Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : University of Illinois Open Source License
3 : Copyright 2003 Theoretical and Computational Biophysics Group,
4 : All rights reserved.
5 :
6 : Developed by: Theoretical and Computational Biophysics Group
7 : University of Illinois at Urbana-Champaign
8 : http://www.ks.uiuc.edu/
9 :
10 : Permission is hereby granted, free of charge, to any person obtaining a copy of
11 : this software and associated documentation files (the Software), to deal with
12 : the Software without restriction, including without limitation the rights to
13 : use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
14 : of the Software, and to permit persons to whom the Software is furnished to
15 : do so, subject to the following conditions:
16 :
17 : Redistributions of source code must retain the above copyright notice,
18 : this list of conditions and the following disclaimers.
19 :
20 : Redistributions in binary form must reproduce the above copyright notice,
21 : this list of conditions and the following disclaimers in the documentation
22 : and/or other materials provided with the distribution.
23 :
24 : Neither the names of Theoretical and Computational Biophysics Group,
25 : University of Illinois at Urbana-Champaign, nor the names of its contributors
26 : may be used to endorse or promote products derived from this Software without
27 : specific prior written permission.
28 :
29 : THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
30 : IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
31 : FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
32 : THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR
33 : OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
34 : ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
35 : OTHER DEALINGS WITH THE SOFTWARE.
36 : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
37 : #if defined(__PLUMED_HAS_MOLFILE_PLUGINS) && ! defined(__PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS)
38 : /***************************************************************************
39 : *cr
40 : *cr (C) Copyright 1995-2009 The Board of Trustees of the
41 : *cr University of Illinois
42 : *cr All Rights Reserved
43 : *cr
44 : ***************************************************************************/
45 :
46 : /***************************************************************************
47 : * RCS INFORMATION:
48 : *
49 : * $RCSfile: crdplugin.c,v $
50 : * $Author: johns $ $Locker: $ $State: Exp $
51 : * $Revision: 1.39 $ $Date: 2013/04/13 03:29:48 $
52 : *
53 : ***************************************************************************/
54 :
55 : /*
56 : * TODO: This plugin should probably be merged with the 'rst7' plugin, since
57 : * the differences between them are minor, and there's no logical reason
58 : * for them to be implemented completely independently as they are now.
59 : * The major differences in formatting are in regard to the 6F12.7 (rst7)
60 : * versus 10F8.3 (crd) ascii floating point conversion modes.
61 : */
62 :
63 : #include "largefiles.h" /* platform dependent 64-bit file I/O defines */
64 :
65 : #include <stdio.h>
66 : #include <stdlib.h>
67 : #include <string.h>
68 : #include "molfile_plugin.h"
69 :
70 : namespace PLMD{
71 : namespace molfile{
72 :
73 : typedef struct {
74 : FILE *file;
75 : int has_box;
76 : int numatoms;
77 : } crddata;
78 :
79 2 : static void *open_crd_read(const char *filename, const char *filetype,
80 : int *natoms) {
81 :
82 : FILE *fd;
83 : crddata *data;
84 :
85 2 : fd = fopen(filename, "rb");
86 2 : if (!fd) return NULL;
87 :
88 : /* first line is title, so skip past it */
89 162 : while (getc(fd) != '\n');
90 :
91 : /*
92 : * CRD's don't store the number of atoms in the timestep, so we assume that
93 : * the application will determine this for us.
94 : */
95 2 : data = (crddata *)malloc(sizeof(crddata));
96 2 : data->file = fd;
97 2 : *natoms = MOLFILE_NUMATOMS_UNKNOWN;
98 : /* filetype "crd" has no box; filetype "crdbox" does. */
99 2 : data->has_box = strcmp(filetype, "crd");
100 2 : return data;
101 : }
102 :
103 : /*
104 : * CRD files with box info are indistinguishable from regular CRD's.
105 : * We regard CRD's with box info as a different file format.
106 : * CRD's don't tell how many atoms there are in each frame. We therefore
107 : * rely on the numatoms field in the molfile_timestep_t parameter.
108 : */
109 5 : static int read_crd_timestep(void *mydata, int natoms, molfile_timestep_t *ts) {
110 : crddata *crd = (crddata *)mydata;
111 : int i, j;
112 : float x, y, z;
113 : float a, b, c;
114 :
115 : /* Read in the atom coordinates */
116 21382 : for (i=0; i<natoms; i++) {
117 21379 : j = fscanf(crd->file, "%f %f %f", &x, &y, &z);
118 21379 : if (j == EOF) {
119 : return MOLFILE_ERROR;
120 21377 : } else if (j <= 0) {
121 0 : fprintf(stderr, "Problem reading CRD file\n");
122 0 : return MOLFILE_ERROR;
123 : }
124 :
125 : /* only save coords if we're given a valid ts pointer */
126 : /* otherwise assume that VMD wants us to skip it. */
127 21377 : if (ts != NULL) {
128 21377 : ts->coords[3*i ] = x;
129 21377 : ts->coords[3*i+1] = y;
130 21377 : ts->coords[3*i+2] = z;
131 : }
132 : }
133 :
134 :
135 : /* Read the PBC box info. */
136 3 : if (crd->has_box) {
137 2 : j = fscanf(crd->file, "%f %f %f", &a, &b, &c);
138 2 : if (j == EOF) {
139 : printf("EOF in box\n");
140 0 : return MOLFILE_ERROR;
141 2 : } else if (j <= 0) {
142 : printf("Problem reading box part of CRD file, scanf returned %d\n",j);
143 0 : return MOLFILE_ERROR;
144 : }
145 :
146 : /* only save coords if we're given a valid ts pointer */
147 : /* otherwise assume that VMD wants us to skip it. */
148 2 : if (ts != NULL) {
149 2 : ts->A = a;
150 2 : ts->B = b;
151 2 : ts->C = c;
152 :
153 : /* XXX periodic cell angles are only stored in the PARM file */
154 : /* we should probably retrieve these from the already-loaded */
155 : /* molecule when possible. */
156 2 : ts->alpha = 90.0;
157 2 : ts->beta = 90.0;
158 2 : ts->gamma = 90.0;
159 : }
160 : }
161 :
162 : return MOLFILE_SUCCESS;
163 : }
164 :
165 2 : static void close_crd_read(void *mydata) {
166 : crddata *crd = (crddata *)mydata;
167 2 : fclose(crd->file);
168 2 : free(crd);
169 2 : }
170 :
171 0 : static void *open_crd_write(const char *path, const char *filetype,
172 : int natoms) {
173 : crddata *crd;
174 : FILE *fd;
175 :
176 0 : fd = fopen(path, "wb");
177 0 : if (!fd) {
178 0 : fprintf(stderr, "Could not open file %s for writing\n", path);
179 0 : return NULL;
180 : }
181 : fprintf(fd, "TITLE : Created by VMD with %d atoms\n", natoms);
182 :
183 0 : crd = (crddata *)malloc(sizeof(crddata));
184 0 : crd->file = fd;
185 0 : crd->numatoms = natoms;
186 0 : crd->has_box = strcmp(filetype, "crd");
187 0 : return crd;
188 : }
189 :
190 0 : static int write_crd_timestep(void *v, const molfile_timestep_t *ts) {
191 : crddata *crd = (crddata *)v;
192 : int i;
193 : int lfdone=0;
194 0 : const int ndata = crd->numatoms * 3;
195 :
196 0 : for (i=0; i<ndata; i++) {
197 : lfdone = 0;
198 0 : fprintf(crd->file, "%8.3f", ts->coords[i]);
199 0 : if ((i+1) % 10 == 0) {
200 0 : fprintf(crd->file, "\n");
201 : lfdone = 1;
202 : }
203 : }
204 0 : if (!lfdone)
205 0 : fprintf(crd->file, "\n");
206 :
207 0 : if (crd->has_box) {
208 0 : fprintf (crd->file, "%8.3f%8.3f%8.3f\n", ts->A, ts->B, ts->C);
209 : }
210 :
211 0 : return MOLFILE_SUCCESS;
212 : }
213 :
214 0 : static void close_crd_write(void *v) {
215 : crddata *crd = (crddata *)v;
216 0 : fclose(crd->file);
217 0 : free(crd);
218 0 : }
219 :
220 : /* registration stuff */
221 :
222 : static molfile_plugin_t plugin;
223 : static molfile_plugin_t crdboxplugin;
224 :
225 10632 : VMDPLUGIN_API int VMDPLUGIN_init(void) {
226 : memset(&plugin, 0, sizeof(molfile_plugin_t));
227 10632 : plugin.abiversion = vmdplugin_ABIVERSION;
228 10632 : plugin.type = MOLFILE_PLUGIN_TYPE;
229 10632 : plugin.name = "crd";
230 10632 : plugin.prettyname = "AMBER Coordinates";
231 10632 : plugin.author = "Justin Gullingsrud, John Stone";
232 : plugin.majorv = 0;
233 10632 : plugin.minorv = 9;
234 10632 : plugin.is_reentrant = VMDPLUGIN_THREADSAFE;
235 10632 : plugin.filename_extension = "mdcrd,crd";
236 10632 : plugin.open_file_read = open_crd_read;
237 10632 : plugin.read_next_timestep = read_crd_timestep;
238 10632 : plugin.close_file_read = close_crd_read;
239 10632 : plugin.open_file_write = open_crd_write;
240 10632 : plugin.write_timestep = write_crd_timestep;
241 10632 : plugin.close_file_write = close_crd_write;
242 :
243 : memcpy(&crdboxplugin, &plugin, sizeof(molfile_plugin_t));
244 10632 : crdboxplugin.name = "crdbox";
245 10632 : crdboxplugin.prettyname = "AMBER Coordinates with Periodic Box";
246 :
247 10632 : return VMDPLUGIN_SUCCESS;
248 : }
249 :
250 10632 : VMDPLUGIN_API int VMDPLUGIN_register(void *v, vmdplugin_register_cb cb) {
251 10632 : (*cb)(v, (vmdplugin_t *)&plugin);
252 10632 : (*cb)(v, (vmdplugin_t *)&crdboxplugin);
253 10632 : return VMDPLUGIN_SUCCESS;
254 : }
255 :
256 0 : VMDPLUGIN_API int VMDPLUGIN_fini(void) { return VMDPLUGIN_SUCCESS; }
257 :
258 : }
259 : }
260 :
261 : #endif
262 :
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