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                                 add_stage(mdrun,STAGE_ANNEAL,&ap);
 521                         }
 522                         else if(!strncmp(word[1],"set_temp",8)) {
 523                                 if(word[2][0]=='c') {
 524                                         stp.type=SET_TEMP_CURRENT;
 525                                         stp.val=0.0;
 526                                 }
 527                                 else {
 528                                         stp.type=SET_TEMP_VALUE;
 529                                         stp.val=atof(word[2]);
 530                                 }
 531                                 add_stage(mdrun,STAGE_SET_TEMP,&stp);
 532                         }
 533                         else if(!strncmp(word[1],"set_timestep",12)) {
 534                                 stsp.tau=atof(word[2]);
 535                                 add_stage(mdrun,STAGE_SET_TIMESTEP,&stsp);
 536                         }
 537                         else {
 538                                 printf("%s unknown stage type: %s\n",
 539                                        ME,word[1]);
 540                                 return -1;
 541                         }
 542                 }
 543                 else {
 544                         printf("%s unknown keyword '%s', skipped!\n",
 545                                ME,word[0]);
 546                         continue;
 547                 }
 548         }
 549
 550         /* close file */
 551         close(fd);
 552
 553         return 0;
 554 }
 555
 556 int check_pressure(t_moldyn *moldyn,t_mdrun *mdrun) {
 557
 558         double delta;
 559
 560         if(!(mdrun->sattr&SATTR_PRELAX)) {
 561                 return TRUE;
 562         }
 563
 564         delta=moldyn->p_avg-moldyn->p_ref;
 565
 566         if(delta<0)
 567                 delta=-delta;
 568
 569         if(delta>mdrun->dp)
 570                 return FALSE;
 571
 572         return TRUE;
 573 }
 574
 575 int check_temperature(t_moldyn *moldyn,t_mdrun *mdrun) {
 576
 577         double delta;
 578
 579         if(!(mdrun->sattr&SATTR_TRELAX))
 580                 return TRUE;
 581
 582         delta=moldyn->t_avg-moldyn->t_ref;
 583
 584         if(delta<0)
 585                 delta=-delta;
 586
 587         if(delta>mdrun->dt)
 588                 return FALSE;
 589
 590         return TRUE;
 591 }
 592
 593 int displace_atom(t_moldyn *moldyn,t_mdrun *mdrun) {
 594
 595         t_displace_atom_params *dap;
 596         t_stage *stage;
 597         t_atom *atom;
 598
 599         stage=mdrun->stage.current->data;
 600         dap=stage->params;
 601
 602         atom=&(moldyn->atom[dap->nr]);
 603         atom->r.x+=dap->dx;
 604         atom->r.y+=dap->dy;
 605         atom->r.z+=dap->dz;
 606
 607         return 0;
 608 }
 609
 610 int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 611
 612         t_insert_atoms_params *iap;
 613         t_stage *stage;
 614         t_atom *atom;
 615         t_3dvec r,v,dist;
 616         double d,dmin,o;
 617         int cnt,i;
 618         double x,y,z;
 619         double x0,y0,z0;
 620         u8 cr_check,run;
 621
 622         stage=mdrun->stage.current->data;
 623         iap=stage->params;
 624
 625         cr_check=FALSE;
 626
 627         v.x=0.0; v.y=0.0; v.z=0.0;
 628         x=0; y=0; z=0;
 629         o=0; dmin=0;
 630
 631         switch(mdrun->lattice) {
 632                 case CUBIC:
 633                         o=0.5*mdrun->lc;
 634                         break;
 635                 case FCC:
 636                         o=0.25*mdrun->lc;
 637                         break;
 638                 case DIAMOND:
 639                 case ZINCBLENDE:
 640                         o=0.125*mdrun->lc;
 641                         break;
 642                 default:
 643                         break;
 644         }
 645
 646         switch(iap->type) {
 647                 case INS_TOTAL:
 648                         x=moldyn->dim.x;
 649                         x0=-x/2.0;
 650                         y=moldyn->dim.y;
 651                         y0=-y/2.0;
 652                         z=moldyn->dim.z;
 653                         z0=-z/2.0;
 654                         cr_check=TRUE;
 655                         break;
 656                 case INS_REGION:
 657                         x=iap->x1-iap->x0;
 658                         x0=iap->x0;
 659                         y=iap->y1-iap->y0;
 660                         y0=iap->y0;
 661                         z=iap->z1-iap->z0;
 662                         z0=iap->z0;
 663                         cr_check=TRUE;
 664                         break;
 665                 case INS_POS:
 666                         x0=iap->x0;
 667                         y0=iap->y0;
 668                         z0=iap->z0;
 669                         cr_check=FALSE;
 670                         break;
 671                 default:
 672                         printf("%s unknown insertion mode: %02x\n",
 673                                ME,iap->type);
 674                         return -1;
 675         }
 676
 677         cnt=0;
 678         while(cnt<iap->ins_atoms) {
 679                 run=1;
 680                 while(run) {
 681                         if(iap->type!=INS_POS) {
 682                                 r.x=rand_get_double(&(moldyn->random))*x;
 683                                 r.y=rand_get_double(&(moldyn->random))*y;
 684                                 r.z=rand_get_double(&(moldyn->random))*z;
 685                         }
 686                         else {
 687                                 r.x=0.0;
 688                                 r.y=0.0;
 689                                 r.z=0.0;
 690                         }
 691                         r.x+=x0;
 692                         r.y+=y0;
 693                         r.z+=z0;
 694                         // offset
 695                         if(iap->type!=INS_TOTAL) {
 696                                 r.x+=o;
 697                                 r.y+=o;
 698                                 r.z+=o;
 699                         }
 700                         run=0;
 701                         if(cr_check==TRUE) {
 702                                 dmin=1000;      // for sure too high!
 703                                 for(i=0;i<moldyn->count;i++) {
 704                                         atom=&(moldyn->atom[i]);
 705                                         v3_sub(&dist,&(atom->r),&r);
 706                                         check_per_bound(moldyn,&dist);
 707                                         d=v3_absolute_square(&dist);
 708                                         if(d<(iap->cr*iap->cr)) {
 709                                                 run=1;
 710                                                 break;
 711                                         }
 712                                         if(d<dmin)
 713                                                 dmin=d;
 714                                 }
 715                         }
 716                 }
 717                 add_atom(moldyn,iap->element,pse_mass[iap->element],
 718                          iap->brand,iap->attr,&r,&v);
 719                 printf("%s atom inserted (%d/%d): %f %f %f\n",
 720                        ME,(iap->cnt_steps+1)*iap->ins_atoms,
 721                        iap->ins_steps*iap->ins_atoms,r.x,r.y,r.z);
 722                 printf("  -> d2 = %f/%f\n",dmin,iap->cr*iap->cr);
 723                 cnt+=1;
 724         }
 725
 726         return 0;
 727 }
 728
 729 int insert_mixed_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 730
 731         t_stage *stage;
 732         t_insert_mixed_atoms_params *imp;
 733         t_atom *atom;
 734         double x,x0,y,y0,z,z0;
 735         double dmin,d,cmin,cmax;
 736         u8 retry;
 737         t_3dvec r,v,dist;
 738         int i;
 739
 740
 741         stage=mdrun->stage.current->data;
 742         imp=stage->params;
 743
 744         x=moldyn->dim.x;
 745         x0=-x/2.0;
 746         y=moldyn->dim.y;
 747         y0=-y/2.0;
 748         z=moldyn->dim.z;
 749         z0=-z/2.0;
 750
 751         v.x=0.0;
 752         v.y=0.0;
 753         v.z=0.0;
 754
 755         cmin=imp->crmin*imp->crmin;
 756         cmax=imp->crmax*imp->crmax;
 757
 758         while(imp->amount1|imp->amount2) {
 759                 if(imp->amount1) {
 760                         retry=1;
 761                         while(retry) {
 762                                 retry=0;
 763                                 r.x=rand_get_double(&(moldyn->random))*x;
 764                                 r.y=rand_get_double(&(moldyn->random))*y;
 765                                 r.z=rand_get_double(&(moldyn->random))*z;
 766                                 r.x+=x0;
 767                                 r.y+=y0;
 768                                 r.z+=z0;
 769                                 dmin=1000.0;    // for sure too high!
 770                                 for(i=0;i<moldyn->count;i++) {
 771                                         atom=&(moldyn->atom[i]);
 772                                         v3_sub(&dist,&(atom->r),&r);
 773                                         check_per_bound(moldyn,&dist);
 774                                         d=v3_absolute_square(&dist);
 775                                         if(d<cmin) {
 776                                                 retry=1;
 777                                                 break;
 778                                         }
 779                                         if(d<dmin)
 780                                                 dmin=d;
 781                                 }
 782                                 if(dmin!=1000.0)
 783                                         if(dmin>cmax)
 784                                                 retry=1;
 785                         }
 786                         add_atom(moldyn,imp->element1,pse_mass[imp->element1],
 787                                  imp->brand1,imp->attr1,&r,&v);
 788                         printf("%s (mixed) atom inserted (%d): %f %f %f\n",
 789                                ME,imp->amount1,r.x,r.y,r.z);
 790                         printf("  -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
 791                         imp->amount1-=1;
 792                 }
 793                 if(imp->amount2) {
 794                         retry=1;
 795                         while(retry) {
 796                                 retry=0;
 797                                 r.x=rand_get_double(&(moldyn->random))*x;
 798                                 r.y=rand_get_double(&(moldyn->random))*y;
 799                                 r.z=rand_get_double(&(moldyn->random))*z;
 800                                 r.x+=x0;
 801                                 r.y+=y0;
 802                                 r.z+=z0;
 803                                 dmin=1000.0;    // for sure too high!
 804                                 for(i=0;i<moldyn->count;i++) {
 805                                         atom=&(moldyn->atom[i]);
 806                                         v3_sub(&dist,&(atom->r),&r);
 807                                         check_per_bound(moldyn,&dist);
 808                                         d=v3_absolute_square(&dist);
 809                                         if(d<cmin) {
 810                                                 retry=1;
 811                                                 break;
 812                                         }
 813                                         if(d<dmin)
 814                                                 dmin=d;
 815                                 }
 816                                 if(dmin!=1000.0)
 817                                         if(dmin>cmax)
 818                                                 retry=1;
 819                         }
 820                         add_atom(moldyn,imp->element2,pse_mass[imp->element2],
 821                                  imp->brand2,imp->attr2,&r,&v);
 822                         printf("%s (mixed) atom inserted (%d): %f %f %f\n",
 823                                ME,imp->amount2,r.x,r.y,r.z);
 824                         printf("  -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
 825                         imp->amount2-=1;
 826                 }
 827         }
 828
 829         return 0;
 830 }
 831
 832 int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
 833
 834         t_stage *stage;
 835         t_chaattr_params *cap;
 836         t_atom *atom;
 837         int i;
 838
 839         stage=mdrun->stage.current->data;
 840         cap=stage->params;
 841
 842         for(i=0;i<moldyn->count;i++) {
 843                 atom=&(moldyn->atom[i]);
 844                 if(cap->type&CHAATTR_ELEMENT) {
 845                         if(cap->element!=atom->element)
 846                                 continue;
 847                 }
 848                 if(cap->type&CHAATTR_REGION) {
 849                         if(cap->x0<atom->r.x)
 850                                 continue;
 851                         if(cap->y0<atom->r.y)
 852                                 continue;
 853                         if(cap->z0<atom->r.z)
 854                                 continue;
 855                         if(cap->x1>atom->r.x)
 856                                 continue;
 857                         if(cap->y1>atom->r.y)
 858                                 continue;
 859                         if(cap->z1>atom->r.z)
 860                                 continue;
 861                 }
 862                 atom->attr=cap->attr;
 863         }
 864
 865         return 0;
 866 }
 867
 868 int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
 869
 870         t_stage *stage;
 871         t_chsattr_params *csp;
 872
 873         stage=mdrun->stage.current->data;
 874         csp=stage->params;
 875
 876         if(csp->type&CHSATTR_PCTRL) {
 877                 if(csp->ptau>0)
 878                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
 879                 else
 880                         set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
 881         }
 882         if(csp->type&CHSATTR_TCTRL) {
 883                 if(csp->ttau>0)
 884                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
 885                 else
 886                         set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
 887         }
 888         if(csp->type&CHSATTR_PRELAX) {
 889                 if(csp->dp<0)
 890                         mdrun->sattr&=(~(SATTR_PRELAX));
 891                 else
 892                         mdrun->sattr|=SATTR_PRELAX;
 893                 mdrun->dp=csp->dp;
 894         }
 895         if(csp->type&CHSATTR_TRELAX) {
 896                 if(csp->dt<0)
 897                         mdrun->sattr&=(~(SATTR_TRELAX));
 898                 else
 899                         mdrun->sattr|=SATTR_TRELAX;
 900                 mdrun->dt=csp->dt;
 901         }
 902         if(csp->type&CHSATTR_AVGRST) {
 903                 if(csp->avgrst)
 904                         mdrun->sattr|=SATTR_AVGRST;
 905                 else
 906                         mdrun->sattr&=(~(SATTR_AVGRST));
 907         }
 908         if(csp->type&CHSATTR_RSTEPS) {
 909                 mdrun->relax_steps=csp->rsteps;
 910         }
 911
 912         return 0;
 913 }
 914
 915 #define stage_print(m)  if(!(stage->executed)) \
 916                                 printf("%s",m)
 917
 918 int mdrun_hook(void *ptr1,void *ptr2) {
 919
 920         t_moldyn *moldyn;
 921         t_mdrun *mdrun;
 922         t_stage *stage;
 923         t_list *sl;
 924         int steps;
 925         u8 change_stage;
 926
 927         t_insert_atoms_params *iap;
 928         t_insert_mixed_atoms_params *imp;
 929         t_continue_params *cp;
 930         t_anneal_params *ap;
 931         t_set_temp_params *stp;
 932         t_set_timestep_params *stsp;
 933
 934         moldyn=ptr1;
 935         mdrun=ptr2;
 936
 937         sl=&(mdrun->stage);
 938
 939         change_stage=FALSE;
 940
 941         /* return immediately if there are no more stage */
 942         if(sl->current==NULL)
 943                 return 0;
 944
 945         /* get stage description */
 946         stage=sl->current->data;
 947
 948         /* steps in next schedule */
 949         steps=mdrun->relax_steps;
 950
 951         /* check whether relaxation steps are necessary */
 952         if((check_pressure(moldyn,mdrun)==TRUE)&\
 953            (check_temperature(moldyn,mdrun)==TRUE)) {
 954
 955                 /* be verbose */
 956                 stage_print("\n###########################\n");
 957                 stage_print("# [mdrun] executing stage #\n");
 958                 stage_print("###########################\n\n");
 959
 960                 /* stage specific stuff */
 961                 switch(stage->type) {
 962                         case STAGE_DISPLACE_ATOM:
 963                                 stage_print("  -> displace atom\n\n");
 964                                 displace_atom(moldyn,mdrun);
 965                                 change_stage=TRUE;
 966                                 break;
 967                         case STAGE_INSERT_ATOMS:
 968                                 stage_print("  -> insert atoms\n\n");
 969                                 iap=stage->params;
 970                                 if(iap->cnt_steps==iap->ins_steps) {
 971                                         change_stage=TRUE;
 972                                         break;
 973                                 }
 974                                 insert_atoms(moldyn,mdrun);
 975                                 iap->cnt_steps+=1;
 976                                 break;
 977
 978
 979
 980                         case STAGE_INSERT_MIXED_ATOMS:
 981                                 stage_print("  -> insert mixed atoms\n\n");
 982                                 imp=stage->params;
 983                                 insert_mixed_atoms(moldyn,mdrun);
 984                                 change_stage=TRUE;
 985                                 break;
 986
 987
 988
 989                         case STAGE_CONTINUE:
 990                                 stage_print("  -> continue\n\n");
 991                                 if(stage->executed==TRUE) {
 992                                         change_stage=TRUE;
 993                                         break;
 994                                 }
 995                                 cp=stage->params;
 996                                 steps=cp->runs;
 997                                 break;
 998                         case STAGE_ANNEAL:
 999                                 stage_print("  -> anneal\n\n");
1000                                 ap=stage->params;
1001                                 if(ap->count==ap->runs) {
1002                                         change_stage=TRUE;
1003                                         break;
1004                                 }
1005                                 if(moldyn->t_ref+ap->dt>=0.0)
1006                                         set_temperature(moldyn,
1007                                                         moldyn->t_ref+ap->dt);
1008                                 ap->count+=1;
1009                                 break;
1010                         case STAGE_CHAATTR:
1011                                 stage_print("  -> change atom attributes\n\n");
1012                                 chaatr(moldyn,mdrun);
1013                                 change_stage=TRUE;
1014                                 break;
1015                         case STAGE_CHSATTR:
1016                                 stage_print("  -> change sys attributes\n\n");
1017                                 chsattr(moldyn,mdrun);
1018                                 change_stage=TRUE;
1019                                 break;
1020                         case STAGE_SET_TEMP:
1021                                 stage_print("  -> set temperature\n\n");
1022                                 stp=stage->params;
1023                                 if(stp->type&SET_TEMP_CURRENT) {
1024                                         set_temperature(moldyn,moldyn->t_avg);
1025                                 }
1026                                 else {
1027                                         set_temperature(moldyn,stp->val);
1028                                 }
1029                                 change_stage=TRUE;
1030                                 break;
1031                         case STAGE_SET_TIMESTEP:
1032                                 stage_print("  -> set timestep\n\n");
1033                                 stsp=stage->params;
1034                                 mdrun->timestep=stsp->tau;
1035                                 change_stage=TRUE;
1036                                 break;
1037                         default:
1038                                 printf("%s unknwon stage type\n",ME);
1039                                 break;
1040                 }
1041
1042                 /* mark as executed */
1043                 stage->executed=TRUE;
1044
1045                 /* change state */
1046                 if(change_stage==TRUE) {
1047                         printf("%s finished stage\n",ME);
1048                         if(list_next_f(sl)==L_NO_NEXT_ELEMENT) {
1049                                 printf("%s no more stages\n",ME);
1050                                 return 0;
1051                         }
1052                         steps=0;
1053                 }
1054
1055         }
1056         else {
1057
1058                 /* averages */
1059                 if(mdrun->sattr&SATTR_AVGRST)
1060                         average_reset(moldyn);
1061
1062         }
1063
1064         /* continue simulation */
1065         moldyn_add_schedule(moldyn,steps,mdrun->timestep);
1066
1067         return 0;
1068 }
1069
1070 int main(int argc,char **argv) {
1071
1072         t_mdrun mdrun;
1073         t_moldyn moldyn;
1074         t_3dvec o;
1075
1076         /* clear structs */
1077         memset(&mdrun,0,sizeof(t_mdrun));
1078         memset(&moldyn,0,sizeof(t_moldyn));
1079
1080         /* parse arguments */
1081         if(mdrun_parse_argv(&mdrun,argc,argv)<0)
1082                 return -1;
1083
1084         /* initialize list system */
1085         list_init_f(&(mdrun.stage));
1086
1087         /* parse config file */
1088         mdrun_parse_config(&mdrun);
1089
1090         /* reset the stage list */
1091         list_reset_f(&(mdrun.stage));
1092
1093         /* sanity check! */
1094
1095         /* prepare simulation */
1096
1097         if(mdrun.continue_file[0]) {
1098                 // read the save file
1099                 moldyn_read_save_file(&moldyn,mdrun.continue_file);
1100                 // manualaadjusting some stuff
1101                 moldyn.argc=argc;
1102                 moldyn.args=argv;
1103                 rand_init(&(moldyn.random),NULL,1);
1104                 moldyn.random.status|=RAND_STAT_VERBOSE;
1105         }
1106         else {
1107                 moldyn_init(&moldyn,argc,argv);
1108         }
1109
1110         if(set_int_alg(&moldyn,mdrun.intalgo)<0)
1111                 return -1;
1112
1113         /* potential */
1114         set_cutoff(&moldyn,mdrun.cutoff);
1115         if(set_potential(&moldyn,mdrun.potential)<0)
1116                 return -1;
1117         switch(mdrun.potential) {
1118                 case MOLDYN_POTENTIAL_AM:
1119                         albe_mult_set_params(&moldyn,
1120                                              mdrun.element1,
1121                                              mdrun.element2);
1122                         break;
1123                 case MOLDYN_POTENTIAL_TM:
1124                         tersoff_mult_set_params(&moldyn,
1125                                                 mdrun.element1,
1126                                                 mdrun.element2);
1127                         break;
1128                 case MOLDYN_POTENTIAL_HO:
1129                         harmonic_oscillator_set_params(&moldyn,mdrun.element1);
1130                         break;
1131                 case MOLDYN_POTENTIAL_LJ:
1132                         lennard_jones_set_params(&moldyn,mdrun.element1);
1133                         break;
1134                 default:
1135                         printf("%s unknown potential: %02x\n",
1136                                ME,mdrun.potential);
1137                         return -1;
1138         }
1139
1140         /* if it is a continue run, reset schedule and skip lattice init */
1141         if(mdrun.continue_file[0]) {
1142                 memset(&(moldyn.schedule),0,sizeof(t_moldyn_schedule));
1143                 goto addsched;
1144         }
1145
1146         /* initial lattice and dimensions */
1147         set_dim(&moldyn,mdrun.dim.x,mdrun.dim.y,mdrun.dim.z,mdrun.vis);
1148         set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
1149         switch(mdrun.lattice) {
1150                 case FCC:
1151                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
1152                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
1153                                        mdrun.ly,mdrun.lz,NULL);
1154                         break;
1155                 case DIAMOND:
1156                         create_lattice(&moldyn,DIAMOND,mdrun.lc,mdrun.element1,
1157                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
1158                                        mdrun.ly,mdrun.lz,NULL);
1159                         break;
1160                 case ZINCBLENDE:
1161                         o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
1162                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
1163                                        mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
1164                                        mdrun.ly,mdrun.lz,&o);
1165                         o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
1166                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
1167                                        mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
1168                                        mdrun.ly,mdrun.lz,&o);
1169                         break;
1170                 case NONE:
1171                         set_nn_dist(&moldyn,mdrun.nnd);
1172                         break;
1173                 default:
1174                         printf("%s unknown lattice type: %02x\n",
1175                                ME,mdrun.lattice);
1176                         return -1;
1177         }
1178         moldyn_bc_check(&moldyn);
1179
1180         /* temperature and pressure */
1181         set_temperature(&moldyn,mdrun.temperature);
1182         set_pressure(&moldyn,mdrun.pressure);
1183         thermal_init(&moldyn,TRUE);
1184
1185 addsched:
1186         /* first schedule */
1187         moldyn_add_schedule(&moldyn,mdrun.prerun,mdrun.timestep);
1188
1189         /* log */
1190         moldyn_set_log_dir(&moldyn,mdrun.sdir);
1191         moldyn_set_report(&moldyn,"CHANGE ME","CHANGE ME TOO");
1192         if(mdrun.elog)
1193                 moldyn_set_log(&moldyn,LOG_TOTAL_ENERGY,mdrun.elog);
1194         if(mdrun.tlog)
1195                 moldyn_set_log(&moldyn,LOG_TEMPERATURE,mdrun.tlog);
1196         if(mdrun.plog)
1197                 moldyn_set_log(&moldyn,LOG_PRESSURE,mdrun.plog);
1198         if(mdrun.vlog)
1199                 moldyn_set_log(&moldyn,LOG_VOLUME,mdrun.vlog);
1200         if(mdrun.visualize)
1201                 moldyn_set_log(&moldyn,VISUAL_STEP,mdrun.visualize);
1202         if(mdrun.save)
1203                 moldyn_set_log(&moldyn,SAVE_STEP,mdrun.save);
1204         moldyn_set_log(&moldyn,CREATE_REPORT,0);
1205         set_avg_skip(&moldyn,mdrun.avgskip);
1206
1207         /* prepare the hook function */
1208         moldyn_set_schedule_hook(&moldyn,&mdrun_hook,&mdrun);
1209
1210         /* run the simulation */
1211         moldyn_integrate(&moldyn);
1212
1213         /* shutdown */
1214         moldyn_shutdown(&moldyn);
1215         del_stages(&mdrun);
1216         list_destroy_f(&(mdrun.stage));
1217
1218         return 0;
1219 }