2 * moldyn.c - molecular dynamics library main file
4 * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
12 #include <sys/types.h>
21 #include "report/report.h"
24 * global variables, pse and atom colors (only needed here)
27 static char *pse_name[]={
49 static char *pse_col[]={
72 * the moldyn functions
75 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
77 printf("[moldyn] init\n");
79 memset(moldyn,0,sizeof(t_moldyn));
84 rand_init(&(moldyn->random),NULL,1);
85 moldyn->random.status|=RAND_STAT_VERBOSE;
90 int moldyn_shutdown(t_moldyn *moldyn) {
92 printf("[moldyn] shutdown\n");
94 moldyn_log_shutdown(moldyn);
95 link_cell_shutdown(moldyn);
96 rand_close(&(moldyn->random));
102 int set_int_alg(t_moldyn *moldyn,u8 algo) {
104 printf("[moldyn] integration algorithm: ");
107 case MOLDYN_INTEGRATE_VERLET:
108 moldyn->integrate=velocity_verlet;
109 printf("velocity verlet\n");
112 printf("unknown integration algorithm: %02x\n",algo);
120 int set_cutoff(t_moldyn *moldyn,double cutoff) {
122 moldyn->cutoff=cutoff;
124 printf("[moldyn] cutoff [A]: %f\n",moldyn->cutoff);
129 int set_bondlen(t_moldyn *moldyn,double b0,double b1,double bm) {
131 moldyn->bondlen[0]=b0*b0;
132 moldyn->bondlen[1]=b1*b1;
134 moldyn->bondlen[2]=b0*b1;
136 moldyn->bondlen[2]=bm*bm;
141 int set_temperature(t_moldyn *moldyn,double t_ref) {
145 printf("[moldyn] temperature [K]: %f\n",moldyn->t_ref);
150 int set_pressure(t_moldyn *moldyn,double p_ref) {
154 printf("[moldyn] pressure [bar]: %f\n",moldyn->p_ref/BAR);
159 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
161 moldyn->pt_scale=(ptype|ttype);
165 printf("[moldyn] p/t scaling:\n");
167 printf(" p: %s",ptype?"yes":"no ");
169 printf(" | type: %02x | factor: %f",ptype,ptc);
172 printf(" t: %s",ttype?"yes":"no ");
174 printf(" | type: %02x | factor: %f",ttype,ttc);
180 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
186 moldyn->volume=x*y*z;
194 moldyn->dv=0.000001*moldyn->volume;
196 printf("[moldyn] dimensions in A and A^3 respectively:\n");
197 printf(" x: %f\n",moldyn->dim.x);
198 printf(" y: %f\n",moldyn->dim.y);
199 printf(" z: %f\n",moldyn->dim.z);
200 printf(" volume: %f\n",moldyn->volume);
201 printf(" visualize simulation box: %s\n",visualize?"yes":"no");
202 printf(" delta volume (pressure calc): %f\n",moldyn->dv);
207 int set_nn_dist(t_moldyn *moldyn,double dist) {
214 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
216 printf("[moldyn] periodic boundary conditions:\n");
219 moldyn->status|=MOLDYN_STAT_PBX;
222 moldyn->status|=MOLDYN_STAT_PBY;
225 moldyn->status|=MOLDYN_STAT_PBZ;
227 printf(" x: %s\n",x?"yes":"no");
228 printf(" y: %s\n",y?"yes":"no");
229 printf(" z: %s\n",z?"yes":"no");
234 int set_potential1b(t_moldyn *moldyn,pf_func1b func) {
241 int set_potential2b(t_moldyn *moldyn,pf_func2b func) {
248 int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func) {
250 moldyn->func3b_j1=func;
255 int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func) {
257 moldyn->func3b_j2=func;
262 int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func) {
264 moldyn->func3b_j3=func;
269 int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func) {
271 moldyn->func3b_k1=func;
276 int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func) {
278 moldyn->func3b_k2=func;
283 int set_potential_params(t_moldyn *moldyn,void *params) {
285 moldyn->pot_params=params;
290 int set_avg_skip(t_moldyn *moldyn,int skip) {
292 printf("[moldyn] skip %d steps before starting average calc\n",skip);
293 moldyn->avg_skip=skip;
298 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
300 strncpy(moldyn->vlsdir,dir,127);
305 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title) {
307 strncpy(moldyn->rauthor,author,63);
308 strncpy(moldyn->rtitle,title,63);
313 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
318 printf("[moldyn] set log: ");
321 case LOG_TOTAL_ENERGY:
322 moldyn->ewrite=timer;
323 snprintf(filename,127,"%s/energy",moldyn->vlsdir);
324 moldyn->efd=open(filename,
325 O_WRONLY|O_CREAT|O_EXCL,
328 perror("[moldyn] energy log fd open");
331 dprintf(moldyn->efd,"# total energy log file\n");
332 printf("total energy (%d)\n",timer);
334 case LOG_TOTAL_MOMENTUM:
335 moldyn->mwrite=timer;
336 snprintf(filename,127,"%s/momentum",moldyn->vlsdir);
337 moldyn->mfd=open(filename,
338 O_WRONLY|O_CREAT|O_EXCL,
341 perror("[moldyn] momentum log fd open");
344 dprintf(moldyn->efd,"# total momentum log file\n");
345 printf("total momentum (%d)\n",timer);
348 moldyn->pwrite=timer;
349 snprintf(filename,127,"%s/pressure",moldyn->vlsdir);
350 moldyn->pfd=open(filename,
351 O_WRONLY|O_CREAT|O_EXCL,
354 perror("[moldyn] pressure log file\n");
357 dprintf(moldyn->pfd,"# pressure log file\n");
358 printf("pressure (%d)\n",timer);
360 case LOG_TEMPERATURE:
361 moldyn->twrite=timer;
362 snprintf(filename,127,"%s/temperature",moldyn->vlsdir);
363 moldyn->tfd=open(filename,
364 O_WRONLY|O_CREAT|O_EXCL,
367 perror("[moldyn] temperature log file\n");
370 dprintf(moldyn->tfd,"# temperature log file\n");
371 printf("temperature (%d)\n",timer);
374 moldyn->swrite=timer;
375 printf("save file (%d)\n",timer);
378 moldyn->vwrite=timer;
379 ret=visual_init(moldyn,moldyn->vlsdir);
381 printf("[moldyn] visual init failure\n");
384 printf("visual file (%d)\n",timer);
387 snprintf(filename,127,"%s/report.tex",moldyn->vlsdir);
388 moldyn->rfd=open(filename,
389 O_WRONLY|O_CREAT|O_EXCL,
392 perror("[moldyn] report fd open");
395 printf("report -> ");
397 snprintf(filename,127,"%s/e_plot.scr",
399 moldyn->epfd=open(filename,
400 O_WRONLY|O_CREAT|O_EXCL,
403 perror("[moldyn] energy plot fd open");
406 dprintf(moldyn->epfd,e_plot_script);
411 snprintf(filename,127,"%s/pressure_plot.scr",
413 moldyn->ppfd=open(filename,
414 O_WRONLY|O_CREAT|O_EXCL,
417 perror("[moldyn] p plot fd open");
420 dprintf(moldyn->ppfd,pressure_plot_script);
425 snprintf(filename,127,"%s/temperature_plot.scr",
427 moldyn->tpfd=open(filename,
428 O_WRONLY|O_CREAT|O_EXCL,
431 perror("[moldyn] t plot fd open");
434 dprintf(moldyn->tpfd,temperature_plot_script);
436 printf("temperature ");
438 dprintf(moldyn->rfd,report_start,
439 moldyn->rauthor,moldyn->rtitle);
443 printf("unknown log type: %02x\n",type);
450 int moldyn_log_shutdown(t_moldyn *moldyn) {
454 printf("[moldyn] log shutdown\n");
458 dprintf(moldyn->rfd,report_energy);
459 snprintf(sc,255,"cd %s && gnuplot e_plot.scr",
464 if(moldyn->mfd) close(moldyn->mfd);
468 dprintf(moldyn->rfd,report_pressure);
469 snprintf(sc,255,"cd %s && gnuplot pressure_plot.scr",
476 dprintf(moldyn->rfd,report_temperature);
477 snprintf(sc,255,"cd %s && gnuplot temperature_plot.scr",
482 dprintf(moldyn->rfd,report_end);
484 snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
487 snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
490 snprintf(sc,255,"cd %s && dvipdf report >/dev/null 2>&1",
499 * creating lattice functions
502 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
503 u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin) {
514 /* how many atoms do we expect */
515 if(type==CUBIC) new*=1;
516 if(type==FCC) new*=4;
517 if(type==DIAMOND) new*=8;
519 /* allocate space for atoms */
520 ptr=realloc(moldyn->atom,(count+new)*sizeof(t_atom));
522 perror("[moldyn] realloc (create lattice)");
526 atom=&(moldyn->atom[count]);
528 /* no atoms on the boundaries (only reason: it looks better!) */
542 set_nn_dist(moldyn,lc);
543 ret=cubic_init(a,b,c,lc,atom,&orig);
547 v3_scale(&orig,&orig,0.5);
548 set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
549 ret=fcc_init(a,b,c,lc,atom,&orig);
553 v3_scale(&orig,&orig,0.25);
554 set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
555 ret=diamond_init(a,b,c,lc,atom,&orig);
558 printf("unknown lattice type (%02x)\n",type);
564 printf("[moldyn] creating lattice failed\n");
565 printf(" amount of atoms\n");
566 printf(" - expected: %d\n",new);
567 printf(" - created: %d\n",ret);
572 printf("[moldyn] created lattice with %d atoms\n",new);
574 for(ret=0;ret<new;ret++) {
575 atom[ret].element=element;
578 atom[ret].brand=brand;
579 atom[ret].tag=count+ret;
580 check_per_bound(moldyn,&(atom[ret].r));
581 atom[ret].r_0=atom[ret].r;
584 /* update total system mass */
585 total_mass_calc(moldyn);
590 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
591 t_3dvec *r,t_3dvec *v) {
598 count=(moldyn->count)++;
600 ptr=realloc(atom,(count+1)*sizeof(t_atom));
602 perror("[moldyn] realloc (add atom)");
610 atom[count].element=element;
611 atom[count].mass=mass;
612 atom[count].brand=brand;
613 atom[count].tag=count;
614 atom[count].attr=attr;
615 check_per_bound(moldyn,&(atom[count].r));
616 atom[count].r_0=atom[count].r;
618 /* update total system mass */
619 total_mass_calc(moldyn);
624 int del_atom(t_moldyn *moldyn,int tag) {
631 new=(t_atom *)malloc((moldyn->count-1)*sizeof(t_atom));
633 perror("[moldyn]malloc (del atom)");
637 for(cnt=0;cnt<tag;cnt++)
640 for(cnt=tag+1;cnt<moldyn->count;cnt++) {
642 new[cnt-1].tag=cnt-1;
654 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
673 v3_copy(&(atom[count].r),&r);
682 for(i=0;i<count;i++) {
683 atom[i].r.x-=(a*lc)/2.0;
684 atom[i].r.y-=(b*lc)/2.0;
685 atom[i].r.z-=(c*lc)/2.0;
691 /* fcc lattice init */
692 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
705 /* construct the basis */
706 memset(basis,0,3*sizeof(t_3dvec));
714 /* fill up the room */
722 v3_copy(&(atom[count].r),&r);
725 /* the three face centered atoms */
727 v3_add(&n,&r,&basis[l]);
728 v3_copy(&(atom[count].r),&n);
737 /* coordinate transformation */
738 for(i=0;i<count;i++) {
739 atom[i].r.x-=(a*lc)/2.0;
740 atom[i].r.y-=(b*lc)/2.0;
741 atom[i].r.z-=(c*lc)/2.0;
747 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
752 count=fcc_init(a,b,c,lc,atom,origin);
758 if(origin) v3_add(&o,&o,origin);
760 count+=fcc_init(a,b,c,lc,&atom[count],&o);
765 int destroy_atoms(t_moldyn *moldyn) {
767 if(moldyn->atom) free(moldyn->atom);
772 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
775 * - gaussian distribution of velocities
776 * - zero total momentum
777 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
782 t_3dvec p_total,delta;
787 random=&(moldyn->random);
789 printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
791 /* gaussian distribution of velocities */
793 for(i=0;i<moldyn->count;i++) {
794 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
796 v=sigma*rand_get_gauss(random);
798 p_total.x+=atom[i].mass*v;
800 v=sigma*rand_get_gauss(random);
802 p_total.y+=atom[i].mass*v;
804 v=sigma*rand_get_gauss(random);
806 p_total.z+=atom[i].mass*v;
809 /* zero total momentum */
810 v3_scale(&p_total,&p_total,1.0/moldyn->count);
811 for(i=0;i<moldyn->count;i++) {
812 v3_scale(&delta,&p_total,1.0/atom[i].mass);
813 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
816 /* velocity scaling */
817 scale_velocity(moldyn,equi_init);
822 double total_mass_calc(t_moldyn *moldyn) {
828 for(i=0;i<moldyn->count;i++)
829 moldyn->mass+=moldyn->atom[i].mass;
834 double temperature_calc(t_moldyn *moldyn) {
836 /* assume up to date kinetic energy, which is 3/2 N k_B T */
838 moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
843 double get_temperature(t_moldyn *moldyn) {
848 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
858 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
861 /* get kinetic energy / temperature & count involved atoms */
864 for(i=0;i<moldyn->count;i++) {
865 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
866 e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
871 if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
872 else return 0; /* no atoms involved in scaling! */
874 /* (temporary) hack for e,t = 0 */
877 if(moldyn->t_ref!=0.0) {
878 thermal_init(moldyn,equi_init);
882 return 0; /* no scaling needed */
886 /* get scaling factor */
887 scale=moldyn->t_ref/moldyn->t;
891 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
892 scale=1.0+(scale-1.0)/moldyn->t_tc;
895 /* velocity scaling */
896 for(i=0;i<moldyn->count;i++) {
897 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
898 v3_scale(&(atom[i].v),&(atom[i].v),scale);
904 double ideal_gas_law_pressure(t_moldyn *moldyn) {
908 p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
913 double virial_sum(t_moldyn *moldyn) {
919 /* virial (sum over atom virials) */
921 for(i=0;i<moldyn->count;i++) {
922 virial=&(moldyn->atom[i].virial);
923 v+=(virial->xx+virial->yy+virial->zz);
927 /* global virial (absolute coordinates) */
928 virial=&(moldyn->gvir);
929 moldyn->gv=virial->xx+virial->yy+virial->zz;
931 return moldyn->virial;
934 double pressure_calc(t_moldyn *moldyn) {
938 * with W = 1/3 sum_i f_i r_i (- skipped!)
939 * virial = sum_i f_i r_i
941 * => P = (2 Ekin + virial) / (3V)
944 /* assume up to date virial & up to date kinetic energy */
946 /* pressure (atom virials) */
947 moldyn->p=2.0*moldyn->ekin+moldyn->virial;
948 moldyn->p/=(3.0*moldyn->volume);
950 /* pressure (absolute coordinates) */
951 moldyn->gp=2.0*moldyn->ekin+moldyn->gv;
952 moldyn->gp/=(3.0*moldyn->volume);
957 int average_and_fluctuation_calc(t_moldyn *moldyn) {
959 if(moldyn->total_steps<moldyn->avg_skip)
962 int denom=moldyn->total_steps+1-moldyn->avg_skip;
964 /* assume up to date energies, temperature, pressure etc */
967 moldyn->k_sum+=moldyn->ekin;
968 moldyn->k2_sum+=(moldyn->ekin*moldyn->ekin);
969 moldyn->k_avg=moldyn->k_sum/denom;
970 moldyn->k2_avg=moldyn->k2_sum/denom;
971 moldyn->dk2_avg=moldyn->k2_avg-(moldyn->k_avg*moldyn->k_avg);
973 /* potential energy */
974 moldyn->v_sum+=moldyn->energy;
975 moldyn->v2_sum+=(moldyn->energy*moldyn->energy);
976 moldyn->v_avg=moldyn->v_sum/denom;
977 moldyn->v2_avg=moldyn->v2_sum/denom;
978 moldyn->dv2_avg=moldyn->v2_avg-(moldyn->v_avg*moldyn->v_avg);
981 moldyn->t_sum+=moldyn->t;
982 moldyn->t_avg=moldyn->t_sum/denom;
985 moldyn->virial_sum+=moldyn->virial;
986 moldyn->virial_avg=moldyn->virial_sum/denom;
987 moldyn->gv_sum+=moldyn->gv;
988 moldyn->gv_avg=moldyn->gv_sum/denom;
991 moldyn->p_sum+=moldyn->p;
992 moldyn->p_avg=moldyn->p_sum/denom;
993 moldyn->gp_sum+=moldyn->gp;
994 moldyn->gp_avg=moldyn->gp_sum/denom;
999 int get_heat_capacity(t_moldyn *moldyn) {
1003 /* averages needed for heat capacity calc */
1004 if(moldyn->total_steps<moldyn->avg_skip)
1007 /* (temperature average)^2 */
1008 temp2=moldyn->t_avg*moldyn->t_avg;
1009 printf("[moldyn] specific heat capacity for T=%f K [J/(kg K)]\n",
1012 /* ideal gas contribution */
1013 ighc=3.0*moldyn->count*K_BOLTZMANN/2.0;
1014 printf(" ideal gas contribution: %f\n",
1015 ighc/moldyn->mass*KILOGRAM/JOULE);
1017 /* specific heat for nvt ensemble */
1018 moldyn->c_v_nvt=moldyn->dv2_avg/(K_BOLTZMANN*temp2)+ighc;
1019 moldyn->c_v_nvt/=moldyn->mass;
1021 /* specific heat for nve ensemble */
1022 moldyn->c_v_nve=ighc/(1.0-(moldyn->dv2_avg/(ighc*K_BOLTZMANN*temp2)));
1023 moldyn->c_v_nve/=moldyn->mass;
1025 printf(" NVE: %f\n",moldyn->c_v_nve*KILOGRAM/JOULE);
1026 printf(" NVT: %f\n",moldyn->c_v_nvt*KILOGRAM/JOULE);
1027 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)));
1032 double thermodynamic_pressure_calc(t_moldyn *moldyn) {
1035 double u_up,u_down,dv;
1047 dv=8*scale*scale*scale*moldyn->volume;
1049 store=malloc(moldyn->count*sizeof(t_atom));
1051 printf("[moldyn] allocating store mem failed\n");
1055 /* save unscaled potential energy + atom/dim configuration */
1056 memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
1059 /* scale up dimension and atom positions */
1060 scale_dim(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
1061 scale_atoms(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
1062 link_cell_shutdown(moldyn);
1063 link_cell_init(moldyn,QUIET);
1064 potential_force_calc(moldyn);
1065 u_up=moldyn->energy;
1067 /* restore atomic configuration + dim */
1068 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
1071 /* scale down dimension and atom positions */
1072 scale_dim(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
1073 scale_atoms(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
1074 link_cell_shutdown(moldyn);
1075 link_cell_init(moldyn,QUIET);
1076 potential_force_calc(moldyn);
1077 u_down=moldyn->energy;
1079 /* calculate pressure */
1080 p=-(u_up-u_down)/dv;
1081 printf("-------> %.10f %.10f %f\n",u_up/EV/moldyn->count,u_down/EV/moldyn->count,p/BAR);
1083 /* restore atomic configuration + dim */
1084 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
1087 /* restore energy */
1088 potential_force_calc(moldyn);
1090 link_cell_shutdown(moldyn);
1091 link_cell_init(moldyn,QUIET);
1096 double get_pressure(t_moldyn *moldyn) {
1102 int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
1114 if(x) dim->x*=scale;
1115 if(y) dim->y*=scale;
1116 if(z) dim->z*=scale;
1121 int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
1132 for(i=0;i<moldyn->count;i++) {
1133 r=&(moldyn->atom[i].r);
1142 int scale_volume(t_moldyn *moldyn) {
1148 vdim=&(moldyn->vis.dim);
1152 /* scaling factor */
1153 if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
1154 scale=1.0-(moldyn->p_ref-moldyn->p)/moldyn->p_tc;
1155 scale=pow(scale,ONE_THIRD);
1158 scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
1160 moldyn->debug=scale;
1162 /* scale the atoms and dimensions */
1163 scale_atoms(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
1164 scale_dim(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
1166 /* visualize dimensions */
1173 /* recalculate scaled volume */
1174 moldyn->volume=dim->x*dim->y*dim->z;
1176 /* adjust/reinit linkcell */
1177 if(((int)(dim->x/moldyn->cutoff)!=lc->nx)||
1178 ((int)(dim->y/moldyn->cutoff)!=lc->ny)||
1179 ((int)(dim->z/moldyn->cutoff)!=lc->nx)) {
1180 link_cell_shutdown(moldyn);
1181 link_cell_init(moldyn,QUIET);
1192 double e_kin_calc(t_moldyn *moldyn) {
1200 for(i=0;i<moldyn->count;i++) {
1201 atom[i].ekin=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
1202 moldyn->ekin+=atom[i].ekin;
1205 return moldyn->ekin;
1208 double get_total_energy(t_moldyn *moldyn) {
1210 return(moldyn->ekin+moldyn->energy);
1213 t_3dvec get_total_p(t_moldyn *moldyn) {
1222 for(i=0;i<moldyn->count;i++) {
1223 v3_scale(&p,&(atom[i].v),atom[i].mass);
1224 v3_add(&p_total,&p_total,&p);
1230 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
1234 /* nn_dist is the nearest neighbour distance */
1236 tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
1245 /* linked list / cell method */
1249 int link_cell_init(t_moldyn *moldyn,u8 vol) {
1257 /* partitioning the md cell */
1258 lc->nx=moldyn->dim.x/moldyn->cutoff;
1259 lc->x=moldyn->dim.x/lc->nx;
1260 lc->ny=moldyn->dim.y/moldyn->cutoff;
1261 lc->y=moldyn->dim.y/lc->ny;
1262 lc->nz=moldyn->dim.z/moldyn->cutoff;
1263 lc->z=moldyn->dim.z/lc->nz;
1265 lc->cells=lc->nx*lc->ny*lc->nz;
1266 lc->subcell=malloc(lc->cells*sizeof(int*));
1269 printf("[moldyn] FATAL: less then 27 subcells!\n");
1272 printf("[moldyn] initializing 'static' linked cells (%d)\n",
1274 printf(" x: %d x %f A\n",lc->nx,lc->x);
1275 printf(" y: %d x %f A\n",lc->ny,lc->y);
1276 printf(" z: %d x %f A\n",lc->nz,lc->z);
1280 for(i=0;i<lc->cells;i++) {
1281 lc->subcell[i]=malloc((MAX_ATOMS_PER_LIST+1)*sizeof(int));
1282 if(lc->subcell[i]==NULL) {
1283 perror("[moldyn] list init (malloc)");
1286 //if(i==0) printf(" --- add one here! %d %p %p ----\n",i,lc->subcell,lc->subcell[0]);
1289 /* update the list */
1290 link_cell_update(moldyn);
1295 int link_cell_update(t_moldyn *moldyn) {
1309 for(i=0;i<lc->cells;i++)
1310 memset(lc->subcell[i],0,(MAX_ATOMS_PER_LIST+1)*sizeof(int));
1312 for(count=0;count<moldyn->count;count++) {
1313 i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
1314 j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
1315 k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
1318 while(lc->subcell[i+j*nx+k*nx*ny][p]!=0)
1321 if(p>=MAX_ATOMS_PER_LIST) {
1322 printf("[moldyn] FATAL: amount of atoms too high!\n");
1326 lc->subcell[i+j*nx+k*nx*ny][p]=count;
1332 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,int **cell) {
1350 cell[0]=lc->subcell[i+j*nx+k*a];
1351 for(ci=-1;ci<=1;ci++) {
1354 if((x<0)||(x>=nx)) {
1358 for(cj=-1;cj<=1;cj++) {
1361 if((y<0)||(y>=ny)) {
1365 for(ck=-1;ck<=1;ck++) {
1368 if((z<0)||(z>=nz)) {
1372 if(!(ci|cj|ck)) continue;
1374 cell[--count2]=lc->subcell[x+y*nx+z*a];
1377 cell[count1++]=lc->subcell[x+y*nx+z*a];
1388 int link_cell_shutdown(t_moldyn *moldyn) {
1396 for(i=0;i<lc->cells;i++)
1398 //printf(" --- free %p , %d\n",lc->subcell[i],i);
1399 free(lc->subcell[i]);
1409 int link_cell_init(t_moldyn *moldyn,u8 vol) {
1416 /* partitioning the md cell */
1417 lc->nx=moldyn->dim.x/moldyn->cutoff;
1418 lc->x=moldyn->dim.x/lc->nx;
1419 lc->ny=moldyn->dim.y/moldyn->cutoff;
1420 lc->y=moldyn->dim.y/lc->ny;
1421 lc->nz=moldyn->dim.z/moldyn->cutoff;
1422 lc->z=moldyn->dim.z/lc->nz;
1424 lc->cells=lc->nx*lc->ny*lc->nz;
1425 lc->subcell=malloc(lc->cells*sizeof(t_list));
1428 printf("[moldyn] FATAL: less then 27 subcells!\n");
1431 printf("[moldyn] initializing 'dynamic' linked cells (%d)\n",
1433 printf(" x: %d x %f A\n",lc->nx,lc->x);
1434 printf(" y: %d x %f A\n",lc->ny,lc->y);
1435 printf(" z: %d x %f A\n",lc->nz,lc->z);
1438 for(i=0;i<lc->cells;i++)
1439 list_init_f(&(lc->subcell[i]));
1441 link_cell_update(moldyn);
1446 int link_cell_update(t_moldyn *moldyn) {
1464 for(i=0;i<lc->cells;i++)
1465 list_destroy_f(&(lc->subcell[i]));
1467 for(count=0;count<moldyn->count;count++) {
1468 i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
1469 j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
1470 k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
1471 list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
1473 //if(i==0&&j==0&&k==0) printf(" --- add one here! %d %p ----\n",count,lc->subcell[0].current);
1479 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
1497 cell[0]=lc->subcell[i+j*nx+k*a];
1498 for(ci=-1;ci<=1;ci++) {
1501 if((x<0)||(x>=nx)) {
1505 for(cj=-1;cj<=1;cj++) {
1508 if((y<0)||(y>=ny)) {
1512 for(ck=-1;ck<=1;ck++) {
1515 if((z<0)||(z>=nz)) {
1519 if(!(ci|cj|ck)) continue;
1521 cell[--count2]=lc->subcell[x+y*nx+z*a];
1524 cell[count1++]=lc->subcell[x+y*nx+z*a];
1535 int link_cell_shutdown(t_moldyn *moldyn) {
1543 for(i=0;i<lc->nx*lc->ny*lc->nz;i++) {
1545 list_destroy_f(&(moldyn->lc.subcell[i]));
1556 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
1560 t_moldyn_schedule *schedule;
1562 schedule=&(moldyn->schedule);
1563 count=++(schedule->total_sched);
1565 ptr=realloc(schedule->runs,count*sizeof(int));
1567 perror("[moldyn] realloc (runs)");
1571 schedule->runs[count-1]=runs;
1573 ptr=realloc(schedule->tau,count*sizeof(double));
1575 perror("[moldyn] realloc (tau)");
1579 schedule->tau[count-1]=tau;
1581 printf("[moldyn] schedule added:\n");
1582 printf(" number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
1588 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
1590 moldyn->schedule.hook=hook;
1591 moldyn->schedule.hook_params=hook_params;
1598 * 'integration of newtons equation' - algorithms
1602 /* start the integration */
1604 int moldyn_integrate(t_moldyn *moldyn) {
1607 unsigned int e,m,s,v,p,t;
1609 t_moldyn_schedule *sched;
1614 double energy_scale;
1615 struct timeval t1,t2;
1618 sched=&(moldyn->schedule);
1621 /* initialize linked cell method */
1622 link_cell_init(moldyn,VERBOSE);
1624 /* logging & visualization */
1632 /* sqaure of some variables */
1633 moldyn->tau_square=moldyn->tau*moldyn->tau;
1634 moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
1636 /* get current time */
1637 gettimeofday(&t1,NULL);
1639 /* calculate initial forces */
1640 potential_force_calc(moldyn);
1645 /* some stupid checks before we actually start calculating bullshit */
1646 if(moldyn->cutoff>0.5*moldyn->dim.x)
1647 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
1648 if(moldyn->cutoff>0.5*moldyn->dim.y)
1649 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
1650 if(moldyn->cutoff>0.5*moldyn->dim.z)
1651 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
1652 ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
1653 if(ds>0.05*moldyn->nnd)
1654 printf("[moldyn] warning: forces too high / tau too small!\n");
1656 /* zero absolute time */
1658 moldyn->total_steps=0;
1660 /* debugging, ignore */
1663 /* tell the world */
1664 printf("[moldyn] integration start, go get a coffee ...\n");
1666 /* executing the schedule */
1668 while(sched->count<sched->total_sched) {
1670 /* setting amount of runs and finite time step size */
1671 moldyn->tau=sched->tau[sched->count];
1672 moldyn->tau_square=moldyn->tau*moldyn->tau;
1673 moldyn->time_steps=sched->runs[sched->count];
1675 /* energy scaling factor (might change!) */
1676 energy_scale=moldyn->count*EV;
1678 /* integration according to schedule */
1680 for(i=0;i<moldyn->time_steps;i++) {
1682 /* integration step */
1683 moldyn->integrate(moldyn);
1685 /* calculate kinetic energy, temperature and pressure */
1687 temperature_calc(moldyn);
1689 pressure_calc(moldyn);
1690 average_and_fluctuation_calc(moldyn);
1693 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
1694 scale_velocity(moldyn,FALSE);
1695 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
1696 scale_volume(moldyn);
1698 /* check for log & visualization */
1700 if(!(moldyn->total_steps%e))
1701 dprintf(moldyn->efd,
1703 moldyn->time,moldyn->ekin/energy_scale,
1704 moldyn->energy/energy_scale,
1705 get_total_energy(moldyn)/energy_scale);
1708 if(!(moldyn->total_steps%m)) {
1709 momentum=get_total_p(moldyn);
1710 dprintf(moldyn->mfd,
1711 "%f %f %f %f %f\n",moldyn->time,
1712 momentum.x,momentum.y,momentum.z,
1713 v3_norm(&momentum));
1717 if(!(moldyn->total_steps%p)) {
1718 dprintf(moldyn->pfd,
1719 "%f %f %f %f %f\n",moldyn->time,
1720 moldyn->p/BAR,moldyn->p_avg/BAR,
1721 moldyn->gp/BAR,moldyn->gp_avg/BAR);
1725 if(!(moldyn->total_steps%t)) {
1726 dprintf(moldyn->tfd,
1728 moldyn->time,moldyn->t,moldyn->t_avg);
1732 if(!(moldyn->total_steps%s)) {
1733 snprintf(dir,128,"%s/s-%07.f.save",
1734 moldyn->vlsdir,moldyn->time);
1735 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT,
1737 if(fd<0) perror("[moldyn] save fd open");
1739 write(fd,moldyn,sizeof(t_moldyn));
1740 write(fd,moldyn->atom,
1741 moldyn->count*sizeof(t_atom));
1747 if(!(moldyn->total_steps%v)) {
1748 visual_atoms(moldyn);
1752 /* display progress */
1753 //if(!(moldyn->total_steps%10)) {
1754 /* get current time */
1755 gettimeofday(&t2,NULL);
1757 printf("\rsched:%d, steps:%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f (%d)",
1759 moldyn->t,moldyn->t_avg,
1760 moldyn->p_avg/BAR,moldyn->gp_avg/BAR,
1762 (int)(t2.tv_sec-t1.tv_sec));
1765 /* copy over time */
1769 /* increase absolute time */
1770 moldyn->time+=moldyn->tau;
1771 moldyn->total_steps+=1;
1775 /* check for hooks */
1777 printf("\n ## schedule hook %d/%d start ##\n",
1778 sched->count+1,sched->total_sched-1);
1779 sched->hook(moldyn,sched->hook_params);
1780 printf(" ## schedule hook end ##\n");
1783 /* increase the schedule counter */
1791 /* velocity verlet */
1793 int velocity_verlet(t_moldyn *moldyn) {
1796 double tau,tau_square,h;
1801 count=moldyn->count;
1803 tau_square=moldyn->tau_square;
1805 for(i=0;i<count;i++) {
1808 v3_scale(&delta,&(atom[i].v),tau);
1809 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1810 v3_scale(&delta,&(atom[i].f),h*tau_square);
1811 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1812 check_per_bound(moldyn,&(atom[i].r));
1814 /* velocities [actually v(t+tau/2)] */
1815 v3_scale(&delta,&(atom[i].f),h*tau);
1816 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1819 /* neighbour list update */
1820 link_cell_update(moldyn);
1822 /* forces depending on chosen potential */
1823 potential_force_calc(moldyn);
1825 for(i=0;i<count;i++) {
1826 /* again velocities [actually v(t+tau)] */
1827 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
1828 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1837 * potentials & corresponding forces & virial routine
1841 /* generic potential and force calculation */
1843 int potential_force_calc(t_moldyn *moldyn) {
1846 t_atom *itom,*jtom,*ktom;
1850 int *neighbour_i[27];
1854 t_list neighbour_i[27];
1855 t_list neighbour_i2[27];
1861 count=moldyn->count;
1871 /* reset global virial */
1872 memset(&(moldyn->gvir),0,sizeof(t_virial));
1874 /* reset force, site energy and virial of every atom */
1875 for(i=0;i<count;i++) {
1878 v3_zero(&(itom[i].f));
1881 virial=(&(itom[i].virial));
1889 /* reset site energy */
1894 /* get energy, force and virial of every atom */
1896 /* first (and only) loop over atoms i */
1897 for(i=0;i<count;i++) {
1899 /* single particle potential/force */
1900 if(itom[i].attr&ATOM_ATTR_1BP)
1902 moldyn->func1b(moldyn,&(itom[i]));
1904 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
1907 /* 2 body pair potential/force */
1909 link_cell_neighbour_index(moldyn,
1910 (itom[i].r.x+moldyn->dim.x/2)/lc->x,
1911 (itom[i].r.y+moldyn->dim.y/2)/lc->y,
1912 (itom[i].r.z+moldyn->dim.z/2)/lc->z,
1917 /* first loop over atoms j */
1918 if(moldyn->func2b) {
1925 while(neighbour_i[j][p]!=0) {
1927 jtom=&(atom[neighbour_i[j][p]]);
1930 if(jtom==&(itom[i]))
1933 if((jtom->attr&ATOM_ATTR_2BP)&
1934 (itom[i].attr&ATOM_ATTR_2BP)) {
1935 moldyn->func2b(moldyn,
1942 this=&(neighbour_i[j]);
1945 if(this->start==NULL)
1949 jtom=this->current->data;
1951 if(jtom==&(itom[i]))
1954 if((jtom->attr&ATOM_ATTR_2BP)&
1955 (itom[i].attr&ATOM_ATTR_2BP)) {
1956 moldyn->func2b(moldyn,
1961 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1967 /* 3 body potential/force */
1969 if(!(itom[i].attr&ATOM_ATTR_3BP))
1972 /* copy the neighbour lists */
1974 /* no copy needed for static lists */
1976 memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
1979 /* second loop over atoms j */
1986 while(neighbour_i[j][p]!=0) {
1988 jtom=&(atom[neighbour_i[j][p]]);
1991 this=&(neighbour_i[j]);
1994 if(this->start==NULL)
1999 jtom=this->current->data;
2002 if(jtom==&(itom[i]))
2005 if(!(jtom->attr&ATOM_ATTR_3BP))
2011 if(moldyn->func3b_j1)
2012 moldyn->func3b_j1(moldyn,
2017 /* in first j loop, 3bp run can be skipped */
2018 if(!(moldyn->run3bp))
2021 /* first loop over atoms k */
2022 if(moldyn->func3b_k1) {
2030 while(neighbour_i[j][q]!=0) {
2032 ktom=&(atom[neighbour_i[k][q]]);
2035 that=&(neighbour_i2[k]);
2038 if(that->start==NULL)
2042 ktom=that->current->data;
2045 if(!(ktom->attr&ATOM_ATTR_3BP))
2051 if(ktom==&(itom[i]))
2054 moldyn->func3b_k1(moldyn,
2062 } while(list_next_f(that)!=\
2070 if(moldyn->func3b_j2)
2071 moldyn->func3b_j2(moldyn,
2076 /* second loop over atoms k */
2077 if(moldyn->func3b_k2) {
2085 while(neighbour_i[j][q]!=0) {
2087 ktom=&(atom[neighbour_i[k][q]]);
2090 that=&(neighbour_i2[k]);
2093 if(that->start==NULL)
2097 ktom=that->current->data;
2100 if(!(ktom->attr&ATOM_ATTR_3BP))
2106 if(ktom==&(itom[i]))
2109 moldyn->func3b_k2(moldyn,
2118 } while(list_next_f(that)!=\
2126 /* 2bp post function */
2127 if(moldyn->func3b_j3) {
2128 moldyn->func3b_j3(moldyn,
2135 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
2150 //printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
2151 if(moldyn->time>DSTART&&moldyn->time<DEND) {
2153 printf(" x: %0.40f\n",moldyn->atom[5832].f.x);
2154 printf(" y: %0.40f\n",moldyn->atom[5832].f.y);
2155 printf(" z: %0.40f\n",moldyn->atom[5832].f.z);
2159 /* calculate global virial */
2160 for(i=0;i<count;i++) {
2161 moldyn->gvir.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
2162 moldyn->gvir.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
2163 moldyn->gvir.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
2164 moldyn->gvir.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
2165 moldyn->gvir.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
2166 moldyn->gvir.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
2173 * virial calculation
2176 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
2177 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
2179 a->virial.xx+=f->x*d->x;
2180 a->virial.yy+=f->y*d->y;
2181 a->virial.zz+=f->z*d->z;
2182 a->virial.xy+=f->x*d->y;
2183 a->virial.xz+=f->x*d->z;
2184 a->virial.yz+=f->y*d->z;
2190 * periodic boundary checking
2193 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
2194 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
2205 if(moldyn->status&MOLDYN_STAT_PBX) {
2206 if(a->x>=x) a->x-=dim->x;
2207 else if(-a->x>x) a->x+=dim->x;
2209 if(moldyn->status&MOLDYN_STAT_PBY) {
2210 if(a->y>=y) a->y-=dim->y;
2211 else if(-a->y>y) a->y+=dim->y;
2213 if(moldyn->status&MOLDYN_STAT_PBZ) {
2214 if(a->z>=z) a->z-=dim->z;
2215 else if(-a->z>z) a->z+=dim->z;
2222 * debugging / critical check functions
2225 int moldyn_bc_check(t_moldyn *moldyn) {
2238 for(i=0;i<moldyn->count;i++) {
2239 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
2240 printf("FATAL: atom %d: x: %.20f (%.20f)\n",
2241 i,atom[i].r.x,dim->x/2);
2242 printf("diagnostic:\n");
2243 printf("-----------\natom.r.x:\n");
2245 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
2248 ((byte)&(1<<k))?1:0,
2251 printf("---------------\nx=dim.x/2:\n");
2253 memcpy(&byte,(u8 *)(&x)+j,1);
2256 ((byte)&(1<<k))?1:0,
2259 if(atom[i].r.x==x) printf("the same!\n");
2260 else printf("different!\n");
2262 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
2263 printf("FATAL: atom %d: y: %.20f (%.20f)\n",
2264 i,atom[i].r.y,dim->y/2);
2265 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
2266 printf("FATAL: atom %d: z: %.20f (%.20f)\n",
2267 i,atom[i].r.z,dim->z/2);
2277 int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
2282 fd=open(file,O_RDONLY);
2284 perror("[moldyn] load save file open");
2288 size=sizeof(t_moldyn);
2289 cnt=read(fd,moldyn,size);
2291 perror("[moldyn] load save file read (moldyn)");
2295 size=moldyn->count*sizeof(t_atom);
2297 moldyn->atom=(t_atom *)malloc(size);
2298 if(moldyn->atom==NULL) {
2299 perror("[moldyn] load save file malloc (atoms)");
2303 cnt=read(fd,moldyn->atom,size);
2305 perror("[moldyn] load save file read (atoms)");
2314 int moldyn_load(t_moldyn *moldyn) {
2322 * post processing functions
2325 int get_line(int fd,char *line,int max) {
2332 if(count==max) return count;
2333 ret=read(fd,line+count,1);
2334 if(ret<=0) return ret;
2335 if(line[count]=='\n') {
2343 int pair_correlation_init(t_moldyn *moldyn,double dr) {
2349 int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
2359 t_list neighbour[27];
2367 unsigned char ibrand;
2371 slots=(int)(moldyn->cutoff/dr);
2374 printf("[moldyn] pair correlation calc info:\n");
2375 printf(" time: %f\n",moldyn->time);
2376 printf(" count: %d\n",moldyn->count);
2377 printf(" cutoff: %f\n",moldyn->cutoff);
2378 printf(" temperature: cur=%f avg=%f\n",moldyn->t,moldyn->t_avg);
2384 stat=(double *)malloc(3*slots*sizeof(double));
2386 perror("[moldyn] pair correlation malloc");
2391 memset(stat,0,3*slots*sizeof(double));
2393 link_cell_init(moldyn,VERBOSE);
2397 for(i=0;i<moldyn->count;i++) {
2398 /* neighbour indexing */
2399 link_cell_neighbour_index(moldyn,
2400 (itom[i].r.x+moldyn->dim.x/2)/lc->x,
2401 (itom[i].r.y+moldyn->dim.y/2)/lc->x,
2402 (itom[i].r.z+moldyn->dim.z/2)/lc->x,
2405 /* brand of atom i */
2406 ibrand=itom[i].brand;
2410 bc=(j<lc->dnlc)?0:1;
2415 while(neighbour[j][p]!=0) {
2417 jtom=&(moldyn->atom[neighbour[j][p]]);
2420 this=&(neighbour[j]);
2423 if(this->start==NULL)
2428 jtom=this->current->data;
2431 if(jtom==&(itom[i]))
2434 /* only count pairs once */
2435 if(itom[i].tag>jtom->tag)
2439 * pair correlation calc
2443 v3_sub(&dist,&(jtom->r),&(itom[i].r));
2444 if(bc) check_per_bound(moldyn,&dist);
2445 d=v3_absolute_square(&dist);
2447 /* ignore if greater cutoff */
2448 if(d>moldyn->cutoff_square)
2451 /* fill the slots */
2455 if(ibrand!=jtom->brand) {
2460 /* type a - type a bonds */
2464 /* type b - type b bonds */
2471 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
2477 for(i=1;i<slots;i++) {
2478 // normalization: 4 pi r r dr
2479 // here: not double counting pairs -> 2 pi r r dr
2480 norm=2*M_PI*moldyn->count*(i*dr*i*dr)*dr;
2482 stat[slots+i]/=norm;
2488 /* todo: store/print pair correlation function */
2494 link_cell_shutdown(moldyn);
2499 int analyze_bonds(t_moldyn *moldyn) {
2508 * visualization code
2511 int visual_init(t_moldyn *moldyn,char *filebase) {
2513 strncpy(moldyn->vis.fb,filebase,128);
2518 int visual_atoms(t_moldyn *moldyn) {
2532 t_list neighbour[27];
2548 sprintf(file,"%s/atomic_conf_%07.f.xyz",v->fb,moldyn->time);
2549 fd=open(file,O_WRONLY|O_CREAT|O_TRUNC,S_IRUSR|S_IWUSR);
2551 perror("open visual save file fd");
2555 /* write the actual data file */
2558 dprintf(fd,"# [P] %d %07.f <%f,%f,%f>\n",
2559 moldyn->count,moldyn->time,help/40.0,help/40.0,-0.8*help);
2561 // atomic configuration
2562 for(i=0;i<moldyn->count;i++) {
2563 // atom type, positions, color and kinetic energy
2564 dprintf(fd,"%s %f %f %f %s %f\n",pse_name[atom[i].element],
2568 pse_col[atom[i].element],
2572 * bond detection should usually be done by potential
2573 * functions. brrrrr! EVIL!
2575 * todo: potentials need to export a 'find_bonds' function!
2578 // bonds between atoms
2579 if(!(atom[i].attr&ATOM_ATTR_VB))
2581 link_cell_neighbour_index(moldyn,
2582 (atom[i].r.x+moldyn->dim.x/2)/lc->x,
2583 (atom[i].r.y+moldyn->dim.y/2)/lc->y,
2584 (atom[i].r.z+moldyn->dim.z/2)/lc->z,
2590 while(neighbour[j][p]!=0) {
2591 btom=&(atom[neighbour[j][p]]);
2594 list_reset_f(&neighbour[j]);
2595 if(neighbour[j].start==NULL)
2598 btom=neighbour[j].current->data;
2600 if(btom==&atom[i]) // skip identical atoms
2602 //if(btom<&atom[i]) // skip half of them
2604 v3_sub(&dist,&(atom[i].r),&(btom->r));
2605 if(bc) check_per_bound(moldyn,&dist);
2606 d2=v3_absolute_square(&dist);
2607 brand=atom[i].brand;
2608 if(brand==btom->brand) {
2609 if(d2>moldyn->bondlen[brand])
2613 if(d2>moldyn->bondlen[2])
2616 dprintf(fd,"# [B] %f %f %f %f %f %f\n",
2617 atom[i].r.x,atom[i].r.y,atom[i].r.z,
2618 btom->r.x,btom->r.y,btom->r.z);
2622 } while(list_next_f(&neighbour[j])!=L_NO_NEXT_ELEMENT);
2629 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2630 -dim.x/2,-dim.y/2,-dim.z/2,
2631 dim.x/2,-dim.y/2,-dim.z/2);
2632 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2633 -dim.x/2,-dim.y/2,-dim.z/2,
2634 -dim.x/2,dim.y/2,-dim.z/2);
2635 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2636 dim.x/2,dim.y/2,-dim.z/2,
2637 dim.x/2,-dim.y/2,-dim.z/2);
2638 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2639 -dim.x/2,dim.y/2,-dim.z/2,
2640 dim.x/2,dim.y/2,-dim.z/2);
2642 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2643 -dim.x/2,-dim.y/2,dim.z/2,
2644 dim.x/2,-dim.y/2,dim.z/2);
2645 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2646 -dim.x/2,-dim.y/2,dim.z/2,
2647 -dim.x/2,dim.y/2,dim.z/2);
2648 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2649 dim.x/2,dim.y/2,dim.z/2,
2650 dim.x/2,-dim.y/2,dim.z/2);
2651 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2652 -dim.x/2,dim.y/2,dim.z/2,
2653 dim.x/2,dim.y/2,dim.z/2);
2655 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2656 -dim.x/2,-dim.y/2,dim.z/2,
2657 -dim.x/2,-dim.y/2,-dim.z/2);
2658 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2659 -dim.x/2,dim.y/2,dim.z/2,
2660 -dim.x/2,dim.y/2,-dim.z/2);
2661 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2662 dim.x/2,-dim.y/2,dim.z/2,
2663 dim.x/2,-dim.y/2,-dim.z/2);
2664 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2665 dim.x/2,dim.y/2,dim.z/2,
2666 dim.x/2,dim.y/2,-dim.z/2);