# | Line 6 | Line 6 | |
---|---|---|
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 | /** | |
# | Line 74 | Line 74 | |
74 | #include "UseTheForce/DarkSide/simParallel_interface.h" | |
75 | #endif | |
76 | ||
77 | < | namespace oopse { |
77 | > | namespace OpenMD { |
78 | std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) { | |
79 | std::map<int, std::set<int> >::iterator i = container.find(index); | |
80 | std::set<int> result; | |
# | Line 969 | Line 969 | namespace oopse { | |
969 | sprintf( painCave.errMsg, | |
970 | "There was an error setting the simulation information in fortran.\n" ); | |
971 | painCave.isFatal = 1; | |
972 | < | painCave.severity = OOPSE_ERROR; |
972 | > | painCave.severity = OPENMD_ERROR; |
973 | simError(); | |
974 | } | |
975 | ||
# | Line 1105 | Line 1105 | namespace oopse { | |
1105 | rsw_ = 0.85 * rcut_; | |
1106 | sprintf(painCave.errMsg, | |
1107 | "SimCreator Warning: No value was set for the switchingRadius.\n" | |
1108 | < | "\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n" |
1108 | > | "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n" |
1109 | "\tswitchingRadius = %f. for this simulation\n", rsw_); | |
1110 | painCave.isFatal = 0; | |
1111 | simError(); | |
# | Line 1113 | Line 1113 | namespace oopse { | |
1113 | rsw_ = rcut_; | |
1114 | sprintf(painCave.errMsg, | |
1115 | "SimCreator Warning: No value was set for the switchingRadius.\n" | |
1116 | < | "\tOOPSE will use the same value as the cutoffRadius.\n" |
1116 | > | "\tOpenMD will use the same value as the cutoffRadius.\n" |
1117 | "\tswitchingRadius = %f. for this simulation\n", rsw_); | |
1118 | painCave.isFatal = 0; | |
1119 | simError(); | |
# | Line 1139 | Line 1139 | namespace oopse { | |
1139 | if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { | |
1140 | sprintf(painCave.errMsg, | |
1141 | "SimCreator Warning: No value was set for the cutoffRadius.\n" | |
1142 | < | "\tOOPSE will use a default value of 15.0 angstroms" |
1142 | > | "\tOpenMD will use a default value of 15.0 angstroms" |
1143 | "\tfor the cutoffRadius.\n"); | |
1144 | painCave.isFatal = 0; | |
1145 | simError(); | |
# | Line 1173 | Line 1173 | namespace oopse { | |
1173 | } else { | |
1174 | sprintf(painCave.errMsg, | |
1175 | "SimCreator Warning: No value was set for switchingRadius.\n" | |
1176 | < | "\tOOPSE will use a default value of\n" |
1176 | > | "\tOpenMD will use a default value of\n" |
1177 | "\t0.85 * cutoffRadius for the switchingRadius\n"); | |
1178 | painCave.isFatal = 0; | |
1179 | simError(); | |
# | Line 1634 | Line 1634 | namespace oopse { | |
1634 | return sdByGlobalIndex_.at(index); | |
1635 | } | |
1636 | */ | |
1637 | < | }//end namespace oopse |
1637 | > | }//end namespace OpenMD |
1638 |
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