mdrun.c

   1 /*
   2  * mdrun.c - main code to run a md simulation
   3  *
   4  * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
   5  *
   6  */
   7
   8 #include "mdrun.h"
   9
  10 /* potential */
  11 #include "potentials/harmonic_oscillator.h"
  12 #include "potentials/lennard_jones.h"
  13 #include "potentials/albe.h"
  14 #ifdef TERSOFF_ORIG
  15 #include "potentials/tersoff_orig.h"
  16 #else
  17 #include "potentials/tersoff.h"
  18 #endif
  19
  20 #define ME      "[mdrun]"
  21
  22 /*
  23  * parse function
  24  */
  25
  26 int mdrun_usage(void) {
  27
  28         printf("%s usage:\n",ME);
  29
  30         return 0;
  31 }
  32
  33 int mdrun_parse_argv(t_mdrun *mdrun,int argc,char **argv) {
  34
  35         int i;
  36
  37         for(i=1;i<argc;i++) {
  38
  39                 if(argv[i][0]!='-') {
  40                         printf("%s unknown switch: %s\n",ME,argv[i]);
  41                         return -1;
  42                 }
  43
  44                 switch(argv[i][1]) {
  45                         case 'c':
  46                                 strncpy(mdrun->cfile,argv[++i],128);
  47                                 break;
  48                         case 's':
  49                                 strncpy(mdrun->sdir,argv[++i],128);
  50                                 break;
  51                         case 'h':
  52                                 mdrun_usage();
  53                                 break;
  54                         default:
  55                                 printf("%s unknown option: %s\n",ME,argv[i]);
  56                                 mdrun_usage();
  57                                 return -1;
  58                 }
  59
  60         }
  61
  62         return 0;
  63 }
  64
  65 int del_stages(t_mdrun *mdrun) {
  66
  67         t_list *sl;
  68         t_stage *stage;
  69
  70         sl=&(mdrun->stage);
  71
  72         list_reset_f(sl);
  73
  74         if(sl->start==NULL)
  75                 return 0;
  76
  77         do {
  78                 stage=sl->current->data;
  79                 free(stage->params);
  80                 free(stage);
  81         } while(list_next_f(sl)!=L_NO_NEXT_ELEMENT);
  82
  83         return 0;
  84 }
  85
  86 int add_stage(t_mdrun *mdrun,u8 type,void *params) {
  87
  88         int psize;
  89
  90         t_stage *stage;
  91
  92         switch(type) {
  93                 case STAGE_DISPLACE_ATOM:
  94                         psize=sizeof(t_displace_atom_params);
  95                         break;
  96                 case STAGE_INSERT_ATOMS:
  97                         psize=sizeof(t_insert_atoms_params);
  98                         break;
  99                 case STAGE_INSERT_MIXED_ATOMS:
 100                         psize=sizeof(t_insert_mixed_atoms_params);
 101                         break;
 102                 case STAGE_CONTINUE:
 103                         psize=sizeof(t_continue_params);
 104                         break;
 105                 case STAGE_ANNEAL:
 106                         psize=sizeof(t_anneal_params);
 107                         break;
 108                 case STAGE_CHAATTR:
 109                         psize=sizeof(t_chaattr_params);
 110                         break;
 111                 case STAGE_CHSATTR:
 112                         psize=sizeof(t_chsattr_params);
 113                         break;
 114                 case STAGE_SET_TEMP:
 115                         psize=sizeof(t_set_temp_params);
 116                         break;
 117                 case STAGE_SET_TIMESTEP:
 118                         psize=sizeof(t_set_timestep_params);
 119                         break;
 120                 default:
 121                         printf("%s unknown stage type: %02x\n",ME,type);
 122                         return -1;
 123         }
 124
 125         stage=malloc(sizeof(t_stage));
 126         if(stage==NULL) {
 127                 perror("[mdrun] malloc (add stage)");
 128                 return -1;
 129         }
 130
 131         stage->type=type;
 132         stage->executed=FALSE;
 133
 134         stage->params=malloc(psize);
 135         if(stage->params==NULL) {
 136                 perror("[mdrun] malloc (stage params)");
 137                 return -1;
 138         }
 139
 140         memcpy(stage->params,params,psize);
 141
 142         list_add_immediate_f(&(mdrun->stage),stage);
 143
 144         return 0;
 145 }
 146
 147 int mdrun_parse_config(t_mdrun *mdrun) {
 148
 149         int fd,ret;
 150         char error[128];
 151         char line[128];
 152         char *wptr;
 153         char word[16][64];
 154         int wcnt;
 155         int i,o;
 156
 157         t_displace_atom_params dap;
 158         t_insert_atoms_params iap;
 159         t_insert_mixed_atoms_params imp;
 160         t_continue_params cp;
 161         t_anneal_params ap;
 162         t_chaattr_params cap;
 163         t_chsattr_params csp;
 164         t_set_temp_params stp;
 165         t_set_timestep_params stsp;
 166
 167         /* open config file */
 168         fd=open(mdrun->cfile,O_RDONLY);
 169         if(fd<0) {
 170                 snprintf(error,128,"%s open cfile %s",ME,mdrun->cfile);
 171                 perror(error);
 172                 return fd;
 173         }
 174
 175         /* read, parse, set */
 176         ret=1;
 177         while(ret>0) {
 178
 179                 /* read */
 180                 ret=get_line(fd,line,128);
 181
 182                 /* parse */
 183
 184                 // ignore # lines and \n
 185                 if((line[0]=='#')|(ret==1))
 186                         continue;
 187
 188                 // reset
 189                 memset(&iap,0,sizeof(t_insert_atoms_params));
 190                 memset(&imp,0,sizeof(t_insert_mixed_atoms_params));
 191                 memset(&cp,0,sizeof(t_continue_params));
 192                 memset(&ap,0,sizeof(t_anneal_params));
 193                 memset(&cap,0,sizeof(t_chaattr_params));
 194                 memset(&csp,0,sizeof(t_chsattr_params));
 195                 memset(&stp,0,sizeof(t_set_temp_params));
 196                 memset(&stsp,0,sizeof(t_set_timestep_params));
 197
 198                 // get command + args
 199                 wcnt=0;
 200                 while(1) {
 201                         if(wcnt)
 202                                 wptr=strtok(NULL," \t");
 203                         else
 204                                 wptr=strtok(line," \t");
 205                         if(wptr==NULL)
 206                                 break;
 207                         strncpy(word[wcnt],wptr,64);
 208                         wcnt+=1;
 209                 }
 210
 211                 if(!strncmp(word[0],"potential",9)) {
 212                         if(!strncmp(word[1],"albe",4))
 213                                 mdrun->potential=MOLDYN_POTENTIAL_AM;
 214                         if(!strncmp(word[1],"tersoff",7))
 215                                 mdrun->potential=MOLDYN_POTENTIAL_TM;
 216                         if(!strncmp(word[1],"ho",2))
 217                                 mdrun->potential=MOLDYN_POTENTIAL_HO;
 218                         if(!strncmp(word[1],"lj",2))
 219                                 mdrun->potential=MOLDYN_POTENTIAL_LJ;
 220                 }
 221                 else if(!strncmp(word[0],"continue",8))
 222                         strncpy(mdrun->continue_file,word[1],128);
 223                 else if(!strncmp(word[0],"cutoff",6))
 224                         mdrun->cutoff=atof(word[1]);
 225                 else if(!strncmp(word[0],"nnd",3))
 226                         mdrun->nnd=atof(word[1]);
 227                 else if(!strncmp(word[0],"intalgo",7)) {
 228                         if(!strncmp(word[1],"verlet",5))
 229                                 mdrun->intalgo=MOLDYN_INTEGRATE_VERLET;
 230                 }
 231                 else if(!strncmp(word[0],"timestep",8))
 232                         mdrun->timestep=atof(word[1]);
 233                 else if(!strncmp(word[0],"volume",6)) {
 234                         mdrun->dim.x=atof(word[1]);
 235                         mdrun->dim.y=atof(word[2]);
 236                         mdrun->dim.z=atof(word[3]);
 237                         if(strncmp(word[4],"0",1))
 238                                 mdrun->vis=TRUE;
 239                 }
 240                 else if(!strncmp(word[0],"pbc",3)) {
 241                         if(strncmp(word[1],"0",1))
 242                                 mdrun->pbcx=TRUE;
 243                         else
 244                                 mdrun->pbcx=FALSE;
 245                         if(strncmp(word[2],"0",1))
 246                                 mdrun->pbcy=TRUE;
 247                         else
 248                                 mdrun->pbcy=FALSE;
 249                         if(strncmp(word[3],"0",1))
 250                                 mdrun->pbcz=TRUE;
 251                         else
 252                                 mdrun->pbcz=FALSE;
 253                 }
 254                 else if(!strncmp(word[0],"temperature",11))
 255                         mdrun->temperature=atof(word[1]);
 256                 else if(!strncmp(word[0],"pressure",8))
 257                         mdrun->pressure=atof(word[1]);
 258                 else if(!strncmp(word[0],"lattice",7)) {
 259                         if(!strncmp(word[1],"zincblende",10))
 260                                 mdrun->lattice=ZINCBLENDE;
 261                         if(!strncmp(word[1],"fcc",3))
 262                                 mdrun->lattice=FCC;
 263                         if(!strncmp(word[1],"diamond",7))
 264                                 mdrun->lattice=DIAMOND;
 265                         if(!strncmp(word[1],"none",4))
 266                                 mdrun->lattice=NONE;
 267                 }
 268                 else if(!strncmp(word[0],"element1",8)) {
 269                         mdrun->element1=atoi(word[1]);
 270                         mdrun->m1=pse_mass[mdrun->element1];
 271                 }
 272                 else if(!strncmp(word[0],"element2",8)) {
 273                         mdrun->element2=atoi(word[1]);
 274                         mdrun->m2=pse_mass[mdrun->element2];
 275                 }
 276                 else if(!strncmp(word[0],"fill",6)) {
 277                         // only lc mode by now
 278                         mdrun->lx=atoi(word[2]);
 279                         mdrun->ly=atoi(word[3]);
 280                         mdrun->lz=atoi(word[4]);
 281                         mdrun->lc=atof(word[5]);
 282                 }
 283                 else if(!strncmp(word[0],"aattr",5)) {
 284                         // for aatrib line we need a special stage
 285                         // containing one schedule of 0 loops ...
 286                         for(i=0;i<strlen(word[1]);i++) {
 287                                 switch(word[1][i]) {
 288                                         case 't':
 289                                                 cap.type|=CHAATTR_TOTALV;
 290                                                 break;
 291                                         case 'r':
 292                                                 cap.type|=CHAATTR_REGION;
 293                                                 break;
 294                                         case 'e':
 295                                                 cap.type|=CHAATTR_ELEMENT;
 296                                                 break;
 297                                         default:
 298                                                 break;
 299                                 }
 300                         }
 301                         i=2;
 302                         if(cap.type&CHAATTR_REGION) {
 303                                 cap.x0=atof(word[1]);
 304                                 cap.y0=atof(word[2]);
 305                                 cap.z0=atof(word[3]);
 306                                 cap.x1=atof(word[4]);
 307                                 cap.y1=atof(word[5]);
 308                                 cap.z1=atof(word[6]);
 309                                 i+=6;
 310                         }
 311                         if(cap.type&CHAATTR_ELEMENT) {
 312                                 cap.element=atoi(word[i]);
 313                                 i+=1;
 314                         }
 315                         for(o=0;o<strlen(word[i]);o++) {
 316                                 switch(word[i][o]) {
 317                                         case 'b':
 318                                                 cap.attr|=ATOM_ATTR_VB;
 319                                                 break;
 320                                         case 'h':
 321                                                 cap.attr|=ATOM_ATTR_HB;
 322                                                 break;
 323                                         case 'v':
 324                                                 cap.attr|=ATOM_ATTR_VA;
 325                                                 break;
 326                                         case 'f':
 327                                                 cap.attr|=ATOM_ATTR_FP;
 328                                                 break;
 329                                         case '1':
 330                                                 cap.attr|=ATOM_ATTR_1BP;
 331                                                 break;
 332                                         case '2':
 333                                                 cap.attr|=ATOM_ATTR_2BP;
 334                                                 break;
 335                                         case '3':
 336                                                 cap.attr|=ATOM_ATTR_3BP;
 337                                                 break;
 338                                         default:
 339                                                 break;
 340                                 }
 341                         }
 342                         add_stage(mdrun,STAGE_CHAATTR,&cap);
 343                 }
 344                 else if(!strncmp(word[0],"sattr",5)) {
 345                         // for satrib line we need a special stage
 346                         // containing one schedule of 0 loops ...
 347                         csp.type=0;
 348                         for(i=1;i<wcnt;i++) {
 349                                 if(!strncmp(word[i],"pctrl",5)) {
 350                                         csp.ptau=0.01/(atof(word[++i])*GPA);
 351                                         csp.type|=CHSATTR_PCTRL;
 352                                 }
 353                                 if(!strncmp(word[i],"tctrl",5)) {
 354                                         csp.ttau=atof(word[++i]);
 355                                         csp.type|=CHSATTR_TCTRL;
 356                                 }
 357                                 if(!strncmp(word[i],"prelax",6)) {
 358                                         csp.dp=atof(word[++i])*BAR;
 359                                         csp.type|=CHSATTR_PRELAX;
 360                                 }
 361                                 if(!strncmp(word[i],"trelax",6)) {
 362                                         csp.dt=atof(word[++i]);
 363                                         csp.type|=CHSATTR_TRELAX;
 364                                 }
 365                                 if(!strncmp(word[i],"rsteps",6)) {
 366                                         csp.rsteps=atoi(word[++i]);
 367                                         csp.type|=CHSATTR_RSTEPS;
 368                                 }
 369                                 if(!strncmp(word[i],"avgrst",6)) {
 370                                         csp.avgrst=atoi(word[++i]);
 371                                         csp.type|=CHSATTR_AVGRST;
 372                                 }
 373                         }
 374                         add_stage(mdrun,STAGE_CHSATTR,&csp);
 375                 }
 376                 else if(!strncmp(word[0],"prerun",6))
 377                         mdrun->prerun=atoi(word[1]);
 378                 else if(!strncmp(word[0],"avgskip",7))
 379                         mdrun->avgskip=atoi(word[1]);
 380                 else if(!strncmp(word[0],"elog",4))
 381                         mdrun->elog=atoi(word[1]);
 382                 else if(!strncmp(word[0],"tlog",4))
 383                         mdrun->tlog=atoi(word[1]);
 384                 else if(!strncmp(word[0],"plog",4))
 385                         mdrun->plog=atoi(word[1]);
 386                 else if(!strncmp(word[0],"vlog",4))
 387                         mdrun->vlog=atoi(word[1]);
 388                 else if(!strncmp(word[0],"save",4))
 389                         mdrun->save=atoi(word[1]);
 390                 else if(!strncmp(word[0],"visualize",9))
 391                         mdrun->visualize=atoi(word[1]);
 392                 else if(!strncmp(word[0],"stage",5)) {
 393                         // for every stage line, add a stage
 394                         if(!strncmp(word[1],"displace",8)) {
 395                                 dap.nr=atoi(word[2]);
 396                                 dap.dx=atof(word[3]);
 397                                 dap.dy=atof(word[4]);
 398                                 dap.dz=atof(word[5]);
 399                                 add_stage(mdrun,STAGE_DISPLACE_ATOM,&dap);
 400                         }
 401                         else if(!strncmp(word[1],"ins_atoms",9)) {
 402                                 iap.ins_steps=atoi(word[2]);
 403                                 iap.ins_atoms=atoi(word[3]);
 404                                 iap.element=atoi(word[4]);
 405                                 iap.brand=atoi(word[5]);
 406                                 for(i=0;i<strlen(word[6]);i++) {
 407                                         switch(word[6][i]) {
 408                                                 case 'b':
 409                                                         iap.attr|=ATOM_ATTR_VB;
 410                                                         break;
 411                                                 case 'h':
 412                                                         iap.attr|=ATOM_ATTR_HB;
 413                                                         break;
 414                                                 case 'v':
 415                                                         iap.attr|=ATOM_ATTR_VA;
 416                                                         break;
 417                                                 case 'f':
 418                                                         iap.attr|=ATOM_ATTR_FP;
 419                                                         break;
 420                                                 case '1':
 421                                                         iap.attr|=ATOM_ATTR_1BP;
 422                                                         break;
 423                                                 case '2':
 424                                                         iap.attr|=ATOM_ATTR_2BP;
 425                                                         break;
 426                                                 case '3':
 427                                                         iap.attr|=ATOM_ATTR_3BP;
 428                                                         break;
 429                                                 default:
 430                                                         break;
 431                                         }
 432                                 }
 433                                 switch(word[7][0]) {
 434                                         // insertion types
 435                                         case 'p':
 436                                                 iap.type=INS_POS;
 437                                                 iap.x0=atof(word[8]);
 438                                                 iap.y0=atof(word[9]);
 439                                                 iap.z0=atof(word[10]);
 440                                                 break;
 441                                         case 'r':
 442                                                 if(word[8][0]=='t') {
 443                                                         iap.type=INS_TOTAL;
 444                                                         iap.cr=atof(word[9]);
 445                                                 }
 446                                                 else {
 447                                                         iap.type=INS_REGION;
 448                                                         iap.x0=atof(word[8]);
 449                                                         iap.y0=atof(word[9]);
 450                                                         iap.z0=atof(word[10]);
 451                                                         iap.x1=atof(word[11]);
 452                                                         iap.y1=atof(word[12]);
 453                                                         iap.z1=atof(word[13]);
 454                                                         iap.cr=atof(word[14]);
 455                                                 }
 456                                         default:
 457                                                 break;
 458                                 }
 459                                 add_stage(mdrun,STAGE_INSERT_ATOMS,&iap);
 460                         }
 461
 462
 463                         // HERE WE GO ...
 464
 465                         else if(!strncmp(word[1],"ins_m_atoms",11)) {
 466                                 imp.element1=atoi(word[2]);
 467                                 imp.element2=atoi(word[3]);
 468                                 imp.amount1=atoi(word[4]);
 469                                 imp.amount2=atoi(word[5]);
 470                                 imp.brand1=atoi(word[6]);
 471                                 imp.brand2=atoi(word[7]);
 472                                 imp.crmin=atof(word[8]);
 473                                 imp.crmax=atof(word[9]);
 474                                 /* do this later ...
 475                                 for(i=0;i<strlen(word[8]);i++) {
 476                                         switch(word[8][i]) {
 477                                                 case 'b':
 478                                                         imp.attr|=ATOM_ATTR_VB;
 479                                                         break;
 480                                                 case 'h':
 481                                                         imp.attr|=ATOM_ATTR_HB;
 482                                                         break;
 483                                                 case 'v':
 484                                                         imp.attr|=ATOM_ATTR_VA;
 485                                                         break;
 486                                                 case 'f':
 487                                                         imp.attr|=ATOM_ATTR_FP;
 488                                                         break;
 489                                                 case '1':
 490                                                         imp.attr|=ATOM_ATTR_1BP;
 491                                                         break;
 492                                                 case '2':
 493                                                         imp.attr|=ATOM_ATTR_2BP;
 494                                                         break;
 495                                                 case '3':
 496                                                         imp.attr|=ATOM_ATTR_3BP;
 497                                                         break;
 498                                                 default:
 499                                                         break;
 500                                         }
 501                                 }
 502                                 */
 503                                 imp.attr1=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
 504                                 imp.attr2=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
 505                                 add_stage(mdrun,STAGE_INSERT_MIXED_ATOMS,&imp);
 506                         }
 507
 508
 509
 510
 511
 512                         else if(!strncmp(word[1],"continue",8)) {
 513                                 cp.runs=atoi(word[2]);
 514                                 add_stage(mdrun,STAGE_CONTINUE,&cp);
 515                         }
 516                         else if(!strncmp(word[1],"anneal",6)) {
 517                                 ap.count=0;
 518                                 ap.runs=atoi(word[2]);
 519                                 ap.dt=atof(word[3]);
 520                                 ap.interval=atoi(word[4]);
 521                                 add_stage(mdrun,STAGE_ANNEAL,&ap);
 522                         }
 523                         else if(!strncmp(word[1],"set_temp",8)) {
 524                                 if(word[2][0]=='c') {
 525                                         stp.type=SET_TEMP_CURRENT;
 526                                         stp.val=0.0;
 527                                 }
 528                                 else {
 529                                         stp.type=SET_TEMP_VALUE;
 530                                         stp.val=atof(word[2]);
 531                                 }
 532                                 add_stage(mdrun,STAGE_SET_TEMP,&stp);
 533                         }
 534                         else if(!strncmp(word[1],"set_timestep",12)) {
 535                                 stsp.tau=atof(word[2]);
 536                                 add_stage(mdrun,STAGE_SET_TIMESTEP,&stsp);
 537                         }
 538                         else {
 539                                 printf("%s unknown stage type: %s\n",
 540                                        ME,word[1]);
 541                                 return -1;
 542                         }
 543                 }
 544                 else {
 545                         printf("%s unknown keyword '%s', skipped!\n",
 546                                ME,word[0]);
 547                         continue;
 548                 }
 549         }
 550
 551         /* close file */
 552         close(fd);
 553
 554         return 0;
 555 }
 556
 557 int check_pressure(t_moldyn *moldyn,t_mdrun *mdrun) {
 558
 559         double delta;
 560
 561         if(!(mdrun->sattr&SATTR_PRELAX)) {
 562                 return TRUE;
 563         }
 564
 565         delta=moldyn->p_avg-moldyn->p_ref;
 566
 567         if(delta<0)
 568                 delta=-delta;
 569
 570         if(delta>mdrun->dp)
 571                 return FALSE;
 572
 573         return TRUE;
 574 }
 575
 576 int check_temperature(t_moldyn *moldyn,t_mdrun *mdrun) {
 577
 578         double delta;
 579
 580         if(!(mdrun->sattr&SATTR_TRELAX))
 581                 return TRUE;
 582
 583         delta=moldyn->t_avg-moldyn->t_ref;
 584
 585         if(delta<0)
 586                 delta=-delta;
 587
 588         if(delta>mdrun->dt)
 589                 return FALSE;
 590
 591         return TRUE;
 592 }
 593
 594 int displace_atom(t_moldyn *moldyn,t_mdrun *mdrun) {
 595
 596         t_displace_atom_params *dap;
 597         t_stage *stage;
 598         t_atom *atom;
 599
 600         stage=mdrun->stage.current->data;
 601         dap=stage->params;
 602
 603         atom=&(moldyn->atom[dap->nr]);
 604         atom->r.x+=dap->dx;
 605         atom->r.y+=dap->dy;
 606         atom->r.z+=dap->dz;
 607
 608         return 0;
 609 }
 610
 611 int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 612
 613         t_insert_atoms_params *iap;
 614         t_stage *stage;
 615         t_atom *atom;
 616         t_3dvec r,v,dist;
 617         double d,dmin,o;
 618         int cnt,i;
 619         double x,y,z;
 620         double x0,y0,z0;
 621         u8 cr_check,run;
 622
 623         stage=mdrun->stage.current->data;
 624         iap=stage->params;
 625
 626         cr_check=FALSE;
 627
 628         v.x=0.0; v.y=0.0; v.z=0.0;
 629         x=0; y=0; z=0;
 630         o=0; dmin=0;
 631
 632         switch(mdrun->lattice) {
 633                 case CUBIC:
 634                         o=0.5*mdrun->lc;
 635                         break;
 636                 case FCC:
 637                         o=0.25*mdrun->lc;
 638                         break;
 639                 case DIAMOND:
 640                 case ZINCBLENDE:
 641                         o=0.125*mdrun->lc;
 642                         break;
 643                 default:
 644                         break;
 645         }
 646
 647         switch(iap->type) {
 648                 case INS_TOTAL:
 649                         x=moldyn->dim.x;
 650                         x0=-x/2.0;
 651                         y=moldyn->dim.y;
 652                         y0=-y/2.0;
 653                         z=moldyn->dim.z;
 654                         z0=-z/2.0;
 655                         cr_check=TRUE;
 656                         break;
 657                 case INS_REGION:
 658                         x=iap->x1-iap->x0;
 659                         x0=iap->x0;
 660                         y=iap->y1-iap->y0;
 661                         y0=iap->y0;
 662                         z=iap->z1-iap->z0;
 663                         z0=iap->z0;
 664                         cr_check=TRUE;
 665                         break;
 666                 case INS_POS:
 667                         x0=iap->x0;
 668                         y0=iap->y0;
 669                         z0=iap->z0;
 670                         cr_check=FALSE;
 671                         break;
 672                 default:
 673                         printf("%s unknown insertion mode: %02x\n",
 674                                ME,iap->type);
 675                         return -1;
 676         }
 677
 678         cnt=0;
 679         while(cnt<iap->ins_atoms) {
 680                 run=1;
 681                 while(run) {
 682                         if(iap->type!=INS_POS) {
 683                                 r.x=rand_get_double(&(moldyn->random))*x;
 684                                 r.y=rand_get_double(&(moldyn->random))*y;
 685                                 r.z=rand_get_double(&(moldyn->random))*z;
 686                         }
 687                         else {
 688                                 r.x=0.0;
 689                                 r.y=0.0;
 690                                 r.z=0.0;
 691                         }
 692                         r.x+=x0;
 693                         r.y+=y0;
 694                         r.z+=z0;
 695                         // offset
 696                         if(iap->type!=INS_TOTAL) {
 697                                 r.x+=o;
 698                                 r.y+=o;
 699                                 r.z+=o;
 700                         }
 701                         run=0;
 702                         if(cr_check==TRUE) {
 703                                 dmin=1000;      // for sure too high!
 704                                 for(i=0;i<moldyn->count;i++) {
 705                                         atom=&(moldyn->atom[i]);
 706                                         v3_sub(&dist,&(atom->r),&r);
 707                                         check_per_bound(moldyn,&dist);
 708                                         d=v3_absolute_square(&dist);
 709                                         if(d<(iap->cr*iap->cr)) {
 710                                                 run=1;
 711                                                 break;
 712                                         }
 713                                         if(d<dmin)
 714                                                 dmin=d;
 715                                 }
 716                         }
 717                 }
 718                 add_atom(moldyn,iap->element,pse_mass[iap->element],
 719                          iap->brand,iap->attr,&r,&v);
 720                 printf("%s atom inserted (%d/%d): %f %f %f\n",
 721                        ME,(iap->cnt_steps+1)*iap->ins_atoms,
 722                        iap->ins_steps*iap->ins_atoms,r.x,r.y,r.z);
 723                 printf("  -> d2 = %f/%f\n",dmin,iap->cr*iap->cr);
 724                 cnt+=1;
 725         }
 726
 727         return 0;
 728 }
 729
 730 int insert_mixed_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 731
 732         t_stage *stage;
 733         t_insert_mixed_atoms_params *imp;
 734         t_atom *atom;
 735         double x,x0,y,y0,z,z0;
 736         double dmin,d,cmin,cmax;
 737         u8 retry;
 738         t_3dvec r,v,dist;
 739         int i;
 740
 741
 742         stage=mdrun->stage.current->data;
 743         imp=stage->params;
 744
 745         x=moldyn->dim.x;
 746         x0=-x/2.0;
 747         y=moldyn->dim.y;
 748         y0=-y/2.0;
 749         z=moldyn->dim.z;
 750         z0=-z/2.0;
 751
 752         v.x=0.0;
 753         v.y=0.0;
 754         v.z=0.0;
 755
 756         cmin=imp->crmin*imp->crmin;
 757         cmax=imp->crmax*imp->crmax;
 758
 759         while(imp->amount1|imp->amount2) {
 760                 if(imp->amount1) {
 761                         retry=1;
 762                         while(retry) {
 763                                 retry=0;
 764                                 r.x=rand_get_double(&(moldyn->random))*x;
 765                                 r.y=rand_get_double(&(moldyn->random))*y;
 766                                 r.z=rand_get_double(&(moldyn->random))*z;
 767                                 r.x+=x0;
 768                                 r.y+=y0;
 769                                 r.z+=z0;
 770                                 dmin=1000.0;    // for sure too high!
 771                                 for(i=0;i<moldyn->count;i++) {
 772                                         atom=&(moldyn->atom[i]);
 773                                         v3_sub(&dist,&(atom->r),&r);
 774                                         check_per_bound(moldyn,&dist);
 775                                         d=v3_absolute_square(&dist);
 776                                         if(d<cmin) {
 777                                                 retry=1;
 778                                                 break;
 779                                         }
 780                                         if(d<dmin)
 781                                                 dmin=d;
 782                                 }
 783                                 if(dmin!=1000.0)
 784                                         if(dmin>cmax)
 785                                                 retry=1;
 786                         }
 787                         add_atom(moldyn,imp->element1,pse_mass[imp->element1],
 788                                  imp->brand1,imp->attr1,&r,&v);
 789                         printf("%s (mixed) atom inserted (%d): %f %f %f\n",
 790                                ME,imp->amount1,r.x,r.y,r.z);
 791                         printf("  -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
 792                         imp->amount1-=1;
 793                 }
 794                 if(imp->amount2) {
 795                         retry=1;
 796                         while(retry) {
 797                                 retry=0;
 798                                 r.x=rand_get_double(&(moldyn->random))*x;
 799                                 r.y=rand_get_double(&(moldyn->random))*y;
 800                                 r.z=rand_get_double(&(moldyn->random))*z;
 801                                 r.x+=x0;
 802                                 r.y+=y0;
 803                                 r.z+=z0;
 804                                 dmin=1000.0;    // for sure too high!
 805                                 for(i=0;i<moldyn->count;i++) {
 806                                         atom=&(moldyn->atom[i]);
 807                                         v3_sub(&dist,&(atom->r),&r);
 808                                         check_per_bound(moldyn,&dist);
 809                                         d=v3_absolute_square(&dist);
 810                                         if(d<cmin) {
 811                                                 retry=1;
 812                                                 break;
 813                                         }
 814                                         if(d<dmin)
 815                                                 dmin=d;
 816                                 }
 817                                 if(dmin!=1000.0)
 818                                         if(dmin>cmax)
 819                                                 retry=1;
 820                         }
 821                         add_atom(moldyn,imp->element2,pse_mass[imp->element2],
 822                                  imp->brand2,imp->attr2,&r,&v);
 823                         printf("%s (mixed) atom inserted (%d): %f %f %f\n",
 824                                ME,imp->amount2,r.x,r.y,r.z);
 825                         printf("  -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
 826                         imp->amount2-=1;
 827                 }
 828         }
 829
 830         return 0;
 831 }
 832
 833 int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
 834
 835         t_stage *stage;
 836         t_chaattr_params *cap;
 837         t_atom *atom;
 838         int i;
 839
 840         stage=mdrun->stage.current->data;
 841         cap=stage->params;
 842
 843         for(i=0;i<moldyn->count;i++) {
 844                 atom=&(moldyn->atom[i]);
 845                 if(cap->type&CHAATTR_ELEMENT) {
 846                         if(cap->element!=atom->element)
 847                                 continue;
 848                 }
 849                 if(cap->type&CHAATTR_REGION) {
 850                         if(cap->x0<atom->r.x)
 851                                 continue;
 852                         if(cap->y0<atom->r.y)
 853                                 continue;
 854                         if(cap->z0<atom->r.z)
 855                                 continue;
 856                         if(cap->x1>atom->r.x)
 857                                 continue;
 858                         if(cap->y1>atom->r.y)
 859                                 continue;
 860                         if(cap->z1>atom->r.z)
 861                                 continue;
 862                 }
 863                 atom->attr=cap->attr;
 864         }
 865
 866         return 0;
 867 }
 868
 869 int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
 870
 871         t_stage *stage;
 872         t_chsattr_params *csp;
 873
 874         stage=mdrun->stage.current->data;
 875         csp=stage->params;
 876
 877         if(csp->type&CHSATTR_PCTRL) {
 878                 if(csp->ptau>0)
 879                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
 880                 else
 881                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
 882         }
 883         if(csp->type&CHSATTR_TCTRL) {
 884                 if(csp->ttau>0)
 885                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
 886                 else
 887                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
 888         }
 889         if(csp->type&CHSATTR_PRELAX) {
 890                 if(csp->dp<0)
 891                         mdrun->sattr&=(~(SATTR_PRELAX));
 892                 else
 893                         mdrun->sattr|=SATTR_PRELAX;
 894                 mdrun->dp=csp->dp;
 895         }
 896         if(csp->type&CHSATTR_TRELAX) {
 897                 if(csp->dt<0)
 898                         mdrun->sattr&=(~(SATTR_TRELAX));
 899                 else
 900                         mdrun->sattr|=SATTR_TRELAX;
 901                 mdrun->dt=csp->dt;
 902         }
 903         if(csp->type&CHSATTR_AVGRST) {
 904                 if(csp->avgrst)
 905                         mdrun->sattr|=SATTR_AVGRST;
 906                 else
 907                         mdrun->sattr&=(~(SATTR_AVGRST));
 908         }
 909         if(csp->type&CHSATTR_RSTEPS) {
 910                 mdrun->relax_steps=csp->rsteps;
 911         }
 912
 913         return 0;
 914 }
 915
 916 #define stage_print(m)  if(!(stage->executed)) \
 917                                 printf("%s",m)
 918
 919 int mdrun_hook(void *ptr1,void *ptr2) {
 920
 921         t_moldyn *moldyn;
 922         t_mdrun *mdrun;
 923         t_stage *stage;
 924         t_list *sl;
 925         int steps;
 926         u8 change_stage;
 927
 928         t_insert_atoms_params *iap;
 929         t_insert_mixed_atoms_params *imp;
 930         t_continue_params *cp;
 931         t_anneal_params *ap;
 932         t_set_temp_params *stp;
 933         t_set_timestep_params *stsp;
 934
 935         moldyn=ptr1;
 936         mdrun=ptr2;
 937
 938         sl=&(mdrun->stage);
 939
 940         change_stage=FALSE;
 941
 942         /* return immediately if there are no more stage */
 943         if(sl->current==NULL)
 944                 return 0;
 945
 946         /* get stage description */
 947         stage=sl->current->data;
 948
 949         /* steps in next schedule */
 950         steps=mdrun->relax_steps;
 951
 952         /* check whether relaxation steps are necessary */
 953         if((check_pressure(moldyn,mdrun)==TRUE)&\
 954            (check_temperature(moldyn,mdrun)==TRUE)) {
 955
 956                 /* be verbose */
 957                 stage_print("\n###########################\n");
 958                 stage_print("# [mdrun] executing stage #\n");
 959                 stage_print("###########################\n\n");
 960
 961                 /* stage specific stuff */
 962                 switch(stage->type) {
 963                         case STAGE_DISPLACE_ATOM:
 964                                 stage_print("  -> displace atom\n\n");
 965                                 displace_atom(moldyn,mdrun);
 966                                 change_stage=TRUE;
 967                                 break;
 968                         case STAGE_INSERT_ATOMS:
 969                                 stage_print("  -> insert atoms\n\n");
 970                                 iap=stage->params;
 971                                 if(iap->cnt_steps==iap->ins_steps) {
 972                                         change_stage=TRUE;
 973                                         break;
 974                                 }
 975                                 insert_atoms(moldyn,mdrun);
 976                                 iap->cnt_steps+=1;
 977                                 break;
 978
 979
 980
 981                         case STAGE_INSERT_MIXED_ATOMS:
 982                                 stage_print("  -> insert mixed atoms\n\n");
 983                                 imp=stage->params;
 984                                 insert_mixed_atoms(moldyn,mdrun);
 985                                 change_stage=TRUE;
 986                                 break;
 987
 988
 989
 990                         case STAGE_CONTINUE:
 991                                 stage_print("  -> continue\n\n");
 992                                 if(stage->executed==TRUE) {
 993                                         change_stage=TRUE;
 994                                         break;
 995                                 }
 996                                 cp=stage->params;
 997                                 steps=cp->runs;
 998                                 break;
 999                         case STAGE_ANNEAL:
1000                                 stage_print("  -> anneal\n\n");
1001                                 ap=stage->params;
1002                                 if(ap->count==ap->runs) {
1003                                         change_stage=TRUE;
1004                                         break;
1005                                 }
1006                                 if(moldyn->t_ref+ap->dt>=0.0)
1007                                         set_temperature(moldyn,
1008                                                         moldyn->t_ref+ap->dt);
1009                                 ap->count+=1;
1010                                 steps=ap->interval;
1011                                 break;
1012                         case STAGE_CHAATTR:
1013                                 stage_print("  -> change atom attributes\n\n");
1014                                 chaatr(moldyn,mdrun);
1015                                 change_stage=TRUE;
1016                                 break;
1017                         case STAGE_CHSATTR:
1018                                 stage_print("  -> change sys attributes\n\n");
1019                                 chsattr(moldyn,mdrun);
1020                                 change_stage=TRUE;
1021                                 break;
1022                         case STAGE_SET_TEMP:
1023                                 stage_print("  -> set temperature\n\n");
1024                                 stp=stage->params;
1025                                 if(stp->type&SET_TEMP_CURRENT) {
1026                                         set_temperature(moldyn,moldyn->t_avg);
1027                                 }
1028                                 else {
1029                                         set_temperature(moldyn,stp->val);
1030                                 }
1031                                 change_stage=TRUE;
1032                                 break;
1033                         case STAGE_SET_TIMESTEP:
1034                                 stage_print("  -> set timestep\n\n");
1035                                 stsp=stage->params;
1036                                 mdrun->timestep=stsp->tau;
1037                                 change_stage=TRUE;
1038                                 break;
1039                         default:
1040                                 printf("%s unknwon stage type\n",ME);
1041                                 break;
1042                 }
1043
1044                 /* mark as executed */
1045                 stage->executed=TRUE;
1046
1047                 /* change state */
1048                 if(change_stage==TRUE) {
1049                         printf("%s finished stage\n",ME);
1050                         if(list_next_f(sl)==L_NO_NEXT_ELEMENT) {
1051                                 printf("%s no more stages\n",ME);
1052                                 return 0;
1053                         }
1054                         steps=0;
1055                 }
1056
1057         }
1058         else {
1059
1060                 /* averages */
1061                 if(mdrun->sattr&SATTR_AVGRST)
1062                         average_reset(moldyn);
1063
1064         }
1065
1066         /* continue simulation */
1067         moldyn_add_schedule(moldyn,steps,mdrun->timestep);
1068
1069         return 0;
1070 }
1071
1072 int main(int argc,char **argv) {
1073
1074         t_mdrun mdrun;
1075         t_moldyn moldyn;
1076         t_3dvec o;
1077
1078         /* clear structs */
1079         memset(&mdrun,0,sizeof(t_mdrun));
1080         memset(&moldyn,0,sizeof(t_moldyn));
1081
1082         /* parse arguments */
1083         if(mdrun_parse_argv(&mdrun,argc,argv)<0)
1084                 return -1;
1085
1086         /* initialize list system */
1087         list_init_f(&(mdrun.stage));
1088
1089         /* parse config file */
1090         mdrun_parse_config(&mdrun);
1091
1092         /* reset the stage list */
1093         list_reset_f(&(mdrun.stage));
1094
1095         /* sanity check! */
1096
1097         /* prepare simulation */
1098
1099         if(mdrun.continue_file[0]) {
1100                 // read the save file
1101                 moldyn_read_save_file(&moldyn,mdrun.continue_file);
1102                 // manualaadjusting some stuff
1103                 moldyn.argc=argc;
1104                 moldyn.args=argv;
1105                 rand_init(&(moldyn.random),NULL,1);
1106                 moldyn.random.status|=RAND_STAT_VERBOSE;
1107         }
1108         else {
1109                 moldyn_init(&moldyn,argc,argv);
1110         }
1111
1112         if(set_int_alg(&moldyn,mdrun.intalgo)<0)
1113                 return -1;
1114
1115         /* potential */
1116         set_cutoff(&moldyn,mdrun.cutoff);
1117         if(set_potential(&moldyn,mdrun.potential)<0)
1118                 return -1;
1119         switch(mdrun.potential) {
1120                 case MOLDYN_POTENTIAL_AM:
1121                         albe_mult_set_params(&moldyn,
1122                                              mdrun.element1,
1123                                              mdrun.element2);
1124                         break;
1125                 case MOLDYN_POTENTIAL_TM:
1126                         tersoff_mult_set_params(&moldyn,
1127                                                 mdrun.element1,
1128                                                 mdrun.element2);
1129                         break;
1130                 case MOLDYN_POTENTIAL_HO:
1131                         harmonic_oscillator_set_params(&moldyn,mdrun.element1);
1132                         break;
1133                 case MOLDYN_POTENTIAL_LJ:
1134                         lennard_jones_set_params(&moldyn,mdrun.element1);
1135                         break;
1136                 default:
1137                         printf("%s unknown potential: %02x\n",
1138                                ME,mdrun.potential);
1139                         return -1;
1140         }
1141
1142         /* if it is a continue run, reset schedule and skip lattice init */
1143         if(mdrun.continue_file[0]) {
1144                 memset(&(moldyn.schedule),0,sizeof(t_moldyn_schedule));
1145                 goto addsched;
1146         }
1147
1148         /* initial lattice and dimensions */
1149         set_dim(&moldyn,mdrun.dim.x,mdrun.dim.y,mdrun.dim.z,mdrun.vis);
1150         set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
1151         switch(mdrun.lattice) {
1152                 case FCC:
1153                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
1154                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
1155                                        mdrun.ly,mdrun.lz,NULL);
1156                         break;
1157                 case DIAMOND:
1158                         create_lattice(&moldyn,DIAMOND,mdrun.lc,mdrun.element1,
1159                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
1160                                        mdrun.ly,mdrun.lz,NULL);
1161                         break;
1162                 case ZINCBLENDE:
1163                         o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
1164                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
1165                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
1166                                        mdrun.ly,mdrun.lz,&o);
1167                         o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
1168                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
1169                                        mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
1170                                        mdrun.ly,mdrun.lz,&o);
1171                         break;
1172                 case NONE:
1173                         set_nn_dist(&moldyn,mdrun.nnd);
1174                         break;
1175                 default:
1176                         printf("%s unknown lattice type: %02x\n",
1177                                ME,mdrun.lattice);
1178                         return -1;
1179         }
1180         moldyn_bc_check(&moldyn);
1181
1182         /* temperature and pressure */
1183         set_temperature(&moldyn,mdrun.temperature);
1184         set_pressure(&moldyn,mdrun.pressure);
1185         thermal_init(&moldyn,TRUE);
1186
1187 addsched:
1188         /* first schedule */
1189         moldyn_add_schedule(&moldyn,mdrun.prerun,mdrun.timestep);
1190
1191         /* log */
1192         moldyn_set_log_dir(&moldyn,mdrun.sdir);
1193         moldyn_set_report(&moldyn,"CHANGE ME","CHANGE ME TOO");
1194         if(mdrun.elog)
1195                 moldyn_set_log(&moldyn,LOG_TOTAL_ENERGY,mdrun.elog);
1196         if(mdrun.tlog)
1197                 moldyn_set_log(&moldyn,LOG_TEMPERATURE,mdrun.tlog);
1198         if(mdrun.plog)
1199                 moldyn_set_log(&moldyn,LOG_PRESSURE,mdrun.plog);
1200         if(mdrun.vlog)
1201                 moldyn_set_log(&moldyn,LOG_VOLUME,mdrun.vlog);
1202         if(mdrun.visualize)
1203                 moldyn_set_log(&moldyn,VISUAL_STEP,mdrun.visualize);
1204         if(mdrun.save)
1205                 moldyn_set_log(&moldyn,SAVE_STEP,mdrun.save);
1206         moldyn_set_log(&moldyn,CREATE_REPORT,0);
1207         set_avg_skip(&moldyn,mdrun.avgskip);
1208
1209         /* prepare the hook function */
1210         moldyn_set_schedule_hook(&moldyn,&mdrun_hook,&mdrun);
1211
1212         /* run the simulation */
1213         moldyn_integrate(&moldyn);
1214
1215         /* shutdown */
1216         moldyn_shutdown(&moldyn);
1217         del_stages(&mdrun);
1218         list_destroy_f(&(mdrun.stage));
1219
1220         return 0;
1221 }