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])*BAR;
 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.brand=atoi(word[5]);
 376                                 for(i=0;i<strlen(word[6]);i++) {
 377                                         switch(word[6][i]) {
 378                                                 case 'b':
 379                                                         iap.attr|=ATOM_ATTR_VB;
 380                                                         break;
 381                                                 case 'h':
 382                                                         iap.attr|=ATOM_ATTR_HB;
 383                                                         break;
 384                                                 case 'v':
 385                                                         iap.attr|=ATOM_ATTR_VA;
 386                                                         break;
 387                                                 case 'f':
 388                                                         iap.attr|=ATOM_ATTR_FP;
 389                                                         break;
 390                                                 case '1':
 391                                                         iap.attr|=ATOM_ATTR_1BP;
 392                                                         break;
 393                                                 case '2':
 394                                                         iap.attr|=ATOM_ATTR_2BP;
 395                                                         break;
 396                                                 case '3':
 397                                                         iap.attr|=ATOM_ATTR_3BP;
 398                                                         break;
 399                                                 default:
 400                                                         break;
 401                                         }
 402                                 }
 403                                 switch(word[7][0]) {
 404                                         // insertion types
 405                                         case 'p':
 406                                                 iap.type=INS_POS;
 407                                                 iap.x0=atof(word[8]);
 408                                                 iap.y0=atof(word[9]);
 409                                                 iap.z0=atof(word[10]);
 410                                                 break;
 411                                         case 'r':
 412                                                 if(word[8][0]=='t') {
 413                                                         iap.type=INS_TOTAL;
 414                                                         iap.cr=atof(word[9]);
 415                                                 }
 416                                                 else {
 417                                                         iap.type=INS_REGION;
 418                                                         iap.x0=atof(word[8]);
 419                                                         iap.y0=atof(word[9]);
 420                                                         iap.z0=atof(word[10]);
 421                                                         iap.x1=atof(word[11]);
 422                                                         iap.y1=atof(word[12]);
 423                                                         iap.z1=atof(word[13]);
 424                                                         iap.cr=atof(word[14]);
 425                                                 }
 426                                         default:
 427                                                 break;
 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
 468         delta=moldyn->p_avg-moldyn->p_ref;
 469
 470         if(delta<0)
 471                 delta=-delta;
 472
 473         if(delta>mdrun->dp)
 474                 return FALSE;
 475
 476         return TRUE;
 477 }
 478
 479 int check_temperature(t_moldyn *moldyn,t_mdrun *mdrun) {
 480
 481         double delta;
 482
 483         if(!(mdrun->sattr&SATTR_TRELAX))
 484                 return TRUE;
 485
 486         delta=moldyn->t_avg-moldyn->t_ref;
 487
 488         if(delta<0)
 489                 delta=-delta;
 490
 491         if(delta>mdrun->dt)
 492                 return FALSE;
 493
 494         return TRUE;
 495 }
 496
 497 int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 498
 499         t_insert_atoms_params *iap;
 500         t_stage *stage;
 501         t_atom *atom;
 502         t_3dvec r,v,dist;
 503         double d,dmin,o;
 504         int cnt,i;
 505         double x,y,z;
 506         double x0,y0,z0;
 507         u8 cr_check,run;
 508
 509         stage=mdrun->stage.current->data;
 510         iap=stage->params;
 511
 512         cr_check=FALSE;
 513
 514         v.x=0.0; v.y=0.0; v.z=0.0;
 515         x=0; y=0; z=0;
 516         o=0; dmin=0;
 517
 518         switch(mdrun->lattice) {
 519                 case CUBIC:
 520                         o=0.5*mdrun->lc;
 521                         break;
 522                 case FCC:
 523                         o=0.25*mdrun->lc;
 524                         break;
 525                 case DIAMOND:
 526                 case ZINCBLENDE:
 527                         o=0.125*mdrun->lc;
 528                         break;
 529                 default:
 530                         break;
 531         }
 532
 533         switch(iap->type) {
 534                 case INS_TOTAL:
 535                         x=moldyn->dim.x;
 536                         x0=-x/2.0;
 537                         y=moldyn->dim.y;
 538                         y0=-y/2.0;
 539                         z=moldyn->dim.z;
 540                         z0=-z/2.0;
 541                         cr_check=TRUE;
 542                         break;
 543                 case INS_REGION:
 544                         x=iap->x1-iap->x0;
 545                         x0=iap->x0;
 546                         y=iap->y1-iap->y0;
 547                         y0=iap->y0;
 548                         z=iap->z1-iap->z0;
 549                         z0=iap->z0;
 550                         cr_check=TRUE;
 551                         break;
 552                 case INS_POS:
 553                         x0=iap->x0;
 554                         y0=iap->y0;
 555                         z0=iap->z0;
 556                         cr_check=FALSE;
 557                         break;
 558                 default:
 559                         printf("%s unknown insertion mode: %02x\n",
 560                                ME,iap->type);
 561                         return -1;
 562         }
 563
 564         cnt=0;
 565         while(cnt<iap->ins_atoms) {
 566                 run=1;
 567                 while(run) {
 568                         if(iap->type!=INS_POS) {
 569                                 r.x=rand_get_double(&(moldyn->random))*x;
 570                                 r.y=rand_get_double(&(moldyn->random))*y;
 571                                 r.z=rand_get_double(&(moldyn->random))*z;
 572                         }
 573                         else {
 574                                 r.x=0.0;
 575                                 r.y=0.0;
 576                                 r.z=0.0;
 577                         }
 578                         r.x+=x0;
 579                         r.y+=y0;
 580                         r.z+=z0;
 581                         // offset
 582                         if(iap->type!=INS_TOTAL) {
 583                                 r.x+=o;
 584                                 r.y+=o;
 585                                 r.z+=o;
 586                         }
 587                         run=0;
 588                         if(cr_check==TRUE) {
 589                                 dmin=1000;      // for sure too high!
 590                                 for(i=0;i<moldyn->count;i++) {
 591                                         atom=&(moldyn->atom[i]);
 592                                         v3_sub(&dist,&(atom->r),&r);
 593                                         check_per_bound(moldyn,&dist);
 594                                         d=v3_absolute_square(&dist);
 595                                         if(d<(iap->cr*iap->cr)) {
 596                                                 run=1;
 597                                                 break;
 598                                         }
 599                                         if(d<dmin)
 600                                                 dmin=d;
 601                                 }
 602                         }
 603                 }
 604                 add_atom(moldyn,iap->element,pse_mass[iap->element],
 605                          iap->brand,iap->attr,&r,&v);
 606                 printf("%s atom inserted (%d/%d): %f %f %f\n",
 607                        ME,(iap->cnt_steps+1)*iap->ins_atoms,
 608                        iap->ins_steps*iap->ins_atoms,r.x,r.y,r.z);
 609                 printf("  -> d2 = %f/%f\n",dmin,iap->cr*iap->cr);
 610                 cnt+=1;
 611         }
 612
 613         return 0;
 614 }
 615
 616 int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
 617
 618         t_stage *stage;
 619         t_chaattr_params *cap;
 620         t_atom *atom;
 621         int i;
 622
 623         stage=mdrun->stage.current->data;
 624         cap=stage->params;
 625
 626         for(i=0;i<moldyn->count;i++) {
 627                 atom=&(moldyn->atom[i]);
 628                 if(cap->type&CHAATTR_ELEMENT) {
 629                         if(cap->element!=atom->element)
 630                                 continue;
 631                 }
 632                 if(cap->type&CHAATTR_REGION) {
 633                         if(cap->x0<atom->r.x)
 634                                 continue;
 635                         if(cap->y0<atom->r.y)
 636                                 continue;
 637                         if(cap->z0<atom->r.z)
 638                                 continue;
 639                         if(cap->x1>atom->r.x)
 640                                 continue;
 641                         if(cap->y1>atom->r.y)
 642                                 continue;
 643                         if(cap->z1>atom->r.z)
 644                                 continue;
 645                 }
 646                 atom->attr=cap->attr;
 647         }
 648
 649         return 0;
 650 }
 651
 652 int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
 653
 654         t_stage *stage;
 655         t_chsattr_params *csp;
 656
 657         stage=mdrun->stage.current->data;
 658         csp=stage->params;
 659
 660         if(csp->type&CHSATTR_PCTRL) {
 661                 if(csp->ptau>0)
 662                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
 663                 else
 664                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
 665         }
 666         if(csp->type&CHSATTR_TCTRL) {
 667                 if(csp->ttau>0)
 668                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
 669                 else
 670                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
 671         }
 672         if(csp->type&CHSATTR_PRELAX) {
 673                 if(csp->dp<0)
 674                         mdrun->sattr&=(~(SATTR_PRELAX));
 675                 else
 676                         mdrun->sattr|=SATTR_PRELAX;
 677                 mdrun->dp=csp->dp;
 678         }
 679         if(csp->type&CHSATTR_TRELAX) {
 680                 if(csp->dt<0)
 681                         mdrun->sattr&=(~(SATTR_TRELAX));
 682                 else
 683                         mdrun->sattr|=SATTR_TRELAX;
 684                 mdrun->dt=csp->dt;
 685         }
 686         if(csp->type&CHSATTR_AVGRST) {
 687                 if(csp->avgrst)
 688                         mdrun->sattr|=SATTR_AVGRST;
 689                 else
 690                         mdrun->sattr&=(~(SATTR_AVGRST));
 691         }
 692         if(csp->type&CHSATTR_RSTEPS) {
 693                 mdrun->relax_steps=csp->rsteps;
 694         }
 695
 696         return 0;
 697 }
 698
 699 #define stage_print(m)  if(!(stage->executed)) \
 700                                 printf("%s",m)
 701
 702 int mdrun_hook(void *ptr1,void *ptr2) {
 703
 704         t_moldyn *moldyn;
 705         t_mdrun *mdrun;
 706         t_stage *stage;
 707         t_list *sl;
 708         int steps;
 709         double tau;
 710         u8 change_stage;
 711
 712         t_insert_atoms_params *iap;
 713         t_continue_params *cp;
 714         t_anneal_params *ap;
 715
 716         moldyn=ptr1;
 717         mdrun=ptr2;
 718
 719         sl=&(mdrun->stage);
 720
 721         change_stage=FALSE;
 722
 723         /* return immediately if there are no more stage */
 724         if(sl->current==NULL)
 725                 return 0;
 726
 727         /* get stage description */
 728         stage=sl->current->data;
 729
 730         /* default steps and tau values */
 731         steps=mdrun->relax_steps;
 732         tau=mdrun->timestep;
 733
 734         /* check whether relaxation steps are necessary */
 735         if((check_pressure(moldyn,mdrun)==TRUE)&\
 736            (check_temperature(moldyn,mdrun)==TRUE)) {
 737
 738                 /* be verbose */
 739                 stage_print("\n###########################\n");
 740                 stage_print("# [mdrun] executing stage #\n");
 741                 stage_print("###########################\n\n");
 742
 743                 /* stage specific stuff */
 744                 switch(stage->type) {
 745                         case STAGE_INSERT_ATOMS:
 746                                 stage_print("  -> insert atoms\n\n");
 747                                 iap=stage->params;
 748                                 if(iap->cnt_steps==iap->ins_steps) {
 749                                         change_stage=TRUE;
 750                                         break;
 751                                 }
 752                                 insert_atoms(moldyn,mdrun);
 753                                 iap->cnt_steps+=1;
 754                                         break;
 755                         case STAGE_CONTINUE:
 756                                 stage_print("  -> continue\n\n");
 757                                 if(stage->executed==TRUE) {
 758                                         change_stage=TRUE;
 759                                         break;
 760                                 }
 761                                 cp=stage->params;
 762                                 steps=cp->runs;
 763                                         break;
 764                         case STAGE_ANNEAL:
 765                                 stage_print("  -> anneal\n\n");
 766                                 ap=stage->params;
 767                                 if(ap->count==ap->runs) {
 768                                         change_stage=TRUE;
 769                                         break;
 770                                 }
 771                                 if(moldyn->t_ref+ap->dt>=0.0)
 772                                         set_temperature(moldyn,
 773                                                         moldyn->t_ref+ap->dt);
 774                                 ap->count+=1;
 775                                 break;
 776                         case STAGE_CHAATTR:
 777                                 stage_print("  -> chaattr\n\n");
 778                                 chaatr(moldyn,mdrun);
 779                                 change_stage=TRUE;
 780                                 break;
 781                         case STAGE_CHSATTR:
 782                                 stage_print("  -> chsattr\n\n");
 783                                 chsattr(moldyn,mdrun);
 784                                 change_stage=TRUE;
 785                                 break;
 786                         default:
 787                                 printf("%s unknwon stage type\n",ME);
 788                                 break;
 789                 }
 790
 791                 /* mark as executed */
 792                 stage->executed=TRUE;
 793
 794                 /* change state */
 795                 if(change_stage==TRUE) {
 796                         printf("%s finished stage\n",ME);
 797                         if(list_next_f(sl)==L_NO_NEXT_ELEMENT) {
 798                                 printf("%s no more stages\n",ME);
 799                                 return 0;
 800                         }
 801                         steps=0;
 802                         tau=mdrun->timestep;
 803                 }
 804
 805         }
 806         else {
 807
 808                 /* averages */
 809                 if(mdrun->sattr&SATTR_AVGRST)
 810                         average_reset(moldyn);
 811
 812         }
 813
 814         /* continue simulation */
 815         moldyn_add_schedule(moldyn,steps,tau);
 816
 817         return 0;
 818 }
 819
 820 int main(int argc,char **argv) {
 821
 822         t_mdrun mdrun;
 823         t_moldyn moldyn;
 824         t_3dvec o;
 825
 826         /* clear structs */
 827         memset(&mdrun,0,sizeof(t_mdrun));
 828         memset(&moldyn,0,sizeof(t_moldyn));
 829
 830         /* parse arguments */
 831         if(mdrun_parse_argv(&mdrun,argc,argv)<0)
 832                 return -1;
 833
 834         /* initialize list system */
 835         list_init_f(&(mdrun.stage));
 836
 837         /* parse config file */
 838         mdrun_parse_config(&mdrun);
 839
 840         /* reset the stage list */
 841         list_reset_f(&(mdrun.stage));
 842
 843         /* sanity check! */
 844
 845         /* prepare simulation */
 846         moldyn_init(&moldyn,argc,argv);
 847         if(set_int_alg(&moldyn,mdrun.intalgo)<0)
 848                 return -1;
 849         set_cutoff(&moldyn,mdrun.cutoff);
 850         if(set_potential(&moldyn,mdrun.potential)<0)
 851                 return -1;
 852         switch(mdrun.potential) {
 853                 case MOLDYN_POTENTIAL_AM:
 854                         albe_mult_set_params(&moldyn,
 855                                              mdrun.element1,
 856                                              mdrun.element2);
 857                         break;
 858                 case MOLDYN_POTENTIAL_TM:
 859                         tersoff_mult_set_params(&moldyn,
 860                                                 mdrun.element1,
 861                                                 mdrun.element2);
 862                         break;
 863                 case MOLDYN_POTENTIAL_HO:
 864                         harmonic_oscillator_set_params(&moldyn,mdrun.element1);
 865                         break;
 866                 case MOLDYN_POTENTIAL_LJ:
 867                         lennard_jones_set_params(&moldyn,mdrun.element1);
 868                         break;
 869                 default:
 870                         printf("%s unknown potential: %02x\n",
 871                                ME,mdrun.potential);
 872                         return -1;
 873         }
 874         set_dim(&moldyn,mdrun.dim.x,mdrun.dim.y,mdrun.dim.z,mdrun.vis);
 875         set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
 876         switch(mdrun.lattice) {
 877                 case FCC:
 878                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
 879                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
 880                                        mdrun.ly,mdrun.lz,NULL);
 881                         break;
 882                 case DIAMOND:
 883                         create_lattice(&moldyn,DIAMOND,mdrun.lc,mdrun.element1,
 884                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
 885                                        mdrun.ly,mdrun.lz,NULL);
 886                         break;
 887                 case ZINCBLENDE:
 888                         o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
 889                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
 890                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
 891                                        mdrun.ly,mdrun.lz,&o);
 892                         o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
 893                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
 894                                        mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
 895                                        mdrun.ly,mdrun.lz,&o);
 896                         break;
 897                 default:
 898                         printf("%s unknown lattice type: %02x\n",
 899                                ME,mdrun.lattice);
 900                         return -1;
 901         }
 902         moldyn_bc_check(&moldyn);
 903         set_temperature(&moldyn,mdrun.temperature);
 904         set_pressure(&moldyn,mdrun.pressure);
 905         thermal_init(&moldyn,TRUE);
 906         moldyn_add_schedule(&moldyn,mdrun.prerun,mdrun.timestep);
 907         moldyn_set_log_dir(&moldyn,mdrun.sdir);
 908         moldyn_set_report(&moldyn,"CHANGE ME","CHANGE ME TOO");
 909         if(mdrun.elog)
 910                 moldyn_set_log(&moldyn,LOG_TOTAL_ENERGY,mdrun.elog);
 911         if(mdrun.tlog)
 912                 moldyn_set_log(&moldyn,LOG_TEMPERATURE,mdrun.tlog);
 913         if(mdrun.plog)
 914                 moldyn_set_log(&moldyn,LOG_PRESSURE,mdrun.plog);
 915         if(mdrun.vlog)
 916                 moldyn_set_log(&moldyn,LOG_VOLUME,mdrun.vlog);
 917         if(mdrun.visualize)
 918                 moldyn_set_log(&moldyn,VISUAL_STEP,mdrun.visualize);
 919         if(mdrun.save)
 920                 moldyn_set_log(&moldyn,SAVE_STEP,mdrun.save);
 921         moldyn_set_log(&moldyn,CREATE_REPORT,0);
 922         set_avg_skip(&moldyn,mdrun.avgskip);
 923
 924         /* prepare the hook function */
 925         moldyn_set_schedule_hook(&moldyn,&mdrun_hook,&mdrun);
 926
 927         /* run the simulation */
 928         moldyn_integrate(&moldyn);
 929
 930         /* shutdown */
 931         moldyn_shutdown(&moldyn);
 932         del_stages(&mdrun);
 933         list_destroy_f(&(mdrun.stage));
 934
 935         return 0;
 936 }