| 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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
#include <iostream> |
| 58 |
|
#include "utils/StringUtils.hpp" |
| 59 |
|
#include "utils/simError.h" |
| 60 |
|
#include "utils/MemoryUtils.hpp" |
| 61 |
< |
using namespace oopse; |
| 61 |
> |
using namespace OpenMD; |
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|
| 63 |
|
struct SDShape{ |
| 64 |
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StuntDouble* sd; |
| 65 |
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Shape* shape; |
| 66 |
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}; |
| 67 |
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void registerHydrodynamicsModels(); |
| 68 |
< |
void calcHydrodynamicsProp(HydrodynamicsModel* model, Shape* shape,double viscosity, double temperature, std::ostream& os, const std::string& prefix); |
| 68 |
> |
void writeHydroProps(std::ostream& os); |
| 69 |
|
|
| 70 |
|
int main(int argc, char* argv[]){ |
| 70 |
– |
//register force fields |
| 71 |
– |
registerForceFields(); |
| 71 |
|
registerHydrodynamicsModels(); |
| 72 |
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|
| 73 |
|
gengetopt_args_info args_info; |
| 88 |
|
exit(1); |
| 89 |
|
} |
| 90 |
|
|
| 92 |
– |
mdFileName = dumpFileName; |
| 93 |
– |
mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md"; |
| 94 |
– |
|
| 91 |
|
if (args_info.output_given){ |
| 92 |
|
prefix = args_info.output_arg; |
| 93 |
|
} else { |
| 94 |
< |
prefix = getPrefix(mdFileName); |
| 94 |
> |
prefix = getPrefix(dumpFileName); |
| 95 |
|
} |
| 96 |
|
std::string outputFilename = prefix + ".diff"; |
| 97 |
|
|
| 98 |
|
//parse md file and set up the system |
| 99 |
|
SimCreator creator; |
| 100 |
< |
SimInfo* info = creator.createSim(mdFileName, true); |
| 100 |
> |
SimInfo* info = creator.createSim(dumpFileName, true); |
| 101 |
|
|
| 102 |
|
SimInfo::MoleculeIterator mi; |
| 103 |
|
Molecule* mol; |
| 109 |
|
identMat(2,2) = 1.0; |
| 110 |
|
|
| 111 |
|
Globals* simParams = info->getSimParams(); |
| 112 |
< |
double temperature; |
| 113 |
< |
double viscosity; |
| 112 |
> |
RealType temperature; |
| 113 |
> |
RealType viscosity; |
| 114 |
|
|
| 115 |
|
if (simParams->haveViscosity()) { |
| 116 |
|
viscosity = simParams->getViscosity(); |
| 123 |
|
if (simParams->haveTargetTemp()) { |
| 124 |
|
temperature = simParams->getTargetTemp(); |
| 125 |
|
} else { |
| 126 |
< |
sprintf(painCave.errMsg, "target temperaturemust be set\n"); |
| 126 |
> |
sprintf(painCave.errMsg, "target temperature must be set\n"); |
| 127 |
|
painCave.isFatal = 1; |
| 128 |
|
simError(); |
| 129 |
|
} |
| 135 |
|
integrableObject = mol->nextIntegrableObject(ii)) { |
| 136 |
|
if (uniqueStuntDoubles.find(integrableObject->getType()) == uniqueStuntDoubles.end()) { |
| 137 |
|
|
| 142 |
– |
SDShape tmp; |
| 143 |
– |
tmp.shape = ShapeBuilder::createShape(integrableObject); |
| 144 |
– |
tmp.sd = integrableObject; |
| 145 |
– |
uniqueStuntDoubles.insert(std::map<std::string, SDShape>::value_type(integrableObject->getType(), tmp)); |
| 138 |
|
integrableObject->setPos(V3Zero); |
| 139 |
|
integrableObject->setA(identMat); |
| 140 |
|
if (integrableObject->isRigidBody()) { |
| 141 |
|
RigidBody* rb = static_cast<RigidBody*>(integrableObject); |
| 142 |
|
rb->updateAtoms(); |
| 143 |
|
} |
| 144 |
+ |
|
| 145 |
+ |
SDShape tmp; |
| 146 |
+ |
tmp.shape = ShapeBuilder::createShape(integrableObject); |
| 147 |
+ |
tmp.sd = integrableObject; |
| 148 |
+ |
uniqueStuntDoubles.insert(std::map<std::string, SDShape>::value_type(integrableObject->getType(), tmp)); |
| 149 |
+ |
|
| 150 |
|
} |
| 151 |
|
} |
| 152 |
|
} |
| 153 |
|
|
| 154 |
|
|
| 155 |
|
|
| 158 |
– |
std::ofstream outputDiff(outputFilename.c_str()); |
| 156 |
|
std::map<std::string, SDShape>::iterator si; |
| 157 |
|
for (si = uniqueStuntDoubles.begin(); si != uniqueStuntDoubles.end(); ++si) { |
| 158 |
|
HydrodynamicsModel* model; |
| 165 |
|
} else { |
| 166 |
|
model = new BeadModel(sd, info); |
| 167 |
|
} |
| 168 |
< |
calcHydrodynamicsProp(model, shape, viscosity, temperature, outputDiff, prefix); |
| 168 |
> |
|
| 169 |
> |
model->init(); |
| 170 |
> |
|
| 171 |
> |
std::ofstream ofs; |
| 172 |
> |
std::stringstream outputBeads; |
| 173 |
> |
outputBeads << prefix << "_" << model->getStuntDoubleName() << ".xyz"; |
| 174 |
> |
ofs.open(outputBeads.str().c_str()); |
| 175 |
> |
model->writeBeads(ofs); |
| 176 |
> |
ofs.close(); |
| 177 |
> |
|
| 178 |
> |
//if beads option is turned on, skip the calculation |
| 179 |
> |
if (!args_info.beads_flag) { |
| 180 |
> |
model->calcHydroProps(shape, viscosity, temperature); |
| 181 |
> |
std::ofstream outputDiff; |
| 182 |
> |
outputDiff.open(outputFilename.c_str()); |
| 183 |
> |
model->writeHydroProps(outputDiff); |
| 184 |
> |
outputDiff.close(); |
| 185 |
> |
} |
| 186 |
> |
|
| 187 |
|
delete model; |
| 188 |
|
} |
| 189 |
|
|
| 199 |
|
HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<AnalyticalModel>("AnalyticalModel")); |
| 200 |
|
|
| 201 |
|
} |
| 187 |
– |
void calcHydrodynamicsProp(HydrodynamicsModel* model, Shape* shape,double viscosity, double temperature, std::ostream& os, const std::string& prefix) { |
| 188 |
– |
|
| 189 |
– |
shape->calcHydroProps(model, viscosity, temperature); |
| 190 |
– |
model->writeHydroProps(os); |
| 191 |
– |
std::ofstream ofs; |
| 192 |
– |
std::stringstream outputBeads; |
| 193 |
– |
outputBeads << prefix << "_" << model->getStuntDoubleName() << ".xyz"; |
| 194 |
– |
ofs.open(outputBeads.str().c_str()); |
| 195 |
– |
model->writeBeads(ofs); |
| 196 |
– |
ofs.close(); |
| 197 |
– |
} |
