OpenMD 3.0
Molecular Dynamics in the Open
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LegendreCorrFunc.cpp
1/*
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31 * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
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/LegendreCorrFunc.hpp"
46
47#include <sstream>
48
50#include "utils/Revision.hpp"
51#include "utils/simError.h"
52
53namespace OpenMD {
54 LegendreCorrFunc::LegendreCorrFunc(SimInfo* info, const std::string& filename,
55 const std::string& sele1,
56 const std::string& sele2, int order) :
57 ObjectACF<Vector3d>(info, filename, sele1, sele2),
58 order_(order) {
59 setCorrFuncType("Legendre Correlation Function");
60 setOutputName(getPrefix(dumpFilename_) + ".lcorr");
61
62 std::stringstream params;
63 params << " order = " << order_;
64 const std::string paramString = params.str();
65 setParameterString(paramString);
66
67 setLabelString("Pn(costheta_x)\tPn(costheta_y)\tPn(costheta_z)");
68
69 LegendrePolynomial polynomial(order);
70 legendre_ = polynomial.getLegendrePolynomial(order);
71
72 rotMats_.resize(nFrames_);
73 }
74
75 int LegendreCorrFunc::computeProperty1(int frame, StuntDouble* sd) {
76 rotMats_[frame].push_back(sd->getA());
77 return rotMats_[frame].size() - 1;
78 }
79
80 Vector3d LegendreCorrFunc::calcCorrVal(int frame1, int frame2, int id1,
81 int id2) {
82 // The lab frame vector corresponding to the body-fixed
83 // z-axis is simply the second column of A.transpose()
84 // or, identically, the second row of A itself.
85 // Similar identites give the 0th and 1st rows of A for
86 // the lab vectors associated with body-fixed x- and y- axes.
87
88 Vector3d v1x = rotMats_[frame1][id1].getRow(0);
89 Vector3d v1y = rotMats_[frame1][id1].getRow(1);
90 Vector3d v1z = rotMats_[frame1][id1].getRow(2);
91
92 Vector3d v2x = rotMats_[frame2][id2].getRow(0);
93 Vector3d v2y = rotMats_[frame2][id2].getRow(1);
94 Vector3d v2z = rotMats_[frame2][id2].getRow(2);
95
96 RealType ux =
97 legendre_.evaluate(dot(v1x, v2x) / (v1x.length() * v2x.length()));
98 RealType uy =
99 legendre_.evaluate(dot(v1y, v2y) / (v1y.length() * v2y.length()));
100 RealType uz =
101 legendre_.evaluate(dot(v1z, v2z) / (v1z.length() * v2z.length()));
102
103 return Vector3d(ux, uy, uz);
104 }
105
106 void LegendreCorrFunc::validateSelection(SelectionManager&) {
107 StuntDouble* sd;
108 int i;
109 for (sd = seleMan1_.beginSelected(i); sd != NULL;
110 sd = seleMan1_.nextSelected(i)) {
111 if (!sd->isDirectional()) {
112 snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
113 "LegendreCorrFunc::validateSelection Error: "
114 "at least one of the selected objects is not Directional\n");
115 painCave.isFatal = 1;
116 simError();
117 }
118 }
119 }
120} // namespace OpenMD
A collection of Legendre Polynomials.
Real evaluate(const Real &x)
Calculates the value of this Polynomial evaluated at the given x value.
StuntDouble * nextSelected(int &i)
Finds the next selected StuntDouble in the selection.
StuntDouble * beginSelected(int &i)
Finds the first selected StuntDouble in the selection.
One of the heavy-weight classes of OpenMD, SimInfo maintains objects and variables relating to the cu...
Definition SimInfo.hpp:93
"Don't move, or you're dead! Stand up! Captain, we've got them!"
RotMat3x3d getA()
Returns the current rotation matrix of this stuntDouble.
bool isDirectional()
Tests if this stuntDouble is a directional one.
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)