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