OpenMD 3.0
Molecular Dynamics in the Open
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SimCreator.hpp
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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/**
46 * @file SimCreator.hpp
47 * @author tlin
48 * @date 11/02/2004
49 * @version 1.0
50 */
51
52#ifndef BRAINS_SIMCREATOR_HPP
53#define BRAINS_SIMCREATOR_HPP
54
55#include <iostream>
56
57#include "brains/ForceField.hpp"
58#include "brains/SimInfo.hpp"
59#include "io/Globals.hpp"
61
62namespace OpenMD {
63
64 /**
65 * @class SimCreator SimCreator.hpp "brains/SimCreator.hpp"
66 *
67 * The only responsibility of SimCreator is to parse the meta-data
68 * file and create a SimInfo instance based on the information
69 * returned by parser.
70 */
71 class SimCreator {
72 public:
73 virtual ~SimCreator() = default;
74
75 /**
76 * Setup Simulation
77 * @return a pointer to SimInfo
78 * @param mdFileName the meta-data file name
79 * @param loadInitCoords should the initial coordinates be loaded from a
80 * file?
81 */
82 SimInfo* createSim(const std::string& mdFileName,
83 bool loadInitCoords = true);
84
85 private:
86 /**
87 * Parses the meta-data file
88 * @param mdFileName the meta-data file name
89 * @param rawMetaData the raw meta-data stream
90 * @param mdFileVersion the version of code used to create the meta-data
91 * file
92 * @param metaDataStartingLine the starting line of the meta-data block
93 * @return a pointer to the simulation parameters in a #Globals object
94 */
95 Globals* parseFile(std::istream& rawMetaData, const std::string& mdFileName,
96 int mdFileVersion, int metaDataStartingLine);
97
98 /** create the molecules belong to current processor*/
99 virtual void createMolecules(SimInfo* info);
100
101 /**
102 * Figure out the data storage layout based on what kinds of
103 * objects are being simulated
104 */
105 void computeStorageLayouts(SimInfo* info);
106
107 /**
108 * Sets the global index for atoms, rigidbodies and cutoff groups
109 * and fill up globalGroupMembership and globalMolMembership
110 * arrays which map atoms' global index to the global index of the
111 * groups (or molecules) they belong to. These array are never
112 * changed during the simulation.
113 */
114 void setGlobalIndex(SimInfo* info);
115
116 void gatherParameters(SimInfo* info, const std::string& mdfile);
117
118 /**
119 * Divide the molecules among the processors
120 */
121
122 void divideMolecules(SimInfo* info);
123
124 /** Load initial coordinates */
125 void loadCoordinates(SimInfo* info, const std::string& mdFileName);
126
127 std::string
128 mdFileName_; // save the meta-data file name which may be used later
129 };
130} // namespace OpenMD
131
132#endif // BRAINS_SIMCREATOR_HPP
The only responsibility of SimCreator is to parse the meta-data file and create a SimInfo instance ba...
SimInfo * createSim(const std::string &mdFileName, bool loadInitCoords=true)
Setup Simulation.
One of the heavy-weight classes of OpenMD, SimInfo maintains objects and variables relating to the cu...
Definition SimInfo.hpp:93
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.