mdrun.c

   1 /*
   2  * mdrun.c - main code to run a md simulation
   3  *
   4  * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
   5  *
   6  */
   7
   8 #include "mdrun.h"
   9
  10 /* potential */
  11 #include "potentials/harmonic_oscillator.h"
  12 #include "potentials/lennard_jones.h"
  13 #include "potentials/albe.h"
  14 #ifdef TERSOFF_ORIG
  15 #include "potentials/tersoff_orig.h"
  16 #else
  17 #include "potentials/tersoff.h"
  18 #endif
  19
  20 #define ME      "[mdrun]"
  21
  22 /*
  23  * parse function
  24  */
  25
  26 int mdrun_usage(void) {
  27
  28         printf("%s usage:\n",ME);
  29
  30         return 0;
  31 }
  32
  33 int mdrun_parse_argv(t_mdrun *mdrun,int argc,char **argv) {
  34
  35         int i;
  36
  37         for(i=1;i<argc;i++) {
  38
  39                 if(argv[i][0]!='-') {
  40                         printf("%s unknown switch: %s\n",ME,argv[i]);
  41                         return -1;
  42                 }
  43
  44                 switch(argv[i][1]) {
  45                         case 'c':
  46                                 strncpy(mdrun->cfile,argv[++i],128);
  47                                 break;
  48                         case 's':
  49                                 strncpy(mdrun->sdir,argv[++i],128);
  50                                 break;
  51                         case 'h':
  52                                 mdrun_usage();
  53                                 break;
  54                         default:
  55                                 printf("%s unknown option: %s\n",ME,argv[i]);
  56                                 mdrun_usage();
  57                                 return -1;
  58                 }
  59
  60         }
  61
  62         return 0;
  63 }
  64
  65 int del_stages(t_mdrun *mdrun) {
  66
  67         t_list *sl;
  68         t_stage *stage;
  69
  70         sl=&(mdrun->stage);
  71
  72         list_reset_f(sl);
  73
  74         if(sl->start==NULL)
  75                 return 0;
  76
  77         do {
  78                 stage=sl->current->data;
  79                 free(stage->params);
  80                 free(stage);
  81         } while(list_next_f(sl)!=L_NO_NEXT_ELEMENT);
  82
  83         return 0;
  84 }
  85
  86 int add_stage(t_mdrun *mdrun,u8 type,void *params) {
  87
  88         int psize;
  89
  90         t_stage *stage;
  91
  92         switch(type) {
  93                 case STAGE_INSERT_ATOMS:
  94                         psize=sizeof(t_insert_atoms_params);
  95                         break;
  96                 case STAGE_CONTINUE:
  97                         psize=sizeof(t_continue_params);
  98                         break;
  99                 case STAGE_ANNEAL:
 100                         psize=sizeof(t_anneal_params);
 101                         break;
 102                 case STAGE_CHAATTR:
 103                         psize=sizeof(t_chaattr_params);
 104                         break;
 105                 case STAGE_CHSATTR:
 106                         psize=sizeof(t_chsattr_params);
 107                         break;
 108                 default:
 109                         printf("%s unknown stage type: %02x\n",ME,type);
 110                         return -1;
 111         }
 112
 113         stage=malloc(sizeof(t_stage));
 114         if(stage==NULL) {
 115                 perror("[mdrun] malloc (add stage)");
 116                 return -1;
 117         }
 118
 119         stage->type=type;
 120         stage->executed=FALSE;
 121
 122         stage->params=malloc(psize);
 123         if(stage->params==NULL) {
 124                 perror("[mdrun] malloc (stage params)");
 125                 return -1;
 126         }
 127
 128         memcpy(stage->params,params,psize);
 129
 130         list_add_immediate_f(&(mdrun->stage),stage);
 131
 132         return 0;
 133 }
 134
 135 int mdrun_parse_config(t_mdrun *mdrun) {
 136
 137         int fd,ret;
 138         char error[128];
 139         char line[128];
 140         char *wptr;
 141         char word[16][32];
 142         int wcnt;
 143         int i;
 144
 145         t_insert_atoms_params iap;
 146         t_continue_params cp;
 147         t_anneal_params ap;
 148         t_chaattr_params cap;
 149         t_chsattr_params csp;
 150
 151         /* open config file */
 152         fd=open(mdrun->cfile,O_RDONLY);
 153         if(fd<0) {
 154                 snprintf(error,128,"%s open cfile %s",ME,mdrun->cfile);
 155                 perror(error);
 156                 return fd;
 157         }
 158
 159         /* read, parse, set */
 160         ret=1;
 161         while(ret>0) {
 162
 163                 /* read */
 164                 ret=get_line(fd,line,128);
 165
 166                 /* parse */
 167
 168                 // ignore # lines and \n
 169                 if((line[0]=='#')|(ret==1))
 170                         continue;
 171
 172                 // reset
 173                 memset(&iap,0,sizeof(t_insert_atoms_params));
 174                 memset(&cp,0,sizeof(t_continue_params));
 175                 memset(&ap,0,sizeof(t_anneal_params));
 176                 memset(&cap,0,sizeof(t_chaattr_params));
 177                 memset(&csp,0,sizeof(t_chsattr_params));
 178
 179                 // get command + args
 180                 wcnt=0;
 181                 while(1) {
 182                         if(wcnt)
 183                                 wptr=strtok(NULL," \t");
 184                         else
 185                                 wptr=strtok(line," \t");
 186                         if(wptr==NULL)
 187                                 break;
 188                         strncpy(word[wcnt],wptr,32);
 189                         wcnt+=1;
 190                 }
 191
 192                 if(!strncmp(word[0],"potential",9)) {
 193                         if(!strncmp(word[1],"albe",4))
 194                                 mdrun->potential=MOLDYN_POTENTIAL_AM;
 195                         if(!strncmp(word[1],"tersoff",7))
 196                                 mdrun->potential=MOLDYN_POTENTIAL_TM;
 197                         if(!strncmp(word[1],"ho",2))
 198                                 mdrun->potential=MOLDYN_POTENTIAL_HO;
 199                         if(!strncmp(word[1],"lj",2))
 200                                 mdrun->potential=MOLDYN_POTENTIAL_LJ;
 201                 }
 202                 else if(!strncmp(word[0],"cutoff",6))
 203                         mdrun->cutoff=atof(word[1]);
 204                 else if(!strncmp(word[0],"intalgo",7)) {
 205                         if(!strncmp(word[1],"verlet",5))
 206                                 mdrun->intalgo=MOLDYN_INTEGRATE_VERLET;
 207                 }
 208                 else if(!strncmp(word[0],"timestep",8))
 209                         mdrun->timestep=atof(word[1]);
 210                 else if(!strncmp(word[0],"volume",6)) {
 211                         mdrun->dim.x=atof(word[1]);
 212                         mdrun->dim.y=atof(word[2]);
 213                         mdrun->dim.z=atof(word[3]);
 214                         if(strncmp(word[4],"0",1))
 215                                 mdrun->vis=TRUE;
 216                 }
 217                 else if(!strncmp(word[0],"pbc",3)) {
 218                         if(strncmp(word[1],"0",1))
 219                                 mdrun->pbcx=TRUE;
 220                         else
 221                                 mdrun->pbcx=FALSE;
 222                         if(strncmp(word[2],"0",1))
 223                                 mdrun->pbcy=TRUE;
 224                         else
 225                                 mdrun->pbcy=FALSE;
 226                         if(strncmp(word[3],"0",1))
 227                                 mdrun->pbcz=TRUE;
 228                         else
 229                                 mdrun->pbcz=FALSE;
 230                 }
 231                 else if(!strncmp(word[0],"temperature",11))
 232                         mdrun->temperature=atof(word[1]);
 233                 else if(!strncmp(word[0],"pressure",8))
 234                         mdrun->pressure=atof(word[1]);
 235                 else if(!strncmp(word[0],"lattice",7)) {
 236                         if(!strncmp(word[1],"zincblende",10))
 237                                 mdrun->lattice=ZINCBLENDE;
 238                         if(!strncmp(word[1],"fcc",3))
 239                                 mdrun->lattice=FCC;
 240                         if(!strncmp(word[1],"diamond",7))
 241                                 mdrun->lattice=DIAMOND;
 242                 }
 243                 else if(!strncmp(word[0],"element1",8)) {
 244                         mdrun->element1=atoi(word[1]);
 245                         switch(mdrun->element1) {
 246                                 case SI:
 247                                         mdrun->m1=M_SI;
 248                                         break;
 249                                 case C:
 250                                         mdrun->m1=M_C;
 251                                         break;
 252                                 default:
 253                                         printf("%s unknown element1: %s|%d\n",
 254                                                ME,word[1],mdrun->element1);
 255                                         return -1;
 256                         }
 257                 }
 258                 else if(!strncmp(word[0],"element2",8)) {
 259                         mdrun->element2=atoi(word[1]);
 260                         switch(mdrun->element2) {
 261                                 case SI:
 262                                         mdrun->m2=M_SI;
 263                                         break;
 264                                 case C:
 265                                         mdrun->m2=M_C;
 266                                         break;
 267                                 default:
 268                                         printf("%s unknown element2: %s|%d\n",
 269                                                ME,word[1],mdrun->element2);
 270                                         return -1;
 271                         }
 272                 }
 273                 else if(!strncmp(word[0],"fill",6)) {
 274                         // only lc mode by now
 275                         mdrun->lx=atoi(word[2]);
 276                         mdrun->ly=atoi(word[3]);
 277                         mdrun->lz=atoi(word[4]);
 278                 }
 279                 else if(!strncmp(word[0],"aattr",5)) {
 280                         // for aatrib line we need a special stage
 281                         // containing one schedule of 0 loops ...
 282                         for(i=0;i<strlen(word[1]);i++) {
 283                                 switch(word[1][i]) {
 284                                         case 't':
 285                                                 cap.type|=CHAATTR_TOTALV;
 286                                                 break;
 287                                         case 'r':
 288                                                 cap.type|=CHAATTR_REGION;
 289                                                 break;
 290                                         case 'e':
 291                                                 cap.type|=CHAATTR_ELEMENT;
 292                                                 break;
 293                                         default:
 294                                                 break;
 295                                 }
 296                         }
 297                         i=1;
 298                         if(cap.type&CHAATTR_REGION) {
 299                                 cap.x0=atof(word[1]);
 300                                 cap.y0=atof(word[2]);
 301                                 cap.z0=atof(word[3]);
 302                                 cap.x1=atof(word[4]);
 303                                 cap.y1=atof(word[5]);
 304                                 cap.z1=atof(word[6]);
 305                                 i+=6;
 306                         }
 307                         if(cap.type&CHAATTR_ELEMENT) {
 308                                 cap.element=atoi(word[i]);
 309                                 i+=1;
 310                         }
 311                         wptr=word[i];
 312                         for(i=0;i<strlen(wptr);i++) {
 313                                 switch(word[2][i]) {
 314                                         case 'b':
 315                                                 cap.attr|=ATOM_ATTR_VB;
 316                                                 break;
 317                                         case 'h':
 318                                                 cap.attr|=ATOM_ATTR_HB;
 319                                                 break;
 320                                         case 'v':
 321                                                 cap.attr|=ATOM_ATTR_VA;
 322                                                 break;
 323                                         case 'f':
 324                                                 cap.attr|=ATOM_ATTR_FP;
 325                                                 break;
 326                                         case '1':
 327                                                 cap.attr|=ATOM_ATTR_1BP;
 328                                                 break;
 329                                         case '2':
 330                                                 cap.attr|=ATOM_ATTR_2BP;
 331                                                 break;
 332                                         case '3':
 333                                                 cap.attr|=ATOM_ATTR_3BP;
 334                                                 break;
 335                                         default:
 336                                                 break;
 337                                 }
 338                         }
 339                         add_stage(mdrun,STAGE_CHAATTR,&cap);
 340                 }
 341                 else if(!strncmp(word[0],"sattr",5)) {
 342                         // for satrib line we need a special stage
 343                         // containing one schedule of 0 loops ...
 344                         for(i=1;i<wcnt;i++) {
 345                                 if(!strncmp(word[i],"pctrl",5)) {
 346                                         csp.ptau=atof(word[++i]);
 347                                 }
 348                                 if(!strncmp(word[i],"tctrl",5)) {
 349                                         csp.ttau=atof(word[++i]);
 350                                 }
 351                                 if(!strncmp(word[i],"prelax",6)) {
 352                                         csp.dp=atof(word[++i]);
 353                                 }
 354                                 if(!strncmp(word[i],"trelax",6)) {
 355                                         csp.dt=atof(word[++i]);
 356                                 }
 357                                 if(!strncmp(word[i],"rsteps",6)) {
 358                                         csp.rsteps=atoi(word[++i]);
 359                                 }
 360                                 if(!strncmp(word[i],"avgrst",6)) {
 361                                         csp.avgrst=atoi(word[++i]);
 362                                 }
 363                         }
 364                         add_stage(mdrun,STAGE_CHSATTR,&csp);
 365                 }
 366                 else if(!strncmp(word[0],"prerun",6))
 367                         mdrun->prerun=atoi(word[1]);
 368                 else if(!strncmp(word[0],"avgskip",7))
 369                         mdrun->avgskip=atoi(word[1]);
 370                 else if(!strncmp(word[0],"elog",4))
 371                         mdrun->elog=atoi(word[1]);
 372                 else if(!strncmp(word[0],"tlog",4))
 373                         mdrun->tlog=atoi(word[1]);
 374                 else if(!strncmp(word[0],"plog",4))
 375                         mdrun->plog=atoi(word[1]);
 376                 else if(!strncmp(word[0],"vlog",4))
 377                         mdrun->vlog=atoi(word[1]);
 378                 else if(!strncmp(word[0],"save",4))
 379                         mdrun->save=atoi(word[1]);
 380                 else if(!strncmp(word[0],"visualize",9))
 381                         mdrun->visualize=atoi(word[1]);
 382                 else if(!strncmp(word[0],"stage",5)) {
 383                         // for every stage line, add a stage
 384                         if(!strncmp(word[1],"ins_atoms",9)) {
 385                                 iap.ins_steps=atoi(word[2]);
 386                                 iap.ins_atoms=atoi(word[3]);
 387                                 iap.element=atoi(word[4]);
 388                                 iap.element=atoi(word[4]);
 389                                 iap.brand=atoi(word[5]);
 390                                 for(i=0;i<strlen(word[6]);i++) {
 391                                         switch(word[6][i]) {
 392                                                 case 'b':
 393                                                         iap.attr|=ATOM_ATTR_VB;
 394                                                         break;
 395                                                 case 'h':
 396                                                         iap.attr|=ATOM_ATTR_HB;
 397                                                         break;
 398                                                 case 'v':
 399                                                         iap.attr|=ATOM_ATTR_VA;
 400                                                         break;
 401                                                 case 'f':
 402                                                         iap.attr|=ATOM_ATTR_FP;
 403                                                         break;
 404                                                 case '1':
 405                                                         iap.attr|=ATOM_ATTR_1BP;
 406                                                         break;
 407                                                 case '2':
 408                                                         iap.attr|=ATOM_ATTR_2BP;
 409                                                         break;
 410                                                 case '3':
 411                                                         iap.attr|=ATOM_ATTR_3BP;
 412                                                         break;
 413                                                 default:
 414                                                         break;
 415                                         }
 416                                 }
 417                                 // only rand mode by now
 418                                 if(word[8][0]=='t')
 419                                         iap.type=INS_TOTAL;
 420                                 else {
 421                                         iap.type=INS_REGION;
 422                                         iap.x0=atof(word[8]);
 423                                         iap.y0=atof(word[9]);
 424                                         iap.z0=atof(word[10]);
 425                                         iap.x1=atof(word[11]);
 426                                         iap.y1=atof(word[12]);
 427                                         iap.z1=atof(word[13]);
 428                                 }
 429                                 add_stage(mdrun,STAGE_INSERT_ATOMS,&iap);
 430                         }
 431                         else if(!strncmp(word[1],"continue",8)) {
 432                                 cp.runs=atoi(word[2]);
 433                                 add_stage(mdrun,STAGE_CONTINUE,&cp);
 434                         }
 435                         else if(!strncmp(word[1],"anneal",6)) {
 436                                 ap.count=0;
 437                                 ap.runs=atoi(word[2]);
 438                                 ap.dt=atof(word[3]);
 439                                 add_stage(mdrun,STAGE_ANNEAL,&ap);
 440                         }
 441                         else {
 442                                 printf("%s unknown stage type: %s\n",
 443                                        ME,word[1]);
 444                                 return -1;
 445                         }
 446                 }
 447                 else {
 448                         printf("%s unknown keyword '%s', skipped!\n",
 449                                ME,word[0]);
 450                         continue;
 451                 }
 452         }
 453
 454         /* close file */
 455         close(fd);
 456
 457         return 0;
 458 }
 459
 460 int check_pressure(t_moldyn *moldyn,t_mdrun *mdrun) {
 461
 462         double delta;
 463
 464         if(!(mdrun->sattr&SATTR_PRELAX))
 465                 return TRUE;
 466
 467         delta=moldyn->p_avg-moldyn->p_ref;
 468
 469         if(delta<0)
 470                 delta=-delta;
 471
 472         if(delta>mdrun->dp)
 473                 return FALSE;
 474
 475         return TRUE;
 476 }
 477
 478 int check_temperature(t_moldyn *moldyn,t_mdrun *mdrun) {
 479
 480         double delta;
 481
 482         if(!(mdrun->sattr&SATTR_TRELAX))
 483                 return TRUE;
 484
 485         delta=moldyn->t_avg-moldyn->t_ref;
 486
 487         if(delta<0)
 488                 delta=-delta;
 489
 490         if(delta>mdrun->dt)
 491                 return FALSE;
 492
 493         return TRUE;
 494 }
 495
 496 int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 497
 498         t_insert_atoms_params *iap;
 499         t_stage *stage;
 500         t_atom *atom;
 501         t_3dvec r,v,dist;
 502         double d,dmin;
 503         int cnt,i;
 504         double x,y,z;
 505         double x0,y0,z0;
 506         u8 cr_check,run;
 507
 508         stage=mdrun->stage.current->data;
 509         iap=stage->params;
 510
 511         cr_check=FALSE;
 512
 513         v.x=0.0; v.y=0.0; v.z=0.0;
 514
 515         switch(iap->type) {
 516                 case INS_TOTAL:
 517                         x=moldyn->dim.x;
 518                         x0=0.0;
 519                         y=moldyn->dim.y;
 520                         y0=0.0;
 521                         z=moldyn->dim.z;
 522                         z0=0.0;
 523                         cr_check=TRUE;
 524                         break;
 525                 case INS_REGION:
 526                         x=iap->x1-iap->x0;
 527                         x0=iap->x0;
 528                         y=iap->y1-iap->y0;
 529                         y0=iap->y0;
 530                         z=iap->z1-iap->z0;
 531                         z0=iap->z0;
 532                         cr_check=TRUE;
 533                         break;
 534                 default:
 535                         printf("%s unknown insertion mode: %02x\n",
 536                                ME,iap->type);
 537                         return -1;
 538         }
 539
 540         cnt=0;
 541         while(cnt<iap->ins_atoms) {
 542                 run=1;
 543                 while(run) {
 544                         r.x=(rand_get_double(&(moldyn->random))-0.5)*x+x0;
 545                         r.y=(rand_get_double(&(moldyn->random))-0.5)*y+y0;
 546                         r.z=(rand_get_double(&(moldyn->random))-0.5)*z+z0;
 547                         run=0;
 548                         if(cr_check==TRUE) {
 549                                 dmin=1000;      // for sure too high!
 550                                 for(i=0;i<moldyn->count;i++) {
 551                                         atom=&(moldyn->atom[i]);
 552                                         v3_sub(&dist,&(atom->r),&r);
 553                                         check_per_bound(moldyn,&dist);
 554                                         d=v3_absolute_square(&dist);
 555                                         if(d<(iap->cr*iap->cr)) {
 556                                                 run=1;
 557                                                 break;
 558                                         }
 559                                         if(d<dmin)
 560                                                 dmin=d;
 561                                 }
 562                         }
 563                 }
 564                 add_atom(moldyn,iap->element,pse_mass[iap->element],
 565                          iap->brand,iap->attr,&r,&v);
 566                 printf("%s atom inserted: %f %f %f | d squared = %f\n",
 567                        ME,r.x,r.y,r.z,dmin);
 568                 cnt+=1;
 569         }
 570
 571         return 0;
 572 }
 573
 574 int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
 575
 576         t_stage *stage;
 577         t_chaattr_params *cap;
 578         t_atom *atom;
 579         int i;
 580
 581         stage=mdrun->stage.current->data;
 582         cap=stage->params;
 583
 584         for(i=0;i<moldyn->count;i++) {
 585                 atom=&(moldyn->atom[i]);
 586                 if(cap->type&CHAATTR_ELEMENT) {
 587                         if(cap->element!=atom->element)
 588                                 continue;
 589                 }
 590                 if(cap->type&CHAATTR_REGION) {
 591                         if(cap->x0<atom->r.x)
 592                                 continue;
 593                         if(cap->y0<atom->r.y)
 594                                 continue;
 595                         if(cap->z0<atom->r.z)
 596                                 continue;
 597                         if(cap->x1>atom->r.x)
 598                                 continue;
 599                         if(cap->y1>atom->r.y)
 600                                 continue;
 601                         if(cap->z1>atom->r.z)
 602                                 continue;
 603                 }
 604                 atom->attr=cap->attr;
 605         }
 606
 607         return 0;
 608 }
 609
 610 int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
 611
 612         t_stage *stage;
 613         t_chsattr_params *csp;
 614
 615         stage=mdrun->stage.current->data;
 616         csp=stage->params;
 617
 618         if(csp->type&CHSATTR_PCTRL) {
 619                 if(csp->ptau>0)
 620                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
 621                 else
 622                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
 623         }
 624         if(csp->type&CHSATTR_TCTRL) {
 625                 if(csp->ttau>0)
 626                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
 627                 else
 628                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
 629         }
 630         if(csp->type&CHSATTR_PRELAX) {
 631                 if(csp->dp<0)
 632                         mdrun->sattr&=(~(SATTR_PRELAX));
 633                 else
 634                         mdrun->sattr|=SATTR_PRELAX;
 635                 mdrun->dp=csp->dp;
 636         }
 637         if(csp->type&CHSATTR_TRELAX) {
 638                 if(csp->dt<0)
 639                         mdrun->sattr&=(~(SATTR_TRELAX));
 640                 else
 641                         mdrun->sattr|=SATTR_TRELAX;
 642                 mdrun->dt=csp->dt;
 643         }
 644         if(csp->type&CHSATTR_AVGRST) {
 645                 if(csp->avgrst)
 646                         mdrun->sattr|=CHSATTR_AVGRST;
 647                 else
 648                         mdrun->sattr&=(~(CHSATTR_AVGRST));
 649         }
 650         if(csp->type&CHSATTR_RSTEPS) {
 651                 mdrun->relax_steps=csp->rsteps;
 652         }
 653
 654         return 0;
 655 }
 656
 657 int mdrun_hook(void *ptr1,void *ptr2) {
 658
 659         t_moldyn *moldyn;
 660         t_mdrun *mdrun;
 661         t_stage *stage;
 662         t_list *sl;
 663         int steps;
 664         double tau;
 665         u8 change_stage;
 666
 667         t_insert_atoms_params *iap;
 668         t_continue_params *cp;
 669         t_anneal_params *ap;
 670
 671         moldyn=ptr1;
 672         mdrun=ptr2;
 673
 674         sl=&(mdrun->stage);
 675
 676         change_stage=FALSE;
 677
 678         /* return immediately if there are no more stage */
 679         if(sl->current==NULL)
 680                 return 0;
 681
 682         /* get stage description */
 683         stage=sl->current->data;
 684
 685         /* default steps and tau values */
 686         steps=mdrun->relax_steps;
 687         tau=mdrun->timestep;
 688
 689         /* check whether relaxation steps are necessary */
 690         if(!((check_pressure(moldyn,mdrun)==FALSE)|\
 691              (check_temperature(moldyn,mdrun)==FALSE))) {
 692
 693                 /* stage specific stuff */
 694                 switch(stage->type) {
 695                         case STAGE_INSERT_ATOMS:
 696                                 iap=stage->params;
 697                                 if(iap->cnt_steps==iap->ins_steps) {
 698                                         change_stage=TRUE;
 699                                         break;
 700                                 }
 701                                 insert_atoms(moldyn,mdrun);
 702                                 iap->cnt_steps+=1;
 703                                         break;
 704                         case STAGE_CONTINUE:
 705                                 if(stage->executed==TRUE) {
 706                                         change_stage=TRUE;
 707                                         break;
 708                                 }
 709                                 cp=stage->params;
 710                                 steps=cp->runs;
 711                                         break;
 712                         case STAGE_ANNEAL:
 713                                 ap=stage->params;
 714                                 if(ap->count==ap->runs) {
 715                                         change_stage=TRUE;
 716                                         break;
 717                                 }
 718                                 set_temperature(moldyn,moldyn->t_ref+ap->dt);
 719                                 ap->count+=1;
 720                                 break;
 721                         case STAGE_CHAATTR:
 722                                 chaatr(moldyn,mdrun);
 723                                 change_stage=TRUE;
 724                                 break;
 725                         case STAGE_CHSATTR:
 726                                 chsattr(moldyn,mdrun);
 727                                 change_stage=TRUE;
 728                                 break;
 729                         default:
 730                                 printf("%s unknwon stage type\n",ME);
 731                                 break;
 732                 }
 733
 734                 /* mark as executed */
 735                 stage->executed=TRUE;
 736
 737                 /* change state */
 738                 if(change_stage==TRUE) {
 739                         printf("%s finished stage\n",ME);
 740                         if(list_next_f(sl)==L_NO_NEXT_ELEMENT) {
 741                                 printf("%s no more stages\n",ME);
 742                                 return 0;
 743                         }
 744                         steps=0;
 745                         tau=mdrun->timestep;
 746                 }
 747
 748         }
 749         else {
 750
 751                 /* averages */
 752                 if(mdrun->sattr&SATTR_AVGRST)
 753                         average_reset(moldyn);
 754
 755         }
 756
 757         /* continue simulation */
 758         moldyn_add_schedule(moldyn,steps,tau);
 759
 760         return 0;
 761 }
 762
 763 int main(int argc,char **argv) {
 764
 765         t_mdrun mdrun;
 766         t_moldyn moldyn;
 767         t_3dvec o;
 768
 769         /* clear mdrun struct */
 770         memset(&mdrun,0,sizeof(t_mdrun));
 771
 772         /* parse arguments */
 773         if(mdrun_parse_argv(&mdrun,argc,argv)<0)
 774                 return -1;
 775
 776         /* initialize list system */
 777         list_init_f(&(mdrun.stage));
 778
 779         /* parse config file */
 780         mdrun_parse_config(&mdrun);
 781
 782         /* reset the stage list */
 783         list_reset_f(&(mdrun.stage));
 784
 785         /* sanity check! */
 786
 787         /* prepare simulation */
 788         moldyn_init(&moldyn,argc,argv);
 789         if(set_int_alg(&moldyn,mdrun.intalgo)<0)
 790                 return -1;
 791         set_cutoff(&moldyn,mdrun.cutoff);
 792         if(set_potential(&moldyn,mdrun.potential)<0)
 793                 return -1;
 794         switch(mdrun.potential) {
 795                 case MOLDYN_POTENTIAL_AM:
 796                         albe_mult_set_params(&moldyn,
 797                                              mdrun.element1,
 798                                              mdrun.element2);
 799                         break;
 800                 case MOLDYN_POTENTIAL_TM:
 801                         tersoff_mult_set_params(&moldyn,
 802                                                 mdrun.element1,
 803                                                 mdrun.element2);
 804                         break;
 805                 case MOLDYN_POTENTIAL_HO:
 806                         harmonic_oscillator_set_params(&moldyn,mdrun.element1);
 807                         break;
 808                 case MOLDYN_POTENTIAL_LJ:
 809                         lennard_jones_set_params(&moldyn,mdrun.element1);
 810                         break;
 811                 default:
 812                         printf("%s unknown potential: %02x\n",
 813                                ME,mdrun.potential);
 814                         return -1;
 815         }
 816         set_dim(&moldyn,mdrun.dim.x,mdrun.dim.y,mdrun.dim.z,mdrun.vis);
 817         set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
 818         switch(mdrun.lattice) {
 819                 case FCC:
 820                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
 821                                        mdrun.m1,0,0,mdrun.lx,
 822                                        mdrun.ly,mdrun.lz,NULL);
 823                         break;
 824                 case DIAMOND:
 825                         create_lattice(&moldyn,DIAMOND,mdrun.lc,mdrun.element1,
 826                                        mdrun.m1,0,0,mdrun.lx,
 827                                        mdrun.ly,mdrun.lz,NULL);
 828                         break;
 829                 case ZINCBLENDE:
 830                         o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
 831                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
 832                                        mdrun.m1,0,0,mdrun.lx,
 833                                        mdrun.ly,mdrun.lz,&o);
 834                         o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
 835                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
 836                                        mdrun.m2,0,1,mdrun.lx,
 837                                        mdrun.ly,mdrun.lz,&o);
 838                         break;
 839                 default:
 840                         printf("%s unknown lattice type: %02x\n",
 841                                ME,mdrun.lattice);
 842                         return -1;
 843         }
 844         moldyn_bc_check(&moldyn);
 845         set_temperature(&moldyn,mdrun.temperature);
 846         set_pressure(&moldyn,mdrun.pressure);
 847         thermal_init(&moldyn,TRUE);
 848         moldyn_add_schedule(&moldyn,mdrun.prerun,mdrun.timestep);
 849         moldyn_set_log_dir(&moldyn,mdrun.sdir);
 850         moldyn_set_report(&moldyn,"CHANGE ME","CHANGE ME TOO");
 851         if(mdrun.elog)
 852                 moldyn_set_log(&moldyn,LOG_TOTAL_ENERGY,mdrun.elog);
 853         if(mdrun.tlog)
 854                 moldyn_set_log(&moldyn,LOG_TEMPERATURE,mdrun.tlog);
 855         if(mdrun.plog)
 856                 moldyn_set_log(&moldyn,LOG_PRESSURE,mdrun.plog);
 857         if(mdrun.vlog)
 858                 moldyn_set_log(&moldyn,LOG_VOLUME,mdrun.vlog);
 859         if(mdrun.visualize)
 860                 moldyn_set_log(&moldyn,VISUAL_STEP,mdrun.visualize);
 861         if(mdrun.save)
 862                 moldyn_set_log(&moldyn,SAVE_STEP,mdrun.save);
 863         moldyn_set_log(&moldyn,CREATE_REPORT,0);
 864         set_avg_skip(&moldyn,mdrun.avgskip);
 865
 866         /* prepare the hook function */
 867         moldyn_set_schedule_hook(&moldyn,&mdrun_hook,&mdrun);
 868
 869         /* run the simulation */
 870         moldyn_integrate(&moldyn);
 871
 872         /* shutdown */
 873         moldyn_shutdown(&moldyn);
 874         del_stages(&mdrun);
 875         list_destroy_f(&(mdrun.stage));
 876
 877         return 0;
 878 }