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 int moldyn_usage(char **argv) {
  27
  28         printf("\n%s usage:\n\n",argv[0]);
  29         printf("--- general options ---\n");
  30         printf("-E <steps> <file> (log total energy)\n");
  31         printf("-M <steps> <file> (log total momentum)\n");
  32         printf("-D <steps> <file> (dump total information)\n");
  33         printf("-S <steps> <filebase> (single save file)\n");
  34         printf("-V <steps> <filebase> (rasmol file)\n");
  35         printf("--- physics options ---\n");
  36         printf("-T <temperature> [K] (%f)\n",MOLDYN_TEMP);
  37         printf("-t <timestep tau> [s] (%.15f)\n",MOLDYN_TAU);
  38         printf("-C <cutoff radius> [m] (%.15f)\n",MOLDYN_CUTOFF);
  39         printf("-R <runs> (%d)\n",MOLDYN_RUNS);
  40         printf(" -- integration algo --\n");
  41         printf("  -I <number> (%d)\n",MOLDYN_INTEGRATE_DEFAULT);
  42         printf("     0: velocity verlet\n");
  43         printf(" -- potential --\n");
  44         printf("  -P <number> <param1 param2 ...>\n");
  45         printf("     0: harmonic oscillator\n");
  46         printf("        param1: spring constant\n");
  47         printf("        param2: equilibrium distance\n");
  48         printf("     1: lennard jones\n");
  49         printf("        param1: epsilon\n");
  50         printf("        param2: sigma\n");
  51         printf("\n");
  52
  53         return 0;
  54 }
  55
  56 int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
  57
  58         int i;
  59         t_ho_params hop;
  60         t_lj_params ljp;
  61         t_tersoff_params tp;
  62         double s,e;
  63
  64         memset(moldyn,0,sizeof(t_moldyn));
  65
  66         /* default values */
  67         moldyn->t=MOLDYN_TEMP;
  68         moldyn->tau=MOLDYN_TAU;
  69         moldyn->time_steps=MOLDYN_RUNS;
  70         moldyn->integrate=velocity_verlet;
  71         moldyn->potential_force_function=lennard_jones;
  72
  73         /* parse argv */
  74         for(i=1;i<argc;i++) {
  75                 if(argv[i][0]=='-') {
  76                         switch(argv[i][1]){
  77                                 case 'E':
  78                                         moldyn->ewrite=atoi(argv[++i]);
  79                                         strncpy(moldyn->efb,argv[++i],64);
  80                                         break;
  81                                 case 'M':
  82                                         moldyn->mwrite=atoi(argv[++i]);
  83                                         strncpy(moldyn->mfb,argv[++i],64);
  84                                         break;
  85                                 case 'S':
  86                                         moldyn->swrite=atoi(argv[++i]);
  87                                         strncpy(moldyn->sfb,argv[++i],64);
  88                                         break;
  89                                 case 'V':
  90                                         moldyn->vwrite=atoi(argv[++i]);
  91                                         strncpy(moldyn->vfb,argv[++i],64);
  92                                         break;
  93                                 case 'T':
  94                                         moldyn->t=atof(argv[++i]);
  95                                         break;
  96                                 case 't':
  97                                         moldyn->tau=atof(argv[++i]);
  98                                         break;
  99                                 case 'C':
 100                                         moldyn->cutoff=atof(argv[++i]);
 101                                         break;
 102                                 case 'R':
 103                                         moldyn->time_steps=atoi(argv[++i]);
 104                                         break;
 105                                 case 'I':
 106         /* integration algorithm */
 107         switch(atoi(argv[++i])) {
 108                 case MOLDYN_INTEGRATE_VERLET:
 109                         moldyn->integrate=velocity_verlet;
 110                         break;
 111                 default:
 112                         printf("unknown integration algo %s\n",argv[i]);
 113                         moldyn_usage(argv);
 114                         return -1;
 115         }
 116
 117                                 case 'P':
 118         /* potential + params */
 119         switch(atoi(argv[++i])) {
 120                 case MOLDYN_POTENTIAL_HO:
 121                         hop.spring_constant=atof(argv[++i]);
 122                         hop.equilibrium_distance=atof(argv[++i]);
 123                         moldyn->pot_params=malloc(sizeof(t_ho_params));
 124                         memcpy(moldyn->pot_params,&hop,sizeof(t_ho_params));
 125                         moldyn->potential_force_function=harmonic_oscillator;
 126                         break;
 127                 case MOLDYN_POTENTIAL_LJ:
 128                         e=atof(argv[++i]);
 129                         s=atof(argv[++i]);
 130                         ljp.epsilon4=4*e;
 131                         ljp.sigma6=s*s*s*s*s*s;
 132                         ljp.sigma12=ljp.sigma6*ljp.sigma6;
 133                         moldyn->pot_params=malloc(sizeof(t_lj_params));
 134                         memcpy(moldyn->pot_params,&ljp,sizeof(t_lj_params));
 135                         moldyn->potential_force_function=lennard_jones;
 136                         break;
 137                 default:
 138                         printf("unknown potential %s\n",argv[i]);
 139                         moldyn_usage(argv);
 140                         return -1;
 141         }
 142
 143                                 default:
 144                                         printf("unknown option %s\n",argv[i]);
 145                                         moldyn_usage(argv);
 146                                         return -1;
 147                         }
 148                 } else {
 149                         moldyn_usage(argv);
 150                         return -1;
 151                 }
 152         }
 153
 154         return 0;
 155 }
 156
 157 int moldyn_log_init(t_moldyn *moldyn) {
 158
 159         moldyn->lvstat=0;
 160         t_visual *vis;
 161
 162         vis=&(moldyn->vis);
 163
 164         if(moldyn->ewrite) {
 165                 moldyn->efd=open(moldyn->efb,O_WRONLY|O_CREAT|O_TRUNC);
 166                 if(moldyn->efd<0) {
 167                         perror("[moldyn] efd open");
 168                         return moldyn->efd;
 169                 }
 170                 dprintf(moldyn->efd,"# moldyn total energy logfile\n");
 171                 moldyn->lvstat|=MOLDYN_LVSTAT_TOTAL_E;
 172         }
 173
 174         if(moldyn->mwrite) {
 175                 moldyn->mfd=open(moldyn->mfb,O_WRONLY|O_CREAT|O_TRUNC);
 176                 if(moldyn->mfd<0) {
 177                         perror("[moldyn] mfd open");
 178                         return moldyn->mfd;
 179                 }
 180                 dprintf(moldyn->mfd,"# moldyn total momentum logfile\n");
 181                 moldyn->lvstat|=MOLDYN_LVSTAT_TOTAL_M;
 182         }
 183
 184         if(moldyn->swrite)
 185                 moldyn->lvstat|=MOLDYN_LVSTAT_SAVE;
 186
 187         if((moldyn->vwrite)&&(vis)) {
 188                 moldyn->visual=vis;
 189                 visual_init(vis,moldyn->vfb);
 190                 moldyn->lvstat|=MOLDYN_LVSTAT_VISUAL;
 191         }
 192
 193         moldyn->lvstat|=MOLDYN_LVSTAT_INITIALIZED;
 194
 195         return 0;
 196 }
 197
 198 int moldyn_log_shutdown(t_moldyn *moldyn) {
 199
 200         if(moldyn->efd) close(moldyn->efd);
 201         if(moldyn->mfd) close(moldyn->efd);
 202         if(moldyn->dfd) close(moldyn->efd);
 203         if(moldyn->visual) visual_tini(moldyn->visual);
 204
 205         return 0;
 206 }
 207
 208 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 209
 210         int ret;
 211
 212         ret=moldyn_parse_argv(moldyn,argc,argv);
 213         if(ret<0) return ret;
 214
 215         ret=moldyn_log_init(moldyn);
 216         if(ret<0) return ret;
 217
 218         rand_init(&(moldyn->random),NULL,1);
 219         moldyn->random.status|=RAND_STAT_VERBOSE;
 220
 221         moldyn->status=0;
 222
 223         return 0;
 224 }
 225
 226 int moldyn_shutdown(t_moldyn *moldyn) {
 227
 228         moldyn_log_shutdown(moldyn);
 229         rand_close(&(moldyn->random));
 230         free(moldyn->atom);
 231
 232         return 0;
 233 }
 234
 235 int create_lattice(u8 type,int element,double mass,double lc,
 236                    int a,int b,int c,t_atom **atom) {
 237
 238         int count;
 239         int ret;
 240         t_3dvec origin;
 241
 242         count=a*b*c;
 243
 244         if(type==FCC) count*=4;
 245         if(type==DIAMOND) count*=8;
 246
 247         *atom=malloc(count*sizeof(t_atom));
 248         if(*atom==NULL) {
 249                 perror("malloc (atoms)");
 250                 return -1;
 251         }
 252
 253         v3_zero(&origin);
 254
 255         switch(type) {
 256                 case FCC:
 257                         ret=fcc_init(a,b,c,lc,*atom,&origin);
 258                         break;
 259                 case DIAMOND:
 260                         ret=diamond_init(a,b,c,lc,*atom,&origin);
 261                         break;
 262                 default:
 263                         printf("unknown lattice type (%02x)\n",type);
 264                         return -1;
 265         }
 266
 267         /* debug */
 268         if(ret!=count) {
 269                 printf("ok, there is something wrong ...\n");
 270                 printf("calculated -> %d atoms\n",count);
 271                 printf("created -> %d atoms\n",ret);
 272                 return -1;
 273         }
 274
 275         while(count) {
 276                 (*atom)[count-1].element=element;
 277                 (*atom)[count-1].mass=mass;
 278                 count-=1;
 279         }
 280
 281         return ret;
 282 }
 283
 284 int destroy_lattice(t_atom *atom) {
 285
 286         if(atom) free(atom);
 287
 288         return 0;
 289 }
 290
 291 int thermal_init(t_moldyn *moldyn) {
 292
 293         /*
 294          * - gaussian distribution of velocities
 295          * - zero total momentum
 296          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 297          */
 298
 299         int i;
 300         double v,sigma;
 301         t_3dvec p_total,delta;
 302         t_atom *atom;
 303         t_random *random;
 304
 305         atom=moldyn->atom;
 306         random=&(moldyn->random);
 307
 308         /* gaussian distribution of velocities */
 309         v3_zero(&p_total);
 310         for(i=0;i<moldyn->count;i++) {
 311                 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t/atom[i].mass);
 312                 /* x direction */
 313                 v=sigma*rand_get_gauss(random);
 314                 atom[i].v.x=v;
 315                 p_total.x+=atom[i].mass*v;
 316                 /* y direction */
 317                 v=sigma*rand_get_gauss(random);
 318                 atom[i].v.y=v;
 319                 p_total.y+=atom[i].mass*v;
 320                 /* z direction */
 321                 v=sigma*rand_get_gauss(random);
 322                 atom[i].v.z=v;
 323                 p_total.z+=atom[i].mass*v;
 324         }
 325
 326         /* zero total momentum */
 327         v3_scale(&p_total,&p_total,1.0/moldyn->count);
 328         for(i=0;i<moldyn->count;i++) {
 329                 v3_scale(&delta,&p_total,1.0/atom[i].mass);
 330                 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
 331         }
 332
 333         /* velocity scaling */
 334         scale_velocity(moldyn);
 335
 336         return 0;
 337 }
 338
 339 int scale_velocity(t_moldyn *moldyn) {
 340
 341         int i;
 342         double e,c;
 343         t_atom *atom;
 344
 345         atom=moldyn->atom;
 346
 347         /*
 348          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 349          */
 350         e=0.0;
 351         for(i=0;i<moldyn->count;i++)
 352                 e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 353         c=sqrt((2.0*e)/(3.0*moldyn->count*K_BOLTZMANN*moldyn->t));
 354         for(i=0;i<moldyn->count;i++)
 355                 v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
 356
 357         return 0;
 358 }
 359
 360 double get_e_kin(t_atom *atom,int count) {
 361
 362         int i;
 363         double e;
 364
 365         e=0.0;
 366
 367         for(i=0;i<count;i++) {
 368                 e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 369         }
 370
 371         return e;
 372 }
 373
 374 double get_e_pot(t_moldyn *moldyn) {
 375
 376         return moldyn->energy;
 377 }
 378
 379 double get_total_energy(t_moldyn *moldyn) {
 380
 381         double e;
 382
 383         e=get_e_kin(moldyn->atom,moldyn->count);
 384         e+=get_e_pot(moldyn);
 385
 386         return e;
 387 }
 388
 389 t_3dvec get_total_p(t_atom *atom, int count) {
 390
 391         t_3dvec p,p_total;
 392         int i;
 393
 394         v3_zero(&p_total);
 395         for(i=0;i<count;i++) {
 396                 v3_scale(&p,&(atom[i].v),atom[i].mass);
 397                 v3_add(&p_total,&p_total,&p);
 398         }
 399
 400         return p_total;
 401 }
 402
 403 double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
 404
 405         double tau;
 406
 407         tau=0.05*nn_dist/(sqrt(3.0*K_BOLTZMANN*t/moldyn->atom[0].mass));
 408         tau*=1.0E-9;
 409         if(tau<moldyn->tau)
 410                 printf("[moldyn] warning: time step  (%f > %.15f)\n",
 411                        moldyn->tau,tau);
 412
 413         return tau;
 414 }
 415
 416 /*
 417  * numerical tricks
 418  */
 419
 420 /* linked list / cell method */
 421
 422 int link_cell_init(t_moldyn *moldyn) {
 423
 424         t_linkcell *lc;
 425         int i;
 426
 427         lc=&(moldyn->lc);
 428
 429         /* list log fd */
 430         lc->listfd=open("/dev/null",O_WRONLY);
 431
 432         /* partitioning the md cell */
 433         lc->nx=moldyn->dim.x/moldyn->cutoff;
 434         lc->x=moldyn->dim.x/lc->nx;
 435         lc->ny=moldyn->dim.y/moldyn->cutoff;
 436         lc->y=moldyn->dim.y/lc->ny;
 437         lc->nz=moldyn->dim.z/moldyn->cutoff;
 438         lc->z=moldyn->dim.z/lc->nz;
 439
 440         lc->cells=lc->nx*lc->ny*lc->nz;
 441         lc->subcell=malloc(lc->cells*sizeof(t_list));
 442
 443         printf("initializing linked cells (%d)\n",lc->cells);
 444
 445         for(i=0;i<lc->cells;i++)
 446                 //list_init(&(lc->subcell[i]),1);
 447                 list_init(&(lc->subcell[i]));
 448
 449         link_cell_update(moldyn);
 450
 451         return 0;
 452 }
 453
 454 int link_cell_update(t_moldyn *moldyn) {
 455
 456         int count,i,j,k;
 457         int nx,ny,nz;
 458         t_atom *atom;
 459         t_linkcell *lc;
 460
 461         atom=moldyn->atom;
 462         lc=&(moldyn->lc);
 463
 464         nx=lc->nx;
 465         ny=lc->ny;
 466         nz=lc->nz;
 467
 468         for(i=0;i<lc->cells;i++)
 469                 list_destroy(&(moldyn->lc.subcell[i]));
 470
 471         for(count=0;count<moedyn->count;count++) {
 472                 i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
 473                 j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
 474                 k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
 475                 list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
 476                                        &(atom[count]));
 477         }
 478
 479         return 0;
 480 }
 481
 482 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 483
 484         t_linkcell *lc;
 485         int a;
 486         int count1,count2;
 487         int ci,cj,ck;
 488         int nx,ny,nz;
 489         int x,y,z;
 490         u8 bx,by,bz;
 491
 492         lc=&(moldyn->lc);
 493         nx=lc->nx;
 494         ny=lc->ny;
 495         nz=lc->nz;
 496         count1=1;
 497         count2=27;
 498         a=nx*ny;
 499
 500
 501         cell[0]=lc->subcell[i+j*nx+k*a];
 502         for(ci=-1;ci<=1;ci++) {
 503                 bx=0;
 504                 x=i+ci;
 505                 if((x<0)||(x>=nx)) {
 506                         x=(x+nx)%nx;
 507                         bx=1;
 508                 }
 509                 for(cj=-1;cj<=1;cj++) {
 510                         by=0;
 511                         y=j+cj;
 512                         if((y<0)||(y>=ny)) {
 513                                 y=(y+ny)%ny;
 514                                 by=1;
 515                         }
 516                         for(ck=-1;ck<=1;ck++) {
 517                                 bz=0;
 518                                 z=k+ck;
 519                                 if((z<0)||(z>=nz)) {
 520                                         z=(z+nz)%nz;
 521                                         bz=1;
 522                                 }
 523                                 if(!(ci|cj|ck)) continue;
 524                                 if(bx|by|bz) {
 525                                         cell[--count2]=lc->subcell[x+y*nx+z*a];
 526                                 }
 527                                 else {
 528                                         cell[count1++]=lc->subcell[x+y*nx+z*a];
 529                                 }
 530                         }
 531                 }
 532         }
 533
 534         lc->dnlc=count2;
 535         lc->countn=27;
 536
 537         return count2;
 538 }
 539
 540 int link_cell_shutdown(t_moldyn *moldyn) {
 541
 542         int i;
 543         t_linkcell *lc;
 544
 545         lc=&(moldyn->lc);
 546
 547         for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
 548                 list_shutdown(&(moldyn->lc.subcell[i]));
 549
 550         if(lc->listfd) close(lc->listfd);
 551
 552         return 0;
 553 }
 554
 555 /*
 556  *
 557  * 'integration of newtons equation' - algorithms
 558  *
 559  */
 560
 561 /* start the integration */
 562
 563 int moldyn_integrate(t_moldyn *moldyn) {
 564
 565         int i;
 566         unsigned int e,m,s,d,v;
 567         t_3dvec p;
 568
 569         int fd;
 570         char fb[128];
 571
 572         /* initialize linked cell method */
 573         link_cell_init(moldyn);
 574
 575         /* logging & visualization */
 576         e=moldyn->ewrite;
 577         m=moldyn->mwrite;
 578         s=moldyn->swrite;
 579         d=moldyn->dwrite;
 580         v=moldyn->vwrite;
 581
 582         if(!(moldyn->lvstat&MOLDYN_LVSTAT_INITIALIZED)) {
 583                 printf("[moldyn] warning, lv system not initialized\n");
 584                 return -1;
 585         }
 586
 587         /* sqaure of some variables */
 588         moldyn->tau_square=moldyn->tau*moldyn->tau;
 589         moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
 590
 591         /* calculate initial forces */
 592         moldyn->potential_force_function(moldyn);
 593
 594         for(i=0;i<moldyn->time_steps;i++) {
 595
 596                 /* integration step */
 597                 moldyn->integrate(moldyn);
 598
 599                 /* check for log & visualization */
 600                 if(e) {
 601                         if(!(i%e))
 602                                 dprintf(moldyn->efd,
 603                                         "%.15f %.45f\n",i*moldyn->tau,
 604                                         get_total_energy(moldyn));
 605                 }
 606                 if(m) {
 607                         if(!(i%m)) {
 608                                 p=get_total_p(moldyn->atom,moldyn->count);
 609                                 dprintf(moldyn->mfd,
 610                                         "%.15f %.45f\n",i*moldyn->tau,
 611                                         v3_norm(&p));
 612                         }
 613                 }
 614                 if(s) {
 615                         if(!(i%s)) {
 616                                 snprintf(fb,128,"%s-%f-%.15f.save",moldyn->sfb,
 617                                          moldyn->t,i*moldyn->tau);
 618                                 fd=open(fb,O_WRONLY|O_TRUNC|O_CREAT);
 619                                 if(fd<0) perror("[moldyn] save fd open");
 620                                 else {
 621                                         write(fd,moldyn,sizeof(t_moldyn));
 622                                         write(fd,moldyn->atom,
 623                                               moldyn->count*sizeof(t_atom));
 624                                 }
 625                                 close(fd);
 626                         }
 627                 }
 628                 if(v) {
 629                         if(!(i%v)) {
 630                                 visual_atoms(moldyn->visual,i*moldyn->tau,
 631                                              moldyn->atom,moldyn->count);
 632                                 printf("\rsteps: %d",i);
 633                                 fflush(stdout);
 634                         }
 635                 }
 636         }
 637
 638         return 0;
 639 }
 640
 641 /* velocity verlet */
 642
 643 int velocity_verlet(t_moldyn *moldyn) {
 644
 645         int i,count;
 646         double tau,tau_square;
 647         t_3dvec delta;
 648         t_atom *atom;
 649
 650         atom=moldyn->atom;
 651         count=moldyn->count;
 652         tau=moldyn->tau;
 653         tau_square=moldyn->tau_square;
 654
 655         for(i=0;i<count;i++) {
 656                 /* new positions */
 657                 v3_scale(&delta,&(atom[i].v),tau);
 658                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 659                 v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
 660                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 661                 v3_per_bound(&(atom[i].r),&(moldyn->dim));
 662
 663                 /* velocities */
 664                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 665                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 666         }
 667
 668         /* neighbour list update */
 669 printf("list update ...\n");
 670         link_cell_update(moldyn);
 671 printf("done\n");
 672
 673         /* forces depending on chosen potential */
 674 printf("calc potential/force ...\n");
 675         potential_force_calc(moldyn);
 676         //moldyn->potential_force_function(moldyn);
 677 printf("done\n");
 678
 679         for(i=0;i<count;i++) {
 680                 /* again velocities */
 681                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 682                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 683         }
 684
 685         return 0;
 686 }
 687
 688
 689 /*
 690  *
 691  * potentials & corresponding forces
 692  *
 693  */
 694
 695 /* generic potential and force calculation */
 696
 697 int potential_force_calc(t_moldyn *moldyn) {
 698
 699         int i,count;
 700         t_atom *atom;
 701         t_linkcell *lc;
 702         t_list neighbour[27];
 703         t_list *this;
 704         double u;
 705         u8 bc,bc3;
 706         int countn,dnlc;
 707
 708         count=moldyn->count;
 709         atom=moldyn->atom;
 710         lc=&(moldyn->lc);
 711
 712         /* reset energy */
 713         moldyn->energy=0.0;
 714
 715         for(i=0;i<count;i++) {
 716
 717                 /* reset force */
 718                 v3_zero(&(atom[i].f));
 719
 720                 /* single particle potential/force */
 721                 if(atom[i].attr&ATOM_ATTR_1BP)
 722                         moldyn->pf_func1b(moldyn,&(atom[i]));
 723
 724                 /* 2 body pair potential/force */
 725                 if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
 726
 727                         link_cell_neighbour_index(moldyn,
 728                                 (atom[i].r.x+moldyn->dim.x/2)/lc->x,
 729                                 (atom[i].r.y+moldyn->dim.y/2)/lc->y,
 730                                 (atom[i].r.z+moldyn->dim.z/2)/lc->z,
 731                                 neighbour);
 732
 733                         countn=lc->countn;
 734                         dnlc=lc->dnlc;
 735
 736                         for(j=0;j<countn;j++) {
 737
 738                                 this=&(neighbour[j]);
 739                                 list_reset(this);
 740
 741                                 if(this->start==NULL)
 742                                         continue;
 743
 744                                 bc=(j<dnlc)?0:1;
 745
 746                                 do {
 747                                         btom=this->current->data;
 748
 749                                         if(btom==&(atom[i]))
 750                                                 continue;
 751
 752                                         if((btom->attr&ATOM_ATTR_2BP)&
 753                                            (atom[i].attr&ATOM_ATTR_2BP))
 754                                                 moldyn->pf_func2b(moldyn,
 755                                                                   &(atom[i]),
 756                                                                   btom,
 757                                                                   bc);
 758
 759                                         /* 3 body potential/force */
 760
 761                                         if(!(atom[i].attr&ATOM_ATTR_3BP)||
 762                                            !(btom->attr&ATOM_ATTR_3BP))
 763                                                 continue;
 764
 765                                         link_cell_neighbour_index(moldyn,
 766                                            (btom->r.x+moldyn->dim.x/2)/lc->x,
 767                                            (btom->r.y+moldyn->dim.y/2)/lc->y,
 768                                            (btom->r.z+moldyn->dim.z/2)/lc->z,
 769                                            neighbourk);
 770
 771                                         for(k=0;k<lc->countn;k++) {
 772
 773                                                 thisk=&(neighbourk[k]);
 774                                                 list_reset(thisk);
 775
 776                                                 if(thisk->start==NULL)
 777                                                         continue;
 778
 779                                                 bck=(k<lc->dnlc)?0:1;
 780
 781                                                 do {
 782
 783                         ktom=thisk->current->data;
 784
 785                         if(!(ktom->attr&ATOM_ATTR_3BP))
 786                                 continue;
 787
 788                         if(ktom==btom)
 789                                 continue;
 790
 791                         if(ktom==&(atom[i]))
 792                                 continue;
 793
 794                         moldyn->pf_func3b(moldyn,&(atom[i]),btom,ktom,bck);
 795
 796                                                 } while(list_next(thisk)!=\
 797                                                         L_NO_NEXT_ELEMENT);
 798
 799                                 } while(list_next(this)!=L_NO_NEXT_ELEMENT);
 800                         }
 801                 }
 802         }
 803
 804         return 0;
 805 }
 806
 807 /*
 808  * periodic boundayr checking
 809  */
 810
 811 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
 812
 813         double x,y,z;
 814
 815         x=0.5*dim->x;
 816         y=0.5*dim->y;
 817         z=0.5*dim->z;
 818
 819         if(moldyn->MOLDYN_ATTR_PBX)
 820                 if(a->x>=x) a->x-=dim->x;
 821                 else if(-a->x>x) a->x+=dim->x;
 822         if(moldyn->MOLDYN_ATTR_PBY)
 823                 if(a->y>=y) a->y-=dim->y;
 824                 else if(-a->y>y) a->y+=dim->y;
 825         if(moldyn->MOLDYN_ATTR_PBZ)
 826                 if(a->z>=z) a->z-=dim->z;
 827                 else if(-a->z>z) a->z+=dim->z;
 828
 829         return 0;
 830 }
 831
 832
 833 /*
 834  * example potentials
 835  */
 836
 837 /* harmonic oscillator potential and force */
 838
 839 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc)) {
 840
 841         t_ho_params *params;
 842         t_3dvec force,distance;
 843         double d;
 844         double sc,equi_dist;
 845
 846         params=moldyn->pot2b_params;
 847         sc=params->spring_constant;
 848         equi_dist=params->equilibrium_distance;
 849
 850         v3_sub(&distance,&(ai->r),&(aj->r);
 851
 852         v3_per_bound(&distance,&(moldyn->dim));
 853         if(bc) check_per_bound(moldyn,&distance);
 854         d=v3_norm(&distance);
 855         if(d<=moldyn->cutoff) {
 856                 /* energy is 1/2 (d-d0)^2, but we will add this twice ... */
 857                 moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
 858                 v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
 859                 v3_add(&(ai->f),&(ai->f),&force);
 860         }
 861
 862         return 0;
 863 }
 864
 865 /* lennard jones potential & force for one sort of atoms */
 866
 867 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 868
 869         t_lj_params *params;
 870         t_3dvec force,distance;
 871         double d,h1,h2,u;
 872         double eps,sig6,sig12;
 873
 874         params=moldyn->pot_params;
 875         eps=params->epsilon4;
 876         sig6=params->sigma6;
 877         sig12=params->sigma12;
 878
 879         v3_sub(&distance,&(ai->r),&(aj->r));
 880         if(bc) check_per_bound(moldyn,&distance);
 881         d=v3_absolute_square(&distance);        /* 1/r^2 */
 882         if(d<=moldyn->cutoff_square) {
 883                 d=1.0/d;                        /* 1/r^2 */
 884                 h2=d*d;                         /* 1/r^4 */
 885                 h2*=d;                          /* 1/r^6 */
 886                 h1=h2*h2;                       /* 1/r^12 */
 887                 /* energy is eps*..., but we will add this twice ... */
 888                 moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
 889                 h2*=d;                          /* 1/r^8 */
 890                 h1*=d;                          /* 1/r^14 */
 891                 h2*=6*sig6;
 892                 h1*=12*sig12;
 893                 d=+h1-h2;
 894                 d*=eps;
 895                 v3_scale(&force,&distance,d);
 896                 v3_add(&(ai->f),&(aj->f),&force);
 897         }
 898
 899         return 0;
 900 }
 901
 902 /*
 903  * tersoff potential & force for 2 sorts of atoms
 904  */
 905
 906 /* tersoff 2 body part */
 907
 908 int tersoff_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 909
 910         t_tersoff_params *params;
 911         t_3dvec dist_ij;
 912         double d_ij;
 913
 914         params=moldyn->pot_params;
 915
 916         /*
 917          * we need: f_c, df_c, f_r, df_r
 918          *
 919          * therefore we need: R, S
 920          */
 921
 922         v3_sub(&dist_ij,&(ai->r),&(aj->r));
 923
 924         if(bc) check_per_bound(moldyn,&dist_ij);
 925
 926         if(ai->bnum==aj->bnum) {
 927                 S=params->S[ai->bnum];
 928                 R=params->R[ai->bnum];
 929         }
 930         else {
 931                 S=params->Smixed;
 932                 R=params->Rmixed;
 933         }
 934
 935         d_ij=v3_norm(&dist_ij);
 936
 937         if(d_ij<=S) {
 938                 f_r=A*exp(-lamda*d_ij);
 939                 df_r=-lambda*f_r/d_ij;
 940                 if(d_ij<R) {
 941                         /* f_c = 1, df_c = 0 */
 942                         v3_scale(&force,&dist_ij,df_r);
 943                 }
 944                 else {
 945                         s_r=S-R;
 946                         arg=PI*(d_ij-R)/s_r;
 947                         f_c=0.5+0.5*cos(arg);
 948                         df_c=-0.5*sin(arg)*(PI/(s_r*d_ij));
 949                         scale=df_c*f_r+df_r*f_c;
 950                         v3_scale(&force,&dist_ij,scale);
 951                         v3_add(&(ai->f),&(ai->f),&force);
 952                 }
 953                 moldyn->energy+=(f_r*f_c);
 954         }
 955
 956         return 0;
 957 }
 958
 959 /* tersoff 3 body part */
 960
 961 int tersoff(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc,u8 bck) {
 962
 963         t_tersoff_params *params;
 964         t_3dvec dist_ij;
 965         double d_ij;
 966
 967         params=moldyn->pot_params;
 968
 969         /* 2 body part of the tersoff potential */
 970
 971         v3_sub(&dist_ij,&(ai->r),&(aj->r));
 972         if(bc) check_per_bound(moldyn,&dist_ij);
 973         d_ij=v3_norm(&dist_ij);
 974                 if(d_ij<=S) {
 975
 976                                 /* determine the tersoff parameters */
 977                                 if(atom[i].element!=btom->element) {
 978                                 S=sqrt(TERSOFF_S[e1]*TERSOFF_S[e2]);
 979                                 R=R_m;
 980                                 A=;
 981                                 lambda=;
 982                                 B=;
 983                                 mu=;
 984                                 chi=;
 985                                 beta=;
 986                                 betaN=;
 987
 988                                 if(d_ij<=R) {
 989                                         df_r=-lambda*A*exp(-lambda*d_ij)/d_ij;
 990                                         v3_scale(&force,&dist_ij,df_r);
 991                                         v3_add(&(atom[i].f),&(atom[i].f),
 992                                                 &force);
 993                                 }
 994                                 else {
 995                                         s_r=S-R;
 996                                         arg1=PI*(d_ij-R)/s_r;
 997                                         f_c=0.5+0.5*cos(arg1);
 998                                         df_c=-0.5*sin(arg1)*(PI/(s_r*d_ij));
 999                                         f_r=A*exp(-lambda*d_ij);
1000                                         df_r=-lambda*f_r/d_ij;
1001                                         scale=df_c*f_r+df_r*f_c;
1002                                         v3_scale(&force,&dist_ij,scale);
1003                                         v3_add(&(atom[i].f),&(atom[i].f),
1004                                                &force);
1005                                 }
1006                         }
1007                         else
1008                                 continue;
1009
1010
1011                         /* end 2 body stuff */
1012
1013                         /* determine cell neighbours of btom */
1014                         ki=(btom->r.x+(moldyn->dim.x/2))/lc->x;
1015                         kj=(btom->r.y+(moldyn->dim.y/2))/lc->y;
1016                         kk=(btom->r.z+(moldyn->dim.z/2))/lc->z;
1017                         ck=link_cell_neighbour_index(moldyn,ki,kj,kk,
1018                                                      neighbourk);
1019
1020                         /* go for zeta - 3 body stuff! */
1021                         zeta=0.0;
1022                         d_ij2=d_ij*d_ij;
1023
1024                         /* cell of btom */
1025                         thisk=&(neighbourk[0]);
1026                         list_reset(thisk);
1027                         do {
1028                                 ktom=thisk->current->data;
1029                                 if(ktom==btom)
1030                                         continue;
1031                                 if(ktom==&(atom[i]))
1032                                         continue;
1033
1034                                 /* 3 body stuff (1) */
1035
1036                                 v3_sub(&dist_ik,ktom,&(atom[i]));
1037                                 d_ik=v3_norm(&dist_ik);
1038                                 if(d_ik<=Sik) {
1039
1040                                 Rik=;
1041                                 Sik=;
1042                                 Aik=;
1043                                 lambda_ik=;
1044                                 Bik=;
1045                                 mu_ik=;
1046                                 omega_ik=;
1047                                 c_i=;
1048                                 d_i=;
1049                                 h_i=;
1050
1051
1052                                         if(d_ik<=Rik) {
1053                                                 f_cik=1.0;
1054                                                 df_cik=0.0;
1055                                         }
1056                                         else {
1057                                                 sik_rik=Sik-Rik;
1058                                                 arg1ik=PI*(d_ik-Rik)/sik_rik;
1059                                                 f_cik=0.5+0.5*cos(arg1ik);
1060                                                 df_cik=-0.5*sin(arg1ik)* \
1061                                                        (PI/(sik_rik*d_ik));
1062                                                 f_rik=Aik*exp(-lambda_ik*d_ik);
1063                                                 f_aik=-Bik*exp(-mu_ik*d_ik);
1064                                         }
1065
1066                                         v3_sub(&distance_jk,ktom,btom);
1067                                         cos_theta=(d_ij2+d_ik*d_ik-d_jk*d_jk)/\
1068                                                   (2*d_ij*d_ik);
1069                                         sin_theta=sqrt(1.0/\
1070                                                   (cos_theta*cos_theta));
1071                                         theta=arccos(cos_theta);
1072
1073
1074                                 }
1075                                 else
1076                                         continue;
1077
1078                                 /* end 3 body stuff (1) */
1079
1080
1081                         } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
1082
1083                         /* direct neighbours of btom cell */
1084                         for(k=1;k<ck;k++) {
1085                                 thisk=&(neighbourk[k]);
1086                                 list_reset(thisk);
1087                                 if(thisk->start!=NULL) {
1088
1089                                 do {
1090                                         ktom=thisk->current->data;
1091                                         if(ktom==&(atom[i]))
1092                                                 continue;
1093
1094                                 /* 3 body stuff (2) */
1095
1096                                 } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
1097
1098                                 }
1099                         }
1100
1101                         /* indirect neighbours of btom cell */
1102                         for(k=ck;k<27;k++) {
1103                                 thisk=&(neighbourk[k]);
1104                                 list_reset(thisk);
1105                                 if(thisk->start!=NULL) {
1106
1107                                 do {
1108                                         ktom=thisk->current->data;
1109                                         if(ktom==&(atom[i]))
1110                                                 continue;
1111
1112                                 /* 3 body stuff */
1113
1114                                 } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
1115
1116                                 }
1117                         }
1118
1119
1120                 } while(list_next(this)!=L_NO_NEXT_ELEMENT);
1121
1122                 /*
1123                  * direct neighbour cells of atom i
1124                  */
1125                 for(j=1;j<c;j++) {
1126                         this=&(neighbour[j]);
1127                         list_reset(this);
1128                         if(this->start!=NULL) {
1129
1130                         do {
1131                                 btom=this->current->data;
1132
1133                                 /* 2 body stuff */
1134
1135
1136                         /* determine cell neighbours of btom */
1137                         ki=(btom->r.x+(moldyn->dim.x/2))/lc->x;
1138                         kj=(btom->r.y+(moldyn->dim.y/2))/lc->y;
1139                         kk=(btom->r.z+(moldyn->dim.z/2))/lc->z;
1140                         ck=link_cell_neighbour_index(moldyn,ki,kj,kk,
1141                                                      neighbourk);
1142
1143                         /* cell of btom */
1144                         thisk=&(neighbourk[0]);
1145                         list_reset(thisk);
1146                         do {
1147                                 ktom=thisk->current->data;
1148                                 if(ktom==btom)
1149                                         continue;
1150                                 if(ktom==&(atom[i]))
1151                                         continue;
1152
1153                                 /* 3 body stuff (1) */
1154
1155                         } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
1156
1157                         /* direct neighbours of btom cell */
1158                         for(k=1;k<ck;k++) {
1159                                 thisk=&(neighbourk[k]);
1160                                 list_reset(thisk);
1161                                 if(thisk->start!=NULL) {
1162
1163                                 do {
1164                                         ktom=thisk->current->data;
1165                                         if(ktom==&(atom[i]))
1166                                                 continue;
1167
1168                                 /* 3 body stuff (2) */
1169
1170                                 } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
1171
1172                                 }
1173                         }
1174
1175                         /* indirect neighbours of btom cell */
1176                         for(k=ck;k<27;k++) {
1177                                 thisk=&(neighbourk[k]);
1178                                 list_reset(thisk);
1179                                 if(thisk->start!=NULL) {
1180
1181                                 do {
1182                                         ktom=thisk->current->data;
1183                                         if(ktom==&(atom[i]))
1184                                                 continue;
1185
1186                                 /* 3 body stuff (3) */
1187
1188                                 } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
1189
1190                                 }
1191                         }
1192
1193
1194                         } while(list_next(this)!=L_NO_NEXT_ELEMENT);
1195
1196                         }
1197                 }
1198
1199                 /*
1200                  * indirect neighbour cells of atom i
1201                  */
1202                 for(j=c;j<27;j++) {
1203                         this=&(neighbour[j]);
1204                         list_reset(this);
1205                         if(this->start!=NULL) {
1206
1207                         do {
1208                                 btom=this->current->data;
1209
1210                                 /* 2 body stuff */
1211
1212
1213                         /* determine cell neighbours of btom */
1214                         ki=(btom->r.x+(moldyn->dim.x/2))/lc->x;
1215                         kj=(btom->r.y+(moldyn->dim.y/2))/lc->y;
1216                         kk=(btom->r.z+(moldyn->dim.z/2))/lc->z;
1217                         ck=link_cell_neighbour_index(moldyn,ki,kj,kk,
1218                                                      neighbourk);
1219
1220                         /* cell of btom */
1221                         thisk=&(neighbourk[0]);
1222                         list_reset(thisk);
1223                         do {
1224                                 ktom=thisk->current->data;
1225                                 if(ktom==btom)
1226                                         continue;
1227                                 if(ktom==&(atom[i]))
1228                                         continue;
1229
1230                                 /* 3 body stuff (1) */
1231
1232                         } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
1233
1234                         /* direct neighbours of btom cell */
1235                         for(k=1;k<ck;k++) {
1236                                 thisk=&(neighbourk[k]);
1237                                 list_reset(thisk);
1238                                 if(thisk->start!=NULL) {
1239
1240                                 do {
1241                                         ktom=thisk->current->data;
1242                                         if(ktom==&(atom[i]))
1243                                                 continue;
1244
1245                                 /* 3 body stuff (2) */
1246
1247                                 } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
1248
1249                                 }
1250                         }
1251
1252                         /* indirect neighbours of btom cell */
1253                         for(k=ck;k<27;k++) {
1254                                 thisk=&(neighbourk[k]);
1255                                 list_reset(thisk);
1256                                 if(thisk->start!=NULL) {
1257
1258                                 do {
1259                                         ktom=thisk->current->data;
1260                                         if(ktom==&(atom[i]))
1261                                                 continue;
1262
1263                                 /* 3 body stuff (3) */
1264
1265                                 } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
1266
1267                                 }
1268                         }
1269
1270
1271                         } while(list_next(this)!=L_NO_NEXT_ELEMENT);
1272
1273                         }
1274                 }
1275
1276         }
1277
1278         moldyn->energy=0.5*u;
1279
1280         return 0;
1281 }
1282