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"
26 int mdrun_usage(void) {
28 printf("%s usage:\n",ME);
33 int mdrun_parse_argv(t_mdrun *mdrun,int argc,char **argv) {
40 printf("%s unknown switch: %s\n",ME,argv[i]);
46 strncpy(mdrun->cfile,argv[++i],128);
49 strncpy(mdrun->sdir,argv[++i],128);
55 printf("%s unknown option: %s\n",ME,argv[i]);
65 int del_stages(t_mdrun *mdrun) {
78 stage=sl->current->data;
81 } while(list_next_f(sl)!=L_NO_NEXT_ELEMENT);
86 int add_stage(t_mdrun *mdrun,u8 type,void *params) {
93 case STAGE_DISPLACE_ATOM:
94 psize=sizeof(t_displace_atom_params);
97 psize=sizeof(t_del_atoms_params);
99 case STAGE_INSERT_ATOMS:
100 psize=sizeof(t_insert_atoms_params);
102 case STAGE_INSERT_MIXED_ATOMS:
103 psize=sizeof(t_insert_mixed_atoms_params);
106 psize=sizeof(t_continue_params);
109 psize=sizeof(t_anneal_params);
112 psize=sizeof(t_chaattr_params);
115 psize=sizeof(t_chsattr_params);
118 psize=sizeof(t_set_temp_params);
120 case STAGE_SET_TIMESTEP:
121 psize=sizeof(t_set_timestep_params);
124 psize=sizeof(t_fill_params);
126 case STAGE_THERMAL_INIT:
130 printf("%s unknown stage type: %02x\n",ME,type);
134 stage=malloc(sizeof(t_stage));
136 perror("[mdrun] malloc (add stage)");
141 stage->executed=FALSE;
143 stage->params=malloc(psize);
144 if(stage->params==NULL) {
145 perror("[mdrun] malloc (stage params)");
149 memcpy(stage->params,params,psize);
151 list_add_immediate_f(&(mdrun->stage),stage);
156 int mdrun_parse_config(t_mdrun *mdrun) {
166 t_displace_atom_params dap;
167 t_insert_atoms_params iap;
168 t_insert_mixed_atoms_params imp;
169 t_continue_params cp;
171 t_chaattr_params cap;
172 t_chsattr_params csp;
173 t_set_temp_params stp;
174 t_set_timestep_params stsp;
176 t_del_atoms_params delp;
178 /* open config file */
179 fd=open(mdrun->cfile,O_RDONLY);
181 snprintf(error,128,"%s open cfile %s",ME,mdrun->cfile);
186 /* read, parse, set */
191 ret=get_line(fd,line,128);
195 // ignore # lines and \n
196 if((line[0]=='#')|(ret==1))
200 memset(&iap,0,sizeof(t_insert_atoms_params));
201 memset(&imp,0,sizeof(t_insert_mixed_atoms_params));
202 memset(&cp,0,sizeof(t_continue_params));
203 memset(&ap,0,sizeof(t_anneal_params));
204 memset(&cap,0,sizeof(t_chaattr_params));
205 memset(&csp,0,sizeof(t_chsattr_params));
206 memset(&stp,0,sizeof(t_set_temp_params));
207 memset(&stsp,0,sizeof(t_set_timestep_params));
208 memset(&fp,0,sizeof(t_fill_params));
209 memset(&delp,0,sizeof(t_del_atoms_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;
297 // parse fill command
300 if(!strncmp(word[i],"lc",2)) {
301 fp.lx=atoi(word[++i]);
302 fp.ly=atoi(word[++i]);
303 fp.lz=atoi(word[++i]);
304 fp.lc=atof(word[++i]);
308 if(!strncmp(word[i],"eb",2)) {
309 fp.fill_element=atoi(word[++i]);
310 fp.fill_brand=atoi(word[++i]);
313 if(word[i][0]=='p') {
318 fp.p_params.type=PART_INSIDE_R;
320 fp.p_params.type=PART_INSIDE_D;
324 fp.p_params.type=PART_OUTSIDE_R;
326 fp.p_params.type=PART_OUTSIDE_D;
331 if((fp.p_params.type==PART_INSIDE_R)||
332 (fp.p_params.type==PART_OUTSIDE_R)) {
333 fp.p_params.r=atof(word[++i]);
334 fp.p_params.p.x=atof(word[++i]);
335 fp.p_params.p.y=atof(word[++i]);
336 fp.p_params.p.z=atof(word[++i]);
338 if((fp.p_params.type==PART_INSIDE_D)||
339 (fp.p_params.type==PART_OUTSIDE_D)) {
340 fp.p_params.p.x=atof(word[++i]);
341 fp.p_params.p.y=atof(word[++i]);
342 fp.p_params.p.z=atof(word[++i]);
343 fp.p_params.d.x=atof(word[++i]);
344 fp.p_params.d.y=atof(word[++i]);
345 fp.p_params.d.z=atof(word[++i]);
349 if(word[i][0]=='d') {
350 switch(word[++i][0]) {
353 fp.d_params.type=DEFECT_TYPE_0D;
354 if(!strncmp(word[i+1],"dbx",3)) {
355 fp.d_params.stype=DEFECT_STYPE_DB_X;
357 if(!strncmp(word[i+1],"dby",3)) {
358 fp.d_params.stype=DEFECT_STYPE_DB_Y;
360 if(!strncmp(word[i+1],"dbz",3)) {
361 fp.d_params.stype=DEFECT_STYPE_DB_Z;
363 if(!strncmp(word[i+1],"dbr",3)) {
364 fp.d_params.stype=DEFECT_STYPE_DB_R;
367 fp.d_params.od=atof(word[++i]);
368 fp.d_params.dd=atof(word[++i]);
369 fp.d_params.element=atoi(word[++i]);
370 fp.d_params.brand=atoi(word[++i]);
372 fp.d_params.attr=ATOM_ATTR_HB|ATOM_ATTR_VA;
373 fp.d_params.attr|=ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP;
377 fp.d_params.type=DEFECT_TYPE_1D;
380 fp.d_params.type=DEFECT_TYPE_2D;
383 fp.d_params.type=DEFECT_TYPE_3D;
393 add_stage(mdrun,STAGE_FILL,&fp);
395 else if(!strncmp(word[0],"thermal_init",12)) {
396 add_stage(mdrun,STAGE_THERMAL_INIT,NULL);
398 else if(!strncmp(word[0],"aattr",5)) {
399 // for aatrib line we need a special stage
400 // containing one schedule of 0 loops ...
401 for(i=0;i<strlen(word[1]);i++) {
404 cap.type|=CHAATTR_TOTALV;
407 cap.type|=CHAATTR_REGION;
410 cap.type|=CHAATTR_ELEMENT;
417 if(cap.type&CHAATTR_REGION) {
418 cap.x0=atof(word[1]);
419 cap.y0=atof(word[2]);
420 cap.z0=atof(word[3]);
421 cap.x1=atof(word[4]);
422 cap.y1=atof(word[5]);
423 cap.z1=atof(word[6]);
426 if(cap.type&CHAATTR_ELEMENT) {
427 cap.element=atoi(word[i]);
430 for(o=0;o<strlen(word[i]);o++) {
433 cap.attr|=ATOM_ATTR_VB;
436 cap.attr|=ATOM_ATTR_HB;
439 cap.attr|=ATOM_ATTR_VA;
442 cap.attr|=ATOM_ATTR_FP;
445 cap.attr|=ATOM_ATTR_1BP;
448 cap.attr|=ATOM_ATTR_2BP;
451 cap.attr|=ATOM_ATTR_3BP;
457 add_stage(mdrun,STAGE_CHAATTR,&cap);
459 else if(!strncmp(word[0],"sattr",5)) {
460 // for satrib line we need a special stage
461 // containing one schedule of 0 loops ...
463 for(i=1;i<wcnt;i++) {
464 if(!strncmp(word[i],"pctrl",5)) {
465 csp.ptau=atof(word[++i]);
467 csp.ptau=0.01/(csp.ptau*GPA);
468 csp.type|=CHSATTR_PCTRL;
470 if(!strncmp(word[i],"tctrl",5)) {
471 csp.ttau=atof(word[++i]);
472 csp.type|=CHSATTR_TCTRL;
474 if(!strncmp(word[i],"prelax",6)) {
475 csp.dp=atof(word[++i])*BAR;
476 csp.type|=CHSATTR_PRELAX;
478 if(!strncmp(word[i],"trelax",6)) {
479 csp.dt=atof(word[++i]);
480 csp.type|=CHSATTR_TRELAX;
482 if(!strncmp(word[i],"rsteps",6)) {
483 csp.rsteps=atoi(word[++i]);
484 csp.type|=CHSATTR_RSTEPS;
486 if(!strncmp(word[i],"avgrst",6)) {
487 csp.avgrst=atoi(word[++i]);
488 csp.type|=CHSATTR_AVGRST;
491 add_stage(mdrun,STAGE_CHSATTR,&csp);
493 else if(!strncmp(word[0],"prerun",6))
494 mdrun->prerun=atoi(word[1]);
495 else if(!strncmp(word[0],"avgskip",7))
496 mdrun->avgskip=atoi(word[1]);
497 else if(!strncmp(word[0],"elog",4))
498 mdrun->elog=atoi(word[1]);
499 else if(!strncmp(word[0],"tlog",4))
500 mdrun->tlog=atoi(word[1]);
501 else if(!strncmp(word[0],"plog",4))
502 mdrun->plog=atoi(word[1]);
503 else if(!strncmp(word[0],"vlog",4))
504 mdrun->vlog=atoi(word[1]);
505 else if(!strncmp(word[0],"save",4))
506 mdrun->save=atoi(word[1]);
507 else if(!strncmp(word[0],"visualize",9))
508 mdrun->visualize=atoi(word[1]);
509 else if(!strncmp(word[0],"stage",5)) {
510 // for every stage line, add a stage
511 if(!strncmp(word[1],"displace",8)) {
512 dap.nr=atoi(word[2]);
513 dap.dx=atof(word[3]);
514 dap.dy=atof(word[4]);
515 dap.dz=atof(word[5]);
516 add_stage(mdrun,STAGE_DISPLACE_ATOM,&dap);
518 else if(!strncmp(word[1],"del_atoms",9)) {
519 delp.o.x=atof(word[2]);
520 delp.o.y=atof(word[3]);
521 delp.o.z=atof(word[4]);
522 delp.r=atof(word[5]);
523 add_stage(mdrun,STAGE_DEL_ATOMS,&delp);
525 else if(!strncmp(word[1],"ins_atoms",9)) {
526 iap.ins_steps=atoi(word[2]);
527 iap.ins_atoms=atoi(word[3]);
528 iap.element=atoi(word[4]);
529 iap.brand=atoi(word[5]);
530 for(i=0;i<strlen(word[6]);i++) {
533 iap.attr|=ATOM_ATTR_VB;
536 iap.attr|=ATOM_ATTR_HB;
539 iap.attr|=ATOM_ATTR_VA;
542 iap.attr|=ATOM_ATTR_FP;
545 iap.attr|=ATOM_ATTR_1BP;
548 iap.attr|=ATOM_ATTR_2BP;
551 iap.attr|=ATOM_ATTR_3BP;
561 iap.x0=atof(word[8]);
562 iap.y0=atof(word[9]);
563 iap.z0=atof(word[10]);
570 iap.cr=atof(word[9]);
574 iap.x0=atof(word[9]);
575 iap.y0=atof(word[10]);
576 iap.z0=atof(word[11]);
577 iap.x1=atof(word[12]);
578 iap.y1=atof(word[13]);
579 iap.z1=atof(word[14]);
580 iap.cr=atof(word[15]);
584 iap.x0=atof(word[9]);
585 iap.y0=atof(word[10]);
586 iap.z0=atof(word[11]);
587 iap.x1=atof(word[12]);
588 iap.cr=atof(word[13]);
596 add_stage(mdrun,STAGE_INSERT_ATOMS,&iap);
602 else if(!strncmp(word[1],"ins_m_atoms",11)) {
603 imp.element1=atoi(word[2]);
604 imp.element2=atoi(word[3]);
605 imp.amount1=atoi(word[4]);
606 imp.amount2=atoi(word[5]);
607 imp.brand1=atoi(word[6]);
608 imp.brand2=atoi(word[7]);
609 imp.crmin=atof(word[8]);
610 imp.crmax=atof(word[9]);
612 for(i=0;i<strlen(word[8]);i++) {
615 imp.attr|=ATOM_ATTR_VB;
618 imp.attr|=ATOM_ATTR_HB;
621 imp.attr|=ATOM_ATTR_VA;
624 imp.attr|=ATOM_ATTR_FP;
627 imp.attr|=ATOM_ATTR_1BP;
630 imp.attr|=ATOM_ATTR_2BP;
633 imp.attr|=ATOM_ATTR_3BP;
640 imp.attr1=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
641 imp.attr2=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
642 add_stage(mdrun,STAGE_INSERT_MIXED_ATOMS,&imp);
649 else if(!strncmp(word[1],"continue",8)) {
650 cp.runs=atoi(word[2]);
651 add_stage(mdrun,STAGE_CONTINUE,&cp);
653 else if(!strncmp(word[1],"anneal",6)) {
655 ap.runs=atoi(word[2]);
657 ap.interval=atoi(word[4]);
658 add_stage(mdrun,STAGE_ANNEAL,&ap);
660 else if(!strncmp(word[1],"set_temp",8)) {
661 if(word[2][0]=='c') {
662 stp.type=SET_TEMP_CURRENT;
666 stp.type=SET_TEMP_VALUE;
667 stp.val=atof(word[2]);
669 add_stage(mdrun,STAGE_SET_TEMP,&stp);
671 else if(!strncmp(word[1],"set_timestep",12)) {
672 stsp.tau=atof(word[2]);
673 add_stage(mdrun,STAGE_SET_TIMESTEP,&stsp);
676 printf("%s unknown stage type: %s\n",
682 printf("%s unknown keyword '%s', skipped!\n",
694 int check_pressure(t_moldyn *moldyn,t_mdrun *mdrun) {
698 if(!(mdrun->sattr&SATTR_PRELAX)) {
702 delta=moldyn->p_avg-moldyn->p_ref;
713 int check_temperature(t_moldyn *moldyn,t_mdrun *mdrun) {
717 if(!(mdrun->sattr&SATTR_TRELAX))
720 delta=moldyn->t_avg-moldyn->t_ref;
731 int displace_atom(t_moldyn *moldyn,t_mdrun *mdrun) {
733 t_displace_atom_params *dap;
737 stage=mdrun->stage.current->data;
740 atom=&(moldyn->atom[dap->nr]);
748 int del_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
751 t_del_atoms_params *delp;
755 stage=mdrun->stage.current->data;
758 for(i=0;i<moldyn->count;i++) {
759 v3_sub(&dist,&(delp->o),&(moldyn->atom[i].r));
760 //printf("%d ----> %f %f %f = %f | %f\n",i,dist.x,dist.y,dist.z,v3_absolute_square(&dist),delp->r*delp->r);
761 if(v3_absolute_square(&dist)<=(delp->r*delp->r)) {
762 del_atom(moldyn,moldyn->atom[i].tag);
763 printf("%s atom deleted: %d %d %d\n",ME,
764 moldyn->atom[i].tag,moldyn->atom[i].element,
765 moldyn->atom[i].brand);
773 int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
775 t_insert_atoms_params *iap;
785 stage=mdrun->stage.current->data;
790 v.x=0.0; v.y=0.0; v.z=0.0;
794 switch(mdrun->lattice) {
844 printf("%s unknown insertion mode: %02x\n",
850 while(cnt<iap->ins_atoms) {
853 if(iap->type!=INS_POS) {
854 r.x=rand_get_double(&(moldyn->random))*x;
855 r.y=rand_get_double(&(moldyn->random))*y;
856 r.z=rand_get_double(&(moldyn->random))*z;
867 if(iap->type!=INS_TOTAL) {
874 dmin=1000; // for sure too high!
875 for(i=0;i<moldyn->count;i++) {
876 atom=&(moldyn->atom[i]);
877 v3_sub(&dist,&(atom->r),&r);
878 check_per_bound(moldyn,&dist);
879 d=v3_absolute_square(&dist);
880 if(d<(iap->cr*iap->cr)) {
888 if(iap->type==INS_SPHERE) {
889 if((r.x-iap->x0)*(r.x-iap->x0)+
890 (r.y-iap->y0)*(r.y-iap->y0)+
891 (r.z-iap->z0)*(r.z-iap->z0)>
897 add_atom(moldyn,iap->element,
898 iap->brand,iap->attr,&r,&v);
899 printf("%s atom inserted (%d/%d): %f %f %f\n",
900 ME,(iap->cnt_steps+1)*iap->ins_atoms,
901 iap->ins_steps*iap->ins_atoms,r.x,r.y,r.z);
902 printf(" -> d2 = %f/%f\n",dmin,iap->cr*iap->cr);
909 int insert_mixed_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
912 t_insert_mixed_atoms_params *imp;
914 double x,x0,y,y0,z,z0;
915 double dmin,d,cmin,cmax;
921 stage=mdrun->stage.current->data;
935 cmin=imp->crmin*imp->crmin;
936 cmax=imp->crmax*imp->crmax;
938 while(imp->amount1|imp->amount2) {
943 r.x=rand_get_double(&(moldyn->random))*x;
944 r.y=rand_get_double(&(moldyn->random))*y;
945 r.z=rand_get_double(&(moldyn->random))*z;
949 dmin=1000.0; // for sure too high!
950 for(i=0;i<moldyn->count;i++) {
951 atom=&(moldyn->atom[i]);
952 v3_sub(&dist,&(atom->r),&r);
953 check_per_bound(moldyn,&dist);
954 d=v3_absolute_square(&dist);
966 add_atom(moldyn,imp->element1,
967 imp->brand1,imp->attr1,&r,&v);
968 printf("%s (mixed) atom inserted (%d): %f %f %f\n",
969 ME,imp->amount1,r.x,r.y,r.z);
970 printf(" -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
977 r.x=rand_get_double(&(moldyn->random))*x;
978 r.y=rand_get_double(&(moldyn->random))*y;
979 r.z=rand_get_double(&(moldyn->random))*z;
983 dmin=1000.0; // for sure too high!
984 for(i=0;i<moldyn->count;i++) {
985 atom=&(moldyn->atom[i]);
986 v3_sub(&dist,&(atom->r),&r);
987 check_per_bound(moldyn,&dist);
988 d=v3_absolute_square(&dist);
1000 add_atom(moldyn,imp->element2,
1001 imp->brand2,imp->attr2,&r,&v);
1002 printf("%s (mixed) atom inserted (%d): %f %f %f\n",
1003 ME,imp->amount2,r.x,r.y,r.z);
1004 printf(" -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
1012 int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
1015 t_chaattr_params *cap;
1019 stage=mdrun->stage.current->data;
1022 for(i=0;i<moldyn->count;i++) {
1023 atom=&(moldyn->atom[i]);
1024 if(cap->type&CHAATTR_ELEMENT) {
1025 if(cap->element!=atom->element)
1028 if(cap->type&CHAATTR_REGION) {
1029 if(cap->x0<atom->r.x)
1031 if(cap->y0<atom->r.y)
1033 if(cap->z0<atom->r.z)
1035 if(cap->x1>atom->r.x)
1037 if(cap->y1>atom->r.y)
1039 if(cap->z1>atom->r.z)
1042 atom->attr=cap->attr;
1048 int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
1051 t_chsattr_params *csp;
1053 stage=mdrun->stage.current->data;
1056 if(csp->type&CHSATTR_PCTRL) {
1058 set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
1060 set_p_scale(moldyn,P_SCALE_NONE,1.0);
1062 if(csp->type&CHSATTR_TCTRL) {
1064 set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
1066 set_t_scale(moldyn,T_SCALE_NONE,1.0);
1068 if(csp->type&CHSATTR_PRELAX) {
1070 mdrun->sattr&=(~(SATTR_PRELAX));
1072 mdrun->sattr|=SATTR_PRELAX;
1075 if(csp->type&CHSATTR_TRELAX) {
1077 mdrun->sattr&=(~(SATTR_TRELAX));
1079 mdrun->sattr|=SATTR_TRELAX;
1082 if(csp->type&CHSATTR_AVGRST) {
1084 mdrun->sattr|=SATTR_AVGRST;
1086 mdrun->sattr&=(~(SATTR_AVGRST));
1088 if(csp->type&CHSATTR_RSTEPS) {
1089 mdrun->relax_steps=csp->rsteps;
1095 #define stage_print(m) if(!(stage->executed)) \
1098 int mdrun_hook(void *ptr1,void *ptr2) {
1108 t_insert_atoms_params *iap;
1109 t_insert_mixed_atoms_params *imp;
1110 t_continue_params *cp;
1111 t_anneal_params *ap;
1112 t_set_temp_params *stp;
1113 t_set_timestep_params *stsp;
1123 /* return immediately if there are no more stage */
1124 if(sl->current==NULL)
1127 /* get stage description */
1128 stage=sl->current->data;
1130 /* steps in next schedule */
1131 steps=mdrun->relax_steps;
1133 /* check whether relaxation steps are necessary */
1134 if((check_pressure(moldyn,mdrun)==TRUE)&\
1135 (check_temperature(moldyn,mdrun)==TRUE)) {
1138 stage_print("\n###########################\n");
1139 stage_print("# [mdrun] executing stage #\n");
1140 stage_print("###########################\n\n");
1142 /* stage specific stuff */
1143 switch(stage->type) {
1144 case STAGE_DISPLACE_ATOM:
1145 stage_print(" -> displace atom\n\n");
1146 displace_atom(moldyn,mdrun);
1149 case STAGE_DEL_ATOMS:
1150 stage_print(" -> del atoms\n\n");
1151 del_atoms(moldyn,mdrun);
1154 case STAGE_INSERT_ATOMS:
1155 stage_print(" -> insert atoms\n\n");
1157 if(iap->cnt_steps==iap->ins_steps) {
1161 insert_atoms(moldyn,mdrun);
1167 case STAGE_INSERT_MIXED_ATOMS:
1168 stage_print(" -> insert mixed atoms\n\n");
1170 insert_mixed_atoms(moldyn,mdrun);
1176 case STAGE_CONTINUE:
1177 stage_print(" -> continue\n\n");
1178 if(stage->executed==TRUE) {
1186 stage_print(" -> anneal\n\n");
1188 if(ap->count==ap->runs) {
1192 if(moldyn->t_ref+ap->dt>=0.0)
1193 set_temperature(moldyn,
1194 moldyn->t_ref+ap->dt);
1199 stage_print(" -> change atom attributes\n\n");
1200 chaatr(moldyn,mdrun);
1204 stage_print(" -> change sys attributes\n\n");
1205 chsattr(moldyn,mdrun);
1208 case STAGE_SET_TEMP:
1209 stage_print(" -> set temperature\n\n");
1211 if(stp->type&SET_TEMP_CURRENT) {
1212 set_temperature(moldyn,moldyn->t_avg);
1215 set_temperature(moldyn,stp->val);
1219 case STAGE_SET_TIMESTEP:
1220 stage_print(" -> set timestep\n\n");
1222 mdrun->timestep=stsp->tau;
1226 stage_print(" -> fill lattice\n\n");
1228 switch(fp->lattice) {
1231 o.x=0.5*0.25*fp->lc;
1234 create_lattice(moldyn,
1237 DEFAULT_ATOM_ATTR,0,
1238 fp->lx,fp->ly,fp->lz,
1245 create_lattice(moldyn,
1248 DEFAULT_ATOM_ATTR,1,
1249 fp->lx,fp->ly,fp->lz,
1257 create_lattice(moldyn,
1262 fp->lx,fp->ly,fp->lz,
1268 moldyn_bc_check(moldyn);
1271 case STAGE_THERMAL_INIT:
1272 stage_print(" -> thermal init\n\n");
1273 thermal_init(moldyn,TRUE);
1277 printf("%s unknwon stage type\n",ME);
1281 /* mark as executed */
1282 stage->executed=TRUE;
1285 if(change_stage==TRUE) {
1286 printf("%s finished stage\n",ME);
1287 if(list_next_f(sl)==L_NO_NEXT_ELEMENT) {
1288 printf("%s no more stages\n",ME);
1298 if(mdrun->sattr&SATTR_AVGRST)
1299 average_reset(moldyn);
1303 /* continue simulation */
1304 moldyn_add_schedule(moldyn,steps,mdrun->timestep);
1309 int main(int argc,char **argv) {
1316 memset(&mdrun,0,sizeof(t_mdrun));
1317 memset(&moldyn,0,sizeof(t_moldyn));
1319 /* parse arguments */
1320 if(mdrun_parse_argv(&mdrun,argc,argv)<0)
1323 /* initialize list system */
1324 list_init_f(&(mdrun.stage));
1326 /* parse config file */
1327 mdrun_parse_config(&mdrun);
1329 /* reset the stage list */
1330 list_reset_f(&(mdrun.stage));
1334 /* prepare simulation */
1336 if(mdrun.continue_file[0]) {
1337 // read the save file
1338 moldyn_read_save_file(&moldyn,mdrun.continue_file);
1339 // manualaadjusting some stuff
1342 rand_init(&(moldyn.random),NULL,1);
1343 moldyn.random.status|=RAND_STAT_VERBOSE;
1346 moldyn_init(&moldyn,argc,argv);
1349 if(set_int_alg(&moldyn,mdrun.intalgo)<0)
1353 set_cutoff(&moldyn,mdrun.cutoff);
1354 if(set_potential(&moldyn,mdrun.potential)<0)
1356 switch(mdrun.potential) {
1357 case MOLDYN_POTENTIAL_AM:
1358 albe_mult_set_params(&moldyn,
1362 case MOLDYN_POTENTIAL_TM:
1363 tersoff_mult_set_params(&moldyn,
1367 case MOLDYN_POTENTIAL_HO:
1368 harmonic_oscillator_set_params(&moldyn,mdrun.element1);
1370 case MOLDYN_POTENTIAL_LJ:
1371 lennard_jones_set_params(&moldyn,mdrun.element1);
1374 printf("%s unknown potential: %02x\n",
1375 ME,mdrun.potential);
1379 /* if it is a continue run, reset schedule and skip lattice init */
1380 if(mdrun.continue_file[0]) {
1381 memset(&(moldyn.schedule),0,sizeof(t_moldyn_schedule));
1385 /* initial lattice and dimensions */
1386 set_dim(&moldyn,mdrun.dim.x,mdrun.dim.y,mdrun.dim.z,mdrun.vis);
1387 set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
1388 /* replaced by fill stage !!
1389 switch(mdrun.lattice) {
1391 create_lattice(&moldyn,FCC,mdrun.lc,mdrun.fill_element,
1392 mdrun.m1,DEFAULT_ATOM_ATTR,
1393 mdrun.fill_brand,mdrun.lx,
1394 mdrun.ly,mdrun.lz,NULL,0,NULL);
1397 create_lattice(&moldyn,DIAMOND,mdrun.lc,
1399 mdrun.m1,DEFAULT_ATOM_ATTR,
1400 mdrun.fill_brand,mdrun.lx,
1401 mdrun.ly,mdrun.lz,NULL,0,NULL);
1404 o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
1405 create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
1406 mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
1407 mdrun.ly,mdrun.lz,&o,0,NULL);
1408 o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
1409 create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
1410 mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
1411 mdrun.ly,mdrun.lz,&o,0,NULL);
1414 set_nn_dist(&moldyn,mdrun.nnd);
1417 printf("%s unknown lattice type: %02x\n",
1421 moldyn_bc_check(&moldyn);
1422 replaced by fill stage !! */
1424 /* temperature and pressure */
1425 set_temperature(&moldyn,mdrun.temperature);
1426 set_pressure(&moldyn,mdrun.pressure);
1427 /* replaced thermal_init stage
1428 thermal_init(&moldyn,TRUE);
1432 /* first schedule */
1433 moldyn_add_schedule(&moldyn,mdrun.prerun,mdrun.timestep);
1436 moldyn_set_log_dir(&moldyn,mdrun.sdir);
1437 moldyn_set_report(&moldyn,"CHANGE ME","CHANGE ME TOO");
1439 moldyn_set_log(&moldyn,LOG_TOTAL_ENERGY,mdrun.elog);
1441 moldyn_set_log(&moldyn,LOG_TEMPERATURE,mdrun.tlog);
1443 moldyn_set_log(&moldyn,LOG_PRESSURE,mdrun.plog);
1445 moldyn_set_log(&moldyn,LOG_VOLUME,mdrun.vlog);
1447 moldyn_set_log(&moldyn,VISUAL_STEP,mdrun.visualize);
1449 moldyn_set_log(&moldyn,SAVE_STEP,mdrun.save);
1450 moldyn_set_log(&moldyn,CREATE_REPORT,0);
1451 set_avg_skip(&moldyn,mdrun.avgskip);
1453 /* prepare the hook function */
1454 moldyn_set_schedule_hook(&moldyn,&mdrun_hook,&mdrun);
1456 /* run the simulation */
1457 moldyn_integrate(&moldyn);
1460 moldyn_shutdown(&moldyn);
1462 list_destroy_f(&(mdrun.stage));