src/ngmx/manager.c

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team,
   6  * check out http://www.gromacs.org for more information.
   7  * Copyright (c) 2012, by the GROMACS development team, led by
   8  * David van der Spoel, Berk Hess, Erik Lindahl, and including many
   9  * others, as listed in the AUTHORS file in the top-level source
  10  * directory and at http://www.gromacs.org.
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  38 #ifdef HAVE_CONFIG_H
  39 #include <config.h>
  40 #endif
  41
  42 #include <sysstuff.h>
  43 #include <string.h>
  44 #include <smalloc.h>
  45 #include <ctype.h>
  46 #include <typedefs.h>
  47 #include <smalloc.h>
  48 #include <tpxio.h>
  49 #include <macros.h>
  50 #include <maths.h>
  51 #include <atomprop.h>
  52 #include <names.h>
  53 #include "manager.h"
  54 #include "futil.h"
  55 #include "pbc.h"
  56 #include "nmol.h"
  57 #include "copyrite.h"
  58 #include "gstat.h"
  59 #include "vec.h"
  60 #include "statutil.h"
  61 #include "string2.h"
  62
  63 static void add_object(t_manager *man,eObject eO,atom_id ai,atom_id aj)
  64 {
  65   srenew(man->obj,++man->nobj);
  66   man->obj[man->nobj-1].eO    = eO;
  67   man->obj[man->nobj-1].eV    = eVNormal;
  68   man->obj[man->nobj-1].color = WHITE;
  69   man->obj[man->nobj-1].ai    = ai;
  70   man->obj[man->nobj-1].aj    = aj;
  71   man->obj[man->nobj-1].z     = 0.0;
  72 }
  73
  74 static void add_bonds(t_manager *man,t_functype func[],
  75                       t_ilist *b,gmx_bool bB[])
  76 {
  77   gmx_bool    *bH=man->bHydro;
  78   t_iatom *ia;
  79   t_iatom type,ai,aj,ak;
  80   int     i,delta,ftype;
  81
  82 #ifdef DEBUG
  83   fprintf(stderr,"Going to make bonds from an ilist with %d entries\n",b->nr);
  84 #endif
  85   ia=b->iatoms;
  86   for(i=0; (i<b->nr); ) {
  87     type  = ia[0];
  88     ai    = ia[1];
  89     ftype = func[type];
  90     delta = interaction_function[ftype].nratoms;
  91
  92     if (ftype == F_SETTLE) {
  93       aj = ia[2];
  94       ak = ia[3];
  95       bB[ai]=bB[aj]=bB[ak]=TRUE;
  96       add_object(man,eOHBond,ai,aj);
  97       add_object(man,eOHBond,ai,ak);
  98     }
  99     else if (IS_CHEMBOND(ftype)) {
 100       aj=ia[2];
 101 #ifdef DEBUG
 102       fprintf(stderr,"Adding bond from %d to %d\n",ai,aj);
 103 #endif
 104       bB[ai]=bB[aj]=TRUE;
 105       if (!(bH[ai] == bH[aj]))
 106         add_object(man,eOHBond,ai,aj);
 107       else if (!bH[ai] && !bH[aj])
 108         add_object(man,eOBond,ai,aj);
 109     }
 110 #ifdef DEBUG
 111     fprintf(stderr,"Type: %5d, delta: %5d\n",type,delta);
 112 #endif
 113     ia += delta+1;
 114     i  += delta+1;
 115   }
 116 }
 117
 118 static void add_bpl(t_manager *man,t_idef *idef,gmx_bool bB[])
 119 {
 120   int ftype;
 121
 122   for(ftype=0; ftype<F_NRE; ftype++)
 123     if (IS_CHEMBOND(ftype) || ftype==F_SETTLE)
 124       add_bonds(man,idef->functype,&idef->il[ftype],bB);
 125 }
 126
 127 static atom_id which_atom(t_manager *man,int x, int y)
 128 {
 129 #define DELTA 5
 130   int i;
 131   iv2 *ix=man->ix;
 132
 133   for(i=0; (i<man->natom); i++) {
 134     if ((abs(ix[i][XX]-x) < DELTA) && (abs(ix[i][YY]-y) < DELTA)) {
 135       if (man->bVis[i])
 136         return (atom_id) i;
 137     }
 138   }
 139   return NO_ATID;
 140 }
 141
 142 static void do_label(t_x11 *x11,t_manager *man,int x,int y,gmx_bool bSet)
 143 {
 144   atom_id ai;
 145   unsigned long   col;
 146
 147   if ((ai=which_atom(man,x,y)) != NO_ATID) {
 148     x=man->ix[ai][XX];
 149     y=man->ix[ai][YY];
 150     if (bSet && !man->bLabel[ai]) {
 151       col=WHITE;
 152       man->bLabel[ai]=TRUE;
 153     }
 154     else if (!bSet && man->bLabel[ai]) {
 155       col=BLUE;
 156       man->bLabel[ai]=FALSE;
 157     }
 158     else
 159       return;
 160     XSetForeground(x11->disp,x11->gc,col);
 161     XDrawString(x11->disp,man->molw->wd.self,x11->gc,x+2,y-2,man->szLab[ai],
 162                 strlen(man->szLab[ai]));
 163     XSetForeground(x11->disp,x11->gc,x11->fg);
 164   }
 165 }
 166
 167 static void show_label(t_x11 *x11,t_manager *man,int x,int y)
 168 {
 169   do_label(x11,man,x,y,TRUE);
 170 }
 171
 172 static void hide_label(t_x11 *x11,t_manager *man,int x,int y)
 173 {
 174   do_label(x11,man,x,y,FALSE);
 175 }
 176
 177 void set_file(t_x11 *x11,t_manager *man,const char *trajectory,
 178               const char *status)
 179 {
 180   gmx_atomprop_t aps;
 181   char         buf[256],quote[256];
 182   t_tpxheader  sh;
 183   t_atoms      *at;
 184   gmx_bool         *bB;
 185   int          i,idum;
 186
 187   read_tpxheader(status,&sh,TRUE,NULL,NULL);
 188   snew(man->ix,sh.natoms);
 189   snew(man->zz,sh.natoms);
 190   snew(man->col,sh.natoms);
 191   snew(man->size,sh.natoms);
 192   snew(man->vdw,sh.natoms);
 193   snew(man->bLabel,sh.natoms);
 194   snew(man->bVis,sh.natoms);
 195   for(i=0; (i<sh.natoms); i++)
 196     man->bVis[i]=FALSE;
 197
 198   man->bPbc=FALSE;
 199
 200   snew(man->szLab,sh.natoms);
 201   snew(man->bHydro,sh.natoms);
 202   snew(bB,sh.natoms);
 203   read_tpx_top(status,NULL,man->box,&man->natom,NULL,NULL,NULL,&man->top);
 204   man->gpbc = gmx_rmpbc_init(&man->top.idef,-1,man->natom,man->box);
 205
 206   man->natom=
 207     read_first_x(man->oenv,&man->status,trajectory,&(man->time),&(man->x),
 208                  man->box);
 209   man->trajfile=strdup(trajectory);
 210   if (man->natom > man->top.atoms.nr)
 211     gmx_fatal(FARGS,"Topology %s (%d atoms) and trajectory %s (%d atoms) "
 212                 "do not match",status,man->top.atoms.nr,
 213                 trajectory,man->natom);
 214
 215   cool_quote(quote,255,NULL);
 216   sprintf(buf,"%s: %s",*man->top.name,quote);
 217   man->title.text = strdup(buf);
 218   man->view       = init_view(man->box);
 219   at  = &(man->top.atoms);
 220   aps = gmx_atomprop_init();
 221   for(i=0; (i<man->natom); i++) {
 222     char *aname=*(at->atomname[i]);
 223     t_resinfo *ri=&at->resinfo[at->atom[i].resind];
 224
 225     man->col[i]=Type2Color(aname);
 226     snew(man->szLab[i],20);
 227     if (ri->ic != ' ') {
 228       sprintf(man->szLab[i],"%s%d%c, %s",*ri->name,ri->nr,ri->ic,aname);
 229     } else {
 230       sprintf(man->szLab[i],"%s%d, %s",*ri->name,ri->nr,aname);
 231     }
 232     man->bHydro[i]=(toupper(aname[0])=='H');
 233     if ( man->bHydro[i] )
 234       man->vdw[i]=0;
 235     else if (!gmx_atomprop_query(aps,epropVDW,*ri->name,aname,&(man->vdw[i])))
 236       man->vdw[i] = 0;
 237   }
 238   gmx_atomprop_destroy(aps);
 239   add_bpl(man,&(man->top.idef),bB);
 240   for(i=0; (i<man->natom); i++)
 241     if (!bB[i])
 242       add_object(man,eOSingle,(atom_id) i,0);
 243   sfree(bB);
 244
 245   ExposeWin(x11->disp,man->molw->wd.self);
 246 }
 247
 248 void step_message(t_x11 *x11,t_manager *man)
 249 {
 250   XEvent letter;
 251
 252   letter.type=ClientMessage;
 253   letter.xclient.display=x11->disp;
 254   letter.xclient.window=man->wd.self;
 255   letter.xclient.message_type=0;
 256   letter.xclient.format=32;
 257   letter.xclient.data.l[0]=IDSTEP;
 258   letter.xclient.data.l[1]=Button1;
 259   XSendEvent(x11->disp,letter.xclient.window,True,0,&letter);
 260 }
 261
 262 gmx_bool ReadMonfile(char *fn,int *nbars, int *bars)
 263 {
 264   FILE *fp;
 265   if ((fp = fopen(fn,"r"))==NULL)
 266     return(FALSE);
 267   else {
 268     for((*nbars)=0; fscanf(fp,"%d",&bars[*nbars])>0; (*nbars)++)
 269       ;
 270     fclose(fp);
 271     return (TRUE);
 272   }
 273 }
 274
 275 static void reset_mols(t_block *mols,matrix box,rvec x[])
 276 {
 277   int  i,m0,m1,j,m;
 278   rvec xcm,icm;
 279   real ix,iy,iz;
 280
 281   for(i=0; (i<mols->nr); i++) {
 282     m0=mols->index[i];
 283     m1=mols->index[i+1];
 284
 285     clear_rvec(xcm);
 286     clear_rvec(icm);
 287
 288     for(j=m0; (j<m1); j++) {
 289       rvec_inc(xcm,x[j]);
 290     }
 291     for(m=0; (m<DIM); m++)
 292       xcm[m]/=(m1-m0);
 293     for(m=0; (m<DIM); m++) {
 294       if (xcm[m] < 0)
 295         icm[m]=box[m][m];
 296       else if (xcm[m] >= box[m][m])
 297         icm[m]=-box[m][m];
 298     }
 299     ix=icm[XX],iy=icm[YY],iz=icm[ZZ];
 300
 301     if ((ix != 0) || (iy != 0) || (iz != 0)) {
 302       for(j=m0; (j<m1); j++) {
 303         x[j][XX]+=ix;
 304         x[j][YY]+=iy;
 305         x[j][ZZ]+=iz;
 306       }
 307     }
 308   }
 309 }
 310
 311 static gmx_bool step_man(t_manager *man,int *nat)
 312 {
 313   static int  ncount=0;
 314   static gmx_bool bWarn = FALSE;
 315   gmx_bool        bEof;
 316   int         dum;
 317   const char *warn;
 318
 319   if (!man->natom) {
 320     fprintf(stderr,"Not initiated yet!");
 321     exit(1);
 322   }
 323   bEof=read_next_x(man->oenv,man->status,&man->time,man->natom,man->x,man->box);
 324   *nat=man->natom;
 325   if (ncount == man->nSkip) {
 326     switch (man->molw->boxtype) {
 327     case esbTri:
 328       put_atoms_in_triclinic_unitcell(ecenterDEF,man->box,man->natom,man->x);
 329       break;
 330     case esbTrunc:
 331       warn = put_atoms_in_compact_unitcell(man->molw->ePBC,ecenterDEF,man->box,
 332                                            man->natom,man->x);
 333       if (warn && !bWarn) {
 334         fprintf(stderr,"\n%s\n",warn);
 335         bWarn = TRUE;
 336       }
 337       break;
 338     case esbRect:
 339     case esbNone:
 340     default:
 341       break;
 342     }
 343     if (man->bPbc) {
 344       gmx_rmpbc(man->gpbc,man->natom,man->box,man->x);
 345       reset_mols(&(man->top.mols),man->box,man->x);
 346     }
 347     ncount=0;
 348   }
 349   else {
 350     if (man->nSkip > 0) {
 351       ncount++;
 352       return step_man(man,nat);
 353     }
 354   }
 355
 356   return bEof;
 357 }
 358
 359 static void HandleClient(t_x11 *x11,t_manager *man,long data[])
 360 {
 361   int  ID,button,x,y;
 362   gmx_bool bPos;
 363   real fac;
 364
 365   ID=data[0];
 366   button=data[1];
 367   x=data[2];
 368   y=data[3];
 369   bPos=(button==Button1);
 370   switch (ID) {
 371   case IDROTX:
 372   case IDROTY:
 373   case IDROTZ:
 374     rotate_3d(man->view,ID-IDROTX,bPos);
 375     draw_mol(x11,man);
 376     break;
 377   case IDZOOM:
 378     if (bPos)
 379       fac=0.8; /* Reduce distance between eye and origin */
 380     else
 381       fac=1.25;
 382
 383     /*  zoom changed to scale by Berk Hess 3-7-96
 384     if (zoom_3d(man->view,fac))
 385       draw_mol(x11,man); */
 386     man->view->sc_x/=fac;
 387     man->view->sc_y/=fac;
 388     draw_mol(x11,man);
 389     break;
 390   case IDTRANSX:
 391   case IDTRANSY:
 392   case IDTRANSZ:
 393     translate_view(man->view,ID-IDTRANSX,bPos);
 394     draw_mol(x11,man);
 395     break;
 396   case IDREWIND:
 397     if (man->status) {
 398       rewind_trj(man->status);
 399       read_next_x(man->oenv,man->status,&(man->time),man->natom,man->x,
 400                   man->box);
 401       man->bEof=FALSE;
 402       draw_mol(x11,man);
 403     }
 404     break;
 405   case IDSTEP: {
 406     int      nat;
 407
 408     nat=0;
 409     if (!step_man(man,&nat)) {
 410       man->bEof=TRUE;
 411       man->bStop=TRUE;
 412     }
 413     else {
 414       if (nat > 0) {
 415         draw_mol(x11,man);
 416         usleep(man->nWait*1000);
 417       }
 418     }
 419     break;
 420   }
 421   case IDFF:
 422     man->bStop=FALSE;
 423     break;
 424   case IDSTOP_ANI:
 425     man->bStop=TRUE;
 426     break;
 427   case IDDRAWMOL:
 428     draw_mol(x11,man);
 429     break;
 430   case IDLABEL:
 431     switch (button) {
 432     case Button1:
 433     case Button2:
 434       show_label(x11,man,x,y);
 435       break;
 436     case Button3:
 437       hide_label(x11,man,x,y);
 438       break;
 439     }
 440     break;
 441   default:
 442     break;
 443   }
 444   if (man->bAnimate && !man->bEof && !man->bStop)
 445     step_message(x11,man);
 446 }
 447
 448 static gmx_bool TitleCallBack(t_x11 *x11,XEvent *event, Window w, void *data)
 449 {
 450   t_windata *wd;
 451
 452   wd=(t_windata *)data;
 453   switch (event->type) {
 454   case Expose:
 455     if (wd->text && (wd->width > 10)) {
 456       XSetForeground(x11->disp,x11->gc,WHITE);
 457       TextInWin(x11,wd,wd->text,eXCenter,eYCenter);
 458       XDrawLine(x11->disp,wd->self,x11->gc,0,wd->height,
 459                 wd->width,wd->height);
 460     }
 461     break;
 462   case ConfigureNotify:
 463     wd->width=event->xconfigure.width;
 464     wd->height=event->xconfigure.height;
 465     break;
 466   }
 467   return FALSE;
 468 }
 469
 470 static gmx_bool ManCallBack(t_x11 *x11,XEvent *event, Window w, void *data)
 471 {
 472   t_manager *man;
 473   int       width,height;
 474
 475   man=(t_manager *)data;
 476   switch(event->type) {
 477   case ConfigureNotify:
 478     width=event->xconfigure.width;
 479     height=event->xconfigure.height;
 480     if ((width!=man->wd.width) || (height!=man->wd.height))
 481       move_man(x11,man,width,height);
 482     break;
 483   case ClientMessage:
 484     HandleClient(x11,man,event->xclient.data.l);
 485     break;
 486   default:
 487     break;
 488   }
 489   return FALSE;
 490 }
 491
 492 void no_labels(t_x11 *x11,t_manager *man)
 493 {
 494   int i;
 495
 496   for(i=0; (i<man->natom); i++)
 497     man->bLabel[i]=FALSE;
 498   draw_mol(x11,man);
 499 }
 500
 501 void move_man(t_x11 *x11,t_manager *man,int width,int height)
 502 {
 503   int x0,y0,mw,mh,hb;
 504   int th;
 505
 506 #ifdef DEBUG
 507   fprintf(stderr,"Move manager %dx%d\n",width,height);
 508 #endif
 509   man->wd.width=width;
 510   man->wd.height=height;
 511
 512   /* Move all subwindows, resize only Mol window */
 513   x0=width-EWIDTH-AIR-4*BORDER;               /* Starting of ewin etc. */
 514   y0=AIR;
 515
 516   /* Mol Window */
 517   mw=x0-2*AIR-4*BORDER;
 518   mh=height-y0-AIR-2*BORDER;
 519   XMoveResizeWindow(x11->disp,man->molw->wd.self,AIR,y0,mw,mh);
 520
 521   /* Title Window */
 522   th=XTextHeight(x11->font);
 523   XMoveResizeWindow(x11->disp,man->title.self,0,0,mw,th+AIR);
 524
 525   /* Legend Window */
 526   XMoveResizeWindow(x11->disp,man->legw->wd.self,x0,y0,EWIDTH,LEGHEIGHT);
 527   y0+=LEGHEIGHT+AIR+2*BORDER;
 528
 529   if (y0 > height)
 530     printf("Error: Windows falling out of main window!\n");
 531
 532   /* Button Box */
 533   hb=height-y0-AIR-2*BORDER;
 534   XMoveResizeWindow(x11->disp,man->bbox->wd.self,x0,y0,EWIDTH,hb);
 535
 536   /* Video Box */
 537   x0=(mw-man->vbox->wd.width)/2;
 538   y0=(mh-2-AIR-man->vbox->wd.height);
 539   XMoveWindow(x11->disp,man->vbox->wd.self,x0,y0);
 540 }
 541
 542 void map_man(t_x11 *x11,t_manager *man)
 543 {
 544   XMapWindow(x11->disp,man->wd.self);
 545   map_mw(x11,man->molw);
 546   XMapWindow(x11->disp,man->title.self);
 547   map_legw(x11,man->legw);
 548   show_but(x11,man->bbox);
 549 }
 550
 551 gmx_bool toggle_animate (t_x11 *x11,t_manager *man)
 552 {
 553   if (man->status) {
 554     man->bAnimate=!man->bAnimate;
 555     man->bStop=TRUE;
 556     man->bEof=FALSE;
 557     if (man->bAnimate)
 558       show_but(x11,man->vbox);
 559     else
 560       hide_but(x11,man->vbox);
 561   }
 562   return man->bAnimate;
 563 }
 564
 565 gmx_bool toggle_pbc (t_manager *man)
 566 {
 567   man->bPbc=!man->bPbc;
 568
 569   return man->bPbc;
 570 }
 571
 572
 573 t_manager *init_man(t_x11 *x11,Window Parent,
 574                     int x,int y,int width,int height,
 575                     unsigned long fg,unsigned long bg,
 576                     int ePBC,matrix box,
 577                     const output_env_t oenv)
 578 {
 579   t_manager *man;
 580
 581   snew(man,1);
 582   man->status=NULL;
 583   man->bPlus=TRUE;
 584   man->bSort=TRUE;
 585   man->oenv=oenv;
 586   InitWin(&(man->wd),x,y,width,height,0,"Manager");
 587   man->wd.self=XCreateSimpleWindow(x11->disp,Parent,man->wd.x, man->wd.y,
 588                                    man->wd.width,man->wd.height,
 589                                    man->wd.bwidth,fg,bg);
 590   x11->RegisterCallback(x11,man->wd.self,Parent,ManCallBack,man);
 591   x11->SetInputMask(x11,man->wd.self,StructureNotifyMask |
 592                     ExposureMask | ButtonPressMask);
 593
 594   /* The order of creating windows is important for the stacking order */
 595   /* Mol Window */
 596   man->molw=init_mw(x11,man->wd.self,0,0,1,1,WHITE,BLUE,ePBC,box);
 597
 598   /* Title Window */
 599   InitWin(&(man->title),0,0,1,1,0,NULL);
 600   man->title.self=XCreateSimpleWindow(x11->disp,man->molw->wd.self,
 601                                       man->title.x,man->title.y,
 602                                       man->title.width,man->title.height,
 603                                       man->title.bwidth,WHITE,BLUE);
 604   x11->RegisterCallback(x11,man->title.self,man->molw->wd.self,
 605                         TitleCallBack,&(man->title));
 606   x11->SetInputMask(x11,man->title.self,ExposureMask | StructureNotifyMask);
 607
 608   /* Button box */
 609   man->bbox=init_bbox(x11,man->wd.self,man->wd.self,1,WHITE,BLUE);
 610
 611   /* Legend Window */
 612   man->legw=init_legw(x11,man->wd.self,0,0,EWIDTH,LEGHEIGHT,WHITE,BLUE);
 613
 614   /* Video Box */
 615   man->vbox=init_vbox(x11,man->molw->wd.self,man->wd.self,WHITE,BLUE);
 616
 617   return man;
 618 }
 619
 620 void done_man(t_x11 *x11,t_manager *man)
 621 {
 622   done_bbox(x11,man->vbox);
 623   done_bbox(x11,man->bbox);
 624   done_mw(x11,man->molw);
 625   done_legw(x11,man->legw);
 626   x11->UnRegisterCallback(x11,man->title.self);
 627   x11->UnRegisterCallback(x11,man->wd.self);
 628   sfree(man->x);
 629   sfree(man->obj);
 630   sfree(man->bHydro);
 631   sfree(man->bLabel);
 632   sfree(man->szLab);
 633   sfree(man->col);
 634   sfree(man);
 635 }
 636
 637 void do_filter(t_x11 *x11,t_manager *man,t_filter *filter)
 638 {
 639   int      i;
 640   atom_id  j;
 641
 642   for(i=0; (i<man->natom); i++)
 643     man->bVis[i]=FALSE;
 644   for(i=0; (i<filter->grps->nr); i++) {
 645     if (filter->bShow[i])
 646       for(j=filter->grps->index[i]; (j<filter->grps->index[i+1]); j++)
 647         man->bVis[filter->grps->a[j]]=TRUE;
 648   }
 649
 650   ExposeWin(x11->disp,man->wd.self);
 651 }