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);
561 int del_atom(t_moldyn *moldyn,int tag) {
568 new=(t_atom *)malloc((moldyn->count-1)*sizeof(t_atom));
570 perror("[moldyn]malloc (del atom)");
574 for(cnt=0;cnt<tag;cnt++)
577 for(cnt=tag+1;cnt<moldyn->count;cnt++) {
579 new[cnt-1].tag=cnt-1;
591 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
610 v3_copy(&(atom[count].r),&r);
619 for(i=0;i<count;i++) {
620 atom[i].r.x-=(a*lc)/2.0;
621 atom[i].r.y-=(b*lc)/2.0;
622 atom[i].r.z-=(c*lc)/2.0;
628 /* fcc lattice init */
629 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
642 /* construct the basis */
643 memset(basis,0,3*sizeof(t_3dvec));
651 /* fill up the room */
659 v3_copy(&(atom[count].r),&r);
662 /* the three face centered atoms */
664 v3_add(&n,&r,&basis[l]);
665 v3_copy(&(atom[count].r),&n);
674 /* coordinate transformation */
675 for(i=0;i<count;i++) {
676 atom[i].r.x-=(a*lc)/2.0;
677 atom[i].r.y-=(b*lc)/2.0;
678 atom[i].r.z-=(c*lc)/2.0;
684 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
689 count=fcc_init(a,b,c,lc,atom,origin);
695 if(origin) v3_add(&o,&o,origin);
697 count+=fcc_init(a,b,c,lc,&atom[count],&o);
702 int destroy_atoms(t_moldyn *moldyn) {
704 if(moldyn->atom) free(moldyn->atom);
709 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
712 * - gaussian distribution of velocities
713 * - zero total momentum
714 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
719 t_3dvec p_total,delta;
724 random=&(moldyn->random);
726 printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
728 /* gaussian distribution of velocities */
730 for(i=0;i<moldyn->count;i++) {
731 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
733 v=sigma*rand_get_gauss(random);
735 p_total.x+=atom[i].mass*v;
737 v=sigma*rand_get_gauss(random);
739 p_total.y+=atom[i].mass*v;
741 v=sigma*rand_get_gauss(random);
743 p_total.z+=atom[i].mass*v;
746 /* zero total momentum */
747 v3_scale(&p_total,&p_total,1.0/moldyn->count);
748 for(i=0;i<moldyn->count;i++) {
749 v3_scale(&delta,&p_total,1.0/atom[i].mass);
750 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
753 /* velocity scaling */
754 scale_velocity(moldyn,equi_init);
759 double total_mass_calc(t_moldyn *moldyn) {
765 for(i=0;i<moldyn->count;i++)
766 moldyn->mass+=moldyn->atom[i].mass;
771 double temperature_calc(t_moldyn *moldyn) {
773 /* assume up to date kinetic energy, which is 3/2 N k_B T */
775 moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
780 double get_temperature(t_moldyn *moldyn) {
785 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
795 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
798 /* get kinetic energy / temperature & count involved atoms */
801 for(i=0;i<moldyn->count;i++) {
802 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
803 e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
808 if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
809 else return 0; /* no atoms involved in scaling! */
811 /* (temporary) hack for e,t = 0 */
814 if(moldyn->t_ref!=0.0) {
815 thermal_init(moldyn,equi_init);
819 return 0; /* no scaling needed */
823 /* get scaling factor */
824 scale=moldyn->t_ref/moldyn->t;
828 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
829 scale=1.0+(scale-1.0)/moldyn->t_tc;
832 /* velocity scaling */
833 for(i=0;i<moldyn->count;i++) {
834 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
835 v3_scale(&(atom[i].v),&(atom[i].v),scale);
841 double ideal_gas_law_pressure(t_moldyn *moldyn) {
845 p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
850 double virial_sum(t_moldyn *moldyn) {
856 /* virial (sum over atom virials) */
858 for(i=0;i<moldyn->count;i++) {
859 virial=&(moldyn->atom[i].virial);
860 v+=(virial->xx+virial->yy+virial->zz);
864 /* global virial (absolute coordinates) */
865 virial=&(moldyn->gvir);
866 moldyn->gv=virial->xx+virial->yy+virial->zz;
868 return moldyn->virial;
871 double pressure_calc(t_moldyn *moldyn) {
875 * with W = 1/3 sum_i f_i r_i (- skipped!)
876 * virial = sum_i f_i r_i
878 * => P = (2 Ekin + virial) / (3V)
881 /* assume up to date virial & up to date kinetic energy */
883 /* pressure (atom virials) */
884 moldyn->p=2.0*moldyn->ekin+moldyn->virial;
885 moldyn->p/=(3.0*moldyn->volume);
887 /* pressure (absolute coordinates) */
888 moldyn->gp=2.0*moldyn->ekin+moldyn->gv;
889 moldyn->gp/=(3.0*moldyn->volume);
894 int average_and_fluctuation_calc(t_moldyn *moldyn) {
896 if(moldyn->total_steps<moldyn->avg_skip)
899 int denom=moldyn->total_steps+1-moldyn->avg_skip;
901 /* assume up to date energies, temperature, pressure etc */
904 moldyn->k_sum+=moldyn->ekin;
905 moldyn->k2_sum+=(moldyn->ekin*moldyn->ekin);
906 moldyn->k_avg=moldyn->k_sum/denom;
907 moldyn->k2_avg=moldyn->k2_sum/denom;
908 moldyn->dk2_avg=moldyn->k2_avg-(moldyn->k_avg*moldyn->k_avg);
910 /* potential energy */
911 moldyn->v_sum+=moldyn->energy;
912 moldyn->v2_sum+=(moldyn->energy*moldyn->energy);
913 moldyn->v_avg=moldyn->v_sum/denom;
914 moldyn->v2_avg=moldyn->v2_sum/denom;
915 moldyn->dv2_avg=moldyn->v2_avg-(moldyn->v_avg*moldyn->v_avg);
918 moldyn->t_sum+=moldyn->t;
919 moldyn->t_avg=moldyn->t_sum/denom;
922 moldyn->virial_sum+=moldyn->virial;
923 moldyn->virial_avg=moldyn->virial_sum/denom;
924 moldyn->gv_sum+=moldyn->gv;
925 moldyn->gv_avg=moldyn->gv_sum/denom;
928 moldyn->p_sum+=moldyn->p;
929 moldyn->p_avg=moldyn->p_sum/denom;
930 moldyn->gp_sum+=moldyn->gp;
931 moldyn->gp_avg=moldyn->gp_sum/denom;
936 int get_heat_capacity(t_moldyn *moldyn) {
940 /* averages needed for heat capacity calc */
941 if(moldyn->total_steps<moldyn->avg_skip)
944 /* (temperature average)^2 */
945 temp2=moldyn->t_avg*moldyn->t_avg;
946 printf("[moldyn] specific heat capacity for T=%f K [J/(kg K)]\n",
949 /* ideal gas contribution */
950 ighc=3.0*moldyn->count*K_BOLTZMANN/2.0;
951 printf(" ideal gas contribution: %f\n",
952 ighc/moldyn->mass*KILOGRAM/JOULE);
954 /* specific heat for nvt ensemble */
955 moldyn->c_v_nvt=moldyn->dv2_avg/(K_BOLTZMANN*temp2)+ighc;
956 moldyn->c_v_nvt/=moldyn->mass;
958 /* specific heat for nve ensemble */
959 moldyn->c_v_nve=ighc/(1.0-(moldyn->dv2_avg/(ighc*K_BOLTZMANN*temp2)));
960 moldyn->c_v_nve/=moldyn->mass;
962 printf(" NVE: %f\n",moldyn->c_v_nve*KILOGRAM/JOULE);
963 printf(" NVT: %f\n",moldyn->c_v_nvt*KILOGRAM/JOULE);
964 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)));
969 double thermodynamic_pressure_calc(t_moldyn *moldyn) {
972 double u_up,u_down,dv;
984 dv=8*scale*scale*scale*moldyn->volume;
986 store=malloc(moldyn->count*sizeof(t_atom));
988 printf("[moldyn] allocating store mem failed\n");
992 /* save unscaled potential energy + atom/dim configuration */
993 memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
996 /* scale up dimension and atom positions */
997 scale_dim(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
998 scale_atoms(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
999 link_cell_shutdown(moldyn);
1000 link_cell_init(moldyn,QUIET);
1001 potential_force_calc(moldyn);
1002 u_up=moldyn->energy;
1004 /* restore atomic configuration + dim */
1005 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
1008 /* scale down dimension and atom positions */
1009 scale_dim(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
1010 scale_atoms(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
1011 link_cell_shutdown(moldyn);
1012 link_cell_init(moldyn,QUIET);
1013 potential_force_calc(moldyn);
1014 u_down=moldyn->energy;
1016 /* calculate pressure */
1017 p=-(u_up-u_down)/dv;
1018 printf("-------> %.10f %.10f %f\n",u_up/EV/moldyn->count,u_down/EV/moldyn->count,p/BAR);
1020 /* restore atomic configuration + dim */
1021 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
1024 /* restore energy */
1025 potential_force_calc(moldyn);
1027 link_cell_shutdown(moldyn);
1028 link_cell_init(moldyn,QUIET);
1033 double get_pressure(t_moldyn *moldyn) {
1039 int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
1051 if(x) dim->x*=scale;
1052 if(y) dim->y*=scale;
1053 if(z) dim->z*=scale;
1058 int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
1069 for(i=0;i<moldyn->count;i++) {
1070 r=&(moldyn->atom[i].r);
1079 int scale_volume(t_moldyn *moldyn) {
1085 vdim=&(moldyn->vis.dim);
1089 /* scaling factor */
1090 if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
1091 scale=1.0-(moldyn->p_ref-moldyn->p)/moldyn->p_tc;
1092 scale=pow(scale,ONE_THIRD);
1095 scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
1097 moldyn->debug=scale;
1099 /* scale the atoms and dimensions */
1100 scale_atoms(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
1101 scale_dim(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
1103 /* visualize dimensions */
1110 /* recalculate scaled volume */
1111 moldyn->volume=dim->x*dim->y*dim->z;
1113 /* adjust/reinit linkcell */
1114 if(((int)(dim->x/moldyn->cutoff)!=lc->nx)||
1115 ((int)(dim->y/moldyn->cutoff)!=lc->ny)||
1116 ((int)(dim->z/moldyn->cutoff)!=lc->nx)) {
1117 link_cell_shutdown(moldyn);
1118 link_cell_init(moldyn,QUIET);
1129 double e_kin_calc(t_moldyn *moldyn) {
1137 for(i=0;i<moldyn->count;i++) {
1138 atom[i].ekin=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
1139 moldyn->ekin+=atom[i].ekin;
1142 return moldyn->ekin;
1145 double get_total_energy(t_moldyn *moldyn) {
1147 return(moldyn->ekin+moldyn->energy);
1150 t_3dvec get_total_p(t_moldyn *moldyn) {
1159 for(i=0;i<moldyn->count;i++) {
1160 v3_scale(&p,&(atom[i].v),atom[i].mass);
1161 v3_add(&p_total,&p_total,&p);
1167 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
1171 /* nn_dist is the nearest neighbour distance */
1173 tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
1182 /* linked list / cell method */
1184 int link_cell_init(t_moldyn *moldyn,u8 vol) {
1191 /* partitioning the md cell */
1192 lc->nx=moldyn->dim.x/moldyn->cutoff;
1193 lc->x=moldyn->dim.x/lc->nx;
1194 lc->ny=moldyn->dim.y/moldyn->cutoff;
1195 lc->y=moldyn->dim.y/lc->ny;
1196 lc->nz=moldyn->dim.z/moldyn->cutoff;
1197 lc->z=moldyn->dim.z/lc->nz;
1199 lc->cells=lc->nx*lc->ny*lc->nz;
1200 lc->subcell=malloc(lc->cells*sizeof(t_list));
1203 printf("[moldyn] FATAL: less then 27 subcells!\n");
1206 printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
1207 printf(" x: %d x %f A\n",lc->nx,lc->x);
1208 printf(" y: %d x %f A\n",lc->ny,lc->y);
1209 printf(" z: %d x %f A\n",lc->nz,lc->z);
1212 for(i=0;i<lc->cells;i++)
1213 list_init_f(&(lc->subcell[i]));
1215 link_cell_update(moldyn);
1220 int link_cell_update(t_moldyn *moldyn) {
1238 for(i=0;i<lc->cells;i++)
1239 list_destroy_f(&(lc->subcell[i]));
1241 for(count=0;count<moldyn->count;count++) {
1242 i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
1243 j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
1244 k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
1245 list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
1252 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
1270 cell[0]=lc->subcell[i+j*nx+k*a];
1271 for(ci=-1;ci<=1;ci++) {
1274 if((x<0)||(x>=nx)) {
1278 for(cj=-1;cj<=1;cj++) {
1281 if((y<0)||(y>=ny)) {
1285 for(ck=-1;ck<=1;ck++) {
1288 if((z<0)||(z>=nz)) {
1292 if(!(ci|cj|ck)) continue;
1294 cell[--count2]=lc->subcell[x+y*nx+z*a];
1297 cell[count1++]=lc->subcell[x+y*nx+z*a];
1308 int link_cell_shutdown(t_moldyn *moldyn) {
1315 for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
1316 list_destroy_f(&(moldyn->lc.subcell[i]));
1323 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
1327 t_moldyn_schedule *schedule;
1329 schedule=&(moldyn->schedule);
1330 count=++(schedule->total_sched);
1332 ptr=realloc(schedule->runs,count*sizeof(int));
1334 perror("[moldyn] realloc (runs)");
1338 schedule->runs[count-1]=runs;
1340 ptr=realloc(schedule->tau,count*sizeof(double));
1342 perror("[moldyn] realloc (tau)");
1346 schedule->tau[count-1]=tau;
1348 printf("[moldyn] schedule added:\n");
1349 printf(" number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
1355 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
1357 moldyn->schedule.hook=hook;
1358 moldyn->schedule.hook_params=hook_params;
1365 * 'integration of newtons equation' - algorithms
1369 /* start the integration */
1371 int moldyn_integrate(t_moldyn *moldyn) {
1374 unsigned int e,m,s,v,p,t;
1376 t_moldyn_schedule *sched;
1381 double energy_scale;
1382 struct timeval t1,t2;
1385 sched=&(moldyn->schedule);
1388 /* initialize linked cell method */
1389 link_cell_init(moldyn,VERBOSE);
1391 /* logging & visualization */
1399 /* sqaure of some variables */
1400 moldyn->tau_square=moldyn->tau*moldyn->tau;
1401 moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
1403 /* get current time */
1404 gettimeofday(&t1,NULL);
1406 /* calculate initial forces */
1407 potential_force_calc(moldyn);
1412 /* some stupid checks before we actually start calculating bullshit */
1413 if(moldyn->cutoff>0.5*moldyn->dim.x)
1414 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
1415 if(moldyn->cutoff>0.5*moldyn->dim.y)
1416 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
1417 if(moldyn->cutoff>0.5*moldyn->dim.z)
1418 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
1419 ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
1420 if(ds>0.05*moldyn->nnd)
1421 printf("[moldyn] warning: forces too high / tau too small!\n");
1423 /* zero absolute time */
1425 moldyn->total_steps=0;
1427 /* debugging, ignore */
1430 /* tell the world */
1431 printf("[moldyn] integration start, go get a coffee ...\n");
1433 /* executing the schedule */
1435 while(sched->count<sched->total_sched) {
1437 /* setting amount of runs and finite time step size */
1438 moldyn->tau=sched->tau[sched->count];
1439 moldyn->tau_square=moldyn->tau*moldyn->tau;
1440 moldyn->time_steps=sched->runs[sched->count];
1442 /* energy scaling factor (might change!) */
1443 energy_scale=moldyn->count*EV;
1445 /* integration according to schedule */
1447 for(i=0;i<moldyn->time_steps;i++) {
1449 /* integration step */
1450 moldyn->integrate(moldyn);
1452 /* calculate kinetic energy, temperature and pressure */
1454 temperature_calc(moldyn);
1456 pressure_calc(moldyn);
1457 average_and_fluctuation_calc(moldyn);
1460 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
1461 scale_velocity(moldyn,FALSE);
1462 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
1463 scale_volume(moldyn);
1465 /* check for log & visualization */
1467 if(!(moldyn->total_steps%e))
1468 dprintf(moldyn->efd,
1470 moldyn->time,moldyn->ekin/energy_scale,
1471 moldyn->energy/energy_scale,
1472 get_total_energy(moldyn)/energy_scale);
1475 if(!(moldyn->total_steps%m)) {
1476 momentum=get_total_p(moldyn);
1477 dprintf(moldyn->mfd,
1478 "%f %f %f %f %f\n",moldyn->time,
1479 momentum.x,momentum.y,momentum.z,
1480 v3_norm(&momentum));
1484 if(!(moldyn->total_steps%p)) {
1485 dprintf(moldyn->pfd,
1486 "%f %f %f %f %f\n",moldyn->time,
1487 moldyn->p/BAR,moldyn->p_avg/BAR,
1488 moldyn->gp/BAR,moldyn->gp_avg/BAR);
1492 if(!(moldyn->total_steps%t)) {
1493 dprintf(moldyn->tfd,
1495 moldyn->time,moldyn->t,moldyn->t_avg);
1499 if(!(moldyn->total_steps%s)) {
1500 snprintf(dir,128,"%s/s-%07.f.save",
1501 moldyn->vlsdir,moldyn->time);
1502 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT,
1504 if(fd<0) perror("[moldyn] save fd open");
1506 write(fd,moldyn,sizeof(t_moldyn));
1507 write(fd,moldyn->atom,
1508 moldyn->count*sizeof(t_atom));
1514 if(!(moldyn->total_steps%v)) {
1515 visual_atoms(&(moldyn->vis),moldyn->time,
1516 moldyn->atom,moldyn->count);
1520 /* display progress */
1521 if(!(moldyn->total_steps%10)) {
1522 /* get current time */
1523 gettimeofday(&t2,NULL);
1525 printf("\rsched:%d, steps:%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f (%d)",
1527 moldyn->t,moldyn->t_avg,
1528 moldyn->p_avg/BAR,moldyn->gp_avg/BAR,
1530 (int)(t2.tv_sec-t1.tv_sec));
1533 /* copy over time */
1537 /* increase absolute time */
1538 moldyn->time+=moldyn->tau;
1539 moldyn->total_steps+=1;
1543 /* check for hooks */
1545 printf("\n ## schedule hook %d/%d start ##\n",
1546 sched->count+1,sched->total_sched-1);
1547 sched->hook(moldyn,sched->hook_params);
1548 printf(" ## schedule hook end ##\n");
1551 /* increase the schedule counter */
1559 /* velocity verlet */
1561 int velocity_verlet(t_moldyn *moldyn) {
1564 double tau,tau_square,h;
1569 count=moldyn->count;
1571 tau_square=moldyn->tau_square;
1573 for(i=0;i<count;i++) {
1576 v3_scale(&delta,&(atom[i].v),tau);
1577 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1578 v3_scale(&delta,&(atom[i].f),h*tau_square);
1579 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1580 check_per_bound(moldyn,&(atom[i].r));
1582 /* velocities [actually v(t+tau/2)] */
1583 v3_scale(&delta,&(atom[i].f),h*tau);
1584 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1587 /* neighbour list update */
1588 link_cell_update(moldyn);
1590 /* forces depending on chosen potential */
1591 potential_force_calc(moldyn);
1593 for(i=0;i<count;i++) {
1594 /* again velocities [actually v(t+tau)] */
1595 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
1596 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1605 * potentials & corresponding forces & virial routine
1609 /* generic potential and force calculation */
1611 int potential_force_calc(t_moldyn *moldyn) {
1614 t_atom *itom,*jtom,*ktom;
1617 t_list neighbour_i[27];
1618 t_list neighbour_i2[27];
1623 count=moldyn->count;
1630 /* reset global virial */
1631 memset(&(moldyn->gvir),0,sizeof(t_virial));
1633 /* reset force, site energy and virial of every atom */
1634 for(i=0;i<count;i++) {
1637 v3_zero(&(itom[i].f));
1640 virial=(&(itom[i].virial));
1648 /* reset site energy */
1653 /* get energy, force and virial of every atom */
1655 /* first (and only) loop over atoms i */
1656 for(i=0;i<count;i++) {
1658 /* single particle potential/force */
1659 if(itom[i].attr&ATOM_ATTR_1BP)
1661 moldyn->func1b(moldyn,&(itom[i]));
1663 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
1666 /* 2 body pair potential/force */
1668 link_cell_neighbour_index(moldyn,
1669 (itom[i].r.x+moldyn->dim.x/2)/lc->x,
1670 (itom[i].r.y+moldyn->dim.y/2)/lc->y,
1671 (itom[i].r.z+moldyn->dim.z/2)/lc->z,
1676 /* first loop over atoms j */
1677 if(moldyn->func2b) {
1680 this=&(neighbour_i[j]);
1683 if(this->start==NULL)
1689 jtom=this->current->data;
1691 if(jtom==&(itom[i]))
1694 if((jtom->attr&ATOM_ATTR_2BP)&
1695 (itom[i].attr&ATOM_ATTR_2BP)) {
1696 moldyn->func2b(moldyn,
1701 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1706 /* 3 body potential/force */
1708 if(!(itom[i].attr&ATOM_ATTR_3BP))
1711 /* copy the neighbour lists */
1712 memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
1714 /* second loop over atoms j */
1717 this=&(neighbour_i[j]);
1720 if(this->start==NULL)
1726 jtom=this->current->data;
1728 if(jtom==&(itom[i]))
1731 if(!(jtom->attr&ATOM_ATTR_3BP))
1737 if(moldyn->func3b_j1)
1738 moldyn->func3b_j1(moldyn,
1743 /* in first j loop, 3bp run can be skipped */
1744 if(!(moldyn->run3bp))
1747 /* first loop over atoms k */
1748 if(moldyn->func3b_k1) {
1752 that=&(neighbour_i2[k]);
1755 if(that->start==NULL)
1762 ktom=that->current->data;
1764 if(!(ktom->attr&ATOM_ATTR_3BP))
1770 if(ktom==&(itom[i]))
1773 moldyn->func3b_k1(moldyn,
1779 } while(list_next_f(that)!=\
1786 if(moldyn->func3b_j2)
1787 moldyn->func3b_j2(moldyn,
1792 /* second loop over atoms k */
1793 if(moldyn->func3b_k2) {
1797 that=&(neighbour_i2[k]);
1800 if(that->start==NULL)
1807 ktom=that->current->data;
1809 if(!(ktom->attr&ATOM_ATTR_3BP))
1815 if(ktom==&(itom[i]))
1818 moldyn->func3b_k2(moldyn,
1824 } while(list_next_f(that)!=\
1831 /* 2bp post function */
1832 if(moldyn->func3b_j3) {
1833 moldyn->func3b_j3(moldyn,
1838 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1852 printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
1855 /* calculate global virial */
1856 for(i=0;i<count;i++) {
1857 moldyn->gvir.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
1858 moldyn->gvir.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
1859 moldyn->gvir.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
1860 moldyn->gvir.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
1861 moldyn->gvir.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
1862 moldyn->gvir.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
1869 * virial calculation
1872 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1873 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1875 a->virial.xx+=f->x*d->x;
1876 a->virial.yy+=f->y*d->y;
1877 a->virial.zz+=f->z*d->z;
1878 a->virial.xy+=f->x*d->y;
1879 a->virial.xz+=f->x*d->z;
1880 a->virial.yz+=f->y*d->z;
1886 * periodic boundary checking
1889 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1890 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1901 if(moldyn->status&MOLDYN_STAT_PBX) {
1902 if(a->x>=x) a->x-=dim->x;
1903 else if(-a->x>x) a->x+=dim->x;
1905 if(moldyn->status&MOLDYN_STAT_PBY) {
1906 if(a->y>=y) a->y-=dim->y;
1907 else if(-a->y>y) a->y+=dim->y;
1909 if(moldyn->status&MOLDYN_STAT_PBZ) {
1910 if(a->z>=z) a->z-=dim->z;
1911 else if(-a->z>z) a->z+=dim->z;
1918 * debugging / critical check functions
1921 int moldyn_bc_check(t_moldyn *moldyn) {
1934 for(i=0;i<moldyn->count;i++) {
1935 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
1936 printf("FATAL: atom %d: x: %.20f (%.20f)\n",
1937 i,atom[i].r.x,dim->x/2);
1938 printf("diagnostic:\n");
1939 printf("-----------\natom.r.x:\n");
1941 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
1944 ((byte)&(1<<k))?1:0,
1947 printf("---------------\nx=dim.x/2:\n");
1949 memcpy(&byte,(u8 *)(&x)+j,1);
1952 ((byte)&(1<<k))?1:0,
1955 if(atom[i].r.x==x) printf("the same!\n");
1956 else printf("different!\n");
1958 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
1959 printf("FATAL: atom %d: y: %.20f (%.20f)\n",
1960 i,atom[i].r.y,dim->y/2);
1961 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
1962 printf("FATAL: atom %d: z: %.20f (%.20f)\n",
1963 i,atom[i].r.z,dim->z/2);
1973 int moldyn_load(t_moldyn *moldyn) {
1981 * post processing functions
1984 int get_line(int fd,char *line,int max) {
1991 if(count==max) return count;
1992 ret=read(fd,line+count,1);
1993 if(ret<=0) return ret;
1994 if(line[count]=='\n') {
2002 int analyze_bonds(t_moldyn *moldyn) {