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41 /* Derived from PluginMgr.C and catdcd.c */
43 /* PluginMgr.C: Copyright: */
44 /***************************************************************************
46 * cr (C) Copyright 1995-2009 The Board of Trustees of the
47 * cr University of Illinois
48 * cr All Rights Reserved
50 Developed by: Theoretical and Computational Biophysics Group
51 University of Illinois at Urbana-Champaign
52 http://www.ks.uiuc.edu/
54 Permission is hereby granted, free of charge, to any person obtaining a copy of
55 this software and associated documentation files (the Software), to deal with
56 the Software without restriction, including without limitation the rights to
57 use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
58 of the Software, and to permit persons to whom the Software is furnished to
59 do so, subject to the following conditions:
61 Redistributions of source code must retain the above copyright notice,
62 this list of conditions and the following disclaimers.
64 Redistributions in binary form must reproduce the above copyright notice,
65 this list of conditions and the following disclaimers in the documentation
66 and/or other materials provided with the distribution.
68 Neither the names of Theoretical and Computational Biophysics Group,
69 University of Illinois at Urbana-Champaign, nor the names of its contributors
70 may be used to endorse or promote products derived from this Software without
71 specific prior written permission.
73 THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
74 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
75 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
76 THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR
77 OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
78 ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
79 OTHER DEALINGS WITH THE SOFTWARE.
80 ***************************************************************************/
82 /* catdcd.c: Copyright: */
83 /*****************************************************************************/
85 /* (C) Copyright 2001-2005 Justin Gullingsrud and the University of Illinois.*/
87 /*****************************************************************************/
95 * Plugin header files; get plugin source from www.ks.uiuc.edu/Research/vmd"
97 #include "external/vmd_molfile/molfile_plugin.h"
98 #include "external/vmd_molfile/vmddlopen.h"
99 #ifndef GMX_NATIVE_WINDOWS
110 #include "types/simple.h"
115 typedef int (*initfunc)(void);
116 typedef int (*regfunc)(void *, vmdplugin_register_cb);
117 typedef int (*finifunc)(void);
121 static int register_cb(void *v, vmdplugin_t *p)
123 const char *key = p->name;
124 t_gmxvmdplugin *vmdplugin = (t_gmxvmdplugin*)v;
126 if (strcmp(key, vmdplugin->filetype) == 0)
128 vmdplugin->api = (molfile_plugin_t *)p;
130 return VMDPLUGIN_SUCCESS;
133 static int load_sharedlibrary_plugins(const char *fullpath, t_gmxvmdplugin* vmdplugin)
135 /* Open the dll; try to execute the init function. */
136 void *handle, *ifunc, *registerfunc;
137 handle = vmddlopen(fullpath);
142 fprintf(debug, "\nUnable to open dynamic library %s.\n%s\n", fullpath, vmddlerror()); /*only to debug because of stdc++ erros */
147 ifunc = vmddlsym(handle, "vmdplugin_init");
148 if (!ifunc || ((initfunc)(ifunc))())
150 printf("\nvmdplugin_init() for %s returned an error; plugin(s) not loaded.\n", fullpath);
155 registerfunc = vmddlsym(handle, "vmdplugin_register");
158 printf("\nDidn't find the register function in %s; plugin(s) not loaded.\n", fullpath);
164 /* Load plugins from the library.*/
165 ((regfunc)registerfunc)(vmdplugin, register_cb);
168 /* in case this library does not support the filetype, close it */
169 if (vmdplugin->api == NULL)
177 /*return: 1: success, 0: last frame, -1: error*/
178 gmx_bool read_next_vmd_frame(t_trxframe *fr)
182 molfile_timestep_t ts;
185 fr->bV = fr->vmdplugin->bV;
188 snew(ts.coords, fr->natoms*3);
191 snew(ts.velocities, fr->natoms*3);
194 ts.coords = (float*)fr->x;
197 ts.velocities = (float*)fr->v;
201 rc = fr->vmdplugin->api->read_next_timestep(fr->vmdplugin->handle, fr->natoms, &ts);
205 fprintf(stderr, "\nError reading input file (error code %d)\n", rc);
209 fr->vmdplugin->api->close_file_read(fr->vmdplugin->handle);
214 for (i = 0; i < fr->natoms; i++)
216 fr->x[i][0] = .1*ts.coords[i*3];
217 fr->x[i][1] = .1*ts.coords[i*3+1];
218 fr->x[i][2] = .1*ts.coords[i*3+2];
221 fr->v[i][0] = .1*ts.velocities[i*3];
222 fr->v[i][1] = .1*ts.velocities[i*3+1];
223 fr->v[i][2] = .1*ts.velocities[i*3+2];
229 sfree(ts.velocities);
232 for (i = 0; i < fr->natoms; i++)
234 svmul(.1, fr->x[i], fr->x[i]);
237 svmul(.1, fr->v[i], fr->v[i]);
244 vec[0] = .1*ts.A; vec[1] = .1*ts.B; vec[2] = .1*ts.C;
245 angle[0] = ts.alpha; angle[1] = ts.beta; angle[2] = ts.gamma;
246 matrix_convert(fr->box, vec, angle);
247 if (fr->vmdplugin->api->abiversion > 10)
250 fr->time = ts.physical_time;
261 static int load_vmd_library(const char *fn, t_gmxvmdplugin *vmdplugin)
263 char pathname[GMX_PATH_MAX], filename[GMX_PATH_MAX];
268 char pathenv_buffer[GMX_PATH_MAX];
269 #ifndef GMX_NATIVE_WINDOWS
271 const char *defpath_suffix = "/plugins/*/molfile";
272 const char *defpathenv = GMX_VMD_PLUGIN_PATH;
275 HANDLE hFind = INVALID_HANDLE_VALUE;
276 char progfolder[GMX_PATH_MAX];
277 char defpathenv[GMX_PATH_MAX];
278 const char *defpath_suffix = "\\plugins\\WIN32\\molfile";
279 SHGetFolderPath(NULL, CSIDL_PROGRAM_FILES, NULL, SHGFP_TYPE_CURRENT, progfolder);
280 sprintf(defpathenv, "%s\\University of Illinois\\VMD\\plugins\\WIN32\\molfile", progfolder);
283 vmdplugin->api = NULL;
284 vmdplugin->filetype = strrchr(fn, '.');
285 if (!vmdplugin->filetype)
289 vmdplugin->filetype++;
291 /* First look for an explicit path given at run time for the
292 * plugins, then an implicit run-time path, and finally for one
293 * given at configure time. This last might be hard-coded to the
294 * default for VMD installs. */
295 pathenv = getenv("VMD_PLUGIN_PATH");
298 pathenv = getenv("VMDDIR");
301 printf("\nNeither VMD_PLUGIN_PATH or VMDDIR set. ");
302 printf("Using default location:\n%s\n", defpathenv);
303 pathenv = defpathenv;
307 printf("\nVMD_PLUGIN_PATH no set, but VMDDIR is set. ");
309 _snprintf_s(pathenv_buffer, sizeof(pathenv_buffer), _TRUNCATE, "%s%s", pathenv, defpath_suffix);
311 snprintf(pathenv_buffer, sizeof(pathenv_buffer), "%s%s", pathenv, defpath_suffix);
313 printf("Using semi-default location:\n%s\n", pathenv_buffer);
314 pathenv = pathenv_buffer;
317 strncpy(pathname, pathenv, sizeof(pathname));
318 #ifndef GMX_NATIVE_WINDOWS
319 strcat(pathname, "/*.so");
320 glob(pathname, 0, NULL, &globbuf);
321 if (globbuf.gl_pathc == 0)
323 printf("\nNo VMD Plugins found\n"
324 "Set the environment variable VMD_PLUGIN_PATH to the molfile folder within the\n"
325 "VMD installation.\n"
326 "The architecture (e.g. 32bit versus 64bit) of Gromacs and VMD has to match.\n");
329 for (i = 0; i < globbuf.gl_pathc && vmdplugin->api == NULL; i++)
331 /* FIXME: Undefined which plugin is chosen if more than one plugin
332 can read a certain file ending. Requires some additional command
333 line option or enviroment variable to specify which plugin should
336 ret |= load_sharedlibrary_plugins(globbuf.gl_pathv[i], vmdplugin);
340 strcat(pathname, "\\*.so");
341 hFind = FindFirstFile(pathname, &ffd);
342 if (INVALID_HANDLE_VALUE == hFind)
344 printf("\nNo VMD Plugins found\n");
349 sprintf(filename, "%s\\%s", pathenv, ffd.cFileName);
350 ret |= load_sharedlibrary_plugins(filename, vmdplugin);
352 while (FindNextFile(hFind, &ffd ) != 0 && vmdplugin->api == NULL);
358 printf("\nCould not open any VMD library.\n");
362 printf("Compiled with dlopen?\n");
366 printf("Last error:\n%s\n", err);
371 if (vmdplugin->api == NULL)
373 printf("\nNo plugin for %s found\n", vmdplugin->filetype);
377 if (vmdplugin->api->abiversion < 10)
379 printf("\nPlugin and/or VMD is too old. At least VMD 1.8.6 is required.\n");
383 printf("\nUsing VMD plugin: %s (%s)\n", vmdplugin->api->name, vmdplugin->api->prettyname);
389 int read_first_vmd_frame(const char *fn, t_trxframe *fr)
391 molfile_timestep_metadata_t *metadata = NULL;
393 snew(fr->vmdplugin, 1);
394 if (!load_vmd_library(fn, fr->vmdplugin))
399 fr->vmdplugin->handle = fr->vmdplugin->api->open_file_read(fn, fr->vmdplugin->filetype, &fr->natoms);
401 if (!fr->vmdplugin->handle)
403 fprintf(stderr, "\nError: could not open file '%s' for reading.\n",
408 if (fr->natoms == MOLFILE_NUMATOMS_UNKNOWN)
410 fprintf(stderr, "\nFormat of file %s does not record number of atoms.\n", fn);
413 else if (fr->natoms == MOLFILE_NUMATOMS_NONE)
415 fprintf(stderr, "\nNo atoms found by VMD plugin in file %s.\n", fn );
418 else if (fr->natoms < 1) /*should not be reached*/
420 fprintf(stderr, "\nUnknown number of atoms %d for VMD plugin opening file %s.\n",
425 snew(fr->x, fr->natoms);
427 fr->vmdplugin->bV = 0;
428 if (fr->vmdplugin->api->abiversion > 10 && fr->vmdplugin->api->read_timestep_metadata)
430 fr->vmdplugin->api->read_timestep_metadata(fr->vmdplugin->handle, metadata);
432 fr->vmdplugin->bV = metadata->has_velocities;
433 if (fr->vmdplugin->bV)
435 snew(fr->v, fr->natoms);
441 "\nThis trajectory is being read with a VMD plug-in from before VMD"
442 "\nversion 1.8, or from a trajectory that lacks time step metadata."
443 "\nEither way, GROMACS cannot tell whether the trajectory has velocities.\n");