# | Line 6 | Line 6 | |
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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 |
9 | > | * 1. Redistributions of source code must retain the above copyright |
10 | * notice, this list of conditions and the following disclaimer. | |
11 | * | |
12 | < | * 3. Redistributions in binary form must reproduce the above copyright |
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. | |
# | Line 37 | Line 28 | |
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 | #ifndef SELECTION_SELECTIONCOMPILER_HPP | |
# | Line 45 | Line 45 | |
45 | #include <string> | |
46 | #include <vector> | |
47 | ||
48 | < | #include "selection/Token.hpp" |
48 | > | #include "selection/SelectionToken.hpp" |
49 | #include "selection/TokenMap.hpp" | |
50 | < | namespace oopse { |
50 | > | #include "brains/SimInfo.hpp" |
51 | ||
52 | + | namespace OpenMD { |
53 | ||
54 | + | |
55 | /** | |
56 | * @class SelectionCompiler SelectionCompiler.hpp "selection/SelectionCompiler.hpp" | |
57 | * @brief compile a selection script to tokens | |
# | Line 148 | Line 150 | namespace oopse { | |
150 | bool isNameValid(const std::string& name); | |
151 | ||
152 | bool compileError(const std::string& errorMsg) { | |
153 | < | std::cerr << "SelectionCompiler Error: " << errorMsg << std::endl; |
153 | > | |
154 | > | sprintf( painCave.errMsg, |
155 | > | "SelectionCompiler Error: %s\n", errorMsg.c_str()); |
156 | > | painCave.severity = OPENMD_ERROR; |
157 | > | painCave.isFatal = 1; |
158 | > | simError(); |
159 | > | |
160 | error = true; | |
161 | this->errorMessage = errorMsg; | |
162 | return false; |
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