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(algo) {
  55                 case MOLDYN_INTEGRATE_VERLET:
  56                         moldyn->integrate=velocity_verlet;
  57                         break;
  58                 default:
  59                         printf("unknown integration algorithm: %02x\n",algo);
  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_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
 110
 111         moldyn->func1b=func;
 112         moldyn->pot1b_params=params;
 113
 114         return 0;
 115 }
 116
 117 int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
 118
 119         moldyn->func2b=func;
 120         moldyn->pot2b_params=params;
 121
 122         return 0;
 123 }
 124
 125 int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
 126
 127         moldyn->func3b=func;
 128         moldyn->pot3b_params=params;
 129
 130         return 0;
 131 }
 132
 133 int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
 134
 135         switch(type) {
 136                 case LOG_TOTAL_ENERGY:
 137                         moldyn->ewrite=timer;
 138                         moldyn->efd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
 139                         if(moldyn->efd<0) {
 140                                 perror("[moldyn] efd open");
 141                                 return moldyn->efd;
 142                         }
 143                         dprintf(moldyn->efd,"# total energy log file\n");
 144                         break;
 145                 case LOG_TOTAL_MOMENTUM:
 146                         moldyn->mwrite=timer;
 147                         moldyn->mfd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
 148                         if(moldyn->mfd<0) {
 149                                 perror("[moldyn] mfd open");
 150                                 return moldyn->mfd;
 151                         }
 152                         dprintf(moldyn->efd,"# total momentum log file\n");
 153                         break;
 154                 case SAVE_STEP:
 155                         moldyn->swrite=timer;
 156                         strncpy(moldyn->sfb,fb,63);
 157                         break;
 158                 case VISUAL_STEP:
 159                         moldyn->vwrite=timer;
 160                         strncpy(moldyn->vfb,fb,63);
 161                         visual_init(&(moldyn->vis),fb);
 162                         break;
 163                 default:
 164                         printf("unknown log mechanism: %02x\n",type);
 165                         return -1;
 166         }
 167
 168         return 0;
 169 }
 170
 171 int moldyn_log_shutdown(t_moldyn *moldyn) {
 172
 173         if(moldyn->efd) close(moldyn->efd);
 174         if(moldyn->mfd) close(moldyn->mfd);
 175         if(moldyn->visual) visual_tini(moldyn->visual);
 176
 177         return 0;
 178 }
 179
 180 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 181                    u8 attr,u8 bnum,int a,int b,int c) {
 182
 183         int count;
 184         int ret;
 185         t_3dvec origin;
 186         t_atom *atom;
 187
 188         count=a*b*c;
 189         atom=moldyn->atom;
 190
 191         if(type==FCC) count*=4;
 192
 193         if(type==DIAMOND) count*=8;
 194
 195         atom=malloc(count*sizeof(t_atom));
 196         if(atom==NULL) {
 197                 perror("malloc (atoms)");
 198                 return -1;
 199         }
 200
 201         v3_zero(&origin);
 202
 203         switch(type) {
 204                 case FCC:
 205                         ret=fcc_init(a,b,c,lc,atom,&origin);
 206                         break;
 207                 case DIAMOND:
 208                         ret=diamond_init(a,b,c,lc,atom,&origin);
 209                         break;
 210                 default:
 211                         printf("unknown lattice type (%02x)\n",type);
 212                         return -1;
 213         }
 214
 215         /* debug */
 216         if(ret!=count) {
 217                 printf("ok, there is something wrong ...\n");
 218                 printf("calculated -> %d atoms\n",count);
 219                 printf("created -> %d atoms\n",ret);
 220                 return -1;
 221         }
 222
 223         moldyn->count=count;
 224
 225         while(count) {
 226                 atom[count-1].element=element;
 227                 atom[count-1].mass=mass;
 228                 atom[count-1].attr=attr;
 229                 atom[count-1].bnum=bnum;
 230                 count-=1;
 231         }
 232
 233         return ret;
 234 }
 235
 236 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
 237              t_3dvec *r,t_3dvec *v) {
 238
 239         t_atom *atom;
 240         void *ptr;
 241         int count;
 242
 243         atom=moldyn->atom;
 244         count=++(moldyn->count);
 245
 246         ptr=realloc(atom,count*sizeof(t_atom));
 247         if(!ptr) {
 248                 perror("[moldyn] realloc (add atom)");
 249                 return -1;
 250         }
 251         moldyn->atom=ptr;
 252
 253         atom=moldyn->atom;
 254         atom->r=*r;
 255         atom->v=*v;
 256         atom->element=element;
 257         atom->bnum=bnum;
 258         atom->attr=attr;
 259
 260         return 0;
 261 }
 262
 263 int destroy_atoms(t_moldyn *moldyn) {
 264
 265         if(moldyn->atom) free(moldyn->atom);
 266
 267         return 0;
 268 }
 269
 270 int thermal_init(t_moldyn *moldyn) {
 271
 272         /*
 273          * - gaussian distribution of velocities
 274          * - zero total momentum
 275          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 276          */
 277
 278         int i;
 279         double v,sigma;
 280         t_3dvec p_total,delta;
 281         t_atom *atom;
 282         t_random *random;
 283
 284         atom=moldyn->atom;
 285         random=&(moldyn->random);
 286
 287         /* gaussian distribution of velocities */
 288         v3_zero(&p_total);
 289         for(i=0;i<moldyn->count;i++) {
 290                 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t/atom[i].mass);
 291                 /* x direction */
 292                 v=sigma*rand_get_gauss(random);
 293                 atom[i].v.x=v;
 294                 p_total.x+=atom[i].mass*v;
 295                 /* y direction */
 296                 v=sigma*rand_get_gauss(random);
 297                 atom[i].v.y=v;
 298                 p_total.y+=atom[i].mass*v;
 299                 /* z direction */
 300                 v=sigma*rand_get_gauss(random);
 301                 atom[i].v.z=v;
 302                 p_total.z+=atom[i].mass*v;
 303         }
 304
 305         /* zero total momentum */
 306         v3_scale(&p_total,&p_total,1.0/moldyn->count);
 307         for(i=0;i<moldyn->count;i++) {
 308                 v3_scale(&delta,&p_total,1.0/atom[i].mass);
 309                 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
 310         }
 311
 312         /* velocity scaling */
 313         scale_velocity(moldyn);
 314
 315         return 0;
 316 }
 317
 318 int scale_velocity(t_moldyn *moldyn) {
 319
 320         int i;
 321         double e,c;
 322         t_atom *atom;
 323
 324         atom=moldyn->atom;
 325
 326         /*
 327          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 328          */
 329         e=0.0;
 330         for(i=0;i<moldyn->count;i++)
 331                 e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 332         c=sqrt((2.0*e)/(3.0*moldyn->count*K_BOLTZMANN*moldyn->t));
 333         for(i=0;i<moldyn->count;i++)
 334                 v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
 335
 336         return 0;
 337 }
 338
 339 double get_e_kin(t_moldyn *moldyn) {
 340
 341         int i;
 342         t_atom *atom;
 343
 344         atom=moldyn->atom;
 345         moldyn->ekin=0.0;
 346
 347         for(i=0;i<moldyn->count;i++)
 348                 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 349
 350         return moldyn->ekin;
 351 }
 352
 353 double get_e_pot(t_moldyn *moldyn) {
 354
 355         return moldyn->energy;
 356 }
 357
 358 double update_e_kin(t_moldyn *moldyn) {
 359
 360         return(get_e_kin(moldyn));
 361 }
 362
 363 double get_total_energy(t_moldyn *moldyn) {
 364
 365         return(moldyn->ekin+moldyn->energy);
 366 }
 367
 368 t_3dvec get_total_p(t_moldyn *moldyn) {
 369
 370         t_3dvec p,p_total;
 371         int i;
 372         t_atom *atom;
 373
 374         atom=moldyn->atom;
 375
 376         v3_zero(&p_total);
 377         for(i=0;i<moldyn->count;i++) {
 378                 v3_scale(&p,&(atom[i].v),atom[i].mass);
 379                 v3_add(&p_total,&p_total,&p);
 380         }
 381
 382         return p_total;
 383 }
 384
 385 double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
 386
 387         double tau;
 388
 389         tau=0.05*nn_dist/(sqrt(3.0*K_BOLTZMANN*t/moldyn->atom[0].mass));
 390         tau*=1.0E-9;
 391         if(tau<moldyn->tau)
 392                 printf("[moldyn] warning: time step  (%f > %.15f)\n",
 393                        moldyn->tau,tau);
 394
 395         return tau;
 396 }
 397
 398 /*
 399  * numerical tricks
 400  */
 401
 402 /* linked list / cell method */
 403
 404 int link_cell_init(t_moldyn *moldyn) {
 405
 406         t_linkcell *lc;
 407         int i;
 408         int fd;
 409
 410         fd=open("/dev/null",O_WRONLY);
 411
 412         lc=&(moldyn->lc);
 413
 414         /* partitioning the md cell */
 415         lc->nx=moldyn->dim.x/moldyn->cutoff;
 416         lc->x=moldyn->dim.x/lc->nx;
 417         lc->ny=moldyn->dim.y/moldyn->cutoff;
 418         lc->y=moldyn->dim.y/lc->ny;
 419         lc->nz=moldyn->dim.z/moldyn->cutoff;
 420         lc->z=moldyn->dim.z/lc->nz;
 421
 422         lc->cells=lc->nx*lc->ny*lc->nz;
 423         lc->subcell=malloc(lc->cells*sizeof(t_list));
 424
 425         printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 426
 427         for(i=0;i<lc->cells;i++)
 428                 //list_init(&(lc->subcell[i]),1);
 429                 list_init(&(lc->subcell[i]),fd);
 430
 431         link_cell_update(moldyn);
 432
 433         return 0;
 434 }
 435
 436 int link_cell_update(t_moldyn *moldyn) {
 437
 438         int count,i,j,k;
 439         int nx,ny,nz;
 440         t_atom *atom;
 441         t_linkcell *lc;
 442
 443         atom=moldyn->atom;
 444         lc=&(moldyn->lc);
 445
 446         nx=lc->nx;
 447         ny=lc->ny;
 448         nz=lc->nz;
 449
 450         for(i=0;i<lc->cells;i++)
 451                 list_destroy(&(moldyn->lc.subcell[i]));
 452
 453         for(count=0;count<moldyn->count;count++) {
 454                 i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
 455                 j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
 456                 k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
 457                 list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
 458                                        &(atom[count]));
 459         }
 460
 461         return 0;
 462 }
 463
 464 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 465
 466         t_linkcell *lc;
 467         int a;
 468         int count1,count2;
 469         int ci,cj,ck;
 470         int nx,ny,nz;
 471         int x,y,z;
 472         u8 bx,by,bz;
 473
 474         lc=&(moldyn->lc);
 475         nx=lc->nx;
 476         ny=lc->ny;
 477         nz=lc->nz;
 478         count1=1;
 479         count2=27;
 480         a=nx*ny;
 481
 482
 483         cell[0]=lc->subcell[i+j*nx+k*a];
 484         for(ci=-1;ci<=1;ci++) {
 485                 bx=0;
 486                 x=i+ci;
 487                 if((x<0)||(x>=nx)) {
 488                         x=(x+nx)%nx;
 489                         bx=1;
 490                 }
 491                 for(cj=-1;cj<=1;cj++) {
 492                         by=0;
 493                         y=j+cj;
 494                         if((y<0)||(y>=ny)) {
 495                                 y=(y+ny)%ny;
 496                                 by=1;
 497                         }
 498                         for(ck=-1;ck<=1;ck++) {
 499                                 bz=0;
 500                                 z=k+ck;
 501                                 if((z<0)||(z>=nz)) {
 502                                         z=(z+nz)%nz;
 503                                         bz=1;
 504                                 }
 505                                 if(!(ci|cj|ck)) continue;
 506                                 if(bx|by|bz) {
 507                                         cell[--count2]=lc->subcell[x+y*nx+z*a];
 508                                 }
 509                                 else {
 510                                         cell[count1++]=lc->subcell[x+y*nx+z*a];
 511                                 }
 512                         }
 513                 }
 514         }
 515
 516         lc->dnlc=count2;
 517         lc->countn=27;
 518
 519         return count2;
 520 }
 521
 522 int link_cell_shutdown(t_moldyn *moldyn) {
 523
 524         int i;
 525         t_linkcell *lc;
 526
 527         lc=&(moldyn->lc);
 528
 529         for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
 530                 list_shutdown(&(moldyn->lc.subcell[i]));
 531
 532         return 0;
 533 }
 534
 535 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
 536
 537         int count;
 538         void *ptr;
 539         t_moldyn_schedule *schedule;
 540
 541         schedule=&(moldyn->schedule);
 542         count=++(schedule->content_count);
 543
 544         ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
 545         if(!ptr) {
 546                 perror("[moldyn] realloc (runs)");
 547                 return -1;
 548         }
 549         moldyn->schedule.runs=ptr;
 550         moldyn->schedule.runs[count-1]=runs;
 551
 552         ptr=realloc(schedule->tau,count*sizeof(double));
 553         if(!ptr) {
 554                 perror("[moldyn] realloc (tau)");
 555                 return -1;
 556         }
 557         moldyn->schedule.tau=ptr;
 558         moldyn->schedule.tau[count-1]=tau;
 559
 560         return 0;
 561 }
 562
 563 int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
 564
 565         moldyn->schedule.hook=hook;
 566         moldyn->schedule.hook_params=hook_params;
 567
 568         return 0;
 569 }
 570
 571 /*
 572  *
 573  * 'integration of newtons equation' - algorithms
 574  *
 575  */
 576
 577 /* start the integration */
 578
 579 int moldyn_integrate(t_moldyn *moldyn) {
 580
 581         int i,sched;
 582         unsigned int e,m,s,v;
 583         t_3dvec p;
 584         t_moldyn_schedule *schedule;
 585
 586         int fd;
 587         char fb[128];
 588
 589         schedule=&(moldyn->schedule);
 590
 591         /* initialize linked cell method */
 592         link_cell_init(moldyn);
 593
 594         /* logging & visualization */
 595         e=moldyn->ewrite;
 596         m=moldyn->mwrite;
 597         s=moldyn->swrite;
 598         v=moldyn->vwrite;
 599
 600         /* sqaure of some variables */
 601         moldyn->tau_square=moldyn->tau*moldyn->tau;
 602         moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
 603
 604         /* calculate initial forces */
 605         potential_force_calc(moldyn);
 606
 607         /* zero absolute time */
 608         moldyn->time=0.0;
 609
 610         for(sched=0;sched<moldyn->schedule.content_count;sched++) {
 611
 612                 /* setting amount of runs and finite time step size */
 613                 moldyn->tau=schedule->tau[sched];
 614                 moldyn->tau_square=moldyn->tau*moldyn->tau;
 615                 moldyn->time_steps=schedule->runs[sched];
 616
 617         /* integration according to schedule */
 618
 619         for(i=0;i<moldyn->time_steps;i++) {
 620
 621                 /* integration step */
 622                 moldyn->integrate(moldyn);
 623
 624                 /* increase absolute time */
 625                 moldyn->time+=moldyn->tau;
 626
 627                 /* check for log & visualization */
 628                 if(e) {
 629                         if(!(i%e))
 630                                 dprintf(moldyn->efd,
 631                                         "%.15f %.45f %.45f %.45f\n",
 632                                         moldyn->time,update_e_kin(moldyn),
 633                                         moldyn->energy,
 634                                         get_total_energy(moldyn));
 635                 }
 636                 if(m) {
 637                         if(!(i%m)) {
 638                                 p=get_total_p(moldyn);
 639                                 dprintf(moldyn->mfd,
 640                                         "%.15f %.45f\n",moldyn->time,
 641                                         v3_norm(&p));
 642                         }
 643                 }
 644                 if(s) {
 645                         if(!(i%s)) {
 646                                 snprintf(fb,128,"%s-%f-%.15f.save",moldyn->sfb,
 647                                          moldyn->t,i*moldyn->tau);
 648                                 fd=open(fb,O_WRONLY|O_TRUNC|O_CREAT);
 649                                 if(fd<0) perror("[moldyn] save fd open");
 650                                 else {
 651                                         write(fd,moldyn,sizeof(t_moldyn));
 652                                         write(fd,moldyn->atom,
 653                                               moldyn->count*sizeof(t_atom));
 654                                 }
 655                                 close(fd);
 656                         }
 657                 }
 658                 if(v) {
 659                         if(!(i%v)) {
 660                                 visual_atoms(&(moldyn->vis),moldyn->time,
 661                                              moldyn->atom,moldyn->count);
 662                                 printf("\rsched: %d, steps: %d",sched,i);
 663                                 fflush(stdout);
 664                         }
 665                 }
 666
 667         }
 668
 669                 /* check for hooks */
 670                 if(schedule->hook)
 671                         schedule->hook(moldyn,schedule->hook_params);
 672
 673         }
 674
 675         return 0;
 676 }
 677
 678 /* velocity verlet */
 679
 680 int velocity_verlet(t_moldyn *moldyn) {
 681
 682         int i,count;
 683         double tau,tau_square;
 684         t_3dvec delta;
 685         t_atom *atom;
 686
 687         atom=moldyn->atom;
 688         count=moldyn->count;
 689         tau=moldyn->tau;
 690         tau_square=moldyn->tau_square;
 691
 692         for(i=0;i<count;i++) {
 693                 /* new positions */
 694                 v3_scale(&delta,&(atom[i].v),tau);
 695                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 696                 v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
 697                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 698                 v3_per_bound(&(atom[i].r),&(moldyn->dim));
 699
 700                 /* velocities */
 701                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 702                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 703         }
 704
 705         /* neighbour list update */
 706         link_cell_update(moldyn);
 707
 708         /* forces depending on chosen potential */
 709         potential_force_calc(moldyn);
 710         //moldyn->potential_force_function(moldyn);
 711
 712         for(i=0;i<count;i++) {
 713                 /* again velocities */
 714                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 715                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 716         }
 717
 718         return 0;
 719 }
 720
 721
 722 /*
 723  *
 724  * potentials & corresponding forces
 725  *
 726  */
 727
 728 /* generic potential and force calculation */
 729
 730 int potential_force_calc(t_moldyn *moldyn) {
 731
 732         int i,j,k,count;
 733         t_atom *atom,*btom,*ktom;
 734         t_linkcell *lc;
 735         t_list neighbour[27];
 736         t_list *this,*thisk,*neighbourk;
 737         u8 bc,bck;
 738         int countn,dnlc;
 739
 740         count=moldyn->count;
 741         atom=moldyn->atom;
 742         lc=&(moldyn->lc);
 743
 744         /* reset energy */
 745         moldyn->energy=0.0;
 746
 747         for(i=0;i<count;i++) {
 748
 749                 /* reset force */
 750                 v3_zero(&(atom[i].f));
 751
 752                 /* single particle potential/force */
 753                 if(atom[i].attr&ATOM_ATTR_1BP)
 754                         moldyn->func1b(moldyn,&(atom[i]));
 755
 756                 /* 2 body pair potential/force */
 757                 if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
 758
 759                         link_cell_neighbour_index(moldyn,
 760                                 (atom[i].r.x+moldyn->dim.x/2)/lc->x,
 761                                 (atom[i].r.y+moldyn->dim.y/2)/lc->y,
 762                                 (atom[i].r.z+moldyn->dim.z/2)/lc->z,
 763                                 neighbour);
 764
 765                         countn=lc->countn;
 766                         dnlc=lc->dnlc;
 767
 768                         for(j=0;j<countn;j++) {
 769
 770                                 this=&(neighbour[j]);
 771                                 list_reset(this);
 772
 773                                 if(this->start==NULL)
 774                                         continue;
 775
 776                                 bc=(j<dnlc)?0:1;
 777
 778                                 do {
 779                                         btom=this->current->data;
 780
 781                                         if(btom==&(atom[i]))
 782                                                 continue;
 783
 784                                         if((btom->attr&ATOM_ATTR_2BP)&
 785                                            (atom[i].attr&ATOM_ATTR_2BP))
 786                                                 moldyn->func2b(moldyn,
 787                                                                &(atom[i]),
 788                                                                btom,
 789                                                                bc);
 790
 791                                         /* 3 body potential/force */
 792
 793                                         if(!(atom[i].attr&ATOM_ATTR_3BP)||
 794                                            !(btom->attr&ATOM_ATTR_3BP))
 795                                                 continue;
 796
 797                                         link_cell_neighbour_index(moldyn,
 798                                            (btom->r.x+moldyn->dim.x/2)/lc->x,
 799                                            (btom->r.y+moldyn->dim.y/2)/lc->y,
 800                                            (btom->r.z+moldyn->dim.z/2)/lc->z,
 801                                            neighbourk);
 802
 803                                         for(k=0;k<lc->countn;k++) {
 804
 805                                                 thisk=&(neighbourk[k]);
 806                                                 list_reset(thisk);
 807
 808                                                 if(thisk->start==NULL)
 809                                                         continue;
 810
 811                                                 bck=(k<lc->dnlc)?0:1;
 812
 813                                                 do {
 814
 815                         ktom=thisk->current->data;
 816
 817                         if(!(ktom->attr&ATOM_ATTR_3BP))
 818                                 continue;
 819
 820                         if(ktom==btom)
 821                                 continue;
 822
 823                         if(ktom==&(atom[i]))
 824                                 continue;
 825
 826                         moldyn->func3b(moldyn,&(atom[i]),btom,ktom,bck);
 827
 828                                                 } while(list_next(thisk)!=\
 829                                                         L_NO_NEXT_ELEMENT);
 830
 831                                         }
 832
 833                                 } while(list_next(this)!=L_NO_NEXT_ELEMENT);
 834                         }
 835                 }
 836         }
 837
 838         return 0;
 839 }
 840
 841 /*
 842  * periodic boundayr checking
 843  */
 844
 845 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
 846
 847         double x,y,z;
 848         t_3dvec *dim;
 849
 850         dim=&(moldyn->dim);
 851
 852         x=0.5*dim->x;
 853         y=0.5*dim->y;
 854         z=0.5*dim->z;
 855
 856         if(moldyn->status&MOLDYN_STAT_PBX) {
 857                 if(a->x>=x) a->x-=dim->x;
 858                 else if(-a->x>x) a->x+=dim->x;
 859         }
 860         if(moldyn->status&MOLDYN_STAT_PBY) {
 861                 if(a->y>=y) a->y-=dim->y;
 862                 else if(-a->y>y) a->y+=dim->y;
 863         }
 864         if(moldyn->status&MOLDYN_STAT_PBZ) {
 865                 if(a->z>=z) a->z-=dim->z;
 866                 else if(-a->z>z) a->z+=dim->z;
 867         }
 868
 869         return 0;
 870 }
 871
 872
 873 /*
 874  * example potentials
 875  */
 876
 877 /* harmonic oscillator potential and force */
 878
 879 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 880
 881         t_ho_params *params;
 882         t_3dvec force,distance;
 883         double d;
 884         double sc,equi_dist;
 885
 886         params=moldyn->pot2b_params;
 887         sc=params->spring_constant;
 888         equi_dist=params->equilibrium_distance;
 889
 890         v3_sub(&distance,&(ai->r),&(aj->r));
 891
 892         v3_per_bound(&distance,&(moldyn->dim));
 893         if(bc) check_per_bound(moldyn,&distance);
 894         d=v3_norm(&distance);
 895         if(d<=moldyn->cutoff) {
 896                 /* energy is 1/2 (d-d0)^2, but we will add this twice ... */
 897                 moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
 898                 v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
 899                 v3_add(&(ai->f),&(ai->f),&force);
 900         }
 901
 902         return 0;
 903 }
 904
 905 /* lennard jones potential & force for one sort of atoms */
 906
 907 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 908
 909         t_lj_params *params;
 910         t_3dvec force,distance;
 911         double d,h1,h2;
 912         double eps,sig6,sig12;
 913
 914         params=moldyn->pot2b_params;
 915         eps=params->epsilon4;
 916         sig6=params->sigma6;
 917         sig12=params->sigma12;
 918
 919         v3_sub(&distance,&(ai->r),&(aj->r));
 920         if(bc) check_per_bound(moldyn,&distance);
 921         d=v3_absolute_square(&distance);        /* 1/r^2 */
 922         if(d<=moldyn->cutoff_square) {
 923                 d=1.0/d;                        /* 1/r^2 */
 924                 h2=d*d;                         /* 1/r^4 */
 925                 h2*=d;                          /* 1/r^6 */
 926                 h1=h2*h2;                       /* 1/r^12 */
 927                 /* energy is eps*..., but we will add this twice ... */
 928                 moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
 929                 h2*=d;                          /* 1/r^8 */
 930                 h1*=d;                          /* 1/r^14 */
 931                 h2*=6*sig6;
 932                 h1*=12*sig12;
 933                 d=+h1-h2;
 934                 d*=eps;
 935                 v3_scale(&force,&distance,d);
 936                 v3_add(&(ai->f),&(aj->f),&force);
 937         }
 938
 939         return 0;
 940 }
 941
 942 /*
 943  * tersoff potential & force for 2 sorts of atoms
 944  */
 945
 946 /* tersoff 1 body part */
 947 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
 948
 949         int num;
 950         t_tersoff_mult_params *params;
 951         t_tersoff_exchange *exchange;
 952
 953         num=ai->bnum;
 954         params=moldyn->pot1b_params;
 955         exchange=&(params->exchange);
 956
 957         /*
 958          * simple: point constant parameters only depending on atom i to
 959          *         their right values
 960          */
 961
 962         exchange->beta=&(params->beta[num]);
 963         exchange->n=&(params->n[num]);
 964         exchange->c=&(params->c[num]);
 965         exchange->d=&(params->d[num]);
 966         exchange->h=&(params->h[num]);
 967
 968         exchange->betan=pow(*(exchange->beta),*(exchange->n));
 969         exchange->c2=params->c[num]*params->c[num];
 970         exchange->d2=params->d[num]*params->d[num];
 971         exchange->c2d2=exchange->c2/exchange->d2;
 972
 973         return 0;
 974 }
 975
 976 /* tersoff 2 body part */
 977 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 978
 979         t_tersoff_mult_params *params;
 980         t_tersoff_exchange *exchange;
 981         t_3dvec dist_ij,force;
 982         double d_ij;
 983         double A,B,R,S,lambda,mu;
 984         double f_r,df_r;
 985         double f_c,df_c;
 986         int num;
 987         double s_r;
 988         double arg;
 989         double scale;
 990
 991         params=moldyn->pot2b_params;
 992         num=ai->bnum;
 993         exchange=&(params->exchange);
 994
 995         exchange->run3bp=0;
 996
 997         /*
 998          * we need: f_c, df_c, f_r, df_r
 999          *
1000          * therefore we need: R, S, A, lambda
1001          */
1002
1003         v3_sub(&dist_ij,&(ai->r),&(aj->r));
1004
1005         if(bc) check_per_bound(moldyn,&dist_ij);
1006
1007         /* save for use in 3bp */ /* REALLY ?!?!?! */
1008         exchange->dist_ij=dist_ij;
1009
1010         /* constants */
1011         if(num==aj->bnum) {
1012                 S=params->S[num];
1013                 R=params->R[num];
1014                 A=params->A[num];
1015                 lambda=params->lambda[num];
1016                 /* more constants depending of atoms i and j, needed in 3bp */
1017                 params->exchange.B=&(params->B[num]);
1018                 params->exchange.mu=&(params->mu[num]);
1019                 mu=params->mu[num];
1020                 params->exchange.chi=1.0;
1021         }
1022         else {
1023                 S=params->Smixed;
1024                 R=params->Rmixed;
1025                 A=params->Amixed;
1026                 lambda=params->lambda_m;
1027                 /* more constants depending of atoms i and j, needed in 3bp */
1028                 params->exchange.B=&(params->Bmixed);
1029                 params->exchange.mu=&(params->mu_m);
1030                 mu=params->mu_m;
1031                 params->exchange.chi=params->chi;
1032         }
1033
1034         d_ij=v3_norm(&dist_ij);
1035
1036         /* save for use in 3bp */
1037         exchange->d_ij=d_ij;
1038
1039         if(d_ij>S)
1040                 return 0;
1041
1042         f_r=A*exp(-lambda*d_ij);
1043         df_r=-lambda*f_r/d_ij;
1044
1045         /* f_a, df_a calc + save for 3bp use */
1046         exchange->f_a=-B*exp(-mu*d_ij);
1047         exchange->df_a=-mu*exchange->f_a/d_ij;
1048
1049         if(d_ij<R) {
1050                 /* f_c = 1, df_c = 0 */
1051                 f_c=1.0;
1052                 df_c=0.0;
1053                 v3_scale(&force,&dist_ij,df_r);
1054         }
1055         else {
1056                 s_r=S-R;
1057                 arg=M_PI*(d_ij-R)/s_r;
1058                 f_c=0.5+0.5*cos(arg);
1059                 df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij));
1060                 scale=df_c*f_r+df_r*f_c;
1061                 v3_scale(&force,&dist_ij,scale);
1062         }
1063
1064         /* add forces */
1065         v3_add(&(ai->f),&(ai->f),&force);
1066         /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
1067         moldyn->energy+=(0.25*f_r*f_c);
1068
1069         /* save for use in 3bp */
1070         exchange->f_c=f_c;
1071         exchange->df_c=df_c;
1072
1073         /* enable the run of 3bp function */
1074         exchange->run3bp=1;
1075
1076         return 0;
1077 }
1078
1079 /* tersoff 3 body part */
1080
1081 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
1082
1083         t_tersoff_mult_params *params;
1084         t_tersoff_exchange *exchange;
1085         t_3dvec dist_ij,dist_ik,dist_jk;
1086         t_3dvec temp,force;
1087         double R,S,s_r;
1088         double d_ij,d_ij2,d_ik,d_jk;
1089         double f_c,df_c,b_ij,f_a,df_a;
1090         double f_c_ik,df_c_ik,arg;
1091         double scale;
1092         double chi;
1093         double n,c,d,h,beta,betan;
1094         double c2,d2,c2d2;
1095         double numer,denom;
1096         double theta,cos_theta,sin_theta;
1097         double d_theta,d_theta1,d_theta2;
1098         double h_cos,h_cos2,d2_h_cos2;
1099         double frac1,bracket1,bracket2,bracket2_n_1,bracket2_n;
1100         double bracket3,bracket3_pow_1,bracket3_pow;
1101         int num;
1102
1103         params=moldyn->pot3b_params;
1104         num=ai->bnum;
1105         exchange=&(params->exchange);
1106
1107         if(!(exchange->run3bp))
1108                 return 0;
1109
1110         /*
1111          * we need: f_c, d_fc, b_ij, db_ij, f_a, df_a
1112          *
1113          * we got f_c, df_c, f_a, df_a from 2bp calculation
1114          */
1115
1116         d_ij=exchange->d_ij;
1117         d_ij2=exchange->d_ij2;
1118
1119         f_a=params->exchange.f_a;
1120         df_a=params->exchange.df_a;
1121
1122         /* d_ij is <= S, as we didn't return so far! */
1123
1124         /*
1125          * calc of b_ij (scalar) and db_ij (vector)
1126          *
1127          * - for b_ij: chi, beta, f_c_ik, w(=1), c, d, h, n, cos_theta
1128          *
1129          * - for db_ij: d_theta, sin_theta, cos_theta, f_c_ik, df_c_ik,
1130          *              w_ik,
1131          *
1132          */
1133
1134
1135         v3_sub(&dist_ik,&(ai->r),&(ak->r));
1136         if(bc) check_per_bound(moldyn,&dist_ik);
1137         d_ik=v3_norm(&dist_ik);
1138
1139         /* constants for f_c_ik calc */
1140         if(num==ak->bnum) {
1141                 R=params->R[num];
1142                 S=params->S[num];
1143         }
1144         else {
1145                 R=params->Rmixed;
1146                 S=params->Smixed;
1147         }
1148
1149         /* calc of f_c_ik */
1150         if(d_ik>S)
1151                 return 0;
1152
1153         if(d_ik<R) {
1154                 /* f_c_ik = 1, df_c_ik = 0 */
1155                 f_c_ik=1.0;
1156                 df_c_ik=0.0;
1157         }
1158         else {
1159                 s_r=S-R;
1160                 arg=M_PI*(d_ik-R)/s_r;
1161                 f_c_ik=0.5+0.5*cos(arg);
1162                 df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik));
1163         }
1164
1165         v3_sub(&dist_jk,&(aj->r),&(ak->r));
1166         if(bc) check_per_bound(moldyn,&dist_jk);
1167         d_jk=v3_norm(&dist_jk);
1168
1169         beta=*(exchange->beta);
1170         betan=exchange->betan;
1171         n=*(exchange->n);
1172         c=*(exchange->c);
1173         d=*(exchange->d);
1174         h=*(exchange->h);
1175         c2=exchange->c2;
1176         d2=exchange->d2;
1177         c2d2=exchange->c2d2;
1178
1179         numer=d_ij2+d_ik*d_ik-d_jk*d_jk;
1180         denom=2*d_ij*d_ik;
1181         cos_theta=numer/denom;
1182         sin_theta=sqrt(1.0-(cos_theta*cos_theta));
1183         theta=acos(cos_theta);
1184         d_theta=(-1.0/sqrt(1.0-cos_theta*cos_theta))/(denom*denom);
1185         d_theta1=2*denom-numer*2*d_ik/d_ij;
1186         d_theta2=2*denom-numer*2*d_ij/d_ik;
1187         d_theta1*=d_theta;
1188         d_theta2*=d_theta;
1189
1190         h_cos=(h-cos_theta);
1191         h_cos2=h_cos*h_cos;
1192         d2_h_cos2=d2-h_cos2;
1193
1194         /* some usefull expressions */
1195         frac1=c2/(d2-h_cos2);
1196         bracket1=1+c2d2-frac1;
1197         bracket2=f_c_ik*bracket1;
1198         bracket2_n_1=pow(bracket2,n-1.0);
1199         bracket2_n=bracket2_n_1*bracket2;
1200         bracket3=1+betan*bracket2_n;
1201         bracket3_pow_1=pow(bracket3,(-1.0/(2.0*n))-1.0);
1202         bracket3_pow=bracket3_pow_1*bracket3;
1203
1204         /* now go on with calc of b_ij and derivation of b_ij */
1205         b_ij=chi*bracket3_pow;
1206
1207         /* derivation of theta */
1208         v3_scale(&force,&dist_ij,d_theta1);
1209         v3_scale(&temp,&dist_ik,d_theta2);
1210         v3_add(&force,&force,&temp);
1211
1212         /* part 1 of derivation of b_ij */
1213         v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac1);
1214
1215         /* part 2 of derivation of b_ij */
1216         v3_scale(&temp,&dist_ik,df_c_ik*bracket1);
1217
1218         /* sum up and scale ... */
1219         v3_add(&temp,&temp,&force);
1220         scale=bracket2_n_1*n*betan*(1+betan*bracket3_pow_1)*chi*(1.0/(2.0*n));
1221         v3_scale(&temp,&temp,scale);
1222
1223         /* now construct an energy and a force out of that */
1224         v3_scale(&temp,&temp,f_a);
1225         v3_scale(&force,&dist_ij,df_a*b_ij);
1226         v3_add(&temp,&temp,&force);
1227         v3_scale(&temp,&temp,f_c);
1228         v3_scale(&force,&dist_ij,df_c*b_ij*f_a);
1229         v3_add(&force,&force,&temp);
1230
1231         /* add forces */
1232         v3_add(&(ai->f),&(ai->f),&force);
1233         /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
1234         moldyn->energy+=(0.25*f_a*b_ij*f_c);
1235
1236         return 0;
1237 }
1238