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_temperature(t_moldyn *moldyn,double t_ref) {
133 printf("[moldyn] temperature [K]: %f\n",moldyn->t_ref);
138 int set_pressure(t_moldyn *moldyn,double p_ref) {
142 printf("[moldyn] pressure [bar]: %f\n",moldyn->p_ref/BAR);
147 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
149 moldyn->pt_scale=(ptype|ttype);
153 printf("[moldyn] p/t scaling:\n");
155 printf(" p: %s",ptype?"yes":"no ");
157 printf(" | type: %02x | factor: %f",ptype,ptc);
160 printf(" t: %s",ttype?"yes":"no ");
162 printf(" | type: %02x | factor: %f",ttype,ttc);
168 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
174 moldyn->volume=x*y*z;
182 moldyn->dv=0.000001*moldyn->volume;
184 printf("[moldyn] dimensions in A and A^3 respectively:\n");
185 printf(" x: %f\n",moldyn->dim.x);
186 printf(" y: %f\n",moldyn->dim.y);
187 printf(" z: %f\n",moldyn->dim.z);
188 printf(" volume: %f\n",moldyn->volume);
189 printf(" visualize simulation box: %s\n",visualize?"yes":"no");
190 printf(" delta volume (pressure calc): %f\n",moldyn->dv);
195 int set_nn_dist(t_moldyn *moldyn,double dist) {
202 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
204 printf("[moldyn] periodic boundary conditions:\n");
207 moldyn->status|=MOLDYN_STAT_PBX;
210 moldyn->status|=MOLDYN_STAT_PBY;
213 moldyn->status|=MOLDYN_STAT_PBZ;
215 printf(" x: %s\n",x?"yes":"no");
216 printf(" y: %s\n",y?"yes":"no");
217 printf(" z: %s\n",z?"yes":"no");
222 int set_potential1b(t_moldyn *moldyn,pf_func1b func) {
229 int set_potential2b(t_moldyn *moldyn,pf_func2b func) {
236 int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func) {
238 moldyn->func3b_j1=func;
243 int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func) {
245 moldyn->func3b_j2=func;
250 int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func) {
252 moldyn->func3b_j3=func;
257 int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func) {
259 moldyn->func3b_k1=func;
264 int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func) {
266 moldyn->func3b_k2=func;
271 int set_potential_params(t_moldyn *moldyn,void *params) {
273 moldyn->pot_params=params;
278 int set_avg_skip(t_moldyn *moldyn,int skip) {
280 printf("[moldyn] skip %d steps before starting average calc\n",skip);
281 moldyn->avg_skip=skip;
286 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
288 strncpy(moldyn->vlsdir,dir,127);
293 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title) {
295 strncpy(moldyn->rauthor,author,63);
296 strncpy(moldyn->rtitle,title,63);
301 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
306 printf("[moldyn] set log: ");
309 case LOG_TOTAL_ENERGY:
310 moldyn->ewrite=timer;
311 snprintf(filename,127,"%s/energy",moldyn->vlsdir);
312 moldyn->efd=open(filename,
313 O_WRONLY|O_CREAT|O_EXCL,
316 perror("[moldyn] energy log fd open");
319 dprintf(moldyn->efd,"# total energy log file\n");
320 printf("total energy (%d)\n",timer);
322 case LOG_TOTAL_MOMENTUM:
323 moldyn->mwrite=timer;
324 snprintf(filename,127,"%s/momentum",moldyn->vlsdir);
325 moldyn->mfd=open(filename,
326 O_WRONLY|O_CREAT|O_EXCL,
329 perror("[moldyn] momentum log fd open");
332 dprintf(moldyn->efd,"# total momentum log file\n");
333 printf("total momentum (%d)\n",timer);
336 moldyn->pwrite=timer;
337 snprintf(filename,127,"%s/pressure",moldyn->vlsdir);
338 moldyn->pfd=open(filename,
339 O_WRONLY|O_CREAT|O_EXCL,
342 perror("[moldyn] pressure log file\n");
345 dprintf(moldyn->pfd,"# pressure log file\n");
346 printf("pressure (%d)\n",timer);
348 case LOG_TEMPERATURE:
349 moldyn->twrite=timer;
350 snprintf(filename,127,"%s/temperature",moldyn->vlsdir);
351 moldyn->tfd=open(filename,
352 O_WRONLY|O_CREAT|O_EXCL,
355 perror("[moldyn] temperature log file\n");
358 dprintf(moldyn->tfd,"# temperature log file\n");
359 printf("temperature (%d)\n",timer);
362 moldyn->swrite=timer;
363 printf("save file (%d)\n",timer);
366 moldyn->vwrite=timer;
367 ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
369 printf("[moldyn] visual init failure\n");
372 printf("visual file (%d)\n",timer);
375 snprintf(filename,127,"%s/report.tex",moldyn->vlsdir);
376 moldyn->rfd=open(filename,
377 O_WRONLY|O_CREAT|O_EXCL,
380 perror("[moldyn] report fd open");
383 printf("report -> ");
385 snprintf(filename,127,"%s/e_plot.scr",
387 moldyn->epfd=open(filename,
388 O_WRONLY|O_CREAT|O_EXCL,
391 perror("[moldyn] energy plot fd open");
394 dprintf(moldyn->epfd,e_plot_script);
399 snprintf(filename,127,"%s/pressure_plot.scr",
401 moldyn->ppfd=open(filename,
402 O_WRONLY|O_CREAT|O_EXCL,
405 perror("[moldyn] p plot fd open");
408 dprintf(moldyn->ppfd,pressure_plot_script);
413 snprintf(filename,127,"%s/temperature_plot.scr",
415 moldyn->tpfd=open(filename,
416 O_WRONLY|O_CREAT|O_EXCL,
419 perror("[moldyn] t plot fd open");
422 dprintf(moldyn->tpfd,temperature_plot_script);
424 printf("temperature ");
426 dprintf(moldyn->rfd,report_start,
427 moldyn->rauthor,moldyn->rtitle);
431 printf("unknown log type: %02x\n",type);
438 int moldyn_log_shutdown(t_moldyn *moldyn) {
442 printf("[moldyn] log shutdown\n");
446 dprintf(moldyn->rfd,report_energy);
447 snprintf(sc,255,"cd %s && gnuplot e_plot.scr",
452 if(moldyn->mfd) close(moldyn->mfd);
456 dprintf(moldyn->rfd,report_pressure);
457 snprintf(sc,255,"cd %s && gnuplot pressure_plot.scr",
464 dprintf(moldyn->rfd,report_temperature);
465 snprintf(sc,255,"cd %s && gnuplot temperature_plot.scr",
470 dprintf(moldyn->rfd,report_end);
472 snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
475 snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
478 snprintf(sc,255,"cd %s && dvipdf report >/dev/null 2>&1",
487 * creating lattice functions
490 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
491 u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin) {
502 /* how many atoms do we expect */
503 if(type==CUBIC) new*=1;
504 if(type==FCC) new*=4;
505 if(type==DIAMOND) new*=8;
507 /* allocate space for atoms */
508 ptr=realloc(moldyn->atom,(count+new)*sizeof(t_atom));
510 perror("[moldyn] realloc (create lattice)");
514 atom=&(moldyn->atom[count]);
516 /* no atoms on the boundaries (only reason: it looks better!) */
530 set_nn_dist(moldyn,lc);
531 ret=cubic_init(a,b,c,lc,atom,&orig);
535 v3_scale(&orig,&orig,0.5);
536 set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
537 ret=fcc_init(a,b,c,lc,atom,&orig);
541 v3_scale(&orig,&orig,0.25);
542 set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
543 ret=diamond_init(a,b,c,lc,atom,&orig);
546 printf("unknown lattice type (%02x)\n",type);
552 printf("[moldyn] creating lattice failed\n");
553 printf(" amount of atoms\n");
554 printf(" - expected: %d\n",new);
555 printf(" - created: %d\n",ret);
560 printf("[moldyn] created lattice with %d atoms\n",new);
562 for(ret=0;ret<new;ret++) {
563 atom[ret].element=element;
566 atom[ret].brand=brand;
567 atom[ret].tag=count+ret;
568 check_per_bound(moldyn,&(atom[ret].r));
569 atom[ret].r_0=atom[ret].r;
572 /* update total system mass */
573 total_mass_calc(moldyn);
578 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
579 t_3dvec *r,t_3dvec *v) {
586 count=(moldyn->count)++;
588 ptr=realloc(atom,(count+1)*sizeof(t_atom));
590 perror("[moldyn] realloc (add atom)");
598 atom[count].element=element;
599 atom[count].mass=mass;
600 atom[count].brand=brand;
601 atom[count].tag=count;
602 atom[count].attr=attr;
603 check_per_bound(moldyn,&(atom[count].r));
604 atom[count].r_0=atom[count].r;
606 /* update total system mass */
607 total_mass_calc(moldyn);
612 int del_atom(t_moldyn *moldyn,int tag) {
619 new=(t_atom *)malloc((moldyn->count-1)*sizeof(t_atom));
621 perror("[moldyn]malloc (del atom)");
625 for(cnt=0;cnt<tag;cnt++)
628 for(cnt=tag+1;cnt<moldyn->count;cnt++) {
630 new[cnt-1].tag=cnt-1;
642 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
661 v3_copy(&(atom[count].r),&r);
670 for(i=0;i<count;i++) {
671 atom[i].r.x-=(a*lc)/2.0;
672 atom[i].r.y-=(b*lc)/2.0;
673 atom[i].r.z-=(c*lc)/2.0;
679 /* fcc lattice init */
680 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
693 /* construct the basis */
694 memset(basis,0,3*sizeof(t_3dvec));
702 /* fill up the room */
710 v3_copy(&(atom[count].r),&r);
713 /* the three face centered atoms */
715 v3_add(&n,&r,&basis[l]);
716 v3_copy(&(atom[count].r),&n);
725 /* coordinate transformation */
726 for(i=0;i<count;i++) {
727 atom[i].r.x-=(a*lc)/2.0;
728 atom[i].r.y-=(b*lc)/2.0;
729 atom[i].r.z-=(c*lc)/2.0;
735 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
740 count=fcc_init(a,b,c,lc,atom,origin);
746 if(origin) v3_add(&o,&o,origin);
748 count+=fcc_init(a,b,c,lc,&atom[count],&o);
753 int destroy_atoms(t_moldyn *moldyn) {
755 if(moldyn->atom) free(moldyn->atom);
760 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
763 * - gaussian distribution of velocities
764 * - zero total momentum
765 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
770 t_3dvec p_total,delta;
775 random=&(moldyn->random);
777 printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
779 /* gaussian distribution of velocities */
781 for(i=0;i<moldyn->count;i++) {
782 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
784 v=sigma*rand_get_gauss(random);
786 p_total.x+=atom[i].mass*v;
788 v=sigma*rand_get_gauss(random);
790 p_total.y+=atom[i].mass*v;
792 v=sigma*rand_get_gauss(random);
794 p_total.z+=atom[i].mass*v;
797 /* zero total momentum */
798 v3_scale(&p_total,&p_total,1.0/moldyn->count);
799 for(i=0;i<moldyn->count;i++) {
800 v3_scale(&delta,&p_total,1.0/atom[i].mass);
801 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
804 /* velocity scaling */
805 scale_velocity(moldyn,equi_init);
810 double total_mass_calc(t_moldyn *moldyn) {
816 for(i=0;i<moldyn->count;i++)
817 moldyn->mass+=moldyn->atom[i].mass;
822 double temperature_calc(t_moldyn *moldyn) {
824 /* assume up to date kinetic energy, which is 3/2 N k_B T */
826 moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
831 double get_temperature(t_moldyn *moldyn) {
836 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
846 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
849 /* get kinetic energy / temperature & count involved atoms */
852 for(i=0;i<moldyn->count;i++) {
853 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
854 e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
859 if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
860 else return 0; /* no atoms involved in scaling! */
862 /* (temporary) hack for e,t = 0 */
865 if(moldyn->t_ref!=0.0) {
866 thermal_init(moldyn,equi_init);
870 return 0; /* no scaling needed */
874 /* get scaling factor */
875 scale=moldyn->t_ref/moldyn->t;
879 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
880 scale=1.0+(scale-1.0)/moldyn->t_tc;
883 /* velocity scaling */
884 for(i=0;i<moldyn->count;i++) {
885 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
886 v3_scale(&(atom[i].v),&(atom[i].v),scale);
892 double ideal_gas_law_pressure(t_moldyn *moldyn) {
896 p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
901 double virial_sum(t_moldyn *moldyn) {
907 /* virial (sum over atom virials) */
909 for(i=0;i<moldyn->count;i++) {
910 virial=&(moldyn->atom[i].virial);
911 v+=(virial->xx+virial->yy+virial->zz);
915 /* global virial (absolute coordinates) */
916 virial=&(moldyn->gvir);
917 moldyn->gv=virial->xx+virial->yy+virial->zz;
919 return moldyn->virial;
922 double pressure_calc(t_moldyn *moldyn) {
926 * with W = 1/3 sum_i f_i r_i (- skipped!)
927 * virial = sum_i f_i r_i
929 * => P = (2 Ekin + virial) / (3V)
932 /* assume up to date virial & up to date kinetic energy */
934 /* pressure (atom virials) */
935 moldyn->p=2.0*moldyn->ekin+moldyn->virial;
936 moldyn->p/=(3.0*moldyn->volume);
938 /* pressure (absolute coordinates) */
939 moldyn->gp=2.0*moldyn->ekin+moldyn->gv;
940 moldyn->gp/=(3.0*moldyn->volume);
945 int average_and_fluctuation_calc(t_moldyn *moldyn) {
947 if(moldyn->total_steps<moldyn->avg_skip)
950 int denom=moldyn->total_steps+1-moldyn->avg_skip;
952 /* assume up to date energies, temperature, pressure etc */
955 moldyn->k_sum+=moldyn->ekin;
956 moldyn->k2_sum+=(moldyn->ekin*moldyn->ekin);
957 moldyn->k_avg=moldyn->k_sum/denom;
958 moldyn->k2_avg=moldyn->k2_sum/denom;
959 moldyn->dk2_avg=moldyn->k2_avg-(moldyn->k_avg*moldyn->k_avg);
961 /* potential energy */
962 moldyn->v_sum+=moldyn->energy;
963 moldyn->v2_sum+=(moldyn->energy*moldyn->energy);
964 moldyn->v_avg=moldyn->v_sum/denom;
965 moldyn->v2_avg=moldyn->v2_sum/denom;
966 moldyn->dv2_avg=moldyn->v2_avg-(moldyn->v_avg*moldyn->v_avg);
969 moldyn->t_sum+=moldyn->t;
970 moldyn->t_avg=moldyn->t_sum/denom;
973 moldyn->virial_sum+=moldyn->virial;
974 moldyn->virial_avg=moldyn->virial_sum/denom;
975 moldyn->gv_sum+=moldyn->gv;
976 moldyn->gv_avg=moldyn->gv_sum/denom;
979 moldyn->p_sum+=moldyn->p;
980 moldyn->p_avg=moldyn->p_sum/denom;
981 moldyn->gp_sum+=moldyn->gp;
982 moldyn->gp_avg=moldyn->gp_sum/denom;
987 int get_heat_capacity(t_moldyn *moldyn) {
991 /* averages needed for heat capacity calc */
992 if(moldyn->total_steps<moldyn->avg_skip)
995 /* (temperature average)^2 */
996 temp2=moldyn->t_avg*moldyn->t_avg;
997 printf("[moldyn] specific heat capacity for T=%f K [J/(kg K)]\n",
1000 /* ideal gas contribution */
1001 ighc=3.0*moldyn->count*K_BOLTZMANN/2.0;
1002 printf(" ideal gas contribution: %f\n",
1003 ighc/moldyn->mass*KILOGRAM/JOULE);
1005 /* specific heat for nvt ensemble */
1006 moldyn->c_v_nvt=moldyn->dv2_avg/(K_BOLTZMANN*temp2)+ighc;
1007 moldyn->c_v_nvt/=moldyn->mass;
1009 /* specific heat for nve ensemble */
1010 moldyn->c_v_nve=ighc/(1.0-(moldyn->dv2_avg/(ighc*K_BOLTZMANN*temp2)));
1011 moldyn->c_v_nve/=moldyn->mass;
1013 printf(" NVE: %f\n",moldyn->c_v_nve*KILOGRAM/JOULE);
1014 printf(" NVT: %f\n",moldyn->c_v_nvt*KILOGRAM/JOULE);
1015 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)));
1020 double thermodynamic_pressure_calc(t_moldyn *moldyn) {
1023 double u_up,u_down,dv;
1035 dv=8*scale*scale*scale*moldyn->volume;
1037 store=malloc(moldyn->count*sizeof(t_atom));
1039 printf("[moldyn] allocating store mem failed\n");
1043 /* save unscaled potential energy + atom/dim configuration */
1044 memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
1047 /* scale up dimension and atom positions */
1048 scale_dim(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
1049 scale_atoms(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
1050 link_cell_shutdown(moldyn);
1051 link_cell_init(moldyn,QUIET);
1052 potential_force_calc(moldyn);
1053 u_up=moldyn->energy;
1055 /* restore atomic configuration + dim */
1056 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
1059 /* scale down dimension and atom positions */
1060 scale_dim(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
1061 scale_atoms(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
1062 link_cell_shutdown(moldyn);
1063 link_cell_init(moldyn,QUIET);
1064 potential_force_calc(moldyn);
1065 u_down=moldyn->energy;
1067 /* calculate pressure */
1068 p=-(u_up-u_down)/dv;
1069 printf("-------> %.10f %.10f %f\n",u_up/EV/moldyn->count,u_down/EV/moldyn->count,p/BAR);
1071 /* restore atomic configuration + dim */
1072 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
1075 /* restore energy */
1076 potential_force_calc(moldyn);
1078 link_cell_shutdown(moldyn);
1079 link_cell_init(moldyn,QUIET);
1084 double get_pressure(t_moldyn *moldyn) {
1090 int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
1102 if(x) dim->x*=scale;
1103 if(y) dim->y*=scale;
1104 if(z) dim->z*=scale;
1109 int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
1120 for(i=0;i<moldyn->count;i++) {
1121 r=&(moldyn->atom[i].r);
1130 int scale_volume(t_moldyn *moldyn) {
1136 vdim=&(moldyn->vis.dim);
1140 /* scaling factor */
1141 if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
1142 scale=1.0-(moldyn->p_ref-moldyn->p)/moldyn->p_tc;
1143 scale=pow(scale,ONE_THIRD);
1146 scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
1148 moldyn->debug=scale;
1150 /* scale the atoms and dimensions */
1151 scale_atoms(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
1152 scale_dim(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
1154 /* visualize dimensions */
1161 /* recalculate scaled volume */
1162 moldyn->volume=dim->x*dim->y*dim->z;
1164 /* adjust/reinit linkcell */
1165 if(((int)(dim->x/moldyn->cutoff)!=lc->nx)||
1166 ((int)(dim->y/moldyn->cutoff)!=lc->ny)||
1167 ((int)(dim->z/moldyn->cutoff)!=lc->nx)) {
1168 link_cell_shutdown(moldyn);
1169 link_cell_init(moldyn,QUIET);
1180 double e_kin_calc(t_moldyn *moldyn) {
1188 for(i=0;i<moldyn->count;i++) {
1189 atom[i].ekin=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
1190 moldyn->ekin+=atom[i].ekin;
1193 return moldyn->ekin;
1196 double get_total_energy(t_moldyn *moldyn) {
1198 return(moldyn->ekin+moldyn->energy);
1201 t_3dvec get_total_p(t_moldyn *moldyn) {
1210 for(i=0;i<moldyn->count;i++) {
1211 v3_scale(&p,&(atom[i].v),atom[i].mass);
1212 v3_add(&p_total,&p_total,&p);
1218 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
1222 /* nn_dist is the nearest neighbour distance */
1224 tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
1233 /* linked list / cell method */
1235 int link_cell_init(t_moldyn *moldyn,u8 vol) {
1242 /* partitioning the md cell */
1243 lc->nx=moldyn->dim.x/moldyn->cutoff;
1244 lc->x=moldyn->dim.x/lc->nx;
1245 lc->ny=moldyn->dim.y/moldyn->cutoff;
1246 lc->y=moldyn->dim.y/lc->ny;
1247 lc->nz=moldyn->dim.z/moldyn->cutoff;
1248 lc->z=moldyn->dim.z/lc->nz;
1250 lc->cells=lc->nx*lc->ny*lc->nz;
1251 lc->subcell=malloc(lc->cells*sizeof(t_list));
1254 printf("[moldyn] FATAL: less then 27 subcells!\n");
1257 printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
1258 printf(" x: %d x %f A\n",lc->nx,lc->x);
1259 printf(" y: %d x %f A\n",lc->ny,lc->y);
1260 printf(" z: %d x %f A\n",lc->nz,lc->z);
1263 for(i=0;i<lc->cells;i++)
1264 list_init_f(&(lc->subcell[i]));
1266 link_cell_update(moldyn);
1271 int link_cell_update(t_moldyn *moldyn) {
1289 for(i=0;i<lc->cells;i++)
1290 list_destroy_f(&(lc->subcell[i]));
1292 for(count=0;count<moldyn->count;count++) {
1293 i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
1294 j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
1295 k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
1296 list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
1303 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
1321 cell[0]=lc->subcell[i+j*nx+k*a];
1322 for(ci=-1;ci<=1;ci++) {
1325 if((x<0)||(x>=nx)) {
1329 for(cj=-1;cj<=1;cj++) {
1332 if((y<0)||(y>=ny)) {
1336 for(ck=-1;ck<=1;ck++) {
1339 if((z<0)||(z>=nz)) {
1343 if(!(ci|cj|ck)) continue;
1345 cell[--count2]=lc->subcell[x+y*nx+z*a];
1348 cell[count1++]=lc->subcell[x+y*nx+z*a];
1359 int link_cell_shutdown(t_moldyn *moldyn) {
1366 for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
1367 list_destroy_f(&(moldyn->lc.subcell[i]));
1374 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
1378 t_moldyn_schedule *schedule;
1380 schedule=&(moldyn->schedule);
1381 count=++(schedule->total_sched);
1383 ptr=realloc(schedule->runs,count*sizeof(int));
1385 perror("[moldyn] realloc (runs)");
1389 schedule->runs[count-1]=runs;
1391 ptr=realloc(schedule->tau,count*sizeof(double));
1393 perror("[moldyn] realloc (tau)");
1397 schedule->tau[count-1]=tau;
1399 printf("[moldyn] schedule added:\n");
1400 printf(" number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
1406 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
1408 moldyn->schedule.hook=hook;
1409 moldyn->schedule.hook_params=hook_params;
1416 * 'integration of newtons equation' - algorithms
1420 /* start the integration */
1422 int moldyn_integrate(t_moldyn *moldyn) {
1425 unsigned int e,m,s,v,p,t;
1427 t_moldyn_schedule *sched;
1432 double energy_scale;
1433 struct timeval t1,t2;
1436 sched=&(moldyn->schedule);
1439 /* initialize linked cell method */
1440 link_cell_init(moldyn,VERBOSE);
1442 /* logging & visualization */
1450 /* sqaure of some variables */
1451 moldyn->tau_square=moldyn->tau*moldyn->tau;
1452 moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
1454 /* get current time */
1455 gettimeofday(&t1,NULL);
1457 /* calculate initial forces */
1458 potential_force_calc(moldyn);
1463 /* some stupid checks before we actually start calculating bullshit */
1464 if(moldyn->cutoff>0.5*moldyn->dim.x)
1465 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
1466 if(moldyn->cutoff>0.5*moldyn->dim.y)
1467 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
1468 if(moldyn->cutoff>0.5*moldyn->dim.z)
1469 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
1470 ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
1471 if(ds>0.05*moldyn->nnd)
1472 printf("[moldyn] warning: forces too high / tau too small!\n");
1474 /* zero absolute time */
1476 moldyn->total_steps=0;
1478 /* debugging, ignore */
1481 /* tell the world */
1482 printf("[moldyn] integration start, go get a coffee ...\n");
1484 /* executing the schedule */
1486 while(sched->count<sched->total_sched) {
1488 /* setting amount of runs and finite time step size */
1489 moldyn->tau=sched->tau[sched->count];
1490 moldyn->tau_square=moldyn->tau*moldyn->tau;
1491 moldyn->time_steps=sched->runs[sched->count];
1493 /* energy scaling factor (might change!) */
1494 energy_scale=moldyn->count*EV;
1496 /* integration according to schedule */
1498 for(i=0;i<moldyn->time_steps;i++) {
1500 /* integration step */
1501 moldyn->integrate(moldyn);
1503 /* calculate kinetic energy, temperature and pressure */
1505 temperature_calc(moldyn);
1507 pressure_calc(moldyn);
1508 average_and_fluctuation_calc(moldyn);
1511 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
1512 scale_velocity(moldyn,FALSE);
1513 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
1514 scale_volume(moldyn);
1516 /* check for log & visualization */
1518 if(!(moldyn->total_steps%e))
1519 dprintf(moldyn->efd,
1521 moldyn->time,moldyn->ekin/energy_scale,
1522 moldyn->energy/energy_scale,
1523 get_total_energy(moldyn)/energy_scale);
1526 if(!(moldyn->total_steps%m)) {
1527 momentum=get_total_p(moldyn);
1528 dprintf(moldyn->mfd,
1529 "%f %f %f %f %f\n",moldyn->time,
1530 momentum.x,momentum.y,momentum.z,
1531 v3_norm(&momentum));
1535 if(!(moldyn->total_steps%p)) {
1536 dprintf(moldyn->pfd,
1537 "%f %f %f %f %f\n",moldyn->time,
1538 moldyn->p/BAR,moldyn->p_avg/BAR,
1539 moldyn->gp/BAR,moldyn->gp_avg/BAR);
1543 if(!(moldyn->total_steps%t)) {
1544 dprintf(moldyn->tfd,
1546 moldyn->time,moldyn->t,moldyn->t_avg);
1550 if(!(moldyn->total_steps%s)) {
1551 snprintf(dir,128,"%s/s-%07.f.save",
1552 moldyn->vlsdir,moldyn->time);
1553 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT,
1555 if(fd<0) perror("[moldyn] save fd open");
1557 write(fd,moldyn,sizeof(t_moldyn));
1558 write(fd,moldyn->atom,
1559 moldyn->count*sizeof(t_atom));
1565 if(!(moldyn->total_steps%v)) {
1566 visual_atoms(&(moldyn->vis),moldyn->time,
1567 moldyn->atom,moldyn->count);
1571 /* display progress */
1572 if(!(moldyn->total_steps%10)) {
1573 /* get current time */
1574 gettimeofday(&t2,NULL);
1576 printf("\rsched:%d, steps:%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f (%d)",
1578 moldyn->t,moldyn->t_avg,
1579 moldyn->p_avg/BAR,moldyn->gp_avg/BAR,
1581 (int)(t2.tv_sec-t1.tv_sec));
1584 /* copy over time */
1588 /* increase absolute time */
1589 moldyn->time+=moldyn->tau;
1590 moldyn->total_steps+=1;
1594 /* check for hooks */
1596 printf("\n ## schedule hook %d/%d start ##\n",
1597 sched->count+1,sched->total_sched-1);
1598 sched->hook(moldyn,sched->hook_params);
1599 printf(" ## schedule hook end ##\n");
1602 /* increase the schedule counter */
1610 /* velocity verlet */
1612 int velocity_verlet(t_moldyn *moldyn) {
1615 double tau,tau_square,h;
1620 count=moldyn->count;
1622 tau_square=moldyn->tau_square;
1624 for(i=0;i<count;i++) {
1627 v3_scale(&delta,&(atom[i].v),tau);
1628 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1629 v3_scale(&delta,&(atom[i].f),h*tau_square);
1630 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1631 check_per_bound(moldyn,&(atom[i].r));
1633 /* velocities [actually v(t+tau/2)] */
1634 v3_scale(&delta,&(atom[i].f),h*tau);
1635 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1638 /* neighbour list update */
1639 link_cell_update(moldyn);
1641 /* forces depending on chosen potential */
1642 potential_force_calc(moldyn);
1644 for(i=0;i<count;i++) {
1645 /* again velocities [actually v(t+tau)] */
1646 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
1647 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1656 * potentials & corresponding forces & virial routine
1660 /* generic potential and force calculation */
1662 int potential_force_calc(t_moldyn *moldyn) {
1665 t_atom *itom,*jtom,*ktom;
1668 t_list neighbour_i[27];
1669 t_list neighbour_i2[27];
1674 count=moldyn->count;
1681 /* reset global virial */
1682 memset(&(moldyn->gvir),0,sizeof(t_virial));
1684 /* reset force, site energy and virial of every atom */
1685 for(i=0;i<count;i++) {
1688 v3_zero(&(itom[i].f));
1691 virial=(&(itom[i].virial));
1699 /* reset site energy */
1704 /* get energy, force and virial of every atom */
1706 /* first (and only) loop over atoms i */
1707 for(i=0;i<count;i++) {
1709 /* single particle potential/force */
1710 if(itom[i].attr&ATOM_ATTR_1BP)
1712 moldyn->func1b(moldyn,&(itom[i]));
1714 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
1717 /* 2 body pair potential/force */
1719 link_cell_neighbour_index(moldyn,
1720 (itom[i].r.x+moldyn->dim.x/2)/lc->x,
1721 (itom[i].r.y+moldyn->dim.y/2)/lc->y,
1722 (itom[i].r.z+moldyn->dim.z/2)/lc->z,
1727 /* first loop over atoms j */
1728 if(moldyn->func2b) {
1731 this=&(neighbour_i[j]);
1734 if(this->start==NULL)
1740 jtom=this->current->data;
1742 if(jtom==&(itom[i]))
1745 if((jtom->attr&ATOM_ATTR_2BP)&
1746 (itom[i].attr&ATOM_ATTR_2BP)) {
1747 moldyn->func2b(moldyn,
1752 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1757 /* 3 body potential/force */
1759 if(!(itom[i].attr&ATOM_ATTR_3BP))
1762 /* copy the neighbour lists */
1763 memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
1765 /* second loop over atoms j */
1768 this=&(neighbour_i[j]);
1771 if(this->start==NULL)
1777 jtom=this->current->data;
1779 if(jtom==&(itom[i]))
1782 if(!(jtom->attr&ATOM_ATTR_3BP))
1788 if(moldyn->func3b_j1)
1789 moldyn->func3b_j1(moldyn,
1794 /* in first j loop, 3bp run can be skipped */
1795 if(!(moldyn->run3bp))
1798 /* first loop over atoms k */
1799 if(moldyn->func3b_k1) {
1803 that=&(neighbour_i2[k]);
1806 if(that->start==NULL)
1813 ktom=that->current->data;
1815 if(!(ktom->attr&ATOM_ATTR_3BP))
1821 if(ktom==&(itom[i]))
1824 moldyn->func3b_k1(moldyn,
1830 } while(list_next_f(that)!=\
1837 if(moldyn->func3b_j2)
1838 moldyn->func3b_j2(moldyn,
1843 /* second loop over atoms k */
1844 if(moldyn->func3b_k2) {
1848 that=&(neighbour_i2[k]);
1851 if(that->start==NULL)
1858 ktom=that->current->data;
1860 if(!(ktom->attr&ATOM_ATTR_3BP))
1866 if(ktom==&(itom[i]))
1869 moldyn->func3b_k2(moldyn,
1875 } while(list_next_f(that)!=\
1882 /* 2bp post function */
1883 if(moldyn->func3b_j3) {
1884 moldyn->func3b_j3(moldyn,
1889 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1903 printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
1906 /* calculate global virial */
1907 for(i=0;i<count;i++) {
1908 moldyn->gvir.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
1909 moldyn->gvir.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
1910 moldyn->gvir.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
1911 moldyn->gvir.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
1912 moldyn->gvir.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
1913 moldyn->gvir.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
1920 * virial calculation
1923 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1924 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1926 a->virial.xx+=f->x*d->x;
1927 a->virial.yy+=f->y*d->y;
1928 a->virial.zz+=f->z*d->z;
1929 a->virial.xy+=f->x*d->y;
1930 a->virial.xz+=f->x*d->z;
1931 a->virial.yz+=f->y*d->z;
1937 * periodic boundary checking
1940 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1941 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1952 if(moldyn->status&MOLDYN_STAT_PBX) {
1953 if(a->x>=x) a->x-=dim->x;
1954 else if(-a->x>x) a->x+=dim->x;
1956 if(moldyn->status&MOLDYN_STAT_PBY) {
1957 if(a->y>=y) a->y-=dim->y;
1958 else if(-a->y>y) a->y+=dim->y;
1960 if(moldyn->status&MOLDYN_STAT_PBZ) {
1961 if(a->z>=z) a->z-=dim->z;
1962 else if(-a->z>z) a->z+=dim->z;
1969 * debugging / critical check functions
1972 int moldyn_bc_check(t_moldyn *moldyn) {
1985 for(i=0;i<moldyn->count;i++) {
1986 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
1987 printf("FATAL: atom %d: x: %.20f (%.20f)\n",
1988 i,atom[i].r.x,dim->x/2);
1989 printf("diagnostic:\n");
1990 printf("-----------\natom.r.x:\n");
1992 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
1995 ((byte)&(1<<k))?1:0,
1998 printf("---------------\nx=dim.x/2:\n");
2000 memcpy(&byte,(u8 *)(&x)+j,1);
2003 ((byte)&(1<<k))?1:0,
2006 if(atom[i].r.x==x) printf("the same!\n");
2007 else printf("different!\n");
2009 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
2010 printf("FATAL: atom %d: y: %.20f (%.20f)\n",
2011 i,atom[i].r.y,dim->y/2);
2012 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
2013 printf("FATAL: atom %d: z: %.20f (%.20f)\n",
2014 i,atom[i].r.z,dim->z/2);
2024 int moldyn_load(t_moldyn *moldyn) {
2032 * post processing functions
2035 int get_line(int fd,char *line,int max) {
2042 if(count==max) return count;
2043 ret=read(fd,line+count,1);
2044 if(ret<=0) return ret;
2045 if(line[count]=='\n') {
2053 int analyze_bonds(t_moldyn *moldyn) {
2062 * visualization code
2065 int visual_init(t_visual *v,char *filebase) {
2069 strncpy(v->fb,filebase,128);
2070 memset(file,0,128+8);
2075 int visual_atoms(t_visual *v,double time,t_atom *atom,int n) {
2088 sprintf(file,"%s/atomic_conf_%07.f.xyz",v->fb,time);
2089 fd=open(file,O_WRONLY|O_CREAT|O_TRUNC,S_IRUSR|S_IWUSR);
2091 perror("open visual save file fd");
2095 /* write the actual data file */
2096 dprintf(fd,"# [P] %d %07.f <%f,%f,%f>\n",
2097 n,time,help/40.0,help/40.0,-0.8*help);
2099 dprintf(fd,"%s %f %f %f %s %f\n",pse_name[atom[i].element],
2103 pse_col[atom[i].element],
2106 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2107 -dim.x/2,-dim.y/2,-dim.z/2,
2108 dim.x/2,-dim.y/2,-dim.z/2);
2109 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2110 -dim.x/2,-dim.y/2,-dim.z/2,
2111 -dim.x/2,dim.y/2,-dim.z/2);
2112 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2113 dim.x/2,dim.y/2,-dim.z/2,
2114 dim.x/2,-dim.y/2,-dim.z/2);
2115 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2116 -dim.x/2,dim.y/2,-dim.z/2,
2117 dim.x/2,dim.y/2,-dim.z/2);
2119 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2120 -dim.x/2,-dim.y/2,dim.z/2,
2121 dim.x/2,-dim.y/2,dim.z/2);
2122 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2123 -dim.x/2,-dim.y/2,dim.z/2,
2124 -dim.x/2,dim.y/2,dim.z/2);
2125 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2126 dim.x/2,dim.y/2,dim.z/2,
2127 dim.x/2,-dim.y/2,dim.z/2);
2128 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2129 -dim.x/2,dim.y/2,dim.z/2,
2130 dim.x/2,dim.y/2,dim.z/2);
2132 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2133 -dim.x/2,-dim.y/2,dim.z/2,
2134 -dim.x/2,-dim.y/2,-dim.z/2);
2135 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2136 -dim.x/2,dim.y/2,dim.z/2,
2137 -dim.x/2,dim.y/2,-dim.z/2);
2138 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2139 dim.x/2,-dim.y/2,dim.z/2,
2140 dim.x/2,-dim.y/2,-dim.z/2);
2141 dprintf(fd,"# [D] %f %f %f %f %f %f\n",
2142 dim.x/2,dim.y/2,dim.z/2,
2143 dim.x/2,dim.y/2,-dim.z/2);