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 set_avg_skip(t_moldyn *moldyn,int skip) {
 222
 223         printf("[moldyn] skip %d steps before starting average calc\n",skip);
 224         moldyn->avg_skip=skip;
 225
 226         return 0;
 227 }
 228
 229 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
 230
 231         strncpy(moldyn->vlsdir,dir,127);
 232
 233         return 0;
 234 }
 235
 236 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title) {
 237
 238         strncpy(moldyn->rauthor,author,63);
 239         strncpy(moldyn->rtitle,title,63);
 240
 241         return 0;
 242 }
 243
 244 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 245
 246         char filename[128];
 247         int ret;
 248
 249         printf("[moldyn] set log: ");
 250
 251         switch(type) {
 252                 case LOG_TOTAL_ENERGY:
 253                         moldyn->ewrite=timer;
 254                         snprintf(filename,127,"%s/energy",moldyn->vlsdir);
 255                         moldyn->efd=open(filename,
 256                                          O_WRONLY|O_CREAT|O_EXCL,
 257                                          S_IRUSR|S_IWUSR);
 258                         if(moldyn->efd<0) {
 259                                 perror("[moldyn] energy log fd open");
 260                                 return moldyn->efd;
 261                         }
 262                         dprintf(moldyn->efd,"# total energy log file\n");
 263                         printf("total energy (%d)\n",timer);
 264                         break;
 265                 case LOG_TOTAL_MOMENTUM:
 266                         moldyn->mwrite=timer;
 267                         snprintf(filename,127,"%s/momentum",moldyn->vlsdir);
 268                         moldyn->mfd=open(filename,
 269                                          O_WRONLY|O_CREAT|O_EXCL,
 270                                          S_IRUSR|S_IWUSR);
 271                         if(moldyn->mfd<0) {
 272                                 perror("[moldyn] momentum log fd open");
 273                                 return moldyn->mfd;
 274                         }
 275                         dprintf(moldyn->efd,"# total momentum log file\n");
 276                         printf("total momentum (%d)\n",timer);
 277                         break;
 278                 case LOG_PRESSURE:
 279                         moldyn->pwrite=timer;
 280                         snprintf(filename,127,"%s/pressure",moldyn->vlsdir);
 281                         moldyn->pfd=open(filename,
 282                                          O_WRONLY|O_CREAT|O_EXCL,
 283                                          S_IRUSR|S_IWUSR);
 284                         if(moldyn->pfd<0) {
 285                                 perror("[moldyn] pressure log file\n");
 286                                 return moldyn->pfd;
 287                         }
 288                         dprintf(moldyn->pfd,"# pressure log file\n");
 289                         printf("pressure (%d)\n",timer);
 290                         break;
 291                 case LOG_TEMPERATURE:
 292                         moldyn->twrite=timer;
 293                         snprintf(filename,127,"%s/temperature",moldyn->vlsdir);
 294                         moldyn->tfd=open(filename,
 295                                          O_WRONLY|O_CREAT|O_EXCL,
 296                                          S_IRUSR|S_IWUSR);
 297                         if(moldyn->tfd<0) {
 298                                 perror("[moldyn] temperature log file\n");
 299                                 return moldyn->tfd;
 300                         }
 301                         dprintf(moldyn->tfd,"# temperature log file\n");
 302                         printf("temperature (%d)\n",timer);
 303                         break;
 304                 case SAVE_STEP:
 305                         moldyn->swrite=timer;
 306                         printf("save file (%d)\n",timer);
 307                         break;
 308                 case VISUAL_STEP:
 309                         moldyn->vwrite=timer;
 310                         ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
 311                         if(ret<0) {
 312                                 printf("[moldyn] visual init failure\n");
 313                                 return ret;
 314                         }
 315                         printf("visual file (%d)\n",timer);
 316                         break;
 317                 case CREATE_REPORT:
 318                         snprintf(filename,127,"%s/report.tex",moldyn->vlsdir);
 319                         moldyn->rfd=open(filename,
 320                                          O_WRONLY|O_CREAT|O_EXCL,
 321                                          S_IRUSR|S_IWUSR);
 322                         if(moldyn->rfd<0) {
 323                                 perror("[moldyn] report fd open");
 324                                 return moldyn->rfd;
 325                         }
 326                         printf("report -> ");
 327                         if(moldyn->efd) {
 328                                 snprintf(filename,127,"%s/e_plot.scr",
 329                                          moldyn->vlsdir);
 330                                 moldyn->epfd=open(filename,
 331                                                  O_WRONLY|O_CREAT|O_EXCL,
 332                                                  S_IRUSR|S_IWUSR);
 333                                 if(moldyn->epfd<0) {
 334                                         perror("[moldyn] energy plot fd open");
 335                                         return moldyn->epfd;
 336                                 }
 337                                 dprintf(moldyn->epfd,e_plot_script);
 338                                 close(moldyn->epfd);
 339                                 printf("energy ");
 340                         }
 341                         if(moldyn->pfd) {
 342                                 snprintf(filename,127,"%s/pressure_plot.scr",
 343                                          moldyn->vlsdir);
 344                                 moldyn->ppfd=open(filename,
 345                                                   O_WRONLY|O_CREAT|O_EXCL,
 346                                                   S_IRUSR|S_IWUSR);
 347                                 if(moldyn->ppfd<0) {
 348                                         perror("[moldyn] p plot fd open");
 349                                         return moldyn->ppfd;
 350                                 }
 351                                 dprintf(moldyn->ppfd,pressure_plot_script);
 352                                 close(moldyn->ppfd);
 353                                 printf("pressure ");
 354                         }
 355                         if(moldyn->tfd) {
 356                                 snprintf(filename,127,"%s/temperature_plot.scr",
 357                                          moldyn->vlsdir);
 358                                 moldyn->tpfd=open(filename,
 359                                                   O_WRONLY|O_CREAT|O_EXCL,
 360                                                   S_IRUSR|S_IWUSR);
 361                                 if(moldyn->tpfd<0) {
 362                                         perror("[moldyn] t plot fd open");
 363                                         return moldyn->tpfd;
 364                                 }
 365                                 dprintf(moldyn->tpfd,temperature_plot_script);
 366                                 close(moldyn->tpfd);
 367                                 printf("temperature ");
 368                         }
 369                         dprintf(moldyn->rfd,report_start,
 370                                 moldyn->rauthor,moldyn->rtitle);
 371                         printf("\n");
 372                         break;
 373                 default:
 374                         printf("unknown log type: %02x\n",type);
 375                         return -1;
 376         }
 377
 378         return 0;
 379 }
 380
 381 int moldyn_log_shutdown(t_moldyn *moldyn) {
 382
 383         char sc[256];
 384
 385         printf("[moldyn] log shutdown\n");
 386         if(moldyn->efd) {
 387                 close(moldyn->efd);
 388                 if(moldyn->rfd) {
 389                         dprintf(moldyn->rfd,report_energy);
 390                         snprintf(sc,255,"cd %s && gnuplot e_plot.scr",
 391                                  moldyn->vlsdir);
 392                         system(sc);
 393                 }
 394         }
 395         if(moldyn->mfd) close(moldyn->mfd);
 396         if(moldyn->pfd) {
 397                 close(moldyn->pfd);
 398                 if(moldyn->rfd)
 399                         dprintf(moldyn->rfd,report_pressure);
 400                         snprintf(sc,255,"cd %s && gnuplot pressure_plot.scr",
 401                                  moldyn->vlsdir);
 402                         system(sc);
 403         }
 404         if(moldyn->tfd) {
 405                 close(moldyn->tfd);
 406                 if(moldyn->rfd)
 407                         dprintf(moldyn->rfd,report_temperature);
 408                         snprintf(sc,255,"cd %s && gnuplot temperature_plot.scr",
 409                                  moldyn->vlsdir);
 410                         system(sc);
 411         }
 412         if(moldyn->rfd) {
 413                 dprintf(moldyn->rfd,report_end);
 414                 close(moldyn->rfd);
 415                 snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
 416                          moldyn->vlsdir);
 417                 system(sc);
 418                 snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
 419                          moldyn->vlsdir);
 420                 system(sc);
 421                 snprintf(sc,255,"cd %s && dvipdf report >/dev/null 2>&1",
 422                          moldyn->vlsdir);
 423                 system(sc);
 424         }
 425         if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
 426
 427         return 0;
 428 }
 429
 430 /*
 431  * creating lattice functions
 432  */
 433
 434 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 435                    u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin) {
 436
 437         int new,count;
 438         int ret;
 439         t_3dvec orig;
 440         void *ptr;
 441         t_atom *atom;
 442
 443         new=a*b*c;
 444         count=moldyn->count;
 445
 446         /* how many atoms do we expect */
 447         if(type==CUBIC) new*=1;
 448         if(type==FCC) new*=4;
 449         if(type==DIAMOND) new*=8;
 450
 451         /* allocate space for atoms */
 452         ptr=realloc(moldyn->atom,(count+new)*sizeof(t_atom));
 453         if(!ptr) {
 454                 perror("[moldyn] realloc (create lattice)");
 455                 return -1;
 456         }
 457         moldyn->atom=ptr;
 458         atom=&(moldyn->atom[count]);
 459
 460         /* no atoms on the boundaries (only reason: it looks better!) */
 461         if(!origin) {
 462                 orig.x=0.5*lc;
 463                 orig.y=0.5*lc;
 464                 orig.z=0.5*lc;
 465         }
 466         else {
 467                 orig.x=origin->x;
 468                 orig.y=origin->y;
 469                 orig.z=origin->z;
 470         }
 471
 472         switch(type) {
 473                 case CUBIC:
 474                         set_nn_dist(moldyn,lc);
 475                         ret=cubic_init(a,b,c,lc,atom,&orig);
 476                         break;
 477                 case FCC:
 478                         if(!origin)
 479                                 v3_scale(&orig,&orig,0.5);
 480                         set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
 481                         ret=fcc_init(a,b,c,lc,atom,&orig);
 482                         break;
 483                 case DIAMOND:
 484                         if(!origin)
 485                                 v3_scale(&orig,&orig,0.25);
 486                         set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
 487                         ret=diamond_init(a,b,c,lc,atom,&orig);
 488                         break;
 489                 default:
 490                         printf("unknown lattice type (%02x)\n",type);
 491                         return -1;
 492         }
 493
 494         /* debug */
 495         if(ret!=new) {
 496                 printf("[moldyn] creating lattice failed\n");
 497                 printf("  amount of atoms\n");
 498                 printf("  - expected: %d\n",new);
 499                 printf("  - created: %d\n",ret);
 500                 return -1;
 501         }
 502
 503         moldyn->count+=new;
 504         printf("[moldyn] created lattice with %d atoms\n",new);
 505
 506         for(ret=0;ret<new;ret++) {
 507                 atom[ret].element=element;
 508                 atom[ret].mass=mass;
 509                 atom[ret].attr=attr;
 510                 atom[ret].brand=brand;
 511                 atom[ret].tag=count+ret;
 512                 check_per_bound(moldyn,&(atom[ret].r));
 513         }
 514
 515         /* update total system mass */
 516         total_mass_calc(moldyn);
 517
 518         return ret;
 519 }
 520
 521 /* cubic init */
 522 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 523
 524         int count;
 525         t_3dvec r;
 526         int i,j,k;
 527         t_3dvec o;
 528
 529         count=0;
 530         if(origin)
 531                 v3_copy(&o,origin);
 532         else
 533                 v3_zero(&o);
 534
 535         r.x=o.x;
 536         for(i=0;i<a;i++) {
 537                 r.y=o.y;
 538                 for(j=0;j<b;j++) {
 539                         r.z=o.z;
 540                         for(k=0;k<c;k++) {
 541                                 v3_copy(&(atom[count].r),&r);
 542                                 count+=1;
 543                                 r.z+=lc;
 544                         }
 545                         r.y+=lc;
 546                 }
 547                 r.x+=lc;
 548         }
 549
 550         for(i=0;i<count;i++) {
 551                 atom[i].r.x-=(a*lc)/2.0;
 552                 atom[i].r.y-=(b*lc)/2.0;
 553                 atom[i].r.z-=(c*lc)/2.0;
 554         }
 555
 556         return count;
 557 }
 558
 559 /* fcc lattice init */
 560 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 561
 562         int count;
 563         int i,j,k,l;
 564         t_3dvec o,r,n;
 565         t_3dvec basis[3];
 566
 567         count=0;
 568         if(origin)
 569                 v3_copy(&o,origin);
 570         else
 571                 v3_zero(&o);
 572
 573         /* construct the basis */
 574         memset(basis,0,3*sizeof(t_3dvec));
 575         basis[0].x=0.5*lc;
 576         basis[0].y=0.5*lc;
 577         basis[1].x=0.5*lc;
 578         basis[1].z=0.5*lc;
 579         basis[2].y=0.5*lc;
 580         basis[2].z=0.5*lc;
 581
 582         /* fill up the room */
 583         r.x=o.x;
 584         for(i=0;i<a;i++) {
 585                 r.y=o.y;
 586                 for(j=0;j<b;j++) {
 587                         r.z=o.z;
 588                         for(k=0;k<c;k++) {
 589                                 /* first atom */
 590                                 v3_copy(&(atom[count].r),&r);
 591                                 count+=1;
 592                                 r.z+=lc;
 593                                 /* the three face centered atoms */
 594                                 for(l=0;l<3;l++) {
 595                                         v3_add(&n,&r,&basis[l]);
 596                                         v3_copy(&(atom[count].r),&n);
 597                                         count+=1;
 598                                 }
 599                         }
 600                         r.y+=lc;
 601                 }
 602                 r.x+=lc;
 603         }
 604
 605         /* coordinate transformation */
 606         for(i=0;i<count;i++) {
 607                 atom[i].r.x-=(a*lc)/2.0;
 608                 atom[i].r.y-=(b*lc)/2.0;
 609                 atom[i].r.z-=(c*lc)/2.0;
 610         }
 611
 612         return count;
 613 }
 614
 615 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 616
 617         int count;
 618         t_3dvec o;
 619
 620         count=fcc_init(a,b,c,lc,atom,origin);
 621
 622         o.x=0.25*lc;
 623         o.y=0.25*lc;
 624         o.z=0.25*lc;
 625
 626         if(origin) v3_add(&o,&o,origin);
 627
 628         count+=fcc_init(a,b,c,lc,&atom[count],&o);
 629
 630         return count;
 631 }
 632
 633 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
 634              t_3dvec *r,t_3dvec *v) {
 635
 636         t_atom *atom;
 637         void *ptr;
 638         int count;
 639
 640         atom=moldyn->atom;
 641         count=(moldyn->count)++;
 642
 643         ptr=realloc(atom,(count+1)*sizeof(t_atom));
 644         if(!ptr) {
 645                 perror("[moldyn] realloc (add atom)");
 646                 return -1;
 647         }
 648         moldyn->atom=ptr;
 649
 650         atom=moldyn->atom;
 651         atom[count].r=*r;
 652         atom[count].v=*v;
 653         atom[count].element=element;
 654         atom[count].mass=mass;
 655         atom[count].brand=brand;
 656         atom[count].tag=count;
 657         atom[count].attr=attr;
 658
 659         /* update total system mass */
 660         total_mass_calc(moldyn);
 661
 662         return 0;
 663 }
 664
 665 int destroy_atoms(t_moldyn *moldyn) {
 666
 667         if(moldyn->atom) free(moldyn->atom);
 668
 669         return 0;
 670 }
 671
 672 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 673
 674         /*
 675          * - gaussian distribution of velocities
 676          * - zero total momentum
 677          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 678          */
 679
 680         int i;
 681         double v,sigma;
 682         t_3dvec p_total,delta;
 683         t_atom *atom;
 684         t_random *random;
 685
 686         atom=moldyn->atom;
 687         random=&(moldyn->random);
 688
 689         printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
 690
 691         /* gaussian distribution of velocities */
 692         v3_zero(&p_total);
 693         for(i=0;i<moldyn->count;i++) {
 694                 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
 695                 /* x direction */
 696                 v=sigma*rand_get_gauss(random);
 697                 atom[i].v.x=v;
 698                 p_total.x+=atom[i].mass*v;
 699                 /* y direction */
 700                 v=sigma*rand_get_gauss(random);
 701                 atom[i].v.y=v;
 702                 p_total.y+=atom[i].mass*v;
 703                 /* z direction */
 704                 v=sigma*rand_get_gauss(random);
 705                 atom[i].v.z=v;
 706                 p_total.z+=atom[i].mass*v;
 707         }
 708
 709         /* zero total momentum */
 710         v3_scale(&p_total,&p_total,1.0/moldyn->count);
 711         for(i=0;i<moldyn->count;i++) {
 712                 v3_scale(&delta,&p_total,1.0/atom[i].mass);
 713                 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
 714         }
 715
 716         /* velocity scaling */
 717         scale_velocity(moldyn,equi_init);
 718
 719         return 0;
 720 }
 721
 722 double total_mass_calc(t_moldyn *moldyn) {
 723
 724         int i;
 725
 726         moldyn->mass=0.0;
 727
 728         for(i=0;i<moldyn->count;i++)
 729                 moldyn->mass+=moldyn->atom[i].mass;
 730
 731         return moldyn->mass;
 732 }
 733
 734 double temperature_calc(t_moldyn *moldyn) {
 735
 736         /* assume up to date kinetic energy, which is 3/2 N k_B T */
 737
 738         moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
 739
 740         return moldyn->t;
 741 }
 742
 743 double get_temperature(t_moldyn *moldyn) {
 744
 745         return moldyn->t;
 746 }
 747
 748 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 749
 750         int i;
 751         double e,scale;
 752         t_atom *atom;
 753         int count;
 754
 755         atom=moldyn->atom;
 756
 757         /*
 758          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 759          */
 760
 761         /* get kinetic energy / temperature & count involved atoms */
 762         e=0.0;
 763         count=0;
 764         for(i=0;i<moldyn->count;i++) {
 765                 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
 766                         e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
 767                         count+=1;
 768                 }
 769         }
 770         e*=0.5;
 771         if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
 772         else return 0;  /* no atoms involved in scaling! */
 773
 774         /* (temporary) hack for e,t = 0 */
 775         if(e==0.0) {
 776         moldyn->t=0.0;
 777                 if(moldyn->t_ref!=0.0) {
 778                         thermal_init(moldyn,equi_init);
 779                         return 0;
 780                 }
 781                 else
 782                         return 0; /* no scaling needed */
 783         }
 784
 785
 786         /* get scaling factor */
 787         scale=moldyn->t_ref/moldyn->t;
 788         if(equi_init&TRUE)
 789                 scale*=2.0;
 790         else
 791                 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
 792                         scale=1.0+(scale-1.0)/moldyn->t_tc;
 793         scale=sqrt(scale);
 794
 795         /* velocity scaling */
 796         for(i=0;i<moldyn->count;i++) {
 797                 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
 798                         v3_scale(&(atom[i].v),&(atom[i].v),scale);
 799         }
 800
 801         return 0;
 802 }
 803
 804 double ideal_gas_law_pressure(t_moldyn *moldyn) {
 805
 806         double p;
 807
 808         p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
 809
 810         return p;
 811 }
 812
 813 double virial_sum(t_moldyn *moldyn) {
 814
 815         int i;
 816         double v;
 817         t_virial *virial;
 818
 819         /* virial (sum over atom virials) */
 820         v=0.0;
 821         for(i=0;i<moldyn->count;i++) {
 822                 virial=&(moldyn->atom[i].virial);
 823                 v+=(virial->xx+virial->yy+virial->zz);
 824         }
 825         moldyn->virial=v;
 826
 827         /* global virial (absolute coordinates) */
 828         virial=&(moldyn->gvir);
 829         moldyn->gv=virial->xx+virial->yy+virial->zz;
 830
 831         return moldyn->virial;
 832 }
 833
 834 double pressure_calc(t_moldyn *moldyn) {
 835
 836         /*
 837          * PV = NkT + <W>
 838          * with W = 1/3 sum_i f_i r_i (- skipped!)
 839          * virial = sum_i f_i r_i
 840          *
 841          * => P = (2 Ekin + virial) / (3V)
 842          */
 843
 844         /* assume up to date virial & up to date kinetic energy */
 845
 846         /* pressure (atom virials) */
 847         moldyn->p=2.0*moldyn->ekin+moldyn->virial;
 848         moldyn->p/=(3.0*moldyn->volume);
 849
 850         /* pressure (absolute coordinates) */
 851         moldyn->gp=2.0*moldyn->ekin+moldyn->gv;
 852         moldyn->gp/=(3.0*moldyn->volume);
 853
 854         return moldyn->p;
 855 }
 856
 857 int average_and_fluctuation_calc(t_moldyn *moldyn) {
 858
 859         if(moldyn->total_steps<moldyn->avg_skip)
 860                 return 0;
 861
 862         int denom=moldyn->total_steps+1-moldyn->avg_skip;
 863
 864         /* assume up to date energies, temperature, pressure etc */
 865
 866         /* kinetic energy */
 867         moldyn->k_sum+=moldyn->ekin;
 868         moldyn->k2_sum+=(moldyn->ekin*moldyn->ekin);
 869         moldyn->k_avg=moldyn->k_sum/denom;
 870         moldyn->k2_avg=moldyn->k2_sum/denom;
 871         moldyn->dk2_avg=moldyn->k2_avg-(moldyn->k_avg*moldyn->k_avg);
 872
 873         /* potential energy */
 874         moldyn->v_sum+=moldyn->energy;
 875         moldyn->v2_sum+=(moldyn->energy*moldyn->energy);
 876         moldyn->v_avg=moldyn->v_sum/denom;
 877         moldyn->v2_avg=moldyn->v2_sum/denom;
 878         moldyn->dv2_avg=moldyn->v2_avg-(moldyn->v_avg*moldyn->v_avg);
 879
 880         /* temperature */
 881         moldyn->t_sum+=moldyn->t;
 882         moldyn->t_avg=moldyn->t_sum/denom;
 883
 884         /* virial */
 885         moldyn->virial_sum+=moldyn->virial;
 886         moldyn->virial_avg=moldyn->virial_sum/denom;
 887         moldyn->gv_sum+=moldyn->gv;
 888         moldyn->gv_avg=moldyn->gv_sum/denom;
 889
 890         /* pressure */
 891         moldyn->p_sum+=moldyn->p;
 892         moldyn->p_avg=moldyn->p_sum/denom;
 893         moldyn->gp_sum+=moldyn->gp;
 894         moldyn->gp_avg=moldyn->gp_sum/denom;
 895
 896         return 0;
 897 }
 898
 899 int get_heat_capacity(t_moldyn *moldyn) {
 900
 901         double temp2,ighc;
 902
 903         /* averages needed for heat capacity calc */
 904         if(moldyn->total_steps<moldyn->avg_skip)
 905                 return 0;
 906
 907         /* (temperature average)^2 */
 908         temp2=moldyn->t_avg*moldyn->t_avg;
 909         printf("[moldyn] specific heat capacity for T=%f K [J/(kg K)]\n",
 910                moldyn->t_avg);
 911
 912         /* ideal gas contribution */
 913         ighc=3.0*moldyn->count*K_BOLTZMANN/2.0;
 914         printf("  ideal gas contribution: %f\n",
 915                ighc/moldyn->mass*KILOGRAM/JOULE);
 916
 917         /* specific heat for nvt ensemble */
 918         moldyn->c_v_nvt=moldyn->dv2_avg/(K_BOLTZMANN*temp2)+ighc;
 919         moldyn->c_v_nvt/=moldyn->mass;
 920
 921         /* specific heat for nve ensemble */
 922         moldyn->c_v_nve=ighc/(1.0-(moldyn->dv2_avg/(ighc*K_BOLTZMANN*temp2)));
 923         moldyn->c_v_nve/=moldyn->mass;
 924
 925         printf("  NVE: %f\n",moldyn->c_v_nve*KILOGRAM/JOULE);
 926         printf("  NVT: %f\n",moldyn->c_v_nvt*KILOGRAM/JOULE);
 927 printf("  --> <dV2> sim: %f experimental: %f\n",moldyn->dv2_avg,1.5*moldyn->count*K_B2*moldyn->t_avg*moldyn->t_avg*(1.0-1.5*moldyn->count*K_BOLTZMANN/(700*moldyn->mass*JOULE/KILOGRAM)));
 928
 929         return 0;
 930 }
 931
 932 double thermodynamic_pressure_calc(t_moldyn *moldyn) {
 933
 934         t_3dvec dim,*tp;
 935         double u_up,u_down,dv;
 936         double scale,p;
 937         t_atom *store;
 938
 939         /*
 940          * dU = - p dV
 941          *
 942          * => p = - dU/dV
 943          *
 944          */
 945
 946         scale=0.00001;
 947         dv=8*scale*scale*scale*moldyn->volume;
 948
 949         store=malloc(moldyn->count*sizeof(t_atom));
 950         if(store==NULL) {
 951                 printf("[moldyn] allocating store mem failed\n");
 952                 return -1;
 953         }
 954
 955         /* save unscaled potential energy + atom/dim configuration */
 956         memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
 957         dim=moldyn->dim;
 958
 959         /* scale up dimension and atom positions */
 960         scale_dim(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
 961         scale_atoms(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
 962         link_cell_shutdown(moldyn);
 963         link_cell_init(moldyn,QUIET);
 964         potential_force_calc(moldyn);
 965         u_up=moldyn->energy;
 966
 967         /* restore atomic configuration + dim */
 968         memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
 969         moldyn->dim=dim;
 970
 971         /* scale down dimension and atom positions */
 972         scale_dim(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
 973         scale_atoms(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
 974         link_cell_shutdown(moldyn);
 975         link_cell_init(moldyn,QUIET);
 976         potential_force_calc(moldyn);
 977         u_down=moldyn->energy;
 978
 979         /* calculate pressure */
 980         p=-(u_up-u_down)/dv;
 981 printf("-------> %.10f %.10f %f\n",u_up/EV/moldyn->count,u_down/EV/moldyn->count,p/BAR);
 982
 983         /* restore atomic configuration + dim */
 984         memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
 985         moldyn->dim=dim;
 986
 987         /* restore energy */
 988         potential_force_calc(moldyn);
 989
 990         link_cell_shutdown(moldyn);
 991         link_cell_init(moldyn,QUIET);
 992
 993         return p;
 994 }
 995
 996 double get_pressure(t_moldyn *moldyn) {
 997
 998         return moldyn->p;
 999
1000 }
1001
1002 int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
1003
1004         t_3dvec *dim;
1005
1006         dim=&(moldyn->dim);
1007
1008         if(dir==SCALE_UP)
1009                 scale=1.0+scale;
1010
1011         if(dir==SCALE_DOWN)
1012                 scale=1.0-scale;
1013
1014         if(x) dim->x*=scale;
1015         if(y) dim->y*=scale;
1016         if(z) dim->z*=scale;
1017
1018         return 0;
1019 }
1020
1021 int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
1022
1023         int i;
1024         t_3dvec *r;
1025
1026         if(dir==SCALE_UP)
1027                 scale=1.0+scale;
1028
1029         if(dir==SCALE_DOWN)
1030                 scale=1.0-scale;
1031
1032         for(i=0;i<moldyn->count;i++) {
1033                 r=&(moldyn->atom[i].r);
1034                 if(x) r->x*=scale;
1035                 if(y) r->y*=scale;
1036                 if(z) r->z*=scale;
1037         }
1038
1039         return 0;
1040 }
1041
1042 int scale_volume(t_moldyn *moldyn) {
1043
1044         t_3dvec *dim,*vdim;
1045         double scale;
1046         t_linkcell *lc;
1047
1048         vdim=&(moldyn->vis.dim);
1049         dim=&(moldyn->dim);
1050         lc=&(moldyn->lc);
1051
1052         /* scaling factor */
1053         if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
1054                 scale=1.0-(moldyn->p_ref-moldyn->p)/moldyn->p_tc;
1055                 scale=pow(scale,ONE_THIRD);
1056         }
1057         else {
1058                 scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
1059         }
1060 moldyn->debug=scale;
1061
1062         /* scale the atoms and dimensions */
1063         scale_atoms(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
1064         scale_dim(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
1065
1066         /* visualize dimensions */
1067         if(vdim->x!=0) {
1068                 vdim->x=dim->x;
1069                 vdim->y=dim->y;
1070                 vdim->z=dim->z;
1071         }
1072
1073         /* recalculate scaled volume */
1074         moldyn->volume=dim->x*dim->y*dim->z;
1075
1076         /* adjust/reinit linkcell */
1077         if(((int)(dim->x/moldyn->cutoff)!=lc->nx)||
1078            ((int)(dim->y/moldyn->cutoff)!=lc->ny)||
1079            ((int)(dim->z/moldyn->cutoff)!=lc->nx)) {
1080                 link_cell_shutdown(moldyn);
1081                 link_cell_init(moldyn,QUIET);
1082         } else {
1083                 lc->x*=scale;
1084                 lc->y*=scale;
1085                 lc->z*=scale;
1086         }
1087
1088         return 0;
1089
1090 }
1091
1092 double e_kin_calc(t_moldyn *moldyn) {
1093
1094         int i;
1095         t_atom *atom;
1096
1097         atom=moldyn->atom;
1098         moldyn->ekin=0.0;
1099
1100         for(i=0;i<moldyn->count;i++)
1101                 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
1102
1103         return moldyn->ekin;
1104 }
1105
1106 double get_total_energy(t_moldyn *moldyn) {
1107
1108         return(moldyn->ekin+moldyn->energy);
1109 }
1110
1111 t_3dvec get_total_p(t_moldyn *moldyn) {
1112
1113         t_3dvec p,p_total;
1114         int i;
1115         t_atom *atom;
1116
1117         atom=moldyn->atom;
1118
1119         v3_zero(&p_total);
1120         for(i=0;i<moldyn->count;i++) {
1121                 v3_scale(&p,&(atom[i].v),atom[i].mass);
1122                 v3_add(&p_total,&p_total,&p);
1123         }
1124
1125         return p_total;
1126 }
1127
1128 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
1129
1130         double tau;
1131
1132         /* nn_dist is the nearest neighbour distance */
1133
1134         tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
1135
1136         return tau;
1137 }
1138
1139 /*
1140  * numerical tricks
1141  */
1142
1143 /* linked list / cell method */
1144
1145 int link_cell_init(t_moldyn *moldyn,u8 vol) {
1146
1147         t_linkcell *lc;
1148         int i;
1149
1150         lc=&(moldyn->lc);
1151
1152         /* partitioning the md cell */
1153         lc->nx=moldyn->dim.x/moldyn->cutoff;
1154         lc->x=moldyn->dim.x/lc->nx;
1155         lc->ny=moldyn->dim.y/moldyn->cutoff;
1156         lc->y=moldyn->dim.y/lc->ny;
1157         lc->nz=moldyn->dim.z/moldyn->cutoff;
1158         lc->z=moldyn->dim.z/lc->nz;
1159
1160         lc->cells=lc->nx*lc->ny*lc->nz;
1161         lc->subcell=malloc(lc->cells*sizeof(t_list));
1162
1163         if(lc->cells<27)
1164                 printf("[moldyn] FATAL: less then 27 subcells!\n");
1165
1166         if(vol) {
1167                 printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
1168                 printf("  x: %d x %f A\n",lc->nx,lc->x);
1169                 printf("  y: %d x %f A\n",lc->ny,lc->y);
1170                 printf("  z: %d x %f A\n",lc->nz,lc->z);
1171         }
1172
1173         for(i=0;i<lc->cells;i++)
1174                 list_init_f(&(lc->subcell[i]));
1175
1176         link_cell_update(moldyn);
1177
1178         return 0;
1179 }
1180
1181 int link_cell_update(t_moldyn *moldyn) {
1182
1183         int count,i,j,k;
1184         int nx,ny;
1185         t_atom *atom;
1186         t_linkcell *lc;
1187         double x,y,z;
1188
1189         atom=moldyn->atom;
1190         lc=&(moldyn->lc);
1191
1192         nx=lc->nx;
1193         ny=lc->ny;
1194
1195         x=moldyn->dim.x/2;
1196         y=moldyn->dim.y/2;
1197         z=moldyn->dim.z/2;
1198
1199         for(i=0;i<lc->cells;i++)
1200                 list_destroy_f(&(lc->subcell[i]));
1201
1202         for(count=0;count<moldyn->count;count++) {
1203                 i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
1204                 j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
1205                 k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
1206                 list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
1207                                      &(atom[count]));
1208         }
1209
1210         return 0;
1211 }
1212
1213 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
1214
1215         t_linkcell *lc;
1216         int a;
1217         int count1,count2;
1218         int ci,cj,ck;
1219         int nx,ny,nz;
1220         int x,y,z;
1221         u8 bx,by,bz;
1222
1223         lc=&(moldyn->lc);
1224         nx=lc->nx;
1225         ny=lc->ny;
1226         nz=lc->nz;
1227         count1=1;
1228         count2=27;
1229         a=nx*ny;
1230
1231         cell[0]=lc->subcell[i+j*nx+k*a];
1232         for(ci=-1;ci<=1;ci++) {
1233                 bx=0;
1234                 x=i+ci;
1235                 if((x<0)||(x>=nx)) {
1236                         x=(x+nx)%nx;
1237                         bx=1;
1238                 }
1239                 for(cj=-1;cj<=1;cj++) {
1240                         by=0;
1241                         y=j+cj;
1242                         if((y<0)||(y>=ny)) {
1243                                 y=(y+ny)%ny;
1244                                 by=1;
1245                         }
1246                         for(ck=-1;ck<=1;ck++) {
1247                                 bz=0;
1248                                 z=k+ck;
1249                                 if((z<0)||(z>=nz)) {
1250                                         z=(z+nz)%nz;
1251                                         bz=1;
1252                                 }
1253                                 if(!(ci|cj|ck)) continue;
1254                                 if(bx|by|bz) {
1255                                         cell[--count2]=lc->subcell[x+y*nx+z*a];
1256                                 }
1257                                 else {
1258                                         cell[count1++]=lc->subcell[x+y*nx+z*a];
1259                                 }
1260                         }
1261                 }
1262         }
1263
1264         lc->dnlc=count1;
1265
1266         return count1;
1267 }
1268
1269 int link_cell_shutdown(t_moldyn *moldyn) {
1270
1271         int i;
1272         t_linkcell *lc;
1273
1274         lc=&(moldyn->lc);
1275
1276         for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
1277                 list_destroy_f(&(moldyn->lc.subcell[i]));
1278
1279         free(lc->subcell);
1280
1281         return 0;
1282 }
1283
1284 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
1285
1286         int count;
1287         void *ptr;
1288         t_moldyn_schedule *schedule;
1289
1290         schedule=&(moldyn->schedule);
1291         count=++(schedule->total_sched);
1292
1293         ptr=realloc(schedule->runs,count*sizeof(int));
1294         if(!ptr) {
1295                 perror("[moldyn] realloc (runs)");
1296                 return -1;
1297         }
1298         schedule->runs=ptr;
1299         schedule->runs[count-1]=runs;
1300
1301         ptr=realloc(schedule->tau,count*sizeof(double));
1302         if(!ptr) {
1303                 perror("[moldyn] realloc (tau)");
1304                 return -1;
1305         }
1306         schedule->tau=ptr;
1307         schedule->tau[count-1]=tau;
1308
1309         printf("[moldyn] schedule added:\n");
1310         printf("  number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
1311
1312
1313         return 0;
1314 }
1315
1316 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
1317
1318         moldyn->schedule.hook=hook;
1319         moldyn->schedule.hook_params=hook_params;
1320
1321         return 0;
1322 }
1323
1324 /*
1325  *
1326  * 'integration of newtons equation' - algorithms
1327  *
1328  */
1329
1330 /* start the integration */
1331
1332 int moldyn_integrate(t_moldyn *moldyn) {
1333
1334         int i;
1335         unsigned int e,m,s,v,p,t;
1336         t_3dvec momentum;
1337         t_moldyn_schedule *sched;
1338         t_atom *atom;
1339         int fd;
1340         char dir[128];
1341         double ds;
1342         double energy_scale;
1343         //double tp;
1344
1345         sched=&(moldyn->schedule);
1346         atom=moldyn->atom;
1347
1348         /* initialize linked cell method */
1349         link_cell_init(moldyn,VERBOSE);
1350
1351         /* logging & visualization */
1352         e=moldyn->ewrite;
1353         m=moldyn->mwrite;
1354         s=moldyn->swrite;
1355         v=moldyn->vwrite;
1356         p=moldyn->pwrite;
1357         t=moldyn->twrite;
1358
1359         /* sqaure of some variables */
1360         moldyn->tau_square=moldyn->tau*moldyn->tau;
1361         moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
1362
1363         /* energy scaling factor */
1364         energy_scale=moldyn->count*EV;
1365
1366         /* calculate initial forces */
1367         potential_force_calc(moldyn);
1368 #ifdef DEBUG
1369 return 0;
1370 #endif
1371
1372         /* some stupid checks before we actually start calculating bullshit */
1373         if(moldyn->cutoff>0.5*moldyn->dim.x)
1374                 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
1375         if(moldyn->cutoff>0.5*moldyn->dim.y)
1376                 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
1377         if(moldyn->cutoff>0.5*moldyn->dim.z)
1378                 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
1379         ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
1380         if(ds>0.05*moldyn->nnd)
1381                 printf("[moldyn] warning: forces too high / tau too small!\n");
1382
1383         /* zero absolute time */
1384         moldyn->time=0.0;
1385         moldyn->total_steps=0;
1386
1387         /* debugging, ignore */
1388         moldyn->debug=0;
1389
1390         /* tell the world */
1391         printf("[moldyn] integration start, go get a coffee ...\n");
1392
1393         /* executing the schedule */
1394         for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
1395
1396                 /* setting amount of runs and finite time step size */
1397                 moldyn->tau=sched->tau[sched->count];
1398                 moldyn->tau_square=moldyn->tau*moldyn->tau;
1399                 moldyn->time_steps=sched->runs[sched->count];
1400
1401         /* integration according to schedule */
1402
1403         for(i=0;i<moldyn->time_steps;i++) {
1404
1405                 /* integration step */
1406                 moldyn->integrate(moldyn);
1407
1408                 /* calculate kinetic energy, temperature and pressure */
1409                 e_kin_calc(moldyn);
1410                 temperature_calc(moldyn);
1411                 virial_sum(moldyn);
1412                 pressure_calc(moldyn);
1413                 average_and_fluctuation_calc(moldyn);
1414
1415                 /* p/t scaling */
1416                 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
1417                         scale_velocity(moldyn,FALSE);
1418                 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
1419                         scale_volume(moldyn);
1420
1421                 /* check for log & visualization */
1422                 if(e) {
1423                         if(!(i%e))
1424                                 dprintf(moldyn->efd,
1425                                         "%f %f %f %f\n",
1426                                         moldyn->time,moldyn->ekin/energy_scale,
1427                                         moldyn->energy/energy_scale,
1428                                         get_total_energy(moldyn)/energy_scale);
1429                 }
1430                 if(m) {
1431                         if(!(i%m)) {
1432                                 momentum=get_total_p(moldyn);
1433                                 dprintf(moldyn->mfd,
1434                                         "%f %f %f %f %f\n",moldyn->time,
1435                                         momentum.x,momentum.y,momentum.z,
1436                                         v3_norm(&momentum));
1437                         }
1438                 }
1439                 if(p) {
1440                         if(!(i%p)) {
1441                                 dprintf(moldyn->pfd,
1442                                         "%f %f %f %f %f\n",moldyn->time,
1443                                          moldyn->p/BAR,moldyn->p_avg/BAR,
1444                                          moldyn->gp/BAR,moldyn->gp_avg/BAR);
1445                         }
1446                 }
1447                 if(t) {
1448                         if(!(i%t)) {
1449                                 dprintf(moldyn->tfd,
1450                                         "%f %f %f\n",
1451                                         moldyn->time,moldyn->t,moldyn->t_avg);
1452                         }
1453                 }
1454                 if(s) {
1455                         if(!(i%s)) {
1456                                 snprintf(dir,128,"%s/s-%07.f.save",
1457                                          moldyn->vlsdir,moldyn->time);
1458                                 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
1459                                 if(fd<0) perror("[moldyn] save fd open");
1460                                 else {
1461                                         write(fd,moldyn,sizeof(t_moldyn));
1462                                         write(fd,moldyn->atom,
1463                                               moldyn->count*sizeof(t_atom));
1464                                 }
1465                                 close(fd);
1466                         }
1467                 }
1468                 if(v) {
1469                         if(!(i%v)) {
1470                                 visual_atoms(&(moldyn->vis),moldyn->time,
1471                                              moldyn->atom,moldyn->count);
1472                         }
1473                 }
1474
1475                 /* display progress */
1476                 if(!(i%10)) {
1477         printf("\rsched:%d, steps:%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f",
1478                sched->count,i,
1479                moldyn->t,moldyn->t_avg,
1480                moldyn->p_avg/BAR,moldyn->p/BAR,
1481                moldyn->volume);
1482         fflush(stdout);
1483                 }
1484
1485                 /* increase absolute time */
1486                 moldyn->time+=moldyn->tau;
1487                 moldyn->total_steps+=1;
1488
1489         }
1490
1491                 /* check for hooks */
1492                 if(sched->count+1<sched->total_sched)
1493                         if(sched->hook) {
1494                                 printf("\n ## schedule hook %d/%d start ##\n",
1495                                        sched->count+1,sched->total_sched);
1496                                 sched->hook(moldyn,sched->hook_params);
1497                                 printf(" ## schedule hook end ##\n");
1498                         }
1499
1500         }
1501
1502         return 0;
1503 }
1504
1505 /* velocity verlet */
1506
1507 int velocity_verlet(t_moldyn *moldyn) {
1508
1509         int i,count;
1510         double tau,tau_square,h;
1511         t_3dvec delta;
1512         t_atom *atom;
1513
1514         atom=moldyn->atom;
1515         count=moldyn->count;
1516         tau=moldyn->tau;
1517         tau_square=moldyn->tau_square;
1518
1519         for(i=0;i<count;i++) {
1520                 /* new positions */
1521                 h=0.5/atom[i].mass;
1522                 v3_scale(&delta,&(atom[i].v),tau);
1523                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1524                 v3_scale(&delta,&(atom[i].f),h*tau_square);
1525                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1526                 check_per_bound(moldyn,&(atom[i].r));
1527
1528                 /* velocities [actually v(t+tau/2)] */
1529                 v3_scale(&delta,&(atom[i].f),h*tau);
1530                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1531         }
1532
1533         /* neighbour list update */
1534         link_cell_update(moldyn);
1535
1536         /* forces depending on chosen potential */
1537         potential_force_calc(moldyn);
1538
1539         for(i=0;i<count;i++) {
1540                 /* again velocities [actually v(t+tau)] */
1541                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
1542                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1543         }
1544
1545         return 0;
1546 }
1547
1548
1549 /*
1550  *
1551  * potentials & corresponding forces & virial routine
1552  *
1553  */
1554
1555 /* generic potential and force calculation */
1556
1557 int potential_force_calc(t_moldyn *moldyn) {
1558
1559         int i,j,k,count;
1560         t_atom *itom,*jtom,*ktom;
1561         t_virial *virial;
1562         t_linkcell *lc;
1563         t_list neighbour_i[27];
1564         t_list neighbour_i2[27];
1565         t_list *this,*that;
1566         u8 bc_ij,bc_ik;
1567         int dnlc;
1568
1569         count=moldyn->count;
1570         itom=moldyn->atom;
1571         lc=&(moldyn->lc);
1572
1573         /* reset energy */
1574         moldyn->energy=0.0;
1575
1576         /* reset global virial */
1577         memset(&(moldyn->gvir),0,sizeof(t_virial));
1578
1579         /* reset force, site energy and virial of every atom */
1580         for(i=0;i<count;i++) {
1581
1582                 /* reset force */
1583                 v3_zero(&(itom[i].f));
1584
1585                 /* reset virial */
1586                 virial=(&(itom[i].virial));
1587                 virial->xx=0.0;
1588                 virial->yy=0.0;
1589                 virial->zz=0.0;
1590                 virial->xy=0.0;
1591                 virial->xz=0.0;
1592                 virial->yz=0.0;
1593
1594                 /* reset site energy */
1595                 itom[i].e=0.0;
1596
1597         }
1598
1599         /* get energy, force and virial of every atom */
1600
1601         /* first (and only) loop over atoms i */
1602         for(i=0;i<count;i++) {
1603
1604                 /* single particle potential/force */
1605                 if(itom[i].attr&ATOM_ATTR_1BP)
1606                         if(moldyn->func1b)
1607                                 moldyn->func1b(moldyn,&(itom[i]));
1608
1609                 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
1610                         continue;
1611
1612                 /* 2 body pair potential/force */
1613
1614                 link_cell_neighbour_index(moldyn,
1615                                           (itom[i].r.x+moldyn->dim.x/2)/lc->x,
1616                                           (itom[i].r.y+moldyn->dim.y/2)/lc->y,
1617                                           (itom[i].r.z+moldyn->dim.z/2)/lc->z,
1618                                           neighbour_i);
1619
1620                 dnlc=lc->dnlc;
1621
1622                 /* first loop over atoms j */
1623                 if(moldyn->func2b) {
1624                         for(j=0;j<27;j++) {
1625
1626                                 this=&(neighbour_i[j]);
1627                                 list_reset_f(this);
1628
1629                                 if(this->start==NULL)
1630                                         continue;
1631
1632                                 bc_ij=(j<dnlc)?0:1;
1633
1634                                 do {
1635                                         jtom=this->current->data;
1636
1637                                         if(jtom==&(itom[i]))
1638                                                 continue;
1639
1640                                         if((jtom->attr&ATOM_ATTR_2BP)&
1641                                            (itom[i].attr&ATOM_ATTR_2BP)) {
1642                                                 moldyn->func2b(moldyn,
1643                                                                &(itom[i]),
1644                                                                jtom,
1645                                                                bc_ij);
1646                                         }
1647                                 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1648
1649                         }
1650                 }
1651
1652                 /* 3 body potential/force */
1653
1654                 if(!(itom[i].attr&ATOM_ATTR_3BP))
1655                         continue;
1656
1657                 /* copy the neighbour lists */
1658                 memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
1659
1660                 /* second loop over atoms j */
1661                 for(j=0;j<27;j++) {
1662
1663                         this=&(neighbour_i[j]);
1664                         list_reset_f(this);
1665
1666                         if(this->start==NULL)
1667                                 continue;
1668
1669                         bc_ij=(j<dnlc)?0:1;
1670
1671                         do {
1672                                 jtom=this->current->data;
1673
1674                                 if(jtom==&(itom[i]))
1675                                         continue;
1676
1677                                 if(!(jtom->attr&ATOM_ATTR_3BP))
1678                                         continue;
1679
1680                                 /* reset 3bp run */
1681                                 moldyn->run3bp=1;
1682
1683                                 if(moldyn->func3b_j1)
1684                                         moldyn->func3b_j1(moldyn,
1685                                                           &(itom[i]),
1686                                                           jtom,
1687                                                           bc_ij);
1688
1689                                 /* in first j loop, 3bp run can be skipped */
1690                                 if(!(moldyn->run3bp))
1691                                         continue;
1692
1693                                 /* first loop over atoms k */
1694                                 if(moldyn->func3b_k1) {
1695
1696                                 for(k=0;k<27;k++) {
1697
1698                                         that=&(neighbour_i2[k]);
1699                                         list_reset_f(that);
1700
1701                                         if(that->start==NULL)
1702                                                 continue;
1703
1704                                         bc_ik=(k<dnlc)?0:1;
1705
1706                                         do {
1707
1708                                                 ktom=that->current->data;
1709
1710                                                 if(!(ktom->attr&ATOM_ATTR_3BP))
1711                                                         continue;
1712
1713                                                 if(ktom==jtom)
1714                                                         continue;
1715
1716                                                 if(ktom==&(itom[i]))
1717                                                         continue;
1718
1719                                                 moldyn->func3b_k1(moldyn,
1720                                                                   &(itom[i]),
1721                                                                   jtom,
1722                                                                   ktom,
1723                                                                   bc_ik|bc_ij);
1724
1725                                         } while(list_next_f(that)!=\
1726                                                 L_NO_NEXT_ELEMENT);
1727
1728                                 }
1729
1730                                 }
1731
1732                                 if(moldyn->func3b_j2)
1733                                         moldyn->func3b_j2(moldyn,
1734                                                           &(itom[i]),
1735                                                           jtom,
1736                                                           bc_ij);
1737
1738                                 /* second loop over atoms k */
1739                                 if(moldyn->func3b_k2) {
1740
1741                                 for(k=0;k<27;k++) {
1742
1743                                         that=&(neighbour_i2[k]);
1744                                         list_reset_f(that);
1745
1746                                         if(that->start==NULL)
1747                                                 continue;
1748
1749                                         bc_ik=(k<dnlc)?0:1;
1750
1751                                         do {
1752
1753                                                 ktom=that->current->data;
1754
1755                                                 if(!(ktom->attr&ATOM_ATTR_3BP))
1756                                                         continue;
1757
1758                                                 if(ktom==jtom)
1759                                                         continue;
1760
1761                                                 if(ktom==&(itom[i]))
1762                                                         continue;
1763
1764                                                 moldyn->func3b_k2(moldyn,
1765                                                                   &(itom[i]),
1766                                                                   jtom,
1767                                                                   ktom,
1768                                                                   bc_ik|bc_ij);
1769
1770                                         } while(list_next_f(that)!=\
1771                                                 L_NO_NEXT_ELEMENT);
1772
1773                                 }
1774
1775                                 }
1776
1777                                 /* 2bp post function */
1778                                 if(moldyn->func3b_j3) {
1779                                         moldyn->func3b_j3(moldyn,
1780                                                           &(itom[i]),
1781                                                           jtom,bc_ij);
1782                                 }
1783
1784                         } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1785
1786                 }
1787
1788 #ifdef DEBUG
1789         //printf("\n\n");
1790 #endif
1791 #ifdef VDEBUG
1792         printf("\n\n");
1793 #endif
1794
1795         }
1796
1797 #ifdef DEBUG
1798         printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
1799 #endif
1800
1801         /* calculate global virial */
1802         for(i=0;i<count;i++) {
1803                 moldyn->gvir.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
1804                 moldyn->gvir.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
1805                 moldyn->gvir.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
1806                 moldyn->gvir.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
1807                 moldyn->gvir.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
1808                 moldyn->gvir.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
1809         }
1810
1811         return 0;
1812 }
1813
1814 /*
1815  * virial calculation
1816  */
1817
1818 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1819 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1820
1821         a->virial.xx+=f->x*d->x;
1822         a->virial.yy+=f->y*d->y;
1823         a->virial.zz+=f->z*d->z;
1824         a->virial.xy+=f->x*d->y;
1825         a->virial.xz+=f->x*d->z;
1826         a->virial.yz+=f->y*d->z;
1827
1828         return 0;
1829 }
1830
1831 /*
1832  * periodic boundary checking
1833  */
1834
1835 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1836 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1837
1838         double x,y,z;
1839         t_3dvec *dim;
1840
1841         dim=&(moldyn->dim);
1842
1843         x=dim->x/2;
1844         y=dim->y/2;
1845         z=dim->z/2;
1846
1847         if(moldyn->status&MOLDYN_STAT_PBX) {
1848                 if(a->x>=x) a->x-=dim->x;
1849                 else if(-a->x>x) a->x+=dim->x;
1850         }
1851         if(moldyn->status&MOLDYN_STAT_PBY) {
1852                 if(a->y>=y) a->y-=dim->y;
1853                 else if(-a->y>y) a->y+=dim->y;
1854         }
1855         if(moldyn->status&MOLDYN_STAT_PBZ) {
1856                 if(a->z>=z) a->z-=dim->z;
1857                 else if(-a->z>z) a->z+=dim->z;
1858         }
1859
1860         return 0;
1861 }
1862
1863 /*
1864  * debugging / critical check functions
1865  */
1866
1867 int moldyn_bc_check(t_moldyn *moldyn) {
1868
1869         t_atom *atom;
1870         t_3dvec *dim;
1871         int i;
1872         double x;
1873         u8 byte;
1874         int j,k;
1875
1876         atom=moldyn->atom;
1877         dim=&(moldyn->dim);
1878         x=dim->x/2;
1879
1880         for(i=0;i<moldyn->count;i++) {
1881                 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
1882                         printf("FATAL: atom %d: x: %.20f (%.20f)\n",
1883                                i,atom[i].r.x,dim->x/2);
1884                         printf("diagnostic:\n");
1885                         printf("-----------\natom.r.x:\n");
1886                         for(j=0;j<8;j++) {
1887                                 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
1888                                 for(k=0;k<8;k++)
1889                                         printf("%d%c",
1890                                         ((byte)&(1<<k))?1:0,
1891                                         (k==7)?'\n':'|');
1892                         }
1893                         printf("---------------\nx=dim.x/2:\n");
1894                         for(j=0;j<8;j++) {
1895                                 memcpy(&byte,(u8 *)(&x)+j,1);
1896                                 for(k=0;k<8;k++)
1897                                         printf("%d%c",
1898                                         ((byte)&(1<<k))?1:0,
1899                                         (k==7)?'\n':'|');
1900                         }
1901                         if(atom[i].r.x==x) printf("the same!\n");
1902                         else printf("different!\n");
1903                 }
1904                 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
1905                         printf("FATAL: atom %d: y: %.20f (%.20f)\n",
1906                                i,atom[i].r.y,dim->y/2);
1907                 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
1908                         printf("FATAL: atom %d: z: %.20f (%.20f)\n",
1909                                i,atom[i].r.z,dim->z/2);
1910         }
1911
1912         return 0;
1913 }
1914
1915 /*
1916  * post processing functions
1917  */
1918
1919 int get_line(int fd,char *line,int max) {
1920
1921         int count,ret;
1922
1923         count=0;
1924
1925         while(1) {
1926                 if(count==max) return count;
1927                 ret=read(fd,line+count,1);
1928                 if(ret<=0) return ret;
1929                 if(line[count]=='\n') {
1930                         line[count]='\0';
1931                         return count+1;
1932                 }
1933                 count+=1;
1934         }
1935 }
1936