src/ngmx/manager.c

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
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  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
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  30  * For more info, check our website at http://www.gromacs.org
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  34  */
  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include <sysstuff.h>
  40 #include <string.h>
  41 #include <smalloc.h>
  42 #include <ctype.h>
  43 #include <typedefs.h>
  44 #include <smalloc.h>
  45 #include <tpxio.h>
  46 #include <macros.h>
  47 #include <maths.h>
  48 #include <atomprop.h>
  49 #include <names.h>
  50 #include "manager.h"
  51 #include "futil.h"
  52 #include "pbc.h"
  53 #include "nmol.h"
  54 #include "copyrite.h"
  55 #include "gstat.h"
  56 #include "vec.h"
  57 #include "statutil.h"
  58 #include "string2.h"
  59
  60 static void add_object(t_manager *man,eObject eO,atom_id ai,atom_id aj)
  61 {
  62   srenew(man->obj,++man->nobj);
  63   man->obj[man->nobj-1].eO    = eO;
  64   man->obj[man->nobj-1].eV    = eVNormal;
  65   man->obj[man->nobj-1].color = WHITE;
  66   man->obj[man->nobj-1].ai    = ai;
  67   man->obj[man->nobj-1].aj    = aj;
  68   man->obj[man->nobj-1].z     = 0.0;
  69 }
  70
  71 static void add_bonds(t_manager *man,t_functype func[],
  72                       t_ilist *b,bool bB[])
  73 {
  74   bool    *bH=man->bHydro;
  75   t_iatom *ia;
  76   t_iatom type,ai,aj,ak;
  77   int     i,delta,ftype;
  78
  79 #ifdef DEBUG
  80   fprintf(stderr,"Going to make bonds from an ilist with %d entries\n",b->nr);
  81 #endif
  82   ia=b->iatoms;
  83   for(i=0; (i<b->nr); ) {
  84     type  = ia[0];
  85     ai    = ia[1];
  86     ftype = func[type];
  87     delta = interaction_function[ftype].nratoms;
  88
  89     if (ftype == F_SETTLE) {
  90       aj=ai+1;
  91       ak=ai+2;
  92       bB[ai]=bB[aj]=bB[ak]=TRUE;
  93       add_object(man,eOHBond,ai,aj);
  94       add_object(man,eOHBond,ai,ak);
  95     }
  96     else if (IS_CHEMBOND(ftype)) {
  97       aj=ia[2];
  98 #ifdef DEBUG
  99       fprintf(stderr,"Adding bond from %d to %d\n",ai,aj);
 100 #endif
 101       bB[ai]=bB[aj]=TRUE;
 102       if (!(bH[ai] == bH[aj]))
 103         add_object(man,eOHBond,ai,aj);
 104       else if (!bH[ai] && !bH[aj])
 105         add_object(man,eOBond,ai,aj);
 106     }
 107 #ifdef DEBUG
 108     fprintf(stderr,"Type: %5d, delta: %5d\n",type,delta);
 109 #endif
 110     ia += delta+1;
 111     i  += delta+1;
 112   }
 113 }
 114
 115 static void add_bpl(t_manager *man,t_idef *idef,bool bB[])
 116 {
 117   int ftype;
 118
 119   for(ftype=0; ftype<F_NRE; ftype++)
 120     if (IS_CHEMBOND(ftype) || ftype==F_SETTLE)
 121       add_bonds(man,idef->functype,&idef->il[ftype],bB);
 122 }
 123
 124 static atom_id which_atom(t_manager *man,int x, int y)
 125 {
 126 #define DELTA 5
 127   int i;
 128   iv2 *ix=man->ix;
 129
 130   for(i=0; (i<man->natom); i++) {
 131     if ((abs(ix[i][XX]-x) < DELTA) && (abs(ix[i][YY]-y) < DELTA)) {
 132       if (man->bVis[i])
 133         return (atom_id) i;
 134     }
 135   }
 136   return NO_ATID;
 137 }
 138
 139 static void do_label(t_x11 *x11,t_manager *man,int x,int y,bool bSet)
 140 {
 141   atom_id ai;
 142   unsigned long   col;
 143
 144   if ((ai=which_atom(man,x,y)) != NO_ATID) {
 145     x=man->ix[ai][XX];
 146     y=man->ix[ai][YY];
 147     if (bSet && !man->bLabel[ai]) {
 148       col=WHITE;
 149       man->bLabel[ai]=TRUE;
 150     }
 151     else if (!bSet && man->bLabel[ai]) {
 152       col=BLUE;
 153       man->bLabel[ai]=FALSE;
 154     }
 155     else
 156       return;
 157     XSetForeground(x11->disp,x11->gc,col);
 158     XDrawString(x11->disp,man->molw->wd.self,x11->gc,x+2,y-2,man->szLab[ai],
 159                 strlen(man->szLab[ai]));
 160     XSetForeground(x11->disp,x11->gc,x11->fg);
 161   }
 162 }
 163
 164 static void show_label(t_x11 *x11,t_manager *man,int x,int y)
 165 {
 166   do_label(x11,man,x,y,TRUE);
 167 }
 168
 169 static void hide_label(t_x11 *x11,t_manager *man,int x,int y)
 170 {
 171   do_label(x11,man,x,y,FALSE);
 172 }
 173
 174 void set_file(t_x11 *x11,t_manager *man,const char *trajectory,
 175               const char *status)
 176 {
 177   gmx_atomprop_t aps;
 178   char         buf[256],quote[256];
 179   t_tpxheader  sh;
 180   t_atoms      *at;
 181   bool         *bB;
 182   int          i,idum;
 183
 184   read_tpxheader(status,&sh,TRUE,NULL,NULL);
 185   snew(man->ix,sh.natoms);
 186   snew(man->zz,sh.natoms);
 187   snew(man->col,sh.natoms);
 188   snew(man->size,sh.natoms);
 189   snew(man->vdw,sh.natoms);
 190   snew(man->bLabel,sh.natoms);
 191   snew(man->bVis,sh.natoms);
 192   for(i=0; (i<sh.natoms); i++)
 193     man->bVis[i]=FALSE;
 194
 195   man->bPbc=FALSE;
 196
 197   snew(man->szLab,sh.natoms);
 198   snew(man->bHydro,sh.natoms);
 199   snew(bB,sh.natoms);
 200   read_tpx_top(status,NULL,man->box,&man->natom,NULL,NULL,NULL,&man->top);
 201
 202   man->natom=
 203     read_first_x(man->oenv,&man->status,trajectory,&(man->time),&(man->x),
 204                  man->box);
 205   man->trajfile=strdup(trajectory);
 206   if (man->natom > man->top.atoms.nr)
 207     gmx_fatal(FARGS,"Topology %s (%d atoms) and trajectory %s (%d atoms) "
 208                 "do not match",status,man->top.atoms.nr,
 209                 trajectory,man->natom);
 210
 211   cool_quote(quote,255,NULL);
 212   sprintf(buf,"%s: %s",*man->top.name,quote);
 213   man->title.text = strdup(buf);
 214   man->view       = init_view(man->box);
 215   at  = &(man->top.atoms);
 216   aps = gmx_atomprop_init();
 217   for(i=0; (i<man->natom); i++) {
 218     char *aname=*(at->atomname[i]);
 219     t_resinfo *ri=&at->resinfo[at->atom[i].resind];
 220
 221     man->col[i]=Type2Color(aname);
 222     snew(man->szLab[i],20);
 223     if (ri->ic != ' ') {
 224       sprintf(man->szLab[i],"%s%d%c, %s",*ri->name,ri->nr,ri->ic,aname);
 225     } else {
 226       sprintf(man->szLab[i],"%s%d, %s",*ri->name,ri->nr,aname);
 227     }
 228     man->bHydro[i]=(toupper(aname[0])=='H');
 229     if ( man->bHydro[i] )
 230       man->vdw[i]=0;
 231     else if (!gmx_atomprop_query(aps,epropVDW,*ri->name,aname,&(man->vdw[i])))
 232       man->vdw[i] = 0;
 233   }
 234   gmx_atomprop_destroy(aps);
 235   add_bpl(man,&(man->top.idef),bB);
 236   for(i=0; (i<man->natom); i++)
 237     if (!bB[i])
 238       add_object(man,eOSingle,(atom_id) i,0);
 239   sfree(bB);
 240
 241   ExposeWin(x11->disp,man->molw->wd.self);
 242 }
 243
 244 void step_message(t_x11 *x11,t_manager *man)
 245 {
 246   XEvent letter;
 247
 248   letter.type=ClientMessage;
 249   letter.xclient.display=x11->disp;
 250   letter.xclient.window=man->wd.self;
 251   letter.xclient.message_type=0;
 252   letter.xclient.format=32;
 253   letter.xclient.data.l[0]=IDSTEP;
 254   letter.xclient.data.l[1]=Button1;
 255   XSendEvent(x11->disp,letter.xclient.window,True,0,&letter);
 256 }
 257
 258 bool ReadMonfile(char *fn,int *nbars, int *bars)
 259 {
 260   FILE *fp;
 261   if ((fp = fopen(fn,"r"))==NULL)
 262     return(FALSE);
 263   else {
 264     for((*nbars)=0; fscanf(fp,"%d",&bars[*nbars])>0; (*nbars)++)
 265       ;
 266     fclose(fp);
 267     return (TRUE);
 268   }
 269 }
 270
 271 static void reset_mols(t_block *mols,matrix box,rvec x[])
 272 {
 273   int  i,m0,m1,j,m;
 274   rvec xcm,icm;
 275   real ix,iy,iz;
 276
 277   for(i=0; (i<mols->nr); i++) {
 278     m0=mols->index[i];
 279     m1=mols->index[i+1];
 280
 281     clear_rvec(xcm);
 282     clear_rvec(icm);
 283
 284     for(j=m0; (j<m1); j++) {
 285       rvec_inc(xcm,x[j]);
 286     }
 287     for(m=0; (m<DIM); m++)
 288       xcm[m]/=(m1-m0);
 289     for(m=0; (m<DIM); m++) {
 290       if (xcm[m] < 0)
 291         icm[m]=box[m][m];
 292       else if (xcm[m] >= box[m][m])
 293         icm[m]=-box[m][m];
 294     }
 295     ix=icm[XX],iy=icm[YY],iz=icm[ZZ];
 296
 297     if ((ix != 0) || (iy != 0) || (iz != 0)) {
 298       for(j=m0; (j<m1); j++) {
 299         x[j][XX]+=ix;
 300         x[j][YY]+=iy;
 301         x[j][ZZ]+=iz;
 302       }
 303     }
 304   }
 305 }
 306
 307 static bool step_man(t_manager *man,int *nat)
 308 {
 309   static int  ncount=0;
 310   static bool bWarn = FALSE;
 311   bool        bEof;
 312   int         dum;
 313   const char *warn;
 314
 315   if (!man->natom) {
 316     fprintf(stderr,"Not initiated yet!");
 317     exit(1);
 318   }
 319   bEof=read_next_x(man->oenv,man->status,&man->time,man->natom,man->x,man->box);
 320   *nat=man->natom;
 321   if (ncount == man->nSkip) {
 322     switch (man->molw->boxtype) {
 323     case esbTri:
 324       put_atoms_in_triclinic_unitcell(ecenterDEF,man->box,man->natom,man->x);
 325       break;
 326     case esbTrunc:
 327       warn = put_atoms_in_compact_unitcell(man->molw->ePBC,ecenterDEF,man->box,
 328                                            man->natom,man->x);
 329       if (warn && !bWarn) {
 330         fprintf(stderr,"\n%s\n",warn);
 331         bWarn = TRUE;
 332       }
 333       break;
 334     case esbRect:
 335     case esbNone:
 336     default:
 337       break;
 338     }
 339     if (man->bPbc) {
 340       rm_pbc(&(man->top.idef),man->molw->ePBC,
 341              man->natom,man->box,man->x,man->x);
 342       reset_mols(&(man->top.mols),man->box,man->x);
 343     }
 344     ncount=0;
 345   }
 346   else {
 347     if (man->nSkip > 0) {
 348       ncount++;
 349       return step_man(man,nat);
 350     }
 351   }
 352
 353   return bEof;
 354 }
 355
 356 static void HandleClient(t_x11 *x11,t_manager *man,long data[])
 357 {
 358   int  ID,button,x,y;
 359   bool bPos;
 360   real fac;
 361
 362   ID=data[0];
 363   button=data[1];
 364   x=data[2];
 365   y=data[3];
 366   bPos=(button==Button1);
 367   switch (ID) {
 368   case IDROTX:
 369   case IDROTY:
 370   case IDROTZ:
 371     rotate_3d(man->view,ID-IDROTX,bPos);
 372     draw_mol(x11,man);
 373     break;
 374   case IDZOOM:
 375     if (bPos)
 376       fac=0.8; /* Reduce distance between eye and origin */
 377     else
 378       fac=1.25;
 379
 380     /*  zoom changed to scale by Berk Hess 3-7-96
 381     if (zoom_3d(man->view,fac))
 382       draw_mol(x11,man); */
 383     man->view->sc_x/=fac;
 384     man->view->sc_y/=fac;
 385     draw_mol(x11,man);
 386     break;
 387   case IDTRANSX:
 388   case IDTRANSY:
 389   case IDTRANSZ:
 390     translate_view(man->view,ID-IDTRANSX,bPos);
 391     draw_mol(x11,man);
 392     break;
 393   case IDREWIND:
 394     if (man->status != -1) {
 395       rewind_trj(man->status);
 396       read_next_x(man->oenv,man->status,&(man->time),man->natom,man->x,
 397                   man->box);
 398       man->bEof=FALSE;
 399       draw_mol(x11,man);
 400     }
 401     break;
 402   case IDSTEP: {
 403     int      nat;
 404
 405     nat=0;
 406     if (!step_man(man,&nat)) {
 407       man->bEof=TRUE;
 408       man->bStop=TRUE;
 409     }
 410     else {
 411       if (nat > 0) {
 412         draw_mol(x11,man);
 413         usleep(man->nWait*1000);
 414       }
 415     }
 416     break;
 417   }
 418   case IDFF:
 419     man->bStop=FALSE;
 420     break;
 421   case IDSTOP_ANI:
 422     man->bStop=TRUE;
 423     break;
 424   case IDDRAWMOL:
 425     draw_mol(x11,man);
 426     break;
 427   case IDLABEL:
 428     switch (button) {
 429     case Button1:
 430     case Button2:
 431       show_label(x11,man,x,y);
 432       break;
 433     case Button3:
 434       hide_label(x11,man,x,y);
 435       break;
 436     }
 437     break;
 438   default:
 439     break;
 440   }
 441   if (man->bAnimate && !man->bEof && !man->bStop)
 442     step_message(x11,man);
 443 }
 444
 445 static bool TitleCallBack(t_x11 *x11,XEvent *event, Window w, void *data)
 446 {
 447   t_windata *wd;
 448
 449   wd=(t_windata *)data;
 450   switch (event->type) {
 451   case Expose:
 452     if (wd->text && (wd->width > 10)) {
 453       XSetForeground(x11->disp,x11->gc,WHITE);
 454       TextInWin(x11,wd,wd->text,eXCenter,eYCenter);
 455       XDrawLine(x11->disp,wd->self,x11->gc,0,wd->height,
 456                 wd->width,wd->height);
 457     }
 458     break;
 459   case ConfigureNotify:
 460     wd->width=event->xconfigure.width;
 461     wd->height=event->xconfigure.height;
 462     break;
 463   }
 464   return FALSE;
 465 }
 466
 467 static bool ManCallBack(t_x11 *x11,XEvent *event, Window w, void *data)
 468 {
 469   t_manager *man;
 470   int       width,height;
 471
 472   man=(t_manager *)data;
 473   switch(event->type) {
 474   case ConfigureNotify:
 475     width=event->xconfigure.width;
 476     height=event->xconfigure.height;
 477     if ((width!=man->wd.width) || (height!=man->wd.height))
 478       move_man(x11,man,width,height);
 479     break;
 480   case ClientMessage:
 481     HandleClient(x11,man,event->xclient.data.l);
 482     break;
 483   default:
 484     break;
 485   }
 486   return FALSE;
 487 }
 488
 489 void no_labels(t_x11 *x11,t_manager *man)
 490 {
 491   int i;
 492
 493   for(i=0; (i<man->natom); i++)
 494     man->bLabel[i]=FALSE;
 495   draw_mol(x11,man);
 496 }
 497
 498 void move_man(t_x11 *x11,t_manager *man,int width,int height)
 499 {
 500   int x0,y0,mw,mh,hb;
 501   int th;
 502
 503 #ifdef DEBUG
 504   fprintf(stderr,"Move manager %dx%d\n",width,height);
 505 #endif
 506   man->wd.width=width;
 507   man->wd.height=height;
 508
 509   /* Move all subwindows, resize only Mol window */
 510   x0=width-EWIDTH-AIR-4*BORDER;               /* Starting of ewin etc. */
 511   y0=AIR;
 512
 513   /* Mol Window */
 514   mw=x0-2*AIR-4*BORDER;
 515   mh=height-y0-AIR-2*BORDER;
 516   XMoveResizeWindow(x11->disp,man->molw->wd.self,AIR,y0,mw,mh);
 517
 518   /* Title Window */
 519   th=XTextHeight(x11->font);
 520   XMoveResizeWindow(x11->disp,man->title.self,0,0,mw,th+AIR);
 521
 522   /* Legend Window */
 523   XMoveResizeWindow(x11->disp,man->legw->wd.self,x0,y0,EWIDTH,LEGHEIGHT);
 524   y0+=LEGHEIGHT+AIR+2*BORDER;
 525
 526   if (y0 > height)
 527     printf("Error: Windows falling out of main window!\n");
 528
 529   /* Button Box */
 530   hb=height-y0-AIR-2*BORDER;
 531   XMoveResizeWindow(x11->disp,man->bbox->wd.self,x0,y0,EWIDTH,hb);
 532
 533   /* Video Box */
 534   x0=(mw-man->vbox->wd.width)/2;
 535   y0=(mh-2-AIR-man->vbox->wd.height);
 536   XMoveWindow(x11->disp,man->vbox->wd.self,x0,y0);
 537 }
 538
 539 void map_man(t_x11 *x11,t_manager *man)
 540 {
 541   XMapWindow(x11->disp,man->wd.self);
 542   map_mw(x11,man->molw);
 543   XMapWindow(x11->disp,man->title.self);
 544   map_legw(x11,man->legw);
 545   show_but(x11,man->bbox);
 546 }
 547
 548 bool toggle_animate (t_x11 *x11,t_manager *man)
 549 {
 550   if (man->status != -1) {
 551     man->bAnimate=!man->bAnimate;
 552     man->bStop=TRUE;
 553     man->bEof=FALSE;
 554     if (man->bAnimate)
 555       show_but(x11,man->vbox);
 556     else
 557       hide_but(x11,man->vbox);
 558   }
 559   return man->bAnimate;
 560 }
 561
 562 bool toggle_pbc (t_manager *man)
 563 {
 564   man->bPbc=!man->bPbc;
 565
 566   return man->bPbc;
 567 }
 568
 569
 570 t_manager *init_man(t_x11 *x11,Window Parent,
 571                     int x,int y,int width,int height,
 572                     unsigned long fg,unsigned long bg,
 573                     int ePBC,matrix box,
 574                     const output_env_t oenv)
 575 {
 576   t_manager *man;
 577
 578   snew(man,1);
 579   man->status=-1;
 580   man->bPlus=TRUE;
 581   man->bSort=TRUE;
 582   man->oenv=oenv;
 583   InitWin(&(man->wd),x,y,width,height,0,"Manager");
 584   man->wd.self=XCreateSimpleWindow(x11->disp,Parent,man->wd.x, man->wd.y,
 585                                    man->wd.width,man->wd.height,
 586                                    man->wd.bwidth,fg,bg);
 587   x11->RegisterCallback(x11,man->wd.self,Parent,ManCallBack,man);
 588   x11->SetInputMask(x11,man->wd.self,StructureNotifyMask |
 589                     ExposureMask | ButtonPressMask);
 590
 591   /* The order of creating windows is important for the stacking order */
 592   /* Mol Window */
 593   man->molw=init_mw(x11,man->wd.self,0,0,1,1,WHITE,BLUE,ePBC,box);
 594
 595   /* Title Window */
 596   InitWin(&(man->title),0,0,1,1,0,NULL);
 597   man->title.self=XCreateSimpleWindow(x11->disp,man->molw->wd.self,
 598                                       man->title.x,man->title.y,
 599                                       man->title.width,man->title.height,
 600                                       man->title.bwidth,WHITE,BLUE);
 601   x11->RegisterCallback(x11,man->title.self,man->molw->wd.self,
 602                         TitleCallBack,&(man->title));
 603   x11->SetInputMask(x11,man->title.self,ExposureMask | StructureNotifyMask);
 604
 605   /* Button box */
 606   man->bbox=init_bbox(x11,man->wd.self,man->wd.self,1,WHITE,BLUE);
 607
 608   /* Legend Window */
 609   man->legw=init_legw(x11,man->wd.self,0,0,EWIDTH,LEGHEIGHT,WHITE,BLUE);
 610
 611   /* Video Box */
 612   man->vbox=init_vbox(x11,man->molw->wd.self,man->wd.self,WHITE,BLUE);
 613
 614   return man;
 615 }
 616
 617 void done_man(t_x11 *x11,t_manager *man)
 618 {
 619   done_bbox(x11,man->vbox);
 620   done_bbox(x11,man->bbox);
 621   done_mw(x11,man->molw);
 622   done_legw(x11,man->legw);
 623   x11->UnRegisterCallback(x11,man->title.self);
 624   x11->UnRegisterCallback(x11,man->wd.self);
 625   sfree(man->x);
 626   sfree(man->obj);
 627   sfree(man->bHydro);
 628   sfree(man->bLabel);
 629   sfree(man->szLab);
 630   sfree(man->col);
 631   sfree(man);
 632 }
 633
 634 void do_filter(t_x11 *x11,t_manager *man,t_filter *filter)
 635 {
 636   int      i;
 637   atom_id  j;
 638
 639   for(i=0; (i<man->natom); i++)
 640     man->bVis[i]=FALSE;
 641   for(i=0; (i<filter->grps->nr); i++) {
 642     if (filter->bShow[i])
 643       for(j=filter->grps->index[i]; (j<filter->grps->index[i+1]); j++)
 644         man->bVis[filter->grps->a[j]]=TRUE;
 645   }
 646
 647   ExposeWin(x11->disp,man->wd.self);
 648 }