src/gmxlib/vmdio.c

   1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
   2  *
   3  *
   4  * This file is part of Gromacs        Copyright (c) 1991-2008
   5  * David van der Spoel, Erik Lindahl, Berk Hess, University of Groningen.
   6  *
   7  * This program is free software; you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation; either version 2
  10  * of the License, or (at your option) any later version.
  11  *
  12  * To help us fund GROMACS development, we humbly ask that you cite
  13  * the research papers on the package. Check out http://www.gromacs.org
  14  *
  15  * And Hey:
  16  * Gnomes, ROck Monsters And Chili Sauce
  17  */
  18 #ifdef HAVE_CONFIG_H
  19 #include <config.h>
  20 #endif
  21
  22
  23
  24 /* Derived from PluginMgr.C and catdcd.c */
  25
  26 /* PluginMgr.C: Copyright: */
  27 /***************************************************************************
  28  *cr
  29  *cr            (C) Copyright 1995-2009 The Board of Trustees of the
  30  *cr                        University of Illinois
  31  *cr                         All Rights Reserved
  32  *cr
  33 Developed by:           Theoretical and Computational Biophysics Group
  34                         University of Illinois at Urbana-Champaign
  35                         http://www.ks.uiuc.edu/
  36
  37 Permission is hereby granted, free of charge, to any person obtaining a copy of
  38 this software and associated documentation files (the Software), to deal with
  39 the Software without restriction, including without limitation the rights to
  40 use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
  41 of the Software, and to permit persons to whom the Software is furnished to
  42 do so, subject to the following conditions:
  43
  44 Redistributions of source code must retain the above copyright notice,
  45 this list of conditions and the following disclaimers.
  46
  47 Redistributions in binary form must reproduce the above copyright notice,
  48 this list of conditions and the following disclaimers in the documentation
  49 and/or other materials provided with the distribution.
  50
  51 Neither the names of Theoretical and Computational Biophysics Group,
  52 University of Illinois at Urbana-Champaign, nor the names of its contributors
  53 may be used to endorse or promote products derived from this Software without
  54 specific prior written permission.
  55
  56 THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  57 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  58 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL
  59 THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR
  60 OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
  61 ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
  62 OTHER DEALINGS WITH THE SOFTWARE.
  63  ***************************************************************************/
  64
  65 /* catdcd.c: Copyright: */
  66 /*****************************************************************************/
  67 /*                                                                           */
  68 /* (C) Copyright 2001-2005 Justin Gullingsrud and the University of Illinois.*/
  69 /*                                                                           */
  70 /*****************************************************************************/
  71
  72 #include <stdlib.h>
  73 #include <stdio.h>
  74 #include <string.h>
  75
  76 /*
  77  * Plugin header files; get plugin source from www.ks.uiuc.edu/Research/vmd"
  78  */
  79 #include "molfile_plugin.h"
  80 #include "vmddlopen.h"
  81 #if !((defined WIN32 || defined _WIN32 || defined WIN64 || defined _WIN64) && !defined __CYGWIN__ && !defined __CYGWIN32__)
  82 #include "glob.h"
  83 #else
  84 #include <windows.h>
  85 #include <shlobj.h>
  86 #endif
  87 #include "smalloc.h"
  88 #include "futil.h"
  89 #include "vmdio.h"
  90
  91
  92 #include "types/simple.h"
  93 #include "vec.h"
  94 #include "gmxfio.h"
  95
  96
  97 typedef int (*initfunc)(void);
  98 typedef int (*regfunc)(void *, vmdplugin_register_cb);
  99 typedef int (*finifunc)(void);
 100
 101
 102
 103 static int register_cb(void *v, vmdplugin_t *p) {
 104     const char *key = p->name;
 105     t_gmxvmdplugin *vmdplugin = (t_gmxvmdplugin*)v;
 106
 107     if (strcmp(key,vmdplugin->filetype)==0)
 108     {
 109         vmdplugin->api = (molfile_plugin_t *)p;
 110     }
 111     return VMDPLUGIN_SUCCESS;
 112 }
 113
 114 static int load_sharedlibrary_plugins(const char *fullpath,t_gmxvmdplugin* vmdplugin) {
 115     /* Open the dll; try to execute the init function. */
 116     void *handle, *ifunc, *registerfunc;
 117     handle = vmddlopen(fullpath);
 118     if (!handle) {
 119         if (debug) fprintf(debug, "\nUnable to open dynamic library %s.\n%s\n",  fullpath, vmddlerror());  /*only to debug because of stdc++ erros */
 120         return 0;
 121     }
 122
 123     ifunc = vmddlsym(handle, "vmdplugin_init");
 124     if (ifunc && ((initfunc)(ifunc))()) {
 125         printf("\nvmdplugin_init() for %s returned an error; plugin(s) not loaded.\n", fullpath);
 126         vmddlclose(handle);
 127         return 0;
 128     }
 129
 130     registerfunc = vmddlsym(handle, "vmdplugin_register");
 131     if (!registerfunc) {
 132         printf("\nDidn't find the register function in %s; plugin(s) not loaded.\n", fullpath);
 133         vmddlclose(handle);
 134         return 0;
 135     } else {
 136         /* Load plugins from the library.*/
 137         ((regfunc)registerfunc)(vmdplugin, register_cb);
 138     }
 139
 140     /* in case this library does not support the filetype, close it */
 141     if (vmdplugin->api == NULL)
 142     {
 143         vmddlclose(handle);
 144     }
 145
 146     return 1;
 147 }
 148
 149 /*return: 1: success, 0: last frame, -1: error*/
 150 gmx_bool read_next_vmd_frame(int status,t_trxframe *fr)
 151 {
 152     int rc,i;
 153     rvec vec, angle;
 154     molfile_timestep_t ts;
 155
 156
 157     fr->bV = fr->vmdplugin.bV;
 158
 159 #ifdef GMX_DOUBLE
 160     snew(ts.coords, fr->natoms*3);
 161     if (fr->bV)
 162     {
 163         snew(ts.velocities, fr->natoms*3);
 164     }
 165 #else
 166     ts.coords = (float*)fr->x;
 167     if (fr->bV)
 168     {
 169         ts.velocities = (float*)fr->v;
 170     }
 171 #endif
 172
 173     rc = fr->vmdplugin.api->read_next_timestep(fr->vmdplugin.handle, fr->natoms, &ts);
 174
 175     if (rc < -1) {
 176         fprintf(stderr, "\nError reading input file (error code %d)\n", rc);
 177     }
 178     if (rc < 0)
 179     {
 180         fr->vmdplugin.api->close_file_read(fr->vmdplugin.handle);
 181         return 0;
 182     }
 183
 184 #ifdef GMX_DOUBLE
 185     for (i=0;i<fr->natoms;i++)
 186     {
 187         fr->x[i][0] = .1*ts.coords[i*3];
 188         fr->x[i][1] = .1*ts.coords[i*3+1];
 189         fr->x[i][2] = .1*ts.coords[i*3+2];
 190         if (fr->bV)
 191         {
 192             fr->v[i][0] = .1*ts.velocities[i*3];
 193             fr->v[i][1] = .1*ts.velocities[i*3+1];
 194             fr->v[i][2] = .1*ts.velocities[i*3+2];
 195         }
 196     }
 197     sfree(ts.coords);
 198     if (fr->bV)
 199     {
 200         sfree(ts.velocities);
 201     }
 202 #else
 203     for (i=0;i<fr->natoms;i++)
 204     {
 205         svmul(.1,fr->x[i],fr->x[i]);
 206         if (fr->bV)
 207         {
 208             svmul(.1,fr->v[i],fr->v[i]);
 209         }
 210     }
 211 #endif
 212
 213     fr->bX = 1;
 214     fr->bBox = 1;
 215     vec[0] = .1*ts.A; vec[1] = .1*ts.B; vec[2] = .1*ts.C;
 216     angle[0] = ts.alpha; angle[1] = ts.beta; angle[2] = ts.gamma;
 217     matrix_convert(fr->box,vec,angle);
 218     if (fr->vmdplugin.api->abiversion>10)
 219     {
 220         fr->bTime = TRUE;
 221         fr->time = ts.physical_time;
 222     }
 223     else
 224     {
 225         fr->bTime = FALSE;
 226     }
 227
 228
 229     return 1;
 230 }
 231
 232 int load_vmd_library(const char *fn, t_gmxvmdplugin *vmdplugin)
 233 {
 234     char pathname[GMX_PATH_MAX],filename[GMX_PATH_MAX];
 235     const char *pathenv;
 236     const char *err;
 237     int i;
 238     int ret=0;
 239 #if !((defined WIN32 || defined _WIN32 || defined WIN64 || defined _WIN64) && !defined __CYGWIN__ && !defined __CYGWIN32__)
 240     glob_t globbuf;
 241     const char *defpathenv = "/usr/local/lib/vmd/plugins/*/molfile";
 242 #else
 243     WIN32_FIND_DATA ffd;
 244     HANDLE hFind = INVALID_HANDLE_VALUE;
 245     char progfolder[GMX_PATH_MAX];
 246     char defpathenv[GMX_PATH_MAX];
 247     SHGetFolderPath(NULL,CSIDL_PROGRAM_FILES,NULL,SHGFP_TYPE_CURRENT,progfolder);
 248     sprintf(defpathenv,"%s\\University of Illinois\\VMD\\plugins\\WIN32\\molfile",progfolder);
 249 #endif
 250
 251     vmdplugin->api = NULL;
 252     vmdplugin->filetype = strrchr(fn,'.');
 253     if (!vmdplugin->filetype)
 254     {
 255         return 0;
 256     }
 257     vmdplugin->filetype++;
 258
 259     pathenv = getenv("VMD_PLUGIN_PATH");
 260     if (pathenv==NULL)
 261     {
 262         printf("\nVMD_PLUGIN_PATH not set. ");
 263         printf("Using default location:\n%s\n",defpathenv);
 264         pathenv=defpathenv;
 265     }
 266     strncpy(pathname,pathenv,sizeof(pathname));
 267 #if !((defined WIN32 || defined _WIN32 || defined WIN64 || defined _WIN64) && !defined __CYGWIN__ && !defined __CYGWIN32__)
 268     strcat(pathname,"/*.so");
 269     glob(pathname, 0, NULL, &globbuf);
 270     if (globbuf.gl_pathc == 0)
 271     {
 272         printf("\nNo VMD Plugins found\n"
 273             "Set the environment variable VMD_PLUGIN_PATH to the molfile folder within the\n"
 274             "VMD installation.\n"
 275             "The architecture (e.g. 32bit versus 64bit) of Gromacs and VMD has to match.\n");
 276         return 0;
 277     }
 278     for (i=0; i<globbuf.gl_pathc && vmdplugin->api == NULL; i++)
 279     {
 280         ret|=load_sharedlibrary_plugins(globbuf.gl_pathv[i],vmdplugin);
 281     }
 282     globfree(&globbuf);
 283 #else
 284     strcat(pathname,"\\*.so");
 285     hFind = FindFirstFile(pathname, &ffd);
 286     if (INVALID_HANDLE_VALUE == hFind)
 287     {
 288         printf("\nNo VMD Plugins found\n");
 289         return 0;
 290     }
 291     do
 292     {
 293         sprintf(filename,"%s\\%s",pathenv,ffd.cFileName);
 294         ret|=load_sharedlibrary_plugins(filename,vmdplugin);
 295     }
 296     while (FindNextFile(hFind, &ffd )  != 0 && vmdplugin->api == NULL );
 297     FindClose(hFind);
 298 #endif
 299
 300     if (!ret)
 301     {
 302         printf("\nCould not open any VMD library.\n");
 303         err = vmddlerror();
 304         if (!err)
 305         {
 306             printf("Compiled with dlopen?\n");
 307         }
 308         else
 309         {
 310             printf("Last error:\n%s\n",err);
 311         }
 312         return 0;
 313     }
 314
 315     if (vmdplugin->api == NULL)
 316     {
 317         printf("\nNo plugin for %s found\n",vmdplugin->filetype);
 318         return 0;
 319     }
 320
 321     printf("\nUsing VMD plugin: %s (%s)\n",vmdplugin->api->name,vmdplugin->api->prettyname);
 322
 323     return 1;
 324
 325 }
 326
 327 int read_first_vmd_frame(int *status,const char *fn,t_trxframe *fr,int flags)
 328 {
 329     molfile_timestep_metadata_t *metadata=NULL;
 330
 331     if (!load_vmd_library(fn,&(fr->vmdplugin)))
 332     {
 333         return 0;
 334     }
 335
 336     fr->vmdplugin.handle = fr->vmdplugin.api->open_file_read(fn, fr->vmdplugin.filetype, &fr->natoms);
 337
 338     if (!fr->vmdplugin.handle) {
 339         fprintf(stderr, "\nError: could not open file '%s' for reading.\n",
 340                 fn);
 341         return 0;
 342     }
 343
 344     if (fr->natoms == MOLFILE_NUMATOMS_UNKNOWN) {
 345         fprintf(stderr, "\nFormat of file %s does not record number of atoms.\n", fn);
 346         return 0;
 347     } else if (fr->natoms == MOLFILE_NUMATOMS_NONE) {
 348         fprintf(stderr, "\nNo atoms found by VMD plugin in file %s.\n", fn );
 349         return 0;
 350     } else if (fr->natoms < 1) { /*should not be reached*/
 351         fprintf(stderr, "\nUnknown number of atoms %d for VMD plugin opening file %s.\n",
 352                 fr->natoms, fn );
 353         return 0;
 354     }
 355
 356     snew(fr->x,fr->natoms);
 357
 358     fr->vmdplugin.bV = 0;
 359     if (fr->vmdplugin.api->abiversion > 10 && fr->vmdplugin.api->read_timestep_metadata)
 360     {
 361         fr->vmdplugin.api->read_timestep_metadata(fr->vmdplugin.handle, metadata);
 362         fr->vmdplugin.bV = metadata->has_velocities;
 363         if (fr->vmdplugin.bV)
 364         {
 365             snew(fr->v,fr->natoms);
 366         }
 367     }
 368     return 1;
 369
 370 }
 371
 372
 373