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"
23 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
25 printf("[moldyn] init\n");
27 memset(moldyn,0,sizeof(t_moldyn));
32 rand_init(&(moldyn->random),NULL,1);
33 moldyn->random.status|=RAND_STAT_VERBOSE;
38 int moldyn_shutdown(t_moldyn *moldyn) {
40 printf("[moldyn] shutdown\n");
42 moldyn_log_shutdown(moldyn);
43 link_cell_shutdown(moldyn);
44 rand_close(&(moldyn->random));
50 int set_int_alg(t_moldyn *moldyn,u8 algo) {
52 printf("[moldyn] integration algorithm: ");
55 case MOLDYN_INTEGRATE_VERLET:
56 moldyn->integrate=velocity_verlet;
57 printf("velocity verlet\n");
60 printf("unknown integration algorithm: %02x\n",algo);
68 int set_cutoff(t_moldyn *moldyn,double cutoff) {
70 moldyn->cutoff=cutoff;
72 printf("[moldyn] cutoff [A]: %f\n",moldyn->cutoff);
77 int set_temperature(t_moldyn *moldyn,double t_ref) {
81 printf("[moldyn] temperature [K]: %f\n",moldyn->t_ref);
86 int set_pressure(t_moldyn *moldyn,double p_ref) {
90 printf("[moldyn] pressure [bar]: %f\n",moldyn->p_ref/BAR);
95 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
97 moldyn->pt_scale=(ptype|ttype);
101 printf("[moldyn] p/t scaling:\n");
103 printf(" p: %s",ptype?"yes":"no ");
105 printf(" | type: %02x | factor: %f",ptype,ptc);
108 printf(" t: %s",ttype?"yes":"no ");
110 printf(" | type: %02x | factor: %f",ttype,ttc);
116 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
122 moldyn->volume=x*y*z;
130 moldyn->dv=0.000001*moldyn->volume;
132 printf("[moldyn] dimensions in A and A^3 respectively:\n");
133 printf(" x: %f\n",moldyn->dim.x);
134 printf(" y: %f\n",moldyn->dim.y);
135 printf(" z: %f\n",moldyn->dim.z);
136 printf(" volume: %f\n",moldyn->volume);
137 printf(" visualize simulation box: %s\n",visualize?"yes":"no");
138 printf(" delta volume (pressure calc): %f\n",moldyn->dv);
143 int set_nn_dist(t_moldyn *moldyn,double dist) {
150 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
152 printf("[moldyn] periodic boundary conditions:\n");
155 moldyn->status|=MOLDYN_STAT_PBX;
158 moldyn->status|=MOLDYN_STAT_PBY;
161 moldyn->status|=MOLDYN_STAT_PBZ;
163 printf(" x: %s\n",x?"yes":"no");
164 printf(" y: %s\n",y?"yes":"no");
165 printf(" z: %s\n",z?"yes":"no");
170 int set_potential1b(t_moldyn *moldyn,pf_func1b func) {
177 int set_potential2b(t_moldyn *moldyn,pf_func2b func) {
184 int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func) {
186 moldyn->func3b_j1=func;
191 int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func) {
193 moldyn->func3b_j2=func;
198 int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func) {
200 moldyn->func3b_j3=func;
205 int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func) {
207 moldyn->func3b_k1=func;
212 int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func) {
214 moldyn->func3b_k2=func;
219 int set_potential_params(t_moldyn *moldyn,void *params) {
221 moldyn->pot_params=params;
226 int set_avg_skip(t_moldyn *moldyn,int skip) {
228 printf("[moldyn] skip %d steps before starting average calc\n",skip);
229 moldyn->avg_skip=skip;
234 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
236 strncpy(moldyn->vlsdir,dir,127);
241 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title) {
243 strncpy(moldyn->rauthor,author,63);
244 strncpy(moldyn->rtitle,title,63);
249 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
254 printf("[moldyn] set log: ");
257 case LOG_TOTAL_ENERGY:
258 moldyn->ewrite=timer;
259 snprintf(filename,127,"%s/energy",moldyn->vlsdir);
260 moldyn->efd=open(filename,
261 O_WRONLY|O_CREAT|O_EXCL,
264 perror("[moldyn] energy log fd open");
267 dprintf(moldyn->efd,"# total energy log file\n");
268 printf("total energy (%d)\n",timer);
270 case LOG_TOTAL_MOMENTUM:
271 moldyn->mwrite=timer;
272 snprintf(filename,127,"%s/momentum",moldyn->vlsdir);
273 moldyn->mfd=open(filename,
274 O_WRONLY|O_CREAT|O_EXCL,
277 perror("[moldyn] momentum log fd open");
280 dprintf(moldyn->efd,"# total momentum log file\n");
281 printf("total momentum (%d)\n",timer);
284 moldyn->pwrite=timer;
285 snprintf(filename,127,"%s/pressure",moldyn->vlsdir);
286 moldyn->pfd=open(filename,
287 O_WRONLY|O_CREAT|O_EXCL,
290 perror("[moldyn] pressure log file\n");
293 dprintf(moldyn->pfd,"# pressure log file\n");
294 printf("pressure (%d)\n",timer);
296 case LOG_TEMPERATURE:
297 moldyn->twrite=timer;
298 snprintf(filename,127,"%s/temperature",moldyn->vlsdir);
299 moldyn->tfd=open(filename,
300 O_WRONLY|O_CREAT|O_EXCL,
303 perror("[moldyn] temperature log file\n");
306 dprintf(moldyn->tfd,"# temperature log file\n");
307 printf("temperature (%d)\n",timer);
310 moldyn->swrite=timer;
311 printf("save file (%d)\n",timer);
314 moldyn->vwrite=timer;
315 ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
317 printf("[moldyn] visual init failure\n");
320 printf("visual file (%d)\n",timer);
323 snprintf(filename,127,"%s/report.tex",moldyn->vlsdir);
324 moldyn->rfd=open(filename,
325 O_WRONLY|O_CREAT|O_EXCL,
328 perror("[moldyn] report fd open");
331 printf("report -> ");
333 snprintf(filename,127,"%s/e_plot.scr",
335 moldyn->epfd=open(filename,
336 O_WRONLY|O_CREAT|O_EXCL,
339 perror("[moldyn] energy plot fd open");
342 dprintf(moldyn->epfd,e_plot_script);
347 snprintf(filename,127,"%s/pressure_plot.scr",
349 moldyn->ppfd=open(filename,
350 O_WRONLY|O_CREAT|O_EXCL,
353 perror("[moldyn] p plot fd open");
356 dprintf(moldyn->ppfd,pressure_plot_script);
361 snprintf(filename,127,"%s/temperature_plot.scr",
363 moldyn->tpfd=open(filename,
364 O_WRONLY|O_CREAT|O_EXCL,
367 perror("[moldyn] t plot fd open");
370 dprintf(moldyn->tpfd,temperature_plot_script);
372 printf("temperature ");
374 dprintf(moldyn->rfd,report_start,
375 moldyn->rauthor,moldyn->rtitle);
379 printf("unknown log type: %02x\n",type);
386 int moldyn_log_shutdown(t_moldyn *moldyn) {
390 printf("[moldyn] log shutdown\n");
394 dprintf(moldyn->rfd,report_energy);
395 snprintf(sc,255,"cd %s && gnuplot e_plot.scr",
400 if(moldyn->mfd) close(moldyn->mfd);
404 dprintf(moldyn->rfd,report_pressure);
405 snprintf(sc,255,"cd %s && gnuplot pressure_plot.scr",
412 dprintf(moldyn->rfd,report_temperature);
413 snprintf(sc,255,"cd %s && gnuplot temperature_plot.scr",
418 dprintf(moldyn->rfd,report_end);
420 snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
423 snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
426 snprintf(sc,255,"cd %s && dvipdf report >/dev/null 2>&1",
430 if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
436 * creating lattice functions
439 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
440 u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin) {
451 /* how many atoms do we expect */
452 if(type==CUBIC) new*=1;
453 if(type==FCC) new*=4;
454 if(type==DIAMOND) new*=8;
456 /* allocate space for atoms */
457 ptr=realloc(moldyn->atom,(count+new)*sizeof(t_atom));
459 perror("[moldyn] realloc (create lattice)");
463 atom=&(moldyn->atom[count]);
465 /* no atoms on the boundaries (only reason: it looks better!) */
479 set_nn_dist(moldyn,lc);
480 ret=cubic_init(a,b,c,lc,atom,&orig);
484 v3_scale(&orig,&orig,0.5);
485 set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
486 ret=fcc_init(a,b,c,lc,atom,&orig);
490 v3_scale(&orig,&orig,0.25);
491 set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
492 ret=diamond_init(a,b,c,lc,atom,&orig);
495 printf("unknown lattice type (%02x)\n",type);
501 printf("[moldyn] creating lattice failed\n");
502 printf(" amount of atoms\n");
503 printf(" - expected: %d\n",new);
504 printf(" - created: %d\n",ret);
509 printf("[moldyn] created lattice with %d atoms\n",new);
511 for(ret=0;ret<new;ret++) {
512 atom[ret].element=element;
515 atom[ret].brand=brand;
516 atom[ret].tag=count+ret;
517 check_per_bound(moldyn,&(atom[ret].r));
518 atom[ret].r_0=atom[ret].r;
521 /* update total system mass */
522 total_mass_calc(moldyn);
527 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
528 t_3dvec *r,t_3dvec *v) {
535 count=(moldyn->count)++;
537 ptr=realloc(atom,(count+1)*sizeof(t_atom));
539 perror("[moldyn] realloc (add atom)");
547 atom[count].element=element;
548 atom[count].mass=mass;
549 atom[count].brand=brand;
550 atom[count].tag=count;
551 atom[count].attr=attr;
552 check_per_bound(moldyn,&(atom[count].r));
553 atom[count].r_0=atom[count].r;
555 /* update total system mass */
556 total_mass_calc(moldyn);
562 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
581 v3_copy(&(atom[count].r),&r);
590 for(i=0;i<count;i++) {
591 atom[i].r.x-=(a*lc)/2.0;
592 atom[i].r.y-=(b*lc)/2.0;
593 atom[i].r.z-=(c*lc)/2.0;
599 /* fcc lattice init */
600 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
613 /* construct the basis */
614 memset(basis,0,3*sizeof(t_3dvec));
622 /* fill up the room */
630 v3_copy(&(atom[count].r),&r);
633 /* the three face centered atoms */
635 v3_add(&n,&r,&basis[l]);
636 v3_copy(&(atom[count].r),&n);
645 /* coordinate transformation */
646 for(i=0;i<count;i++) {
647 atom[i].r.x-=(a*lc)/2.0;
648 atom[i].r.y-=(b*lc)/2.0;
649 atom[i].r.z-=(c*lc)/2.0;
655 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
660 count=fcc_init(a,b,c,lc,atom,origin);
666 if(origin) v3_add(&o,&o,origin);
668 count+=fcc_init(a,b,c,lc,&atom[count],&o);
673 int destroy_atoms(t_moldyn *moldyn) {
675 if(moldyn->atom) free(moldyn->atom);
680 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
683 * - gaussian distribution of velocities
684 * - zero total momentum
685 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
690 t_3dvec p_total,delta;
695 random=&(moldyn->random);
697 printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
699 /* gaussian distribution of velocities */
701 for(i=0;i<moldyn->count;i++) {
702 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
704 v=sigma*rand_get_gauss(random);
706 p_total.x+=atom[i].mass*v;
708 v=sigma*rand_get_gauss(random);
710 p_total.y+=atom[i].mass*v;
712 v=sigma*rand_get_gauss(random);
714 p_total.z+=atom[i].mass*v;
717 /* zero total momentum */
718 v3_scale(&p_total,&p_total,1.0/moldyn->count);
719 for(i=0;i<moldyn->count;i++) {
720 v3_scale(&delta,&p_total,1.0/atom[i].mass);
721 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
724 /* velocity scaling */
725 scale_velocity(moldyn,equi_init);
730 double total_mass_calc(t_moldyn *moldyn) {
736 for(i=0;i<moldyn->count;i++)
737 moldyn->mass+=moldyn->atom[i].mass;
742 double temperature_calc(t_moldyn *moldyn) {
744 /* assume up to date kinetic energy, which is 3/2 N k_B T */
746 moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
751 double get_temperature(t_moldyn *moldyn) {
756 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
766 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
769 /* get kinetic energy / temperature & count involved atoms */
772 for(i=0;i<moldyn->count;i++) {
773 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
774 e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
779 if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
780 else return 0; /* no atoms involved in scaling! */
782 /* (temporary) hack for e,t = 0 */
785 if(moldyn->t_ref!=0.0) {
786 thermal_init(moldyn,equi_init);
790 return 0; /* no scaling needed */
794 /* get scaling factor */
795 scale=moldyn->t_ref/moldyn->t;
799 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
800 scale=1.0+(scale-1.0)/moldyn->t_tc;
803 /* velocity scaling */
804 for(i=0;i<moldyn->count;i++) {
805 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
806 v3_scale(&(atom[i].v),&(atom[i].v),scale);
812 double ideal_gas_law_pressure(t_moldyn *moldyn) {
816 p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
821 double virial_sum(t_moldyn *moldyn) {
827 /* virial (sum over atom virials) */
829 for(i=0;i<moldyn->count;i++) {
830 virial=&(moldyn->atom[i].virial);
831 v+=(virial->xx+virial->yy+virial->zz);
835 /* global virial (absolute coordinates) */
836 virial=&(moldyn->gvir);
837 moldyn->gv=virial->xx+virial->yy+virial->zz;
839 return moldyn->virial;
842 double pressure_calc(t_moldyn *moldyn) {
846 * with W = 1/3 sum_i f_i r_i (- skipped!)
847 * virial = sum_i f_i r_i
849 * => P = (2 Ekin + virial) / (3V)
852 /* assume up to date virial & up to date kinetic energy */
854 /* pressure (atom virials) */
855 moldyn->p=2.0*moldyn->ekin+moldyn->virial;
856 moldyn->p/=(3.0*moldyn->volume);
858 /* pressure (absolute coordinates) */
859 moldyn->gp=2.0*moldyn->ekin+moldyn->gv;
860 moldyn->gp/=(3.0*moldyn->volume);
865 int average_and_fluctuation_calc(t_moldyn *moldyn) {
867 if(moldyn->total_steps<moldyn->avg_skip)
870 int denom=moldyn->total_steps+1-moldyn->avg_skip;
872 /* assume up to date energies, temperature, pressure etc */
875 moldyn->k_sum+=moldyn->ekin;
876 moldyn->k2_sum+=(moldyn->ekin*moldyn->ekin);
877 moldyn->k_avg=moldyn->k_sum/denom;
878 moldyn->k2_avg=moldyn->k2_sum/denom;
879 moldyn->dk2_avg=moldyn->k2_avg-(moldyn->k_avg*moldyn->k_avg);
881 /* potential energy */
882 moldyn->v_sum+=moldyn->energy;
883 moldyn->v2_sum+=(moldyn->energy*moldyn->energy);
884 moldyn->v_avg=moldyn->v_sum/denom;
885 moldyn->v2_avg=moldyn->v2_sum/denom;
886 moldyn->dv2_avg=moldyn->v2_avg-(moldyn->v_avg*moldyn->v_avg);
889 moldyn->t_sum+=moldyn->t;
890 moldyn->t_avg=moldyn->t_sum/denom;
893 moldyn->virial_sum+=moldyn->virial;
894 moldyn->virial_avg=moldyn->virial_sum/denom;
895 moldyn->gv_sum+=moldyn->gv;
896 moldyn->gv_avg=moldyn->gv_sum/denom;
899 moldyn->p_sum+=moldyn->p;
900 moldyn->p_avg=moldyn->p_sum/denom;
901 moldyn->gp_sum+=moldyn->gp;
902 moldyn->gp_avg=moldyn->gp_sum/denom;
907 int get_heat_capacity(t_moldyn *moldyn) {
911 /* averages needed for heat capacity calc */
912 if(moldyn->total_steps<moldyn->avg_skip)
915 /* (temperature average)^2 */
916 temp2=moldyn->t_avg*moldyn->t_avg;
917 printf("[moldyn] specific heat capacity for T=%f K [J/(kg K)]\n",
920 /* ideal gas contribution */
921 ighc=3.0*moldyn->count*K_BOLTZMANN/2.0;
922 printf(" ideal gas contribution: %f\n",
923 ighc/moldyn->mass*KILOGRAM/JOULE);
925 /* specific heat for nvt ensemble */
926 moldyn->c_v_nvt=moldyn->dv2_avg/(K_BOLTZMANN*temp2)+ighc;
927 moldyn->c_v_nvt/=moldyn->mass;
929 /* specific heat for nve ensemble */
930 moldyn->c_v_nve=ighc/(1.0-(moldyn->dv2_avg/(ighc*K_BOLTZMANN*temp2)));
931 moldyn->c_v_nve/=moldyn->mass;
933 printf(" NVE: %f\n",moldyn->c_v_nve*KILOGRAM/JOULE);
934 printf(" NVT: %f\n",moldyn->c_v_nvt*KILOGRAM/JOULE);
935 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)));
940 double thermodynamic_pressure_calc(t_moldyn *moldyn) {
943 double u_up,u_down,dv;
955 dv=8*scale*scale*scale*moldyn->volume;
957 store=malloc(moldyn->count*sizeof(t_atom));
959 printf("[moldyn] allocating store mem failed\n");
963 /* save unscaled potential energy + atom/dim configuration */
964 memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
967 /* scale up dimension and atom positions */
968 scale_dim(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
969 scale_atoms(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
970 link_cell_shutdown(moldyn);
971 link_cell_init(moldyn,QUIET);
972 potential_force_calc(moldyn);
975 /* restore atomic configuration + dim */
976 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
979 /* scale down dimension and atom positions */
980 scale_dim(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
981 scale_atoms(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
982 link_cell_shutdown(moldyn);
983 link_cell_init(moldyn,QUIET);
984 potential_force_calc(moldyn);
985 u_down=moldyn->energy;
987 /* calculate pressure */
989 printf("-------> %.10f %.10f %f\n",u_up/EV/moldyn->count,u_down/EV/moldyn->count,p/BAR);
991 /* restore atomic configuration + dim */
992 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
996 potential_force_calc(moldyn);
998 link_cell_shutdown(moldyn);
999 link_cell_init(moldyn,QUIET);
1004 double get_pressure(t_moldyn *moldyn) {
1010 int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
1022 if(x) dim->x*=scale;
1023 if(y) dim->y*=scale;
1024 if(z) dim->z*=scale;
1029 int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
1040 for(i=0;i<moldyn->count;i++) {
1041 r=&(moldyn->atom[i].r);
1050 int scale_volume(t_moldyn *moldyn) {
1056 vdim=&(moldyn->vis.dim);
1060 /* scaling factor */
1061 if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
1062 scale=1.0-(moldyn->p_ref-moldyn->p)/moldyn->p_tc;
1063 scale=pow(scale,ONE_THIRD);
1066 scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
1068 moldyn->debug=scale;
1070 /* scale the atoms and dimensions */
1071 scale_atoms(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
1072 scale_dim(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
1074 /* visualize dimensions */
1081 /* recalculate scaled volume */
1082 moldyn->volume=dim->x*dim->y*dim->z;
1084 /* adjust/reinit linkcell */
1085 if(((int)(dim->x/moldyn->cutoff)!=lc->nx)||
1086 ((int)(dim->y/moldyn->cutoff)!=lc->ny)||
1087 ((int)(dim->z/moldyn->cutoff)!=lc->nx)) {
1088 link_cell_shutdown(moldyn);
1089 link_cell_init(moldyn,QUIET);
1100 double e_kin_calc(t_moldyn *moldyn) {
1108 for(i=0;i<moldyn->count;i++) {
1109 atom[i].ekin=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
1110 moldyn->ekin+=atom[i].ekin;
1113 return moldyn->ekin;
1116 double get_total_energy(t_moldyn *moldyn) {
1118 return(moldyn->ekin+moldyn->energy);
1121 t_3dvec get_total_p(t_moldyn *moldyn) {
1130 for(i=0;i<moldyn->count;i++) {
1131 v3_scale(&p,&(atom[i].v),atom[i].mass);
1132 v3_add(&p_total,&p_total,&p);
1138 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
1142 /* nn_dist is the nearest neighbour distance */
1144 tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
1153 /* linked list / cell method */
1155 int link_cell_init(t_moldyn *moldyn,u8 vol) {
1162 /* partitioning the md cell */
1163 lc->nx=moldyn->dim.x/moldyn->cutoff;
1164 lc->x=moldyn->dim.x/lc->nx;
1165 lc->ny=moldyn->dim.y/moldyn->cutoff;
1166 lc->y=moldyn->dim.y/lc->ny;
1167 lc->nz=moldyn->dim.z/moldyn->cutoff;
1168 lc->z=moldyn->dim.z/lc->nz;
1170 lc->cells=lc->nx*lc->ny*lc->nz;
1171 lc->subcell=malloc(lc->cells*sizeof(t_list));
1174 printf("[moldyn] FATAL: less then 27 subcells!\n");
1177 printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
1178 printf(" x: %d x %f A\n",lc->nx,lc->x);
1179 printf(" y: %d x %f A\n",lc->ny,lc->y);
1180 printf(" z: %d x %f A\n",lc->nz,lc->z);
1183 for(i=0;i<lc->cells;i++)
1184 list_init_f(&(lc->subcell[i]));
1186 link_cell_update(moldyn);
1191 int link_cell_update(t_moldyn *moldyn) {
1209 for(i=0;i<lc->cells;i++)
1210 list_destroy_f(&(lc->subcell[i]));
1212 for(count=0;count<moldyn->count;count++) {
1213 i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
1214 j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
1215 k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
1216 list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
1223 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
1241 cell[0]=lc->subcell[i+j*nx+k*a];
1242 for(ci=-1;ci<=1;ci++) {
1245 if((x<0)||(x>=nx)) {
1249 for(cj=-1;cj<=1;cj++) {
1252 if((y<0)||(y>=ny)) {
1256 for(ck=-1;ck<=1;ck++) {
1259 if((z<0)||(z>=nz)) {
1263 if(!(ci|cj|ck)) continue;
1265 cell[--count2]=lc->subcell[x+y*nx+z*a];
1268 cell[count1++]=lc->subcell[x+y*nx+z*a];
1279 int link_cell_shutdown(t_moldyn *moldyn) {
1286 for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
1287 list_destroy_f(&(moldyn->lc.subcell[i]));
1294 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
1298 t_moldyn_schedule *schedule;
1300 schedule=&(moldyn->schedule);
1301 count=++(schedule->total_sched);
1303 ptr=realloc(schedule->runs,count*sizeof(int));
1305 perror("[moldyn] realloc (runs)");
1309 schedule->runs[count-1]=runs;
1311 ptr=realloc(schedule->tau,count*sizeof(double));
1313 perror("[moldyn] realloc (tau)");
1317 schedule->tau[count-1]=tau;
1319 printf("[moldyn] schedule added:\n");
1320 printf(" number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
1326 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
1328 moldyn->schedule.hook=hook;
1329 moldyn->schedule.hook_params=hook_params;
1336 * 'integration of newtons equation' - algorithms
1340 /* start the integration */
1342 int moldyn_integrate(t_moldyn *moldyn) {
1345 unsigned int e,m,s,v,p,t;
1347 t_moldyn_schedule *sched;
1352 double energy_scale;
1353 struct timeval t1,t2;
1356 sched=&(moldyn->schedule);
1359 /* initialize linked cell method */
1360 link_cell_init(moldyn,VERBOSE);
1362 /* logging & visualization */
1370 /* sqaure of some variables */
1371 moldyn->tau_square=moldyn->tau*moldyn->tau;
1372 moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
1374 /* get current time */
1375 gettimeofday(&t1,NULL);
1377 /* calculate initial forces */
1378 potential_force_calc(moldyn);
1383 /* some stupid checks before we actually start calculating bullshit */
1384 if(moldyn->cutoff>0.5*moldyn->dim.x)
1385 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
1386 if(moldyn->cutoff>0.5*moldyn->dim.y)
1387 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
1388 if(moldyn->cutoff>0.5*moldyn->dim.z)
1389 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
1390 ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
1391 if(ds>0.05*moldyn->nnd)
1392 printf("[moldyn] warning: forces too high / tau too small!\n");
1394 /* zero absolute time */
1396 moldyn->total_steps=0;
1398 /* debugging, ignore */
1401 /* tell the world */
1402 printf("[moldyn] integration start, go get a coffee ...\n");
1404 /* executing the schedule */
1406 while(sched->count<sched->total_sched) {
1408 /* setting amount of runs and finite time step size */
1409 moldyn->tau=sched->tau[sched->count];
1410 moldyn->tau_square=moldyn->tau*moldyn->tau;
1411 moldyn->time_steps=sched->runs[sched->count];
1413 /* energy scaling factor (might change!) */
1414 energy_scale=moldyn->count*EV;
1416 /* integration according to schedule */
1418 for(i=0;i<moldyn->time_steps;i++) {
1420 /* integration step */
1421 moldyn->integrate(moldyn);
1423 /* calculate kinetic energy, temperature and pressure */
1425 temperature_calc(moldyn);
1427 pressure_calc(moldyn);
1428 average_and_fluctuation_calc(moldyn);
1431 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
1432 scale_velocity(moldyn,FALSE);
1433 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
1434 scale_volume(moldyn);
1436 /* check for log & visualization */
1438 if(!(moldyn->total_steps%e))
1439 dprintf(moldyn->efd,
1441 moldyn->time,moldyn->ekin/energy_scale,
1442 moldyn->energy/energy_scale,
1443 get_total_energy(moldyn)/energy_scale);
1446 if(!(moldyn->total_steps%m)) {
1447 momentum=get_total_p(moldyn);
1448 dprintf(moldyn->mfd,
1449 "%f %f %f %f %f\n",moldyn->time,
1450 momentum.x,momentum.y,momentum.z,
1451 v3_norm(&momentum));
1455 if(!(moldyn->total_steps%p)) {
1456 dprintf(moldyn->pfd,
1457 "%f %f %f %f %f\n",moldyn->time,
1458 moldyn->p/BAR,moldyn->p_avg/BAR,
1459 moldyn->gp/BAR,moldyn->gp_avg/BAR);
1463 if(!(moldyn->total_steps%t)) {
1464 dprintf(moldyn->tfd,
1466 moldyn->time,moldyn->t,moldyn->t_avg);
1470 if(!(moldyn->total_steps%s)) {
1471 snprintf(dir,128,"%s/s-%07.f.save",
1472 moldyn->vlsdir,moldyn->time);
1473 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT,
1475 if(fd<0) perror("[moldyn] save fd open");
1477 write(fd,moldyn,sizeof(t_moldyn));
1478 write(fd,moldyn->atom,
1479 moldyn->count*sizeof(t_atom));
1485 if(!(moldyn->total_steps%v)) {
1486 visual_atoms(&(moldyn->vis),moldyn->time,
1487 moldyn->atom,moldyn->count);
1491 /* display progress */
1492 if(!(moldyn->total_steps%10)) {
1493 /* get current time */
1494 gettimeofday(&t2,NULL);
1496 printf("\rsched:%d, steps:%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f (%d)",
1498 moldyn->t,moldyn->t_avg,
1499 moldyn->p_avg/BAR,moldyn->gp_avg/BAR,
1501 (int)(t2.tv_sec-t1.tv_sec));
1504 /* copy over time */
1508 /* increase absolute time */
1509 moldyn->time+=moldyn->tau;
1510 moldyn->total_steps+=1;
1514 /* check for hooks */
1516 printf("\n ## schedule hook %d/%d start ##\n",
1517 sched->count+1,sched->total_sched-1);
1518 sched->hook(moldyn,sched->hook_params);
1519 printf(" ## schedule hook end ##\n");
1522 /* increase the schedule counter */
1530 /* velocity verlet */
1532 int velocity_verlet(t_moldyn *moldyn) {
1535 double tau,tau_square,h;
1540 count=moldyn->count;
1542 tau_square=moldyn->tau_square;
1544 for(i=0;i<count;i++) {
1547 v3_scale(&delta,&(atom[i].v),tau);
1548 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1549 v3_scale(&delta,&(atom[i].f),h*tau_square);
1550 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1551 check_per_bound(moldyn,&(atom[i].r));
1553 /* velocities [actually v(t+tau/2)] */
1554 v3_scale(&delta,&(atom[i].f),h*tau);
1555 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1558 /* neighbour list update */
1559 link_cell_update(moldyn);
1561 /* forces depending on chosen potential */
1562 potential_force_calc(moldyn);
1564 for(i=0;i<count;i++) {
1565 /* again velocities [actually v(t+tau)] */
1566 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
1567 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1576 * potentials & corresponding forces & virial routine
1580 /* generic potential and force calculation */
1582 int potential_force_calc(t_moldyn *moldyn) {
1585 t_atom *itom,*jtom,*ktom;
1588 t_list neighbour_i[27];
1589 t_list neighbour_i2[27];
1594 count=moldyn->count;
1601 /* reset global virial */
1602 memset(&(moldyn->gvir),0,sizeof(t_virial));
1604 /* reset force, site energy and virial of every atom */
1605 for(i=0;i<count;i++) {
1608 v3_zero(&(itom[i].f));
1611 virial=(&(itom[i].virial));
1619 /* reset site energy */
1624 /* get energy, force and virial of every atom */
1626 /* first (and only) loop over atoms i */
1627 for(i=0;i<count;i++) {
1629 /* single particle potential/force */
1630 if(itom[i].attr&ATOM_ATTR_1BP)
1632 moldyn->func1b(moldyn,&(itom[i]));
1634 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
1637 /* 2 body pair potential/force */
1639 link_cell_neighbour_index(moldyn,
1640 (itom[i].r.x+moldyn->dim.x/2)/lc->x,
1641 (itom[i].r.y+moldyn->dim.y/2)/lc->y,
1642 (itom[i].r.z+moldyn->dim.z/2)/lc->z,
1647 /* first loop over atoms j */
1648 if(moldyn->func2b) {
1651 this=&(neighbour_i[j]);
1654 if(this->start==NULL)
1660 jtom=this->current->data;
1662 if(jtom==&(itom[i]))
1665 if((jtom->attr&ATOM_ATTR_2BP)&
1666 (itom[i].attr&ATOM_ATTR_2BP)) {
1667 moldyn->func2b(moldyn,
1672 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1677 /* 3 body potential/force */
1679 if(!(itom[i].attr&ATOM_ATTR_3BP))
1682 /* copy the neighbour lists */
1683 memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
1685 /* second loop over atoms j */
1688 this=&(neighbour_i[j]);
1691 if(this->start==NULL)
1697 jtom=this->current->data;
1699 if(jtom==&(itom[i]))
1702 if(!(jtom->attr&ATOM_ATTR_3BP))
1708 if(moldyn->func3b_j1)
1709 moldyn->func3b_j1(moldyn,
1714 /* in first j loop, 3bp run can be skipped */
1715 if(!(moldyn->run3bp))
1718 /* first loop over atoms k */
1719 if(moldyn->func3b_k1) {
1723 that=&(neighbour_i2[k]);
1726 if(that->start==NULL)
1733 ktom=that->current->data;
1735 if(!(ktom->attr&ATOM_ATTR_3BP))
1741 if(ktom==&(itom[i]))
1744 moldyn->func3b_k1(moldyn,
1750 } while(list_next_f(that)!=\
1757 if(moldyn->func3b_j2)
1758 moldyn->func3b_j2(moldyn,
1763 /* second loop over atoms k */
1764 if(moldyn->func3b_k2) {
1768 that=&(neighbour_i2[k]);
1771 if(that->start==NULL)
1778 ktom=that->current->data;
1780 if(!(ktom->attr&ATOM_ATTR_3BP))
1786 if(ktom==&(itom[i]))
1789 moldyn->func3b_k2(moldyn,
1795 } while(list_next_f(that)!=\
1802 /* 2bp post function */
1803 if(moldyn->func3b_j3) {
1804 moldyn->func3b_j3(moldyn,
1809 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1823 printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
1826 /* calculate global virial */
1827 for(i=0;i<count;i++) {
1828 moldyn->gvir.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
1829 moldyn->gvir.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
1830 moldyn->gvir.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
1831 moldyn->gvir.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
1832 moldyn->gvir.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
1833 moldyn->gvir.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
1840 * virial calculation
1843 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1844 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1846 a->virial.xx+=f->x*d->x;
1847 a->virial.yy+=f->y*d->y;
1848 a->virial.zz+=f->z*d->z;
1849 a->virial.xy+=f->x*d->y;
1850 a->virial.xz+=f->x*d->z;
1851 a->virial.yz+=f->y*d->z;
1857 * periodic boundary checking
1860 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1861 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1872 if(moldyn->status&MOLDYN_STAT_PBX) {
1873 if(a->x>=x) a->x-=dim->x;
1874 else if(-a->x>x) a->x+=dim->x;
1876 if(moldyn->status&MOLDYN_STAT_PBY) {
1877 if(a->y>=y) a->y-=dim->y;
1878 else if(-a->y>y) a->y+=dim->y;
1880 if(moldyn->status&MOLDYN_STAT_PBZ) {
1881 if(a->z>=z) a->z-=dim->z;
1882 else if(-a->z>z) a->z+=dim->z;
1889 * debugging / critical check functions
1892 int moldyn_bc_check(t_moldyn *moldyn) {
1905 for(i=0;i<moldyn->count;i++) {
1906 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
1907 printf("FATAL: atom %d: x: %.20f (%.20f)\n",
1908 i,atom[i].r.x,dim->x/2);
1909 printf("diagnostic:\n");
1910 printf("-----------\natom.r.x:\n");
1912 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
1915 ((byte)&(1<<k))?1:0,
1918 printf("---------------\nx=dim.x/2:\n");
1920 memcpy(&byte,(u8 *)(&x)+j,1);
1923 ((byte)&(1<<k))?1:0,
1926 if(atom[i].r.x==x) printf("the same!\n");
1927 else printf("different!\n");
1929 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
1930 printf("FATAL: atom %d: y: %.20f (%.20f)\n",
1931 i,atom[i].r.y,dim->y/2);
1932 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
1933 printf("FATAL: atom %d: z: %.20f (%.20f)\n",
1934 i,atom[i].r.z,dim->z/2);
1944 int moldyn_load(t_moldyn *moldyn) {
1952 * post processing functions
1955 int get_line(int fd,char *line,int max) {
1962 if(count==max) return count;
1963 ret=read(fd,line+count,1);
1964 if(ret<=0) return ret;
1965 if(line[count]=='\n') {
1973 int analyze_bonds(t_moldyn *moldyn) {