OpenMD 3.0
Molecular Dynamics in the Open
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DirectionalRCorrFunc.cpp
1/*
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32 * research, please cite the appropriate papers when you publish your
33 * work. Good starting points are:
34 *
35 * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
36 * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
37 * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
38 * [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
39 * [5] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
40 * [6] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
41 * [7] Lamichhane, Newman & Gezelter, J. Chem. Phys. 141, 134110 (2014).
42 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
43 */
44
45#include "applications/dynamicProps/DirectionalRCorrFunc.hpp"
46
47#include "utils/Revision.hpp"
48
49namespace OpenMD {
50 DirectionalRCorrFunc::DirectionalRCorrFunc(SimInfo* info,
51 const std::string& filename,
52 const std::string& sele1,
53 const std::string& sele2) :
54 ObjectACF<Vector3d>(info, filename, sele1, sele2) {
55 setCorrFuncType("DirectionalRCorrFunc");
56 setOutputName(getPrefix(dumpFilename_) + ".drcorr");
57 setLabelString("r2\trparallel\trperpendicular");
58 positions_.resize(nFrames_);
59 rotMats_.resize(nFrames_);
60 }
61
62 int DirectionalRCorrFunc::computeProperty1(int frame, StuntDouble* sd) {
63 positions_[frame].push_back(sd->getPos());
64 rotMats_[frame].push_back(sd->getA());
65 return positions_[frame].size() - 1;
66 }
67
68 Vector3d DirectionalRCorrFunc::calcCorrVal(int frame1, int frame2, int id1,
69 int id2) {
70 Vector3d diff = positions_[frame2][id2] - positions_[frame1][id1];
71
72 // The lab frame vector corresponding to the body-fixed
73 // z-axis is simply the second column of A.transpose()
74 // or, identically, the second row of A itself.
75
76 Vector3d u1 = rotMats_[frame1][id1].getRow(2);
77 RealType u1l = u1.length();
78
79 RealType rsq = diff.lengthSquare();
80 RealType rpar = dot(diff, u1) / u1l;
81 RealType rpar2 = rpar * rpar;
82 RealType rperp2 = rsq - rpar2;
83
84 return Vector3d(rsq, rpar2, rperp2);
85 }
86
87 void DirectionalRCorrFunc::validateSelection(SelectionManager&) {
88 StuntDouble* sd;
89 int i;
90 for (sd = seleMan1_.beginSelected(i); sd != NULL;
91 sd = seleMan1_.nextSelected(i)) {
92 if (!sd->isDirectional()) {
93 snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
94 "DirectionalRCorrFunc::validateSelection Error: "
95 "at least one of the selected objects is not Directional\n");
96 painCave.isFatal = 1;
97 simError();
98 }
99 }
100 }
101} // namespace OpenMD
Real length()
Returns the length of this vector.
Definition Vector.hpp:393
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.
Real dot(const DynamicVector< Real > &v1, const DynamicVector< Real > &v2)
Returns the dot product of two DynamicVectors.
std::string getPrefix(const std::string &str)