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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
106 #include "gromacs/fileio/gmxfio.h"
107 #include "gromacs/fileio/trx.h"
108 #include "gromacs/math/vec.h"
109 #include "gromacs/utility/basedefinitions.h"
110 #include "gromacs/utility/futil.h"
111 #include "gromacs/utility/smalloc.h"
114 typedef int (*initfunc)(void);
115 typedef int (*regfunc)(void *, vmdplugin_register_cb);
116 typedef int (*finifunc)(void);
120 static int register_cb(void *v, vmdplugin_t *p)
122 const char *key = p->name;
123 t_gmxvmdplugin *vmdplugin = (t_gmxvmdplugin*)v;
125 if (strcmp(key, vmdplugin->filetype) == 0)
127 vmdplugin->api = (molfile_plugin_t *)p;
129 return VMDPLUGIN_SUCCESS;
132 static int load_sharedlibrary_plugins(const char *fullpath, t_gmxvmdplugin* vmdplugin)
134 /* Open the dll; try to execute the init function. */
135 void *handle, *ifunc, *registerfunc;
136 handle = vmddlopen(fullpath);
141 fprintf(debug, "\nUnable to open dynamic library %s.\n%s\n", fullpath, vmddlerror()); /*only to debug because of stdc++ erros */
146 ifunc = vmddlsym(handle, "vmdplugin_init");
147 if (!ifunc || ((initfunc)(ifunc))())
149 printf("\nvmdplugin_init() for %s returned an error; plugin(s) not loaded.\n", fullpath);
154 registerfunc = vmddlsym(handle, "vmdplugin_register");
157 printf("\nDidn't find the register function in %s; plugin(s) not loaded.\n", fullpath);
163 /* Load plugins from the library.*/
164 ((regfunc)registerfunc)(vmdplugin, register_cb);
167 /* in case this library does not support the filetype, close it */
168 if (vmdplugin->api == NULL)
176 /*return: 1: success, 0: last frame, -1: error*/
177 gmx_bool read_next_vmd_frame(t_trxframe *fr)
181 molfile_timestep_t ts;
184 fr->bV = fr->vmdplugin->bV;
187 snew(ts.coords, fr->natoms*3);
190 snew(ts.velocities, fr->natoms*3);
193 ts.coords = (float*)fr->x;
196 ts.velocities = (float*)fr->v;
200 rc = fr->vmdplugin->api->read_next_timestep(fr->vmdplugin->handle, fr->natoms, &ts);
204 fprintf(stderr, "\nError reading input file (error code %d)\n", rc);
208 fr->vmdplugin->api->close_file_read(fr->vmdplugin->handle);
213 for (i = 0; i < fr->natoms; i++)
215 fr->x[i][0] = .1*ts.coords[i*3];
216 fr->x[i][1] = .1*ts.coords[i*3+1];
217 fr->x[i][2] = .1*ts.coords[i*3+2];
220 fr->v[i][0] = .1*ts.velocities[i*3];
221 fr->v[i][1] = .1*ts.velocities[i*3+1];
222 fr->v[i][2] = .1*ts.velocities[i*3+2];
228 sfree(ts.velocities);
231 for (i = 0; i < fr->natoms; i++)
233 svmul(.1, fr->x[i], fr->x[i]);
236 svmul(.1, fr->v[i], fr->v[i]);
243 vec[0] = .1*ts.A; vec[1] = .1*ts.B; vec[2] = .1*ts.C;
244 angle[0] = ts.alpha; angle[1] = ts.beta; angle[2] = ts.gamma;
245 matrix_convert(fr->box, vec, angle);
246 if (fr->vmdplugin->api->abiversion > 10)
249 fr->time = ts.physical_time;
260 static int load_vmd_library(const char *fn, t_gmxvmdplugin *vmdplugin)
262 char pathname[GMX_PATH_MAX], filename[GMX_PATH_MAX];
267 char pathenv_buffer[GMX_PATH_MAX];
268 #ifndef GMX_NATIVE_WINDOWS
270 const char *defpath_suffix = "/plugins/*/molfile";
271 const char *defpathenv = GMX_VMD_PLUGIN_PATH;
274 HANDLE hFind = INVALID_HANDLE_VALUE;
275 char progfolder[GMX_PATH_MAX];
276 char defpathenv[GMX_PATH_MAX];
277 const char *defpath_suffix = "\\plugins\\WIN32\\molfile";
278 SHGetFolderPath(NULL, CSIDL_PROGRAM_FILES, NULL, SHGFP_TYPE_CURRENT, progfolder);
279 sprintf(defpathenv, "%s\\University of Illinois\\VMD\\plugins\\WIN32\\molfile", progfolder);
282 vmdplugin->api = NULL;
283 vmdplugin->filetype = strrchr(fn, '.');
284 if (!vmdplugin->filetype)
288 vmdplugin->filetype++;
290 /* First look for an explicit path given at run time for the
291 * plugins, then an implicit run-time path, and finally for one
292 * given at configure time. This last might be hard-coded to the
293 * default for VMD installs. */
294 pathenv = getenv("VMD_PLUGIN_PATH");
297 pathenv = getenv("VMDDIR");
300 printf("\nNeither VMD_PLUGIN_PATH or VMDDIR set. ");
301 printf("Using default location:\n%s\n", defpathenv);
302 pathenv = defpathenv;
306 printf("\nVMD_PLUGIN_PATH no set, but VMDDIR is set. ");
308 _snprintf_s(pathenv_buffer, sizeof(pathenv_buffer), _TRUNCATE, "%s%s", pathenv, defpath_suffix);
310 snprintf(pathenv_buffer, sizeof(pathenv_buffer), "%s%s", pathenv, defpath_suffix);
312 printf("Using semi-default location:\n%s\n", pathenv_buffer);
313 pathenv = pathenv_buffer;
316 strncpy(pathname, pathenv, sizeof(pathname));
317 #ifndef GMX_NATIVE_WINDOWS
318 strcat(pathname, "/*.so");
319 glob(pathname, 0, NULL, &globbuf);
320 if (globbuf.gl_pathc == 0)
322 printf("\nNo VMD Plugins found\n"
323 "Set the environment variable VMD_PLUGIN_PATH to the molfile folder within the\n"
324 "VMD installation.\n"
325 "The architecture (e.g. 32bit versus 64bit) of Gromacs and VMD has to match.\n");
328 for (i = 0; i < globbuf.gl_pathc && vmdplugin->api == NULL; i++)
330 /* FIXME: Undefined which plugin is chosen if more than one plugin
331 can read a certain file ending. Requires some additional command
332 line option or enviroment variable to specify which plugin should
335 ret |= load_sharedlibrary_plugins(globbuf.gl_pathv[i], vmdplugin);
339 strcat(pathname, "\\*.so");
340 hFind = FindFirstFile(pathname, &ffd);
341 if (INVALID_HANDLE_VALUE == hFind)
343 printf("\nNo VMD Plugins found\n");
348 sprintf(filename, "%s\\%s", pathenv, ffd.cFileName);
349 ret |= load_sharedlibrary_plugins(filename, vmdplugin);
351 while (FindNextFile(hFind, &ffd ) != 0 && vmdplugin->api == NULL);
357 printf("\nCould not open any VMD library.\n");
361 printf("Compiled with dlopen?\n");
365 printf("Last error:\n%s\n", err);
370 if (vmdplugin->api == NULL)
372 printf("\nNo plugin for %s found\n", vmdplugin->filetype);
376 if (vmdplugin->api->abiversion < 10)
378 printf("\nPlugin and/or VMD is too old. At least VMD 1.8.6 is required.\n");
382 printf("\nUsing VMD plugin: %s (%s)\n", vmdplugin->api->name, vmdplugin->api->prettyname);
388 int read_first_vmd_frame(const char *fn, t_trxframe *fr)
390 molfile_timestep_metadata_t *metadata = NULL;
392 snew(fr->vmdplugin, 1);
393 if (!load_vmd_library(fn, fr->vmdplugin))
398 fr->vmdplugin->handle = fr->vmdplugin->api->open_file_read(fn, fr->vmdplugin->filetype, &fr->natoms);
400 if (!fr->vmdplugin->handle)
402 fprintf(stderr, "\nError: could not open file '%s' for reading.\n",
407 if (fr->natoms == MOLFILE_NUMATOMS_UNKNOWN)
409 fprintf(stderr, "\nFormat of file %s does not record number of atoms.\n", fn);
412 else if (fr->natoms == MOLFILE_NUMATOMS_NONE)
414 fprintf(stderr, "\nNo atoms found by VMD plugin in file %s.\n", fn );
417 else if (fr->natoms < 1) /*should not be reached*/
419 fprintf(stderr, "\nUnknown number of atoms %d for VMD plugin opening file %s.\n",
424 snew(fr->x, fr->natoms);
426 fr->vmdplugin->bV = 0;
427 if (fr->vmdplugin->api->abiversion > 10 && fr->vmdplugin->api->read_timestep_metadata)
429 fr->vmdplugin->api->read_timestep_metadata(fr->vmdplugin->handle, metadata);
431 fr->vmdplugin->bV = metadata->has_velocities;
432 if (fr->vmdplugin->bV)
434 snew(fr->v, fr->natoms);
440 "\nThis trajectory is being read with a VMD plug-in from before VMD"
441 "\nversion 1.8, or from a trajectory that lacks time step metadata."
442 "\nEither way, GROMACS cannot tell whether the trajectory has velocities.\n");