| 6 |
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* redistribute this software in source and binary code form, provided |
| 7 |
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* 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 |
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* 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 |
+ |
* |
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+ |
* 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 |
|
|
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|
#include <iostream> |
| 46 |
|
#include "brains/Register.hpp" |
| 47 |
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#include "brains/SimCreator.hpp" |
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#include "brains/SimInfo.hpp" |
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+ |
#include "utils/StringUtils.hpp" |
| 50 |
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#include "utils/simError.h" |
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|
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#include "applications/dynamicProps/DynamicPropsCmd.h" |
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#include "applications/dynamicProps/RadialRCorrFunc.hpp" |
| 58 |
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#include "applications/dynamicProps/ThetaCorrFunc.hpp" |
| 59 |
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#include "applications/dynamicProps/DirectionalRCorrFunc.hpp" |
| 60 |
+ |
#include "applications/dynamicProps/EnergyCorrFunc.hpp" |
| 61 |
+ |
#include "applications/dynamicProps/StressCorrFunc.hpp" |
| 62 |
+ |
#include "applications/dynamicProps/SystemDipoleCorrFunc.hpp" |
| 63 |
+ |
#include "applications/dynamicProps/MomentumCorrFunc.hpp" |
| 64 |
|
|
| 65 |
|
|
| 66 |
< |
using namespace oopse; |
| 66 |
> |
using namespace OpenMD; |
| 67 |
|
|
| 68 |
|
int main(int argc, char* argv[]){ |
| 69 |
|
|
| 87 |
|
if (args_info.sele1_given) { |
| 88 |
|
sele1 = args_info.sele1_arg; |
| 89 |
|
}else { |
| 90 |
< |
char* sele1Env= getenv("OOPSE_SELE1"); |
| 90 |
> |
char* sele1Env= getenv("SELECTION1"); |
| 91 |
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if (sele1Env) { |
| 92 |
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sele1 = sele1Env; |
| 93 |
|
}else { |
| 94 |
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sprintf( painCave.errMsg, |
| 95 |
< |
"neither --sele1 option nor $OOPSE_SELE1 is set"); |
| 96 |
< |
painCave.severity = OOPSE_ERROR; |
| 95 |
> |
"neither --sele1 option nor $SELECTION1 is set"); |
| 96 |
> |
painCave.severity = OPENMD_ERROR; |
| 97 |
|
painCave.isFatal = 1; |
| 98 |
|
simError(); |
| 99 |
|
} |
| 102 |
|
if (args_info.sele2_given) { |
| 103 |
|
sele2 = args_info.sele2_arg; |
| 104 |
|
}else { |
| 105 |
< |
char* sele2Env = getenv("OOPSE_SELE2"); |
| 105 |
> |
char* sele2Env = getenv("SELECTION2"); |
| 106 |
|
if (sele2Env) { |
| 107 |
|
sele2 = sele2Env; |
| 108 |
|
} else { |
| 110 |
|
} |
| 111 |
|
} |
| 112 |
|
|
| 113 |
+ |
// use the memory string to figure out how much memory we can use: |
| 114 |
+ |
char *end; |
| 115 |
+ |
long long int memSize = memparse(args_info.memory_arg, &end); |
| 116 |
+ |
sprintf( painCave.errMsg, |
| 117 |
+ |
"Amount of memory being used: %llu bytes\n", memSize); |
| 118 |
+ |
painCave.severity = OPENMD_INFO; |
| 119 |
+ |
painCave.isFatal = 0; |
| 120 |
+ |
simError(); |
| 121 |
+ |
|
| 122 |
|
//parse md file and set up the system |
| 123 |
|
SimCreator creator; |
| 124 |
|
SimInfo* info = creator.createSim(dumpFileName, false); |
| 125 |
|
|
| 126 |
|
|
| 127 |
|
TimeCorrFunc* corrFunc; |
| 128 |
< |
if (args_info.dcorr_given){ |
| 129 |
< |
corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2); |
| 128 |
> |
if(args_info.sdcorr_given){ |
| 129 |
> |
corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 130 |
> |
} else if (args_info.dcorr_given){ |
| 131 |
> |
corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 132 |
|
} else if (args_info.rcorr_given) { |
| 133 |
< |
corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2); |
| 133 |
> |
corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 134 |
|
} else if (args_info.r_rcorr_given) { |
| 135 |
< |
corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2); |
| 135 |
> |
corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 136 |
|
} else if (args_info.thetacorr_given) { |
| 137 |
< |
corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2); |
| 137 |
> |
corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 138 |
|
} else if (args_info.drcorr_given) { |
| 139 |
< |
corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2); |
| 140 |
< |
} |
| 141 |
< |
else if (args_info.vcorr_given) { |
| 142 |
< |
corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2); |
| 139 |
> |
corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 140 |
> |
} else if (args_info.vcorr_given) { |
| 141 |
> |
corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 142 |
> |
} else if (args_info.helfandEcorr_given){ |
| 143 |
> |
corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 144 |
> |
} else if (args_info.stresscorr_given){ |
| 145 |
> |
corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 146 |
> |
} else if (args_info.momentum_given){ |
| 147 |
> |
corrFunc = new MomentumCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 148 |
|
} else if (args_info.lcorr_given) { |
| 149 |
|
int order; |
| 150 |
|
if (args_info.order_given) |
| 152 |
|
else { |
| 153 |
|
sprintf( painCave.errMsg, |
| 154 |
|
"--order must be set if --lcoor is set\n"); |
| 155 |
< |
painCave.severity = OOPSE_ERROR; |
| 155 |
> |
painCave.severity = OPENMD_ERROR; |
| 156 |
|
painCave.isFatal = 1; |
| 157 |
|
simError(); |
| 158 |
|
} |
| 159 |
|
|
| 160 |
< |
corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order); |
| 160 |
> |
corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize); |
| 161 |
|
} |
| 162 |
|
|
| 163 |
|
if (args_info.output_given) { |
