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_ref) {
  75
  76         moldyn->t_ref=t_ref;
  77
  78         return 0;
  79 }
  80
  81 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
  82
  83         moldyn->pt_scale=(ptype|ttype);
  84         moldyn->t_tc=ttc;
  85         moldyn->p_tc=ptc;
  86
  87         return 0;
  88 }
  89
  90 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
  91
  92         moldyn->dim.x=x;
  93         moldyn->dim.y=y;
  94         moldyn->dim.z=z;
  95
  96         if(visualize) {
  97                 moldyn->vis.dim.x=x;
  98                 moldyn->vis.dim.y=y;
  99                 moldyn->vis.dim.z=z;
 100         }
 101
 102         return 0;
 103 }
 104
 105 int set_nn_dist(t_moldyn *moldyn,double dist) {
 106
 107         moldyn->nnd=dist;
 108
 109         return 0;
 110 }
 111
 112 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 113
 114         if(x)
 115                 moldyn->status|=MOLDYN_STAT_PBX;
 116
 117         if(y)
 118                 moldyn->status|=MOLDYN_STAT_PBY;
 119
 120         if(z)
 121                 moldyn->status|=MOLDYN_STAT_PBZ;
 122
 123         return 0;
 124 }
 125
 126 int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
 127
 128         moldyn->func1b=func;
 129         moldyn->pot1b_params=params;
 130
 131         return 0;
 132 }
 133
 134 int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
 135
 136         moldyn->func2b=func;
 137         moldyn->pot2b_params=params;
 138
 139         return 0;
 140 }
 141
 142 int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
 143
 144         moldyn->func3b=func;
 145         moldyn->pot3b_params=params;
 146
 147         return 0;
 148 }
 149
 150 int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
 151
 152         switch(type) {
 153                 case LOG_TOTAL_ENERGY:
 154                         moldyn->ewrite=timer;
 155                         moldyn->efd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
 156                         if(moldyn->efd<0) {
 157                                 perror("[moldyn] efd open");
 158                                 return moldyn->efd;
 159                         }
 160                         dprintf(moldyn->efd,"# total energy log file\n");
 161                         break;
 162                 case LOG_TOTAL_MOMENTUM:
 163                         moldyn->mwrite=timer;
 164                         moldyn->mfd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
 165                         if(moldyn->mfd<0) {
 166                                 perror("[moldyn] mfd open");
 167                                 return moldyn->mfd;
 168                         }
 169                         dprintf(moldyn->efd,"# total momentum log file\n");
 170                         break;
 171                 case SAVE_STEP:
 172                         moldyn->swrite=timer;
 173                         strncpy(moldyn->sfb,fb,63);
 174                         break;
 175                 case VISUAL_STEP:
 176                         moldyn->vwrite=timer;
 177                         strncpy(moldyn->vfb,fb,63);
 178                         visual_init(&(moldyn->vis),fb);
 179                         break;
 180                 default:
 181                         printf("unknown log mechanism: %02x\n",type);
 182                         return -1;
 183         }
 184
 185         return 0;
 186 }
 187
 188 int moldyn_log_shutdown(t_moldyn *moldyn) {
 189
 190         printf("[moldyn] log shutdown\n");
 191         if(moldyn->efd) close(moldyn->efd);
 192         if(moldyn->mfd) close(moldyn->mfd);
 193         if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
 194
 195         return 0;
 196 }
 197
 198 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 199                    u8 attr,u8 bnum,int a,int b,int c) {
 200
 201         int count;
 202         int ret;
 203         t_3dvec origin;
 204
 205         count=a*b*c;
 206
 207         if(type==FCC) count*=4;
 208
 209         if(type==DIAMOND) count*=8;
 210
 211         moldyn->atom=malloc(count*sizeof(t_atom));
 212         if(moldyn->atom==NULL) {
 213                 perror("malloc (atoms)");
 214                 return -1;
 215         }
 216
 217         v3_zero(&origin);
 218
 219         switch(type) {
 220                 case FCC:
 221                         ret=fcc_init(a,b,c,lc,moldyn->atom,&origin);
 222                         break;
 223                 case DIAMOND:
 224                         ret=diamond_init(a,b,c,lc,moldyn->atom,&origin);
 225                         break;
 226                 default:
 227                         printf("unknown lattice type (%02x)\n",type);
 228                         return -1;
 229         }
 230
 231         /* debug */
 232         if(ret!=count) {
 233                 printf("ok, there is something wrong ...\n");
 234                 printf("calculated -> %d atoms\n",count);
 235                 printf("created -> %d atoms\n",ret);
 236                 return -1;
 237         }
 238
 239         moldyn->count=count;
 240         printf("[moldyn] created lattice with %d atoms\n",count);
 241
 242         while(count) {
 243                 count-=1;
 244                 moldyn->atom[count].element=element;
 245                 moldyn->atom[count].mass=mass;
 246                 moldyn->atom[count].attr=attr;
 247                 moldyn->atom[count].bnum=bnum;
 248                 check_per_bound(moldyn,&(moldyn->atom[count].r));
 249         }
 250
 251
 252         return ret;
 253 }
 254
 255 int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
 256              t_3dvec *r,t_3dvec *v) {
 257
 258         t_atom *atom;
 259         void *ptr;
 260         int count;
 261
 262         atom=moldyn->atom;
 263         count=++(moldyn->count);
 264
 265         ptr=realloc(atom,count*sizeof(t_atom));
 266         if(!ptr) {
 267                 perror("[moldyn] realloc (add atom)");
 268                 return -1;
 269         }
 270         moldyn->atom=ptr;
 271
 272         atom=moldyn->atom;
 273         atom[count-1].r=*r;
 274         atom[count-1].v=*v;
 275         atom[count-1].element=element;
 276         atom[count-1].mass=mass;
 277         atom[count-1].bnum=bnum;
 278         atom[count-1].attr=attr;
 279
 280         return 0;
 281 }
 282
 283 int destroy_atoms(t_moldyn *moldyn) {
 284
 285         if(moldyn->atom) free(moldyn->atom);
 286
 287         return 0;
 288 }
 289
 290 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 291
 292         /*
 293          * - gaussian distribution of velocities
 294          * - zero total momentum
 295          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 296          */
 297
 298         int i;
 299         double v,sigma;
 300         t_3dvec p_total,delta;
 301         t_atom *atom;
 302         t_random *random;
 303
 304         atom=moldyn->atom;
 305         random=&(moldyn->random);
 306
 307         /* gaussian distribution of velocities */
 308         v3_zero(&p_total);
 309         for(i=0;i<moldyn->count;i++) {
 310                 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
 311                 /* x direction */
 312                 v=sigma*rand_get_gauss(random);
 313                 atom[i].v.x=v;
 314                 p_total.x+=atom[i].mass*v;
 315                 /* y direction */
 316                 v=sigma*rand_get_gauss(random);
 317                 atom[i].v.y=v;
 318                 p_total.y+=atom[i].mass*v;
 319                 /* z direction */
 320                 v=sigma*rand_get_gauss(random);
 321                 atom[i].v.z=v;
 322                 p_total.z+=atom[i].mass*v;
 323         }
 324
 325         /* zero total momentum */
 326         v3_scale(&p_total,&p_total,1.0/moldyn->count);
 327         for(i=0;i<moldyn->count;i++) {
 328                 v3_scale(&delta,&p_total,1.0/atom[i].mass);
 329                 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
 330         }
 331
 332         /* velocity scaling */
 333         scale_velocity(moldyn,equi_init);
 334
 335         return 0;
 336 }
 337
 338 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 339
 340         int i;
 341         double e,scale;
 342         t_atom *atom;
 343         int count;
 344
 345         atom=moldyn->atom;
 346
 347         /*
 348          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 349          */
 350
 351         /* get kinetic energy / temperature & count involved atoms */
 352         e=0.0;
 353         count=0;
 354         for(i=0;i<moldyn->count;i++) {
 355                 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
 356                         e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 357                         count+=1;
 358                 }
 359         }
 360         if(count!=0) moldyn->t=(2.0*e)/(3.0*count*K_BOLTZMANN);
 361         else return 0;  /* no atoms involved in scaling! */
 362
 363         /* (temporary) hack for e,t = 0 */
 364         if(e==0.0) {
 365         moldyn->t=0.0;
 366                 if(moldyn->t_ref!=0.0)
 367                         thermal_init(moldyn,equi_init);
 368                 else
 369                         return 0; /* no scaling needed */
 370         }
 371
 372
 373         /* get scaling factor */
 374         scale=moldyn->t_ref/moldyn->t;
 375         if(equi_init&TRUE)
 376                 scale*=2.0;
 377         else
 378                 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
 379                         scale=1.0+moldyn->tau*(scale-1.0)/moldyn->t_tc;
 380         scale=sqrt(scale);
 381
 382         /* velocity scaling */
 383         for(i=0;i<moldyn->count;i++)
 384                 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
 385                         v3_scale(&(atom[i].v),&(atom[i].v),scale);
 386
 387         return 0;
 388 }
 389
 390 double get_e_kin(t_moldyn *moldyn) {
 391
 392         int i;
 393         t_atom *atom;
 394
 395         atom=moldyn->atom;
 396         moldyn->ekin=0.0;
 397
 398         for(i=0;i<moldyn->count;i++)
 399                 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 400
 401         return moldyn->ekin;
 402 }
 403
 404 double get_e_pot(t_moldyn *moldyn) {
 405
 406         return moldyn->energy;
 407 }
 408
 409 double update_e_kin(t_moldyn *moldyn) {
 410
 411         return(get_e_kin(moldyn));
 412 }
 413
 414 double get_total_energy(t_moldyn *moldyn) {
 415
 416         return(moldyn->ekin+moldyn->energy);
 417 }
 418
 419 t_3dvec get_total_p(t_moldyn *moldyn) {
 420
 421         t_3dvec p,p_total;
 422         int i;
 423         t_atom *atom;
 424
 425         atom=moldyn->atom;
 426
 427         v3_zero(&p_total);
 428         for(i=0;i<moldyn->count;i++) {
 429                 v3_scale(&p,&(atom[i].v),atom[i].mass);
 430                 v3_add(&p_total,&p_total,&p);
 431         }
 432
 433         return p_total;
 434 }
 435
 436 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
 437
 438         double tau;
 439
 440         /* nn_dist is the nearest neighbour distance */
 441
 442         if(moldyn->t==5.0) {
 443                 printf("[moldyn] i do not estimate timesteps below %f K!\n",
 444                        MOLDYN_CRITICAL_EST_TEMP);
 445                 return 23.42;
 446         }
 447
 448         tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
 449
 450         return tau;
 451 }
 452
 453 /*
 454  * numerical tricks
 455  */
 456
 457 /* linked list / cell method */
 458
 459 int link_cell_init(t_moldyn *moldyn) {
 460
 461         t_linkcell *lc;
 462         int i;
 463         int fd;
 464
 465         fd=open("/dev/null",O_WRONLY);
 466
 467         lc=&(moldyn->lc);
 468
 469         /* partitioning the md cell */
 470         lc->nx=moldyn->dim.x/moldyn->cutoff;
 471         lc->x=moldyn->dim.x/lc->nx;
 472         lc->ny=moldyn->dim.y/moldyn->cutoff;
 473         lc->y=moldyn->dim.y/lc->ny;
 474         lc->nz=moldyn->dim.z/moldyn->cutoff;
 475         lc->z=moldyn->dim.z/lc->nz;
 476
 477         lc->cells=lc->nx*lc->ny*lc->nz;
 478         lc->subcell=malloc(lc->cells*sizeof(t_list));
 479
 480         printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 481
 482         for(i=0;i<lc->cells;i++)
 483                 //list_init(&(lc->subcell[i]),1);
 484                 list_init(&(lc->subcell[i]),fd);
 485
 486         link_cell_update(moldyn);
 487
 488         return 0;
 489 }
 490
 491 int link_cell_update(t_moldyn *moldyn) {
 492
 493         int count,i,j,k;
 494         int nx,ny,nz;
 495         t_atom *atom;
 496         t_linkcell *lc;
 497
 498         atom=moldyn->atom;
 499         lc=&(moldyn->lc);
 500
 501         nx=lc->nx;
 502         ny=lc->ny;
 503         nz=lc->nz;
 504
 505         for(i=0;i<lc->cells;i++)
 506                 list_destroy(&(moldyn->lc.subcell[i]));
 507
 508         for(count=0;count<moldyn->count;count++) {
 509                 i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
 510                 j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
 511                 k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
 512                 list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
 513                                        &(atom[count]));
 514         }
 515
 516         return 0;
 517 }
 518
 519 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 520
 521         t_linkcell *lc;
 522         int a;
 523         int count1,count2;
 524         int ci,cj,ck;
 525         int nx,ny,nz;
 526         int x,y,z;
 527         u8 bx,by,bz;
 528
 529         lc=&(moldyn->lc);
 530         nx=lc->nx;
 531         ny=lc->ny;
 532         nz=lc->nz;
 533         count1=1;
 534         count2=27;
 535         a=nx*ny;
 536
 537         cell[0]=lc->subcell[i+j*nx+k*a];
 538         for(ci=-1;ci<=1;ci++) {
 539                 bx=0;
 540                 x=i+ci;
 541                 if((x<0)||(x>=nx)) {
 542                         x=(x+nx)%nx;
 543                         bx=1;
 544                 }
 545                 for(cj=-1;cj<=1;cj++) {
 546                         by=0;
 547                         y=j+cj;
 548                         if((y<0)||(y>=ny)) {
 549                                 y=(y+ny)%ny;
 550                                 by=1;
 551                         }
 552                         for(ck=-1;ck<=1;ck++) {
 553                                 bz=0;
 554                                 z=k+ck;
 555                                 if((z<0)||(z>=nz)) {
 556                                         z=(z+nz)%nz;
 557                                         bz=1;
 558                                 }
 559                                 if(!(ci|cj|ck)) continue;
 560                                 if(bx|by|bz) {
 561                                         cell[--count2]=lc->subcell[x+y*nx+z*a];
 562                                 }
 563                                 else {
 564                                         cell[count1++]=lc->subcell[x+y*nx+z*a];
 565                                 }
 566                         }
 567                 }
 568         }
 569
 570         lc->dnlc=count1;
 571         lc->countn=27;
 572
 573         return count2;
 574 }
 575
 576 int link_cell_shutdown(t_moldyn *moldyn) {
 577
 578         int i;
 579         t_linkcell *lc;
 580
 581         lc=&(moldyn->lc);
 582
 583         for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
 584                 list_shutdown(&(moldyn->lc.subcell[i]));
 585
 586         return 0;
 587 }
 588
 589 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
 590
 591         int count;
 592         void *ptr;
 593         t_moldyn_schedule *schedule;
 594
 595         schedule=&(moldyn->schedule);
 596         count=++(schedule->content_count);
 597
 598         ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
 599         if(!ptr) {
 600                 perror("[moldyn] realloc (runs)");
 601                 return -1;
 602         }
 603         moldyn->schedule.runs=ptr;
 604         moldyn->schedule.runs[count-1]=runs;
 605
 606         ptr=realloc(schedule->tau,count*sizeof(double));
 607         if(!ptr) {
 608                 perror("[moldyn] realloc (tau)");
 609                 return -1;
 610         }
 611         moldyn->schedule.tau=ptr;
 612         moldyn->schedule.tau[count-1]=tau;
 613
 614         return 0;
 615 }
 616
 617 int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
 618
 619         moldyn->schedule.hook=hook;
 620         moldyn->schedule.hook_params=hook_params;
 621
 622         return 0;
 623 }
 624
 625 /*
 626  *
 627  * 'integration of newtons equation' - algorithms
 628  *
 629  */
 630
 631 /* start the integration */
 632
 633 int moldyn_integrate(t_moldyn *moldyn) {
 634
 635         int i,sched;
 636         unsigned int e,m,s,v;
 637         t_3dvec p;
 638         t_moldyn_schedule *schedule;
 639         t_atom *atom;
 640         int fd;
 641         char fb[128];
 642         double ds;
 643
 644         schedule=&(moldyn->schedule);
 645         atom=moldyn->atom;
 646
 647         /* initialize linked cell method */
 648         link_cell_init(moldyn);
 649
 650         /* logging & visualization */
 651         e=moldyn->ewrite;
 652         m=moldyn->mwrite;
 653         s=moldyn->swrite;
 654         v=moldyn->vwrite;
 655
 656         /* sqaure of some variables */
 657         moldyn->tau_square=moldyn->tau*moldyn->tau;
 658         moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
 659         /* calculate initial forces */
 660         potential_force_calc(moldyn);
 661
 662         /* do some checks before we actually start calculating bullshit */
 663         if(moldyn->cutoff>0.5*moldyn->dim.x)
 664                 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
 665         if(moldyn->cutoff>0.5*moldyn->dim.y)
 666                 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
 667         if(moldyn->cutoff>0.5*moldyn->dim.z)
 668                 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
 669         ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
 670         if(ds>0.05*moldyn->nnd)
 671                 printf("[moldyn] warning: forces too high / tau too small!\n");
 672
 673         /* zero absolute time */
 674         moldyn->time=0.0;
 675         for(sched=0;sched<moldyn->schedule.content_count;sched++) {
 676
 677                 /* setting amount of runs and finite time step size */
 678                 moldyn->tau=schedule->tau[sched];
 679                 moldyn->tau_square=moldyn->tau*moldyn->tau;
 680                 moldyn->time_steps=schedule->runs[sched];
 681
 682         /* integration according to schedule */
 683
 684         for(i=0;i<moldyn->time_steps;i++) {
 685
 686                 /* integration step */
 687                 moldyn->integrate(moldyn);
 688
 689                 /* p/t scaling */
 690                 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
 691                         scale_velocity(moldyn,FALSE);
 692
 693                 /* increase absolute time */
 694                 moldyn->time+=moldyn->tau;
 695
 696                 /* check for log & visualization */
 697                 if(e) {
 698                         if(!(i%e))
 699                                 dprintf(moldyn->efd,
 700                                         "%.15f %.45f %.45f %.45f\n",
 701                                         moldyn->time,update_e_kin(moldyn),
 702                                         moldyn->energy,
 703                                         get_total_energy(moldyn));
 704                 }
 705                 if(m) {
 706                         if(!(i%m)) {
 707                                 p=get_total_p(moldyn);
 708                                 dprintf(moldyn->mfd,
 709                                         "%.15f %.45f\n",moldyn->time,
 710                                         v3_norm(&p));
 711                         }
 712                 }
 713                 if(s) {
 714                         if(!(i%s)) {
 715                                 snprintf(fb,128,"%s-%f-%.15f.save",moldyn->sfb,
 716                                          moldyn->t,i*moldyn->tau);
 717                                 fd=open(fb,O_WRONLY|O_TRUNC|O_CREAT);
 718                                 if(fd<0) perror("[moldyn] save fd open");
 719                                 else {
 720                                         write(fd,moldyn,sizeof(t_moldyn));
 721                                         write(fd,moldyn->atom,
 722                                               moldyn->count*sizeof(t_atom));
 723                                 }
 724                                 close(fd);
 725                         }
 726                 }
 727                 if(v) {
 728                         if(!(i%v)) {
 729                                 visual_atoms(&(moldyn->vis),moldyn->time,
 730                                              moldyn->atom,moldyn->count);
 731                                 printf("\rsched: %d, steps: %d",sched,i);
 732                                 fflush(stdout);
 733                         }
 734                 }
 735
 736         }
 737
 738                 /* check for hooks */
 739                 if(schedule->hook)
 740                         schedule->hook(moldyn,schedule->hook_params);
 741
 742         }
 743
 744         return 0;
 745 }
 746
 747 /* velocity verlet */
 748
 749 int velocity_verlet(t_moldyn *moldyn) {
 750
 751         int i,count;
 752         double tau,tau_square;
 753         t_3dvec delta;
 754         t_atom *atom;
 755
 756         atom=moldyn->atom;
 757         count=moldyn->count;
 758         tau=moldyn->tau;
 759         tau_square=moldyn->tau_square;
 760
 761         for(i=0;i<count;i++) {
 762                 /* new positions */
 763                 v3_scale(&delta,&(atom[i].v),tau);
 764                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 765                 v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
 766                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 767                 check_per_bound(moldyn,&(atom[i].r));
 768
 769                 /* velocities */
 770                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 771                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 772         }
 773
 774         /* neighbour list update */
 775         link_cell_update(moldyn);
 776
 777         /* forces depending on chosen potential */
 778         potential_force_calc(moldyn);
 779         //moldyn->potential_force_function(moldyn);
 780
 781         for(i=0;i<count;i++) {
 782                 /* again velocities */
 783                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 784                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 785         }
 786
 787         return 0;
 788 }
 789
 790
 791 /*
 792  *
 793  * potentials & corresponding forces
 794  *
 795  */
 796
 797 /* generic potential and force calculation */
 798
 799 int potential_force_calc(t_moldyn *moldyn) {
 800
 801         int i,j,k,count;
 802         t_atom *itom,*jtom,*ktom;
 803         t_linkcell *lc;
 804         t_list neighbour_i[27];
 805         t_list neighbour_i2[27];
 806         //t_list neighbour_j[27];
 807         t_list *this,*that;
 808         u8 bc_ij,bc_ijk;
 809         int countn,dnlc;
 810
 811         count=moldyn->count;
 812         itom=moldyn->atom;
 813         lc=&(moldyn->lc);
 814
 815         /* reset energy */
 816         moldyn->energy=0.0;
 817
 818         for(i=0;i<count;i++) {
 819
 820                 /* reset force */
 821                 v3_zero(&(itom[i].f));
 822
 823                 /* single particle potential/force */
 824                 if(itom[i].attr&ATOM_ATTR_1BP)
 825                         moldyn->func1b(moldyn,&(itom[i]));
 826
 827                 /* 2 body pair potential/force */
 828                 if(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
 829
 830                         link_cell_neighbour_index(moldyn,
 831                                 (itom[i].r.x+moldyn->dim.x/2)/lc->x,
 832                                 (itom[i].r.y+moldyn->dim.y/2)/lc->y,
 833                                 (itom[i].r.z+moldyn->dim.z/2)/lc->z,
 834                                 neighbour_i);
 835
 836                         countn=lc->countn;
 837                         dnlc=lc->dnlc;
 838
 839                         for(j=0;j<countn;j++) {
 840
 841                                 this=&(neighbour_i[j]);
 842                                 list_reset(this);
 843
 844                                 if(this->start==NULL)
 845                                         continue;
 846
 847                                 bc_ij=(j<dnlc)?0:1;
 848
 849                                 do {
 850                                         jtom=this->current->data;
 851
 852                                         if(jtom==&(itom[i]))
 853                                                 continue;
 854
 855                                         if((jtom->attr&ATOM_ATTR_2BP)&
 856                                            (itom[i].attr&ATOM_ATTR_2BP))
 857                                                 moldyn->func2b(moldyn,
 858                                                                &(itom[i]),
 859                                                                jtom,
 860                                                                bc_ij);
 861
 862                                         /* 3 body potential/force */
 863
 864                                         if(!(itom[i].attr&ATOM_ATTR_3BP)||
 865                                            !(jtom->attr&ATOM_ATTR_3BP))
 866                                                 continue;
 867
 868                         /*
 869                          * according to mr. nordlund, we dont need to take the
 870                          * sum over all atoms now, as 'this is centered' around
 871                          * atom i ...
 872                          * i am not quite sure though! there is a not vanishing
 873                          * part even if f_c_ik is zero ...
 874                          * this analytical potentials suck!
 875                          * switching from mc to md to dft soon!
 876                          */
 877
 878                         //              link_cell_neighbour_index(moldyn,
 879                         //                 (jtom->r.x+moldyn->dim.x/2)/lc->x,
 880                         //                 (jtom->r.y+moldyn->dim.y/2)/lc->y,
 881                         //                 (jtom->r.z+moldyn->dim.z/2)/lc->z,
 882                         //                 neighbour_j);
 883
 884 //                                      /* neighbours of j */
 885 //                                      for(k=0;k<lc->countn;k++) {
 886 //
 887 //                                              that=&(neighbour_j[k]);
 888 //                                              list_reset(that);
 889 //
 890 //                                              if(that->start==NULL)
 891 //                                                      continue;
 892 //
 893 //                                              bc_ijk=(k<lc->dnlc)?0:1;
 894 //
 895 //                                              do {
 896 //
 897 //                      ktom=that->current->data;
 898 //
 899 //                      if(!(ktom->attr&ATOM_ATTR_3BP))
 900 //                              continue;
 901 //
 902 //                      if(ktom==jtom)
 903 //                              continue;
 904 //
 905 //                      if(ktom==&(itom[i]))
 906 //                              continue;
 907 //
 908 //                      moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
 909 //
 910 /*                                              } while(list_next(that)!=\ */
 911 //                                                      L_NO_NEXT_ELEMENT);
 912 //
 913 //                                      }
 914
 915                                         /* copy the neighbour lists */
 916                                         memcpy(neighbour_i2,neighbour_i,
 917                                                27*sizeof(t_list));
 918
 919                                         /* get neighbours of i */
 920                                         for(k=0;k<countn;k++) {
 921
 922                                                 that=&(neighbour_i2[k]);
 923                                                 list_reset(that);
 924
 925                                                 if(that->start==NULL)
 926                                                         continue;
 927
 928                                                 bc_ijk=(k<dnlc)?0:1;
 929
 930                                                 do {
 931
 932                         ktom=that->current->data;
 933
 934                         if(!(ktom->attr&ATOM_ATTR_3BP))
 935                                 continue;
 936
 937                         if(ktom==jtom)
 938                                 continue;
 939
 940                         if(ktom==&(itom[i]))
 941                                 continue;
 942
 943 printf("Debug: atom %d before 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[i],jtom,ktom,itom[i].r.x,itom[i].f.x,itom[i].v.x);
 944                         moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
 945 printf("Debug: atom %d after 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[i],jtom,ktom,itom[i].r.x,itom[i].f.x,itom[i].v.x);
 946
 947                                                 } while(list_next(that)!=\
 948                                                         L_NO_NEXT_ELEMENT);
 949
 950                                         }
 951
 952                                 } while(list_next(this)!=L_NO_NEXT_ELEMENT);
 953                         }
 954                 }
 955         }
 956
 957         return 0;
 958 }
 959
 960 /*
 961  * periodic boundayr checking
 962  */
 963
 964 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
 965
 966         double x,y,z;
 967         t_3dvec *dim;
 968
 969         dim=&(moldyn->dim);
 970
 971         x=0.5*dim->x;
 972         y=0.5*dim->y;
 973         z=0.5*dim->z;
 974
 975         if(moldyn->status&MOLDYN_STAT_PBX) {
 976                 if(a->x>=x) a->x-=dim->x;
 977                 else if(-a->x>x) a->x+=dim->x;
 978         }
 979         if(moldyn->status&MOLDYN_STAT_PBY) {
 980                 if(a->y>=y) a->y-=dim->y;
 981                 else if(-a->y>y) a->y+=dim->y;
 982         }
 983         if(moldyn->status&MOLDYN_STAT_PBZ) {
 984                 if(a->z>=z) a->z-=dim->z;
 985                 else if(-a->z>z) a->z+=dim->z;
 986         }
 987
 988         return 0;
 989 }
 990
 991
 992 /*
 993  * example potentials
 994  */
 995
 996 /* harmonic oscillator potential and force */
 997
 998 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 999
1000         t_ho_params *params;
1001         t_3dvec force,distance;
1002         double d;
1003         double sc,equi_dist;
1004
1005         params=moldyn->pot2b_params;
1006         sc=params->spring_constant;
1007         equi_dist=params->equilibrium_distance;
1008
1009         v3_sub(&distance,&(ai->r),&(aj->r));
1010
1011         if(bc) check_per_bound(moldyn,&distance);
1012         d=v3_norm(&distance);
1013         if(d<=moldyn->cutoff) {
1014                 /* energy is 1/2 (d-d0)^2, but we will add this twice ... */
1015                 moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
1016                 v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
1017                 v3_add(&(ai->f),&(ai->f),&force);
1018         }
1019
1020         return 0;
1021 }
1022
1023 /* lennard jones potential & force for one sort of atoms */
1024
1025 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1026
1027         t_lj_params *params;
1028         t_3dvec force,distance;
1029         double d,h1,h2;
1030         double eps,sig6,sig12;
1031
1032         params=moldyn->pot2b_params;
1033         eps=params->epsilon4;
1034         sig6=params->sigma6;
1035         sig12=params->sigma12;
1036
1037         v3_sub(&distance,&(ai->r),&(aj->r));
1038         if(bc) check_per_bound(moldyn,&distance);
1039         d=v3_absolute_square(&distance);        /* 1/r^2 */
1040         if(d<=moldyn->cutoff_square) {
1041                 d=1.0/d;                        /* 1/r^2 */
1042                 h2=d*d;                         /* 1/r^4 */
1043                 h2*=d;                          /* 1/r^6 */
1044                 h1=h2*h2;                       /* 1/r^12 */
1045                 /* energy is eps*..., but we will add this twice ... */
1046                 moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
1047                 h2*=d;                          /* 1/r^8 */
1048                 h1*=d;                          /* 1/r^14 */
1049                 h2*=6*sig6;
1050                 h1*=12*sig12;
1051                 d=+h1-h2;
1052                 d*=eps;
1053                 v3_scale(&force,&distance,d);
1054                 v3_add(&(ai->f),&(ai->f),&force);
1055         }
1056
1057         return 0;
1058 }
1059
1060 /*
1061  * tersoff potential & force for 2 sorts of atoms
1062  */
1063
1064 /* create mixed terms from parameters and set them */
1065 int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
1066
1067         printf("[moldyn] tersoff parameter completion\n");
1068         p->Smixed=sqrt(p->S[0]*p->S[1]);
1069         p->Rmixed=sqrt(p->R[0]*p->R[1]);
1070         p->Amixed=sqrt(p->A[0]*p->A[1]);
1071         p->Bmixed=sqrt(p->B[0]*p->B[1]);
1072         p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
1073         p->mu_m=0.5*(p->mu[0]+p->mu[1]);
1074
1075         return 0;
1076 }
1077
1078 /* tersoff 1 body part */
1079 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
1080
1081         int num;
1082         t_tersoff_mult_params *params;
1083         t_tersoff_exchange *exchange;
1084
1085         num=ai->bnum;
1086         params=moldyn->pot1b_params;
1087         exchange=&(params->exchange);
1088
1089         /*
1090          * simple: point constant parameters only depending on atom i to
1091          *         their right values
1092          */
1093
1094         exchange->beta=&(params->beta[num]);
1095         exchange->n=&(params->n[num]);
1096         exchange->c=&(params->c[num]);
1097         exchange->d=&(params->d[num]);
1098         exchange->h=&(params->h[num]);
1099
1100         exchange->betan=pow(*(exchange->beta),*(exchange->n));
1101         exchange->c2=params->c[num]*params->c[num];
1102         exchange->d2=params->d[num]*params->d[num];
1103         exchange->c2d2=exchange->c2/exchange->d2;
1104
1105         return 0;
1106 }
1107
1108 /* tersoff 2 body part */
1109 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1110
1111         t_tersoff_mult_params *params;
1112         t_tersoff_exchange *exchange;
1113         t_3dvec dist_ij,force;
1114         double d_ij;
1115         double A,B,R,S,lambda,mu;
1116         double f_r,df_r;
1117         double f_c,df_c;
1118         int num;
1119         double s_r;
1120         double arg;
1121         double scale;
1122
1123         params=moldyn->pot2b_params;
1124         num=ai->bnum;
1125         exchange=&(params->exchange);
1126
1127         exchange->run3bp=0;
1128
1129         /*
1130          * we need: f_c, df_c, f_r, df_r
1131          *
1132          * therefore we need: R, S, A, lambda
1133          */
1134
1135         v3_sub(&dist_ij,&(ai->r),&(aj->r));
1136
1137         if(bc) check_per_bound(moldyn,&dist_ij);
1138
1139         d_ij=v3_norm(&dist_ij);
1140
1141         /* save for use in 3bp */
1142         exchange->dist_ij=dist_ij; /* <- needed ? */
1143         exchange->d_ij=d_ij;
1144
1145         /* constants */
1146         if(num==aj->bnum) {
1147                 S=params->S[num];
1148                 R=params->R[num];
1149                 A=params->A[num];
1150                 lambda=params->lambda[num];
1151                 /* more constants depending of atoms i and j, needed in 3bp */
1152                 params->exchange.B=&(params->B[num]);
1153                 params->exchange.mu=&(params->mu[num]);
1154                 mu=params->mu[num];
1155                 params->exchange.chi=1.0;
1156         }
1157         else {
1158                 S=params->Smixed;
1159                 R=params->Rmixed;
1160                 A=params->Amixed;
1161                 lambda=params->lambda_m;
1162                 /* more constants depending of atoms i and j, needed in 3bp */
1163                 params->exchange.B=&(params->Bmixed);
1164                 params->exchange.mu=&(params->mu_m);
1165                 mu=params->mu_m;
1166                 params->exchange.chi=params->chi;
1167         }
1168
1169         if(d_ij>S)
1170                 return 0;
1171
1172         f_r=A*exp(-lambda*d_ij);
1173         df_r=-lambda*f_r/d_ij;
1174
1175         /* f_a, df_a calc + save for 3bp use */
1176         exchange->f_a=-B*exp(-mu*d_ij);
1177         exchange->df_a=-mu*exchange->f_a/d_ij;
1178
1179         if(d_ij<R) {
1180                 /* f_c = 1, df_c = 0 */
1181                 f_c=1.0;
1182                 df_c=0.0;
1183                 v3_scale(&force,&dist_ij,df_r);
1184         }
1185         else {
1186                 s_r=S-R;
1187                 arg=M_PI*(d_ij-R)/s_r;
1188                 f_c=0.5+0.5*cos(arg);
1189                 df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij));
1190                 scale=df_c*f_r+df_r*f_c;
1191                 v3_scale(&force,&dist_ij,scale);
1192         }
1193
1194         /* add forces */
1195         v3_add(&(ai->f),&(ai->f),&force);
1196         /* energy is 0.5 f_r f_c ... */
1197         moldyn->energy+=(0.5*f_r*f_c);
1198
1199         /* save for use in 3bp */
1200         exchange->f_c=f_c;
1201         exchange->df_c=df_c;
1202
1203         /* enable the run of 3bp function */
1204         exchange->run3bp=1;
1205
1206         return 0;
1207 }
1208
1209 /* tersoff 3 body part */
1210
1211 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
1212
1213         t_tersoff_mult_params *params;
1214         t_tersoff_exchange *exchange;
1215         t_3dvec dist_ij,dist_ik,dist_jk;
1216         t_3dvec temp,force;
1217         double R,S,s_r;
1218         double d_ij,d_ij2,d_ik,d_jk;
1219         double f_c,df_c,b_ij,f_a,df_a;
1220         double f_c_ik,df_c_ik,arg;
1221         double scale;
1222         double chi;
1223         double n,c,d,h,beta,betan;
1224         double c2,d2,c2d2;
1225         double numer,denom;
1226         double theta,cos_theta,sin_theta;
1227         double d_theta,d_theta1,d_theta2;
1228         double h_cos,h_cos2,d2_h_cos2;
1229         double frac1,bracket1,bracket2,bracket2_n_1,bracket2_n;
1230         double bracket3,bracket3_pow_1,bracket3_pow;
1231         int num;
1232
1233         params=moldyn->pot3b_params;
1234         num=ai->bnum;
1235         exchange=&(params->exchange);
1236
1237         if(!(exchange->run3bp))
1238                 return 0;
1239
1240         /*
1241          * we need: f_c, d_fc, b_ij, db_ij, f_a, df_a
1242          *
1243          * we got f_c, df_c, f_a, df_a from 2bp calculation
1244          */
1245
1246         d_ij=exchange->d_ij;
1247         d_ij2=exchange->d_ij2;
1248
1249         f_a=params->exchange.f_a;
1250         df_a=params->exchange.df_a;
1251
1252         /* d_ij is <= S, as we didn't return so far! */
1253
1254         /*
1255          * calc of b_ij (scalar) and db_ij (vector)
1256          *
1257          * - for b_ij: chi, beta, f_c_ik, w(=1), c, d, h, n, cos_theta
1258          *
1259          * - for db_ij: d_theta, sin_theta, cos_theta, f_c_ik, df_c_ik,
1260          *              w_ik,
1261          *
1262          */
1263
1264
1265         v3_sub(&dist_ik,&(ai->r),&(ak->r));
1266         if(bc) check_per_bound(moldyn,&dist_ik);
1267         d_ik=v3_norm(&dist_ik);
1268
1269         /* constants for f_c_ik calc */
1270         if(num==ak->bnum) {
1271                 R=params->R[num];
1272                 S=params->S[num];
1273         }
1274         else {
1275                 R=params->Rmixed;
1276                 S=params->Smixed;
1277         }
1278
1279         /* calc of f_c_ik */
1280         if(d_ik>S)
1281                 return 0;
1282
1283         if(d_ik<R) {
1284                 /* f_c_ik = 1, df_c_ik = 0 */
1285                 f_c_ik=1.0;
1286                 df_c_ik=0.0;
1287         }
1288         else {
1289                 s_r=S-R;
1290                 arg=M_PI*(d_ik-R)/s_r;
1291                 f_c_ik=0.5+0.5*cos(arg);
1292                 df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik));
1293         }
1294
1295         v3_sub(&dist_jk,&(aj->r),&(ak->r));
1296         if(bc) check_per_bound(moldyn,&dist_jk);
1297         d_jk=v3_norm(&dist_jk);
1298
1299         beta=*(exchange->beta);
1300         betan=exchange->betan;
1301         n=*(exchange->n);
1302         c=*(exchange->c);
1303         d=*(exchange->d);
1304         h=*(exchange->h);
1305         c2=exchange->c2;
1306         d2=exchange->d2;
1307         c2d2=exchange->c2d2;
1308
1309         numer=d_ij2+d_ik*d_ik-d_jk*d_jk;
1310         denom=2*d_ij*d_ik;
1311         cos_theta=numer/denom;
1312         sin_theta=sqrt(1.0-(cos_theta*cos_theta));
1313         theta=acos(cos_theta);
1314         d_theta=(-1.0/sqrt(1.0-cos_theta*cos_theta))/(denom*denom);
1315         d_theta1=2*denom-numer*2*d_ik/d_ij;
1316         d_theta2=2*denom-numer*2*d_ij/d_ik;
1317         d_theta1*=d_theta;
1318         d_theta2*=d_theta;
1319
1320         h_cos=(h-cos_theta);
1321         h_cos2=h_cos*h_cos;
1322         d2_h_cos2=d2-h_cos2;
1323
1324         /* some usefull expressions */
1325         frac1=c2/(d2-h_cos2);
1326         bracket1=1+c2d2-frac1;
1327         bracket2=f_c_ik*bracket1;
1328         bracket2_n_1=pow(bracket2,n-1.0);
1329         bracket2_n=bracket2_n_1*bracket2;
1330         bracket3=1+betan*bracket2_n;
1331         bracket3_pow_1=pow(bracket3,(-1.0/(2.0*n))-1.0);
1332         bracket3_pow=bracket3_pow_1*bracket3;
1333
1334         /* now go on with calc of b_ij and derivation of b_ij */
1335         b_ij=chi*bracket3_pow;
1336
1337         /* derivation of theta */
1338         v3_scale(&force,&dist_ij,d_theta1);
1339         v3_scale(&temp,&dist_ik,d_theta2);
1340         v3_add(&force,&force,&temp);
1341
1342         /* part 1 of derivation of b_ij */
1343         v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac1);
1344
1345         /* part 2 of derivation of b_ij */
1346         v3_scale(&temp,&dist_ik,df_c_ik*bracket1);
1347
1348         /* sum up and scale ... */
1349         v3_add(&temp,&temp,&force);
1350         scale=bracket2_n_1*n*betan*(1+betan*bracket3_pow_1)*chi*(1.0/(2.0*n));
1351         v3_scale(&temp,&temp,scale);
1352
1353         /* now construct an energy and a force out of that */
1354         v3_scale(&temp,&temp,f_a);
1355         v3_scale(&force,&dist_ij,df_a*b_ij);
1356         v3_add(&temp,&temp,&force);
1357         v3_scale(&temp,&temp,f_c);
1358         v3_scale(&force,&dist_ij,df_c*b_ij*f_a);
1359         v3_add(&force,&force,&temp);
1360
1361         /* add forces */
1362         v3_add(&(ai->f),&(ai->f),&force);
1363         /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
1364         moldyn->energy+=(0.25*f_a*b_ij*f_c);
1365
1366         return 0;
1367 }
1368