OpenMD 3.0
Molecular Dynamics in the Open
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FreqFlucCorrFunc.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
46
47#include <string>
48
49#include "applications/dynamicProps/TimeCorrFunc.hpp"
50#include "brains/SimInfo.hpp"
51#include "math/Vector3.hpp"
52#include "primitives/Atom.hpp"
54#include "types/MultipoleAdapter.hpp"
55#include "utils/StringUtils.hpp"
56#include "utils/simError.h"
57
58namespace OpenMD {
59
60 FreqFlucCorrFunc::FreqFlucCorrFunc(SimInfo* info, const std::string& filename,
61 const std::string& sele1,
62 const std::string& sele2) :
63 ObjectACF<RealType>(info, filename, sele1, sele2) {
64 setCorrFuncType("FreqFluc Correlation Function");
65 setOutputName(getPrefix(dumpFilename_) + ".ffcorr");
66 }
67
68 int FreqFlucCorrFunc::computeProperty1(int frame, StuntDouble* sd) {
69 Vector3d e = sd->getElectricField();
70 Vector3d u;
71 if (sd->isRigidBody()) {
72 u = sd->getA().getRow(2);
73 } else {
74 AtomType* at = static_cast<Atom*>(sd)->getAtomType();
75 MultipoleAdapter ma = MultipoleAdapter(at);
76
77 if (ma.isDipole()) { u = sd->getDipole(); }
78 }
79
80 RealType uedot = dot(u, e);
81 ueStats_.add(uedot);
82
83 ue_[frame].push_back(uedot);
84 return ue_[frame].size() - 1;
85 }
86
87 RealType FreqFlucCorrFunc::calcCorrVal(int frame1, int frame2, int id1,
88 int id2) {
89 RealType mean = ueStats_.getAverage();
90
91 return (ue_[frame1][id1] - mean) * (ue_[frame2][id2] - mean);
92 }
93
94 void FreqFlucCorrFunc::validateSelection(SelectionManager&) {
95 StuntDouble* sd;
96 int i;
97 for (sd = seleMan1_.beginSelected(i); sd != NULL;
98 sd = seleMan1_.nextSelected(i)) {
99 if (!sd->isRigidBody()) {
100 AtomType* at = static_cast<Atom*>(sd)->getAtomType();
101 MultipoleAdapter ma = MultipoleAdapter(at);
102
103 if (!ma.isDipole()) {
104 snprintf(
105 painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
106 "FreqFlucCorrFunc::validateSelection Error: selection is not a "
107 "RigidBody "
108 "or does\n"
109 "\tnot have a dipole\n");
110 painCave.isFatal = 1;
111 simError();
112 }
113 }
114 }
115 }
116} // namespace OpenMD
Frequency Fluctuation Correlation Function.
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)