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 /* pse */
  21 #define PSE_MASS
  22 #include "pse.h"
  23 #undef PSE_MASS
  24
  25 #define ME      "[mdrun]"
  26
  27 /*
  28  * parse function
  29  */
  30
  31 int mdrun_usage(void) {
  32
  33         printf("%s usage:\n",ME);
  34
  35         return 0;
  36 }
  37
  38 int mdrun_parse_argv(t_mdrun *mdrun,int argc,char **argv) {
  39
  40         int i;
  41
  42         for(i=1;i<argc;i++) {
  43
  44                 if(argv[i][0]!='-') {
  45                         printf("%s unknown switch: %s\n",ME,argv[i]);
  46                         return -1;
  47                 }
  48
  49                 switch(argv[i][1]) {
  50                         case 'c':
  51                                 strncpy(mdrun->cfile,argv[++i],128);
  52                                 break;
  53                         case 's':
  54                                 strncpy(mdrun->sdir,argv[++i],128);
  55                                 break;
  56                         case 'h':
  57                                 mdrun_usage();
  58                                 break;
  59                         default:
  60                                 printf("%s unknown option: %s\n",ME,argv[i]);
  61                                 mdrun_usage();
  62                                 return -1;
  63                 }
  64
  65         }
  66
  67         return 0;
  68 }
  69
  70 int del_stages(t_mdrun *mdrun) {
  71
  72         t_list *sl;
  73         t_stage *stage;
  74
  75         sl=&(mdrun->stage);
  76
  77         list_reset_f(sl);
  78
  79         if(sl->start==NULL)
  80                 return 0;
  81
  82         do {
  83                 stage=sl->current->data;
  84                 free(stage->params);
  85                 free(stage);
  86         } while(list_next_f(sl)!=L_NO_NEXT_ELEMENT);
  87
  88         return 0;
  89 }
  90
  91 int add_stage(t_mdrun *mdrun,u8 type,void *params) {
  92
  93         int psize;
  94
  95         t_stage *stage;
  96
  97         switch(type) {
  98                 case STAGE_DISPLACE_ATOM:
  99                         psize=sizeof(t_displace_atom_params);
 100                         break;
 101                 case STAGE_INSERT_ATOMS:
 102                         psize=sizeof(t_insert_atoms_params);
 103                         break;
 104                 case STAGE_INSERT_MIXED_ATOMS:
 105                         psize=sizeof(t_insert_mixed_atoms_params);
 106                         break;
 107                 case STAGE_CONTINUE:
 108                         psize=sizeof(t_continue_params);
 109                         break;
 110                 case STAGE_ANNEAL:
 111                         psize=sizeof(t_anneal_params);
 112                         break;
 113                 case STAGE_CHAATTR:
 114                         psize=sizeof(t_chaattr_params);
 115                         break;
 116                 case STAGE_CHSATTR:
 117                         psize=sizeof(t_chsattr_params);
 118                         break;
 119                 case STAGE_SET_TEMP:
 120                         psize=sizeof(t_set_temp_params);
 121                         break;
 122                 case STAGE_SET_TIMESTEP:
 123                         psize=sizeof(t_set_timestep_params);
 124                         break;
 125                 case STAGE_FILL:
 126                         psize=sizeof(t_fill_params);
 127                         break;
 128                 case STAGE_THERMAL_INIT:
 129                         psize=0;
 130                         break;
 131                 default:
 132                         printf("%s unknown stage type: %02x\n",ME,type);
 133                         return -1;
 134         }
 135
 136         stage=malloc(sizeof(t_stage));
 137         if(stage==NULL) {
 138                 perror("[mdrun] malloc (add stage)");
 139                 return -1;
 140         }
 141
 142         stage->type=type;
 143         stage->executed=FALSE;
 144
 145         stage->params=malloc(psize);
 146         if(stage->params==NULL) {
 147                 perror("[mdrun] malloc (stage params)");
 148                 return -1;
 149         }
 150
 151         memcpy(stage->params,params,psize);
 152
 153         list_add_immediate_f(&(mdrun->stage),stage);
 154
 155         return 0;
 156 }
 157
 158 int mdrun_parse_config(t_mdrun *mdrun) {
 159
 160         int fd,ret;
 161         char error[128];
 162         char line[128];
 163         char *wptr;
 164         char word[16][64];
 165         int wcnt;
 166         int i,o;
 167
 168         t_displace_atom_params dap;
 169         t_insert_atoms_params iap;
 170         t_insert_mixed_atoms_params imp;
 171         t_continue_params cp;
 172         t_anneal_params ap;
 173         t_chaattr_params cap;
 174         t_chsattr_params csp;
 175         t_set_temp_params stp;
 176         t_set_timestep_params stsp;
 177         t_fill_params fp;
 178
 179         /* open config file */
 180         fd=open(mdrun->cfile,O_RDONLY);
 181         if(fd<0) {
 182                 snprintf(error,128,"%s open cfile %s",ME,mdrun->cfile);
 183                 perror(error);
 184                 return fd;
 185         }
 186
 187         /* read, parse, set */
 188         ret=1;
 189         while(ret>0) {
 190
 191                 /* read */
 192                 ret=get_line(fd,line,128);
 193
 194                 /* parse */
 195
 196                 // ignore # lines and \n
 197                 if((line[0]=='#')|(ret==1))
 198                         continue;
 199
 200                 // reset
 201                 memset(&iap,0,sizeof(t_insert_atoms_params));
 202                 memset(&imp,0,sizeof(t_insert_mixed_atoms_params));
 203                 memset(&cp,0,sizeof(t_continue_params));
 204                 memset(&ap,0,sizeof(t_anneal_params));
 205                 memset(&cap,0,sizeof(t_chaattr_params));
 206                 memset(&csp,0,sizeof(t_chsattr_params));
 207                 memset(&stp,0,sizeof(t_set_temp_params));
 208                 memset(&stsp,0,sizeof(t_set_timestep_params));
 209                 memset(&fp,0,sizeof(t_fill_params));
 210
 211                 // get command + args
 212                 wcnt=0;
 213                 while(1) {
 214                         if(wcnt)
 215                                 wptr=strtok(NULL," \t");
 216                         else
 217                                 wptr=strtok(line," \t");
 218                         if(wptr==NULL)
 219                                 break;
 220                         strncpy(word[wcnt],wptr,64);
 221                         wcnt+=1;
 222                 }
 223
 224                 if(!strncmp(word[0],"potential",9)) {
 225                         if(!strncmp(word[1],"albe",4))
 226                                 mdrun->potential=MOLDYN_POTENTIAL_AM;
 227                         if(!strncmp(word[1],"tersoff",7))
 228                                 mdrun->potential=MOLDYN_POTENTIAL_TM;
 229                         if(!strncmp(word[1],"ho",2))
 230                                 mdrun->potential=MOLDYN_POTENTIAL_HO;
 231                         if(!strncmp(word[1],"lj",2))
 232                                 mdrun->potential=MOLDYN_POTENTIAL_LJ;
 233                 }
 234                 else if(!strncmp(word[0],"continue",8))
 235                         strncpy(mdrun->continue_file,word[1],128);
 236                 else if(!strncmp(word[0],"cutoff",6))
 237                         mdrun->cutoff=atof(word[1]);
 238                 else if(!strncmp(word[0],"nnd",3))
 239                         mdrun->nnd=atof(word[1]);
 240                 else if(!strncmp(word[0],"intalgo",7)) {
 241                         if(!strncmp(word[1],"verlet",5))
 242                                 mdrun->intalgo=MOLDYN_INTEGRATE_VERLET;
 243                 }
 244                 else if(!strncmp(word[0],"timestep",8))
 245                         mdrun->timestep=atof(word[1]);
 246                 else if(!strncmp(word[0],"volume",6)) {
 247                         mdrun->dim.x=atof(word[1]);
 248                         mdrun->dim.y=atof(word[2]);
 249                         mdrun->dim.z=atof(word[3]);
 250                         if(strncmp(word[4],"0",1))
 251                                 mdrun->vis=TRUE;
 252                 }
 253                 else if(!strncmp(word[0],"pbc",3)) {
 254                         if(strncmp(word[1],"0",1))
 255                                 mdrun->pbcx=TRUE;
 256                         else
 257                                 mdrun->pbcx=FALSE;
 258                         if(strncmp(word[2],"0",1))
 259                                 mdrun->pbcy=TRUE;
 260                         else
 261                                 mdrun->pbcy=FALSE;
 262                         if(strncmp(word[3],"0",1))
 263                                 mdrun->pbcz=TRUE;
 264                         else
 265                                 mdrun->pbcz=FALSE;
 266                 }
 267                 else if(!strncmp(word[0],"temperature",11))
 268                         mdrun->temperature=atof(word[1]);
 269                 else if(!strncmp(word[0],"pressure",8))
 270                         mdrun->pressure=atof(word[1]);
 271                 else if(!strncmp(word[0],"lattice",7)) {
 272                         if(!strncmp(word[1],"zincblende",10))
 273                                 mdrun->lattice=ZINCBLENDE;
 274                         if(!strncmp(word[1],"fcc",3))
 275                                 mdrun->lattice=FCC;
 276                         if(!strncmp(word[1],"diamond",7))
 277                                 mdrun->lattice=DIAMOND;
 278                         if(!strncmp(word[1],"none",4))
 279                                 mdrun->lattice=NONE;
 280                         if(wcnt==3)
 281                                 mdrun->lc=atof(word[2]);
 282                 }
 283                 else if(!strncmp(word[0],"element1",8)) {
 284                         mdrun->element1=atoi(word[1]);
 285                 }
 286                 else if(!strncmp(word[0],"element2",8)) {
 287                         mdrun->element2=atoi(word[1]);
 288                 }
 289                 else if(!strncmp(word[0],"fill",6)) {
 290                         // default values
 291                         fp.fill_element=mdrun->element1;
 292                         fp.fill_brand=0;
 293                         fp.lattice=mdrun->lattice;
 294                         fp.p_params.type=0;
 295                         fp.d_params.type=0;
 296                         // parse fill command
 297                         i=1;
 298                         while(i<wcnt) {
 299                                 if(!strncmp(word[i],"lc",2)) {
 300                                         fp.lx=atoi(word[++i]);
 301                                         fp.ly=atoi(word[++i]);
 302                                         fp.lz=atoi(word[++i]);
 303                                         fp.lc=atof(word[++i]);
 304                                         mdrun->lc=fp.lc;
 305                                 }
 306                                 if(!strncmp(word[i],"eb",2)) {
 307                                         fp.fill_element=atoi(word[++i]);
 308                                         fp.fill_brand=atoi(word[++i]);
 309                                 }
 310                                 if(word[i][0]=='p') {
 311                                         i+=1;
 312                                         switch(word[i][0]) {
 313                                         case 'i':
 314                                                 if(word[i][1]=='r')
 315                                                 fp.p_params.type=PART_INSIDE_R;
 316                                                 else
 317                                                 fp.p_params.type=PART_INSIDE_D;
 318                                                 break;
 319                                         case 'o':
 320                                                 if(word[i][1]=='r')
 321                                                 fp.p_params.type=PART_OUTSIDE_R;
 322                                                 else
 323                                                 fp.p_params.type=PART_OUTSIDE_D;
 324                                                 break;
 325                                         default:
 326                                                 break;
 327                                         }
 328                                         if((fp.p_params.type==PART_INSIDE_R)||
 329                                           (fp.p_params.type==PART_OUTSIDE_R)) {
 330                                                 fp.p_params.r=atof(word[++i]);
 331                                                 fp.p_params.p.x=atof(word[++i]);
 332                                                 fp.p_params.p.y=atof(word[++i]);
 333                                                 fp.p_params.p.z=atof(word[++i]);
 334                                         }
 335                                         if((fp.p_params.type==PART_INSIDE_D)||
 336                                            (fp.p_params.type==PART_OUTSIDE_D)) {
 337                                                 fp.p_params.p.x=atof(word[++i]);
 338                                                 fp.p_params.p.y=atof(word[++i]);
 339                                                 fp.p_params.p.z=atof(word[++i]);
 340                                                 fp.p_params.d.x=atof(word[++i]);
 341                                                 fp.p_params.d.y=atof(word[++i]);
 342                                                 fp.p_params.d.z=atof(word[++i]);
 343                                         }
 344                                 }
 345                                 if(word[i][0]=='d') {
 346                                         switch(word[++i][0]) {
 347                                                 case '0':
 348
 349                                 fp.d_params.type=DEFECT_TYPE_0D;
 350                                 if(!strncmp(word[i+1],"dbx",3)) {
 351                                         fp.d_params.stype=DEFECT_STYPE_DB_X;
 352                                 }
 353                                 if(!strncmp(word[i+1],"dby",3)) {
 354                                         fp.d_params.stype=DEFECT_STYPE_DB_Y;
 355                                 }
 356                                 if(!strncmp(word[i+1],"dbz",3)) {
 357                                         fp.d_params.stype=DEFECT_STYPE_DB_Z;
 358                                 }
 359                                 if(!strncmp(word[i+1],"dbr",3)) {
 360                                         fp.d_params.stype=DEFECT_STYPE_DB_R;
 361                                 }
 362                                 i+=1;
 363                                 fp.d_params.od=atof(word[++i]);
 364                                 fp.d_params.dd=atof(word[++i]);
 365                                 fp.d_params.element=atoi(word[++i]);
 366                                 fp.d_params.brand=atoi(word[++i]);
 367                                 // parsed in future
 368                 fp.d_params.attr=ATOM_ATTR_HB|ATOM_ATTR_VA;
 369                 fp.d_params.attr|=ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP;
 370                                 break;
 371
 372                                                 case '1':
 373                                 fp.d_params.type=DEFECT_TYPE_1D;
 374                                 break;
 375                                                 case '2':
 376                                 fp.d_params.type=DEFECT_TYPE_2D;
 377                                 break;
 378                                                 case '3':
 379                                 fp.d_params.type=DEFECT_TYPE_3D;
 380                                 break;
 381                                                 default:
 382                                                         break;
 383                                         }
 384
 385                                 }
 386                                 i+=1;
 387                         }
 388                         add_stage(mdrun,STAGE_FILL,&fp);
 389                 }
 390                 else if(!strncmp(word[0],"thermal_init",12)) {
 391                         add_stage(mdrun,STAGE_THERMAL_INIT,NULL);
 392                 }
 393                 else if(!strncmp(word[0],"aattr",5)) {
 394                         // for aatrib line we need a special stage
 395                         // containing one schedule of 0 loops ...
 396                         for(i=0;i<strlen(word[1]);i++) {
 397                                 switch(word[1][i]) {
 398                                         case 't':
 399                                                 cap.type|=CHAATTR_TOTALV;
 400                                                 break;
 401                                         case 'r':
 402                                                 cap.type|=CHAATTR_REGION;
 403                                                 break;
 404                                         case 'e':
 405                                                 cap.type|=CHAATTR_ELEMENT;
 406                                                 break;
 407                                         default:
 408                                                 break;
 409                                 }
 410                         }
 411                         i=2;
 412                         if(cap.type&CHAATTR_REGION) {
 413                                 cap.x0=atof(word[1]);
 414                                 cap.y0=atof(word[2]);
 415                                 cap.z0=atof(word[3]);
 416                                 cap.x1=atof(word[4]);
 417                                 cap.y1=atof(word[5]);
 418                                 cap.z1=atof(word[6]);
 419                                 i+=6;
 420                         }
 421                         if(cap.type&CHAATTR_ELEMENT) {
 422                                 cap.element=atoi(word[i]);
 423                                 i+=1;
 424                         }
 425                         for(o=0;o<strlen(word[i]);o++) {
 426                                 switch(word[i][o]) {
 427                                         case 'b':
 428                                                 cap.attr|=ATOM_ATTR_VB;
 429                                                 break;
 430                                         case 'h':
 431                                                 cap.attr|=ATOM_ATTR_HB;
 432                                                 break;
 433                                         case 'v':
 434                                                 cap.attr|=ATOM_ATTR_VA;
 435                                                 break;
 436                                         case 'f':
 437                                                 cap.attr|=ATOM_ATTR_FP;
 438                                                 break;
 439                                         case '1':
 440                                                 cap.attr|=ATOM_ATTR_1BP;
 441                                                 break;
 442                                         case '2':
 443                                                 cap.attr|=ATOM_ATTR_2BP;
 444                                                 break;
 445                                         case '3':
 446                                                 cap.attr|=ATOM_ATTR_3BP;
 447                                                 break;
 448                                         default:
 449                                                 break;
 450                                 }
 451                         }
 452                         add_stage(mdrun,STAGE_CHAATTR,&cap);
 453                 }
 454                 else if(!strncmp(word[0],"sattr",5)) {
 455                         // for satrib line we need a special stage
 456                         // containing one schedule of 0 loops ...
 457                         csp.type=0;
 458                         for(i=1;i<wcnt;i++) {
 459                                 if(!strncmp(word[i],"pctrl",5)) {
 460                                         csp.ptau=0.01/(atof(word[++i])*GPA);
 461                                         csp.type|=CHSATTR_PCTRL;
 462                                 }
 463                                 if(!strncmp(word[i],"tctrl",5)) {
 464                                         csp.ttau=atof(word[++i]);
 465                                         csp.type|=CHSATTR_TCTRL;
 466                                 }
 467                                 if(!strncmp(word[i],"prelax",6)) {
 468                                         csp.dp=atof(word[++i])*BAR;
 469                                         csp.type|=CHSATTR_PRELAX;
 470                                 }
 471                                 if(!strncmp(word[i],"trelax",6)) {
 472                                         csp.dt=atof(word[++i]);
 473                                         csp.type|=CHSATTR_TRELAX;
 474                                 }
 475                                 if(!strncmp(word[i],"rsteps",6)) {
 476                                         csp.rsteps=atoi(word[++i]);
 477                                         csp.type|=CHSATTR_RSTEPS;
 478                                 }
 479                                 if(!strncmp(word[i],"avgrst",6)) {
 480                                         csp.avgrst=atoi(word[++i]);
 481                                         csp.type|=CHSATTR_AVGRST;
 482                                 }
 483                         }
 484                         add_stage(mdrun,STAGE_CHSATTR,&csp);
 485                 }
 486                 else if(!strncmp(word[0],"prerun",6))
 487                         mdrun->prerun=atoi(word[1]);
 488                 else if(!strncmp(word[0],"avgskip",7))
 489                         mdrun->avgskip=atoi(word[1]);
 490                 else if(!strncmp(word[0],"elog",4))
 491                         mdrun->elog=atoi(word[1]);
 492                 else if(!strncmp(word[0],"tlog",4))
 493                         mdrun->tlog=atoi(word[1]);
 494                 else if(!strncmp(word[0],"plog",4))
 495                         mdrun->plog=atoi(word[1]);
 496                 else if(!strncmp(word[0],"vlog",4))
 497                         mdrun->vlog=atoi(word[1]);
 498                 else if(!strncmp(word[0],"save",4))
 499                         mdrun->save=atoi(word[1]);
 500                 else if(!strncmp(word[0],"visualize",9))
 501                         mdrun->visualize=atoi(word[1]);
 502                 else if(!strncmp(word[0],"stage",5)) {
 503                         // for every stage line, add a stage
 504                         if(!strncmp(word[1],"displace",8)) {
 505                                 dap.nr=atoi(word[2]);
 506                                 dap.dx=atof(word[3]);
 507                                 dap.dy=atof(word[4]);
 508                                 dap.dz=atof(word[5]);
 509                                 add_stage(mdrun,STAGE_DISPLACE_ATOM,&dap);
 510                         }
 511                         else if(!strncmp(word[1],"ins_atoms",9)) {
 512                                 iap.ins_steps=atoi(word[2]);
 513                                 iap.ins_atoms=atoi(word[3]);
 514                                 iap.element=atoi(word[4]);
 515                                 iap.brand=atoi(word[5]);
 516                                 for(i=0;i<strlen(word[6]);i++) {
 517                                         switch(word[6][i]) {
 518                                                 case 'b':
 519                                                         iap.attr|=ATOM_ATTR_VB;
 520                                                         break;
 521                                                 case 'h':
 522                                                         iap.attr|=ATOM_ATTR_HB;
 523                                                         break;
 524                                                 case 'v':
 525                                                         iap.attr|=ATOM_ATTR_VA;
 526                                                         break;
 527                                                 case 'f':
 528                                                         iap.attr|=ATOM_ATTR_FP;
 529                                                         break;
 530                                                 case '1':
 531                                                         iap.attr|=ATOM_ATTR_1BP;
 532                                                         break;
 533                                                 case '2':
 534                                                         iap.attr|=ATOM_ATTR_2BP;
 535                                                         break;
 536                                                 case '3':
 537                                                         iap.attr|=ATOM_ATTR_3BP;
 538                                                         break;
 539                                                 default:
 540                                                         break;
 541                                         }
 542                                 }
 543                                 switch(word[7][0]) {
 544                                         // insertion types
 545                                         case 'p':
 546                                                 iap.type=INS_POS;
 547                                                 iap.x0=atof(word[8]);
 548                                                 iap.y0=atof(word[9]);
 549                                                 iap.z0=atof(word[10]);
 550                                                 break;
 551                                         case 'r':
 552                                                 if(word[8][0]=='t') {
 553                                                         iap.type=INS_TOTAL;
 554                                                         iap.cr=atof(word[9]);
 555                                                 }
 556                                                 else {
 557                                                         iap.type=INS_REGION;
 558                                                         iap.x0=atof(word[8]);
 559                                                         iap.y0=atof(word[9]);
 560                                                         iap.z0=atof(word[10]);
 561                                                         iap.x1=atof(word[11]);
 562                                                         iap.y1=atof(word[12]);
 563                                                         iap.z1=atof(word[13]);
 564                                                         iap.cr=atof(word[14]);
 565                                                 }
 566                                         default:
 567                                                 break;
 568                                 }
 569                                 add_stage(mdrun,STAGE_INSERT_ATOMS,&iap);
 570                         }
 571
 572
 573                         // HERE WE GO ...
 574
 575                         else if(!strncmp(word[1],"ins_m_atoms",11)) {
 576                                 imp.element1=atoi(word[2]);
 577                                 imp.element2=atoi(word[3]);
 578                                 imp.amount1=atoi(word[4]);
 579                                 imp.amount2=atoi(word[5]);
 580                                 imp.brand1=atoi(word[6]);
 581                                 imp.brand2=atoi(word[7]);
 582                                 imp.crmin=atof(word[8]);
 583                                 imp.crmax=atof(word[9]);
 584                                 /* do this later ...
 585                                 for(i=0;i<strlen(word[8]);i++) {
 586                                         switch(word[8][i]) {
 587                                                 case 'b':
 588                                                         imp.attr|=ATOM_ATTR_VB;
 589                                                         break;
 590                                                 case 'h':
 591                                                         imp.attr|=ATOM_ATTR_HB;
 592                                                         break;
 593                                                 case 'v':
 594                                                         imp.attr|=ATOM_ATTR_VA;
 595                                                         break;
 596                                                 case 'f':
 597                                                         imp.attr|=ATOM_ATTR_FP;
 598                                                         break;
 599                                                 case '1':
 600                                                         imp.attr|=ATOM_ATTR_1BP;
 601                                                         break;
 602                                                 case '2':
 603                                                         imp.attr|=ATOM_ATTR_2BP;
 604                                                         break;
 605                                                 case '3':
 606                                                         imp.attr|=ATOM_ATTR_3BP;
 607                                                         break;
 608                                                 default:
 609                                                         break;
 610                                         }
 611                                 }
 612                                 */
 613                                 imp.attr1=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
 614                                 imp.attr2=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
 615                                 add_stage(mdrun,STAGE_INSERT_MIXED_ATOMS,&imp);
 616                         }
 617
 618
 619
 620
 621
 622                         else if(!strncmp(word[1],"continue",8)) {
 623                                 cp.runs=atoi(word[2]);
 624                                 add_stage(mdrun,STAGE_CONTINUE,&cp);
 625                         }
 626                         else if(!strncmp(word[1],"anneal",6)) {
 627                                 ap.count=0;
 628                                 ap.runs=atoi(word[2]);
 629                                 ap.dt=atof(word[3]);
 630                                 ap.interval=atoi(word[4]);
 631                                 add_stage(mdrun,STAGE_ANNEAL,&ap);
 632                         }
 633                         else if(!strncmp(word[1],"set_temp",8)) {
 634                                 if(word[2][0]=='c') {
 635                                         stp.type=SET_TEMP_CURRENT;
 636                                         stp.val=0.0;
 637                                 }
 638                                 else {
 639                                         stp.type=SET_TEMP_VALUE;
 640                                         stp.val=atof(word[2]);
 641                                 }
 642                                 add_stage(mdrun,STAGE_SET_TEMP,&stp);
 643                         }
 644                         else if(!strncmp(word[1],"set_timestep",12)) {
 645                                 stsp.tau=atof(word[2]);
 646                                 add_stage(mdrun,STAGE_SET_TIMESTEP,&stsp);
 647                         }
 648                         else {
 649                                 printf("%s unknown stage type: %s\n",
 650                                        ME,word[1]);
 651                                 return -1;
 652                         }
 653                 }
 654                 else {
 655                         printf("%s unknown keyword '%s', skipped!\n",
 656                                ME,word[0]);
 657                         continue;
 658                 }
 659         }
 660
 661         /* close file */
 662         close(fd);
 663
 664         return 0;
 665 }
 666
 667 int check_pressure(t_moldyn *moldyn,t_mdrun *mdrun) {
 668
 669         double delta;
 670
 671         if(!(mdrun->sattr&SATTR_PRELAX)) {
 672                 return TRUE;
 673         }
 674
 675         delta=moldyn->p_avg-moldyn->p_ref;
 676
 677         if(delta<0)
 678                 delta=-delta;
 679
 680         if(delta>mdrun->dp)
 681                 return FALSE;
 682
 683         return TRUE;
 684 }
 685
 686 int check_temperature(t_moldyn *moldyn,t_mdrun *mdrun) {
 687
 688         double delta;
 689
 690         if(!(mdrun->sattr&SATTR_TRELAX))
 691                 return TRUE;
 692
 693         delta=moldyn->t_avg-moldyn->t_ref;
 694
 695         if(delta<0)
 696                 delta=-delta;
 697
 698         if(delta>mdrun->dt)
 699                 return FALSE;
 700
 701         return TRUE;
 702 }
 703
 704 int displace_atom(t_moldyn *moldyn,t_mdrun *mdrun) {
 705
 706         t_displace_atom_params *dap;
 707         t_stage *stage;
 708         t_atom *atom;
 709
 710         stage=mdrun->stage.current->data;
 711         dap=stage->params;
 712
 713         atom=&(moldyn->atom[dap->nr]);
 714         atom->r.x+=dap->dx;
 715         atom->r.y+=dap->dy;
 716         atom->r.z+=dap->dz;
 717
 718         return 0;
 719 }
 720
 721 int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 722
 723         t_insert_atoms_params *iap;
 724         t_stage *stage;
 725         t_atom *atom;
 726         t_3dvec r,v,dist;
 727         double d,dmin,o;
 728         int cnt,i;
 729         double x,y,z;
 730         double x0,y0,z0;
 731         u8 cr_check,run;
 732
 733         stage=mdrun->stage.current->data;
 734         iap=stage->params;
 735
 736         cr_check=FALSE;
 737
 738         v.x=0.0; v.y=0.0; v.z=0.0;
 739         x=0; y=0; z=0;
 740         o=0; dmin=0;
 741
 742         switch(mdrun->lattice) {
 743                 case CUBIC:
 744                         o=0.5*mdrun->lc;
 745                         break;
 746                 case FCC:
 747                         o=0.25*mdrun->lc;
 748                         break;
 749                 case DIAMOND:
 750                 case ZINCBLENDE:
 751                         o=0.125*mdrun->lc;
 752                         break;
 753                 default:
 754                         break;
 755         }
 756
 757         switch(iap->type) {
 758                 case INS_TOTAL:
 759                         x=moldyn->dim.x;
 760                         x0=-x/2.0;
 761                         y=moldyn->dim.y;
 762                         y0=-y/2.0;
 763                         z=moldyn->dim.z;
 764                         z0=-z/2.0;
 765                         cr_check=TRUE;
 766                         break;
 767                 case INS_REGION:
 768                         x=iap->x1-iap->x0;
 769                         x0=iap->x0;
 770                         y=iap->y1-iap->y0;
 771                         y0=iap->y0;
 772                         z=iap->z1-iap->z0;
 773                         z0=iap->z0;
 774                         cr_check=TRUE;
 775                         break;
 776                 case INS_POS:
 777                         x0=iap->x0;
 778                         y0=iap->y0;
 779                         z0=iap->z0;
 780                         cr_check=FALSE;
 781                         break;
 782                 default:
 783                         printf("%s unknown insertion mode: %02x\n",
 784                                ME,iap->type);
 785                         return -1;
 786         }
 787
 788         cnt=0;
 789         while(cnt<iap->ins_atoms) {
 790                 run=1;
 791                 while(run) {
 792                         if(iap->type!=INS_POS) {
 793                                 r.x=rand_get_double(&(moldyn->random))*x;
 794                                 r.y=rand_get_double(&(moldyn->random))*y;
 795                                 r.z=rand_get_double(&(moldyn->random))*z;
 796                         }
 797                         else {
 798                                 r.x=0.0;
 799                                 r.y=0.0;
 800                                 r.z=0.0;
 801                         }
 802                         r.x+=x0;
 803                         r.y+=y0;
 804                         r.z+=z0;
 805                         // offset
 806                         if(iap->type!=INS_TOTAL) {
 807                                 r.x+=o;
 808                                 r.y+=o;
 809                                 r.z+=o;
 810                         }
 811                         run=0;
 812                         if(cr_check==TRUE) {
 813                                 dmin=1000;      // for sure too high!
 814                                 for(i=0;i<moldyn->count;i++) {
 815                                         atom=&(moldyn->atom[i]);
 816                                         v3_sub(&dist,&(atom->r),&r);
 817                                         check_per_bound(moldyn,&dist);
 818                                         d=v3_absolute_square(&dist);
 819                                         if(d<(iap->cr*iap->cr)) {
 820                                                 run=1;
 821                                                 break;
 822                                         }
 823                                         if(d<dmin)
 824                                                 dmin=d;
 825                                 }
 826                         }
 827                 }
 828                 add_atom(moldyn,iap->element,
 829                          iap->brand,iap->attr,&r,&v);
 830                 printf("%s atom inserted (%d/%d): %f %f %f\n",
 831                        ME,(iap->cnt_steps+1)*iap->ins_atoms,
 832                        iap->ins_steps*iap->ins_atoms,r.x,r.y,r.z);
 833                 printf("  -> d2 = %f/%f\n",dmin,iap->cr*iap->cr);
 834                 cnt+=1;
 835         }
 836
 837         return 0;
 838 }
 839
 840 int insert_mixed_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 841
 842         t_stage *stage;
 843         t_insert_mixed_atoms_params *imp;
 844         t_atom *atom;
 845         double x,x0,y,y0,z,z0;
 846         double dmin,d,cmin,cmax;
 847         u8 retry;
 848         t_3dvec r,v,dist;
 849         int i;
 850
 851
 852         stage=mdrun->stage.current->data;
 853         imp=stage->params;
 854
 855         x=moldyn->dim.x;
 856         x0=-x/2.0;
 857         y=moldyn->dim.y;
 858         y0=-y/2.0;
 859         z=moldyn->dim.z;
 860         z0=-z/2.0;
 861
 862         v.x=0.0;
 863         v.y=0.0;
 864         v.z=0.0;
 865
 866         cmin=imp->crmin*imp->crmin;
 867         cmax=imp->crmax*imp->crmax;
 868
 869         while(imp->amount1|imp->amount2) {
 870                 if(imp->amount1) {
 871                         retry=1;
 872                         while(retry) {
 873                                 retry=0;
 874                                 r.x=rand_get_double(&(moldyn->random))*x;
 875                                 r.y=rand_get_double(&(moldyn->random))*y;
 876                                 r.z=rand_get_double(&(moldyn->random))*z;
 877                                 r.x+=x0;
 878                                 r.y+=y0;
 879                                 r.z+=z0;
 880                                 dmin=1000.0;    // for sure too high!
 881                                 for(i=0;i<moldyn->count;i++) {
 882                                         atom=&(moldyn->atom[i]);
 883                                         v3_sub(&dist,&(atom->r),&r);
 884                                         check_per_bound(moldyn,&dist);
 885                                         d=v3_absolute_square(&dist);
 886                                         if(d<cmin) {
 887                                                 retry=1;
 888                                                 break;
 889                                         }
 890                                         if(d<dmin)
 891                                                 dmin=d;
 892                                 }
 893                                 if(dmin!=1000.0)
 894                                         if(dmin>cmax)
 895                                                 retry=1;
 896                         }
 897                         add_atom(moldyn,imp->element1,
 898                                  imp->brand1,imp->attr1,&r,&v);
 899                         printf("%s (mixed) atom inserted (%d): %f %f %f\n",
 900                                ME,imp->amount1,r.x,r.y,r.z);
 901                         printf("  -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
 902                         imp->amount1-=1;
 903                 }
 904                 if(imp->amount2) {
 905                         retry=1;
 906                         while(retry) {
 907                                 retry=0;
 908                                 r.x=rand_get_double(&(moldyn->random))*x;
 909                                 r.y=rand_get_double(&(moldyn->random))*y;
 910                                 r.z=rand_get_double(&(moldyn->random))*z;
 911                                 r.x+=x0;
 912                                 r.y+=y0;
 913                                 r.z+=z0;
 914                                 dmin=1000.0;    // for sure too high!
 915                                 for(i=0;i<moldyn->count;i++) {
 916                                         atom=&(moldyn->atom[i]);
 917                                         v3_sub(&dist,&(atom->r),&r);
 918                                         check_per_bound(moldyn,&dist);
 919                                         d=v3_absolute_square(&dist);
 920                                         if(d<cmin) {
 921                                                 retry=1;
 922                                                 break;
 923                                         }
 924                                         if(d<dmin)
 925                                                 dmin=d;
 926                                 }
 927                                 if(dmin!=1000.0)
 928                                         if(dmin>cmax)
 929                                                 retry=1;
 930                         }
 931                         add_atom(moldyn,imp->element2,
 932                                  imp->brand2,imp->attr2,&r,&v);
 933                         printf("%s (mixed) atom inserted (%d): %f %f %f\n",
 934                                ME,imp->amount2,r.x,r.y,r.z);
 935                         printf("  -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
 936                         imp->amount2-=1;
 937                 }
 938         }
 939
 940         return 0;
 941 }
 942
 943 int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
 944
 945         t_stage *stage;
 946         t_chaattr_params *cap;
 947         t_atom *atom;
 948         int i;
 949
 950         stage=mdrun->stage.current->data;
 951         cap=stage->params;
 952
 953         for(i=0;i<moldyn->count;i++) {
 954                 atom=&(moldyn->atom[i]);
 955                 if(cap->type&CHAATTR_ELEMENT) {
 956                         if(cap->element!=atom->element)
 957                                 continue;
 958                 }
 959                 if(cap->type&CHAATTR_REGION) {
 960                         if(cap->x0<atom->r.x)
 961                                 continue;
 962                         if(cap->y0<atom->r.y)
 963                                 continue;
 964                         if(cap->z0<atom->r.z)
 965                                 continue;
 966                         if(cap->x1>atom->r.x)
 967                                 continue;
 968                         if(cap->y1>atom->r.y)
 969                                 continue;
 970                         if(cap->z1>atom->r.z)
 971                                 continue;
 972                 }
 973                 atom->attr=cap->attr;
 974         }
 975
 976         return 0;
 977 }
 978
 979 int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
 980
 981         t_stage *stage;
 982         t_chsattr_params *csp;
 983
 984         stage=mdrun->stage.current->data;
 985         csp=stage->params;
 986
 987         if(csp->type&CHSATTR_PCTRL) {
 988                 if(csp->ptau>0)
 989                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
 990                 else
 991                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
 992         }
 993         if(csp->type&CHSATTR_TCTRL) {
 994                 if(csp->ttau>0)
 995                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
 996                 else
 997                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
 998         }
 999         if(csp->type&CHSATTR_PRELAX) {
1000                 if(csp->dp<0)
1001                         mdrun->sattr&=(~(SATTR_PRELAX));
1002                 else
1003                         mdrun->sattr|=SATTR_PRELAX;
1004                 mdrun->dp=csp->dp;
1005         }
1006         if(csp->type&CHSATTR_TRELAX) {
1007                 if(csp->dt<0)
1008                         mdrun->sattr&=(~(SATTR_TRELAX));
1009                 else
1010                         mdrun->sattr|=SATTR_TRELAX;
1011                 mdrun->dt=csp->dt;
1012         }
1013         if(csp->type&CHSATTR_AVGRST) {
1014                 if(csp->avgrst)
1015                         mdrun->sattr|=SATTR_AVGRST;
1016                 else
1017                         mdrun->sattr&=(~(SATTR_AVGRST));
1018         }
1019         if(csp->type&CHSATTR_RSTEPS) {
1020                 mdrun->relax_steps=csp->rsteps;
1021         }
1022
1023         return 0;
1024 }
1025
1026 #define stage_print(m)  if(!(stage->executed)) \
1027                                 printf("%s",m)
1028
1029 int mdrun_hook(void *ptr1,void *ptr2) {
1030
1031         t_moldyn *moldyn;
1032         t_mdrun *mdrun;
1033         t_stage *stage;
1034         t_list *sl;
1035         int steps;
1036         u8 change_stage;
1037         t_3dvec o;
1038
1039         t_insert_atoms_params *iap;
1040         t_insert_mixed_atoms_params *imp;
1041         t_continue_params *cp;
1042         t_anneal_params *ap;
1043         t_set_temp_params *stp;
1044         t_set_timestep_params *stsp;
1045         t_fill_params *fp;
1046
1047         moldyn=ptr1;
1048         mdrun=ptr2;
1049
1050         sl=&(mdrun->stage);
1051
1052         change_stage=FALSE;
1053
1054         /* return immediately if there are no more stage */
1055         if(sl->current==NULL)
1056                 return 0;
1057
1058         /* get stage description */
1059         stage=sl->current->data;
1060
1061         /* steps in next schedule */
1062         steps=mdrun->relax_steps;
1063
1064         /* check whether relaxation steps are necessary */
1065         if((check_pressure(moldyn,mdrun)==TRUE)&\
1066            (check_temperature(moldyn,mdrun)==TRUE)) {
1067
1068                 /* be verbose */
1069                 stage_print("\n###########################\n");
1070                 stage_print("# [mdrun] executing stage #\n");
1071                 stage_print("###########################\n\n");
1072
1073                 /* stage specific stuff */
1074                 switch(stage->type) {
1075                         case STAGE_DISPLACE_ATOM:
1076                                 stage_print("  -> displace atom\n\n");
1077                                 displace_atom(moldyn,mdrun);
1078                                 change_stage=TRUE;
1079                                 break;
1080                         case STAGE_INSERT_ATOMS:
1081                                 stage_print("  -> insert atoms\n\n");
1082                                 iap=stage->params;
1083                                 if(iap->cnt_steps==iap->ins_steps) {
1084                                         change_stage=TRUE;
1085                                         break;
1086                                 }
1087                                 insert_atoms(moldyn,mdrun);
1088                                 iap->cnt_steps+=1;
1089                                 break;
1090
1091
1092
1093                         case STAGE_INSERT_MIXED_ATOMS:
1094                                 stage_print("  -> insert mixed atoms\n\n");
1095                                 imp=stage->params;
1096                                 insert_mixed_atoms(moldyn,mdrun);
1097                                 change_stage=TRUE;
1098                                 break;
1099
1100
1101
1102                         case STAGE_CONTINUE:
1103                                 stage_print("  -> continue\n\n");
1104                                 if(stage->executed==TRUE) {
1105                                         change_stage=TRUE;
1106                                         break;
1107                                 }
1108                                 cp=stage->params;
1109                                 steps=cp->runs;
1110                                 break;
1111                         case STAGE_ANNEAL:
1112                                 stage_print("  -> anneal\n\n");
1113                                 ap=stage->params;
1114                                 if(ap->count==ap->runs) {
1115                                         change_stage=TRUE;
1116                                         break;
1117                                 }
1118                                 if(moldyn->t_ref+ap->dt>=0.0)
1119                                         set_temperature(moldyn,
1120                                                         moldyn->t_ref+ap->dt);
1121                                 ap->count+=1;
1122                                 steps=ap->interval;
1123                                 break;
1124                         case STAGE_CHAATTR:
1125                                 stage_print("  -> change atom attributes\n\n");
1126                                 chaatr(moldyn,mdrun);
1127                                 change_stage=TRUE;
1128                                 break;
1129                         case STAGE_CHSATTR:
1130                                 stage_print("  -> change sys attributes\n\n");
1131                                 chsattr(moldyn,mdrun);
1132                                 change_stage=TRUE;
1133                                 break;
1134                         case STAGE_SET_TEMP:
1135                                 stage_print("  -> set temperature\n\n");
1136                                 stp=stage->params;
1137                                 if(stp->type&SET_TEMP_CURRENT) {
1138                                         set_temperature(moldyn,moldyn->t_avg);
1139                                 }
1140                                 else {
1141                                         set_temperature(moldyn,stp->val);
1142                                 }
1143                                 change_stage=TRUE;
1144                                 break;
1145                         case STAGE_SET_TIMESTEP:
1146                                 stage_print("  -> set timestep\n\n");
1147                                 stsp=stage->params;
1148                                 mdrun->timestep=stsp->tau;
1149                                 change_stage=TRUE;
1150                                 break;
1151                         case STAGE_FILL:
1152                                 stage_print("  -> fill lattice\n\n");
1153                                 fp=stage->params;
1154                                 switch(fp->lattice) {
1155                                         case ZINCBLENDE:
1156
1157                                         o.x=0.5*0.25*fp->lc;
1158                                         o.y=o.x;
1159                                         o.z=o.x;
1160                                         create_lattice(moldyn,
1161                                                        FCC,fp->lc,
1162                                                        mdrun->element1,
1163                                                        DEFAULT_ATOM_ATTR,0,
1164                                                        fp->lx,fp->ly,fp->lz,
1165                                                        &o,
1166                                                        &(fp->p_params),
1167                                                        &(fp->d_params));
1168                                         o.x+=0.25*fp->lc;
1169                                         o.y=o.x;
1170                                         o.z=o.x;
1171                                         create_lattice(moldyn,
1172                                                        FCC,fp->lc,
1173                                                        mdrun->element2,
1174                                                        DEFAULT_ATOM_ATTR,1,
1175                                                        fp->lx,fp->ly,fp->lz,
1176                                                        &o,
1177                                                        &(fp->p_params),
1178                                                        &(fp->d_params));
1179                                         break;
1180
1181                                         default:
1182
1183                                         create_lattice(moldyn,
1184                                                        fp->lattice,fp->lc,
1185                                                        mdrun->element1,
1186                                                        DEFAULT_ATOM_ATTR,0,
1187                                                        fp->lx,fp->ly,fp->lz,
1188                                                        NULL,
1189                                                        &(fp->p_params),
1190                                                        &(fp->d_params));
1191                                         break;
1192                                 }
1193                                 moldyn_bc_check(moldyn);
1194                                 change_stage=TRUE;
1195                                 break;
1196                         case STAGE_THERMAL_INIT:
1197                                 stage_print("  -> thermal init\n\n");
1198                                 thermal_init(moldyn,TRUE);
1199                                 change_stage=TRUE;
1200                                 break;
1201                         default:
1202                                 printf("%s unknwon stage type\n",ME);
1203                                 break;
1204                 }
1205
1206                 /* mark as executed */
1207                 stage->executed=TRUE;
1208
1209                 /* change state */
1210                 if(change_stage==TRUE) {
1211                         printf("%s finished stage\n",ME);
1212                         if(list_next_f(sl)==L_NO_NEXT_ELEMENT) {
1213                                 printf("%s no more stages\n",ME);
1214                                 return 0;
1215                         }
1216                         steps=0;
1217                 }
1218
1219         }
1220         else {
1221
1222                 /* averages */
1223                 if(mdrun->sattr&SATTR_AVGRST)
1224                         average_reset(moldyn);
1225
1226         }
1227
1228         /* continue simulation */
1229         moldyn_add_schedule(moldyn,steps,mdrun->timestep);
1230
1231         return 0;
1232 }
1233
1234 int main(int argc,char **argv) {
1235
1236         t_mdrun mdrun;
1237         t_moldyn moldyn;
1238         //t_3dvec o;
1239
1240         /* clear structs */
1241         memset(&mdrun,0,sizeof(t_mdrun));
1242         memset(&moldyn,0,sizeof(t_moldyn));
1243
1244         /* parse arguments */
1245         if(mdrun_parse_argv(&mdrun,argc,argv)<0)
1246                 return -1;
1247
1248         /* initialize list system */
1249         list_init_f(&(mdrun.stage));
1250
1251         /* parse config file */
1252         mdrun_parse_config(&mdrun);
1253
1254         /* reset the stage list */
1255         list_reset_f(&(mdrun.stage));
1256
1257         /* sanity check! */
1258
1259         /* prepare simulation */
1260
1261         if(mdrun.continue_file[0]) {
1262                 // read the save file
1263                 moldyn_read_save_file(&moldyn,mdrun.continue_file);
1264                 // manualaadjusting some stuff
1265                 moldyn.argc=argc;
1266                 moldyn.args=argv;
1267                 rand_init(&(moldyn.random),NULL,1);
1268                 moldyn.random.status|=RAND_STAT_VERBOSE;
1269         }
1270         else {
1271                 moldyn_init(&moldyn,argc,argv);
1272         }
1273
1274         if(set_int_alg(&moldyn,mdrun.intalgo)<0)
1275                 return -1;
1276
1277         /* potential */
1278         set_cutoff(&moldyn,mdrun.cutoff);
1279         if(set_potential(&moldyn,mdrun.potential)<0)
1280                 return -1;
1281         switch(mdrun.potential) {
1282                 case MOLDYN_POTENTIAL_AM:
1283                         albe_mult_set_params(&moldyn,
1284                                              mdrun.element1,
1285                                              mdrun.element2);
1286                         break;
1287                 case MOLDYN_POTENTIAL_TM:
1288                         tersoff_mult_set_params(&moldyn,
1289                                                 mdrun.element1,
1290                                                 mdrun.element2);
1291                         break;
1292                 case MOLDYN_POTENTIAL_HO:
1293                         harmonic_oscillator_set_params(&moldyn,mdrun.element1);
1294                         break;
1295                 case MOLDYN_POTENTIAL_LJ:
1296                         lennard_jones_set_params(&moldyn,mdrun.element1);
1297                         break;
1298                 default:
1299                         printf("%s unknown potential: %02x\n",
1300                                ME,mdrun.potential);
1301                         return -1;
1302         }
1303
1304         /* if it is a continue run, reset schedule and skip lattice init */
1305         if(mdrun.continue_file[0]) {
1306                 memset(&(moldyn.schedule),0,sizeof(t_moldyn_schedule));
1307                 goto addsched;
1308         }
1309
1310         /* initial lattice and dimensions */
1311         set_dim(&moldyn,mdrun.dim.x,mdrun.dim.y,mdrun.dim.z,mdrun.vis);
1312         set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
1313         /* replaced by fill stage !!
1314         switch(mdrun.lattice) {
1315                 case FCC:
1316                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.fill_element,
1317                                        mdrun.m1,DEFAULT_ATOM_ATTR,
1318                                        mdrun.fill_brand,mdrun.lx,
1319                                        mdrun.ly,mdrun.lz,NULL,0,NULL);
1320                         break;
1321                 case DIAMOND:
1322                         create_lattice(&moldyn,DIAMOND,mdrun.lc,
1323                                        mdrun.fill_element,
1324                                        mdrun.m1,DEFAULT_ATOM_ATTR,
1325                                        mdrun.fill_brand,mdrun.lx,
1326                                        mdrun.ly,mdrun.lz,NULL,0,NULL);
1327                         break;
1328                 case ZINCBLENDE:
1329                         o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
1330                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
1331                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
1332                                        mdrun.ly,mdrun.lz,&o,0,NULL);
1333                         o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
1334                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
1335                                        mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
1336                                        mdrun.ly,mdrun.lz,&o,0,NULL);
1337                         break;
1338                 case NONE:
1339                         set_nn_dist(&moldyn,mdrun.nnd);
1340                         break;
1341                 default:
1342                         printf("%s unknown lattice type: %02x\n",
1343                                ME,mdrun.lattice);
1344                         return -1;
1345         }
1346         moldyn_bc_check(&moldyn);
1347         replaced by fill stage !! */
1348
1349         /* temperature and pressure */
1350         set_temperature(&moldyn,mdrun.temperature);
1351         set_pressure(&moldyn,mdrun.pressure);
1352         /* replaced thermal_init stage
1353         thermal_init(&moldyn,TRUE);
1354         */
1355
1356 addsched:
1357         /* first schedule */
1358         moldyn_add_schedule(&moldyn,mdrun.prerun,mdrun.timestep);
1359
1360         /* log */
1361         moldyn_set_log_dir(&moldyn,mdrun.sdir);
1362         moldyn_set_report(&moldyn,"CHANGE ME","CHANGE ME TOO");
1363         if(mdrun.elog)
1364                 moldyn_set_log(&moldyn,LOG_TOTAL_ENERGY,mdrun.elog);
1365         if(mdrun.tlog)
1366                 moldyn_set_log(&moldyn,LOG_TEMPERATURE,mdrun.tlog);
1367         if(mdrun.plog)
1368                 moldyn_set_log(&moldyn,LOG_PRESSURE,mdrun.plog);
1369         if(mdrun.vlog)
1370                 moldyn_set_log(&moldyn,LOG_VOLUME,mdrun.vlog);
1371         if(mdrun.visualize)
1372                 moldyn_set_log(&moldyn,VISUAL_STEP,mdrun.visualize);
1373         if(mdrun.save)
1374                 moldyn_set_log(&moldyn,SAVE_STEP,mdrun.save);
1375         moldyn_set_log(&moldyn,CREATE_REPORT,0);
1376         set_avg_skip(&moldyn,mdrun.avgskip);
1377
1378         /* prepare the hook function */
1379         moldyn_set_schedule_hook(&moldyn,&mdrun_hook,&mdrun);
1380
1381         /* run the simulation */
1382         moldyn_integrate(&moldyn);
1383
1384         /* shutdown */
1385         moldyn_shutdown(&moldyn);
1386         del_stages(&mdrun);
1387         list_destroy_f(&(mdrun.stage));
1388
1389         return 0;
1390 }