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 1 body part */
 907 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
 908
 909         int num;
 910         t_tersoff_mult_params *params;
 911         t_tersoff_exchange *exchange;
 912
 913         num=ai->bnum;
 914         params=moldyn->pot1b_params;
 915         exchange=&(params->exchange);
 916
 917         /*
 918          * simple: point constant parameters only depending on atom i to
 919          *         their right values
 920          */
 921
 922         exchange->beta=&(params->beta[num]);
 923         exchange->n=&(params->n[num]);
 924         exchange->c=&(params->c[num]);
 925         exchange->d=&(params->d[num]);
 926         exchange->h=&(params->h[num]);
 927
 928         exchange->betan=pow(*(exchange->beta),*(exchange->n));
 929         exchange->c2=params->c[num]*params->c[num];
 930         exchange->d2=params->d[num]*params->d[num];
 931         exchange->c2d2=exchange->c2/exchange->d2;
 932
 933         return 0;
 934 }
 935
 936 /* tersoff 2 body part */
 937 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 938
 939         t_tersoff_mult_params *params;
 940         t_tersoff_exchange *exchange;
 941         t_3dvec dist_ij;
 942         double d_ij;
 943         double A,B,R,S,lambda;
 944         int num;
 945
 946         params=moldyn->pot_params;
 947         num=ai->bnum;
 948         exchange=&(params->exchange);
 949
 950         exchange->run3bp=0;
 951
 952         /*
 953          * we need: f_c, df_c, f_r, df_r
 954          *
 955          * therefore we need: R, S, A, lambda
 956          */
 957
 958         v3_sub(&dist_ij,&(ai->r),&(aj->r));
 959
 960         if(bc) check_per_bound(moldyn,&dist_ij);
 961
 962         /* save for use in 3bp */ /* REALLY ?!?!?! */
 963         exchange->dist_ij=dist_ij;
 964
 965         /* constants */
 966         if(num==aj->bnum) {
 967                 S=params->S[num];
 968                 R=params->R[num];
 969                 A=params->A[num];
 970                 lambda=params->lambda[num];
 971                 /* more constants depending of atoms i and j, needed in 3bp */
 972                 params->exchange.B=&(params->B[num]);
 973                 params->exchange.mu=params->mu[num];
 974                 params->exchange.chi=1.0;
 975         }
 976         else {
 977                 S=params->Smixed;
 978                 R=params->Rmixed;
 979                 A=params->Amixed;
 980                 lambda=params->lambda_m;
 981                 /* more constants depending of atoms i and j, needed in 3bp */
 982                 params->exchange.B=&(params->Bmixed);
 983                 params->exchange.mu=&(params->mu_m);
 984                 params->exchange.chi=params->chi;
 985         }
 986
 987         d_ij=v3_norm(&dist_ij);
 988
 989         /* save for use in 3bp */
 990         exchange->d_ij=d_ij;
 991
 992         if(d_ij>S)
 993                 return 0;
 994
 995         f_r=A*exp(-lamda*d_ij);
 996         df_r=-lambda*f_r/d_ij;
 997
 998         /* f_a, df_a calc + save for 3bp use */
 999         exchange->f_a=-B*exp(-mu*d_ij);
1000         exchange->df_a=-mu*exchange->f_a/d_ij;
1001
1002         if(d_ij<R) {
1003                 /* f_c = 1, df_c = 0 */
1004                 f_c=1.0;
1005                 df_c=0.0;
1006                 v3_scale(&force,&dist_ij,df_r);
1007         }
1008         else {
1009                 s_r=S-R;
1010                 arg=PI*(d_ij-R)/s_r;
1011                 f_c=0.5+0.5*cos(arg);
1012                 df_c=-0.5*sin(arg)*(PI/(s_r*d_ij));
1013                 scale=df_c*f_r+df_r*f_c;
1014                 v3_scale(&force,&dist_ij,scale);
1015         }
1016
1017         /* add forces */
1018         v3_add(&(ai->f),&(ai->f),&force);
1019         /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
1020         moldyn->energy+=(0.25*f_r*f_c);
1021
1022         /* save for use in 3bp */
1023         exchange->f_c=f_c;
1024         exchange->df_c=df_c;
1025
1026         /* enable the run of 3bp function */
1027         exchange->run3bp=1;
1028
1029         return 0;
1030 }
1031
1032 /* tersoff 3 body part */
1033
1034 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
1035
1036         t_tersoff_mult_params *params;
1037         t_tersoff_exchange *exchange;
1038         t_3dvec dist_ij,dist_ik,dist_jk;
1039         t_3dvec temp,force;
1040         double R,S,s_r;
1041         double d_ij,d_ik,d_jk;
1042         double f_c,df_c,b_ij,f_a,df_a;
1043         double n,c,d,h,neta,betan,betan_1;
1044         double theta,cos_theta,sin_theta;
1045         int num;
1046
1047         params=moldyn->pot_params;
1048         num=ai->bnum;
1049         exchange=params->exchange;
1050
1051         if(!(exchange->run3bp))
1052                 return 0;
1053
1054         /*
1055          * we need: f_c, d_fc, b_ij, db_ij, f_a, df_a
1056          *
1057          * we got f_c, df_c, f_a, df_a from 2bp calculation
1058          */
1059
1060         d_ij=exchange->d_ij;
1061         d_ij2=exchange->d_ij2;
1062
1063         f_a=params->exchange.f_a;
1064         df_a=params->exchange.df_a;
1065
1066         /* d_ij is <= S, as we didn't return so far! */
1067
1068         /*
1069          * calc of b_ij (scalar) and db_ij (vector)
1070          *
1071          * - for b_ij: chi, beta, f_c_ik, w(=1), c, d, h, n, cos_theta
1072          *
1073          * - for db_ij: d_theta, sin_theta, cos_theta, f_c_ik, df_c_ik,
1074          *              w_ik,
1075          *
1076          */
1077
1078
1079         v3_sub(&dist_ik,&(aj->i),&(ak->r));
1080         if(bc) check_per_bound(moldyn,&dist_ik);
1081         d_ik=v3_norm(&dist_ik);
1082
1083         /* constants for f_c_ik calc */
1084         if(num==ak->bnum) {
1085                 R=params->R[num];
1086                 S=params->S[num];
1087         }
1088         else {
1089                 R=params->Rmixed;
1090                 S=params->Smixed;
1091         }
1092
1093         /* calc of f_c_ik */
1094         if(d_ik>S)
1095                 return 0;
1096
1097         if(d_ik<R) {
1098                 /* f_c_ik = 1, df_c_ik = 0 */
1099                 f_c_ik=1.0;
1100                 df_c_ik=0.0;
1101         }
1102         else {
1103                 s_r=S-R;
1104                 arg=PI*(d_ik-R)/s_r;
1105                 f_c_ik=0.5+0.5*cos(arg);
1106                 df_c_ik=-0.5*sin(arg)*(PI/(s_r*d_ik));
1107         }
1108
1109         v3_sub(&dist_jk,&(aj->r),&(ak->r));
1110         if(bc) check_per_bound(moldyn,&dist_jk);
1111         d_jk=v3_norm(&dist_jk);
1112
1113         beta=*(exchange->beta);
1114         betan=exchange->betan;
1115         n=*(exchange->n);
1116         c=*(exchange->c);
1117         d=*(exchange->d);
1118         h=*(exchange->h);
1119         c2=exchange->c2;
1120         d2=exchange->d2;
1121         c2d2=exchange->c2d2;
1122
1123         numer=d_ij2+d_ik*d_ik-d_jk*d_jk;
1124         denom=2*d_ij*d_ik;
1125         cos_theta=numer/denom;
1126         sin_theta=sqrt(1.0-(cos_theta*cos_theta));
1127         theta=arccos(cos_theta);
1128         d_theta=(-1.0/sqrt(1.0-cos_theta*cos_theta))/(denom*denom);
1129         d_theta1=2*denom-numer*2*d_ik/d_ij;
1130         d_theta2=2*denom-numer*2*d_ij/d_ik;
1131         d_theta1*=d_theta;
1132         d_theta2*=d_theta;
1133
1134         h_cos=(h-cos_theta);
1135         h_cos2=h_cos*h_cos;
1136         d2_h_cos2=d2-h_cos2;
1137
1138         /* some usefull expressions */
1139         frac1=c2/(d2-h_cos2);
1140         bracket1=1+c2d2-frac1;
1141         bracket2=f_c_ik*bracket1;
1142         bracket2_n_1=pow(bracket2,n-1.0);
1143         bracket2_n=bracket2_n_1*bracket2;
1144         bracket3=1+betan*bracket2_n;
1145         bracket3_pow_1=pow(bracket3,(-1.0/(2.0*n))-1.0);
1146         bracket3_pow=bracket3_pow_1*bracket3;
1147
1148         /* now go on with calc of b_ij and derivation of b_ij */
1149         b_ij=chi*bracket3_pow;
1150
1151         /* derivation of theta */
1152         v3_scale(&force,&dist_ij,d1_theta);
1153         v3_scale(&temp,&dist_ik,d_theta2);
1154         v3_add(&force,&force,&temp);
1155
1156         /* part 1 of derivation of b_ij */
1157         v3_scale(&force,sin_theta*2*h_cos*f_c_ik*frac1);
1158
1159         /* part 2 of derivation of b_ij */
1160         v3_scale(&temp,&dist_ik,df_c_ik*bracket1);
1161
1162         /* sum up and scale ... */
1163         v3_add(&temp,&temp,&force);
1164         scale=bracket2_n_1*n*betan*(1+betan*bracket3_pow_1)*chi*(1.0/(2.0*n));
1165         v3_scale(&temp,&temp,scale);
1166
1167         /* now construct an energy and a force out of that */
1168         v3_scale(&temp,&temp,f_a);
1169         v3_scale(&force,&dist_ij,df_a*b_ij);
1170         v3_add(&temp,&temp,&force);
1171         v3_scale(&temp,&temp,f_c);
1172         v3_scale(&force,&dist_ij,df_c*b_ij*f_a);
1173         v3_add(&force,&force,&temp);
1174
1175         /* add forces */
1176         v3_add(&(ai->f),&(ai->f),&force);
1177         /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
1178         moldyn->energy+=(0.25*f_a*b_ij*f_c);
1179
1180         return 0;
1181 }
1182