OpenMD 3.1
Molecular Dynamics in the Open
Loading...
Searching...
No Matches
HydroIO.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 HYDRODYNAMICS_HYDROIO_HPP
46#define HYDRODYNAMICS_HYDROIO_HPP
47
48#include <map>
49
50#include "hydrodynamics/HydroProp.hpp"
51
52#if defined(NLOHMANN_JSON)
53#include <nlohmann/json.hpp>
54using ordered_json = nlohmann::ordered_json;
55using json = nlohmann::json;
56#elif defined(RAPID_JSON)
57#define RAPIDJSON_NOMEMBERITERATORCLASS
58#include <rapidjson/document.h>
59#include <rapidjson/error/en.h>
60#include <rapidjson/istreamwrapper.h>
61#include <rapidjson/ostreamwrapper.h>
62#include <rapidjson/prettywriter.h>
63using namespace rapidjson;
64#endif
65
66namespace OpenMD {
67 class HydroIO {
68 public:
69 HydroIO() {}
70
71 ~HydroIO();
72
73 void openDocument(std::istream& is);
74
75 void openWriter(std::ostream& os);
76 void writeHydroProp(HydroProp* hp, RealType viscosity, RealType temperature,
77 std::ostream& os);
78 void closeWriter(std::ostream& os);
79
80 std::map<std::string, HydroProp*> parseHydroFile(const std::string& f);
81
82 void interpretHydroProp(HydroProp* hp, RealType viscosity,
83 RealType temperature);
84
85 private:
86#if defined(NLOHMANN_JSON)
87 ordered_json j_;
88#elif defined(RAPID_JSON)
89 std::ostream* os_;
90 rapidjson::OStreamWrapper* osw_;
91 rapidjson::PrettyWriter<rapidjson::OStreamWrapper> w_;
92 rapidjson::Document d_;
93#endif
94 bool writerOpen_;
95 };
96} // namespace OpenMD
97
98#endif
Container for information about the hydrodynamic behavior of objects interacting with surroundings.
Definition HydroProp.hpp:74
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.