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 */
1247 int link_cell_init(t_moldyn *moldyn,u8 vol) {
1254 /* partitioning the md cell */
1255 lc->nx=moldyn->dim.x/moldyn->cutoff;
1256 lc->x=moldyn->dim.x/lc->nx;
1257 lc->ny=moldyn->dim.y/moldyn->cutoff;
1258 lc->y=moldyn->dim.y/lc->ny;
1259 lc->nz=moldyn->dim.z/moldyn->cutoff;
1260 lc->z=moldyn->dim.z/lc->nz;
1262 lc->cells=lc->nx*lc->ny*lc->nz;
1263 lc->subcell=malloc(lc->cells*sizeof(t_list));
1266 printf("[moldyn] FATAL: less then 27 subcells!\n");
1269 printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
1270 printf(" x: %d x %f A\n",lc->nx,lc->x);
1271 printf(" y: %d x %f A\n",lc->ny,lc->y);
1272 printf(" z: %d x %f A\n",lc->nz,lc->z);
1275 for(i=0;i<lc->cells;i++)
1276 list_init_f(&(lc->subcell[i]));
1278 link_cell_update(moldyn);
1283 int link_cell_update(t_moldyn *moldyn) {
1301 for(i=0;i<lc->cells;i++)
1302 list_destroy_f(&(lc->subcell[i]));
1304 for(count=0;count<moldyn->count;count++) {
1305 i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
1306 j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
1307 k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
1308 list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
1315 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
1333 cell[0]=lc->subcell[i+j*nx+k*a];
1334 for(ci=-1;ci<=1;ci++) {
1337 if((x<0)||(x>=nx)) {
1341 for(cj=-1;cj<=1;cj++) {
1344 if((y<0)||(y>=ny)) {
1348 for(ck=-1;ck<=1;ck++) {
1351 if((z<0)||(z>=nz)) {
1355 if(!(ci|cj|ck)) continue;
1357 cell[--count2]=lc->subcell[x+y*nx+z*a];
1360 cell[count1++]=lc->subcell[x+y*nx+z*a];
1371 int link_cell_shutdown(t_moldyn *moldyn) {
1378 for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
1379 list_destroy_f(&(moldyn->lc.subcell[i]));
1386 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
1390 t_moldyn_schedule *schedule;
1392 schedule=&(moldyn->schedule);
1393 count=++(schedule->total_sched);
1395 ptr=realloc(schedule->runs,count*sizeof(int));
1397 perror("[moldyn] realloc (runs)");
1401 schedule->runs[count-1]=runs;
1403 ptr=realloc(schedule->tau,count*sizeof(double));
1405 perror("[moldyn] realloc (tau)");
1409 schedule->tau[count-1]=tau;
1411 printf("[moldyn] schedule added:\n");
1412 printf(" number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
1418 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
1420 moldyn->schedule.hook=hook;
1421 moldyn->schedule.hook_params=hook_params;
1428 * 'integration of newtons equation' - algorithms
1432 /* start the integration */
1434 int moldyn_integrate(t_moldyn *moldyn) {
1437 unsigned int e,m,s,v,p,t;
1439 t_moldyn_schedule *sched;
1444 double energy_scale;
1445 struct timeval t1,t2;
1448 sched=&(moldyn->schedule);
1451 /* initialize linked cell method */
1452 link_cell_init(moldyn,VERBOSE);
1454 /* logging & visualization */
1462 /* sqaure of some variables */
1463 moldyn->tau_square=moldyn->tau*moldyn->tau;
1464 moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
1466 /* get current time */
1467 gettimeofday(&t1,NULL);
1469 /* calculate initial forces */
1470 potential_force_calc(moldyn);
1475 /* some stupid checks before we actually start calculating bullshit */
1476 if(moldyn->cutoff>0.5*moldyn->dim.x)
1477 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
1478 if(moldyn->cutoff>0.5*moldyn->dim.y)
1479 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
1480 if(moldyn->cutoff>0.5*moldyn->dim.z)
1481 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
1482 ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
1483 if(ds>0.05*moldyn->nnd)
1484 printf("[moldyn] warning: forces too high / tau too small!\n");
1486 /* zero absolute time */
1488 moldyn->total_steps=0;
1490 /* debugging, ignore */
1493 /* tell the world */
1494 printf("[moldyn] integration start, go get a coffee ...\n");
1496 /* executing the schedule */
1498 while(sched->count<sched->total_sched) {
1500 /* setting amount of runs and finite time step size */
1501 moldyn->tau=sched->tau[sched->count];
1502 moldyn->tau_square=moldyn->tau*moldyn->tau;
1503 moldyn->time_steps=sched->runs[sched->count];
1505 /* energy scaling factor (might change!) */
1506 energy_scale=moldyn->count*EV;
1508 /* integration according to schedule */
1510 for(i=0;i<moldyn->time_steps;i++) {
1512 /* integration step */
1513 moldyn->integrate(moldyn);
1515 /* calculate kinetic energy, temperature and pressure */
1517 temperature_calc(moldyn);
1519 pressure_calc(moldyn);
1520 average_and_fluctuation_calc(moldyn);
1523 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
1524 scale_velocity(moldyn,FALSE);
1525 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
1526 scale_volume(moldyn);
1528 /* check for log & visualization */
1530 if(!(moldyn->total_steps%e))
1531 dprintf(moldyn->efd,
1533 moldyn->time,moldyn->ekin/energy_scale,
1534 moldyn->energy/energy_scale,
1535 get_total_energy(moldyn)/energy_scale);
1538 if(!(moldyn->total_steps%m)) {
1539 momentum=get_total_p(moldyn);
1540 dprintf(moldyn->mfd,
1541 "%f %f %f %f %f\n",moldyn->time,
1542 momentum.x,momentum.y,momentum.z,
1543 v3_norm(&momentum));
1547 if(!(moldyn->total_steps%p)) {
1548 dprintf(moldyn->pfd,
1549 "%f %f %f %f %f\n",moldyn->time,
1550 moldyn->p/BAR,moldyn->p_avg/BAR,
1551 moldyn->gp/BAR,moldyn->gp_avg/BAR);
1555 if(!(moldyn->total_steps%t)) {
1556 dprintf(moldyn->tfd,
1558 moldyn->time,moldyn->t,moldyn->t_avg);
1562 if(!(moldyn->total_steps%s)) {
1563 snprintf(dir,128,"%s/s-%07.f.save",
1564 moldyn->vlsdir,moldyn->time);
1565 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT,
1567 if(fd<0) perror("[moldyn] save fd open");
1569 write(fd,moldyn,sizeof(t_moldyn));
1570 write(fd,moldyn->atom,
1571 moldyn->count*sizeof(t_atom));
1577 if(!(moldyn->total_steps%v)) {
1578 visual_atoms(moldyn);
1582 /* display progress */
1583 if(!(moldyn->total_steps%10)) {
1584 /* get current time */
1585 gettimeofday(&t2,NULL);
1587 printf("\rsched:%d, steps:%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f (%d)",
1589 moldyn->t,moldyn->t_avg,
1590 moldyn->p_avg/BAR,moldyn->gp_avg/BAR,
1592 (int)(t2.tv_sec-t1.tv_sec));
1595 /* copy over time */
1599 /* increase absolute time */
1600 moldyn->time+=moldyn->tau;
1601 moldyn->total_steps+=1;
1605 /* check for hooks */
1607 printf("\n ## schedule hook %d/%d start ##\n",
1608 sched->count+1,sched->total_sched-1);
1609 sched->hook(moldyn,sched->hook_params);
1610 printf(" ## schedule hook end ##\n");
1613 /* increase the schedule counter */
1621 /* velocity verlet */
1623 int velocity_verlet(t_moldyn *moldyn) {
1626 double tau,tau_square,h;
1631 count=moldyn->count;
1633 tau_square=moldyn->tau_square;
1635 for(i=0;i<count;i++) {
1638 v3_scale(&delta,&(atom[i].v),tau);
1639 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1640 v3_scale(&delta,&(atom[i].f),h*tau_square);
1641 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1642 check_per_bound(moldyn,&(atom[i].r));
1644 /* velocities [actually v(t+tau/2)] */
1645 v3_scale(&delta,&(atom[i].f),h*tau);
1646 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1649 /* neighbour list update */
1650 link_cell_update(moldyn);
1652 /* forces depending on chosen potential */
1653 potential_force_calc(moldyn);
1655 for(i=0;i<count;i++) {
1656 /* again velocities [actually v(t+tau)] */
1657 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
1658 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1667 * potentials & corresponding forces & virial routine
1671 /* generic potential and force calculation */
1673 int potential_force_calc(t_moldyn *moldyn) {
1676 t_atom *itom,*jtom,*ktom;
1679 t_list neighbour_i[27];
1680 t_list neighbour_i2[27];
1685 count=moldyn->count;
1692 /* reset global virial */
1693 memset(&(moldyn->gvir),0,sizeof(t_virial));
1695 /* reset force, site energy and virial of every atom */
1696 for(i=0;i<count;i++) {
1699 v3_zero(&(itom[i].f));
1702 virial=(&(itom[i].virial));
1710 /* reset site energy */
1715 /* get energy, force and virial of every atom */
1717 /* first (and only) loop over atoms i */
1718 for(i=0;i<count;i++) {
1720 /* single particle potential/force */
1721 if(itom[i].attr&ATOM_ATTR_1BP)
1723 moldyn->func1b(moldyn,&(itom[i]));
1725 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
1728 /* 2 body pair potential/force */
1730 link_cell_neighbour_index(moldyn,
1731 (itom[i].r.x+moldyn->dim.x/2)/lc->x,
1732 (itom[i].r.y+moldyn->dim.y/2)/lc->y,
1733 (itom[i].r.z+moldyn->dim.z/2)/lc->z,
1738 /* first loop over atoms j */
1739 if(moldyn->func2b) {
1742 this=&(neighbour_i[j]);
1745 if(this->start==NULL)
1751 jtom=this->current->data;
1753 if(jtom==&(itom[i]))
1756 if((jtom->attr&ATOM_ATTR_2BP)&
1757 (itom[i].attr&ATOM_ATTR_2BP)) {
1758 moldyn->func2b(moldyn,
1763 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1768 /* 3 body potential/force */
1770 if(!(itom[i].attr&ATOM_ATTR_3BP))
1773 /* copy the neighbour lists */
1774 memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
1776 /* second loop over atoms j */
1779 this=&(neighbour_i[j]);
1782 if(this->start==NULL)
1788 jtom=this->current->data;
1790 if(jtom==&(itom[i]))
1793 if(!(jtom->attr&ATOM_ATTR_3BP))
1799 if(moldyn->func3b_j1)
1800 moldyn->func3b_j1(moldyn,
1805 /* in first j loop, 3bp run can be skipped */
1806 if(!(moldyn->run3bp))
1809 /* first loop over atoms k */
1810 if(moldyn->func3b_k1) {
1814 that=&(neighbour_i2[k]);
1817 if(that->start==NULL)
1824 ktom=that->current->data;
1826 if(!(ktom->attr&ATOM_ATTR_3BP))
1832 if(ktom==&(itom[i]))
1835 moldyn->func3b_k1(moldyn,
1841 } while(list_next_f(that)!=\
1848 if(moldyn->func3b_j2)
1849 moldyn->func3b_j2(moldyn,
1854 /* second loop over atoms k */
1855 if(moldyn->func3b_k2) {
1859 that=&(neighbour_i2[k]);
1862 if(that->start==NULL)
1869 ktom=that->current->data;
1871 if(!(ktom->attr&ATOM_ATTR_3BP))
1877 if(ktom==&(itom[i]))
1880 moldyn->func3b_k2(moldyn,
1886 } while(list_next_f(that)!=\
1893 /* 2bp post function */
1894 if(moldyn->func3b_j3) {
1895 moldyn->func3b_j3(moldyn,
1900 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1914 printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
1917 /* calculate global virial */
1918 for(i=0;i<count;i++) {
1919 moldyn->gvir.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
1920 moldyn->gvir.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
1921 moldyn->gvir.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
1922 moldyn->gvir.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
1923 moldyn->gvir.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
1924 moldyn->gvir.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
1931 * virial calculation
1934 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1935 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1937 a->virial.xx+=f->x*d->x;
1938 a->virial.yy+=f->y*d->y;
1939 a->virial.zz+=f->z*d->z;
1940 a->virial.xy+=f->x*d->y;
1941 a->virial.xz+=f->x*d->z;
1942 a->virial.yz+=f->y*d->z;
1948 * periodic boundary checking
1951 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1952 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1963 if(moldyn->status&MOLDYN_STAT_PBX) {
1964 if(a->x>=x) a->x-=dim->x;
1965 else if(-a->x>x) a->x+=dim->x;
1967 if(moldyn->status&MOLDYN_STAT_PBY) {
1968 if(a->y>=y) a->y-=dim->y;
1969 else if(-a->y>y) a->y+=dim->y;
1971 if(moldyn->status&MOLDYN_STAT_PBZ) {
1972 if(a->z>=z) a->z-=dim->z;
1973 else if(-a->z>z) a->z+=dim->z;
1980 * debugging / critical check functions
1983 int moldyn_bc_check(t_moldyn *moldyn) {
1996 for(i=0;i<moldyn->count;i++) {
1997 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
1998 printf("FATAL: atom %d: x: %.20f (%.20f)\n",
1999 i,atom[i].r.x,dim->x/2);
2000 printf("diagnostic:\n");
2001 printf("-----------\natom.r.x:\n");
2003 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
2006 ((byte)&(1<<k))?1:0,
2009 printf("---------------\nx=dim.x/2:\n");
2011 memcpy(&byte,(u8 *)(&x)+j,1);
2014 ((byte)&(1<<k))?1:0,
2017 if(atom[i].r.x==x) printf("the same!\n");
2018 else printf("different!\n");
2020 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
2021 printf("FATAL: atom %d: y: %.20f (%.20f)\n",
2022 i,atom[i].r.y,dim->y/2);
2023 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
2024 printf("FATAL: atom %d: z: %.20f (%.20f)\n",
2025 i,atom[i].r.z,dim->z/2);
2035 int moldyn_load(t_moldyn *moldyn) {
2043 * post processing functions
2046 int get_line(int fd,char *line,int max) {
2053 if(count==max) return count;
2054 ret=read(fd,line+count,1);
2055 if(ret<=0) return ret;
2056 if(line[count]=='\n') {
2064 int analyze_bonds(t_moldyn *moldyn) {
2073 * visualization code
2076 int visual_init(t_moldyn *moldyn,char *filebase) {
2078 strncpy(moldyn->vis.fb,filebase,128);
2083 int visual_atoms(t_moldyn *moldyn) {
2093 t_list neighbour[27];
2108 sprintf(file,"%s/atomic_conf_%07.f.xyz",v->fb,moldyn->time);
2109 fd=open(file,O_WRONLY|O_CREAT|O_TRUNC,S_IRUSR|S_IWUSR);
2111 perror("open visual save file fd");
2115 /* write the actual data file */
2118 dprintf(fd,"# [P] %d %07.f <%f,%f,%f>\n",
2119 moldyn->count,moldyn->time,help/40.0,help/40.0,-0.8*help);
2121 // atomic configuration
2122 for(i=0;i<moldyn->count;i++) {
2123 // atom type, positions, color and kinetic energy
2124 dprintf(fd,"%s %f %f %f %s %f\n",pse_name[atom[i].element],
2128 pse_col[atom[i].element],
2132 * bond detection should usually be done by potential
2133 * functions. brrrrr! EVIL!
2135 * todo: potentials need to export a 'find_bonds' function!
2138 // bonds between atoms
2139 if(!(atom[i].attr&ATOM_ATTR_VB))
2141 link_cell_neighbour_index(moldyn,
2142 (atom[i].r.x+moldyn->dim.x/2)/lc->x,
2143 (atom[i].r.y+moldyn->dim.y/2)/lc->y,
2144 (atom[i].r.z+moldyn->dim.z/2)/lc->z,
2147 list_reset_f(&neighbour[j]);
2148 if(neighbour[j].start==NULL)
2152 btom=neighbour[j].current->data;
2153 if(btom==&atom[i]) // skip identical atoms
2155 //if(btom<&atom[i]) // skip half of them
2157 v3_sub(&dist,&(atom[i].r),&(btom->r));
2158 if(bc) check_per_bound(moldyn,&dist);
2159 d2=v3_absolute_square(&dist);
2160 brand=atom[i].brand;
2161 if(brand==btom->brand) {
2162 if(d2>moldyn->bondlen[brand])
2166 if(d2>moldyn->bondlen[2])
2169 dprintf(fd,"# [B] %f %f %f %f %f %f\n",
2170 atom[i].r.x,atom[i].r.y,atom[i].r.z,
2171 btom->r.x,btom->r.y,btom->r.z);
2172 } while(list_next_f(&neighbour[j])!=L_NO_NEXT_ELEMENT);
2178 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2179 -dim.x/2,-dim.y/2,-dim.z/2,
2180 dim.x/2,-dim.y/2,-dim.z/2);
2181 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2182 -dim.x/2,-dim.y/2,-dim.z/2,
2183 -dim.x/2,dim.y/2,-dim.z/2);
2184 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2185 dim.x/2,dim.y/2,-dim.z/2,
2186 dim.x/2,-dim.y/2,-dim.z/2);
2187 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2188 -dim.x/2,dim.y/2,-dim.z/2,
2189 dim.x/2,dim.y/2,-dim.z/2);
2191 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2192 -dim.x/2,-dim.y/2,dim.z/2,
2193 dim.x/2,-dim.y/2,dim.z/2);
2194 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2195 -dim.x/2,-dim.y/2,dim.z/2,
2196 -dim.x/2,dim.y/2,dim.z/2);
2197 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2198 dim.x/2,dim.y/2,dim.z/2,
2199 dim.x/2,-dim.y/2,dim.z/2);
2200 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2201 -dim.x/2,dim.y/2,dim.z/2,
2202 dim.x/2,dim.y/2,dim.z/2);
2204 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2205 -dim.x/2,-dim.y/2,dim.z/2,
2206 -dim.x/2,-dim.y/2,-dim.z/2);
2207 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2208 -dim.x/2,dim.y/2,dim.z/2,
2209 -dim.x/2,dim.y/2,-dim.z/2);
2210 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2211 dim.x/2,-dim.y/2,dim.z/2,
2212 dim.x/2,-dim.y/2,-dim.z/2);
2213 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2214 dim.x/2,dim.y/2,dim.z/2,
2215 dim.x/2,dim.y/2,-dim.z/2);