2 * moldyn.c - molecular dynamics library main file
4 * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
12 #include <sys/types.h>
19 #include "report/report.h"
21 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
23 printf("[moldyn] init\n");
25 memset(moldyn,0,sizeof(t_moldyn));
27 rand_init(&(moldyn->random),NULL,1);
28 moldyn->random.status|=RAND_STAT_VERBOSE;
33 int moldyn_shutdown(t_moldyn *moldyn) {
35 printf("[moldyn] shutdown\n");
37 moldyn_log_shutdown(moldyn);
38 link_cell_shutdown(moldyn);
39 rand_close(&(moldyn->random));
45 int set_int_alg(t_moldyn *moldyn,u8 algo) {
47 printf("[moldyn] integration algorithm: ");
50 case MOLDYN_INTEGRATE_VERLET:
51 moldyn->integrate=velocity_verlet;
52 printf("velocity verlet\n");
55 printf("unknown integration algorithm: %02x\n",algo);
63 int set_cutoff(t_moldyn *moldyn,double cutoff) {
65 moldyn->cutoff=cutoff;
67 printf("[moldyn] cutoff [A]: %f\n",moldyn->cutoff);
72 int set_temperature(t_moldyn *moldyn,double t_ref) {
76 printf("[moldyn] temperature [K]: %f\n",moldyn->t_ref);
81 int set_pressure(t_moldyn *moldyn,double p_ref) {
85 printf("[moldyn] pressure [atm]: %f\n",moldyn->p_ref/ATM);
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 set_nn_dist(moldyn,lc);
351 ret=cubic_init(a,b,c,lc,atom,&origin);
354 set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
355 ret=fcc_init(a,b,c,lc,atom,NULL);
358 set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
359 ret=diamond_init(a,b,c,lc,atom,&origin);
362 printf("unknown lattice type (%02x)\n",type);
368 printf("[moldyn] creating lattice failed\n");
369 printf(" amount of atoms\n");
370 printf(" - expected: %d\n",new);
371 printf(" - created: %d\n",ret);
376 printf("[moldyn] created lattice with %d atoms\n",new);
378 for(ret=0;ret<new;ret++) {
379 atom[ret].element=element;
382 atom[ret].brand=brand;
383 atom[ret].tag=count+ret;
384 check_per_bound(moldyn,&(atom[ret].r));
391 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
410 v3_copy(&(atom[count].r),&r);
419 for(i=0;i<count;i++) {
420 atom[i].r.x-=(a*lc)/2.0;
421 atom[i].r.y-=(b*lc)/2.0;
422 atom[i].r.z-=(c*lc)/2.0;
428 /* fcc lattice init */
429 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
442 if(origin) v3_copy(&o,origin);
445 /* construct the basis */
448 if(i!=j) help[j]=0.5*lc;
451 v3_set(&basis[i],help);
457 /* fill up the room */
464 v3_copy(&(atom[count].r),&r);
465 atom[count].element=1;
468 v3_add(&n,&r,&basis[i]);
472 v3_copy(&(atom[count].r),&n);
483 /* coordinate transformation */
489 v3_sub(&(atom[i].r),&(atom[i].r),&n);
494 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
499 count=fcc_init(a,b,c,lc,atom,origin);
505 if(origin) v3_add(&o,&o,origin);
507 count+=fcc_init(a,b,c,lc,&atom[count],&o);
512 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
513 t_3dvec *r,t_3dvec *v) {
520 count=(moldyn->count)++;
522 ptr=realloc(atom,(count+1)*sizeof(t_atom));
524 perror("[moldyn] realloc (add atom)");
532 atom[count].element=element;
533 atom[count].mass=mass;
534 atom[count].brand=brand;
535 atom[count].tag=count;
536 atom[count].attr=attr;
541 int destroy_atoms(t_moldyn *moldyn) {
543 if(moldyn->atom) free(moldyn->atom);
548 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
551 * - gaussian distribution of velocities
552 * - zero total momentum
553 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
558 t_3dvec p_total,delta;
563 random=&(moldyn->random);
565 printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
567 /* gaussian distribution of velocities */
569 for(i=0;i<moldyn->count;i++) {
570 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
572 v=sigma*rand_get_gauss(random);
574 p_total.x+=atom[i].mass*v;
576 v=sigma*rand_get_gauss(random);
578 p_total.y+=atom[i].mass*v;
580 v=sigma*rand_get_gauss(random);
582 p_total.z+=atom[i].mass*v;
585 /* zero total momentum */
586 v3_scale(&p_total,&p_total,1.0/moldyn->count);
587 for(i=0;i<moldyn->count;i++) {
588 v3_scale(&delta,&p_total,1.0/atom[i].mass);
589 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
592 /* velocity scaling */
593 scale_velocity(moldyn,equi_init);
598 double temperature_calc(t_moldyn *moldyn) {
600 /* assume up to date kinetic energy, which is 3/2 N k_B T */
602 moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
607 double get_temperature(t_moldyn *moldyn) {
612 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
622 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
625 /* get kinetic energy / temperature & count involved atoms */
628 for(i=0;i<moldyn->count;i++) {
629 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
630 e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
635 if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
636 else return 0; /* no atoms involved in scaling! */
638 /* (temporary) hack for e,t = 0 */
641 if(moldyn->t_ref!=0.0) {
642 thermal_init(moldyn,equi_init);
646 return 0; /* no scaling needed */
650 /* get scaling factor */
651 scale=moldyn->t_ref/moldyn->t;
655 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
656 scale=1.0+(scale-1.0)/moldyn->t_tc;
659 /* velocity scaling */
660 for(i=0;i<moldyn->count;i++) {
661 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
662 v3_scale(&(atom[i].v),&(atom[i].v),scale);
668 double ideal_gas_law_pressure(t_moldyn *moldyn) {
672 p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
677 double pressure_calc(t_moldyn *moldyn) {
684 * P = 1/(3V) sum_i ( p_i^2 / 2m + f_i r_i )
690 for(i=0;i<moldyn->count;i++) {
691 virial=&(moldyn->atom[i].virial);
692 v+=(virial->xx+virial->yy+virial->zz);
695 /* assume up to date kinetic energy */
696 moldyn->p=2.0*moldyn->ekin+v;
697 moldyn->p/=(3.0*moldyn->volume);
702 double thermodynamic_pressure_calc(t_moldyn *moldyn) {
710 store=malloc(moldyn->count*sizeof(t_atom));
712 printf("[moldyn] allocating store mem failed\n");
716 /* save unscaled potential energy + atom/dim configuration */
718 memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
721 /* derivative with respect to x direction */
722 scale=1.0+moldyn->dv/(moldyn->dim.y*moldyn->dim.z);
723 scale_dim(moldyn,scale,TRUE,0,0);
724 scale_atoms(moldyn,scale,TRUE,0,0);
725 link_cell_shutdown(moldyn);
726 link_cell_init(moldyn,QUIET);
727 potential_force_calc(moldyn);
728 tp->x=(moldyn->energy-u)/moldyn->dv;
731 /* restore atomic configuration + dim */
732 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
735 /* derivative with respect to y direction */
736 scale=1.0+moldyn->dv/(moldyn->dim.x*moldyn->dim.z);
737 scale_dim(moldyn,scale,0,TRUE,0);
738 scale_atoms(moldyn,scale,0,TRUE,0);
739 link_cell_shutdown(moldyn);
740 link_cell_init(moldyn,QUIET);
741 potential_force_calc(moldyn);
742 tp->y=(moldyn->energy-u)/moldyn->dv;
745 /* restore atomic configuration + dim */
746 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
749 /* derivative with respect to z direction */
750 scale=1.0+moldyn->dv/(moldyn->dim.x*moldyn->dim.y);
751 scale_dim(moldyn,scale,0,0,TRUE);
752 scale_atoms(moldyn,scale,0,0,TRUE);
753 link_cell_shutdown(moldyn);
754 link_cell_init(moldyn,QUIET);
755 potential_force_calc(moldyn);
756 tp->z=(moldyn->energy-u)/moldyn->dv;
759 /* restore atomic configuration + dim */
760 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
763 printf("dU/dV komp addiert = %f %f %f\n",tp->x,tp->y,tp->z);
765 scale=1.0+pow(moldyn->dv/moldyn->volume,ONE_THIRD);
767 printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
768 scale_dim(moldyn,scale,1,1,1);
769 scale_atoms(moldyn,scale,1,1,1);
770 link_cell_shutdown(moldyn);
771 link_cell_init(moldyn,QUIET);
772 potential_force_calc(moldyn);
773 printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
775 printf("dU/dV einfach = %f\n",((moldyn->energy-u)/moldyn->dv)/ATM);
777 /* restore atomic configuration + dim */
778 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
784 link_cell_shutdown(moldyn);
785 link_cell_init(moldyn,QUIET);
790 double get_pressure(t_moldyn *moldyn) {
796 int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
809 int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
814 for(i=0;i<moldyn->count;i++) {
815 r=&(moldyn->atom[i].r);
824 int scale_volume(t_moldyn *moldyn) {
830 vdim=&(moldyn->vis.dim);
835 if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
836 scale=1.0-(moldyn->p_ref-moldyn->p)/moldyn->p_tc;
837 scale=pow(scale,ONE_THIRD);
840 scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
844 /* scale the atoms and dimensions */
845 scale_atoms(moldyn,scale,TRUE,TRUE,TRUE);
846 scale_dim(moldyn,scale,TRUE,TRUE,TRUE);
848 /* visualize dimensions */
855 /* recalculate scaled volume */
856 moldyn->volume=dim->x*dim->y*dim->z;
858 /* adjust/reinit linkcell */
859 if(((int)(dim->x/moldyn->cutoff)!=lc->nx)||
860 ((int)(dim->y/moldyn->cutoff)!=lc->ny)||
861 ((int)(dim->z/moldyn->cutoff)!=lc->nx)) {
862 link_cell_shutdown(moldyn);
863 link_cell_init(moldyn,QUIET);
874 double get_e_kin(t_moldyn *moldyn) {
882 for(i=0;i<moldyn->count;i++)
883 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
888 double update_e_kin(t_moldyn *moldyn) {
890 return(get_e_kin(moldyn));
893 double get_total_energy(t_moldyn *moldyn) {
895 return(moldyn->ekin+moldyn->energy);
898 t_3dvec get_total_p(t_moldyn *moldyn) {
907 for(i=0;i<moldyn->count;i++) {
908 v3_scale(&p,&(atom[i].v),atom[i].mass);
909 v3_add(&p_total,&p_total,&p);
915 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
919 /* nn_dist is the nearest neighbour distance */
921 tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
930 /* linked list / cell method */
932 int link_cell_init(t_moldyn *moldyn,u8 vol) {
939 /* partitioning the md cell */
940 lc->nx=moldyn->dim.x/moldyn->cutoff;
941 lc->x=moldyn->dim.x/lc->nx;
942 lc->ny=moldyn->dim.y/moldyn->cutoff;
943 lc->y=moldyn->dim.y/lc->ny;
944 lc->nz=moldyn->dim.z/moldyn->cutoff;
945 lc->z=moldyn->dim.z/lc->nz;
947 lc->cells=lc->nx*lc->ny*lc->nz;
948 lc->subcell=malloc(lc->cells*sizeof(t_list));
951 printf("[moldyn] FATAL: less then 27 subcells!\n");
953 if(vol) printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
955 for(i=0;i<lc->cells;i++)
956 list_init_f(&(lc->subcell[i]));
958 link_cell_update(moldyn);
963 int link_cell_update(t_moldyn *moldyn) {
981 for(i=0;i<lc->cells;i++)
982 list_destroy_f(&(lc->subcell[i]));
984 for(count=0;count<moldyn->count;count++) {
985 i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
986 j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
987 k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
988 list_add_immediate_f(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
995 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
1013 cell[0]=lc->subcell[i+j*nx+k*a];
1014 for(ci=-1;ci<=1;ci++) {
1017 if((x<0)||(x>=nx)) {
1021 for(cj=-1;cj<=1;cj++) {
1024 if((y<0)||(y>=ny)) {
1028 for(ck=-1;ck<=1;ck++) {
1031 if((z<0)||(z>=nz)) {
1035 if(!(ci|cj|ck)) continue;
1037 cell[--count2]=lc->subcell[x+y*nx+z*a];
1040 cell[count1++]=lc->subcell[x+y*nx+z*a];
1051 int link_cell_shutdown(t_moldyn *moldyn) {
1058 for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
1059 list_destroy_f(&(moldyn->lc.subcell[i]));
1066 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
1070 t_moldyn_schedule *schedule;
1072 schedule=&(moldyn->schedule);
1073 count=++(schedule->total_sched);
1075 ptr=realloc(schedule->runs,count*sizeof(int));
1077 perror("[moldyn] realloc (runs)");
1081 schedule->runs[count-1]=runs;
1083 ptr=realloc(schedule->tau,count*sizeof(double));
1085 perror("[moldyn] realloc (tau)");
1089 schedule->tau[count-1]=tau;
1091 printf("[moldyn] schedule added:\n");
1092 printf(" number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
1098 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
1100 moldyn->schedule.hook=hook;
1101 moldyn->schedule.hook_params=hook_params;
1108 * 'integration of newtons equation' - algorithms
1112 /* start the integration */
1114 int moldyn_integrate(t_moldyn *moldyn) {
1117 unsigned int e,m,s,v;
1119 t_moldyn_schedule *sched;
1124 double energy_scale;
1126 sched=&(moldyn->schedule);
1129 /* initialize linked cell method */
1130 link_cell_init(moldyn,VERBOSE);
1132 /* logging & visualization */
1138 /* sqaure of some variables */
1139 moldyn->tau_square=moldyn->tau*moldyn->tau;
1140 moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
1142 /* energy scaling factor */
1143 energy_scale=moldyn->count*EV;
1145 /* calculate initial forces */
1146 potential_force_calc(moldyn);
1148 /* some stupid checks before we actually start calculating bullshit */
1149 if(moldyn->cutoff>0.5*moldyn->dim.x)
1150 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
1151 if(moldyn->cutoff>0.5*moldyn->dim.y)
1152 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
1153 if(moldyn->cutoff>0.5*moldyn->dim.z)
1154 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
1155 ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
1156 if(ds>0.05*moldyn->nnd)
1157 printf("[moldyn] warning: forces too high / tau too small!\n");
1159 /* zero absolute time */
1162 /* debugging, ignore */
1165 /* tell the world */
1166 printf("[moldyn] integration start, go get a coffee ...\n");
1168 /* executing the schedule */
1169 for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
1171 /* setting amount of runs and finite time step size */
1172 moldyn->tau=sched->tau[sched->count];
1173 moldyn->tau_square=moldyn->tau*moldyn->tau;
1174 moldyn->time_steps=sched->runs[sched->count];
1176 /* integration according to schedule */
1178 for(i=0;i<moldyn->time_steps;i++) {
1180 /* integration step */
1181 moldyn->integrate(moldyn);
1183 /* calculate kinetic energy, temperature and pressure */
1184 update_e_kin(moldyn);
1185 temperature_calc(moldyn);
1186 pressure_calc(moldyn);
1187 //thermodynamic_pressure_calc(moldyn);
1190 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
1191 scale_velocity(moldyn,FALSE);
1192 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
1193 scale_volume(moldyn);
1195 /* check for log & visualization */
1198 dprintf(moldyn->efd,
1200 moldyn->time,moldyn->ekin/energy_scale,
1201 moldyn->energy/energy_scale,
1202 get_total_energy(moldyn)/energy_scale);
1206 p=get_total_p(moldyn);
1207 dprintf(moldyn->mfd,
1208 "%f %f\n",moldyn->time,v3_norm(&p));
1213 snprintf(dir,128,"%s/s-%07.f.save",
1214 moldyn->vlsdir,moldyn->time);
1215 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
1216 if(fd<0) perror("[moldyn] save fd open");
1218 write(fd,moldyn,sizeof(t_moldyn));
1219 write(fd,moldyn->atom,
1220 moldyn->count*sizeof(t_atom));
1227 visual_atoms(&(moldyn->vis),moldyn->time,
1228 moldyn->atom,moldyn->count);
1229 printf("\rsched: %d, steps: %d, T: %f, P: %f V: %f",
1231 moldyn->t,moldyn->p/ATM,moldyn->volume);
1236 /* increase absolute time */
1237 moldyn->time+=moldyn->tau;
1241 /* check for hooks */
1243 sched->hook(moldyn,sched->hook_params);
1245 /* get a new info line */
1253 /* velocity verlet */
1255 int velocity_verlet(t_moldyn *moldyn) {
1258 double tau,tau_square,h;
1263 count=moldyn->count;
1265 tau_square=moldyn->tau_square;
1267 for(i=0;i<count;i++) {
1270 v3_scale(&delta,&(atom[i].v),tau);
1271 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1272 v3_scale(&delta,&(atom[i].f),h*tau_square);
1273 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1274 check_per_bound(moldyn,&(atom[i].r));
1276 /* velocities [actually v(t+tau/2)] */
1277 v3_scale(&delta,&(atom[i].f),h*tau);
1278 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1281 /* neighbour list update */
1282 link_cell_update(moldyn);
1284 /* forces depending on chosen potential */
1285 potential_force_calc(moldyn);
1287 for(i=0;i<count;i++) {
1288 /* again velocities [actually v(t+tau)] */
1289 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
1290 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1299 * potentials & corresponding forces & virial routine
1303 /* generic potential and force calculation */
1305 int potential_force_calc(t_moldyn *moldyn) {
1308 t_atom *itom,*jtom,*ktom;
1311 t_list neighbour_i[27];
1312 t_list neighbour_i2[27];
1317 count=moldyn->count;
1324 /* reset force, site energy and virial of every atom */
1325 for(i=0;i<count;i++) {
1328 v3_zero(&(itom[i].f));
1331 virial=(&(itom[i].virial));
1339 /* reset site energy */
1344 /* get energy,force and virial of every atom */
1345 for(i=0;i<count;i++) {
1347 /* single particle potential/force */
1348 if(itom[i].attr&ATOM_ATTR_1BP)
1349 moldyn->func1b(moldyn,&(itom[i]));
1351 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
1354 /* 2 body pair potential/force */
1356 link_cell_neighbour_index(moldyn,
1357 (itom[i].r.x+moldyn->dim.x/2)/lc->x,
1358 (itom[i].r.y+moldyn->dim.y/2)/lc->y,
1359 (itom[i].r.z+moldyn->dim.z/2)/lc->z,
1366 this=&(neighbour_i[j]);
1369 if(this->start==NULL)
1375 jtom=this->current->data;
1377 if(jtom==&(itom[i]))
1380 if((jtom->attr&ATOM_ATTR_2BP)&
1381 (itom[i].attr&ATOM_ATTR_2BP)) {
1382 moldyn->func2b(moldyn,
1388 /* 3 body potential/force */
1390 if(!(itom[i].attr&ATOM_ATTR_3BP)||
1391 !(jtom->attr&ATOM_ATTR_3BP))
1394 /* copy the neighbour lists */
1395 memcpy(neighbour_i2,neighbour_i,
1398 /* get neighbours of i */
1401 that=&(neighbour_i2[k]);
1404 if(that->start==NULL)
1411 ktom=that->current->data;
1413 if(!(ktom->attr&ATOM_ATTR_3BP))
1419 if(ktom==&(itom[i]))
1422 moldyn->func3b(moldyn,
1428 } while(list_next_f(that)!=\
1433 /* 2bp post function */
1434 if(moldyn->func2b_post) {
1435 moldyn->func2b_post(moldyn,
1440 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1457 * virial calculation
1460 inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1462 a->virial.xx+=f->x*d->x;
1463 a->virial.yy+=f->y*d->y;
1464 a->virial.zz+=f->z*d->z;
1465 a->virial.xy+=f->x*d->y;
1466 a->virial.xz+=f->x*d->z;
1467 a->virial.yz+=f->y*d->z;
1473 * periodic boundayr checking
1476 inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1487 if(moldyn->status&MOLDYN_STAT_PBX) {
1488 if(a->x>=x) a->x-=dim->x;
1489 else if(-a->x>x) a->x+=dim->x;
1491 if(moldyn->status&MOLDYN_STAT_PBY) {
1492 if(a->y>=y) a->y-=dim->y;
1493 else if(-a->y>y) a->y+=dim->y;
1495 if(moldyn->status&MOLDYN_STAT_PBZ) {
1496 if(a->z>=z) a->z-=dim->z;
1497 else if(-a->z>z) a->z+=dim->z;
1505 * example potentials
1508 /* harmonic oscillator potential and force */
1510 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1512 t_ho_params *params;
1513 t_3dvec force,distance;
1515 double sc,equi_dist;
1517 params=moldyn->pot2b_params;
1518 sc=params->spring_constant;
1519 equi_dist=params->equilibrium_distance;
1523 v3_sub(&distance,&(aj->r),&(ai->r));
1525 if(bc) check_per_bound(moldyn,&distance);
1526 d=v3_norm(&distance);
1527 if(d<=moldyn->cutoff) {
1528 moldyn->energy+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
1529 /* f = -grad E; grad r_ij = -1 1/r_ij distance */
1530 f=sc*(1.0-equi_dist/d);
1531 v3_scale(&force,&distance,f);
1532 v3_add(&(ai->f),&(ai->f),&force);
1533 virial_calc(ai,&force,&distance);
1534 virial_calc(aj,&force,&distance); /* f and d signe switched */
1535 v3_scale(&force,&distance,-f);
1536 v3_add(&(aj->f),&(aj->f),&force);
1542 /* lennard jones potential & force for one sort of atoms */
1544 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1546 t_lj_params *params;
1547 t_3dvec force,distance;
1549 double eps,sig6,sig12;
1551 params=moldyn->pot2b_params;
1552 eps=params->epsilon4;
1553 sig6=params->sigma6;
1554 sig12=params->sigma12;
1558 v3_sub(&distance,&(aj->r),&(ai->r));
1559 if(bc) check_per_bound(moldyn,&distance);
1560 d=v3_absolute_square(&distance); /* 1/r^2 */
1561 if(d<=moldyn->cutoff_square) {
1562 d=1.0/d; /* 1/r^2 */
1565 h1=h2*h2; /* 1/r^12 */
1566 moldyn->energy+=(eps*(sig12*h1-sig6*h2)-params->uc);
1573 v3_scale(&force,&distance,d);
1574 v3_add(&(aj->f),&(aj->f),&force);
1575 v3_scale(&force,&force,-1.0); /* f = - grad E */
1576 v3_add(&(ai->f),&(ai->f),&force);
1577 virial_calc(ai,&force,&distance);
1578 virial_calc(aj,&force,&distance); /* f and d signe switched */
1585 * tersoff potential & force for 2 sorts of atoms
1588 /* create mixed terms from parameters and set them */
1589 int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
1591 printf("[moldyn] tersoff parameter completion\n");
1592 p->S2[0]=p->S[0]*p->S[0];
1593 p->S2[1]=p->S[1]*p->S[1];
1594 p->Smixed=sqrt(p->S[0]*p->S[1]);
1595 p->S2mixed=p->Smixed*p->Smixed;
1596 p->Rmixed=sqrt(p->R[0]*p->R[1]);
1597 p->Amixed=sqrt(p->A[0]*p->A[1]);
1598 p->Bmixed=sqrt(p->B[0]*p->B[1]);
1599 p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
1600 p->mu_m=0.5*(p->mu[0]+p->mu[1]);
1602 printf("[moldyn] tersoff mult parameter info:\n");
1603 printf(" S (A) | %f | %f | %f\n",p->S[0],p->S[1],p->Smixed);
1604 printf(" R (A) | %f | %f | %f\n",p->R[0],p->R[1],p->Rmixed);
1605 printf(" A (eV) | %f | %f | %f\n",p->A[0]/EV,p->A[1]/EV,p->Amixed/EV);
1606 printf(" B (eV) | %f | %f | %f\n",p->B[0]/EV,p->B[1]/EV,p->Bmixed/EV);
1607 printf(" lambda | %f | %f | %f\n",p->lambda[0],p->lambda[1],
1609 printf(" mu | %f | %f | %f\n",p->mu[0],p->mu[1],p->mu_m);
1610 printf(" beta | %.10f | %.10f\n",p->beta[0],p->beta[1]);
1611 printf(" n | %f | %f\n",p->n[0],p->n[1]);
1612 printf(" c | %f | %f\n",p->c[0],p->c[1]);
1613 printf(" d | %f | %f\n",p->d[0],p->d[1]);
1614 printf(" h | %f | %f\n",p->h[0],p->h[1]);
1615 printf(" chi | %f \n",p->chi);
1620 /* tersoff 1 body part */
1621 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
1624 t_tersoff_mult_params *params;
1625 t_tersoff_exchange *exchange;
1628 params=moldyn->pot1b_params;
1629 exchange=&(params->exchange);
1632 * simple: point constant parameters only depending on atom i to
1633 * their right values
1636 exchange->beta_i=&(params->beta[brand]);
1637 exchange->n_i=&(params->n[brand]);
1638 exchange->c_i=&(params->c[brand]);
1639 exchange->d_i=&(params->d[brand]);
1640 exchange->h_i=&(params->h[brand]);
1642 exchange->betaini=pow(*(exchange->beta_i),*(exchange->n_i));
1643 exchange->ci2=params->c[brand]*params->c[brand];
1644 exchange->di2=params->d[brand]*params->d[brand];
1645 exchange->ci2di2=exchange->ci2/exchange->di2;
1650 /* tersoff 2 body part */
1651 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1653 t_tersoff_mult_params *params;
1654 t_tersoff_exchange *exchange;
1655 t_3dvec dist_ij,force;
1657 double A,B,R,S,S2,lambda,mu;
1664 params=moldyn->pot2b_params;
1666 exchange=&(params->exchange);
1668 /* clear 3bp and 2bp post run */
1670 exchange->run2bp_post=0;
1672 /* reset S > r > R mark */
1673 exchange->d_ij_between_rs=0;
1676 * calc of 2bp contribution of V_ij and dV_ij/ji
1678 * for Vij and dV_ij we need:
1682 * for dV_ji we need:
1683 * - f_c_ji = f_c_ij, df_c_ji = df_c_ij
1684 * - f_r_ji = f_r_ij; df_r_ji = df_r_ij
1689 if(brand==ai->brand) {
1691 S2=params->S2[brand];
1695 lambda=params->lambda[brand];
1696 mu=params->mu[brand];
1705 lambda=params->lambda_m;
1707 params->exchange.chi=params->chi;
1711 v3_sub(&dist_ij,&(aj->r),&(ai->r));
1712 if(bc) check_per_bound(moldyn,&dist_ij);
1713 d_ij2=v3_absolute_square(&dist_ij);
1715 /* if d_ij2 > S2 => no force & potential energy contribution */
1719 /* now we will need the distance */
1720 //d_ij=v3_norm(&dist_ij);
1723 /* save for use in 3bp */
1724 exchange->d_ij=d_ij;
1725 exchange->d_ij2=d_ij2;
1726 exchange->dist_ij=dist_ij;
1728 /* more constants */
1729 exchange->beta_j=&(params->beta[brand]);
1730 exchange->n_j=&(params->n[brand]);
1731 exchange->c_j=&(params->c[brand]);
1732 exchange->d_j=&(params->d[brand]);
1733 exchange->h_j=&(params->h[brand]);
1734 if(brand==ai->brand) {
1735 exchange->betajnj=exchange->betaini;
1736 exchange->cj2=exchange->ci2;
1737 exchange->dj2=exchange->di2;
1738 exchange->cj2dj2=exchange->ci2di2;
1741 exchange->betajnj=pow(*(exchange->beta_j),*(exchange->n_j));
1742 exchange->cj2=params->c[brand]*params->c[brand];
1743 exchange->dj2=params->d[brand]*params->d[brand];
1744 exchange->cj2dj2=exchange->cj2/exchange->dj2;
1747 /* f_r_ij = f_r_ji, df_r_ij = df_r_ji */
1748 f_r=A*exp(-lambda*d_ij);
1749 df_r=lambda*f_r/d_ij;
1751 /* f_a, df_a calc (again, same for ij and ji) | save for later use! */
1752 exchange->f_a=-B*exp(-mu*d_ij);
1753 exchange->df_a=mu*exchange->f_a/d_ij;
1755 /* f_c, df_c calc (again, same for ij and ji) */
1757 /* f_c = 1, df_c = 0 */
1760 /* two body contribution (ij, ji) */
1761 v3_scale(&force,&dist_ij,-df_r);
1765 arg=M_PI*(d_ij-R)/s_r;
1766 f_c=0.5+0.5*cos(arg);
1767 df_c=0.5*sin(arg)*(M_PI/(s_r*d_ij));
1768 /* two body contribution (ij, ji) */
1769 v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
1770 /* tell 3bp that S > r > R */
1771 exchange->d_ij_between_rs=1;
1774 /* add forces of 2bp (ij, ji) contribution
1775 * dVij = dVji and we sum up both: no 1/2) */
1776 v3_add(&(ai->f),&(ai->f),&force);
1779 ai->virial.xx-=force.x*dist_ij.x;
1780 ai->virial.yy-=force.y*dist_ij.y;
1781 ai->virial.zz-=force.z*dist_ij.z;
1782 ai->virial.xy-=force.x*dist_ij.y;
1783 ai->virial.xz-=force.x*dist_ij.z;
1784 ai->virial.yz-=force.y*dist_ij.z;
1787 if(ai==&(moldyn->atom[0])) {
1788 printf("dVij, dVji (2bp) contrib:\n");
1789 printf("%f | %f\n",force.x,ai->f.x);
1790 printf("%f | %f\n",force.y,ai->f.y);
1791 printf("%f | %f\n",force.z,ai->f.z);
1795 if(ai==&(moldyn->atom[0])) {
1796 printf("dVij, dVji (2bp) contrib:\n");
1797 printf("%f | %f\n",force.x*dist_ij.x,ai->virial.xx);
1798 printf("%f | %f\n",force.y*dist_ij.y,ai->virial.yy);
1799 printf("%f | %f\n",force.z*dist_ij.z,ai->virial.zz);
1803 /* energy 2bp contribution (ij, ji) is 0.5 f_r f_c ... */
1804 moldyn->energy+=(0.5*f_r*f_c);
1806 /* save for use in 3bp */
1808 exchange->df_c=df_c;
1810 /* enable the run of 3bp function and 2bp post processing */
1812 exchange->run2bp_post=1;
1814 /* reset 3bp sums */
1815 exchange->zeta_ij=0.0;
1816 exchange->zeta_ji=0.0;
1817 v3_zero(&(exchange->dzeta_ij));
1818 v3_zero(&(exchange->dzeta_ji));
1823 /* tersoff 2 body post part */
1825 int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1828 * here we have to allow for the 3bp sums
1831 * - zeta_ij, dzeta_ij
1832 * - zeta_ji, dzeta_ji
1834 * to compute the 3bp contribution to:
1840 t_tersoff_mult_params *params;
1841 t_tersoff_exchange *exchange;
1846 double f_c,df_c,f_a,df_a;
1847 double chi,ni,betaini,nj,betajnj;
1850 params=moldyn->pot2b_params;
1851 exchange=&(params->exchange);
1853 /* we do not run if f_c_ij was detected to be 0! */
1854 if(!(exchange->run2bp_post))
1858 df_c=exchange->df_c;
1860 df_a=exchange->df_a;
1861 betaini=exchange->betaini;
1862 betajnj=exchange->betajnj;
1863 ni=*(exchange->n_i);
1864 nj=*(exchange->n_j);
1866 dist_ij=&(exchange->dist_ij);
1869 zeta=exchange->zeta_ij;
1871 moldyn->debug++; /* just for debugging ... */
1873 v3_scale(&force,dist_ij,df_a*b*f_c);
1876 tmp=betaini*pow(zeta,ni-1.0); /* beta^n * zeta^n-1 */
1877 b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
1878 db=chi*pow(b,-1.0/(2*ni)-1); /* x(...)^(-1/2n - 1) */
1880 db*=-0.5*tmp; /* db_ij */
1881 v3_scale(&force,&(exchange->dzeta_ij),f_a*db);
1882 v3_scale(&temp,dist_ij,df_a*b);
1883 v3_add(&force,&force,&temp);
1884 v3_scale(&force,&force,f_c);
1886 v3_scale(&temp,dist_ij,df_c*b*f_a);
1887 v3_add(&force,&force,&temp);
1888 v3_scale(&force,&force,-0.5);
1891 v3_add(&(ai->f),&(ai->f),&force);
1894 ai->virial.xx-=force.x*dist_ij->x;
1895 ai->virial.yy-=force.y*dist_ij->y;
1896 ai->virial.zz-=force.z*dist_ij->z;
1897 ai->virial.xy-=force.x*dist_ij->y;
1898 ai->virial.xz-=force.x*dist_ij->z;
1899 ai->virial.yz-=force.y*dist_ij->z;
1902 if(ai==&(moldyn->atom[0])) {
1903 printf("dVij (3bp) contrib:\n");
1904 printf("%f | %f\n",force.x,ai->f.x);
1905 printf("%f | %f\n",force.y,ai->f.y);
1906 printf("%f | %f\n",force.z,ai->f.z);
1910 if(ai==&(moldyn->atom[0])) {
1911 printf("dVij (3bp) contrib:\n");
1912 printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
1913 printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
1914 printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
1918 /* add energy of 3bp sum */
1919 moldyn->energy+=(0.5*f_c*b*f_a);
1922 zeta=exchange->zeta_ji;
1926 v3_scale(&force,dist_ij,df_a*b*f_c);
1929 tmp=betajnj*pow(zeta,nj-1.0); /* beta^n * zeta^n-1 */
1930 b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
1931 db=chi*pow(b,-1.0/(2*nj)-1); /* x(...)^(-1/2n - 1) */
1933 db*=-0.5*tmp; /* db_ij */
1934 v3_scale(&force,&(exchange->dzeta_ji),f_a*db);
1935 v3_scale(&temp,dist_ij,df_a*b);
1936 v3_add(&force,&force,&temp);
1937 v3_scale(&force,&force,f_c);
1939 v3_scale(&temp,dist_ij,df_c*b*f_a);
1940 v3_add(&force,&force,&temp);
1941 v3_scale(&force,&force,-0.5);
1944 v3_add(&(ai->f),&(ai->f),&force);
1946 /* virial - plus sign, as dist_ij = - dist_ji - (really??) */
1947 // TEST ... with a minus instead
1948 ai->virial.xx-=force.x*dist_ij->x;
1949 ai->virial.yy-=force.y*dist_ij->y;
1950 ai->virial.zz-=force.z*dist_ij->z;
1951 ai->virial.xy-=force.x*dist_ij->y;
1952 ai->virial.xz-=force.x*dist_ij->z;
1953 ai->virial.yz-=force.y*dist_ij->z;
1956 if(ai==&(moldyn->atom[0])) {
1957 printf("dVji (3bp) contrib:\n");
1958 printf("%f | %f\n",force.x,ai->f.x);
1959 printf("%f | %f\n",force.y,ai->f.y);
1960 printf("%f | %f\n",force.z,ai->f.z);
1964 if(ai==&(moldyn->atom[0])) {
1965 printf("dVji (3bp) contrib:\n");
1966 printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
1967 printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
1968 printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
1975 /* tersoff 3 body part */
1977 int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
1979 t_tersoff_mult_params *params;
1980 t_tersoff_exchange *exchange;
1981 t_3dvec dist_ij,dist_ik,dist_jk;
1982 t_3dvec temp1,temp2;
1986 double d_ij,d_ik,d_jk,d_ij2,d_ik2,d_jk2;
1989 double f_c_ik,df_c_ik,arg;
1993 double cos_theta,d_costheta1,d_costheta2;
1994 double h_cos,d2_h_cos2;
1995 double frac,g,zeta,chi;
1999 params=moldyn->pot3b_params;
2000 exchange=&(params->exchange);
2002 if(!(exchange->run3bp))
2006 * calc of 3bp contribution of V_ij and dV_ij/ji/jk &
2007 * 2bp contribution of dV_jk
2009 * for Vij and dV_ij we still need:
2010 * - b_ij, db_ij (zeta_ij)
2011 * - f_c_ik, df_c_ik, constants_i, cos_theta_ijk, d_costheta_ijk
2013 * for dV_ji we still need:
2014 * - b_ji, db_ji (zeta_ji)
2015 * - f_c_jk, d_c_jk, constants_j, cos_theta_jik, d_costheta_jik
2017 * for dV_jk we need:
2021 * - f_c_ji, df_c_ji, constants_j, cos_theta_jki, d_costheta_jki
2029 /* dist_ij, d_ij - this is < S_ij ! */
2030 dist_ij=exchange->dist_ij;
2031 d_ij=exchange->d_ij;
2032 d_ij2=exchange->d_ij2;
2034 /* f_c_ij, df_c_ij (same for ji) */
2036 df_c=exchange->df_c;
2039 * calculate unknown values now ...
2042 /* V_ij and dV_ij stuff (in b_ij there is f_c_ik) */
2045 v3_sub(&dist_ik,&(ak->r),&(ai->r));
2046 if(bc) check_per_bound(moldyn,&dist_ik);
2047 d_ik2=v3_absolute_square(&dist_ik);
2051 if(brand==ak->brand) {
2054 S2=params->S2[brand];
2062 /* zeta_ij/dzeta_ij contribution only for d_ik < S */
2065 /* now we need d_ik */
2068 /* get constants_i from exchange data */
2075 c2d2=exchange->ci2di2;
2077 /* cosine of theta_ijk by scalaproduct */
2078 rr=v3_scalar_product(&dist_ij,&dist_ik);
2084 d_costheta1=cos_theta/d_ij2-tmp;
2085 d_costheta2=cos_theta/d_ik2-tmp;
2087 /* some usefull values */
2088 h_cos=(h-cos_theta);
2089 d2_h_cos2=d2+(h_cos*h_cos);
2090 frac=c2/(d2_h_cos2);
2095 /* d_costheta_ij and dg(cos_theta) - needed in any case! */
2096 v3_scale(&temp1,&dist_ij,d_costheta1);
2097 v3_scale(&temp2,&dist_ik,d_costheta2);
2098 v3_add(&temp1,&temp1,&temp2);
2099 v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
2101 /* f_c_ik & df_c_ik + {d,}zeta contribution */
2102 dzeta=&(exchange->dzeta_ij);
2106 // => df_c_ik=0.0; of course we do not set this!
2109 exchange->zeta_ij+=g;
2112 v3_add(dzeta,dzeta,&temp1);
2117 arg=M_PI*(d_ik-R)/s_r;
2118 f_c_ik=0.5+0.5*cos(arg);
2119 df_c_ik=0.5*sin(arg)*(M_PI/(s_r*d_ik));
2122 exchange->zeta_ij+=f_c_ik*g;
2125 v3_scale(&temp1,&temp1,f_c_ik);
2126 v3_scale(&temp2,&dist_ik,g*df_c_ik);
2127 v3_add(&temp1,&temp1,&temp2);
2128 v3_add(dzeta,dzeta,&temp1);
2132 /* dV_ji stuff (in b_ji there is f_c_jk) + dV_jk stuff! */
2135 v3_sub(&dist_jk,&(ak->r),&(aj->r));
2136 if(bc) check_per_bound(moldyn,&dist_jk);
2137 d_jk2=v3_absolute_square(&dist_jk);
2141 if(brand==ak->brand) {
2144 S2=params->S2[brand];
2146 mu=params->mu[brand];
2158 /* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */
2161 /* now we need d_ik */
2164 /* constants_j from exchange data */
2171 c2d2=exchange->cj2dj2;
2173 /* cosine of theta_jik by scalaproduct */
2174 rr=-v3_scalar_product(&dist_ij,&dist_jk); /* -1, as ij -> ji */
2180 d_costheta2=cos_theta/d_ij2;
2182 /* some usefull values */
2183 h_cos=(h-cos_theta);
2184 d2_h_cos2=d2+(h_cos*h_cos);
2185 frac=c2/(d2_h_cos2);
2190 /* d_costheta_jik and dg(cos_theta) - needed in any case! */
2191 v3_scale(&temp1,&dist_jk,d_costheta1);
2192 v3_scale(&temp2,&dist_ij,-d_costheta2); /* ji -> ij => -1 */
2193 //v3_add(&temp1,&temp1,&temp2);
2194 v3_sub(&temp1,&temp1,&temp2); /* there is a minus! */
2195 v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
2197 /* store dg in temp2 and use it for dVjk later */
2198 v3_copy(&temp2,&temp1);
2200 /* f_c_jk + {d,}zeta contribution (df_c_jk = 0) */
2201 dzeta=&(exchange->dzeta_ji);
2207 exchange->zeta_ji+=g;
2210 v3_add(dzeta,dzeta,&temp1);
2215 arg=M_PI*(d_jk-R)/s_r;
2216 f_c_jk=0.5+0.5*cos(arg);
2219 exchange->zeta_ji+=f_c_jk*g;
2222 v3_scale(&temp1,&temp1,f_c_jk);
2223 v3_add(dzeta,dzeta,&temp1);
2226 /* dV_jk stuff | add force contribution on atom i immediately */
2227 if(exchange->d_ij_between_rs) {
2229 v3_scale(&temp1,&temp2,f_c);
2230 v3_scale(&temp2,&dist_ij,df_c*g);
2231 v3_add(&temp2,&temp2,&temp1); /* -> dzeta_jk in temp2 */
2235 // dzeta_jk is simply dg, which is stored in temp2
2237 /* betajnj * zeta_jk ^ nj-1 */
2238 tmp=exchange->betajnj*pow(zeta,(n-1.0));
2239 tmp=-chi/2.0*pow((1+tmp*zeta),(-1.0/(2.0*n)-1))*tmp;
2240 v3_scale(&temp2,&temp2,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
2241 v3_add(&(ai->f),&(ai->f),&temp2); /* -1 skipped in f_a calc ^ */
2242 /* scaled with 0.5 ^ */
2245 ai->virial.xx-=temp2.x*dist_jk.x;
2246 ai->virial.yy-=temp2.y*dist_jk.y;
2247 ai->virial.zz-=temp2.z*dist_jk.z;
2248 ai->virial.xy-=temp2.x*dist_jk.y;
2249 ai->virial.xz-=temp2.x*dist_jk.z;
2250 ai->virial.yz-=temp2.y*dist_jk.z;
2253 if(ai==&(moldyn->atom[0])) {
2254 printf("dVjk (3bp) contrib:\n");
2255 printf("%f | %f\n",temp2.x,ai->f.x);
2256 printf("%f | %f\n",temp2.y,ai->f.y);
2257 printf("%f | %f\n",temp2.z,ai->f.z);
2261 if(ai==&(moldyn->atom[0])) {
2262 printf("dVjk (3bp) contrib:\n");
2263 printf("%f | %f\n",temp2.x*dist_jk.x,ai->virial.xx);
2264 printf("%f | %f\n",temp2.y*dist_jk.y,ai->virial.yy);
2265 printf("%f | %f\n",temp2.z*dist_jk.z,ai->virial.zz);
2276 * debugging / critical check functions
2279 int moldyn_bc_check(t_moldyn *moldyn) {
2292 for(i=0;i<moldyn->count;i++) {
2293 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
2294 printf("FATAL: atom %d: x: %.20f (%.20f)\n",
2295 i,atom[i].r.x,dim->x/2);
2296 printf("diagnostic:\n");
2297 printf("-----------\natom.r.x:\n");
2299 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
2302 ((byte)&(1<<k))?1:0,
2305 printf("---------------\nx=dim.x/2:\n");
2307 memcpy(&byte,(u8 *)(&x)+j,1);
2310 ((byte)&(1<<k))?1:0,
2313 if(atom[i].r.x==x) printf("the same!\n");
2314 else printf("different!\n");
2316 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
2317 printf("FATAL: atom %d: y: %.20f (%.20f)\n",
2318 i,atom[i].r.y,dim->y/2);
2319 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
2320 printf("FATAL: atom %d: z: %.20f (%.20f)\n",
2321 i,atom[i].r.z,dim->z/2);