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,t_3dvec *origin) {
 425
 426         int new,count;
 427         int ret;
 428         t_3dvec orig;
 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         if(!origin) {
 451                 orig.x=0.5*lc;
 452                 orig.y=0.5*lc;
 453                 orig.z=0.5*lc;
 454         }
 455         else {
 456                 orig.x=origin->x;
 457                 orig.y=origin->y;
 458                 orig.z=origin->z;
 459         }
 460
 461         switch(type) {
 462                 case CUBIC:
 463                         set_nn_dist(moldyn,lc);
 464                         ret=cubic_init(a,b,c,lc,atom,&orig);
 465                         break;
 466                 case FCC:
 467                         if(!origin)
 468                                 v3_scale(&orig,&orig,0.5);
 469                         set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
 470                         ret=fcc_init(a,b,c,lc,atom,&orig);
 471                         break;
 472                 case DIAMOND:
 473                         if(!origin)
 474                                 v3_scale(&orig,&orig,0.25);
 475                         set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
 476                         ret=diamond_init(a,b,c,lc,atom,&orig);
 477                         break;
 478                 default:
 479                         printf("unknown lattice type (%02x)\n",type);
 480                         return -1;
 481         }
 482
 483         /* debug */
 484         if(ret!=new) {
 485                 printf("[moldyn] creating lattice failed\n");
 486                 printf("  amount of atoms\n");
 487                 printf("  - expected: %d\n",new);
 488                 printf("  - created: %d\n",ret);
 489                 return -1;
 490         }
 491
 492         moldyn->count+=new;
 493         printf("[moldyn] created lattice with %d atoms\n",new);
 494
 495         for(ret=0;ret<new;ret++) {
 496                 atom[ret].element=element;
 497                 atom[ret].mass=mass;
 498                 atom[ret].attr=attr;
 499                 atom[ret].brand=brand;
 500                 atom[ret].tag=count+ret;
 501                 check_per_bound(moldyn,&(atom[ret].r));
 502         }
 503
 504         return ret;
 505 }
 506
 507 /* cubic init */
 508 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 509
 510         int count;
 511         t_3dvec r;
 512         int i,j,k;
 513         t_3dvec o;
 514
 515         count=0;
 516         if(origin)
 517                 v3_copy(&o,origin);
 518         else
 519                 v3_zero(&o);
 520
 521         r.x=o.x;
 522         for(i=0;i<a;i++) {
 523                 r.y=o.y;
 524                 for(j=0;j<b;j++) {
 525                         r.z=o.z;
 526                         for(k=0;k<c;k++) {
 527                                 v3_copy(&(atom[count].r),&r);
 528                                 count+=1;
 529                                 r.z+=lc;
 530                         }
 531                         r.y+=lc;
 532                 }
 533                 r.x+=lc;
 534         }
 535
 536         for(i=0;i<count;i++) {
 537                 atom[i].r.x-=(a*lc)/2.0;
 538                 atom[i].r.y-=(b*lc)/2.0;
 539                 atom[i].r.z-=(c*lc)/2.0;
 540         }
 541
 542         return count;
 543 }
 544
 545 /* fcc lattice init */
 546 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 547
 548         int count;
 549         int i,j,k,l;
 550         t_3dvec o,r,n;
 551         t_3dvec basis[3];
 552
 553         count=0;
 554         if(origin)
 555                 v3_copy(&o,origin);
 556         else
 557                 v3_zero(&o);
 558
 559         /* construct the basis */
 560         memset(basis,0,3*sizeof(t_3dvec));
 561         basis[0].x=0.5*lc;
 562         basis[0].y=0.5*lc;
 563         basis[1].x=0.5*lc;
 564         basis[1].z=0.5*lc;
 565         basis[2].y=0.5*lc;
 566         basis[2].z=0.5*lc;
 567
 568         /* fill up the room */
 569         r.x=o.x;
 570         for(i=0;i<a;i++) {
 571                 r.y=o.y;
 572                 for(j=0;j<b;j++) {
 573                         r.z=o.z;
 574                         for(k=0;k<c;k++) {
 575                                 /* first atom */
 576                                 v3_copy(&(atom[count].r),&r);
 577                                 count+=1;
 578                                 r.z+=lc;
 579                                 /* the three face centered atoms */
 580                                 for(l=0;l<3;l++) {
 581                                         v3_add(&n,&r,&basis[l]);
 582                                         v3_copy(&(atom[count].r),&n);
 583                                         count+=1;
 584                                 }
 585                         }
 586                         r.y+=lc;
 587                 }
 588                 r.x+=lc;
 589         }
 590
 591         /* coordinate transformation */
 592         for(i=0;i<count;i++) {
 593                 atom[i].r.x-=(a*lc)/2.0;
 594                 atom[i].r.y-=(b*lc)/2.0;
 595                 atom[i].r.z-=(c*lc)/2.0;
 596         }
 597
 598         return count;
 599 }
 600
 601 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 602
 603         int count;
 604         t_3dvec o;
 605
 606         count=fcc_init(a,b,c,lc,atom,origin);
 607
 608         o.x=0.25*lc;
 609         o.y=0.25*lc;
 610         o.z=0.25*lc;
 611
 612         if(origin) v3_add(&o,&o,origin);
 613
 614         count+=fcc_init(a,b,c,lc,&atom[count],&o);
 615
 616         return count;
 617 }
 618
 619 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
 620              t_3dvec *r,t_3dvec *v) {
 621
 622         t_atom *atom;
 623         void *ptr;
 624         int count;
 625
 626         atom=moldyn->atom;
 627         count=(moldyn->count)++;
 628
 629         ptr=realloc(atom,(count+1)*sizeof(t_atom));
 630         if(!ptr) {
 631                 perror("[moldyn] realloc (add atom)");
 632                 return -1;
 633         }
 634         moldyn->atom=ptr;
 635
 636         atom=moldyn->atom;
 637         atom[count].r=*r;
 638         atom[count].v=*v;
 639         atom[count].element=element;
 640         atom[count].mass=mass;
 641         atom[count].brand=brand;
 642         atom[count].tag=count;
 643         atom[count].attr=attr;
 644
 645         return 0;
 646 }
 647
 648 int destroy_atoms(t_moldyn *moldyn) {
 649
 650         if(moldyn->atom) free(moldyn->atom);
 651
 652         return 0;
 653 }
 654
 655 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 656
 657         /*
 658          * - gaussian distribution of velocities
 659          * - zero total momentum
 660          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 661          */
 662
 663         int i;
 664         double v,sigma;
 665         t_3dvec p_total,delta;
 666         t_atom *atom;
 667         t_random *random;
 668
 669         atom=moldyn->atom;
 670         random=&(moldyn->random);
 671
 672         printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
 673
 674         /* gaussian distribution of velocities */
 675         v3_zero(&p_total);
 676         for(i=0;i<moldyn->count;i++) {
 677                 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
 678                 /* x direction */
 679                 v=sigma*rand_get_gauss(random);
 680                 atom[i].v.x=v;
 681                 p_total.x+=atom[i].mass*v;
 682                 /* y direction */
 683                 v=sigma*rand_get_gauss(random);
 684                 atom[i].v.y=v;
 685                 p_total.y+=atom[i].mass*v;
 686                 /* z direction */
 687                 v=sigma*rand_get_gauss(random);
 688                 atom[i].v.z=v;
 689                 p_total.z+=atom[i].mass*v;
 690         }
 691
 692         /* zero total momentum */
 693         v3_scale(&p_total,&p_total,1.0/moldyn->count);
 694         for(i=0;i<moldyn->count;i++) {
 695                 v3_scale(&delta,&p_total,1.0/atom[i].mass);
 696                 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
 697         }
 698
 699         /* velocity scaling */
 700         scale_velocity(moldyn,equi_init);
 701
 702         return 0;
 703 }
 704
 705 double temperature_calc(t_moldyn *moldyn) {
 706
 707         /* assume up to date kinetic energy, which is 3/2 N k_B T */
 708
 709         moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
 710         moldyn->t_sum+=moldyn->t;
 711         moldyn->mean_t=moldyn->t_sum/moldyn->total_steps;
 712
 713         return moldyn->t;
 714 }
 715
 716 double get_temperature(t_moldyn *moldyn) {
 717
 718         return moldyn->t;
 719 }
 720
 721 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 722
 723         int i;
 724         double e,scale;
 725         t_atom *atom;
 726         int count;
 727
 728         atom=moldyn->atom;
 729
 730         /*
 731          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 732          */
 733
 734         /* get kinetic energy / temperature & count involved atoms */
 735         e=0.0;
 736         count=0;
 737         for(i=0;i<moldyn->count;i++) {
 738                 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
 739                         e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
 740                         count+=1;
 741                 }
 742         }
 743         e*=0.5;
 744         if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
 745         else return 0;  /* no atoms involved in scaling! */
 746
 747         /* (temporary) hack for e,t = 0 */
 748         if(e==0.0) {
 749         moldyn->t=0.0;
 750                 if(moldyn->t_ref!=0.0) {
 751                         thermal_init(moldyn,equi_init);
 752                         return 0;
 753                 }
 754                 else
 755                         return 0; /* no scaling needed */
 756         }
 757
 758
 759         /* get scaling factor */
 760         scale=moldyn->t_ref/moldyn->t;
 761         if(equi_init&TRUE)
 762                 scale*=2.0;
 763         else
 764                 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
 765                         scale=1.0+(scale-1.0)/moldyn->t_tc;
 766         scale=sqrt(scale);
 767
 768         /* velocity scaling */
 769         for(i=0;i<moldyn->count;i++) {
 770                 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
 771                         v3_scale(&(atom[i].v),&(atom[i].v),scale);
 772         }
 773
 774         return 0;
 775 }
 776
 777 double ideal_gas_law_pressure(t_moldyn *moldyn) {
 778
 779         double p;
 780
 781         p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
 782
 783         return p;
 784 }
 785
 786 double pressure_calc(t_moldyn *moldyn) {
 787
 788         int i;
 789         double v;
 790         t_virial *virial;
 791
 792         /*
 793          * PV = NkT + <W>
 794          * W = 1/3 sum_i f_i r_i
 795          * virial = sum_i f_i r_i
 796          *
 797          * => P = (2 Ekin + virial) / (3V)
 798          */
 799
 800         v=0.0;
 801         for(i=0;i<moldyn->count;i++) {
 802                 virial=&(moldyn->atom[i].virial);
 803                 v+=(virial->xx+virial->yy+virial->zz);
 804         }
 805
 806         /* virial sum and mean virial */
 807         moldyn->virial_sum+=v;
 808         moldyn->mean_v=moldyn->virial_sum/moldyn->total_steps;
 809
 810         /* assume up to date kinetic energy */
 811         moldyn->p=2.0*moldyn->ekin+moldyn->mean_v;
 812         moldyn->p/=(3.0*moldyn->volume);
 813         moldyn->p_sum+=moldyn->p;
 814         moldyn->mean_p=moldyn->p_sum/moldyn->total_steps;
 815
 816         /* pressure from 'absolute coordinates' virial */
 817         virial=&(moldyn->virial);
 818         v=virial->xx+virial->yy+virial->zz;
 819         moldyn->gp=2.0*moldyn->ekin+v;
 820         moldyn->gp/=(3.0*moldyn->volume);
 821         moldyn->gp_sum+=moldyn->gp;
 822         moldyn->mean_gp=moldyn->gp_sum/moldyn->total_steps;
 823
 824         return moldyn->p;
 825 }
 826
 827 double thermodynamic_pressure_calc(t_moldyn *moldyn) {
 828
 829         t_3dvec dim,*tp;
 830         double u_up,u_down,dv;
 831         double scale,p;
 832         t_atom *store;
 833
 834         /*
 835          * dU = - p dV
 836          *
 837          * => p = - dU/dV
 838          *
 839          */
 840
 841         scale=0.00001;
 842         dv=8*scale*scale*scale*moldyn->volume;
 843
 844         store=malloc(moldyn->count*sizeof(t_atom));
 845         if(store==NULL) {
 846                 printf("[moldyn] allocating store mem failed\n");
 847                 return -1;
 848         }
 849
 850         /* save unscaled potential energy + atom/dim configuration */
 851         memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
 852         dim=moldyn->dim;
 853
 854         /* scale up dimension and atom positions */
 855         scale_dim(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
 856         scale_atoms(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
 857         link_cell_shutdown(moldyn);
 858         link_cell_init(moldyn,QUIET);
 859         potential_force_calc(moldyn);
 860         u_up=moldyn->energy;
 861
 862         /* restore atomic configuration + dim */
 863         memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
 864         moldyn->dim=dim;
 865
 866         /* scale down dimension and atom positions */
 867         scale_dim(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
 868         scale_atoms(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
 869         link_cell_shutdown(moldyn);
 870         link_cell_init(moldyn,QUIET);
 871         potential_force_calc(moldyn);
 872         u_down=moldyn->energy;
 873
 874         /* calculate pressure */
 875         p=-(u_up-u_down)/dv;
 876 printf("-------> %.10f %.10f %f\n",u_up/EV/moldyn->count,u_down/EV/moldyn->count,p/BAR);
 877
 878         /* restore atomic configuration + dim */
 879         memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
 880         moldyn->dim=dim;
 881
 882         /* restore energy */
 883         potential_force_calc(moldyn);
 884
 885         link_cell_shutdown(moldyn);
 886         link_cell_init(moldyn,QUIET);
 887
 888         return p;
 889 }
 890
 891 double get_pressure(t_moldyn *moldyn) {
 892
 893         return moldyn->p;
 894
 895 }
 896
 897 int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
 898
 899         t_3dvec *dim;
 900
 901         dim=&(moldyn->dim);
 902
 903         if(dir==SCALE_UP)
 904                 scale=1.0+scale;
 905
 906         if(dir==SCALE_DOWN)
 907                 scale=1.0-scale;
 908
 909         if(x) dim->x*=scale;
 910         if(y) dim->y*=scale;
 911         if(z) dim->z*=scale;
 912
 913         return 0;
 914 }
 915
 916 int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
 917
 918         int i;
 919         t_3dvec *r;
 920
 921         if(dir==SCALE_UP)
 922                 scale=1.0+scale;
 923
 924         if(dir==SCALE_DOWN)
 925                 scale=1.0-scale;
 926
 927         for(i=0;i<moldyn->count;i++) {
 928                 r=&(moldyn->atom[i].r);
 929                 if(x) r->x*=scale;
 930                 if(y) r->y*=scale;
 931                 if(z) r->z*=scale;
 932         }
 933
 934         return 0;
 935 }
 936
 937 int scale_volume(t_moldyn *moldyn) {
 938
 939         t_3dvec *dim,*vdim;
 940         double scale;
 941         t_linkcell *lc;
 942
 943         vdim=&(moldyn->vis.dim);
 944         dim=&(moldyn->dim);
 945         lc=&(moldyn->lc);
 946
 947         /* scaling factor */
 948         if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
 949                 scale=1.0-(moldyn->p_ref-moldyn->p)/moldyn->p_tc;
 950                 scale=pow(scale,ONE_THIRD);
 951         }
 952         else {
 953                 scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
 954         }
 955 moldyn->debug=scale;
 956
 957         /* scale the atoms and dimensions */
 958         scale_atoms(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
 959         scale_dim(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
 960
 961         /* visualize dimensions */
 962         if(vdim->x!=0) {
 963                 vdim->x=dim->x;
 964                 vdim->y=dim->y;
 965                 vdim->z=dim->z;
 966         }
 967
 968         /* recalculate scaled volume */
 969         moldyn->volume=dim->x*dim->y*dim->z;
 970
 971         /* adjust/reinit linkcell */
 972         if(((int)(dim->x/moldyn->cutoff)!=lc->nx)||
 973            ((int)(dim->y/moldyn->cutoff)!=lc->ny)||
 974            ((int)(dim->z/moldyn->cutoff)!=lc->nx)) {
 975                 link_cell_shutdown(moldyn);
 976                 link_cell_init(moldyn,QUIET);
 977         } else {
 978                 lc->x*=scale;
 979                 lc->y*=scale;
 980                 lc->z*=scale;
 981         }
 982
 983         return 0;
 984
 985 }
 986
 987 double e_kin_calc(t_moldyn *moldyn) {
 988
 989         int i;
 990         t_atom *atom;
 991
 992         atom=moldyn->atom;
 993         moldyn->ekin=0.0;
 994
 995         for(i=0;i<moldyn->count;i++)
 996                 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 997
 998         return moldyn->ekin;
 999 }
1000
1001 double get_total_energy(t_moldyn *moldyn) {
1002
1003         return(moldyn->ekin+moldyn->energy);
1004 }
1005
1006 t_3dvec get_total_p(t_moldyn *moldyn) {
1007
1008         t_3dvec p,p_total;
1009         int i;
1010         t_atom *atom;
1011
1012         atom=moldyn->atom;
1013
1014         v3_zero(&p_total);
1015         for(i=0;i<moldyn->count;i++) {
1016                 v3_scale(&p,&(atom[i].v),atom[i].mass);
1017                 v3_add(&p_total,&p_total,&p);
1018         }
1019
1020         return p_total;
1021 }
1022
1023 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
1024
1025         double tau;
1026
1027         /* nn_dist is the nearest neighbour distance */
1028
1029         tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
1030
1031         return tau;
1032 }
1033
1034 /*
1035  * numerical tricks
1036  */
1037
1038 /* linked list / cell method */
1039
1040 int link_cell_init(t_moldyn *moldyn,u8 vol) {
1041
1042         t_linkcell *lc;
1043         int i;
1044
1045         lc=&(moldyn->lc);
1046
1047         /* partitioning the md cell */
1048         lc->nx=moldyn->dim.x/moldyn->cutoff;
1049         lc->x=moldyn->dim.x/lc->nx;
1050         lc->ny=moldyn->dim.y/moldyn->cutoff;
1051         lc->y=moldyn->dim.y/lc->ny;
1052         lc->nz=moldyn->dim.z/moldyn->cutoff;
1053         lc->z=moldyn->dim.z/lc->nz;
1054
1055         lc->cells=lc->nx*lc->ny*lc->nz;
1056         lc->subcell=malloc(lc->cells*sizeof(t_list));
1057
1058         if(lc->cells<27)
1059                 printf("[moldyn] FATAL: less then 27 subcells!\n");
1060
1061         if(vol) {
1062                 printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
1063                 printf("  x: %d x %f A\n",lc->nx,lc->x);
1064                 printf("  y: %d x %f A\n",lc->ny,lc->y);
1065                 printf("  z: %d x %f A\n",lc->nz,lc->z);
1066         }
1067
1068         for(i=0;i<lc->cells;i++)
1069                 list_init_f(&(lc->subcell[i]));
1070
1071         link_cell_update(moldyn);
1072
1073         return 0;
1074 }
1075
1076 int link_cell_update(t_moldyn *moldyn) {
1077
1078         int count,i,j,k;
1079         int nx,ny;
1080         t_atom *atom;
1081         t_linkcell *lc;
1082         double x,y,z;
1083
1084         atom=moldyn->atom;
1085         lc=&(moldyn->lc);
1086
1087         nx=lc->nx;
1088         ny=lc->ny;
1089
1090         x=moldyn->dim.x/2;
1091         y=moldyn->dim.y/2;
1092         z=moldyn->dim.z/2;
1093
1094         for(i=0;i<lc->cells;i++)
1095                 list_destroy_f(&(lc->subcell[i]));
1096
1097         for(count=0;count<moldyn->count;count++) {
1098                 i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
1099                 j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
1100                 k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
1101                 list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
1102                                      &(atom[count]));
1103         }
1104
1105         return 0;
1106 }
1107
1108 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
1109
1110         t_linkcell *lc;
1111         int a;
1112         int count1,count2;
1113         int ci,cj,ck;
1114         int nx,ny,nz;
1115         int x,y,z;
1116         u8 bx,by,bz;
1117
1118         lc=&(moldyn->lc);
1119         nx=lc->nx;
1120         ny=lc->ny;
1121         nz=lc->nz;
1122         count1=1;
1123         count2=27;
1124         a=nx*ny;
1125
1126         cell[0]=lc->subcell[i+j*nx+k*a];
1127         for(ci=-1;ci<=1;ci++) {
1128                 bx=0;
1129                 x=i+ci;
1130                 if((x<0)||(x>=nx)) {
1131                         x=(x+nx)%nx;
1132                         bx=1;
1133                 }
1134                 for(cj=-1;cj<=1;cj++) {
1135                         by=0;
1136                         y=j+cj;
1137                         if((y<0)||(y>=ny)) {
1138                                 y=(y+ny)%ny;
1139                                 by=1;
1140                         }
1141                         for(ck=-1;ck<=1;ck++) {
1142                                 bz=0;
1143                                 z=k+ck;
1144                                 if((z<0)||(z>=nz)) {
1145                                         z=(z+nz)%nz;
1146                                         bz=1;
1147                                 }
1148                                 if(!(ci|cj|ck)) continue;
1149                                 if(bx|by|bz) {
1150                                         cell[--count2]=lc->subcell[x+y*nx+z*a];
1151                                 }
1152                                 else {
1153                                         cell[count1++]=lc->subcell[x+y*nx+z*a];
1154                                 }
1155                         }
1156                 }
1157         }
1158
1159         lc->dnlc=count1;
1160
1161         return count1;
1162 }
1163
1164 int link_cell_shutdown(t_moldyn *moldyn) {
1165
1166         int i;
1167         t_linkcell *lc;
1168
1169         lc=&(moldyn->lc);
1170
1171         for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
1172                 list_destroy_f(&(moldyn->lc.subcell[i]));
1173
1174         free(lc->subcell);
1175
1176         return 0;
1177 }
1178
1179 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
1180
1181         int count;
1182         void *ptr;
1183         t_moldyn_schedule *schedule;
1184
1185         schedule=&(moldyn->schedule);
1186         count=++(schedule->total_sched);
1187
1188         ptr=realloc(schedule->runs,count*sizeof(int));
1189         if(!ptr) {
1190                 perror("[moldyn] realloc (runs)");
1191                 return -1;
1192         }
1193         schedule->runs=ptr;
1194         schedule->runs[count-1]=runs;
1195
1196         ptr=realloc(schedule->tau,count*sizeof(double));
1197         if(!ptr) {
1198                 perror("[moldyn] realloc (tau)");
1199                 return -1;
1200         }
1201         schedule->tau=ptr;
1202         schedule->tau[count-1]=tau;
1203
1204         printf("[moldyn] schedule added:\n");
1205         printf("  number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
1206
1207
1208         return 0;
1209 }
1210
1211 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
1212
1213         moldyn->schedule.hook=hook;
1214         moldyn->schedule.hook_params=hook_params;
1215
1216         return 0;
1217 }
1218
1219 /*
1220  *
1221  * 'integration of newtons equation' - algorithms
1222  *
1223  */
1224
1225 /* start the integration */
1226
1227 int moldyn_integrate(t_moldyn *moldyn) {
1228
1229         int i;
1230         unsigned int e,m,s,v,p,t;
1231         t_3dvec momentum;
1232         t_moldyn_schedule *sched;
1233         t_atom *atom;
1234         int fd;
1235         char dir[128];
1236         double ds;
1237         double energy_scale;
1238         //double tp;
1239
1240         sched=&(moldyn->schedule);
1241         atom=moldyn->atom;
1242
1243         /* initialize linked cell method */
1244         link_cell_init(moldyn,VERBOSE);
1245
1246         /* logging & visualization */
1247         e=moldyn->ewrite;
1248         m=moldyn->mwrite;
1249         s=moldyn->swrite;
1250         v=moldyn->vwrite;
1251         p=moldyn->pwrite;
1252         t=moldyn->twrite;
1253
1254         /* sqaure of some variables */
1255         moldyn->tau_square=moldyn->tau*moldyn->tau;
1256         moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
1257
1258         /* energy scaling factor */
1259         energy_scale=moldyn->count*EV;
1260
1261         /* calculate initial forces */
1262         potential_force_calc(moldyn);
1263 #ifdef DEBUG
1264 return 0;
1265 #endif
1266
1267         /* some stupid checks before we actually start calculating bullshit */
1268         if(moldyn->cutoff>0.5*moldyn->dim.x)
1269                 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
1270         if(moldyn->cutoff>0.5*moldyn->dim.y)
1271                 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
1272         if(moldyn->cutoff>0.5*moldyn->dim.z)
1273                 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
1274         ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
1275         if(ds>0.05*moldyn->nnd)
1276                 printf("[moldyn] warning: forces too high / tau too small!\n");
1277
1278         /* zero absolute time */
1279         moldyn->time=0.0;
1280         moldyn->total_steps=0;
1281
1282         /* debugging, ignore */
1283         moldyn->debug=0;
1284
1285         /* tell the world */
1286         printf("[moldyn] integration start, go get a coffee ...\n");
1287
1288         /* executing the schedule */
1289         for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
1290
1291                 /* setting amount of runs and finite time step size */
1292                 moldyn->tau=sched->tau[sched->count];
1293                 moldyn->tau_square=moldyn->tau*moldyn->tau;
1294                 moldyn->time_steps=sched->runs[sched->count];
1295
1296         /* integration according to schedule */
1297
1298         for(i=0;i<moldyn->time_steps;i++) {
1299
1300                 /* integration step */
1301                 moldyn->integrate(moldyn);
1302
1303                 /* calculate kinetic energy, temperature and pressure */
1304                 e_kin_calc(moldyn);
1305                 temperature_calc(moldyn);
1306                 pressure_calc(moldyn);
1307                 //tp=thermodynamic_pressure_calc(moldyn);
1308 //printf("thermodynamic p: %f\n",thermodynamic_pressure_calc(moldyn)/BAR);
1309
1310                 /* p/t scaling */
1311                 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
1312                         scale_velocity(moldyn,FALSE);
1313                 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
1314                         scale_volume(moldyn);
1315
1316                 /* check for log & visualization */
1317                 if(e) {
1318                         if(!(i%e))
1319                                 dprintf(moldyn->efd,
1320                                         "%f %f %f %f\n",
1321                                         moldyn->time,moldyn->ekin/energy_scale,
1322                                         moldyn->energy/energy_scale,
1323                                         get_total_energy(moldyn)/energy_scale);
1324                 }
1325                 if(m) {
1326                         if(!(i%m)) {
1327                                 momentum=get_total_p(moldyn);
1328                                 dprintf(moldyn->mfd,
1329                                         "%f %f %f %f %f\n",moldyn->time,
1330                                         momentum.x,momentum.y,momentum.z,
1331                                         v3_norm(&momentum));
1332                         }
1333                 }
1334                 if(p) {
1335                         if(!(i%p)) {
1336                                 dprintf(moldyn->pfd,
1337                                         "%f %f %f %f %f\n",moldyn->time,
1338                                          moldyn->p/BAR,moldyn->mean_p/BAR,
1339                                          moldyn->gp/BAR,moldyn->mean_gp/BAR);
1340                         }
1341                 }
1342                 if(t) {
1343                         if(!(i%t)) {
1344                                 dprintf(moldyn->tfd,
1345                                         "%f %f %f\n",
1346                                         moldyn->time,moldyn->t,moldyn->mean_t);
1347                         }
1348                 }
1349                 if(s) {
1350                         if(!(i%s)) {
1351                                 snprintf(dir,128,"%s/s-%07.f.save",
1352                                          moldyn->vlsdir,moldyn->time);
1353                                 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
1354                                 if(fd<0) perror("[moldyn] save fd open");
1355                                 else {
1356                                         write(fd,moldyn,sizeof(t_moldyn));
1357                                         write(fd,moldyn->atom,
1358                                               moldyn->count*sizeof(t_atom));
1359                                 }
1360                                 close(fd);
1361                         }
1362                 }
1363                 if(v) {
1364                         if(!(i%v)) {
1365                                 visual_atoms(&(moldyn->vis),moldyn->time,
1366                                              moldyn->atom,moldyn->count);
1367                         }
1368                 }
1369
1370                 /* display progress */
1371                 if(!(i%10)) {
1372                         printf("\rsched: %d, steps: %d, T: %f, P: %f %f V: %f",
1373                                sched->count,i,
1374                                moldyn->mean_t,
1375                                moldyn->mean_p/BAR,
1376                                moldyn->mean_gp/BAR,
1377                                moldyn->volume);
1378                         fflush(stdout);
1379                 }
1380
1381                 /* increase absolute time */
1382                 moldyn->time+=moldyn->tau;
1383                 moldyn->total_steps+=1;
1384
1385         }
1386
1387                 /* check for hooks */
1388                 if(sched->hook)
1389                         sched->hook(moldyn,sched->hook_params);
1390
1391                 /* get a new info line */
1392                 printf("\n");
1393
1394         }
1395
1396         return 0;
1397 }
1398
1399 /* velocity verlet */
1400
1401 int velocity_verlet(t_moldyn *moldyn) {
1402
1403         int i,count;
1404         double tau,tau_square,h;
1405         t_3dvec delta;
1406         t_atom *atom;
1407
1408         atom=moldyn->atom;
1409         count=moldyn->count;
1410         tau=moldyn->tau;
1411         tau_square=moldyn->tau_square;
1412
1413         for(i=0;i<count;i++) {
1414                 /* new positions */
1415                 h=0.5/atom[i].mass;
1416                 v3_scale(&delta,&(atom[i].v),tau);
1417                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1418                 v3_scale(&delta,&(atom[i].f),h*tau_square);
1419                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1420                 check_per_bound(moldyn,&(atom[i].r));
1421
1422                 /* velocities [actually v(t+tau/2)] */
1423                 v3_scale(&delta,&(atom[i].f),h*tau);
1424                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1425         }
1426
1427         /* neighbour list update */
1428         link_cell_update(moldyn);
1429
1430         /* forces depending on chosen potential */
1431         potential_force_calc(moldyn);
1432
1433         for(i=0;i<count;i++) {
1434                 /* again velocities [actually v(t+tau)] */
1435                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
1436                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1437         }
1438
1439         return 0;
1440 }
1441
1442
1443 /*
1444  *
1445  * potentials & corresponding forces & virial routine
1446  *
1447  */
1448
1449 /* generic potential and force calculation */
1450
1451 int potential_force_calc(t_moldyn *moldyn) {
1452
1453         int i,j,k,count;
1454         t_atom *itom,*jtom,*ktom;
1455         t_virial *virial;
1456         t_linkcell *lc;
1457         t_list neighbour_i[27];
1458         t_list neighbour_i2[27];
1459         t_list *this,*that;
1460         u8 bc_ij,bc_ik;
1461         int dnlc;
1462
1463         count=moldyn->count;
1464         itom=moldyn->atom;
1465         lc=&(moldyn->lc);
1466
1467         /* reset energy */
1468         moldyn->energy=0.0;
1469
1470         /* reset global virial */
1471         memset(&(moldyn->virial),0,sizeof(t_virial));
1472
1473         /* reset force, site energy and virial of every atom */
1474         for(i=0;i<count;i++) {
1475
1476                 /* reset force */
1477                 v3_zero(&(itom[i].f));
1478
1479                 /* reset virial */
1480                 virial=(&(itom[i].virial));
1481                 virial->xx=0.0;
1482                 virial->yy=0.0;
1483                 virial->zz=0.0;
1484                 virial->xy=0.0;
1485                 virial->xz=0.0;
1486                 virial->yz=0.0;
1487
1488                 /* reset site energy */
1489                 itom[i].e=0.0;
1490
1491         }
1492
1493         /* get energy, force and virial of every atom */
1494
1495         /* first (and only) loop over atoms i */
1496         for(i=0;i<count;i++) {
1497
1498                 /* single particle potential/force */
1499                 if(itom[i].attr&ATOM_ATTR_1BP)
1500                         if(moldyn->func1b)
1501                                 moldyn->func1b(moldyn,&(itom[i]));
1502
1503                 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
1504                         continue;
1505
1506                 /* 2 body pair potential/force */
1507
1508                 link_cell_neighbour_index(moldyn,
1509                                           (itom[i].r.x+moldyn->dim.x/2)/lc->x,
1510                                           (itom[i].r.y+moldyn->dim.y/2)/lc->y,
1511                                           (itom[i].r.z+moldyn->dim.z/2)/lc->z,
1512                                           neighbour_i);
1513
1514                 dnlc=lc->dnlc;
1515
1516                 /* first loop over atoms j */
1517                 if(moldyn->func2b) {
1518                         for(j=0;j<27;j++) {
1519
1520                                 this=&(neighbour_i[j]);
1521                                 list_reset_f(this);
1522
1523                                 if(this->start==NULL)
1524                                         continue;
1525
1526                                 bc_ij=(j<dnlc)?0:1;
1527
1528                                 do {
1529                                         jtom=this->current->data;
1530
1531                                         if(jtom==&(itom[i]))
1532                                                 continue;
1533
1534                                         if((jtom->attr&ATOM_ATTR_2BP)&
1535                                            (itom[i].attr&ATOM_ATTR_2BP)) {
1536                                                 moldyn->func2b(moldyn,
1537                                                                &(itom[i]),
1538                                                                jtom,
1539                                                                bc_ij);
1540                                         }
1541                                 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1542
1543                         }
1544                 }
1545
1546                 /* 3 body potential/force */
1547
1548                 if(!(itom[i].attr&ATOM_ATTR_3BP))
1549                         continue;
1550
1551                 /* copy the neighbour lists */
1552                 memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
1553
1554                 /* second loop over atoms j */
1555                 for(j=0;j<27;j++) {
1556
1557                         this=&(neighbour_i[j]);
1558                         list_reset_f(this);
1559
1560                         if(this->start==NULL)
1561                                 continue;
1562
1563                         bc_ij=(j<dnlc)?0:1;
1564
1565                         do {
1566                                 jtom=this->current->data;
1567
1568                                 if(jtom==&(itom[i]))
1569                                         continue;
1570
1571                                 if(!(jtom->attr&ATOM_ATTR_3BP))
1572                                         continue;
1573
1574                                 /* reset 3bp run */
1575                                 moldyn->run3bp=1;
1576
1577                                 if(moldyn->func3b_j1)
1578                                         moldyn->func3b_j1(moldyn,
1579                                                           &(itom[i]),
1580                                                           jtom,
1581                                                           bc_ij);
1582
1583                                 /* in first j loop, 3bp run can be skipped */
1584                                 if(!(moldyn->run3bp))
1585                                         continue;
1586
1587                                 /* first loop over atoms k */
1588                                 if(moldyn->func3b_k1) {
1589
1590                                 for(k=0;k<27;k++) {
1591
1592                                         that=&(neighbour_i2[k]);
1593                                         list_reset_f(that);
1594
1595                                         if(that->start==NULL)
1596                                                 continue;
1597
1598                                         bc_ik=(k<dnlc)?0:1;
1599
1600                                         do {
1601
1602                                                 ktom=that->current->data;
1603
1604                                                 if(!(ktom->attr&ATOM_ATTR_3BP))
1605                                                         continue;
1606
1607                                                 if(ktom==jtom)
1608                                                         continue;
1609
1610                                                 if(ktom==&(itom[i]))
1611                                                         continue;
1612
1613                                                 moldyn->func3b_k1(moldyn,
1614                                                                   &(itom[i]),
1615                                                                   jtom,
1616                                                                   ktom,
1617                                                                   bc_ik|bc_ij);
1618
1619                                         } while(list_next_f(that)!=\
1620                                                 L_NO_NEXT_ELEMENT);
1621
1622                                 }
1623
1624                                 }
1625
1626                                 if(moldyn->func3b_j2)
1627                                         moldyn->func3b_j2(moldyn,
1628                                                           &(itom[i]),
1629                                                           jtom,
1630                                                           bc_ij);
1631
1632                                 /* second loop over atoms k */
1633                                 if(moldyn->func3b_k2) {
1634
1635                                 for(k=0;k<27;k++) {
1636
1637                                         that=&(neighbour_i2[k]);
1638                                         list_reset_f(that);
1639
1640                                         if(that->start==NULL)
1641                                                 continue;
1642
1643                                         bc_ik=(k<dnlc)?0:1;
1644
1645                                         do {
1646
1647                                                 ktom=that->current->data;
1648
1649                                                 if(!(ktom->attr&ATOM_ATTR_3BP))
1650                                                         continue;
1651
1652                                                 if(ktom==jtom)
1653                                                         continue;
1654
1655                                                 if(ktom==&(itom[i]))
1656                                                         continue;
1657
1658                                                 moldyn->func3b_k2(moldyn,
1659                                                                   &(itom[i]),
1660                                                                   jtom,
1661                                                                   ktom,
1662                                                                   bc_ik|bc_ij);
1663
1664                                         } while(list_next_f(that)!=\
1665                                                 L_NO_NEXT_ELEMENT);
1666
1667                                 }
1668
1669                                 }
1670
1671                                 /* 2bp post function */
1672                                 if(moldyn->func3b_j3) {
1673                                         moldyn->func3b_j3(moldyn,
1674                                                           &(itom[i]),
1675                                                           jtom,bc_ij);
1676                                 }
1677
1678                         } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1679
1680                 }
1681
1682 #ifdef DEBUG
1683         //printf("\n\n");
1684 #endif
1685 #ifdef VDEBUG
1686         printf("\n\n");
1687 #endif
1688
1689         }
1690
1691 #ifdef DEBUG
1692         printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
1693 #endif
1694
1695         /* calculate global virial */
1696         for(i=0;i<count;i++) {
1697                 moldyn->virial.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
1698                 moldyn->virial.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
1699                 moldyn->virial.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
1700                 moldyn->virial.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
1701                 moldyn->virial.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
1702                 moldyn->virial.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
1703         }
1704
1705         return 0;
1706 }
1707
1708 /*
1709  * virial calculation
1710  */
1711
1712 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1713 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1714
1715         a->virial.xx+=f->x*d->x;
1716         a->virial.yy+=f->y*d->y;
1717         a->virial.zz+=f->z*d->z;
1718         a->virial.xy+=f->x*d->y;
1719         a->virial.xz+=f->x*d->z;
1720         a->virial.yz+=f->y*d->z;
1721
1722         return 0;
1723 }
1724
1725 /*
1726  * periodic boundary checking
1727  */
1728
1729 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1730 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1731
1732         double x,y,z;
1733         t_3dvec *dim;
1734
1735         dim=&(moldyn->dim);
1736
1737         x=dim->x/2;
1738         y=dim->y/2;
1739         z=dim->z/2;
1740
1741         if(moldyn->status&MOLDYN_STAT_PBX) {
1742                 if(a->x>=x) a->x-=dim->x;
1743                 else if(-a->x>x) a->x+=dim->x;
1744         }
1745         if(moldyn->status&MOLDYN_STAT_PBY) {
1746                 if(a->y>=y) a->y-=dim->y;
1747                 else if(-a->y>y) a->y+=dim->y;
1748         }
1749         if(moldyn->status&MOLDYN_STAT_PBZ) {
1750                 if(a->z>=z) a->z-=dim->z;
1751                 else if(-a->z>z) a->z+=dim->z;
1752         }
1753
1754         return 0;
1755 }
1756
1757 /*
1758  * debugging / critical check functions
1759  */
1760
1761 int moldyn_bc_check(t_moldyn *moldyn) {
1762
1763         t_atom *atom;
1764         t_3dvec *dim;
1765         int i;
1766         double x;
1767         u8 byte;
1768         int j,k;
1769
1770         atom=moldyn->atom;
1771         dim=&(moldyn->dim);
1772         x=dim->x/2;
1773
1774         for(i=0;i<moldyn->count;i++) {
1775                 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
1776                         printf("FATAL: atom %d: x: %.20f (%.20f)\n",
1777                                i,atom[i].r.x,dim->x/2);
1778                         printf("diagnostic:\n");
1779                         printf("-----------\natom.r.x:\n");
1780                         for(j=0;j<8;j++) {
1781                                 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
1782                                 for(k=0;k<8;k++)
1783                                         printf("%d%c",
1784                                         ((byte)&(1<<k))?1:0,
1785                                         (k==7)?'\n':'|');
1786                         }
1787                         printf("---------------\nx=dim.x/2:\n");
1788                         for(j=0;j<8;j++) {
1789                                 memcpy(&byte,(u8 *)(&x)+j,1);
1790                                 for(k=0;k<8;k++)
1791                                         printf("%d%c",
1792                                         ((byte)&(1<<k))?1:0,
1793                                         (k==7)?'\n':'|');
1794                         }
1795                         if(atom[i].r.x==x) printf("the same!\n");
1796                         else printf("different!\n");
1797                 }
1798                 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
1799                         printf("FATAL: atom %d: y: %.20f (%.20f)\n",
1800                                i,atom[i].r.y,dim->y/2);
1801                 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
1802                         printf("FATAL: atom %d: z: %.20f (%.20f)\n",
1803                                i,atom[i].r.z,dim->z/2);
1804         }
1805
1806         return 0;
1807 }
1808
1809 /*
1810  * postprocessing functions
1811  */
1812 #define LINE_MAX 128
1813 int read_line(int fd,char *line) {
1814
1815         int count,ret;
1816
1817         count=0;
1818
1819         while(1) {
1820                 if(count==LINE_MAX) return count;
1821                 ret=read(fd,line+count,1);
1822                 if(ret<0) return ret;
1823                 if(line[count]=='\n') {
1824                         line[count]='\0';
1825                         return count+1;
1826                 }
1827                 count+=1;
1828         }
1829 }
1830
1831 int calc_fluctuations(double start,double end,char *file) {
1832
1833         int fd;
1834         int count,ret;
1835         double time,pot,kin,tot;
1836         double p_m,k_m,t_m;
1837         double p2_m,k2_m,t2_m;
1838         double p_sum,k_sum,t_sum;
1839         char buf[LINE_MAX];
1840
1841         fd=open(file,O_RDONLY);
1842         if(fd<0) {
1843                 perror("[moldyn] post proc open");
1844                 return fd;
1845         }
1846
1847         /* first calc the averages */
1848         p_sum=0.0;
1849         k_sum=0.0;
1850         t_sum=0.0;
1851         count=0;
1852         while(1) {
1853                 ret=read_line(fd,buf);
1854                 if(ret<0) break;
1855 printf("%d\n",ret);
1856                 if(buf[0]=='#') continue;
1857                 sscanf(buf,"%lf %lf %lf %lf",&time,&kin,&pot,&tot);
1858 printf("%f %f %f %f\n",time,pot,kin,tot);
1859                 //if(time>end) break;
1860                 if((time>=start)&(time<=end)) {
1861                         p_sum+=pot;
1862                         k_sum+=kin;
1863                         t_sum+=tot;
1864                         count+=1;
1865                 }
1866         }
1867
1868         p_m=p_sum/count;
1869         k_m=k_sum/count;
1870         t_m=t_sum/count;
1871
1872         /* mean square fluctuations */
1873         if(lseek(fd,SEEK_SET,0)<0) {
1874                 perror("[moldyn] lseek");
1875                 return -1;
1876         }
1877         count=0;
1878         p_sum=0.0;
1879         k_sum=0.0;
1880         t_sum=0.0;
1881         while(1) {
1882                 ret=read_line(fd,buf);
1883                 if(ret<0) break;
1884                 if(buf[0]=='#') continue;
1885                 sscanf(buf,"%lf %lf %lf %lf",&time,&kin,&pot,&tot);
1886                 if(time>end) break;
1887                 if((time>=start)&(time<=end)) {
1888                         p_sum+=((pot-p_m)*(pot-p_m));
1889                         k_sum+=((kin-k_m)*(kin-k_m));
1890                         t_sum+=((tot-t_m)*(tot-t_m));
1891                         count+=1;
1892                 }
1893         }
1894
1895         p2_m=p_sum/count;
1896         k2_m=k_sum/count;
1897         t2_m=t_sum/count;
1898
1899         printf("[moldyn] fluctuations (%f - %f):\n",start,end);
1900         printf("  - averages   : %f %f %f\n",k_m,p_m,t_m);
1901         printf("  - mean square: %f %f %f\n",k2_m,p2_m,t2_m);
1902
1903         close(fd);
1904
1905         return 0;
1906 }