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         moldyn_log_shutdown(moldyn);
  45         link_cell_shutdown(moldyn);
  46         moldyn_log_shutdown(moldyn);
  47         rand_close(&(moldyn->random));
  48         free(moldyn->atom);
  49
  50         return 0;
  51 }
  52
  53 int set_int_alg(t_moldyn *moldyn,u8 algo) {
  54
  55         switch(algo) {
  56                 case MOLDYN_INTEGRATE_VERLET:
  57                         moldyn->integrate=velocity_verlet;
  58                         break;
  59                 default:
  60                         printf("unknown integration algorithm: %02x\n",algo);
  61                         return -1;
  62         }
  63
  64         return 0;
  65 }
  66
  67 int set_cutoff(t_moldyn *moldyn,double cutoff) {
  68
  69         moldyn->cutoff=cutoff;
  70
  71         return 0;
  72 }
  73
  74 int set_temperature(t_moldyn *moldyn,double t) {
  75
  76         moldyn->t=t;
  77
  78         return 0;
  79 }
  80
  81 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
  82
  83         moldyn->dim.x=x;
  84         moldyn->dim.y=y;
  85         moldyn->dim.z=z;
  86
  87         if(visualize) {
  88                 moldyn->vis.dim.x=x;
  89                 moldyn->vis.dim.y=y;
  90                 moldyn->vis.dim.z=z;
  91         }
  92
  93         return 0;
  94 }
  95
  96 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
  97
  98         if(x)
  99                 moldyn->status|=MOLDYN_STAT_PBX;
 100
 101         if(y)
 102                 moldyn->status|=MOLDYN_STAT_PBY;
 103
 104         if(z)
 105                 moldyn->status|=MOLDYN_STAT_PBZ;
 106
 107         return 0;
 108 }
 109
 110 int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
 111
 112         moldyn->func1b=func;
 113         moldyn->pot1b_params=params;
 114
 115         return 0;
 116 }
 117
 118 int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
 119
 120         moldyn->func2b=func;
 121         moldyn->pot2b_params=params;
 122
 123         return 0;
 124 }
 125
 126 int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
 127
 128         moldyn->func3b=func;
 129         moldyn->pot3b_params=params;
 130
 131         return 0;
 132 }
 133
 134 int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
 135
 136         switch(type) {
 137                 case LOG_TOTAL_ENERGY:
 138                         moldyn->ewrite=timer;
 139                         moldyn->efd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
 140                         if(moldyn->efd<0) {
 141                                 perror("[moldyn] efd open");
 142                                 return moldyn->efd;
 143                         }
 144                         dprintf(moldyn->efd,"# total energy log file\n");
 145                         break;
 146                 case LOG_TOTAL_MOMENTUM:
 147                         moldyn->mwrite=timer;
 148                         moldyn->mfd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
 149                         if(moldyn->mfd<0) {
 150                                 perror("[moldyn] mfd open");
 151                                 return moldyn->mfd;
 152                         }
 153                         dprintf(moldyn->efd,"# total momentum log file\n");
 154                         break;
 155                 case SAVE_STEP:
 156                         moldyn->swrite=timer;
 157                         strncpy(moldyn->sfb,fb,63);
 158                         break;
 159                 case VISUAL_STEP:
 160                         moldyn->vwrite=timer;
 161                         strncpy(moldyn->vfb,fb,63);
 162                         visual_init(&(moldyn->vis),fb);
 163                         break;
 164                 default:
 165                         printf("unknown log mechanism: %02x\n",type);
 166                         return -1;
 167         }
 168
 169         return 0;
 170 }
 171
 172 int moldyn_log_shutdown(t_moldyn *moldyn) {
 173
 174         if(moldyn->efd) close(moldyn->efd);
 175         if(moldyn->mfd) close(moldyn->mfd);
 176         if(moldyn->visual) visual_tini(moldyn->visual);
 177
 178         return 0;
 179 }
 180
 181 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 182                    u8 attr,u8 bnum,int a,int b,int c) {
 183
 184         int count;
 185         int ret;
 186         t_3dvec origin;
 187         t_atom *atom;
 188
 189         count=a*b*c;
 190         atom=moldyn->atom;
 191
 192         if(type==FCC) count*=4;
 193
 194         if(type==DIAMOND) count*=8;
 195
 196         atom=malloc(count*sizeof(t_atom));
 197         if(atom==NULL) {
 198                 perror("malloc (atoms)");
 199                 return -1;
 200         }
 201
 202         v3_zero(&origin);
 203
 204         switch(type) {
 205                 case FCC:
 206                         ret=fcc_init(a,b,c,lc,atom,&origin);
 207                         break;
 208                 case DIAMOND:
 209                         ret=diamond_init(a,b,c,lc,atom,&origin);
 210                         break;
 211                 default:
 212                         printf("unknown lattice type (%02x)\n",type);
 213                         return -1;
 214         }
 215
 216         /* debug */
 217         if(ret!=count) {
 218                 printf("ok, there is something wrong ...\n");
 219                 printf("calculated -> %d atoms\n",count);
 220                 printf("created -> %d atoms\n",ret);
 221                 return -1;
 222         }
 223
 224         moldyn->count=count;
 225
 226         while(count) {
 227                 atom[count-1].element=element;
 228                 atom[count-1].mass=mass;
 229                 atom[count-1].attr=attr;
 230                 atom[count-1].bnum=bnum;
 231                 count-=1;
 232         }
 233
 234         return ret;
 235 }
 236
 237 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
 238              t_3dvec *r,t_3dvec *v) {
 239
 240         t_atom *atom;
 241         void *ptr;
 242         int count;
 243
 244         atom=moldyn->atom;
 245         count=++(moldyn->count);
 246
 247         ptr=realloc(atom,count*sizeof(t_atom));
 248         if(!ptr) {
 249                 perror("[moldyn] realloc (add atom)");
 250                 return -1;
 251         }
 252         moldyn->atom=ptr;
 253
 254         atom=moldyn->atom;
 255         atom->r=*r;
 256         atom->v=*v;
 257         atom->element=element;
 258         atom->bnum=bnum;
 259         atom->attr=attr;
 260
 261         return 0;
 262 }
 263
 264 int destroy_atoms(t_moldyn *moldyn) {
 265
 266         if(moldyn->atom) free(moldyn->atom);
 267
 268         return 0;
 269 }
 270
 271 int thermal_init(t_moldyn *moldyn) {
 272
 273         /*
 274          * - gaussian distribution of velocities
 275          * - zero total momentum
 276          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 277          */
 278
 279         int i;
 280         double v,sigma;
 281         t_3dvec p_total,delta;
 282         t_atom *atom;
 283         t_random *random;
 284
 285         atom=moldyn->atom;
 286         random=&(moldyn->random);
 287
 288         /* gaussian distribution of velocities */
 289         v3_zero(&p_total);
 290         for(i=0;i<moldyn->count;i++) {
 291                 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t/atom[i].mass);
 292                 /* x direction */
 293                 v=sigma*rand_get_gauss(random);
 294                 atom[i].v.x=v;
 295                 p_total.x+=atom[i].mass*v;
 296                 /* y direction */
 297                 v=sigma*rand_get_gauss(random);
 298                 atom[i].v.y=v;
 299                 p_total.y+=atom[i].mass*v;
 300                 /* z direction */
 301                 v=sigma*rand_get_gauss(random);
 302                 atom[i].v.z=v;
 303                 p_total.z+=atom[i].mass*v;
 304         }
 305
 306         /* zero total momentum */
 307         v3_scale(&p_total,&p_total,1.0/moldyn->count);
 308         for(i=0;i<moldyn->count;i++) {
 309                 v3_scale(&delta,&p_total,1.0/atom[i].mass);
 310                 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
 311         }
 312
 313         /* velocity scaling */
 314         scale_velocity(moldyn);
 315
 316         return 0;
 317 }
 318
 319 int scale_velocity(t_moldyn *moldyn) {
 320
 321         int i;
 322         double e,c;
 323         t_atom *atom;
 324
 325         atom=moldyn->atom;
 326
 327         /*
 328          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 329          */
 330         e=0.0;
 331         for(i=0;i<moldyn->count;i++)
 332                 e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 333         c=sqrt((2.0*e)/(3.0*moldyn->count*K_BOLTZMANN*moldyn->t));
 334         for(i=0;i<moldyn->count;i++)
 335                 v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
 336
 337         return 0;
 338 }
 339
 340 double get_e_kin(t_moldyn *moldyn) {
 341
 342         int i;
 343         t_atom *atom;
 344
 345         atom=moldyn->atom;
 346         moldyn->ekin=0.0;
 347
 348         for(i=0;i<moldyn->count;i++)
 349                 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 350
 351         return moldyn->ekin;
 352 }
 353
 354 double get_e_pot(t_moldyn *moldyn) {
 355
 356         return moldyn->energy;
 357 }
 358
 359 double update_e_kin(t_moldyn *moldyn) {
 360
 361         return(get_e_kin(moldyn));
 362 }
 363
 364 double get_total_energy(t_moldyn *moldyn) {
 365
 366         return(moldyn->ekin+moldyn->energy);
 367 }
 368
 369 t_3dvec get_total_p(t_moldyn *moldyn) {
 370
 371         t_3dvec p,p_total;
 372         int i;
 373         t_atom *atom;
 374
 375         atom=moldyn->atom;
 376
 377         v3_zero(&p_total);
 378         for(i=0;i<moldyn->count;i++) {
 379                 v3_scale(&p,&(atom[i].v),atom[i].mass);
 380                 v3_add(&p_total,&p_total,&p);
 381         }
 382
 383         return p_total;
 384 }
 385
 386 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
 387
 388         double tau;
 389
 390         /* nn_dist is the nearest neighbour distance */
 391
 392         if(moldyn->t==5.0) {
 393                 printf("[moldyn] i do not estimate timesteps below %f K!\n",
 394                        MOLDYN_CRITICAL_EST_TEMP);
 395                 return 23.42;
 396         }
 397
 398         tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
 399
 400         return tau;
 401 }
 402
 403 /*
 404  * numerical tricks
 405  */
 406
 407 /* linked list / cell method */
 408
 409 int link_cell_init(t_moldyn *moldyn) {
 410
 411         t_linkcell *lc;
 412         int i;
 413         int fd;
 414
 415         fd=open("/dev/null",O_WRONLY);
 416
 417         lc=&(moldyn->lc);
 418
 419         /* partitioning the md cell */
 420         lc->nx=moldyn->dim.x/moldyn->cutoff;
 421         lc->x=moldyn->dim.x/lc->nx;
 422         lc->ny=moldyn->dim.y/moldyn->cutoff;
 423         lc->y=moldyn->dim.y/lc->ny;
 424         lc->nz=moldyn->dim.z/moldyn->cutoff;
 425         lc->z=moldyn->dim.z/lc->nz;
 426
 427         lc->cells=lc->nx*lc->ny*lc->nz;
 428         lc->subcell=malloc(lc->cells*sizeof(t_list));
 429
 430         printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 431
 432         for(i=0;i<lc->cells;i++)
 433                 //list_init(&(lc->subcell[i]),1);
 434                 list_init(&(lc->subcell[i]),fd);
 435
 436         link_cell_update(moldyn);
 437
 438         return 0;
 439 }
 440
 441 int link_cell_update(t_moldyn *moldyn) {
 442
 443         int count,i,j,k;
 444         int nx,ny,nz;
 445         t_atom *atom;
 446         t_linkcell *lc;
 447
 448         atom=moldyn->atom;
 449         lc=&(moldyn->lc);
 450
 451         nx=lc->nx;
 452         ny=lc->ny;
 453         nz=lc->nz;
 454
 455         for(i=0;i<lc->cells;i++)
 456                 list_destroy(&(moldyn->lc.subcell[i]));
 457
 458         for(count=0;count<moldyn->count;count++) {
 459                 i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
 460                 j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
 461                 k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
 462                 list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
 463                                        &(atom[count]));
 464         }
 465
 466         return 0;
 467 }
 468
 469 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 470
 471         t_linkcell *lc;
 472         int a;
 473         int count1,count2;
 474         int ci,cj,ck;
 475         int nx,ny,nz;
 476         int x,y,z;
 477         u8 bx,by,bz;
 478
 479         lc=&(moldyn->lc);
 480         nx=lc->nx;
 481         ny=lc->ny;
 482         nz=lc->nz;
 483         count1=1;
 484         count2=27;
 485         a=nx*ny;
 486
 487
 488         cell[0]=lc->subcell[i+j*nx+k*a];
 489         for(ci=-1;ci<=1;ci++) {
 490                 bx=0;
 491                 x=i+ci;
 492                 if((x<0)||(x>=nx)) {
 493                         x=(x+nx)%nx;
 494                         bx=1;
 495                 }
 496                 for(cj=-1;cj<=1;cj++) {
 497                         by=0;
 498                         y=j+cj;
 499                         if((y<0)||(y>=ny)) {
 500                                 y=(y+ny)%ny;
 501                                 by=1;
 502                         }
 503                         for(ck=-1;ck<=1;ck++) {
 504                                 bz=0;
 505                                 z=k+ck;
 506                                 if((z<0)||(z>=nz)) {
 507                                         z=(z+nz)%nz;
 508                                         bz=1;
 509                                 }
 510                                 if(!(ci|cj|ck)) continue;
 511                                 if(bx|by|bz) {
 512                                         cell[--count2]=lc->subcell[x+y*nx+z*a];
 513                                 }
 514                                 else {
 515                                         cell[count1++]=lc->subcell[x+y*nx+z*a];
 516                                 }
 517                         }
 518                 }
 519         }
 520
 521         lc->dnlc=count2;
 522         lc->countn=27;
 523
 524         return count2;
 525 }
 526
 527 int link_cell_shutdown(t_moldyn *moldyn) {
 528
 529         int i;
 530         t_linkcell *lc;
 531
 532         lc=&(moldyn->lc);
 533
 534         for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
 535                 list_shutdown(&(moldyn->lc.subcell[i]));
 536
 537         return 0;
 538 }
 539
 540 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
 541
 542         int count;
 543         void *ptr;
 544         t_moldyn_schedule *schedule;
 545
 546         schedule=&(moldyn->schedule);
 547         count=++(schedule->content_count);
 548
 549         ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
 550         if(!ptr) {
 551                 perror("[moldyn] realloc (runs)");
 552                 return -1;
 553         }
 554         moldyn->schedule.runs=ptr;
 555         moldyn->schedule.runs[count-1]=runs;
 556
 557         ptr=realloc(schedule->tau,count*sizeof(double));
 558         if(!ptr) {
 559                 perror("[moldyn] realloc (tau)");
 560                 return -1;
 561         }
 562         moldyn->schedule.tau=ptr;
 563         moldyn->schedule.tau[count-1]=tau;
 564
 565         return 0;
 566 }
 567
 568 int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
 569
 570         moldyn->schedule.hook=hook;
 571         moldyn->schedule.hook_params=hook_params;
 572
 573         return 0;
 574 }
 575
 576 /*
 577  *
 578  * 'integration of newtons equation' - algorithms
 579  *
 580  */
 581
 582 /* start the integration */
 583
 584 int moldyn_integrate(t_moldyn *moldyn) {
 585
 586         int i,sched;
 587         unsigned int e,m,s,v;
 588         t_3dvec p;
 589         t_moldyn_schedule *schedule;
 590
 591         int fd;
 592         char fb[128];
 593
 594         schedule=&(moldyn->schedule);
 595
 596         /* initialize linked cell method */
 597         link_cell_init(moldyn);
 598
 599         /* logging & visualization */
 600         e=moldyn->ewrite;
 601         m=moldyn->mwrite;
 602         s=moldyn->swrite;
 603         v=moldyn->vwrite;
 604
 605         /* sqaure of some variables */
 606         moldyn->tau_square=moldyn->tau*moldyn->tau;
 607         moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
 608
 609         /* calculate initial forces */
 610         potential_force_calc(moldyn);
 611
 612         /* zero absolute time */
 613         moldyn->time=0.0;
 614
 615         for(sched=0;sched<moldyn->schedule.content_count;sched++) {
 616
 617                 /* setting amount of runs and finite time step size */
 618                 moldyn->tau=schedule->tau[sched];
 619                 moldyn->tau_square=moldyn->tau*moldyn->tau;
 620                 moldyn->time_steps=schedule->runs[sched];
 621
 622         /* integration according to schedule */
 623
 624         for(i=0;i<moldyn->time_steps;i++) {
 625
 626                 /* integration step */
 627                 moldyn->integrate(moldyn);
 628
 629                 /* increase absolute time */
 630                 moldyn->time+=moldyn->tau;
 631
 632                 /* check for log & visualization */
 633                 if(e) {
 634                         if(!(i%e))
 635                                 dprintf(moldyn->efd,
 636                                         "%.15f %.45f %.45f %.45f\n",
 637                                         moldyn->time,update_e_kin(moldyn),
 638                                         moldyn->energy,
 639                                         get_total_energy(moldyn));
 640                 }
 641                 if(m) {
 642                         if(!(i%m)) {
 643                                 p=get_total_p(moldyn);
 644                                 dprintf(moldyn->mfd,
 645                                         "%.15f %.45f\n",moldyn->time,
 646                                         v3_norm(&p));
 647                         }
 648                 }
 649                 if(s) {
 650                         if(!(i%s)) {
 651                                 snprintf(fb,128,"%s-%f-%.15f.save",moldyn->sfb,
 652                                          moldyn->t,i*moldyn->tau);
 653                                 fd=open(fb,O_WRONLY|O_TRUNC|O_CREAT);
 654                                 if(fd<0) perror("[moldyn] save fd open");
 655                                 else {
 656                                         write(fd,moldyn,sizeof(t_moldyn));
 657                                         write(fd,moldyn->atom,
 658                                               moldyn->count*sizeof(t_atom));
 659                                 }
 660                                 close(fd);
 661                         }
 662                 }
 663                 if(v) {
 664                         if(!(i%v)) {
 665                                 visual_atoms(&(moldyn->vis),moldyn->time,
 666                                              moldyn->atom,moldyn->count);
 667                                 printf("\rsched: %d, steps: %d",sched,i);
 668                                 fflush(stdout);
 669                         }
 670                 }
 671
 672         }
 673
 674                 /* check for hooks */
 675                 if(schedule->hook)
 676                         schedule->hook(moldyn,schedule->hook_params);
 677
 678         }
 679
 680         return 0;
 681 }
 682
 683 /* velocity verlet */
 684
 685 int velocity_verlet(t_moldyn *moldyn) {
 686
 687         int i,count;
 688         double tau,tau_square;
 689         t_3dvec delta;
 690         t_atom *atom;
 691
 692         atom=moldyn->atom;
 693         count=moldyn->count;
 694         tau=moldyn->tau;
 695         tau_square=moldyn->tau_square;
 696
 697         for(i=0;i<count;i++) {
 698                 /* new positions */
 699                 v3_scale(&delta,&(atom[i].v),tau);
 700                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 701                 v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
 702                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 703                 v3_per_bound(&(atom[i].r),&(moldyn->dim));
 704
 705                 /* velocities */
 706                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 707                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 708         }
 709
 710         /* neighbour list update */
 711         link_cell_update(moldyn);
 712
 713         /* forces depending on chosen potential */
 714         potential_force_calc(moldyn);
 715         //moldyn->potential_force_function(moldyn);
 716
 717         for(i=0;i<count;i++) {
 718                 /* again velocities */
 719                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 720                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 721         }
 722
 723         return 0;
 724 }
 725
 726
 727 /*
 728  *
 729  * potentials & corresponding forces
 730  *
 731  */
 732
 733 /* generic potential and force calculation */
 734
 735 int potential_force_calc(t_moldyn *moldyn) {
 736
 737         int i,j,k,count;
 738         t_atom *atom,*btom,*ktom;
 739         t_linkcell *lc;
 740         t_list neighbour[27];
 741         t_list *this,*thisk,*neighbourk;
 742         u8 bc,bck;
 743         int countn,dnlc;
 744
 745         count=moldyn->count;
 746         atom=moldyn->atom;
 747         lc=&(moldyn->lc);
 748
 749         /* reset energy */
 750         moldyn->energy=0.0;
 751
 752 printf("DEBUG: count = %d\n",count);
 753         for(i=0;i<count;i++) {
 754
 755                 /* reset force */
 756                 v3_zero(&(atom[i].f));
 757
 758                 /* single particle potential/force */
 759                 if(atom[i].attr&ATOM_ATTR_1BP)
 760                         moldyn->func1b(moldyn,&(atom[i]));
 761
 762                 /* 2 body pair potential/force */
 763                 if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
 764
 765 printf("DEBUG: processing atom %d\n",i);
 766                         link_cell_neighbour_index(moldyn,
 767                                 (atom[i].r.x+moldyn->dim.x/2)/lc->x,
 768                                 (atom[i].r.y+moldyn->dim.y/2)/lc->y,
 769                                 (atom[i].r.z+moldyn->dim.z/2)/lc->z,
 770                                 neighbour);
 771
 772                         countn=lc->countn;
 773                         dnlc=lc->dnlc;
 774
 775 printf("DEBUG: countn = %d - dnslc = %d\n",countn,dnlc);
 776                         for(j=0;j<countn;j++) {
 777
 778                                 this=&(neighbour[j]);
 779                                 list_reset(this);
 780
 781                                 if(this->start==NULL)
 782                                         continue;
 783
 784                                 bc=(j<dnlc)?0:1;
 785
 786                                 do {
 787                                         btom=this->current->data;
 788
 789                                         if(btom==&(atom[i]))
 790                                                 continue;
 791
 792                                         if((btom->attr&ATOM_ATTR_2BP)&
 793                                            (atom[i].attr&ATOM_ATTR_2BP))
 794 printf("DEBUG: calling func2b\n");
 795                                                 moldyn->func2b(moldyn,
 796                                                                &(atom[i]),
 797                                                                btom,
 798                                                                bc);
 799
 800                                         /* 3 body potential/force */
 801
 802                                         if(!(atom[i].attr&ATOM_ATTR_3BP)||
 803                                            !(btom->attr&ATOM_ATTR_3BP))
 804                                                 continue;
 805
 806                                         link_cell_neighbour_index(moldyn,
 807                                            (btom->r.x+moldyn->dim.x/2)/lc->x,
 808                                            (btom->r.y+moldyn->dim.y/2)/lc->y,
 809                                            (btom->r.z+moldyn->dim.z/2)/lc->z,
 810                                            neighbourk);
 811
 812                                         for(k=0;k<lc->countn;k++) {
 813
 814                                                 thisk=&(neighbourk[k]);
 815                                                 list_reset(thisk);
 816
 817                                                 if(thisk->start==NULL)
 818                                                         continue;
 819
 820                                                 bck=(k<lc->dnlc)?0:1;
 821
 822                                                 do {
 823
 824                         ktom=thisk->current->data;
 825
 826                         if(!(ktom->attr&ATOM_ATTR_3BP))
 827                                 continue;
 828
 829                         if(ktom==btom)
 830                                 continue;
 831
 832                         if(ktom==&(atom[i]))
 833                                 continue;
 834
 835                         moldyn->func3b(moldyn,&(atom[i]),btom,ktom,bck);
 836
 837                                                 } while(list_next(thisk)!=\
 838                                                         L_NO_NEXT_ELEMENT);
 839
 840                                         }
 841
 842                                 } while(list_next(this)!=L_NO_NEXT_ELEMENT);
 843                         }
 844                 }
 845         }
 846
 847         return 0;
 848 }
 849
 850 /*
 851  * periodic boundayr checking
 852  */
 853
 854 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
 855
 856         double x,y,z;
 857         t_3dvec *dim;
 858
 859         dim=&(moldyn->dim);
 860
 861         x=0.5*dim->x;
 862         y=0.5*dim->y;
 863         z=0.5*dim->z;
 864
 865         if(moldyn->status&MOLDYN_STAT_PBX) {
 866                 if(a->x>=x) a->x-=dim->x;
 867                 else if(-a->x>x) a->x+=dim->x;
 868         }
 869         if(moldyn->status&MOLDYN_STAT_PBY) {
 870                 if(a->y>=y) a->y-=dim->y;
 871                 else if(-a->y>y) a->y+=dim->y;
 872         }
 873         if(moldyn->status&MOLDYN_STAT_PBZ) {
 874                 if(a->z>=z) a->z-=dim->z;
 875                 else if(-a->z>z) a->z+=dim->z;
 876         }
 877
 878         return 0;
 879 }
 880
 881
 882 /*
 883  * example potentials
 884  */
 885
 886 /* harmonic oscillator potential and force */
 887
 888 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 889
 890         t_ho_params *params;
 891         t_3dvec force,distance;
 892         double d;
 893         double sc,equi_dist;
 894
 895         params=moldyn->pot2b_params;
 896         sc=params->spring_constant;
 897         equi_dist=params->equilibrium_distance;
 898
 899         v3_sub(&distance,&(ai->r),&(aj->r));
 900
 901         v3_per_bound(&distance,&(moldyn->dim));
 902         if(bc) check_per_bound(moldyn,&distance);
 903         d=v3_norm(&distance);
 904         if(d<=moldyn->cutoff) {
 905                 /* energy is 1/2 (d-d0)^2, but we will add this twice ... */
 906                 moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
 907                 v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
 908                 v3_add(&(ai->f),&(ai->f),&force);
 909         }
 910
 911         return 0;
 912 }
 913
 914 /* lennard jones potential & force for one sort of atoms */
 915
 916 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 917
 918         t_lj_params *params;
 919         t_3dvec force,distance;
 920         double d,h1,h2;
 921         double eps,sig6,sig12;
 922
 923         params=moldyn->pot2b_params;
 924         eps=params->epsilon4;
 925         sig6=params->sigma6;
 926         sig12=params->sigma12;
 927
 928         v3_sub(&distance,&(ai->r),&(aj->r));
 929         if(bc) check_per_bound(moldyn,&distance);
 930         d=v3_absolute_square(&distance);        /* 1/r^2 */
 931         if(d<=moldyn->cutoff_square) {
 932                 d=1.0/d;                        /* 1/r^2 */
 933                 h2=d*d;                         /* 1/r^4 */
 934                 h2*=d;                          /* 1/r^6 */
 935                 h1=h2*h2;                       /* 1/r^12 */
 936                 /* energy is eps*..., but we will add this twice ... */
 937                 moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
 938                 h2*=d;                          /* 1/r^8 */
 939                 h1*=d;                          /* 1/r^14 */
 940                 h2*=6*sig6;
 941                 h1*=12*sig12;
 942                 d=+h1-h2;
 943                 d*=eps;
 944                 v3_scale(&force,&distance,d);
 945                 v3_add(&(ai->f),&(aj->f),&force);
 946         }
 947
 948         return 0;
 949 }
 950
 951 /*
 952  * tersoff potential & force for 2 sorts of atoms
 953  */
 954
 955 /* tersoff 1 body part */
 956 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
 957
 958         int num;
 959         t_tersoff_mult_params *params;
 960         t_tersoff_exchange *exchange;
 961
 962         num=ai->bnum;
 963         params=moldyn->pot1b_params;
 964         exchange=&(params->exchange);
 965
 966         /*
 967          * simple: point constant parameters only depending on atom i to
 968          *         their right values
 969          */
 970
 971         exchange->beta=&(params->beta[num]);
 972         exchange->n=&(params->n[num]);
 973         exchange->c=&(params->c[num]);
 974         exchange->d=&(params->d[num]);
 975         exchange->h=&(params->h[num]);
 976
 977         exchange->betan=pow(*(exchange->beta),*(exchange->n));
 978         exchange->c2=params->c[num]*params->c[num];
 979         exchange->d2=params->d[num]*params->d[num];
 980         exchange->c2d2=exchange->c2/exchange->d2;
 981
 982         return 0;
 983 }
 984
 985 /* tersoff 2 body part */
 986 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 987
 988         t_tersoff_mult_params *params;
 989         t_tersoff_exchange *exchange;
 990         t_3dvec dist_ij,force;
 991         double d_ij;
 992         double A,B,R,S,lambda,mu;
 993         double f_r,df_r;
 994         double f_c,df_c;
 995         int num;
 996         double s_r;
 997         double arg;
 998         double scale;
 999
1000         params=moldyn->pot2b_params;
1001         num=ai->bnum;
1002         exchange=&(params->exchange);
1003
1004         exchange->run3bp=0;
1005
1006         /*
1007          * we need: f_c, df_c, f_r, df_r
1008          *
1009          * therefore we need: R, S, A, lambda
1010          */
1011
1012         v3_sub(&dist_ij,&(ai->r),&(aj->r));
1013
1014         if(bc) check_per_bound(moldyn,&dist_ij);
1015
1016         /* save for use in 3bp */ /* REALLY ?!?!?! */
1017         exchange->dist_ij=dist_ij;
1018
1019         /* constants */
1020         if(num==aj->bnum) {
1021                 S=params->S[num];
1022                 R=params->R[num];
1023                 A=params->A[num];
1024                 lambda=params->lambda[num];
1025                 /* more constants depending of atoms i and j, needed in 3bp */
1026                 params->exchange.B=&(params->B[num]);
1027                 params->exchange.mu=&(params->mu[num]);
1028                 mu=params->mu[num];
1029                 params->exchange.chi=1.0;
1030         }
1031         else {
1032                 S=params->Smixed;
1033                 R=params->Rmixed;
1034                 A=params->Amixed;
1035                 lambda=params->lambda_m;
1036                 /* more constants depending of atoms i and j, needed in 3bp */
1037                 params->exchange.B=&(params->Bmixed);
1038                 params->exchange.mu=&(params->mu_m);
1039                 mu=params->mu_m;
1040                 params->exchange.chi=params->chi;
1041         }
1042
1043         d_ij=v3_norm(&dist_ij);
1044
1045         /* save for use in 3bp */
1046         exchange->d_ij=d_ij;
1047
1048         if(d_ij>S)
1049                 return 0;
1050
1051         f_r=A*exp(-lambda*d_ij);
1052         df_r=-lambda*f_r/d_ij;
1053
1054         /* f_a, df_a calc + save for 3bp use */
1055         exchange->f_a=-B*exp(-mu*d_ij);
1056         exchange->df_a=-mu*exchange->f_a/d_ij;
1057
1058         if(d_ij<R) {
1059                 /* f_c = 1, df_c = 0 */
1060                 f_c=1.0;
1061                 df_c=0.0;
1062                 v3_scale(&force,&dist_ij,df_r);
1063         }
1064         else {
1065                 s_r=S-R;
1066                 arg=M_PI*(d_ij-R)/s_r;
1067                 f_c=0.5+0.5*cos(arg);
1068                 df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij));
1069                 scale=df_c*f_r+df_r*f_c;
1070                 v3_scale(&force,&dist_ij,scale);
1071         }
1072
1073         /* add forces */
1074         v3_add(&(ai->f),&(ai->f),&force);
1075         /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
1076         moldyn->energy+=(0.25*f_r*f_c);
1077
1078         /* save for use in 3bp */
1079         exchange->f_c=f_c;
1080         exchange->df_c=df_c;
1081
1082         /* enable the run of 3bp function */
1083         exchange->run3bp=1;
1084
1085         return 0;
1086 }
1087
1088 /* tersoff 3 body part */
1089
1090 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
1091
1092         t_tersoff_mult_params *params;
1093         t_tersoff_exchange *exchange;
1094         t_3dvec dist_ij,dist_ik,dist_jk;
1095         t_3dvec temp,force;
1096         double R,S,s_r;
1097         double d_ij,d_ij2,d_ik,d_jk;
1098         double f_c,df_c,b_ij,f_a,df_a;
1099         double f_c_ik,df_c_ik,arg;
1100         double scale;
1101         double chi;
1102         double n,c,d,h,beta,betan;
1103         double c2,d2,c2d2;
1104         double numer,denom;
1105         double theta,cos_theta,sin_theta;
1106         double d_theta,d_theta1,d_theta2;
1107         double h_cos,h_cos2,d2_h_cos2;
1108         double frac1,bracket1,bracket2,bracket2_n_1,bracket2_n;
1109         double bracket3,bracket3_pow_1,bracket3_pow;
1110         int num;
1111
1112         params=moldyn->pot3b_params;
1113         num=ai->bnum;
1114         exchange=&(params->exchange);
1115
1116         if(!(exchange->run3bp))
1117                 return 0;
1118
1119         /*
1120          * we need: f_c, d_fc, b_ij, db_ij, f_a, df_a
1121          *
1122          * we got f_c, df_c, f_a, df_a from 2bp calculation
1123          */
1124
1125         d_ij=exchange->d_ij;
1126         d_ij2=exchange->d_ij2;
1127
1128         f_a=params->exchange.f_a;
1129         df_a=params->exchange.df_a;
1130
1131         /* d_ij is <= S, as we didn't return so far! */
1132
1133         /*
1134          * calc of b_ij (scalar) and db_ij (vector)
1135          *
1136          * - for b_ij: chi, beta, f_c_ik, w(=1), c, d, h, n, cos_theta
1137          *
1138          * - for db_ij: d_theta, sin_theta, cos_theta, f_c_ik, df_c_ik,
1139          *              w_ik,
1140          *
1141          */
1142
1143
1144         v3_sub(&dist_ik,&(ai->r),&(ak->r));
1145         if(bc) check_per_bound(moldyn,&dist_ik);
1146         d_ik=v3_norm(&dist_ik);
1147
1148         /* constants for f_c_ik calc */
1149         if(num==ak->bnum) {
1150                 R=params->R[num];
1151                 S=params->S[num];
1152         }
1153         else {
1154                 R=params->Rmixed;
1155                 S=params->Smixed;
1156         }
1157
1158         /* calc of f_c_ik */
1159         if(d_ik>S)
1160                 return 0;
1161
1162         if(d_ik<R) {
1163                 /* f_c_ik = 1, df_c_ik = 0 */
1164                 f_c_ik=1.0;
1165                 df_c_ik=0.0;
1166         }
1167         else {
1168                 s_r=S-R;
1169                 arg=M_PI*(d_ik-R)/s_r;
1170                 f_c_ik=0.5+0.5*cos(arg);
1171                 df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik));
1172         }
1173
1174         v3_sub(&dist_jk,&(aj->r),&(ak->r));
1175         if(bc) check_per_bound(moldyn,&dist_jk);
1176         d_jk=v3_norm(&dist_jk);
1177
1178         beta=*(exchange->beta);
1179         betan=exchange->betan;
1180         n=*(exchange->n);
1181         c=*(exchange->c);
1182         d=*(exchange->d);
1183         h=*(exchange->h);
1184         c2=exchange->c2;
1185         d2=exchange->d2;
1186         c2d2=exchange->c2d2;
1187
1188         numer=d_ij2+d_ik*d_ik-d_jk*d_jk;
1189         denom=2*d_ij*d_ik;
1190         cos_theta=numer/denom;
1191         sin_theta=sqrt(1.0-(cos_theta*cos_theta));
1192         theta=acos(cos_theta);
1193         d_theta=(-1.0/sqrt(1.0-cos_theta*cos_theta))/(denom*denom);
1194         d_theta1=2*denom-numer*2*d_ik/d_ij;
1195         d_theta2=2*denom-numer*2*d_ij/d_ik;
1196         d_theta1*=d_theta;
1197         d_theta2*=d_theta;
1198
1199         h_cos=(h-cos_theta);
1200         h_cos2=h_cos*h_cos;
1201         d2_h_cos2=d2-h_cos2;
1202
1203         /* some usefull expressions */
1204         frac1=c2/(d2-h_cos2);
1205         bracket1=1+c2d2-frac1;
1206         bracket2=f_c_ik*bracket1;
1207         bracket2_n_1=pow(bracket2,n-1.0);
1208         bracket2_n=bracket2_n_1*bracket2;
1209         bracket3=1+betan*bracket2_n;
1210         bracket3_pow_1=pow(bracket3,(-1.0/(2.0*n))-1.0);
1211         bracket3_pow=bracket3_pow_1*bracket3;
1212
1213         /* now go on with calc of b_ij and derivation of b_ij */
1214         b_ij=chi*bracket3_pow;
1215
1216         /* derivation of theta */
1217         v3_scale(&force,&dist_ij,d_theta1);
1218         v3_scale(&temp,&dist_ik,d_theta2);
1219         v3_add(&force,&force,&temp);
1220
1221         /* part 1 of derivation of b_ij */
1222         v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac1);
1223
1224         /* part 2 of derivation of b_ij */
1225         v3_scale(&temp,&dist_ik,df_c_ik*bracket1);
1226
1227         /* sum up and scale ... */
1228         v3_add(&temp,&temp,&force);
1229         scale=bracket2_n_1*n*betan*(1+betan*bracket3_pow_1)*chi*(1.0/(2.0*n));
1230         v3_scale(&temp,&temp,scale);
1231
1232         /* now construct an energy and a force out of that */
1233         v3_scale(&temp,&temp,f_a);
1234         v3_scale(&force,&dist_ij,df_a*b_ij);
1235         v3_add(&temp,&temp,&force);
1236         v3_scale(&temp,&temp,f_c);
1237         v3_scale(&force,&dist_ij,df_c*b_ij*f_a);
1238         v3_add(&force,&force,&temp);
1239
1240         /* add forces */
1241         v3_add(&(ai->f),&(ai->f),&force);
1242         /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
1243         moldyn->energy+=(0.25*f_a*b_ij*f_c);
1244
1245         return 0;
1246 }
1247