2 * moldyn.c - molecular dynamics library main file
4 * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
12 #include <sys/types.h>
20 #include <fpu_control.h>
26 #if defined PTHREADS || defined VISUAL_THREAD
31 #include "report/report.h"
33 /* potential includes */
34 #include "potentials/harmonic_oscillator.h"
35 #include "potentials/lennard_jones.h"
36 #include "potentials/albe.h"
38 #include "potentials/tersoff_orig.h"
40 #include "potentials/tersoff.h"
54 pthread_mutex_t *amutex;
55 pthread_mutex_t emutex;
59 /* fully constrained relaxation technique - global pointers */
66 * the moldyn functions
69 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
71 printf("[moldyn] init\n");
73 /* only needed if compiled without -msse2 (float-store prob!) */
76 memset(moldyn,0,sizeof(t_moldyn));
81 rand_init(&(moldyn->random),NULL,1);
82 moldyn->random.status|=RAND_STAT_VERBOSE;
85 pthread_mutex_init(&emutex,NULL);
88 #ifdef CONSTRAINT_110_5832
89 printf("\n\n\nWARNING! WARNING! WARNING!\n\n\n");
90 printf("\n\n\n!! -- constraints enabled -- !!\n\n\n");
92 #ifdef CONSTRAINT_11X_5832
93 printf("\n\n\nWARNING! WARNING! WARNING!\n\n\n");
94 printf("\n\n\n!! -- constraints enabled -- !!\n\n\n");
99 int moldyn_shutdown(t_moldyn *moldyn) {
105 printf("[moldyn] shutdown\n");
108 for(i=0;i<moldyn->count;i++)
109 pthread_mutex_destroy(&(amutex[i]));
111 pthread_mutex_destroy(&emutex);
114 moldyn_log_shutdown(moldyn);
115 link_cell_shutdown(moldyn);
116 rand_close(&(moldyn->random));
122 int set_int_alg(t_moldyn *moldyn,u8 algo) {
124 printf("[moldyn] integration algorithm: ");
127 case MOLDYN_INTEGRATE_VERLET:
128 moldyn->integrate=velocity_verlet;
129 printf("velocity verlet\n");
132 printf("unknown integration algorithm: %02x\n",algo);
140 int set_cutoff(t_moldyn *moldyn,double cutoff) {
142 moldyn->cutoff=cutoff;
143 moldyn->cutoff_square=cutoff*cutoff;
145 printf("[moldyn] cutoff [A]: %f\n",moldyn->cutoff);
150 int set_temperature(t_moldyn *moldyn,double t_ref) {
154 printf("[moldyn] temperature [K]: %f\n",moldyn->t_ref);
159 int set_pressure(t_moldyn *moldyn,double p_ref) {
163 printf("[moldyn] pressure [bar]: %f\n",moldyn->p_ref/BAR);
168 int set_p_scale(t_moldyn *moldyn,u8 ptype,double ptc) {
170 moldyn->pt_scale&=(~(P_SCALE_MASK));
171 moldyn->pt_scale|=ptype;
174 printf("[moldyn] p scaling:\n");
176 printf(" p: %s",ptype?"yes":"no ");
178 printf(" | type: %02x | factor: %f",ptype,ptc);
184 int set_t_scale(t_moldyn *moldyn,u8 ttype,double ttc) {
186 moldyn->pt_scale&=(~(T_SCALE_MASK));
187 moldyn->pt_scale|=ttype;
190 printf("[moldyn] t scaling:\n");
192 printf(" t: %s",ttype?"yes":"no ");
194 printf(" | type: %02x | factor: %f",ttype,ttc);
200 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
202 moldyn->pt_scale=(ptype|ttype);
206 printf("[moldyn] p/t scaling:\n");
208 printf(" p: %s",ptype?"yes":"no ");
210 printf(" | type: %02x | factor: %f",ptype,ptc);
213 printf(" t: %s",ttype?"yes":"no ");
215 printf(" | type: %02x | factor: %f",ttype,ttc);
221 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
227 moldyn->volume=x*y*z;
235 printf("[moldyn] dimensions in A and A^3 respectively:\n");
236 printf(" x: %f\n",moldyn->dim.x);
237 printf(" y: %f\n",moldyn->dim.y);
238 printf(" z: %f\n",moldyn->dim.z);
239 printf(" volume: %f\n",moldyn->volume);
240 printf(" visualize simulation box: %s\n",visualize?"yes":"no");
245 int set_nn_dist(t_moldyn *moldyn,double dist) {
252 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
254 printf("[moldyn] periodic boundary conditions:\n");
257 moldyn->status|=MOLDYN_STAT_PBX;
260 moldyn->status|=MOLDYN_STAT_PBY;
263 moldyn->status|=MOLDYN_STAT_PBZ;
265 printf(" x: %s\n",x?"yes":"no");
266 printf(" y: %s\n",y?"yes":"no");
267 printf(" z: %s\n",z?"yes":"no");
272 int set_potential(t_moldyn *moldyn,u8 type) {
275 case MOLDYN_POTENTIAL_TM:
276 //moldyn->func1b=tersoff_mult_1bp;
277 moldyn->func3b_j1=tersoff_mult_3bp_j1;
278 moldyn->func3b_k1=tersoff_mult_3bp_k1;
279 moldyn->func3b_j2=tersoff_mult_3bp_j2;
280 moldyn->func3b_k2=tersoff_mult_3bp_k2;
281 moldyn->check_2b_bond=tersoff_mult_check_2b_bond;
283 case MOLDYN_POTENTIAL_AM:
284 moldyn->func3b_j1=albe_mult_3bp_j1;
285 moldyn->func3b_k1=albe_mult_3bp_k1;
286 moldyn->func3b_j2=albe_mult_3bp_j2;
287 moldyn->func3b_k2=albe_mult_3bp_k2;
288 moldyn->check_2b_bond=albe_mult_check_2b_bond;
290 case MOLDYN_POTENTIAL_HO:
291 moldyn->func2b=harmonic_oscillator;
292 moldyn->check_2b_bond=harmonic_oscillator_check_2b_bond;
294 case MOLDYN_POTENTIAL_LJ:
295 moldyn->func2b=lennard_jones;
296 moldyn->check_2b_bond=lennard_jones_check_2b_bond;
299 printf("[moldyn] set potential: unknown type %02x\n",
307 int set_avg_skip(t_moldyn *moldyn,int skip) {
309 printf("[moldyn] skip %d steps before starting average calc\n",skip);
310 moldyn->avg_skip=skip;
315 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
317 strncpy(moldyn->vlsdir,dir,127);
322 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title) {
324 strncpy(moldyn->rauthor,author,63);
325 strncpy(moldyn->rtitle,title,63);
330 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
335 printf("[moldyn] set log: ");
338 case LOG_TOTAL_ENERGY:
339 moldyn->ewrite=timer;
340 snprintf(filename,127,"%s/energy",moldyn->vlsdir);
341 moldyn->efd=open(filename,
342 O_WRONLY|O_CREAT|O_EXCL,
345 perror("[moldyn] energy log fd open");
348 dprintf(moldyn->efd,"# total energy log file\n");
349 printf("total energy (%d)\n",timer);
351 case LOG_TOTAL_MOMENTUM:
352 moldyn->mwrite=timer;
353 snprintf(filename,127,"%s/momentum",moldyn->vlsdir);
354 moldyn->mfd=open(filename,
355 O_WRONLY|O_CREAT|O_EXCL,
358 perror("[moldyn] momentum log fd open");
361 dprintf(moldyn->efd,"# total momentum log file\n");
362 printf("total momentum (%d)\n",timer);
365 moldyn->pwrite=timer;
366 snprintf(filename,127,"%s/pressure",moldyn->vlsdir);
367 moldyn->pfd=open(filename,
368 O_WRONLY|O_CREAT|O_EXCL,
371 perror("[moldyn] pressure log file\n");
374 dprintf(moldyn->pfd,"# pressure log file\n");
375 printf("pressure (%d)\n",timer);
377 case LOG_TEMPERATURE:
378 moldyn->twrite=timer;
379 snprintf(filename,127,"%s/temperature",moldyn->vlsdir);
380 moldyn->tfd=open(filename,
381 O_WRONLY|O_CREAT|O_EXCL,
384 perror("[moldyn] temperature log file\n");
387 dprintf(moldyn->tfd,"# temperature log file\n");
388 printf("temperature (%d)\n",timer);
391 moldyn->vwrite=timer;
392 snprintf(filename,127,"%s/volume",moldyn->vlsdir);
393 moldyn->vfd=open(filename,
394 O_WRONLY|O_CREAT|O_EXCL,
397 perror("[moldyn] volume log file\n");
400 dprintf(moldyn->vfd,"# volume log file\n");
401 printf("volume (%d)\n",timer);
404 moldyn->swrite=timer;
405 printf("save file (%d)\n",timer);
408 moldyn->awrite=timer;
409 ret=visual_init(moldyn,moldyn->vlsdir);
411 printf("[moldyn] visual init failure\n");
414 printf("visual file (%d)\n",timer);
417 snprintf(filename,127,"%s/report.tex",moldyn->vlsdir);
418 moldyn->rfd=open(filename,
419 O_WRONLY|O_CREAT|O_EXCL,
422 perror("[moldyn] report fd open");
425 printf("report -> ");
427 snprintf(filename,127,"%s/e_plot.scr",
429 moldyn->epfd=open(filename,
430 O_WRONLY|O_CREAT|O_EXCL,
433 perror("[moldyn] energy plot fd open");
436 dprintf(moldyn->epfd,e_plot_script);
441 snprintf(filename,127,"%s/pressure_plot.scr",
443 moldyn->ppfd=open(filename,
444 O_WRONLY|O_CREAT|O_EXCL,
447 perror("[moldyn] p plot fd open");
450 dprintf(moldyn->ppfd,pressure_plot_script);
455 snprintf(filename,127,"%s/temperature_plot.scr",
457 moldyn->tpfd=open(filename,
458 O_WRONLY|O_CREAT|O_EXCL,
461 perror("[moldyn] t plot fd open");
464 dprintf(moldyn->tpfd,temperature_plot_script);
466 printf("temperature ");
468 dprintf(moldyn->rfd,report_start,
469 moldyn->rauthor,moldyn->rtitle);
473 printf("unknown log type: %02x\n",type);
480 int moldyn_log_shutdown(t_moldyn *moldyn) {
484 printf("[moldyn] log shutdown\n");
488 dprintf(moldyn->rfd,report_energy);
489 snprintf(sc,255,"cd %s && gnuplot e_plot.scr",
494 if(moldyn->mfd) close(moldyn->mfd);
498 dprintf(moldyn->rfd,report_pressure);
499 snprintf(sc,255,"cd %s && gnuplot pressure_plot.scr",
506 dprintf(moldyn->rfd,report_temperature);
507 snprintf(sc,255,"cd %s && gnuplot temperature_plot.scr",
512 dprintf(moldyn->rfd,report_end);
514 snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
517 snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
520 snprintf(sc,255,"cd %s && dvipdf report >/dev/null 2>&1",
529 * creating lattice functions
532 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,
533 u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin,
534 t_part_params *p_params,t_defect_params *d_params,
535 t_offset_params *o_params) {
544 pthread_mutex_t *mutex;
550 /* how many atoms do we expect */
553 printf("[moldyn] WARNING: create 'none' lattice called");
555 if(type==CUBIC) new*=1;
556 if(type==FCC) new*=4;
557 if(type==DIAMOND) new*=8;
561 switch(d_params->stype) {
562 case DEFECT_STYPE_DB_X:
563 case DEFECT_STYPE_DB_Y:
564 case DEFECT_STYPE_DB_Z:
565 case DEFECT_STYPE_DB_R:
569 printf("[moldyn] WARNING: cl unknown defect\n");
574 /* allocate space for atoms */
575 ptr=realloc(moldyn->atom,(count+new)*sizeof(t_atom));
577 perror("[moldyn] realloc (create lattice)");
581 atom=&(moldyn->atom[count]);
584 ptr=realloc(amutex,(count+new)*sizeof(pthread_mutex_t));
586 perror("[moldyn] mutex realloc (add atom)");
590 mutex=&(amutex[count]);
593 /* no atoms on the boundaries (only reason: it looks better!) */
608 v3_add(&orig,&orig,&(o_params->o));
609 set_nn_dist(moldyn,lc);
610 ret=cubic_init(a,b,c,lc,atom,&orig,p_params,d_params);
611 strcpy(name,"cubic");
615 v3_scale(&orig,&orig,0.5);
617 v3_add(&orig,&orig,&(o_params->o));
618 set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
619 ret=fcc_init(a,b,c,lc,atom,&orig,p_params,d_params);
624 v3_scale(&orig,&orig,0.25);
626 v3_add(&orig,&orig,&(o_params->o));
627 set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
628 ret=diamond_init(a,b,c,lc,atom,&orig,p_params,d_params);
629 strcpy(name,"diamond");
632 printf("unknown lattice type (%02x)\n",type);
638 printf("[moldyn] creating %s lattice (lc=%f) incomplete\n",
640 printf(" (ignore for partial lattice creation)\n");
641 printf(" amount of atoms\n");
642 printf(" - expected: %d\n",new);
643 printf(" - created: %d\n",ret);
648 printf("[moldyn] created %s lattice with %d atoms\n",name,ret);
650 for(new=0;new<ret;new++) {
651 atom[new].element=element;
652 atom[new].mass=pse_mass[element];
654 atom[new].brand=brand;
655 atom[new].tag=count+new;
656 check_per_bound(moldyn,&(atom[new].r));
657 atom[new].r_0=atom[new].r;
659 pthread_mutex_init(&(mutex[new]),NULL);
663 atom[new].element=d_params->element;
664 atom[new].mass=pse_mass[d_params->element];
665 atom[new].attr=d_params->attr;
666 atom[new].brand=d_params->brand;
667 atom[new].tag=count+new;
668 check_per_bound(moldyn,&(atom[new].r));
669 atom[new].r_0=atom[new].r;
671 pthread_mutex_init(&(mutex[new]),NULL);
677 ptr=realloc(moldyn->atom,moldyn->count*sizeof(t_atom));
679 perror("[moldyn] realloc (create lattice - alloc fix)");
684 // WHAT ABOUT AMUTEX !!!!
687 ptr=realloc(moldyn->lc.subcell->list,moldyn->count*sizeof(int));
689 perror("[moldyn] list realloc (create lattice)");
692 moldyn->lc.subcell->list=ptr;
695 /* update total system mass */
696 total_mass_calc(moldyn);
701 int add_atom(t_moldyn *moldyn,int element,u8 brand,u8 attr,
702 t_3dvec *r,t_3dvec *v) {
709 count=(moldyn->count)++; // asshole style!
711 ptr=realloc(atom,(count+1)*sizeof(t_atom));
713 perror("[moldyn] realloc (add atom)");
719 ptr=realloc(moldyn->lc.subcell->list,(count+1)*sizeof(int));
721 perror("[moldyn] list realloc (add atom)");
724 moldyn->lc.subcell->list=ptr;
728 ptr=realloc(amutex,(count+1)*sizeof(pthread_mutex_t));
730 perror("[moldyn] mutex realloc (add atom)");
734 pthread_mutex_init(&(amutex[count]),NULL);
739 /* initialize new atom */
740 memset(&(atom[count]),0,sizeof(t_atom));
743 atom[count].element=element;
744 atom[count].mass=pse_mass[element];
745 atom[count].brand=brand;
746 atom[count].tag=count;
747 atom[count].attr=attr;
748 check_per_bound(moldyn,&(atom[count].r));
749 atom[count].r_0=atom[count].r;
751 /* update total system mass */
752 total_mass_calc(moldyn);
757 int del_atom(t_moldyn *moldyn,int tag) {
761 #if defined LOWMEM_LISTS || defined PTHREADS
767 new=(t_atom *)malloc((moldyn->count-1)*sizeof(t_atom));
769 perror("[moldyn]malloc (del atom)");
773 for(cnt=0;cnt<tag;cnt++)
776 for(cnt=tag+1;cnt<moldyn->count;cnt++) {
778 new[cnt-1].tag=cnt-1;
787 ptr=realloc(moldyn->lc.subcell->list,moldyn->count*sizeof(int));
789 perror("[moldyn] list realloc (del atom)");
792 moldyn->lc.subcell->list=ptr;
794 link_cell_update(moldyn);
798 ptr=realloc(amutex,moldyn->count*sizeof(pthread_mutex_t));
800 perror("[moldyn] mutex realloc (add atom)");
804 pthread_mutex_destroy(&(amutex[moldyn->count+1]));
811 #define set_atom_positions(pos) \
812 if(d_params->type) {\
813 d_o.x=0; d_o.y=0; d_o.z=0;\
814 d_d.x=0; d_d.y=0; d_d.z=0;\
815 switch(d_params->stype) {\
816 case DEFECT_STYPE_DB_X:\
820 case DEFECT_STYPE_DB_Y:\
824 case DEFECT_STYPE_DB_Z:\
828 case DEFECT_STYPE_DB_R:\
831 printf("[moldyn] WARNING: unknown defect\n");\
834 v3_add(&dr,&pos,&d_o);\
835 v3_copy(&(atom[count].r),&dr);\
837 v3_add(&dr,&pos,&d_d);\
838 v3_copy(&(atom[count].r),&dr);\
842 v3_copy(&(atom[count].r),&pos);\
847 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin,
848 t_part_params *p_params,t_defect_params *d_params) {
868 /* shift partition values */
870 p.x=p_params->p.x+(a*lc)/2.0;
871 p.y=p_params->p.y+(b*lc)/2.0;
872 p.z=p_params->p.z+(c*lc)/2.0;
881 switch(p_params->type) {
884 if(v3_absolute_square(&dist)<
885 (p_params->r*p_params->r)) {
886 set_atom_positions(r);
891 if(v3_absolute_square(&dist)>=
892 (p_params->r*p_params->r)) {
893 set_atom_positions(r);
898 if((fabs(dist.x)<p_params->d.x)&&
899 (fabs(dist.y)<p_params->d.y)&&
900 (fabs(dist.z)<p_params->d.z)) {
901 set_atom_positions(r);
906 if((fabs(dist.x)>=p_params->d.x)||
907 (fabs(dist.y)>=p_params->d.y)||
908 (fabs(dist.z)>=p_params->d.z)) {
909 set_atom_positions(r);
913 set_atom_positions(r);
923 for(i=0;i<count;i++) {
924 atom[i].r.x-=(a*lc)/2.0;
925 atom[i].r.y-=(b*lc)/2.0;
926 atom[i].r.z-=(c*lc)/2.0;
932 /* fcc lattice init */
933 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin,
934 t_part_params *p_params,t_defect_params *d_params) {
952 /* construct the basis */
953 memset(basis,0,3*sizeof(t_3dvec));
961 /* shift partition values */
963 p.x=p_params->p.x+(a*lc)/2.0;
964 p.y=p_params->p.y+(b*lc)/2.0;
965 p.z=p_params->p.z+(c*lc)/2.0;
968 /* fill up the room */
976 switch(p_params->type) {
979 if(v3_absolute_square(&dist)<
980 (p_params->r*p_params->r)) {
981 set_atom_positions(r);
986 if(v3_absolute_square(&dist)>=
987 (p_params->r*p_params->r)) {
988 set_atom_positions(r);
993 if((fabs(dist.x)<p_params->d.x)&&
994 (fabs(dist.y)<p_params->d.y)&&
995 (fabs(dist.z)<p_params->d.z)) {
996 set_atom_positions(r);
1000 v3_sub(&dist,&r,&p);
1001 if((fabs(dist.x)>=p_params->d.x)||
1002 (fabs(dist.y)>=p_params->d.y)||
1003 (fabs(dist.z)>=p_params->d.z)) {
1004 set_atom_positions(r);
1008 set_atom_positions(r);
1011 /* the three face centered atoms */
1013 v3_add(&n,&r,&basis[l]);
1014 switch(p_params->type) {
1016 v3_sub(&dist,&n,&p);
1017 if(v3_absolute_square(&dist)<
1018 (p_params->r*p_params->r)) {
1019 set_atom_positions(n);
1022 case PART_OUTSIDE_R:
1023 v3_sub(&dist,&n,&p);
1024 if(v3_absolute_square(&dist)>=
1025 (p_params->r*p_params->r)) {
1026 set_atom_positions(n);
1030 v3_sub(&dist,&n,&p);
1031 if((fabs(dist.x)<p_params->d.x)&&
1032 (fabs(dist.y)<p_params->d.y)&&
1033 (fabs(dist.z)<p_params->d.z)) {
1034 set_atom_positions(n);
1037 case PART_OUTSIDE_D:
1038 v3_sub(&dist,&n,&p);
1039 if((fabs(dist.x)>=p_params->d.x)||
1040 (fabs(dist.y)>=p_params->d.y)||
1041 (fabs(dist.z)>=p_params->d.z)) {
1042 set_atom_positions(n);
1046 set_atom_positions(n);
1057 /* coordinate transformation */
1058 for(i=0;i<count;i++) {
1059 atom[i].r.x-=(a*lc)/2.0;
1060 atom[i].r.y-=(b*lc)/2.0;
1061 atom[i].r.z-=(c*lc)/2.0;
1067 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin,
1068 t_part_params *p_params,t_defect_params *d_params) {
1073 count=fcc_init(a,b,c,lc,atom,origin,p_params,d_params);
1079 if(origin) v3_add(&o,&o,origin);
1081 count+=fcc_init(a,b,c,lc,&atom[count],&o,p_params,d_params);
1086 int destroy_atoms(t_moldyn *moldyn) {
1088 if(moldyn->atom) free(moldyn->atom);
1093 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
1096 * - gaussian distribution of velocities
1097 * - zero total momentum
1098 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
1103 t_3dvec p_total,delta;
1108 random=&(moldyn->random);
1110 printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
1112 /* gaussian distribution of velocities */
1114 for(i=0;i<moldyn->count;i++) {
1115 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
1117 v=sigma*rand_get_gauss(random);
1119 p_total.x+=atom[i].mass*v;
1121 v=sigma*rand_get_gauss(random);
1123 p_total.y+=atom[i].mass*v;
1125 v=sigma*rand_get_gauss(random);
1127 p_total.z+=atom[i].mass*v;
1130 /* zero total momentum */
1131 v3_scale(&p_total,&p_total,1.0/moldyn->count);
1132 for(i=0;i<moldyn->count;i++) {
1133 v3_scale(&delta,&p_total,1.0/atom[i].mass);
1134 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
1137 /* velocity scaling */
1138 scale_velocity(moldyn,equi_init);
1143 double total_mass_calc(t_moldyn *moldyn) {
1149 for(i=0;i<moldyn->count;i++)
1150 moldyn->mass+=moldyn->atom[i].mass;
1152 return moldyn->mass;
1155 double temperature_calc(t_moldyn *moldyn) {
1157 /* assume up to date kinetic energy, which is 3/2 N k_B T */
1160 moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
1166 double get_temperature(t_moldyn *moldyn) {
1171 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
1181 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
1184 /* get kinetic energy / temperature & count involved atoms */
1187 for(i=0;i<moldyn->count;i++) {
1188 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
1189 e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
1194 if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
1195 else return 0; /* no atoms involved in scaling! */
1197 /* (temporary) hack for e,t = 0 */
1200 if(moldyn->t_ref!=0.0) {
1201 thermal_init(moldyn,equi_init);
1205 return 0; /* no scaling needed */
1209 /* get scaling factor */
1210 scale=moldyn->t_ref/moldyn->t;
1214 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
1215 scale=1.0+(scale-1.0)*moldyn->tau/moldyn->t_tc;
1218 /* velocity scaling */
1219 for(i=0;i<moldyn->count;i++) {
1220 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
1221 v3_scale(&(atom[i].v),&(atom[i].v),scale);
1227 double ideal_gas_law_pressure(t_moldyn *moldyn) {
1231 p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
1236 double virial_sum(t_moldyn *moldyn) {
1241 /* virial (sum over atom virials) */
1249 for(i=0;i<moldyn->count;i++) {
1250 virial=&(moldyn->atom[i].virial);
1251 moldyn->virial+=(virial->xx+virial->yy+virial->zz);
1252 moldyn->vir.xx+=virial->xx;
1253 moldyn->vir.yy+=virial->yy;
1254 moldyn->vir.zz+=virial->zz;
1255 moldyn->vir.xy+=virial->xy;
1256 moldyn->vir.xz+=virial->xz;
1257 moldyn->vir.yz+=virial->yz;
1260 /* global virial (absolute coordinates) */
1261 //virial=&(moldyn->gvir);
1262 //moldyn->gv=virial->xx+virial->yy+virial->zz;
1264 return moldyn->virial;
1267 double pressure_calc(t_moldyn *moldyn) {
1271 * with W = 1/3 sum_i f_i r_i (- skipped!)
1272 * virial = sum_i f_i r_i
1274 * => P = (2 Ekin + virial) / (3V)
1277 /* assume up to date virial & up to date kinetic energy */
1279 /* pressure (atom virials) */
1280 moldyn->p=2.0*moldyn->ekin+moldyn->virial;
1281 moldyn->p/=(3.0*moldyn->volume);
1283 //moldyn->px=2.0*moldyn->ekinx+moldyn->vir.xx;
1284 //moldyn->px/=moldyn->volume;
1285 //moldyn->py=2.0*moldyn->ekiny+moldyn->vir.yy;
1286 //moldyn->py/=moldyn->volume;
1287 //moldyn->pz=2.0*moldyn->ekinz+moldyn->vir.zz;
1288 //moldyn->pz/=moldyn->volume;
1290 /* pressure (absolute coordinates) */
1291 //moldyn->gp=2.0*moldyn->ekin+moldyn->gv;
1292 //moldyn->gp/=(3.0*moldyn->volume);
1297 int average_reset(t_moldyn *moldyn) {
1299 printf("[moldyn] average reset\n");
1301 /* update skip value */
1302 moldyn->avg_skip=moldyn->total_steps;
1304 /* kinetic energy */
1308 /* potential energy */
1316 moldyn->virial_sum=0.0;
1317 //moldyn->gv_sum=0.0;
1321 //moldyn->gp_sum=0.0;
1327 int average_and_fluctuation_calc(t_moldyn *moldyn) {
1331 if(moldyn->total_steps<moldyn->avg_skip)
1334 denom=moldyn->total_steps+1-moldyn->avg_skip;
1336 /* assume up to date energies, temperature, pressure etc */
1338 /* kinetic energy */
1339 moldyn->k_sum+=moldyn->ekin;
1340 moldyn->k2_sum+=(moldyn->ekin*moldyn->ekin);
1341 moldyn->k_avg=moldyn->k_sum/denom;
1342 moldyn->k2_avg=moldyn->k2_sum/denom;
1343 moldyn->dk2_avg=moldyn->k2_avg-(moldyn->k_avg*moldyn->k_avg);
1345 /* potential energy */
1346 moldyn->v_sum+=moldyn->energy;
1347 moldyn->v2_sum+=(moldyn->energy*moldyn->energy);
1348 moldyn->v_avg=moldyn->v_sum/denom;
1349 moldyn->v2_avg=moldyn->v2_sum/denom;
1350 moldyn->dv2_avg=moldyn->v2_avg-(moldyn->v_avg*moldyn->v_avg);
1353 moldyn->t_sum+=moldyn->t;
1354 moldyn->t_avg=moldyn->t_sum/denom;
1357 moldyn->virial_sum+=moldyn->virial;
1358 moldyn->virial_avg=moldyn->virial_sum/denom;
1359 //moldyn->gv_sum+=moldyn->gv;
1360 //moldyn->gv_avg=moldyn->gv_sum/denom;
1363 moldyn->p_sum+=moldyn->p;
1364 moldyn->p_avg=moldyn->p_sum/denom;
1365 //moldyn->gp_sum+=moldyn->gp;
1366 //moldyn->gp_avg=moldyn->gp_sum/denom;
1367 moldyn->tp_sum+=moldyn->tp;
1368 moldyn->tp_avg=moldyn->tp_sum/denom;
1373 int get_heat_capacity(t_moldyn *moldyn) {
1377 /* averages needed for heat capacity calc */
1378 if(moldyn->total_steps<moldyn->avg_skip)
1381 /* (temperature average)^2 */
1382 temp2=moldyn->t_avg*moldyn->t_avg;
1383 printf("[moldyn] specific heat capacity for T=%f K [J/(kg K)]\n",
1386 /* ideal gas contribution */
1387 ighc=3.0*moldyn->count*K_BOLTZMANN/2.0;
1388 printf(" ideal gas contribution: %f\n",
1389 ighc/moldyn->mass*KILOGRAM/JOULE);
1391 /* specific heat for nvt ensemble */
1392 moldyn->c_v_nvt=moldyn->dv2_avg/(K_BOLTZMANN*temp2)+ighc;
1393 moldyn->c_v_nvt/=moldyn->mass;
1395 /* specific heat for nve ensemble */
1396 moldyn->c_v_nve=ighc/(1.0-(moldyn->dv2_avg/(ighc*K_BOLTZMANN*temp2)));
1397 moldyn->c_v_nve/=moldyn->mass;
1399 printf(" NVE: %f\n",moldyn->c_v_nve*KILOGRAM/JOULE);
1400 printf(" NVT: %f\n",moldyn->c_v_nvt*KILOGRAM/JOULE);
1401 printf(" --> <dV2> sim: %f experimental: %f\n",moldyn->dv2_avg,1.5*moldyn->count*K_B2*moldyn->t_avg*moldyn->t_avg*(1.0-1.5*moldyn->count*K_BOLTZMANN/(700*moldyn->mass*JOULE/KILOGRAM)));
1406 double thermodynamic_pressure_calc(t_moldyn *moldyn) {
1422 /* store atomic configuration + dimension */
1423 store=malloc(moldyn->count*sizeof(t_atom));
1425 printf("[moldyn] allocating store mem failed\n");
1428 memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
1433 h=(1.0-sd)*(1.0-sd)*(1.0-sd);
1434 su=pow(2.0-h,ONE_THIRD)-1.0;
1435 dv=(1.0-h)*moldyn->volume;
1437 /* scale up dimension and atom positions */
1438 scale_dim(moldyn,SCALE_UP,su,TRUE,TRUE,TRUE);
1439 scale_atoms(moldyn,SCALE_UP,su,TRUE,TRUE,TRUE);
1440 link_cell_shutdown(moldyn);
1441 link_cell_init(moldyn,QUIET);
1442 potential_force_calc(moldyn);
1445 /* restore atomic configuration + dim */
1446 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
1449 /* scale down dimension and atom positions */
1450 scale_dim(moldyn,SCALE_DOWN,sd,TRUE,TRUE,TRUE);
1451 scale_atoms(moldyn,SCALE_DOWN,sd,TRUE,TRUE,TRUE);
1452 link_cell_shutdown(moldyn);
1453 link_cell_init(moldyn,QUIET);
1454 potential_force_calc(moldyn);
1457 /* calculate pressure */
1458 moldyn->tp=-(y1-y0)/(2.0*dv);
1460 /* restore atomic configuration */
1461 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
1463 link_cell_shutdown(moldyn);
1464 link_cell_init(moldyn,QUIET);
1465 //potential_force_calc(moldyn);
1467 /* free store buffer */
1474 double get_pressure(t_moldyn *moldyn) {
1480 int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
1492 if(x) dim->x*=scale;
1493 if(y) dim->y*=scale;
1494 if(z) dim->z*=scale;
1499 int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
1510 for(i=0;i<moldyn->count;i++) {
1511 r=&(moldyn->atom[i].r);
1520 int scale_atoms_ind(t_moldyn *moldyn,double x,double y,double z) {
1525 for(i=0;i<moldyn->count;i++) {
1526 r=&(moldyn->atom[i].r);
1535 int scale_dim_ind(t_moldyn *moldyn,double x,double y,double z) {
1548 int scale_volume(t_moldyn *moldyn) {
1555 vdim=&(moldyn->vis.dim);
1559 /* scaling factor */
1560 if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
1561 scale=1.0-(moldyn->p_ref-moldyn->p)*moldyn->p_tc*moldyn->tau;
1562 scale=pow(scale,ONE_THIRD);
1565 scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
1570 sx=1.0-(moldyn->p_ref-moldyn->px)*moldyn->p_tc*moldyn->tau;
1571 sy=1.0-(moldyn->p_ref-moldyn->py)*moldyn->p_tc*moldyn->tau;
1572 sz=1.0-(moldyn->p_ref-moldyn->pz)*moldyn->p_tc*moldyn->tau;
1573 sx=pow(sx,ONE_THIRD);
1574 sy=pow(sy,ONE_THIRD);
1575 sz=pow(sz,ONE_THIRD);
1578 /* scale the atoms and dimensions */
1579 scale_atoms(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
1580 scale_dim(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
1581 //scale_atoms_ind(moldyn,sx,sy,sz);
1582 //scale_dim_ind(moldyn,sx,sy,sz);
1584 /* visualize dimensions */
1591 /* recalculate scaled volume */
1592 moldyn->volume=dim->x*dim->y*dim->z;
1594 /* adjust/reinit linkcell */
1595 if(((int)(dim->x/moldyn->cutoff)!=lc->nx)||
1596 ((int)(dim->y/moldyn->cutoff)!=lc->ny)||
1597 ((int)(dim->z/moldyn->cutoff)!=lc->nx)) {
1598 link_cell_shutdown(moldyn);
1599 link_cell_init(moldyn,QUIET);
1613 double e_kin_calc(t_moldyn *moldyn) {
1620 //moldyn->ekinx=0.0;
1621 //moldyn->ekiny=0.0;
1622 //moldyn->ekinz=0.0;
1624 for(i=0;i<moldyn->count;i++) {
1625 atom[i].ekin=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
1626 moldyn->ekin+=atom[i].ekin;
1627 //moldyn->ekinx+=0.5*atom[i].mass*atom[i].v.x*atom[i].v.x;
1628 //moldyn->ekiny+=0.5*atom[i].mass*atom[i].v.y*atom[i].v.y;
1629 //moldyn->ekinz+=0.5*atom[i].mass*atom[i].v.z*atom[i].v.z;
1632 return moldyn->ekin;
1635 double get_total_energy(t_moldyn *moldyn) {
1637 return(moldyn->ekin+moldyn->energy);
1640 t_3dvec get_total_p(t_moldyn *moldyn) {
1649 for(i=0;i<moldyn->count;i++) {
1650 v3_scale(&p,&(atom[i].v),atom[i].mass);
1651 v3_add(&p_total,&p_total,&p);
1657 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
1661 /* nn_dist is the nearest neighbour distance */
1663 tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
1672 /* linked list / cell method */
1674 int link_cell_init(t_moldyn *moldyn,u8 vol) {
1677 #ifndef LOWMEM_LISTS
1683 /* partitioning the md cell */
1684 lc->nx=moldyn->dim.x/moldyn->cutoff;
1685 lc->x=moldyn->dim.x/lc->nx;
1686 lc->ny=moldyn->dim.y/moldyn->cutoff;
1687 lc->y=moldyn->dim.y/lc->ny;
1688 lc->nz=moldyn->dim.z/moldyn->cutoff;
1689 lc->z=moldyn->dim.z/lc->nz;
1690 lc->cells=lc->nx*lc->ny*lc->nz;
1693 lc->subcell=malloc(lc->cells*sizeof(int*));
1695 lc->subcell=malloc(sizeof(t_lowmem_list));
1697 lc->subcell=malloc(lc->cells*sizeof(t_list));
1700 if(lc->subcell==NULL) {
1701 perror("[moldyn] cell init (malloc)");
1706 printf("[moldyn] FATAL: less then 27 subcells! (%d)\n",
1711 printf("[moldyn] initializing 'static' linked cells (%d)\n",
1714 printf("[moldyn] initializing 'lowmem' linked cells (%d)\n",
1717 printf("[moldyn] initializing 'dynamic' linked cells (%d)\n",
1720 printf(" x: %d x %f A\n",lc->nx,lc->x);
1721 printf(" y: %d x %f A\n",lc->ny,lc->y);
1722 printf(" z: %d x %f A\n",lc->nz,lc->z);
1727 for(i=0;i<lc->cells;i++) {
1728 lc->subcell[i]=malloc((MAX_ATOMS_PER_LIST+1)*sizeof(int));
1729 if(lc->subcell[i]==NULL) {
1730 perror("[moldyn] list init (malloc)");
1735 printf(" ---> %d malloc %p (%p)\n",
1736 i,lc->subcell[0],lc->subcell);
1740 lc->subcell->head=malloc(lc->cells*sizeof(int));
1741 if(lc->subcell->head==NULL) {
1742 perror("[moldyn] head init (malloc)");
1745 lc->subcell->list=malloc(moldyn->count*sizeof(int));
1746 if(lc->subcell->list==NULL) {
1747 perror("[moldyn] list init (malloc)");
1751 for(i=0;i<lc->cells;i++)
1752 list_init_f(&(lc->subcell[i]));
1755 /* update the list */
1756 link_cell_update(moldyn);
1761 int link_cell_update(t_moldyn *moldyn) {
1779 for(i=0;i<lc->cells;i++)
1781 memset(lc->subcell[i],-1,(MAX_ATOMS_PER_LIST+1)*sizeof(int));
1783 lc->subcell->head[i]=-1;
1785 list_destroy_f(&(lc->subcell[i]));
1788 for(count=0;count<moldyn->count;count++) {
1789 i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
1790 j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
1791 k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
1795 while(lc->subcell[i+j*nx+k*nxy][p]!=-1)
1798 if(p>=MAX_ATOMS_PER_LIST) {
1799 printf("[moldyn] FATAL: amount of atoms too high!\n");
1803 lc->subcell[i+j*nx+k*nxy][p]=count;
1806 lc->subcell->list[count]=lc->subcell->head[p];
1807 lc->subcell->head[p]=count;
1809 list_add_immediate_f(&(lc->subcell[i+j*nx+k*nxy]),
1813 printf(" ---> %d %d malloc %p (%p)\n",
1814 i,count,lc->subcell[i].current,lc->subcell);
1822 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,
1848 if(i>=nx||j>=ny||k>=nz)
1849 printf("[moldyn] WARNING: lcni %d/%d %d/%d %d/%d\n",
1852 #ifndef LOWMEM_LISTS
1853 cell[0]=lc->subcell[i+j*nx+k*a];
1855 cell[0]=lc->subcell->head[i+j*nx+k*a];
1857 for(ci=-1;ci<=1;ci++) {
1860 if((x<0)||(x>=nx)) {
1864 for(cj=-1;cj<=1;cj++) {
1867 if((y<0)||(y>=ny)) {
1871 for(ck=-1;ck<=1;ck++) {
1874 if((z<0)||(z>=nz)) {
1878 if(!(ci|cj|ck)) continue;
1880 #ifndef LOWMEM_LISTS
1881 cell[--count2]=lc->subcell[x+y*nx+z*a];
1883 cell[--count2]=lc->subcell->head[x+y*nx+z*a];
1888 #ifndef LOWMEM_LISTS
1889 cell[count1++]=lc->subcell[x+y*nx+z*a];
1891 cell[count1++]=lc->subcell->head[x+y*nx+z*a];
1903 int link_cell_shutdown(t_moldyn *moldyn) {
1905 #ifndef LOWMEM_LISTS
1913 free(lc->subcell->head);
1914 free(lc->subcell->list);
1918 for(i=0;i<lc->cells;i++) {
1920 free(lc->subcell[i]);
1922 //printf(" ---> %d free %p\n",i,lc->subcell[i].start);
1923 list_destroy_f(&(lc->subcell[i]));
1933 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
1937 t_moldyn_schedule *schedule;
1939 schedule=&(moldyn->schedule);
1940 count=++(schedule->total_sched);
1942 ptr=realloc(schedule->runs,count*sizeof(int));
1944 perror("[moldyn] realloc (runs)");
1948 schedule->runs[count-1]=runs;
1950 ptr=realloc(schedule->tau,count*sizeof(double));
1952 perror("[moldyn] realloc (tau)");
1956 schedule->tau[count-1]=tau;
1958 printf("[moldyn] schedule added:\n");
1959 printf(" number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
1965 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
1967 moldyn->schedule.hook=hook;
1968 moldyn->schedule.hook_params=hook_params;
1975 * 'integration of newtons equation' - algorithms
1979 /* start the integration */
1981 int moldyn_integrate(t_moldyn *moldyn) {
1984 unsigned int e,m,s,v,p,t,a;
1986 t_moldyn_schedule *sched;
1991 double energy_scale;
1992 struct timeval t1,t2;
1995 #ifdef VISUAL_THREAD
1997 pthread_t io_thread;
2006 sched=&(moldyn->schedule);
2009 /* initialize linked cell method */
2010 link_cell_init(moldyn,VERBOSE);
2012 /* logging & visualization */
2021 /* sqaure of some variables */
2022 moldyn->tau_square=moldyn->tau*moldyn->tau;
2024 /* get current time */
2025 gettimeofday(&t1,NULL);
2027 /* calculate initial forces */
2028 potential_force_calc(moldyn);
2033 /* some stupid checks before we actually start calculating bullshit */
2034 if(moldyn->cutoff>0.5*moldyn->dim.x)
2035 printf("[moldyn] WARNING: cutoff > 0.5 x dim.x\n");
2036 if(moldyn->cutoff>0.5*moldyn->dim.y)
2037 printf("[moldyn] WARNING: cutoff > 0.5 x dim.y\n");
2038 if(moldyn->cutoff>0.5*moldyn->dim.z)
2039 printf("[moldyn] WARNING: cutoff > 0.5 x dim.z\n");
2041 ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
2042 if(ds>0.05*moldyn->nnd)
2043 printf("[moldyn] WARNING: forces too high / tau too small!\n");
2046 /* zero absolute time */
2047 // should have right values!
2049 //moldyn->total_steps=0;
2051 /* debugging, ignore */
2054 /* zero & init moldyn copy */
2055 #ifdef VISUAL_THREAD
2056 memset(&md_copy,0,sizeof(t_moldyn));
2057 atom_copy=malloc(moldyn->count*sizeof(t_atom));
2058 if(atom_copy==NULL) {
2059 perror("[moldyn] malloc atom copy (init)");
2065 printf("##################\n");
2066 printf("# USING PTHREADS #\n");
2067 printf("##################\n");
2069 /* tell the world */
2070 printf("[moldyn] integration start, go get a coffee ...\n");
2072 /* executing the schedule */
2074 while(sched->count<sched->total_sched) {
2076 /* setting amount of runs and finite time step size */
2077 moldyn->tau=sched->tau[sched->count];
2078 moldyn->tau_square=moldyn->tau*moldyn->tau;
2079 moldyn->time_steps=sched->runs[sched->count];
2081 /* energy scaling factor (might change!) */
2082 energy_scale=moldyn->count*EV;
2084 /* integration according to schedule */
2086 for(i=0;i<moldyn->time_steps;i++) {
2088 /* integration step */
2089 moldyn->integrate(moldyn);
2091 /* calculate kinetic energy, temperature and pressure */
2093 temperature_calc(moldyn);
2095 pressure_calc(moldyn);
2097 thermodynamic_pressure_calc(moldyn);
2098 printf("\n\nDEBUG: numeric pressure calc: %f\n\n",
2102 /* calculate fluctuations + averages */
2103 average_and_fluctuation_calc(moldyn);
2106 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
2107 scale_velocity(moldyn,FALSE);
2108 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
2109 scale_volume(moldyn);
2111 /* check for log & visualization */
2113 if(!(moldyn->total_steps%e))
2114 dprintf(moldyn->efd,
2115 "%f %f %f %f %f %f\n",
2116 moldyn->time,moldyn->ekin/energy_scale,
2117 moldyn->energy/energy_scale,
2118 get_total_energy(moldyn)/energy_scale,
2119 moldyn->ekin/EV,moldyn->energy/EV);
2122 if(!(moldyn->total_steps%m)) {
2123 momentum=get_total_p(moldyn);
2124 dprintf(moldyn->mfd,
2125 "%f %f %f %f %f\n",moldyn->time,
2126 momentum.x,momentum.y,momentum.z,
2127 v3_norm(&momentum));
2131 if(!(moldyn->total_steps%p)) {
2132 dprintf(moldyn->pfd,
2133 "%f %f %f %f %f %f %f\n",moldyn->time,
2134 moldyn->p/BAR,moldyn->p_avg/BAR,
2135 moldyn->p/BAR,moldyn->p_avg/BAR,
2136 moldyn->tp/BAR,moldyn->tp_avg/BAR);
2140 if(!(moldyn->total_steps%t)) {
2141 dprintf(moldyn->tfd,
2143 moldyn->time,moldyn->t,moldyn->t_avg);
2147 if(!(moldyn->total_steps%v)) {
2148 dprintf(moldyn->vfd,
2149 "%f %f %f %f %f\n",moldyn->time,
2157 if(!(moldyn->total_steps%s)) {
2158 snprintf(dir,128,"%s/s-%08.f.save",
2159 moldyn->vlsdir,moldyn->time);
2160 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT,
2162 if(fd<0) perror("[moldyn] save fd open");
2164 write(fd,moldyn,sizeof(t_moldyn));
2165 write(fd,moldyn->atom,
2166 moldyn->count*sizeof(t_atom));
2172 if(!(moldyn->total_steps%a)) {
2173 #ifdef VISUAL_THREAD
2174 /* check whether thread has not terminated yet */
2176 ret=pthread_join(io_thread,NULL);
2179 /* prepare and start thread */
2180 if(moldyn->count!=md_copy.count) {
2184 memcpy(&md_copy,moldyn,sizeof(t_moldyn));
2186 atom_copy=malloc(moldyn->count*sizeof(t_atom));
2187 if(atom_copy==NULL) {
2188 perror("[moldyn] malloc atom copy (change)");
2192 md_copy.atom=atom_copy;
2193 memcpy(atom_copy,moldyn->atom,moldyn->count*sizeof(t_atom));
2195 ret=pthread_create(&io_thread,NULL,visual_atoms,&md_copy);
2197 perror("[moldyn] create visual atoms thread\n");
2201 visual_atoms(moldyn);
2206 /* display progress */
2210 /* get current time */
2211 gettimeofday(&t2,NULL);
2213 printf("sched:%d, steps:%d/%d, T:%4.1f/%4.1f P:%4.1f/%4.1f V:%6.1f (%d)\n",
2214 sched->count,i,moldyn->total_steps,
2215 moldyn->t,moldyn->t_avg,
2217 moldyn->p/BAR,moldyn->p_avg/BAR,
2219 moldyn->p/BAR,(moldyn->p-2.0*moldyn->ekin/(3.0*moldyn->volume))/BAR,
2222 (int)(t2.tv_sec-t1.tv_sec));
2226 /* copy over time */
2232 /* increase absolute time */
2233 moldyn->time+=moldyn->tau;
2234 moldyn->total_steps+=1;
2238 /* check for hooks */
2240 printf("\n ## schedule hook %d start ##\n",
2242 sched->hook(moldyn,sched->hook_params);
2243 printf(" ## schedule hook end ##\n");
2246 /* increase the schedule counter */
2251 /* writing a final save file! */
2253 snprintf(dir,128,"%s/s-final.save",moldyn->vlsdir);
2254 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT,S_IRUSR|S_IWUSR);
2255 if(fd<0) perror("[moldyn] save fd open");
2257 write(fd,moldyn,sizeof(t_moldyn));
2258 write(fd,moldyn->atom,
2259 moldyn->count*sizeof(t_atom));
2263 /* writing a final visual file! */
2265 visual_atoms(moldyn);
2270 /* velocity verlet */
2272 int velocity_verlet(t_moldyn *moldyn) {
2275 double tau,tau_square,h;
2278 #ifdef CONSTRAINT_11X_5832
2284 count=moldyn->count;
2286 tau_square=moldyn->tau_square;
2288 #ifdef CONSTRAINT_110_5832
2290 atom[5832].f.x=0.5*(atom[5832].f.x-atom[5832].f.y);
2291 atom[5832].f.y=-atom[5832].f.x;
2294 #ifdef CONSTRAINT_11X_5832
2298 yt=atom[5832].f.y*cos(-0.16935129)-atom[5832].f.z*sin(-0.16935129);
2299 zt=atom[5832].f.y*sin(-0.16935129)+atom[5832].f.z*cos(-0.16935129);
2301 xtt=xt*cos(M_PI/4.0)-yt*sin(M_PI/4.0);
2302 ytt=xt*sin(M_PI/4.0)+yt*sin(M_PI/4.0);
2304 // apply constraints
2306 // first trafo backwards
2307 xt=xtt*cos(M_PI/4.0)+ytt*sin(M_PI/4.0);
2308 yt=-xtt*sin(M_PI/4.0)+ytt*sin(M_PI/4.0);
2310 // second trafo backwards
2312 atom[5832].f.y=yt*cos(-0.16935129)+zt*sin(-0.16935129);
2313 atom[5832].f.z=-yt*sin(-0.16935129)+zt*cos(-0.16935129);
2316 for(i=0;i<count;i++) {
2317 /* check whether fixed atom */
2318 if(atom[i].attr&ATOM_ATTR_FP)
2322 v3_scale(&delta,&(atom[i].v),tau);
2323 #ifdef CONSTRAINT_110_5832
2329 #ifdef CONSTRAINT_11X_5832
2333 yt=delta.y*cos(-0.16935129)-delta.z*sin(-0.16935129);
2334 zt=delta.y*sin(-0.16935129)+delta.z*cos(-0.16935129);
2336 xtt=xt*cos(M_PI/4.0)-yt*sin(M_PI/4.0);
2337 ytt=xt*sin(M_PI/4.0)+yt*sin(M_PI/4.0);
2339 // apply constraints
2341 // first trafo backwards
2342 xt=xtt*cos(M_PI/4.0)+ytt*sin(M_PI/4.0);
2343 yt=-xtt*sin(M_PI/4.0)+ytt*sin(M_PI/4.0);
2345 // second trafo backwards
2347 delta.y=yt*cos(-0.16935129)+zt*sin(-0.16935129);
2348 delta.z=-yt*sin(-0.16935129)+zt*cos(-0.16935129);
2353 v3_add(&(atom[i].r),&(atom[i].r),&delta);
2355 v3_scale(&delta,&(atom[i].f),h*tau_square);
2356 #ifdef CONSTRAINT_110_5832
2362 #ifdef CONSTRAINT_11X_5832
2366 yt=delta.y*cos(-0.16935129)-delta.z*sin(-0.16935129);
2367 zt=delta.y*sin(-0.16935129)+delta.z*cos(-0.16935129);
2369 xtt=xt*cos(M_PI/4.0)-yt*sin(M_PI/4.0);
2370 ytt=xt*sin(M_PI/4.0)+yt*sin(M_PI/4.0);
2372 // apply constraints
2374 // first trafo backwards
2375 xt=xtt*cos(M_PI/4.0)+ytt*sin(M_PI/4.0);
2376 yt=-xtt*sin(M_PI/4.0)+ytt*sin(M_PI/4.0);
2378 // second trafo backwards
2380 delta.y=yt*cos(-0.16935129)+zt*sin(-0.16935129);
2381 delta.z=-yt*sin(-0.16935129)+zt*cos(-0.16935129);
2385 v3_add(&(atom[i].r),&(atom[i].r),&delta);
2386 //check_per_bound_and_care_for_pbc(moldyn,&(atom[i]));
2387 check_per_bound(moldyn,&(atom[i].r));
2389 /* velocities [actually v(t+tau/2)] */
2390 v3_scale(&delta,&(atom[i].f),h*tau);
2391 v3_add(&(atom[i].v),&(atom[i].v),&delta);
2394 /* criticial check */
2395 moldyn_bc_check(moldyn);
2397 /* neighbour list update */
2398 link_cell_update(moldyn);
2400 /* forces depending on chosen potential */
2402 // if albe, use albe force calc routine
2403 //if(moldyn->func3b_j1==albe_mult_3bp_j1)
2404 // albe_potential_force_calc(moldyn);
2406 potential_force_calc(moldyn);
2408 albe_potential_force_calc(moldyn);
2411 #ifdef CONSTRAINT_110_5832
2413 atom[5832].f.x=0.5*(atom[5832].f.x-atom[5832].f.y);
2414 atom[5832].f.y=-atom[5832].f.x;
2417 #ifdef CONSTRAINT_11X_5832
2421 yt=atom[5832].f.y*cos(-0.16935129)-atom[5832].f.z*sin(-0.16935129);
2422 zt=atom[5832].f.y*sin(-0.16935129)+atom[5832].f.z*cos(-0.16935129);
2424 xtt=xt*cos(M_PI/4.0)-yt*sin(M_PI/4.0);
2425 ytt=xt*sin(M_PI/4.0)+yt*sin(M_PI/4.0);
2427 // apply constraints
2429 // first trafo backwards
2430 xt=xtt*cos(M_PI/4.0)+ytt*sin(M_PI/4.0);
2431 yt=-xtt*sin(M_PI/4.0)+ytt*sin(M_PI/4.0);
2433 // second trafo backwards
2435 atom[5832].f.y=yt*cos(-0.16935129)+zt*sin(-0.16935129);
2436 atom[5832].f.z=-yt*sin(-0.16935129)+zt*cos(-0.16935129);
2439 for(i=0;i<count;i++) {
2440 /* check whether fixed atom */
2441 if(atom[i].attr&ATOM_ATTR_FP)
2443 /* again velocities [actually v(t+tau)] */
2444 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
2445 v3_add(&(atom[i].v),&(atom[i].v),&delta);
2454 * potentials & corresponding forces & virial routine
2458 /* generic potential and force calculation */
2460 int potential_force_calc(t_moldyn *moldyn) {
2463 t_atom *itom,*jtom,*ktom;
2467 int *neighbour_i[27];
2471 int neighbour_i[27];
2474 t_list neighbour_i[27];
2475 t_list neighbour_i2[27];
2481 count=moldyn->count;
2491 /* reset global virial */
2492 memset(&(moldyn->gvir),0,sizeof(t_virial));
2494 /* reset force, site energy and virial of every atom */
2496 i=omp_get_thread_num();
2497 #pragma omp parallel for private(virial)
2499 for(i=0;i<count;i++) {
2502 v3_zero(&(itom[i].f));
2505 virial=(&(itom[i].virial));
2513 /* reset site energy */
2518 /* get energy, force and virial of every atom */
2520 /* first (and only) loop over atoms i */
2521 for(i=0;i<count;i++) {
2523 /* single particle potential/force */
2524 if(itom[i].attr&ATOM_ATTR_1BP)
2526 moldyn->func1b(moldyn,&(itom[i]));
2528 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
2531 /* 2 body pair potential/force */
2533 link_cell_neighbour_index(moldyn,
2534 (itom[i].r.x+moldyn->dim.x/2)/lc->x,
2535 (itom[i].r.y+moldyn->dim.y/2)/lc->y,
2536 (itom[i].r.z+moldyn->dim.z/2)/lc->z,
2541 /* first loop over atoms j */
2542 if(moldyn->func2b) {
2549 while(neighbour_i[j][p]!=-1) {
2551 jtom=&(atom[neighbour_i[j][p]]);
2559 p=lc->subcell->list[p];
2561 this=&(neighbour_i[j]);
2564 if(this->start==NULL)
2568 jtom=this->current->data;
2571 if(jtom==&(itom[i]))
2574 if((jtom->attr&ATOM_ATTR_2BP)&
2575 (itom[i].attr&ATOM_ATTR_2BP)) {
2576 moldyn->func2b(moldyn,
2586 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
2592 /* 3 body potential/force */
2594 if(!(itom[i].attr&ATOM_ATTR_3BP))
2597 /* copy the neighbour lists */
2599 /* no copy needed for static lists */
2601 /* no copy needed for lowmem lists */
2603 memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
2606 /* second loop over atoms j */
2613 while(neighbour_i[j][p]!=-1) {
2615 jtom=&(atom[neighbour_i[j][p]]);
2623 p=lc->subcell->list[p];
2625 this=&(neighbour_i[j]);
2628 if(this->start==NULL)
2633 jtom=this->current->data;
2636 if(jtom==&(itom[i]))
2639 if(!(jtom->attr&ATOM_ATTR_3BP))
2645 if(moldyn->func3b_j1)
2646 moldyn->func3b_j1(moldyn,
2651 /* in first j loop, 3bp run can be skipped */
2652 if(!(moldyn->run3bp))
2655 /* first loop over atoms k */
2656 if(moldyn->func3b_k1) {
2664 while(neighbour_i[k][q]!=-1) {
2666 ktom=&(atom[neighbour_i[k][q]]);
2674 q=lc->subcell->list[q];
2676 that=&(neighbour_i2[k]);
2679 if(that->start==NULL)
2683 ktom=that->current->data;
2686 if(!(ktom->attr&ATOM_ATTR_3BP))
2692 if(ktom==&(itom[i]))
2695 moldyn->func3b_k1(moldyn,
2706 } while(list_next_f(that)!=\
2714 if(moldyn->func3b_j2)
2715 moldyn->func3b_j2(moldyn,
2720 /* second loop over atoms k */
2721 if(moldyn->func3b_k2) {
2729 while(neighbour_i[k][q]!=-1) {
2731 ktom=&(atom[neighbour_i[k][q]]);
2739 q=lc->subcell->list[q];
2741 that=&(neighbour_i2[k]);
2744 if(that->start==NULL)
2748 ktom=that->current->data;
2751 if(!(ktom->attr&ATOM_ATTR_3BP))
2757 if(ktom==&(itom[i]))
2760 moldyn->func3b_k2(moldyn,
2771 } while(list_next_f(that)!=\
2779 /* 2bp post function */
2780 if(moldyn->func3b_j3) {
2781 moldyn->func3b_j3(moldyn,
2790 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
2805 //printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
2806 if(moldyn->time>DSTART&&moldyn->time<DEND) {
2808 printf(" x: %0.40f\n",moldyn->atom[DATOM].f.x);
2809 printf(" y: %0.40f\n",moldyn->atom[DATOM].f.y);
2810 printf(" z: %0.40f\n",moldyn->atom[DATOM].f.z);
2814 /* some postprocessing */
2816 #pragma omp parallel for
2818 for(i=0;i<count;i++) {
2819 /* calculate global virial */
2820 moldyn->gvir.xx+=itom[i].r.x*itom[i].f.x;
2821 moldyn->gvir.yy+=itom[i].r.y*itom[i].f.y;
2822 moldyn->gvir.zz+=itom[i].r.z*itom[i].f.z;
2823 moldyn->gvir.xy+=itom[i].r.y*itom[i].f.x;
2824 moldyn->gvir.xz+=itom[i].r.z*itom[i].f.x;
2825 moldyn->gvir.yz+=itom[i].r.z*itom[i].f.y;
2827 /* check forces regarding the given timestep */
2828 if(v3_norm(&(itom[i].f))>\
2829 0.1*moldyn->nnd*itom[i].mass/moldyn->tau_square)
2830 printf("[moldyn] WARNING: pfc (high force: atom %d)\n",
2838 * virial calculation
2841 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
2842 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
2844 a->virial.xx+=f->x*d->x;
2845 a->virial.yy+=f->y*d->y;
2846 a->virial.zz+=f->z*d->z;
2847 a->virial.xy+=f->x*d->y;
2848 a->virial.xz+=f->x*d->z;
2849 a->virial.yz+=f->y*d->z;
2855 * periodic boundary checking
2858 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
2859 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
2870 if(moldyn->status&MOLDYN_STAT_PBX) {
2871 if(a->x>=x) a->x-=dim->x;
2872 else if(-a->x>x) a->x+=dim->x;
2874 if(moldyn->status&MOLDYN_STAT_PBY) {
2875 if(a->y>=y) a->y-=dim->y;
2876 else if(-a->y>y) a->y+=dim->y;
2878 if(moldyn->status&MOLDYN_STAT_PBZ) {
2879 if(a->z>=z) a->z-=dim->z;
2880 else if(-a->z>z) a->z+=dim->z;
2886 int check_per_bound_and_care_for_pbc(t_moldyn *moldyn,t_atom *a) {
2897 if(moldyn->status&MOLDYN_STAT_PBX) {
2902 else if(-a->r.x>x) {
2907 if(moldyn->status&MOLDYN_STAT_PBY) {
2912 else if(-a->r.y>y) {
2917 if(moldyn->status&MOLDYN_STAT_PBZ) {
2922 else if(-a->r.z>z) {
2932 * debugging / critical check functions
2935 int moldyn_bc_check(t_moldyn *moldyn) {
2948 for(i=0;i<moldyn->count;i++) {
2949 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
2950 printf("FATAL: atom %d: x: %.20f (%.20f)\n",
2951 i,atom[i].r.x,dim->x/2);
2952 printf("diagnostic:\n");
2953 printf("-----------\natom.r.x:\n");
2955 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
2958 ((byte)&(1<<k))?1:0,
2961 printf("---------------\nx=dim.x/2:\n");
2963 memcpy(&byte,(u8 *)(&x)+j,1);
2966 ((byte)&(1<<k))?1:0,
2969 if(atom[i].r.x==x) printf("the same!\n");
2970 else printf("different!\n");
2972 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
2973 printf("FATAL: atom %d: y: %.20f (%.20f)\n",
2974 i,atom[i].r.y,dim->y/2);
2975 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
2976 printf("FATAL: atom %d: z: %.20f (%.20f)\n",
2977 i,atom[i].r.z,dim->z/2);
2987 int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
2994 fd=open(file,O_RDONLY);
2996 perror("[moldyn] load save file open");
3000 fsize=lseek(fd,0,SEEK_END);
3001 lseek(fd,0,SEEK_SET);
3003 size=sizeof(t_moldyn);
3006 cnt=read(fd,moldyn,size);
3008 perror("[moldyn] load save file read (moldyn)");
3014 size=moldyn->count*sizeof(t_atom);
3016 /* correcting possible atom data offset */
3018 if(fsize!=sizeof(t_moldyn)+size) {
3019 corr=fsize-sizeof(t_moldyn)-size;
3020 printf("[moldyn] WARNING: lsf (illegal file size)\n");
3021 printf(" modifying offset:\n");
3022 printf(" - current pos: %d\n",sizeof(t_moldyn));
3023 printf(" - atom size: %d\n",size);
3024 printf(" - file size: %d\n",fsize);
3025 printf(" => correction: %d\n",corr);
3026 lseek(fd,corr,SEEK_CUR);
3029 moldyn->atom=(t_atom *)malloc(size);
3030 if(moldyn->atom==NULL) {
3031 perror("[moldyn] load save file malloc (atoms)");
3036 cnt=read(fd,moldyn->atom,size);
3038 perror("[moldyn] load save file read (atoms)");
3045 amutex=malloc(moldyn->count*sizeof(pthread_mutex_t));
3047 perror("[moldyn] load save file (mutexes)");
3050 for(cnt=0;cnt<moldyn->count;cnt++)
3051 pthread_mutex_init(&(amutex[cnt]),NULL);
3059 int moldyn_free_save_file(t_moldyn *moldyn) {
3066 int moldyn_load(t_moldyn *moldyn) {
3074 * function to find/callback all combinations of 2 body bonds
3077 int process_2b_bonds(t_moldyn *moldyn,void *data,
3078 int (*process)(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
3079 void *data,u8 bc)) {
3089 t_list neighbour[27];
3099 for(i=0;i<moldyn->count;i++) {
3100 /* neighbour indexing */
3101 link_cell_neighbour_index(moldyn,
3102 (itom[i].r.x+moldyn->dim.x/2)/lc->x,
3103 (itom[i].r.y+moldyn->dim.y/2)/lc->x,
3104 (itom[i].r.z+moldyn->dim.z/2)/lc->x,
3109 bc=(j<lc->dnlc)?0:1;
3114 while(neighbour[j][p]!=-1) {
3116 jtom=&(moldyn->atom[neighbour[j][p]]);
3124 p=lc->subcell->list[p];
3126 this=&(neighbour[j]);
3129 if(this->start==NULL)
3134 jtom=this->current->data;
3138 process(moldyn,&(itom[i]),jtom,data,bc);
3145 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
3155 * function to find neighboured atoms
3158 int process_neighbours(t_moldyn *moldyn,void *data,t_atom *atom,
3159 int (*process)(t_moldyn *moldyn,t_atom *atom,t_atom *natom,
3160 void *data,u8 bc)) {
3170 t_list neighbour[27];
3179 /* neighbour indexing */
3180 link_cell_neighbour_index(moldyn,
3181 (atom->r.x+moldyn->dim.x/2)/lc->x,
3182 (atom->r.y+moldyn->dim.y/2)/lc->x,
3183 (atom->r.z+moldyn->dim.z/2)/lc->x,
3188 bc=(j<lc->dnlc)?0:1;
3193 while(neighbour[j][p]!=-1) {
3195 natom=&(moldyn->atom[neighbour[j][p]]);
3202 natom=&(moldyn->atom[p]);
3203 p=lc->subcell->list[p];
3205 this=&(neighbour[j]);
3208 if(this->start==NULL)
3213 natom=this->current->data;
3217 process(moldyn,atom,natom,data,bc);
3224 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
3233 * post processing functions
3236 int get_line(int fd,char *line,int max) {
3243 if(count==max) return count;
3244 ret=read(fd,line+count,1);
3245 if(ret<=0) return ret;
3246 if(line[count]=='\n') {
3247 memset(line+count,0,max-count-1);
3255 int pair_correlation_init(t_moldyn *moldyn,double dr) {
3261 int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc) {
3278 for(i=0;i<moldyn->count;i++) {
3280 /* care for pb crossing */
3281 final_r.x=atom[i].r.x+atom[i].pbc[0]*moldyn->dim.x;
3282 final_r.y=atom[i].r.y+atom[i].pbc[1]*moldyn->dim.y;
3283 final_r.z=atom[i].r.z+atom[i].pbc[2]*moldyn->dim.z;
3284 /* calculate distance */
3285 v3_sub(&dist,&final_r,&(atom[i].r_0));
3286 d2=v3_absolute_square(&dist);
3300 dc[0]*=(1.0/(6.0*moldyn->time*a_cnt));
3301 dc[1]*=(1.0/(6.0*moldyn->time*b_cnt));
3302 dc[2]*=(1.0/(6.0*moldyn->time*moldyn->count));
3307 int calculate_msd(t_moldyn *moldyn,double *msd) {
3324 for(i=0;i<moldyn->count;i++) {
3326 /* care for pb crossing */
3327 if(atom[i].pbc[0]|atom[i].pbc[1]|atom[i].pbc[2]) {
3328 printf("[moldyn] msd pb crossings for atom %d\n",i);
3329 printf(" x: %d y: %d z: %d\n",
3330 atom[i].pbc[0],atom[i].pbc[1],atom[i].pbc[2]);
3332 final_r.x=atom[i].r.x+atom[i].pbc[0]*moldyn->dim.x;
3333 final_r.y=atom[i].r.y+atom[i].pbc[1]*moldyn->dim.y;
3334 final_r.z=atom[i].r.z+atom[i].pbc[2]*moldyn->dim.z;
3335 /* calculate distance */
3336 v3_sub(&dist,&final_r,&(atom[i].r_0));
3337 d2=v3_absolute_square(&dist);
3353 msd[2]/=moldyn->count;
3358 int bonding_analyze(t_moldyn *moldyn,double *cnt) {
3363 int calculate_pair_correlation_process(t_moldyn *moldyn,t_atom *itom,
3364 t_atom *jtom,void *data,u8 bc) {
3371 /* only count pairs once,
3372 * skip same atoms */
3373 if(itom->tag>=jtom->tag)
3377 * pair correlation calc
3384 v3_sub(&dist,&(jtom->r),&(itom->r));
3385 if(bc) check_per_bound(moldyn,&dist);
3386 d=v3_absolute_square(&dist);
3388 /* ignore if greater cutoff */
3389 if(d>moldyn->cutoff_square)
3392 /* fill the slots */
3396 /* should never happen but it does 8) -
3397 * related to -ffloat-store problem! */
3399 printf("[moldyn] WARNING: pcc (%d/%d)",
3405 if(itom->brand!=jtom->brand) {
3410 /* type a - type a bonds */
3412 pcc->stat[s+pcc->o1]+=1;
3414 /* type b - type b bonds */
3415 pcc->stat[s+pcc->o2]+=1;
3421 int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
3428 pcc.o1=moldyn->cutoff/dr;
3431 if(pcc.o1*dr<=moldyn->cutoff)
3432 printf("[moldyn] WARNING: pcc (low #slots)\n");
3434 printf("[moldyn] pair correlation calc info:\n");
3435 printf(" time: %f\n",moldyn->time);
3436 printf(" count: %d\n",moldyn->count);
3437 printf(" cutoff: %f\n",moldyn->cutoff);
3438 printf(" temperature: cur=%f avg=%f\n",moldyn->t,moldyn->t_avg);
3441 pcc.stat=(double *)ptr;
3444 pcc.stat=(double *)malloc(3*pcc.o1*sizeof(double));
3445 if(pcc.stat==NULL) {
3446 perror("[moldyn] pair correlation malloc");
3451 memset(pcc.stat,0,3*pcc.o1*sizeof(double));
3454 process_2b_bonds(moldyn,&pcc,calculate_pair_correlation_process);
3457 for(i=1;i<pcc.o1;i++) {
3458 // normalization: 4 pi r^2 dr
3459 // here: not double counting pairs -> 2 pi r r dr
3460 // ... and actually it's a constant times r^2
3463 pcc.stat[pcc.o1+i]/=norm;
3464 pcc.stat[pcc.o2+i]/=norm;
3469 /* todo: store/print pair correlation function */
3476 int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
3483 if(itom->tag>=jtom->tag)
3487 v3_sub(&dist,&(jtom->r),&(itom->r));
3488 if(bc) check_per_bound(moldyn,&dist);
3489 d=v3_absolute_square(&dist);
3491 /* ignore if greater or equal cutoff */
3492 if(d>moldyn->cutoff_square)
3495 /* check for potential bond */
3496 if(moldyn->check_2b_bond(moldyn,itom,jtom,bc)==FALSE)
3499 /* now count this bonding ... */
3502 /* increase total bond counter
3507 ba->acnt[jtom->tag]+=1;
3509 ba->bcnt[jtom->tag]+=1;
3512 ba->acnt[itom->tag]+=1;
3514 ba->bcnt[itom->tag]+=1;
3519 int bond_analyze(t_moldyn *moldyn,double *quality) {
3530 ba.acnt=malloc(moldyn->count*sizeof(int));
3532 perror("[moldyn] bond analyze malloc (a)");
3535 memset(ba.acnt,0,moldyn->count*sizeof(int));
3537 ba.bcnt=malloc(moldyn->count*sizeof(int));
3539 perror("[moldyn] bond analyze malloc (b)");
3542 memset(ba.bcnt,0,moldyn->count*sizeof(int));
3551 process_2b_bonds(moldyn,&ba,bond_analyze_process);
3553 for(i=0;i<moldyn->count;i++) {
3554 if(atom[i].brand==0) {
3555 if((ba.acnt[i]==0)&(ba.bcnt[i]==4))
3557 if((ba.acnt[i]==0)&(ba.bcnt[i]==3))
3561 if((ba.acnt[i]==4)&(ba.bcnt[i]==0)) {
3565 if((ba.acnt[i]==3)&(ba.bcnt[i]==0)) {
3574 quality[0]=1.0*ccnt4/bcnt;
3575 quality[1]=1.0*ccnt3/bcnt;
3578 printf("[moldyn] bond analyze: %f %f\n",
3579 1.0*ccnt4/bcnt,1.0*ccnt3/bcnt);
3586 * visualization code
3589 int visual_init(t_moldyn *moldyn,char *filebase) {
3591 strncpy(moldyn->vis.fb,filebase,128);
3596 int visual_bonds_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
3603 if(itom->tag>=jtom->tag)
3606 if(moldyn->check_2b_bond(moldyn,itom,jtom,bc)==FALSE)
3609 if((itom->attr&ATOM_ATTR_VB)|(jtom->attr&ATOM_ATTR_VB))
3610 dprintf(vb->fd,"# [B] %f %f %f %f %f %f\n",
3611 itom->r.x,itom->r.y,itom->r.z,
3612 jtom->r.x,jtom->r.y,jtom->r.z);
3617 #ifdef VISUAL_THREAD
3618 void *visual_atoms(void *ptr) {
3620 int visual_atoms(t_moldyn *moldyn) {
3631 #ifdef VISUAL_THREAD
3645 sprintf(file,"%s/atomic_conf_%08.f.xyz",v->fb,moldyn->time);
3646 vb.fd=open(file,O_WRONLY|O_CREAT|O_TRUNC,S_IRUSR|S_IWUSR);
3648 perror("open visual save file fd");
3649 #ifndef VISUAL_THREAD
3654 /* write the actual data file */
3657 dprintf(vb.fd,"# [P] %d %08.f <%f,%f,%f>\n",
3658 moldyn->count,moldyn->time,help/40.0,help/40.0,-0.8*help);
3660 // atomic configuration
3661 for(i=0;i<moldyn->count;i++) {
3662 v3_sub(&strain,&(atom[i].r),&(atom[i].r_0));
3663 check_per_bound(moldyn,&strain);
3664 // atom type, positions, color and kinetic energy
3665 dprintf(vb.fd,"%s %f %f %f %s %f\n",pse_name[atom[i].element],
3669 pse_col[atom[i].element],
3671 sqrt(v3_absolute_square(&strain)));
3674 // bonds between atoms
3675 #ifndef VISUAL_THREAD
3676 process_2b_bonds(moldyn,&vb,visual_bonds_process);
3681 dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
3682 -dim.x/2,-dim.y/2,-dim.z/2,
3683 dim.x/2,-dim.y/2,-dim.z/2);
3684 dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
3685 -dim.x/2,-dim.y/2,-dim.z/2,
3686 -dim.x/2,dim.y/2,-dim.z/2);
3687 dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
3688 dim.x/2,dim.y/2,-dim.z/2,
3689 dim.x/2,-dim.y/2,-dim.z/2);
3690 dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
3691 -dim.x/2,dim.y/2,-dim.z/2,
3692 dim.x/2,dim.y/2,-dim.z/2);
3694 dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
3695 -dim.x/2,-dim.y/2,dim.z/2,
3696 dim.x/2,-dim.y/2,dim.z/2);
3697 dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
3698 -dim.x/2,-dim.y/2,dim.z/2,
3699 -dim.x/2,dim.y/2,dim.z/2);
3700 dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
3701 dim.x/2,dim.y/2,dim.z/2,
3702 dim.x/2,-dim.y/2,dim.z/2);
3703 dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
3704 -dim.x/2,dim.y/2,dim.z/2,
3705 dim.x/2,dim.y/2,dim.z/2);
3707 dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
3708 -dim.x/2,-dim.y/2,dim.z/2,
3709 -dim.x/2,-dim.y/2,-dim.z/2);
3710 dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
3711 -dim.x/2,dim.y/2,dim.z/2,
3712 -dim.x/2,dim.y/2,-dim.z/2);
3713 dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
3714 dim.x/2,-dim.y/2,dim.z/2,
3715 dim.x/2,-dim.y/2,-dim.z/2);
3716 dprintf(vb.fd,"# [D] %f %f %f %f %f %f\n",
3717 dim.x/2,dim.y/2,dim.z/2,
3718 dim.x/2,dim.y/2,-dim.z/2);
3723 #ifdef VISUAL_THREAD
3734 * fpu cntrol functions
3737 // set rounding to double (eliminates -ffloat-store!)
3738 int fpu_set_rtd(void) {
3744 ctrl&=~_FPU_EXTENDED;