# | 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 | /** | |
# | 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 446 | Line 446 | namespace oopse { | |
446 | b = torsion->getAtomB()->getGlobalIndex(); | |
447 | c = torsion->getAtomC()->getGlobalIndex(); | |
448 | d = torsion->getAtomD()->getGlobalIndex(); | |
449 | < | |
449 | > | |
450 | if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) { | |
451 | oneTwoInteractions_.addPair(a, b); | |
452 | oneTwoInteractions_.addPair(b, c); | |
# | Line 763 | Line 763 | namespace oopse { | |
763 | useRF = 0; | |
764 | useSF = 0; | |
765 | useSP = 0; | |
766 | + | useBoxDipole = 0; |
767 | ||
768 | ||
769 | if (simParams_->haveElectrostaticSummationMethod()) { | |
# | Line 950 | Line 951 | namespace oopse { | |
951 | nOneThree = oneThreeInteractions_.getSize(); | |
952 | nOneFour = oneFourInteractions_.getSize(); | |
953 | ||
953 | – | std::cerr << "exculdes:\n"; |
954 | – | std::cerr << excludedInteractions_; |
955 | – | std::cerr << "\noneTwo:\n"; |
956 | – | std::cerr << oneTwoInteractions_; |
957 | – | std::cerr << "\noneThree:\n"; |
958 | – | std::cerr << oneThreeInteractions_; |
959 | – | std::cerr << "\noneFour:\n"; |
960 | – | std::cerr << oneFourInteractions_; |
961 | – | |
954 | int* excludeList = excludedInteractions_.getPairList(); | |
955 | int* oneTwoList = oneTwoInteractions_.getPairList(); | |
956 | int* oneThreeList = oneThreeInteractions_.getPairList(); | |
# | Line 977 | 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 1061 | Line 1053 | namespace oopse { | |
1053 | int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default | |
1054 | ||
1055 | // Set LJ shifting bools to false | |
1056 | < | ljsp_ = false; |
1057 | < | ljsf_ = false; |
1056 | > | ljsp_ = 0; |
1057 | > | ljsf_ = 0; |
1058 | ||
1059 | std::string myPolicy; | |
1060 | if (forceFieldOptions_.haveCutoffPolicy()){ | |
# | Line 1113 | 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 1121 | 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 1133 | Line 1125 | namespace oopse { | |
1125 | toUpper(myMethod); | |
1126 | ||
1127 | if (myMethod == "SHIFTED_POTENTIAL") { | |
1128 | < | ljsp_ = true; |
1128 | > | ljsp_ = 1; |
1129 | } else if (myMethod == "SHIFTED_FORCE") { | |
1130 | < | ljsf_ = true; |
1130 | > | ljsf_ = 1; |
1131 | } | |
1132 | } | |
1133 | + | |
1134 | notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_); | |
1135 | ||
1136 | } else { | |
# | Line 1146 | 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 1159 | Line 1152 | namespace oopse { | |
1152 | // For the time being, we're tethering the LJ shifted behavior to the | |
1153 | // electrostaticSummationMethod keyword options | |
1154 | if (myMethod == "SHIFTED_POTENTIAL") { | |
1155 | < | ljsp_ = true; |
1155 | > | ljsp_ = 1; |
1156 | } else if (myMethod == "SHIFTED_FORCE") { | |
1157 | < | ljsf_ = true; |
1157 | > | ljsf_ = 1; |
1158 | } | |
1159 | if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") { | |
1160 | if (simParams_->haveSwitchingRadius()){ | |
# | Line 1180 | 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 1641 | Line 1634 | namespace oopse { | |
1634 | return sdByGlobalIndex_.at(index); | |
1635 | } | |
1636 | */ | |
1637 | < | }//end namespace oopse |
1637 | > | }//end namespace OpenMD |
1638 |
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