| 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, 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 |
|
|
| 43 |
|
#include <algorithm> |
| 47 |
|
#include "io/DumpReader.hpp" |
| 48 |
|
#include "primitives/Molecule.hpp" |
| 49 |
|
#include "utils/NumericConstant.hpp" |
| 50 |
< |
namespace oopse { |
| 50 |
> |
#include "types/LennardJonesAdapter.hpp" |
| 51 |
|
|
| 52 |
+ |
namespace OpenMD { |
| 53 |
|
|
| 54 |
< |
DensityPlot::DensityPlot(SimInfo* info, const std::string& filename, const std::string& sele, const std::string& cmSele, RealType len, int nrbins) |
| 55 |
< |
: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info), |
| 56 |
< |
cmSelectionScript_(cmSele), cmEvaluator_(info), cmSeleMan_(info), |
| 57 |
< |
len_(len), nRBins_(nrbins), halfLen_(len/2) { |
| 54 |
> |
|
| 55 |
> |
DensityPlot::DensityPlot(SimInfo* info, const std::string& filename, |
| 56 |
> |
const std::string& sele, const std::string& cmSele, |
| 57 |
> |
RealType len, int nrbins) |
| 58 |
> |
: StaticAnalyser(info, filename), |
| 59 |
> |
len_(len), halfLen_(len/2), nRBins_(nrbins), |
| 60 |
> |
selectionScript_(sele), seleMan_(info), evaluator_(info), |
| 61 |
> |
cmSelectionScript_(cmSele), cmSeleMan_(info), cmEvaluator_(info) { |
| 62 |
|
|
| 63 |
|
setOutputName(getPrefix(filename) + ".density"); |
| 64 |
< |
|
| 64 |
> |
|
| 65 |
|
deltaR_ = len_ /nRBins_; |
| 66 |
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histogram_.resize(nRBins_); |
| 67 |
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density_.resize(nRBins_); |
| 77 |
|
cmEvaluator_.loadScriptString(cmSele); |
| 78 |
|
if (!cmEvaluator_.isDynamic()) { |
| 79 |
|
cmSeleMan_.setSelectionSet(cmEvaluator_.evaluate()); |
| 80 |
< |
} |
| 75 |
< |
|
| 76 |
< |
|
| 80 |
> |
} |
| 81 |
|
} |
| 82 |
|
|
| 83 |
< |
void DensityPlot::process() { |
| 84 |
< |
Molecule* mol; |
| 85 |
< |
RigidBody* rb; |
| 86 |
< |
SimInfo::MoleculeIterator mi; |
| 87 |
< |
Molecule::RigidBodyIterator rbIter; |
| 84 |
< |
|
| 85 |
< |
DumpReader reader(info_, dumpFilename_); |
| 86 |
< |
int nFrames = reader.getNFrames(); |
| 87 |
< |
for (int i = 0; i < nFrames; i += step_) { |
| 88 |
< |
reader.readFrame(i); |
| 89 |
< |
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 83 |
> |
void DensityPlot::process() { |
| 84 |
> |
Molecule* mol; |
| 85 |
> |
RigidBody* rb; |
| 86 |
> |
SimInfo::MoleculeIterator mi; |
| 87 |
> |
Molecule::RigidBodyIterator rbIter; |
| 88 |
|
|
| 89 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 89 |
> |
DumpReader reader(info_, dumpFilename_); |
| 90 |
> |
int nFrames = reader.getNFrames(); |
| 91 |
> |
for (int i = 0; i < nFrames; i += step_) { |
| 92 |
> |
reader.readFrame(i); |
| 93 |
> |
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 94 |
> |
|
| 95 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 96 |
> |
mol = info_->nextMolecule(mi)) { |
| 97 |
|
//change the positions of atoms which belong to the rigidbodies |
| 98 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 99 |
< |
rb->updateAtoms(); |
| 98 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 99 |
> |
rb = mol->nextRigidBody(rbIter)) { |
| 100 |
> |
rb->updateAtoms(); |
| 101 |
|
} |
| 102 |
|
|
| 103 |
< |
} |
| 103 |
> |
} |
| 104 |
|
|
| 105 |
< |
if (evaluator_.isDynamic()) { |
| 105 |
> |
if (evaluator_.isDynamic()) { |
| 106 |
|
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 107 |
< |
} |
| 107 |
> |
} |
| 108 |
|
|
| 109 |
< |
if (cmEvaluator_.isDynamic()) { |
| 109 |
> |
if (cmEvaluator_.isDynamic()) { |
| 110 |
|
cmSeleMan_.setSelectionSet(cmEvaluator_.evaluate()); |
| 111 |
< |
} |
| 111 |
> |
} |
| 112 |
|
|
| 113 |
< |
Vector3d origin = calcNewOrigin(); |
| 113 |
> |
Vector3d origin = calcNewOrigin(); |
| 114 |
|
|
| 115 |
< |
Mat3x3d hmat = currentSnapshot_->getHmat(); |
| 116 |
< |
RealType slabVolume = deltaR_ * hmat(0, 0) * hmat(1, 1); |
| 117 |
< |
int k; |
| 118 |
< |
for (StuntDouble* sd = seleMan_.beginSelected(k); sd != NULL; sd = seleMan_.nextSelected(k)) { |
| 115 |
> |
Mat3x3d hmat = currentSnapshot_->getHmat(); |
| 116 |
> |
RealType slabVolume = deltaR_ * hmat(0, 0) * hmat(1, 1); |
| 117 |
> |
int k; |
| 118 |
> |
for (StuntDouble* sd = seleMan_.beginSelected(k); sd != NULL; |
| 119 |
> |
sd = seleMan_.nextSelected(k)) { |
| 120 |
|
|
| 121 |
|
|
| 122 |
< |
if (!sd->isAtom()) { |
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< |
sprintf( painCave.errMsg, "Can not calculate electron density if it is not atom\n"); |
| 124 |
< |
painCave.severity = OOPSE_ERROR; |
| 125 |
< |
painCave.isFatal = 1; |
| 126 |
< |
simError(); |
| 127 |
< |
} |
| 122 |
> |
if (!sd->isAtom()) { |
| 123 |
> |
sprintf( painCave.errMsg, |
| 124 |
> |
"Can not calculate electron density if it is not atom\n"); |
| 125 |
> |
painCave.severity = OPENMD_ERROR; |
| 126 |
> |
painCave.isFatal = 1; |
| 127 |
> |
simError(); |
| 128 |
> |
} |
| 129 |
|
|
| 130 |
< |
Atom* atom = static_cast<Atom*>(sd); |
| 131 |
< |
GenericData* data = atom->getAtomType()->getPropertyByName("nelectron"); |
| 132 |
< |
if (data == NULL) { |
| 133 |
< |
sprintf( painCave.errMsg, "Can not find Parameters for nelectron\n"); |
| 134 |
< |
painCave.severity = OOPSE_ERROR; |
| 135 |
< |
painCave.isFatal = 1; |
| 136 |
< |
simError(); |
| 137 |
< |
} |
| 130 |
> |
Atom* atom = static_cast<Atom*>(sd); |
| 131 |
> |
GenericData* data = atom->getAtomType()->getPropertyByName("nelectron"); |
| 132 |
> |
if (data == NULL) { |
| 133 |
> |
sprintf( painCave.errMsg, "Can not find Parameters for nelectron\n"); |
| 134 |
> |
painCave.severity = OPENMD_ERROR; |
| 135 |
> |
painCave.isFatal = 1; |
| 136 |
> |
simError(); |
| 137 |
> |
} |
| 138 |
|
|
| 139 |
< |
DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data); |
| 140 |
< |
if (doubleData == NULL) { |
| 141 |
< |
sprintf( painCave.errMsg, |
| 142 |
< |
"Can not cast GenericData to DoubleGenericData\n"); |
| 143 |
< |
painCave.severity = OOPSE_ERROR; |
| 144 |
< |
painCave.isFatal = 1; |
| 145 |
< |
simError(); |
| 146 |
< |
} |
| 139 |
> |
DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data); |
| 140 |
> |
if (doubleData == NULL) { |
| 141 |
> |
sprintf( painCave.errMsg, |
| 142 |
> |
"Can not cast GenericData to DoubleGenericData\n"); |
| 143 |
> |
painCave.severity = OPENMD_ERROR; |
| 144 |
> |
painCave.isFatal = 1; |
| 145 |
> |
simError(); |
| 146 |
> |
} |
| 147 |
|
|
| 148 |
< |
RealType nelectron = doubleData->getData(); |
| 149 |
< |
|
| 150 |
< |
data = atom->getAtomType()->getPropertyByName("LennardJones"); |
| 151 |
< |
if (data == NULL) { |
| 144 |
< |
sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n"); |
| 145 |
< |
painCave.severity = OOPSE_ERROR; |
| 146 |
< |
painCave.isFatal = 1; |
| 147 |
< |
simError(); |
| 148 |
< |
} |
| 149 |
< |
|
| 150 |
< |
LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
| 151 |
< |
if (ljData == NULL) { |
| 152 |
< |
sprintf( painCave.errMsg, |
| 153 |
< |
"Can not cast GenericData to LJParam\n"); |
| 154 |
< |
painCave.severity = OOPSE_ERROR; |
| 155 |
< |
painCave.isFatal = 1; |
| 156 |
< |
simError(); |
| 157 |
< |
} |
| 158 |
< |
|
| 159 |
< |
LJParam ljParam = ljData->getData(); |
| 160 |
< |
RealType sigma = ljParam.sigma * 0.5; |
| 161 |
< |
RealType sigma2 = sigma * sigma; |
| 162 |
< |
|
| 163 |
< |
Vector3d pos = sd->getPos() - origin; |
| 164 |
< |
for (int j =0; j < nRBins_; ++j) { |
| 165 |
< |
Vector3d tmp(pos); |
| 166 |
< |
RealType zdist =j * deltaR_ - halfLen_; |
| 167 |
< |
tmp[2] += zdist; |
| 168 |
< |
if (usePeriodicBoundaryConditions_) |
| 169 |
< |
currentSnapshot_->wrapVector(tmp); |
| 170 |
< |
|
| 171 |
< |
RealType wrappedZdist = tmp.z() + halfLen_; |
| 172 |
< |
if (wrappedZdist < 0.0 || wrappedZdist > len_) { |
| 173 |
< |
continue; |
| 174 |
< |
} |
| 175 |
< |
|
| 176 |
< |
int which =wrappedZdist / deltaR_; |
| 177 |
< |
density_[which] += nelectron * exp(-zdist*zdist/(sigma2*2.0)) /(slabVolume* sqrt(2*NumericConstant::PI*sigma*sigma)); |
| 178 |
< |
|
| 179 |
< |
} |
| 148 |
> |
RealType nelectron = doubleData->getData(); |
| 149 |
> |
LennardJonesAdapter lja = LennardJonesAdapter(atom->getAtomType()); |
| 150 |
> |
RealType sigma = lja.getSigma() * 0.5; |
| 151 |
> |
RealType sigma2 = sigma * sigma; |
| 152 |
|
|
| 153 |
< |
|
| 154 |
< |
|
| 155 |
< |
} |
| 153 |
> |
Vector3d pos = sd->getPos() - origin; |
| 154 |
> |
for (int j =0; j < nRBins_; ++j) { |
| 155 |
> |
Vector3d tmp(pos); |
| 156 |
> |
RealType zdist =j * deltaR_ - halfLen_; |
| 157 |
> |
tmp[2] += zdist; |
| 158 |
> |
if (usePeriodicBoundaryConditions_) |
| 159 |
> |
currentSnapshot_->wrapVector(tmp); |
| 160 |
> |
|
| 161 |
> |
RealType wrappedZdist = tmp.z() + halfLen_; |
| 162 |
> |
if (wrappedZdist < 0.0 || wrappedZdist > len_) { |
| 163 |
> |
continue; |
| 164 |
> |
} |
| 165 |
> |
|
| 166 |
> |
int which = int(wrappedZdist / deltaR_); |
| 167 |
> |
density_[which] += nelectron * exp(-zdist*zdist/(sigma2*2.0)) /(slabVolume* sqrt(2*NumericConstant::PI*sigma*sigma)); |
| 168 |
> |
|
| 169 |
> |
} |
| 170 |
> |
} |
| 171 |
|
} |
| 172 |
< |
|
| 173 |
< |
int nProcessed = nFrames /step_; |
| 174 |
< |
std::transform(density_.begin(), density_.end(), density_.begin(), std::bind2nd(std::divides<RealType>(), nProcessed)); |
| 175 |
< |
writeDensity(); |
| 172 |
> |
|
| 173 |
> |
int nProcessed = nFrames /step_; |
| 174 |
> |
std::transform(density_.begin(), density_.end(), density_.begin(), |
| 175 |
> |
std::bind2nd(std::divides<RealType>(), nProcessed)); |
| 176 |
> |
writeDensity(); |
| 177 |
|
|
| 178 |
|
|
| 179 |
|
|
| 180 |
< |
} |
| 180 |
> |
} |
| 181 |
|
|
| 182 |
< |
Vector3d DensityPlot::calcNewOrigin() { |
| 182 |
> |
Vector3d DensityPlot::calcNewOrigin() { |
| 183 |
|
|
| 184 |
|
int i; |
| 185 |
|
Vector3d newOrigin(0.0); |
| 186 |
|
RealType totalMass = 0.0; |
| 187 |
< |
for (StuntDouble* sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) { |
| 188 |
< |
RealType mass = sd->getMass(); |
| 189 |
< |
totalMass += mass; |
| 190 |
< |
newOrigin += sd->getPos() * mass; |
| 187 |
> |
for (StuntDouble* sd = seleMan_.beginSelected(i); sd != NULL; |
| 188 |
> |
sd = seleMan_.nextSelected(i)) { |
| 189 |
> |
RealType mass = sd->getMass(); |
| 190 |
> |
totalMass += mass; |
| 191 |
> |
newOrigin += sd->getPos() * mass; |
| 192 |
|
} |
| 193 |
|
newOrigin /= totalMass; |
| 194 |
|
return newOrigin; |
| 195 |
< |
} |
| 195 |
> |
} |
| 196 |
|
|
| 197 |
< |
void DensityPlot::writeDensity() { |
| 197 |
> |
void DensityPlot::writeDensity() { |
| 198 |
|
std::ofstream ofs(outputFilename_.c_str(), std::ios::binary); |
| 199 |
|
if (ofs.is_open()) { |
| 200 |
|
ofs << "#g(x, y, z)\n"; |
| 201 |
|
ofs << "#selection: (" << selectionScript_ << ")\n"; |
| 202 |
|
ofs << "#cmSelection:(" << cmSelectionScript_ << ")\n"; |
| 203 |
< |
ofs << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "\tdeltaR = " << deltaR_ <<"\n"; |
| 204 |
< |
for (int i = 0; i < histogram_.size(); ++i) { |
| 205 |
< |
ofs << i*deltaR_ - halfLen_ <<"\t" << density_[i]<< std::endl; |
| 203 |
> |
ofs << "#nRBins = " << nRBins_ << "\t maxLen = " |
| 204 |
> |
<< len_ << "\tdeltaR = " << deltaR_ <<"\n"; |
| 205 |
> |
for (unsigned int i = 0; i < histogram_.size(); ++i) { |
| 206 |
> |
ofs << i*deltaR_ - halfLen_ <<"\t" << density_[i]<< std::endl; |
| 207 |
|
} |
| 208 |
|
} else { |
| 209 |
|
|
| 210 |
< |
sprintf(painCave.errMsg, "DensityPlot: unable to open %s\n", outputFilename_.c_str()); |
| 210 |
> |
sprintf(painCave.errMsg, "DensityPlot: unable to open %s\n", |
| 211 |
> |
outputFilename_.c_str()); |
| 212 |
|
painCave.isFatal = 1; |
| 213 |
|
simError(); |
| 214 |
|
} |
| 216 |
|
ofs.close(); |
| 217 |
|
|
| 218 |
|
|
| 219 |
< |
} |
| 219 |
> |
} |
| 220 |
|
|
| 221 |
|
} |
| 222 |
|
|
