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1 | < | /* |
2 | < | * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
3 | < | * |
4 | < | * The University of Notre Dame grants you ("Licensee") a |
5 | < | * non-exclusive, royalty free, license to use, modify and |
6 | < | * redistribute this software in source and binary code form, provided |
7 | < | * that the following conditions are met: |
8 | < | * |
9 | < | * 1. Acknowledgement of the program authors must be made in any |
10 | < | * publication of scientific results based in part on use of the |
11 | < | * program. An acceptable form of acknowledgement is citation of |
12 | < | * the article in which the program was described (Matthew |
13 | < | * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
14 | < | * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
15 | < | * Parallel Simulation Engine for Molecular Dynamics," |
16 | < | * J. Comput. Chem. 26, pp. 252-271 (2005)) |
17 | < | * |
18 | < | * 2. Redistributions of source code must retain the above copyright |
19 | < | * notice, this list of conditions and the following disclaimer. |
20 | < | * |
21 | < | * 3. Redistributions in binary form must reproduce the above copyright |
22 | < | * notice, this list of conditions and the following disclaimer in the |
23 | < | * documentation and/or other materials provided with the |
24 | < | * distribution. |
25 | < | * |
26 | < | * This software is provided "AS IS," without a warranty of any |
27 | < | * kind. All express or implied conditions, representations and |
28 | < | * warranties, including any implied warranty of merchantability, |
29 | < | * fitness for a particular purpose or non-infringement, are hereby |
30 | < | * excluded. The University of Notre Dame and its licensors shall not |
31 | < | * be liable for any damages suffered by licensee as a result of |
32 | < | * using, modifying or distributing the software or its |
33 | < | * derivatives. In no event will the University of Notre Dame or its |
34 | < | * licensors be liable for any lost revenue, profit or data, or for |
35 | < | * direct, indirect, special, consequential, incidental or punitive |
36 | < | * damages, however caused and regardless of the theory of liability, |
37 | < | * arising out of the use of or inability to use software, even if the |
38 | < | * University of Notre Dame has been advised of the possibility of |
39 | < | * such damages. |
40 | < | */ |
1 | > | /* |
2 | > | * Copyright (c) 2009 The University of Notre Dame. All Rights Reserved. |
3 | > | * |
4 | > | * The University of Notre Dame grants you ("Licensee") a |
5 | > | * non-exclusive, royalty free, license to use, modify and |
6 | > | * redistribute this software in source and binary code form, provided |
7 | > | * that the following conditions are met: |
8 | > | * |
9 | > | * 1. Redistributions of source code must retain the above copyright |
10 | > | * notice, this list of conditions and the following disclaimer. |
11 | > | * |
12 | > | * 2. Redistributions in binary form must reproduce the above copyright |
13 | > | * notice, this list of conditions and the following disclaimer in the |
14 | > | * documentation and/or other materials provided with the |
15 | > | * distribution. |
16 | > | * |
17 | > | * This software is provided "AS IS," without a warranty of any |
18 | > | * kind. All express or implied conditions, representations and |
19 | > | * warranties, including any implied warranty of merchantability, |
20 | > | * fitness for a particular purpose or non-infringement, are hereby |
21 | > | * excluded. The University of Notre Dame and its licensors shall not |
22 | > | * be liable for any damages suffered by licensee as a result of |
23 | > | * using, modifying or distributing the software or its |
24 | > | * derivatives. In no event will the University of Notre Dame or its |
25 | > | * licensors be liable for any lost revenue, profit or data, or for |
26 | > | * direct, indirect, special, consequential, incidental or punitive |
27 | > | * damages, however caused and regardless of the theory of liability, |
28 | > | * arising out of the use of or inability to use software, even if the |
29 | > | * University of Notre Dame has been advised of the possibility of |
30 | > | * such damages. |
31 | > | * |
32 | > | * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
33 | > | * research, please cite the appropriate papers when you publish your |
34 | > | * work. Good starting points are: |
35 | > | * |
36 | > | * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
37 | > | * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
38 | > | * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
39 | > | * [4] Vardeman & Gezelter, in progress (2009). |
40 | > | */ |
41 | ||
42 | #define _LARGEFILE_SOURCE64 | |
43 | #define _FILE_OFFSET_BITS 64 | |
# | Line 67 | Line 67 | |
67 | #endif // is_mpi | |
68 | ||
69 | ||
70 | < | namespace oopse { |
70 | > | namespace OpenMD { |
71 | ||
72 | DumpReader::DumpReader(SimInfo* info, const std::string& filename) | |
73 | : info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) { | |
# | Line 392 | Line 392 | namespace oopse { | |
392 | q[3] = tokenizer.nextTokenAsDouble(); | |
393 | ||
394 | RealType qlen = q.length(); | |
395 | < | if (qlen < oopse::epsilon) { //check quaternion is not equal to 0 |
395 | > | if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0 |
396 | ||
397 | sprintf(painCave.errMsg, | |
398 | "DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n"); | |
# | Line 549 | Line 549 | namespace oopse { | |
549 | } | |
550 | ||
551 | ||
552 | < | }//end namespace oopse |
552 | > | }//end namespace OpenMD |
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