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