OpenMD 3.0
Molecular Dynamics in the Open
Loading...
Searching...
No Matches
SpatialStatistics.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 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#ifndef APPLICATIONS_STATICPROPS_SPATIALSTATISTICS_HPP
46#define APPLICATIONS_STATICPROPS_SPATIALSTATISTICS_HPP
47
48#include <string>
49#include <vector>
50
51#include "applications/staticProps/StaticAnalyser.hpp"
52#include "brains/SimInfo.hpp"
53#include "brains/Snapshot.hpp"
55#include "math/Vector3.hpp"
57#include "selection/SelectionEvaluator.hpp"
58#include "selection/SelectionManager.hpp"
59
60namespace OpenMD {
61
63 public:
64 SpatialStatistics(SimInfo* info, const std::string& filename,
65 const std::string& sele, int nbins);
66
67 virtual void process();
68 virtual void processFrame(int frame);
69 virtual int getBin(Vector3d pos) = 0;
70 virtual void processStuntDouble(StuntDouble* sd, int bin) = 0;
71
72 protected:
73 Snapshot* currentSnapshot_;
74 int nProcessed_;
75 std::string selectionScript_;
76 SelectionEvaluator evaluator_;
77 SelectionManager seleMan_;
78 };
79
81 public:
82 SlabStatistics(SimInfo* info, const std::string& filename,
83 const std::string& sele, int nbins, int axis);
84
85 virtual int getBin(Vector3d pos);
86 virtual void processFrame(int frame);
87
88 protected:
89 Mat3x3d hmat_;
90 RealType volume_;
91 int axis_;
92 std::string axisLabel_;
93 };
94
96 public:
97 ShellStatistics(SimInfo* info, const std::string& filename,
98 const std::string& sele, const std::string& comsele,
99 int nbins, RealType binWidth);
100
101 virtual void processFrame(int frame);
102 virtual int getBin(Vector3d pos);
103 void setCoordinateOrigin(Vector3d co) { coordinateOrigin_ = co; }
104
105 protected:
106 Vector3d coordinateOrigin_;
107 RealType binWidth_;
108 std::string comSele_;
109 SelectionManager comSeleMan_;
110 SelectionEvaluator comEvaluator_;
111 };
112} // namespace OpenMD
113
114#endif
"selection/SelectionEvaluator"
One of the heavy-weight classes of OpenMD, SimInfo maintains objects and variables relating to the cu...
Definition SimInfo.hpp:93
The Snapshot class is a repository storing dynamic data during a Simulation.
Definition Snapshot.hpp:147
"Don't move, or you're dead! Stand up! Captain, we've got them!"
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.