OpenMD 3.0
Molecular Dynamics in the Open
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COMVel.cpp
1/*
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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#include "applications/sequentialProps/COMVel.hpp"
46
47#include <algorithm>
48#include <functional>
49
50#include "io/DumpReader.hpp"
52#include "utils/Revision.hpp"
53#include "utils/simError.h"
54
55namespace OpenMD {
56
57 COMVel::COMVel(SimInfo* info, const std::string& filename,
58 const std::string& sele1, const std::string& sele2) :
59 SequentialAnalyzer(info, filename, sele1, sele2) {
60 setOutputName(getPrefix(filename) + ".comVel");
61 }
62
63 void COMVel::doFrame(int) {
64 StuntDouble* sd;
65 int i;
66
67 if (evaluator1_.isDynamic()) {
68 seleMan1_.setSelectionSet(evaluator1_.evaluate());
69 }
70
71 RealType mtot = 0.0;
72 Vector3d comVel(V3Zero);
73 RealType mass;
74
75 for (sd = seleMan1_.beginSelected(i); sd != NULL;
76 sd = seleMan1_.nextSelected(i)) {
77 mass = sd->getMass();
78 mtot += mass;
79 comVel += sd->getVel() * mass;
80 }
81
82 comVel /= mtot;
83
84 values_.push_back(comVel);
85 }
86
87 void COMVel::writeSequence() {
88 std::ofstream ofs(outputFilename_.c_str(), std::ios::binary);
89
90 if (ofs.is_open()) {
91 Revision r;
92
93 ofs << "# " << getSequenceType() << "\n";
94 ofs << "# OpenMD " << r.getFullRevision() << "\n";
95 ofs << "# " << r.getBuildDate() << "\n";
96 ofs << "# selection script1: \"" << selectionScript1_;
97 ofs << "\"\tselection script2: \"" << selectionScript2_ << "\"\n";
98 if (!paramString_.empty())
99 ofs << "# parameters: " << paramString_ << "\n";
100
101 ofs << "#time\tvalue\n";
102
103 for (unsigned int i = 0; i < times_.size(); ++i) {
104 ofs << times_[i] << "\t" << values_[i].x() << "\t" << values_[i].y()
105 << "\t" << values_[i].z() << "\n";
106 }
107
108 } else {
109 snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
110 "COMVel::writeSequence Error: failed to open %s\n",
111 outputFilename_.c_str());
112 painCave.isFatal = 1;
113 simError();
114 }
115
116 ofs.close();
117 }
118} // namespace OpenMD
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.
std::string getPrefix(const std::string &str)