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: %f\n",moldyn->t_ref);
81 int set_pressure(t_moldyn *moldyn,double p_ref) {
85 printf("[moldyn] pressure: %f\n",moldyn->p_ref);
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,void *params) {
168 moldyn->pot1b_params=params;
173 int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
176 moldyn->pot2b_params=params;
181 int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) {
183 moldyn->func2b_post=func;
184 moldyn->pot2b_params=params;
189 int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
192 moldyn->pot3b_params=params;
197 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
199 strncpy(moldyn->vlsdir,dir,127);
204 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title) {
206 strncpy(moldyn->rauthor,author,63);
207 strncpy(moldyn->rtitle,title,63);
212 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
217 printf("[moldyn] set log: ");
220 case LOG_TOTAL_ENERGY:
221 moldyn->ewrite=timer;
222 snprintf(filename,127,"%s/energy",moldyn->vlsdir);
223 moldyn->efd=open(filename,
224 O_WRONLY|O_CREAT|O_EXCL,
227 perror("[moldyn] energy log fd open");
230 dprintf(moldyn->efd,"# total energy log file\n");
231 printf("total energy (%d)\n",timer);
233 case LOG_TOTAL_MOMENTUM:
234 moldyn->mwrite=timer;
235 snprintf(filename,127,"%s/momentum",moldyn->vlsdir);
236 moldyn->mfd=open(filename,
237 O_WRONLY|O_CREAT|O_EXCL,
240 perror("[moldyn] momentum log fd open");
243 dprintf(moldyn->efd,"# total momentum log file\n");
244 printf("total momentum (%d)\n",timer);
247 moldyn->swrite=timer;
248 printf("save file (%d)\n",timer);
251 moldyn->vwrite=timer;
252 ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
254 printf("[moldyn] visual init failure\n");
257 printf("visual file (%d)\n",timer);
260 snprintf(filename,127,"%s/report.tex",moldyn->vlsdir);
261 moldyn->rfd=open(filename,
262 O_WRONLY|O_CREAT|O_EXCL,
265 perror("[moldyn] report fd open");
268 snprintf(filename,127,"%s/plot.scr",moldyn->vlsdir);
269 moldyn->pfd=open(filename,
270 O_WRONLY|O_CREAT|O_EXCL,
273 perror("[moldyn] plot fd open");
276 dprintf(moldyn->rfd,report_start,
277 moldyn->rauthor,moldyn->rtitle);
278 dprintf(moldyn->pfd,plot_script);
282 printf("unknown log type: %02x\n",type);
289 int moldyn_log_shutdown(t_moldyn *moldyn) {
293 printf("[moldyn] log shutdown\n");
294 if(moldyn->efd) close(moldyn->efd);
295 if(moldyn->mfd) close(moldyn->mfd);
297 dprintf(moldyn->rfd,report_end);
299 snprintf(sc,255,"cd %s && gnuplot plot.scr",moldyn->vlsdir);
301 snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
303 snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
305 snprintf(sc,255,"cd %s && dvipdf report",moldyn->vlsdir);
308 if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
314 * creating lattice functions
317 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
318 u8 attr,u8 brand,int a,int b,int c) {
329 /* how many atoms do we expect */
330 if(type==CUBIC) new*=1;
331 if(type==FCC) new*=4;
332 if(type==DIAMOND) new*=8;
334 /* allocate space for atoms */
335 ptr=realloc(moldyn->atom,(count+new)*sizeof(t_atom));
337 perror("[moldyn] realloc (create lattice)");
341 atom=&(moldyn->atom[count]);
347 ret=cubic_init(a,b,c,lc,atom,NULL);
350 ret=fcc_init(a,b,c,lc,atom,NULL);
353 ret=diamond_init(a,b,c,lc,atom,&origin);
356 printf("unknown lattice type (%02x)\n",type);
362 printf("[moldyn] creating lattice failed\n");
363 printf(" amount of atoms\n");
364 printf(" - expected: %d\n",new);
365 printf(" - created: %d\n",ret);
370 printf("[moldyn] created lattice with %d atoms\n",new);
372 for(ret=0;ret<new;ret++) {
373 atom[ret].element=element;
376 atom[ret].brand=brand;
377 atom[ret].tag=count+ret;
378 check_per_bound(moldyn,&(atom[ret].r));
385 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
404 v3_copy(&(atom[count].r),&r);
413 for(i=0;i<count;i++) {
414 atom[i].r.x-=(a*lc)/2.0;
415 atom[i].r.y-=(b*lc)/2.0;
416 atom[i].r.z-=(c*lc)/2.0;
422 /* fcc lattice init */
423 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
436 if(origin) v3_copy(&o,origin);
439 /* construct the basis */
442 if(i!=j) help[j]=0.5*lc;
445 v3_set(&basis[i],help);
451 /* fill up the room */
458 v3_copy(&(atom[count].r),&r);
459 atom[count].element=1;
462 v3_add(&n,&r,&basis[i]);
466 v3_copy(&(atom[count].r),&n);
477 /* coordinate transformation */
483 v3_sub(&(atom[i].r),&(atom[i].r),&n);
488 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
493 count=fcc_init(a,b,c,lc,atom,origin);
499 if(origin) v3_add(&o,&o,origin);
501 count+=fcc_init(a,b,c,lc,&atom[count],&o);
506 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
507 t_3dvec *r,t_3dvec *v) {
514 count=(moldyn->count)++;
516 ptr=realloc(atom,(count+1)*sizeof(t_atom));
518 perror("[moldyn] realloc (add atom)");
526 atom[count].element=element;
527 atom[count].mass=mass;
528 atom[count].brand=brand;
529 atom[count].tag=count;
530 atom[count].attr=attr;
535 int destroy_atoms(t_moldyn *moldyn) {
537 if(moldyn->atom) free(moldyn->atom);
542 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
545 * - gaussian distribution of velocities
546 * - zero total momentum
547 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
552 t_3dvec p_total,delta;
557 random=&(moldyn->random);
559 printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
561 /* gaussian distribution of velocities */
563 for(i=0;i<moldyn->count;i++) {
564 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
566 v=sigma*rand_get_gauss(random);
568 p_total.x+=atom[i].mass*v;
570 v=sigma*rand_get_gauss(random);
572 p_total.y+=atom[i].mass*v;
574 v=sigma*rand_get_gauss(random);
576 p_total.z+=atom[i].mass*v;
579 /* zero total momentum */
580 v3_scale(&p_total,&p_total,1.0/moldyn->count);
581 for(i=0;i<moldyn->count;i++) {
582 v3_scale(&delta,&p_total,1.0/atom[i].mass);
583 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
586 /* velocity scaling */
587 scale_velocity(moldyn,equi_init);
592 double temperature_calc(t_moldyn *moldyn) {
594 /* assume up to date kinetic energy, which is 3/2 N k_B T */
596 moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
601 double get_temperature(t_moldyn *moldyn) {
606 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
616 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
619 /* get kinetic energy / temperature & count involved atoms */
622 for(i=0;i<moldyn->count;i++) {
623 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
624 e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
629 if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
630 else return 0; /* no atoms involved in scaling! */
632 /* (temporary) hack for e,t = 0 */
635 if(moldyn->t_ref!=0.0) {
636 thermal_init(moldyn,equi_init);
640 return 0; /* no scaling needed */
644 /* get scaling factor */
645 scale=moldyn->t_ref/moldyn->t;
649 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
650 scale=1.0+(scale-1.0)/moldyn->t_tc;
653 /* velocity scaling */
654 for(i=0;i<moldyn->count;i++) {
655 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
656 v3_scale(&(atom[i].v),&(atom[i].v),scale);
662 double ideal_gas_law_pressure(t_moldyn *moldyn) {
666 p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
671 double pressure_calc(t_moldyn *moldyn) {
678 * P = 1/(3V) sum_i ( p_i^2 / 2m + f_i r_i )
684 for(i=0;i<moldyn->count;i++) {
685 virial=&(moldyn->atom[i].virial);
686 v+=(virial->xx+virial->yy+virial->zz);
689 /* assume up to date kinetic energy */
690 moldyn->p=2.0*moldyn->ekin+v;
691 moldyn->p/=(3.0*moldyn->volume);
696 double thermodynamic_pressure_calc(t_moldyn *moldyn) {
704 store=malloc(moldyn->count*sizeof(t_atom));
706 printf("[moldyn] allocating store mem failed\n");
710 /* save unscaled potential energy + atom/dim configuration */
712 memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
715 /* derivative with respect to x direction */
716 scale=1.0+moldyn->dv/(moldyn->dim.y*moldyn->dim.z);
717 scale_dim(moldyn,scale,TRUE,0,0);
718 scale_atoms(moldyn,scale,TRUE,0,0);
719 link_cell_shutdown(moldyn);
720 link_cell_init(moldyn);
721 potential_force_calc(moldyn);
722 tp->x=(moldyn->energy-u)/moldyn->dv;
725 /* restore atomic configuration + dim */
726 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
729 /* derivative with respect to y direction */
730 scale=1.0+moldyn->dv/(moldyn->dim.x*moldyn->dim.z);
731 scale_dim(moldyn,scale,0,TRUE,0);
732 scale_atoms(moldyn,scale,0,TRUE,0);
733 link_cell_shutdown(moldyn);
734 link_cell_init(moldyn);
735 potential_force_calc(moldyn);
736 tp->y=(moldyn->energy-u)/moldyn->dv;
739 /* restore atomic configuration + dim */
740 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
743 /* derivative with respect to z direction */
744 scale=1.0+moldyn->dv/(moldyn->dim.x*moldyn->dim.y);
745 scale_dim(moldyn,scale,0,0,TRUE);
746 scale_atoms(moldyn,scale,0,0,TRUE);
747 link_cell_shutdown(moldyn);
748 link_cell_init(moldyn);
749 potential_force_calc(moldyn);
750 tp->z=(moldyn->energy-u)/moldyn->dv;
753 /* restore atomic configuration + dim */
754 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
757 printf("dU/dV komp addiert = %f %f %f\n",tp->x,tp->y,tp->z);
759 scale=1.0+pow(moldyn->dv/moldyn->volume,ONE_THIRD);
761 printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
762 scale_dim(moldyn,scale,1,1,1);
763 scale_atoms(moldyn,scale,1,1,1);
764 link_cell_shutdown(moldyn);
765 link_cell_init(moldyn);
766 potential_force_calc(moldyn);
767 printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
769 printf("dU/dV einfach = %f\n",((moldyn->energy-u)/moldyn->dv)/ATM);
771 /* restore atomic configuration + dim */
772 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
778 link_cell_shutdown(moldyn);
779 link_cell_init(moldyn);
784 double get_pressure(t_moldyn *moldyn) {
790 int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
803 int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
808 for(i=0;i<moldyn->count;i++) {
809 r=&(moldyn->atom[i].r);
818 int scale_volume(t_moldyn *moldyn) {
829 vdim=&(moldyn->vis.dim);
832 memset(&virial,0,sizeof(t_virial));
834 for(i=0;i<moldyn->count;i++) {
835 virial.xx+=atom[i].virial.xx;
836 virial.yy+=atom[i].virial.yy;
837 virial.zz+=atom[i].virial.zz;
838 virial.xy+=atom[i].virial.xy;
839 virial.xz+=atom[i].virial.xz;
840 virial.yz+=atom[i].virial.yz;
843 /* just a guess so far ... */
844 v=virial.xx+virial.yy+virial.zz;
847 /* get pressure from virial */
848 moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t+ONE_THIRD*v;
849 moldyn->p/=moldyn->volume;
850 printf("%f | %f\n",moldyn->p/(ATM),moldyn->p_ref/ATM);
853 if(moldyn->pt_scale&P_SCALE_BERENDSEN)
854 scale=3*sqrt(1-(moldyn->p_ref-moldyn->p)/moldyn->p_tc);
856 /* should actually never be used */
857 scale=pow(moldyn->p/moldyn->p_ref,1.0/3.0);
859 printf("scale = %f\n",scale);
864 if(vdim->x) vdim->x=dim->x;
865 if(vdim->y) vdim->y=dim->y;
866 if(vdim->z) vdim->z=dim->z;
867 moldyn->volume*=(scale*scale*scale);
869 /* check whether we need a new linkcell init */
870 if((dim->x/moldyn->cutoff!=lc->nx)||
871 (dim->y/moldyn->cutoff!=lc->ny)||
872 (dim->z/moldyn->cutoff!=lc->nx)) {
873 link_cell_shutdown(moldyn);
874 link_cell_init(moldyn);
881 double get_e_kin(t_moldyn *moldyn) {
889 for(i=0;i<moldyn->count;i++)
890 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
895 double update_e_kin(t_moldyn *moldyn) {
897 return(get_e_kin(moldyn));
900 double get_total_energy(t_moldyn *moldyn) {
902 return(moldyn->ekin+moldyn->energy);
905 t_3dvec get_total_p(t_moldyn *moldyn) {
914 for(i=0;i<moldyn->count;i++) {
915 v3_scale(&p,&(atom[i].v),atom[i].mass);
916 v3_add(&p_total,&p_total,&p);
922 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
926 /* nn_dist is the nearest neighbour distance */
928 tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
937 /* linked list / cell method */
939 int link_cell_init(t_moldyn *moldyn) {
946 /* partitioning the md cell */
947 lc->nx=moldyn->dim.x/moldyn->cutoff;
948 lc->x=moldyn->dim.x/lc->nx;
949 lc->ny=moldyn->dim.y/moldyn->cutoff;
950 lc->y=moldyn->dim.y/lc->ny;
951 lc->nz=moldyn->dim.z/moldyn->cutoff;
952 lc->z=moldyn->dim.z/lc->nz;
954 lc->cells=lc->nx*lc->ny*lc->nz;
955 lc->subcell=malloc(lc->cells*sizeof(t_list));
958 printf("[moldyn] FATAL: less then 27 subcells!\n");
960 printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
962 for(i=0;i<lc->cells;i++)
963 list_init_f(&(lc->subcell[i]));
965 link_cell_update(moldyn);
970 int link_cell_update(t_moldyn *moldyn) {
988 for(i=0;i<lc->cells;i++)
989 list_destroy_f(&(lc->subcell[i]));
991 for(count=0;count<moldyn->count;count++) {
992 i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
993 j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
994 k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
995 list_add_immediate_f(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
1002 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
1020 cell[0]=lc->subcell[i+j*nx+k*a];
1021 for(ci=-1;ci<=1;ci++) {
1024 if((x<0)||(x>=nx)) {
1028 for(cj=-1;cj<=1;cj++) {
1031 if((y<0)||(y>=ny)) {
1035 for(ck=-1;ck<=1;ck++) {
1038 if((z<0)||(z>=nz)) {
1042 if(!(ci|cj|ck)) continue;
1044 cell[--count2]=lc->subcell[x+y*nx+z*a];
1047 cell[count1++]=lc->subcell[x+y*nx+z*a];
1058 int link_cell_shutdown(t_moldyn *moldyn) {
1065 for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
1066 list_destroy_f(&(moldyn->lc.subcell[i]));
1073 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
1077 t_moldyn_schedule *schedule;
1079 schedule=&(moldyn->schedule);
1080 count=++(schedule->total_sched);
1082 ptr=realloc(schedule->runs,count*sizeof(int));
1084 perror("[moldyn] realloc (runs)");
1088 schedule->runs[count-1]=runs;
1090 ptr=realloc(schedule->tau,count*sizeof(double));
1092 perror("[moldyn] realloc (tau)");
1096 schedule->tau[count-1]=tau;
1098 printf("[moldyn] schedule added:\n");
1099 printf(" number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
1105 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
1107 moldyn->schedule.hook=hook;
1108 moldyn->schedule.hook_params=hook_params;
1115 * 'integration of newtons equation' - algorithms
1119 /* start the integration */
1121 int moldyn_integrate(t_moldyn *moldyn) {
1124 unsigned int e,m,s,v;
1126 t_moldyn_schedule *sched;
1131 double energy_scale;
1133 sched=&(moldyn->schedule);
1136 /* initialize linked cell method */
1137 link_cell_init(moldyn);
1139 /* logging & visualization */
1145 /* sqaure of some variables */
1146 moldyn->tau_square=moldyn->tau*moldyn->tau;
1147 moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
1149 /* energy scaling factor */
1150 energy_scale=moldyn->count*EV;
1152 /* calculate initial forces */
1153 potential_force_calc(moldyn);
1155 /* some stupid checks before we actually start calculating bullshit */
1156 if(moldyn->cutoff>0.5*moldyn->dim.x)
1157 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
1158 if(moldyn->cutoff>0.5*moldyn->dim.y)
1159 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
1160 if(moldyn->cutoff>0.5*moldyn->dim.z)
1161 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
1162 ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
1163 if(ds>0.05*moldyn->nnd)
1164 printf("[moldyn] warning: forces too high / tau too small!\n");
1166 /* zero absolute time */
1169 /* debugging, ignore */
1172 /* tell the world */
1173 printf("[moldyn] integration start, go get a coffee ...\n");
1175 /* executing the schedule */
1176 for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
1178 /* setting amount of runs and finite time step size */
1179 moldyn->tau=sched->tau[sched->count];
1180 moldyn->tau_square=moldyn->tau*moldyn->tau;
1181 moldyn->time_steps=sched->runs[sched->count];
1183 /* integration according to schedule */
1185 for(i=0;i<moldyn->time_steps;i++) {
1187 /* integration step */
1188 moldyn->integrate(moldyn);
1191 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
1192 scale_velocity(moldyn,FALSE);
1193 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
1194 scale_volume(moldyn);
1196 update_e_kin(moldyn);
1197 temperature_calc(moldyn);
1198 pressure_calc(moldyn);
1199 //thermodynamic_pressure_calc(moldyn);
1201 /* check for log & visualization */
1204 dprintf(moldyn->efd,
1206 moldyn->time,moldyn->ekin/energy_scale,
1207 moldyn->energy/energy_scale,
1208 get_total_energy(moldyn)/energy_scale);
1212 p=get_total_p(moldyn);
1213 dprintf(moldyn->mfd,
1214 "%f %f\n",moldyn->time,v3_norm(&p));
1219 snprintf(dir,128,"%s/s-%07.f.save",
1220 moldyn->vlsdir,moldyn->time);
1221 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
1222 if(fd<0) perror("[moldyn] save fd open");
1224 write(fd,moldyn,sizeof(t_moldyn));
1225 write(fd,moldyn->atom,
1226 moldyn->count*sizeof(t_atom));
1233 visual_atoms(&(moldyn->vis),moldyn->time,
1234 moldyn->atom,moldyn->count);
1235 printf("\rsched: %d, steps: %d, debug: %f | %f",
1236 sched->count,i,moldyn->p/ATM,moldyn->p/ATM);
1241 /* increase absolute time */
1242 moldyn->time+=moldyn->tau;
1246 /* check for hooks */
1248 sched->hook(moldyn,sched->hook_params);
1250 /* get a new info line */
1258 /* velocity verlet */
1260 int velocity_verlet(t_moldyn *moldyn) {
1263 double tau,tau_square,h;
1268 count=moldyn->count;
1270 tau_square=moldyn->tau_square;
1272 for(i=0;i<count;i++) {
1275 v3_scale(&delta,&(atom[i].v),tau);
1276 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1277 v3_scale(&delta,&(atom[i].f),h*tau_square);
1278 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1279 check_per_bound(moldyn,&(atom[i].r));
1281 /* velocities [actually v(t+tau/2)] */
1282 v3_scale(&delta,&(atom[i].f),h*tau);
1283 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1286 /* neighbour list update */
1287 link_cell_update(moldyn);
1289 /* forces depending on chosen potential */
1290 potential_force_calc(moldyn);
1292 for(i=0;i<count;i++) {
1293 /* again velocities [actually v(t+tau)] */
1294 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
1295 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1304 * potentials & corresponding forces & virial routine
1308 /* generic potential and force calculation */
1310 int potential_force_calc(t_moldyn *moldyn) {
1313 t_atom *itom,*jtom,*ktom;
1316 t_list neighbour_i[27];
1317 t_list neighbour_i2[27];
1322 count=moldyn->count;
1329 /* reset force, site energy and virial of every atom */
1330 for(i=0;i<count;i++) {
1333 v3_zero(&(itom[i].f));
1336 virial=(&(itom[i].virial));
1344 /* reset site energy */
1349 /* get energy,force and virial of every atom */
1350 for(i=0;i<count;i++) {
1352 /* single particle potential/force */
1353 if(itom[i].attr&ATOM_ATTR_1BP)
1354 moldyn->func1b(moldyn,&(itom[i]));
1356 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
1359 /* 2 body pair potential/force */
1361 link_cell_neighbour_index(moldyn,
1362 (itom[i].r.x+moldyn->dim.x/2)/lc->x,
1363 (itom[i].r.y+moldyn->dim.y/2)/lc->y,
1364 (itom[i].r.z+moldyn->dim.z/2)/lc->z,
1371 this=&(neighbour_i[j]);
1374 if(this->start==NULL)
1380 jtom=this->current->data;
1382 if(jtom==&(itom[i]))
1385 if((jtom->attr&ATOM_ATTR_2BP)&
1386 (itom[i].attr&ATOM_ATTR_2BP)) {
1387 moldyn->func2b(moldyn,
1393 /* 3 body potential/force */
1395 if(!(itom[i].attr&ATOM_ATTR_3BP)||
1396 !(jtom->attr&ATOM_ATTR_3BP))
1399 /* copy the neighbour lists */
1400 memcpy(neighbour_i2,neighbour_i,
1403 /* get neighbours of i */
1406 that=&(neighbour_i2[k]);
1409 if(that->start==NULL)
1416 ktom=that->current->data;
1418 if(!(ktom->attr&ATOM_ATTR_3BP))
1424 if(ktom==&(itom[i]))
1427 moldyn->func3b(moldyn,
1433 } while(list_next_f(that)!=\
1438 /* 2bp post function */
1439 if(moldyn->func2b_post) {
1440 moldyn->func2b_post(moldyn,
1445 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1462 * virial calculation
1465 inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1467 a->virial.xx+=f->x*d->x;
1468 a->virial.yy+=f->y*d->y;
1469 a->virial.zz+=f->z*d->z;
1470 a->virial.xy+=f->x*d->y;
1471 a->virial.xz+=f->x*d->z;
1472 a->virial.yz+=f->y*d->z;
1478 * periodic boundayr checking
1481 inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1492 if(moldyn->status&MOLDYN_STAT_PBX) {
1493 if(a->x>=x) a->x-=dim->x;
1494 else if(-a->x>x) a->x+=dim->x;
1496 if(moldyn->status&MOLDYN_STAT_PBY) {
1497 if(a->y>=y) a->y-=dim->y;
1498 else if(-a->y>y) a->y+=dim->y;
1500 if(moldyn->status&MOLDYN_STAT_PBZ) {
1501 if(a->z>=z) a->z-=dim->z;
1502 else if(-a->z>z) a->z+=dim->z;
1510 * example potentials
1513 /* harmonic oscillator potential and force */
1515 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1517 t_ho_params *params;
1518 t_3dvec force,distance;
1520 double sc,equi_dist;
1522 params=moldyn->pot2b_params;
1523 sc=params->spring_constant;
1524 equi_dist=params->equilibrium_distance;
1528 v3_sub(&distance,&(aj->r),&(ai->r));
1530 if(bc) check_per_bound(moldyn,&distance);
1531 d=v3_norm(&distance);
1532 if(d<=moldyn->cutoff) {
1533 moldyn->energy+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
1534 /* f = -grad E; grad r_ij = -1 1/r_ij distance */
1535 f=sc*(1.0-equi_dist/d);
1536 v3_scale(&force,&distance,f);
1537 v3_add(&(ai->f),&(ai->f),&force);
1538 virial_calc(ai,&force,&distance);
1539 virial_calc(aj,&force,&distance); /* f and d signe switched */
1540 v3_scale(&force,&distance,-f);
1541 v3_add(&(aj->f),&(aj->f),&force);
1547 /* lennard jones potential & force for one sort of atoms */
1549 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1551 t_lj_params *params;
1552 t_3dvec force,distance;
1554 double eps,sig6,sig12;
1556 params=moldyn->pot2b_params;
1557 eps=params->epsilon4;
1558 sig6=params->sigma6;
1559 sig12=params->sigma12;
1563 v3_sub(&distance,&(aj->r),&(ai->r));
1564 if(bc) check_per_bound(moldyn,&distance);
1565 d=v3_absolute_square(&distance); /* 1/r^2 */
1566 if(d<=moldyn->cutoff_square) {
1567 d=1.0/d; /* 1/r^2 */
1570 h1=h2*h2; /* 1/r^12 */
1571 moldyn->energy+=(eps*(sig12*h1-sig6*h2)-params->uc);
1578 v3_scale(&force,&distance,d);
1579 v3_add(&(aj->f),&(aj->f),&force);
1580 v3_scale(&force,&force,-1.0); /* f = - grad E */
1581 v3_add(&(ai->f),&(ai->f),&force);
1582 virial_calc(ai,&force,&distance);
1583 virial_calc(aj,&force,&distance); /* f and d signe switched */
1590 * tersoff potential & force for 2 sorts of atoms
1593 /* create mixed terms from parameters and set them */
1594 int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
1596 printf("[moldyn] tersoff parameter completion\n");
1597 p->S2[0]=p->S[0]*p->S[0];
1598 p->S2[1]=p->S[1]*p->S[1];
1599 p->Smixed=sqrt(p->S[0]*p->S[1]);
1600 p->S2mixed=p->Smixed*p->Smixed;
1601 p->Rmixed=sqrt(p->R[0]*p->R[1]);
1602 p->Amixed=sqrt(p->A[0]*p->A[1]);
1603 p->Bmixed=sqrt(p->B[0]*p->B[1]);
1604 p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
1605 p->mu_m=0.5*(p->mu[0]+p->mu[1]);
1607 printf("[moldyn] tersoff mult parameter info:\n");
1608 printf(" S (A) | %f | %f | %f\n",p->S[0],p->S[1],p->Smixed);
1609 printf(" R (A) | %f | %f | %f\n",p->R[0],p->R[1],p->Rmixed);
1610 printf(" A (eV) | %f | %f | %f\n",p->A[0]/EV,p->A[1]/EV,p->Amixed/EV);
1611 printf(" B (eV) | %f | %f | %f\n",p->B[0]/EV,p->B[1]/EV,p->Bmixed/EV);
1612 printf(" lambda | %f | %f | %f\n",p->lambda[0],p->lambda[1],
1614 printf(" mu | %f | %f | %f\n",p->mu[0],p->mu[1],p->mu_m);
1615 printf(" beta | %.10f | %.10f\n",p->beta[0],p->beta[1]);
1616 printf(" n | %f | %f\n",p->n[0],p->n[1]);
1617 printf(" c | %f | %f\n",p->c[0],p->c[1]);
1618 printf(" d | %f | %f\n",p->d[0],p->d[1]);
1619 printf(" h | %f | %f\n",p->h[0],p->h[1]);
1620 printf(" chi | %f \n",p->chi);
1625 /* tersoff 1 body part */
1626 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
1629 t_tersoff_mult_params *params;
1630 t_tersoff_exchange *exchange;
1633 params=moldyn->pot1b_params;
1634 exchange=&(params->exchange);
1637 * simple: point constant parameters only depending on atom i to
1638 * their right values
1641 exchange->beta_i=&(params->beta[brand]);
1642 exchange->n_i=&(params->n[brand]);
1643 exchange->c_i=&(params->c[brand]);
1644 exchange->d_i=&(params->d[brand]);
1645 exchange->h_i=&(params->h[brand]);
1647 exchange->betaini=pow(*(exchange->beta_i),*(exchange->n_i));
1648 exchange->ci2=params->c[brand]*params->c[brand];
1649 exchange->di2=params->d[brand]*params->d[brand];
1650 exchange->ci2di2=exchange->ci2/exchange->di2;
1655 /* tersoff 2 body part */
1656 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1658 t_tersoff_mult_params *params;
1659 t_tersoff_exchange *exchange;
1660 t_3dvec dist_ij,force;
1662 double A,B,R,S,S2,lambda,mu;
1669 params=moldyn->pot2b_params;
1671 exchange=&(params->exchange);
1673 /* clear 3bp and 2bp post run */
1675 exchange->run2bp_post=0;
1677 /* reset S > r > R mark */
1678 exchange->d_ij_between_rs=0;
1681 * calc of 2bp contribution of V_ij and dV_ij/ji
1683 * for Vij and dV_ij we need:
1687 * for dV_ji we need:
1688 * - f_c_ji = f_c_ij, df_c_ji = df_c_ij
1689 * - f_r_ji = f_r_ij; df_r_ji = df_r_ij
1694 if(brand==ai->brand) {
1696 S2=params->S2[brand];
1700 lambda=params->lambda[brand];
1701 mu=params->mu[brand];
1710 lambda=params->lambda_m;
1712 params->exchange.chi=params->chi;
1716 v3_sub(&dist_ij,&(aj->r),&(ai->r));
1717 if(bc) check_per_bound(moldyn,&dist_ij);
1718 d_ij2=v3_absolute_square(&dist_ij);
1720 /* if d_ij2 > S2 => no force & potential energy contribution */
1724 /* now we will need the distance */
1725 //d_ij=v3_norm(&dist_ij);
1728 /* save for use in 3bp */
1729 exchange->d_ij=d_ij;
1730 exchange->d_ij2=d_ij2;
1731 exchange->dist_ij=dist_ij;
1733 /* more constants */
1734 exchange->beta_j=&(params->beta[brand]);
1735 exchange->n_j=&(params->n[brand]);
1736 exchange->c_j=&(params->c[brand]);
1737 exchange->d_j=&(params->d[brand]);
1738 exchange->h_j=&(params->h[brand]);
1739 if(brand==ai->brand) {
1740 exchange->betajnj=exchange->betaini;
1741 exchange->cj2=exchange->ci2;
1742 exchange->dj2=exchange->di2;
1743 exchange->cj2dj2=exchange->ci2di2;
1746 exchange->betajnj=pow(*(exchange->beta_j),*(exchange->n_j));
1747 exchange->cj2=params->c[brand]*params->c[brand];
1748 exchange->dj2=params->d[brand]*params->d[brand];
1749 exchange->cj2dj2=exchange->cj2/exchange->dj2;
1752 /* f_r_ij = f_r_ji, df_r_ij = df_r_ji */
1753 f_r=A*exp(-lambda*d_ij);
1754 df_r=lambda*f_r/d_ij;
1756 /* f_a, df_a calc (again, same for ij and ji) | save for later use! */
1757 exchange->f_a=-B*exp(-mu*d_ij);
1758 exchange->df_a=mu*exchange->f_a/d_ij;
1760 /* f_c, df_c calc (again, same for ij and ji) */
1762 /* f_c = 1, df_c = 0 */
1765 /* two body contribution (ij, ji) */
1766 v3_scale(&force,&dist_ij,-df_r);
1770 arg=M_PI*(d_ij-R)/s_r;
1771 f_c=0.5+0.5*cos(arg);
1772 df_c=0.5*sin(arg)*(M_PI/(s_r*d_ij));
1773 /* two body contribution (ij, ji) */
1774 v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
1775 /* tell 3bp that S > r > R */
1776 exchange->d_ij_between_rs=1;
1779 /* add forces of 2bp (ij, ji) contribution
1780 * dVij = dVji and we sum up both: no 1/2) */
1781 v3_add(&(ai->f),&(ai->f),&force);
1784 ai->virial.xx-=force.x*dist_ij.x;
1785 ai->virial.yy-=force.y*dist_ij.y;
1786 ai->virial.zz-=force.z*dist_ij.z;
1787 ai->virial.xy-=force.x*dist_ij.y;
1788 ai->virial.xz-=force.x*dist_ij.z;
1789 ai->virial.yz-=force.y*dist_ij.z;
1792 if(ai==&(moldyn->atom[0])) {
1793 printf("dVij, dVji (2bp) contrib:\n");
1794 printf("%f | %f\n",force.x,ai->f.x);
1795 printf("%f | %f\n",force.y,ai->f.y);
1796 printf("%f | %f\n",force.z,ai->f.z);
1800 if(ai==&(moldyn->atom[0])) {
1801 printf("dVij, dVji (2bp) contrib:\n");
1802 printf("%f | %f\n",force.x*dist_ij.x,ai->virial.xx);
1803 printf("%f | %f\n",force.y*dist_ij.y,ai->virial.yy);
1804 printf("%f | %f\n",force.z*dist_ij.z,ai->virial.zz);
1808 /* energy 2bp contribution (ij, ji) is 0.5 f_r f_c ... */
1809 moldyn->energy+=(0.5*f_r*f_c);
1811 /* save for use in 3bp */
1813 exchange->df_c=df_c;
1815 /* enable the run of 3bp function and 2bp post processing */
1817 exchange->run2bp_post=1;
1819 /* reset 3bp sums */
1820 exchange->zeta_ij=0.0;
1821 exchange->zeta_ji=0.0;
1822 v3_zero(&(exchange->dzeta_ij));
1823 v3_zero(&(exchange->dzeta_ji));
1828 /* tersoff 2 body post part */
1830 int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1833 * here we have to allow for the 3bp sums
1836 * - zeta_ij, dzeta_ij
1837 * - zeta_ji, dzeta_ji
1839 * to compute the 3bp contribution to:
1845 t_tersoff_mult_params *params;
1846 t_tersoff_exchange *exchange;
1851 double f_c,df_c,f_a,df_a;
1852 double chi,ni,betaini,nj,betajnj;
1855 params=moldyn->pot2b_params;
1856 exchange=&(params->exchange);
1858 /* we do not run if f_c_ij was detected to be 0! */
1859 if(!(exchange->run2bp_post))
1863 df_c=exchange->df_c;
1865 df_a=exchange->df_a;
1866 betaini=exchange->betaini;
1867 betajnj=exchange->betajnj;
1868 ni=*(exchange->n_i);
1869 nj=*(exchange->n_j);
1871 dist_ij=&(exchange->dist_ij);
1874 zeta=exchange->zeta_ij;
1876 moldyn->debug++; /* just for debugging ... */
1878 v3_scale(&force,dist_ij,df_a*b*f_c);
1881 tmp=betaini*pow(zeta,ni-1.0); /* beta^n * zeta^n-1 */
1882 b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
1883 db=chi*pow(b,-1.0/(2*ni)-1); /* x(...)^(-1/2n - 1) */
1885 db*=-0.5*tmp; /* db_ij */
1886 v3_scale(&force,&(exchange->dzeta_ij),f_a*db);
1887 v3_scale(&temp,dist_ij,df_a*b);
1888 v3_add(&force,&force,&temp);
1889 v3_scale(&force,&force,f_c);
1891 v3_scale(&temp,dist_ij,df_c*b*f_a);
1892 v3_add(&force,&force,&temp);
1893 v3_scale(&force,&force,-0.5);
1896 v3_add(&(ai->f),&(ai->f),&force);
1899 ai->virial.xx-=force.x*dist_ij->x;
1900 ai->virial.yy-=force.y*dist_ij->y;
1901 ai->virial.zz-=force.z*dist_ij->z;
1902 ai->virial.xy-=force.x*dist_ij->y;
1903 ai->virial.xz-=force.x*dist_ij->z;
1904 ai->virial.yz-=force.y*dist_ij->z;
1907 if(ai==&(moldyn->atom[0])) {
1908 printf("dVij (3bp) contrib:\n");
1909 printf("%f | %f\n",force.x,ai->f.x);
1910 printf("%f | %f\n",force.y,ai->f.y);
1911 printf("%f | %f\n",force.z,ai->f.z);
1915 if(ai==&(moldyn->atom[0])) {
1916 printf("dVij (3bp) contrib:\n");
1917 printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
1918 printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
1919 printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
1923 /* add energy of 3bp sum */
1924 moldyn->energy+=(0.5*f_c*b*f_a);
1927 zeta=exchange->zeta_ji;
1931 v3_scale(&force,dist_ij,df_a*b*f_c);
1934 tmp=betajnj*pow(zeta,nj-1.0); /* beta^n * zeta^n-1 */
1935 b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
1936 db=chi*pow(b,-1.0/(2*nj)-1); /* x(...)^(-1/2n - 1) */
1938 db*=-0.5*tmp; /* db_ij */
1939 v3_scale(&force,&(exchange->dzeta_ji),f_a*db);
1940 v3_scale(&temp,dist_ij,df_a*b);
1941 v3_add(&force,&force,&temp);
1942 v3_scale(&force,&force,f_c);
1944 v3_scale(&temp,dist_ij,df_c*b*f_a);
1945 v3_add(&force,&force,&temp);
1946 v3_scale(&force,&force,-0.5);
1949 v3_add(&(ai->f),&(ai->f),&force);
1951 /* virial - plus sign, as dist_ij = - dist_ji - (really??) */
1952 // TEST ... with a minus instead
1953 ai->virial.xx-=force.x*dist_ij->x;
1954 ai->virial.yy-=force.y*dist_ij->y;
1955 ai->virial.zz-=force.z*dist_ij->z;
1956 ai->virial.xy-=force.x*dist_ij->y;
1957 ai->virial.xz-=force.x*dist_ij->z;
1958 ai->virial.yz-=force.y*dist_ij->z;
1961 if(ai==&(moldyn->atom[0])) {
1962 printf("dVji (3bp) contrib:\n");
1963 printf("%f | %f\n",force.x,ai->f.x);
1964 printf("%f | %f\n",force.y,ai->f.y);
1965 printf("%f | %f\n",force.z,ai->f.z);
1969 if(ai==&(moldyn->atom[0])) {
1970 printf("dVji (3bp) contrib:\n");
1971 printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
1972 printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
1973 printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
1980 /* tersoff 3 body part */
1982 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
1984 t_tersoff_mult_params *params;
1985 t_tersoff_exchange *exchange;
1986 t_3dvec dist_ij,dist_ik,dist_jk;
1987 t_3dvec temp1,temp2;
1991 double d_ij,d_ik,d_jk,d_ij2,d_ik2,d_jk2;
1994 double f_c_ik,df_c_ik,arg;
1998 double cos_theta,d_costheta1,d_costheta2;
1999 double h_cos,d2_h_cos2;
2000 double frac,g,zeta,chi;
2004 params=moldyn->pot3b_params;
2005 exchange=&(params->exchange);
2007 if(!(exchange->run3bp))
2011 * calc of 3bp contribution of V_ij and dV_ij/ji/jk &
2012 * 2bp contribution of dV_jk
2014 * for Vij and dV_ij we still need:
2015 * - b_ij, db_ij (zeta_ij)
2016 * - f_c_ik, df_c_ik, constants_i, cos_theta_ijk, d_costheta_ijk
2018 * for dV_ji we still need:
2019 * - b_ji, db_ji (zeta_ji)
2020 * - f_c_jk, d_c_jk, constants_j, cos_theta_jik, d_costheta_jik
2022 * for dV_jk we need:
2026 * - f_c_ji, df_c_ji, constants_j, cos_theta_jki, d_costheta_jki
2034 /* dist_ij, d_ij - this is < S_ij ! */
2035 dist_ij=exchange->dist_ij;
2036 d_ij=exchange->d_ij;
2037 d_ij2=exchange->d_ij2;
2039 /* f_c_ij, df_c_ij (same for ji) */
2041 df_c=exchange->df_c;
2044 * calculate unknown values now ...
2047 /* V_ij and dV_ij stuff (in b_ij there is f_c_ik) */
2050 v3_sub(&dist_ik,&(ak->r),&(ai->r));
2051 if(bc) check_per_bound(moldyn,&dist_ik);
2052 d_ik2=v3_absolute_square(&dist_ik);
2056 if(brand==ak->brand) {
2059 S2=params->S2[brand];
2067 /* zeta_ij/dzeta_ij contribution only for d_ik < S */
2070 /* now we need d_ik */
2073 /* get constants_i from exchange data */
2080 c2d2=exchange->ci2di2;
2082 /* cosine of theta_ijk by scalaproduct */
2083 rr=v3_scalar_product(&dist_ij,&dist_ik);
2089 d_costheta1=cos_theta/d_ij2-tmp;
2090 d_costheta2=cos_theta/d_ik2-tmp;
2092 /* some usefull values */
2093 h_cos=(h-cos_theta);
2094 d2_h_cos2=d2+(h_cos*h_cos);
2095 frac=c2/(d2_h_cos2);
2100 /* d_costheta_ij and dg(cos_theta) - needed in any case! */
2101 v3_scale(&temp1,&dist_ij,d_costheta1);
2102 v3_scale(&temp2,&dist_ik,d_costheta2);
2103 v3_add(&temp1,&temp1,&temp2);
2104 v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
2106 /* f_c_ik & df_c_ik + {d,}zeta contribution */
2107 dzeta=&(exchange->dzeta_ij);
2111 // => df_c_ik=0.0; of course we do not set this!
2114 exchange->zeta_ij+=g;
2117 v3_add(dzeta,dzeta,&temp1);
2122 arg=M_PI*(d_ik-R)/s_r;
2123 f_c_ik=0.5+0.5*cos(arg);
2124 df_c_ik=0.5*sin(arg)*(M_PI/(s_r*d_ik));
2127 exchange->zeta_ij+=f_c_ik*g;
2130 v3_scale(&temp1,&temp1,f_c_ik);
2131 v3_scale(&temp2,&dist_ik,g*df_c_ik);
2132 v3_add(&temp1,&temp1,&temp2);
2133 v3_add(dzeta,dzeta,&temp1);
2137 /* dV_ji stuff (in b_ji there is f_c_jk) + dV_jk stuff! */
2140 v3_sub(&dist_jk,&(ak->r),&(aj->r));
2141 if(bc) check_per_bound(moldyn,&dist_jk);
2142 d_jk2=v3_absolute_square(&dist_jk);
2146 if(brand==ak->brand) {
2149 S2=params->S2[brand];
2151 mu=params->mu[brand];
2163 /* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */
2166 /* now we need d_ik */
2169 /* constants_j from exchange data */
2176 c2d2=exchange->cj2dj2;
2178 /* cosine of theta_jik by scalaproduct */
2179 rr=-v3_scalar_product(&dist_ij,&dist_jk); /* -1, as ij -> ji */
2185 d_costheta2=cos_theta/d_ij2;
2187 /* some usefull values */
2188 h_cos=(h-cos_theta);
2189 d2_h_cos2=d2+(h_cos*h_cos);
2190 frac=c2/(d2_h_cos2);
2195 /* d_costheta_jik and dg(cos_theta) - needed in any case! */
2196 v3_scale(&temp1,&dist_jk,d_costheta1);
2197 v3_scale(&temp2,&dist_ij,-d_costheta2); /* ji -> ij => -1 */
2198 //v3_add(&temp1,&temp1,&temp2);
2199 v3_sub(&temp1,&temp1,&temp2); /* there is a minus! */
2200 v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
2202 /* store dg in temp2 and use it for dVjk later */
2203 v3_copy(&temp2,&temp1);
2205 /* f_c_jk + {d,}zeta contribution (df_c_jk = 0) */
2206 dzeta=&(exchange->dzeta_ji);
2212 exchange->zeta_ji+=g;
2215 v3_add(dzeta,dzeta,&temp1);
2220 arg=M_PI*(d_jk-R)/s_r;
2221 f_c_jk=0.5+0.5*cos(arg);
2224 exchange->zeta_ji+=f_c_jk*g;
2227 v3_scale(&temp1,&temp1,f_c_jk);
2228 v3_add(dzeta,dzeta,&temp1);
2231 /* dV_jk stuff | add force contribution on atom i immediately */
2232 if(exchange->d_ij_between_rs) {
2234 v3_scale(&temp1,&temp2,f_c);
2235 v3_scale(&temp2,&dist_ij,df_c*g);
2236 v3_add(&temp2,&temp2,&temp1); /* -> dzeta_jk in temp2 */
2240 // dzeta_jk is simply dg, which is stored in temp2
2242 /* betajnj * zeta_jk ^ nj-1 */
2243 tmp=exchange->betajnj*pow(zeta,(n-1.0));
2244 tmp=-chi/2.0*pow((1+tmp*zeta),(-1.0/(2.0*n)-1))*tmp;
2245 v3_scale(&temp2,&temp2,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
2246 v3_add(&(ai->f),&(ai->f),&temp2); /* -1 skipped in f_a calc ^ */
2247 /* scaled with 0.5 ^ */
2250 ai->virial.xx-=temp2.x*dist_jk.x;
2251 ai->virial.yy-=temp2.y*dist_jk.y;
2252 ai->virial.zz-=temp2.z*dist_jk.z;
2253 ai->virial.xy-=temp2.x*dist_jk.y;
2254 ai->virial.xz-=temp2.x*dist_jk.z;
2255 ai->virial.yz-=temp2.y*dist_jk.z;
2258 if(ai==&(moldyn->atom[0])) {
2259 printf("dVjk (3bp) contrib:\n");
2260 printf("%f | %f\n",temp2.x,ai->f.x);
2261 printf("%f | %f\n",temp2.y,ai->f.y);
2262 printf("%f | %f\n",temp2.z,ai->f.z);
2266 if(ai==&(moldyn->atom[0])) {
2267 printf("dVjk (3bp) contrib:\n");
2268 printf("%f | %f\n",temp2.x*dist_jk.x,ai->virial.xx);
2269 printf("%f | %f\n",temp2.y*dist_jk.y,ai->virial.yy);
2270 printf("%f | %f\n",temp2.z*dist_jk.z,ai->virial.zz);
2281 * debugging / critical check functions
2284 int moldyn_bc_check(t_moldyn *moldyn) {
2297 for(i=0;i<moldyn->count;i++) {
2298 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
2299 printf("FATAL: atom %d: x: %.20f (%.20f)\n",
2300 i,atom[i].r.x,dim->x/2);
2301 printf("diagnostic:\n");
2302 printf("-----------\natom.r.x:\n");
2304 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
2307 ((byte)&(1<<k))?1:0,
2310 printf("---------------\nx=dim.x/2:\n");
2312 memcpy(&byte,(u8 *)(&x)+j,1);
2315 ((byte)&(1<<k))?1:0,
2318 if(atom[i].r.x==x) printf("the same!\n");
2319 else printf("different!\n");
2321 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
2322 printf("FATAL: atom %d: y: %.20f (%.20f)\n",
2323 i,atom[i].r.y,dim->y/2);
2324 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
2325 printf("FATAL: atom %d: z: %.20f (%.20f)\n",
2326 i,atom[i].r.z,dim->z/2);