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 set_avg_skip(t_moldyn *moldyn,int skip) {
223 printf("[moldyn] skip %d steps before starting average calc\n",skip);
224 moldyn->avg_skip=skip;
229 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
231 strncpy(moldyn->vlsdir,dir,127);
236 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title) {
238 strncpy(moldyn->rauthor,author,63);
239 strncpy(moldyn->rtitle,title,63);
244 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
249 printf("[moldyn] set log: ");
252 case LOG_TOTAL_ENERGY:
253 moldyn->ewrite=timer;
254 snprintf(filename,127,"%s/energy",moldyn->vlsdir);
255 moldyn->efd=open(filename,
256 O_WRONLY|O_CREAT|O_EXCL,
259 perror("[moldyn] energy log fd open");
262 dprintf(moldyn->efd,"# total energy log file\n");
263 printf("total energy (%d)\n",timer);
265 case LOG_TOTAL_MOMENTUM:
266 moldyn->mwrite=timer;
267 snprintf(filename,127,"%s/momentum",moldyn->vlsdir);
268 moldyn->mfd=open(filename,
269 O_WRONLY|O_CREAT|O_EXCL,
272 perror("[moldyn] momentum log fd open");
275 dprintf(moldyn->efd,"# total momentum log file\n");
276 printf("total momentum (%d)\n",timer);
279 moldyn->pwrite=timer;
280 snprintf(filename,127,"%s/pressure",moldyn->vlsdir);
281 moldyn->pfd=open(filename,
282 O_WRONLY|O_CREAT|O_EXCL,
285 perror("[moldyn] pressure log file\n");
288 dprintf(moldyn->pfd,"# pressure log file\n");
289 printf("pressure (%d)\n",timer);
291 case LOG_TEMPERATURE:
292 moldyn->twrite=timer;
293 snprintf(filename,127,"%s/temperature",moldyn->vlsdir);
294 moldyn->tfd=open(filename,
295 O_WRONLY|O_CREAT|O_EXCL,
298 perror("[moldyn] temperature log file\n");
301 dprintf(moldyn->tfd,"# temperature log file\n");
302 printf("temperature (%d)\n",timer);
305 moldyn->swrite=timer;
306 printf("save file (%d)\n",timer);
309 moldyn->vwrite=timer;
310 ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
312 printf("[moldyn] visual init failure\n");
315 printf("visual file (%d)\n",timer);
318 snprintf(filename,127,"%s/report.tex",moldyn->vlsdir);
319 moldyn->rfd=open(filename,
320 O_WRONLY|O_CREAT|O_EXCL,
323 perror("[moldyn] report fd open");
326 printf("report -> ");
328 snprintf(filename,127,"%s/e_plot.scr",
330 moldyn->epfd=open(filename,
331 O_WRONLY|O_CREAT|O_EXCL,
334 perror("[moldyn] energy plot fd open");
337 dprintf(moldyn->epfd,e_plot_script);
342 snprintf(filename,127,"%s/pressure_plot.scr",
344 moldyn->ppfd=open(filename,
345 O_WRONLY|O_CREAT|O_EXCL,
348 perror("[moldyn] p plot fd open");
351 dprintf(moldyn->ppfd,pressure_plot_script);
356 snprintf(filename,127,"%s/temperature_plot.scr",
358 moldyn->tpfd=open(filename,
359 O_WRONLY|O_CREAT|O_EXCL,
362 perror("[moldyn] t plot fd open");
365 dprintf(moldyn->tpfd,temperature_plot_script);
367 printf("temperature ");
369 dprintf(moldyn->rfd,report_start,
370 moldyn->rauthor,moldyn->rtitle);
374 printf("unknown log type: %02x\n",type);
381 int moldyn_log_shutdown(t_moldyn *moldyn) {
385 printf("[moldyn] log shutdown\n");
389 dprintf(moldyn->rfd,report_energy);
390 snprintf(sc,255,"cd %s && gnuplot e_plot.scr",
395 if(moldyn->mfd) close(moldyn->mfd);
399 dprintf(moldyn->rfd,report_pressure);
400 snprintf(sc,255,"cd %s && gnuplot pressure_plot.scr",
407 dprintf(moldyn->rfd,report_temperature);
408 snprintf(sc,255,"cd %s && gnuplot temperature_plot.scr",
413 dprintf(moldyn->rfd,report_end);
415 snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
418 snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
421 snprintf(sc,255,"cd %s && dvipdf report >/dev/null 2>&1",
425 if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
431 * creating lattice functions
434 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
435 u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin) {
446 /* how many atoms do we expect */
447 if(type==CUBIC) new*=1;
448 if(type==FCC) new*=4;
449 if(type==DIAMOND) new*=8;
451 /* allocate space for atoms */
452 ptr=realloc(moldyn->atom,(count+new)*sizeof(t_atom));
454 perror("[moldyn] realloc (create lattice)");
458 atom=&(moldyn->atom[count]);
460 /* no atoms on the boundaries (only reason: it looks better!) */
474 set_nn_dist(moldyn,lc);
475 ret=cubic_init(a,b,c,lc,atom,&orig);
479 v3_scale(&orig,&orig,0.5);
480 set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
481 ret=fcc_init(a,b,c,lc,atom,&orig);
485 v3_scale(&orig,&orig,0.25);
486 set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
487 ret=diamond_init(a,b,c,lc,atom,&orig);
490 printf("unknown lattice type (%02x)\n",type);
496 printf("[moldyn] creating lattice failed\n");
497 printf(" amount of atoms\n");
498 printf(" - expected: %d\n",new);
499 printf(" - created: %d\n",ret);
504 printf("[moldyn] created lattice with %d atoms\n",new);
506 for(ret=0;ret<new;ret++) {
507 atom[ret].element=element;
510 atom[ret].brand=brand;
511 atom[ret].tag=count+ret;
512 check_per_bound(moldyn,&(atom[ret].r));
513 atom[ret].r_0=atom[ret].r;
516 /* update total system mass */
517 total_mass_calc(moldyn);
522 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
523 t_3dvec *r,t_3dvec *v) {
530 count=(moldyn->count)++;
532 ptr=realloc(atom,(count+1)*sizeof(t_atom));
534 perror("[moldyn] realloc (add atom)");
542 atom[count].element=element;
543 atom[count].mass=mass;
544 atom[count].brand=brand;
545 atom[count].tag=count;
546 atom[count].attr=attr;
547 check_per_bound(moldyn,&(atom[count].r));
548 atom[count].r_0=atom[count].r;
550 /* update total system mass */
551 total_mass_calc(moldyn);
557 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
576 v3_copy(&(atom[count].r),&r);
585 for(i=0;i<count;i++) {
586 atom[i].r.x-=(a*lc)/2.0;
587 atom[i].r.y-=(b*lc)/2.0;
588 atom[i].r.z-=(c*lc)/2.0;
594 /* fcc lattice init */
595 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
608 /* construct the basis */
609 memset(basis,0,3*sizeof(t_3dvec));
617 /* fill up the room */
625 v3_copy(&(atom[count].r),&r);
628 /* the three face centered atoms */
630 v3_add(&n,&r,&basis[l]);
631 v3_copy(&(atom[count].r),&n);
640 /* coordinate transformation */
641 for(i=0;i<count;i++) {
642 atom[i].r.x-=(a*lc)/2.0;
643 atom[i].r.y-=(b*lc)/2.0;
644 atom[i].r.z-=(c*lc)/2.0;
650 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
655 count=fcc_init(a,b,c,lc,atom,origin);
661 if(origin) v3_add(&o,&o,origin);
663 count+=fcc_init(a,b,c,lc,&atom[count],&o);
668 int destroy_atoms(t_moldyn *moldyn) {
670 if(moldyn->atom) free(moldyn->atom);
675 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
678 * - gaussian distribution of velocities
679 * - zero total momentum
680 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
685 t_3dvec p_total,delta;
690 random=&(moldyn->random);
692 printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
694 /* gaussian distribution of velocities */
696 for(i=0;i<moldyn->count;i++) {
697 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
699 v=sigma*rand_get_gauss(random);
701 p_total.x+=atom[i].mass*v;
703 v=sigma*rand_get_gauss(random);
705 p_total.y+=atom[i].mass*v;
707 v=sigma*rand_get_gauss(random);
709 p_total.z+=atom[i].mass*v;
712 /* zero total momentum */
713 v3_scale(&p_total,&p_total,1.0/moldyn->count);
714 for(i=0;i<moldyn->count;i++) {
715 v3_scale(&delta,&p_total,1.0/atom[i].mass);
716 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
719 /* velocity scaling */
720 scale_velocity(moldyn,equi_init);
725 double total_mass_calc(t_moldyn *moldyn) {
731 for(i=0;i<moldyn->count;i++)
732 moldyn->mass+=moldyn->atom[i].mass;
737 double temperature_calc(t_moldyn *moldyn) {
739 /* assume up to date kinetic energy, which is 3/2 N k_B T */
741 moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
746 double get_temperature(t_moldyn *moldyn) {
751 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
761 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
764 /* get kinetic energy / temperature & count involved atoms */
767 for(i=0;i<moldyn->count;i++) {
768 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
769 e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
774 if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
775 else return 0; /* no atoms involved in scaling! */
777 /* (temporary) hack for e,t = 0 */
780 if(moldyn->t_ref!=0.0) {
781 thermal_init(moldyn,equi_init);
785 return 0; /* no scaling needed */
789 /* get scaling factor */
790 scale=moldyn->t_ref/moldyn->t;
794 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
795 scale=1.0+(scale-1.0)/moldyn->t_tc;
798 /* velocity scaling */
799 for(i=0;i<moldyn->count;i++) {
800 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
801 v3_scale(&(atom[i].v),&(atom[i].v),scale);
807 double ideal_gas_law_pressure(t_moldyn *moldyn) {
811 p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
816 double virial_sum(t_moldyn *moldyn) {
822 /* virial (sum over atom virials) */
824 for(i=0;i<moldyn->count;i++) {
825 virial=&(moldyn->atom[i].virial);
826 v+=(virial->xx+virial->yy+virial->zz);
830 /* global virial (absolute coordinates) */
831 virial=&(moldyn->gvir);
832 moldyn->gv=virial->xx+virial->yy+virial->zz;
834 return moldyn->virial;
837 double pressure_calc(t_moldyn *moldyn) {
841 * with W = 1/3 sum_i f_i r_i (- skipped!)
842 * virial = sum_i f_i r_i
844 * => P = (2 Ekin + virial) / (3V)
847 /* assume up to date virial & up to date kinetic energy */
849 /* pressure (atom virials) */
850 moldyn->p=2.0*moldyn->ekin+moldyn->virial;
851 moldyn->p/=(3.0*moldyn->volume);
853 /* pressure (absolute coordinates) */
854 moldyn->gp=2.0*moldyn->ekin+moldyn->gv;
855 moldyn->gp/=(3.0*moldyn->volume);
860 int average_and_fluctuation_calc(t_moldyn *moldyn) {
862 if(moldyn->total_steps<moldyn->avg_skip)
865 int denom=moldyn->total_steps+1-moldyn->avg_skip;
867 /* assume up to date energies, temperature, pressure etc */
870 moldyn->k_sum+=moldyn->ekin;
871 moldyn->k2_sum+=(moldyn->ekin*moldyn->ekin);
872 moldyn->k_avg=moldyn->k_sum/denom;
873 moldyn->k2_avg=moldyn->k2_sum/denom;
874 moldyn->dk2_avg=moldyn->k2_avg-(moldyn->k_avg*moldyn->k_avg);
876 /* potential energy */
877 moldyn->v_sum+=moldyn->energy;
878 moldyn->v2_sum+=(moldyn->energy*moldyn->energy);
879 moldyn->v_avg=moldyn->v_sum/denom;
880 moldyn->v2_avg=moldyn->v2_sum/denom;
881 moldyn->dv2_avg=moldyn->v2_avg-(moldyn->v_avg*moldyn->v_avg);
884 moldyn->t_sum+=moldyn->t;
885 moldyn->t_avg=moldyn->t_sum/denom;
888 moldyn->virial_sum+=moldyn->virial;
889 moldyn->virial_avg=moldyn->virial_sum/denom;
890 moldyn->gv_sum+=moldyn->gv;
891 moldyn->gv_avg=moldyn->gv_sum/denom;
894 moldyn->p_sum+=moldyn->p;
895 moldyn->p_avg=moldyn->p_sum/denom;
896 moldyn->gp_sum+=moldyn->gp;
897 moldyn->gp_avg=moldyn->gp_sum/denom;
902 int get_heat_capacity(t_moldyn *moldyn) {
906 /* averages needed for heat capacity calc */
907 if(moldyn->total_steps<moldyn->avg_skip)
910 /* (temperature average)^2 */
911 temp2=moldyn->t_avg*moldyn->t_avg;
912 printf("[moldyn] specific heat capacity for T=%f K [J/(kg K)]\n",
915 /* ideal gas contribution */
916 ighc=3.0*moldyn->count*K_BOLTZMANN/2.0;
917 printf(" ideal gas contribution: %f\n",
918 ighc/moldyn->mass*KILOGRAM/JOULE);
920 /* specific heat for nvt ensemble */
921 moldyn->c_v_nvt=moldyn->dv2_avg/(K_BOLTZMANN*temp2)+ighc;
922 moldyn->c_v_nvt/=moldyn->mass;
924 /* specific heat for nve ensemble */
925 moldyn->c_v_nve=ighc/(1.0-(moldyn->dv2_avg/(ighc*K_BOLTZMANN*temp2)));
926 moldyn->c_v_nve/=moldyn->mass;
928 printf(" NVE: %f\n",moldyn->c_v_nve*KILOGRAM/JOULE);
929 printf(" NVT: %f\n",moldyn->c_v_nvt*KILOGRAM/JOULE);
930 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)));
935 double thermodynamic_pressure_calc(t_moldyn *moldyn) {
938 double u_up,u_down,dv;
950 dv=8*scale*scale*scale*moldyn->volume;
952 store=malloc(moldyn->count*sizeof(t_atom));
954 printf("[moldyn] allocating store mem failed\n");
958 /* save unscaled potential energy + atom/dim configuration */
959 memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
962 /* scale up dimension and atom positions */
963 scale_dim(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
964 scale_atoms(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
965 link_cell_shutdown(moldyn);
966 link_cell_init(moldyn,QUIET);
967 potential_force_calc(moldyn);
970 /* restore atomic configuration + dim */
971 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
974 /* scale down dimension and atom positions */
975 scale_dim(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
976 scale_atoms(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
977 link_cell_shutdown(moldyn);
978 link_cell_init(moldyn,QUIET);
979 potential_force_calc(moldyn);
980 u_down=moldyn->energy;
982 /* calculate pressure */
984 printf("-------> %.10f %.10f %f\n",u_up/EV/moldyn->count,u_down/EV/moldyn->count,p/BAR);
986 /* restore atomic configuration + dim */
987 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
991 potential_force_calc(moldyn);
993 link_cell_shutdown(moldyn);
994 link_cell_init(moldyn,QUIET);
999 double get_pressure(t_moldyn *moldyn) {
1005 int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
1017 if(x) dim->x*=scale;
1018 if(y) dim->y*=scale;
1019 if(z) dim->z*=scale;
1024 int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
1035 for(i=0;i<moldyn->count;i++) {
1036 r=&(moldyn->atom[i].r);
1045 int scale_volume(t_moldyn *moldyn) {
1051 vdim=&(moldyn->vis.dim);
1055 /* scaling factor */
1056 if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
1057 scale=1.0-(moldyn->p_ref-moldyn->p)/moldyn->p_tc;
1058 scale=pow(scale,ONE_THIRD);
1061 scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
1063 moldyn->debug=scale;
1065 /* scale the atoms and dimensions */
1066 scale_atoms(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
1067 scale_dim(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
1069 /* visualize dimensions */
1076 /* recalculate scaled volume */
1077 moldyn->volume=dim->x*dim->y*dim->z;
1079 /* adjust/reinit linkcell */
1080 if(((int)(dim->x/moldyn->cutoff)!=lc->nx)||
1081 ((int)(dim->y/moldyn->cutoff)!=lc->ny)||
1082 ((int)(dim->z/moldyn->cutoff)!=lc->nx)) {
1083 link_cell_shutdown(moldyn);
1084 link_cell_init(moldyn,QUIET);
1095 double e_kin_calc(t_moldyn *moldyn) {
1103 for(i=0;i<moldyn->count;i++) {
1104 atom[i].ekin=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
1105 moldyn->ekin+=atom[i].ekin;
1108 return moldyn->ekin;
1111 double get_total_energy(t_moldyn *moldyn) {
1113 return(moldyn->ekin+moldyn->energy);
1116 t_3dvec get_total_p(t_moldyn *moldyn) {
1125 for(i=0;i<moldyn->count;i++) {
1126 v3_scale(&p,&(atom[i].v),atom[i].mass);
1127 v3_add(&p_total,&p_total,&p);
1133 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
1137 /* nn_dist is the nearest neighbour distance */
1139 tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
1148 /* linked list / cell method */
1150 int link_cell_init(t_moldyn *moldyn,u8 vol) {
1157 /* partitioning the md cell */
1158 lc->nx=moldyn->dim.x/moldyn->cutoff;
1159 lc->x=moldyn->dim.x/lc->nx;
1160 lc->ny=moldyn->dim.y/moldyn->cutoff;
1161 lc->y=moldyn->dim.y/lc->ny;
1162 lc->nz=moldyn->dim.z/moldyn->cutoff;
1163 lc->z=moldyn->dim.z/lc->nz;
1165 lc->cells=lc->nx*lc->ny*lc->nz;
1166 lc->subcell=malloc(lc->cells*sizeof(t_list));
1169 printf("[moldyn] FATAL: less then 27 subcells!\n");
1172 printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
1173 printf(" x: %d x %f A\n",lc->nx,lc->x);
1174 printf(" y: %d x %f A\n",lc->ny,lc->y);
1175 printf(" z: %d x %f A\n",lc->nz,lc->z);
1178 for(i=0;i<lc->cells;i++)
1179 list_init_f(&(lc->subcell[i]));
1181 link_cell_update(moldyn);
1186 int link_cell_update(t_moldyn *moldyn) {
1204 for(i=0;i<lc->cells;i++)
1205 list_destroy_f(&(lc->subcell[i]));
1207 for(count=0;count<moldyn->count;count++) {
1208 i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
1209 j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
1210 k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
1211 list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
1218 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
1236 cell[0]=lc->subcell[i+j*nx+k*a];
1237 for(ci=-1;ci<=1;ci++) {
1240 if((x<0)||(x>=nx)) {
1244 for(cj=-1;cj<=1;cj++) {
1247 if((y<0)||(y>=ny)) {
1251 for(ck=-1;ck<=1;ck++) {
1254 if((z<0)||(z>=nz)) {
1258 if(!(ci|cj|ck)) continue;
1260 cell[--count2]=lc->subcell[x+y*nx+z*a];
1263 cell[count1++]=lc->subcell[x+y*nx+z*a];
1274 int link_cell_shutdown(t_moldyn *moldyn) {
1281 for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
1282 list_destroy_f(&(moldyn->lc.subcell[i]));
1289 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
1293 t_moldyn_schedule *schedule;
1295 schedule=&(moldyn->schedule);
1296 count=++(schedule->total_sched);
1298 ptr=realloc(schedule->runs,count*sizeof(int));
1300 perror("[moldyn] realloc (runs)");
1304 schedule->runs[count-1]=runs;
1306 ptr=realloc(schedule->tau,count*sizeof(double));
1308 perror("[moldyn] realloc (tau)");
1312 schedule->tau[count-1]=tau;
1314 printf("[moldyn] schedule added:\n");
1315 printf(" number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
1321 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
1323 moldyn->schedule.hook=hook;
1324 moldyn->schedule.hook_params=hook_params;
1331 * 'integration of newtons equation' - algorithms
1335 /* start the integration */
1337 int moldyn_integrate(t_moldyn *moldyn) {
1340 unsigned int e,m,s,v,p,t;
1342 t_moldyn_schedule *sched;
1347 double energy_scale;
1350 sched=&(moldyn->schedule);
1353 /* initialize linked cell method */
1354 link_cell_init(moldyn,VERBOSE);
1356 /* logging & visualization */
1364 /* sqaure of some variables */
1365 moldyn->tau_square=moldyn->tau*moldyn->tau;
1366 moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
1368 /* energy scaling factor */
1369 energy_scale=moldyn->count*EV;
1371 /* calculate initial forces */
1372 potential_force_calc(moldyn);
1377 /* some stupid checks before we actually start calculating bullshit */
1378 if(moldyn->cutoff>0.5*moldyn->dim.x)
1379 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
1380 if(moldyn->cutoff>0.5*moldyn->dim.y)
1381 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
1382 if(moldyn->cutoff>0.5*moldyn->dim.z)
1383 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
1384 ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
1385 if(ds>0.05*moldyn->nnd)
1386 printf("[moldyn] warning: forces too high / tau too small!\n");
1388 /* zero absolute time */
1390 moldyn->total_steps=0;
1392 /* debugging, ignore */
1395 /* tell the world */
1396 printf("[moldyn] integration start, go get a coffee ...\n");
1398 /* executing the schedule */
1400 while(sched->count<sched->total_sched) {
1402 /* setting amount of runs and finite time step size */
1403 moldyn->tau=sched->tau[sched->count];
1404 moldyn->tau_square=moldyn->tau*moldyn->tau;
1405 moldyn->time_steps=sched->runs[sched->count];
1407 /* integration according to schedule */
1409 for(i=0;i<moldyn->time_steps;i++) {
1411 /* integration step */
1412 moldyn->integrate(moldyn);
1414 /* calculate kinetic energy, temperature and pressure */
1416 temperature_calc(moldyn);
1418 pressure_calc(moldyn);
1419 average_and_fluctuation_calc(moldyn);
1422 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
1423 scale_velocity(moldyn,FALSE);
1424 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
1425 scale_volume(moldyn);
1427 /* check for log & visualization */
1430 dprintf(moldyn->efd,
1432 moldyn->time,moldyn->ekin/energy_scale,
1433 moldyn->energy/energy_scale,
1434 get_total_energy(moldyn)/energy_scale);
1438 momentum=get_total_p(moldyn);
1439 dprintf(moldyn->mfd,
1440 "%f %f %f %f %f\n",moldyn->time,
1441 momentum.x,momentum.y,momentum.z,
1442 v3_norm(&momentum));
1447 dprintf(moldyn->pfd,
1448 "%f %f %f %f %f\n",moldyn->time,
1449 moldyn->p/BAR,moldyn->p_avg/BAR,
1450 moldyn->gp/BAR,moldyn->gp_avg/BAR);
1455 dprintf(moldyn->tfd,
1457 moldyn->time,moldyn->t,moldyn->t_avg);
1462 snprintf(dir,128,"%s/s-%07.f.save",
1463 moldyn->vlsdir,moldyn->time);
1464 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
1465 if(fd<0) perror("[moldyn] save fd open");
1467 write(fd,moldyn,sizeof(t_moldyn));
1468 write(fd,moldyn->atom,
1469 moldyn->count*sizeof(t_atom));
1476 visual_atoms(&(moldyn->vis),moldyn->time,
1477 moldyn->atom,moldyn->count);
1481 /* display progress */
1483 printf("\rsched:%d, steps:%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f",
1485 moldyn->t,moldyn->t_avg,
1486 moldyn->p_avg/BAR,moldyn->p/BAR,
1491 /* increase absolute time */
1492 moldyn->time+=moldyn->tau;
1493 moldyn->total_steps+=1;
1497 /* check for hooks */
1499 printf("\n ## schedule hook %d/%d start ##\n",
1500 sched->count+1,sched->total_sched-1);
1501 sched->hook(moldyn,sched->hook_params);
1502 printf(" ## schedule hook end ##\n");
1505 /* increase the schedule counter */
1513 /* velocity verlet */
1515 int velocity_verlet(t_moldyn *moldyn) {
1518 double tau,tau_square,h;
1523 count=moldyn->count;
1525 tau_square=moldyn->tau_square;
1527 for(i=0;i<count;i++) {
1530 v3_scale(&delta,&(atom[i].v),tau);
1531 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1532 v3_scale(&delta,&(atom[i].f),h*tau_square);
1533 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1534 check_per_bound(moldyn,&(atom[i].r));
1536 /* velocities [actually v(t+tau/2)] */
1537 v3_scale(&delta,&(atom[i].f),h*tau);
1538 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1541 /* neighbour list update */
1542 link_cell_update(moldyn);
1544 /* forces depending on chosen potential */
1545 potential_force_calc(moldyn);
1547 for(i=0;i<count;i++) {
1548 /* again velocities [actually v(t+tau)] */
1549 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
1550 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1559 * potentials & corresponding forces & virial routine
1563 /* generic potential and force calculation */
1565 int potential_force_calc(t_moldyn *moldyn) {
1568 t_atom *itom,*jtom,*ktom;
1571 t_list neighbour_i[27];
1572 t_list neighbour_i2[27];
1577 count=moldyn->count;
1584 /* reset global virial */
1585 memset(&(moldyn->gvir),0,sizeof(t_virial));
1587 /* reset force, site energy and virial of every atom */
1588 for(i=0;i<count;i++) {
1591 v3_zero(&(itom[i].f));
1594 virial=(&(itom[i].virial));
1602 /* reset site energy */
1607 /* get energy, force and virial of every atom */
1609 /* first (and only) loop over atoms i */
1610 for(i=0;i<count;i++) {
1612 /* single particle potential/force */
1613 if(itom[i].attr&ATOM_ATTR_1BP)
1615 moldyn->func1b(moldyn,&(itom[i]));
1617 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
1620 /* 2 body pair potential/force */
1622 link_cell_neighbour_index(moldyn,
1623 (itom[i].r.x+moldyn->dim.x/2)/lc->x,
1624 (itom[i].r.y+moldyn->dim.y/2)/lc->y,
1625 (itom[i].r.z+moldyn->dim.z/2)/lc->z,
1630 /* first loop over atoms j */
1631 if(moldyn->func2b) {
1634 this=&(neighbour_i[j]);
1637 if(this->start==NULL)
1643 jtom=this->current->data;
1645 if(jtom==&(itom[i]))
1648 if((jtom->attr&ATOM_ATTR_2BP)&
1649 (itom[i].attr&ATOM_ATTR_2BP)) {
1650 moldyn->func2b(moldyn,
1655 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1660 /* 3 body potential/force */
1662 if(!(itom[i].attr&ATOM_ATTR_3BP))
1665 /* copy the neighbour lists */
1666 memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
1668 /* second loop over atoms j */
1671 this=&(neighbour_i[j]);
1674 if(this->start==NULL)
1680 jtom=this->current->data;
1682 if(jtom==&(itom[i]))
1685 if(!(jtom->attr&ATOM_ATTR_3BP))
1691 if(moldyn->func3b_j1)
1692 moldyn->func3b_j1(moldyn,
1697 /* in first j loop, 3bp run can be skipped */
1698 if(!(moldyn->run3bp))
1701 /* first loop over atoms k */
1702 if(moldyn->func3b_k1) {
1706 that=&(neighbour_i2[k]);
1709 if(that->start==NULL)
1716 ktom=that->current->data;
1718 if(!(ktom->attr&ATOM_ATTR_3BP))
1724 if(ktom==&(itom[i]))
1727 moldyn->func3b_k1(moldyn,
1733 } while(list_next_f(that)!=\
1740 if(moldyn->func3b_j2)
1741 moldyn->func3b_j2(moldyn,
1746 /* second loop over atoms k */
1747 if(moldyn->func3b_k2) {
1751 that=&(neighbour_i2[k]);
1754 if(that->start==NULL)
1761 ktom=that->current->data;
1763 if(!(ktom->attr&ATOM_ATTR_3BP))
1769 if(ktom==&(itom[i]))
1772 moldyn->func3b_k2(moldyn,
1778 } while(list_next_f(that)!=\
1785 /* 2bp post function */
1786 if(moldyn->func3b_j3) {
1787 moldyn->func3b_j3(moldyn,
1792 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1806 printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
1809 /* calculate global virial */
1810 for(i=0;i<count;i++) {
1811 moldyn->gvir.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
1812 moldyn->gvir.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
1813 moldyn->gvir.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
1814 moldyn->gvir.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
1815 moldyn->gvir.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
1816 moldyn->gvir.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
1823 * virial calculation
1826 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1827 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1829 a->virial.xx+=f->x*d->x;
1830 a->virial.yy+=f->y*d->y;
1831 a->virial.zz+=f->z*d->z;
1832 a->virial.xy+=f->x*d->y;
1833 a->virial.xz+=f->x*d->z;
1834 a->virial.yz+=f->y*d->z;
1840 * periodic boundary checking
1843 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1844 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1855 if(moldyn->status&MOLDYN_STAT_PBX) {
1856 if(a->x>=x) a->x-=dim->x;
1857 else if(-a->x>x) a->x+=dim->x;
1859 if(moldyn->status&MOLDYN_STAT_PBY) {
1860 if(a->y>=y) a->y-=dim->y;
1861 else if(-a->y>y) a->y+=dim->y;
1863 if(moldyn->status&MOLDYN_STAT_PBZ) {
1864 if(a->z>=z) a->z-=dim->z;
1865 else if(-a->z>z) a->z+=dim->z;
1872 * debugging / critical check functions
1875 int moldyn_bc_check(t_moldyn *moldyn) {
1888 for(i=0;i<moldyn->count;i++) {
1889 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
1890 printf("FATAL: atom %d: x: %.20f (%.20f)\n",
1891 i,atom[i].r.x,dim->x/2);
1892 printf("diagnostic:\n");
1893 printf("-----------\natom.r.x:\n");
1895 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
1898 ((byte)&(1<<k))?1:0,
1901 printf("---------------\nx=dim.x/2:\n");
1903 memcpy(&byte,(u8 *)(&x)+j,1);
1906 ((byte)&(1<<k))?1:0,
1909 if(atom[i].r.x==x) printf("the same!\n");
1910 else printf("different!\n");
1912 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
1913 printf("FATAL: atom %d: y: %.20f (%.20f)\n",
1914 i,atom[i].r.y,dim->y/2);
1915 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
1916 printf("FATAL: atom %d: z: %.20f (%.20f)\n",
1917 i,atom[i].r.z,dim->z/2);
1924 * post processing functions
1927 int get_line(int fd,char *line,int max) {
1934 if(count==max) return count;
1935 ret=read(fd,line+count,1);
1936 if(ret<=0) return ret;
1937 if(line[count]=='\n') {