2 * moldyn.c - molecular dynamics library main file
4 * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
12 #include <sys/types.h>
19 #include "report/report.h"
21 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
23 printf("[moldyn] init\n");
25 memset(moldyn,0,sizeof(t_moldyn));
27 rand_init(&(moldyn->random),NULL,1);
28 moldyn->random.status|=RAND_STAT_VERBOSE;
33 int moldyn_shutdown(t_moldyn *moldyn) {
35 printf("[moldyn] shutdown\n");
37 moldyn_log_shutdown(moldyn);
38 link_cell_shutdown(moldyn);
39 rand_close(&(moldyn->random));
45 int set_int_alg(t_moldyn *moldyn,u8 algo) {
47 printf("[moldyn] integration algorithm: ");
50 case MOLDYN_INTEGRATE_VERLET:
51 moldyn->integrate=velocity_verlet;
52 printf("velocity verlet\n");
55 printf("unknown integration algorithm: %02x\n",algo);
63 int set_cutoff(t_moldyn *moldyn,double cutoff) {
65 moldyn->cutoff=cutoff;
67 printf("[moldyn] cutoff [A]: %f\n",moldyn->cutoff);
72 int set_temperature(t_moldyn *moldyn,double t_ref) {
76 printf("[moldyn] temperature [K]: %f\n",moldyn->t_ref);
81 int set_pressure(t_moldyn *moldyn,double p_ref) {
85 printf("[moldyn] pressure [bar]: %f\n",moldyn->p_ref/BAR);
90 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
92 moldyn->pt_scale=(ptype|ttype);
96 printf("[moldyn] p/t scaling:\n");
98 printf(" p: %s",ptype?"yes":"no ");
100 printf(" | type: %02x | factor: %f",ptype,ptc);
103 printf(" t: %s",ttype?"yes":"no ");
105 printf(" | type: %02x | factor: %f",ttype,ttc);
111 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
117 moldyn->volume=x*y*z;
125 moldyn->dv=0.000001*moldyn->volume;
127 printf("[moldyn] dimensions in A and A^3 respectively:\n");
128 printf(" x: %f\n",moldyn->dim.x);
129 printf(" y: %f\n",moldyn->dim.y);
130 printf(" z: %f\n",moldyn->dim.z);
131 printf(" volume: %f\n",moldyn->volume);
132 printf(" visualize simulation box: %s\n",visualize?"yes":"no");
133 printf(" delta volume (pressure calc): %f\n",moldyn->dv);
138 int set_nn_dist(t_moldyn *moldyn,double dist) {
145 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
147 printf("[moldyn] periodic boundary conditions:\n");
150 moldyn->status|=MOLDYN_STAT_PBX;
153 moldyn->status|=MOLDYN_STAT_PBY;
156 moldyn->status|=MOLDYN_STAT_PBZ;
158 printf(" x: %s\n",x?"yes":"no");
159 printf(" y: %s\n",y?"yes":"no");
160 printf(" z: %s\n",z?"yes":"no");
165 int set_potential1b(t_moldyn *moldyn,pf_func1b func) {
172 int set_potential2b(t_moldyn *moldyn,pf_func2b func) {
179 int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func) {
181 moldyn->func3b_j1=func;
186 int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func) {
188 moldyn->func3b_j2=func;
193 int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func) {
195 moldyn->func3b_j3=func;
200 int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func) {
202 moldyn->func3b_k1=func;
207 int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func) {
209 moldyn->func3b_k2=func;
214 int set_potential_params(t_moldyn *moldyn,void *params) {
216 moldyn->pot_params=params;
221 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
223 strncpy(moldyn->vlsdir,dir,127);
228 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title) {
230 strncpy(moldyn->rauthor,author,63);
231 strncpy(moldyn->rtitle,title,63);
236 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
241 printf("[moldyn] set log: ");
244 case LOG_TOTAL_ENERGY:
245 moldyn->ewrite=timer;
246 snprintf(filename,127,"%s/energy",moldyn->vlsdir);
247 moldyn->efd=open(filename,
248 O_WRONLY|O_CREAT|O_EXCL,
251 perror("[moldyn] energy log fd open");
254 dprintf(moldyn->efd,"# total energy log file\n");
255 printf("total energy (%d)\n",timer);
257 case LOG_TOTAL_MOMENTUM:
258 moldyn->mwrite=timer;
259 snprintf(filename,127,"%s/momentum",moldyn->vlsdir);
260 moldyn->mfd=open(filename,
261 O_WRONLY|O_CREAT|O_EXCL,
264 perror("[moldyn] momentum log fd open");
267 dprintf(moldyn->efd,"# total momentum log file\n");
268 printf("total momentum (%d)\n",timer);
271 moldyn->pwrite=timer;
272 snprintf(filename,127,"%s/pressure",moldyn->vlsdir);
273 moldyn->pfd=open(filename,
274 O_WRONLY|O_CREAT|O_EXCL,
277 perror("[moldyn] pressure log file\n");
280 dprintf(moldyn->pfd,"# pressure log file\n");
281 printf("pressure (%d)\n",timer);
283 case LOG_TEMPERATURE:
284 moldyn->twrite=timer;
285 snprintf(filename,127,"%s/temperature",moldyn->vlsdir);
286 moldyn->tfd=open(filename,
287 O_WRONLY|O_CREAT|O_EXCL,
290 perror("[moldyn] temperature log file\n");
293 dprintf(moldyn->tfd,"# temperature log file\n");
294 printf("temperature (%d)\n",timer);
297 moldyn->swrite=timer;
298 printf("save file (%d)\n",timer);
301 moldyn->vwrite=timer;
302 ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
304 printf("[moldyn] visual init failure\n");
307 printf("visual file (%d)\n",timer);
310 snprintf(filename,127,"%s/report.tex",moldyn->vlsdir);
311 moldyn->rfd=open(filename,
312 O_WRONLY|O_CREAT|O_EXCL,
315 perror("[moldyn] report fd open");
318 printf("report -> ");
320 snprintf(filename,127,"%s/e_plot.scr",
322 moldyn->epfd=open(filename,
323 O_WRONLY|O_CREAT|O_EXCL,
326 perror("[moldyn] energy plot fd open");
329 dprintf(moldyn->epfd,e_plot_script);
334 snprintf(filename,127,"%s/pressure_plot.scr",
336 moldyn->ppfd=open(filename,
337 O_WRONLY|O_CREAT|O_EXCL,
340 perror("[moldyn] p plot fd open");
343 dprintf(moldyn->ppfd,pressure_plot_script);
348 snprintf(filename,127,"%s/temperature_plot.scr",
350 moldyn->tpfd=open(filename,
351 O_WRONLY|O_CREAT|O_EXCL,
354 perror("[moldyn] t plot fd open");
357 dprintf(moldyn->tpfd,temperature_plot_script);
359 printf("temperature ");
361 dprintf(moldyn->rfd,report_start,
362 moldyn->rauthor,moldyn->rtitle);
366 printf("unknown log type: %02x\n",type);
373 int moldyn_log_shutdown(t_moldyn *moldyn) {
377 printf("[moldyn] log shutdown\n");
381 dprintf(moldyn->rfd,report_energy);
382 snprintf(sc,255,"cd %s && gnuplot e_plot.scr",
387 if(moldyn->mfd) close(moldyn->mfd);
391 dprintf(moldyn->rfd,report_pressure);
392 snprintf(sc,255,"cd %s && gnuplot pressure_plot.scr",
399 dprintf(moldyn->rfd,report_temperature);
400 snprintf(sc,255,"cd %s && gnuplot temperature_plot.scr",
405 dprintf(moldyn->rfd,report_end);
407 snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
410 snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
413 snprintf(sc,255,"cd %s && dvipdf report >/dev/null 2>&1",
417 if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
423 * creating lattice functions
426 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
427 u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin) {
438 /* how many atoms do we expect */
439 if(type==CUBIC) new*=1;
440 if(type==FCC) new*=4;
441 if(type==DIAMOND) new*=8;
443 /* allocate space for atoms */
444 ptr=realloc(moldyn->atom,(count+new)*sizeof(t_atom));
446 perror("[moldyn] realloc (create lattice)");
450 atom=&(moldyn->atom[count]);
452 /* no atoms on the boundaries (only reason: it looks better!) */
466 set_nn_dist(moldyn,lc);
467 ret=cubic_init(a,b,c,lc,atom,&orig);
471 v3_scale(&orig,&orig,0.5);
472 set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
473 ret=fcc_init(a,b,c,lc,atom,&orig);
477 v3_scale(&orig,&orig,0.25);
478 set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
479 ret=diamond_init(a,b,c,lc,atom,&orig);
482 printf("unknown lattice type (%02x)\n",type);
488 printf("[moldyn] creating lattice failed\n");
489 printf(" amount of atoms\n");
490 printf(" - expected: %d\n",new);
491 printf(" - created: %d\n",ret);
496 printf("[moldyn] created lattice with %d atoms\n",new);
498 for(ret=0;ret<new;ret++) {
499 atom[ret].element=element;
502 atom[ret].brand=brand;
503 atom[ret].tag=count+ret;
504 check_per_bound(moldyn,&(atom[ret].r));
511 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
530 v3_copy(&(atom[count].r),&r);
539 for(i=0;i<count;i++) {
540 atom[i].r.x-=(a*lc)/2.0;
541 atom[i].r.y-=(b*lc)/2.0;
542 atom[i].r.z-=(c*lc)/2.0;
548 /* fcc lattice init */
549 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
562 /* construct the basis */
563 memset(basis,0,3*sizeof(t_3dvec));
571 /* fill up the room */
579 v3_copy(&(atom[count].r),&r);
582 /* the three face centered atoms */
584 v3_add(&n,&r,&basis[l]);
585 v3_copy(&(atom[count].r),&n);
594 /* coordinate transformation */
595 for(i=0;i<count;i++) {
596 atom[i].r.x-=(a*lc)/2.0;
597 atom[i].r.y-=(b*lc)/2.0;
598 atom[i].r.z-=(c*lc)/2.0;
604 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
609 count=fcc_init(a,b,c,lc,atom,origin);
615 if(origin) v3_add(&o,&o,origin);
617 count+=fcc_init(a,b,c,lc,&atom[count],&o);
622 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
623 t_3dvec *r,t_3dvec *v) {
630 count=(moldyn->count)++;
632 ptr=realloc(atom,(count+1)*sizeof(t_atom));
634 perror("[moldyn] realloc (add atom)");
642 atom[count].element=element;
643 atom[count].mass=mass;
644 atom[count].brand=brand;
645 atom[count].tag=count;
646 atom[count].attr=attr;
651 int destroy_atoms(t_moldyn *moldyn) {
653 if(moldyn->atom) free(moldyn->atom);
658 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
661 * - gaussian distribution of velocities
662 * - zero total momentum
663 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
668 t_3dvec p_total,delta;
673 random=&(moldyn->random);
675 printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
677 /* gaussian distribution of velocities */
679 for(i=0;i<moldyn->count;i++) {
680 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
682 v=sigma*rand_get_gauss(random);
684 p_total.x+=atom[i].mass*v;
686 v=sigma*rand_get_gauss(random);
688 p_total.y+=atom[i].mass*v;
690 v=sigma*rand_get_gauss(random);
692 p_total.z+=atom[i].mass*v;
695 /* zero total momentum */
696 v3_scale(&p_total,&p_total,1.0/moldyn->count);
697 for(i=0;i<moldyn->count;i++) {
698 v3_scale(&delta,&p_total,1.0/atom[i].mass);
699 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
702 /* velocity scaling */
703 scale_velocity(moldyn,equi_init);
708 double temperature_calc(t_moldyn *moldyn) {
710 /* assume up to date kinetic energy, which is 3/2 N k_B T */
712 moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
713 moldyn->t_sum+=moldyn->t;
714 moldyn->mean_t=moldyn->t_sum/moldyn->total_steps;
719 double get_temperature(t_moldyn *moldyn) {
724 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
734 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
737 /* get kinetic energy / temperature & count involved atoms */
740 for(i=0;i<moldyn->count;i++) {
741 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
742 e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
747 if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
748 else return 0; /* no atoms involved in scaling! */
750 /* (temporary) hack for e,t = 0 */
753 if(moldyn->t_ref!=0.0) {
754 thermal_init(moldyn,equi_init);
758 return 0; /* no scaling needed */
762 /* get scaling factor */
763 scale=moldyn->t_ref/moldyn->t;
767 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
768 scale=1.0+(scale-1.0)/moldyn->t_tc;
771 /* velocity scaling */
772 for(i=0;i<moldyn->count;i++) {
773 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
774 v3_scale(&(atom[i].v),&(atom[i].v),scale);
780 double ideal_gas_law_pressure(t_moldyn *moldyn) {
784 p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
789 double pressure_calc(t_moldyn *moldyn) {
797 * W = 1/3 sum_i f_i r_i
798 * virial = sum_i f_i r_i
800 * => P = (2 Ekin + virial) / (3V)
804 for(i=0;i<moldyn->count;i++) {
805 virial=&(moldyn->atom[i].virial);
806 v+=(virial->xx+virial->yy+virial->zz);
809 /* virial sum and mean virial */
810 moldyn->virial_sum+=v;
811 moldyn->mean_v=moldyn->virial_sum/moldyn->total_steps;
813 /* assume up to date kinetic energy */
814 moldyn->p=2.0*moldyn->ekin+moldyn->mean_v;
815 moldyn->p/=(3.0*moldyn->volume);
816 moldyn->p_sum+=moldyn->p;
817 moldyn->mean_p=moldyn->p_sum/moldyn->total_steps;
819 /* pressure from 'absolute coordinates' virial */
820 virial=&(moldyn->virial);
821 v=virial->xx+virial->yy+virial->zz;
822 moldyn->gp=2.0*moldyn->ekin+v;
823 moldyn->gp/=(3.0*moldyn->volume);
824 moldyn->gp_sum+=moldyn->gp;
825 moldyn->mean_gp=moldyn->gp_sum/moldyn->total_steps;
830 double thermodynamic_pressure_calc(t_moldyn *moldyn) {
833 double u_up,u_down,dv;
845 dv=8*scale*scale*scale*moldyn->volume;
847 store=malloc(moldyn->count*sizeof(t_atom));
849 printf("[moldyn] allocating store mem failed\n");
853 /* save unscaled potential energy + atom/dim configuration */
854 memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
857 /* scale up dimension and atom positions */
858 scale_dim(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
859 scale_atoms(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
860 link_cell_shutdown(moldyn);
861 link_cell_init(moldyn,QUIET);
862 potential_force_calc(moldyn);
865 /* restore atomic configuration + dim */
866 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
869 /* scale down dimension and atom positions */
870 scale_dim(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
871 scale_atoms(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
872 link_cell_shutdown(moldyn);
873 link_cell_init(moldyn,QUIET);
874 potential_force_calc(moldyn);
875 u_down=moldyn->energy;
877 /* calculate pressure */
879 printf("-------> %.10f %.10f %f\n",u_up/EV/moldyn->count,u_down/EV/moldyn->count,p/BAR);
881 /* restore atomic configuration + dim */
882 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
886 potential_force_calc(moldyn);
888 link_cell_shutdown(moldyn);
889 link_cell_init(moldyn,QUIET);
894 double get_pressure(t_moldyn *moldyn) {
900 int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
919 int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
930 for(i=0;i<moldyn->count;i++) {
931 r=&(moldyn->atom[i].r);
940 int scale_volume(t_moldyn *moldyn) {
946 vdim=&(moldyn->vis.dim);
951 if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
952 scale=1.0-(moldyn->p_ref-moldyn->p)/moldyn->p_tc;
953 scale=pow(scale,ONE_THIRD);
956 scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
960 /* scale the atoms and dimensions */
961 scale_atoms(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
962 scale_dim(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
964 /* visualize dimensions */
971 /* recalculate scaled volume */
972 moldyn->volume=dim->x*dim->y*dim->z;
974 /* adjust/reinit linkcell */
975 if(((int)(dim->x/moldyn->cutoff)!=lc->nx)||
976 ((int)(dim->y/moldyn->cutoff)!=lc->ny)||
977 ((int)(dim->z/moldyn->cutoff)!=lc->nx)) {
978 link_cell_shutdown(moldyn);
979 link_cell_init(moldyn,QUIET);
990 double e_kin_calc(t_moldyn *moldyn) {
998 for(i=0;i<moldyn->count;i++)
999 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
1001 return moldyn->ekin;
1004 double get_total_energy(t_moldyn *moldyn) {
1006 return(moldyn->ekin+moldyn->energy);
1009 t_3dvec get_total_p(t_moldyn *moldyn) {
1018 for(i=0;i<moldyn->count;i++) {
1019 v3_scale(&p,&(atom[i].v),atom[i].mass);
1020 v3_add(&p_total,&p_total,&p);
1026 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
1030 /* nn_dist is the nearest neighbour distance */
1032 tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
1041 /* linked list / cell method */
1043 int link_cell_init(t_moldyn *moldyn,u8 vol) {
1050 /* partitioning the md cell */
1051 lc->nx=moldyn->dim.x/moldyn->cutoff;
1052 lc->x=moldyn->dim.x/lc->nx;
1053 lc->ny=moldyn->dim.y/moldyn->cutoff;
1054 lc->y=moldyn->dim.y/lc->ny;
1055 lc->nz=moldyn->dim.z/moldyn->cutoff;
1056 lc->z=moldyn->dim.z/lc->nz;
1058 lc->cells=lc->nx*lc->ny*lc->nz;
1059 lc->subcell=malloc(lc->cells*sizeof(t_list));
1062 printf("[moldyn] FATAL: less then 27 subcells!\n");
1065 printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
1066 printf(" x: %d x %f A\n",lc->nx,lc->x);
1067 printf(" y: %d x %f A\n",lc->ny,lc->y);
1068 printf(" z: %d x %f A\n",lc->nz,lc->z);
1071 for(i=0;i<lc->cells;i++)
1072 list_init_f(&(lc->subcell[i]));
1074 link_cell_update(moldyn);
1079 int link_cell_update(t_moldyn *moldyn) {
1097 for(i=0;i<lc->cells;i++)
1098 list_destroy_f(&(lc->subcell[i]));
1100 for(count=0;count<moldyn->count;count++) {
1101 i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
1102 j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
1103 k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
1104 list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
1111 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
1129 cell[0]=lc->subcell[i+j*nx+k*a];
1130 for(ci=-1;ci<=1;ci++) {
1133 if((x<0)||(x>=nx)) {
1137 for(cj=-1;cj<=1;cj++) {
1140 if((y<0)||(y>=ny)) {
1144 for(ck=-1;ck<=1;ck++) {
1147 if((z<0)||(z>=nz)) {
1151 if(!(ci|cj|ck)) continue;
1153 cell[--count2]=lc->subcell[x+y*nx+z*a];
1156 cell[count1++]=lc->subcell[x+y*nx+z*a];
1167 int link_cell_shutdown(t_moldyn *moldyn) {
1174 for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
1175 list_destroy_f(&(moldyn->lc.subcell[i]));
1182 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
1186 t_moldyn_schedule *schedule;
1188 schedule=&(moldyn->schedule);
1189 count=++(schedule->total_sched);
1191 ptr=realloc(schedule->runs,count*sizeof(int));
1193 perror("[moldyn] realloc (runs)");
1197 schedule->runs[count-1]=runs;
1199 ptr=realloc(schedule->tau,count*sizeof(double));
1201 perror("[moldyn] realloc (tau)");
1205 schedule->tau[count-1]=tau;
1207 printf("[moldyn] schedule added:\n");
1208 printf(" number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
1214 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
1216 moldyn->schedule.hook=hook;
1217 moldyn->schedule.hook_params=hook_params;
1224 * 'integration of newtons equation' - algorithms
1228 /* start the integration */
1230 int moldyn_integrate(t_moldyn *moldyn) {
1233 unsigned int e,m,s,v,p,t;
1235 t_moldyn_schedule *sched;
1240 double energy_scale;
1243 sched=&(moldyn->schedule);
1246 /* initialize linked cell method */
1247 link_cell_init(moldyn,VERBOSE);
1249 /* logging & visualization */
1257 /* sqaure of some variables */
1258 moldyn->tau_square=moldyn->tau*moldyn->tau;
1259 moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
1261 /* energy scaling factor */
1262 energy_scale=moldyn->count*EV;
1264 /* calculate initial forces */
1265 potential_force_calc(moldyn);
1270 /* some stupid checks before we actually start calculating bullshit */
1271 if(moldyn->cutoff>0.5*moldyn->dim.x)
1272 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
1273 if(moldyn->cutoff>0.5*moldyn->dim.y)
1274 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
1275 if(moldyn->cutoff>0.5*moldyn->dim.z)
1276 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
1277 ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
1278 if(ds>0.05*moldyn->nnd)
1279 printf("[moldyn] warning: forces too high / tau too small!\n");
1281 /* zero absolute time */
1283 moldyn->total_steps=0;
1285 /* debugging, ignore */
1288 /* tell the world */
1289 printf("[moldyn] integration start, go get a coffee ...\n");
1291 /* executing the schedule */
1292 for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
1294 /* setting amount of runs and finite time step size */
1295 moldyn->tau=sched->tau[sched->count];
1296 moldyn->tau_square=moldyn->tau*moldyn->tau;
1297 moldyn->time_steps=sched->runs[sched->count];
1299 /* integration according to schedule */
1301 for(i=0;i<moldyn->time_steps;i++) {
1303 /* integration step */
1304 moldyn->integrate(moldyn);
1306 /* calculate kinetic energy, temperature and pressure */
1308 temperature_calc(moldyn);
1309 pressure_calc(moldyn);
1310 //tp=thermodynamic_pressure_calc(moldyn);
1311 //printf("thermodynamic p: %f\n",thermodynamic_pressure_calc(moldyn)/BAR);
1314 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
1315 scale_velocity(moldyn,FALSE);
1316 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
1317 scale_volume(moldyn);
1319 /* check for log & visualization */
1322 dprintf(moldyn->efd,
1324 moldyn->time,moldyn->ekin/energy_scale,
1325 moldyn->energy/energy_scale,
1326 get_total_energy(moldyn)/energy_scale);
1330 momentum=get_total_p(moldyn);
1331 dprintf(moldyn->mfd,
1332 "%f %f %f %f %f\n",moldyn->time,
1333 momentum.x,momentum.y,momentum.z,
1334 v3_norm(&momentum));
1339 dprintf(moldyn->pfd,
1340 "%f %f %f %f %f\n",moldyn->time,
1341 moldyn->p/BAR,moldyn->mean_p/BAR,
1342 moldyn->gp/BAR,moldyn->mean_gp/BAR);
1347 dprintf(moldyn->tfd,
1349 moldyn->time,moldyn->t,moldyn->mean_t);
1354 snprintf(dir,128,"%s/s-%07.f.save",
1355 moldyn->vlsdir,moldyn->time);
1356 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
1357 if(fd<0) perror("[moldyn] save fd open");
1359 write(fd,moldyn,sizeof(t_moldyn));
1360 write(fd,moldyn->atom,
1361 moldyn->count*sizeof(t_atom));
1368 visual_atoms(&(moldyn->vis),moldyn->time,
1369 moldyn->atom,moldyn->count);
1373 /* display progress */
1375 printf("\rsched: %d, steps: %d, T: %f, P: %f %f V: %f",
1379 moldyn->mean_gp/BAR,
1384 /* increase absolute time */
1385 moldyn->time+=moldyn->tau;
1386 moldyn->total_steps+=1;
1390 /* check for hooks */
1391 if(sched->count+1<sched->total_sched)
1393 sched->hook(moldyn,sched->hook_params);
1395 /* get a new info line */
1403 /* velocity verlet */
1405 int velocity_verlet(t_moldyn *moldyn) {
1408 double tau,tau_square,h;
1413 count=moldyn->count;
1415 tau_square=moldyn->tau_square;
1417 for(i=0;i<count;i++) {
1420 v3_scale(&delta,&(atom[i].v),tau);
1421 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1422 v3_scale(&delta,&(atom[i].f),h*tau_square);
1423 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1424 check_per_bound(moldyn,&(atom[i].r));
1426 /* velocities [actually v(t+tau/2)] */
1427 v3_scale(&delta,&(atom[i].f),h*tau);
1428 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1431 /* neighbour list update */
1432 link_cell_update(moldyn);
1434 /* forces depending on chosen potential */
1435 potential_force_calc(moldyn);
1437 for(i=0;i<count;i++) {
1438 /* again velocities [actually v(t+tau)] */
1439 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
1440 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1449 * potentials & corresponding forces & virial routine
1453 /* generic potential and force calculation */
1455 int potential_force_calc(t_moldyn *moldyn) {
1458 t_atom *itom,*jtom,*ktom;
1461 t_list neighbour_i[27];
1462 t_list neighbour_i2[27];
1467 count=moldyn->count;
1474 /* reset global virial */
1475 memset(&(moldyn->virial),0,sizeof(t_virial));
1477 /* reset force, site energy and virial of every atom */
1478 for(i=0;i<count;i++) {
1481 v3_zero(&(itom[i].f));
1484 virial=(&(itom[i].virial));
1492 /* reset site energy */
1497 /* get energy, force and virial of every atom */
1499 /* first (and only) loop over atoms i */
1500 for(i=0;i<count;i++) {
1502 /* single particle potential/force */
1503 if(itom[i].attr&ATOM_ATTR_1BP)
1505 moldyn->func1b(moldyn,&(itom[i]));
1507 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
1510 /* 2 body pair potential/force */
1512 link_cell_neighbour_index(moldyn,
1513 (itom[i].r.x+moldyn->dim.x/2)/lc->x,
1514 (itom[i].r.y+moldyn->dim.y/2)/lc->y,
1515 (itom[i].r.z+moldyn->dim.z/2)/lc->z,
1520 /* first loop over atoms j */
1521 if(moldyn->func2b) {
1524 this=&(neighbour_i[j]);
1527 if(this->start==NULL)
1533 jtom=this->current->data;
1535 if(jtom==&(itom[i]))
1538 if((jtom->attr&ATOM_ATTR_2BP)&
1539 (itom[i].attr&ATOM_ATTR_2BP)) {
1540 moldyn->func2b(moldyn,
1545 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1550 /* 3 body potential/force */
1552 if(!(itom[i].attr&ATOM_ATTR_3BP))
1555 /* copy the neighbour lists */
1556 memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
1558 /* second loop over atoms j */
1561 this=&(neighbour_i[j]);
1564 if(this->start==NULL)
1570 jtom=this->current->data;
1572 if(jtom==&(itom[i]))
1575 if(!(jtom->attr&ATOM_ATTR_3BP))
1581 if(moldyn->func3b_j1)
1582 moldyn->func3b_j1(moldyn,
1587 /* in first j loop, 3bp run can be skipped */
1588 if(!(moldyn->run3bp))
1591 /* first loop over atoms k */
1592 if(moldyn->func3b_k1) {
1596 that=&(neighbour_i2[k]);
1599 if(that->start==NULL)
1606 ktom=that->current->data;
1608 if(!(ktom->attr&ATOM_ATTR_3BP))
1614 if(ktom==&(itom[i]))
1617 moldyn->func3b_k1(moldyn,
1623 } while(list_next_f(that)!=\
1630 if(moldyn->func3b_j2)
1631 moldyn->func3b_j2(moldyn,
1636 /* second loop over atoms k */
1637 if(moldyn->func3b_k2) {
1641 that=&(neighbour_i2[k]);
1644 if(that->start==NULL)
1651 ktom=that->current->data;
1653 if(!(ktom->attr&ATOM_ATTR_3BP))
1659 if(ktom==&(itom[i]))
1662 moldyn->func3b_k2(moldyn,
1668 } while(list_next_f(that)!=\
1675 /* 2bp post function */
1676 if(moldyn->func3b_j3) {
1677 moldyn->func3b_j3(moldyn,
1682 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1696 printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
1699 /* calculate global virial */
1700 for(i=0;i<count;i++) {
1701 moldyn->virial.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
1702 moldyn->virial.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
1703 moldyn->virial.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
1704 moldyn->virial.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
1705 moldyn->virial.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
1706 moldyn->virial.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
1713 * virial calculation
1716 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1717 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1719 a->virial.xx+=f->x*d->x;
1720 a->virial.yy+=f->y*d->y;
1721 a->virial.zz+=f->z*d->z;
1722 a->virial.xy+=f->x*d->y;
1723 a->virial.xz+=f->x*d->z;
1724 a->virial.yz+=f->y*d->z;
1730 * periodic boundary checking
1733 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1734 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1745 if(moldyn->status&MOLDYN_STAT_PBX) {
1746 if(a->x>=x) a->x-=dim->x;
1747 else if(-a->x>x) a->x+=dim->x;
1749 if(moldyn->status&MOLDYN_STAT_PBY) {
1750 if(a->y>=y) a->y-=dim->y;
1751 else if(-a->y>y) a->y+=dim->y;
1753 if(moldyn->status&MOLDYN_STAT_PBZ) {
1754 if(a->z>=z) a->z-=dim->z;
1755 else if(-a->z>z) a->z+=dim->z;
1762 * debugging / critical check functions
1765 int moldyn_bc_check(t_moldyn *moldyn) {
1778 for(i=0;i<moldyn->count;i++) {
1779 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
1780 printf("FATAL: atom %d: x: %.20f (%.20f)\n",
1781 i,atom[i].r.x,dim->x/2);
1782 printf("diagnostic:\n");
1783 printf("-----------\natom.r.x:\n");
1785 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
1788 ((byte)&(1<<k))?1:0,
1791 printf("---------------\nx=dim.x/2:\n");
1793 memcpy(&byte,(u8 *)(&x)+j,1);
1796 ((byte)&(1<<k))?1:0,
1799 if(atom[i].r.x==x) printf("the same!\n");
1800 else printf("different!\n");
1802 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
1803 printf("FATAL: atom %d: y: %.20f (%.20f)\n",
1804 i,atom[i].r.y,dim->y/2);
1805 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
1806 printf("FATAL: atom %d: z: %.20f (%.20f)\n",
1807 i,atom[i].r.z,dim->z/2);
1814 * postprocessing functions
1817 int get_line(int fd,char *line,int max) {
1824 if(count==max) return count;
1825 ret=read(fd,line+count,1);
1826 if(ret<=0) return ret;
1827 if(line[count]=='\n') {
1835 int calc_fluctuations(double start,double end,t_moldyn *moldyn) {
1839 double time,pot,kin,tot;
1840 double p_sum,k_sum,t_sum;
1841 double p2_sum,k2_sum,t2_sum;
1845 printf("[moldyn] calculating energy fluctuations [eV]:\n");
1847 snprintf(file,128+7,"%s/energy",moldyn->vlsdir);
1848 fd=open(file,O_RDONLY);
1850 perror("[moldyn] post proc energy open");
1854 /* calc the averages of A and A^2 */
1860 ret=get_line(fd,buf,63);
1862 if(buf[0]=='#') continue;
1863 sscanf(buf,"%lf %lf %lf %lf",&time,&kin,&pot,&tot);
1864 if(time<start) continue;
1876 moldyn->k_m=k_sum/count;
1877 moldyn->p_m=p_sum/count;
1878 moldyn->t_m=t_sum/count;
1881 moldyn->dk2_m=k2_sum/count-moldyn->k_m*moldyn->k_m;
1882 moldyn->dp2_m=p2_sum/count-moldyn->p_m*moldyn->p_m;
1883 moldyn->dt2_m=t2_sum/count-moldyn->t_m*moldyn->t_m;
1885 printf(" averages : %f %f %f\n",moldyn->k_m,
1888 printf(" mean square: %f %f %f\n",moldyn->dk2_m,
1897 int get_heat_capacity(t_moldyn *moldyn) {
1899 double temp2,mass,ighc;
1902 /* (temperature average)^2 */
1903 temp2=2.0*moldyn->k_m*EV/(3.0*K_BOLTZMANN);
1904 printf("[moldyn] specific heat capacity for T=%f K [J/(kg K)]\n",temp2);
1909 for(i=0;i<moldyn->count;i++)
1910 mass+=moldyn->atom[i].mass;
1912 /* ideal gas contribution */
1913 ighc=3.0*moldyn->count*K_BOLTZMANN/2.0;
1914 printf(" ideal gas contribution: %f\n",ighc/mass*KILOGRAM/JOULE);
1916 moldyn->c_v_nvt=moldyn->dp2_m*moldyn->count*moldyn->count*EV/(K_BOLTZMANN*temp2)+ighc;
1917 moldyn->c_v_nvt/=mass;
1918 moldyn->c_v_nve=ighc/(1.0-(moldyn->dp2_m*moldyn->count*moldyn->count*EV/(ighc*K_BOLTZMANN*temp2)));
1919 moldyn->c_v_nve/=mass;
1921 printf(" NVE: %f\n",moldyn->c_v_nve*KILOGRAM/JOULE);
1922 printf(" NVT: %f\n",moldyn->c_v_nvt*KILOGRAM/JOULE);