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,o;
 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],"nnd",3))
 205                         mdrun->nnd=atof(word[1]);
 206                 else if(!strncmp(word[0],"intalgo",7)) {
 207                         if(!strncmp(word[1],"verlet",5))
 208                                 mdrun->intalgo=MOLDYN_INTEGRATE_VERLET;
 209                 }
 210                 else if(!strncmp(word[0],"timestep",8))
 211                         mdrun->timestep=atof(word[1]);
 212                 else if(!strncmp(word[0],"volume",6)) {
 213                         mdrun->dim.x=atof(word[1]);
 214                         mdrun->dim.y=atof(word[2]);
 215                         mdrun->dim.z=atof(word[3]);
 216                         if(strncmp(word[4],"0",1))
 217                                 mdrun->vis=TRUE;
 218                 }
 219                 else if(!strncmp(word[0],"pbc",3)) {
 220                         if(strncmp(word[1],"0",1))
 221                                 mdrun->pbcx=TRUE;
 222                         else
 223                                 mdrun->pbcx=FALSE;
 224                         if(strncmp(word[2],"0",1))
 225                                 mdrun->pbcy=TRUE;
 226                         else
 227                                 mdrun->pbcy=FALSE;
 228                         if(strncmp(word[3],"0",1))
 229                                 mdrun->pbcz=TRUE;
 230                         else
 231                                 mdrun->pbcz=FALSE;
 232                 }
 233                 else if(!strncmp(word[0],"temperature",11))
 234                         mdrun->temperature=atof(word[1]);
 235                 else if(!strncmp(word[0],"pressure",8))
 236                         mdrun->pressure=atof(word[1]);
 237                 else if(!strncmp(word[0],"lattice",7)) {
 238                         if(!strncmp(word[1],"zincblende",10))
 239                                 mdrun->lattice=ZINCBLENDE;
 240                         if(!strncmp(word[1],"fcc",3))
 241                                 mdrun->lattice=FCC;
 242                         if(!strncmp(word[1],"diamond",7))
 243                                 mdrun->lattice=DIAMOND;
 244                 }
 245                 else if(!strncmp(word[0],"element1",8)) {
 246                         mdrun->element1=atoi(word[1]);
 247                         mdrun->m1=pse_mass[mdrun->element1];
 248                 }
 249                 else if(!strncmp(word[0],"element2",8)) {
 250                         mdrun->element2=atoi(word[1]);
 251                         mdrun->m2=pse_mass[mdrun->element2];
 252                 }
 253                 else if(!strncmp(word[0],"fill",6)) {
 254                         // only lc mode by now
 255                         mdrun->lx=atoi(word[2]);
 256                         mdrun->ly=atoi(word[3]);
 257                         mdrun->lz=atoi(word[4]);
 258                         mdrun->lc=atof(word[5]);
 259                 }
 260                 else if(!strncmp(word[0],"aattr",5)) {
 261                         // for aatrib line we need a special stage
 262                         // containing one schedule of 0 loops ...
 263                         for(i=0;i<strlen(word[1]);i++) {
 264                                 switch(word[1][i]) {
 265                                         case 't':
 266                                                 cap.type|=CHAATTR_TOTALV;
 267                                                 break;
 268                                         case 'r':
 269                                                 cap.type|=CHAATTR_REGION;
 270                                                 break;
 271                                         case 'e':
 272                                                 cap.type|=CHAATTR_ELEMENT;
 273                                                 break;
 274                                         default:
 275                                                 break;
 276                                 }
 277                         }
 278                         i=2;
 279                         if(cap.type&CHAATTR_REGION) {
 280                                 cap.x0=atof(word[1]);
 281                                 cap.y0=atof(word[2]);
 282                                 cap.z0=atof(word[3]);
 283                                 cap.x1=atof(word[4]);
 284                                 cap.y1=atof(word[5]);
 285                                 cap.z1=atof(word[6]);
 286                                 i+=6;
 287                         }
 288                         if(cap.type&CHAATTR_ELEMENT) {
 289                                 cap.element=atoi(word[i]);
 290                                 i+=1;
 291                         }
 292                         for(o=0;o<strlen(word[i]);o++) {
 293                                 switch(word[i][o]) {
 294                                         case 'b':
 295                                                 cap.attr|=ATOM_ATTR_VB;
 296                                                 break;
 297                                         case 'h':
 298                                                 cap.attr|=ATOM_ATTR_HB;
 299                                                 break;
 300                                         case 'v':
 301                                                 cap.attr|=ATOM_ATTR_VA;
 302                                                 break;
 303                                         case 'f':
 304                                                 cap.attr|=ATOM_ATTR_FP;
 305                                                 break;
 306                                         case '1':
 307                                                 cap.attr|=ATOM_ATTR_1BP;
 308                                                 break;
 309                                         case '2':
 310                                                 cap.attr|=ATOM_ATTR_2BP;
 311                                                 break;
 312                                         case '3':
 313                                                 cap.attr|=ATOM_ATTR_3BP;
 314                                                 break;
 315                                         default:
 316                                                 break;
 317                                 }
 318                         }
 319                         add_stage(mdrun,STAGE_CHAATTR,&cap);
 320                 }
 321                 else if(!strncmp(word[0],"sattr",5)) {
 322                         // for satrib line we need a special stage
 323                         // containing one schedule of 0 loops ...
 324                         csp.type=0;
 325                         for(i=1;i<wcnt;i++) {
 326                                 if(!strncmp(word[i],"pctrl",5)) {
 327                                         csp.ptau=0.01/(atof(word[++i])*GPA);
 328                                         csp.type|=CHSATTR_PCTRL;
 329                                 }
 330                                 if(!strncmp(word[i],"tctrl",5)) {
 331                                         csp.ttau=atof(word[++i]);
 332                                         csp.type|=CHSATTR_TCTRL;
 333                                 }
 334                                 if(!strncmp(word[i],"prelax",6)) {
 335                                         csp.dp=atof(word[++i]);
 336                                         csp.type|=CHSATTR_PRELAX;
 337                                 }
 338                                 if(!strncmp(word[i],"trelax",6)) {
 339                                         csp.dt=atof(word[++i]);
 340                                         csp.type|=CHSATTR_TRELAX;
 341                                 }
 342                                 if(!strncmp(word[i],"rsteps",6)) {
 343                                         csp.rsteps=atoi(word[++i]);
 344                                         csp.type|=CHSATTR_RSTEPS;
 345                                 }
 346                                 if(!strncmp(word[i],"avgrst",6)) {
 347                                         csp.avgrst=atoi(word[++i]);
 348                                         csp.type|=CHSATTR_AVGRST;
 349                                 }
 350                         }
 351                         add_stage(mdrun,STAGE_CHSATTR,&csp);
 352                 }
 353                 else if(!strncmp(word[0],"prerun",6))
 354                         mdrun->prerun=atoi(word[1]);
 355                 else if(!strncmp(word[0],"avgskip",7))
 356                         mdrun->avgskip=atoi(word[1]);
 357                 else if(!strncmp(word[0],"elog",4))
 358                         mdrun->elog=atoi(word[1]);
 359                 else if(!strncmp(word[0],"tlog",4))
 360                         mdrun->tlog=atoi(word[1]);
 361                 else if(!strncmp(word[0],"plog",4))
 362                         mdrun->plog=atoi(word[1]);
 363                 else if(!strncmp(word[0],"vlog",4))
 364                         mdrun->vlog=atoi(word[1]);
 365                 else if(!strncmp(word[0],"save",4))
 366                         mdrun->save=atoi(word[1]);
 367                 else if(!strncmp(word[0],"visualize",9))
 368                         mdrun->visualize=atoi(word[1]);
 369                 else if(!strncmp(word[0],"stage",5)) {
 370                         // for every stage line, add a stage
 371                         if(!strncmp(word[1],"ins_atoms",9)) {
 372                                 iap.ins_steps=atoi(word[2]);
 373                                 iap.ins_atoms=atoi(word[3]);
 374                                 iap.element=atoi(word[4]);
 375                                 iap.element=atoi(word[4]);
 376                                 iap.brand=atoi(word[5]);
 377                                 for(i=0;i<strlen(word[6]);i++) {
 378                                         switch(word[6][i]) {
 379                                                 case 'b':
 380                                                         iap.attr|=ATOM_ATTR_VB;
 381                                                         break;
 382                                                 case 'h':
 383                                                         iap.attr|=ATOM_ATTR_HB;
 384                                                         break;
 385                                                 case 'v':
 386                                                         iap.attr|=ATOM_ATTR_VA;
 387                                                         break;
 388                                                 case 'f':
 389                                                         iap.attr|=ATOM_ATTR_FP;
 390                                                         break;
 391                                                 case '1':
 392                                                         iap.attr|=ATOM_ATTR_1BP;
 393                                                         break;
 394                                                 case '2':
 395                                                         iap.attr|=ATOM_ATTR_2BP;
 396                                                         break;
 397                                                 case '3':
 398                                                         iap.attr|=ATOM_ATTR_3BP;
 399                                                         break;
 400                                                 default:
 401                                                         break;
 402                                         }
 403                                 }
 404                                 // only rand mode by now
 405                                 if(word[8][0]=='t')
 406                                         iap.type=INS_TOTAL;
 407                                 else {
 408                                         iap.type=INS_REGION;
 409                                         iap.x0=atof(word[8]);
 410                                         iap.y0=atof(word[9]);
 411                                         iap.z0=atof(word[10]);
 412                                         iap.x1=atof(word[11]);
 413                                         iap.y1=atof(word[12]);
 414                                         iap.z1=atof(word[13]);
 415                                 }
 416                                 add_stage(mdrun,STAGE_INSERT_ATOMS,&iap);
 417                         }
 418                         else if(!strncmp(word[1],"continue",8)) {
 419                                 cp.runs=atoi(word[2]);
 420                                 add_stage(mdrun,STAGE_CONTINUE,&cp);
 421                         }
 422                         else if(!strncmp(word[1],"anneal",6)) {
 423                                 ap.count=0;
 424                                 ap.runs=atoi(word[2]);
 425                                 ap.dt=atof(word[3]);
 426                                 add_stage(mdrun,STAGE_ANNEAL,&ap);
 427                         }
 428                         else {
 429                                 printf("%s unknown stage type: %s\n",
 430                                        ME,word[1]);
 431                                 return -1;
 432                         }
 433                 }
 434                 else {
 435                         printf("%s unknown keyword '%s', skipped!\n",
 436                                ME,word[0]);
 437                         continue;
 438                 }
 439         }
 440
 441         /* close file */
 442         close(fd);
 443
 444         return 0;
 445 }
 446
 447 int check_pressure(t_moldyn *moldyn,t_mdrun *mdrun) {
 448
 449         double delta;
 450
 451         if(!(mdrun->sattr&SATTR_PRELAX))
 452                 return TRUE;
 453
 454         delta=moldyn->p_avg-moldyn->p_ref;
 455
 456         if(delta<0)
 457                 delta=-delta;
 458
 459         if(delta>mdrun->dp)
 460                 return FALSE;
 461
 462         return TRUE;
 463 }
 464
 465 int check_temperature(t_moldyn *moldyn,t_mdrun *mdrun) {
 466
 467         double delta;
 468
 469         if(!(mdrun->sattr&SATTR_TRELAX))
 470                 return TRUE;
 471
 472         delta=moldyn->t_avg-moldyn->t_ref;
 473
 474         if(delta<0)
 475                 delta=-delta;
 476
 477         if(delta>mdrun->dt)
 478                 return FALSE;
 479
 480         return TRUE;
 481 }
 482
 483 int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 484
 485         t_insert_atoms_params *iap;
 486         t_stage *stage;
 487         t_atom *atom;
 488         t_3dvec r,v,dist;
 489         double d,dmin;
 490         int cnt,i;
 491         double x,y,z;
 492         double x0,y0,z0;
 493         u8 cr_check,run;
 494
 495         stage=mdrun->stage.current->data;
 496         iap=stage->params;
 497
 498         cr_check=FALSE;
 499
 500         v.x=0.0; v.y=0.0; v.z=0.0;
 501
 502         switch(iap->type) {
 503                 case INS_TOTAL:
 504                         x=moldyn->dim.x;
 505                         x0=0.0;
 506                         y=moldyn->dim.y;
 507                         y0=0.0;
 508                         z=moldyn->dim.z;
 509                         z0=0.0;
 510                         cr_check=TRUE;
 511                         break;
 512                 case INS_REGION:
 513                         x=iap->x1-iap->x0;
 514                         x0=iap->x0;
 515                         y=iap->y1-iap->y0;
 516                         y0=iap->y0;
 517                         z=iap->z1-iap->z0;
 518                         z0=iap->z0;
 519                         cr_check=TRUE;
 520                         break;
 521                 default:
 522                         printf("%s unknown insertion mode: %02x\n",
 523                                ME,iap->type);
 524                         return -1;
 525         }
 526
 527         cnt=0;
 528         while(cnt<iap->ins_atoms) {
 529                 run=1;
 530                 while(run) {
 531                         r.x=(rand_get_double(&(moldyn->random))-0.5)*x+x0;
 532                         r.y=(rand_get_double(&(moldyn->random))-0.5)*y+y0;
 533                         r.z=(rand_get_double(&(moldyn->random))-0.5)*z+z0;
 534                         run=0;
 535                         if(cr_check==TRUE) {
 536                                 dmin=1000;      // for sure too high!
 537                                 for(i=0;i<moldyn->count;i++) {
 538                                         atom=&(moldyn->atom[i]);
 539                                         v3_sub(&dist,&(atom->r),&r);
 540                                         check_per_bound(moldyn,&dist);
 541                                         d=v3_absolute_square(&dist);
 542                                         if(d<(iap->cr*iap->cr)) {
 543                                                 run=1;
 544                                                 break;
 545                                         }
 546                                         if(d<dmin)
 547                                                 dmin=d;
 548                                 }
 549                         }
 550                 }
 551                 add_atom(moldyn,iap->element,pse_mass[iap->element],
 552                          iap->brand,iap->attr,&r,&v);
 553                 printf("%s atom inserted: %f %f %f | d squared = %f\n",
 554                        ME,r.x,r.y,r.z,dmin);
 555                 cnt+=1;
 556         }
 557
 558         return 0;
 559 }
 560
 561 int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
 562
 563         t_stage *stage;
 564         t_chaattr_params *cap;
 565         t_atom *atom;
 566         int i;
 567
 568         stage=mdrun->stage.current->data;
 569         cap=stage->params;
 570
 571         for(i=0;i<moldyn->count;i++) {
 572                 atom=&(moldyn->atom[i]);
 573                 if(cap->type&CHAATTR_ELEMENT) {
 574                         if(cap->element!=atom->element)
 575                                 continue;
 576                 }
 577                 if(cap->type&CHAATTR_REGION) {
 578                         if(cap->x0<atom->r.x)
 579                                 continue;
 580                         if(cap->y0<atom->r.y)
 581                                 continue;
 582                         if(cap->z0<atom->r.z)
 583                                 continue;
 584                         if(cap->x1>atom->r.x)
 585                                 continue;
 586                         if(cap->y1>atom->r.y)
 587                                 continue;
 588                         if(cap->z1>atom->r.z)
 589                                 continue;
 590                 }
 591                 atom->attr=cap->attr;
 592         }
 593
 594         return 0;
 595 }
 596
 597 int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
 598
 599         t_stage *stage;
 600         t_chsattr_params *csp;
 601
 602         stage=mdrun->stage.current->data;
 603         csp=stage->params;
 604
 605         if(csp->type&CHSATTR_PCTRL) {
 606                 if(csp->ptau>0)
 607                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
 608                 else
 609                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
 610         }
 611         if(csp->type&CHSATTR_TCTRL) {
 612                 if(csp->ttau>0)
 613                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
 614                 else
 615                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
 616         }
 617         if(csp->type&CHSATTR_PRELAX) {
 618                 if(csp->dp<0)
 619                         mdrun->sattr&=(~(SATTR_PRELAX));
 620                 else
 621                         mdrun->sattr|=SATTR_PRELAX;
 622                 mdrun->dp=csp->dp;
 623         }
 624         if(csp->type&CHSATTR_TRELAX) {
 625                 if(csp->dt<0)
 626                         mdrun->sattr&=(~(SATTR_TRELAX));
 627                 else
 628                         mdrun->sattr|=SATTR_TRELAX;
 629                 mdrun->dt=csp->dt;
 630         }
 631         if(csp->type&CHSATTR_AVGRST) {
 632                 if(csp->avgrst)
 633                         mdrun->sattr|=SATTR_AVGRST;
 634                 else
 635                         mdrun->sattr&=(~(SATTR_AVGRST));
 636         }
 637         if(csp->type&CHSATTR_RSTEPS) {
 638                 mdrun->relax_steps=csp->rsteps;
 639         }
 640
 641         return 0;
 642 }
 643
 644 #define stage_print(m)  if(!(stage->executed)) \
 645                                 printf("%s",m)
 646
 647 int mdrun_hook(void *ptr1,void *ptr2) {
 648
 649         t_moldyn *moldyn;
 650         t_mdrun *mdrun;
 651         t_stage *stage;
 652         t_list *sl;
 653         int steps;
 654         double tau;
 655         u8 change_stage;
 656
 657         t_insert_atoms_params *iap;
 658         t_continue_params *cp;
 659         t_anneal_params *ap;
 660
 661         moldyn=ptr1;
 662         mdrun=ptr2;
 663
 664         sl=&(mdrun->stage);
 665
 666         change_stage=FALSE;
 667
 668         /* return immediately if there are no more stage */
 669         if(sl->current==NULL)
 670                 return 0;
 671
 672         /* get stage description */
 673         stage=sl->current->data;
 674
 675         /* default steps and tau values */
 676         steps=mdrun->relax_steps;
 677         tau=mdrun->timestep;
 678
 679         /* check whether relaxation steps are necessary */
 680         if(!((check_pressure(moldyn,mdrun)==FALSE)|\
 681              (check_temperature(moldyn,mdrun)==FALSE))) {
 682
 683                 /* be verbose */
 684                 stage_print("\n###########################\n");
 685                 stage_print("# [mdrun] executing stage #\n");
 686                 stage_print("###########################\n\n");
 687
 688                 /* stage specific stuff */
 689                 switch(stage->type) {
 690                         case STAGE_INSERT_ATOMS:
 691                                 stage_print("  -> insert atoms\n\n");
 692                                 iap=stage->params;
 693                                 if(iap->cnt_steps==iap->ins_steps) {
 694                                         change_stage=TRUE;
 695                                         break;
 696                                 }
 697                                 insert_atoms(moldyn,mdrun);
 698                                 iap->cnt_steps+=1;
 699                                         break;
 700                         case STAGE_CONTINUE:
 701                                 stage_print("  -> continue\n\n");
 702                                 if(stage->executed==TRUE) {
 703                                         change_stage=TRUE;
 704                                         break;
 705                                 }
 706                                 cp=stage->params;
 707                                 steps=cp->runs;
 708                                         break;
 709                         case STAGE_ANNEAL:
 710                                 stage_print("  -> anneal\n\n");
 711                                 ap=stage->params;
 712                                 if(ap->count==ap->runs) {
 713                                         change_stage=TRUE;
 714                                         break;
 715                                 }
 716                                 set_temperature(moldyn,moldyn->t_ref+ap->dt);
 717                                 ap->count+=1;
 718                                 break;
 719                         case STAGE_CHAATTR:
 720                                 stage_print("  -> chaattr\n\n");
 721                                 chaatr(moldyn,mdrun);
 722                                 change_stage=TRUE;
 723                                 break;
 724                         case STAGE_CHSATTR:
 725                                 stage_print("  -> chsattr\n\n");
 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 structs */
 770         memset(&mdrun,0,sizeof(t_mdrun));
 771         memset(&moldyn,0,sizeof(t_moldyn));
 772
 773         /* parse arguments */
 774         if(mdrun_parse_argv(&mdrun,argc,argv)<0)
 775                 return -1;
 776
 777         /* initialize list system */
 778         list_init_f(&(mdrun.stage));
 779
 780         /* parse config file */
 781         mdrun_parse_config(&mdrun);
 782
 783         /* reset the stage list */
 784         list_reset_f(&(mdrun.stage));
 785
 786         /* sanity check! */
 787
 788         /* prepare simulation */
 789         moldyn_init(&moldyn,argc,argv);
 790         if(set_int_alg(&moldyn,mdrun.intalgo)<0)
 791                 return -1;
 792         set_cutoff(&moldyn,mdrun.cutoff);
 793         if(set_potential(&moldyn,mdrun.potential)<0)
 794                 return -1;
 795         switch(mdrun.potential) {
 796                 case MOLDYN_POTENTIAL_AM:
 797                         albe_mult_set_params(&moldyn,
 798                                              mdrun.element1,
 799                                              mdrun.element2);
 800                         break;
 801                 case MOLDYN_POTENTIAL_TM:
 802                         tersoff_mult_set_params(&moldyn,
 803                                                 mdrun.element1,
 804                                                 mdrun.element2);
 805                         break;
 806                 case MOLDYN_POTENTIAL_HO:
 807                         harmonic_oscillator_set_params(&moldyn,mdrun.element1);
 808                         break;
 809                 case MOLDYN_POTENTIAL_LJ:
 810                         lennard_jones_set_params(&moldyn,mdrun.element1);
 811                         break;
 812                 default:
 813                         printf("%s unknown potential: %02x\n",
 814                                ME,mdrun.potential);
 815                         return -1;
 816         }
 817         set_dim(&moldyn,mdrun.dim.x,mdrun.dim.y,mdrun.dim.z,mdrun.vis);
 818         set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
 819         switch(mdrun.lattice) {
 820                 case FCC:
 821                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
 822                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
 823                                        mdrun.ly,mdrun.lz,NULL);
 824                         break;
 825                 case DIAMOND:
 826                         create_lattice(&moldyn,DIAMOND,mdrun.lc,mdrun.element1,
 827                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
 828                                        mdrun.ly,mdrun.lz,NULL);
 829                         break;
 830                 case ZINCBLENDE:
 831                         o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
 832                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
 833                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
 834                                        mdrun.ly,mdrun.lz,&o);
 835                         o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
 836                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
 837                                        mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
 838                                        mdrun.ly,mdrun.lz,&o);
 839                         break;
 840                 default:
 841                         printf("%s unknown lattice type: %02x\n",
 842                                ME,mdrun.lattice);
 843                         return -1;
 844         }
 845         moldyn_bc_check(&moldyn);
 846         set_temperature(&moldyn,mdrun.temperature);
 847         set_pressure(&moldyn,mdrun.pressure);
 848         thermal_init(&moldyn,TRUE);
 849         moldyn_add_schedule(&moldyn,mdrun.prerun,mdrun.timestep);
 850         moldyn_set_log_dir(&moldyn,mdrun.sdir);
 851         moldyn_set_report(&moldyn,"CHANGE ME","CHANGE ME TOO");
 852         if(mdrun.elog)
 853                 moldyn_set_log(&moldyn,LOG_TOTAL_ENERGY,mdrun.elog);
 854         if(mdrun.tlog)
 855                 moldyn_set_log(&moldyn,LOG_TEMPERATURE,mdrun.tlog);
 856         if(mdrun.plog)
 857                 moldyn_set_log(&moldyn,LOG_PRESSURE,mdrun.plog);
 858         if(mdrun.vlog)
 859                 moldyn_set_log(&moldyn,LOG_VOLUME,mdrun.vlog);
 860         if(mdrun.visualize)
 861                 moldyn_set_log(&moldyn,VISUAL_STEP,mdrun.visualize);
 862         if(mdrun.save)
 863                 moldyn_set_log(&moldyn,SAVE_STEP,mdrun.save);
 864         moldyn_set_log(&moldyn,CREATE_REPORT,0);
 865         set_avg_skip(&moldyn,mdrun.avgskip);
 866
 867         /* prepare the hook function */
 868         moldyn_set_schedule_hook(&moldyn,&mdrun_hook,&mdrun);
 869
 870         /* run the simulation */
 871         moldyn_integrate(&moldyn);
 872
 873         /* shutdown */
 874         moldyn_shutdown(&moldyn);
 875         del_stages(&mdrun);
 876         list_destroy_f(&(mdrun.stage));
 877
 878         return 0;
 879 }