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_DEL_ATOMS:
 102                         psize=sizeof(t_del_atoms_params);
 103                         break;
 104                 case STAGE_INSERT_ATOMS:
 105                         psize=sizeof(t_insert_atoms_params);
 106                         break;
 107                 case STAGE_INSERT_MIXED_ATOMS:
 108                         psize=sizeof(t_insert_mixed_atoms_params);
 109                         break;
 110                 case STAGE_CONTINUE:
 111                         psize=sizeof(t_continue_params);
 112                         break;
 113                 case STAGE_ANNEAL:
 114                         psize=sizeof(t_anneal_params);
 115                         break;
 116                 case STAGE_CHAATTR:
 117                         psize=sizeof(t_chaattr_params);
 118                         break;
 119                 case STAGE_CHSATTR:
 120                         psize=sizeof(t_chsattr_params);
 121                         break;
 122                 case STAGE_SET_TEMP:
 123                         psize=sizeof(t_set_temp_params);
 124                         break;
 125                 case STAGE_SET_TIMESTEP:
 126                         psize=sizeof(t_set_timestep_params);
 127                         break;
 128                 case STAGE_FILL:
 129                         psize=sizeof(t_fill_params);
 130                         break;
 131                 case STAGE_THERMAL_INIT:
 132                         psize=0;
 133                         break;
 134                 default:
 135                         printf("%s unknown stage type: %02x\n",ME,type);
 136                         return -1;
 137         }
 138
 139         stage=malloc(sizeof(t_stage));
 140         if(stage==NULL) {
 141                 perror("[mdrun] malloc (add stage)");
 142                 return -1;
 143         }
 144
 145         stage->type=type;
 146         stage->executed=FALSE;
 147
 148         stage->params=malloc(psize);
 149         if(stage->params==NULL) {
 150                 perror("[mdrun] malloc (stage params)");
 151                 return -1;
 152         }
 153
 154         memcpy(stage->params,params,psize);
 155
 156         list_add_immediate_f(&(mdrun->stage),stage);
 157
 158         return 0;
 159 }
 160
 161 int mdrun_parse_config(t_mdrun *mdrun) {
 162
 163         int fd,ret;
 164         char error[128];
 165         char line[128];
 166         char *wptr;
 167         char word[32][64];
 168         int wcnt;
 169         int i,o;
 170
 171         t_displace_atom_params dap;
 172         t_insert_atoms_params iap;
 173         t_insert_mixed_atoms_params imp;
 174         t_continue_params cp;
 175         t_anneal_params ap;
 176         t_chaattr_params cap;
 177         t_chsattr_params csp;
 178         t_set_temp_params stp;
 179         t_set_timestep_params stsp;
 180         t_fill_params fp;
 181         t_del_atoms_params delp;
 182
 183         /* open config file */
 184         fd=open(mdrun->cfile,O_RDONLY);
 185         if(fd<0) {
 186                 snprintf(error,128,"%s open cfile %s",ME,mdrun->cfile);
 187                 perror(error);
 188                 return fd;
 189         }
 190
 191         /* read, parse, set */
 192         ret=1;
 193         while(ret>0) {
 194
 195                 /* read */
 196                 ret=get_line(fd,line,128);
 197
 198                 /* parse */
 199
 200                 // ignore # lines and \n
 201                 if((line[0]=='#')|(ret==1))
 202                         continue;
 203
 204                 // reset
 205                 memset(&iap,0,sizeof(t_insert_atoms_params));
 206                 memset(&imp,0,sizeof(t_insert_mixed_atoms_params));
 207                 memset(&cp,0,sizeof(t_continue_params));
 208                 memset(&ap,0,sizeof(t_anneal_params));
 209                 memset(&cap,0,sizeof(t_chaattr_params));
 210                 memset(&csp,0,sizeof(t_chsattr_params));
 211                 memset(&stp,0,sizeof(t_set_temp_params));
 212                 memset(&stsp,0,sizeof(t_set_timestep_params));
 213                 memset(&fp,0,sizeof(t_fill_params));
 214                 memset(&delp,0,sizeof(t_del_atoms_params));
 215
 216                 // get command + args
 217                 wcnt=0;
 218                 while(1) {
 219                         if(wcnt)
 220                                 wptr=strtok(NULL," \t");
 221                         else
 222                                 wptr=strtok(line," \t");
 223                         if(wptr==NULL)
 224                                 break;
 225                         strncpy(word[wcnt],wptr,64);
 226                         wcnt+=1;
 227                 }
 228
 229                 if(!strncmp(word[0],"potential",9)) {
 230                         if(!strncmp(word[1],"albe",4))
 231                                 mdrun->potential=MOLDYN_POTENTIAL_AM;
 232                         if(!strncmp(word[1],"tersoff",7))
 233                                 mdrun->potential=MOLDYN_POTENTIAL_TM;
 234                         if(!strncmp(word[1],"ho",2))
 235                                 mdrun->potential=MOLDYN_POTENTIAL_HO;
 236                         if(!strncmp(word[1],"lj",2))
 237                                 mdrun->potential=MOLDYN_POTENTIAL_LJ;
 238                 }
 239                 else if(!strncmp(word[0],"continue",8))
 240                         strncpy(mdrun->continue_file,word[1],128);
 241                 else if(!strncmp(word[0],"cutoff",6))
 242                         mdrun->cutoff=atof(word[1]);
 243                 else if(!strncmp(word[0],"nnd",3))
 244                         mdrun->nnd=atof(word[1]);
 245                 else if(!strncmp(word[0],"intalgo",7)) {
 246                         if(!strncmp(word[1],"verlet",5))
 247                                 mdrun->intalgo=MOLDYN_INTEGRATE_VERLET;
 248                 }
 249                 else if(!strncmp(word[0],"timestep",8))
 250                         mdrun->timestep=atof(word[1]);
 251                 else if(!strncmp(word[0],"volume",6)) {
 252                         mdrun->dim.x=atof(word[1]);
 253                         mdrun->dim.y=atof(word[2]);
 254                         mdrun->dim.z=atof(word[3]);
 255                         if(strncmp(word[4],"0",1))
 256                                 mdrun->vis=TRUE;
 257                 }
 258                 else if(!strncmp(word[0],"pbc",3)) {
 259                         if(strncmp(word[1],"0",1))
 260                                 mdrun->pbcx=TRUE;
 261                         else
 262                                 mdrun->pbcx=FALSE;
 263                         if(strncmp(word[2],"0",1))
 264                                 mdrun->pbcy=TRUE;
 265                         else
 266                                 mdrun->pbcy=FALSE;
 267                         if(strncmp(word[3],"0",1))
 268                                 mdrun->pbcz=TRUE;
 269                         else
 270                                 mdrun->pbcz=FALSE;
 271                 }
 272                 else if(!strncmp(word[0],"temperature",11))
 273                         mdrun->temperature=atof(word[1]);
 274                 else if(!strncmp(word[0],"pressure",8))
 275                         mdrun->pressure=atof(word[1]);
 276                 else if(!strncmp(word[0],"lattice",7)) {
 277                         if(!strncmp(word[1],"zincblende",10))
 278                                 mdrun->lattice=ZINCBLENDE;
 279                         if(!strncmp(word[1],"fcc",3))
 280                                 mdrun->lattice=FCC;
 281                         if(!strncmp(word[1],"diamond",7))
 282                                 mdrun->lattice=DIAMOND;
 283                         if(!strncmp(word[1],"none",4))
 284                                 mdrun->lattice=NONE;
 285                         if(wcnt==3)
 286                                 mdrun->lc=atof(word[2]);
 287                 }
 288                 else if(!strncmp(word[0],"element1",8)) {
 289                         mdrun->element1=atoi(word[1]);
 290                 }
 291                 else if(!strncmp(word[0],"element2",8)) {
 292                         mdrun->element2=atoi(word[1]);
 293                 }
 294                 else if(!strncmp(word[0],"fill",6)) {
 295                         // default values
 296                         fp.fill_element=mdrun->element1;
 297                         fp.fill_brand=0;
 298                         fp.lattice=mdrun->lattice;
 299                         fp.p_params.type=0;
 300                         fp.d_params.type=0;
 301                         fp.d_params.stype=0;
 302                         // parse fill command
 303                         i=1;
 304                         while(i<wcnt) {
 305                                 if(!strncmp(word[i],"lc",2)) {
 306                                         fp.lx=atoi(word[++i]);
 307                                         fp.ly=atoi(word[++i]);
 308                                         fp.lz=atoi(word[++i]);
 309                                         fp.lc=atof(word[++i]);
 310                                         mdrun->lc=fp.lc;
 311                                         continue;
 312                                 }
 313                                 if(!strncmp(word[i],"eb",2)) {
 314                                         fp.fill_element=atoi(word[++i]);
 315                                         fp.fill_brand=atoi(word[++i]);
 316                                         continue;
 317                                 }
 318                                 if(word[i][0]=='p') {
 319                                         i+=1;
 320                                         switch(word[i][0]) {
 321                                         case 'i':
 322                                                 if(word[i][1]=='r')
 323                                                 fp.p_params.type=PART_INSIDE_R;
 324                                                 else
 325                                                 fp.p_params.type=PART_INSIDE_D;
 326                                                 break;
 327                                         case 'o':
 328                                                 if(word[i][1]=='r')
 329                                                 fp.p_params.type=PART_OUTSIDE_R;
 330                                                 else
 331                                                 fp.p_params.type=PART_OUTSIDE_D;
 332                                                 break;
 333                                         default:
 334                                                 break;
 335                                         }
 336                                         if((fp.p_params.type==PART_INSIDE_R)||
 337                                           (fp.p_params.type==PART_OUTSIDE_R)) {
 338                                                 fp.p_params.r=atof(word[++i]);
 339                                                 fp.p_params.p.x=atof(word[++i]);
 340                                                 fp.p_params.p.y=atof(word[++i]);
 341                                                 fp.p_params.p.z=atof(word[++i]);
 342                                         }
 343                                         if((fp.p_params.type==PART_INSIDE_D)||
 344                                            (fp.p_params.type==PART_OUTSIDE_D)) {
 345                                                 fp.p_params.p.x=atof(word[++i]);
 346                                                 fp.p_params.p.y=atof(word[++i]);
 347                                                 fp.p_params.p.z=atof(word[++i]);
 348                                                 fp.p_params.d.x=atof(word[++i]);
 349                                                 fp.p_params.d.y=atof(word[++i]);
 350                                                 fp.p_params.d.z=atof(word[++i]);
 351                                         }
 352                                         continue;
 353                                 }
 354                                 if(word[i][0]=='d') {
 355                                         switch(word[++i][0]) {
 356                                                 case '0':
 357
 358                                 fp.d_params.type=DEFECT_TYPE_0D;
 359                                 if(!strncmp(word[i+1],"dbx",3)) {
 360                                         fp.d_params.stype=DEFECT_STYPE_DB_X;
 361                                 }
 362                                 if(!strncmp(word[i+1],"dby",3)) {
 363                                         fp.d_params.stype=DEFECT_STYPE_DB_Y;
 364                                 }
 365                                 if(!strncmp(word[i+1],"dbz",3)) {
 366                                         fp.d_params.stype=DEFECT_STYPE_DB_Z;
 367                                 }
 368                                 if(!strncmp(word[i+1],"dbr",3)) {
 369                                         fp.d_params.stype=DEFECT_STYPE_DB_R;
 370                                 }
 371                                 i+=1;
 372                                 fp.d_params.od=atof(word[++i]);
 373                                 fp.d_params.dd=atof(word[++i]);
 374                                 fp.d_params.element=atoi(word[++i]);
 375                                 fp.d_params.brand=atoi(word[++i]);
 376                                 // parsed in future
 377                 fp.d_params.attr=ATOM_ATTR_HB|ATOM_ATTR_VA;
 378                 fp.d_params.attr|=ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP;
 379                                 break;
 380
 381                                                 case '1':
 382                                 fp.d_params.type=DEFECT_TYPE_1D;
 383                                 break;
 384                                                 case '2':
 385                                 fp.d_params.type=DEFECT_TYPE_2D;
 386                                 break;
 387                                                 case '3':
 388                                 fp.d_params.type=DEFECT_TYPE_3D;
 389                                 break;
 390                                                 default:
 391                                                         break;
 392                                         }
 393                                         continue;
 394
 395                                 }
 396                                 i+=1;
 397                         }
 398                         add_stage(mdrun,STAGE_FILL,&fp);
 399                 }
 400                 else if(!strncmp(word[0],"thermal_init",12)) {
 401                         add_stage(mdrun,STAGE_THERMAL_INIT,NULL);
 402                 }
 403                 else if(!strncmp(word[0],"aattr",5)) {
 404                         // for aatrib line we need a special stage
 405                         // containing one schedule of 0 loops ...
 406                         for(i=0;i<strlen(word[1]);i++) {
 407                                 switch(word[1][i]) {
 408                                         case 't':
 409                                                 cap.type|=CHAATTR_TOTALV;
 410                                                 break;
 411                                         case 'r':
 412                                                 cap.type|=CHAATTR_REGION;
 413                                                 break;
 414                                         case 'e':
 415                                                 cap.type|=CHAATTR_ELEMENT;
 416                                                 break;
 417                                         default:
 418                                                 break;
 419                                 }
 420                         }
 421                         i=2;
 422                         if(cap.type&CHAATTR_REGION) {
 423                                 cap.x0=atof(word[1]);
 424                                 cap.y0=atof(word[2]);
 425                                 cap.z0=atof(word[3]);
 426                                 cap.x1=atof(word[4]);
 427                                 cap.y1=atof(word[5]);
 428                                 cap.z1=atof(word[6]);
 429                                 i+=6;
 430                         }
 431                         if(cap.type&CHAATTR_ELEMENT) {
 432                                 cap.element=atoi(word[i]);
 433                                 i+=1;
 434                         }
 435                         for(o=0;o<strlen(word[i]);o++) {
 436                                 switch(word[i][o]) {
 437                                         case 'b':
 438                                                 cap.attr|=ATOM_ATTR_VB;
 439                                                 break;
 440                                         case 'h':
 441                                                 cap.attr|=ATOM_ATTR_HB;
 442                                                 break;
 443                                         case 'v':
 444                                                 cap.attr|=ATOM_ATTR_VA;
 445                                                 break;
 446                                         case 'f':
 447                                                 cap.attr|=ATOM_ATTR_FP;
 448                                                 break;
 449                                         case '1':
 450                                                 cap.attr|=ATOM_ATTR_1BP;
 451                                                 break;
 452                                         case '2':
 453                                                 cap.attr|=ATOM_ATTR_2BP;
 454                                                 break;
 455                                         case '3':
 456                                                 cap.attr|=ATOM_ATTR_3BP;
 457                                                 break;
 458                                         default:
 459                                                 break;
 460                                 }
 461                         }
 462                         add_stage(mdrun,STAGE_CHAATTR,&cap);
 463                 }
 464                 else if(!strncmp(word[0],"sattr",5)) {
 465                         // for satrib line we need a special stage
 466                         // containing one schedule of 0 loops ...
 467                         csp.type=0;
 468                         for(i=1;i<wcnt;i++) {
 469                                 if(!strncmp(word[i],"pctrl",5)) {
 470                                         csp.ptau=0.01/(atof(word[++i])*GPA);
 471                                         csp.type|=CHSATTR_PCTRL;
 472                                 }
 473                                 if(!strncmp(word[i],"tctrl",5)) {
 474                                         csp.ttau=atof(word[++i]);
 475                                         csp.type|=CHSATTR_TCTRL;
 476                                 }
 477                                 if(!strncmp(word[i],"prelax",6)) {
 478                                         csp.dp=atof(word[++i])*BAR;
 479                                         csp.type|=CHSATTR_PRELAX;
 480                                 }
 481                                 if(!strncmp(word[i],"trelax",6)) {
 482                                         csp.dt=atof(word[++i]);
 483                                         csp.type|=CHSATTR_TRELAX;
 484                                 }
 485                                 if(!strncmp(word[i],"rsteps",6)) {
 486                                         csp.rsteps=atoi(word[++i]);
 487                                         csp.type|=CHSATTR_RSTEPS;
 488                                 }
 489                                 if(!strncmp(word[i],"avgrst",6)) {
 490                                         csp.avgrst=atoi(word[++i]);
 491                                         csp.type|=CHSATTR_AVGRST;
 492                                 }
 493                         }
 494                         add_stage(mdrun,STAGE_CHSATTR,&csp);
 495                 }
 496                 else if(!strncmp(word[0],"prerun",6))
 497                         mdrun->prerun=atoi(word[1]);
 498                 else if(!strncmp(word[0],"avgskip",7))
 499                         mdrun->avgskip=atoi(word[1]);
 500                 else if(!strncmp(word[0],"elog",4))
 501                         mdrun->elog=atoi(word[1]);
 502                 else if(!strncmp(word[0],"tlog",4))
 503                         mdrun->tlog=atoi(word[1]);
 504                 else if(!strncmp(word[0],"plog",4))
 505                         mdrun->plog=atoi(word[1]);
 506                 else if(!strncmp(word[0],"vlog",4))
 507                         mdrun->vlog=atoi(word[1]);
 508                 else if(!strncmp(word[0],"save",4))
 509                         mdrun->save=atoi(word[1]);
 510                 else if(!strncmp(word[0],"visualize",9))
 511                         mdrun->visualize=atoi(word[1]);
 512                 else if(!strncmp(word[0],"stage",5)) {
 513                         // for every stage line, add a stage
 514                         if(!strncmp(word[1],"displace",8)) {
 515                                 dap.nr=atoi(word[2]);
 516                                 dap.dx=atof(word[3]);
 517                                 dap.dy=atof(word[4]);
 518                                 dap.dz=atof(word[5]);
 519                                 add_stage(mdrun,STAGE_DISPLACE_ATOM,&dap);
 520                         }
 521                         else if(!strncmp(word[1],"del_atoms",9)) {
 522                                 delp.o.x=atof(word[2]);
 523                                 delp.o.y=atof(word[3]);
 524                                 delp.o.z=atof(word[4]);
 525                                 delp.r=atof(word[5]);
 526                                 add_stage(mdrun,STAGE_DEL_ATOMS,&delp);
 527                         }
 528                         else if(!strncmp(word[1],"ins_atoms",9)) {
 529                                 iap.ins_steps=atoi(word[2]);
 530                                 iap.ins_atoms=atoi(word[3]);
 531                                 iap.element=atoi(word[4]);
 532                                 iap.brand=atoi(word[5]);
 533                                 for(i=0;i<strlen(word[6]);i++) {
 534                                         switch(word[6][i]) {
 535                                                 case 'b':
 536                                                         iap.attr|=ATOM_ATTR_VB;
 537                                                         break;
 538                                                 case 'h':
 539                                                         iap.attr|=ATOM_ATTR_HB;
 540                                                         break;
 541                                                 case 'v':
 542                                                         iap.attr|=ATOM_ATTR_VA;
 543                                                         break;
 544                                                 case 'f':
 545                                                         iap.attr|=ATOM_ATTR_FP;
 546                                                         break;
 547                                                 case '1':
 548                                                         iap.attr|=ATOM_ATTR_1BP;
 549                                                         break;
 550                                                 case '2':
 551                                                         iap.attr|=ATOM_ATTR_2BP;
 552                                                         break;
 553                                                 case '3':
 554                                                         iap.attr|=ATOM_ATTR_3BP;
 555                                                         break;
 556                                                 default:
 557                                                         break;
 558                                         }
 559                                 }
 560                                 switch(word[7][0]) {
 561                                         // insertion types
 562                                         case 'p':
 563                                                 iap.type=INS_POS;
 564                                                 iap.x0=atof(word[8]);
 565                                                 iap.y0=atof(word[9]);
 566                                                 iap.z0=atof(word[10]);
 567                                                 break;
 568                                         case 'r':
 569                                                 switch(word[8][0]) {
 570
 571                                                 case 't':
 572                                                         iap.type=INS_TOTAL;
 573                                                         iap.cr=atof(word[9]);
 574                                                         break;
 575                                                 case 'r':
 576                                                         iap.type=INS_RECT;
 577                                                         iap.x0=atof(word[9]);
 578                                                         iap.y0=atof(word[10]);
 579                                                         iap.z0=atof(word[11]);
 580                                                         iap.x1=atof(word[12]);
 581                                                         iap.y1=atof(word[13]);
 582                                                         iap.z1=atof(word[14]);
 583                                                         iap.cr=atof(word[15]);
 584                                                         break;
 585                                                 case 's':
 586                                                         iap.type=INS_SPHERE;
 587                                                         iap.x0=atof(word[9]);
 588                                                         iap.y0=atof(word[10]);
 589                                                         iap.z0=atof(word[11]);
 590                                                         iap.x1=atof(word[12]);
 591                                                         iap.cr=atof(word[13]);
 592                                                         break;
 593                                                 default:
 594                                                         break;
 595                                                 }
 596                                         default:
 597                                                 break;
 598                                 }
 599                                 add_stage(mdrun,STAGE_INSERT_ATOMS,&iap);
 600                         }
 601
 602
 603                         // HERE WE GO ...
 604
 605                         else if(!strncmp(word[1],"ins_m_atoms",11)) {
 606                                 imp.element1=atoi(word[2]);
 607                                 imp.element2=atoi(word[3]);
 608                                 imp.amount1=atoi(word[4]);
 609                                 imp.amount2=atoi(word[5]);
 610                                 imp.brand1=atoi(word[6]);
 611                                 imp.brand2=atoi(word[7]);
 612                                 imp.crmin=atof(word[8]);
 613                                 imp.crmax=atof(word[9]);
 614                                 /* do this later ...
 615                                 for(i=0;i<strlen(word[8]);i++) {
 616                                         switch(word[8][i]) {
 617                                                 case 'b':
 618                                                         imp.attr|=ATOM_ATTR_VB;
 619                                                         break;
 620                                                 case 'h':
 621                                                         imp.attr|=ATOM_ATTR_HB;
 622                                                         break;
 623                                                 case 'v':
 624                                                         imp.attr|=ATOM_ATTR_VA;
 625                                                         break;
 626                                                 case 'f':
 627                                                         imp.attr|=ATOM_ATTR_FP;
 628                                                         break;
 629                                                 case '1':
 630                                                         imp.attr|=ATOM_ATTR_1BP;
 631                                                         break;
 632                                                 case '2':
 633                                                         imp.attr|=ATOM_ATTR_2BP;
 634                                                         break;
 635                                                 case '3':
 636                                                         imp.attr|=ATOM_ATTR_3BP;
 637                                                         break;
 638                                                 default:
 639                                                         break;
 640                                         }
 641                                 }
 642                                 */
 643                                 imp.attr1=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
 644                                 imp.attr2=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
 645                                 add_stage(mdrun,STAGE_INSERT_MIXED_ATOMS,&imp);
 646                         }
 647
 648
 649
 650
 651
 652                         else if(!strncmp(word[1],"continue",8)) {
 653                                 cp.runs=atoi(word[2]);
 654                                 add_stage(mdrun,STAGE_CONTINUE,&cp);
 655                         }
 656                         else if(!strncmp(word[1],"anneal",6)) {
 657                                 ap.count=0;
 658                                 ap.runs=atoi(word[2]);
 659                                 ap.dt=atof(word[3]);
 660                                 ap.interval=atoi(word[4]);
 661                                 add_stage(mdrun,STAGE_ANNEAL,&ap);
 662                         }
 663                         else if(!strncmp(word[1],"set_temp",8)) {
 664                                 if(word[2][0]=='c') {
 665                                         stp.type=SET_TEMP_CURRENT;
 666                                         stp.val=0.0;
 667                                 }
 668                                 else {
 669                                         stp.type=SET_TEMP_VALUE;
 670                                         stp.val=atof(word[2]);
 671                                 }
 672                                 add_stage(mdrun,STAGE_SET_TEMP,&stp);
 673                         }
 674                         else if(!strncmp(word[1],"set_timestep",12)) {
 675                                 stsp.tau=atof(word[2]);
 676                                 add_stage(mdrun,STAGE_SET_TIMESTEP,&stsp);
 677                         }
 678                         else {
 679                                 printf("%s unknown stage type: %s\n",
 680                                        ME,word[1]);
 681                                 return -1;
 682                         }
 683                 }
 684                 else {
 685                         printf("%s unknown keyword '%s', skipped!\n",
 686                                ME,word[0]);
 687                         continue;
 688                 }
 689         }
 690
 691         /* close file */
 692         close(fd);
 693
 694         return 0;
 695 }
 696
 697 int check_pressure(t_moldyn *moldyn,t_mdrun *mdrun) {
 698
 699         double delta;
 700
 701         if(!(mdrun->sattr&SATTR_PRELAX)) {
 702                 return TRUE;
 703         }
 704
 705         delta=moldyn->p_avg-moldyn->p_ref;
 706
 707         if(delta<0)
 708                 delta=-delta;
 709
 710         if(delta>mdrun->dp)
 711                 return FALSE;
 712
 713         return TRUE;
 714 }
 715
 716 int check_temperature(t_moldyn *moldyn,t_mdrun *mdrun) {
 717
 718         double delta;
 719
 720         if(!(mdrun->sattr&SATTR_TRELAX))
 721                 return TRUE;
 722
 723         delta=moldyn->t_avg-moldyn->t_ref;
 724
 725         if(delta<0)
 726                 delta=-delta;
 727
 728         if(delta>mdrun->dt)
 729                 return FALSE;
 730
 731         return TRUE;
 732 }
 733
 734 int displace_atom(t_moldyn *moldyn,t_mdrun *mdrun) {
 735
 736         t_displace_atom_params *dap;
 737         t_stage *stage;
 738         t_atom *atom;
 739
 740         stage=mdrun->stage.current->data;
 741         dap=stage->params;
 742
 743         atom=&(moldyn->atom[dap->nr]);
 744         atom->r.x+=dap->dx;
 745         atom->r.y+=dap->dy;
 746         atom->r.z+=dap->dz;
 747
 748         return 0;
 749 }
 750
 751 int del_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 752
 753         t_stage *stage;
 754         t_del_atoms_params *delp;
 755         int i;
 756         t_3dvec dist;
 757
 758         stage=mdrun->stage.current->data;
 759         delp=stage->params;
 760
 761         for(i=0;i<moldyn->count;i++) {
 762                 v3_sub(&dist,&(delp->o),&(moldyn->atom[i].r));
 763 //printf("%d ----> %f %f %f = %f | %f\n",i,dist.x,dist.y,dist.z,v3_absolute_square(&dist),delp->r*delp->r);
 764                 if(v3_absolute_square(&dist)<=(delp->r*delp->r)) {
 765                         del_atom(moldyn,moldyn->atom[i].tag);
 766                         printf("%s atom deleted: %d %d %d\n",ME,
 767                                moldyn->atom[i].tag,moldyn->atom[i].element,
 768                                moldyn->atom[i].brand);
 769                 }
 770         }
 771
 772         return 0;
 773
 774 }
 775
 776 int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 777
 778         t_insert_atoms_params *iap;
 779         t_stage *stage;
 780         t_atom *atom;
 781         t_3dvec r,v,dist;
 782         double d,dmin,o;
 783         int cnt,i;
 784         double x,y,z;
 785         double x0,y0,z0;
 786         u8 cr_check,run;
 787
 788         stage=mdrun->stage.current->data;
 789         iap=stage->params;
 790
 791         cr_check=FALSE;
 792
 793         v.x=0.0; v.y=0.0; v.z=0.0;
 794         x=0; y=0; z=0;
 795         o=0; dmin=0;
 796
 797         switch(mdrun->lattice) {
 798                 case CUBIC:
 799                         o=0.5*mdrun->lc;
 800                         break;
 801                 case FCC:
 802                         o=0.25*mdrun->lc;
 803                         break;
 804                 case DIAMOND:
 805                 case ZINCBLENDE:
 806                         o=0.125*mdrun->lc;
 807                         break;
 808                 default:
 809                         break;
 810         }
 811
 812         switch(iap->type) {
 813                 case INS_TOTAL:
 814                         x=moldyn->dim.x;
 815                         x0=-x/2.0;
 816                         y=moldyn->dim.y;
 817                         y0=-y/2.0;
 818                         z=moldyn->dim.z;
 819                         z0=-z/2.0;
 820                         cr_check=TRUE;
 821                         break;
 822                 case INS_RECT:
 823                         x=iap->x1-iap->x0;
 824                         x0=iap->x0;
 825                         y=iap->y1-iap->y0;
 826                         y0=iap->y0;
 827                         z=iap->z1-iap->z0;
 828                         z0=iap->z0;
 829                         cr_check=TRUE;
 830                         break;
 831                 case INS_SPHERE:
 832                         x=2.0*iap->x1;
 833                         x0=iap->x0-iap->x1;
 834                         y=x;
 835                         y0=iap->y0-iap->x1;
 836                         z=x;
 837                         z0=iap->z0-iap->x1;
 838                         cr_check=TRUE;
 839                         break;
 840                 case INS_POS:
 841                         x0=iap->x0;
 842                         y0=iap->y0;
 843                         z0=iap->z0;
 844                         cr_check=FALSE;
 845                         break;
 846                 default:
 847                         printf("%s unknown insertion mode: %02x\n",
 848                                ME,iap->type);
 849                         return -1;
 850         }
 851
 852         cnt=0;
 853         while(cnt<iap->ins_atoms) {
 854                 run=1;
 855                 while(run) {
 856                         if(iap->type!=INS_POS) {
 857                                 r.x=rand_get_double(&(moldyn->random))*x;
 858                                 r.y=rand_get_double(&(moldyn->random))*y;
 859                                 r.z=rand_get_double(&(moldyn->random))*z;
 860                         }
 861                         else {
 862                                 r.x=0.0;
 863                                 r.y=0.0;
 864                                 r.z=0.0;
 865                         }
 866                         r.x+=x0;
 867                         r.y+=y0;
 868                         r.z+=z0;
 869                         // offset
 870                         if(iap->type!=INS_TOTAL) {
 871                                 r.x+=o;
 872                                 r.y+=o;
 873                                 r.z+=o;
 874                         }
 875                         run=0;
 876                         if(cr_check==TRUE) {
 877                                 dmin=1000;      // for sure too high!
 878                                 for(i=0;i<moldyn->count;i++) {
 879                                         atom=&(moldyn->atom[i]);
 880                                         v3_sub(&dist,&(atom->r),&r);
 881                                         check_per_bound(moldyn,&dist);
 882                                         d=v3_absolute_square(&dist);
 883                                         if(d<(iap->cr*iap->cr)) {
 884                                                 run=1;
 885                                                 break;
 886                                         }
 887                                         if(d<dmin)
 888                                                 dmin=d;
 889                                 }
 890                         }
 891                         if(iap->type==INS_SPHERE) {
 892                                 if((r.x-iap->x0)*(r.x-iap->x0)+
 893                                    (r.y-iap->y0)*(r.y-iap->y0)+
 894                                    (r.z-iap->z0)*(r.z-iap->z0)>
 895                                    (iap->x1*iap->x1)) {
 896                                         run=1;
 897                                 }
 898                         }
 899                 }
 900                 add_atom(moldyn,iap->element,
 901                          iap->brand,iap->attr,&r,&v);
 902                 printf("%s atom inserted (%d/%d): %f %f %f\n",
 903                        ME,(iap->cnt_steps+1)*iap->ins_atoms,
 904                        iap->ins_steps*iap->ins_atoms,r.x,r.y,r.z);
 905                 printf("  -> d2 = %f/%f\n",dmin,iap->cr*iap->cr);
 906                 cnt+=1;
 907         }
 908
 909         return 0;
 910 }
 911
 912 int insert_mixed_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 913
 914         t_stage *stage;
 915         t_insert_mixed_atoms_params *imp;
 916         t_atom *atom;
 917         double x,x0,y,y0,z,z0;
 918         double dmin,d,cmin,cmax;
 919         u8 retry;
 920         t_3dvec r,v,dist;
 921         int i;
 922
 923
 924         stage=mdrun->stage.current->data;
 925         imp=stage->params;
 926
 927         x=moldyn->dim.x;
 928         x0=-x/2.0;
 929         y=moldyn->dim.y;
 930         y0=-y/2.0;
 931         z=moldyn->dim.z;
 932         z0=-z/2.0;
 933
 934         v.x=0.0;
 935         v.y=0.0;
 936         v.z=0.0;
 937
 938         cmin=imp->crmin*imp->crmin;
 939         cmax=imp->crmax*imp->crmax;
 940
 941         while(imp->amount1|imp->amount2) {
 942                 if(imp->amount1) {
 943                         retry=1;
 944                         while(retry) {
 945                                 retry=0;
 946                                 r.x=rand_get_double(&(moldyn->random))*x;
 947                                 r.y=rand_get_double(&(moldyn->random))*y;
 948                                 r.z=rand_get_double(&(moldyn->random))*z;
 949                                 r.x+=x0;
 950                                 r.y+=y0;
 951                                 r.z+=z0;
 952                                 dmin=1000.0;    // for sure too high!
 953                                 for(i=0;i<moldyn->count;i++) {
 954                                         atom=&(moldyn->atom[i]);
 955                                         v3_sub(&dist,&(atom->r),&r);
 956                                         check_per_bound(moldyn,&dist);
 957                                         d=v3_absolute_square(&dist);
 958                                         if(d<cmin) {
 959                                                 retry=1;
 960                                                 break;
 961                                         }
 962                                         if(d<dmin)
 963                                                 dmin=d;
 964                                 }
 965                                 if(dmin!=1000.0)
 966                                         if(dmin>cmax)
 967                                                 retry=1;
 968                         }
 969                         add_atom(moldyn,imp->element1,
 970                                  imp->brand1,imp->attr1,&r,&v);
 971                         printf("%s (mixed) atom inserted (%d): %f %f %f\n",
 972                                ME,imp->amount1,r.x,r.y,r.z);
 973                         printf("  -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
 974                         imp->amount1-=1;
 975                 }
 976                 if(imp->amount2) {
 977                         retry=1;
 978                         while(retry) {
 979                                 retry=0;
 980                                 r.x=rand_get_double(&(moldyn->random))*x;
 981                                 r.y=rand_get_double(&(moldyn->random))*y;
 982                                 r.z=rand_get_double(&(moldyn->random))*z;
 983                                 r.x+=x0;
 984                                 r.y+=y0;
 985                                 r.z+=z0;
 986                                 dmin=1000.0;    // for sure too high!
 987                                 for(i=0;i<moldyn->count;i++) {
 988                                         atom=&(moldyn->atom[i]);
 989                                         v3_sub(&dist,&(atom->r),&r);
 990                                         check_per_bound(moldyn,&dist);
 991                                         d=v3_absolute_square(&dist);
 992                                         if(d<cmin) {
 993                                                 retry=1;
 994                                                 break;
 995                                         }
 996                                         if(d<dmin)
 997                                                 dmin=d;
 998                                 }
 999                                 if(dmin!=1000.0)
1000                                         if(dmin>cmax)
1001                                                 retry=1;
1002                         }
1003                         add_atom(moldyn,imp->element2,
1004                                  imp->brand2,imp->attr2,&r,&v);
1005                         printf("%s (mixed) atom inserted (%d): %f %f %f\n",
1006                                ME,imp->amount2,r.x,r.y,r.z);
1007                         printf("  -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
1008                         imp->amount2-=1;
1009                 }
1010         }
1011
1012         return 0;
1013 }
1014
1015 int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
1016
1017         t_stage *stage;
1018         t_chaattr_params *cap;
1019         t_atom *atom;
1020         int i;
1021
1022         stage=mdrun->stage.current->data;
1023         cap=stage->params;
1024
1025         for(i=0;i<moldyn->count;i++) {
1026                 atom=&(moldyn->atom[i]);
1027                 if(cap->type&CHAATTR_ELEMENT) {
1028                         if(cap->element!=atom->element)
1029                                 continue;
1030                 }
1031                 if(cap->type&CHAATTR_REGION) {
1032                         if(cap->x0<atom->r.x)
1033                                 continue;
1034                         if(cap->y0<atom->r.y)
1035                                 continue;
1036                         if(cap->z0<atom->r.z)
1037                                 continue;
1038                         if(cap->x1>atom->r.x)
1039                                 continue;
1040                         if(cap->y1>atom->r.y)
1041                                 continue;
1042                         if(cap->z1>atom->r.z)
1043                                 continue;
1044                 }
1045                 atom->attr=cap->attr;
1046         }
1047
1048         return 0;
1049 }
1050
1051 int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
1052
1053         t_stage *stage;
1054         t_chsattr_params *csp;
1055
1056         stage=mdrun->stage.current->data;
1057         csp=stage->params;
1058
1059         if(csp->type&CHSATTR_PCTRL) {
1060                 if(csp->ptau>0)
1061                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
1062                 else
1063                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
1064         }
1065         if(csp->type&CHSATTR_TCTRL) {
1066                 if(csp->ttau>0)
1067                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
1068                 else
1069                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
1070         }
1071         if(csp->type&CHSATTR_PRELAX) {
1072                 if(csp->dp<0)
1073                         mdrun->sattr&=(~(SATTR_PRELAX));
1074                 else
1075                         mdrun->sattr|=SATTR_PRELAX;
1076                 mdrun->dp=csp->dp;
1077         }
1078         if(csp->type&CHSATTR_TRELAX) {
1079                 if(csp->dt<0)
1080                         mdrun->sattr&=(~(SATTR_TRELAX));
1081                 else
1082                         mdrun->sattr|=SATTR_TRELAX;
1083                 mdrun->dt=csp->dt;
1084         }
1085         if(csp->type&CHSATTR_AVGRST) {
1086                 if(csp->avgrst)
1087                         mdrun->sattr|=SATTR_AVGRST;
1088                 else
1089                         mdrun->sattr&=(~(SATTR_AVGRST));
1090         }
1091         if(csp->type&CHSATTR_RSTEPS) {
1092                 mdrun->relax_steps=csp->rsteps;
1093         }
1094
1095         return 0;
1096 }
1097
1098 #define stage_print(m)  if(!(stage->executed)) \
1099                                 printf("%s",m)
1100
1101 int mdrun_hook(void *ptr1,void *ptr2) {
1102
1103         t_moldyn *moldyn;
1104         t_mdrun *mdrun;
1105         t_stage *stage;
1106         t_list *sl;
1107         int steps;
1108         u8 change_stage;
1109         t_3dvec o;
1110
1111         t_insert_atoms_params *iap;
1112         t_insert_mixed_atoms_params *imp;
1113         t_continue_params *cp;
1114         t_anneal_params *ap;
1115         t_set_temp_params *stp;
1116         t_set_timestep_params *stsp;
1117         t_fill_params *fp;
1118
1119         moldyn=ptr1;
1120         mdrun=ptr2;
1121
1122         sl=&(mdrun->stage);
1123
1124         change_stage=FALSE;
1125
1126         /* return immediately if there are no more stage */
1127         if(sl->current==NULL)
1128                 return 0;
1129
1130         /* get stage description */
1131         stage=sl->current->data;
1132
1133         /* steps in next schedule */
1134         steps=mdrun->relax_steps;
1135
1136         /* check whether relaxation steps are necessary */
1137         if((check_pressure(moldyn,mdrun)==TRUE)&\
1138            (check_temperature(moldyn,mdrun)==TRUE)) {
1139
1140                 /* be verbose */
1141                 stage_print("\n###########################\n");
1142                 stage_print("# [mdrun] executing stage #\n");
1143                 stage_print("###########################\n\n");
1144
1145                 /* stage specific stuff */
1146                 switch(stage->type) {
1147                         case STAGE_DISPLACE_ATOM:
1148                                 stage_print("  -> displace atom\n\n");
1149                                 displace_atom(moldyn,mdrun);
1150                                 change_stage=TRUE;
1151                                 break;
1152                         case STAGE_DEL_ATOMS:
1153                                 stage_print(" -> del atoms\n\n");
1154                                 del_atoms(moldyn,mdrun);
1155                                 change_stage=TRUE;
1156                                 break;
1157                         case STAGE_INSERT_ATOMS:
1158                                 stage_print("  -> insert atoms\n\n");
1159                                 iap=stage->params;
1160                                 if(iap->cnt_steps==iap->ins_steps) {
1161                                         change_stage=TRUE;
1162                                         break;
1163                                 }
1164                                 insert_atoms(moldyn,mdrun);
1165                                 iap->cnt_steps+=1;
1166                                 break;
1167
1168
1169
1170                         case STAGE_INSERT_MIXED_ATOMS:
1171                                 stage_print("  -> insert mixed atoms\n\n");
1172                                 imp=stage->params;
1173                                 insert_mixed_atoms(moldyn,mdrun);
1174                                 change_stage=TRUE;
1175                                 break;
1176
1177
1178
1179                         case STAGE_CONTINUE:
1180                                 stage_print("  -> continue\n\n");
1181                                 if(stage->executed==TRUE) {
1182                                         change_stage=TRUE;
1183                                         break;
1184                                 }
1185                                 cp=stage->params;
1186                                 steps=cp->runs;
1187                                 break;
1188                         case STAGE_ANNEAL:
1189                                 stage_print("  -> anneal\n\n");
1190                                 ap=stage->params;
1191                                 if(ap->count==ap->runs) {
1192                                         change_stage=TRUE;
1193                                         break;
1194                                 }
1195                                 if(moldyn->t_ref+ap->dt>=0.0)
1196                                         set_temperature(moldyn,
1197                                                         moldyn->t_ref+ap->dt);
1198                                 ap->count+=1;
1199                                 steps=ap->interval;
1200                                 break;
1201                         case STAGE_CHAATTR:
1202                                 stage_print("  -> change atom attributes\n\n");
1203                                 chaatr(moldyn,mdrun);
1204                                 change_stage=TRUE;
1205                                 break;
1206                         case STAGE_CHSATTR:
1207                                 stage_print("  -> change sys attributes\n\n");
1208                                 chsattr(moldyn,mdrun);
1209                                 change_stage=TRUE;
1210                                 break;
1211                         case STAGE_SET_TEMP:
1212                                 stage_print("  -> set temperature\n\n");
1213                                 stp=stage->params;
1214                                 if(stp->type&SET_TEMP_CURRENT) {
1215                                         set_temperature(moldyn,moldyn->t_avg);
1216                                 }
1217                                 else {
1218                                         set_temperature(moldyn,stp->val);
1219                                 }
1220                                 change_stage=TRUE;
1221                                 break;
1222                         case STAGE_SET_TIMESTEP:
1223                                 stage_print("  -> set timestep\n\n");
1224                                 stsp=stage->params;
1225                                 mdrun->timestep=stsp->tau;
1226                                 change_stage=TRUE;
1227                                 break;
1228                         case STAGE_FILL:
1229                                 stage_print("  -> fill lattice\n\n");
1230                                 fp=stage->params;
1231                                 switch(fp->lattice) {
1232                                         case ZINCBLENDE:
1233
1234                                         o.x=0.5*0.25*fp->lc;
1235                                         o.y=o.x;
1236                                         o.z=o.x;
1237                                         create_lattice(moldyn,
1238                                                        FCC,fp->lc,
1239                                                        mdrun->element1,
1240                                                        DEFAULT_ATOM_ATTR,0,
1241                                                        fp->lx,fp->ly,fp->lz,
1242                                                        &o,
1243                                                        &(fp->p_params),
1244                                                        &(fp->d_params));
1245                                         o.x+=0.25*fp->lc;
1246                                         o.y=o.x;
1247                                         o.z=o.x;
1248                                         create_lattice(moldyn,
1249                                                        FCC,fp->lc,
1250                                                        mdrun->element2,
1251                                                        DEFAULT_ATOM_ATTR,1,
1252                                                        fp->lx,fp->ly,fp->lz,
1253                                                        &o,
1254                                                        &(fp->p_params),
1255                                                        &(fp->d_params));
1256                                         break;
1257
1258                                         default:
1259
1260                                         create_lattice(moldyn,
1261                                                        fp->lattice,fp->lc,
1262                                                        fp->fill_element,
1263                                                        DEFAULT_ATOM_ATTR,
1264                                                        fp->fill_brand,
1265                                                        fp->lx,fp->ly,fp->lz,
1266                                                        NULL,
1267                                                        &(fp->p_params),
1268                                                        &(fp->d_params));
1269                                         break;
1270                                 }
1271                                 moldyn_bc_check(moldyn);
1272                                 change_stage=TRUE;
1273                                 break;
1274                         case STAGE_THERMAL_INIT:
1275                                 stage_print("  -> thermal init\n\n");
1276                                 thermal_init(moldyn,TRUE);
1277                                 change_stage=TRUE;
1278                                 break;
1279                         default:
1280                                 printf("%s unknwon stage type\n",ME);
1281                                 break;
1282                 }
1283
1284                 /* mark as executed */
1285                 stage->executed=TRUE;
1286
1287                 /* change state */
1288                 if(change_stage==TRUE) {
1289                         printf("%s finished stage\n",ME);
1290                         if(list_next_f(sl)==L_NO_NEXT_ELEMENT) {
1291                                 printf("%s no more stages\n",ME);
1292                                 return 0;
1293                         }
1294                         steps=0;
1295                 }
1296
1297         }
1298         else {
1299
1300                 /* averages */
1301                 if(mdrun->sattr&SATTR_AVGRST)
1302                         average_reset(moldyn);
1303
1304         }
1305
1306         /* continue simulation */
1307         moldyn_add_schedule(moldyn,steps,mdrun->timestep);
1308
1309         return 0;
1310 }
1311
1312 int main(int argc,char **argv) {
1313
1314         t_mdrun mdrun;
1315         t_moldyn moldyn;
1316         //t_3dvec o;
1317
1318         /* clear structs */
1319         memset(&mdrun,0,sizeof(t_mdrun));
1320         memset(&moldyn,0,sizeof(t_moldyn));
1321
1322         /* parse arguments */
1323         if(mdrun_parse_argv(&mdrun,argc,argv)<0)
1324                 return -1;
1325
1326         /* initialize list system */
1327         list_init_f(&(mdrun.stage));
1328
1329         /* parse config file */
1330         mdrun_parse_config(&mdrun);
1331
1332         /* reset the stage list */
1333         list_reset_f(&(mdrun.stage));
1334
1335         /* sanity check! */
1336
1337         /* prepare simulation */
1338
1339         if(mdrun.continue_file[0]) {
1340                 // read the save file
1341                 moldyn_read_save_file(&moldyn,mdrun.continue_file);
1342                 // manualaadjusting some stuff
1343                 moldyn.argc=argc;
1344                 moldyn.args=argv;
1345                 rand_init(&(moldyn.random),NULL,1);
1346                 moldyn.random.status|=RAND_STAT_VERBOSE;
1347         }
1348         else {
1349                 moldyn_init(&moldyn,argc,argv);
1350         }
1351
1352         if(set_int_alg(&moldyn,mdrun.intalgo)<0)
1353                 return -1;
1354
1355         /* potential */
1356         set_cutoff(&moldyn,mdrun.cutoff);
1357         if(set_potential(&moldyn,mdrun.potential)<0)
1358                 return -1;
1359         switch(mdrun.potential) {
1360                 case MOLDYN_POTENTIAL_AM:
1361                         albe_mult_set_params(&moldyn,
1362                                              mdrun.element1,
1363                                              mdrun.element2);
1364                         break;
1365                 case MOLDYN_POTENTIAL_TM:
1366                         tersoff_mult_set_params(&moldyn,
1367                                                 mdrun.element1,
1368                                                 mdrun.element2);
1369                         break;
1370                 case MOLDYN_POTENTIAL_HO:
1371                         harmonic_oscillator_set_params(&moldyn,mdrun.element1);
1372                         break;
1373                 case MOLDYN_POTENTIAL_LJ:
1374                         lennard_jones_set_params(&moldyn,mdrun.element1);
1375                         break;
1376                 default:
1377                         printf("%s unknown potential: %02x\n",
1378                                ME,mdrun.potential);
1379                         return -1;
1380         }
1381
1382         /* if it is a continue run, reset schedule and skip lattice init */
1383         if(mdrun.continue_file[0]) {
1384                 memset(&(moldyn.schedule),0,sizeof(t_moldyn_schedule));
1385                 goto addsched;
1386         }
1387
1388         /* initial lattice and dimensions */
1389         set_dim(&moldyn,mdrun.dim.x,mdrun.dim.y,mdrun.dim.z,mdrun.vis);
1390         set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
1391         /* replaced by fill stage !!
1392         switch(mdrun.lattice) {
1393                 case FCC:
1394                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.fill_element,
1395                                        mdrun.m1,DEFAULT_ATOM_ATTR,
1396                                        mdrun.fill_brand,mdrun.lx,
1397                                        mdrun.ly,mdrun.lz,NULL,0,NULL);
1398                         break;
1399                 case DIAMOND:
1400                         create_lattice(&moldyn,DIAMOND,mdrun.lc,
1401                                        mdrun.fill_element,
1402                                        mdrun.m1,DEFAULT_ATOM_ATTR,
1403                                        mdrun.fill_brand,mdrun.lx,
1404                                        mdrun.ly,mdrun.lz,NULL,0,NULL);
1405                         break;
1406                 case ZINCBLENDE:
1407                         o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
1408                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
1409                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
1410                                        mdrun.ly,mdrun.lz,&o,0,NULL);
1411                         o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
1412                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
1413                                        mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
1414                                        mdrun.ly,mdrun.lz,&o,0,NULL);
1415                         break;
1416                 case NONE:
1417                         set_nn_dist(&moldyn,mdrun.nnd);
1418                         break;
1419                 default:
1420                         printf("%s unknown lattice type: %02x\n",
1421                                ME,mdrun.lattice);
1422                         return -1;
1423         }
1424         moldyn_bc_check(&moldyn);
1425         replaced by fill stage !! */
1426
1427         /* temperature and pressure */
1428         set_temperature(&moldyn,mdrun.temperature);
1429         set_pressure(&moldyn,mdrun.pressure);
1430         /* replaced thermal_init stage
1431         thermal_init(&moldyn,TRUE);
1432         */
1433
1434 addsched:
1435         /* first schedule */
1436         moldyn_add_schedule(&moldyn,mdrun.prerun,mdrun.timestep);
1437
1438         /* log */
1439         moldyn_set_log_dir(&moldyn,mdrun.sdir);
1440         moldyn_set_report(&moldyn,"CHANGE ME","CHANGE ME TOO");
1441         if(mdrun.elog)
1442                 moldyn_set_log(&moldyn,LOG_TOTAL_ENERGY,mdrun.elog);
1443         if(mdrun.tlog)
1444                 moldyn_set_log(&moldyn,LOG_TEMPERATURE,mdrun.tlog);
1445         if(mdrun.plog)
1446                 moldyn_set_log(&moldyn,LOG_PRESSURE,mdrun.plog);
1447         if(mdrun.vlog)
1448                 moldyn_set_log(&moldyn,LOG_VOLUME,mdrun.vlog);
1449         if(mdrun.visualize)
1450                 moldyn_set_log(&moldyn,VISUAL_STEP,mdrun.visualize);
1451         if(mdrun.save)
1452                 moldyn_set_log(&moldyn,SAVE_STEP,mdrun.save);
1453         moldyn_set_log(&moldyn,CREATE_REPORT,0);
1454         set_avg_skip(&moldyn,mdrun.avgskip);
1455
1456         /* prepare the hook function */
1457         moldyn_set_schedule_hook(&moldyn,&mdrun_hook,&mdrun);
1458
1459         /* run the simulation */
1460         moldyn_integrate(&moldyn);
1461
1462         /* shutdown */
1463         moldyn_shutdown(&moldyn);
1464         del_stages(&mdrun);
1465         list_destroy_f(&(mdrun.stage));
1466
1467         return 0;
1468 }