OpenMD 3.0
Molecular Dynamics in the Open
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ChargeAtomTypesSectionParser.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/ChargeAtomTypesSectionParser.hpp"
46
47#include "brains/ForceField.hpp"
48#include "types/FixedChargeAdapter.hpp"
49#include "utils/simError.h"
50
51namespace OpenMD {
52
53 ChargeAtomTypesSectionParser::ChargeAtomTypesSectionParser(
54 ForceFieldOptions& options) :
55 options_(options) {
56 setSectionName("ChargeAtomTypes");
57 }
58
59 void ChargeAtomTypesSectionParser::parseLine(ForceField& ff,
60 const std::string& line,
61 int lineNo) {
62 StringTokenizer tokenizer(line);
63 int nTokens = tokenizer.countTokens();
64
65 if (nTokens < 2) {
66 snprintf(
67 painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
68 "ChargeAtomTypesSectionParser Error: Not enough tokens at line %d\n",
69 lineNo);
70 painCave.isFatal = 1;
71 simError();
72 } else {
73 RealType cus_ = options_.getChargeUnitScaling();
74
75 std::string atomTypeName = tokenizer.nextToken();
76
77 AtomType* atomType = ff.getAtomType(atomTypeName);
78 if (atomType != NULL) {
79 FixedChargeAdapter fca = FixedChargeAdapter(atomType);
80 RealType charge = cus_ * tokenizer.nextTokenAsDouble();
81 fca.makeFixedCharge(charge);
82 } else {
83 snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
84 "ChargeAtomTypesSectionParser Error: Can not find matching "
85 "AtomType at "
86 "line %d\n",
87 lineNo);
88 painCave.isFatal = 1;
89 simError();
90 }
91 }
92 }
93} // namespace OpenMD
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.