OpenMD 3.0
Molecular Dynamics in the Open
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BendTypesSectionParser.cpp
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#include "io/BendTypesSectionParser.hpp"
46
47#include "brains/ForceField.hpp"
48#include "types/BendTypeParser.hpp"
49#include "utils/simError.h"
50
51namespace OpenMD {
52
53 BendTypesSectionParser::BendTypesSectionParser(ForceFieldOptions& options) :
54 options_(options) {
55 setSectionName("BendTypes");
56 }
57
58 void BendTypesSectionParser::parseLine(ForceField& ff,
59 const std::string& line, int lineNo) {
60 StringTokenizer tokenizer(line);
61 BendTypeParser btParser;
62 BendType* bendType = NULL;
63
64 int nTokens = tokenizer.countTokens();
65
66 if (nTokens < 5) {
67 snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
68 "BendTypesSectionParser Error: Not enough tokens at line %d\n",
69 lineNo);
70 painCave.isFatal = 1;
71 simError();
72 return;
73 }
74
75 std::string at1 = tokenizer.nextToken();
76 std::string at2 = tokenizer.nextToken();
77 std::string at3 = tokenizer.nextToken();
78 std::string remainder = tokenizer.getRemainingString();
79 RealType kScale = options_.getBendForceConstantScaling();
80
81 try {
82 bendType = btParser.parseLine(remainder, kScale);
83 } catch (OpenMDException& e) {
84 snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
85 "BendTypesSectionParser Error: %s "
86 "at line %d\n",
87 e.what(), lineNo);
88 painCave.isFatal = 1;
89 simError();
90 }
91
92 if (bendType != NULL) { ff.addBendType(at1, at2, at3, bendType); }
93 }
94} // namespace OpenMD
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.