moldyn.c

   1 /*
   2  * moldyn.c - molecular dynamics library main file
   3  *
   4  * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
   5  *
   6  */
   7
   8 #define _GNU_SOURCE
   9 #include <stdio.h>
  10 #include <stdlib.h>
  11 #include <string.h>
  12 #include <sys/types.h>
  13 #include <sys/stat.h>
  14 #include <fcntl.h>
  15 #include <unistd.h>
  16 #include <math.h>
  17
  18 #include "moldyn.h"
  19 #include "report/report.h"
  20
  21 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
  22
  23         printf("[moldyn] init\n");
  24
  25         memset(moldyn,0,sizeof(t_moldyn));
  26
  27         rand_init(&(moldyn->random),NULL,1);
  28         moldyn->random.status|=RAND_STAT_VERBOSE;
  29
  30         return 0;
  31 }
  32
  33 int moldyn_shutdown(t_moldyn *moldyn) {
  34
  35         printf("[moldyn] shutdown\n");
  36
  37         moldyn_log_shutdown(moldyn);
  38         link_cell_shutdown(moldyn);
  39         rand_close(&(moldyn->random));
  40         free(moldyn->atom);
  41
  42         return 0;
  43 }
  44
  45 int set_int_alg(t_moldyn *moldyn,u8 algo) {
  46
  47         printf("[moldyn] integration algorithm: ");
  48
  49         switch(algo) {
  50                 case MOLDYN_INTEGRATE_VERLET:
  51                         moldyn->integrate=velocity_verlet;
  52                         printf("velocity verlet\n");
  53                         break;
  54                 default:
  55                         printf("unknown integration algorithm: %02x\n",algo);
  56                         printf("unknown\n");
  57                         return -1;
  58         }
  59
  60         return 0;
  61 }
  62
  63 int set_cutoff(t_moldyn *moldyn,double cutoff) {
  64
  65         moldyn->cutoff=cutoff;
  66
  67         printf("[moldyn] cutoff [A]: %f\n",moldyn->cutoff);
  68
  69         return 0;
  70 }
  71
  72 int set_temperature(t_moldyn *moldyn,double t_ref) {
  73
  74         moldyn->t_ref=t_ref;
  75
  76         printf("[moldyn] temperature [K]: %f\n",moldyn->t_ref);
  77
  78         return 0;
  79 }
  80
  81 int set_pressure(t_moldyn *moldyn,double p_ref) {
  82
  83         moldyn->p_ref=p_ref;
  84
  85         printf("[moldyn] pressure [atm]: %f\n",moldyn->p_ref/ATM);
  86
  87         return 0;
  88 }
  89
  90 int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
  91
  92         moldyn->pt_scale=(ptype|ttype);
  93         moldyn->t_tc=ttc;
  94         moldyn->p_tc=ptc;
  95
  96         printf("[moldyn] p/t scaling:\n");
  97
  98         printf("  p: %s",ptype?"yes":"no ");
  99         if(ptype)
 100                 printf(" | type: %02x | factor: %f",ptype,ptc);
 101         printf("\n");
 102
 103         printf("  t: %s",ttype?"yes":"no ");
 104         if(ttype)
 105                 printf(" | type: %02x | factor: %f",ttype,ttc);
 106         printf("\n");
 107
 108         return 0;
 109 }
 110
 111 int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
 112
 113         moldyn->dim.x=x;
 114         moldyn->dim.y=y;
 115         moldyn->dim.z=z;
 116
 117         moldyn->volume=x*y*z;
 118
 119         if(visualize) {
 120                 moldyn->vis.dim.x=x;
 121                 moldyn->vis.dim.y=y;
 122                 moldyn->vis.dim.z=z;
 123         }
 124
 125         moldyn->dv=0.000001*moldyn->volume;
 126
 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);
 134
 135         return 0;
 136 }
 137
 138 int set_nn_dist(t_moldyn *moldyn,double dist) {
 139
 140         moldyn->nnd=dist;
 141
 142         return 0;
 143 }
 144
 145 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 146
 147         printf("[moldyn] periodic boundary conditions:\n");
 148
 149         if(x)
 150                 moldyn->status|=MOLDYN_STAT_PBX;
 151
 152         if(y)
 153                 moldyn->status|=MOLDYN_STAT_PBY;
 154
 155         if(z)
 156                 moldyn->status|=MOLDYN_STAT_PBZ;
 157
 158         printf("  x: %s\n",x?"yes":"no");
 159         printf("  y: %s\n",y?"yes":"no");
 160         printf("  z: %s\n",z?"yes":"no");
 161
 162         return 0;
 163 }
 164
 165 int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
 166
 167         moldyn->func1b=func;
 168         moldyn->pot1b_params=params;
 169
 170         return 0;
 171 }
 172
 173 int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
 174
 175         moldyn->func2b=func;
 176         moldyn->pot2b_params=params;
 177
 178         return 0;
 179 }
 180
 181 int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) {
 182
 183         moldyn->func2b_post=func;
 184         moldyn->pot2b_params=params;
 185
 186         return 0;
 187 }
 188
 189 int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
 190
 191         moldyn->func3b=func;
 192         moldyn->pot3b_params=params;
 193
 194         return 0;
 195 }
 196
 197 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
 198
 199         strncpy(moldyn->vlsdir,dir,127);
 200
 201         return 0;
 202 }
 203
 204 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title) {
 205
 206         strncpy(moldyn->rauthor,author,63);
 207         strncpy(moldyn->rtitle,title,63);
 208
 209         return 0;
 210 }
 211
 212 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 213
 214         char filename[128];
 215         int ret;
 216
 217         printf("[moldyn] set log: ");
 218
 219         switch(type) {
 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,
 225                                          S_IRUSR|S_IWUSR);
 226                         if(moldyn->efd<0) {
 227                                 perror("[moldyn] energy log fd open");
 228                                 return moldyn->efd;
 229                         }
 230                         dprintf(moldyn->efd,"# total energy log file\n");
 231                         printf("total energy (%d)\n",timer);
 232                         break;
 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,
 238                                          S_IRUSR|S_IWUSR);
 239                         if(moldyn->mfd<0) {
 240                                 perror("[moldyn] momentum log fd open");
 241                                 return moldyn->mfd;
 242                         }
 243                         dprintf(moldyn->efd,"# total momentum log file\n");
 244                         printf("total momentum (%d)\n",timer);
 245                         break;
 246                 case SAVE_STEP:
 247                         moldyn->swrite=timer;
 248                         printf("save file (%d)\n",timer);
 249                         break;
 250                 case VISUAL_STEP:
 251                         moldyn->vwrite=timer;
 252                         ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
 253                         if(ret<0) {
 254                                 printf("[moldyn] visual init failure\n");
 255                                 return ret;
 256                         }
 257                         printf("visual file (%d)\n",timer);
 258                         break;
 259                 case CREATE_REPORT:
 260                         snprintf(filename,127,"%s/report.tex",moldyn->vlsdir);
 261                         moldyn->rfd=open(filename,
 262                                          O_WRONLY|O_CREAT|O_EXCL,
 263                                          S_IRUSR|S_IWUSR);
 264                         if(moldyn->rfd<0) {
 265                                 perror("[moldyn] report fd open");
 266                                 return moldyn->rfd;
 267                         }
 268                         snprintf(filename,127,"%s/plot.scr",moldyn->vlsdir);
 269                         moldyn->pfd=open(filename,
 270                                          O_WRONLY|O_CREAT|O_EXCL,
 271                                          S_IRUSR|S_IWUSR);
 272                         if(moldyn->pfd<0) {
 273                                 perror("[moldyn] plot fd open");
 274                                 return moldyn->pfd;
 275                         }
 276                         dprintf(moldyn->rfd,report_start,
 277                                 moldyn->rauthor,moldyn->rtitle);
 278                         dprintf(moldyn->pfd,plot_script);
 279                         close(moldyn->pfd);
 280                         break;
 281                 default:
 282                         printf("unknown log type: %02x\n",type);
 283                         return -1;
 284         }
 285
 286         return 0;
 287 }
 288
 289 int moldyn_log_shutdown(t_moldyn *moldyn) {
 290
 291         char sc[256];
 292
 293         printf("[moldyn] log shutdown\n");
 294         if(moldyn->efd) close(moldyn->efd);
 295         if(moldyn->mfd) close(moldyn->mfd);
 296         if(moldyn->rfd) {
 297                 dprintf(moldyn->rfd,report_end);
 298                 close(moldyn->rfd);
 299                 snprintf(sc,255,"cd %s && gnuplot plot.scr",moldyn->vlsdir);
 300                 system(sc);
 301                 snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
 302                 system(sc);
 303                 snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
 304                 system(sc);
 305                 snprintf(sc,255,"cd %s && dvipdf report",moldyn->vlsdir);
 306                 system(sc);
 307         }
 308         if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
 309
 310         return 0;
 311 }
 312
 313 /*
 314  * creating lattice functions
 315  */
 316
 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) {
 319
 320         int new,count;
 321         int ret;
 322         t_3dvec origin;
 323         void *ptr;
 324         t_atom *atom;
 325
 326         new=a*b*c;
 327         count=moldyn->count;
 328
 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;
 333
 334         /* allocate space for atoms */
 335         ptr=realloc(moldyn->atom,(count+new)*sizeof(t_atom));
 336         if(!ptr) {
 337                 perror("[moldyn] realloc (create lattice)");
 338                 return -1;
 339         }
 340         moldyn->atom=ptr;
 341         atom=&(moldyn->atom[count]);
 342
 343         /* no atoms on the boundaries (only reason: it looks better!) */
 344         origin.x=0.5*lc;
 345         origin.y=0.5*lc;
 346         origin.z=0.5*lc;
 347
 348         switch(type) {
 349                 case CUBIC:
 350                         set_nn_dist(moldyn,lc);
 351                         ret=cubic_init(a,b,c,lc,atom,&origin);
 352                         break;
 353                 case FCC:
 354                         v3_scale(&origin,&origin,0.5);
 355                         set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
 356                         ret=fcc_init(a,b,c,lc,atom,&origin);
 357                         break;
 358                 case DIAMOND:
 359                         v3_scale(&origin,&origin,0.25);
 360                         set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
 361                         ret=diamond_init(a,b,c,lc,atom,&origin);
 362                         break;
 363                 default:
 364                         printf("unknown lattice type (%02x)\n",type);
 365                         return -1;
 366         }
 367
 368         /* debug */
 369         if(ret!=new) {
 370                 printf("[moldyn] creating lattice failed\n");
 371                 printf("  amount of atoms\n");
 372                 printf("  - expected: %d\n",new);
 373                 printf("  - created: %d\n",ret);
 374                 return -1;
 375         }
 376
 377         moldyn->count+=new;
 378         printf("[moldyn] created lattice with %d atoms\n",new);
 379
 380         for(ret=0;ret<new;ret++) {
 381                 atom[ret].element=element;
 382                 atom[ret].mass=mass;
 383                 atom[ret].attr=attr;
 384                 atom[ret].brand=brand;
 385                 atom[ret].tag=count+ret;
 386                 check_per_bound(moldyn,&(atom[ret].r));
 387         }
 388
 389         return ret;
 390 }
 391
 392 /* cubic init */
 393 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 394
 395         int count;
 396         t_3dvec r;
 397         int i,j,k;
 398         t_3dvec o;
 399
 400         count=0;
 401         if(origin)
 402                 v3_copy(&o,origin);
 403         else
 404                 v3_zero(&o);
 405
 406         r.x=o.x;
 407         for(i=0;i<a;i++) {
 408                 r.y=o.y;
 409                 for(j=0;j<b;j++) {
 410                         r.z=o.z;
 411                         for(k=0;k<c;k++) {
 412                                 v3_copy(&(atom[count].r),&r);
 413                                 count+=1;
 414                                 r.z+=lc;
 415                         }
 416                         r.y+=lc;
 417                 }
 418                 r.x+=lc;
 419         }
 420
 421         for(i=0;i<count;i++) {
 422                 atom[i].r.x-=(a*lc)/2.0;
 423                 atom[i].r.y-=(b*lc)/2.0;
 424                 atom[i].r.z-=(c*lc)/2.0;
 425         }
 426
 427         return count;
 428 }
 429
 430 /* fcc lattice init */
 431 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 432
 433         int count;
 434         int i,j,k,l;
 435         t_3dvec o,r,n;
 436         t_3dvec basis[3];
 437
 438         count=0;
 439         if(origin)
 440                 v3_copy(&o,origin);
 441         else
 442                 v3_zero(&o);
 443
 444         /* construct the basis */
 445         memset(basis,0,3*sizeof(t_3dvec));
 446         basis[0].x=0.5*lc;
 447         basis[0].y=0.5*lc;
 448         basis[1].x=0.5*lc;
 449         basis[1].z=0.5*lc;
 450         basis[2].y=0.5*lc;
 451         basis[2].z=0.5*lc;
 452
 453         /* fill up the room */
 454         r.x=o.x;
 455         for(i=0;i<a;i++) {
 456                 r.y=o.y;
 457                 for(j=0;j<b;j++) {
 458                         r.z=o.z;
 459                         for(k=0;k<c;k++) {
 460                                 /* first atom */
 461                                 v3_copy(&(atom[count].r),&r);
 462                                 count+=1;
 463                                 r.z+=lc;
 464                                 /* the three face centered atoms */
 465                                 for(l=0;l<3;l++) {
 466                                         v3_add(&n,&r,&basis[l]);
 467                                         v3_copy(&(atom[count].r),&n);
 468                                         count+=1;
 469                                 }
 470                         }
 471                         r.y+=lc;
 472                 }
 473                 r.x+=lc;
 474         }
 475
 476         /* coordinate transformation */
 477         for(i=0;i<count;i++) {
 478                 atom[i].r.x-=(a*lc)/2.0;
 479                 atom[i].r.y-=(b*lc)/2.0;
 480                 atom[i].r.z-=(c*lc)/2.0;
 481         }
 482
 483         return count;
 484 }
 485
 486 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 487
 488         int count;
 489         t_3dvec o;
 490
 491         count=fcc_init(a,b,c,lc,atom,origin);
 492
 493         o.x=0.25*lc;
 494         o.y=0.25*lc;
 495         o.z=0.25*lc;
 496
 497         if(origin) v3_add(&o,&o,origin);
 498
 499         count+=fcc_init(a,b,c,lc,&atom[count],&o);
 500
 501         return count;
 502 }
 503
 504 int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
 505              t_3dvec *r,t_3dvec *v) {
 506
 507         t_atom *atom;
 508         void *ptr;
 509         int count;
 510
 511         atom=moldyn->atom;
 512         count=(moldyn->count)++;
 513
 514         ptr=realloc(atom,(count+1)*sizeof(t_atom));
 515         if(!ptr) {
 516                 perror("[moldyn] realloc (add atom)");
 517                 return -1;
 518         }
 519         moldyn->atom=ptr;
 520
 521         atom=moldyn->atom;
 522         atom[count].r=*r;
 523         atom[count].v=*v;
 524         atom[count].element=element;
 525         atom[count].mass=mass;
 526         atom[count].brand=brand;
 527         atom[count].tag=count;
 528         atom[count].attr=attr;
 529
 530         return 0;
 531 }
 532
 533 int destroy_atoms(t_moldyn *moldyn) {
 534
 535         if(moldyn->atom) free(moldyn->atom);
 536
 537         return 0;
 538 }
 539
 540 int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 541
 542         /*
 543          * - gaussian distribution of velocities
 544          * - zero total momentum
 545          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 546          */
 547
 548         int i;
 549         double v,sigma;
 550         t_3dvec p_total,delta;
 551         t_atom *atom;
 552         t_random *random;
 553
 554         atom=moldyn->atom;
 555         random=&(moldyn->random);
 556
 557         printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
 558
 559         /* gaussian distribution of velocities */
 560         v3_zero(&p_total);
 561         for(i=0;i<moldyn->count;i++) {
 562                 sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
 563                 /* x direction */
 564                 v=sigma*rand_get_gauss(random);
 565                 atom[i].v.x=v;
 566                 p_total.x+=atom[i].mass*v;
 567                 /* y direction */
 568                 v=sigma*rand_get_gauss(random);
 569                 atom[i].v.y=v;
 570                 p_total.y+=atom[i].mass*v;
 571                 /* z direction */
 572                 v=sigma*rand_get_gauss(random);
 573                 atom[i].v.z=v;
 574                 p_total.z+=atom[i].mass*v;
 575         }
 576
 577         /* zero total momentum */
 578         v3_scale(&p_total,&p_total,1.0/moldyn->count);
 579         for(i=0;i<moldyn->count;i++) {
 580                 v3_scale(&delta,&p_total,1.0/atom[i].mass);
 581                 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
 582         }
 583
 584         /* velocity scaling */
 585         scale_velocity(moldyn,equi_init);
 586
 587         return 0;
 588 }
 589
 590 double temperature_calc(t_moldyn *moldyn) {
 591
 592         /* assume up to date kinetic energy, which is 3/2 N k_B T */
 593
 594         moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
 595
 596         return moldyn->t;
 597 }
 598
 599 double get_temperature(t_moldyn *moldyn) {
 600
 601         return moldyn->t;
 602 }
 603
 604 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 605
 606         int i;
 607         double e,scale;
 608         t_atom *atom;
 609         int count;
 610
 611         atom=moldyn->atom;
 612
 613         /*
 614          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 615          */
 616
 617         /* get kinetic energy / temperature & count involved atoms */
 618         e=0.0;
 619         count=0;
 620         for(i=0;i<moldyn->count;i++) {
 621                 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
 622                         e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
 623                         count+=1;
 624                 }
 625         }
 626         e*=0.5;
 627         if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
 628         else return 0;  /* no atoms involved in scaling! */
 629
 630         /* (temporary) hack for e,t = 0 */
 631         if(e==0.0) {
 632         moldyn->t=0.0;
 633                 if(moldyn->t_ref!=0.0) {
 634                         thermal_init(moldyn,equi_init);
 635                         return 0;
 636                 }
 637                 else
 638                         return 0; /* no scaling needed */
 639         }
 640
 641
 642         /* get scaling factor */
 643         scale=moldyn->t_ref/moldyn->t;
 644         if(equi_init&TRUE)
 645                 scale*=2.0;
 646         else
 647                 if(moldyn->pt_scale&T_SCALE_BERENDSEN)
 648                         scale=1.0+(scale-1.0)/moldyn->t_tc;
 649         scale=sqrt(scale);
 650
 651         /* velocity scaling */
 652         for(i=0;i<moldyn->count;i++) {
 653                 if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
 654                         v3_scale(&(atom[i].v),&(atom[i].v),scale);
 655         }
 656
 657         return 0;
 658 }
 659
 660 double ideal_gas_law_pressure(t_moldyn *moldyn) {
 661
 662         double p;
 663
 664         p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
 665
 666         return p;
 667 }
 668
 669 double pressure_calc(t_moldyn *moldyn) {
 670
 671         int i;
 672         double v;
 673         t_virial *virial;
 674
 675         /*
 676          * P = 1/(3V) sum_i ( p_i^2 / 2m + f_i r_i )
 677          *
 678          * virial = f_i r_i
 679          */
 680
 681         v=0.0;
 682         for(i=0;i<moldyn->count;i++) {
 683                 virial=&(moldyn->atom[i].virial);
 684                 v+=(virial->xx+virial->yy+virial->zz);
 685         }
 686
 687         /* assume up to date kinetic energy */
 688         moldyn->p=2.0*moldyn->ekin+v;
 689         moldyn->p/=(3.0*moldyn->volume);
 690
 691         return moldyn->p;
 692 }
 693
 694 double thermodynamic_pressure_calc(t_moldyn *moldyn) {
 695
 696         t_3dvec dim,*tp;
 697         double u,p;
 698         double scale;
 699         t_atom *store;
 700
 701         tp=&(moldyn->tp);
 702         store=malloc(moldyn->count*sizeof(t_atom));
 703         if(store==NULL) {
 704                 printf("[moldyn] allocating store mem failed\n");
 705                 return -1;
 706         }
 707
 708         /* save unscaled potential energy + atom/dim configuration */
 709         u=moldyn->energy;
 710         memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
 711         dim=moldyn->dim;
 712
 713         /* derivative with respect to x direction */
 714         scale=1.0+moldyn->dv/(moldyn->dim.y*moldyn->dim.z);
 715         scale_dim(moldyn,scale,TRUE,0,0);
 716         scale_atoms(moldyn,scale,TRUE,0,0);
 717         link_cell_shutdown(moldyn);
 718         link_cell_init(moldyn,QUIET);
 719         potential_force_calc(moldyn);
 720         tp->x=(moldyn->energy-u)/moldyn->dv;
 721         p=tp->x*tp->x;
 722
 723         /* restore atomic configuration + dim */
 724         memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
 725         moldyn->dim=dim;
 726
 727         /* derivative with respect to y direction */
 728         scale=1.0+moldyn->dv/(moldyn->dim.x*moldyn->dim.z);
 729         scale_dim(moldyn,scale,0,TRUE,0);
 730         scale_atoms(moldyn,scale,0,TRUE,0);
 731         link_cell_shutdown(moldyn);
 732         link_cell_init(moldyn,QUIET);
 733         potential_force_calc(moldyn);
 734         tp->y=(moldyn->energy-u)/moldyn->dv;
 735         p+=tp->y*tp->y;
 736
 737         /* restore atomic configuration + dim */
 738         memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
 739         moldyn->dim=dim;
 740
 741         /* derivative with respect to z direction */
 742         scale=1.0+moldyn->dv/(moldyn->dim.x*moldyn->dim.y);
 743         scale_dim(moldyn,scale,0,0,TRUE);
 744         scale_atoms(moldyn,scale,0,0,TRUE);
 745         link_cell_shutdown(moldyn);
 746         link_cell_init(moldyn,QUIET);
 747         potential_force_calc(moldyn);
 748         tp->z=(moldyn->energy-u)/moldyn->dv;
 749         p+=tp->z*tp->z;
 750
 751         /* restore atomic configuration + dim */
 752         memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
 753         moldyn->dim=dim;
 754
 755         printf("dU/dV komp addiert = %f %f %f\n",tp->x,tp->y,tp->z);
 756
 757         scale=1.0+pow(moldyn->dv/moldyn->volume,ONE_THIRD);
 758
 759 printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
 760         scale_dim(moldyn,scale,1,1,1);
 761         scale_atoms(moldyn,scale,1,1,1);
 762         link_cell_shutdown(moldyn);
 763         link_cell_init(moldyn,QUIET);
 764         potential_force_calc(moldyn);
 765 printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
 766
 767         printf("dU/dV einfach = %f\n",((moldyn->energy-u)/moldyn->dv)/ATM);
 768
 769         /* restore atomic configuration + dim */
 770         memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
 771         moldyn->dim=dim;
 772
 773         /* restore energy */
 774         moldyn->energy=u;
 775
 776         link_cell_shutdown(moldyn);
 777         link_cell_init(moldyn,QUIET);
 778
 779         return sqrt(p);
 780 }
 781
 782 double get_pressure(t_moldyn *moldyn) {
 783
 784         return moldyn->p;
 785
 786 }
 787
 788 int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
 789
 790         t_3dvec *dim;
 791
 792         dim=&(moldyn->dim);
 793
 794         if(x) dim->x*=scale;
 795         if(y) dim->y*=scale;
 796         if(z) dim->z*=scale;
 797
 798         return 0;
 799 }
 800
 801 int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
 802
 803         int i;
 804         t_3dvec *r;
 805
 806         for(i=0;i<moldyn->count;i++) {
 807                 r=&(moldyn->atom[i].r);
 808                 if(x) r->x*=scale;
 809                 if(y) r->y*=scale;
 810                 if(z) r->z*=scale;
 811         }
 812
 813         return 0;
 814 }
 815
 816 int scale_volume(t_moldyn *moldyn) {
 817
 818         t_3dvec *dim,*vdim;
 819         double scale;
 820         t_linkcell *lc;
 821
 822         vdim=&(moldyn->vis.dim);
 823         dim=&(moldyn->dim);
 824         lc=&(moldyn->lc);
 825
 826         /* scaling factor */
 827         if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
 828                 scale=1.0-(moldyn->p_ref-moldyn->p)/moldyn->p_tc;
 829                 scale=pow(scale,ONE_THIRD);
 830         }
 831         else {
 832                 scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
 833         }
 834 moldyn->debug=scale;
 835
 836         /* scale the atoms and dimensions */
 837         scale_atoms(moldyn,scale,TRUE,TRUE,TRUE);
 838         scale_dim(moldyn,scale,TRUE,TRUE,TRUE);
 839
 840         /* visualize dimensions */
 841         if(vdim->x!=0) {
 842                 vdim->x=dim->x;
 843                 vdim->y=dim->y;
 844                 vdim->z=dim->z;
 845         }
 846
 847         /* recalculate scaled volume */
 848         moldyn->volume=dim->x*dim->y*dim->z;
 849
 850         /* adjust/reinit linkcell */
 851         if(((int)(dim->x/moldyn->cutoff)!=lc->nx)||
 852            ((int)(dim->y/moldyn->cutoff)!=lc->ny)||
 853            ((int)(dim->z/moldyn->cutoff)!=lc->nx)) {
 854                 link_cell_shutdown(moldyn);
 855                 link_cell_init(moldyn,QUIET);
 856         } else {
 857                 lc->x*=scale;
 858                 lc->y*=scale;
 859                 lc->z*=scale;
 860         }
 861
 862         return 0;
 863
 864 }
 865
 866 double get_e_kin(t_moldyn *moldyn) {
 867
 868         int i;
 869         t_atom *atom;
 870
 871         atom=moldyn->atom;
 872         moldyn->ekin=0.0;
 873
 874         for(i=0;i<moldyn->count;i++)
 875                 moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 876
 877         return moldyn->ekin;
 878 }
 879
 880 double update_e_kin(t_moldyn *moldyn) {
 881
 882         return(get_e_kin(moldyn));
 883 }
 884
 885 double get_total_energy(t_moldyn *moldyn) {
 886
 887         return(moldyn->ekin+moldyn->energy);
 888 }
 889
 890 t_3dvec get_total_p(t_moldyn *moldyn) {
 891
 892         t_3dvec p,p_total;
 893         int i;
 894         t_atom *atom;
 895
 896         atom=moldyn->atom;
 897
 898         v3_zero(&p_total);
 899         for(i=0;i<moldyn->count;i++) {
 900                 v3_scale(&p,&(atom[i].v),atom[i].mass);
 901                 v3_add(&p_total,&p_total,&p);
 902         }
 903
 904         return p_total;
 905 }
 906
 907 double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
 908
 909         double tau;
 910
 911         /* nn_dist is the nearest neighbour distance */
 912
 913         tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
 914
 915         return tau;
 916 }
 917
 918 /*
 919  * numerical tricks
 920  */
 921
 922 /* linked list / cell method */
 923
 924 int link_cell_init(t_moldyn *moldyn,u8 vol) {
 925
 926         t_linkcell *lc;
 927         int i;
 928
 929         lc=&(moldyn->lc);
 930
 931         /* partitioning the md cell */
 932         lc->nx=moldyn->dim.x/moldyn->cutoff;
 933         lc->x=moldyn->dim.x/lc->nx;
 934         lc->ny=moldyn->dim.y/moldyn->cutoff;
 935         lc->y=moldyn->dim.y/lc->ny;
 936         lc->nz=moldyn->dim.z/moldyn->cutoff;
 937         lc->z=moldyn->dim.z/lc->nz;
 938
 939         lc->cells=lc->nx*lc->ny*lc->nz;
 940         lc->subcell=malloc(lc->cells*sizeof(t_list));
 941
 942         if(lc->cells<27)
 943                 printf("[moldyn] FATAL: less then 27 subcells!\n");
 944
 945         if(vol) printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 946
 947         for(i=0;i<lc->cells;i++)
 948                 list_init_f(&(lc->subcell[i]));
 949
 950         link_cell_update(moldyn);
 951
 952         return 0;
 953 }
 954
 955 int link_cell_update(t_moldyn *moldyn) {
 956
 957         int count,i,j,k;
 958         int nx,ny;
 959         t_atom *atom;
 960         t_linkcell *lc;
 961         double x,y,z;
 962
 963         atom=moldyn->atom;
 964         lc=&(moldyn->lc);
 965
 966         nx=lc->nx;
 967         ny=lc->ny;
 968
 969         x=moldyn->dim.x/2;
 970         y=moldyn->dim.y/2;
 971         z=moldyn->dim.z/2;
 972
 973         for(i=0;i<lc->cells;i++)
 974                 list_destroy_f(&(lc->subcell[i]));
 975
 976         for(count=0;count<moldyn->count;count++) {
 977                 i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
 978                 j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
 979                 k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
 980                 list_add_immediate_f(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
 981                                      &(atom[count]));
 982         }
 983
 984         return 0;
 985 }
 986
 987 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 988
 989         t_linkcell *lc;
 990         int a;
 991         int count1,count2;
 992         int ci,cj,ck;
 993         int nx,ny,nz;
 994         int x,y,z;
 995         u8 bx,by,bz;
 996
 997         lc=&(moldyn->lc);
 998         nx=lc->nx;
 999         ny=lc->ny;
1000         nz=lc->nz;
1001         count1=1;
1002         count2=27;
1003         a=nx*ny;
1004
1005         cell[0]=lc->subcell[i+j*nx+k*a];
1006         for(ci=-1;ci<=1;ci++) {
1007                 bx=0;
1008                 x=i+ci;
1009                 if((x<0)||(x>=nx)) {
1010                         x=(x+nx)%nx;
1011                         bx=1;
1012                 }
1013                 for(cj=-1;cj<=1;cj++) {
1014                         by=0;
1015                         y=j+cj;
1016                         if((y<0)||(y>=ny)) {
1017                                 y=(y+ny)%ny;
1018                                 by=1;
1019                         }
1020                         for(ck=-1;ck<=1;ck++) {
1021                                 bz=0;
1022                                 z=k+ck;
1023                                 if((z<0)||(z>=nz)) {
1024                                         z=(z+nz)%nz;
1025                                         bz=1;
1026                                 }
1027                                 if(!(ci|cj|ck)) continue;
1028                                 if(bx|by|bz) {
1029                                         cell[--count2]=lc->subcell[x+y*nx+z*a];
1030                                 }
1031                                 else {
1032                                         cell[count1++]=lc->subcell[x+y*nx+z*a];
1033                                 }
1034                         }
1035                 }
1036         }
1037
1038         lc->dnlc=count1;
1039
1040         return count1;
1041 }
1042
1043 int link_cell_shutdown(t_moldyn *moldyn) {
1044
1045         int i;
1046         t_linkcell *lc;
1047
1048         lc=&(moldyn->lc);
1049
1050         for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
1051                 list_destroy_f(&(moldyn->lc.subcell[i]));
1052
1053         free(lc->subcell);
1054
1055         return 0;
1056 }
1057
1058 int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
1059
1060         int count;
1061         void *ptr;
1062         t_moldyn_schedule *schedule;
1063
1064         schedule=&(moldyn->schedule);
1065         count=++(schedule->total_sched);
1066
1067         ptr=realloc(schedule->runs,count*sizeof(int));
1068         if(!ptr) {
1069                 perror("[moldyn] realloc (runs)");
1070                 return -1;
1071         }
1072         schedule->runs=ptr;
1073         schedule->runs[count-1]=runs;
1074
1075         ptr=realloc(schedule->tau,count*sizeof(double));
1076         if(!ptr) {
1077                 perror("[moldyn] realloc (tau)");
1078                 return -1;
1079         }
1080         schedule->tau=ptr;
1081         schedule->tau[count-1]=tau;
1082
1083         printf("[moldyn] schedule added:\n");
1084         printf("  number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
1085
1086
1087         return 0;
1088 }
1089
1090 int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
1091
1092         moldyn->schedule.hook=hook;
1093         moldyn->schedule.hook_params=hook_params;
1094
1095         return 0;
1096 }
1097
1098 /*
1099  *
1100  * 'integration of newtons equation' - algorithms
1101  *
1102  */
1103
1104 /* start the integration */
1105
1106 int moldyn_integrate(t_moldyn *moldyn) {
1107
1108         int i;
1109         unsigned int e,m,s,v;
1110         t_3dvec p;
1111         t_moldyn_schedule *sched;
1112         t_atom *atom;
1113         int fd;
1114         char dir[128];
1115         double ds;
1116         double energy_scale;
1117
1118         sched=&(moldyn->schedule);
1119         atom=moldyn->atom;
1120
1121         /* initialize linked cell method */
1122         link_cell_init(moldyn,VERBOSE);
1123
1124         /* logging & visualization */
1125         e=moldyn->ewrite;
1126         m=moldyn->mwrite;
1127         s=moldyn->swrite;
1128         v=moldyn->vwrite;
1129
1130         /* sqaure of some variables */
1131         moldyn->tau_square=moldyn->tau*moldyn->tau;
1132         moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
1133
1134         /* energy scaling factor */
1135         energy_scale=moldyn->count*EV;
1136
1137         /* calculate initial forces */
1138         potential_force_calc(moldyn);
1139
1140         /* some stupid checks before we actually start calculating bullshit */
1141         if(moldyn->cutoff>0.5*moldyn->dim.x)
1142                 printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
1143         if(moldyn->cutoff>0.5*moldyn->dim.y)
1144                 printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
1145         if(moldyn->cutoff>0.5*moldyn->dim.z)
1146                 printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
1147         ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
1148         if(ds>0.05*moldyn->nnd)
1149                 printf("[moldyn] warning: forces too high / tau too small!\n");
1150
1151         /* zero absolute time */
1152         moldyn->time=0.0;
1153
1154         /* debugging, ignore */
1155         moldyn->debug=0;
1156
1157         /* tell the world */
1158         printf("[moldyn] integration start, go get a coffee ...\n");
1159
1160         /* executing the schedule */
1161         for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
1162
1163                 /* setting amount of runs and finite time step size */
1164                 moldyn->tau=sched->tau[sched->count];
1165                 moldyn->tau_square=moldyn->tau*moldyn->tau;
1166                 moldyn->time_steps=sched->runs[sched->count];
1167
1168         /* integration according to schedule */
1169
1170         for(i=0;i<moldyn->time_steps;i++) {
1171
1172                 /* integration step */
1173                 moldyn->integrate(moldyn);
1174
1175                 /* calculate kinetic energy, temperature and pressure */
1176                 update_e_kin(moldyn);
1177                 temperature_calc(moldyn);
1178                 pressure_calc(moldyn);
1179                 //thermodynamic_pressure_calc(moldyn);
1180
1181                 /* p/t scaling */
1182                 if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
1183                         scale_velocity(moldyn,FALSE);
1184                 if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
1185                         scale_volume(moldyn);
1186
1187                 /* check for log & visualization */
1188                 if(e) {
1189                         if(!(i%e))
1190                                 dprintf(moldyn->efd,
1191                                         "%f %f %f %f\n",
1192                                         moldyn->time,moldyn->ekin/energy_scale,
1193                                         moldyn->energy/energy_scale,
1194                                         get_total_energy(moldyn)/energy_scale);
1195                 }
1196                 if(m) {
1197                         if(!(i%m)) {
1198                                 p=get_total_p(moldyn);
1199                                 dprintf(moldyn->mfd,
1200                                         "%f %f\n",moldyn->time,v3_norm(&p));
1201                         }
1202                 }
1203                 if(s) {
1204                         if(!(i%s)) {
1205                                 snprintf(dir,128,"%s/s-%07.f.save",
1206                                          moldyn->vlsdir,moldyn->time);
1207                                 fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
1208                                 if(fd<0) perror("[moldyn] save fd open");
1209                                 else {
1210                                         write(fd,moldyn,sizeof(t_moldyn));
1211                                         write(fd,moldyn->atom,
1212                                               moldyn->count*sizeof(t_atom));
1213                                 }
1214                                 close(fd);
1215                         }
1216                 }
1217                 if(v) {
1218                         if(!(i%v)) {
1219                                 visual_atoms(&(moldyn->vis),moldyn->time,
1220                                              moldyn->atom,moldyn->count);
1221                                 printf("\rsched: %d, steps: %d, T: %f, P: %f V: %f",
1222                                        sched->count,i,
1223                                        moldyn->t,moldyn->p/ATM,moldyn->volume);
1224                                 fflush(stdout);
1225                         }
1226                 }
1227
1228                 /* increase absolute time */
1229                 moldyn->time+=moldyn->tau;
1230
1231         }
1232
1233                 /* check for hooks */
1234                 if(sched->hook)
1235                         sched->hook(moldyn,sched->hook_params);
1236
1237                 /* get a new info line */
1238                 printf("\n");
1239
1240         }
1241
1242         return 0;
1243 }
1244
1245 /* velocity verlet */
1246
1247 int velocity_verlet(t_moldyn *moldyn) {
1248
1249         int i,count;
1250         double tau,tau_square,h;
1251         t_3dvec delta;
1252         t_atom *atom;
1253
1254         atom=moldyn->atom;
1255         count=moldyn->count;
1256         tau=moldyn->tau;
1257         tau_square=moldyn->tau_square;
1258
1259         for(i=0;i<count;i++) {
1260                 /* new positions */
1261                 h=0.5/atom[i].mass;
1262                 v3_scale(&delta,&(atom[i].v),tau);
1263                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1264                 v3_scale(&delta,&(atom[i].f),h*tau_square);
1265                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
1266                 check_per_bound(moldyn,&(atom[i].r));
1267
1268                 /* velocities [actually v(t+tau/2)] */
1269                 v3_scale(&delta,&(atom[i].f),h*tau);
1270                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1271         }
1272
1273         /* neighbour list update */
1274         link_cell_update(moldyn);
1275
1276         /* forces depending on chosen potential */
1277         potential_force_calc(moldyn);
1278
1279         for(i=0;i<count;i++) {
1280                 /* again velocities [actually v(t+tau)] */
1281                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
1282                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
1283         }
1284
1285         return 0;
1286 }
1287
1288
1289 /*
1290  *
1291  * potentials & corresponding forces & virial routine
1292  *
1293  */
1294
1295 /* generic potential and force calculation */
1296
1297 int potential_force_calc(t_moldyn *moldyn) {
1298
1299         int i,j,k,count;
1300         t_atom *itom,*jtom,*ktom;
1301         t_virial *virial;
1302         t_linkcell *lc;
1303         t_list neighbour_i[27];
1304         t_list neighbour_i2[27];
1305         t_list *this,*that;
1306         u8 bc_ij,bc_ik;
1307         int dnlc;
1308
1309         count=moldyn->count;
1310         itom=moldyn->atom;
1311         lc=&(moldyn->lc);
1312
1313         /* reset energy */
1314         moldyn->energy=0.0;
1315
1316         /* reset force, site energy and virial of every atom */
1317         for(i=0;i<count;i++) {
1318
1319                 /* reset force */
1320                 v3_zero(&(itom[i].f));
1321
1322                 /* reset virial */
1323                 virial=(&(itom[i].virial));
1324                 virial->xx=0.0;
1325                 virial->yy=0.0;
1326                 virial->zz=0.0;
1327                 virial->xy=0.0;
1328                 virial->xz=0.0;
1329                 virial->yz=0.0;
1330
1331                 /* reset site energy */
1332                 itom[i].e=0.0;
1333
1334         }
1335
1336         /* get energy,force and virial of every atom */
1337         for(i=0;i<count;i++) {
1338
1339                 /* single particle potential/force */
1340                 if(itom[i].attr&ATOM_ATTR_1BP)
1341                         moldyn->func1b(moldyn,&(itom[i]));
1342
1343                 if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
1344                         continue;
1345
1346                 /* 2 body pair potential/force */
1347
1348                 link_cell_neighbour_index(moldyn,
1349                                           (itom[i].r.x+moldyn->dim.x/2)/lc->x,
1350                                           (itom[i].r.y+moldyn->dim.y/2)/lc->y,
1351                                           (itom[i].r.z+moldyn->dim.z/2)/lc->z,
1352                                           neighbour_i);
1353
1354                 dnlc=lc->dnlc;
1355
1356                 for(j=0;j<27;j++) {
1357
1358                         this=&(neighbour_i[j]);
1359                         list_reset_f(this);
1360
1361                         if(this->start==NULL)
1362                                 continue;
1363
1364                         bc_ij=(j<dnlc)?0:1;
1365
1366                         do {
1367                                 jtom=this->current->data;
1368
1369                                 if(jtom==&(itom[i]))
1370                                         continue;
1371
1372                                 if((jtom->attr&ATOM_ATTR_2BP)&
1373                                    (itom[i].attr&ATOM_ATTR_2BP)) {
1374                                         moldyn->func2b(moldyn,
1375                                                        &(itom[i]),
1376                                                        jtom,
1377                                                        bc_ij);
1378                                 }
1379
1380                                 /* 3 body potential/force */
1381
1382                                 if(!(itom[i].attr&ATOM_ATTR_3BP)||
1383                                    !(jtom->attr&ATOM_ATTR_3BP))
1384                                         continue;
1385
1386                                 /* copy the neighbour lists */
1387                                 memcpy(neighbour_i2,neighbour_i,
1388                                        27*sizeof(t_list));
1389
1390                                 /* get neighbours of i */
1391                                 for(k=0;k<27;k++) {
1392
1393                                         that=&(neighbour_i2[k]);
1394                                         list_reset_f(that);
1395
1396                                         if(that->start==NULL)
1397                                                 continue;
1398
1399                                         bc_ik=(k<dnlc)?0:1;
1400
1401                                         do {
1402
1403                                                 ktom=that->current->data;
1404
1405                                                 if(!(ktom->attr&ATOM_ATTR_3BP))
1406                                                         continue;
1407
1408                                                 if(ktom==jtom)
1409                                                         continue;
1410
1411                                                 if(ktom==&(itom[i]))
1412                                                         continue;
1413
1414                                                 moldyn->func3b(moldyn,
1415                                                                &(itom[i]),
1416                                                                jtom,
1417                                                                ktom,
1418                                                                bc_ik|bc_ij);
1419
1420                                         } while(list_next_f(that)!=\
1421                                                 L_NO_NEXT_ELEMENT);
1422
1423                                 }
1424
1425                                 /* 2bp post function */
1426                                 if(moldyn->func2b_post) {
1427                                         moldyn->func2b_post(moldyn,
1428                                                             &(itom[i]),
1429                                                             jtom,bc_ij);
1430                                 }
1431
1432                         } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
1433
1434                 }
1435
1436         }
1437
1438 #ifdef DEBUG
1439 printf("\n\n");
1440 #endif
1441 #ifdef VDEBUG
1442 printf("\n\n");
1443 #endif
1444
1445         return 0;
1446 }
1447
1448 /*
1449  * virial calculation
1450  */
1451
1452 inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
1453
1454         a->virial.xx+=f->x*d->x;
1455         a->virial.yy+=f->y*d->y;
1456         a->virial.zz+=f->z*d->z;
1457         a->virial.xy+=f->x*d->y;
1458         a->virial.xz+=f->x*d->z;
1459         a->virial.yz+=f->y*d->z;
1460
1461         return 0;
1462 }
1463
1464 /*
1465  * periodic boundayr checking
1466  */
1467
1468 inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
1469
1470         double x,y,z;
1471         t_3dvec *dim;
1472
1473         dim=&(moldyn->dim);
1474
1475         x=dim->x/2;
1476         y=dim->y/2;
1477         z=dim->z/2;
1478
1479         if(moldyn->status&MOLDYN_STAT_PBX) {
1480                 if(a->x>=x) a->x-=dim->x;
1481                 else if(-a->x>x) a->x+=dim->x;
1482         }
1483         if(moldyn->status&MOLDYN_STAT_PBY) {
1484                 if(a->y>=y) a->y-=dim->y;
1485                 else if(-a->y>y) a->y+=dim->y;
1486         }
1487         if(moldyn->status&MOLDYN_STAT_PBZ) {
1488                 if(a->z>=z) a->z-=dim->z;
1489                 else if(-a->z>z) a->z+=dim->z;
1490         }
1491
1492         return 0;
1493 }
1494
1495
1496 /*
1497  * example potentials
1498  */
1499
1500 /* harmonic oscillator potential and force */
1501
1502 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
1503
1504         t_ho_params *params;
1505         t_3dvec force,distance;
1506         double d,f;
1507         double sc,equi_dist;
1508
1509         params=moldyn->pot2b_params;
1510         sc=params->spring_constant;
1511         equi_dist=params->equilibrium_distance;
1512
1513         if(ai<aj) return 0;
1514
1515         v3_sub(&distance,&(aj->r),&(ai->r));
1516
1517         if(bc) check_per_bound(moldyn,&distance);
1518         d=v3_norm(&distance);
1519         if(d<=moldyn->cutoff) {
1520                 moldyn->energy+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
1521                 /* f = -grad E; grad r_ij = -1 1/r_ij distance */
1522                 f=sc*(1.0-equi_dist/d);
1523                 v3_scale(&force,&distance,f);
1524                 v3_add(&(ai->f),&(ai->f),&force);
1525                 virial_calc(ai,&force,&distance);
1526                 virial_calc(aj,&force,&distance); /* f and d signe switched */
1527                 v3_scale(&force,&distance,-f);
1528                 v3_add(&(aj->f),&(aj->f),&force);
1529         }
1530
1531         return 0;
1532 }
1533
1534 /*
1535  * debugging / critical check functions
1536  */
1537
1538 int moldyn_bc_check(t_moldyn *moldyn) {
1539
1540         t_atom *atom;
1541         t_3dvec *dim;
1542         int i;
1543         double x;
1544         u8 byte;
1545         int j,k;
1546
1547         atom=moldyn->atom;
1548         dim=&(moldyn->dim);
1549         x=dim->x/2;
1550
1551         for(i=0;i<moldyn->count;i++) {
1552                 if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
1553                         printf("FATAL: atom %d: x: %.20f (%.20f)\n",
1554                                i,atom[i].r.x,dim->x/2);
1555                         printf("diagnostic:\n");
1556                         printf("-----------\natom.r.x:\n");
1557                         for(j=0;j<8;j++) {
1558                                 memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
1559                                 for(k=0;k<8;k++)
1560                                         printf("%d%c",
1561                                         ((byte)&(1<<k))?1:0,
1562                                         (k==7)?'\n':'|');
1563                         }
1564                         printf("---------------\nx=dim.x/2:\n");
1565                         for(j=0;j<8;j++) {
1566                                 memcpy(&byte,(u8 *)(&x)+j,1);
1567                                 for(k=0;k<8;k++)
1568                                         printf("%d%c",
1569                                         ((byte)&(1<<k))?1:0,
1570                                         (k==7)?'\n':'|');
1571                         }
1572                         if(atom[i].r.x==x) printf("the same!\n");
1573                         else printf("different!\n");
1574                 }
1575                 if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
1576                         printf("FATAL: atom %d: y: %.20f (%.20f)\n",
1577                                i,atom[i].r.y,dim->y/2);
1578                 if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
1579                         printf("FATAL: atom %d: z: %.20f (%.20f)\n",
1580                                i,atom[i].r.z,dim->z/2);
1581         }
1582
1583         return 0;
1584 }