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 mdrun_parse_config(t_mdrun *mdrun) {
  66
  67         int fd,ret;
  68         char error[128];
  69         char line[128];
  70         char *wptr;
  71         char word[16][32];
  72         int wcnt;
  73
  74         /* open config file */
  75         fd=open(mdrun->cfile,O_RDONLY);
  76         if(fd<0) {
  77                 snprintf(error,128,"%s open cfile %s",ME,mdrun->cfile);
  78                 perror(error);
  79                 return fd;
  80         }
  81
  82         /* read, parse, set */
  83         ret=1;
  84         while(ret>0) {
  85
  86                 /* read */
  87                 ret=get_line(fd,line,128);
  88
  89                 /* parse */
  90
  91                 // ignore # lines and \n
  92                 if((line[0]=='#')|(ret==1))
  93                         continue;
  94
  95                 // get command + args
  96                 wcnt=0;
  97                 while(1) {
  98                         if(wcnt)
  99                                 wptr=strtok(NULL," \t");
 100                         else
 101                                 wptr=strtok(line," \t");
 102                         if(wptr==NULL)
 103                                 break;
 104                         strncpy(word[wcnt],wptr,32);
 105                         wcnt+=1;
 106                 }
 107
 108                 if(!strncmp(word[0],"potential",9)) {
 109                         if(!strncmp(word[1],"albe",4))
 110                                 mdrun->potential=MOLDYN_POTENTIAL_AM;
 111                         if(!strncmp(word[1],"tersoff",7))
 112                                 mdrun->potential=MOLDYN_POTENTIAL_TM;
 113                         if(!strncmp(word[1],"ho",2))
 114                                 mdrun->potential=MOLDYN_POTENTIAL_HO;
 115                         if(!strncmp(word[1],"lj",2))
 116                                 mdrun->potential=MOLDYN_POTENTIAL_LJ;
 117                 }
 118                 else if(!strncmp(word[0],"cutoff",6))
 119                         mdrun->cutoff=atof(word[1]);
 120                 else if(!strncmp(word[0],"intalgo",7)) {
 121                         if(!strncmp(word[1],"verlet",5))
 122                                 mdrun->intalgo=MOLDYN_INTEGRATE_VERLET;
 123                 }
 124                 else if(!strncmp(word[0],"timestep",8))
 125                         mdrun->timestep=atof(word[1]);
 126                 else if(!strncmp(word[0],"volume",6)) {
 127                         mdrun->dim.x=atof(word[1]);
 128                         mdrun->dim.y=atof(word[2]);
 129                         mdrun->dim.z=atof(word[3]);
 130                         if(strncmp(word[4],"0",1))
 131                                 mdrun->vis=TRUE;
 132                 }
 133                 else if(!strncmp(word[0],"pbc",3)) {
 134                         if(strncmp(word[1],"0",1))
 135                                 mdrun->pbcx=TRUE;
 136                         else
 137                                 mdrun->pbcx=FALSE;
 138                         if(strncmp(word[2],"0",1))
 139                                 mdrun->pbcy=TRUE;
 140                         else
 141                                 mdrun->pbcy=FALSE;
 142                         if(strncmp(word[3],"0",1))
 143                                 mdrun->pbcz=TRUE;
 144                         else
 145                                 mdrun->pbcz=FALSE;
 146                 }
 147                 else if(!strncmp(word[0],"temperature",11))
 148                         mdrun->temperature=atof(word[1]);
 149                 else if(!strncmp(word[0],"pressure",8))
 150                         mdrun->pressure=atof(word[1]);
 151                 else if(!strncmp(word[0],"lattice",7)) {
 152                         if(!strncmp(word[1],"zincblende",10))
 153                                 mdrun->lattice=ZINCBLENDE;
 154                         if(!strncmp(word[1],"fcc",3))
 155                                 mdrun->lattice=FCC;
 156                         if(!strncmp(word[1],"diamond",7))
 157                                 mdrun->lattice=DIAMOND;
 158                 }
 159                 else if(!strncmp(word[0],"element1",8)) {
 160                         mdrun->element1=atoi(word[1]);
 161                         switch(mdrun->element1) {
 162                                 case SI:
 163                                         mdrun->m1=M_SI;
 164                                         break;
 165                                 case C:
 166                                         mdrun->m1=M_C;
 167                                         break;
 168                                 default:
 169                                         printf("%s unknown element1: %s|%d\n",
 170                                                ME,word[1],mdrun->element1);
 171                                         return -1;
 172                         }
 173                 }
 174                 else if(!strncmp(word[0],"element2",8)) {
 175                         mdrun->element2=atoi(word[1]);
 176                         switch(mdrun->element2) {
 177                                 case SI:
 178                                         mdrun->m2=M_SI;
 179                                         break;
 180                                 case C:
 181                                         mdrun->m2=M_C;
 182                                         break;
 183                                 default:
 184                                         printf("%s unknown element2: %s|%d\n",
 185                                                ME,word[1],mdrun->element2);
 186                                         return -1;
 187                         }
 188                 }
 189                 else if(!strncmp(word[0],"filllc",6)) {
 190                         mdrun->lx=atoi(word[1]);
 191                         mdrun->ly=atoi(word[2]);
 192                         mdrun->lz=atoi(word[3]);
 193                 }
 194                 else if(!strncmp(word[0],"aattrib",7)) {
 195                         // for aatrib line we need a special stage
 196                         // containing one schedule of 0 loops ...
 197                         printf("%s aattrib: %s\n",ME,word[1]);
 198                 }
 199                 else if(!strncmp(word[0],"eattrib",7)) {
 200                         mdrun->p_tau=atof(word[1]);
 201                         mdrun->t_tau=atof(word[2]);
 202                 }
 203                 else if(!strncmp(word[0],"prerun",6))
 204                         mdrun->prerun=atoi(word[1]);
 205                 else if(!strncmp(word[0],"avgskip",7))
 206                         mdrun->avgskip=atoi(word[1]);
 207                 else if(!strncmp(word[0],"elog",4))
 208                         mdrun->elog=atoi(word[1]);
 209                 else if(!strncmp(word[0],"tlog",4))
 210                         mdrun->tlog=atoi(word[1]);
 211                 else if(!strncmp(word[0],"plog",4))
 212                         mdrun->plog=atoi(word[1]);
 213                 else if(!strncmp(word[0],"vlog",4))
 214                         mdrun->vlog=atoi(word[1]);
 215                 else if(!strncmp(word[0],"save",4))
 216                         mdrun->save=atoi(word[1]);
 217                 else if(!strncmp(word[0],"visualize",9))
 218                         mdrun->visualize=atoi(word[1]);
 219                 else if(!strncmp(word[0],"stage",5)) {
 220                         // for every stage line, add a stage
 221                         printf("%s stage: %s\n",ME,word[1]);
 222                 }
 223                 else {
 224                         printf("%s unknown command %s, skipped!\n",ME,wptr);
 225                         continue;
 226                 }
 227         }
 228
 229         return 0;
 230 }
 231
 232 int main(int argc,char **argv) {
 233
 234         t_mdrun mdrun;
 235         t_moldyn moldyn;
 236         t_3dvec o;
 237
 238         /* clear mdrun struct */
 239         memset(&mdrun,0,sizeof(t_mdrun));
 240
 241         /* parse arguments */
 242         if(mdrun_parse_argv(&mdrun,argc,argv)<0)
 243                 return -1;
 244
 245         /* parse config file */
 246         mdrun_parse_config(&mdrun);
 247
 248         /* sanity check! */
 249
 250         /* prepare simulation */
 251         moldyn_init(&moldyn,argc,argv);
 252         if(set_int_alg(&moldyn,mdrun.intalgo)<0)
 253                 return -1;
 254         set_cutoff(&moldyn,mdrun.cutoff);
 255         if(set_potential(&moldyn,mdrun.potential)<0)
 256                 return -1;
 257         switch(mdrun.potential) {
 258                 case MOLDYN_POTENTIAL_AM:
 259                         albe_mult_set_params(&moldyn,
 260                                              mdrun.element1,
 261                                              mdrun.element2);
 262                         break;
 263                 case MOLDYN_POTENTIAL_TM:
 264                         tersoff_mult_set_params(&moldyn,
 265                                                 mdrun.element1,
 266                                                 mdrun.element2);
 267                         break;
 268                 case MOLDYN_POTENTIAL_HO:
 269                         harmonic_oscillator_set_params(&moldyn,mdrun.element1);
 270                         break;
 271                 case MOLDYN_POTENTIAL_LJ:
 272                         lennard_jones_set_params(&moldyn,mdrun.element1);
 273                         break;
 274                 default:
 275                         printf("%s unknown potential: %02x\n",
 276                                ME,mdrun.potential);
 277                         return -1;
 278         }
 279         set_dim(&moldyn,mdrun.dim.x,mdrun.dim.y,mdrun.dim.z,mdrun.vis);
 280         set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
 281         switch(mdrun.lattice) {
 282                 case FCC:
 283                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
 284                                        mdrun.m1,0,0,mdrun.lx,
 285                                        mdrun.ly,mdrun.lz,NULL);
 286                         break;
 287                 case DIAMOND:
 288                         create_lattice(&moldyn,DIAMOND,mdrun.lc,mdrun.element1,
 289                                        mdrun.m1,0,0,mdrun.lx,
 290                                        mdrun.ly,mdrun.lz,NULL);
 291                         break;
 292                 case ZINCBLENDE:
 293                         o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
 294                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
 295                                        mdrun.m1,0,0,mdrun.lx,
 296                                        mdrun.ly,mdrun.lz,&o);
 297                         o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
 298                         create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
 299                                        mdrun.m2,0,0,mdrun.lx,
 300                                        mdrun.ly,mdrun.lz,&o);
 301                         break;
 302                 default:
 303                         printf("%s unknown lattice type: %02x\n",
 304                                ME,mdrun.lattice);
 305                         return -1;
 306         }
 307         moldyn_bc_check(&moldyn);
 308         set_temperature(&moldyn,mdrun.temperature);
 309         set_pressure(&moldyn,mdrun.pressure);
 310         thermal_init(&moldyn,TRUE);
 311         moldyn_add_schedule(&moldyn,mdrun.prerun,mdrun.timestep);
 312         moldyn_set_log_dir(&moldyn,mdrun.sdir);
 313         moldyn_set_report(&moldyn,"CHANGE ME","CHANGE ME TOO");
 314         if(mdrun.elog)
 315                 moldyn_set_log(&moldyn,LOG_TOTAL_ENERGY,mdrun.elog);
 316         if(mdrun.tlog)
 317                 moldyn_set_log(&moldyn,LOG_TEMPERATURE,mdrun.tlog);
 318         if(mdrun.plog)
 319                 moldyn_set_log(&moldyn,LOG_PRESSURE,mdrun.plog);
 320         if(mdrun.vlog)
 321                 moldyn_set_log(&moldyn,LOG_VOLUME,mdrun.vlog);
 322         if(mdrun.visualize)
 323                 moldyn_set_log(&moldyn,VISUAL_STEP,mdrun.visualize);
 324         if(mdrun.save)
 325                 moldyn_set_log(&moldyn,SAVE_STEP,mdrun.save);
 326         moldyn_set_log(&moldyn,CREATE_REPORT,0);
 327         set_avg_skip(&moldyn,mdrun.avgskip);
 328
 329         /* prepare the hook function */
 330
 331         /* run the simulation */
 332         moldyn_integrate(&moldyn);
 333
 334         /* shutdown */
 335         moldyn_shutdown(&moldyn);
 336
 337         return 0;
 338 }