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         printf("[moldyn] shutdown\n");
  45         moldyn_log_shutdown(moldyn);
  46         link_cell_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         printf("[moldyn] log shutdown\n");
 175         if(moldyn->efd) close(moldyn->efd);
 176         if(moldyn->mfd) close(moldyn->mfd);
 177         if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
 178
 179         return 0;
 180 }
 181
 182 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 183                    u8 attr,u8 bnum,int a,int b,int c) {
 184
 185         int count;
 186         int ret;
 187         t_3dvec origin;
 188
 189         count=a*b*c;
 190
 191         if(type==FCC) count*=4;
 192
 193         if(type==DIAMOND) count*=8;
 194
 195         moldyn->atom=malloc(count*sizeof(t_atom));
 196         if(moldyn->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,moldyn->atom,&origin);
 206                         break;
 207                 case DIAMOND:
 208                         ret=diamond_init(a,b,c,lc,moldyn->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                 moldyn->atom[count-1].element=element;
 227                 moldyn->atom[count-1].mass=mass;
 228                 moldyn->atom[count-1].attr=attr;
 229                 moldyn->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[count-1].r=*r;
 255         atom[count-1].v=*v;
 256         atom[count-1].element=element;
 257         atom[count-1].mass=mass;
 258         atom[count-1].bnum=bnum;
 259         atom[count-1].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
 331         if(moldyn->t==0.0) {
 332                 printf("[moldyn] no velocity scaling for T = 0 K\n");
 333                 return -1;
 334         }
 335
 336         e=0.0;
 337         for(i=0;i<moldyn->count;i++)
 338                 e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 339         c=sqrt((2.0*e)/(3.0*moldyn->count*K_BOLTZMANN*moldyn->t));
 340         for(i=0;i<moldyn->count;i++)
 341                 v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
 342
 343         return 0;
 344 }
 345
 346 double get_e_kin(t_moldyn *moldyn) {
 347
 348         int i;
 349         t_atom *atom;
 350
 351         atom=moldyn->atom;
 352         moldyn->ekin=0.0;
 353
 354         for(i=0;i<moldyn->count;i++)
 355                 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 356
 357         return moldyn->ekin;
 358 }
 359
 360 double get_e_pot(t_moldyn *moldyn) {
 361
 362         return moldyn->energy;
 363 }
 364
 365 double update_e_kin(t_moldyn *moldyn) {
 366
 367         return(get_e_kin(moldyn));
 368 }
 369
 370 double get_total_energy(t_moldyn *moldyn) {
 371
 372         return(moldyn->ekin+moldyn->energy);
 373 }
 374
 375 t_3dvec get_total_p(t_moldyn *moldyn) {
 376
 377         t_3dvec p,p_total;
 378         int i;
 379         t_atom *atom;
 380
 381         atom=moldyn->atom;
 382
 383         v3_zero(&p_total);
 384         for(i=0;i<moldyn->count;i++) {
 385                 v3_scale(&p,&(atom[i].v),atom[i].mass);
 386                 v3_add(&p_total,&p_total,&p);
 387         }
 388
 389         return p_total;
 390 }
 391
 392 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
 393
 394         double tau;
 395
 396         /* nn_dist is the nearest neighbour distance */
 397
 398         if(moldyn->t==5.0) {
 399                 printf("[moldyn] i do not estimate timesteps below %f K!\n",
 400                        MOLDYN_CRITICAL_EST_TEMP);
 401                 return 23.42;
 402         }
 403
 404         tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
 405
 406         return tau;
 407 }
 408
 409 /*
 410  * numerical tricks
 411  */
 412
 413 /* linked list / cell method */
 414
 415 int link_cell_init(t_moldyn *moldyn) {
 416
 417         t_linkcell *lc;
 418         int i;
 419         int fd;
 420
 421         fd=open("/dev/null",O_WRONLY);
 422
 423         lc=&(moldyn->lc);
 424
 425         /* partitioning the md cell */
 426         lc->nx=moldyn->dim.x/moldyn->cutoff;
 427         lc->x=moldyn->dim.x/lc->nx;
 428         lc->ny=moldyn->dim.y/moldyn->cutoff;
 429         lc->y=moldyn->dim.y/lc->ny;
 430         lc->nz=moldyn->dim.z/moldyn->cutoff;
 431         lc->z=moldyn->dim.z/lc->nz;
 432
 433         lc->cells=lc->nx*lc->ny*lc->nz;
 434         lc->subcell=malloc(lc->cells*sizeof(t_list));
 435
 436         printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 437
 438         for(i=0;i<lc->cells;i++)
 439                 //list_init(&(lc->subcell[i]),1);
 440                 list_init(&(lc->subcell[i]),fd);
 441
 442         link_cell_update(moldyn);
 443
 444         return 0;
 445 }
 446
 447 int link_cell_update(t_moldyn *moldyn) {
 448
 449         int count,i,j,k;
 450         int nx,ny,nz;
 451         t_atom *atom;
 452         t_linkcell *lc;
 453
 454         atom=moldyn->atom;
 455         lc=&(moldyn->lc);
 456
 457         nx=lc->nx;
 458         ny=lc->ny;
 459         nz=lc->nz;
 460
 461         for(i=0;i<lc->cells;i++)
 462                 list_destroy(&(moldyn->lc.subcell[i]));
 463
 464         for(count=0;count<moldyn->count;count++) {
 465                 i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
 466                 j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
 467                 k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
 468                 list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
 469                                        &(atom[count]));
 470         }
 471
 472         return 0;
 473 }
 474
 475 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 476
 477         t_linkcell *lc;
 478         int a;
 479         int count1,count2;
 480         int ci,cj,ck;
 481         int nx,ny,nz;
 482         int x,y,z;
 483         u8 bx,by,bz;
 484
 485         lc=&(moldyn->lc);
 486         nx=lc->nx;
 487         ny=lc->ny;
 488         nz=lc->nz;
 489         count1=1;
 490         count2=27;
 491         a=nx*ny;
 492
 493
 494         cell[0]=lc->subcell[i+j*nx+k*a];
 495         for(ci=-1;ci<=1;ci++) {
 496                 bx=0;
 497                 x=i+ci;
 498                 if((x<0)||(x>=nx)) {
 499                         x=(x+nx)%nx;
 500                         bx=1;
 501                 }
 502                 for(cj=-1;cj<=1;cj++) {
 503                         by=0;
 504                         y=j+cj;
 505                         if((y<0)||(y>=ny)) {
 506                                 y=(y+ny)%ny;
 507                                 by=1;
 508                         }
 509                         for(ck=-1;ck<=1;ck++) {
 510                                 bz=0;
 511                                 z=k+ck;
 512                                 if((z<0)||(z>=nz)) {
 513                                         z=(z+nz)%nz;
 514                                         bz=1;
 515                                 }
 516                                 if(!(ci|cj|ck)) continue;
 517                                 if(bx|by|bz) {
 518                                         cell[--count2]=lc->subcell[x+y*nx+z*a];
 519                                 }
 520                                 else {
 521                                         cell[count1++]=lc->subcell[x+y*nx+z*a];
 522                                 }
 523                         }
 524                 }
 525         }
 526
 527         lc->dnlc=count2;
 528         lc->countn=27;
 529
 530         return count2;
 531 }
 532
 533 int link_cell_shutdown(t_moldyn *moldyn) {
 534
 535         int i;
 536         t_linkcell *lc;
 537
 538         lc=&(moldyn->lc);
 539
 540         for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
 541                 list_shutdown(&(moldyn->lc.subcell[i]));
 542
 543         return 0;
 544 }
 545
 546 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
 547
 548         int count;
 549         void *ptr;
 550         t_moldyn_schedule *schedule;
 551
 552         schedule=&(moldyn->schedule);
 553         count=++(schedule->content_count);
 554
 555         ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
 556         if(!ptr) {
 557                 perror("[moldyn] realloc (runs)");
 558                 return -1;
 559         }
 560         moldyn->schedule.runs=ptr;
 561         moldyn->schedule.runs[count-1]=runs;
 562
 563         ptr=realloc(schedule->tau,count*sizeof(double));
 564         if(!ptr) {
 565                 perror("[moldyn] realloc (tau)");
 566                 return -1;
 567         }
 568         moldyn->schedule.tau=ptr;
 569         moldyn->schedule.tau[count-1]=tau;
 570
 571         return 0;
 572 }
 573
 574 int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
 575
 576         moldyn->schedule.hook=hook;
 577         moldyn->schedule.hook_params=hook_params;
 578
 579         return 0;
 580 }
 581
 582 /*
 583  *
 584  * 'integration of newtons equation' - algorithms
 585  *
 586  */
 587
 588 /* start the integration */
 589
 590 int moldyn_integrate(t_moldyn *moldyn) {
 591
 592         int i,sched;
 593         unsigned int e,m,s,v;
 594         t_3dvec p;
 595         t_moldyn_schedule *schedule;
 596         t_atom *atom;
 597
 598         int fd;
 599         char fb[128];
 600
 601         schedule=&(moldyn->schedule);
 602         atom=moldyn->atom;
 603
 604         /* initialize linked cell method */
 605         link_cell_init(moldyn);
 606
 607         /* logging & visualization */
 608         e=moldyn->ewrite;
 609         m=moldyn->mwrite;
 610         s=moldyn->swrite;
 611         v=moldyn->vwrite;
 612
 613         /* sqaure of some variables */
 614         moldyn->tau_square=moldyn->tau*moldyn->tau;
 615         moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
 616
 617         /* calculate initial forces */
 618         potential_force_calc(moldyn);
 619
 620         /* zero absolute time */
 621         moldyn->time=0.0;
 622
 623         for(sched=0;sched<moldyn->schedule.content_count;sched++) {
 624
 625                 /* setting amount of runs and finite time step size */
 626                 moldyn->tau=schedule->tau[sched];
 627                 moldyn->tau_square=moldyn->tau*moldyn->tau;
 628                 moldyn->time_steps=schedule->runs[sched];
 629
 630         /* integration according to schedule */
 631
 632         for(i=0;i<moldyn->time_steps;i++) {
 633
 634                 /* integration step */
 635                 moldyn->integrate(moldyn);
 636
 637                 /* increase absolute time */
 638                 moldyn->time+=moldyn->tau;
 639
 640                 /* check for log & visualization */
 641                 if(e) {
 642                         if(!(i%e))
 643                                 dprintf(moldyn->efd,
 644                                         "%.15f %.45f %.45f %.45f\n",
 645                                         moldyn->time,update_e_kin(moldyn),
 646                                         moldyn->energy,
 647                                         get_total_energy(moldyn));
 648                 }
 649                 if(m) {
 650                         if(!(i%m)) {
 651                                 p=get_total_p(moldyn);
 652                                 dprintf(moldyn->mfd,
 653                                         "%.15f %.45f\n",moldyn->time,
 654                                         v3_norm(&p));
 655                         }
 656                 }
 657                 if(s) {
 658                         if(!(i%s)) {
 659                                 snprintf(fb,128,"%s-%f-%.15f.save",moldyn->sfb,
 660                                          moldyn->t,i*moldyn->tau);
 661                                 fd=open(fb,O_WRONLY|O_TRUNC|O_CREAT);
 662                                 if(fd<0) perror("[moldyn] save fd open");
 663                                 else {
 664                                         write(fd,moldyn,sizeof(t_moldyn));
 665                                         write(fd,moldyn->atom,
 666                                               moldyn->count*sizeof(t_atom));
 667                                 }
 668                                 close(fd);
 669                         }
 670                 }
 671                 if(v) {
 672                         if(!(i%v)) {
 673                                 visual_atoms(&(moldyn->vis),moldyn->time,
 674                                              moldyn->atom,moldyn->count);
 675                                 printf("\rsched: %d, steps: %d",sched,i);
 676                                 fflush(stdout);
 677                         }
 678                 }
 679
 680         }
 681
 682                 /* check for hooks */
 683                 if(schedule->hook)
 684                         schedule->hook(moldyn,schedule->hook_params);
 685
 686         }
 687
 688         return 0;
 689 }
 690
 691 /* velocity verlet */
 692
 693 int velocity_verlet(t_moldyn *moldyn) {
 694
 695         int i,count;
 696         double tau,tau_square;
 697         t_3dvec delta;
 698         t_atom *atom;
 699
 700         atom=moldyn->atom;
 701         count=moldyn->count;
 702         tau=moldyn->tau;
 703         tau_square=moldyn->tau_square;
 704
 705         for(i=0;i<count;i++) {
 706                 /* new positions */
 707                 v3_scale(&delta,&(atom[i].v),tau);
 708                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 709                 v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
 710                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 711                 check_per_bound(moldyn,&(atom[i].r));
 712
 713                 /* 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         /* neighbour list update */
 719         link_cell_update(moldyn);
 720
 721         /* forces depending on chosen potential */
 722         potential_force_calc(moldyn);
 723         //moldyn->potential_force_function(moldyn);
 724
 725         for(i=0;i<count;i++) {
 726                 /* again velocities */
 727                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 728                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 729         }
 730
 731         return 0;
 732 }
 733
 734
 735 /*
 736  *
 737  * potentials & corresponding forces
 738  *
 739  */
 740
 741 /* generic potential and force calculation */
 742
 743 int potential_force_calc(t_moldyn *moldyn) {
 744
 745         int i,j,k,count;
 746         t_atom *atom,*btom,*ktom;
 747         t_linkcell *lc;
 748         t_list neighbour[27];
 749         t_list *this,*thisk,*neighbourk;
 750         u8 bc,bck;
 751         int countn,dnlc;
 752
 753         count=moldyn->count;
 754         atom=moldyn->atom;
 755         lc=&(moldyn->lc);
 756
 757         /* reset energy */
 758         moldyn->energy=0.0;
 759
 760         for(i=0;i<count;i++) {
 761 printf("BAR %d %d\n",i,count);
 762
 763                 /* reset force */
 764                 v3_zero(&(atom[i].f));
 765
 766                 /* single particle potential/force */
 767                 if(atom[i].attr&ATOM_ATTR_1BP)
 768                         moldyn->func1b(moldyn,&(atom[i]));
 769
 770                 /* 2 body pair potential/force */
 771                 if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
 772
 773                         link_cell_neighbour_index(moldyn,
 774                                 (atom[i].r.x+moldyn->dim.x/2)/lc->x,
 775                                 (atom[i].r.y+moldyn->dim.y/2)/lc->y,
 776                                 (atom[i].r.z+moldyn->dim.z/2)/lc->z,
 777                                 neighbour);
 778
 779                         countn=lc->countn;
 780                         dnlc=lc->dnlc;
 781
 782                         for(j=0;j<countn;j++) {
 783
 784                                 this=&(neighbour[j]);
 785                                 list_reset(this);
 786
 787                                 if(this->start==NULL)
 788                                         continue;
 789
 790                                 bc=(j<dnlc)?0:1;
 791
 792                                 do {
 793                                         btom=this->current->data;
 794
 795                                         if(btom==&(atom[i]))
 796                                                 continue;
 797
 798                                         if((btom->attr&ATOM_ATTR_2BP)&
 799                                            (atom[i].attr&ATOM_ATTR_2BP))
 800                                                 moldyn->func2b(moldyn,
 801                                                                &(atom[i]),
 802                                                                btom,
 803                                                                bc);
 804
 805                                         /* 3 body potential/force */
 806
 807                                         if(!(atom[i].attr&ATOM_ATTR_3BP)||
 808                                            !(btom->attr&ATOM_ATTR_3BP))
 809                                                 continue;
 810
 811                                         link_cell_neighbour_index(moldyn,
 812                                            (btom->r.x+moldyn->dim.x/2)/lc->x,
 813                                            (btom->r.y+moldyn->dim.y/2)/lc->y,
 814                                            (btom->r.z+moldyn->dim.z/2)/lc->z,
 815                                            neighbourk);
 816
 817                                         for(k=0;k<lc->countn;k++) {
 818
 819                                                 thisk=&(neighbourk[k]);
 820                                                 list_reset(thisk);
 821
 822                                                 if(thisk->start==NULL)
 823                                                         continue;
 824
 825                                                 bck=(k<lc->dnlc)?0:1;
 826
 827                                                 do {
 828
 829                         ktom=thisk->current->data;
 830
 831                         if(!(ktom->attr&ATOM_ATTR_3BP))
 832                                 continue;
 833
 834                         if(ktom==btom)
 835                                 continue;
 836
 837                         if(ktom==&(atom[i]))
 838                                 continue;
 839
 840                         moldyn->func3b(moldyn,&(atom[i]),btom,ktom,bck);
 841
 842                                                 } while(list_next(thisk)!=\
 843                                                         L_NO_NEXT_ELEMENT);
 844
 845                                         }
 846
 847                                 } while(list_next(this)!=L_NO_NEXT_ELEMENT);
 848                         }
 849                 }
 850         }
 851
 852         return 0;
 853 }
 854
 855 /*
 856  * periodic boundayr checking
 857  */
 858
 859 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
 860
 861         double x,y,z;
 862         t_3dvec *dim;
 863
 864         dim=&(moldyn->dim);
 865
 866         x=0.5*dim->x;
 867         y=0.5*dim->y;
 868         z=0.5*dim->z;
 869
 870         if(moldyn->status&MOLDYN_STAT_PBX) {
 871                 if(a->x>=x) a->x-=dim->x;
 872                 else if(-a->x>x) a->x+=dim->x;
 873         }
 874         if(moldyn->status&MOLDYN_STAT_PBY) {
 875                 if(a->y>=y) a->y-=dim->y;
 876                 else if(-a->y>y) a->y+=dim->y;
 877         }
 878         if(moldyn->status&MOLDYN_STAT_PBZ) {
 879                 if(a->z>=z) a->z-=dim->z;
 880                 else if(-a->z>z) a->z+=dim->z;
 881         }
 882
 883         return 0;
 884 }
 885
 886
 887 /*
 888  * example potentials
 889  */
 890
 891 /* harmonic oscillator potential and force */
 892
 893 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 894
 895         t_ho_params *params;
 896         t_3dvec force,distance;
 897         double d;
 898         double sc,equi_dist;
 899
 900         params=moldyn->pot2b_params;
 901         sc=params->spring_constant;
 902         equi_dist=params->equilibrium_distance;
 903
 904         v3_sub(&distance,&(ai->r),&(aj->r));
 905
 906         if(bc) check_per_bound(moldyn,&distance);
 907         d=v3_norm(&distance);
 908         if(d<=moldyn->cutoff) {
 909                 /* energy is 1/2 (d-d0)^2, but we will add this twice ... */
 910                 moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
 911                 v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
 912                 v3_add(&(ai->f),&(ai->f),&force);
 913         }
 914
 915         return 0;
 916 }
 917
 918 /* lennard jones potential & force for one sort of atoms */
 919
 920 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 921
 922         t_lj_params *params;
 923         t_3dvec force,distance;
 924         double d,h1,h2;
 925         double eps,sig6,sig12;
 926
 927         params=moldyn->pot2b_params;
 928         eps=params->epsilon4;
 929         sig6=params->sigma6;
 930         sig12=params->sigma12;
 931
 932         v3_sub(&distance,&(ai->r),&(aj->r));
 933         if(bc) check_per_bound(moldyn,&distance);
 934         d=v3_absolute_square(&distance);        /* 1/r^2 */
 935         if(d<=moldyn->cutoff_square) {
 936                 d=1.0/d;                        /* 1/r^2 */
 937                 h2=d*d;                         /* 1/r^4 */
 938                 h2*=d;                          /* 1/r^6 */
 939                 h1=h2*h2;                       /* 1/r^12 */
 940                 /* energy is eps*..., but we will add this twice ... */
 941                 moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
 942                 h2*=d;                          /* 1/r^8 */
 943                 h1*=d;                          /* 1/r^14 */
 944                 h2*=6*sig6;
 945                 h1*=12*sig12;
 946                 d=+h1-h2;
 947                 d*=eps;
 948                 v3_scale(&force,&distance,d);
 949                 v3_add(&(ai->f),&(ai->f),&force);
 950         }
 951
 952         return 0;
 953 }
 954
 955 /*
 956  * tersoff potential & force for 2 sorts of atoms
 957  */
 958
 959 /* tersoff 1 body part */
 960 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
 961
 962         int num;
 963         t_tersoff_mult_params *params;
 964         t_tersoff_exchange *exchange;
 965
 966         num=ai->bnum;
 967         params=moldyn->pot1b_params;
 968         exchange=&(params->exchange);
 969
 970         /*
 971          * simple: point constant parameters only depending on atom i to
 972          *         their right values
 973          */
 974
 975         exchange->beta=&(params->beta[num]);
 976         exchange->n=&(params->n[num]);
 977         exchange->c=&(params->c[num]);
 978         exchange->d=&(params->d[num]);
 979         exchange->h=&(params->h[num]);
 980
 981         exchange->betan=pow(*(exchange->beta),*(exchange->n));
 982         exchange->c2=params->c[num]*params->c[num];
 983         exchange->d2=params->d[num]*params->d[num];
 984         exchange->c2d2=exchange->c2/exchange->d2;
 985
 986         return 0;
 987 }
 988
 989 /* tersoff 2 body part */
 990 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 991
 992         t_tersoff_mult_params *params;
 993         t_tersoff_exchange *exchange;
 994         t_3dvec dist_ij,force;
 995         double d_ij;
 996         double A,B,R,S,lambda,mu;
 997         double f_r,df_r;
 998         double f_c,df_c;
 999         int num;
1000         double s_r;
1001         double arg;
1002         double scale;
1003
1004         params=moldyn->pot2b_params;
1005         num=ai->bnum;
1006         exchange=&(params->exchange);
1007
1008         exchange->run3bp=0;
1009
1010         /*
1011          * we need: f_c, df_c, f_r, df_r
1012          *
1013          * therefore we need: R, S, A, lambda
1014          */
1015
1016         v3_sub(&dist_ij,&(ai->r),&(aj->r));
1017
1018         if(bc) check_per_bound(moldyn,&dist_ij);
1019
1020         /* save for use in 3bp */ /* REALLY ?!?!?! */
1021         exchange->dist_ij=dist_ij;
1022
1023         /* constants */
1024         if(num==aj->bnum) {
1025                 S=params->S[num];
1026                 R=params->R[num];
1027                 A=params->A[num];
1028                 lambda=params->lambda[num];
1029                 /* more constants depending of atoms i and j, needed in 3bp */
1030                 params->exchange.B=&(params->B[num]);
1031                 params->exchange.mu=&(params->mu[num]);
1032                 mu=params->mu[num];
1033                 params->exchange.chi=1.0;
1034         }
1035         else {
1036                 S=params->Smixed;
1037                 R=params->Rmixed;
1038                 A=params->Amixed;
1039                 lambda=params->lambda_m;
1040                 /* more constants depending of atoms i and j, needed in 3bp */
1041                 params->exchange.B=&(params->Bmixed);
1042                 params->exchange.mu=&(params->mu_m);
1043                 mu=params->mu_m;
1044                 params->exchange.chi=params->chi;
1045         }
1046
1047         d_ij=v3_norm(&dist_ij);
1048
1049         /* save for use in 3bp */
1050         exchange->d_ij=d_ij;
1051
1052         if(d_ij>S)
1053                 return 0;
1054
1055         f_r=A*exp(-lambda*d_ij);
1056         df_r=-lambda*f_r/d_ij;
1057
1058         /* f_a, df_a calc + save for 3bp use */
1059         exchange->f_a=-B*exp(-mu*d_ij);
1060         exchange->df_a=-mu*exchange->f_a/d_ij;
1061
1062         if(d_ij<R) {
1063                 /* f_c = 1, df_c = 0 */
1064                 f_c=1.0;
1065                 df_c=0.0;
1066                 v3_scale(&force,&dist_ij,df_r);
1067         }
1068         else {
1069                 s_r=S-R;
1070                 arg=M_PI*(d_ij-R)/s_r;
1071                 f_c=0.5+0.5*cos(arg);
1072                 df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij));
1073                 scale=df_c*f_r+df_r*f_c;
1074                 v3_scale(&force,&dist_ij,scale);
1075         }
1076
1077         /* add forces */
1078         v3_add(&(ai->f),&(ai->f),&force);
1079         /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
1080         moldyn->energy+=(0.25*f_r*f_c);
1081
1082         /* save for use in 3bp */
1083         exchange->f_c=f_c;
1084         exchange->df_c=df_c;
1085
1086         /* enable the run of 3bp function */
1087         exchange->run3bp=1;
1088
1089         return 0;
1090 }
1091
1092 /* tersoff 3 body part */
1093
1094 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
1095
1096         t_tersoff_mult_params *params;
1097         t_tersoff_exchange *exchange;
1098         t_3dvec dist_ij,dist_ik,dist_jk;
1099         t_3dvec temp,force;
1100         double R,S,s_r;
1101         double d_ij,d_ij2,d_ik,d_jk;
1102         double f_c,df_c,b_ij,f_a,df_a;
1103         double f_c_ik,df_c_ik,arg;
1104         double scale;
1105         double chi;
1106         double n,c,d,h,beta,betan;
1107         double c2,d2,c2d2;
1108         double numer,denom;
1109         double theta,cos_theta,sin_theta;
1110         double d_theta,d_theta1,d_theta2;
1111         double h_cos,h_cos2,d2_h_cos2;
1112         double frac1,bracket1,bracket2,bracket2_n_1,bracket2_n;
1113         double bracket3,bracket3_pow_1,bracket3_pow;
1114         int num;
1115
1116         params=moldyn->pot3b_params;
1117         num=ai->bnum;
1118         exchange=&(params->exchange);
1119
1120         if(!(exchange->run3bp))
1121                 return 0;
1122
1123         /*
1124          * we need: f_c, d_fc, b_ij, db_ij, f_a, df_a
1125          *
1126          * we got f_c, df_c, f_a, df_a from 2bp calculation
1127          */
1128
1129         d_ij=exchange->d_ij;
1130         d_ij2=exchange->d_ij2;
1131
1132         f_a=params->exchange.f_a;
1133         df_a=params->exchange.df_a;
1134
1135         /* d_ij is <= S, as we didn't return so far! */
1136
1137         /*
1138          * calc of b_ij (scalar) and db_ij (vector)
1139          *
1140          * - for b_ij: chi, beta, f_c_ik, w(=1), c, d, h, n, cos_theta
1141          *
1142          * - for db_ij: d_theta, sin_theta, cos_theta, f_c_ik, df_c_ik,
1143          *              w_ik,
1144          *
1145          */
1146
1147
1148         v3_sub(&dist_ik,&(ai->r),&(ak->r));
1149         if(bc) check_per_bound(moldyn,&dist_ik);
1150         d_ik=v3_norm(&dist_ik);
1151
1152         /* constants for f_c_ik calc */
1153         if(num==ak->bnum) {
1154                 R=params->R[num];
1155                 S=params->S[num];
1156         }
1157         else {
1158                 R=params->Rmixed;
1159                 S=params->Smixed;
1160         }
1161
1162         /* calc of f_c_ik */
1163         if(d_ik>S)
1164                 return 0;
1165
1166         if(d_ik<R) {
1167                 /* f_c_ik = 1, df_c_ik = 0 */
1168                 f_c_ik=1.0;
1169                 df_c_ik=0.0;
1170         }
1171         else {
1172                 s_r=S-R;
1173                 arg=M_PI*(d_ik-R)/s_r;
1174                 f_c_ik=0.5+0.5*cos(arg);
1175                 df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik));
1176         }
1177
1178         v3_sub(&dist_jk,&(aj->r),&(ak->r));
1179         if(bc) check_per_bound(moldyn,&dist_jk);
1180         d_jk=v3_norm(&dist_jk);
1181
1182         beta=*(exchange->beta);
1183         betan=exchange->betan;
1184         n=*(exchange->n);
1185         c=*(exchange->c);
1186         d=*(exchange->d);
1187         h=*(exchange->h);
1188         c2=exchange->c2;
1189         d2=exchange->d2;
1190         c2d2=exchange->c2d2;
1191
1192         numer=d_ij2+d_ik*d_ik-d_jk*d_jk;
1193         denom=2*d_ij*d_ik;
1194         cos_theta=numer/denom;
1195         sin_theta=sqrt(1.0-(cos_theta*cos_theta));
1196         theta=acos(cos_theta);
1197         d_theta=(-1.0/sqrt(1.0-cos_theta*cos_theta))/(denom*denom);
1198         d_theta1=2*denom-numer*2*d_ik/d_ij;
1199         d_theta2=2*denom-numer*2*d_ij/d_ik;
1200         d_theta1*=d_theta;
1201         d_theta2*=d_theta;
1202
1203         h_cos=(h-cos_theta);
1204         h_cos2=h_cos*h_cos;
1205         d2_h_cos2=d2-h_cos2;
1206
1207         /* some usefull expressions */
1208         frac1=c2/(d2-h_cos2);
1209         bracket1=1+c2d2-frac1;
1210         bracket2=f_c_ik*bracket1;
1211         bracket2_n_1=pow(bracket2,n-1.0);
1212         bracket2_n=bracket2_n_1*bracket2;
1213         bracket3=1+betan*bracket2_n;
1214         bracket3_pow_1=pow(bracket3,(-1.0/(2.0*n))-1.0);
1215         bracket3_pow=bracket3_pow_1*bracket3;
1216
1217         /* now go on with calc of b_ij and derivation of b_ij */
1218         b_ij=chi*bracket3_pow;
1219
1220         /* derivation of theta */
1221         v3_scale(&force,&dist_ij,d_theta1);
1222         v3_scale(&temp,&dist_ik,d_theta2);
1223         v3_add(&force,&force,&temp);
1224
1225         /* part 1 of derivation of b_ij */
1226         v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac1);
1227
1228         /* part 2 of derivation of b_ij */
1229         v3_scale(&temp,&dist_ik,df_c_ik*bracket1);
1230
1231         /* sum up and scale ... */
1232         v3_add(&temp,&temp,&force);
1233         scale=bracket2_n_1*n*betan*(1+betan*bracket3_pow_1)*chi*(1.0/(2.0*n));
1234         v3_scale(&temp,&temp,scale);
1235
1236         /* now construct an energy and a force out of that */
1237         v3_scale(&temp,&temp,f_a);
1238         v3_scale(&force,&dist_ij,df_a*b_ij);
1239         v3_add(&temp,&temp,&force);
1240         v3_scale(&temp,&temp,f_c);
1241         v3_scale(&force,&dist_ij,df_c*b_ij*f_a);
1242         v3_add(&force,&force,&temp);
1243
1244         /* add forces */
1245         v3_add(&(ai->f),&(ai->f),&force);
1246         /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
1247         moldyn->energy+=(0.25*f_a*b_ij*f_c);
1248
1249         return 0;
1250 }
1251