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_INSERT_ATOMS:
94 psize=sizeof(t_insert_atoms_params);
97 psize=sizeof(t_continue_params);
100 psize=sizeof(t_anneal_params);
103 psize=sizeof(t_chaattr_params);
106 psize=sizeof(t_chsattr_params);
109 printf("%s unknown stage type: %02x\n",ME,type);
113 stage=malloc(sizeof(t_stage));
115 perror("[mdrun] malloc (add stage)");
120 stage->executed=FALSE;
122 stage->params=malloc(psize);
123 if(stage->params==NULL) {
124 perror("[mdrun] malloc (stage params)");
128 memcpy(stage->params,params,psize);
130 list_add_immediate_f(&(mdrun->stage),stage);
135 int mdrun_parse_config(t_mdrun *mdrun) {
145 t_insert_atoms_params iap;
146 t_continue_params cp;
148 t_chaattr_params cap;
149 t_chsattr_params csp;
151 /* open config file */
152 fd=open(mdrun->cfile,O_RDONLY);
154 snprintf(error,128,"%s open cfile %s",ME,mdrun->cfile);
159 /* read, parse, set */
164 ret=get_line(fd,line,128);
168 // ignore # lines and \n
169 if((line[0]=='#')|(ret==1))
173 memset(&iap,0,sizeof(t_insert_atoms_params));
174 memset(&cp,0,sizeof(t_continue_params));
175 memset(&ap,0,sizeof(t_anneal_params));
176 memset(&cap,0,sizeof(t_chaattr_params));
177 memset(&csp,0,sizeof(t_chsattr_params));
179 // get command + args
183 wptr=strtok(NULL," \t");
185 wptr=strtok(line," \t");
188 strncpy(word[wcnt],wptr,32);
192 if(!strncmp(word[0],"potential",9)) {
193 if(!strncmp(word[1],"albe",4))
194 mdrun->potential=MOLDYN_POTENTIAL_AM;
195 if(!strncmp(word[1],"tersoff",7))
196 mdrun->potential=MOLDYN_POTENTIAL_TM;
197 if(!strncmp(word[1],"ho",2))
198 mdrun->potential=MOLDYN_POTENTIAL_HO;
199 if(!strncmp(word[1],"lj",2))
200 mdrun->potential=MOLDYN_POTENTIAL_LJ;
202 else if(!strncmp(word[0],"cutoff",6))
203 mdrun->cutoff=atof(word[1]);
204 else if(!strncmp(word[0],"intalgo",7)) {
205 if(!strncmp(word[1],"verlet",5))
206 mdrun->intalgo=MOLDYN_INTEGRATE_VERLET;
208 else if(!strncmp(word[0],"timestep",8))
209 mdrun->timestep=atof(word[1]);
210 else if(!strncmp(word[0],"volume",6)) {
211 mdrun->dim.x=atof(word[1]);
212 mdrun->dim.y=atof(word[2]);
213 mdrun->dim.z=atof(word[3]);
214 if(strncmp(word[4],"0",1))
217 else if(!strncmp(word[0],"pbc",3)) {
218 if(strncmp(word[1],"0",1))
222 if(strncmp(word[2],"0",1))
226 if(strncmp(word[3],"0",1))
231 else if(!strncmp(word[0],"temperature",11))
232 mdrun->temperature=atof(word[1]);
233 else if(!strncmp(word[0],"pressure",8))
234 mdrun->pressure=atof(word[1]);
235 else if(!strncmp(word[0],"lattice",7)) {
236 if(!strncmp(word[1],"zincblende",10))
237 mdrun->lattice=ZINCBLENDE;
238 if(!strncmp(word[1],"fcc",3))
240 if(!strncmp(word[1],"diamond",7))
241 mdrun->lattice=DIAMOND;
243 else if(!strncmp(word[0],"element1",8)) {
244 mdrun->element1=atoi(word[1]);
245 switch(mdrun->element1) {
253 printf("%s unknown element1: %s|%d\n",
254 ME,word[1],mdrun->element1);
258 else if(!strncmp(word[0],"element2",8)) {
259 mdrun->element2=atoi(word[1]);
260 switch(mdrun->element2) {
268 printf("%s unknown element2: %s|%d\n",
269 ME,word[1],mdrun->element2);
273 else if(!strncmp(word[0],"fill",6)) {
274 // only lc mode by now
275 mdrun->lx=atoi(word[2]);
276 mdrun->ly=atoi(word[3]);
277 mdrun->lz=atoi(word[4]);
279 else if(!strncmp(word[0],"aattr",5)) {
280 // for aatrib line we need a special stage
281 // containing one schedule of 0 loops ...
282 for(i=0;i<strlen(word[1]);i++) {
285 cap.type|=CHAATTR_TOTALV;
288 cap.type|=CHAATTR_REGION;
291 cap.type|=CHAATTR_ELEMENT;
298 if(cap.type&CHAATTR_REGION) {
299 cap.x0=atof(word[1]);
300 cap.y0=atof(word[2]);
301 cap.z0=atof(word[3]);
302 cap.x1=atof(word[4]);
303 cap.y1=atof(word[5]);
304 cap.z1=atof(word[6]);
307 if(cap.type&CHAATTR_ELEMENT) {
308 cap.element=atoi(word[i]);
312 for(i=0;i<strlen(wptr);i++) {
315 cap.attr|=ATOM_ATTR_VB;
318 cap.attr|=ATOM_ATTR_HB;
321 cap.attr|=ATOM_ATTR_VA;
324 cap.attr|=ATOM_ATTR_FP;
327 cap.attr|=ATOM_ATTR_1BP;
330 cap.attr|=ATOM_ATTR_2BP;
333 cap.attr|=ATOM_ATTR_3BP;
339 add_stage(mdrun,STAGE_CHAATTR,&cap);
341 else if(!strncmp(word[0],"sattr",5)) {
342 // for satrib line we need a special stage
343 // containing one schedule of 0 loops ...
344 for(i=1;i<wcnt;i++) {
345 if(!strncmp(word[i],"pctrl",5)) {
346 csp.ptau=atof(word[++i]);
348 if(!strncmp(word[i],"tctrl",5)) {
349 csp.ttau=atof(word[++i]);
351 if(!strncmp(word[i],"prelax",6)) {
352 csp.dp=atof(word[++i]);
354 if(!strncmp(word[i],"trelax",6)) {
355 csp.dt=atof(word[++i]);
357 if(!strncmp(word[i],"rsteps",6)) {
358 csp.rsteps=atoi(word[++i]);
360 if(!strncmp(word[i],"avgrst",6)) {
361 csp.avgrst=atoi(word[++i]);
364 add_stage(mdrun,STAGE_CHSATTR,&csp);
366 else if(!strncmp(word[0],"prerun",6))
367 mdrun->prerun=atoi(word[1]);
368 else if(!strncmp(word[0],"avgskip",7))
369 mdrun->avgskip=atoi(word[1]);
370 else if(!strncmp(word[0],"elog",4))
371 mdrun->elog=atoi(word[1]);
372 else if(!strncmp(word[0],"tlog",4))
373 mdrun->tlog=atoi(word[1]);
374 else if(!strncmp(word[0],"plog",4))
375 mdrun->plog=atoi(word[1]);
376 else if(!strncmp(word[0],"vlog",4))
377 mdrun->vlog=atoi(word[1]);
378 else if(!strncmp(word[0],"save",4))
379 mdrun->save=atoi(word[1]);
380 else if(!strncmp(word[0],"visualize",9))
381 mdrun->visualize=atoi(word[1]);
382 else if(!strncmp(word[0],"stage",5)) {
383 // for every stage line, add a stage
384 if(!strncmp(word[1],"ins_atoms",9)) {
385 iap.ins_steps=atoi(word[2]);
386 iap.ins_atoms=atoi(word[3]);
387 iap.element=atoi(word[4]);
388 iap.element=atoi(word[4]);
389 iap.brand=atoi(word[5]);
390 for(i=0;i<strlen(word[6]);i++) {
393 iap.attr|=ATOM_ATTR_VB;
396 iap.attr|=ATOM_ATTR_HB;
399 iap.attr|=ATOM_ATTR_VA;
402 iap.attr|=ATOM_ATTR_FP;
405 iap.attr|=ATOM_ATTR_1BP;
408 iap.attr|=ATOM_ATTR_2BP;
411 iap.attr|=ATOM_ATTR_3BP;
417 // only rand mode by now
422 iap.x0=atof(word[8]);
423 iap.y0=atof(word[9]);
424 iap.z0=atof(word[10]);
425 iap.x1=atof(word[11]);
426 iap.y1=atof(word[12]);
427 iap.z1=atof(word[13]);
429 add_stage(mdrun,STAGE_INSERT_ATOMS,&iap);
431 else if(!strncmp(word[1],"continue",8)) {
432 cp.runs=atoi(word[2]);
433 add_stage(mdrun,STAGE_CONTINUE,&cp);
435 else if(!strncmp(word[1],"anneal",6)) {
437 ap.runs=atoi(word[2]);
439 add_stage(mdrun,STAGE_ANNEAL,&ap);
442 printf("%s unknown stage type: %s\n",
448 printf("%s unknown keyword '%s', skipped!\n",
460 int check_pressure(t_moldyn *moldyn,t_mdrun *mdrun) {
464 if(!(mdrun->sattr&SATTR_PRELAX))
467 delta=moldyn->p_avg-moldyn->p_ref;
478 int check_temperature(t_moldyn *moldyn,t_mdrun *mdrun) {
482 if(!(mdrun->sattr&SATTR_TRELAX))
485 delta=moldyn->t_avg-moldyn->t_ref;
496 int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
498 t_insert_atoms_params *iap;
508 stage=mdrun->stage.current->data;
513 v.x=0.0; v.y=0.0; v.z=0.0;
535 printf("%s unknown insertion mode: %02x\n",
541 while(cnt<iap->ins_atoms) {
544 r.x=(rand_get_double(&(moldyn->random))-0.5)*x+x0;
545 r.y=(rand_get_double(&(moldyn->random))-0.5)*y+y0;
546 r.z=(rand_get_double(&(moldyn->random))-0.5)*z+z0;
549 dmin=1000; // for sure too high!
550 for(i=0;i<moldyn->count;i++) {
551 atom=&(moldyn->atom[i]);
552 v3_sub(&dist,&(atom->r),&r);
553 check_per_bound(moldyn,&dist);
554 d=v3_absolute_square(&dist);
555 if(d<(iap->cr*iap->cr)) {
564 add_atom(moldyn,iap->element,pse_mass[iap->element],
565 iap->brand,iap->attr,&r,&v);
566 printf("%s atom inserted: %f %f %f | d squared = %f\n",
567 ME,r.x,r.y,r.z,dmin);
574 int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
577 t_chaattr_params *cap;
581 stage=mdrun->stage.current->data;
584 for(i=0;i<moldyn->count;i++) {
585 atom=&(moldyn->atom[i]);
586 if(cap->type&CHAATTR_ELEMENT) {
587 if(cap->element!=atom->element)
590 if(cap->type&CHAATTR_REGION) {
591 if(cap->x0<atom->r.x)
593 if(cap->y0<atom->r.y)
595 if(cap->z0<atom->r.z)
597 if(cap->x1>atom->r.x)
599 if(cap->y1>atom->r.y)
601 if(cap->z1>atom->r.z)
604 atom->attr=cap->attr;
610 int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
613 t_chsattr_params *csp;
615 stage=mdrun->stage.current->data;
618 if(csp->type&CHSATTR_PCTRL) {
620 set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
622 set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
624 if(csp->type&CHSATTR_TCTRL) {
626 set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
628 set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
630 if(csp->type&CHSATTR_PRELAX) {
632 mdrun->sattr&=(~(SATTR_PRELAX));
634 mdrun->sattr|=SATTR_PRELAX;
637 if(csp->type&CHSATTR_TRELAX) {
639 mdrun->sattr&=(~(SATTR_TRELAX));
641 mdrun->sattr|=SATTR_TRELAX;
644 if(csp->type&CHSATTR_AVGRST) {
646 mdrun->sattr|=CHSATTR_AVGRST;
648 mdrun->sattr&=(~(CHSATTR_AVGRST));
650 if(csp->type&CHSATTR_RSTEPS) {
651 mdrun->relax_steps=csp->rsteps;
657 int mdrun_hook(void *ptr1,void *ptr2) {
667 t_insert_atoms_params *iap;
668 t_continue_params *cp;
678 /* return immediately if there are no more stage */
679 if(sl->current==NULL)
682 /* get stage description */
683 stage=sl->current->data;
685 /* default steps and tau values */
686 steps=mdrun->relax_steps;
689 /* check whether relaxation steps are necessary */
690 if(!((check_pressure(moldyn,mdrun)==FALSE)|\
691 (check_temperature(moldyn,mdrun)==FALSE))) {
693 /* stage specific stuff */
694 switch(stage->type) {
695 case STAGE_INSERT_ATOMS:
697 if(iap->cnt_steps==iap->ins_steps) {
701 insert_atoms(moldyn,mdrun);
705 if(stage->executed==TRUE) {
714 if(ap->count==ap->runs) {
718 set_temperature(moldyn,moldyn->t_ref+ap->dt);
722 chaatr(moldyn,mdrun);
726 chsattr(moldyn,mdrun);
730 printf("%s unknwon stage type\n",ME);
734 /* mark as executed */
735 stage->executed=TRUE;
738 if(change_stage==TRUE) {
739 printf("%s finished stage\n",ME);
740 if(list_next_f(sl)==L_NO_NEXT_ELEMENT) {
741 printf("%s no more stages\n",ME);
752 if(mdrun->sattr&SATTR_AVGRST)
753 average_reset(moldyn);
757 /* continue simulation */
758 moldyn_add_schedule(moldyn,steps,tau);
763 int main(int argc,char **argv) {
769 /* clear mdrun struct */
770 memset(&mdrun,0,sizeof(t_mdrun));
772 /* parse arguments */
773 if(mdrun_parse_argv(&mdrun,argc,argv)<0)
776 /* initialize list system */
777 list_init_f(&(mdrun.stage));
779 /* parse config file */
780 mdrun_parse_config(&mdrun);
782 /* reset the stage list */
783 list_reset_f(&(mdrun.stage));
787 /* prepare simulation */
788 moldyn_init(&moldyn,argc,argv);
789 if(set_int_alg(&moldyn,mdrun.intalgo)<0)
791 set_cutoff(&moldyn,mdrun.cutoff);
792 if(set_potential(&moldyn,mdrun.potential)<0)
794 switch(mdrun.potential) {
795 case MOLDYN_POTENTIAL_AM:
796 albe_mult_set_params(&moldyn,
800 case MOLDYN_POTENTIAL_TM:
801 tersoff_mult_set_params(&moldyn,
805 case MOLDYN_POTENTIAL_HO:
806 harmonic_oscillator_set_params(&moldyn,mdrun.element1);
808 case MOLDYN_POTENTIAL_LJ:
809 lennard_jones_set_params(&moldyn,mdrun.element1);
812 printf("%s unknown potential: %02x\n",
816 set_dim(&moldyn,mdrun.dim.x,mdrun.dim.y,mdrun.dim.z,mdrun.vis);
817 set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
818 switch(mdrun.lattice) {
820 create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
821 mdrun.m1,0,0,mdrun.lx,
822 mdrun.ly,mdrun.lz,NULL);
825 create_lattice(&moldyn,DIAMOND,mdrun.lc,mdrun.element1,
826 mdrun.m1,0,0,mdrun.lx,
827 mdrun.ly,mdrun.lz,NULL);
830 o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
831 create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
832 mdrun.m1,0,0,mdrun.lx,
833 mdrun.ly,mdrun.lz,&o);
834 o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
835 create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
836 mdrun.m2,0,1,mdrun.lx,
837 mdrun.ly,mdrun.lz,&o);
840 printf("%s unknown lattice type: %02x\n",
844 moldyn_bc_check(&moldyn);
845 set_temperature(&moldyn,mdrun.temperature);
846 set_pressure(&moldyn,mdrun.pressure);
847 thermal_init(&moldyn,TRUE);
848 moldyn_add_schedule(&moldyn,mdrun.prerun,mdrun.timestep);
849 moldyn_set_log_dir(&moldyn,mdrun.sdir);
850 moldyn_set_report(&moldyn,"CHANGE ME","CHANGE ME TOO");
852 moldyn_set_log(&moldyn,LOG_TOTAL_ENERGY,mdrun.elog);
854 moldyn_set_log(&moldyn,LOG_TEMPERATURE,mdrun.tlog);
856 moldyn_set_log(&moldyn,LOG_PRESSURE,mdrun.plog);
858 moldyn_set_log(&moldyn,LOG_VOLUME,mdrun.vlog);
860 moldyn_set_log(&moldyn,VISUAL_STEP,mdrun.visualize);
862 moldyn_set_log(&moldyn,SAVE_STEP,mdrun.save);
863 moldyn_set_log(&moldyn,CREATE_REPORT,0);
864 set_avg_skip(&moldyn,mdrun.avgskip);
866 /* prepare the hook function */
867 moldyn_set_schedule_hook(&moldyn,&mdrun_hook,&mdrun);
869 /* run the simulation */
870 moldyn_integrate(&moldyn);
873 moldyn_shutdown(&moldyn);
875 list_destroy_f(&(mdrun.stage));