| 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 |
|
* 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, 234107 (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 |
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|
| 43 |
|
#include <iostream> |
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|
#include "applications/hydrodynamics/HydrodynamicsModel.hpp" |
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#include "applications/hydrodynamics/HydrodynamicsModelCreator.hpp" |
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#include "applications/hydrodynamics/HydrodynamicsModelFactory.hpp" |
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+ |
#include "applications/hydrodynamics/AnalyticalModel.hpp" |
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#include "applications/hydrodynamics/BeadModel.hpp" |
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#include "applications/hydrodynamics/RoughShell.hpp" |
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+ |
#include "applications/hydrodynamics/ShapeBuilder.hpp" |
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#include "brains/Register.hpp" |
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|
#include "brains/SimCreator.hpp" |
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#include "brains/SimInfo.hpp" |
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+ |
#include "utils/StringUtils.hpp" |
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+ |
#include "utils/simError.h" |
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+ |
#include "utils/MemoryUtils.hpp" |
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+ |
using namespace OpenMD; |
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|
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< |
using namespace oopse; |
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< |
|
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< |
/** Register different hydrodynamics models */ |
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> |
struct SDShape{ |
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> |
StuntDouble* sd; |
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> |
Shape* shape; |
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> |
}; |
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void registerHydrodynamicsModels(); |
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+ |
void writeHydroProps(std::ostream& os); |
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|
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– |
bool calcHydrodynamicsProp(const std::string& modelType, StuntDouble* sd, const DynamicProperty& param, std::ostream& os, const std::string& prefix); |
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– |
|
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int main(int argc, char* argv[]){ |
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//register force fields |
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registerForceFields(); |
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registerHydrodynamicsModels(); |
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|
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gengetopt_args_info args_info; |
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exit(1); |
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} |
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|
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– |
mdFileName = dumpFileName; |
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– |
mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md"; |
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– |
|
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if (args_info.output_given){ |
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prefix = args_info.output_arg; |
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} else { |
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prefix = "hydro"; |
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> |
prefix = getPrefix(dumpFileName); |
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} |
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std::string outputFilename = prefix + ".diff"; |
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< |
|
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DynamicProperty param; |
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param.insert(DynamicProperty::value_type("Viscosity", args_info.viscosity_arg)); |
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< |
param.insert(DynamicProperty::value_type("Temperature", args_info.temperature_arg)); |
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< |
|
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< |
if (args_info.sigma_given) { |
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< |
param.insert(DynamicProperty::value_type("Sigma", args_info.sigma_arg)); |
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< |
} |
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< |
|
| 104 |
< |
|
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> |
|
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//parse md file and set up the system |
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SimCreator creator; |
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< |
SimInfo* info = creator.createSim(mdFileName, true); |
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> |
SimInfo* info = creator.createSim(dumpFileName, true); |
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|
|
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SimInfo::MoleculeIterator mi; |
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Molecule* mol; |
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Molecule::IntegrableObjectIterator ii; |
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< |
StuntDouble* integrableObject; |
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> |
StuntDouble* sd; |
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Mat3x3d identMat; |
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identMat(0,0) = 1.0; |
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|
identMat(1,1) = 1.0; |
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|
identMat(2,2) = 1.0; |
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< |
|
| 111 |
< |
|
| 112 |
< |
std::map<std::string, StuntDouble*> uniqueStuntDoubles; |
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< |
|
| 114 |
< |
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 115 |
< |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 116 |
< |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 117 |
< |
if (uniqueStuntDoubles.find(integrableObject->getType()) == uniqueStuntDoubles.end()) { |
| 118 |
< |
uniqueStuntDoubles.insert(std::map<std::string, StuntDouble*>::value_type(integrableObject->getType(), integrableObject)); |
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< |
integrableObject->setPos(V3Zero); |
| 120 |
< |
integrableObject->setA(identMat); |
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< |
if (integrableObject->isRigidBody()) { |
| 129 |
< |
RigidBody* rb = static_cast<RigidBody*>(integrableObject); |
| 130 |
< |
rb->updateAtoms(); |
| 131 |
< |
} |
| 132 |
< |
} |
| 133 |
< |
} |
| 110 |
> |
|
| 111 |
> |
Globals* simParams = info->getSimParams(); |
| 112 |
> |
RealType temperature; |
| 113 |
> |
RealType viscosity; |
| 114 |
> |
|
| 115 |
> |
if (simParams->haveViscosity()) { |
| 116 |
> |
viscosity = simParams->getViscosity(); |
| 117 |
> |
} else { |
| 118 |
> |
sprintf(painCave.errMsg, "viscosity must be set\n"); |
| 119 |
> |
painCave.isFatal = 1; |
| 120 |
> |
simError(); |
| 121 |
|
} |
| 122 |
|
|
| 123 |
< |
std::map<std::string, StuntDouble*>::iterator iter; |
| 124 |
< |
std::ofstream outputDiff(outputFilename.c_str()); |
| 125 |
< |
for (iter = uniqueStuntDoubles.begin(); iter != uniqueStuntDoubles.end(); ++iter) { |
| 126 |
< |
calcHydrodynamicsProp(args_info.model_arg, iter->second, param, outputDiff, prefix); |
| 123 |
> |
if (simParams->haveTargetTemp()) { |
| 124 |
> |
temperature = simParams->getTargetTemp(); |
| 125 |
> |
} else { |
| 126 |
> |
sprintf(painCave.errMsg, "target temperature must be set\n"); |
| 127 |
> |
painCave.isFatal = 1; |
| 128 |
> |
simError(); |
| 129 |
|
} |
| 130 |
+ |
|
| 131 |
+ |
std::map<std::string, SDShape> uniqueStuntDoubles; |
| 132 |
|
|
| 133 |
+ |
for (mol = info->beginMolecule(mi); mol != NULL; |
| 134 |
+ |
mol = info->nextMolecule(mi)) { |
| 135 |
+ |
|
| 136 |
+ |
for (sd = mol->beginIntegrableObject(ii); sd != NULL; |
| 137 |
+ |
sd = mol->nextIntegrableObject(ii)) { |
| 138 |
+ |
|
| 139 |
+ |
if (uniqueStuntDoubles.find(sd->getType()) == uniqueStuntDoubles.end()) { |
| 140 |
+ |
|
| 141 |
+ |
sd->setPos(V3Zero); |
| 142 |
+ |
sd->setA(identMat); |
| 143 |
+ |
if (sd->isRigidBody()) { |
| 144 |
+ |
RigidBody* rb = static_cast<RigidBody*>(sd); |
| 145 |
+ |
rb->updateAtoms(); |
| 146 |
+ |
} |
| 147 |
+ |
|
| 148 |
+ |
SDShape tmp; |
| 149 |
+ |
tmp.shape = ShapeBuilder::createShape(sd); |
| 150 |
+ |
tmp.sd = sd; |
| 151 |
+ |
uniqueStuntDoubles.insert(std::map<std::string, SDShape>::value_type(sd->getType(), tmp)); |
| 152 |
+ |
|
| 153 |
+ |
} |
| 154 |
+ |
} |
| 155 |
+ |
} |
| 156 |
+ |
|
| 157 |
+ |
|
| 158 |
+ |
|
| 159 |
+ |
std::map<std::string, SDShape>::iterator si; |
| 160 |
+ |
for (si = uniqueStuntDoubles.begin(); si != uniqueStuntDoubles.end(); ++si) { |
| 161 |
+ |
HydrodynamicsModel* model; |
| 162 |
+ |
Shape* shape = si->second.shape; |
| 163 |
+ |
StuntDouble* sd = si->second.sd;; |
| 164 |
+ |
if (args_info.model_given) { |
| 165 |
+ |
model = HydrodynamicsModelFactory::getInstance()->createHydrodynamicsModel(args_info.model_arg, sd, info); |
| 166 |
+ |
} else if (shape->hasAnalyticalSolution()) { |
| 167 |
+ |
model = new AnalyticalModel(sd, info); |
| 168 |
+ |
} else { |
| 169 |
+ |
model = new BeadModel(sd, info); |
| 170 |
+ |
} |
| 171 |
+ |
|
| 172 |
+ |
model->init(); |
| 173 |
+ |
|
| 174 |
+ |
std::ofstream ofs; |
| 175 |
+ |
std::stringstream outputBeads; |
| 176 |
+ |
outputBeads << prefix << "_" << model->getStuntDoubleName() << ".xyz"; |
| 177 |
+ |
ofs.open(outputBeads.str().c_str()); |
| 178 |
+ |
model->writeBeads(ofs); |
| 179 |
+ |
ofs.close(); |
| 180 |
+ |
|
| 181 |
+ |
//if beads option is turned on, skip the calculation |
| 182 |
+ |
if (!args_info.beads_flag) { |
| 183 |
+ |
model->calcHydroProps(shape, viscosity, temperature); |
| 184 |
+ |
std::ofstream outputDiff; |
| 185 |
+ |
outputDiff.open(outputFilename.c_str()); |
| 186 |
+ |
model->writeHydroProps(outputDiff); |
| 187 |
+ |
outputDiff.close(); |
| 188 |
+ |
} |
| 189 |
+ |
|
| 190 |
+ |
delete model; |
| 191 |
+ |
} |
| 192 |
+ |
|
| 193 |
+ |
|
| 194 |
+ |
//MemoryUtils::deletePointers(shapes); |
| 195 |
|
delete info; |
| 196 |
|
|
| 197 |
|
} |
| 198 |
|
|
| 199 |
|
void registerHydrodynamicsModels() { |
| 200 |
< |
HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<RoughShell>("RoughShell")); |
| 201 |
< |
HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<BeadModel>("BeadModel")); |
| 202 |
< |
|
| 200 |
> |
HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<RoughShell>("RoughShell")); |
| 201 |
> |
HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<BeadModel>("BeadModel")); |
| 202 |
> |
HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<AnalyticalModel>("AnalyticalModel")); |
| 203 |
|
} |
| 151 |
– |
|
| 152 |
– |
bool calcHydrodynamicsProp(const std::string& modelType, StuntDouble* sd, const DynamicProperty& param, std::ostream& os, const std::string& prefix) { |
| 153 |
– |
HydrodynamicsModel* hydroModel = HydrodynamicsModelFactory::getInstance()->createHydrodynamicsModel(modelType, sd, param); |
| 154 |
– |
bool ret = false; |
| 155 |
– |
if (hydroModel == NULL) { |
| 156 |
– |
std::cout << "Integrator Factory can not create " << modelType <<std::endl; |
| 157 |
– |
} |
| 158 |
– |
|
| 159 |
– |
if (hydroModel->calcHydrodyanmicsProps()) { |
| 160 |
– |
ret = true; |
| 161 |
– |
hydroModel->writeDiffCenterAndDiffTensor(os); |
| 162 |
– |
|
| 163 |
– |
std::ofstream ofs; |
| 164 |
– |
std::stringstream outputBeads; |
| 165 |
– |
outputBeads << prefix << "_" << sd->getType() << ".xyz"; |
| 166 |
– |
ofs.open(outputBeads.str().c_str()); |
| 167 |
– |
hydroModel->writeBeads(ofs); |
| 168 |
– |
ofs.close(); |
| 169 |
– |
} |
| 170 |
– |
|
| 171 |
– |
delete hydroModel; |
| 172 |
– |
|
| 173 |
– |
return ret; |
| 174 |
– |
} |
