| 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 |
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* 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 |
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* 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 |
+ |
* |
| 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). |
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*/ |
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|
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#include <algorithm> |
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#include "RadialDistrFunc.hpp" |
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#include "io/DumpReader.hpp" |
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#include "primitives/Molecule.hpp" |
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namespace oopse { |
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> |
namespace OpenMD { |
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|
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< |
RadialDistrFunc:: RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2) |
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: info_(info), currentSnapshot_(NULL), dumpFilename_(filename), step_(1), |
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selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), seleMan1_(info), seleMan2_(info){ |
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> |
RadialDistrFunc::RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2) |
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> |
: StaticAnalyser(info, filename), |
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> |
selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), |
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seleMan1_(info), seleMan2_(info), common_(info), sele1_minus_common_(info), sele2_minus_common_(info){ |
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|
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evaluator1_.loadScriptString(sele1); |
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evaluator2_.loadScriptString(sele2); |
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> |
evaluator1_.loadScriptString(sele1); |
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> |
evaluator2_.loadScriptString(sele2); |
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|
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if (!evaluator1_.isDynamic()) { |
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seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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} |
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if (!evaluator2_.isDynamic()) { |
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< |
seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
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} |
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> |
if (!evaluator1_.isDynamic()) { |
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> |
seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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> |
validateSelection1(seleMan1_); |
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> |
} |
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> |
if (!evaluator2_.isDynamic()) { |
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> |
seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
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> |
validateSelection2(seleMan2_); |
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> |
} |
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|
|
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< |
if (!evaluator1_.isDynamic() && !evaluator2_.isDynamic()) { |
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> |
if (!evaluator1_.isDynamic() && !evaluator2_.isDynamic()) { |
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|
//if all selections are static, we can precompute the number of real pairs |
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+ |
common_ = seleMan1_ & seleMan2_; |
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+ |
sele1_minus_common_ = seleMan1_ - common_; |
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+ |
sele2_minus_common_ = seleMan2_ - common_; |
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|
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int nSelected1 = seleMan1_.getSelectionCount(); |
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int nSelected2 = seleMan2_.getSelectionCount(); |
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< |
|
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BitSet bs = seleMan1_.getSelectionSet(); |
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bs &= seleMan2_.getSelectionSet(); |
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< |
int nIntersect = bs.countBits(); |
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|
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nRealPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; |
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} |
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> |
int nIntersect = common_.getSelectionCount(); |
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> |
|
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> |
nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; |
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} |
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|
|
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< |
} |
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> |
} |
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|
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< |
void RadialDistrFunc::process() { |
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> |
void RadialDistrFunc::process() { |
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Molecule* mol; |
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RigidBody* rb; |
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SimInfo::MoleculeIterator mi; |
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|
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DumpReader reader(info_, dumpFilename_); |
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int nFrames = reader.getNFrames(); |
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nProcessed_ = nFrames / step_ + 1; |
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> |
nProcessed_ = nFrames / step_; |
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> |
|
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for (int i = 0; i < nFrames; i += step_) { |
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< |
reader.readFrame(i); |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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> |
reader.readFrame(i); |
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> |
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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|
|
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< |
if (evaluator1_.isDynamic()) { |
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< |
seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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} |
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< |
if (evaluator2_.isDynamic()) { |
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< |
seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
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< |
} |
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> |
if (evaluator1_.isDynamic()) { |
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> |
seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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> |
validateSelection1(seleMan1_); |
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> |
} |
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> |
if (evaluator2_.isDynamic()) { |
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> |
seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
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> |
validateSelection2(seleMan2_); |
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> |
} |
| 106 |
|
|
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< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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> |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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|
|
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< |
//change the positions of atoms which belong to the rigidbodies |
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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rb->updateAtoms(); |
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< |
} |
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} |
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> |
//change the positions of atoms which belong to the rigidbodies |
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> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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> |
rb->updateAtoms(); |
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> |
} |
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> |
} |
| 114 |
|
|
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< |
initalizeHistogram(); |
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> |
initalizeHistogram(); |
| 116 |
|
|
| 110 |
– |
StuntDouble* sd1; |
| 111 |
– |
int j; |
| 112 |
– |
for (sd1 = seleMan1_.beginSelected(j); sd1 != NULL; sd1 = seleMan1_.nextSelected(j)) { |
| 117 |
|
|
| 118 |
< |
StuntDouble* sd2; |
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int k; |
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< |
for (sd2 = seleMan2_.beginSelected(k); sd2 != NULL; sd2 = seleMan2_.nextSelected(k)) { |
| 121 |
< |
if (sd1 != sd2) { |
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< |
collectHistogram(sd1, sd2); |
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< |
} |
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< |
} |
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< |
} |
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> |
|
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> |
//selections may overlap. |
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> |
// |
| 121 |
> |
// |s1 -c | c | |
| 122 |
> |
// | c |s2 - c| |
| 123 |
> |
// |
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> |
// s1 : number of selected stuntdoubles in selection1 |
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> |
// s2 : number of selected stuntdoubles in selection2 |
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> |
// c : number of intersect stuntdouble between selection1 and selection2 |
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> |
//when loop over the pairs, we can divide the looping into 3 stages |
| 128 |
> |
//stage 1 : [s1-c] [s2] |
| 129 |
> |
//stage 2 : [c] [s2 - c] |
| 130 |
> |
//stage 3 : [c] [c] |
| 131 |
> |
//stage 1 and stage 2 are completly non-overlapping |
| 132 |
> |
//stage 3 are completely overlapping |
| 133 |
|
|
| 134 |
< |
processHistogram(); |
| 134 |
> |
if (evaluator1_.isDynamic() || evaluator2_.isDynamic()) { |
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> |
common_ = seleMan1_ & seleMan2_; |
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> |
sele1_minus_common_ = seleMan1_ - common_; |
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> |
sele2_minus_common_ = seleMan2_ - common_; |
| 138 |
> |
int nSelected1 = seleMan1_.getSelectionCount(); |
| 139 |
> |
int nSelected2 = seleMan2_.getSelectionCount(); |
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> |
int nIntersect = common_.getSelectionCount(); |
| 141 |
> |
|
| 142 |
> |
nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; |
| 143 |
> |
} |
| 144 |
> |
processNonOverlapping(sele1_minus_common_, seleMan2_); |
| 145 |
> |
processNonOverlapping(common_, sele2_minus_common_); |
| 146 |
> |
processOverlapping(common_); |
| 147 |
> |
|
| 148 |
> |
processHistogram(); |
| 149 |
|
|
| 150 |
|
} |
| 151 |
|
|
| 152 |
|
postProcess(); |
| 153 |
|
|
| 154 |
|
writeRdf(); |
| 155 |
< |
} |
| 155 |
> |
} |
| 156 |
|
|
| 157 |
< |
int RadialDistrFunc::getNRealPairs() { |
| 158 |
< |
if (evaluator1_.isDynamic() || evaluator2_.isDynamic()) { |
| 159 |
< |
//if one of the selection is static, need to recompute it |
| 157 |
> |
void RadialDistrFunc::processNonOverlapping( SelectionManager& sman1, SelectionManager& sman2) { |
| 158 |
> |
StuntDouble* sd1; |
| 159 |
> |
StuntDouble* sd2; |
| 160 |
> |
int i; |
| 161 |
> |
int j; |
| 162 |
> |
|
| 163 |
> |
for (sd1 = sman1.beginSelected(i); sd1 != NULL; sd1 = sman1.nextSelected(i)) { |
| 164 |
|
|
| 165 |
< |
int nSelected1 = seleMan1_.getSelectionCount(); |
| 166 |
< |
int nSelected2 = seleMan2_.getSelectionCount(); |
| 165 |
> |
for (sd2 = sman2.beginSelected(j); sd2 != NULL; sd2 = sman2.nextSelected(j)) { |
| 166 |
> |
collectHistogram(sd1, sd2); |
| 167 |
> |
} |
| 168 |
> |
} |
| 169 |
|
|
| 170 |
< |
BitSet bs = seleMan1_.getSelectionSet(); |
| 140 |
< |
bs &= seleMan2_.getSelectionSet(); |
| 141 |
< |
int nIntersect = bs.countBits(); |
| 170 |
> |
} |
| 171 |
|
|
| 172 |
< |
nRealPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; |
| 172 |
> |
void RadialDistrFunc::processOverlapping( SelectionManager& sman) { |
| 173 |
> |
StuntDouble* sd1; |
| 174 |
> |
StuntDouble* sd2; |
| 175 |
> |
int i; |
| 176 |
> |
int j; |
| 177 |
> |
|
| 178 |
> |
//basically, it is the same as below loop |
| 179 |
> |
//for (int i = 0; i < n; ++i ) |
| 180 |
> |
// for (int j = i + 1; j < n; ++j) {} |
| 181 |
> |
|
| 182 |
> |
for (sd1 = sman.beginSelected(i); sd1 != NULL; sd1 = sman.nextSelected(i)) { |
| 183 |
> |
for (j = i, sd2 = sman.nextSelected(j); sd2 != NULL; sd2 = sman.nextSelected(j)) { |
| 184 |
> |
collectHistogram(sd1, sd2); |
| 185 |
> |
} |
| 186 |
|
} |
| 187 |
|
|
| 188 |
< |
return nRealPairs_; |
| 147 |
< |
} |
| 188 |
> |
} |
| 189 |
|
|
| 190 |
|
} |
