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 #include "report/report.h"
  20
  21 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
  22
  23         printf("[moldyn] init\n");
  24
  25         memset(moldyn,0,sizeof(t_moldyn));
  26
  27         rand_init(&(moldyn->random),NULL,1);
  28         moldyn->random.status|=RAND_STAT_VERBOSE;
  29
  30         return 0;
  31 }
  32
  33 int moldyn_shutdown(t_moldyn *moldyn) {
  34
  35         printf("[moldyn] shutdown\n");
  36
  37         moldyn_log_shutdown(moldyn);
  38         link_cell_shutdown(moldyn);
  39         rand_close(&(moldyn->random));
  40         free(moldyn->atom);
  41
  42         return 0;
  43 }
  44
  45 int set_int_alg(t_moldyn *moldyn,u8 algo) {
  46
  47         printf("[moldyn] integration algorithm: ");
  48
  49         switch(algo) {
  50                 case MOLDYN_INTEGRATE_VERLET:
  51                         moldyn->integrate=velocity_verlet;
  52                         printf("velocity verlet\n");
  53                         break;
  54                 default:
  55                         printf("unknown integration algorithm: %02x\n",algo);
  56                         printf("unknown\n");
  57                         return -1;
  58         }
  59
  60         return 0;
  61 }
  62
  63 int set_cutoff(t_moldyn *moldyn,double cutoff) {
  64
  65         moldyn->cutoff=cutoff;
  66
  67         printf("[moldyn] cutoff [A]: %f\n",moldyn->cutoff);
  68
  69         return 0;
  70 }
  71
  72 int set_temperature(t_moldyn *moldyn,double t_ref) {
  73
  74         moldyn->t_ref=t_ref;
  75
  76         printf("[moldyn] temperature [K]: %f\n",moldyn->t_ref);
  77
  78         return 0;
  79 }
  80
  81 int set_pressure(t_moldyn *moldyn,double p_ref) {
  82
  83         moldyn->p_ref=p_ref;
  84
  85         printf("[moldyn] pressure [bar]: %f\n",moldyn->p_ref/BAR);
  86
  87         return 0;
  88 }
  89
  90 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
  91
  92         moldyn->pt_scale=(ptype|ttype);
  93         moldyn->t_tc=ttc;
  94         moldyn->p_tc=ptc;
  95
  96         printf("[moldyn] p/t scaling:\n");
  97
  98         printf("  p: %s",ptype?"yes":"no ");
  99         if(ptype)
 100                 printf(" | type: %02x | factor: %f",ptype,ptc);
 101         printf("\n");
 102
 103         printf("  t: %s",ttype?"yes":"no ");
 104         if(ttype)
 105                 printf(" | type: %02x | factor: %f",ttype,ttc);
 106         printf("\n");
 107
 108         return 0;
 109 }
 110
 111 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
 112
 113         moldyn->dim.x=x;
 114         moldyn->dim.y=y;
 115         moldyn->dim.z=z;
 116
 117         moldyn->volume=x*y*z;
 118
 119         if(visualize) {
 120                 moldyn->vis.dim.x=x;
 121                 moldyn->vis.dim.y=y;
 122                 moldyn->vis.dim.z=z;
 123         }
 124
 125         moldyn->dv=0.000001*moldyn->volume;
 126
 127         printf("[moldyn] dimensions in A and A^3 respectively:\n");
 128         printf("  x: %f\n",moldyn->dim.x);
 129         printf("  y: %f\n",moldyn->dim.y);
 130         printf("  z: %f\n",moldyn->dim.z);
 131         printf("  volume: %f\n",moldyn->volume);
 132         printf("  visualize simulation box: %s\n",visualize?"yes":"no");
 133         printf("  delta volume (pressure calc): %f\n",moldyn->dv);
 134
 135         return 0;
 136 }
 137
 138 int set_nn_dist(t_moldyn *moldyn,double dist) {
 139
 140         moldyn->nnd=dist;
 141
 142         return 0;
 143 }
 144
 145 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 146
 147         printf("[moldyn] periodic boundary conditions:\n");
 148
 149         if(x)
 150                 moldyn->status|=MOLDYN_STAT_PBX;
 151
 152         if(y)
 153                 moldyn->status|=MOLDYN_STAT_PBY;
 154
 155         if(z)
 156                 moldyn->status|=MOLDYN_STAT_PBZ;
 157
 158         printf("  x: %s\n",x?"yes":"no");
 159         printf("  y: %s\n",y?"yes":"no");
 160         printf("  z: %s\n",z?"yes":"no");
 161
 162         return 0;
 163 }
 164
 165 int set_potential1b(t_moldyn *moldyn,pf_func1b func) {
 166
 167         moldyn->func1b=func;
 168
 169         return 0;
 170 }
 171
 172 int set_potential2b(t_moldyn *moldyn,pf_func2b func) {
 173
 174         moldyn->func2b=func;
 175
 176         return 0;
 177 }
 178
 179 int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func) {
 180
 181         moldyn->func3b_j1=func;
 182
 183         return 0;
 184 }
 185
 186 int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func) {
 187
 188         moldyn->func3b_j2=func;
 189
 190         return 0;
 191 }
 192
 193 int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func) {
 194
 195         moldyn->func3b_j3=func;
 196
 197         return 0;
 198 }
 199
 200 int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func) {
 201
 202         moldyn->func3b_k1=func;
 203
 204         return 0;
 205 }
 206
 207 int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func) {
 208
 209         moldyn->func3b_k2=func;
 210
 211         return 0;
 212 }
 213
 214 int set_potential_params(t_moldyn *moldyn,void *params) {
 215
 216         moldyn->pot_params=params;
 217
 218         return 0;
 219 }
 220
 221 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
 222
 223         strncpy(moldyn->vlsdir,dir,127);
 224
 225         return 0;
 226 }
 227
 228 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title) {
 229
 230         strncpy(moldyn->rauthor,author,63);
 231         strncpy(moldyn->rtitle,title,63);
 232
 233         return 0;
 234 }
 235
 236 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 237
 238         char filename[128];
 239         int ret;
 240
 241         printf("[moldyn] set log: ");
 242
 243         switch(type) {
 244                 case LOG_TOTAL_ENERGY:
 245                         moldyn->ewrite=timer;
 246                         snprintf(filename,127,"%s/energy",moldyn->vlsdir);
 247                         moldyn->efd=open(filename,
 248                                          O_WRONLY|O_CREAT|O_EXCL,
 249                                          S_IRUSR|S_IWUSR);
 250                         if(moldyn->efd<0) {
 251                                 perror("[moldyn] energy log fd open");
 252                                 return moldyn->efd;
 253                         }
 254                         dprintf(moldyn->efd,"# total energy log file\n");
 255                         printf("total energy (%d)\n",timer);
 256                         break;
 257                 case LOG_TOTAL_MOMENTUM:
 258                         moldyn->mwrite=timer;
 259                         snprintf(filename,127,"%s/momentum",moldyn->vlsdir);
 260                         moldyn->mfd=open(filename,
 261                                          O_WRONLY|O_CREAT|O_EXCL,
 262                                          S_IRUSR|S_IWUSR);
 263                         if(moldyn->mfd<0) {
 264                                 perror("[moldyn] momentum log fd open");
 265                                 return moldyn->mfd;
 266                         }
 267                         dprintf(moldyn->efd,"# total momentum log file\n");
 268                         printf("total momentum (%d)\n",timer);
 269                         break;
 270                 case LOG_PRESSURE:
 271                         moldyn->pwrite=timer;
 272                         snprintf(filename,127,"%s/pressure",moldyn->vlsdir);
 273                         moldyn->pfd=open(filename,
 274                                          O_WRONLY|O_CREAT|O_EXCL,
 275                                          S_IRUSR|S_IWUSR);
 276                         if(moldyn->pfd<0) {
 277                                 perror("[moldyn] pressure log file\n");
 278                                 return moldyn->pfd;
 279                         }
 280                         dprintf(moldyn->pfd,"# pressure log file\n");
 281                         printf("pressure (%d)\n",timer);
 282                         break;
 283                 case LOG_TEMPERATURE:
 284                         moldyn->twrite=timer;
 285                         snprintf(filename,127,"%s/temperature",moldyn->vlsdir);
 286                         moldyn->tfd=open(filename,
 287                                          O_WRONLY|O_CREAT|O_EXCL,
 288                                          S_IRUSR|S_IWUSR);
 289                         if(moldyn->tfd<0) {
 290                                 perror("[moldyn] temperature log file\n");
 291                                 return moldyn->tfd;
 292                         }
 293                         dprintf(moldyn->tfd,"# temperature log file\n");
 294                         printf("temperature (%d)\n",timer);
 295                         break;
 296                 case SAVE_STEP:
 297                         moldyn->swrite=timer;
 298                         printf("save file (%d)\n",timer);
 299                         break;
 300                 case VISUAL_STEP:
 301                         moldyn->vwrite=timer;
 302                         ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
 303                         if(ret<0) {
 304                                 printf("[moldyn] visual init failure\n");
 305                                 return ret;
 306                         }
 307                         printf("visual file (%d)\n",timer);
 308                         break;
 309                 case CREATE_REPORT:
 310                         snprintf(filename,127,"%s/report.tex",moldyn->vlsdir);
 311                         moldyn->rfd=open(filename,
 312                                          O_WRONLY|O_CREAT|O_EXCL,
 313                                          S_IRUSR|S_IWUSR);
 314                         if(moldyn->rfd<0) {
 315                                 perror("[moldyn] report fd open");
 316                                 return moldyn->rfd;
 317                         }
 318                         printf("report -> ");
 319                         if(moldyn->efd) {
 320                                 snprintf(filename,127,"%s/e_plot.scr",
 321                                          moldyn->vlsdir);
 322                                 moldyn->epfd=open(filename,
 323                                                  O_WRONLY|O_CREAT|O_EXCL,
 324                                                  S_IRUSR|S_IWUSR);
 325                                 if(moldyn->epfd<0) {
 326                                         perror("[moldyn] energy plot fd open");
 327                                         return moldyn->epfd;
 328                                 }
 329                                 dprintf(moldyn->epfd,e_plot_script);
 330                                 close(moldyn->epfd);
 331                                 printf("energy ");
 332                         }
 333                         if(moldyn->pfd) {
 334                                 snprintf(filename,127,"%s/pressure_plot.scr",
 335                                          moldyn->vlsdir);
 336                                 moldyn->ppfd=open(filename,
 337                                                   O_WRONLY|O_CREAT|O_EXCL,
 338                                                   S_IRUSR|S_IWUSR);
 339                                 if(moldyn->ppfd<0) {
 340                                         perror("[moldyn] p plot fd open");
 341                                         return moldyn->ppfd;
 342                                 }
 343                                 dprintf(moldyn->ppfd,pressure_plot_script);
 344                                 close(moldyn->ppfd);
 345                                 printf("pressure ");
 346                         }
 347                         if(moldyn->tfd) {
 348                                 snprintf(filename,127,"%s/temperature_plot.scr",
 349                                          moldyn->vlsdir);
 350                                 moldyn->tpfd=open(filename,
 351                                                   O_WRONLY|O_CREAT|O_EXCL,
 352                                                   S_IRUSR|S_IWUSR);
 353                                 if(moldyn->tpfd<0) {
 354                                         perror("[moldyn] t plot fd open");
 355                                         return moldyn->tpfd;
 356                                 }
 357                                 dprintf(moldyn->tpfd,temperature_plot_script);
 358                                 close(moldyn->tpfd);
 359                                 printf("temperature ");
 360                         }
 361                         dprintf(moldyn->rfd,report_start,
 362                                 moldyn->rauthor,moldyn->rtitle);
 363                         printf("\n");
 364                         break;
 365                 default:
 366                         printf("unknown log type: %02x\n",type);
 367                         return -1;
 368         }
 369
 370         return 0;
 371 }
 372
 373 int moldyn_log_shutdown(t_moldyn *moldyn) {
 374
 375         char sc[256];
 376
 377         printf("[moldyn] log shutdown\n");
 378         if(moldyn->efd) {
 379                 close(moldyn->efd);
 380                 if(moldyn->rfd) {
 381                         dprintf(moldyn->rfd,report_energy);
 382                         snprintf(sc,255,"cd %s && gnuplot e_plot.scr",
 383                                  moldyn->vlsdir);
 384                         system(sc);
 385                 }
 386         }
 387         if(moldyn->mfd) close(moldyn->mfd);
 388         if(moldyn->pfd) {
 389                 close(moldyn->pfd);
 390                 if(moldyn->rfd)
 391                         dprintf(moldyn->rfd,report_pressure);
 392                         snprintf(sc,255,"cd %s && gnuplot pressure_plot.scr",
 393                                  moldyn->vlsdir);
 394                         system(sc);
 395         }
 396         if(moldyn->tfd) {
 397                 close(moldyn->tfd);
 398                 if(moldyn->rfd)
 399                         dprintf(moldyn->rfd,report_temperature);
 400                         snprintf(sc,255,"cd %s && gnuplot temperature_plot.scr",
 401                                  moldyn->vlsdir);
 402                         system(sc);
 403         }
 404         if(moldyn->rfd) {
 405                 dprintf(moldyn->rfd,report_end);
 406                 close(moldyn->rfd);
 407                 snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
 408                 system(sc);
 409                 snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
 410                 system(sc);
 411                 snprintf(sc,255,"cd %s && dvipdf report",moldyn->vlsdir);
 412                 system(sc);
 413         }
 414         if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
 415
 416         return 0;
 417 }
 418
 419 /*
 420  * creating lattice functions
 421  */
 422
 423 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 424                    u8 attr,u8 brand,int a,int b,int c) {
 425
 426         int new,count;
 427         int ret;
 428         t_3dvec origin;
 429         void *ptr;
 430         t_atom *atom;
 431
 432         new=a*b*c;
 433         count=moldyn->count;
 434
 435         /* how many atoms do we expect */
 436         if(type==CUBIC) new*=1;
 437         if(type==FCC) new*=4;
 438         if(type==DIAMOND) new*=8;
 439
 440         /* allocate space for atoms */
 441         ptr=realloc(moldyn->atom,(count+new)*sizeof(t_atom));
 442         if(!ptr) {
 443                 perror("[moldyn] realloc (create lattice)");
 444                 return -1;
 445         }
 446         moldyn->atom=ptr;
 447         atom=&(moldyn->atom[count]);
 448
 449         /* no atoms on the boundaries (only reason: it looks better!) */
 450         origin.x=0.5*lc;
 451         origin.y=0.5*lc;
 452         origin.z=0.5*lc;
 453
 454         switch(type) {
 455                 case CUBIC:
 456                         set_nn_dist(moldyn,lc);
 457                         ret=cubic_init(a,b,c,lc,atom,&origin);
 458                         break;
 459                 case FCC:
 460                         v3_scale(&origin,&origin,0.5);
 461                         set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
 462                         ret=fcc_init(a,b,c,lc,atom,&origin);
 463                         break;
 464                 case DIAMOND:
 465                         v3_scale(&origin,&origin,0.25);
 466                         set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
 467                         ret=diamond_init(a,b,c,lc,atom,&origin);
 468                         break;
 469                 default:
 470                         printf("unknown lattice type (%02x)\n",type);
 471                         return -1;
 472         }
 473
 474         /* debug */
 475         if(ret!=new) {
 476                 printf("[moldyn] creating lattice failed\n");
 477                 printf("  amount of atoms\n");
 478                 printf("  - expected: %d\n",new);
 479                 printf("  - created: %d\n",ret);
 480                 return -1;
 481         }
 482
 483         moldyn->count+=new;
 484         printf("[moldyn] created lattice with %d atoms\n",new);
 485
 486         for(ret=0;ret<new;ret++) {
 487                 atom[ret].element=element;
 488                 atom[ret].mass=mass;
 489                 atom[ret].attr=attr;
 490                 atom[ret].brand=brand;
 491                 atom[ret].tag=count+ret;
 492                 check_per_bound(moldyn,&(atom[ret].r));
 493         }
 494
 495         return ret;
 496 }
 497
 498 /* cubic init */
 499 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 500
 501         int count;
 502         t_3dvec r;
 503         int i,j,k;
 504         t_3dvec o;
 505
 506         count=0;
 507         if(origin)
 508                 v3_copy(&o,origin);
 509         else
 510                 v3_zero(&o);
 511
 512         r.x=o.x;
 513         for(i=0;i<a;i++) {
 514                 r.y=o.y;
 515                 for(j=0;j<b;j++) {
 516                         r.z=o.z;
 517                         for(k=0;k<c;k++) {
 518                                 v3_copy(&(atom[count].r),&r);
 519                                 count+=1;
 520                                 r.z+=lc;
 521                         }
 522                         r.y+=lc;
 523                 }
 524                 r.x+=lc;
 525         }
 526
 527         for(i=0;i<count;i++) {
 528                 atom[i].r.x-=(a*lc)/2.0;
 529                 atom[i].r.y-=(b*lc)/2.0;
 530                 atom[i].r.z-=(c*lc)/2.0;
 531         }
 532
 533         return count;
 534 }
 535
 536 /* fcc lattice init */
 537 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 538
 539         int count;
 540         int i,j,k,l;
 541         t_3dvec o,r,n;
 542         t_3dvec basis[3];
 543
 544         count=0;
 545         if(origin)
 546                 v3_copy(&o,origin);
 547         else
 548                 v3_zero(&o);
 549
 550         /* construct the basis */
 551         memset(basis,0,3*sizeof(t_3dvec));
 552         basis[0].x=0.5*lc;
 553         basis[0].y=0.5*lc;
 554         basis[1].x=0.5*lc;
 555         basis[1].z=0.5*lc;
 556         basis[2].y=0.5*lc;
 557         basis[2].z=0.5*lc;
 558
 559         /* fill up the room */
 560         r.x=o.x;
 561         for(i=0;i<a;i++) {
 562                 r.y=o.y;
 563                 for(j=0;j<b;j++) {
 564                         r.z=o.z;
 565                         for(k=0;k<c;k++) {
 566                                 /* first atom */
 567                                 v3_copy(&(atom[count].r),&r);
 568                                 count+=1;
 569                                 r.z+=lc;
 570                                 /* the three face centered atoms */
 571                                 for(l=0;l<3;l++) {
 572                                         v3_add(&n,&r,&basis[l]);
 573                                         v3_copy(&(atom[count].r),&n);
 574                                         count+=1;
 575                                 }
 576                         }
 577                         r.y+=lc;
 578                 }
 579                 r.x+=lc;
 580         }
 581
 582         /* coordinate transformation */
 583         for(i=0;i<count;i++) {
 584                 atom[i].r.x-=(a*lc)/2.0;
 585                 atom[i].r.y-=(b*lc)/2.0;
 586                 atom[i].r.z-=(c*lc)/2.0;
 587         }
 588
 589         return count;
 590 }
 591
 592 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 593
 594         int count;
 595         t_3dvec o;
 596
 597         count=fcc_init(a,b,c,lc,atom,origin);
 598
 599         o.x=0.25*lc;
 600         o.y=0.25*lc;
 601         o.z=0.25*lc;
 602
 603         if(origin) v3_add(&o,&o,origin);
 604
 605         count+=fcc_init(a,b,c,lc,&atom[count],&o);
 606
 607         return count;
 608 }
 609
 610 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
 611              t_3dvec *r,t_3dvec *v) {
 612
 613         t_atom *atom;
 614         void *ptr;
 615         int count;
 616
 617         atom=moldyn->atom;
 618         count=(moldyn->count)++;
 619
 620         ptr=realloc(atom,(count+1)*sizeof(t_atom));
 621         if(!ptr) {
 622                 perror("[moldyn] realloc (add atom)");
 623                 return -1;
 624         }
 625         moldyn->atom=ptr;
 626
 627         atom=moldyn->atom;
 628         atom[count].r=*r;
 629         atom[count].v=*v;
 630         atom[count].element=element;
 631         atom[count].mass=mass;
 632         atom[count].brand=brand;
 633         atom[count].tag=count;
 634         atom[count].attr=attr;
 635
 636         return 0;
 637 }
 638
 639 int destroy_atoms(t_moldyn *moldyn) {
 640
 641         if(moldyn->atom) free(moldyn->atom);
 642
 643         return 0;
 644 }
 645
 646 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 647
 648         /*
 649          * - gaussian distribution of velocities
 650          * - zero total momentum
 651          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 652          */
 653
 654         int i;
 655         double v,sigma;
 656         t_3dvec p_total,delta;
 657         t_atom *atom;
 658         t_random *random;
 659
 660         atom=moldyn->atom;
 661         random=&(moldyn->random);
 662
 663         printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
 664
 665         /* gaussian distribution of velocities */
 666         v3_zero(&p_total);
 667         for(i=0;i<moldyn->count;i++) {
 668                 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
 669                 /* x direction */
 670                 v=sigma*rand_get_gauss(random);
 671                 atom[i].v.x=v;
 672                 p_total.x+=atom[i].mass*v;
 673                 /* y direction */
 674                 v=sigma*rand_get_gauss(random);
 675                 atom[i].v.y=v;
 676                 p_total.y+=atom[i].mass*v;
 677                 /* z direction */
 678                 v=sigma*rand_get_gauss(random);
 679                 atom[i].v.z=v;
 680                 p_total.z+=atom[i].mass*v;
 681         }
 682
 683         /* zero total momentum */
 684         v3_scale(&p_total,&p_total,1.0/moldyn->count);
 685         for(i=0;i<moldyn->count;i++) {
 686                 v3_scale(&delta,&p_total,1.0/atom[i].mass);
 687                 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
 688         }
 689
 690         /* velocity scaling */
 691         scale_velocity(moldyn,equi_init);
 692
 693         return 0;
 694 }
 695
 696 double temperature_calc(t_moldyn *moldyn) {
 697
 698         /* assume up to date kinetic energy, which is 3/2 N k_B T */
 699
 700         moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
 701         moldyn->t_sum+=moldyn->t;
 702         moldyn->mean_t=moldyn->t_sum/moldyn->total_steps;
 703
 704         return moldyn->t;
 705 }
 706
 707 double get_temperature(t_moldyn *moldyn) {
 708
 709         return moldyn->t;
 710 }
 711
 712 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 713
 714         int i;
 715         double e,scale;
 716         t_atom *atom;
 717         int count;
 718
 719         atom=moldyn->atom;
 720
 721         /*
 722          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 723          */
 724
 725         /* get kinetic energy / temperature & count involved atoms */
 726         e=0.0;
 727         count=0;
 728         for(i=0;i<moldyn->count;i++) {
 729                 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
 730                         e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
 731                         count+=1;
 732                 }
 733         }
 734         e*=0.5;
 735         if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
 736         else return 0;  /* no atoms involved in scaling! */
 737
 738         /* (temporary) hack for e,t = 0 */
 739         if(e==0.0) {
 740         moldyn->t=0.0;
 741                 if(moldyn->t_ref!=0.0) {
 742                         thermal_init(moldyn,equi_init);
 743                         return 0;
 744                 }
 745                 else
 746                         return 0; /* no scaling needed */
 747         }
 748
 749
 750         /* get scaling factor */
 751         scale=moldyn->t_ref/moldyn->t;
 752         if(equi_init&TRUE)
 753                 scale*=2.0;
 754         else
 755                 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
 756                         scale=1.0+(scale-1.0)/moldyn->t_tc;
 757         scale=sqrt(scale);
 758
 759         /* velocity scaling */
 760         for(i=0;i<moldyn->count;i++) {
 761                 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
 762                         v3_scale(&(atom[i].v),&(atom[i].v),scale);
 763         }
 764
 765         return 0;
 766 }
 767
 768 double ideal_gas_law_pressure(t_moldyn *moldyn) {
 769
 770         double p;
 771
 772         p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
 773
 774         return p;
 775 }
 776
 777 double pressure_calc(t_moldyn *moldyn) {
 778
 779         int i;
 780         double v;
 781         t_virial *virial;
 782
 783         /*
 784          * PV = NkT + <W>
 785          * W = 1/3 sum_i f_i r_i
 786          * virial = sum_i f_i r_i
 787          *
 788          * => P = (2 Ekin + virial) / (3V)
 789          */
 790
 791         v=0.0;
 792         for(i=0;i<moldyn->count;i++) {
 793                 virial=&(moldyn->atom[i].virial);
 794                 v+=(virial->xx+virial->yy+virial->zz);
 795         }
 796
 797         /* assume up to date kinetic energy */
 798         moldyn->p=2.0*moldyn->ekin+v;
 799         moldyn->p/=(3.0*moldyn->volume);
 800         moldyn->p_sum+=moldyn->p;
 801         moldyn->mean_p=moldyn->p_sum/moldyn->total_steps;
 802
 803         /* pressure from 'absolute coordinates' virial */
 804         virial=&(moldyn->virial);
 805         v=virial->xx+virial->yy+virial->zz;
 806         moldyn->gp=2.0*moldyn->ekin+v;
 807         moldyn->gp/=(3.0*moldyn->volume);
 808         moldyn->gp_sum+=moldyn->gp;
 809         moldyn->mean_gp=moldyn->gp_sum/moldyn->total_steps;
 810
 811         return moldyn->p;
 812 }
 813
 814 double thermodynamic_pressure_calc(t_moldyn *moldyn) {
 815
 816         t_3dvec dim,*tp;
 817         double u,p;
 818         double scale,dv;
 819         t_atom *store;
 820
 821         /*
 822          * dU = - p dV
 823          *
 824          * => p = - dU/dV
 825          *
 826          * dV: dx,y,z = 0.001 x,y,z
 827          */
 828
 829         scale=1.00000000000001;
 830 printf("\n\nP-DEBUG:\n");
 831
 832         tp=&(moldyn->tp);
 833         store=malloc(moldyn->count*sizeof(t_atom));
 834         if(store==NULL) {
 835                 printf("[moldyn] allocating store mem failed\n");
 836                 return -1;
 837         }
 838
 839         /* save unscaled potential energy + atom/dim configuration */
 840         u=moldyn->energy;
 841         memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
 842         dim=moldyn->dim;
 843
 844         /* derivative with respect to x direction */
 845         scale_dim(moldyn,scale,TRUE,0,0);
 846         scale_atoms(moldyn,scale,TRUE,0,0);
 847         dv=0.00000000000001*moldyn->dim.x*moldyn->dim.y*moldyn->dim.z;
 848         link_cell_shutdown(moldyn);
 849         link_cell_init(moldyn,QUIET);
 850         potential_force_calc(moldyn);
 851         tp->x=(moldyn->energy-u)/dv;
 852         p=tp->x*tp->x;
 853
 854         /* restore atomic configuration + dim */
 855         memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
 856         moldyn->dim=dim;
 857
 858         /* derivative with respect to y direction */
 859         scale_dim(moldyn,scale,0,TRUE,0);
 860         scale_atoms(moldyn,scale,0,TRUE,0);
 861         dv=0.00000000000001*moldyn->dim.y*moldyn->dim.x*moldyn->dim.z;
 862         link_cell_shutdown(moldyn);
 863         link_cell_init(moldyn,QUIET);
 864         potential_force_calc(moldyn);
 865         tp->y=(moldyn->energy-u)/dv;
 866         p+=tp->y*tp->y;
 867
 868         /* restore atomic configuration + dim */
 869         memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
 870         moldyn->dim=dim;
 871
 872         /* derivative with respect to z direction */
 873         scale_dim(moldyn,scale,0,0,TRUE);
 874         scale_atoms(moldyn,scale,0,0,TRUE);
 875         dv=0.00000000000001*moldyn->dim.z*moldyn->dim.x*moldyn->dim.y;
 876         link_cell_shutdown(moldyn);
 877         link_cell_init(moldyn,QUIET);
 878         potential_force_calc(moldyn);
 879         tp->z=(moldyn->energy-u)/dv;
 880         p+=tp->z*tp->z;
 881
 882         /* restore atomic configuration + dim */
 883         memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
 884         moldyn->dim=dim;
 885
 886         /* restore energy */
 887         moldyn->energy=u;
 888
 889         link_cell_shutdown(moldyn);
 890         link_cell_init(moldyn,QUIET);
 891
 892         return sqrt(p);
 893 }
 894
 895 double get_pressure(t_moldyn *moldyn) {
 896
 897         return moldyn->p;
 898
 899 }
 900
 901 int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
 902
 903         t_3dvec *dim;
 904
 905         dim=&(moldyn->dim);
 906
 907         if(x) dim->x*=scale;
 908         if(y) dim->y*=scale;
 909         if(z) dim->z*=scale;
 910
 911         return 0;
 912 }
 913
 914 int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
 915
 916         int i;
 917         t_3dvec *r;
 918
 919         for(i=0;i<moldyn->count;i++) {
 920                 r=&(moldyn->atom[i].r);
 921                 if(x) r->x*=scale;
 922                 if(y) r->y*=scale;
 923                 if(z) r->z*=scale;
 924         }
 925
 926         return 0;
 927 }
 928
 929 int scale_volume(t_moldyn *moldyn) {
 930
 931         t_3dvec *dim,*vdim;
 932         double scale;
 933         t_linkcell *lc;
 934
 935         vdim=&(moldyn->vis.dim);
 936         dim=&(moldyn->dim);
 937         lc=&(moldyn->lc);
 938
 939         /* scaling factor */
 940         if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
 941                 scale=1.0-(moldyn->p_ref-moldyn->p)/moldyn->p_tc;
 942                 scale=pow(scale,ONE_THIRD);
 943         }
 944         else {
 945                 scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
 946         }
 947 moldyn->debug=scale;
 948
 949         /* scale the atoms and dimensions */
 950         scale_atoms(moldyn,scale,TRUE,TRUE,TRUE);
 951         scale_dim(moldyn,scale,TRUE,TRUE,TRUE);
 952
 953         /* visualize dimensions */
 954         if(vdim->x!=0) {
 955                 vdim->x=dim->x;
 956                 vdim->y=dim->y;
 957                 vdim->z=dim->z;
 958         }
 959
 960         /* recalculate scaled volume */
 961         moldyn->volume=dim->x*dim->y*dim->z;
 962
 963         /* adjust/reinit linkcell */
 964         if(((int)(dim->x/moldyn->cutoff)!=lc->nx)||
 965            ((int)(dim->y/moldyn->cutoff)!=lc->ny)||
 966            ((int)(dim->z/moldyn->cutoff)!=lc->nx)) {
 967                 link_cell_shutdown(moldyn);
 968                 link_cell_init(moldyn,QUIET);
 969         } else {
 970                 lc->x*=scale;
 971                 lc->y*=scale;
 972                 lc->z*=scale;
 973         }
 974
 975         return 0;
 976
 977 }
 978
 979 double e_kin_calc(t_moldyn *moldyn) {
 980
 981         int i;
 982         t_atom *atom;
 983
 984         atom=moldyn->atom;
 985         moldyn->ekin=0.0;
 986
 987         for(i=0;i<moldyn->count;i++)
 988                 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 989
 990         return moldyn->ekin;
 991 }
 992
 993 double get_total_energy(t_moldyn *moldyn) {
 994
 995         return(moldyn->ekin+moldyn->energy);
 996 }
 997
 998 t_3dvec get_total_p(t_moldyn *moldyn) {
 999
1000         t_3dvec p,p_total;
1001         int i;
1002         t_atom *atom;
1003
1004         atom=moldyn->atom;
1005
1006         v3_zero(&p_total);
1007         for(i=0;i<moldyn->count;i++) {
1008                 v3_scale(&p,&(atom[i].v),atom[i].mass);
1009                 v3_add(&p_total,&p_total,&p);
1010         }
1011
1012         return p_total;
1013 }
1014
1015 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
1016
1017         double tau;
1018
1019         /* nn_dist is the nearest neighbour distance */
1020
1021         tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
1022
1023         return tau;
1024 }
1025
1026 /*
1027  * numerical tricks
1028  */
1029
1030 /* linked list / cell method */
1031
1032 int link_cell_init(t_moldyn *moldyn,u8 vol) {
1033
1034         t_linkcell *lc;
1035         int i;
1036
1037         lc=&(moldyn->lc);
1038
1039         /* partitioning the md cell */
1040         lc->nx=moldyn->dim.x/moldyn->cutoff;
1041         lc->x=moldyn->dim.x/lc->nx;
1042         lc->ny=moldyn->dim.y/moldyn->cutoff;
1043         lc->y=moldyn->dim.y/lc->ny;
1044         lc->nz=moldyn->dim.z/moldyn->cutoff;
1045         lc->z=moldyn->dim.z/lc->nz;
1046
1047         lc->cells=lc->nx*lc->ny*lc->nz;
1048         lc->subcell=malloc(lc->cells*sizeof(t_list));
1049
1050         if(lc->cells<27)
1051                 printf("[moldyn] FATAL: less then 27 subcells!\n");
1052
1053         if(vol) {
1054                 printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
1055                 printf("  x: %d x %f A\n",lc->nx,lc->x);
1056                 printf("  y: %d x %f A\n",lc->ny,lc->y);
1057                 printf("  z: %d x %f A\n",lc->nz,lc->z);
1058         }
1059
1060         for(i=0;i<lc->cells;i++)
1061                 list_init_f(&(lc->subcell[i]));
1062
1063         link_cell_update(moldyn);
1064
1065         return 0;
1066 }
1067
1068 int link_cell_update(t_moldyn *moldyn) {
1069
1070         int count,i,j,k;
1071         int nx,ny;
1072         t_atom *atom;
1073         t_linkcell *lc;
1074         double x,y,z;
1075
1076         atom=moldyn->atom;
1077         lc=&(moldyn->lc);
1078
1079         nx=lc->nx;
1080         ny=lc->ny;
1081
1082         x=moldyn->dim.x/2;
1083         y=moldyn->dim.y/2;
1084         z=moldyn->dim.z/2;
1085
1086         for(i=0;i<lc->cells;i++)
1087                 list_destroy_f(&(lc->subcell[i]));
1088
1089         for(count=0;count<moldyn->count;count++) {
1090                 i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
1091                 j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
1092                 k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
1093                 list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
1094                                      &(atom[count]));
1095         }
1096
1097         return 0;
1098 }
1099
1100 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
1101
1102         t_linkcell *lc;
1103         int a;
1104         int count1,count2;
1105         int ci,cj,ck;
1106         int nx,ny,nz;
1107         int x,y,z;
1108         u8 bx,by,bz;
1109
1110         lc=&(moldyn->lc);
1111         nx=lc->nx;
1112         ny=lc->ny;
1113         nz=lc->nz;
1114         count1=1;
1115         count2=27;
1116         a=nx*ny;
1117
1118         cell[0]=lc->subcell[i+j*nx+k*a];
1119         for(ci=-1;ci<=1;ci++) {
1120                 bx=0;
1121                 x=i+ci;
1122                 if((x<0)||(x>=nx)) {
1123                         x=(x+nx)%nx;
1124                         bx=1;
1125                 }
1126                 for(cj=-1;cj<=1;cj++) {
1127                         by=0;
1128                         y=j+cj;
1129                         if((y<0)||(y>=ny)) {
1130                                 y=(y+ny)%ny;
1131                                 by=1;
1132                         }
1133                         for(ck=-1;ck<=1;ck++) {
1134                                 bz=0;
1135                                 z=k+ck;
1136                                 if((z<0)||(z>=nz)) {
1137                                         z=(z+nz)%nz;
1138                                         bz=1;
1139                                 }
1140                                 if(!(ci|cj|ck)) continue;
1141                                 if(bx|by|bz) {
1142                                         cell[--count2]=lc->subcell[x+y*nx+z*a];
1143                                 }
1144                                 else {
1145                                         cell[count1++]=lc->subcell[x+y*nx+z*a];
1146                                 }
1147                         }
1148                 }
1149         }
1150
1151         lc->dnlc=count1;
1152
1153         return count1;
1154 }
1155
1156 int link_cell_shutdown(t_moldyn *moldyn) {
1157
1158         int i;
1159         t_linkcell *lc;
1160
1161         lc=&(moldyn->lc);
1162
1163         for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
1164                 list_destroy_f(&(moldyn->lc.subcell[i]));
1165
1166         free(lc->subcell);
1167
1168         return 0;
1169 }
1170
1171 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
1172
1173         int count;
1174         void *ptr;
1175         t_moldyn_schedule *schedule;
1176
1177         schedule=&(moldyn->schedule);
1178         count=++(schedule->total_sched);
1179
1180         ptr=realloc(schedule->runs,count*sizeof(int));
1181         if(!ptr) {
1182                 perror("[moldyn] realloc (runs)");
1183                 return -1;
1184         }
1185         schedule->runs=ptr;
1186         schedule->runs[count-1]=runs;
1187
1188         ptr=realloc(schedule->tau,count*sizeof(double));
1189         if(!ptr) {
1190                 perror("[moldyn] realloc (tau)");
1191                 return -1;
1192         }
1193         schedule->tau=ptr;
1194         schedule->tau[count-1]=tau;
1195
1196         printf("[moldyn] schedule added:\n");
1197         printf("  number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
1198
1199
1200         return 0;
1201 }
1202
1203 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
1204
1205         moldyn->schedule.hook=hook;
1206         moldyn->schedule.hook_params=hook_params;
1207
1208         return 0;
1209 }
1210
1211 /*
1212  *
1213  * 'integration of newtons equation' - algorithms
1214  *
1215  */
1216
1217 /* start the integration */
1218
1219 int moldyn_integrate(t_moldyn *moldyn) {
1220
1221         int i;
1222         unsigned int e,m,s,v,p,t;
1223         t_3dvec momentum;
1224         t_moldyn_schedule *sched;
1225         t_atom *atom;
1226         int fd;
1227         char dir[128];
1228         double ds;
1229         double energy_scale;
1230         //double tp;
1231
1232         sched=&(moldyn->schedule);
1233         atom=moldyn->atom;
1234
1235         /* initialize linked cell method */
1236         link_cell_init(moldyn,VERBOSE);
1237
1238         /* logging & visualization */
1239         e=moldyn->ewrite;
1240         m=moldyn->mwrite;
1241         s=moldyn->swrite;
1242         v=moldyn->vwrite;
1243         p=moldyn->pwrite;
1244         t=moldyn->twrite;
1245
1246         /* sqaure of some variables */
1247         moldyn->tau_square=moldyn->tau*moldyn->tau;
1248         moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
1249
1250         /* energy scaling factor */
1251         energy_scale=moldyn->count*EV;
1252
1253         /* calculate initial forces */
1254         potential_force_calc(moldyn);
1255
1256         /* some stupid checks before we actually start calculating bullshit */
1257         if(moldyn->cutoff>0.5*moldyn->dim.x)
1258                 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
1259         if(moldyn->cutoff>0.5*moldyn->dim.y)
1260                 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
1261         if(moldyn->cutoff>0.5*moldyn->dim.z)
1262                 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
1263         ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
1264         if(ds>0.05*moldyn->nnd)
1265                 printf("[moldyn] warning: forces too high / tau too small!\n");
1266
1267         /* zero absolute time */
1268         moldyn->time=0.0;
1269         moldyn->total_steps=0;
1270
1271         /* debugging, ignore */
1272         moldyn->debug=0;
1273
1274         /* tell the world */
1275         printf("[moldyn] integration start, go get a coffee ...\n");
1276
1277         /* executing the schedule */
1278         for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
1279
1280                 /* setting amount of runs and finite time step size */
1281                 moldyn->tau=sched->tau[sched->count];
1282                 moldyn->tau_square=moldyn->tau*moldyn->tau;
1283                 moldyn->time_steps=sched->runs[sched->count];
1284
1285         /* integration according to schedule */
1286
1287         for(i=0;i<moldyn->time_steps;i++) {
1288
1289                 /* integration step */
1290                 moldyn->integrate(moldyn);
1291
1292                 /* calculate kinetic energy, temperature and pressure */
1293                 e_kin_calc(moldyn);
1294                 temperature_calc(moldyn);
1295                 pressure_calc(moldyn);
1296                 //tp=thermodynamic_pressure_calc(moldyn);
1297 //printf("thermodynamic p: %f %f %f - %f\n",moldyn->tp.x/BAR,moldyn->tp.y/BAR,moldyn->tp.z/BAR,tp/BAR);
1298
1299                 /* p/t scaling */
1300                 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
1301                         scale_velocity(moldyn,FALSE);
1302                 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
1303                         scale_volume(moldyn);
1304
1305                 /* check for log & visualization */
1306                 if(e) {
1307                         if(!(i%e))
1308                                 dprintf(moldyn->efd,
1309                                         "%f %f %f %f\n",
1310                                         moldyn->time,moldyn->ekin/energy_scale,
1311                                         moldyn->energy/energy_scale,
1312                                         get_total_energy(moldyn)/energy_scale);
1313                 }
1314                 if(m) {
1315                         if(!(i%m)) {
1316                                 momentum=get_total_p(moldyn);
1317                                 dprintf(moldyn->mfd,
1318                                         "%f %f %f %f %f\n",moldyn->time,
1319                                         momentum.x,momentum.y,momentum.z,
1320                                         v3_norm(&momentum));
1321                         }
1322                 }
1323                 if(p) {
1324                         if(!(i%p)) {
1325                                 dprintf(moldyn->pfd,
1326                                         "%f %f %f %f %f\n",moldyn->time,
1327                                          moldyn->p/BAR,moldyn->mean_p/BAR,
1328                                          moldyn->gp/BAR,moldyn->mean_gp/BAR);
1329                         }
1330                 }
1331                 if(t) {
1332                         if(!(i%t)) {
1333                                 dprintf(moldyn->tfd,
1334                                         "%f %f %f\n",
1335                                         moldyn->time,moldyn->t,moldyn->mean_t);
1336                         }
1337                 }
1338                 if(s) {
1339                         if(!(i%s)) {
1340                                 snprintf(dir,128,"%s/s-%07.f.save",
1341                                          moldyn->vlsdir,moldyn->time);
1342                                 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
1343                                 if(fd<0) perror("[moldyn] save fd open");
1344                                 else {
1345                                         write(fd,moldyn,sizeof(t_moldyn));
1346                                         write(fd,moldyn->atom,
1347                                               moldyn->count*sizeof(t_atom));
1348                                 }
1349                                 close(fd);
1350                         }
1351                 }
1352                 if(v) {
1353                         if(!(i%v)) {
1354                                 visual_atoms(&(moldyn->vis),moldyn->time,
1355                                              moldyn->atom,moldyn->count);
1356                         }
1357                 }
1358
1359                 /* display progress */
1360                 if(!(i%10)) {
1361                         printf("\rsched: %d, steps: %d, T: %f, P: %f %f V: %f",
1362                                sched->count,i,
1363                                moldyn->mean_t,
1364                                moldyn->mean_p/BAR,
1365                                moldyn->mean_gp/BAR,
1366                                moldyn->volume);
1367                         fflush(stdout);
1368                 }
1369
1370                 /* increase absolute time */
1371                 moldyn->time+=moldyn->tau;
1372                 moldyn->total_steps+=1;
1373
1374         }
1375
1376                 /* check for hooks */
1377                 if(sched->hook)
1378                         sched->hook(moldyn,sched->hook_params);
1379
1380                 /* get a new info line */
1381                 printf("\n");
1382
1383         }
1384
1385         return 0;
1386 }
1387
1388 /* velocity verlet */
1389
1390 int velocity_verlet(t_moldyn *moldyn) {
1391
1392         int i,count;
1393         double tau,tau_square,h;
1394         t_3dvec delta;
1395         t_atom *atom;
1396
1397         atom=moldyn->atom;
1398         count=moldyn->count;
1399         tau=moldyn->tau;
1400         tau_square=moldyn->tau_square;
1401
1402         for(i=0;i<count;i++) {
1403                 /* new positions */
1404                 h=0.5/atom[i].mass;
1405                 v3_scale(&delta,&(atom[i].v),tau);
1406                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1407                 v3_scale(&delta,&(atom[i].f),h*tau_square);
1408                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1409                 check_per_bound(moldyn,&(atom[i].r));
1410
1411                 /* velocities [actually v(t+tau/2)] */
1412                 v3_scale(&delta,&(atom[i].f),h*tau);
1413                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1414         }
1415
1416         /* neighbour list update */
1417         link_cell_update(moldyn);
1418
1419         /* forces depending on chosen potential */
1420         potential_force_calc(moldyn);
1421
1422         for(i=0;i<count;i++) {
1423                 /* again velocities [actually v(t+tau)] */
1424                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
1425                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1426         }
1427
1428         return 0;
1429 }
1430
1431
1432 /*
1433  *
1434  * potentials & corresponding forces & virial routine
1435  *
1436  */
1437
1438 /* generic potential and force calculation */
1439
1440 int potential_force_calc(t_moldyn *moldyn) {
1441
1442         int i,j,k,count;
1443         t_atom *itom,*jtom,*ktom;
1444         t_virial *virial;
1445         t_linkcell *lc;
1446         t_list neighbour_i[27];
1447         t_list neighbour_i2[27];
1448         t_list *this,*that;
1449         u8 bc_ij,bc_ik;
1450         int dnlc;
1451
1452         count=moldyn->count;
1453         itom=moldyn->atom;
1454         lc=&(moldyn->lc);
1455
1456         /* reset energy */
1457         moldyn->energy=0.0;
1458
1459         /* reset global virial */
1460         memset(&(moldyn->virial),0,sizeof(t_virial));
1461
1462         /* reset force, site energy and virial of every atom */
1463         for(i=0;i<count;i++) {
1464
1465                 /* reset force */
1466                 v3_zero(&(itom[i].f));
1467
1468                 /* reset virial */
1469                 virial=(&(itom[i].virial));
1470                 virial->xx=0.0;
1471                 virial->yy=0.0;
1472                 virial->zz=0.0;
1473                 virial->xy=0.0;
1474                 virial->xz=0.0;
1475                 virial->yz=0.0;
1476
1477                 /* reset site energy */
1478                 itom[i].e=0.0;
1479
1480         }
1481
1482         /* get energy, force and virial of every atom */
1483
1484         /* first (and only) loop over atoms i */
1485         for(i=0;i<count;i++) {
1486
1487                 /* single particle potential/force */
1488                 if(itom[i].attr&ATOM_ATTR_1BP)
1489                         moldyn->func1b(moldyn,&(itom[i]));
1490
1491                 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
1492                         continue;
1493
1494                 /* 2 body pair potential/force */
1495
1496                 link_cell_neighbour_index(moldyn,
1497                                           (itom[i].r.x+moldyn->dim.x/2)/lc->x,
1498                                           (itom[i].r.y+moldyn->dim.y/2)/lc->y,
1499                                           (itom[i].r.z+moldyn->dim.z/2)/lc->z,
1500                                           neighbour_i);
1501
1502                 dnlc=lc->dnlc;
1503
1504                 /* first loop over atoms j */
1505                 if(moldyn->func2b) {
1506                         for(j=0;j<27;j++) {
1507
1508                                 this=&(neighbour_i[j]);
1509                                 list_reset_f(this);
1510
1511                                 if(this->start==NULL)
1512                                         continue;
1513
1514                                 bc_ij=(j<dnlc)?0:1;
1515
1516                                 do {
1517                                         jtom=this->current->data;
1518
1519                                         if(jtom==&(itom[i]))
1520                                                 continue;
1521
1522                                         if((jtom->attr&ATOM_ATTR_2BP)&
1523                                            (itom[i].attr&ATOM_ATTR_2BP)) {
1524                                                 moldyn->func2b(moldyn,
1525                                                                &(itom[i]),
1526                                                                jtom,
1527                                                                bc_ij);
1528                                         }
1529                                 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1530
1531                         }
1532                 }
1533
1534                 /* 3 body potential/force */
1535
1536                 if(!(itom[i].attr&ATOM_ATTR_3BP))
1537                         continue;
1538
1539                 /* copy the neighbour lists */
1540                 memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
1541
1542                 /* second loop over atoms j */
1543                 for(j=0;j<27;j++) {
1544
1545                         this=&(neighbour_i[j]);
1546                         list_reset_f(this);
1547
1548                         if(this->start==NULL)
1549                                 continue;
1550
1551                         bc_ij=(j<dnlc)?0:1;
1552
1553                         do {
1554                                 jtom=this->current->data;
1555
1556                                 if(jtom==&(itom[i]))
1557                                         continue;
1558
1559                                 if(!(jtom->attr&ATOM_ATTR_3BP))
1560                                         continue;
1561
1562                                 /* reset 3bp run */
1563                                 moldyn->run3bp=1;
1564
1565                                 if(moldyn->func3b_j1)
1566                                         moldyn->func3b_j1(moldyn,
1567                                                           &(itom[i]),
1568                                                           jtom,
1569                                                           bc_ij);
1570
1571                                 /* in first j loop, 3bp run can be skipped */
1572                                 if(!(moldyn->run3bp))
1573                                         continue;
1574
1575                                 /* first loop over atoms k */
1576                                 if(moldyn->func3b_k1) {
1577
1578                                 for(k=0;k<27;k++) {
1579
1580                                         that=&(neighbour_i2[k]);
1581                                         list_reset_f(that);
1582
1583                                         if(that->start==NULL)
1584                                                 continue;
1585
1586                                         bc_ik=(k<dnlc)?0:1;
1587
1588                                         do {
1589
1590                                                 ktom=that->current->data;
1591
1592                                                 if(!(ktom->attr&ATOM_ATTR_3BP))
1593                                                         continue;
1594
1595                                                 if(ktom==jtom)
1596                                                         continue;
1597
1598                                                 if(ktom==&(itom[i]))
1599                                                         continue;
1600
1601                                                 moldyn->func3b_k1(moldyn,
1602                                                                   &(itom[i]),
1603                                                                   jtom,
1604                                                                   ktom,
1605                                                                   bc_ik|bc_ij);
1606
1607                                         } while(list_next_f(that)!=\
1608                                                 L_NO_NEXT_ELEMENT);
1609
1610                                 }
1611
1612                                 }
1613
1614                                 if(moldyn->func3b_j2)
1615                                         moldyn->func3b_j2(moldyn,
1616                                                           &(itom[i]),
1617                                                           jtom,
1618                                                           bc_ij);
1619
1620                                 /* second loop over atoms k */
1621                                 if(moldyn->func3b_k2) {
1622
1623                                 for(k=0;k<27;k++) {
1624
1625                                         that=&(neighbour_i2[k]);
1626                                         list_reset_f(that);
1627
1628                                         if(that->start==NULL)
1629                                                 continue;
1630
1631                                         bc_ik=(k<dnlc)?0:1;
1632
1633                                         do {
1634
1635                                                 ktom=that->current->data;
1636
1637                                                 if(!(ktom->attr&ATOM_ATTR_3BP))
1638                                                         continue;
1639
1640                                                 if(ktom==jtom)
1641                                                         continue;
1642
1643                                                 if(ktom==&(itom[i]))
1644                                                         continue;
1645
1646                                                 moldyn->func3b_k2(moldyn,
1647                                                                   &(itom[i]),
1648                                                                   jtom,
1649                                                                   ktom,
1650                                                                   bc_ik|bc_ij);
1651
1652                                         } while(list_next_f(that)!=\
1653                                                 L_NO_NEXT_ELEMENT);
1654
1655                                 }
1656
1657                                 }
1658
1659                                 /* 2bp post function */
1660                                 if(moldyn->func3b_j3) {
1661                                         moldyn->func3b_j3(moldyn,
1662                                                           &(itom[i]),
1663                                                           jtom,bc_ij);
1664                                 }
1665
1666                         } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1667
1668                 }
1669
1670 #ifdef DEBUG
1671         //printf("\n\n");
1672 #endif
1673 #ifdef VDEBUG
1674         printf("\n\n");
1675 #endif
1676
1677         }
1678
1679 #ifdef DEBUG
1680         printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
1681 #endif
1682
1683         /* calculate global virial */
1684         for(i=0;i<count;i++) {
1685                 moldyn->virial.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
1686                 moldyn->virial.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
1687                 moldyn->virial.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
1688                 moldyn->virial.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
1689                 moldyn->virial.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
1690                 moldyn->virial.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
1691         }
1692
1693         return 0;
1694 }
1695
1696 /*
1697  * virial calculation
1698  */
1699
1700 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1701 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1702
1703         a->virial.xx+=f->x*d->x;
1704         a->virial.yy+=f->y*d->y;
1705         a->virial.zz+=f->z*d->z;
1706         a->virial.xy+=f->x*d->y;
1707         a->virial.xz+=f->x*d->z;
1708         a->virial.yz+=f->y*d->z;
1709
1710         return 0;
1711 }
1712
1713 /*
1714  * periodic boundary checking
1715  */
1716
1717 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1718 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1719
1720         double x,y,z;
1721         t_3dvec *dim;
1722
1723         dim=&(moldyn->dim);
1724
1725         x=dim->x/2;
1726         y=dim->y/2;
1727         z=dim->z/2;
1728
1729         if(moldyn->status&MOLDYN_STAT_PBX) {
1730                 if(a->x>=x) a->x-=dim->x;
1731                 else if(-a->x>x) a->x+=dim->x;
1732         }
1733         if(moldyn->status&MOLDYN_STAT_PBY) {
1734                 if(a->y>=y) a->y-=dim->y;
1735                 else if(-a->y>y) a->y+=dim->y;
1736         }
1737         if(moldyn->status&MOLDYN_STAT_PBZ) {
1738                 if(a->z>=z) a->z-=dim->z;
1739                 else if(-a->z>z) a->z+=dim->z;
1740         }
1741
1742         return 0;
1743 }
1744
1745 /*
1746  * debugging / critical check functions
1747  */
1748
1749 int moldyn_bc_check(t_moldyn *moldyn) {
1750
1751         t_atom *atom;
1752         t_3dvec *dim;
1753         int i;
1754         double x;
1755         u8 byte;
1756         int j,k;
1757
1758         atom=moldyn->atom;
1759         dim=&(moldyn->dim);
1760         x=dim->x/2;
1761
1762         for(i=0;i<moldyn->count;i++) {
1763                 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
1764                         printf("FATAL: atom %d: x: %.20f (%.20f)\n",
1765                                i,atom[i].r.x,dim->x/2);
1766                         printf("diagnostic:\n");
1767                         printf("-----------\natom.r.x:\n");
1768                         for(j=0;j<8;j++) {
1769                                 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
1770                                 for(k=0;k<8;k++)
1771                                         printf("%d%c",
1772                                         ((byte)&(1<<k))?1:0,
1773                                         (k==7)?'\n':'|');
1774                         }
1775                         printf("---------------\nx=dim.x/2:\n");
1776                         for(j=0;j<8;j++) {
1777                                 memcpy(&byte,(u8 *)(&x)+j,1);
1778                                 for(k=0;k<8;k++)
1779                                         printf("%d%c",
1780                                         ((byte)&(1<<k))?1:0,
1781                                         (k==7)?'\n':'|');
1782                         }
1783                         if(atom[i].r.x==x) printf("the same!\n");
1784                         else printf("different!\n");
1785                 }
1786                 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
1787                         printf("FATAL: atom %d: y: %.20f (%.20f)\n",
1788                                i,atom[i].r.y,dim->y/2);
1789                 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
1790                         printf("FATAL: atom %d: z: %.20f (%.20f)\n",
1791                                i,atom[i].r.z,dim->z/2);
1792         }
1793
1794         return 0;
1795 }