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_DEL_ATOMS:
102 psize=sizeof(t_del_atoms_params);
104 case STAGE_INSERT_ATOMS:
105 psize=sizeof(t_insert_atoms_params);
107 case STAGE_INSERT_MIXED_ATOMS:
108 psize=sizeof(t_insert_mixed_atoms_params);
111 psize=sizeof(t_continue_params);
114 psize=sizeof(t_anneal_params);
117 psize=sizeof(t_chaattr_params);
120 psize=sizeof(t_chsattr_params);
123 psize=sizeof(t_set_temp_params);
125 case STAGE_SET_TIMESTEP:
126 psize=sizeof(t_set_timestep_params);
129 psize=sizeof(t_fill_params);
131 case STAGE_THERMAL_INIT:
135 printf("%s unknown stage type: %02x\n",ME,type);
139 stage=malloc(sizeof(t_stage));
141 perror("[mdrun] malloc (add stage)");
146 stage->executed=FALSE;
148 stage->params=malloc(psize);
149 if(stage->params==NULL) {
150 perror("[mdrun] malloc (stage params)");
154 memcpy(stage->params,params,psize);
156 list_add_immediate_f(&(mdrun->stage),stage);
161 int mdrun_parse_config(t_mdrun *mdrun) {
171 t_displace_atom_params dap;
172 t_insert_atoms_params iap;
173 t_insert_mixed_atoms_params imp;
174 t_continue_params cp;
176 t_chaattr_params cap;
177 t_chsattr_params csp;
178 t_set_temp_params stp;
179 t_set_timestep_params stsp;
181 t_del_atoms_params delp;
183 /* open config file */
184 fd=open(mdrun->cfile,O_RDONLY);
186 snprintf(error,128,"%s open cfile %s",ME,mdrun->cfile);
191 /* read, parse, set */
196 ret=get_line(fd,line,128);
200 // ignore # lines and \n
201 if((line[0]=='#')|(ret==1))
205 memset(&iap,0,sizeof(t_insert_atoms_params));
206 memset(&imp,0,sizeof(t_insert_mixed_atoms_params));
207 memset(&cp,0,sizeof(t_continue_params));
208 memset(&ap,0,sizeof(t_anneal_params));
209 memset(&cap,0,sizeof(t_chaattr_params));
210 memset(&csp,0,sizeof(t_chsattr_params));
211 memset(&stp,0,sizeof(t_set_temp_params));
212 memset(&stsp,0,sizeof(t_set_timestep_params));
213 memset(&fp,0,sizeof(t_fill_params));
214 memset(&delp,0,sizeof(t_del_atoms_params));
216 // get command + args
220 wptr=strtok(NULL," \t");
222 wptr=strtok(line," \t");
225 strncpy(word[wcnt],wptr,64);
229 if(!strncmp(word[0],"potential",9)) {
230 if(!strncmp(word[1],"albe",4))
231 mdrun->potential=MOLDYN_POTENTIAL_AM;
232 if(!strncmp(word[1],"tersoff",7))
233 mdrun->potential=MOLDYN_POTENTIAL_TM;
234 if(!strncmp(word[1],"ho",2))
235 mdrun->potential=MOLDYN_POTENTIAL_HO;
236 if(!strncmp(word[1],"lj",2))
237 mdrun->potential=MOLDYN_POTENTIAL_LJ;
239 else if(!strncmp(word[0],"continue",8))
240 strncpy(mdrun->continue_file,word[1],128);
241 else if(!strncmp(word[0],"cutoff",6))
242 mdrun->cutoff=atof(word[1]);
243 else if(!strncmp(word[0],"nnd",3))
244 mdrun->nnd=atof(word[1]);
245 else if(!strncmp(word[0],"intalgo",7)) {
246 if(!strncmp(word[1],"verlet",5))
247 mdrun->intalgo=MOLDYN_INTEGRATE_VERLET;
249 else if(!strncmp(word[0],"timestep",8))
250 mdrun->timestep=atof(word[1]);
251 else if(!strncmp(word[0],"volume",6)) {
252 mdrun->dim.x=atof(word[1]);
253 mdrun->dim.y=atof(word[2]);
254 mdrun->dim.z=atof(word[3]);
255 if(strncmp(word[4],"0",1))
258 else if(!strncmp(word[0],"pbc",3)) {
259 if(strncmp(word[1],"0",1))
263 if(strncmp(word[2],"0",1))
267 if(strncmp(word[3],"0",1))
272 else if(!strncmp(word[0],"temperature",11))
273 mdrun->temperature=atof(word[1]);
274 else if(!strncmp(word[0],"pressure",8))
275 mdrun->pressure=atof(word[1]);
276 else if(!strncmp(word[0],"lattice",7)) {
277 if(!strncmp(word[1],"zincblende",10))
278 mdrun->lattice=ZINCBLENDE;
279 if(!strncmp(word[1],"fcc",3))
281 if(!strncmp(word[1],"diamond",7))
282 mdrun->lattice=DIAMOND;
283 if(!strncmp(word[1],"none",4))
286 mdrun->lc=atof(word[2]);
288 else if(!strncmp(word[0],"element1",8)) {
289 mdrun->element1=atoi(word[1]);
291 else if(!strncmp(word[0],"element2",8)) {
292 mdrun->element2=atoi(word[1]);
294 else if(!strncmp(word[0],"fill",6)) {
296 fp.fill_element=mdrun->element1;
298 fp.lattice=mdrun->lattice;
302 // parse fill command
305 if(!strncmp(word[i],"lc",2)) {
306 fp.lx=atoi(word[++i]);
307 fp.ly=atoi(word[++i]);
308 fp.lz=atoi(word[++i]);
309 fp.lc=atof(word[++i]);
313 if(!strncmp(word[i],"eb",2)) {
314 fp.fill_element=atoi(word[++i]);
315 fp.fill_brand=atoi(word[++i]);
318 if(word[i][0]=='p') {
323 fp.p_params.type=PART_INSIDE_R;
325 fp.p_params.type=PART_INSIDE_D;
329 fp.p_params.type=PART_OUTSIDE_R;
331 fp.p_params.type=PART_OUTSIDE_D;
336 if((fp.p_params.type==PART_INSIDE_R)||
337 (fp.p_params.type==PART_OUTSIDE_R)) {
338 fp.p_params.r=atof(word[++i]);
339 fp.p_params.p.x=atof(word[++i]);
340 fp.p_params.p.y=atof(word[++i]);
341 fp.p_params.p.z=atof(word[++i]);
343 if((fp.p_params.type==PART_INSIDE_D)||
344 (fp.p_params.type==PART_OUTSIDE_D)) {
345 fp.p_params.p.x=atof(word[++i]);
346 fp.p_params.p.y=atof(word[++i]);
347 fp.p_params.p.z=atof(word[++i]);
348 fp.p_params.d.x=atof(word[++i]);
349 fp.p_params.d.y=atof(word[++i]);
350 fp.p_params.d.z=atof(word[++i]);
354 if(word[i][0]=='d') {
355 switch(word[++i][0]) {
358 fp.d_params.type=DEFECT_TYPE_0D;
359 if(!strncmp(word[i+1],"dbx",3)) {
360 fp.d_params.stype=DEFECT_STYPE_DB_X;
362 if(!strncmp(word[i+1],"dby",3)) {
363 fp.d_params.stype=DEFECT_STYPE_DB_Y;
365 if(!strncmp(word[i+1],"dbz",3)) {
366 fp.d_params.stype=DEFECT_STYPE_DB_Z;
368 if(!strncmp(word[i+1],"dbr",3)) {
369 fp.d_params.stype=DEFECT_STYPE_DB_R;
372 fp.d_params.od=atof(word[++i]);
373 fp.d_params.dd=atof(word[++i]);
374 fp.d_params.element=atoi(word[++i]);
375 fp.d_params.brand=atoi(word[++i]);
377 fp.d_params.attr=ATOM_ATTR_HB|ATOM_ATTR_VA;
378 fp.d_params.attr|=ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP;
382 fp.d_params.type=DEFECT_TYPE_1D;
385 fp.d_params.type=DEFECT_TYPE_2D;
388 fp.d_params.type=DEFECT_TYPE_3D;
398 add_stage(mdrun,STAGE_FILL,&fp);
400 else if(!strncmp(word[0],"thermal_init",12)) {
401 add_stage(mdrun,STAGE_THERMAL_INIT,NULL);
403 else if(!strncmp(word[0],"aattr",5)) {
404 // for aatrib line we need a special stage
405 // containing one schedule of 0 loops ...
406 for(i=0;i<strlen(word[1]);i++) {
409 cap.type|=CHAATTR_TOTALV;
412 cap.type|=CHAATTR_REGION;
415 cap.type|=CHAATTR_ELEMENT;
422 if(cap.type&CHAATTR_REGION) {
423 cap.x0=atof(word[1]);
424 cap.y0=atof(word[2]);
425 cap.z0=atof(word[3]);
426 cap.x1=atof(word[4]);
427 cap.y1=atof(word[5]);
428 cap.z1=atof(word[6]);
431 if(cap.type&CHAATTR_ELEMENT) {
432 cap.element=atoi(word[i]);
435 for(o=0;o<strlen(word[i]);o++) {
438 cap.attr|=ATOM_ATTR_VB;
441 cap.attr|=ATOM_ATTR_HB;
444 cap.attr|=ATOM_ATTR_VA;
447 cap.attr|=ATOM_ATTR_FP;
450 cap.attr|=ATOM_ATTR_1BP;
453 cap.attr|=ATOM_ATTR_2BP;
456 cap.attr|=ATOM_ATTR_3BP;
462 add_stage(mdrun,STAGE_CHAATTR,&cap);
464 else if(!strncmp(word[0],"sattr",5)) {
465 // for satrib line we need a special stage
466 // containing one schedule of 0 loops ...
468 for(i=1;i<wcnt;i++) {
469 if(!strncmp(word[i],"pctrl",5)) {
470 csp.ptau=0.01/(atof(word[++i])*GPA);
471 csp.type|=CHSATTR_PCTRL;
473 if(!strncmp(word[i],"tctrl",5)) {
474 csp.ttau=atof(word[++i]);
475 csp.type|=CHSATTR_TCTRL;
477 if(!strncmp(word[i],"prelax",6)) {
478 csp.dp=atof(word[++i])*BAR;
479 csp.type|=CHSATTR_PRELAX;
481 if(!strncmp(word[i],"trelax",6)) {
482 csp.dt=atof(word[++i]);
483 csp.type|=CHSATTR_TRELAX;
485 if(!strncmp(word[i],"rsteps",6)) {
486 csp.rsteps=atoi(word[++i]);
487 csp.type|=CHSATTR_RSTEPS;
489 if(!strncmp(word[i],"avgrst",6)) {
490 csp.avgrst=atoi(word[++i]);
491 csp.type|=CHSATTR_AVGRST;
494 add_stage(mdrun,STAGE_CHSATTR,&csp);
496 else if(!strncmp(word[0],"prerun",6))
497 mdrun->prerun=atoi(word[1]);
498 else if(!strncmp(word[0],"avgskip",7))
499 mdrun->avgskip=atoi(word[1]);
500 else if(!strncmp(word[0],"elog",4))
501 mdrun->elog=atoi(word[1]);
502 else if(!strncmp(word[0],"tlog",4))
503 mdrun->tlog=atoi(word[1]);
504 else if(!strncmp(word[0],"plog",4))
505 mdrun->plog=atoi(word[1]);
506 else if(!strncmp(word[0],"vlog",4))
507 mdrun->vlog=atoi(word[1]);
508 else if(!strncmp(word[0],"save",4))
509 mdrun->save=atoi(word[1]);
510 else if(!strncmp(word[0],"visualize",9))
511 mdrun->visualize=atoi(word[1]);
512 else if(!strncmp(word[0],"stage",5)) {
513 // for every stage line, add a stage
514 if(!strncmp(word[1],"displace",8)) {
515 dap.nr=atoi(word[2]);
516 dap.dx=atof(word[3]);
517 dap.dy=atof(word[4]);
518 dap.dz=atof(word[5]);
519 add_stage(mdrun,STAGE_DISPLACE_ATOM,&dap);
521 else if(!strncmp(word[1],"del_atoms",9)) {
522 delp.o.x=atof(word[2]);
523 delp.o.y=atof(word[3]);
524 delp.o.z=atof(word[4]);
525 delp.r=atof(word[5]);
526 add_stage(mdrun,STAGE_DEL_ATOMS,&delp);
528 else if(!strncmp(word[1],"ins_atoms",9)) {
529 iap.ins_steps=atoi(word[2]);
530 iap.ins_atoms=atoi(word[3]);
531 iap.element=atoi(word[4]);
532 iap.brand=atoi(word[5]);
533 for(i=0;i<strlen(word[6]);i++) {
536 iap.attr|=ATOM_ATTR_VB;
539 iap.attr|=ATOM_ATTR_HB;
542 iap.attr|=ATOM_ATTR_VA;
545 iap.attr|=ATOM_ATTR_FP;
548 iap.attr|=ATOM_ATTR_1BP;
551 iap.attr|=ATOM_ATTR_2BP;
554 iap.attr|=ATOM_ATTR_3BP;
564 iap.x0=atof(word[8]);
565 iap.y0=atof(word[9]);
566 iap.z0=atof(word[10]);
573 iap.cr=atof(word[9]);
577 iap.x0=atof(word[9]);
578 iap.y0=atof(word[10]);
579 iap.z0=atof(word[11]);
580 iap.x1=atof(word[12]);
581 iap.y1=atof(word[13]);
582 iap.z1=atof(word[14]);
583 iap.cr=atof(word[15]);
587 iap.x0=atof(word[9]);
588 iap.y0=atof(word[10]);
589 iap.z0=atof(word[11]);
590 iap.x1=atof(word[12]);
591 iap.cr=atof(word[13]);
599 add_stage(mdrun,STAGE_INSERT_ATOMS,&iap);
605 else if(!strncmp(word[1],"ins_m_atoms",11)) {
606 imp.element1=atoi(word[2]);
607 imp.element2=atoi(word[3]);
608 imp.amount1=atoi(word[4]);
609 imp.amount2=atoi(word[5]);
610 imp.brand1=atoi(word[6]);
611 imp.brand2=atoi(word[7]);
612 imp.crmin=atof(word[8]);
613 imp.crmax=atof(word[9]);
615 for(i=0;i<strlen(word[8]);i++) {
618 imp.attr|=ATOM_ATTR_VB;
621 imp.attr|=ATOM_ATTR_HB;
624 imp.attr|=ATOM_ATTR_VA;
627 imp.attr|=ATOM_ATTR_FP;
630 imp.attr|=ATOM_ATTR_1BP;
633 imp.attr|=ATOM_ATTR_2BP;
636 imp.attr|=ATOM_ATTR_3BP;
643 imp.attr1=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
644 imp.attr2=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
645 add_stage(mdrun,STAGE_INSERT_MIXED_ATOMS,&imp);
652 else if(!strncmp(word[1],"continue",8)) {
653 cp.runs=atoi(word[2]);
654 add_stage(mdrun,STAGE_CONTINUE,&cp);
656 else if(!strncmp(word[1],"anneal",6)) {
658 ap.runs=atoi(word[2]);
660 ap.interval=atoi(word[4]);
661 add_stage(mdrun,STAGE_ANNEAL,&ap);
663 else if(!strncmp(word[1],"set_temp",8)) {
664 if(word[2][0]=='c') {
665 stp.type=SET_TEMP_CURRENT;
669 stp.type=SET_TEMP_VALUE;
670 stp.val=atof(word[2]);
672 add_stage(mdrun,STAGE_SET_TEMP,&stp);
674 else if(!strncmp(word[1],"set_timestep",12)) {
675 stsp.tau=atof(word[2]);
676 add_stage(mdrun,STAGE_SET_TIMESTEP,&stsp);
679 printf("%s unknown stage type: %s\n",
685 printf("%s unknown keyword '%s', skipped!\n",
697 int check_pressure(t_moldyn *moldyn,t_mdrun *mdrun) {
701 if(!(mdrun->sattr&SATTR_PRELAX)) {
705 delta=moldyn->p_avg-moldyn->p_ref;
716 int check_temperature(t_moldyn *moldyn,t_mdrun *mdrun) {
720 if(!(mdrun->sattr&SATTR_TRELAX))
723 delta=moldyn->t_avg-moldyn->t_ref;
734 int displace_atom(t_moldyn *moldyn,t_mdrun *mdrun) {
736 t_displace_atom_params *dap;
740 stage=mdrun->stage.current->data;
743 atom=&(moldyn->atom[dap->nr]);
751 int del_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
754 t_del_atoms_params *delp;
758 stage=mdrun->stage.current->data;
761 for(i=0;i<moldyn->count;i++) {
762 v3_sub(&dist,&(delp->o),&(moldyn->atom[i].r));
763 //printf("%d ----> %f %f %f = %f | %f\n",i,dist.x,dist.y,dist.z,v3_absolute_square(&dist),delp->r*delp->r);
764 if(v3_absolute_square(&dist)<=(delp->r*delp->r)) {
765 del_atom(moldyn,moldyn->atom[i].tag);
766 printf("%s atom deleted: %d %d %d\n",ME,
767 moldyn->atom[i].tag,moldyn->atom[i].element,
768 moldyn->atom[i].brand);
776 int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
778 t_insert_atoms_params *iap;
788 stage=mdrun->stage.current->data;
793 v.x=0.0; v.y=0.0; v.z=0.0;
797 switch(mdrun->lattice) {
847 printf("%s unknown insertion mode: %02x\n",
853 while(cnt<iap->ins_atoms) {
856 if(iap->type!=INS_POS) {
857 r.x=rand_get_double(&(moldyn->random))*x;
858 r.y=rand_get_double(&(moldyn->random))*y;
859 r.z=rand_get_double(&(moldyn->random))*z;
870 if(iap->type!=INS_TOTAL) {
877 dmin=1000; // for sure too high!
878 for(i=0;i<moldyn->count;i++) {
879 atom=&(moldyn->atom[i]);
880 v3_sub(&dist,&(atom->r),&r);
881 check_per_bound(moldyn,&dist);
882 d=v3_absolute_square(&dist);
883 if(d<(iap->cr*iap->cr)) {
891 if(iap->type==INS_SPHERE) {
892 if((r.x-iap->x0)*(r.x-iap->x0)+
893 (r.y-iap->y0)*(r.y-iap->y0)+
894 (r.z-iap->z0)*(r.z-iap->z0)>
900 add_atom(moldyn,iap->element,
901 iap->brand,iap->attr,&r,&v);
902 printf("%s atom inserted (%d/%d): %f %f %f\n",
903 ME,(iap->cnt_steps+1)*iap->ins_atoms,
904 iap->ins_steps*iap->ins_atoms,r.x,r.y,r.z);
905 printf(" -> d2 = %f/%f\n",dmin,iap->cr*iap->cr);
912 int insert_mixed_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
915 t_insert_mixed_atoms_params *imp;
917 double x,x0,y,y0,z,z0;
918 double dmin,d,cmin,cmax;
924 stage=mdrun->stage.current->data;
938 cmin=imp->crmin*imp->crmin;
939 cmax=imp->crmax*imp->crmax;
941 while(imp->amount1|imp->amount2) {
946 r.x=rand_get_double(&(moldyn->random))*x;
947 r.y=rand_get_double(&(moldyn->random))*y;
948 r.z=rand_get_double(&(moldyn->random))*z;
952 dmin=1000.0; // for sure too high!
953 for(i=0;i<moldyn->count;i++) {
954 atom=&(moldyn->atom[i]);
955 v3_sub(&dist,&(atom->r),&r);
956 check_per_bound(moldyn,&dist);
957 d=v3_absolute_square(&dist);
969 add_atom(moldyn,imp->element1,
970 imp->brand1,imp->attr1,&r,&v);
971 printf("%s (mixed) atom inserted (%d): %f %f %f\n",
972 ME,imp->amount1,r.x,r.y,r.z);
973 printf(" -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
980 r.x=rand_get_double(&(moldyn->random))*x;
981 r.y=rand_get_double(&(moldyn->random))*y;
982 r.z=rand_get_double(&(moldyn->random))*z;
986 dmin=1000.0; // for sure too high!
987 for(i=0;i<moldyn->count;i++) {
988 atom=&(moldyn->atom[i]);
989 v3_sub(&dist,&(atom->r),&r);
990 check_per_bound(moldyn,&dist);
991 d=v3_absolute_square(&dist);
1003 add_atom(moldyn,imp->element2,
1004 imp->brand2,imp->attr2,&r,&v);
1005 printf("%s (mixed) atom inserted (%d): %f %f %f\n",
1006 ME,imp->amount2,r.x,r.y,r.z);
1007 printf(" -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
1015 int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
1018 t_chaattr_params *cap;
1022 stage=mdrun->stage.current->data;
1025 for(i=0;i<moldyn->count;i++) {
1026 atom=&(moldyn->atom[i]);
1027 if(cap->type&CHAATTR_ELEMENT) {
1028 if(cap->element!=atom->element)
1031 if(cap->type&CHAATTR_REGION) {
1032 if(cap->x0<atom->r.x)
1034 if(cap->y0<atom->r.y)
1036 if(cap->z0<atom->r.z)
1038 if(cap->x1>atom->r.x)
1040 if(cap->y1>atom->r.y)
1042 if(cap->z1>atom->r.z)
1045 atom->attr=cap->attr;
1051 int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
1054 t_chsattr_params *csp;
1056 stage=mdrun->stage.current->data;
1059 if(csp->type&CHSATTR_PCTRL) {
1061 set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
1063 set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
1065 if(csp->type&CHSATTR_TCTRL) {
1067 set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
1069 set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
1071 if(csp->type&CHSATTR_PRELAX) {
1073 mdrun->sattr&=(~(SATTR_PRELAX));
1075 mdrun->sattr|=SATTR_PRELAX;
1078 if(csp->type&CHSATTR_TRELAX) {
1080 mdrun->sattr&=(~(SATTR_TRELAX));
1082 mdrun->sattr|=SATTR_TRELAX;
1085 if(csp->type&CHSATTR_AVGRST) {
1087 mdrun->sattr|=SATTR_AVGRST;
1089 mdrun->sattr&=(~(SATTR_AVGRST));
1091 if(csp->type&CHSATTR_RSTEPS) {
1092 mdrun->relax_steps=csp->rsteps;
1098 #define stage_print(m) if(!(stage->executed)) \
1101 int mdrun_hook(void *ptr1,void *ptr2) {
1111 t_insert_atoms_params *iap;
1112 t_insert_mixed_atoms_params *imp;
1113 t_continue_params *cp;
1114 t_anneal_params *ap;
1115 t_set_temp_params *stp;
1116 t_set_timestep_params *stsp;
1126 /* return immediately if there are no more stage */
1127 if(sl->current==NULL)
1130 /* get stage description */
1131 stage=sl->current->data;
1133 /* steps in next schedule */
1134 steps=mdrun->relax_steps;
1136 /* check whether relaxation steps are necessary */
1137 if((check_pressure(moldyn,mdrun)==TRUE)&\
1138 (check_temperature(moldyn,mdrun)==TRUE)) {
1141 stage_print("\n###########################\n");
1142 stage_print("# [mdrun] executing stage #\n");
1143 stage_print("###########################\n\n");
1145 /* stage specific stuff */
1146 switch(stage->type) {
1147 case STAGE_DISPLACE_ATOM:
1148 stage_print(" -> displace atom\n\n");
1149 displace_atom(moldyn,mdrun);
1152 case STAGE_DEL_ATOMS:
1153 stage_print(" -> del atoms\n\n");
1154 del_atoms(moldyn,mdrun);
1157 case STAGE_INSERT_ATOMS:
1158 stage_print(" -> insert atoms\n\n");
1160 if(iap->cnt_steps==iap->ins_steps) {
1164 insert_atoms(moldyn,mdrun);
1170 case STAGE_INSERT_MIXED_ATOMS:
1171 stage_print(" -> insert mixed atoms\n\n");
1173 insert_mixed_atoms(moldyn,mdrun);
1179 case STAGE_CONTINUE:
1180 stage_print(" -> continue\n\n");
1181 if(stage->executed==TRUE) {
1189 stage_print(" -> anneal\n\n");
1191 if(ap->count==ap->runs) {
1195 if(moldyn->t_ref+ap->dt>=0.0)
1196 set_temperature(moldyn,
1197 moldyn->t_ref+ap->dt);
1202 stage_print(" -> change atom attributes\n\n");
1203 chaatr(moldyn,mdrun);
1207 stage_print(" -> change sys attributes\n\n");
1208 chsattr(moldyn,mdrun);
1211 case STAGE_SET_TEMP:
1212 stage_print(" -> set temperature\n\n");
1214 if(stp->type&SET_TEMP_CURRENT) {
1215 set_temperature(moldyn,moldyn->t_avg);
1218 set_temperature(moldyn,stp->val);
1222 case STAGE_SET_TIMESTEP:
1223 stage_print(" -> set timestep\n\n");
1225 mdrun->timestep=stsp->tau;
1229 stage_print(" -> fill lattice\n\n");
1231 switch(fp->lattice) {
1234 o.x=0.5*0.25*fp->lc;
1237 create_lattice(moldyn,
1240 DEFAULT_ATOM_ATTR,0,
1241 fp->lx,fp->ly,fp->lz,
1248 create_lattice(moldyn,
1251 DEFAULT_ATOM_ATTR,1,
1252 fp->lx,fp->ly,fp->lz,
1260 create_lattice(moldyn,
1265 fp->lx,fp->ly,fp->lz,
1271 moldyn_bc_check(moldyn);
1274 case STAGE_THERMAL_INIT:
1275 stage_print(" -> thermal init\n\n");
1276 thermal_init(moldyn,TRUE);
1280 printf("%s unknwon stage type\n",ME);
1284 /* mark as executed */
1285 stage->executed=TRUE;
1288 if(change_stage==TRUE) {
1289 printf("%s finished stage\n",ME);
1290 if(list_next_f(sl)==L_NO_NEXT_ELEMENT) {
1291 printf("%s no more stages\n",ME);
1301 if(mdrun->sattr&SATTR_AVGRST)
1302 average_reset(moldyn);
1306 /* continue simulation */
1307 moldyn_add_schedule(moldyn,steps,mdrun->timestep);
1312 int main(int argc,char **argv) {
1319 memset(&mdrun,0,sizeof(t_mdrun));
1320 memset(&moldyn,0,sizeof(t_moldyn));
1322 /* parse arguments */
1323 if(mdrun_parse_argv(&mdrun,argc,argv)<0)
1326 /* initialize list system */
1327 list_init_f(&(mdrun.stage));
1329 /* parse config file */
1330 mdrun_parse_config(&mdrun);
1332 /* reset the stage list */
1333 list_reset_f(&(mdrun.stage));
1337 /* prepare simulation */
1339 if(mdrun.continue_file[0]) {
1340 // read the save file
1341 moldyn_read_save_file(&moldyn,mdrun.continue_file);
1342 // manualaadjusting some stuff
1345 rand_init(&(moldyn.random),NULL,1);
1346 moldyn.random.status|=RAND_STAT_VERBOSE;
1349 moldyn_init(&moldyn,argc,argv);
1352 if(set_int_alg(&moldyn,mdrun.intalgo)<0)
1356 set_cutoff(&moldyn,mdrun.cutoff);
1357 if(set_potential(&moldyn,mdrun.potential)<0)
1359 switch(mdrun.potential) {
1360 case MOLDYN_POTENTIAL_AM:
1361 albe_mult_set_params(&moldyn,
1365 case MOLDYN_POTENTIAL_TM:
1366 tersoff_mult_set_params(&moldyn,
1370 case MOLDYN_POTENTIAL_HO:
1371 harmonic_oscillator_set_params(&moldyn,mdrun.element1);
1373 case MOLDYN_POTENTIAL_LJ:
1374 lennard_jones_set_params(&moldyn,mdrun.element1);
1377 printf("%s unknown potential: %02x\n",
1378 ME,mdrun.potential);
1382 /* if it is a continue run, reset schedule and skip lattice init */
1383 if(mdrun.continue_file[0]) {
1384 memset(&(moldyn.schedule),0,sizeof(t_moldyn_schedule));
1388 /* initial lattice and dimensions */
1389 set_dim(&moldyn,mdrun.dim.x,mdrun.dim.y,mdrun.dim.z,mdrun.vis);
1390 set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
1391 /* replaced by fill stage !!
1392 switch(mdrun.lattice) {
1394 create_lattice(&moldyn,FCC,mdrun.lc,mdrun.fill_element,
1395 mdrun.m1,DEFAULT_ATOM_ATTR,
1396 mdrun.fill_brand,mdrun.lx,
1397 mdrun.ly,mdrun.lz,NULL,0,NULL);
1400 create_lattice(&moldyn,DIAMOND,mdrun.lc,
1402 mdrun.m1,DEFAULT_ATOM_ATTR,
1403 mdrun.fill_brand,mdrun.lx,
1404 mdrun.ly,mdrun.lz,NULL,0,NULL);
1407 o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
1408 create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
1409 mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
1410 mdrun.ly,mdrun.lz,&o,0,NULL);
1411 o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
1412 create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
1413 mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
1414 mdrun.ly,mdrun.lz,&o,0,NULL);
1417 set_nn_dist(&moldyn,mdrun.nnd);
1420 printf("%s unknown lattice type: %02x\n",
1424 moldyn_bc_check(&moldyn);
1425 replaced by fill stage !! */
1427 /* temperature and pressure */
1428 set_temperature(&moldyn,mdrun.temperature);
1429 set_pressure(&moldyn,mdrun.pressure);
1430 /* replaced thermal_init stage
1431 thermal_init(&moldyn,TRUE);
1435 /* first schedule */
1436 moldyn_add_schedule(&moldyn,mdrun.prerun,mdrun.timestep);
1439 moldyn_set_log_dir(&moldyn,mdrun.sdir);
1440 moldyn_set_report(&moldyn,"CHANGE ME","CHANGE ME TOO");
1442 moldyn_set_log(&moldyn,LOG_TOTAL_ENERGY,mdrun.elog);
1444 moldyn_set_log(&moldyn,LOG_TEMPERATURE,mdrun.tlog);
1446 moldyn_set_log(&moldyn,LOG_PRESSURE,mdrun.plog);
1448 moldyn_set_log(&moldyn,LOG_VOLUME,mdrun.vlog);
1450 moldyn_set_log(&moldyn,VISUAL_STEP,mdrun.visualize);
1452 moldyn_set_log(&moldyn,SAVE_STEP,mdrun.save);
1453 moldyn_set_log(&moldyn,CREATE_REPORT,0);
1454 set_avg_skip(&moldyn,mdrun.avgskip);
1456 /* prepare the hook function */
1457 moldyn_set_schedule_hook(&moldyn,&mdrun_hook,&mdrun);
1459 /* run the simulation */
1460 moldyn_integrate(&moldyn);
1463 moldyn_shutdown(&moldyn);
1465 list_destroy_f(&(mdrun.stage));