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[32][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                         fp.d_params.stype=0;
 297                         // parse fill command
 298                         i=1;
 299                         while(i<wcnt) {
 300                                 if(!strncmp(word[i],"lc",2)) {
 301                                         fp.lx=atoi(word[++i]);
 302                                         fp.ly=atoi(word[++i]);
 303                                         fp.lz=atoi(word[++i]);
 304                                         fp.lc=atof(word[++i]);
 305                                         mdrun->lc=fp.lc;
 306                                 }
 307                                 if(!strncmp(word[i],"eb",2)) {
 308                                         fp.fill_element=atoi(word[++i]);
 309                                         fp.fill_brand=atoi(word[++i]);
 310                                 }
 311                                 if(word[i][0]=='p') {
 312                                         i+=1;
 313                                         switch(word[i][0]) {
 314                                         case 'i':
 315                                                 if(word[i][1]=='r')
 316                                                 fp.p_params.type=PART_INSIDE_R;
 317                                                 else
 318                                                 fp.p_params.type=PART_INSIDE_D;
 319                                                 break;
 320                                         case 'o':
 321                                                 if(word[i][1]=='r')
 322                                                 fp.p_params.type=PART_OUTSIDE_R;
 323                                                 else
 324                                                 fp.p_params.type=PART_OUTSIDE_D;
 325                                                 break;
 326                                         default:
 327                                                 break;
 328                                         }
 329                                         if((fp.p_params.type==PART_INSIDE_R)||
 330                                           (fp.p_params.type==PART_OUTSIDE_R)) {
 331                                                 fp.p_params.r=atof(word[++i]);
 332                                                 fp.p_params.p.x=atof(word[++i]);
 333                                                 fp.p_params.p.y=atof(word[++i]);
 334                                                 fp.p_params.p.z=atof(word[++i]);
 335                                         }
 336                                         if((fp.p_params.type==PART_INSIDE_D)||
 337                                            (fp.p_params.type==PART_OUTSIDE_D)) {
 338                                                 fp.p_params.p.x=atof(word[++i]);
 339                                                 fp.p_params.p.y=atof(word[++i]);
 340                                                 fp.p_params.p.z=atof(word[++i]);
 341                                                 fp.p_params.d.x=atof(word[++i]);
 342                                                 fp.p_params.d.y=atof(word[++i]);
 343                                                 fp.p_params.d.z=atof(word[++i]);
 344                                         }
 345                                 }
 346                                 if(word[i][0]=='d') {
 347                                         switch(word[++i][0]) {
 348                                                 case '0':
 349
 350                                 fp.d_params.type=DEFECT_TYPE_0D;
 351                                 if(!strncmp(word[i+1],"dbx",3)) {
 352                                         fp.d_params.stype=DEFECT_STYPE_DB_X;
 353                                 }
 354                                 if(!strncmp(word[i+1],"dby",3)) {
 355                                         fp.d_params.stype=DEFECT_STYPE_DB_Y;
 356                                 }
 357                                 if(!strncmp(word[i+1],"dbz",3)) {
 358                                         fp.d_params.stype=DEFECT_STYPE_DB_Z;
 359                                 }
 360                                 if(!strncmp(word[i+1],"dbr",3)) {
 361                                         fp.d_params.stype=DEFECT_STYPE_DB_R;
 362                                 }
 363                                 i+=1;
 364                                 fp.d_params.od=atof(word[++i]);
 365                                 fp.d_params.dd=atof(word[++i]);
 366                                 fp.d_params.element=atoi(word[++i]);
 367                                 fp.d_params.brand=atoi(word[++i]);
 368                                 // parsed in future
 369                 fp.d_params.attr=ATOM_ATTR_HB|ATOM_ATTR_VA;
 370                 fp.d_params.attr|=ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP;
 371                                 break;
 372
 373                                                 case '1':
 374                                 fp.d_params.type=DEFECT_TYPE_1D;
 375                                 break;
 376                                                 case '2':
 377                                 fp.d_params.type=DEFECT_TYPE_2D;
 378                                 break;
 379                                                 case '3':
 380                                 fp.d_params.type=DEFECT_TYPE_3D;
 381                                 break;
 382                                                 default:
 383                                                         break;
 384                                         }
 385
 386                                 }
 387                                 i+=1;
 388                         }
 389                         add_stage(mdrun,STAGE_FILL,&fp);
 390                 }
 391                 else if(!strncmp(word[0],"thermal_init",12)) {
 392                         add_stage(mdrun,STAGE_THERMAL_INIT,NULL);
 393                 }
 394                 else if(!strncmp(word[0],"aattr",5)) {
 395                         // for aatrib line we need a special stage
 396                         // containing one schedule of 0 loops ...
 397                         for(i=0;i<strlen(word[1]);i++) {
 398                                 switch(word[1][i]) {
 399                                         case 't':
 400                                                 cap.type|=CHAATTR_TOTALV;
 401                                                 break;
 402                                         case 'r':
 403                                                 cap.type|=CHAATTR_REGION;
 404                                                 break;
 405                                         case 'e':
 406                                                 cap.type|=CHAATTR_ELEMENT;
 407                                                 break;
 408                                         default:
 409                                                 break;
 410                                 }
 411                         }
 412                         i=2;
 413                         if(cap.type&CHAATTR_REGION) {
 414                                 cap.x0=atof(word[1]);
 415                                 cap.y0=atof(word[2]);
 416                                 cap.z0=atof(word[3]);
 417                                 cap.x1=atof(word[4]);
 418                                 cap.y1=atof(word[5]);
 419                                 cap.z1=atof(word[6]);
 420                                 i+=6;
 421                         }
 422                         if(cap.type&CHAATTR_ELEMENT) {
 423                                 cap.element=atoi(word[i]);
 424                                 i+=1;
 425                         }
 426                         for(o=0;o<strlen(word[i]);o++) {
 427                                 switch(word[i][o]) {
 428                                         case 'b':
 429                                                 cap.attr|=ATOM_ATTR_VB;
 430                                                 break;
 431                                         case 'h':
 432                                                 cap.attr|=ATOM_ATTR_HB;
 433                                                 break;
 434                                         case 'v':
 435                                                 cap.attr|=ATOM_ATTR_VA;
 436                                                 break;
 437                                         case 'f':
 438                                                 cap.attr|=ATOM_ATTR_FP;
 439                                                 break;
 440                                         case '1':
 441                                                 cap.attr|=ATOM_ATTR_1BP;
 442                                                 break;
 443                                         case '2':
 444                                                 cap.attr|=ATOM_ATTR_2BP;
 445                                                 break;
 446                                         case '3':
 447                                                 cap.attr|=ATOM_ATTR_3BP;
 448                                                 break;
 449                                         default:
 450                                                 break;
 451                                 }
 452                         }
 453                         add_stage(mdrun,STAGE_CHAATTR,&cap);
 454                 }
 455                 else if(!strncmp(word[0],"sattr",5)) {
 456                         // for satrib line we need a special stage
 457                         // containing one schedule of 0 loops ...
 458                         csp.type=0;
 459                         for(i=1;i<wcnt;i++) {
 460                                 if(!strncmp(word[i],"pctrl",5)) {
 461                                         csp.ptau=0.01/(atof(word[++i])*GPA);
 462                                         csp.type|=CHSATTR_PCTRL;
 463                                 }
 464                                 if(!strncmp(word[i],"tctrl",5)) {
 465                                         csp.ttau=atof(word[++i]);
 466                                         csp.type|=CHSATTR_TCTRL;
 467                                 }
 468                                 if(!strncmp(word[i],"prelax",6)) {
 469                                         csp.dp=atof(word[++i])*BAR;
 470                                         csp.type|=CHSATTR_PRELAX;
 471                                 }
 472                                 if(!strncmp(word[i],"trelax",6)) {
 473                                         csp.dt=atof(word[++i]);
 474                                         csp.type|=CHSATTR_TRELAX;
 475                                 }
 476                                 if(!strncmp(word[i],"rsteps",6)) {
 477                                         csp.rsteps=atoi(word[++i]);
 478                                         csp.type|=CHSATTR_RSTEPS;
 479                                 }
 480                                 if(!strncmp(word[i],"avgrst",6)) {
 481                                         csp.avgrst=atoi(word[++i]);
 482                                         csp.type|=CHSATTR_AVGRST;
 483                                 }
 484                         }
 485                         add_stage(mdrun,STAGE_CHSATTR,&csp);
 486                 }
 487                 else if(!strncmp(word[0],"prerun",6))
 488                         mdrun->prerun=atoi(word[1]);
 489                 else if(!strncmp(word[0],"avgskip",7))
 490                         mdrun->avgskip=atoi(word[1]);
 491                 else if(!strncmp(word[0],"elog",4))
 492                         mdrun->elog=atoi(word[1]);
 493                 else if(!strncmp(word[0],"tlog",4))
 494                         mdrun->tlog=atoi(word[1]);
 495                 else if(!strncmp(word[0],"plog",4))
 496                         mdrun->plog=atoi(word[1]);
 497                 else if(!strncmp(word[0],"vlog",4))
 498                         mdrun->vlog=atoi(word[1]);
 499                 else if(!strncmp(word[0],"save",4))
 500                         mdrun->save=atoi(word[1]);
 501                 else if(!strncmp(word[0],"visualize",9))
 502                         mdrun->visualize=atoi(word[1]);
 503                 else if(!strncmp(word[0],"stage",5)) {
 504                         // for every stage line, add a stage
 505                         if(!strncmp(word[1],"displace",8)) {
 506                                 dap.nr=atoi(word[2]);
 507                                 dap.dx=atof(word[3]);
 508                                 dap.dy=atof(word[4]);
 509                                 dap.dz=atof(word[5]);
 510                                 add_stage(mdrun,STAGE_DISPLACE_ATOM,&dap);
 511                         }
 512                         else if(!strncmp(word[1],"ins_atoms",9)) {
 513                                 iap.ins_steps=atoi(word[2]);
 514                                 iap.ins_atoms=atoi(word[3]);
 515                                 iap.element=atoi(word[4]);
 516                                 iap.brand=atoi(word[5]);
 517                                 for(i=0;i<strlen(word[6]);i++) {
 518                                         switch(word[6][i]) {
 519                                                 case 'b':
 520                                                         iap.attr|=ATOM_ATTR_VB;
 521                                                         break;
 522                                                 case 'h':
 523                                                         iap.attr|=ATOM_ATTR_HB;
 524                                                         break;
 525                                                 case 'v':
 526                                                         iap.attr|=ATOM_ATTR_VA;
 527                                                         break;
 528                                                 case 'f':
 529                                                         iap.attr|=ATOM_ATTR_FP;
 530                                                         break;
 531                                                 case '1':
 532                                                         iap.attr|=ATOM_ATTR_1BP;
 533                                                         break;
 534                                                 case '2':
 535                                                         iap.attr|=ATOM_ATTR_2BP;
 536                                                         break;
 537                                                 case '3':
 538                                                         iap.attr|=ATOM_ATTR_3BP;
 539                                                         break;
 540                                                 default:
 541                                                         break;
 542                                         }
 543                                 }
 544                                 switch(word[7][0]) {
 545                                         // insertion types
 546                                         case 'p':
 547                                                 iap.type=INS_POS;
 548                                                 iap.x0=atof(word[8]);
 549                                                 iap.y0=atof(word[9]);
 550                                                 iap.z0=atof(word[10]);
 551                                                 break;
 552                                         case 'r':
 553                                                 switch(word[8][0]) {
 554
 555                                                 case 't':
 556                                                         iap.type=INS_TOTAL;
 557                                                         iap.cr=atof(word[9]);
 558                                                         break;
 559                                                 case 'r':
 560                                                         iap.type=INS_RECT;
 561                                                         iap.x0=atof(word[9]);
 562                                                         iap.y0=atof(word[10]);
 563                                                         iap.z0=atof(word[11]);
 564                                                         iap.x1=atof(word[12]);
 565                                                         iap.y1=atof(word[13]);
 566                                                         iap.z1=atof(word[14]);
 567                                                         iap.cr=atof(word[15]);
 568                                                         break;
 569                                                 case 's':
 570                                                         iap.type=INS_SPHERE;
 571                                                         iap.x0=atof(word[9]);
 572                                                         iap.y0=atof(word[10]);
 573                                                         iap.z0=atof(word[11]);
 574                                                         iap.x1=atof(word[12]);
 575                                                         iap.cr=atof(word[13]);
 576                                                         break;
 577                                                 default:
 578                                                         break;
 579                                                 }
 580                                         default:
 581                                                 break;
 582                                 }
 583                                 add_stage(mdrun,STAGE_INSERT_ATOMS,&iap);
 584                         }
 585
 586
 587                         // HERE WE GO ...
 588
 589                         else if(!strncmp(word[1],"ins_m_atoms",11)) {
 590                                 imp.element1=atoi(word[2]);
 591                                 imp.element2=atoi(word[3]);
 592                                 imp.amount1=atoi(word[4]);
 593                                 imp.amount2=atoi(word[5]);
 594                                 imp.brand1=atoi(word[6]);
 595                                 imp.brand2=atoi(word[7]);
 596                                 imp.crmin=atof(word[8]);
 597                                 imp.crmax=atof(word[9]);
 598                                 /* do this later ...
 599                                 for(i=0;i<strlen(word[8]);i++) {
 600                                         switch(word[8][i]) {
 601                                                 case 'b':
 602                                                         imp.attr|=ATOM_ATTR_VB;
 603                                                         break;
 604                                                 case 'h':
 605                                                         imp.attr|=ATOM_ATTR_HB;
 606                                                         break;
 607                                                 case 'v':
 608                                                         imp.attr|=ATOM_ATTR_VA;
 609                                                         break;
 610                                                 case 'f':
 611                                                         imp.attr|=ATOM_ATTR_FP;
 612                                                         break;
 613                                                 case '1':
 614                                                         imp.attr|=ATOM_ATTR_1BP;
 615                                                         break;
 616                                                 case '2':
 617                                                         imp.attr|=ATOM_ATTR_2BP;
 618                                                         break;
 619                                                 case '3':
 620                                                         imp.attr|=ATOM_ATTR_3BP;
 621                                                         break;
 622                                                 default:
 623                                                         break;
 624                                         }
 625                                 }
 626                                 */
 627                                 imp.attr1=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
 628                                 imp.attr2=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
 629                                 add_stage(mdrun,STAGE_INSERT_MIXED_ATOMS,&imp);
 630                         }
 631
 632
 633
 634
 635
 636                         else if(!strncmp(word[1],"continue",8)) {
 637                                 cp.runs=atoi(word[2]);
 638                                 add_stage(mdrun,STAGE_CONTINUE,&cp);
 639                         }
 640                         else if(!strncmp(word[1],"anneal",6)) {
 641                                 ap.count=0;
 642                                 ap.runs=atoi(word[2]);
 643                                 ap.dt=atof(word[3]);
 644                                 ap.interval=atoi(word[4]);
 645                                 add_stage(mdrun,STAGE_ANNEAL,&ap);
 646                         }
 647                         else if(!strncmp(word[1],"set_temp",8)) {
 648                                 if(word[2][0]=='c') {
 649                                         stp.type=SET_TEMP_CURRENT;
 650                                         stp.val=0.0;
 651                                 }
 652                                 else {
 653                                         stp.type=SET_TEMP_VALUE;
 654                                         stp.val=atof(word[2]);
 655                                 }
 656                                 add_stage(mdrun,STAGE_SET_TEMP,&stp);
 657                         }
 658                         else if(!strncmp(word[1],"set_timestep",12)) {
 659                                 stsp.tau=atof(word[2]);
 660                                 add_stage(mdrun,STAGE_SET_TIMESTEP,&stsp);
 661                         }
 662                         else {
 663                                 printf("%s unknown stage type: %s\n",
 664                                        ME,word[1]);
 665                                 return -1;
 666                         }
 667                 }
 668                 else {
 669                         printf("%s unknown keyword '%s', skipped!\n",
 670                                ME,word[0]);
 671                         continue;
 672                 }
 673         }
 674
 675         /* close file */
 676         close(fd);
 677
 678         return 0;
 679 }
 680
 681 int check_pressure(t_moldyn *moldyn,t_mdrun *mdrun) {
 682
 683         double delta;
 684
 685         if(!(mdrun->sattr&SATTR_PRELAX)) {
 686                 return TRUE;
 687         }
 688
 689         delta=moldyn->p_avg-moldyn->p_ref;
 690
 691         if(delta<0)
 692                 delta=-delta;
 693
 694         if(delta>mdrun->dp)
 695                 return FALSE;
 696
 697         return TRUE;
 698 }
 699
 700 int check_temperature(t_moldyn *moldyn,t_mdrun *mdrun) {
 701
 702         double delta;
 703
 704         if(!(mdrun->sattr&SATTR_TRELAX))
 705                 return TRUE;
 706
 707         delta=moldyn->t_avg-moldyn->t_ref;
 708
 709         if(delta<0)
 710                 delta=-delta;
 711
 712         if(delta>mdrun->dt)
 713                 return FALSE;
 714
 715         return TRUE;
 716 }
 717
 718 int displace_atom(t_moldyn *moldyn,t_mdrun *mdrun) {
 719
 720         t_displace_atom_params *dap;
 721         t_stage *stage;
 722         t_atom *atom;
 723
 724         stage=mdrun->stage.current->data;
 725         dap=stage->params;
 726
 727         atom=&(moldyn->atom[dap->nr]);
 728         atom->r.x+=dap->dx;
 729         atom->r.y+=dap->dy;
 730         atom->r.z+=dap->dz;
 731
 732         return 0;
 733 }
 734
 735 int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 736
 737         t_insert_atoms_params *iap;
 738         t_stage *stage;
 739         t_atom *atom;
 740         t_3dvec r,v,dist;
 741         double d,dmin,o;
 742         int cnt,i;
 743         double x,y,z;
 744         double x0,y0,z0;
 745         u8 cr_check,run;
 746
 747         stage=mdrun->stage.current->data;
 748         iap=stage->params;
 749
 750         cr_check=FALSE;
 751
 752         v.x=0.0; v.y=0.0; v.z=0.0;
 753         x=0; y=0; z=0;
 754         o=0; dmin=0;
 755
 756         switch(mdrun->lattice) {
 757                 case CUBIC:
 758                         o=0.5*mdrun->lc;
 759                         break;
 760                 case FCC:
 761                         o=0.25*mdrun->lc;
 762                         break;
 763                 case DIAMOND:
 764                 case ZINCBLENDE:
 765                         o=0.125*mdrun->lc;
 766                         break;
 767                 default:
 768                         break;
 769         }
 770
 771         switch(iap->type) {
 772                 case INS_TOTAL:
 773                         x=moldyn->dim.x;
 774                         x0=-x/2.0;
 775                         y=moldyn->dim.y;
 776                         y0=-y/2.0;
 777                         z=moldyn->dim.z;
 778                         z0=-z/2.0;
 779                         cr_check=TRUE;
 780                         break;
 781                 case INS_RECT:
 782                         x=iap->x1-iap->x0;
 783                         x0=iap->x0;
 784                         y=iap->y1-iap->y0;
 785                         y0=iap->y0;
 786                         z=iap->z1-iap->z0;
 787                         z0=iap->z0;
 788                         cr_check=TRUE;
 789                         break;
 790                 case INS_SPHERE:
 791                         x=2.0*iap->x1;
 792                         x0=iap->x0-iap->x1;
 793                         y=x;
 794                         y0=iap->y0-iap->x1;
 795                         z=x;
 796                         z0=iap->z0-iap->x1;
 797                         cr_check=TRUE;
 798                         break;
 799                 case INS_POS:
 800                         x0=iap->x0;
 801                         y0=iap->y0;
 802                         z0=iap->z0;
 803                         cr_check=FALSE;
 804                         break;
 805                 default:
 806                         printf("%s unknown insertion mode: %02x\n",
 807                                ME,iap->type);
 808                         return -1;
 809         }
 810
 811         cnt=0;
 812         while(cnt<iap->ins_atoms) {
 813                 run=1;
 814                 while(run) {
 815                         if(iap->type!=INS_POS) {
 816                                 r.x=rand_get_double(&(moldyn->random))*x;
 817                                 r.y=rand_get_double(&(moldyn->random))*y;
 818                                 r.z=rand_get_double(&(moldyn->random))*z;
 819                         }
 820                         else {
 821                                 r.x=0.0;
 822                                 r.y=0.0;
 823                                 r.z=0.0;
 824                         }
 825                         r.x+=x0;
 826                         r.y+=y0;
 827                         r.z+=z0;
 828                         // offset
 829                         if(iap->type!=INS_TOTAL) {
 830                                 r.x+=o;
 831                                 r.y+=o;
 832                                 r.z+=o;
 833                         }
 834                         run=0;
 835                         if(cr_check==TRUE) {
 836                                 dmin=1000;      // for sure too high!
 837                                 for(i=0;i<moldyn->count;i++) {
 838                                         atom=&(moldyn->atom[i]);
 839                                         v3_sub(&dist,&(atom->r),&r);
 840                                         check_per_bound(moldyn,&dist);
 841                                         d=v3_absolute_square(&dist);
 842                                         if(d<(iap->cr*iap->cr)) {
 843                                                 run=1;
 844                                                 break;
 845                                         }
 846                                         if(d<dmin)
 847                                                 dmin=d;
 848                                 }
 849                         }
 850                         if(iap->type==INS_SPHERE) {
 851                                 if((r.x-iap->x0)*(r.x-iap->x0)+
 852                                    (r.y-iap->y0)*(r.y-iap->y0)+
 853                                    (r.z-iap->z0)*(r.z-iap->z0)>
 854                                    (iap->x1*iap->x1)) {
 855                                         run=1;
 856                                 }
 857                         }
 858                 }
 859                 add_atom(moldyn,iap->element,
 860                          iap->brand,iap->attr,&r,&v);
 861                 printf("%s atom inserted (%d/%d): %f %f %f\n",
 862                        ME,(iap->cnt_steps+1)*iap->ins_atoms,
 863                        iap->ins_steps*iap->ins_atoms,r.x,r.y,r.z);
 864                 printf("  -> d2 = %f/%f\n",dmin,iap->cr*iap->cr);
 865                 cnt+=1;
 866         }
 867
 868         return 0;
 869 }
 870
 871 int insert_mixed_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 872
 873         t_stage *stage;
 874         t_insert_mixed_atoms_params *imp;
 875         t_atom *atom;
 876         double x,x0,y,y0,z,z0;
 877         double dmin,d,cmin,cmax;
 878         u8 retry;
 879         t_3dvec r,v,dist;
 880         int i;
 881
 882
 883         stage=mdrun->stage.current->data;
 884         imp=stage->params;
 885
 886         x=moldyn->dim.x;
 887         x0=-x/2.0;
 888         y=moldyn->dim.y;
 889         y0=-y/2.0;
 890         z=moldyn->dim.z;
 891         z0=-z/2.0;
 892
 893         v.x=0.0;
 894         v.y=0.0;
 895         v.z=0.0;
 896
 897         cmin=imp->crmin*imp->crmin;
 898         cmax=imp->crmax*imp->crmax;
 899
 900         while(imp->amount1|imp->amount2) {
 901                 if(imp->amount1) {
 902                         retry=1;
 903                         while(retry) {
 904                                 retry=0;
 905                                 r.x=rand_get_double(&(moldyn->random))*x;
 906                                 r.y=rand_get_double(&(moldyn->random))*y;
 907                                 r.z=rand_get_double(&(moldyn->random))*z;
 908                                 r.x+=x0;
 909                                 r.y+=y0;
 910                                 r.z+=z0;
 911                                 dmin=1000.0;    // for sure too high!
 912                                 for(i=0;i<moldyn->count;i++) {
 913                                         atom=&(moldyn->atom[i]);
 914                                         v3_sub(&dist,&(atom->r),&r);
 915                                         check_per_bound(moldyn,&dist);
 916                                         d=v3_absolute_square(&dist);
 917                                         if(d<cmin) {
 918                                                 retry=1;
 919                                                 break;
 920                                         }
 921                                         if(d<dmin)
 922                                                 dmin=d;
 923                                 }
 924                                 if(dmin!=1000.0)
 925                                         if(dmin>cmax)
 926                                                 retry=1;
 927                         }
 928                         add_atom(moldyn,imp->element1,
 929                                  imp->brand1,imp->attr1,&r,&v);
 930                         printf("%s (mixed) atom inserted (%d): %f %f %f\n",
 931                                ME,imp->amount1,r.x,r.y,r.z);
 932                         printf("  -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
 933                         imp->amount1-=1;
 934                 }
 935                 if(imp->amount2) {
 936                         retry=1;
 937                         while(retry) {
 938                                 retry=0;
 939                                 r.x=rand_get_double(&(moldyn->random))*x;
 940                                 r.y=rand_get_double(&(moldyn->random))*y;
 941                                 r.z=rand_get_double(&(moldyn->random))*z;
 942                                 r.x+=x0;
 943                                 r.y+=y0;
 944                                 r.z+=z0;
 945                                 dmin=1000.0;    // for sure too high!
 946                                 for(i=0;i<moldyn->count;i++) {
 947                                         atom=&(moldyn->atom[i]);
 948                                         v3_sub(&dist,&(atom->r),&r);
 949                                         check_per_bound(moldyn,&dist);
 950                                         d=v3_absolute_square(&dist);
 951                                         if(d<cmin) {
 952                                                 retry=1;
 953                                                 break;
 954                                         }
 955                                         if(d<dmin)
 956                                                 dmin=d;
 957                                 }
 958                                 if(dmin!=1000.0)
 959                                         if(dmin>cmax)
 960                                                 retry=1;
 961                         }
 962                         add_atom(moldyn,imp->element2,
 963                                  imp->brand2,imp->attr2,&r,&v);
 964                         printf("%s (mixed) atom inserted (%d): %f %f %f\n",
 965                                ME,imp->amount2,r.x,r.y,r.z);
 966                         printf("  -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
 967                         imp->amount2-=1;
 968                 }
 969         }
 970
 971         return 0;
 972 }
 973
 974 int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
 975
 976         t_stage *stage;
 977         t_chaattr_params *cap;
 978         t_atom *atom;
 979         int i;
 980
 981         stage=mdrun->stage.current->data;
 982         cap=stage->params;
 983
 984         for(i=0;i<moldyn->count;i++) {
 985                 atom=&(moldyn->atom[i]);
 986                 if(cap->type&CHAATTR_ELEMENT) {
 987                         if(cap->element!=atom->element)
 988                                 continue;
 989                 }
 990                 if(cap->type&CHAATTR_REGION) {
 991                         if(cap->x0<atom->r.x)
 992                                 continue;
 993                         if(cap->y0<atom->r.y)
 994                                 continue;
 995                         if(cap->z0<atom->r.z)
 996                                 continue;
 997                         if(cap->x1>atom->r.x)
 998                                 continue;
 999                         if(cap->y1>atom->r.y)
1000                                 continue;
1001                         if(cap->z1>atom->r.z)
1002                                 continue;
1003                 }
1004                 atom->attr=cap->attr;
1005         }
1006
1007         return 0;
1008 }
1009
1010 int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
1011
1012         t_stage *stage;
1013         t_chsattr_params *csp;
1014
1015         stage=mdrun->stage.current->data;
1016         csp=stage->params;
1017
1018         if(csp->type&CHSATTR_PCTRL) {
1019                 if(csp->ptau>0)
1020                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
1021                 else
1022                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
1023         }
1024         if(csp->type&CHSATTR_TCTRL) {
1025                 if(csp->ttau>0)
1026                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
1027                 else
1028                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
1029         }
1030         if(csp->type&CHSATTR_PRELAX) {
1031                 if(csp->dp<0)
1032                         mdrun->sattr&=(~(SATTR_PRELAX));
1033                 else
1034                         mdrun->sattr|=SATTR_PRELAX;
1035                 mdrun->dp=csp->dp;
1036         }
1037         if(csp->type&CHSATTR_TRELAX) {
1038                 if(csp->dt<0)
1039                         mdrun->sattr&=(~(SATTR_TRELAX));
1040                 else
1041                         mdrun->sattr|=SATTR_TRELAX;
1042                 mdrun->dt=csp->dt;
1043         }
1044         if(csp->type&CHSATTR_AVGRST) {
1045                 if(csp->avgrst)
1046                         mdrun->sattr|=SATTR_AVGRST;
1047                 else
1048                         mdrun->sattr&=(~(SATTR_AVGRST));
1049         }
1050         if(csp->type&CHSATTR_RSTEPS) {
1051                 mdrun->relax_steps=csp->rsteps;
1052         }
1053
1054         return 0;
1055 }
1056
1057 #define stage_print(m)  if(!(stage->executed)) \
1058                                 printf("%s",m)
1059
1060 int mdrun_hook(void *ptr1,void *ptr2) {
1061
1062         t_moldyn *moldyn;
1063         t_mdrun *mdrun;
1064         t_stage *stage;
1065         t_list *sl;
1066         int steps;
1067         u8 change_stage;
1068         t_3dvec o;
1069
1070         t_insert_atoms_params *iap;
1071         t_insert_mixed_atoms_params *imp;
1072         t_continue_params *cp;
1073         t_anneal_params *ap;
1074         t_set_temp_params *stp;
1075         t_set_timestep_params *stsp;
1076         t_fill_params *fp;
1077
1078         moldyn=ptr1;
1079         mdrun=ptr2;
1080
1081         sl=&(mdrun->stage);
1082
1083         change_stage=FALSE;
1084
1085         /* return immediately if there are no more stage */
1086         if(sl->current==NULL)
1087                 return 0;
1088
1089         /* get stage description */
1090         stage=sl->current->data;
1091
1092         /* steps in next schedule */
1093         steps=mdrun->relax_steps;
1094
1095         /* check whether relaxation steps are necessary */
1096         if((check_pressure(moldyn,mdrun)==TRUE)&\
1097            (check_temperature(moldyn,mdrun)==TRUE)) {
1098
1099                 /* be verbose */
1100                 stage_print("\n###########################\n");
1101                 stage_print("# [mdrun] executing stage #\n");
1102                 stage_print("###########################\n\n");
1103
1104                 /* stage specific stuff */
1105                 switch(stage->type) {
1106                         case STAGE_DISPLACE_ATOM:
1107                                 stage_print("  -> displace atom\n\n");
1108                                 displace_atom(moldyn,mdrun);
1109                                 change_stage=TRUE;
1110                                 break;
1111                         case STAGE_INSERT_ATOMS:
1112                                 stage_print("  -> insert atoms\n\n");
1113                                 iap=stage->params;
1114                                 if(iap->cnt_steps==iap->ins_steps) {
1115                                         change_stage=TRUE;
1116                                         break;
1117                                 }
1118                                 insert_atoms(moldyn,mdrun);
1119                                 iap->cnt_steps+=1;
1120                                 break;
1121
1122
1123
1124                         case STAGE_INSERT_MIXED_ATOMS:
1125                                 stage_print("  -> insert mixed atoms\n\n");
1126                                 imp=stage->params;
1127                                 insert_mixed_atoms(moldyn,mdrun);
1128                                 change_stage=TRUE;
1129                                 break;
1130
1131
1132
1133                         case STAGE_CONTINUE:
1134                                 stage_print("  -> continue\n\n");
1135                                 if(stage->executed==TRUE) {
1136                                         change_stage=TRUE;
1137                                         break;
1138                                 }
1139                                 cp=stage->params;
1140                                 steps=cp->runs;
1141                                 break;
1142                         case STAGE_ANNEAL:
1143                                 stage_print("  -> anneal\n\n");
1144                                 ap=stage->params;
1145                                 if(ap->count==ap->runs) {
1146                                         change_stage=TRUE;
1147                                         break;
1148                                 }
1149                                 if(moldyn->t_ref+ap->dt>=0.0)
1150                                         set_temperature(moldyn,
1151                                                         moldyn->t_ref+ap->dt);
1152                                 ap->count+=1;
1153                                 steps=ap->interval;
1154                                 break;
1155                         case STAGE_CHAATTR:
1156                                 stage_print("  -> change atom attributes\n\n");
1157                                 chaatr(moldyn,mdrun);
1158                                 change_stage=TRUE;
1159                                 break;
1160                         case STAGE_CHSATTR:
1161                                 stage_print("  -> change sys attributes\n\n");
1162                                 chsattr(moldyn,mdrun);
1163                                 change_stage=TRUE;
1164                                 break;
1165                         case STAGE_SET_TEMP:
1166                                 stage_print("  -> set temperature\n\n");
1167                                 stp=stage->params;
1168                                 if(stp->type&SET_TEMP_CURRENT) {
1169                                         set_temperature(moldyn,moldyn->t_avg);
1170                                 }
1171                                 else {
1172                                         set_temperature(moldyn,stp->val);
1173                                 }
1174                                 change_stage=TRUE;
1175                                 break;
1176                         case STAGE_SET_TIMESTEP:
1177                                 stage_print("  -> set timestep\n\n");
1178                                 stsp=stage->params;
1179                                 mdrun->timestep=stsp->tau;
1180                                 change_stage=TRUE;
1181                                 break;
1182                         case STAGE_FILL:
1183                                 stage_print("  -> fill lattice\n\n");
1184                                 fp=stage->params;
1185                                 switch(fp->lattice) {
1186                                         case ZINCBLENDE:
1187
1188                                         o.x=0.5*0.25*fp->lc;
1189                                         o.y=o.x;
1190                                         o.z=o.x;
1191                                         create_lattice(moldyn,
1192                                                        FCC,fp->lc,
1193                                                        mdrun->element1,
1194                                                        DEFAULT_ATOM_ATTR,0,
1195                                                        fp->lx,fp->ly,fp->lz,
1196                                                        &o,
1197                                                        &(fp->p_params),
1198                                                        &(fp->d_params));
1199                                         o.x+=0.25*fp->lc;
1200                                         o.y=o.x;
1201                                         o.z=o.x;
1202                                         create_lattice(moldyn,
1203                                                        FCC,fp->lc,
1204                                                        mdrun->element2,
1205                                                        DEFAULT_ATOM_ATTR,1,
1206                                                        fp->lx,fp->ly,fp->lz,
1207                                                        &o,
1208                                                        &(fp->p_params),
1209                                                        &(fp->d_params));
1210                                         break;
1211
1212                                         default:
1213
1214                                         create_lattice(moldyn,
1215                                                        fp->lattice,fp->lc,
1216                                                        mdrun->element1,
1217                                                        DEFAULT_ATOM_ATTR,0,
1218                                                        fp->lx,fp->ly,fp->lz,
1219                                                        NULL,
1220                                                        &(fp->p_params),
1221                                                        &(fp->d_params));
1222                                         break;
1223                                 }
1224                                 moldyn_bc_check(moldyn);
1225                                 change_stage=TRUE;
1226                                 break;
1227                         case STAGE_THERMAL_INIT:
1228                                 stage_print("  -> thermal init\n\n");
1229                                 thermal_init(moldyn,TRUE);
1230                                 change_stage=TRUE;
1231                                 break;
1232                         default:
1233                                 printf("%s unknwon stage type\n",ME);
1234                                 break;
1235                 }
1236
1237                 /* mark as executed */
1238                 stage->executed=TRUE;
1239
1240                 /* change state */
1241                 if(change_stage==TRUE) {
1242                         printf("%s finished stage\n",ME);
1243                         if(list_next_f(sl)==L_NO_NEXT_ELEMENT) {
1244                                 printf("%s no more stages\n",ME);
1245                                 return 0;
1246                         }
1247                         steps=0;
1248                 }
1249
1250         }
1251         else {
1252
1253                 /* averages */
1254                 if(mdrun->sattr&SATTR_AVGRST)
1255                         average_reset(moldyn);
1256
1257         }
1258
1259         /* continue simulation */
1260         moldyn_add_schedule(moldyn,steps,mdrun->timestep);
1261
1262         return 0;
1263 }
1264
1265 int main(int argc,char **argv) {
1266
1267         t_mdrun mdrun;
1268         t_moldyn moldyn;
1269         //t_3dvec o;
1270
1271         /* clear structs */
1272         memset(&mdrun,0,sizeof(t_mdrun));
1273         memset(&moldyn,0,sizeof(t_moldyn));
1274
1275         /* parse arguments */
1276         if(mdrun_parse_argv(&mdrun,argc,argv)<0)
1277                 return -1;
1278
1279         /* initialize list system */
1280         list_init_f(&(mdrun.stage));
1281
1282         /* parse config file */
1283         mdrun_parse_config(&mdrun);
1284
1285         /* reset the stage list */
1286         list_reset_f(&(mdrun.stage));
1287
1288         /* sanity check! */
1289
1290         /* prepare simulation */
1291
1292         if(mdrun.continue_file[0]) {
1293                 // read the save file
1294                 moldyn_read_save_file(&moldyn,mdrun.continue_file);
1295                 // manualaadjusting some stuff
1296                 moldyn.argc=argc;
1297                 moldyn.args=argv;
1298                 rand_init(&(moldyn.random),NULL,1);
1299                 moldyn.random.status|=RAND_STAT_VERBOSE;
1300         }
1301         else {
1302                 moldyn_init(&moldyn,argc,argv);
1303         }
1304
1305         if(set_int_alg(&moldyn,mdrun.intalgo)<0)
1306                 return -1;
1307
1308         /* potential */
1309         set_cutoff(&moldyn,mdrun.cutoff);
1310         if(set_potential(&moldyn,mdrun.potential)<0)
1311                 return -1;
1312         switch(mdrun.potential) {
1313                 case MOLDYN_POTENTIAL_AM:
1314                         albe_mult_set_params(&moldyn,
1315                                              mdrun.element1,
1316                                              mdrun.element2);
1317                         break;
1318                 case MOLDYN_POTENTIAL_TM:
1319                         tersoff_mult_set_params(&moldyn,
1320                                                 mdrun.element1,
1321                                                 mdrun.element2);
1322                         break;
1323                 case MOLDYN_POTENTIAL_HO:
1324                         harmonic_oscillator_set_params(&moldyn,mdrun.element1);
1325                         break;
1326                 case MOLDYN_POTENTIAL_LJ:
1327                         lennard_jones_set_params(&moldyn,mdrun.element1);
1328                         break;
1329                 default:
1330                         printf("%s unknown potential: %02x\n",
1331                                ME,mdrun.potential);
1332                         return -1;
1333         }
1334
1335         /* if it is a continue run, reset schedule and skip lattice init */
1336         if(mdrun.continue_file[0]) {
1337                 memset(&(moldyn.schedule),0,sizeof(t_moldyn_schedule));
1338                 goto addsched;
1339         }
1340
1341         /* initial lattice and dimensions */
1342         set_dim(&moldyn,mdrun.dim.x,mdrun.dim.y,mdrun.dim.z,mdrun.vis);
1343         set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
1344         /* replaced by fill stage !!
1345         switch(mdrun.lattice) {
1346                 case FCC:
1347                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.fill_element,
1348                                        mdrun.m1,DEFAULT_ATOM_ATTR,
1349                                        mdrun.fill_brand,mdrun.lx,
1350                                        mdrun.ly,mdrun.lz,NULL,0,NULL);
1351                         break;
1352                 case DIAMOND:
1353                         create_lattice(&moldyn,DIAMOND,mdrun.lc,
1354                                        mdrun.fill_element,
1355                                        mdrun.m1,DEFAULT_ATOM_ATTR,
1356                                        mdrun.fill_brand,mdrun.lx,
1357                                        mdrun.ly,mdrun.lz,NULL,0,NULL);
1358                         break;
1359                 case ZINCBLENDE:
1360                         o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
1361                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
1362                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
1363                                        mdrun.ly,mdrun.lz,&o,0,NULL);
1364                         o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
1365                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
1366                                        mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
1367                                        mdrun.ly,mdrun.lz,&o,0,NULL);
1368                         break;
1369                 case NONE:
1370                         set_nn_dist(&moldyn,mdrun.nnd);
1371                         break;
1372                 default:
1373                         printf("%s unknown lattice type: %02x\n",
1374                                ME,mdrun.lattice);
1375                         return -1;
1376         }
1377         moldyn_bc_check(&moldyn);
1378         replaced by fill stage !! */
1379
1380         /* temperature and pressure */
1381         set_temperature(&moldyn,mdrun.temperature);
1382         set_pressure(&moldyn,mdrun.pressure);
1383         /* replaced thermal_init stage
1384         thermal_init(&moldyn,TRUE);
1385         */
1386
1387 addsched:
1388         /* first schedule */
1389         moldyn_add_schedule(&moldyn,mdrun.prerun,mdrun.timestep);
1390
1391         /* log */
1392         moldyn_set_log_dir(&moldyn,mdrun.sdir);
1393         moldyn_set_report(&moldyn,"CHANGE ME","CHANGE ME TOO");
1394         if(mdrun.elog)
1395                 moldyn_set_log(&moldyn,LOG_TOTAL_ENERGY,mdrun.elog);
1396         if(mdrun.tlog)
1397                 moldyn_set_log(&moldyn,LOG_TEMPERATURE,mdrun.tlog);
1398         if(mdrun.plog)
1399                 moldyn_set_log(&moldyn,LOG_PRESSURE,mdrun.plog);
1400         if(mdrun.vlog)
1401                 moldyn_set_log(&moldyn,LOG_VOLUME,mdrun.vlog);
1402         if(mdrun.visualize)
1403                 moldyn_set_log(&moldyn,VISUAL_STEP,mdrun.visualize);
1404         if(mdrun.save)
1405                 moldyn_set_log(&moldyn,SAVE_STEP,mdrun.save);
1406         moldyn_set_log(&moldyn,CREATE_REPORT,0);
1407         set_avg_skip(&moldyn,mdrun.avgskip);
1408
1409         /* prepare the hook function */
1410         moldyn_set_schedule_hook(&moldyn,&mdrun_hook,&mdrun);
1411
1412         /* run the simulation */
1413         moldyn_integrate(&moldyn);
1414
1415         /* shutdown */
1416         moldyn_shutdown(&moldyn);
1417         del_stages(&mdrun);
1418         list_destroy_f(&(mdrun.stage));
1419
1420         return 0;
1421 }