2 * mdrun.c - main code to run a md simulation
4 * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
11 #include "potentials/harmonic_oscillator.h"
12 #include "potentials/lennard_jones.h"
13 #include "potentials/albe.h"
15 #include "potentials/tersoff_orig.h"
17 #include "potentials/tersoff.h"
31 int mdrun_usage(void) {
33 printf("%s usage:\n",ME);
38 int mdrun_parse_argv(t_mdrun *mdrun,int argc,char **argv) {
45 printf("%s unknown switch: %s\n",ME,argv[i]);
51 strncpy(mdrun->cfile,argv[++i],128);
54 strncpy(mdrun->sdir,argv[++i],128);
60 printf("%s unknown option: %s\n",ME,argv[i]);
70 int del_stages(t_mdrun *mdrun) {
83 stage=sl->current->data;
86 } while(list_next_f(sl)!=L_NO_NEXT_ELEMENT);
91 int add_stage(t_mdrun *mdrun,u8 type,void *params) {
98 case STAGE_DISPLACE_ATOM:
99 psize=sizeof(t_displace_atom_params);
101 case STAGE_INSERT_ATOMS:
102 psize=sizeof(t_insert_atoms_params);
104 case STAGE_INSERT_MIXED_ATOMS:
105 psize=sizeof(t_insert_mixed_atoms_params);
108 psize=sizeof(t_continue_params);
111 psize=sizeof(t_anneal_params);
114 psize=sizeof(t_chaattr_params);
117 psize=sizeof(t_chsattr_params);
120 psize=sizeof(t_set_temp_params);
122 case STAGE_SET_TIMESTEP:
123 psize=sizeof(t_set_timestep_params);
126 psize=sizeof(t_fill_params);
128 case STAGE_THERMAL_INIT:
132 printf("%s unknown stage type: %02x\n",ME,type);
136 stage=malloc(sizeof(t_stage));
138 perror("[mdrun] malloc (add stage)");
143 stage->executed=FALSE;
145 stage->params=malloc(psize);
146 if(stage->params==NULL) {
147 perror("[mdrun] malloc (stage params)");
151 memcpy(stage->params,params,psize);
153 list_add_immediate_f(&(mdrun->stage),stage);
158 int mdrun_parse_config(t_mdrun *mdrun) {
168 t_displace_atom_params dap;
169 t_insert_atoms_params iap;
170 t_insert_mixed_atoms_params imp;
171 t_continue_params cp;
173 t_chaattr_params cap;
174 t_chsattr_params csp;
175 t_set_temp_params stp;
176 t_set_timestep_params stsp;
179 /* open config file */
180 fd=open(mdrun->cfile,O_RDONLY);
182 snprintf(error,128,"%s open cfile %s",ME,mdrun->cfile);
187 /* read, parse, set */
192 ret=get_line(fd,line,128);
196 // ignore # lines and \n
197 if((line[0]=='#')|(ret==1))
201 memset(&iap,0,sizeof(t_insert_atoms_params));
202 memset(&imp,0,sizeof(t_insert_mixed_atoms_params));
203 memset(&cp,0,sizeof(t_continue_params));
204 memset(&ap,0,sizeof(t_anneal_params));
205 memset(&cap,0,sizeof(t_chaattr_params));
206 memset(&csp,0,sizeof(t_chsattr_params));
207 memset(&stp,0,sizeof(t_set_temp_params));
208 memset(&stsp,0,sizeof(t_set_timestep_params));
209 memset(&fp,0,sizeof(t_fill_params));
211 // get command + args
215 wptr=strtok(NULL," \t");
217 wptr=strtok(line," \t");
220 strncpy(word[wcnt],wptr,64);
224 if(!strncmp(word[0],"potential",9)) {
225 if(!strncmp(word[1],"albe",4))
226 mdrun->potential=MOLDYN_POTENTIAL_AM;
227 if(!strncmp(word[1],"tersoff",7))
228 mdrun->potential=MOLDYN_POTENTIAL_TM;
229 if(!strncmp(word[1],"ho",2))
230 mdrun->potential=MOLDYN_POTENTIAL_HO;
231 if(!strncmp(word[1],"lj",2))
232 mdrun->potential=MOLDYN_POTENTIAL_LJ;
234 else if(!strncmp(word[0],"continue",8))
235 strncpy(mdrun->continue_file,word[1],128);
236 else if(!strncmp(word[0],"cutoff",6))
237 mdrun->cutoff=atof(word[1]);
238 else if(!strncmp(word[0],"nnd",3))
239 mdrun->nnd=atof(word[1]);
240 else if(!strncmp(word[0],"intalgo",7)) {
241 if(!strncmp(word[1],"verlet",5))
242 mdrun->intalgo=MOLDYN_INTEGRATE_VERLET;
244 else if(!strncmp(word[0],"timestep",8))
245 mdrun->timestep=atof(word[1]);
246 else if(!strncmp(word[0],"volume",6)) {
247 mdrun->dim.x=atof(word[1]);
248 mdrun->dim.y=atof(word[2]);
249 mdrun->dim.z=atof(word[3]);
250 if(strncmp(word[4],"0",1))
253 else if(!strncmp(word[0],"pbc",3)) {
254 if(strncmp(word[1],"0",1))
258 if(strncmp(word[2],"0",1))
262 if(strncmp(word[3],"0",1))
267 else if(!strncmp(word[0],"temperature",11))
268 mdrun->temperature=atof(word[1]);
269 else if(!strncmp(word[0],"pressure",8))
270 mdrun->pressure=atof(word[1]);
271 else if(!strncmp(word[0],"lattice",7)) {
272 if(!strncmp(word[1],"zincblende",10))
273 mdrun->lattice=ZINCBLENDE;
274 if(!strncmp(word[1],"fcc",3))
276 if(!strncmp(word[1],"diamond",7))
277 mdrun->lattice=DIAMOND;
278 if(!strncmp(word[1],"none",4))
281 mdrun->lc=atof(word[2]);
283 else if(!strncmp(word[0],"element1",8)) {
284 mdrun->element1=atoi(word[1]);
286 else if(!strncmp(word[0],"element2",8)) {
287 mdrun->element2=atoi(word[1]);
289 else if(!strncmp(word[0],"fill",6)) {
291 fp.fill_element=mdrun->element1;
293 fp.lattice=mdrun->lattice;
296 // parse fill command
299 if(!strncmp(word[i],"lc",2)) {
300 fp.lx=atoi(word[++i]);
301 fp.ly=atoi(word[++i]);
302 fp.lz=atoi(word[++i]);
303 fp.lc=atof(word[++i]);
306 if(!strncmp(word[i],"eb",2)) {
307 fp.fill_element=atoi(word[++i]);
308 fp.fill_brand=atoi(word[++i]);
310 if(word[i][0]=='p') {
315 fp.p_params.type=PART_INSIDE_R;
317 fp.p_params.type=PART_INSIDE_D;
321 fp.p_params.type=PART_OUTSIDE_R;
323 fp.p_params.type=PART_OUTSIDE_D;
328 if((fp.p_params.type==PART_INSIDE_R)||
329 (fp.p_params.type==PART_OUTSIDE_R)) {
330 fp.p_params.r=atof(word[++i]);
331 fp.p_params.p.x=atof(word[++i]);
332 fp.p_params.p.y=atof(word[++i]);
333 fp.p_params.p.z=atof(word[++i]);
335 if((fp.p_params.type==PART_INSIDE_D)||
336 (fp.p_params.type==PART_OUTSIDE_D)) {
337 fp.p_params.p.x=atof(word[++i]);
338 fp.p_params.p.y=atof(word[++i]);
339 fp.p_params.p.z=atof(word[++i]);
340 fp.p_params.d.x=atof(word[++i]);
341 fp.p_params.d.y=atof(word[++i]);
342 fp.p_params.d.z=atof(word[++i]);
345 if(word[i][0]=='d') {
346 switch(word[++i][0]) {
349 fp.d_params.type=DEFECT_TYPE_0D;
350 if(!strncmp(word[i+1],"dbx",3)) {
351 fp.d_params.stype=DEFECT_STYPE_DB_X;
353 if(!strncmp(word[i+1],"dby",3)) {
354 fp.d_params.stype=DEFECT_STYPE_DB_Y;
356 if(!strncmp(word[i+1],"dbz",3)) {
357 fp.d_params.stype=DEFECT_STYPE_DB_Z;
359 if(!strncmp(word[i+1],"dbr",3)) {
360 fp.d_params.stype=DEFECT_STYPE_DB_R;
363 fp.d_params.od=atof(word[++i]);
364 fp.d_params.dd=atof(word[++i]);
365 fp.d_params.element=atoi(word[++i]);
366 fp.d_params.brand=atoi(word[++i]);
368 fp.d_params.attr=ATOM_ATTR_HB|ATOM_ATTR_VA;
369 fp.d_params.attr|=ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP;
373 fp.d_params.type=DEFECT_TYPE_1D;
376 fp.d_params.type=DEFECT_TYPE_2D;
379 fp.d_params.type=DEFECT_TYPE_3D;
388 add_stage(mdrun,STAGE_FILL,&fp);
390 else if(!strncmp(word[0],"thermal_init",12)) {
391 add_stage(mdrun,STAGE_THERMAL_INIT,NULL);
393 else if(!strncmp(word[0],"aattr",5)) {
394 // for aatrib line we need a special stage
395 // containing one schedule of 0 loops ...
396 for(i=0;i<strlen(word[1]);i++) {
399 cap.type|=CHAATTR_TOTALV;
402 cap.type|=CHAATTR_REGION;
405 cap.type|=CHAATTR_ELEMENT;
412 if(cap.type&CHAATTR_REGION) {
413 cap.x0=atof(word[1]);
414 cap.y0=atof(word[2]);
415 cap.z0=atof(word[3]);
416 cap.x1=atof(word[4]);
417 cap.y1=atof(word[5]);
418 cap.z1=atof(word[6]);
421 if(cap.type&CHAATTR_ELEMENT) {
422 cap.element=atoi(word[i]);
425 for(o=0;o<strlen(word[i]);o++) {
428 cap.attr|=ATOM_ATTR_VB;
431 cap.attr|=ATOM_ATTR_HB;
434 cap.attr|=ATOM_ATTR_VA;
437 cap.attr|=ATOM_ATTR_FP;
440 cap.attr|=ATOM_ATTR_1BP;
443 cap.attr|=ATOM_ATTR_2BP;
446 cap.attr|=ATOM_ATTR_3BP;
452 add_stage(mdrun,STAGE_CHAATTR,&cap);
454 else if(!strncmp(word[0],"sattr",5)) {
455 // for satrib line we need a special stage
456 // containing one schedule of 0 loops ...
458 for(i=1;i<wcnt;i++) {
459 if(!strncmp(word[i],"pctrl",5)) {
460 csp.ptau=0.01/(atof(word[++i])*GPA);
461 csp.type|=CHSATTR_PCTRL;
463 if(!strncmp(word[i],"tctrl",5)) {
464 csp.ttau=atof(word[++i]);
465 csp.type|=CHSATTR_TCTRL;
467 if(!strncmp(word[i],"prelax",6)) {
468 csp.dp=atof(word[++i])*BAR;
469 csp.type|=CHSATTR_PRELAX;
471 if(!strncmp(word[i],"trelax",6)) {
472 csp.dt=atof(word[++i]);
473 csp.type|=CHSATTR_TRELAX;
475 if(!strncmp(word[i],"rsteps",6)) {
476 csp.rsteps=atoi(word[++i]);
477 csp.type|=CHSATTR_RSTEPS;
479 if(!strncmp(word[i],"avgrst",6)) {
480 csp.avgrst=atoi(word[++i]);
481 csp.type|=CHSATTR_AVGRST;
484 add_stage(mdrun,STAGE_CHSATTR,&csp);
486 else if(!strncmp(word[0],"prerun",6))
487 mdrun->prerun=atoi(word[1]);
488 else if(!strncmp(word[0],"avgskip",7))
489 mdrun->avgskip=atoi(word[1]);
490 else if(!strncmp(word[0],"elog",4))
491 mdrun->elog=atoi(word[1]);
492 else if(!strncmp(word[0],"tlog",4))
493 mdrun->tlog=atoi(word[1]);
494 else if(!strncmp(word[0],"plog",4))
495 mdrun->plog=atoi(word[1]);
496 else if(!strncmp(word[0],"vlog",4))
497 mdrun->vlog=atoi(word[1]);
498 else if(!strncmp(word[0],"save",4))
499 mdrun->save=atoi(word[1]);
500 else if(!strncmp(word[0],"visualize",9))
501 mdrun->visualize=atoi(word[1]);
502 else if(!strncmp(word[0],"stage",5)) {
503 // for every stage line, add a stage
504 if(!strncmp(word[1],"displace",8)) {
505 dap.nr=atoi(word[2]);
506 dap.dx=atof(word[3]);
507 dap.dy=atof(word[4]);
508 dap.dz=atof(word[5]);
509 add_stage(mdrun,STAGE_DISPLACE_ATOM,&dap);
511 else if(!strncmp(word[1],"ins_atoms",9)) {
512 iap.ins_steps=atoi(word[2]);
513 iap.ins_atoms=atoi(word[3]);
514 iap.element=atoi(word[4]);
515 iap.brand=atoi(word[5]);
516 for(i=0;i<strlen(word[6]);i++) {
519 iap.attr|=ATOM_ATTR_VB;
522 iap.attr|=ATOM_ATTR_HB;
525 iap.attr|=ATOM_ATTR_VA;
528 iap.attr|=ATOM_ATTR_FP;
531 iap.attr|=ATOM_ATTR_1BP;
534 iap.attr|=ATOM_ATTR_2BP;
537 iap.attr|=ATOM_ATTR_3BP;
547 iap.x0=atof(word[8]);
548 iap.y0=atof(word[9]);
549 iap.z0=atof(word[10]);
552 if(word[8][0]=='t') {
554 iap.cr=atof(word[9]);
558 iap.x0=atof(word[8]);
559 iap.y0=atof(word[9]);
560 iap.z0=atof(word[10]);
561 iap.x1=atof(word[11]);
562 iap.y1=atof(word[12]);
563 iap.z1=atof(word[13]);
564 iap.cr=atof(word[14]);
569 add_stage(mdrun,STAGE_INSERT_ATOMS,&iap);
575 else if(!strncmp(word[1],"ins_m_atoms",11)) {
576 imp.element1=atoi(word[2]);
577 imp.element2=atoi(word[3]);
578 imp.amount1=atoi(word[4]);
579 imp.amount2=atoi(word[5]);
580 imp.brand1=atoi(word[6]);
581 imp.brand2=atoi(word[7]);
582 imp.crmin=atof(word[8]);
583 imp.crmax=atof(word[9]);
585 for(i=0;i<strlen(word[8]);i++) {
588 imp.attr|=ATOM_ATTR_VB;
591 imp.attr|=ATOM_ATTR_HB;
594 imp.attr|=ATOM_ATTR_VA;
597 imp.attr|=ATOM_ATTR_FP;
600 imp.attr|=ATOM_ATTR_1BP;
603 imp.attr|=ATOM_ATTR_2BP;
606 imp.attr|=ATOM_ATTR_3BP;
613 imp.attr1=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
614 imp.attr2=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
615 add_stage(mdrun,STAGE_INSERT_MIXED_ATOMS,&imp);
622 else if(!strncmp(word[1],"continue",8)) {
623 cp.runs=atoi(word[2]);
624 add_stage(mdrun,STAGE_CONTINUE,&cp);
626 else if(!strncmp(word[1],"anneal",6)) {
628 ap.runs=atoi(word[2]);
630 ap.interval=atoi(word[4]);
631 add_stage(mdrun,STAGE_ANNEAL,&ap);
633 else if(!strncmp(word[1],"set_temp",8)) {
634 if(word[2][0]=='c') {
635 stp.type=SET_TEMP_CURRENT;
639 stp.type=SET_TEMP_VALUE;
640 stp.val=atof(word[2]);
642 add_stage(mdrun,STAGE_SET_TEMP,&stp);
644 else if(!strncmp(word[1],"set_timestep",12)) {
645 stsp.tau=atof(word[2]);
646 add_stage(mdrun,STAGE_SET_TIMESTEP,&stsp);
649 printf("%s unknown stage type: %s\n",
655 printf("%s unknown keyword '%s', skipped!\n",
667 int check_pressure(t_moldyn *moldyn,t_mdrun *mdrun) {
671 if(!(mdrun->sattr&SATTR_PRELAX)) {
675 delta=moldyn->p_avg-moldyn->p_ref;
686 int check_temperature(t_moldyn *moldyn,t_mdrun *mdrun) {
690 if(!(mdrun->sattr&SATTR_TRELAX))
693 delta=moldyn->t_avg-moldyn->t_ref;
704 int displace_atom(t_moldyn *moldyn,t_mdrun *mdrun) {
706 t_displace_atom_params *dap;
710 stage=mdrun->stage.current->data;
713 atom=&(moldyn->atom[dap->nr]);
721 int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
723 t_insert_atoms_params *iap;
733 stage=mdrun->stage.current->data;
738 v.x=0.0; v.y=0.0; v.z=0.0;
742 switch(mdrun->lattice) {
783 printf("%s unknown insertion mode: %02x\n",
789 while(cnt<iap->ins_atoms) {
792 if(iap->type!=INS_POS) {
793 r.x=rand_get_double(&(moldyn->random))*x;
794 r.y=rand_get_double(&(moldyn->random))*y;
795 r.z=rand_get_double(&(moldyn->random))*z;
806 if(iap->type!=INS_TOTAL) {
813 dmin=1000; // for sure too high!
814 for(i=0;i<moldyn->count;i++) {
815 atom=&(moldyn->atom[i]);
816 v3_sub(&dist,&(atom->r),&r);
817 check_per_bound(moldyn,&dist);
818 d=v3_absolute_square(&dist);
819 if(d<(iap->cr*iap->cr)) {
828 add_atom(moldyn,iap->element,
829 iap->brand,iap->attr,&r,&v);
830 printf("%s atom inserted (%d/%d): %f %f %f\n",
831 ME,(iap->cnt_steps+1)*iap->ins_atoms,
832 iap->ins_steps*iap->ins_atoms,r.x,r.y,r.z);
833 printf(" -> d2 = %f/%f\n",dmin,iap->cr*iap->cr);
840 int insert_mixed_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
843 t_insert_mixed_atoms_params *imp;
845 double x,x0,y,y0,z,z0;
846 double dmin,d,cmin,cmax;
852 stage=mdrun->stage.current->data;
866 cmin=imp->crmin*imp->crmin;
867 cmax=imp->crmax*imp->crmax;
869 while(imp->amount1|imp->amount2) {
874 r.x=rand_get_double(&(moldyn->random))*x;
875 r.y=rand_get_double(&(moldyn->random))*y;
876 r.z=rand_get_double(&(moldyn->random))*z;
880 dmin=1000.0; // for sure too high!
881 for(i=0;i<moldyn->count;i++) {
882 atom=&(moldyn->atom[i]);
883 v3_sub(&dist,&(atom->r),&r);
884 check_per_bound(moldyn,&dist);
885 d=v3_absolute_square(&dist);
897 add_atom(moldyn,imp->element1,
898 imp->brand1,imp->attr1,&r,&v);
899 printf("%s (mixed) atom inserted (%d): %f %f %f\n",
900 ME,imp->amount1,r.x,r.y,r.z);
901 printf(" -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
908 r.x=rand_get_double(&(moldyn->random))*x;
909 r.y=rand_get_double(&(moldyn->random))*y;
910 r.z=rand_get_double(&(moldyn->random))*z;
914 dmin=1000.0; // for sure too high!
915 for(i=0;i<moldyn->count;i++) {
916 atom=&(moldyn->atom[i]);
917 v3_sub(&dist,&(atom->r),&r);
918 check_per_bound(moldyn,&dist);
919 d=v3_absolute_square(&dist);
931 add_atom(moldyn,imp->element2,
932 imp->brand2,imp->attr2,&r,&v);
933 printf("%s (mixed) atom inserted (%d): %f %f %f\n",
934 ME,imp->amount2,r.x,r.y,r.z);
935 printf(" -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
943 int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
946 t_chaattr_params *cap;
950 stage=mdrun->stage.current->data;
953 for(i=0;i<moldyn->count;i++) {
954 atom=&(moldyn->atom[i]);
955 if(cap->type&CHAATTR_ELEMENT) {
956 if(cap->element!=atom->element)
959 if(cap->type&CHAATTR_REGION) {
960 if(cap->x0<atom->r.x)
962 if(cap->y0<atom->r.y)
964 if(cap->z0<atom->r.z)
966 if(cap->x1>atom->r.x)
968 if(cap->y1>atom->r.y)
970 if(cap->z1>atom->r.z)
973 atom->attr=cap->attr;
979 int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
982 t_chsattr_params *csp;
984 stage=mdrun->stage.current->data;
987 if(csp->type&CHSATTR_PCTRL) {
989 set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
991 set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
993 if(csp->type&CHSATTR_TCTRL) {
995 set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
997 set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
999 if(csp->type&CHSATTR_PRELAX) {
1001 mdrun->sattr&=(~(SATTR_PRELAX));
1003 mdrun->sattr|=SATTR_PRELAX;
1006 if(csp->type&CHSATTR_TRELAX) {
1008 mdrun->sattr&=(~(SATTR_TRELAX));
1010 mdrun->sattr|=SATTR_TRELAX;
1013 if(csp->type&CHSATTR_AVGRST) {
1015 mdrun->sattr|=SATTR_AVGRST;
1017 mdrun->sattr&=(~(SATTR_AVGRST));
1019 if(csp->type&CHSATTR_RSTEPS) {
1020 mdrun->relax_steps=csp->rsteps;
1026 #define stage_print(m) if(!(stage->executed)) \
1029 int mdrun_hook(void *ptr1,void *ptr2) {
1039 t_insert_atoms_params *iap;
1040 t_insert_mixed_atoms_params *imp;
1041 t_continue_params *cp;
1042 t_anneal_params *ap;
1043 t_set_temp_params *stp;
1044 t_set_timestep_params *stsp;
1054 /* return immediately if there are no more stage */
1055 if(sl->current==NULL)
1058 /* get stage description */
1059 stage=sl->current->data;
1061 /* steps in next schedule */
1062 steps=mdrun->relax_steps;
1064 /* check whether relaxation steps are necessary */
1065 if((check_pressure(moldyn,mdrun)==TRUE)&\
1066 (check_temperature(moldyn,mdrun)==TRUE)) {
1069 stage_print("\n###########################\n");
1070 stage_print("# [mdrun] executing stage #\n");
1071 stage_print("###########################\n\n");
1073 /* stage specific stuff */
1074 switch(stage->type) {
1075 case STAGE_DISPLACE_ATOM:
1076 stage_print(" -> displace atom\n\n");
1077 displace_atom(moldyn,mdrun);
1080 case STAGE_INSERT_ATOMS:
1081 stage_print(" -> insert atoms\n\n");
1083 if(iap->cnt_steps==iap->ins_steps) {
1087 insert_atoms(moldyn,mdrun);
1093 case STAGE_INSERT_MIXED_ATOMS:
1094 stage_print(" -> insert mixed atoms\n\n");
1096 insert_mixed_atoms(moldyn,mdrun);
1102 case STAGE_CONTINUE:
1103 stage_print(" -> continue\n\n");
1104 if(stage->executed==TRUE) {
1112 stage_print(" -> anneal\n\n");
1114 if(ap->count==ap->runs) {
1118 if(moldyn->t_ref+ap->dt>=0.0)
1119 set_temperature(moldyn,
1120 moldyn->t_ref+ap->dt);
1125 stage_print(" -> change atom attributes\n\n");
1126 chaatr(moldyn,mdrun);
1130 stage_print(" -> change sys attributes\n\n");
1131 chsattr(moldyn,mdrun);
1134 case STAGE_SET_TEMP:
1135 stage_print(" -> set temperature\n\n");
1137 if(stp->type&SET_TEMP_CURRENT) {
1138 set_temperature(moldyn,moldyn->t_avg);
1141 set_temperature(moldyn,stp->val);
1145 case STAGE_SET_TIMESTEP:
1146 stage_print(" -> set timestep\n\n");
1148 mdrun->timestep=stsp->tau;
1152 stage_print(" -> fill lattice\n\n");
1154 switch(fp->lattice) {
1157 o.x=0.5*0.25*fp->lc;
1160 create_lattice(moldyn,
1163 DEFAULT_ATOM_ATTR,0,
1164 fp->lx,fp->ly,fp->lz,
1171 create_lattice(moldyn,
1174 DEFAULT_ATOM_ATTR,1,
1175 fp->lx,fp->ly,fp->lz,
1183 create_lattice(moldyn,
1186 DEFAULT_ATOM_ATTR,0,
1187 fp->lx,fp->ly,fp->lz,
1193 moldyn_bc_check(moldyn);
1196 case STAGE_THERMAL_INIT:
1197 stage_print(" -> thermal init\n\n");
1198 thermal_init(moldyn,TRUE);
1202 printf("%s unknwon stage type\n",ME);
1206 /* mark as executed */
1207 stage->executed=TRUE;
1210 if(change_stage==TRUE) {
1211 printf("%s finished stage\n",ME);
1212 if(list_next_f(sl)==L_NO_NEXT_ELEMENT) {
1213 printf("%s no more stages\n",ME);
1223 if(mdrun->sattr&SATTR_AVGRST)
1224 average_reset(moldyn);
1228 /* continue simulation */
1229 moldyn_add_schedule(moldyn,steps,mdrun->timestep);
1234 int main(int argc,char **argv) {
1241 memset(&mdrun,0,sizeof(t_mdrun));
1242 memset(&moldyn,0,sizeof(t_moldyn));
1244 /* parse arguments */
1245 if(mdrun_parse_argv(&mdrun,argc,argv)<0)
1248 /* initialize list system */
1249 list_init_f(&(mdrun.stage));
1251 /* parse config file */
1252 mdrun_parse_config(&mdrun);
1254 /* reset the stage list */
1255 list_reset_f(&(mdrun.stage));
1259 /* prepare simulation */
1261 if(mdrun.continue_file[0]) {
1262 // read the save file
1263 moldyn_read_save_file(&moldyn,mdrun.continue_file);
1264 // manualaadjusting some stuff
1267 rand_init(&(moldyn.random),NULL,1);
1268 moldyn.random.status|=RAND_STAT_VERBOSE;
1271 moldyn_init(&moldyn,argc,argv);
1274 if(set_int_alg(&moldyn,mdrun.intalgo)<0)
1278 set_cutoff(&moldyn,mdrun.cutoff);
1279 if(set_potential(&moldyn,mdrun.potential)<0)
1281 switch(mdrun.potential) {
1282 case MOLDYN_POTENTIAL_AM:
1283 albe_mult_set_params(&moldyn,
1287 case MOLDYN_POTENTIAL_TM:
1288 tersoff_mult_set_params(&moldyn,
1292 case MOLDYN_POTENTIAL_HO:
1293 harmonic_oscillator_set_params(&moldyn,mdrun.element1);
1295 case MOLDYN_POTENTIAL_LJ:
1296 lennard_jones_set_params(&moldyn,mdrun.element1);
1299 printf("%s unknown potential: %02x\n",
1300 ME,mdrun.potential);
1304 /* if it is a continue run, reset schedule and skip lattice init */
1305 if(mdrun.continue_file[0]) {
1306 memset(&(moldyn.schedule),0,sizeof(t_moldyn_schedule));
1310 /* initial lattice and dimensions */
1311 set_dim(&moldyn,mdrun.dim.x,mdrun.dim.y,mdrun.dim.z,mdrun.vis);
1312 set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
1313 /* replaced by fill stage !!
1314 switch(mdrun.lattice) {
1316 create_lattice(&moldyn,FCC,mdrun.lc,mdrun.fill_element,
1317 mdrun.m1,DEFAULT_ATOM_ATTR,
1318 mdrun.fill_brand,mdrun.lx,
1319 mdrun.ly,mdrun.lz,NULL,0,NULL);
1322 create_lattice(&moldyn,DIAMOND,mdrun.lc,
1324 mdrun.m1,DEFAULT_ATOM_ATTR,
1325 mdrun.fill_brand,mdrun.lx,
1326 mdrun.ly,mdrun.lz,NULL,0,NULL);
1329 o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
1330 create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
1331 mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
1332 mdrun.ly,mdrun.lz,&o,0,NULL);
1333 o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
1334 create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
1335 mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
1336 mdrun.ly,mdrun.lz,&o,0,NULL);
1339 set_nn_dist(&moldyn,mdrun.nnd);
1342 printf("%s unknown lattice type: %02x\n",
1346 moldyn_bc_check(&moldyn);
1347 replaced by fill stage !! */
1349 /* temperature and pressure */
1350 set_temperature(&moldyn,mdrun.temperature);
1351 set_pressure(&moldyn,mdrun.pressure);
1352 /* replaced thermal_init stage
1353 thermal_init(&moldyn,TRUE);
1357 /* first schedule */
1358 moldyn_add_schedule(&moldyn,mdrun.prerun,mdrun.timestep);
1361 moldyn_set_log_dir(&moldyn,mdrun.sdir);
1362 moldyn_set_report(&moldyn,"CHANGE ME","CHANGE ME TOO");
1364 moldyn_set_log(&moldyn,LOG_TOTAL_ENERGY,mdrun.elog);
1366 moldyn_set_log(&moldyn,LOG_TEMPERATURE,mdrun.tlog);
1368 moldyn_set_log(&moldyn,LOG_PRESSURE,mdrun.plog);
1370 moldyn_set_log(&moldyn,LOG_VOLUME,mdrun.vlog);
1372 moldyn_set_log(&moldyn,VISUAL_STEP,mdrun.visualize);
1374 moldyn_set_log(&moldyn,SAVE_STEP,mdrun.save);
1375 moldyn_set_log(&moldyn,CREATE_REPORT,0);
1376 set_avg_skip(&moldyn,mdrun.avgskip);
1378 /* prepare the hook function */
1379 moldyn_set_schedule_hook(&moldyn,&mdrun_hook,&mdrun);
1381 /* run the simulation */
1382 moldyn_integrate(&moldyn);
1385 moldyn_shutdown(&moldyn);
1387 list_destroy_f(&(mdrun.stage));