moldyn.c

   1 /*
   2  * moldyn.c - molecular dynamics library main file
   3  *
   4  * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
   5  *
   6  */
   7
   8 #define _GNU_SOURCE
   9 #include <stdio.h>
  10 #include <stdlib.h>
  11 #include <string.h>
  12 #include <sys/types.h>
  13 #include <sys/stat.h>
  14 #include <fcntl.h>
  15 #include <unistd.h>
  16 #include <math.h>
  17
  18 #include "moldyn.h"
  19
  20 #include "math/math.h"
  21 #include "init/init.h"
  22 #include "random/random.h"
  23 #include "visual/visual.h"
  24 #include "list/list.h"
  25
  26
  27 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
  28
  29         //int ret;
  30
  31         //ret=moldyn_parse_argv(moldyn,argc,argv);
  32         //if(ret<0) return ret;
  33
  34         memset(moldyn,0,sizeof(t_moldyn));
  35
  36         rand_init(&(moldyn->random),NULL,1);
  37         moldyn->random.status|=RAND_STAT_VERBOSE;
  38
  39         return 0;
  40 }
  41
  42 int moldyn_shutdown(t_moldyn *moldyn) {
  43
  44         printf("[moldyn] shutdown\n");
  45         moldyn_log_shutdown(moldyn);
  46         link_cell_shutdown(moldyn);
  47         rand_close(&(moldyn->random));
  48         free(moldyn->atom);
  49
  50         return 0;
  51 }
  52
  53 int set_int_alg(t_moldyn *moldyn,u8 algo) {
  54
  55         switch(algo) {
  56                 case MOLDYN_INTEGRATE_VERLET:
  57                         moldyn->integrate=velocity_verlet;
  58                         break;
  59                 default:
  60                         printf("unknown integration algorithm: %02x\n",algo);
  61                         return -1;
  62         }
  63
  64         return 0;
  65 }
  66
  67 int set_cutoff(t_moldyn *moldyn,double cutoff) {
  68
  69         moldyn->cutoff=cutoff;
  70
  71         return 0;
  72 }
  73
  74 int set_temperature(t_moldyn *moldyn,double t) {
  75
  76         moldyn->t=t;
  77
  78         return 0;
  79 }
  80
  81 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
  82
  83         moldyn->dim.x=x;
  84         moldyn->dim.y=y;
  85         moldyn->dim.z=z;
  86
  87         if(visualize) {
  88                 moldyn->vis.dim.x=x;
  89                 moldyn->vis.dim.y=y;
  90                 moldyn->vis.dim.z=z;
  91         }
  92
  93         return 0;
  94 }
  95
  96 int set_nn_dist(t_moldyn *moldyn,double dist) {
  97
  98         moldyn->nnd=dist;
  99
 100         return 0;
 101 }
 102
 103 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 104
 105         if(x)
 106                 moldyn->status|=MOLDYN_STAT_PBX;
 107
 108         if(y)
 109                 moldyn->status|=MOLDYN_STAT_PBY;
 110
 111         if(z)
 112                 moldyn->status|=MOLDYN_STAT_PBZ;
 113
 114         return 0;
 115 }
 116
 117 int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
 118
 119         moldyn->func1b=func;
 120         moldyn->pot1b_params=params;
 121
 122         return 0;
 123 }
 124
 125 int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
 126
 127         moldyn->func2b=func;
 128         moldyn->pot2b_params=params;
 129
 130         return 0;
 131 }
 132
 133 int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
 134
 135         moldyn->func3b=func;
 136         moldyn->pot3b_params=params;
 137
 138         return 0;
 139 }
 140
 141 int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
 142
 143         switch(type) {
 144                 case LOG_TOTAL_ENERGY:
 145                         moldyn->ewrite=timer;
 146                         moldyn->efd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
 147                         if(moldyn->efd<0) {
 148                                 perror("[moldyn] efd open");
 149                                 return moldyn->efd;
 150                         }
 151                         dprintf(moldyn->efd,"# total energy log file\n");
 152                         break;
 153                 case LOG_TOTAL_MOMENTUM:
 154                         moldyn->mwrite=timer;
 155                         moldyn->mfd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
 156                         if(moldyn->mfd<0) {
 157                                 perror("[moldyn] mfd open");
 158                                 return moldyn->mfd;
 159                         }
 160                         dprintf(moldyn->efd,"# total momentum log file\n");
 161                         break;
 162                 case SAVE_STEP:
 163                         moldyn->swrite=timer;
 164                         strncpy(moldyn->sfb,fb,63);
 165                         break;
 166                 case VISUAL_STEP:
 167                         moldyn->vwrite=timer;
 168                         strncpy(moldyn->vfb,fb,63);
 169                         visual_init(&(moldyn->vis),fb);
 170                         break;
 171                 default:
 172                         printf("unknown log mechanism: %02x\n",type);
 173                         return -1;
 174         }
 175
 176         return 0;
 177 }
 178
 179 int moldyn_log_shutdown(t_moldyn *moldyn) {
 180
 181         printf("[moldyn] log shutdown\n");
 182         if(moldyn->efd) close(moldyn->efd);
 183         if(moldyn->mfd) close(moldyn->mfd);
 184         if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
 185
 186         return 0;
 187 }
 188
 189 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 190                    u8 attr,u8 bnum,int a,int b,int c) {
 191
 192         int count;
 193         int ret;
 194         t_3dvec origin;
 195
 196         count=a*b*c;
 197
 198         if(type==FCC) count*=4;
 199
 200         if(type==DIAMOND) count*=8;
 201
 202         moldyn->atom=malloc(count*sizeof(t_atom));
 203         if(moldyn->atom==NULL) {
 204                 perror("malloc (atoms)");
 205                 return -1;
 206         }
 207
 208         v3_zero(&origin);
 209
 210         switch(type) {
 211                 case FCC:
 212                         ret=fcc_init(a,b,c,lc,moldyn->atom,&origin);
 213                         break;
 214                 case DIAMOND:
 215                         ret=diamond_init(a,b,c,lc,moldyn->atom,&origin);
 216                         break;
 217                 default:
 218                         printf("unknown lattice type (%02x)\n",type);
 219                         return -1;
 220         }
 221
 222         /* debug */
 223         if(ret!=count) {
 224                 printf("ok, there is something wrong ...\n");
 225                 printf("calculated -> %d atoms\n",count);
 226                 printf("created -> %d atoms\n",ret);
 227                 return -1;
 228         }
 229
 230         moldyn->count=count;
 231         printf("[moldyn] created lattice with %d atoms\n",count);
 232
 233         while(count) {
 234                 moldyn->atom[count-1].element=element;
 235                 moldyn->atom[count-1].mass=mass;
 236                 moldyn->atom[count-1].attr=attr;
 237                 moldyn->atom[count-1].bnum=bnum;
 238                 count-=1;
 239         }
 240
 241         return ret;
 242 }
 243
 244 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
 245              t_3dvec *r,t_3dvec *v) {
 246
 247         t_atom *atom;
 248         void *ptr;
 249         int count;
 250
 251         atom=moldyn->atom;
 252         count=++(moldyn->count);
 253
 254         ptr=realloc(atom,count*sizeof(t_atom));
 255         if(!ptr) {
 256                 perror("[moldyn] realloc (add atom)");
 257                 return -1;
 258         }
 259         moldyn->atom=ptr;
 260
 261         atom=moldyn->atom;
 262         atom[count-1].r=*r;
 263         atom[count-1].v=*v;
 264         atom[count-1].element=element;
 265         atom[count-1].mass=mass;
 266         atom[count-1].bnum=bnum;
 267         atom[count-1].attr=attr;
 268
 269         return 0;
 270 }
 271
 272 int destroy_atoms(t_moldyn *moldyn) {
 273
 274         if(moldyn->atom) free(moldyn->atom);
 275
 276         return 0;
 277 }
 278
 279 int thermal_init(t_moldyn *moldyn) {
 280
 281         /*
 282          * - gaussian distribution of velocities
 283          * - zero total momentum
 284          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 285          */
 286
 287         int i;
 288         double v,sigma;
 289         t_3dvec p_total,delta;
 290         t_atom *atom;
 291         t_random *random;
 292
 293         atom=moldyn->atom;
 294         random=&(moldyn->random);
 295
 296         /* gaussian distribution of velocities */
 297         v3_zero(&p_total);
 298         for(i=0;i<moldyn->count;i++) {
 299                 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t/atom[i].mass);
 300                 /* x direction */
 301                 v=sigma*rand_get_gauss(random);
 302                 atom[i].v.x=v;
 303                 p_total.x+=atom[i].mass*v;
 304                 /* y direction */
 305                 v=sigma*rand_get_gauss(random);
 306                 atom[i].v.y=v;
 307                 p_total.y+=atom[i].mass*v;
 308                 /* z direction */
 309                 v=sigma*rand_get_gauss(random);
 310                 atom[i].v.z=v;
 311                 p_total.z+=atom[i].mass*v;
 312         }
 313
 314         /* zero total momentum */
 315         v3_scale(&p_total,&p_total,1.0/moldyn->count);
 316         for(i=0;i<moldyn->count;i++) {
 317                 v3_scale(&delta,&p_total,1.0/atom[i].mass);
 318                 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
 319         }
 320
 321         /* velocity scaling */
 322         scale_velocity(moldyn,VSCALE_INIT_EQUI);
 323
 324         return 0;
 325 }
 326
 327 int scale_velocity(t_moldyn *moldyn,u8 type) {
 328
 329         int i;
 330         double e,scale;
 331         t_atom *atom;
 332
 333         atom=moldyn->atom;
 334
 335         /*
 336          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 337          */
 338
 339         e=0.0;
 340         for(i=0;i<moldyn->count;i++)
 341                 e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 342         scale=(1.5*moldyn->count*K_BOLTZMANN*moldyn->t)/e;
 343         if(type&VSCALE_INIT_EQUI) scale*=2.0; /* equipartition theorem */
 344         scale=sqrt(scale);
 345         for(i=0;i<moldyn->count;i++)
 346                 v3_scale(&(atom[i].v),&(atom[i].v),scale);
 347
 348         return 0;
 349 }
 350
 351 double get_e_kin(t_moldyn *moldyn) {
 352
 353         int i;
 354         t_atom *atom;
 355
 356         atom=moldyn->atom;
 357         moldyn->ekin=0.0;
 358
 359         for(i=0;i<moldyn->count;i++)
 360                 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 361
 362         return moldyn->ekin;
 363 }
 364
 365 double get_e_pot(t_moldyn *moldyn) {
 366
 367         return moldyn->energy;
 368 }
 369
 370 double update_e_kin(t_moldyn *moldyn) {
 371
 372         return(get_e_kin(moldyn));
 373 }
 374
 375 double get_total_energy(t_moldyn *moldyn) {
 376
 377         return(moldyn->ekin+moldyn->energy);
 378 }
 379
 380 t_3dvec get_total_p(t_moldyn *moldyn) {
 381
 382         t_3dvec p,p_total;
 383         int i;
 384         t_atom *atom;
 385
 386         atom=moldyn->atom;
 387
 388         v3_zero(&p_total);
 389         for(i=0;i<moldyn->count;i++) {
 390                 v3_scale(&p,&(atom[i].v),atom[i].mass);
 391                 v3_add(&p_total,&p_total,&p);
 392         }
 393
 394         return p_total;
 395 }
 396
 397 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
 398
 399         double tau;
 400
 401         /* nn_dist is the nearest neighbour distance */
 402
 403         if(moldyn->t==5.0) {
 404                 printf("[moldyn] i do not estimate timesteps below %f K!\n",
 405                        MOLDYN_CRITICAL_EST_TEMP);
 406                 return 23.42;
 407         }
 408
 409         tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
 410
 411         return tau;
 412 }
 413
 414 /*
 415  * numerical tricks
 416  */
 417
 418 /* linked list / cell method */
 419
 420 int link_cell_init(t_moldyn *moldyn) {
 421
 422         t_linkcell *lc;
 423         int i;
 424         int fd;
 425
 426         fd=open("/dev/null",O_WRONLY);
 427
 428         lc=&(moldyn->lc);
 429
 430         /* partitioning the md cell */
 431         lc->nx=moldyn->dim.x/moldyn->cutoff;
 432         lc->x=moldyn->dim.x/lc->nx;
 433         lc->ny=moldyn->dim.y/moldyn->cutoff;
 434         lc->y=moldyn->dim.y/lc->ny;
 435         lc->nz=moldyn->dim.z/moldyn->cutoff;
 436         lc->z=moldyn->dim.z/lc->nz;
 437
 438         lc->cells=lc->nx*lc->ny*lc->nz;
 439         lc->subcell=malloc(lc->cells*sizeof(t_list));
 440
 441         printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 442
 443         for(i=0;i<lc->cells;i++)
 444                 //list_init(&(lc->subcell[i]),1);
 445                 list_init(&(lc->subcell[i]),fd);
 446
 447         link_cell_update(moldyn);
 448
 449         return 0;
 450 }
 451
 452 int link_cell_update(t_moldyn *moldyn) {
 453
 454         int count,i,j,k;
 455         int nx,ny,nz;
 456         t_atom *atom;
 457         t_linkcell *lc;
 458
 459         atom=moldyn->atom;
 460         lc=&(moldyn->lc);
 461
 462         nx=lc->nx;
 463         ny=lc->ny;
 464         nz=lc->nz;
 465
 466         for(i=0;i<lc->cells;i++)
 467                 list_destroy(&(moldyn->lc.subcell[i]));
 468
 469         for(count=0;count<moldyn->count;count++) {
 470                 i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
 471                 j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
 472                 k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
 473                 list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
 474                                        &(atom[count]));
 475         }
 476
 477         return 0;
 478 }
 479
 480 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 481
 482         t_linkcell *lc;
 483         int a;
 484         int count1,count2;
 485         int ci,cj,ck;
 486         int nx,ny,nz;
 487         int x,y,z;
 488         u8 bx,by,bz;
 489
 490         lc=&(moldyn->lc);
 491         nx=lc->nx;
 492         ny=lc->ny;
 493         nz=lc->nz;
 494         count1=1;
 495         count2=27;
 496         a=nx*ny;
 497
 498
 499         cell[0]=lc->subcell[i+j*nx+k*a];
 500         for(ci=-1;ci<=1;ci++) {
 501                 bx=0;
 502                 x=i+ci;
 503                 if((x<0)||(x>=nx)) {
 504                         x=(x+nx)%nx;
 505                         bx=1;
 506                 }
 507                 for(cj=-1;cj<=1;cj++) {
 508                         by=0;
 509                         y=j+cj;
 510                         if((y<0)||(y>=ny)) {
 511                                 y=(y+ny)%ny;
 512                                 by=1;
 513                         }
 514                         for(ck=-1;ck<=1;ck++) {
 515                                 bz=0;
 516                                 z=k+ck;
 517                                 if((z<0)||(z>=nz)) {
 518                                         z=(z+nz)%nz;
 519                                         bz=1;
 520                                 }
 521                                 if(!(ci|cj|ck)) continue;
 522                                 if(bx|by|bz) {
 523                                         cell[--count2]=lc->subcell[x+y*nx+z*a];
 524                                 }
 525                                 else {
 526                                         cell[count1++]=lc->subcell[x+y*nx+z*a];
 527                                 }
 528                         }
 529                 }
 530         }
 531
 532         lc->dnlc=count2;
 533         lc->countn=27;
 534
 535         return count2;
 536 }
 537
 538 int link_cell_shutdown(t_moldyn *moldyn) {
 539
 540         int i;
 541         t_linkcell *lc;
 542
 543         lc=&(moldyn->lc);
 544
 545         for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
 546                 list_shutdown(&(moldyn->lc.subcell[i]));
 547
 548         return 0;
 549 }
 550
 551 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
 552
 553         int count;
 554         void *ptr;
 555         t_moldyn_schedule *schedule;
 556
 557         schedule=&(moldyn->schedule);
 558         count=++(schedule->content_count);
 559
 560         ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
 561         if(!ptr) {
 562                 perror("[moldyn] realloc (runs)");
 563                 return -1;
 564         }
 565         moldyn->schedule.runs=ptr;
 566         moldyn->schedule.runs[count-1]=runs;
 567
 568         ptr=realloc(schedule->tau,count*sizeof(double));
 569         if(!ptr) {
 570                 perror("[moldyn] realloc (tau)");
 571                 return -1;
 572         }
 573         moldyn->schedule.tau=ptr;
 574         moldyn->schedule.tau[count-1]=tau;
 575
 576         return 0;
 577 }
 578
 579 int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
 580
 581         moldyn->schedule.hook=hook;
 582         moldyn->schedule.hook_params=hook_params;
 583
 584         return 0;
 585 }
 586
 587 /*
 588  *
 589  * 'integration of newtons equation' - algorithms
 590  *
 591  */
 592
 593 /* start the integration */
 594
 595 int moldyn_integrate(t_moldyn *moldyn) {
 596
 597         int i,sched;
 598         unsigned int e,m,s,v;
 599         t_3dvec p;
 600         t_moldyn_schedule *schedule;
 601         t_atom *atom;
 602         int fd;
 603         char fb[128];
 604         double ds;
 605
 606         schedule=&(moldyn->schedule);
 607         atom=moldyn->atom;
 608
 609         /* initialize linked cell method */
 610         link_cell_init(moldyn);
 611
 612         /* logging & visualization */
 613         e=moldyn->ewrite;
 614         m=moldyn->mwrite;
 615         s=moldyn->swrite;
 616         v=moldyn->vwrite;
 617
 618         /* sqaure of some variables */
 619         moldyn->tau_square=moldyn->tau*moldyn->tau;
 620         moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
 621
 622         /* calculate initial forces */
 623         potential_force_calc(moldyn);
 624
 625         /* do some checks before we actually start calculating bullshit */
 626         if(moldyn->cutoff>0.5*moldyn->dim.x)
 627                 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
 628         if(moldyn->cutoff>0.5*moldyn->dim.y)
 629                 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
 630         if(moldyn->cutoff>0.5*moldyn->dim.z)
 631                 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
 632         ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
 633         if(ds>0.05*moldyn->nnd)
 634                 printf("[moldyn] warning: forces too high / tau too small!\n");
 635
 636         /* zero absolute time */
 637         moldyn->time=0.0;
 638
 639         for(sched=0;sched<moldyn->schedule.content_count;sched++) {
 640
 641                 /* setting amount of runs and finite time step size */
 642                 moldyn->tau=schedule->tau[sched];
 643                 moldyn->tau_square=moldyn->tau*moldyn->tau;
 644                 moldyn->time_steps=schedule->runs[sched];
 645
 646         /* integration according to schedule */
 647
 648         for(i=0;i<moldyn->time_steps;i++) {
 649
 650                 /* integration step */
 651                 moldyn->integrate(moldyn);
 652
 653                 /* increase absolute time */
 654                 moldyn->time+=moldyn->tau;
 655
 656                 /* check for log & visualization */
 657                 if(e) {
 658                         if(!(i%e))
 659                                 dprintf(moldyn->efd,
 660                                         "%.15f %.45f %.45f %.45f\n",
 661                                         moldyn->time,update_e_kin(moldyn),
 662                                         moldyn->energy,
 663                                         get_total_energy(moldyn));
 664                 }
 665                 if(m) {
 666                         if(!(i%m)) {
 667                                 p=get_total_p(moldyn);
 668                                 dprintf(moldyn->mfd,
 669                                         "%.15f %.45f\n",moldyn->time,
 670                                         v3_norm(&p));
 671                         }
 672                 }
 673                 if(s) {
 674                         if(!(i%s)) {
 675                                 snprintf(fb,128,"%s-%f-%.15f.save",moldyn->sfb,
 676                                          moldyn->t,i*moldyn->tau);
 677                                 fd=open(fb,O_WRONLY|O_TRUNC|O_CREAT);
 678                                 if(fd<0) perror("[moldyn] save fd open");
 679                                 else {
 680                                         write(fd,moldyn,sizeof(t_moldyn));
 681                                         write(fd,moldyn->atom,
 682                                               moldyn->count*sizeof(t_atom));
 683                                 }
 684                                 close(fd);
 685                         }
 686                 }
 687                 if(v) {
 688                         if(!(i%v)) {
 689                                 visual_atoms(&(moldyn->vis),moldyn->time,
 690                                              moldyn->atom,moldyn->count);
 691                                 printf("\rsched: %d, steps: %d",sched,i);
 692                                 fflush(stdout);
 693                         }
 694                 }
 695
 696         }
 697
 698                 /* check for hooks */
 699                 if(schedule->hook)
 700                         schedule->hook(moldyn,schedule->hook_params);
 701
 702         }
 703
 704         return 0;
 705 }
 706
 707 /* velocity verlet */
 708
 709 int velocity_verlet(t_moldyn *moldyn) {
 710
 711         int i,count;
 712         double tau,tau_square;
 713         t_3dvec delta;
 714         t_atom *atom;
 715
 716         atom=moldyn->atom;
 717         count=moldyn->count;
 718         tau=moldyn->tau;
 719         tau_square=moldyn->tau_square;
 720
 721         for(i=0;i<count;i++) {
 722                 /* new positions */
 723                 v3_scale(&delta,&(atom[i].v),tau);
 724                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 725                 v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
 726                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 727                 check_per_bound(moldyn,&(atom[i].r));
 728
 729                 /* velocities */
 730                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 731                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 732         }
 733
 734         /* neighbour list update */
 735         link_cell_update(moldyn);
 736
 737         /* forces depending on chosen potential */
 738         potential_force_calc(moldyn);
 739         //moldyn->potential_force_function(moldyn);
 740
 741         for(i=0;i<count;i++) {
 742                 /* again velocities */
 743                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 744                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 745         }
 746
 747         return 0;
 748 }
 749
 750
 751 /*
 752  *
 753  * potentials & corresponding forces
 754  *
 755  */
 756
 757 /* generic potential and force calculation */
 758
 759 int potential_force_calc(t_moldyn *moldyn) {
 760
 761         int i,j,k,count;
 762         t_atom *atom,*btom,*ktom;
 763         t_linkcell *lc;
 764         t_list neighbour[27];
 765         t_list *this,*thisk,*neighbourk;
 766         u8 bc,bck;
 767         int countn,dnlc;
 768
 769         count=moldyn->count;
 770         atom=moldyn->atom;
 771         lc=&(moldyn->lc);
 772
 773         /* reset energy */
 774         moldyn->energy=0.0;
 775
 776         for(i=0;i<count;i++) {
 777
 778                 /* reset force */
 779                 v3_zero(&(atom[i].f));
 780
 781                 /* single particle potential/force */
 782                 if(atom[i].attr&ATOM_ATTR_1BP)
 783                         moldyn->func1b(moldyn,&(atom[i]));
 784
 785                 /* 2 body pair potential/force */
 786                 if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
 787
 788                         link_cell_neighbour_index(moldyn,
 789                                 (atom[i].r.x+moldyn->dim.x/2)/lc->x,
 790                                 (atom[i].r.y+moldyn->dim.y/2)/lc->y,
 791                                 (atom[i].r.z+moldyn->dim.z/2)/lc->z,
 792                                 neighbour);
 793
 794                         countn=lc->countn;
 795                         dnlc=lc->dnlc;
 796
 797                         for(j=0;j<countn;j++) {
 798
 799                                 this=&(neighbour[j]);
 800                                 list_reset(this);
 801
 802                                 if(this->start==NULL)
 803                                         continue;
 804
 805                                 bc=(j<dnlc)?0:1;
 806
 807                                 do {
 808                                         btom=this->current->data;
 809
 810                                         if(btom==&(atom[i]))
 811                                                 continue;
 812
 813                                         if((btom->attr&ATOM_ATTR_2BP)&
 814                                            (atom[i].attr&ATOM_ATTR_2BP))
 815                                                 moldyn->func2b(moldyn,
 816                                                                &(atom[i]),
 817                                                                btom,
 818                                                                bc);
 819
 820                                         /* 3 body potential/force */
 821
 822                                         if(!(atom[i].attr&ATOM_ATTR_3BP)||
 823                                            !(btom->attr&ATOM_ATTR_3BP))
 824                                                 continue;
 825
 826                                         link_cell_neighbour_index(moldyn,
 827                                            (btom->r.x+moldyn->dim.x/2)/lc->x,
 828                                            (btom->r.y+moldyn->dim.y/2)/lc->y,
 829                                            (btom->r.z+moldyn->dim.z/2)/lc->z,
 830                                            neighbourk);
 831
 832                                         for(k=0;k<lc->countn;k++) {
 833
 834                                                 thisk=&(neighbourk[k]);
 835                                                 list_reset(thisk);
 836
 837                                                 if(thisk->start==NULL)
 838                                                         continue;
 839
 840                                                 bck=(k<lc->dnlc)?0:1;
 841
 842                                                 do {
 843
 844                         ktom=thisk->current->data;
 845
 846                         if(!(ktom->attr&ATOM_ATTR_3BP))
 847                                 continue;
 848
 849                         if(ktom==btom)
 850                                 continue;
 851
 852                         if(ktom==&(atom[i]))
 853                                 continue;
 854
 855                         moldyn->func3b(moldyn,&(atom[i]),btom,ktom,bck);
 856
 857                                                 } while(list_next(thisk)!=\
 858                                                         L_NO_NEXT_ELEMENT);
 859
 860                                         }
 861
 862                                 } while(list_next(this)!=L_NO_NEXT_ELEMENT);
 863                         }
 864                 }
 865         }
 866
 867         return 0;
 868 }
 869
 870 /*
 871  * periodic boundayr checking
 872  */
 873
 874 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
 875
 876         double x,y,z;
 877         t_3dvec *dim;
 878
 879         dim=&(moldyn->dim);
 880
 881         x=0.5*dim->x;
 882         y=0.5*dim->y;
 883         z=0.5*dim->z;
 884
 885         if(moldyn->status&MOLDYN_STAT_PBX) {
 886                 if(a->x>=x) a->x-=dim->x;
 887                 else if(-a->x>x) a->x+=dim->x;
 888         }
 889         if(moldyn->status&MOLDYN_STAT_PBY) {
 890                 if(a->y>=y) a->y-=dim->y;
 891                 else if(-a->y>y) a->y+=dim->y;
 892         }
 893         if(moldyn->status&MOLDYN_STAT_PBZ) {
 894                 if(a->z>=z) a->z-=dim->z;
 895                 else if(-a->z>z) a->z+=dim->z;
 896         }
 897
 898         return 0;
 899 }
 900
 901
 902 /*
 903  * example potentials
 904  */
 905
 906 /* harmonic oscillator potential and force */
 907
 908 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 909
 910         t_ho_params *params;
 911         t_3dvec force,distance;
 912         double d;
 913         double sc,equi_dist;
 914
 915         params=moldyn->pot2b_params;
 916         sc=params->spring_constant;
 917         equi_dist=params->equilibrium_distance;
 918
 919         v3_sub(&distance,&(ai->r),&(aj->r));
 920
 921         if(bc) check_per_bound(moldyn,&distance);
 922         d=v3_norm(&distance);
 923         if(d<=moldyn->cutoff) {
 924                 /* energy is 1/2 (d-d0)^2, but we will add this twice ... */
 925                 moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
 926                 v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
 927                 v3_add(&(ai->f),&(ai->f),&force);
 928         }
 929
 930         return 0;
 931 }
 932
 933 /* lennard jones potential & force for one sort of atoms */
 934
 935 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 936
 937         t_lj_params *params;
 938         t_3dvec force,distance;
 939         double d,h1,h2;
 940         double eps,sig6,sig12;
 941
 942         params=moldyn->pot2b_params;
 943         eps=params->epsilon4;
 944         sig6=params->sigma6;
 945         sig12=params->sigma12;
 946
 947         v3_sub(&distance,&(ai->r),&(aj->r));
 948         if(bc) check_per_bound(moldyn,&distance);
 949         d=v3_absolute_square(&distance);        /* 1/r^2 */
 950         if(d<=moldyn->cutoff_square) {
 951                 d=1.0/d;                        /* 1/r^2 */
 952                 h2=d*d;                         /* 1/r^4 */
 953                 h2*=d;                          /* 1/r^6 */
 954                 h1=h2*h2;                       /* 1/r^12 */
 955                 /* energy is eps*..., but we will add this twice ... */
 956                 moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
 957                 h2*=d;                          /* 1/r^8 */
 958                 h1*=d;                          /* 1/r^14 */
 959                 h2*=6*sig6;
 960                 h1*=12*sig12;
 961                 d=+h1-h2;
 962                 d*=eps;
 963                 v3_scale(&force,&distance,d);
 964                 v3_add(&(ai->f),&(ai->f),&force);
 965         }
 966
 967         return 0;
 968 }
 969
 970 /*
 971  * tersoff potential & force for 2 sorts of atoms
 972  */
 973
 974 /* tersoff 1 body part */
 975 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
 976
 977         int num;
 978         t_tersoff_mult_params *params;
 979         t_tersoff_exchange *exchange;
 980
 981         num=ai->bnum;
 982         params=moldyn->pot1b_params;
 983         exchange=&(params->exchange);
 984
 985         /*
 986          * simple: point constant parameters only depending on atom i to
 987          *         their right values
 988          */
 989
 990         exchange->beta=&(params->beta[num]);
 991         exchange->n=&(params->n[num]);
 992         exchange->c=&(params->c[num]);
 993         exchange->d=&(params->d[num]);
 994         exchange->h=&(params->h[num]);
 995
 996         exchange->betan=pow(*(exchange->beta),*(exchange->n));
 997         exchange->c2=params->c[num]*params->c[num];
 998         exchange->d2=params->d[num]*params->d[num];
 999         exchange->c2d2=exchange->c2/exchange->d2;
1000
1001         return 0;
1002 }
1003
1004 /* tersoff 2 body part */
1005 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1006
1007         t_tersoff_mult_params *params;
1008         t_tersoff_exchange *exchange;
1009         t_3dvec dist_ij,force;
1010         double d_ij;
1011         double A,B,R,S,lambda,mu;
1012         double f_r,df_r;
1013         double f_c,df_c;
1014         int num;
1015         double s_r;
1016         double arg;
1017         double scale;
1018
1019         params=moldyn->pot2b_params;
1020         num=ai->bnum;
1021         exchange=&(params->exchange);
1022
1023         exchange->run3bp=0;
1024
1025         /*
1026          * we need: f_c, df_c, f_r, df_r
1027          *
1028          * therefore we need: R, S, A, lambda
1029          */
1030
1031         v3_sub(&dist_ij,&(ai->r),&(aj->r));
1032
1033         if(bc) check_per_bound(moldyn,&dist_ij);
1034
1035         /* save for use in 3bp */ /* REALLY ?!?!?! */
1036         exchange->dist_ij=dist_ij;
1037
1038         /* constants */
1039         if(num==aj->bnum) {
1040                 S=params->S[num];
1041                 R=params->R[num];
1042                 A=params->A[num];
1043                 lambda=params->lambda[num];
1044                 /* more constants depending of atoms i and j, needed in 3bp */
1045                 params->exchange.B=&(params->B[num]);
1046                 params->exchange.mu=&(params->mu[num]);
1047                 mu=params->mu[num];
1048                 params->exchange.chi=1.0;
1049         }
1050         else {
1051                 S=params->Smixed;
1052                 R=params->Rmixed;
1053                 A=params->Amixed;
1054                 lambda=params->lambda_m;
1055                 /* more constants depending of atoms i and j, needed in 3bp */
1056                 params->exchange.B=&(params->Bmixed);
1057                 params->exchange.mu=&(params->mu_m);
1058                 mu=params->mu_m;
1059                 params->exchange.chi=params->chi;
1060         }
1061
1062         d_ij=v3_norm(&dist_ij);
1063
1064         /* save for use in 3bp */
1065         exchange->d_ij=d_ij;
1066
1067         if(d_ij>S)
1068                 return 0;
1069
1070         f_r=A*exp(-lambda*d_ij);
1071         df_r=-lambda*f_r/d_ij;
1072
1073         /* f_a, df_a calc + save for 3bp use */
1074         exchange->f_a=-B*exp(-mu*d_ij);
1075         exchange->df_a=-mu*exchange->f_a/d_ij;
1076
1077         if(d_ij<R) {
1078                 /* f_c = 1, df_c = 0 */
1079                 f_c=1.0;
1080                 df_c=0.0;
1081                 v3_scale(&force,&dist_ij,df_r);
1082         }
1083         else {
1084                 s_r=S-R;
1085                 arg=M_PI*(d_ij-R)/s_r;
1086                 f_c=0.5+0.5*cos(arg);
1087                 df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij));
1088                 scale=df_c*f_r+df_r*f_c;
1089                 v3_scale(&force,&dist_ij,scale);
1090         }
1091
1092         /* add forces */
1093         v3_add(&(ai->f),&(ai->f),&force);
1094         /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
1095         moldyn->energy+=(0.25*f_r*f_c);
1096
1097         /* save for use in 3bp */
1098         exchange->f_c=f_c;
1099         exchange->df_c=df_c;
1100
1101         /* enable the run of 3bp function */
1102         exchange->run3bp=1;
1103
1104         return 0;
1105 }
1106
1107 /* tersoff 3 body part */
1108
1109 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
1110
1111         t_tersoff_mult_params *params;
1112         t_tersoff_exchange *exchange;
1113         t_3dvec dist_ij,dist_ik,dist_jk;
1114         t_3dvec temp,force;
1115         double R,S,s_r;
1116         double d_ij,d_ij2,d_ik,d_jk;
1117         double f_c,df_c,b_ij,f_a,df_a;
1118         double f_c_ik,df_c_ik,arg;
1119         double scale;
1120         double chi;
1121         double n,c,d,h,beta,betan;
1122         double c2,d2,c2d2;
1123         double numer,denom;
1124         double theta,cos_theta,sin_theta;
1125         double d_theta,d_theta1,d_theta2;
1126         double h_cos,h_cos2,d2_h_cos2;
1127         double frac1,bracket1,bracket2,bracket2_n_1,bracket2_n;
1128         double bracket3,bracket3_pow_1,bracket3_pow;
1129         int num;
1130
1131         params=moldyn->pot3b_params;
1132         num=ai->bnum;
1133         exchange=&(params->exchange);
1134
1135         if(!(exchange->run3bp))
1136                 return 0;
1137
1138         /*
1139          * we need: f_c, d_fc, b_ij, db_ij, f_a, df_a
1140          *
1141          * we got f_c, df_c, f_a, df_a from 2bp calculation
1142          */
1143
1144         d_ij=exchange->d_ij;
1145         d_ij2=exchange->d_ij2;
1146
1147         f_a=params->exchange.f_a;
1148         df_a=params->exchange.df_a;
1149
1150         /* d_ij is <= S, as we didn't return so far! */
1151
1152         /*
1153          * calc of b_ij (scalar) and db_ij (vector)
1154          *
1155          * - for b_ij: chi, beta, f_c_ik, w(=1), c, d, h, n, cos_theta
1156          *
1157          * - for db_ij: d_theta, sin_theta, cos_theta, f_c_ik, df_c_ik,
1158          *              w_ik,
1159          *
1160          */
1161
1162
1163         v3_sub(&dist_ik,&(ai->r),&(ak->r));
1164         if(bc) check_per_bound(moldyn,&dist_ik);
1165         d_ik=v3_norm(&dist_ik);
1166
1167         /* constants for f_c_ik calc */
1168         if(num==ak->bnum) {
1169                 R=params->R[num];
1170                 S=params->S[num];
1171         }
1172         else {
1173                 R=params->Rmixed;
1174                 S=params->Smixed;
1175         }
1176
1177         /* calc of f_c_ik */
1178         if(d_ik>S)
1179                 return 0;
1180
1181         if(d_ik<R) {
1182                 /* f_c_ik = 1, df_c_ik = 0 */
1183                 f_c_ik=1.0;
1184                 df_c_ik=0.0;
1185         }
1186         else {
1187                 s_r=S-R;
1188                 arg=M_PI*(d_ik-R)/s_r;
1189                 f_c_ik=0.5+0.5*cos(arg);
1190                 df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik));
1191         }
1192
1193         v3_sub(&dist_jk,&(aj->r),&(ak->r));
1194         if(bc) check_per_bound(moldyn,&dist_jk);
1195         d_jk=v3_norm(&dist_jk);
1196
1197         beta=*(exchange->beta);
1198         betan=exchange->betan;
1199         n=*(exchange->n);
1200         c=*(exchange->c);
1201         d=*(exchange->d);
1202         h=*(exchange->h);
1203         c2=exchange->c2;
1204         d2=exchange->d2;
1205         c2d2=exchange->c2d2;
1206
1207         numer=d_ij2+d_ik*d_ik-d_jk*d_jk;
1208         denom=2*d_ij*d_ik;
1209         cos_theta=numer/denom;
1210         sin_theta=sqrt(1.0-(cos_theta*cos_theta));
1211         theta=acos(cos_theta);
1212         d_theta=(-1.0/sqrt(1.0-cos_theta*cos_theta))/(denom*denom);
1213         d_theta1=2*denom-numer*2*d_ik/d_ij;
1214         d_theta2=2*denom-numer*2*d_ij/d_ik;
1215         d_theta1*=d_theta;
1216         d_theta2*=d_theta;
1217
1218         h_cos=(h-cos_theta);
1219         h_cos2=h_cos*h_cos;
1220         d2_h_cos2=d2-h_cos2;
1221
1222         /* some usefull expressions */
1223         frac1=c2/(d2-h_cos2);
1224         bracket1=1+c2d2-frac1;
1225         bracket2=f_c_ik*bracket1;
1226         bracket2_n_1=pow(bracket2,n-1.0);
1227         bracket2_n=bracket2_n_1*bracket2;
1228         bracket3=1+betan*bracket2_n;
1229         bracket3_pow_1=pow(bracket3,(-1.0/(2.0*n))-1.0);
1230         bracket3_pow=bracket3_pow_1*bracket3;
1231
1232         /* now go on with calc of b_ij and derivation of b_ij */
1233         b_ij=chi*bracket3_pow;
1234
1235         /* derivation of theta */
1236         v3_scale(&force,&dist_ij,d_theta1);
1237         v3_scale(&temp,&dist_ik,d_theta2);
1238         v3_add(&force,&force,&temp);
1239
1240         /* part 1 of derivation of b_ij */
1241         v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac1);
1242
1243         /* part 2 of derivation of b_ij */
1244         v3_scale(&temp,&dist_ik,df_c_ik*bracket1);
1245
1246         /* sum up and scale ... */
1247         v3_add(&temp,&temp,&force);
1248         scale=bracket2_n_1*n*betan*(1+betan*bracket3_pow_1)*chi*(1.0/(2.0*n));
1249         v3_scale(&temp,&temp,scale);
1250
1251         /* now construct an energy and a force out of that */
1252         v3_scale(&temp,&temp,f_a);
1253         v3_scale(&force,&dist_ij,df_a*b_ij);
1254         v3_add(&temp,&temp,&force);
1255         v3_scale(&temp,&temp,f_c);
1256         v3_scale(&force,&dist_ij,df_c*b_ij*f_a);
1257         v3_add(&force,&force,&temp);
1258
1259         /* add forces */
1260         v3_add(&(ai->f),&(ai->f),&force);
1261         /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
1262         moldyn->energy+=(0.25*f_a*b_ij*f_c);
1263
1264         return 0;
1265 }
1266