| 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). |
| 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> |
| 45 |
|
#include "RadialDistrFunc.hpp" |
| 46 |
|
#include "io/DumpReader.hpp" |
| 47 |
|
#include "primitives/Molecule.hpp" |
| 48 |
+ |
|
| 49 |
|
namespace OpenMD { |
| 50 |
|
|
| 51 |
< |
RadialDistrFunc::RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2) |
| 52 |
< |
: StaticAnalyser(info, filename), |
| 53 |
< |
selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), |
| 54 |
< |
seleMan1_(info), seleMan2_(info), common_(info), sele1_minus_common_(info), sele2_minus_common_(info){ |
| 51 |
> |
RadialDistrFunc::RadialDistrFunc(SimInfo* info, |
| 52 |
> |
const std::string& filename, |
| 53 |
> |
const std::string& sele1, |
| 54 |
> |
const std::string& sele2) |
| 55 |
> |
: StaticAnalyser(info, filename), selectionScript1_(sele1), |
| 56 |
> |
selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), |
| 57 |
> |
seleMan1_(info), seleMan2_(info), common_(info), |
| 58 |
> |
sele1_minus_common_(info), sele2_minus_common_(info) { |
| 59 |
|
|
| 60 |
|
evaluator1_.loadScriptString(sele1); |
| 61 |
|
evaluator2_.loadScriptString(sele2); |
| 70 |
|
} |
| 71 |
|
|
| 72 |
|
if (!evaluator1_.isDynamic() && !evaluator2_.isDynamic()) { |
| 73 |
< |
//if all selections are static, we can precompute the number of real pairs |
| 73 |
> |
// If all selections are static, we can precompute the number |
| 74 |
> |
// of real pairs. |
| 75 |
|
common_ = seleMan1_ & seleMan2_; |
| 76 |
|
sele1_minus_common_ = seleMan1_ - common_; |
| 77 |
|
sele2_minus_common_ = seleMan2_ - common_; |
| 80 |
|
int nSelected2 = seleMan2_.getSelectionCount(); |
| 81 |
|
int nIntersect = common_.getSelectionCount(); |
| 82 |
|
|
| 83 |
< |
nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; |
| 83 |
> |
nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; |
| 84 |
|
} |
| 85 |
|
|
| 86 |
|
} |
| 110 |
|
validateSelection2(seleMan2_); |
| 111 |
|
} |
| 112 |
|
|
| 113 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 113 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 114 |
> |
mol = info_->nextMolecule(mi)) { |
| 115 |
|
|
| 116 |
< |
//change the positions of atoms which belong to the rigidbodies |
| 117 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 116 |
> |
// Change the positions of atoms which belong to the RigidBodies |
| 117 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 118 |
> |
rb = mol->nextRigidBody(rbIter)) { |
| 119 |
|
rb->updateAtoms(); |
| 120 |
|
} |
| 121 |
|
} |
| 122 |
|
|
| 123 |
|
initalizeHistogram(); |
| 115 |
– |
|
| 116 |
– |
|
| 124 |
|
|
| 125 |
< |
//selections may overlap. |
| 125 |
> |
// Selections may overlap, and we need a bit of logic to deal |
| 126 |
> |
// with this. |
| 127 |
|
// |
| 128 |
< |
// |s1 -c | c | |
| 129 |
< |
// | c |s2 - c| |
| 128 |
> |
// | s1 | |
| 129 |
> |
// | s1 -c | c | |
| 130 |
> |
// | c | s2 - c | |
| 131 |
> |
// | s2 | |
| 132 |
|
// |
| 133 |
< |
// s1 : number of selected stuntdoubles in selection1 |
| 134 |
< |
// s2 : number of selected stuntdoubles in selection2 |
| 135 |
< |
// c : number of intersect stuntdouble between selection1 and selection2 |
| 136 |
< |
//when loop over the pairs, we can divide the looping into 3 stages |
| 137 |
< |
//stage 1 : [s1-c] [s2] |
| 138 |
< |
//stage 2 : [c] [s2 - c] |
| 139 |
< |
//stage 3 : [c] [c] |
| 140 |
< |
//stage 1 and stage 2 are completly non-overlapping |
| 141 |
< |
//stage 3 are completely overlapping |
| 133 |
> |
// s1 : Set of StuntDoubles in selection1 |
| 134 |
> |
// s2 : Set of StuntDoubles in selection2 |
| 135 |
> |
// c : Intersection of selection1 and selection2 |
| 136 |
> |
// |
| 137 |
> |
// When we loop over the pairs, we can divide the looping into 3 |
| 138 |
> |
// stages: |
| 139 |
> |
// |
| 140 |
> |
// Stage 1 : [s1-c] [s2] |
| 141 |
> |
// Stage 2 : [c] [s2 - c] |
| 142 |
> |
// Stage 3 : [c] [c] |
| 143 |
> |
// Stages 1 and 2 are completely non-overlapping. |
| 144 |
> |
// Stage 3 is completely overlapping. |
| 145 |
|
|
| 146 |
|
if (evaluator1_.isDynamic() || evaluator2_.isDynamic()) { |
| 147 |
|
common_ = seleMan1_ & seleMan2_; |
| 153 |
|
|
| 154 |
|
nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2; |
| 155 |
|
} |
| 156 |
+ |
|
| 157 |
|
processNonOverlapping(sele1_minus_common_, seleMan2_); |
| 158 |
< |
processNonOverlapping(common_, sele2_minus_common_); |
| 158 |
> |
processNonOverlapping(common_, sele2_minus_common_); |
| 159 |
|
processOverlapping(common_); |
| 160 |
|
|
| 161 |
|
processHistogram(); |
| 167 |
|
writeRdf(); |
| 168 |
|
} |
| 169 |
|
|
| 170 |
< |
void RadialDistrFunc::processNonOverlapping( SelectionManager& sman1, SelectionManager& sman2) { |
| 170 |
> |
void RadialDistrFunc::processNonOverlapping( SelectionManager& sman1, |
| 171 |
> |
SelectionManager& sman2) { |
| 172 |
|
StuntDouble* sd1; |
| 173 |
|
StuntDouble* sd2; |
| 174 |
|
int i; |
| 175 |
|
int j; |
| 176 |
|
|
| 177 |
< |
for (sd1 = sman1.beginSelected(i); sd1 != NULL; sd1 = sman1.nextSelected(i)) { |
| 177 |
> |
// This is the same as a non-overlapping pairwise loop structure: |
| 178 |
> |
// for (int i = 0; i < ni ; ++i ) { |
| 179 |
> |
// for (int j = 0; j < nj; ++j) {} |
| 180 |
> |
// } |
| 181 |
|
|
| 182 |
< |
for (sd2 = sman2.beginSelected(j); sd2 != NULL; sd2 = sman2.nextSelected(j)) { |
| 182 |
> |
for (sd1 = sman1.beginSelected(i); sd1 != NULL; |
| 183 |
> |
sd1 = sman1.nextSelected(i)) { |
| 184 |
> |
for (sd2 = sman2.beginSelected(j); sd2 != NULL; |
| 185 |
> |
sd2 = sman2.nextSelected(j)) { |
| 186 |
|
collectHistogram(sd1, sd2); |
| 187 |
< |
} |
| 187 |
> |
} |
| 188 |
|
} |
| 168 |
– |
|
| 189 |
|
} |
| 190 |
|
|
| 191 |
|
void RadialDistrFunc::processOverlapping( SelectionManager& sman) { |
| 194 |
|
int i; |
| 195 |
|
int j; |
| 196 |
|
|
| 197 |
< |
//basically, it is the same as below loop |
| 198 |
< |
//for (int i = 0; i < n; ++i ) |
| 199 |
< |
// for (int j = i + 1; j < n; ++j) {} |
| 197 |
> |
// This is the same as a pairwise loop structure: |
| 198 |
> |
// for (int i = 0; i < n-1 ; ++i ) { |
| 199 |
> |
// for (int j = i + 1; j < n; ++j) {} |
| 200 |
> |
// } |
| 201 |
|
|
| 202 |
< |
for (sd1 = sman.beginSelected(i); sd1 != NULL; sd1 = sman.nextSelected(i)) { |
| 203 |
< |
for (j = i, sd2 = sman.nextSelected(j); sd2 != NULL; sd2 = sman.nextSelected(j)) { |
| 202 |
> |
for (sd1 = sman.beginSelected(i); sd1 != NULL; |
| 203 |
> |
sd1 = sman.nextSelected(i)) { |
| 204 |
> |
for (j = i, sd2 = sman.nextSelected(j); sd2 != NULL; |
| 205 |
> |
sd2 = sman.nextSelected(j)) { |
| 206 |
|
collectHistogram(sd1, sd2); |
| 207 |
|
} |
| 208 |
|
} |
| 186 |
– |
|
| 209 |
|
} |
| 188 |
– |
|
| 210 |
|
} |
