src/programs/view/manager.cpp

   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  * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
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  37 #include "gmxpre.h"
  38
  39 #include "manager.h"
  40
  41 #include "config.h"
  42
  43 #include <cctype>
  44 #include <cstdio>
  45 #include <cstdlib>
  46 #include <cstring>
  47
  48 #include <string>
  49
  50 #ifdef HAVE_UNISTD_H
  51 #include <unistd.h> // for usleep()
  52 #endif
  53
  54 #include "gromacs/fileio/tpxio.h"
  55 #include "gromacs/math/utilities.h"
  56 #include "gromacs/math/vec.h"
  57 #include "gromacs/mdtypes/md_enums.h"
  58 #include "gromacs/pbcutil/pbc.h"
  59 #include "gromacs/topology/atomprop.h"
  60 #include "gromacs/topology/ifunc.h"
  61 #include "gromacs/utility/coolstuff.h"
  62 #include "gromacs/utility/cstringutil.h"
  63 #include "gromacs/utility/fatalerror.h"
  64 #include "gromacs/utility/futil.h"
  65 #include "gromacs/utility/smalloc.h"
  66 #include "gromacs/utility/stringutil.h"
  67
  68 #include "3dview.h"
  69 #include "nmol.h"
  70
  71 static void add_object(t_manager *man, eObject eO, int ai, int aj)
  72 {
  73     srenew(man->obj, ++man->nobj);
  74     man->obj[man->nobj-1].eO    = eO;
  75     man->obj[man->nobj-1].eV    = eVNormal;
  76     man->obj[man->nobj-1].color = WHITE;
  77     man->obj[man->nobj-1].ai    = ai;
  78     man->obj[man->nobj-1].aj    = aj;
  79     man->obj[man->nobj-1].z     = 0.0;
  80 }
  81
  82 static void add_bonds(t_manager *man, t_functype func[],
  83                       t_ilist *b, bool bB[])
  84 {
  85     bool        *bH = man->bHydro;
  86     t_iatom     *ia;
  87     t_iatom      type, ai, aj, ak;
  88     int          i, delta, ftype;
  89
  90 #ifdef DEBUG
  91     std::fprintf(stderr, "Going to make bonds from an ilist with %d entries\n", b->nr);
  92 #endif
  93     ia = b->iatoms;
  94     for (i = 0; (i < b->nr); )
  95     {
  96         type  = ia[0];
  97         ai    = ia[1];
  98         ftype = func[type];
  99         delta = interaction_function[ftype].nratoms;
 100
 101         if (ftype == F_SETTLE)
 102         {
 103             aj     = ia[2];
 104             ak     = ia[3];
 105             bB[ai] = bB[aj] = bB[ak] = true;
 106             add_object(man, eOHBond, ai, aj);
 107             add_object(man, eOHBond, ai, ak);
 108         }
 109         else if (IS_CHEMBOND(ftype))
 110         {
 111             aj = ia[2];
 112 #ifdef DEBUG
 113             std::fprintf(stderr, "Adding bond from %d to %d\n", ai, aj);
 114 #endif
 115             bB[ai] = bB[aj] = true;
 116             if (!(bH[ai] == bH[aj]))
 117             {
 118                 add_object(man, eOHBond, ai, aj);
 119             }
 120             else if (!bH[ai] && !bH[aj])
 121             {
 122                 add_object(man, eOBond, ai, aj);
 123             }
 124         }
 125 #ifdef DEBUG
 126         std::fprintf(stderr, "Type: %5d, delta: %5d\n", type, delta);
 127 #endif
 128         ia += delta+1;
 129         i  += delta+1;
 130     }
 131 }
 132
 133 static void add_bpl(t_manager *man, t_idef *idef, bool bB[])
 134 {
 135     int ftype;
 136
 137     for (ftype = 0; ftype < F_NRE; ftype++)
 138     {
 139         if (IS_CHEMBOND(ftype) || ftype == F_SETTLE)
 140         {
 141             add_bonds(man, idef->functype, &idef->il[ftype], bB);
 142         }
 143     }
 144 }
 145
 146 static int which_atom(t_manager *man, int x, int y)
 147 {
 148 #define DELTA 5
 149     int  i;
 150     iv2 *ix = man->ix;
 151
 152     for (i = 0; (i < man->natom); i++)
 153     {
 154         if ((std::abs(ix[i][XX]-x) < DELTA) && (std::abs(ix[i][YY]-y) < DELTA))
 155         {
 156             if (man->bVis[i])
 157             {
 158                 return (int) i;
 159             }
 160         }
 161     }
 162     return -1;
 163 }
 164
 165 static void do_label(t_x11 *x11, t_manager *man, int x, int y, bool bSet)
 166 {
 167     int             ai;
 168     unsigned long   col;
 169
 170     if ((ai = which_atom(man, x, y)) != -1)
 171     {
 172         x = man->ix[ai][XX];
 173         y = man->ix[ai][YY];
 174         if (bSet && !man->bLabel[ai])
 175         {
 176             col             = WHITE;
 177             man->bLabel[ai] = true;
 178         }
 179         else if (!bSet && man->bLabel[ai])
 180         {
 181             col             = BLUE;
 182             man->bLabel[ai] = false;
 183         }
 184         else
 185         {
 186             return;
 187         }
 188         XSetForeground(x11->disp, x11->gc, col);
 189         XDrawString(x11->disp, man->molw->wd.self, x11->gc, x+2, y-2, man->szLab[ai],
 190                     std::strlen(man->szLab[ai]));
 191         XSetForeground(x11->disp, x11->gc, x11->fg);
 192     }
 193 }
 194
 195 static void show_label(t_x11 *x11, t_manager *man, int x, int y)
 196 {
 197     do_label(x11, man, x, y, true);
 198 }
 199
 200 static void hide_label(t_x11 *x11, t_manager *man, int x, int y)
 201 {
 202     do_label(x11, man, x, y, false);
 203 }
 204
 205 void set_file(t_x11 *x11, t_manager *man, const char *trajectory,
 206               const char *status)
 207 {
 208     gmx_atomprop_t    aps;
 209     t_tpxheader       sh;
 210     t_atoms          *at;
 211     bool             *bB;
 212     int               i;
 213
 214     read_tpxheader(status, &sh, true);
 215     snew(man->ix, sh.natoms);
 216     snew(man->zz, sh.natoms);
 217     snew(man->col, sh.natoms);
 218     snew(man->size, sh.natoms);
 219     snew(man->vdw, sh.natoms);
 220     snew(man->bLabel, sh.natoms);
 221     snew(man->bVis, sh.natoms);
 222     for (i = 0; (i < sh.natoms); i++)
 223     {
 224         man->bVis[i] = false;
 225     }
 226
 227     man->bPbc = false;
 228
 229     snew(man->szLab, sh.natoms);
 230     snew(man->bHydro, sh.natoms);
 231     snew(bB, sh.natoms);
 232     read_tpx_top(status, NULL, man->box, &man->natom, NULL, NULL, &man->top);
 233     man->gpbc = gmx_rmpbc_init(&man->top.idef, -1, man->natom);
 234
 235     man->natom =
 236         read_first_x(man->oenv, &man->status, trajectory, &(man->time), &(man->x),
 237                      man->box);
 238     man->trajfile = gmx_strdup(trajectory);
 239     if (man->natom > man->top.atoms.nr)
 240     {
 241         gmx_fatal(FARGS, "Topology %s (%d atoms) and trajectory %s (%d atoms) "
 242                   "do not match", status, man->top.atoms.nr,
 243                   trajectory, man->natom);
 244     }
 245
 246     man->title.text = gmx_strdup(gmx::formatString("%s: %s", *man->top.name, gmx::getCoolQuote().c_str()).c_str());
 247     man->view       = init_view(man->box);
 248     at              = &(man->top.atoms);
 249     aps             = gmx_atomprop_init();
 250     for (i = 0; (i < man->natom); i++)
 251     {
 252         char      *aname = *(at->atomname[i]);
 253         t_resinfo *ri    = &at->resinfo[at->atom[i].resind];
 254
 255         man->col[i] = Type2Color(aname);
 256         snew(man->szLab[i], 20);
 257         if (ri->ic != ' ')
 258         {
 259             std::sprintf(man->szLab[i], "%s%d%c, %s", *ri->name, ri->nr, ri->ic, aname);
 260         }
 261         else
 262         {
 263             std::sprintf(man->szLab[i], "%s%d, %s", *ri->name, ri->nr, aname);
 264         }
 265         man->bHydro[i] = (toupper(aname[0]) == 'H');
 266         if (man->bHydro[i])
 267         {
 268             man->vdw[i] = 0;
 269         }
 270         else if (!gmx_atomprop_query(aps, epropVDW, *ri->name, aname, &(man->vdw[i])))
 271         {
 272             man->vdw[i] = 0;
 273         }
 274     }
 275     gmx_atomprop_destroy(aps);
 276     add_bpl(man, &(man->top.idef), bB);
 277     for (i = 0; (i < man->natom); i++)
 278     {
 279         if (!bB[i])
 280         {
 281             add_object(man, eOSingle, (int) i, 0);
 282         }
 283     }
 284     sfree(bB);
 285
 286     ExposeWin(x11->disp, man->molw->wd.self);
 287 }
 288
 289 void step_message(t_x11 *x11, t_manager *man)
 290 {
 291     XEvent letter;
 292
 293     letter.type                 = ClientMessage;
 294     letter.xclient.display      = x11->disp;
 295     letter.xclient.window       = man->wd.self;
 296     letter.xclient.message_type = 0;
 297     letter.xclient.format       = 32;
 298     letter.xclient.data.l[0]    = IDSTEP;
 299     letter.xclient.data.l[1]    = Button1;
 300     XSendEvent(x11->disp, letter.xclient.window, True, 0, &letter);
 301 }
 302
 303 static void reset_mols(t_block *mols, matrix box, rvec x[])
 304 {
 305     int  i, m0, m1, j, m;
 306     rvec xcm, icm;
 307     real ix, iy, iz;
 308
 309     for (i = 0; (i < mols->nr); i++)
 310     {
 311         m0 = mols->index[i];
 312         m1 = mols->index[i+1];
 313
 314         clear_rvec(xcm);
 315         clear_rvec(icm);
 316
 317         for (j = m0; (j < m1); j++)
 318         {
 319             rvec_inc(xcm, x[j]);
 320         }
 321         for (m = 0; (m < DIM); m++)
 322         {
 323             xcm[m] /= (m1-m0);
 324         }
 325         for (m = 0; (m < DIM); m++)
 326         {
 327             if (xcm[m] < 0)
 328             {
 329                 icm[m] = box[m][m];
 330             }
 331             else if (xcm[m] >= box[m][m])
 332             {
 333                 icm[m] = -box[m][m];
 334             }
 335         }
 336         ix = icm[XX], iy = icm[YY], iz = icm[ZZ];
 337
 338         if ((ix != 0) || (iy != 0) || (iz != 0))
 339         {
 340             for (j = m0; (j < m1); j++)
 341             {
 342                 x[j][XX] += ix;
 343                 x[j][YY] += iy;
 344                 x[j][ZZ] += iz;
 345             }
 346         }
 347     }
 348 }
 349
 350 static bool step_man(t_manager *man, int *nat)
 351 {
 352     static int      ncount = 0;
 353     bool            bEof;
 354
 355     if (!man->natom)
 356     {
 357         std::fprintf(stderr, "Not initiated yet!");
 358         std::exit(1);
 359     }
 360     bEof = read_next_x(man->oenv, man->status, &man->time, man->x, man->box);
 361     *nat = man->natom;
 362     if (ncount == man->nSkip)
 363     {
 364         switch (man->molw->boxtype)
 365         {
 366             case esbTri:
 367                 put_atoms_in_triclinic_unitcell(ecenterDEF, man->box, man->natom, man->x);
 368                 break;
 369             case esbTrunc:
 370                 put_atoms_in_compact_unitcell(man->molw->ePBC, ecenterDEF, man->box,
 371                                               man->natom, man->x);
 372                 break;
 373             case esbRect:
 374             case esbNone:
 375             default:
 376                 break;
 377         }
 378         if (man->bPbc)
 379         {
 380             gmx_rmpbc(man->gpbc, man->natom, man->box, man->x);
 381             reset_mols(&(man->top.mols), man->box, man->x);
 382         }
 383         ncount = 0;
 384     }
 385     else
 386     {
 387         if (man->nSkip > 0)
 388         {
 389             ncount++;
 390             return step_man(man, nat);
 391         }
 392     }
 393
 394     return bEof;
 395 }
 396
 397 static void HandleClient(t_x11 *x11, t_manager *man, long data[])
 398 {
 399     int  ID, button, x, y;
 400     bool bPos;
 401     real fac;
 402
 403     ID     = data[0];
 404     button = data[1];
 405     x      = data[2];
 406     y      = data[3];
 407     bPos   = (button == Button1);
 408     switch (ID)
 409     {
 410         case IDROTX:
 411         case IDROTY:
 412         case IDROTZ:
 413             rotate_3d(man->view, ID-IDROTX, bPos);
 414             draw_mol(x11, man);
 415             break;
 416         case IDZOOM:
 417             if (bPos)
 418             {
 419                 fac = 0.8; /* Reduce distance between eye and origin */
 420             }
 421             else
 422             {
 423                 fac = 1.25;
 424             }
 425
 426             /*  zoom changed to scale by Berk Hess 3-7-96
 427                if (zoom_3d(man->view,fac))
 428                draw_mol(x11,man); */
 429             man->view->sc_x /= fac;
 430             man->view->sc_y /= fac;
 431             draw_mol(x11, man);
 432             break;
 433         case IDTRANSX:
 434         case IDTRANSY:
 435         case IDTRANSZ:
 436             translate_view(man->view, ID-IDTRANSX, bPos);
 437             draw_mol(x11, man);
 438             break;
 439         case IDREWIND:
 440             if (man->status)
 441             {
 442                 rewind_trj(man->status);
 443                 read_next_x(man->oenv, man->status, &(man->time), man->x,
 444                             man->box);
 445                 man->bEof = false;
 446                 draw_mol(x11, man);
 447             }
 448             break;
 449         case IDSTEP:
 450         {
 451             int      nat;
 452
 453             nat = 0;
 454             if (!step_man(man, &nat))
 455             {
 456                 man->bEof  = true;
 457                 man->bStop = true;
 458             }
 459             else
 460             {
 461                 if (nat > 0)
 462                 {
 463                     draw_mol(x11, man);
 464                     usleep(man->nWait*1000);
 465                 }
 466             }
 467             break;
 468         }
 469         case IDFF:
 470             man->bStop = false;
 471             break;
 472         case IDSTOP_ANI:
 473             man->bStop = true;
 474             break;
 475         case IDDRAWMOL:
 476             draw_mol(x11, man);
 477             break;
 478         case IDLABEL:
 479             switch (button)
 480             {
 481                 case Button1:
 482                 case Button2:
 483                     show_label(x11, man, x, y);
 484                     break;
 485                 case Button3:
 486                     hide_label(x11, man, x, y);
 487                     break;
 488             }
 489             break;
 490         default:
 491             break;
 492     }
 493     if (man->bAnimate && !man->bEof && !man->bStop)
 494     {
 495         step_message(x11, man);
 496     }
 497 }
 498
 499 static bool TitleCallBack(t_x11 *x11, XEvent *event, Window /*w*/, void *data)
 500 {
 501     t_windata *wd;
 502
 503     wd = (t_windata *)data;
 504     switch (event->type)
 505     {
 506         case Expose:
 507             if (wd->text && (wd->width > 10))
 508             {
 509                 XSetForeground(x11->disp, x11->gc, WHITE);
 510                 TextInWin(x11, wd, wd->text, eXCenter, eYCenter);
 511                 XDrawLine(x11->disp, wd->self, x11->gc, 0, wd->height,
 512                           wd->width, wd->height);
 513             }
 514             break;
 515         case ConfigureNotify:
 516             wd->width  = event->xconfigure.width;
 517             wd->height = event->xconfigure.height;
 518             break;
 519     }
 520     return false;
 521 }
 522
 523 static bool ManCallBack(t_x11 *x11, XEvent *event, Window /*w*/, void *data)
 524 {
 525     t_manager *man;
 526     int        width, height;
 527
 528     man = (t_manager *)data;
 529     switch (event->type)
 530     {
 531         case ConfigureNotify:
 532             width  = event->xconfigure.width;
 533             height = event->xconfigure.height;
 534             if ((width != man->wd.width) || (height != man->wd.height))
 535             {
 536                 move_man(x11, man, width, height);
 537             }
 538             break;
 539         case ClientMessage:
 540             HandleClient(x11, man, event->xclient.data.l);
 541             break;
 542         default:
 543             break;
 544     }
 545     return false;
 546 }
 547
 548 void no_labels(t_x11 *x11, t_manager *man)
 549 {
 550     int i;
 551
 552     for (i = 0; (i < man->natom); i++)
 553     {
 554         man->bLabel[i] = false;
 555     }
 556     draw_mol(x11, man);
 557 }
 558
 559 void move_man(t_x11 *x11, t_manager *man, int width, int height)
 560 {
 561     int x0, y0, mw, mh, hb;
 562     int th;
 563
 564 #ifdef DEBUG
 565     std::fprintf(stderr, "Move manager %dx%d\n", width, height);
 566 #endif
 567     man->wd.width  = width;
 568     man->wd.height = height;
 569
 570     /* Move all subwindows, resize only Mol window */
 571     x0 = width-EWIDTH-AIR-4*BORDER;           /* Starting of ewin etc. */
 572     y0 = AIR;
 573
 574     /* Mol Window */
 575     mw = x0-2*AIR-4*BORDER;
 576     mh = height-y0-AIR-2*BORDER;
 577     XMoveResizeWindow(x11->disp, man->molw->wd.self, AIR, y0, mw, mh);
 578
 579     /* Title Window */
 580     th = XTextHeight(x11->font);
 581     XMoveResizeWindow(x11->disp, man->title.self, 0, 0, mw, th+AIR);
 582
 583     /* Legend Window */
 584     XMoveResizeWindow(x11->disp, man->legw->wd.self, x0, y0, EWIDTH, LEGHEIGHT);
 585     y0 += LEGHEIGHT+AIR+2*BORDER;
 586
 587     if (y0 > height)
 588     {
 589         std::printf("Error: Windows falling out of main window!\n");
 590     }
 591
 592     /* Button Box */
 593     hb = height-y0-AIR-2*BORDER;
 594     XMoveResizeWindow(x11->disp, man->bbox->wd.self, x0, y0, EWIDTH, hb);
 595
 596     /* Video Box */
 597     x0 = (mw-man->vbox->wd.width)/2;
 598     y0 = (mh-2-AIR-man->vbox->wd.height);
 599     XMoveWindow(x11->disp, man->vbox->wd.self, x0, y0);
 600 }
 601
 602 void map_man(t_x11 *x11, t_manager *man)
 603 {
 604     XMapWindow(x11->disp, man->wd.self);
 605     map_mw(x11, man->molw);
 606     XMapWindow(x11->disp, man->title.self);
 607     map_legw(x11, man->legw);
 608     show_but(x11, man->bbox);
 609 }
 610
 611 bool toggle_animate (t_x11 *x11, t_manager *man)
 612 {
 613     if (man->status)
 614     {
 615         man->bAnimate = !man->bAnimate;
 616         man->bStop    = true;
 617         man->bEof     = false;
 618         if (man->bAnimate)
 619         {
 620             show_but(x11, man->vbox);
 621         }
 622         else
 623         {
 624             hide_but(x11, man->vbox);
 625         }
 626     }
 627     return man->bAnimate;
 628 }
 629
 630 bool toggle_pbc (t_manager *man)
 631 {
 632     man->bPbc = !man->bPbc;
 633
 634     return man->bPbc;
 635 }
 636
 637
 638 t_manager *init_man(t_x11 *x11, Window Parent,
 639                     int x, int y, int width, int height,
 640                     unsigned long fg, unsigned long bg,
 641                     int ePBC, matrix box,
 642                     gmx_output_env_t *oenv)
 643 {
 644     t_manager *man;
 645
 646     snew(man, 1);
 647     man->status = NULL;
 648     man->bPlus  = true;
 649     man->bSort  = true;
 650     man->oenv   = oenv;
 651     InitWin(&(man->wd), x, y, width, height, 0, "Manager");
 652     man->wd.self = XCreateSimpleWindow(x11->disp, Parent, man->wd.x, man->wd.y,
 653                                        man->wd.width, man->wd.height,
 654                                        man->wd.bwidth, fg, bg);
 655     x11->RegisterCallback(x11, man->wd.self, Parent, ManCallBack, man);
 656     x11->SetInputMask(x11, man->wd.self, StructureNotifyMask |
 657                       ExposureMask | ButtonPressMask);
 658
 659     /* The order of creating windows is important for the stacking order */
 660     /* Mol Window */
 661     man->molw = init_mw(x11, man->wd.self, 0, 0, 1, 1, WHITE, BLUE, ePBC, box);
 662
 663     /* Title Window */
 664     InitWin(&(man->title), 0, 0, 1, 1, 0, NULL);
 665     man->title.self = XCreateSimpleWindow(x11->disp, man->molw->wd.self,
 666                                           man->title.x, man->title.y,
 667                                           man->title.width, man->title.height,
 668                                           man->title.bwidth, WHITE, BLUE);
 669     x11->RegisterCallback(x11, man->title.self, man->molw->wd.self,
 670                           TitleCallBack, &(man->title));
 671     x11->SetInputMask(x11, man->title.self, ExposureMask | StructureNotifyMask);
 672
 673     /* Button box */
 674     man->bbox = init_bbox(x11, man->wd.self, man->wd.self, 1, WHITE, BLUE);
 675
 676     /* Legend Window */
 677     man->legw = init_legw(x11, man->wd.self, 0, 0, EWIDTH, LEGHEIGHT, WHITE, BLUE);
 678
 679     /* Video Box */
 680     man->vbox = init_vbox(x11, man->molw->wd.self, man->wd.self, WHITE, BLUE);
 681
 682     return man;
 683 }
 684
 685 void done_man(t_x11 *x11, t_manager *man)
 686 {
 687     done_bbox(x11, man->vbox);
 688     done_bbox(x11, man->bbox);
 689     done_mw(x11, man->molw);
 690     done_legw(x11, man->legw);
 691     x11->UnRegisterCallback(x11, man->title.self);
 692     x11->UnRegisterCallback(x11, man->wd.self);
 693     sfree(man->x);
 694     sfree(man->obj);
 695     sfree(man->bHydro);
 696     sfree(man->bLabel);
 697     sfree(man->szLab);
 698     sfree(man->col);
 699     sfree(man);
 700 }
 701
 702 void do_filter(t_x11 *x11, t_manager *man, t_filter *filter)
 703 {
 704     int      i;
 705     int      j;
 706
 707     for (i = 0; (i < man->natom); i++)
 708     {
 709         man->bVis[i] = false;
 710     }
 711     for (i = 0; (i < filter->grps->nr); i++)
 712     {
 713         if (filter->bShow[i])
 714         {
 715             for (j = filter->grps->index[i]; (j < filter->grps->index[i+1]); j++)
 716             {
 717                 man->bVis[filter->grps->a[j]] = true;
 718             }
 719         }
 720     }
 721
 722     ExposeWin(x11->disp, man->wd.self);
 723 }