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 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
  21
  22         memset(moldyn,0,sizeof(t_moldyn));
  23
  24         rand_init(&(moldyn->random),NULL,1);
  25         moldyn->random.status|=RAND_STAT_VERBOSE;
  26
  27         return 0;
  28 }
  29
  30 int moldyn_shutdown(t_moldyn *moldyn) {
  31
  32         printf("[moldyn] shutdown\n");
  33         moldyn_log_shutdown(moldyn);
  34         link_cell_shutdown(moldyn);
  35         rand_close(&(moldyn->random));
  36         free(moldyn->atom);
  37
  38         return 0;
  39 }
  40
  41 int set_int_alg(t_moldyn *moldyn,u8 algo) {
  42
  43         switch(algo) {
  44                 case MOLDYN_INTEGRATE_VERLET:
  45                         moldyn->integrate=velocity_verlet;
  46                         break;
  47                 default:
  48                         printf("unknown integration algorithm: %02x\n",algo);
  49                         return -1;
  50         }
  51
  52         return 0;
  53 }
  54
  55 int set_cutoff(t_moldyn *moldyn,double cutoff) {
  56
  57         moldyn->cutoff=cutoff;
  58
  59         return 0;
  60 }
  61
  62 int set_temperature(t_moldyn *moldyn,double t_ref) {
  63
  64         moldyn->t_ref=t_ref;
  65
  66         return 0;
  67 }
  68
  69 int set_pressure(t_moldyn *moldyn,double p_ref) {
  70
  71         moldyn->p_ref=p_ref;
  72
  73         return 0;
  74 }
  75
  76 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
  77
  78         moldyn->pt_scale=(ptype|ttype);
  79         moldyn->t_tc=ttc;
  80         moldyn->p_tc=ptc;
  81
  82         return 0;
  83 }
  84
  85 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
  86
  87         moldyn->dim.x=x;
  88         moldyn->dim.y=y;
  89         moldyn->dim.z=z;
  90
  91         moldyn->volume=x*y*z;
  92
  93         if(visualize) {
  94                 moldyn->vis.dim.x=x;
  95                 moldyn->vis.dim.y=y;
  96                 moldyn->vis.dim.z=z;
  97         }
  98
  99         printf("[moldyn] dimensions in A and A^3 respectively:\n");
 100         printf("  x: %f\n",moldyn->dim.x);
 101         printf("  y: %f\n",moldyn->dim.y);
 102         printf("  z: %f\n",moldyn->dim.z);
 103         printf("  volume: %f\n",moldyn->volume);
 104         printf("  visualize simulation box: %s\n",visualize?"on":"off");
 105
 106         return 0;
 107 }
 108
 109 int set_nn_dist(t_moldyn *moldyn,double dist) {
 110
 111         moldyn->nnd=dist;
 112
 113         return 0;
 114 }
 115
 116 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 117
 118         if(x)
 119                 moldyn->status|=MOLDYN_STAT_PBX;
 120
 121         if(y)
 122                 moldyn->status|=MOLDYN_STAT_PBY;
 123
 124         if(z)
 125                 moldyn->status|=MOLDYN_STAT_PBZ;
 126
 127         return 0;
 128 }
 129
 130 int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
 131
 132         moldyn->func1b=func;
 133         moldyn->pot1b_params=params;
 134
 135         return 0;
 136 }
 137
 138 int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
 139
 140         moldyn->func2b=func;
 141         moldyn->pot2b_params=params;
 142
 143         return 0;
 144 }
 145
 146 int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) {
 147
 148         moldyn->func2b_post=func;
 149         moldyn->pot2b_params=params;
 150
 151         return 0;
 152 }
 153
 154 int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
 155
 156         moldyn->func3b=func;
 157         moldyn->pot3b_params=params;
 158
 159         return 0;
 160 }
 161
 162 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
 163
 164         strncpy(moldyn->vlsdir,dir,127);
 165
 166         return 0;
 167 }
 168
 169 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 170
 171         char filename[128];
 172         int ret;
 173
 174         switch(type) {
 175                 case LOG_TOTAL_ENERGY:
 176                         moldyn->ewrite=timer;
 177                         snprintf(filename,127,"%s/energy",moldyn->vlsdir);
 178                         moldyn->efd=open(filename,
 179                                          O_WRONLY|O_CREAT|O_EXCL,
 180                                          S_IRUSR|S_IWUSR);
 181                         if(moldyn->efd<0) {
 182                                 perror("[moldyn] energy log fd open");
 183                                 return moldyn->efd;
 184                         }
 185                         dprintf(moldyn->efd,"# total energy log file\n");
 186                         break;
 187                 case LOG_TOTAL_MOMENTUM:
 188                         moldyn->mwrite=timer;
 189                         snprintf(filename,127,"%s/momentum",moldyn->vlsdir);
 190                         moldyn->mfd=open(filename,
 191                                          O_WRONLY|O_CREAT|O_EXCL,
 192                                          S_IRUSR|S_IWUSR);
 193                         if(moldyn->mfd<0) {
 194                                 perror("[moldyn] momentum log fd open");
 195                                 return moldyn->mfd;
 196                         }
 197                         dprintf(moldyn->efd,"# total momentum log file\n");
 198                         break;
 199                 case SAVE_STEP:
 200                         moldyn->swrite=timer;
 201                         break;
 202                 case VISUAL_STEP:
 203                         moldyn->vwrite=timer;
 204                         ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
 205                         if(ret<0) {
 206                                 printf("[moldyn] visual init failure\n");
 207                                 return ret;
 208                         }
 209                         break;
 210                 default:
 211                         printf("[moldyn] unknown log mechanism: %02x\n",type);
 212                         return -1;
 213         }
 214
 215         return 0;
 216 }
 217
 218 int moldyn_log_shutdown(t_moldyn *moldyn) {
 219
 220         printf("[moldyn] log shutdown\n");
 221         if(moldyn->efd) close(moldyn->efd);
 222         if(moldyn->mfd) close(moldyn->mfd);
 223         if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
 224
 225         return 0;
 226 }
 227
 228 /*
 229  * creating lattice functions
 230  */
 231
 232 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 233                    u8 attr,u8 bnum,int a,int b,int c) {
 234
 235         int count;
 236         int ret;
 237         t_3dvec origin;
 238
 239         count=a*b*c;
 240
 241         /* how many atoms do we expect */
 242         if(type==FCC) count*=4;
 243         if(type==DIAMOND) count*=8;
 244
 245         /* allocate space for atoms */
 246         moldyn->atom=malloc(count*sizeof(t_atom));
 247         if(moldyn->atom==NULL) {
 248                 perror("malloc (atoms)");
 249                 return -1;
 250         }
 251
 252         v3_zero(&origin);
 253
 254         switch(type) {
 255                 case FCC:
 256                         ret=fcc_init(a,b,c,lc,moldyn->atom,&origin);
 257                         break;
 258                 case DIAMOND:
 259                         ret=diamond_init(a,b,c,lc,moldyn->atom,&origin);
 260                         break;
 261                 default:
 262                         printf("unknown lattice type (%02x)\n",type);
 263                         return -1;
 264         }
 265
 266         /* debug */
 267         if(ret!=count) {
 268                 printf("[moldyn] creating lattice failed\n");
 269                 printf("  amount of atoms\n");
 270                 printf("  - expected: %d\n",count);
 271                 printf("  - created: %d\n",ret);
 272                 return -1;
 273         }
 274
 275         moldyn->count=count;
 276         printf("[moldyn] created lattice with %d atoms\n",count);
 277
 278         while(count) {
 279                 count-=1;
 280                 moldyn->atom[count].element=element;
 281                 moldyn->atom[count].mass=mass;
 282                 moldyn->atom[count].attr=attr;
 283                 moldyn->atom[count].bnum=bnum;
 284                 check_per_bound(moldyn,&(moldyn->atom[count].r));
 285         }
 286
 287         return ret;
 288 }
 289
 290 /* fcc lattice init */
 291 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 292
 293         int count;
 294         int i,j;
 295         t_3dvec o,r,n;
 296         t_3dvec basis[3];
 297         double help[3];
 298         double x,y,z;
 299
 300         x=a*lc;
 301         y=b*lc;
 302         z=c*lc;
 303
 304         if(origin) v3_copy(&o,origin);
 305         else v3_zero(&o);
 306
 307         /* construct the basis */
 308         for(i=0;i<3;i++) {
 309                 for(j=0;j<3;j++) {
 310                         if(i!=j) help[j]=0.5*lc;
 311                         else help[j]=.0;
 312                 }
 313                 v3_set(&basis[i],help);
 314         }
 315
 316         v3_zero(&r);
 317         count=0;
 318
 319         /* fill up the room */
 320         r.x=o.x;
 321         while(r.x<x) {
 322                 r.y=o.y;
 323                 while(r.y<y) {
 324                         r.z=o.z;
 325                         while(r.z<z) {
 326                                 v3_copy(&(atom[count].r),&r);
 327                                 atom[count].element=1;
 328                                 count+=1;
 329                                 for(i=0;i<3;i++) {
 330                                         v3_add(&n,&r,&basis[i]);
 331                                         if((n.x<x+o.x)&&
 332                                            (n.y<y+o.y)&&
 333                                            (n.z<z+o.z)) {
 334                                                 v3_copy(&(atom[count].r),&n);
 335                                                 count+=1;
 336                                         }
 337                                 }
 338                                 r.z+=lc;
 339                         }
 340                         r.y+=lc;
 341                 }
 342                 r.x+=lc;
 343         }
 344
 345         /* coordinate transformation */
 346         help[0]=x/2.0;
 347         help[1]=y/2.0;
 348         help[2]=z/2.0;
 349         v3_set(&n,help);
 350         for(i=0;i<count;i++)
 351                 v3_sub(&(atom[i].r),&(atom[i].r),&n);
 352
 353         return count;
 354 }
 355
 356 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 357
 358         int count;
 359         t_3dvec o;
 360
 361         count=fcc_init(a,b,c,lc,atom,origin);
 362
 363         o.x=0.25*lc;
 364         o.y=0.25*lc;
 365         o.z=0.25*lc;
 366
 367         if(origin) v3_add(&o,&o,origin);
 368
 369         count+=fcc_init(a,b,c,lc,&atom[count],&o);
 370
 371         return count;
 372 }
 373
 374 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
 375              t_3dvec *r,t_3dvec *v) {
 376
 377         t_atom *atom;
 378         void *ptr;
 379         int count;
 380
 381         atom=moldyn->atom;
 382         count=++(moldyn->count);
 383
 384         ptr=realloc(atom,count*sizeof(t_atom));
 385         if(!ptr) {
 386                 perror("[moldyn] realloc (add atom)");
 387                 return -1;
 388         }
 389         moldyn->atom=ptr;
 390
 391         atom=moldyn->atom;
 392         atom[count-1].r=*r;
 393         atom[count-1].v=*v;
 394         atom[count-1].element=element;
 395         atom[count-1].mass=mass;
 396         atom[count-1].bnum=bnum;
 397         atom[count-1].attr=attr;
 398
 399         return 0;
 400 }
 401
 402 int destroy_atoms(t_moldyn *moldyn) {
 403
 404         if(moldyn->atom) free(moldyn->atom);
 405
 406         return 0;
 407 }
 408
 409 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 410
 411         /*
 412          * - gaussian distribution of velocities
 413          * - zero total momentum
 414          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 415          */
 416
 417         int i;
 418         double v,sigma;
 419         t_3dvec p_total,delta;
 420         t_atom *atom;
 421         t_random *random;
 422
 423         atom=moldyn->atom;
 424         random=&(moldyn->random);
 425
 426         /* gaussian distribution of velocities */
 427         v3_zero(&p_total);
 428         for(i=0;i<moldyn->count;i++) {
 429                 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
 430                 /* x direction */
 431                 v=sigma*rand_get_gauss(random);
 432                 atom[i].v.x=v;
 433                 p_total.x+=atom[i].mass*v;
 434                 /* y direction */
 435                 v=sigma*rand_get_gauss(random);
 436                 atom[i].v.y=v;
 437                 p_total.y+=atom[i].mass*v;
 438                 /* z direction */
 439                 v=sigma*rand_get_gauss(random);
 440                 atom[i].v.z=v;
 441                 p_total.z+=atom[i].mass*v;
 442         }
 443
 444         /* zero total momentum */
 445         v3_scale(&p_total,&p_total,1.0/moldyn->count);
 446         for(i=0;i<moldyn->count;i++) {
 447                 v3_scale(&delta,&p_total,1.0/atom[i].mass);
 448                 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
 449         }
 450
 451         /* velocity scaling */
 452         scale_velocity(moldyn,equi_init);
 453
 454         return 0;
 455 }
 456
 457 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 458
 459         int i;
 460         double e,scale;
 461         t_atom *atom;
 462         int count;
 463
 464         atom=moldyn->atom;
 465
 466         /*
 467          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 468          */
 469
 470         /* get kinetic energy / temperature & count involved atoms */
 471         e=0.0;
 472         count=0;
 473         for(i=0;i<moldyn->count;i++) {
 474                 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
 475                         e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 476                         count+=1;
 477                 }
 478         }
 479         if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
 480         else return 0;  /* no atoms involved in scaling! */
 481
 482         /* (temporary) hack for e,t = 0 */
 483         if(e==0.0) {
 484         moldyn->t=0.0;
 485                 if(moldyn->t_ref!=0.0) {
 486                         thermal_init(moldyn,equi_init);
 487                         return 0;
 488                 }
 489                 else
 490                         return 0; /* no scaling needed */
 491         }
 492
 493
 494         /* get scaling factor */
 495         scale=moldyn->t_ref/moldyn->t;
 496         if(equi_init&TRUE)
 497                 scale*=2.0;
 498         else
 499                 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
 500                         scale=1.0+(scale-1.0)/moldyn->t_tc;
 501         scale=sqrt(scale);
 502
 503         /* velocity scaling */
 504         for(i=0;i<moldyn->count;i++) {
 505                 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
 506                         v3_scale(&(atom[i].v),&(atom[i].v),scale);
 507         }
 508
 509         return 0;
 510 }
 511
 512 int scale_volume(t_moldyn *moldyn) {
 513
 514         t_atom *atom;
 515         t_3dvec *dim,*vdim;
 516         double virial,scale;
 517         t_linkcell *lc;
 518         int i;
 519
 520         atom=moldyn->atom;
 521         dim=&(moldyn->dim);
 522         vdim=&(moldyn->vis.dim);
 523         lc=&(moldyn->lc);
 524
 525         for(i=0;i<moldyn->count;i++)
 526                 virial+=v3_norm(&(atom[i].virial));
 527
 528 printf("%f\n",virial);
 529         /* get pressure from virial */
 530         moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t-ONE_THIRD*virial;
 531         moldyn->p/=moldyn->volume;
 532 printf("%f\n",moldyn->p/(ATM));
 533
 534         /* scale factor */
 535         if(moldyn->pt_scale&P_SCALE_BERENDSEN)
 536                 scale=3*sqrt(1-(moldyn->p_ref-moldyn->p)/moldyn->p_tc);
 537         else
 538                 /* should actually never be used */
 539                 scale=pow(moldyn->p/moldyn->p_ref,1.0/3.0);
 540
 541 printf("scale = %f\n",scale);
 542         /* actual scaling */
 543         dim->x*=scale;
 544         dim->y*=scale;
 545         dim->z*=scale;
 546         if(vdim->x) vdim->x=dim->x;
 547         if(vdim->y) vdim->y=dim->y;
 548         if(vdim->z) vdim->z=dim->z;
 549         moldyn->volume*=(scale*scale*scale);
 550
 551         /* check whether we need a new linkcell init */
 552         if((dim->x/moldyn->cutoff!=lc->nx)||
 553            (dim->y/moldyn->cutoff!=lc->ny)||
 554            (dim->z/moldyn->cutoff!=lc->nx)) {
 555                 link_cell_shutdown(moldyn);
 556                 link_cell_init(moldyn);
 557         }
 558
 559         return 0;
 560
 561 }
 562
 563 double get_e_kin(t_moldyn *moldyn) {
 564
 565         int i;
 566         t_atom *atom;
 567
 568         atom=moldyn->atom;
 569         moldyn->ekin=0.0;
 570
 571         for(i=0;i<moldyn->count;i++)
 572                 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 573
 574         return moldyn->ekin;
 575 }
 576
 577 double get_e_pot(t_moldyn *moldyn) {
 578
 579         return moldyn->energy;
 580 }
 581
 582 double update_e_kin(t_moldyn *moldyn) {
 583
 584         return(get_e_kin(moldyn));
 585 }
 586
 587 double get_total_energy(t_moldyn *moldyn) {
 588
 589         return(moldyn->ekin+moldyn->energy);
 590 }
 591
 592 t_3dvec get_total_p(t_moldyn *moldyn) {
 593
 594         t_3dvec p,p_total;
 595         int i;
 596         t_atom *atom;
 597
 598         atom=moldyn->atom;
 599
 600         v3_zero(&p_total);
 601         for(i=0;i<moldyn->count;i++) {
 602                 v3_scale(&p,&(atom[i].v),atom[i].mass);
 603                 v3_add(&p_total,&p_total,&p);
 604         }
 605
 606         return p_total;
 607 }
 608
 609 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
 610
 611         double tau;
 612
 613         /* nn_dist is the nearest neighbour distance */
 614
 615         tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
 616
 617         return tau;
 618 }
 619
 620 /*
 621  * numerical tricks
 622  */
 623
 624 /* linked list / cell method */
 625
 626 int link_cell_init(t_moldyn *moldyn) {
 627
 628         t_linkcell *lc;
 629         int i;
 630
 631         lc=&(moldyn->lc);
 632
 633         /* partitioning the md cell */
 634         lc->nx=moldyn->dim.x/moldyn->cutoff;
 635         lc->x=moldyn->dim.x/lc->nx;
 636         lc->ny=moldyn->dim.y/moldyn->cutoff;
 637         lc->y=moldyn->dim.y/lc->ny;
 638         lc->nz=moldyn->dim.z/moldyn->cutoff;
 639         lc->z=moldyn->dim.z/lc->nz;
 640
 641         lc->cells=lc->nx*lc->ny*lc->nz;
 642         lc->subcell=malloc(lc->cells*sizeof(t_list));
 643
 644         printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 645
 646         for(i=0;i<lc->cells;i++)
 647                 list_init_f(&(lc->subcell[i]));
 648
 649         link_cell_update(moldyn);
 650
 651         return 0;
 652 }
 653
 654 int link_cell_update(t_moldyn *moldyn) {
 655
 656         int count,i,j,k;
 657         int nx,ny;
 658         t_atom *atom;
 659         t_linkcell *lc;
 660         double x,y,z;
 661
 662         atom=moldyn->atom;
 663         lc=&(moldyn->lc);
 664
 665         nx=lc->nx;
 666         ny=lc->ny;
 667
 668         x=moldyn->dim.x/2;
 669         y=moldyn->dim.y/2;
 670         z=moldyn->dim.z/2;
 671
 672         for(i=0;i<lc->cells;i++)
 673                 list_destroy_f(&(lc->subcell[i]));
 674
 675         for(count=0;count<moldyn->count;count++) {
 676                 i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
 677                 j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
 678                 k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
 679                 list_add_immediate_f(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
 680                                      &(atom[count]));
 681         }
 682
 683         return 0;
 684 }
 685
 686 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 687
 688         t_linkcell *lc;
 689         int a;
 690         int count1,count2;
 691         int ci,cj,ck;
 692         int nx,ny,nz;
 693         int x,y,z;
 694         u8 bx,by,bz;
 695
 696         lc=&(moldyn->lc);
 697         nx=lc->nx;
 698         ny=lc->ny;
 699         nz=lc->nz;
 700         count1=1;
 701         count2=27;
 702         a=nx*ny;
 703
 704         cell[0]=lc->subcell[i+j*nx+k*a];
 705         for(ci=-1;ci<=1;ci++) {
 706                 bx=0;
 707                 x=i+ci;
 708                 if((x<0)||(x>=nx)) {
 709                         x=(x+nx)%nx;
 710                         bx=1;
 711                 }
 712                 for(cj=-1;cj<=1;cj++) {
 713                         by=0;
 714                         y=j+cj;
 715                         if((y<0)||(y>=ny)) {
 716                                 y=(y+ny)%ny;
 717                                 by=1;
 718                         }
 719                         for(ck=-1;ck<=1;ck++) {
 720                                 bz=0;
 721                                 z=k+ck;
 722                                 if((z<0)||(z>=nz)) {
 723                                         z=(z+nz)%nz;
 724                                         bz=1;
 725                                 }
 726                                 if(!(ci|cj|ck)) continue;
 727                                 if(bx|by|bz) {
 728                                         cell[--count2]=lc->subcell[x+y*nx+z*a];
 729                                 }
 730                                 else {
 731                                         cell[count1++]=lc->subcell[x+y*nx+z*a];
 732                                 }
 733                         }
 734                 }
 735         }
 736
 737         lc->dnlc=count1;
 738
 739         return count1;
 740 }
 741
 742 int link_cell_shutdown(t_moldyn *moldyn) {
 743
 744         int i;
 745         t_linkcell *lc;
 746
 747         lc=&(moldyn->lc);
 748
 749         for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
 750                 list_destroy_f(&(moldyn->lc.subcell[i]));
 751
 752         free(lc->subcell);
 753
 754         return 0;
 755 }
 756
 757 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
 758
 759         int count;
 760         void *ptr;
 761         t_moldyn_schedule *schedule;
 762
 763         schedule=&(moldyn->schedule);
 764         count=++(schedule->content_count);
 765
 766         ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
 767         if(!ptr) {
 768                 perror("[moldyn] realloc (runs)");
 769                 return -1;
 770         }
 771         moldyn->schedule.runs=ptr;
 772         moldyn->schedule.runs[count-1]=runs;
 773
 774         ptr=realloc(schedule->tau,count*sizeof(double));
 775         if(!ptr) {
 776                 perror("[moldyn] realloc (tau)");
 777                 return -1;
 778         }
 779         moldyn->schedule.tau=ptr;
 780         moldyn->schedule.tau[count-1]=tau;
 781
 782         return 0;
 783 }
 784
 785 int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
 786
 787         moldyn->schedule.hook=hook;
 788         moldyn->schedule.hook_params=hook_params;
 789
 790         return 0;
 791 }
 792
 793 /*
 794  *
 795  * 'integration of newtons equation' - algorithms
 796  *
 797  */
 798
 799 /* start the integration */
 800
 801 int moldyn_integrate(t_moldyn *moldyn) {
 802
 803         int i,sched;
 804         unsigned int e,m,s,v;
 805         t_3dvec p;
 806         t_moldyn_schedule *schedule;
 807         t_atom *atom;
 808         int fd;
 809         char dir[128];
 810         double ds;
 811
 812         schedule=&(moldyn->schedule);
 813         atom=moldyn->atom;
 814
 815         /* initialize linked cell method */
 816         link_cell_init(moldyn);
 817
 818         /* logging & visualization */
 819         e=moldyn->ewrite;
 820         m=moldyn->mwrite;
 821         s=moldyn->swrite;
 822         v=moldyn->vwrite;
 823
 824         /* sqaure of some variables */
 825         moldyn->tau_square=moldyn->tau*moldyn->tau;
 826         moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
 827
 828         /* calculate initial forces */
 829         potential_force_calc(moldyn);
 830
 831         /* some stupid checks before we actually start calculating bullshit */
 832         if(moldyn->cutoff>0.5*moldyn->dim.x)
 833                 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
 834         if(moldyn->cutoff>0.5*moldyn->dim.y)
 835                 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
 836         if(moldyn->cutoff>0.5*moldyn->dim.z)
 837                 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
 838         ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
 839         if(ds>0.05*moldyn->nnd)
 840                 printf("[moldyn] warning: forces too high / tau too small!\n");
 841
 842         /* zero absolute time */
 843         moldyn->time=0.0;
 844
 845         /* debugging, ignore */
 846         moldyn->debug=0;
 847
 848         /* executing the schedule */
 849         for(sched=0;sched<moldyn->schedule.content_count;sched++) {
 850
 851                 /* setting amount of runs and finite time step size */
 852                 moldyn->tau=schedule->tau[sched];
 853                 moldyn->tau_square=moldyn->tau*moldyn->tau;
 854                 moldyn->time_steps=schedule->runs[sched];
 855
 856         /* integration according to schedule */
 857
 858         for(i=0;i<moldyn->time_steps;i++) {
 859
 860                 /* integration step */
 861                 moldyn->integrate(moldyn);
 862
 863                 /* p/t scaling */
 864                 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
 865                         scale_velocity(moldyn,FALSE);
 866                 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
 867                         scale_volume(moldyn);
 868
 869                 /* check for log & visualization */
 870                 if(e) {
 871                         if(!(i%e))
 872                                 dprintf(moldyn->efd,
 873                                         "%f %f %f %f\n",
 874                                         moldyn->time,update_e_kin(moldyn),
 875                                         moldyn->energy,
 876                                         get_total_energy(moldyn));
 877                 }
 878                 if(m) {
 879                         if(!(i%m)) {
 880                                 p=get_total_p(moldyn);
 881                                 dprintf(moldyn->mfd,
 882                                         "%f %f\n",moldyn->time,v3_norm(&p));
 883                         }
 884                 }
 885                 if(s) {
 886                         if(!(i%s)) {
 887                                 snprintf(dir,128,"%s/s-%07.f.save",
 888                                          moldyn->vlsdir,moldyn->time);
 889                                 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
 890                                 if(fd<0) perror("[moldyn] save fd open");
 891                                 else {
 892                                         write(fd,moldyn,sizeof(t_moldyn));
 893                                         write(fd,moldyn->atom,
 894                                               moldyn->count*sizeof(t_atom));
 895                                 }
 896                                 close(fd);
 897                         }
 898                 }
 899                 if(v) {
 900                         if(!(i%v)) {
 901                                 visual_atoms(&(moldyn->vis),moldyn->time,
 902                                              moldyn->atom,moldyn->count);
 903                                 printf("\rsched: %d, steps: %d, debug: %d",
 904                                        sched,i,moldyn->debug);
 905                                 fflush(stdout);
 906                         }
 907                 }
 908
 909                 /* increase absolute time */
 910                 moldyn->time+=moldyn->tau;
 911
 912         }
 913
 914                 /* check for hooks */
 915                 if(schedule->hook)
 916                         schedule->hook(moldyn,schedule->hook_params);
 917
 918                 /* get a new info line */
 919                 printf("\n");
 920
 921         }
 922
 923         return 0;
 924 }
 925
 926 /* velocity verlet */
 927
 928 int velocity_verlet(t_moldyn *moldyn) {
 929
 930         int i,count;
 931         double tau,tau_square;
 932         t_3dvec delta;
 933         t_atom *atom;
 934
 935         atom=moldyn->atom;
 936         count=moldyn->count;
 937         tau=moldyn->tau;
 938         tau_square=moldyn->tau_square;
 939
 940         for(i=0;i<count;i++) {
 941                 /* new positions */
 942                 v3_scale(&delta,&(atom[i].v),tau);
 943                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 944                 v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
 945                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 946                 check_per_bound(moldyn,&(atom[i].r));
 947
 948                 /* velocities */
 949                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 950                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 951         }
 952
 953         /* neighbour list update */
 954         link_cell_update(moldyn);
 955
 956         /* forces depending on chosen potential */
 957         potential_force_calc(moldyn);
 958
 959         for(i=0;i<count;i++) {
 960                 /* again velocities */
 961                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 962                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 963         }
 964
 965         return 0;
 966 }
 967
 968
 969 /*
 970  *
 971  * potentials & corresponding forces
 972  *
 973  */
 974
 975 /* generic potential and force calculation */
 976
 977 int potential_force_calc(t_moldyn *moldyn) {
 978
 979         int i,j,k,count;
 980         t_atom *itom,*jtom,*ktom;
 981         t_linkcell *lc;
 982         t_list neighbour_i[27];
 983         t_list neighbour_i2[27];
 984         t_list *this,*that;
 985         u8 bc_ij,bc_ik;
 986         int dnlc;
 987
 988         count=moldyn->count;
 989         itom=moldyn->atom;
 990         lc=&(moldyn->lc);
 991
 992         /* reset energy */
 993         moldyn->energy=0.0;
 994
 995         /* get energy and force of every atom */
 996         for(i=0;i<count;i++) {
 997
 998                 /* reset force */
 999                 v3_zero(&(itom[i].f));
1000
1001                 /* reset viral of atom i */
1002                 v3_zero(&(itom[i].virial));
1003
1004                 /* reset site energy */
1005                 itom[i].e=0.0;
1006
1007                 /* single particle potential/force */
1008                 if(itom[i].attr&ATOM_ATTR_1BP)
1009                         moldyn->func1b(moldyn,&(itom[i]));
1010
1011                 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
1012                         continue;
1013
1014                 /* 2 body pair potential/force */
1015
1016                 link_cell_neighbour_index(moldyn,
1017                                           (itom[i].r.x+moldyn->dim.x/2)/lc->x,
1018                                           (itom[i].r.y+moldyn->dim.y/2)/lc->y,
1019                                           (itom[i].r.z+moldyn->dim.z/2)/lc->z,
1020                                           neighbour_i);
1021
1022                 dnlc=lc->dnlc;
1023
1024                 for(j=0;j<27;j++) {
1025
1026                         this=&(neighbour_i[j]);
1027                         list_reset_f(this);
1028
1029                         if(this->start==NULL)
1030                                 continue;
1031
1032                         bc_ij=(j<dnlc)?0:1;
1033
1034                         do {
1035                                 jtom=this->current->data;
1036
1037                                 if(jtom==&(itom[i]))
1038                                         continue;
1039
1040                                 if((jtom->attr&ATOM_ATTR_2BP)&
1041                                    (itom[i].attr&ATOM_ATTR_2BP)) {
1042                                         moldyn->func2b(moldyn,
1043                                                        &(itom[i]),
1044                                                        jtom,
1045                                                        bc_ij);
1046                                 }
1047
1048                                 /* 3 body potential/force */
1049
1050                                 if(!(itom[i].attr&ATOM_ATTR_3BP)||
1051                                    !(jtom->attr&ATOM_ATTR_3BP))
1052                                         continue;
1053
1054                                 /* copy the neighbour lists */
1055                                 memcpy(neighbour_i2,neighbour_i,
1056                                        27*sizeof(t_list));
1057
1058                                 /* get neighbours of i */
1059                                 for(k=0;k<27;k++) {
1060
1061                                         that=&(neighbour_i2[k]);
1062                                         list_reset_f(that);
1063
1064                                         if(that->start==NULL)
1065                                                 continue;
1066
1067                                         bc_ik=(k<dnlc)?0:1;
1068
1069                                         do {
1070
1071                                                 ktom=that->current->data;
1072
1073                                                 if(!(ktom->attr&ATOM_ATTR_3BP))
1074                                                         continue;
1075
1076                                                 if(ktom==jtom)
1077                                                         continue;
1078
1079                                                 if(ktom==&(itom[i]))
1080                                                         continue;
1081
1082                                                 moldyn->func3b(moldyn,
1083                                                                &(itom[i]),
1084                                                                jtom,
1085                                                                ktom,
1086                                                                bc_ik|bc_ij);
1087
1088                                         } while(list_next_f(that)!=\
1089                                                 L_NO_NEXT_ELEMENT);
1090
1091                                 }
1092
1093                                 /* 2bp post function */
1094                                 if(moldyn->func2b_post) {
1095                                         moldyn->func2b_post(moldyn,
1096                                                             &(itom[i]),
1097                                                             jtom,bc_ij);
1098                                 }
1099
1100                         } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1101
1102                 }
1103
1104         }
1105
1106         return 0;
1107 }
1108
1109 /*
1110  * periodic boundayr checking
1111  */
1112
1113 inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1114
1115         double x,y,z;
1116         t_3dvec *dim;
1117
1118         dim=&(moldyn->dim);
1119
1120         x=dim->x/2;
1121         y=dim->y/2;
1122         z=dim->z/2;
1123
1124         if(moldyn->status&MOLDYN_STAT_PBX) {
1125                 if(a->x>=x) a->x-=dim->x;
1126                 else if(-a->x>x) a->x+=dim->x;
1127         }
1128         if(moldyn->status&MOLDYN_STAT_PBY) {
1129                 if(a->y>=y) a->y-=dim->y;
1130                 else if(-a->y>y) a->y+=dim->y;
1131         }
1132         if(moldyn->status&MOLDYN_STAT_PBZ) {
1133                 if(a->z>=z) a->z-=dim->z;
1134                 else if(-a->z>z) a->z+=dim->z;
1135         }
1136
1137         return 0;
1138 }
1139
1140
1141 /*
1142  * example potentials
1143  */
1144
1145 /* harmonic oscillator potential and force */
1146
1147 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1148
1149         t_ho_params *params;
1150         t_3dvec force,distance;
1151         double d;
1152         double sc,equi_dist;
1153
1154         params=moldyn->pot2b_params;
1155         sc=params->spring_constant;
1156         equi_dist=params->equilibrium_distance;
1157
1158         v3_sub(&distance,&(aj->r),&(ai->r));
1159
1160         if(bc) check_per_bound(moldyn,&distance);
1161         d=v3_norm(&distance);
1162         if(d<=moldyn->cutoff) {
1163                 /* energy is 1/2 (d-d0)^2, but we will add this twice ... */
1164                 moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
1165                 /* f = -grad E; grad r_ij = -1 1/r_ij distance */
1166                 v3_scale(&force,&distance,sc*(1.0-(equi_dist/d)));
1167                 v3_add(&(ai->f),&(ai->f),&force);
1168         }
1169
1170         return 0;
1171 }
1172
1173 /* lennard jones potential & force for one sort of atoms */
1174
1175 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1176
1177         t_lj_params *params;
1178         t_3dvec force,distance;
1179         double d,h1,h2;
1180         double eps,sig6,sig12;
1181
1182         params=moldyn->pot2b_params;
1183         eps=params->epsilon4;
1184         sig6=params->sigma6;
1185         sig12=params->sigma12;
1186
1187         v3_sub(&distance,&(aj->r),&(ai->r));
1188         if(bc) check_per_bound(moldyn,&distance);
1189         d=v3_absolute_square(&distance);        /* 1/r^2 */
1190         if(d<=moldyn->cutoff_square) {
1191                 d=1.0/d;                        /* 1/r^2 */
1192                 h2=d*d;                         /* 1/r^4 */
1193                 h2*=d;                          /* 1/r^6 */
1194                 h1=h2*h2;                       /* 1/r^12 */
1195                 /* energy is eps*..., but we will add this twice ... */
1196                 moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
1197                 h2*=d;                          /* 1/r^8 */
1198                 h1*=d;                          /* 1/r^14 */
1199                 h2*=6*sig6;
1200                 h1*=12*sig12;
1201                 d=+h1-h2;
1202                 d*=eps;
1203                 v3_scale(&force,&distance,-1.0*d); /* f = - grad E */
1204                 v3_add(&(ai->f),&(ai->f),&force);
1205         }
1206
1207         return 0;
1208 }
1209
1210 /*
1211  * tersoff potential & force for 2 sorts of atoms
1212  */
1213
1214 /* create mixed terms from parameters and set them */
1215 int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
1216
1217         printf("[moldyn] tersoff parameter completion\n");
1218         p->Smixed=sqrt(p->S[0]*p->S[1]);
1219         p->Rmixed=sqrt(p->R[0]*p->R[1]);
1220         p->Amixed=sqrt(p->A[0]*p->A[1]);
1221         p->Bmixed=sqrt(p->B[0]*p->B[1]);
1222         p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
1223         p->mu_m=0.5*(p->mu[0]+p->mu[1]);
1224
1225         printf("[moldyn] tersoff mult parameter info:\n");
1226         printf("  S (A)  | %f | %f | %f\n",p->S[0],p->S[1],p->Smixed);
1227         printf("  R (A)  | %f | %f | %f\n",p->R[0],p->R[1],p->Rmixed);
1228         printf("  A (eV) | %f | %f | %f\n",p->A[0]/EV,p->A[1]/EV,p->Amixed/EV);
1229         printf("  B (eV) | %f | %f | %f\n",p->B[0]/EV,p->B[1]/EV,p->Bmixed/EV);
1230         printf("  lambda | %f | %f | %f\n",p->lambda[0],p->lambda[1],
1231                                           p->lambda_m);
1232         printf("  mu     | %f | %f | %f\n",p->mu[0],p->mu[1],p->mu_m);
1233         printf("  beta   | %.10f | %.10f\n",p->beta[0],p->beta[1]);
1234         printf("  n      | %f | %f\n",p->n[0],p->n[1]);
1235         printf("  c      | %f | %f\n",p->c[0],p->c[1]);
1236         printf("  d      | %f | %f\n",p->d[0],p->d[1]);
1237         printf("  h      | %f | %f\n",p->h[0],p->h[1]);
1238         printf("  chi    | %f \n",p->chi);
1239
1240         return 0;
1241 }
1242
1243 /* tersoff 1 body part */
1244 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
1245
1246         int num;
1247         t_tersoff_mult_params *params;
1248         t_tersoff_exchange *exchange;
1249
1250         num=ai->bnum;
1251         params=moldyn->pot1b_params;
1252         exchange=&(params->exchange);
1253
1254         /*
1255          * simple: point constant parameters only depending on atom i to
1256          *         their right values
1257          */
1258
1259         exchange->beta_i=&(params->beta[num]);
1260         exchange->n_i=&(params->n[num]);
1261         exchange->c_i=&(params->c[num]);
1262         exchange->d_i=&(params->d[num]);
1263         exchange->h_i=&(params->h[num]);
1264
1265         exchange->betaini=pow(*(exchange->beta_i),*(exchange->n_i));
1266         exchange->ci2=params->c[num]*params->c[num];
1267         exchange->di2=params->d[num]*params->d[num];
1268         exchange->ci2di2=exchange->ci2/exchange->di2;
1269
1270         return 0;
1271 }
1272
1273 /* tersoff 2 body part */
1274 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1275
1276         t_tersoff_mult_params *params;
1277         t_tersoff_exchange *exchange;
1278         t_3dvec dist_ij,force;
1279         double d_ij;
1280         double A,B,R,S,lambda,mu;
1281         double f_r,df_r;
1282         double f_c,df_c;
1283         int num;
1284         double s_r;
1285         double arg;
1286
1287         params=moldyn->pot2b_params;
1288         num=aj->bnum;
1289         exchange=&(params->exchange);
1290
1291         /* clear 3bp and 2bp post run */
1292         exchange->run3bp=0;
1293         exchange->run2bp_post=0;
1294
1295         /* reset S > r > R mark */
1296         exchange->d_ij_between_rs=0;
1297
1298         /*
1299          * calc of 2bp contribution of V_ij and dV_ij/ji
1300          *
1301          * for Vij and dV_ij we need:
1302          * - f_c_ij, df_c_ij
1303          * - f_r_ij, df_r_ij
1304          *
1305          * for dV_ji we need:
1306          * - f_c_ji = f_c_ij, df_c_ji = df_c_ij
1307          * - f_r_ji = f_r_ij; df_r_ji = df_r_ij
1308          *
1309          */
1310
1311         /* dist_ij, d_ij */
1312         v3_sub(&dist_ij,&(aj->r),&(ai->r));
1313         if(bc) check_per_bound(moldyn,&dist_ij);
1314         d_ij=v3_norm(&dist_ij);
1315
1316         /* save for use in 3bp */
1317         exchange->d_ij=d_ij;
1318         exchange->dist_ij=dist_ij;
1319
1320         /* constants */
1321         if(num==ai->bnum) {
1322                 S=params->S[num];
1323                 R=params->R[num];
1324                 A=params->A[num];
1325                 B=params->B[num];
1326                 lambda=params->lambda[num];
1327                 mu=params->mu[num];
1328                 exchange->chi=1.0;
1329         }
1330         else {
1331                 S=params->Smixed;
1332                 R=params->Rmixed;
1333                 A=params->Amixed;
1334                 B=params->Bmixed;
1335                 lambda=params->lambda_m;
1336                 mu=params->mu_m;
1337                 params->exchange.chi=params->chi;
1338         }
1339
1340         /* if d_ij > S => no force & potential energy contribution */
1341         if(d_ij>S)
1342                 return 0;
1343
1344         /* more constants */
1345         exchange->beta_j=&(params->beta[num]);
1346         exchange->n_j=&(params->n[num]);
1347         exchange->c_j=&(params->c[num]);
1348         exchange->d_j=&(params->d[num]);
1349         exchange->h_j=&(params->h[num]);
1350         if(num==ai->bnum) {
1351                 exchange->betajnj=exchange->betaini;
1352                 exchange->cj2=exchange->ci2;
1353                 exchange->dj2=exchange->di2;
1354                 exchange->cj2dj2=exchange->ci2di2;
1355         }
1356         else {
1357                 exchange->betajnj=pow(*(exchange->beta_j),*(exchange->n_j));
1358                 exchange->cj2=params->c[num]*params->c[num];
1359                 exchange->dj2=params->d[num]*params->d[num];
1360                 exchange->cj2dj2=exchange->cj2/exchange->dj2;
1361         }
1362
1363         /* f_r_ij = f_r_ji, df_r_ij = df_r_ji */
1364         f_r=A*exp(-lambda*d_ij);
1365         df_r=lambda*f_r/d_ij;
1366
1367         /* f_a, df_a calc (again, same for ij and ji) | save for later use! */
1368         exchange->f_a=-B*exp(-mu*d_ij);
1369         exchange->df_a=mu*exchange->f_a/d_ij;
1370
1371         /* f_c, df_c calc (again, same for ij and ji) */
1372         if(d_ij<R) {
1373                 /* f_c = 1, df_c = 0 */
1374                 f_c=1.0;
1375                 df_c=0.0;
1376                 /* two body contribution (ij, ji) */
1377                 v3_scale(&force,&dist_ij,-df_r);
1378         }
1379         else {
1380                 s_r=S-R;
1381                 arg=M_PI*(d_ij-R)/s_r;
1382                 f_c=0.5+0.5*cos(arg);
1383                 //df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij)); /* MARK! */
1384                 df_c=0.5*sin(arg)*(M_PI/(s_r*d_ij));
1385                 /* two body contribution (ij, ji) */
1386                 v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
1387                 /* tell 3bp that S > r > R */
1388                 exchange->d_ij_between_rs=1;
1389         }
1390
1391         /* add forces of 2bp (ij, ji) contribution
1392          * dVij = dVji and we sum up both: no 1/2) */
1393         v3_add(&(ai->f),&(ai->f),&force);
1394
1395         /* energy 2bp contribution (ij, ji) is 0.5 f_r f_c ... */
1396         moldyn->energy+=(0.5*f_r*f_c);
1397
1398         /* save for use in 3bp */
1399         exchange->f_c=f_c;
1400         exchange->df_c=df_c;
1401
1402         /* enable the run of 3bp function and 2bp post processing */
1403         exchange->run3bp=1;
1404         exchange->run2bp_post=1;
1405
1406         /* reset 3bp sums */
1407         exchange->zeta_ij=0.0;
1408         exchange->zeta_ji=0.0;
1409         v3_zero(&(exchange->dzeta_ij));
1410         v3_zero(&(exchange->dzeta_ji));
1411
1412         return 0;
1413 }
1414
1415 /* tersoff 2 body post part */
1416
1417 int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1418
1419         /*
1420          * here we have to allow for the 3bp sums
1421          *
1422          * that is:
1423          * - zeta_ij, dzeta_ij
1424          * - zeta_ji, dzeta_ji
1425          *
1426          * to compute the 3bp contribution to:
1427          * - Vij, dVij
1428          * - dVji
1429          *
1430          */
1431
1432         t_tersoff_mult_params *params;
1433         t_tersoff_exchange *exchange;
1434
1435         t_3dvec force,temp;
1436         t_3dvec *dist_ij;
1437         double b,db,tmp;
1438         double f_c,df_c,f_a,df_a;
1439         double chi,ni,betaini,nj,betajnj;
1440         double zeta;
1441
1442         params=moldyn->pot2b_params;
1443         exchange=&(params->exchange);
1444
1445         /* we do not run if f_c_ij was detected to be 0! */
1446         if(!(exchange->run2bp_post))
1447                 return 0;
1448
1449         f_c=exchange->f_c;
1450         df_c=exchange->df_c;
1451         f_a=exchange->f_a;
1452         df_a=exchange->df_a;
1453         betaini=exchange->betaini;
1454         betajnj=exchange->betajnj;
1455         ni=*(exchange->n_i);
1456         nj=*(exchange->n_j);
1457         chi=exchange->chi;
1458         dist_ij=&(exchange->dist_ij);
1459
1460         /* Vij and dVij */
1461         zeta=exchange->zeta_ij;
1462         if(zeta==0.0) {
1463                 moldyn->debug++;                /* just for debugging ... */
1464                 db=0.0;
1465                 b=chi;
1466                 v3_scale(&force,dist_ij,df_a*b*f_c);
1467         }
1468         else {
1469                 tmp=betaini*pow(zeta,ni-1.0);           /* beta^n * zeta^n-1 */
1470                 b=(1+zeta*tmp);                         /* 1 + beta^n zeta^n */
1471                 db=chi*pow(b,-1.0/(2*ni)-1);            /* x(...)^(-1/2n - 1) */
1472                 b=db*b;                                 /* b_ij */
1473                 db*=-0.5*tmp;                           /* db_ij */
1474                 v3_scale(&force,&(exchange->dzeta_ij),f_a*db);
1475                 v3_scale(&temp,dist_ij,df_a*b);
1476                 v3_add(&force,&force,&temp);
1477                 v3_scale(&force,&force,f_c);
1478         }
1479         v3_scale(&temp,dist_ij,df_c*b*f_a);
1480         v3_add(&force,&force,&temp);
1481         v3_scale(&force,&force,-0.5);
1482
1483         /* add force */
1484         v3_add(&(ai->f),&(ai->f),&force);
1485
1486         /* add energy of 3bp sum */
1487         moldyn->energy+=(0.5*f_c*b*f_a);
1488
1489         /* dVji */
1490         zeta=exchange->zeta_ji;
1491         if(zeta==0.0) {
1492                 moldyn->debug++;
1493                 b=chi;
1494                 v3_scale(&force,dist_ij,df_a*b*f_c);
1495         }
1496         else {
1497                 tmp=betajnj*pow(zeta,nj-1.0);           /* beta^n * zeta^n-1 */
1498                 b=(1+zeta*tmp);                         /* 1 + beta^n zeta^n */
1499                 db=chi*pow(b,-1.0/(2*nj)-1);            /* x(...)^(-1/2n - 1) */
1500                 b=db*b;                                 /* b_ij */
1501                 db*=-0.5*tmp;                           /* db_ij */
1502                 v3_scale(&force,&(exchange->dzeta_ji),f_a*db);
1503                 v3_scale(&temp,dist_ij,df_a*b);
1504                 v3_add(&force,&force,&temp);
1505                 v3_scale(&force,&force,f_c);
1506         }
1507         v3_scale(&temp,dist_ij,df_c*b*f_a);
1508         v3_add(&force,&force,&temp);
1509         v3_scale(&force,&force,-0.5);
1510
1511         /* add force */
1512         v3_add(&(ai->f),&(ai->f),&force);
1513
1514         return 0;
1515 }
1516
1517 /* tersoff 3 body part */
1518
1519 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
1520
1521         t_tersoff_mult_params *params;
1522         t_tersoff_exchange *exchange;
1523         t_3dvec dist_ij,dist_ik,dist_jk;
1524         t_3dvec temp1,temp2;
1525         t_3dvec *dzeta;
1526         double R,S,s_r;
1527         double B,mu;
1528         double d_ij,d_ik,d_jk;
1529         double rr,dd;
1530         double f_c,df_c;
1531         double f_c_ik,df_c_ik,arg;
1532         double f_c_jk;
1533         double n,c,d,h;
1534         double c2,d2,c2d2;
1535         double cos_theta,d_costheta1,d_costheta2;
1536         double h_cos,d2_h_cos2;
1537         double frac,g,zeta,chi;
1538         double tmp;
1539         int num;
1540
1541         params=moldyn->pot3b_params;
1542         exchange=&(params->exchange);
1543
1544         if(!(exchange->run3bp))
1545                 return 0;
1546
1547         /*
1548          * calc of 3bp contribution of V_ij and dV_ij/ji/jk &
1549          * 2bp contribution of dV_jk
1550          *
1551          * for Vij and dV_ij we still need:
1552          * - b_ij, db_ij (zeta_ij)
1553          *   - f_c_ik, df_c_ik, constants_i, cos_theta_ijk, d_costheta_ijk
1554          *
1555          * for dV_ji we still need:
1556          * - b_ji, db_ji (zeta_ji)
1557          *   - f_c_jk, d_c_jk, constants_j, cos_theta_jik, d_costheta_jik
1558          *
1559          * for dV_jk we need:
1560          * - f_c_jk
1561          * - f_a_jk
1562          * - db_jk (zeta_jk)
1563          *   - f_c_ji, df_c_ji, constants_j, cos_theta_jki, d_costheta_jki
1564          *
1565          */
1566
1567         /*
1568          * get exchange data
1569          */
1570
1571         /* dist_ij, d_ij - this is < S_ij ! */
1572         dist_ij=exchange->dist_ij;
1573         d_ij=exchange->d_ij;
1574
1575         /* f_c_ij, df_c_ij (same for ji) */
1576         f_c=exchange->f_c;
1577         df_c=exchange->df_c;
1578
1579         /*
1580          * calculate unknown values now ...
1581          */
1582
1583         /* V_ij and dV_ij stuff (in b_ij there is f_c_ik) */
1584
1585         /* dist_ik, d_ik */
1586         v3_sub(&dist_ik,&(ak->r),&(ai->r));
1587         if(bc) check_per_bound(moldyn,&dist_ik);
1588         d_ik=v3_norm(&dist_ik);
1589
1590         /* ik constants */
1591         num=ai->bnum;
1592         if(num==ak->bnum) {
1593                 R=params->R[num];
1594                 S=params->S[num];
1595         }
1596         else {
1597                 R=params->Rmixed;
1598                 S=params->Smixed;
1599         }
1600
1601         /* zeta_ij/dzeta_ij contribution only for d_ik < S */
1602         if(d_ik<S) {
1603
1604                 /* get constants_i from exchange data */
1605                 n=*(exchange->n_i);
1606                 c=*(exchange->c_i);
1607                 d=*(exchange->d_i);
1608                 h=*(exchange->h_i);
1609                 c2=exchange->ci2;
1610                 d2=exchange->di2;
1611                 c2d2=exchange->ci2di2;
1612
1613                 /* cosine of theta_ijk by scalaproduct */
1614                 rr=v3_scalar_product(&dist_ij,&dist_ik);
1615                 dd=d_ij*d_ik;
1616                 cos_theta=rr/dd;
1617
1618                 /* d_costheta */
1619                 tmp=1.0/dd;
1620                 d_costheta1=cos_theta/(d_ij*d_ij)-tmp;
1621                 d_costheta2=cos_theta/(d_ik*d_ik)-tmp;
1622
1623                 /* some usefull values */
1624                 h_cos=(h-cos_theta);
1625                 d2_h_cos2=d2+(h_cos*h_cos);
1626                 frac=c2/(d2_h_cos2);
1627
1628                 /* g(cos_theta) */
1629                 g=1.0+c2d2-frac;
1630
1631                 /* d_costheta_ij and dg(cos_theta) - needed in any case! */
1632                 v3_scale(&temp1,&dist_ij,d_costheta1);
1633                 v3_scale(&temp2,&dist_ik,d_costheta2);
1634                 v3_add(&temp1,&temp1,&temp2);
1635                 v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
1636
1637                 /* f_c_ik & df_c_ik + {d,}zeta contribution */
1638                 dzeta=&(exchange->dzeta_ij);
1639                 if(d_ik<R) {
1640                         /* {d,}f_c_ik */
1641                         // => f_c_ik=1.0;
1642                         // => df_c_ik=0.0; of course we do not set this!
1643
1644                         /* zeta_ij */
1645                         exchange->zeta_ij+=g;
1646
1647                         /* dzeta_ij */
1648                         v3_add(dzeta,dzeta,&temp1);
1649                 }
1650                 else {
1651                         /* {d,}f_c_ik */
1652                         s_r=S-R;
1653                         arg=M_PI*(d_ik-R)/s_r;
1654                         f_c_ik=0.5+0.5*cos(arg);
1655                         //df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik)); /* MARK */
1656                         df_c_ik=0.5*sin(arg)*(M_PI/(s_r*d_ik));
1657
1658                         /* zeta_ij */
1659                         exchange->zeta_ij+=f_c_ik*g;
1660
1661                         /* dzeta_ij */
1662                         v3_scale(&temp1,&temp1,f_c_ik);
1663                         v3_scale(&temp2,&dist_ik,g*df_c_ik);
1664                         v3_add(&temp1,&temp1,&temp2);
1665                         v3_add(dzeta,dzeta,&temp1);
1666                 }
1667         }
1668
1669         /* dV_ji stuff (in b_ji there is f_c_jk) + dV_jk stuff! */
1670
1671         /* dist_jk, d_jk */
1672         v3_sub(&dist_jk,&(ak->r),&(aj->r));
1673         if(bc) check_per_bound(moldyn,&dist_jk);
1674         d_jk=v3_norm(&dist_jk);
1675
1676         /* jk constants */
1677         num=aj->bnum;
1678         if(num==ak->bnum) {
1679                 R=params->R[num];
1680                 S=params->S[num];
1681                 B=params->B[num];
1682                 mu=params->mu[num];
1683                 chi=1.0;
1684         }
1685         else {
1686                 R=params->Rmixed;
1687                 S=params->Smixed;
1688                 B=params->Bmixed;
1689                 mu=params->mu_m;
1690                 chi=params->chi;
1691         }
1692
1693         /* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */
1694         if(d_jk<S) {
1695
1696                 /* constants_j from exchange data */
1697                 n=*(exchange->n_j);
1698                 c=*(exchange->c_j);
1699                 d=*(exchange->d_j);
1700                 h=*(exchange->h_j);
1701                 c2=exchange->cj2;
1702                 d2=exchange->dj2;
1703                 c2d2=exchange->cj2dj2;
1704
1705                 /* cosine of theta_jik by scalaproduct */
1706                 rr=-v3_scalar_product(&dist_ij,&dist_jk); /* -1, as ij -> ji */
1707                 dd=d_ij*d_jk;
1708                 cos_theta=rr/dd;
1709
1710                 /* d_costheta */
1711                 d_costheta1=1.0/dd;
1712                 d_costheta2=cos_theta/(d_ij*d_ij);
1713
1714                 /* some usefull values */
1715                 h_cos=(h-cos_theta);
1716                 d2_h_cos2=d2+(h_cos*h_cos);
1717                 frac=c2/(d2_h_cos2);
1718
1719                 /* g(cos_theta) */
1720                 g=1.0+c2d2-frac;
1721
1722                 /* d_costheta_ij and dg(cos_theta) - needed in any case! */
1723                 v3_scale(&temp1,&dist_jk,d_costheta1);
1724                 v3_scale(&temp2,&dist_ij,-d_costheta2); /* ji -> ij => -1 */
1725                 v3_add(&temp1,&temp1,&temp2);
1726                 v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
1727
1728                 /* store dg in temp2 and use it for dVjk later */
1729                 v3_copy(&temp2,&temp1);
1730
1731                 /* f_c_jk + {d,}zeta contribution (df_c_jk = 0) */
1732                 dzeta=&(exchange->dzeta_ji);
1733                 if(d_jk<R) {
1734                         /* f_c_jk */
1735                         f_c_jk=1.0;
1736
1737                         /* zeta_ji */
1738                         exchange->zeta_ji+=g;
1739
1740                         /* dzeta_ji */
1741                         v3_add(dzeta,dzeta,&temp1);
1742                 }
1743                 else {
1744                         /* f_c_jk */
1745                         s_r=S-R;
1746                         arg=M_PI*(d_jk-R)/s_r;
1747                         f_c_jk=0.5+0.5*cos(arg);
1748
1749                         /* zeta_ji */
1750                         exchange->zeta_ji+=f_c_jk*g;
1751
1752                         /* dzeta_ji */
1753                         v3_scale(&temp1,&temp1,f_c_jk);
1754                         v3_add(dzeta,dzeta,&temp1);
1755                 }
1756
1757                 /* dV_jk stuff | add force contribution on atom i immediately */
1758                 if(exchange->d_ij_between_rs) {
1759                         zeta=f_c*g;
1760                         v3_scale(&temp1,&temp2,f_c);
1761                         v3_scale(&temp2,&dist_ij,df_c*g);
1762                         v3_add(&temp2,&temp2,&temp1); /* -> dzeta_jk in temp2 */
1763                 }
1764                 else {
1765                         zeta=g;
1766                         // dzeta_jk is simply dg, which is stored in temp2
1767                 }
1768                 /* betajnj * zeta_jk ^ nj-1 */
1769                 tmp=exchange->betajnj*pow(zeta,(n-1.0));
1770                 tmp=-chi/2.0*pow((1+tmp*zeta),(-1.0/(2.0*n)-1))*tmp;
1771                 v3_scale(&temp2,&temp2,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
1772                 v3_add(&(ai->f),&(ai->f),&temp2); /* -1 skipped in f_a calc ^ */
1773                                                   /* scaled with 0.5 ^ */
1774
1775         }
1776
1777         return 0;
1778 }
1779
1780
1781 /*
1782  * debugging / critical check functions
1783  */
1784
1785 int moldyn_bc_check(t_moldyn *moldyn) {
1786
1787         t_atom *atom;
1788         t_3dvec *dim;
1789         int i;
1790 double x;
1791 u8 byte;
1792 int j,k;
1793
1794         atom=moldyn->atom;
1795         dim=&(moldyn->dim);
1796 x=dim->x/2;
1797
1798         for(i=0;i<moldyn->count;i++) {
1799                 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
1800                         printf("FATAL: atom %d: x: %.20f (%.20f)\n",
1801                                i,atom[i].r.x,dim->x/2);
1802                         printf("diagnostic:\n");
1803                         printf("-----------\natom.r.x:\n");
1804                         for(j=0;j<8;j++) {
1805                                 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
1806                                 for(k=0;k<8;k++)
1807                                         printf("%d%c",
1808                                         ((byte)&(1<<k))?1:0,
1809                                         (k==7)?'\n':'|');
1810                         }
1811                         printf("---------------\nx=dim.x/2:\n");
1812                         for(j=0;j<8;j++) {
1813                                 memcpy(&byte,(u8 *)(&x)+j,1);
1814                                 for(k=0;k<8;k++)
1815                                         printf("%d%c",
1816                                         ((byte)&(1<<k))?1:0,
1817                                         (k==7)?'\n':'|');
1818                         }
1819                         if(atom[i].r.x==x) printf("the same!\n");
1820                         else printf("different!\n");
1821                 }
1822                 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
1823                         printf("FATAL: atom %d: y: %.20f (%.20f)\n",
1824                                i,atom[i].r.y,dim->y/2);
1825                 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
1826                         printf("FATAL: atom %d: z: %.20f (%.20f)\n",
1827                                i,atom[i].r.z,dim->z/2);
1828         }
1829
1830         return 0;
1831 }