2 * moldyn.c - molecular dynamics library main file
4 * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
12 #include <sys/types.h>
19 #include "report/report.h"
21 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
23 printf("[moldyn] init\n");
25 memset(moldyn,0,sizeof(t_moldyn));
27 rand_init(&(moldyn->random),NULL,1);
28 moldyn->random.status|=RAND_STAT_VERBOSE;
33 int moldyn_shutdown(t_moldyn *moldyn) {
35 printf("[moldyn] shutdown\n");
37 moldyn_log_shutdown(moldyn);
38 link_cell_shutdown(moldyn);
39 rand_close(&(moldyn->random));
45 int set_int_alg(t_moldyn *moldyn,u8 algo) {
47 printf("[moldyn] integration algorithm: ");
50 case MOLDYN_INTEGRATE_VERLET:
51 moldyn->integrate=velocity_verlet;
52 printf("velocity verlet\n");
55 printf("unknown integration algorithm: %02x\n",algo);
63 int set_cutoff(t_moldyn *moldyn,double cutoff) {
65 moldyn->cutoff=cutoff;
67 printf("[moldyn] cutoff [A]: %f\n",moldyn->cutoff);
72 int set_temperature(t_moldyn *moldyn,double t_ref) {
76 printf("[moldyn] temperature [K]: %f\n",moldyn->t_ref);
81 int set_pressure(t_moldyn *moldyn,double p_ref) {
85 printf("[moldyn] pressure [bar]: %f\n",moldyn->p_ref/BAR);
90 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
92 moldyn->pt_scale=(ptype|ttype);
96 printf("[moldyn] p/t scaling:\n");
98 printf(" p: %s",ptype?"yes":"no ");
100 printf(" | type: %02x | factor: %f",ptype,ptc);
103 printf(" t: %s",ttype?"yes":"no ");
105 printf(" | type: %02x | factor: %f",ttype,ttc);
111 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
117 moldyn->volume=x*y*z;
125 moldyn->dv=0.000001*moldyn->volume;
127 printf("[moldyn] dimensions in A and A^3 respectively:\n");
128 printf(" x: %f\n",moldyn->dim.x);
129 printf(" y: %f\n",moldyn->dim.y);
130 printf(" z: %f\n",moldyn->dim.z);
131 printf(" volume: %f\n",moldyn->volume);
132 printf(" visualize simulation box: %s\n",visualize?"yes":"no");
133 printf(" delta volume (pressure calc): %f\n",moldyn->dv);
138 int set_nn_dist(t_moldyn *moldyn,double dist) {
145 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
147 printf("[moldyn] periodic boundary conditions:\n");
150 moldyn->status|=MOLDYN_STAT_PBX;
153 moldyn->status|=MOLDYN_STAT_PBY;
156 moldyn->status|=MOLDYN_STAT_PBZ;
158 printf(" x: %s\n",x?"yes":"no");
159 printf(" y: %s\n",y?"yes":"no");
160 printf(" z: %s\n",z?"yes":"no");
165 int set_potential1b(t_moldyn *moldyn,pf_func1b func) {
172 int set_potential2b(t_moldyn *moldyn,pf_func2b func) {
179 int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func) {
181 moldyn->func3b_j1=func;
186 int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func) {
188 moldyn->func3b_j2=func;
193 int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func) {
195 moldyn->func3b_j3=func;
200 int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func) {
202 moldyn->func3b_k1=func;
207 int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func) {
209 moldyn->func3b_k2=func;
214 int set_potential_params(t_moldyn *moldyn,void *params) {
216 moldyn->pot_params=params;
221 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
223 strncpy(moldyn->vlsdir,dir,127);
228 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title) {
230 strncpy(moldyn->rauthor,author,63);
231 strncpy(moldyn->rtitle,title,63);
236 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
241 printf("[moldyn] set log: ");
244 case LOG_TOTAL_ENERGY:
245 moldyn->ewrite=timer;
246 snprintf(filename,127,"%s/energy",moldyn->vlsdir);
247 moldyn->efd=open(filename,
248 O_WRONLY|O_CREAT|O_EXCL,
251 perror("[moldyn] energy log fd open");
254 dprintf(moldyn->efd,"# total energy log file\n");
255 printf("total energy (%d)\n",timer);
257 case LOG_TOTAL_MOMENTUM:
258 moldyn->mwrite=timer;
259 snprintf(filename,127,"%s/momentum",moldyn->vlsdir);
260 moldyn->mfd=open(filename,
261 O_WRONLY|O_CREAT|O_EXCL,
264 perror("[moldyn] momentum log fd open");
267 dprintf(moldyn->efd,"# total momentum log file\n");
268 printf("total momentum (%d)\n",timer);
271 moldyn->pwrite=timer;
272 snprintf(filename,127,"%s/pressure",moldyn->vlsdir);
273 moldyn->pfd=open(filename,
274 O_WRONLY|O_CREAT|O_EXCL,
277 perror("[moldyn] pressure log file\n");
280 dprintf(moldyn->pfd,"# pressure log file\n");
281 printf("pressure (%d)\n",timer);
283 case LOG_TEMPERATURE:
284 moldyn->twrite=timer;
285 snprintf(filename,127,"%s/temperature",moldyn->vlsdir);
286 moldyn->tfd=open(filename,
287 O_WRONLY|O_CREAT|O_EXCL,
290 perror("[moldyn] temperature log file\n");
293 dprintf(moldyn->tfd,"# temperature log file\n");
294 printf("temperature (%d)\n",timer);
297 moldyn->swrite=timer;
298 printf("save file (%d)\n",timer);
301 moldyn->vwrite=timer;
302 ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
304 printf("[moldyn] visual init failure\n");
307 printf("visual file (%d)\n",timer);
310 snprintf(filename,127,"%s/report.tex",moldyn->vlsdir);
311 moldyn->rfd=open(filename,
312 O_WRONLY|O_CREAT|O_EXCL,
315 perror("[moldyn] report fd open");
318 printf("report -> ");
320 snprintf(filename,127,"%s/e_plot.scr",
322 moldyn->epfd=open(filename,
323 O_WRONLY|O_CREAT|O_EXCL,
326 perror("[moldyn] energy plot fd open");
329 dprintf(moldyn->epfd,e_plot_script);
334 snprintf(filename,127,"%s/pressure_plot.scr",
336 moldyn->ppfd=open(filename,
337 O_WRONLY|O_CREAT|O_EXCL,
340 perror("[moldyn] p plot fd open");
343 dprintf(moldyn->ppfd,pressure_plot_script);
348 snprintf(filename,127,"%s/temperature_plot.scr",
350 moldyn->tpfd=open(filename,
351 O_WRONLY|O_CREAT|O_EXCL,
354 perror("[moldyn] t plot fd open");
357 dprintf(moldyn->tpfd,temperature_plot_script);
359 printf("temperature ");
361 dprintf(moldyn->rfd,report_start,
362 moldyn->rauthor,moldyn->rtitle);
366 printf("unknown log type: %02x\n",type);
373 int moldyn_log_shutdown(t_moldyn *moldyn) {
377 printf("[moldyn] log shutdown\n");
381 dprintf(moldyn->rfd,report_energy);
382 snprintf(sc,255,"cd %s && gnuplot e_plot.scr",
387 if(moldyn->mfd) close(moldyn->mfd);
391 dprintf(moldyn->rfd,report_pressure);
392 snprintf(sc,255,"cd %s && gnuplot pressure_plot.scr",
399 dprintf(moldyn->rfd,report_temperature);
400 snprintf(sc,255,"cd %s && gnuplot temperature_plot.scr",
405 dprintf(moldyn->rfd,report_end);
407 snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
409 snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
411 snprintf(sc,255,"cd %s && dvipdf report",moldyn->vlsdir);
414 if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
420 * creating lattice functions
423 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
424 u8 attr,u8 brand,int a,int b,int c) {
435 /* how many atoms do we expect */
436 if(type==CUBIC) new*=1;
437 if(type==FCC) new*=4;
438 if(type==DIAMOND) new*=8;
440 /* allocate space for atoms */
441 ptr=realloc(moldyn->atom,(count+new)*sizeof(t_atom));
443 perror("[moldyn] realloc (create lattice)");
447 atom=&(moldyn->atom[count]);
449 /* no atoms on the boundaries (only reason: it looks better!) */
456 set_nn_dist(moldyn,lc);
457 ret=cubic_init(a,b,c,lc,atom,&origin);
460 v3_scale(&origin,&origin,0.5);
461 set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
462 ret=fcc_init(a,b,c,lc,atom,&origin);
465 v3_scale(&origin,&origin,0.25);
466 set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
467 ret=diamond_init(a,b,c,lc,atom,&origin);
470 printf("unknown lattice type (%02x)\n",type);
476 printf("[moldyn] creating lattice failed\n");
477 printf(" amount of atoms\n");
478 printf(" - expected: %d\n",new);
479 printf(" - created: %d\n",ret);
484 printf("[moldyn] created lattice with %d atoms\n",new);
486 for(ret=0;ret<new;ret++) {
487 atom[ret].element=element;
490 atom[ret].brand=brand;
491 atom[ret].tag=count+ret;
492 check_per_bound(moldyn,&(atom[ret].r));
499 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
518 v3_copy(&(atom[count].r),&r);
527 for(i=0;i<count;i++) {
528 atom[i].r.x-=(a*lc)/2.0;
529 atom[i].r.y-=(b*lc)/2.0;
530 atom[i].r.z-=(c*lc)/2.0;
536 /* fcc lattice init */
537 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
550 /* construct the basis */
551 memset(basis,0,3*sizeof(t_3dvec));
559 /* fill up the room */
567 v3_copy(&(atom[count].r),&r);
570 /* the three face centered atoms */
572 v3_add(&n,&r,&basis[l]);
573 v3_copy(&(atom[count].r),&n);
582 /* coordinate transformation */
583 for(i=0;i<count;i++) {
584 atom[i].r.x-=(a*lc)/2.0;
585 atom[i].r.y-=(b*lc)/2.0;
586 atom[i].r.z-=(c*lc)/2.0;
592 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
597 count=fcc_init(a,b,c,lc,atom,origin);
603 if(origin) v3_add(&o,&o,origin);
605 count+=fcc_init(a,b,c,lc,&atom[count],&o);
610 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
611 t_3dvec *r,t_3dvec *v) {
618 count=(moldyn->count)++;
620 ptr=realloc(atom,(count+1)*sizeof(t_atom));
622 perror("[moldyn] realloc (add atom)");
630 atom[count].element=element;
631 atom[count].mass=mass;
632 atom[count].brand=brand;
633 atom[count].tag=count;
634 atom[count].attr=attr;
639 int destroy_atoms(t_moldyn *moldyn) {
641 if(moldyn->atom) free(moldyn->atom);
646 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
649 * - gaussian distribution of velocities
650 * - zero total momentum
651 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
656 t_3dvec p_total,delta;
661 random=&(moldyn->random);
663 printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
665 /* gaussian distribution of velocities */
667 for(i=0;i<moldyn->count;i++) {
668 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
670 v=sigma*rand_get_gauss(random);
672 p_total.x+=atom[i].mass*v;
674 v=sigma*rand_get_gauss(random);
676 p_total.y+=atom[i].mass*v;
678 v=sigma*rand_get_gauss(random);
680 p_total.z+=atom[i].mass*v;
683 /* zero total momentum */
684 v3_scale(&p_total,&p_total,1.0/moldyn->count);
685 for(i=0;i<moldyn->count;i++) {
686 v3_scale(&delta,&p_total,1.0/atom[i].mass);
687 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
690 /* velocity scaling */
691 scale_velocity(moldyn,equi_init);
696 double temperature_calc(t_moldyn *moldyn) {
698 /* assume up to date kinetic energy, which is 3/2 N k_B T */
700 moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
701 moldyn->t_sum+=moldyn->t;
702 moldyn->mean_t=moldyn->t_sum/moldyn->total_steps;
707 double get_temperature(t_moldyn *moldyn) {
712 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
722 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
725 /* get kinetic energy / temperature & count involved atoms */
728 for(i=0;i<moldyn->count;i++) {
729 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
730 e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
735 if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
736 else return 0; /* no atoms involved in scaling! */
738 /* (temporary) hack for e,t = 0 */
741 if(moldyn->t_ref!=0.0) {
742 thermal_init(moldyn,equi_init);
746 return 0; /* no scaling needed */
750 /* get scaling factor */
751 scale=moldyn->t_ref/moldyn->t;
755 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
756 scale=1.0+(scale-1.0)/moldyn->t_tc;
759 /* velocity scaling */
760 for(i=0;i<moldyn->count;i++) {
761 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
762 v3_scale(&(atom[i].v),&(atom[i].v),scale);
768 double ideal_gas_law_pressure(t_moldyn *moldyn) {
772 p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
777 double pressure_calc(t_moldyn *moldyn) {
785 * W = 1/3 sum_i f_i r_i
786 * virial = sum_i f_i r_i
788 * => P = (2 Ekin + virial) / (3V)
792 for(i=0;i<moldyn->count;i++) {
793 virial=&(moldyn->atom[i].virial);
794 v+=(virial->xx+virial->yy+virial->zz);
797 /* assume up to date kinetic energy */
798 moldyn->p=2.0*moldyn->ekin+v;
799 moldyn->p/=(3.0*moldyn->volume);
800 moldyn->p_sum+=moldyn->p;
801 moldyn->mean_p=moldyn->p_sum/moldyn->total_steps;
803 /* pressure from 'absolute coordinates' virial */
804 virial=&(moldyn->virial);
805 v=virial->xx+virial->yy+virial->zz;
806 moldyn->gp=2.0*moldyn->ekin+v;
807 moldyn->gp/=(3.0*moldyn->volume);
808 moldyn->gp_sum+=moldyn->gp;
809 moldyn->mean_gp=moldyn->gp_sum/moldyn->total_steps;
814 double thermodynamic_pressure_calc(t_moldyn *moldyn) {
826 * dV: dx,y,z = 0.001 x,y,z
829 scale=1.00000000000001;
830 printf("\n\nP-DEBUG:\n");
833 store=malloc(moldyn->count*sizeof(t_atom));
835 printf("[moldyn] allocating store mem failed\n");
839 /* save unscaled potential energy + atom/dim configuration */
841 memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
844 /* derivative with respect to x direction */
845 scale_dim(moldyn,scale,TRUE,0,0);
846 scale_atoms(moldyn,scale,TRUE,0,0);
847 dv=0.00000000000001*moldyn->dim.x*moldyn->dim.y*moldyn->dim.z;
848 link_cell_shutdown(moldyn);
849 link_cell_init(moldyn,QUIET);
850 potential_force_calc(moldyn);
851 tp->x=(moldyn->energy-u)/dv;
854 /* restore atomic configuration + dim */
855 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
858 /* derivative with respect to y direction */
859 scale_dim(moldyn,scale,0,TRUE,0);
860 scale_atoms(moldyn,scale,0,TRUE,0);
861 dv=0.00000000000001*moldyn->dim.y*moldyn->dim.x*moldyn->dim.z;
862 link_cell_shutdown(moldyn);
863 link_cell_init(moldyn,QUIET);
864 potential_force_calc(moldyn);
865 tp->y=(moldyn->energy-u)/dv;
868 /* restore atomic configuration + dim */
869 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
872 /* derivative with respect to z direction */
873 scale_dim(moldyn,scale,0,0,TRUE);
874 scale_atoms(moldyn,scale,0,0,TRUE);
875 dv=0.00000000000001*moldyn->dim.z*moldyn->dim.x*moldyn->dim.y;
876 link_cell_shutdown(moldyn);
877 link_cell_init(moldyn,QUIET);
878 potential_force_calc(moldyn);
879 tp->z=(moldyn->energy-u)/dv;
882 /* restore atomic configuration + dim */
883 memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
889 link_cell_shutdown(moldyn);
890 link_cell_init(moldyn,QUIET);
895 double get_pressure(t_moldyn *moldyn) {
901 int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
914 int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
919 for(i=0;i<moldyn->count;i++) {
920 r=&(moldyn->atom[i].r);
929 int scale_volume(t_moldyn *moldyn) {
935 vdim=&(moldyn->vis.dim);
940 if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
941 scale=1.0-(moldyn->p_ref-moldyn->p)/moldyn->p_tc;
942 scale=pow(scale,ONE_THIRD);
945 scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
949 /* scale the atoms and dimensions */
950 scale_atoms(moldyn,scale,TRUE,TRUE,TRUE);
951 scale_dim(moldyn,scale,TRUE,TRUE,TRUE);
953 /* visualize dimensions */
960 /* recalculate scaled volume */
961 moldyn->volume=dim->x*dim->y*dim->z;
963 /* adjust/reinit linkcell */
964 if(((int)(dim->x/moldyn->cutoff)!=lc->nx)||
965 ((int)(dim->y/moldyn->cutoff)!=lc->ny)||
966 ((int)(dim->z/moldyn->cutoff)!=lc->nx)) {
967 link_cell_shutdown(moldyn);
968 link_cell_init(moldyn,QUIET);
979 double e_kin_calc(t_moldyn *moldyn) {
987 for(i=0;i<moldyn->count;i++)
988 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
993 double get_total_energy(t_moldyn *moldyn) {
995 return(moldyn->ekin+moldyn->energy);
998 t_3dvec get_total_p(t_moldyn *moldyn) {
1007 for(i=0;i<moldyn->count;i++) {
1008 v3_scale(&p,&(atom[i].v),atom[i].mass);
1009 v3_add(&p_total,&p_total,&p);
1015 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
1019 /* nn_dist is the nearest neighbour distance */
1021 tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
1030 /* linked list / cell method */
1032 int link_cell_init(t_moldyn *moldyn,u8 vol) {
1039 /* partitioning the md cell */
1040 lc->nx=moldyn->dim.x/moldyn->cutoff;
1041 lc->x=moldyn->dim.x/lc->nx;
1042 lc->ny=moldyn->dim.y/moldyn->cutoff;
1043 lc->y=moldyn->dim.y/lc->ny;
1044 lc->nz=moldyn->dim.z/moldyn->cutoff;
1045 lc->z=moldyn->dim.z/lc->nz;
1047 lc->cells=lc->nx*lc->ny*lc->nz;
1048 lc->subcell=malloc(lc->cells*sizeof(t_list));
1051 printf("[moldyn] FATAL: less then 27 subcells!\n");
1054 printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
1055 printf(" x: %d x %f A\n",lc->nx,lc->x);
1056 printf(" y: %d x %f A\n",lc->ny,lc->y);
1057 printf(" z: %d x %f A\n",lc->nz,lc->z);
1060 for(i=0;i<lc->cells;i++)
1061 list_init_f(&(lc->subcell[i]));
1063 link_cell_update(moldyn);
1068 int link_cell_update(t_moldyn *moldyn) {
1086 for(i=0;i<lc->cells;i++)
1087 list_destroy_f(&(lc->subcell[i]));
1089 for(count=0;count<moldyn->count;count++) {
1090 i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
1091 j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
1092 k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
1093 list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
1100 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
1118 cell[0]=lc->subcell[i+j*nx+k*a];
1119 for(ci=-1;ci<=1;ci++) {
1122 if((x<0)||(x>=nx)) {
1126 for(cj=-1;cj<=1;cj++) {
1129 if((y<0)||(y>=ny)) {
1133 for(ck=-1;ck<=1;ck++) {
1136 if((z<0)||(z>=nz)) {
1140 if(!(ci|cj|ck)) continue;
1142 cell[--count2]=lc->subcell[x+y*nx+z*a];
1145 cell[count1++]=lc->subcell[x+y*nx+z*a];
1156 int link_cell_shutdown(t_moldyn *moldyn) {
1163 for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
1164 list_destroy_f(&(moldyn->lc.subcell[i]));
1171 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
1175 t_moldyn_schedule *schedule;
1177 schedule=&(moldyn->schedule);
1178 count=++(schedule->total_sched);
1180 ptr=realloc(schedule->runs,count*sizeof(int));
1182 perror("[moldyn] realloc (runs)");
1186 schedule->runs[count-1]=runs;
1188 ptr=realloc(schedule->tau,count*sizeof(double));
1190 perror("[moldyn] realloc (tau)");
1194 schedule->tau[count-1]=tau;
1196 printf("[moldyn] schedule added:\n");
1197 printf(" number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
1203 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
1205 moldyn->schedule.hook=hook;
1206 moldyn->schedule.hook_params=hook_params;
1213 * 'integration of newtons equation' - algorithms
1217 /* start the integration */
1219 int moldyn_integrate(t_moldyn *moldyn) {
1222 unsigned int e,m,s,v,p,t;
1224 t_moldyn_schedule *sched;
1229 double energy_scale;
1232 sched=&(moldyn->schedule);
1235 /* initialize linked cell method */
1236 link_cell_init(moldyn,VERBOSE);
1238 /* logging & visualization */
1246 /* sqaure of some variables */
1247 moldyn->tau_square=moldyn->tau*moldyn->tau;
1248 moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
1250 /* energy scaling factor */
1251 energy_scale=moldyn->count*EV;
1253 /* calculate initial forces */
1254 potential_force_calc(moldyn);
1256 /* some stupid checks before we actually start calculating bullshit */
1257 if(moldyn->cutoff>0.5*moldyn->dim.x)
1258 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
1259 if(moldyn->cutoff>0.5*moldyn->dim.y)
1260 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
1261 if(moldyn->cutoff>0.5*moldyn->dim.z)
1262 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
1263 ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
1264 if(ds>0.05*moldyn->nnd)
1265 printf("[moldyn] warning: forces too high / tau too small!\n");
1267 /* zero absolute time */
1269 moldyn->total_steps=0;
1271 /* debugging, ignore */
1274 /* tell the world */
1275 printf("[moldyn] integration start, go get a coffee ...\n");
1277 /* executing the schedule */
1278 for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
1280 /* setting amount of runs and finite time step size */
1281 moldyn->tau=sched->tau[sched->count];
1282 moldyn->tau_square=moldyn->tau*moldyn->tau;
1283 moldyn->time_steps=sched->runs[sched->count];
1285 /* integration according to schedule */
1287 for(i=0;i<moldyn->time_steps;i++) {
1289 /* integration step */
1290 moldyn->integrate(moldyn);
1292 /* calculate kinetic energy, temperature and pressure */
1294 temperature_calc(moldyn);
1295 pressure_calc(moldyn);
1296 //tp=thermodynamic_pressure_calc(moldyn);
1297 //printf("thermodynamic p: %f %f %f - %f\n",moldyn->tp.x/BAR,moldyn->tp.y/BAR,moldyn->tp.z/BAR,tp/BAR);
1300 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
1301 scale_velocity(moldyn,FALSE);
1302 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
1303 scale_volume(moldyn);
1305 /* check for log & visualization */
1308 dprintf(moldyn->efd,
1310 moldyn->time,moldyn->ekin/energy_scale,
1311 moldyn->energy/energy_scale,
1312 get_total_energy(moldyn)/energy_scale);
1316 momentum=get_total_p(moldyn);
1317 dprintf(moldyn->mfd,
1318 "%f %f %f %f %f\n",moldyn->time,
1319 momentum.x,momentum.y,momentum.z,
1320 v3_norm(&momentum));
1325 dprintf(moldyn->pfd,
1326 "%f %f %f %f %f\n",moldyn->time,
1327 moldyn->p/BAR,moldyn->mean_p/BAR,
1328 moldyn->gp/BAR,moldyn->mean_gp/BAR);
1333 dprintf(moldyn->tfd,
1335 moldyn->time,moldyn->t,moldyn->mean_t);
1340 snprintf(dir,128,"%s/s-%07.f.save",
1341 moldyn->vlsdir,moldyn->time);
1342 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
1343 if(fd<0) perror("[moldyn] save fd open");
1345 write(fd,moldyn,sizeof(t_moldyn));
1346 write(fd,moldyn->atom,
1347 moldyn->count*sizeof(t_atom));
1354 visual_atoms(&(moldyn->vis),moldyn->time,
1355 moldyn->atom,moldyn->count);
1359 /* display progress */
1361 printf("\rsched: %d, steps: %d, T: %f, P: %f %f V: %f",
1365 moldyn->mean_gp/BAR,
1370 /* increase absolute time */
1371 moldyn->time+=moldyn->tau;
1372 moldyn->total_steps+=1;
1376 /* check for hooks */
1378 sched->hook(moldyn,sched->hook_params);
1380 /* get a new info line */
1388 /* velocity verlet */
1390 int velocity_verlet(t_moldyn *moldyn) {
1393 double tau,tau_square,h;
1398 count=moldyn->count;
1400 tau_square=moldyn->tau_square;
1402 for(i=0;i<count;i++) {
1405 v3_scale(&delta,&(atom[i].v),tau);
1406 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1407 v3_scale(&delta,&(atom[i].f),h*tau_square);
1408 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1409 check_per_bound(moldyn,&(atom[i].r));
1411 /* velocities [actually v(t+tau/2)] */
1412 v3_scale(&delta,&(atom[i].f),h*tau);
1413 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1416 /* neighbour list update */
1417 link_cell_update(moldyn);
1419 /* forces depending on chosen potential */
1420 potential_force_calc(moldyn);
1422 for(i=0;i<count;i++) {
1423 /* again velocities [actually v(t+tau)] */
1424 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
1425 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1434 * potentials & corresponding forces & virial routine
1438 /* generic potential and force calculation */
1440 int potential_force_calc(t_moldyn *moldyn) {
1443 t_atom *itom,*jtom,*ktom;
1446 t_list neighbour_i[27];
1447 t_list neighbour_i2[27];
1452 count=moldyn->count;
1459 /* reset global virial */
1460 memset(&(moldyn->virial),0,sizeof(t_virial));
1462 /* reset force, site energy and virial of every atom */
1463 for(i=0;i<count;i++) {
1466 v3_zero(&(itom[i].f));
1469 virial=(&(itom[i].virial));
1477 /* reset site energy */
1482 /* get energy, force and virial of every atom */
1484 /* first (and only) loop over atoms i */
1485 for(i=0;i<count;i++) {
1487 /* single particle potential/force */
1488 if(itom[i].attr&ATOM_ATTR_1BP)
1489 moldyn->func1b(moldyn,&(itom[i]));
1491 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
1494 /* 2 body pair potential/force */
1496 link_cell_neighbour_index(moldyn,
1497 (itom[i].r.x+moldyn->dim.x/2)/lc->x,
1498 (itom[i].r.y+moldyn->dim.y/2)/lc->y,
1499 (itom[i].r.z+moldyn->dim.z/2)/lc->z,
1504 /* first loop over atoms j */
1505 if(moldyn->func2b) {
1508 this=&(neighbour_i[j]);
1511 if(this->start==NULL)
1517 jtom=this->current->data;
1519 if(jtom==&(itom[i]))
1522 if((jtom->attr&ATOM_ATTR_2BP)&
1523 (itom[i].attr&ATOM_ATTR_2BP)) {
1524 moldyn->func2b(moldyn,
1529 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1534 /* 3 body potential/force */
1536 if(!(itom[i].attr&ATOM_ATTR_3BP))
1539 /* copy the neighbour lists */
1540 memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
1542 /* second loop over atoms j */
1545 this=&(neighbour_i[j]);
1548 if(this->start==NULL)
1554 jtom=this->current->data;
1556 if(jtom==&(itom[i]))
1559 if(!(jtom->attr&ATOM_ATTR_3BP))
1565 if(moldyn->func3b_j1)
1566 moldyn->func3b_j1(moldyn,
1571 /* in first j loop, 3bp run can be skipped */
1572 if(!(moldyn->run3bp))
1575 /* first loop over atoms k */
1576 if(moldyn->func3b_k1) {
1580 that=&(neighbour_i2[k]);
1583 if(that->start==NULL)
1590 ktom=that->current->data;
1592 if(!(ktom->attr&ATOM_ATTR_3BP))
1598 if(ktom==&(itom[i]))
1601 moldyn->func3b_k1(moldyn,
1607 } while(list_next_f(that)!=\
1614 if(moldyn->func3b_j2)
1615 moldyn->func3b_j2(moldyn,
1620 /* second loop over atoms k */
1621 if(moldyn->func3b_k2) {
1625 that=&(neighbour_i2[k]);
1628 if(that->start==NULL)
1635 ktom=that->current->data;
1637 if(!(ktom->attr&ATOM_ATTR_3BP))
1643 if(ktom==&(itom[i]))
1646 moldyn->func3b_k2(moldyn,
1652 } while(list_next_f(that)!=\
1659 /* 2bp post function */
1660 if(moldyn->func3b_j3) {
1661 moldyn->func3b_j3(moldyn,
1666 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1680 printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
1683 /* calculate global virial */
1684 for(i=0;i<count;i++) {
1685 moldyn->virial.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
1686 moldyn->virial.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
1687 moldyn->virial.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
1688 moldyn->virial.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
1689 moldyn->virial.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
1690 moldyn->virial.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
1697 * virial calculation
1700 //inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1701 int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1703 a->virial.xx+=f->x*d->x;
1704 a->virial.yy+=f->y*d->y;
1705 a->virial.zz+=f->z*d->z;
1706 a->virial.xy+=f->x*d->y;
1707 a->virial.xz+=f->x*d->z;
1708 a->virial.yz+=f->y*d->z;
1714 * periodic boundary checking
1717 //inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1718 int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1729 if(moldyn->status&MOLDYN_STAT_PBX) {
1730 if(a->x>=x) a->x-=dim->x;
1731 else if(-a->x>x) a->x+=dim->x;
1733 if(moldyn->status&MOLDYN_STAT_PBY) {
1734 if(a->y>=y) a->y-=dim->y;
1735 else if(-a->y>y) a->y+=dim->y;
1737 if(moldyn->status&MOLDYN_STAT_PBZ) {
1738 if(a->z>=z) a->z-=dim->z;
1739 else if(-a->z>z) a->z+=dim->z;
1746 * debugging / critical check functions
1749 int moldyn_bc_check(t_moldyn *moldyn) {
1762 for(i=0;i<moldyn->count;i++) {
1763 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
1764 printf("FATAL: atom %d: x: %.20f (%.20f)\n",
1765 i,atom[i].r.x,dim->x/2);
1766 printf("diagnostic:\n");
1767 printf("-----------\natom.r.x:\n");
1769 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
1772 ((byte)&(1<<k))?1:0,
1775 printf("---------------\nx=dim.x/2:\n");
1777 memcpy(&byte,(u8 *)(&x)+j,1);
1780 ((byte)&(1<<k))?1:0,
1783 if(atom[i].r.x==x) printf("the same!\n");
1784 else printf("different!\n");
1786 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
1787 printf("FATAL: atom %d: y: %.20f (%.20f)\n",
1788 i,atom[i].r.y,dim->y/2);
1789 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
1790 printf("FATAL: atom %d: z: %.20f (%.20f)\n",
1791 i,atom[i].r.z,dim->z/2);