| 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. |
| 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 |
|
*/ |
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|
|
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|
/** |
| 74 |
|
#include "UseTheForce/DarkSide/simParallel_interface.h" |
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|
#endif |
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|
|
| 77 |
< |
namespace oopse { |
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> |
namespace OpenMD { |
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|
std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) { |
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std::map<int, std::set<int> >::iterator i = container.find(index); |
| 80 |
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std::set<int> result; |
| 409 |
|
|
| 410 |
|
a = bond->getAtomA()->getGlobalIndex(); |
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|
b = bond->getAtomB()->getGlobalIndex(); |
| 412 |
< |
|
| 412 |
> |
|
| 413 |
|
if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) { |
| 414 |
|
oneTwoInteractions_.addPair(a, b); |
| 415 |
|
} else { |
| 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 |
|
|
| 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()){ |
| 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(); |
| 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(); |
| 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 { |
| 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(); |
| 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()){ |
| 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(); |
| 1634 |
|
return sdByGlobalIndex_.at(index); |
| 1635 |
|
} |
| 1636 |
|
*/ |
| 1637 |
< |
}//end namespace oopse |
| 1637 |
> |
}//end namespace OpenMD |
| 1638 |
|
|
