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",moldyn->vlsdir);
409 snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
411 snprintf(sc,255,"cd %s && dvipdf report",moldyn->vlsdir);
414 if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
420 * creating lattice functions
423 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
424 u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin) {
435 /* how many atoms do we expect */
436 if(type==CUBIC) new*=1;
437 if(type==FCC) new*=4;
438 if(type==DIAMOND) new*=8;
440 /* allocate space for atoms */
441 ptr=realloc(moldyn->atom,(count+new)*sizeof(t_atom));
443 perror("[moldyn] realloc (create lattice)");
447 atom=&(moldyn->atom[count]);
449 /* no atoms on the boundaries (only reason: it looks better!) */
463 set_nn_dist(moldyn,lc);
464 ret=cubic_init(a,b,c,lc,atom,&orig);
468 v3_scale(&orig,&orig,0.5);
469 set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
470 ret=fcc_init(a,b,c,lc,atom,&orig);
474 v3_scale(&orig,&orig,0.25);
475 set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
476 ret=diamond_init(a,b,c,lc,atom,&orig);
479 printf("unknown lattice type (%02x)\n",type);
485 printf("[moldyn] creating lattice failed\n");
486 printf(" amount of atoms\n");
487 printf(" - expected: %d\n",new);
488 printf(" - created: %d\n",ret);
493 printf("[moldyn] created lattice with %d atoms\n",new);
495 for(ret=0;ret<new;ret++) {
496 atom[ret].element=element;
499 atom[ret].brand=brand;
500 atom[ret].tag=count+ret;
501 check_per_bound(moldyn,&(atom[ret].r));
508 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
527 v3_copy(&(atom[count].r),&r);
536 for(i=0;i<count;i++) {
537 atom[i].r.x-=(a*lc)/2.0;
538 atom[i].r.y-=(b*lc)/2.0;
539 atom[i].r.z-=(c*lc)/2.0;
545 /* fcc lattice init */
546 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
559 /* construct the basis */
560 memset(basis,0,3*sizeof(t_3dvec));
568 /* fill up the room */
576 v3_copy(&(atom[count].r),&r);
579 /* the three face centered atoms */
581 v3_add(&n,&r,&basis[l]);
582 v3_copy(&(atom[count].r),&n);
591 /* coordinate transformation */
592 for(i=0;i<count;i++) {
593 atom[i].r.x-=(a*lc)/2.0;
594 atom[i].r.y-=(b*lc)/2.0;
595 atom[i].r.z-=(c*lc)/2.0;
601 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
606 count=fcc_init(a,b,c,lc,atom,origin);
612 if(origin) v3_add(&o,&o,origin);
614 count+=fcc_init(a,b,c,lc,&atom[count],&o);
619 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
620 t_3dvec *r,t_3dvec *v) {
627 count=(moldyn->count)++;
629 ptr=realloc(atom,(count+1)*sizeof(t_atom));
631 perror("[moldyn] realloc (add atom)");
639 atom[count].element=element;
640 atom[count].mass=mass;
641 atom[count].brand=brand;
642 atom[count].tag=count;
643 atom[count].attr=attr;
648 int destroy_atoms(t_moldyn *moldyn) {
650 if(moldyn->atom) free(moldyn->atom);
655 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
658 * - gaussian distribution of velocities
659 * - zero total momentum
660 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
665 t_3dvec p_total,delta;
670 random=&(moldyn->random);
672 printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
674 /* gaussian distribution of velocities */
676 for(i=0;i<moldyn->count;i++) {
677 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
679 v=sigma*rand_get_gauss(random);
681 p_total.x+=atom[i].mass*v;
683 v=sigma*rand_get_gauss(random);
685 p_total.y+=atom[i].mass*v;
687 v=sigma*rand_get_gauss(random);
689 p_total.z+=atom[i].mass*v;
692 /* zero total momentum */
693 v3_scale(&p_total,&p_total,1.0/moldyn->count);
694 for(i=0;i<moldyn->count;i++) {
695 v3_scale(&delta,&p_total,1.0/atom[i].mass);
696 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
699 /* velocity scaling */
700 scale_velocity(moldyn,equi_init);
705 double temperature_calc(t_moldyn *moldyn) {
707 /* assume up to date kinetic energy, which is 3/2 N k_B T */
709 moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
710 moldyn->t_sum+=moldyn->t;
711 moldyn->mean_t=moldyn->t_sum/moldyn->total_steps;
716 double get_temperature(t_moldyn *moldyn) {
721 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
731 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
734 /* get kinetic energy / temperature & count involved atoms */
737 for(i=0;i<moldyn->count;i++) {
738 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
739 e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
744 if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
745 else return 0; /* no atoms involved in scaling! */
747 /* (temporary) hack for e,t = 0 */
750 if(moldyn->t_ref!=0.0) {
751 thermal_init(moldyn,equi_init);
755 return 0; /* no scaling needed */
759 /* get scaling factor */
760 scale=moldyn->t_ref/moldyn->t;
764 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
765 scale=1.0+(scale-1.0)/moldyn->t_tc;
768 /* velocity scaling */
769 for(i=0;i<moldyn->count;i++) {
770 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
771 v3_scale(&(atom[i].v),&(atom[i].v),scale);
777 double ideal_gas_law_pressure(t_moldyn *moldyn) {
781 p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
786 double pressure_calc(t_moldyn *moldyn) {
794 * W = 1/3 sum_i f_i r_i
795 * virial = sum_i f_i r_i
797 * => P = (2 Ekin + virial) / (3V)
801 for(i=0;i<moldyn->count;i++) {
802 virial=&(moldyn->atom[i].virial);
803 v+=(virial->xx+virial->yy+virial->zz);
806 /* virial sum and mean virial */
807 moldyn->virial_sum+=v;
808 moldyn->mean_v=moldyn->virial_sum/moldyn->total_steps;
810 /* assume up to date kinetic energy */
811 moldyn->p=2.0*moldyn->ekin+moldyn->mean_v;
812 moldyn->p/=(3.0*moldyn->volume);
813 moldyn->p_sum+=moldyn->p;
814 moldyn->mean_p=moldyn->p_sum/moldyn->total_steps;
816 /* pressure from 'absolute coordinates' virial */
817 virial=&(moldyn->virial);
818 v=virial->xx+virial->yy+virial->zz;
819 moldyn->gp=2.0*moldyn->ekin+v;
820 moldyn->gp/=(3.0*moldyn->volume);
821 moldyn->gp_sum+=moldyn->gp;
822 moldyn->mean_gp=moldyn->gp_sum/moldyn->total_steps;
827 double thermodynamic_pressure_calc(t_moldyn *moldyn) {
830 double u_up,u_down,dv;
842 dv=8*scale*scale*scale*moldyn->volume;
844 store=malloc(moldyn->count*sizeof(t_atom));
846 printf("[moldyn] allocating store mem failed\n");
850 /* save unscaled potential energy + atom/dim configuration */
851 memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
854 /* scale up dimension and atom positions */
855 scale_dim(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
856 scale_atoms(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
857 link_cell_shutdown(moldyn);
858 link_cell_init(moldyn,QUIET);
859 potential_force_calc(moldyn);
862 /* restore atomic configuration + dim */
863 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
866 /* scale down dimension and atom positions */
867 scale_dim(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
868 scale_atoms(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
869 link_cell_shutdown(moldyn);
870 link_cell_init(moldyn,QUIET);
871 potential_force_calc(moldyn);
872 u_down=moldyn->energy;
874 /* calculate pressure */
876 printf("-------> %.10f %.10f %f\n",u_up/EV/moldyn->count,u_down/EV/moldyn->count,p/BAR);
878 /* restore atomic configuration + dim */
879 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
883 potential_force_calc(moldyn);
885 link_cell_shutdown(moldyn);
886 link_cell_init(moldyn,QUIET);
891 double get_pressure(t_moldyn *moldyn) {
897 int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
916 int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
927 for(i=0;i<moldyn->count;i++) {
928 r=&(moldyn->atom[i].r);
937 int scale_volume(t_moldyn *moldyn) {
943 vdim=&(moldyn->vis.dim);
948 if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
949 scale=1.0-(moldyn->p_ref-moldyn->p)/moldyn->p_tc;
950 scale=pow(scale,ONE_THIRD);
953 scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
957 /* scale the atoms and dimensions */
958 scale_atoms(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
959 scale_dim(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
961 /* visualize dimensions */
968 /* recalculate scaled volume */
969 moldyn->volume=dim->x*dim->y*dim->z;
971 /* adjust/reinit linkcell */
972 if(((int)(dim->x/moldyn->cutoff)!=lc->nx)||
973 ((int)(dim->y/moldyn->cutoff)!=lc->ny)||
974 ((int)(dim->z/moldyn->cutoff)!=lc->nx)) {
975 link_cell_shutdown(moldyn);
976 link_cell_init(moldyn,QUIET);
987 double e_kin_calc(t_moldyn *moldyn) {
995 for(i=0;i<moldyn->count;i++)
996 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
1001 double get_total_energy(t_moldyn *moldyn) {
1003 return(moldyn->ekin+moldyn->energy);
1006 t_3dvec get_total_p(t_moldyn *moldyn) {
1015 for(i=0;i<moldyn->count;i++) {
1016 v3_scale(&p,&(atom[i].v),atom[i].mass);
1017 v3_add(&p_total,&p_total,&p);
1023 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
1027 /* nn_dist is the nearest neighbour distance */
1029 tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
1038 /* linked list / cell method */
1040 int link_cell_init(t_moldyn *moldyn,u8 vol) {
1047 /* partitioning the md cell */
1048 lc->nx=moldyn->dim.x/moldyn->cutoff;
1049 lc->x=moldyn->dim.x/lc->nx;
1050 lc->ny=moldyn->dim.y/moldyn->cutoff;
1051 lc->y=moldyn->dim.y/lc->ny;
1052 lc->nz=moldyn->dim.z/moldyn->cutoff;
1053 lc->z=moldyn->dim.z/lc->nz;
1055 lc->cells=lc->nx*lc->ny*lc->nz;
1056 lc->subcell=malloc(lc->cells*sizeof(t_list));
1059 printf("[moldyn] FATAL: less then 27 subcells!\n");
1062 printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
1063 printf(" x: %d x %f A\n",lc->nx,lc->x);
1064 printf(" y: %d x %f A\n",lc->ny,lc->y);
1065 printf(" z: %d x %f A\n",lc->nz,lc->z);
1068 for(i=0;i<lc->cells;i++)
1069 list_init_f(&(lc->subcell[i]));
1071 link_cell_update(moldyn);
1076 int link_cell_update(t_moldyn *moldyn) {
1094 for(i=0;i<lc->cells;i++)
1095 list_destroy_f(&(lc->subcell[i]));
1097 for(count=0;count<moldyn->count;count++) {
1098 i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
1099 j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
1100 k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
1101 list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
1108 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
1126 cell[0]=lc->subcell[i+j*nx+k*a];
1127 for(ci=-1;ci<=1;ci++) {
1130 if((x<0)||(x>=nx)) {
1134 for(cj=-1;cj<=1;cj++) {
1137 if((y<0)||(y>=ny)) {
1141 for(ck=-1;ck<=1;ck++) {
1144 if((z<0)||(z>=nz)) {
1148 if(!(ci|cj|ck)) continue;
1150 cell[--count2]=lc->subcell[x+y*nx+z*a];
1153 cell[count1++]=lc->subcell[x+y*nx+z*a];
1164 int link_cell_shutdown(t_moldyn *moldyn) {
1171 for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
1172 list_destroy_f(&(moldyn->lc.subcell[i]));
1179 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
1183 t_moldyn_schedule *schedule;
1185 schedule=&(moldyn->schedule);
1186 count=++(schedule->total_sched);
1188 ptr=realloc(schedule->runs,count*sizeof(int));
1190 perror("[moldyn] realloc (runs)");
1194 schedule->runs[count-1]=runs;
1196 ptr=realloc(schedule->tau,count*sizeof(double));
1198 perror("[moldyn] realloc (tau)");
1202 schedule->tau[count-1]=tau;
1204 printf("[moldyn] schedule added:\n");
1205 printf(" number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
1211 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
1213 moldyn->schedule.hook=hook;
1214 moldyn->schedule.hook_params=hook_params;
1221 * 'integration of newtons equation' - algorithms
1225 /* start the integration */
1227 int moldyn_integrate(t_moldyn *moldyn) {
1230 unsigned int e,m,s,v,p,t;
1232 t_moldyn_schedule *sched;
1237 double energy_scale;
1240 sched=&(moldyn->schedule);
1243 /* initialize linked cell method */
1244 link_cell_init(moldyn,VERBOSE);
1246 /* logging & visualization */
1254 /* sqaure of some variables */
1255 moldyn->tau_square=moldyn->tau*moldyn->tau;
1256 moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
1258 /* energy scaling factor */
1259 energy_scale=moldyn->count*EV;
1261 /* calculate initial forces */
1262 potential_force_calc(moldyn);
1267 /* some stupid checks before we actually start calculating bullshit */
1268 if(moldyn->cutoff>0.5*moldyn->dim.x)
1269 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
1270 if(moldyn->cutoff>0.5*moldyn->dim.y)
1271 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
1272 if(moldyn->cutoff>0.5*moldyn->dim.z)
1273 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
1274 ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
1275 if(ds>0.05*moldyn->nnd)
1276 printf("[moldyn] warning: forces too high / tau too small!\n");
1278 /* zero absolute time */
1280 moldyn->total_steps=0;
1282 /* debugging, ignore */
1285 /* tell the world */
1286 printf("[moldyn] integration start, go get a coffee ...\n");
1288 /* executing the schedule */
1289 for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
1291 /* setting amount of runs and finite time step size */
1292 moldyn->tau=sched->tau[sched->count];
1293 moldyn->tau_square=moldyn->tau*moldyn->tau;
1294 moldyn->time_steps=sched->runs[sched->count];
1296 /* integration according to schedule */
1298 for(i=0;i<moldyn->time_steps;i++) {
1300 /* integration step */
1301 moldyn->integrate(moldyn);
1303 /* calculate kinetic energy, temperature and pressure */
1305 temperature_calc(moldyn);
1306 pressure_calc(moldyn);
1307 //tp=thermodynamic_pressure_calc(moldyn);
1308 //printf("thermodynamic p: %f\n",thermodynamic_pressure_calc(moldyn)/BAR);
1311 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
1312 scale_velocity(moldyn,FALSE);
1313 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
1314 scale_volume(moldyn);
1316 /* check for log & visualization */
1319 dprintf(moldyn->efd,
1321 moldyn->time,moldyn->ekin/energy_scale,
1322 moldyn->energy/energy_scale,
1323 get_total_energy(moldyn)/energy_scale);
1327 momentum=get_total_p(moldyn);
1328 dprintf(moldyn->mfd,
1329 "%f %f %f %f %f\n",moldyn->time,
1330 momentum.x,momentum.y,momentum.z,
1331 v3_norm(&momentum));
1336 dprintf(moldyn->pfd,
1337 "%f %f %f %f %f\n",moldyn->time,
1338 moldyn->p/BAR,moldyn->mean_p/BAR,
1339 moldyn->gp/BAR,moldyn->mean_gp/BAR);
1344 dprintf(moldyn->tfd,
1346 moldyn->time,moldyn->t,moldyn->mean_t);
1351 snprintf(dir,128,"%s/s-%07.f.save",
1352 moldyn->vlsdir,moldyn->time);
1353 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
1354 if(fd<0) perror("[moldyn] save fd open");
1356 write(fd,moldyn,sizeof(t_moldyn));
1357 write(fd,moldyn->atom,
1358 moldyn->count*sizeof(t_atom));
1365 visual_atoms(&(moldyn->vis),moldyn->time,
1366 moldyn->atom,moldyn->count);
1370 /* display progress */
1372 printf("\rsched: %d, steps: %d, T: %f, P: %f %f V: %f",
1376 moldyn->mean_gp/BAR,
1381 /* increase absolute time */
1382 moldyn->time+=moldyn->tau;
1383 moldyn->total_steps+=1;
1387 /* check for hooks */
1389 sched->hook(moldyn,sched->hook_params);
1391 /* get a new info line */
1399 /* velocity verlet */
1401 int velocity_verlet(t_moldyn *moldyn) {
1404 double tau,tau_square,h;
1409 count=moldyn->count;
1411 tau_square=moldyn->tau_square;
1413 for(i=0;i<count;i++) {
1416 v3_scale(&delta,&(atom[i].v),tau);
1417 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1418 v3_scale(&delta,&(atom[i].f),h*tau_square);
1419 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1420 check_per_bound(moldyn,&(atom[i].r));
1422 /* velocities [actually v(t+tau/2)] */
1423 v3_scale(&delta,&(atom[i].f),h*tau);
1424 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1427 /* neighbour list update */
1428 link_cell_update(moldyn);
1430 /* forces depending on chosen potential */
1431 potential_force_calc(moldyn);
1433 for(i=0;i<count;i++) {
1434 /* again velocities [actually v(t+tau)] */
1435 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
1436 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1445 * potentials & corresponding forces & virial routine
1449 /* generic potential and force calculation */
1451 int potential_force_calc(t_moldyn *moldyn) {
1454 t_atom *itom,*jtom,*ktom;
1457 t_list neighbour_i[27];
1458 t_list neighbour_i2[27];
1463 count=moldyn->count;
1470 /* reset global virial */
1471 memset(&(moldyn->virial),0,sizeof(t_virial));
1473 /* reset force, site energy and virial of every atom */
1474 for(i=0;i<count;i++) {
1477 v3_zero(&(itom[i].f));
1480 virial=(&(itom[i].virial));
1488 /* reset site energy */
1493 /* get energy, force and virial of every atom */
1495 /* first (and only) loop over atoms i */
1496 for(i=0;i<count;i++) {
1498 /* single particle potential/force */
1499 if(itom[i].attr&ATOM_ATTR_1BP)
1501 moldyn->func1b(moldyn,&(itom[i]));
1503 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
1506 /* 2 body pair potential/force */
1508 link_cell_neighbour_index(moldyn,
1509 (itom[i].r.x+moldyn->dim.x/2)/lc->x,
1510 (itom[i].r.y+moldyn->dim.y/2)/lc->y,
1511 (itom[i].r.z+moldyn->dim.z/2)/lc->z,
1516 /* first loop over atoms j */
1517 if(moldyn->func2b) {
1520 this=&(neighbour_i[j]);
1523 if(this->start==NULL)
1529 jtom=this->current->data;
1531 if(jtom==&(itom[i]))
1534 if((jtom->attr&ATOM_ATTR_2BP)&
1535 (itom[i].attr&ATOM_ATTR_2BP)) {
1536 moldyn->func2b(moldyn,
1541 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1546 /* 3 body potential/force */
1548 if(!(itom[i].attr&ATOM_ATTR_3BP))
1551 /* copy the neighbour lists */
1552 memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
1554 /* second loop over atoms j */
1557 this=&(neighbour_i[j]);
1560 if(this->start==NULL)
1566 jtom=this->current->data;
1568 if(jtom==&(itom[i]))
1571 if(!(jtom->attr&ATOM_ATTR_3BP))
1577 if(moldyn->func3b_j1)
1578 moldyn->func3b_j1(moldyn,
1583 /* in first j loop, 3bp run can be skipped */
1584 if(!(moldyn->run3bp))
1587 /* first loop over atoms k */
1588 if(moldyn->func3b_k1) {
1592 that=&(neighbour_i2[k]);
1595 if(that->start==NULL)
1602 ktom=that->current->data;
1604 if(!(ktom->attr&ATOM_ATTR_3BP))
1610 if(ktom==&(itom[i]))
1613 moldyn->func3b_k1(moldyn,
1619 } while(list_next_f(that)!=\
1626 if(moldyn->func3b_j2)
1627 moldyn->func3b_j2(moldyn,
1632 /* second loop over atoms k */
1633 if(moldyn->func3b_k2) {
1637 that=&(neighbour_i2[k]);
1640 if(that->start==NULL)
1647 ktom=that->current->data;
1649 if(!(ktom->attr&ATOM_ATTR_3BP))
1655 if(ktom==&(itom[i]))
1658 moldyn->func3b_k2(moldyn,
1664 } while(list_next_f(that)!=\
1671 /* 2bp post function */
1672 if(moldyn->func3b_j3) {
1673 moldyn->func3b_j3(moldyn,
1678 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1692 printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
1695 /* calculate global virial */
1696 for(i=0;i<count;i++) {
1697 moldyn->virial.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
1698 moldyn->virial.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
1699 moldyn->virial.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
1700 moldyn->virial.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
1701 moldyn->virial.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
1702 moldyn->virial.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
1709 * virial calculation
1712 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1713 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1715 a->virial.xx+=f->x*d->x;
1716 a->virial.yy+=f->y*d->y;
1717 a->virial.zz+=f->z*d->z;
1718 a->virial.xy+=f->x*d->y;
1719 a->virial.xz+=f->x*d->z;
1720 a->virial.yz+=f->y*d->z;
1726 * periodic boundary checking
1729 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1730 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1741 if(moldyn->status&MOLDYN_STAT_PBX) {
1742 if(a->x>=x) a->x-=dim->x;
1743 else if(-a->x>x) a->x+=dim->x;
1745 if(moldyn->status&MOLDYN_STAT_PBY) {
1746 if(a->y>=y) a->y-=dim->y;
1747 else if(-a->y>y) a->y+=dim->y;
1749 if(moldyn->status&MOLDYN_STAT_PBZ) {
1750 if(a->z>=z) a->z-=dim->z;
1751 else if(-a->z>z) a->z+=dim->z;
1758 * debugging / critical check functions
1761 int moldyn_bc_check(t_moldyn *moldyn) {
1774 for(i=0;i<moldyn->count;i++) {
1775 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
1776 printf("FATAL: atom %d: x: %.20f (%.20f)\n",
1777 i,atom[i].r.x,dim->x/2);
1778 printf("diagnostic:\n");
1779 printf("-----------\natom.r.x:\n");
1781 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
1784 ((byte)&(1<<k))?1:0,
1787 printf("---------------\nx=dim.x/2:\n");
1789 memcpy(&byte,(u8 *)(&x)+j,1);
1792 ((byte)&(1<<k))?1:0,
1795 if(atom[i].r.x==x) printf("the same!\n");
1796 else printf("different!\n");
1798 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
1799 printf("FATAL: atom %d: y: %.20f (%.20f)\n",
1800 i,atom[i].r.y,dim->y/2);
1801 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
1802 printf("FATAL: atom %d: z: %.20f (%.20f)\n",
1803 i,atom[i].r.z,dim->z/2);
1810 * postprocessing functions
1812 #define LINE_MAX 128
1813 int read_line(int fd,char *line) {
1820 if(count==LINE_MAX) return count;
1821 ret=read(fd,line+count,1);
1822 if(ret<0) return ret;
1823 if(line[count]=='\n') {
1831 int calc_fluctuations(double start,double end,char *file) {
1835 double time,pot,kin,tot;
1837 double p2_m,k2_m,t2_m;
1838 double p_sum,k_sum,t_sum;
1841 fd=open(file,O_RDONLY);
1843 perror("[moldyn] post proc open");
1847 /* first calc the averages */
1853 ret=read_line(fd,buf);
1856 if(buf[0]=='#') continue;
1857 sscanf(buf,"%lf %lf %lf %lf",&time,&kin,&pot,&tot);
1858 printf("%f %f %f %f\n",time,pot,kin,tot);
1859 //if(time>end) break;
1860 if((time>=start)&(time<=end)) {
1872 /* mean square fluctuations */
1873 if(lseek(fd,SEEK_SET,0)<0) {
1874 perror("[moldyn] lseek");
1882 ret=read_line(fd,buf);
1884 if(buf[0]=='#') continue;
1885 sscanf(buf,"%lf %lf %lf %lf",&time,&kin,&pot,&tot);
1887 if((time>=start)&(time<=end)) {
1888 p_sum+=((pot-p_m)*(pot-p_m));
1889 k_sum+=((kin-k_m)*(kin-k_m));
1890 t_sum+=((tot-t_m)*(tot-t_m));
1899 printf("[moldyn] fluctuations (%f - %f):\n",start,end);
1900 printf(" - averages : %f %f %f\n",k_m,p_m,t_m);
1901 printf(" - mean square: %f %f %f\n",k2_m,p2_m,t2_m);