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