OpenMD 3.0
Molecular Dynamics in the Open
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CharmmTorsionType.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 "types/CharmmTorsionType.hpp"
46
47#include <config.h>
48
49#include <algorithm>
50#include <cmath>
51#include <fstream>
52
53#include "math/ChebyshevT.hpp"
54#include "math/ChebyshevU.hpp"
55
56namespace OpenMD {
57
58 CharmmTorsionType::CharmmTorsionType(
59 std::vector<CharmmTorsionParameter>& parameters) :
61 C_(0.0) {
62 std::vector<CharmmTorsionParameter>::iterator i;
63 i = std::max_element(parameters.begin(), parameters.end(),
65 if (i != parameters.end()) {
66 int maxPower = i->n;
67 ChebyshevT T(maxPower);
68 ChebyshevU U(maxPower);
69
70 // convert parameters of charmm type torsion into
71 // Polynomial parameters
72
73 for (i = parameters.begin(); i != parameters.end(); ++i) {
74 DoublePolynomial cosTerm = T.getChebyshevPolynomial(i->n);
75 cosTerm *= (cos(i->delta) * i->kchi);
76
77 // should check that i->n is >= 1
78 DoublePolynomial sinTerm = U.getChebyshevPolynomial(i->n - 1);
79 sinTerm *= -(sin(i->delta) * i->kchi);
80
81 T_ += cosTerm;
82 U_ += sinTerm;
83 C_ += i->kchi;
84 }
85 }
86 }
87
88 void CharmmTorsionType::calcForce(RealType cosPhi, RealType& V,
89 RealType& dVdCosPhi) {
90 // check roundoff
91 if (cosPhi > 1.0) {
92 cosPhi = 1.0;
93 } else if (cosPhi < -1.0) {
94 cosPhi = -1.0;
95 }
96
97 RealType sinPhi = sqrt(1.0 - cosPhi * cosPhi);
98
99 // trick to avoid divergence in angles near 0 and pi:
100
101 if (fabs(sinPhi) < 1.0E-6) { sinPhi = copysign(1.0E-6, sinPhi); }
102
103 V = C_ + T_.evaluate(cosPhi) + U_.evaluate(cosPhi) * sinPhi;
104 dVdCosPhi = T_.evaluateDerivative(cosPhi);
105 // Chain rule for U * sinPhi term:
106 dVdCosPhi += U_.evaluateDerivative(cosPhi) * sinPhi;
107 dVdCosPhi += U_.evaluate(cosPhi) / (2.0 * sinPhi);
108 }
109} // namespace OpenMD
A collection of Chebyshev Polynomials.
A collection of Chebyshev Polynomials.
Real evaluateDerivative(const Real &x)
Returns the first derivative of this polynomial.
Real evaluate(const Real &x)
Calculates the value of this Polynomial evaluated at the given x value.
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.