1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
4 * This file is part of Gromacs Copyright (c) 1991-2008
5 * David van der Spoel, Erik Lindahl, Berk Hess, University of Groningen.
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.
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
16 * Gnomes, ROck Monsters And Chili Sauce
21 #include "gmx_header_config.h"
25 /* Derived from PluginMgr.C and catdcd.c */
27 /* PluginMgr.C: Copyright: */
28 /***************************************************************************
30 *cr (C) Copyright 1995-2009 The Board of Trustees of the
31 *cr University of Illinois
32 *cr All Rights Reserved
34 Developed by: Theoretical and Computational Biophysics Group
35 University of Illinois at Urbana-Champaign
36 http://www.ks.uiuc.edu/
38 Permission is hereby granted, free of charge, to any person obtaining a copy of
39 this software and associated documentation files (the Software), to deal with
40 the Software without restriction, including without limitation the rights to
41 use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
42 of the Software, and to permit persons to whom the Software is furnished to
43 do so, subject to the following conditions:
45 Redistributions of source code must retain the above copyright notice,
46 this list of conditions and the following disclaimers.
48 Redistributions in binary form must reproduce the above copyright notice,
49 this list of conditions and the following disclaimers in the documentation
50 and/or other materials provided with the distribution.
52 Neither the names of Theoretical and Computational Biophysics Group,
53 University of Illinois at Urbana-Champaign, nor the names of its contributors
54 may be used to endorse or promote products derived from this Software without
55 specific prior written permission.
57 THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
58 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
59 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
60 THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR
61 OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
62 ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
63 OTHER DEALINGS WITH THE SOFTWARE.
64 ***************************************************************************/
66 /* catdcd.c: Copyright: */
67 /*****************************************************************************/
69 /* (C) Copyright 2001-2005 Justin Gullingsrud and the University of Illinois.*/
71 /*****************************************************************************/
79 * Plugin header files; get plugin source from www.ks.uiuc.edu/Research/vmd"
81 #include "molfile_plugin.h"
82 #include "vmddlopen.h"
83 #ifndef GMX_NATIVE_WINDOWS
94 #include "types/simple.h"
99 typedef int (*initfunc)(void);
100 typedef int (*regfunc)(void *, vmdplugin_register_cb);
101 typedef int (*finifunc)(void);
105 static int register_cb(void *v, vmdplugin_t *p) {
106 const char *key = p->name;
107 t_gmxvmdplugin *vmdplugin = (t_gmxvmdplugin*)v;
109 if (strcmp(key,vmdplugin->filetype)==0)
111 vmdplugin->api = (molfile_plugin_t *)p;
113 return VMDPLUGIN_SUCCESS;
116 static int load_sharedlibrary_plugins(const char *fullpath,t_gmxvmdplugin* vmdplugin) {
117 /* Open the dll; try to execute the init function. */
118 void *handle, *ifunc, *registerfunc;
119 handle = vmddlopen(fullpath);
121 if (debug) fprintf(debug, "\nUnable to open dynamic library %s.\n%s\n", fullpath, vmddlerror()); /*only to debug because of stdc++ erros */
125 ifunc = vmddlsym(handle, "vmdplugin_init");
126 if (!ifunc || ((initfunc)(ifunc))()) {
127 printf("\nvmdplugin_init() for %s returned an error; plugin(s) not loaded.\n", fullpath);
132 registerfunc = vmddlsym(handle, "vmdplugin_register");
134 printf("\nDidn't find the register function in %s; plugin(s) not loaded.\n", fullpath);
138 /* Load plugins from the library.*/
139 ((regfunc)registerfunc)(vmdplugin, register_cb);
142 /* in case this library does not support the filetype, close it */
143 if (vmdplugin->api == NULL)
151 /*return: 1: success, 0: last frame, -1: error*/
152 gmx_bool read_next_vmd_frame(int status,t_trxframe *fr)
156 molfile_timestep_t ts;
159 fr->bV = fr->vmdplugin->bV;
162 snew(ts.coords, fr->natoms*3);
165 snew(ts.velocities, fr->natoms*3);
168 ts.coords = (float*)fr->x;
171 ts.velocities = (float*)fr->v;
175 rc = fr->vmdplugin->api->read_next_timestep(fr->vmdplugin->handle, fr->natoms, &ts);
178 fprintf(stderr, "\nError reading input file (error code %d)\n", rc);
182 fr->vmdplugin->api->close_file_read(fr->vmdplugin->handle);
187 for (i=0;i<fr->natoms;i++)
189 fr->x[i][0] = .1*ts.coords[i*3];
190 fr->x[i][1] = .1*ts.coords[i*3+1];
191 fr->x[i][2] = .1*ts.coords[i*3+2];
194 fr->v[i][0] = .1*ts.velocities[i*3];
195 fr->v[i][1] = .1*ts.velocities[i*3+1];
196 fr->v[i][2] = .1*ts.velocities[i*3+2];
202 sfree(ts.velocities);
205 for (i=0;i<fr->natoms;i++)
207 svmul(.1,fr->x[i],fr->x[i]);
210 svmul(.1,fr->v[i],fr->v[i]);
217 vec[0] = .1*ts.A; vec[1] = .1*ts.B; vec[2] = .1*ts.C;
218 angle[0] = ts.alpha; angle[1] = ts.beta; angle[2] = ts.gamma;
219 matrix_convert(fr->box,vec,angle);
220 if (fr->vmdplugin->api->abiversion>10)
223 fr->time = ts.physical_time;
234 static int load_vmd_library(const char *fn, t_gmxvmdplugin *vmdplugin)
236 char pathname[GMX_PATH_MAX],filename[GMX_PATH_MAX];
241 char pathenv_buffer[GMX_PATH_MAX];
242 #ifndef GMX_NATIVE_WINDOWS
244 const char *defpath_suffix = "/plugins/*/molfile";
245 const char *defpathenv = GMX_VMD_PLUGIN_PATH;
248 HANDLE hFind = INVALID_HANDLE_VALUE;
249 char progfolder[GMX_PATH_MAX];
250 char defpathenv[GMX_PATH_MAX];
251 const char *defpath_suffix = "\\plugins\\WIN32\\molfile";
252 SHGetFolderPath(NULL,CSIDL_PROGRAM_FILES,NULL,SHGFP_TYPE_CURRENT,progfolder);
253 sprintf(defpathenv,"%s\\University of Illinois\\VMD\\plugins\\WIN32\\molfile",progfolder);
256 vmdplugin->api = NULL;
257 vmdplugin->filetype = strrchr(fn,'.');
258 if (!vmdplugin->filetype)
262 vmdplugin->filetype++;
264 /* First look for an explicit path given at run time for the
265 * plugins, then an implicit run-time path, and finally for one
266 * given at configure time. This last might be hard-coded to the
267 * default for VMD installs. */
268 pathenv = getenv("VMD_PLUGIN_PATH");
271 pathenv = getenv("VMDDIR");
274 printf("\nNeither VMD_PLUGIN_PATH or VMDDIR set. ");
275 printf("Using default location:\n%s\n",defpathenv);
280 printf("\nVMD_PLUGIN_PATH no set, but VMDDIR is set. ");
282 _snprintf_s(pathenv_buffer, sizeof(pathenv_buffer), _TRUNCATE, "%s%s", pathenv, defpath_suffix);
284 snprintf(pathenv_buffer, sizeof(pathenv_buffer), "%s%s", pathenv, defpath_suffix);
286 printf("Using semi-default location:\n%s\n",pathenv_buffer);
287 pathenv = pathenv_buffer;
290 strncpy(pathname,pathenv,sizeof(pathname));
291 #ifndef GMX_NATIVE_WINDOWS
292 strcat(pathname,"/*.so");
293 glob(pathname, 0, NULL, &globbuf);
294 if (globbuf.gl_pathc == 0)
296 printf("\nNo VMD Plugins found\n"
297 "Set the environment variable VMD_PLUGIN_PATH to the molfile folder within the\n"
298 "VMD installation.\n"
299 "The architecture (e.g. 32bit versus 64bit) of Gromacs and VMD has to match.\n");
302 for (i=0; i<globbuf.gl_pathc && vmdplugin->api == NULL; i++)
304 /* FIXME: Undefined which plugin is chosen if more than one plugin
305 can read a certain file ending. Requires some additional command
306 line option or enviroment variable to specify which plugin should
309 ret|=load_sharedlibrary_plugins(globbuf.gl_pathv[i],vmdplugin);
313 strcat(pathname,"\\*.so");
314 hFind = FindFirstFile(pathname, &ffd);
315 if (INVALID_HANDLE_VALUE == hFind)
317 printf("\nNo VMD Plugins found\n");
322 sprintf(filename,"%s\\%s",pathenv,ffd.cFileName);
323 ret|=load_sharedlibrary_plugins(filename,vmdplugin);
325 while (FindNextFile(hFind, &ffd ) != 0 && vmdplugin->api == NULL );
331 printf("\nCould not open any VMD library.\n");
335 printf("Compiled with dlopen?\n");
339 printf("Last error:\n%s\n",err);
344 if (vmdplugin->api == NULL)
346 printf("\nNo plugin for %s found\n",vmdplugin->filetype);
350 if (vmdplugin->api->abiversion < 10)
352 printf("\nPlugin and/or VMD is too old. At least VMD 1.8.6 is required.\n");
356 printf("\nUsing VMD plugin: %s (%s)\n",vmdplugin->api->name,vmdplugin->api->prettyname);
362 int read_first_vmd_frame(int *status,const char *fn,t_trxframe *fr,int flags)
364 molfile_timestep_metadata_t *metadata=NULL;
366 snew(fr->vmdplugin,1);
367 if (!load_vmd_library(fn,fr->vmdplugin))
372 fr->vmdplugin->handle = fr->vmdplugin->api->open_file_read(fn, fr->vmdplugin->filetype, &fr->natoms);
374 if (!fr->vmdplugin->handle) {
375 fprintf(stderr, "\nError: could not open file '%s' for reading.\n",
380 if (fr->natoms == MOLFILE_NUMATOMS_UNKNOWN) {
381 fprintf(stderr, "\nFormat of file %s does not record number of atoms.\n", fn);
383 } else if (fr->natoms == MOLFILE_NUMATOMS_NONE) {
384 fprintf(stderr, "\nNo atoms found by VMD plugin in file %s.\n", fn );
386 } else if (fr->natoms < 1) { /*should not be reached*/
387 fprintf(stderr, "\nUnknown number of atoms %d for VMD plugin opening file %s.\n",
392 snew(fr->x,fr->natoms);
394 fr->vmdplugin->bV = 0;
395 if (fr->vmdplugin->api->abiversion > 10 && fr->vmdplugin->api->read_timestep_metadata)
397 fr->vmdplugin->api->read_timestep_metadata(fr->vmdplugin->handle, metadata);
399 fr->vmdplugin->bV = metadata->has_velocities;
400 if (fr->vmdplugin->bV)
402 snew(fr->v,fr->natoms);
408 "\nThis trajectory is being read with a VMD plug-in from before VMD"
409 "\nversion 1.8, or from a trajectory that lacks time step metadata."
410 "\nEither way, GROMACS cannot tell whether the trajectory has velocities.\n");