */
 703                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 704                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 705         }
 706
 707         return 0;
 708 }
 709
 710
 711 /*
 712  *
 713  * potentials & corresponding forces
 714  *
 715  */
 716
 717 /* generic potential and force calculation */
 718
 719 int potential_force_calc(t_moldyn *moldyn) {
 720
 721         int i,count;
 722         t_atom *atom;
 723         t_linkcell *lc;
 724         t_list neighbour[27];
 725         t_list *this;
 726         double u;
 727         u8 bc,bc3;
 728         int countn,dnlc;
 729
 730         count=moldyn->count;
 731         atom=moldyn->atom;
 732         lc=&(moldyn->lc);
 733
 734         /* reset energy */
 735         moldyn->energy=0.0;
 736
 737         for(i=0;i<count;i++) {
 738
 739                 /* reset force */
 740                 v3_zero(&(atom[i].f));
 741
 742                 /* single particle potential/force */
 743                 if(atom[i].attr&ATOM_ATTR_1BP)
 744                         moldyn->pf_func1b(moldyn,&(atom[i]));
 745
 746                 /* 2 body pair potential/force */
 747                 if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
 748
 749                         link_cell_neighbour_index(moldyn,
 750                                 (atom[i].r.x+moldyn->dim.x/2)/lc->x,
 751                                 (atom[i].r.y+moldyn->dim.y/2)/lc->y,
 752                                 (atom[i].r.z+moldyn->dim.z/2)/lc->z,
 753                                 neighbour);
 754
 755                         countn=lc->countn;
 756                         dnlc=lc->dnlc;
 757
 758                         for(j=0;j<countn;j++) {
 759
 760                                 this=&(neighbour[j]);
 761                                 list_reset(this);
 762
 763                                 if(this->start==NULL)
 764                                         continue;
 765
 766                                 bc=(j<dnlc)?0:1;
 767
 768                                 do {
 769                                         btom=this->current->data;
 770
 771                                         if(btom==&(atom[i]))
 772                                                 continue;
 773
 774                                         if((btom->attr&ATOM_ATTR_2BP)&
 775                                            (atom[i].attr&ATOM_ATTR_2BP))
 776                                                 moldyn->pf_func2b(moldyn,
 777                                                                   &(atom[i]),
 778                                                                   btom,
 779                                                                   bc);
 780
 781                                         /* 3 body potential/force */
 782
 783                                         if(!(atom[i].attr&ATOM_ATTR_3BP)||
 784                                            !(btom->attr&ATOM_ATTR_3BP))
 785                                                 continue;
 786
 787                                         link_cell_neighbour_index(moldyn,
 788                                            (btom->r.x+moldyn->dim.x/2)/lc->x,
 789                                            (btom->r.y+moldyn->dim.y/2)/lc->y,
 790                                            (btom->r.z+moldyn->dim.z/2)/lc->z,
 791                                            neighbourk);
 792
 793                                         for(k=0;k<lc->countn;k++) {
 794
 795                                                 thisk=&(neighbourk[k]);
 796                                                 list_reset(thisk);
 797
 798                                                 if(thisk->start==NULL)
 799                                                         continue;
 800
 801                                                 bck=(k<lc->dnlc)?0:1;
 802
 803                                                 do {
 804
 805                         ktom=thisk->current->data;
 806
 807                         if(!(ktom->attr&ATOM_ATTR_3BP))
 808                                 continue;
 809
 810                         if(ktom==btom)
 811                                 continue;
 812
 813                         if(ktom==&(atom[i]))
 814                                 continue;
 815
 816                         moldyn->pf_func3b(moldyn,&(atom[i]),btom,ktom,bck);
 817
 818                                                 } while(list_next(thisk)!=\
 819                                                         L_NO_NEXT_ELEMENT);
 820
 821                                 } while(list_next(this)!=L_NO_NEXT_ELEMENT);
 822                         }
 823                 }
 824         }
 825
 826         return 0;
 827 }
 828
 829 /*
 830  * periodic boundayr checking
 831  */
 832
 833 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
 834
 835         double x,y,z;
 836
 837         x=0.5*dim->x;
 838         y=0.5*dim->y;
 839         z=0.5*dim->z;
 840
 841         if(moldyn->MOLDYN_ATTR_PBX)
 842                 if(a->x>=x) a->x-=dim->x;
 843                 else if(-a->x>x) a->x+=dim->x;
 844         if(moldyn->MOLDYN_ATTR_PBY)
 845                 if(a->y>=y) a->y-=dim->y;
 846                 else if(-a->y>y) a->y+=dim->y;
 847         if(moldyn->MOLDYN_ATTR_PBZ)
 848                 if(a->z>=z) a->z-=dim->z;
 849                 else if(-a->z>z) a->z+=dim->z;
 850
 851         return 0;
 852 }
 853
 854
 855 /*
 856  * example potentials
 857  */
 858
 859 /* harmonic oscillator potential and force */
 860
 861 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc)) {
 862
 863         t_ho_params *params;
 864         t_3dvec force,distance;
 865         double d;
 866         double sc,equi_dist;
 867
 868         params=moldyn->pot2b_params;
 869         sc=params->spring_constant;
 870         equi_dist=params->equilibrium_distance;
 871
 872         v3_sub(&distance,&(ai->r),&(aj->r);
 873
 874         v3_per_bound(&distance,&(moldyn->dim));
 875         if(bc) check_per_bound(moldyn,&distance);
 876         d=v3_norm(&distance);
 877         if(d<=moldyn->cutoff) {
 878                 /* energy is 1/2 (d-d0)^2, but we will add this twice ... */
 879                 moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
 880                 v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
 881                 v3_add(&(ai->f),&(ai->f),&force);
 882         }
 883
 884         return 0;
 885 }
 886
 887 /* lennard jones potential & force for one sort of atoms */
 888
 889 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 890
 891         t_lj_params *params;
 892         t_3dvec force,distance;
 893         double d,h1,h2,u;
 894         double eps,sig6,sig12;
 895
 896         params=moldyn->pot_params;
 897         eps=params->epsilon4;
 898         sig6=params->sigma6;
 899         sig12=params->sigma12;
 900
 901         v3_sub(&distance,&(ai->r),&(aj->r));
 902         if(bc) check_per_bound(moldyn,&distance);
 903         d=v3_absolute_square(&distance);        /* 1/r^2 */
 904         if(d<=moldyn->cutoff_square) {
 905                 d=1.0/d;                        /* 1/r^2 */
 906                 h2=d*d;                         /* 1/r^4 */
 907                 h2*=d;                          /* 1/r^6 */
 908                 h1=h2*h2;                       /* 1/r^12 */
 909                 /* energy is eps*..., but we will add this twice ... */
 910                 moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
 911                 h2*=d;                          /* 1/r^8 */
 912                 h1*=d;                          /* 1/r^14 */
 913                 h2*=6*sig6;
 914                 h1*=12*sig12;
 915                 d=+h1-h2;
 916                 d*=eps;
 917                 v3_scale(&force,&distance,d);
 918                 v3_add(&(ai->f),&(aj->f),&force);
 919         }
 920
 921         return 0;
 922 }
 923
 924 /*
 925  * tersoff potential & force for 2 sorts of atoms
 926  */
 927
 928 /* tersoff 1 body part */
 929 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
 930
 931         int num;
 932         t_tersoff_mult_params *params;
 933         t_tersoff_exchange *exchange;
 934
 935         num=ai->bnum;
 936         params=moldyn->pot1b_params;
 937         exchange=&(params->exchange);
 938
 939         /*
 940          * simple: point constant parameters only depending on atom i to
 941          *         their right values
 942          */
 943
 944         exchange->beta=&(params->beta[num]);
 945         exchange->n=&(params->n[num]);
 946         exchange->c=&(params->c[num]);
 947         exchange->d=&(params->d[num]);
 948         exchange->h=&(params->h[num]);
 949
 950         exchange->betan=pow(*(exchange->beta),*(exchange->n));
 951         exchange->c2=params->c[num]*params->c[num];
 952         exchange->d2=params->d[num]*params->d[num];
 953         exchange->c2d2=exchange->c2/exchange->d2;
 954
 955         return 0;
 956 }
 957
 958 /* tersoff 2 body part */
 959 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 960
 961         t_tersoff_mult_params *params;
 962         t_tersoff_exchange *exchange;
 963         t_3dvec dist_ij;
 964         double d_ij;
 965         double A,B,R,S,lambda;
 966         int num;
 967
 968         params=moldyn->pot_params;
 969         num=ai->bnum;
 970         exchange=&(params->exchange);
 971
 972         exchange->run3bp=0;
 973
 974         /*
 975          * we need: f_c, df_c, f_r, df_r
 976          *
 977          * therefore we need: R, S, A, lambda
 978          */
 979
 980         v3_sub(&dist_ij,&(ai->r),&(aj->r));
 981
 982         if(bc) check_per_bound(moldyn,&dist_ij);
 983
 984         /* save for use in 3bp */ /* REALLY ?!?!?! */
 985         exchange->dist_ij=dist_ij;
 986
 987         /* constants */
 988         if(num==aj->bnum) {
 989                 S=params->S[num];
 990                 R=params->R[num];
 991                 A=params->A[num];
 992                 lambda=params->lambda[num];
 993                 /* more constants depending of atoms i and j, needed in 3bp */
 994                 params->exchange.B=&(params->B[num]);
 995                 params->exchange.mu=params->mu[num];
 996                 params->exchange.chi=1.0;
 997         }
 998         else {
 999                 S=params->Smixed;
1000                 R=params->Rmixed;
1001                 A=params->Amixed;
1002                 lambda=params->lambda_m;
1003                 /* more constants depending of atoms i and j, needed in 3bp */
1004                 params->exchange.B=&(params->Bmixed);
1005                 params->exchange.mu=&(params->mu_m);
1006                 params->exchange.chi=params->chi;
1007         }
1008
1009         d_ij=v3_norm(&dist_ij);
1010
1011         /* save for use in 3bp */
1012         exchange->d_ij=d_ij;
1013
1014         if(d_ij>S)
1015                 return 0;
1016
1017         f_r=A*exp(-lamda*d_ij);
1018         df_r=-lambda*f_r/d_ij;
1019
1020         /* f_a, df_a calc + save for 3bp use */
1021         exchange->f_a=-B*exp(-mu*d_ij);
1022         exchange->df_a=-mu*exchange->f_a/d_ij;
1023
1024         if(d_ij<R) {
1025                 /* f_c = 1, df_c = 0 */
1026                 f_c=1.0;
1027                 df_c=0.0;
1028                 v3_scale(&force,&dist_ij,df_r);
1029         }
1030         else {
1031                 s_r=S-R;
1032                 arg=PI*(d_ij-R)/s_r;
1033                 f_c=0.5+0.5*cos(arg);
1034                 df_c=-0.5*sin(arg)*(PI/(s_r*d_ij));
1035                 scale=df_c*f_r+df_r*f_c;
1036                 v3_scale(&force,&dist_ij,scale);
1037         }
1038
1039         /* add forces */
1040         v3_add(&(ai->f),&(ai->f),&force);
1041         /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
1042         moldyn->energy+=(0.25*f_r*f_c);
1043
1044         /* save for use in 3bp */
1045         exchange->f_c=f_c;
1046         exchange->df_c=df_c;
1047
1048         /* enable the run of 3bp function */
1049         exchange->run3bp=1;
1050
1051         return 0;
1052 }
1053
1054 /* tersoff 3 body part */
1055
1056 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
1057
1058         t_tersoff_mult_params *params;
1059         t_tersoff_exchange *exchange;
1060         t_3dvec dist_ij,dist_ik,dist_jk;
1061         t_3dvec temp,force;
1062         double R,S,s_r;
1063         double d_ij,d_ik,d_jk;
1064         double f_c,df_c,b_ij,f_a,df_a;
1065         double n,c,d,h,neta,betan,betan_1;
1066         double theta,cos_theta,sin_theta;
1067         int num;
1068
1069         params=moldyn->pot_params;
1070         num=ai->bnum;
1071         exchange=params->exchange;
1072
1073         if(!(exchange->run3bp))
1074                 return 0;
1075
1076         /*
1077          * we need: f_c, d_fc, b_ij, db_ij, f_a, df_a
1078          *
1079          * we got f_c, df_c, f_a, df_a from 2bp calculation
1080          */
1081
1082         d_ij=exchange->d_ij;
1083         d_ij2=exchange->d_ij2;
1084
1085         f_a=params->exchange.f_a;
1086         df_a=params->exchange.df_a;
1087
1088         /* d_ij is <= S, as we didn't return so far! */
1089
1090         /*
1091          * calc of b_ij (scalar) and db_ij (vector)
1092          *
1093          * - for b_ij: chi, beta, f_c_ik, w(=1), c, d, h, n, cos_theta
1094          *
1095          * - for db_ij: d_theta, sin_theta, cos_theta, f_c_ik, df_c_ik,
1096          *              w_ik,
1097          *
1098          */
1099
1100
1101         v3_sub(&dist_ik,&(aj->i),&(ak->r));
1102         if(bc) check_per_bound(moldyn,&dist_ik);
1103         d_ik=v3_norm(&dist_ik);
1104
1105         /* constants for f_c_ik calc */
1106         if(num==ak->bnum) {
1107                 R=params->R[num];
1108                 S=params->S[num];
1109         }
1110         else {
1111                 R=params->Rmixed;
1112                 S=params->Smixed;
1113         }
1114
1115         /* calc of f_c_ik */
1116         if(d_ik>S)
1117                 return 0;
1118
1119         if(d_ik<R) {
1120                 /* f_c_ik = 1, df_c_ik = 0 */
1121                 f_c_ik=1.0;
1122                 df_c_ik=0.0;
1123         }
1124         else {
1125                 s_r=S-R;
1126                 arg=PI*(d_ik-R)/s_r;
1127                 f_c_ik=0.5+0.5*cos(arg);
1128                 df_c_ik=-0.5*sin(arg)*(PI/(s_r*d_ik));
1129         }
1130
1131         v3_sub(&dist_jk,&(aj->r),&(ak->r));
1132         if(bc) check_per_bound(moldyn,&dist_jk);
1133         d_jk=v3_norm(&dist_jk);
1134
1135         beta=*(exchange->beta);
1136         betan=exchange->betan;
1137         n=*(exchange->n);
1138         c=*(exchange->c);
1139         d=*(exchange->d);
1140         h=*(exchange->h);
1141         c2=exchange->c2;
1142         d2=exchange->d2;
1143         c2d2=exchange->c2d2;
1144
1145         numer=d_ij2+d_ik*d_ik-d_jk*d_jk;
1146         denom=2*d_ij*d_ik;
1147         cos_theta=numer/denom;
1148         sin_theta=sqrt(1.0-(cos_theta*cos_theta));
1149         theta=arccos(cos_theta);
1150         d_theta=(-1.0/sqrt(1.0-cos_theta*cos_theta))/(denom*denom);
1151         d_theta1=2*denom-numer*2*d_ik/d_ij;
1152         d_theta2=2*denom-numer*2*d_ij/d_ik;
1153         d_theta1*=d_theta;
1154         d_theta2*=d_theta;
1155
1156         h_cos=(h-cos_theta);
1157         h_cos2=h_cos*h_cos;
1158         d2_h_cos2=d2-h_cos2;
1159
1160         /* some usefull expressions */
1161         frac1=c2/(d2-h_cos2);
1162         bracket1=1+c2d2-frac1;
1163         bracket2=f_c_ik*bracket1;
1164         bracket2_n_1=pow(bracket2,n-1.0);
1165         bracket2_n=bracket2_n_1*bracket2;
1166         bracket3=1+betan*bracket2_n;
1167         bracket3_pow_1=pow(bracket3,(-1.0/(2.0*n))-1.0);
1168         bracket3_pow=bracket3_pow_1*bracket3;
1169
1170         /* now go on with calc of b_ij and derivation of b_ij */
1171         b_ij=chi*bracket3_pow;
1172
1173         /* derivation of theta */
1174         v3_scale(&force,&dist_ij,d1_theta);
1175         v3_scale(&temp,&dist_ik,d_theta2);
1176         v3_add(&force,&force,&temp);
1177
1178         /* part 1 of derivation of b_ij */
1179         v3_scale(&force,sin_theta*2*h_cos*f_c_ik*frac1);
1180
1181         /* part 2 of derivation of b_ij */
1182         v3_scale(&temp,&dist_ik,df_c_ik*bracket1);
1183
1184         /* sum up and scale ... */
1185         v3_add(&temp,&temp,&force);
1186         scale=bracket2_n_1*n*betan*(1+betan*bracket3_pow_1)*chi*(1.0/(2.0*n));
1187         v3_scale(&temp,&temp,scale);
1188
1189         /* now construct an energy and a force out of that */
1190         v3_scale(&temp,&temp,f_a);
1191         v3_scale(&force,&dist_ij,df_a*b_ij);
1192         v3_add(&temp,&temp,&force);
1193         v3_scale(&temp,&temp,f_c);
1194         v3_scale(&force,&dist_ij,df_c*b_ij*f_a);
1195         v3_add(&force,&force,&temp);
1196
1197         /* add forces */
1198         v3_add(&(ai->f),&(ai->f),&force);
1199         /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
1200         moldyn->energy+=(0.25*f_a*b_ij*f_c);
1201
1202         return 0;
1203 }
1204