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39 /* Derived from PluginMgr.C and catdcd.c */
41 /* PluginMgr.C: Copyright: */
42 /***************************************************************************
44 * cr (C) Copyright 1995-2009 The Board of Trustees of the
45 * cr University of Illinois
46 * cr All Rights Reserved
48 Developed by: Theoretical and Computational Biophysics Group
49 University of Illinois at Urbana-Champaign
50 http://www.ks.uiuc.edu/
52 Permission is hereby granted, free of charge, to any person obtaining a copy of
53 this software and associated documentation files (the Software), to deal with
54 the Software without restriction, including without limitation the rights to
55 use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
56 of the Software, and to permit persons to whom the Software is furnished to
57 do so, subject to the following conditions:
59 Redistributions of source code must retain the above copyright notice,
60 this list of conditions and the following disclaimers.
62 Redistributions in binary form must reproduce the above copyright notice,
63 this list of conditions and the following disclaimers in the documentation
64 and/or other materials provided with the distribution.
66 Neither the names of Theoretical and Computational Biophysics Group,
67 University of Illinois at Urbana-Champaign, nor the names of its contributors
68 may be used to endorse or promote products derived from this Software without
69 specific prior written permission.
71 THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
72 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
73 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
74 THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR
75 OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
76 ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
77 OTHER DEALINGS WITH THE SOFTWARE.
78 ***************************************************************************/
80 /* catdcd.c: Copyright: */
81 /*****************************************************************************/
83 /* (C) Copyright 2001-2005 Justin Gullingsrud and the University of Illinois.*/
85 /*****************************************************************************/
93 * Plugin header files; get plugin source from www.ks.uiuc.edu/Research/vmd"
95 #include "external/vmd_molfile/molfile_plugin.h"
96 #include "external/vmd_molfile/vmddlopen.h"
97 #ifndef GMX_NATIVE_WINDOWS
104 #include "gromacs/fileio/gmxfio.h"
105 #include "gromacs/fileio/trx.h"
106 #include "gromacs/math/vec.h"
107 #include "gromacs/utility/basedefinitions.h"
108 #include "gromacs/utility/futil.h"
109 #include "gromacs/utility/smalloc.h"
112 typedef int (*initfunc)(void);
113 typedef int (*regfunc)(void *, vmdplugin_register_cb);
114 typedef int (*finifunc)(void);
118 static int register_cb(void *v, vmdplugin_t *p)
120 const char *key = p->name;
121 t_gmxvmdplugin *vmdplugin = (t_gmxvmdplugin*)v;
123 if (strcmp(key, vmdplugin->filetype) == 0)
125 vmdplugin->api = (molfile_plugin_t *)p;
127 return VMDPLUGIN_SUCCESS;
130 static int load_sharedlibrary_plugins(const char *fullpath, t_gmxvmdplugin* vmdplugin)
132 /* Open the dll; try to execute the init function. */
133 void *handle, *ifunc, *registerfunc;
134 handle = vmddlopen(fullpath);
139 fprintf(debug, "\nUnable to open dynamic library %s.\n%s\n", fullpath, vmddlerror()); /*only to debug because of stdc++ erros */
144 ifunc = vmddlsym(handle, "vmdplugin_init");
145 if (!ifunc || ((initfunc)(ifunc))())
147 printf("\nvmdplugin_init() for %s returned an error; plugin(s) not loaded.\n", fullpath);
152 registerfunc = vmddlsym(handle, "vmdplugin_register");
155 printf("\nDidn't find the register function in %s; plugin(s) not loaded.\n", fullpath);
161 /* Load plugins from the library.*/
162 ((regfunc)registerfunc)(vmdplugin, register_cb);
165 /* in case this library does not support the filetype, close it */
166 if (vmdplugin->api == NULL)
174 /*return: 1: success, 0: last frame, -1: error*/
175 gmx_bool read_next_vmd_frame(t_trxframe *fr)
179 molfile_timestep_t ts;
182 fr->bV = fr->vmdplugin->bV;
185 snew(ts.coords, fr->natoms*3);
188 snew(ts.velocities, fr->natoms*3);
191 ts.coords = (float*)fr->x;
194 ts.velocities = (float*)fr->v;
198 rc = fr->vmdplugin->api->read_next_timestep(fr->vmdplugin->handle, fr->natoms, &ts);
202 fprintf(stderr, "\nError reading input file (error code %d)\n", rc);
206 fr->vmdplugin->api->close_file_read(fr->vmdplugin->handle);
211 for (i = 0; i < fr->natoms; i++)
213 fr->x[i][0] = .1*ts.coords[i*3];
214 fr->x[i][1] = .1*ts.coords[i*3+1];
215 fr->x[i][2] = .1*ts.coords[i*3+2];
218 fr->v[i][0] = .1*ts.velocities[i*3];
219 fr->v[i][1] = .1*ts.velocities[i*3+1];
220 fr->v[i][2] = .1*ts.velocities[i*3+2];
226 sfree(ts.velocities);
229 for (i = 0; i < fr->natoms; i++)
231 svmul(.1, fr->x[i], fr->x[i]);
234 svmul(.1, fr->v[i], fr->v[i]);
241 vec[0] = .1*ts.A; vec[1] = .1*ts.B; vec[2] = .1*ts.C;
242 angle[0] = ts.alpha; angle[1] = ts.beta; angle[2] = ts.gamma;
243 matrix_convert(fr->box, vec, angle);
244 if (fr->vmdplugin->api->abiversion > 10)
247 fr->time = ts.physical_time;
258 static int load_vmd_library(const char *fn, t_gmxvmdplugin *vmdplugin)
260 char pathname[GMX_PATH_MAX], filename[GMX_PATH_MAX];
265 char pathenv_buffer[GMX_PATH_MAX];
266 #ifndef GMX_NATIVE_WINDOWS
268 const char *defpath_suffix = "/plugins/*/molfile";
269 const char *defpathenv = GMX_VMD_PLUGIN_PATH;
272 HANDLE hFind = INVALID_HANDLE_VALUE;
273 char progfolder[GMX_PATH_MAX];
274 char defpathenv[GMX_PATH_MAX];
275 const char *defpath_suffix = "\\plugins\\WIN32\\molfile";
276 SHGetFolderPath(NULL, CSIDL_PROGRAM_FILES, NULL, SHGFP_TYPE_CURRENT, progfolder);
277 sprintf(defpathenv, "%s\\University of Illinois\\VMD\\plugins\\WIN32\\molfile", progfolder);
280 vmdplugin->api = NULL;
281 vmdplugin->filetype = strrchr(fn, '.');
282 if (!vmdplugin->filetype)
286 vmdplugin->filetype++;
288 /* First look for an explicit path given at run time for the
289 * plugins, then an implicit run-time path, and finally for one
290 * given at configure time. This last might be hard-coded to the
291 * default for VMD installs. */
292 pathenv = getenv("VMD_PLUGIN_PATH");
295 pathenv = getenv("VMDDIR");
298 printf("\nNeither VMD_PLUGIN_PATH or VMDDIR set. ");
299 printf("Using default location:\n%s\n", defpathenv);
300 pathenv = defpathenv;
304 printf("\nVMD_PLUGIN_PATH no set, but VMDDIR is set. ");
306 _snprintf_s(pathenv_buffer, sizeof(pathenv_buffer), _TRUNCATE, "%s%s", pathenv, defpath_suffix);
308 snprintf(pathenv_buffer, sizeof(pathenv_buffer), "%s%s", pathenv, defpath_suffix);
310 printf("Using semi-default location:\n%s\n", pathenv_buffer);
311 pathenv = pathenv_buffer;
314 strncpy(pathname, pathenv, sizeof(pathname));
315 #ifndef GMX_NATIVE_WINDOWS
316 strcat(pathname, "/*.so");
317 glob(pathname, 0, NULL, &globbuf);
318 if (globbuf.gl_pathc == 0)
320 printf("\nNo VMD Plugins found\n"
321 "Set the environment variable VMD_PLUGIN_PATH to the molfile folder within the\n"
322 "VMD installation.\n"
323 "The architecture (e.g. 32bit versus 64bit) of Gromacs and VMD has to match.\n");
326 for (i = 0; i < globbuf.gl_pathc && vmdplugin->api == NULL; i++)
328 /* FIXME: Undefined which plugin is chosen if more than one plugin
329 can read a certain file ending. Requires some additional command
330 line option or enviroment variable to specify which plugin should
333 ret |= load_sharedlibrary_plugins(globbuf.gl_pathv[i], vmdplugin);
337 strcat(pathname, "\\*.so");
338 hFind = FindFirstFile(pathname, &ffd);
339 if (INVALID_HANDLE_VALUE == hFind)
341 printf("\nNo VMD Plugins found\n");
346 sprintf(filename, "%s\\%s", pathenv, ffd.cFileName);
347 ret |= load_sharedlibrary_plugins(filename, vmdplugin);
349 while (FindNextFile(hFind, &ffd ) != 0 && vmdplugin->api == NULL);
355 printf("\nCould not open any VMD library.\n");
359 printf("Compiled with dlopen?\n");
363 printf("Last error:\n%s\n", err);
368 if (vmdplugin->api == NULL)
370 printf("\nNo plugin for %s found\n", vmdplugin->filetype);
374 if (vmdplugin->api->abiversion < 10)
376 printf("\nPlugin and/or VMD is too old. At least VMD 1.8.6 is required.\n");
380 printf("\nUsing VMD plugin: %s (%s)\n", vmdplugin->api->name, vmdplugin->api->prettyname);
386 int read_first_vmd_frame(const char *fn, t_trxframe *fr)
388 molfile_timestep_metadata_t *metadata = NULL;
390 snew(fr->vmdplugin, 1);
391 if (!load_vmd_library(fn, fr->vmdplugin))
396 fr->vmdplugin->handle = fr->vmdplugin->api->open_file_read(fn, fr->vmdplugin->filetype, &fr->natoms);
398 if (!fr->vmdplugin->handle)
400 fprintf(stderr, "\nError: could not open file '%s' for reading.\n",
405 if (fr->natoms == MOLFILE_NUMATOMS_UNKNOWN)
407 fprintf(stderr, "\nFormat of file %s does not record number of atoms.\n", fn);
410 else if (fr->natoms == MOLFILE_NUMATOMS_NONE)
412 fprintf(stderr, "\nNo atoms found by VMD plugin in file %s.\n", fn );
415 else if (fr->natoms < 1) /*should not be reached*/
417 fprintf(stderr, "\nUnknown number of atoms %d for VMD plugin opening file %s.\n",
422 snew(fr->x, fr->natoms);
424 fr->vmdplugin->bV = 0;
425 if (fr->vmdplugin->api->abiversion > 10 && fr->vmdplugin->api->read_timestep_metadata)
427 fr->vmdplugin->api->read_timestep_metadata(fr->vmdplugin->handle, metadata);
429 fr->vmdplugin->bV = metadata->has_velocities;
430 if (fr->vmdplugin->bV)
432 snew(fr->v, fr->natoms);
438 "\nThis trajectory is being read with a VMD plug-in from before VMD"
439 "\nversion 1.8, or from a trajectory that lacks time step metadata."
440 "\nEither way, GROMACS cannot tell whether the trajectory has velocities.\n");