OpenMD
3.2
Molecular Dynamics in the Open
Toggle main menu visibility
Loading...
Searching...
No Matches
LangevinHullForceModifier.hpp
1
/*
2
* Copyright (c) 2004-present, The University of Notre Dame. All rights
3
* reserved.
4
*
5
* Redistribution and use in source and binary forms, with or without
6
* modification, are permitted provided that the following conditions are met:
7
*
8
* 1. Redistributions of source code must retain the above copyright notice,
9
* this list of conditions and the following disclaimer.
10
*
11
* 2. Redistributions in binary form must reproduce the above copyright notice,
12
* this list of conditions and the following disclaimer in the documentation
13
* and/or other materials provided with the distribution.
14
*
15
* 3. Neither the name of the copyright holder nor the names of its
16
* contributors may be used to endorse or promote products derived from
17
* this software without specific prior written permission.
18
*
19
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
20
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
21
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
22
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
23
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
24
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
25
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
26
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
27
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
28
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
29
* POSSIBILITY OF SUCH DAMAGE.
30
*
31
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
32
* research, please cite the following paper when you publish your work:
33
*
34
* [1] Drisko et al., J. Open Source Softw. 9, 7004 (2024).
35
*
36
* Good starting points for code and simulation methodology are:
37
*
38
* [2] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
39
* [3] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
40
* [4] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
41
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
42
* [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
43
* [7] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
44
* [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
45
* [9] Drisko & Gezelter, J. Chem. Theory Comput. 20, 4986-4997 (2024).
46
*/
47
48
#ifndef INTEGRATOR_LANGEVINHULLFORCEMODIFIER_HPP
49
#define INTEGRATOR_LANGEVINHULLFORCEMODIFIER_HPP
50
51
#include <map>
52
#include <memory>
53
#include <vector>
54
55
#include "
brains/ForceManager.hpp
"
56
#include "brains/Thermo.hpp"
57
#include "brains/Velocitizer.hpp"
58
#include "math/Hull.hpp"
59
#include "math/Triangle.hpp"
60
#include "
primitives/Molecule.hpp
"
61
#include "utils/RandNumGen.hpp"
62
63
using namespace
std;
64
namespace
OpenMD
{
65
66
/**
67
* @class LangevinHullForceModifier
68
* Force modifier for NPT Langevin Hull Dynamics applying friction
69
* and random forces as well as torques. Stochastic force is
70
* determined by the area of surface triangles on the convex hull.
71
* See: Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011),
72
* and Kohanoff et al. CHEMPHYSCHEM 6, 1848-1852 (2005).
73
*/
74
class
LangevinHullForceModifier :
public
ForceModifier {
75
public
:
76
LangevinHullForceModifier(
SimInfo
* info);
77
~LangevinHullForceModifier();
78
79
void
modifyForces()
override
;
80
81
private
:
82
std::vector<Vector3d> genTriangleForces(
int
nTriangles);
83
84
Globals
* simParams_;
85
Utils::RandNumGenPtr randNumGen_;
86
std::normal_distribution<RealType> forceDistribution_;
87
std::unique_ptr<Velocitizer> veloMunge {
nullptr
};
88
89
RealType dt_;
90
RealType targetTemp_;
91
RealType targetPressure_;
92
RealType viscosity_;
93
94
enum
HullTypeEnum { hullConvex, hullAlphaShape, hullUnknown };
95
96
std::map<string, HullTypeEnum> stringToEnumMap_;
97
HullTypeEnum hullType_;
98
99
bool
doThermalCoupling_;
100
bool
doPressureCoupling_;
101
102
Hull
* surfaceMesh_;
103
std::vector<StuntDouble*> localSites_;
104
};
105
}
// namespace OpenMD
106
107
#endif
// INTEGRATOR_LANGEVINHULLFORCEMODIFIER_HPP
ForceManager.hpp
Molecule.hpp
OpenMD::Globals
Definition
Globals.hpp:70
OpenMD::Hull
Definition
Hull.hpp:62
OpenMD::SimInfo
One of the heavy-weight classes of OpenMD, SimInfo maintains objects and variables relating to the cu...
Definition
SimInfo.hpp:96
OpenMD
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.
Definition
ActionCorrFunc.cpp:63
integrators
LangevinHullForceModifier.hpp
Generated on
for OpenMD by
1.17.0