OpenMD 3.2
Molecular Dynamics in the Open
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SimplePreprocessor.hpp
1/*
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30 *
31 * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
32 * research, please cite the following paper when you publish your work:
33 *
34 * [1] Drisko et al., J. Open Source Softw. 9, 7004 (2024).
35 *
36 * Good starting points for code and simulation methodology are:
37 *
38 * [2] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
39 * [3] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
40 * [4] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
41 * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
42 * [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
43 * [7] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
44 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
45 * [9] Drisko & Gezelter, J. Chem. Theory Comput. 20, 4986-4997 (2024).
46 */
47
48#ifndef OMDPARSER_SIMPLEPREPROCESSOR_HPP
49#define OMDPARSER_SIMPLEPREPROCESSOR_HPP
50#include <iostream>
51#include <set>
52#include <fstream>
53#include <sstream>
55#include "utils/Trim.hpp"
56#include "utils/OpenMDException.hpp"
57#include "utils/simError.h"
58
59
60/**
61 * @class SimplePreprocessor
62 * @brief A simple preprocessor.
63 * @note only supports \#include \#ifdef, \#ifndef, \#endif, \#define and \#undef, c-like multiple line
64 * comment is not supported, macro substitute is not supported.
65 */
66namespace OpenMD {
68 public:
69 bool preprocess(std::istream& myStream, const std::string& filename, int startingLine, ostream& os) {
70 std::set<std::string> defineSet;
71 std::stack<bool> ifStates;
72
73 ifStates.push(true);
74 return doPreprocess(myStream, filename, startingLine, os, defineSet, ifStates);
75 }
76
77 private:
78 bool doPreprocess(std::istream& myStream, const std::string& filename, int startingLine, ostream& os, std::set<std::string>& defineSet, std::stack<bool>& ifStates) {
79 //std::ifstream input(filename.c_str());
80 //if (!input.is_open()) {
81 // std::stringstream ss;
82 // ss << "Can not open " << filename << " for preprocessing\n";
83 //
84 // snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
85 // "Can not open (%s) for processing. \n"
86 // "\tPlease check md file name syntax.\n", filename.c_str());
87 //
88 // painCave.isFatal = 1;
89 // simError();
90 //
91 // throw OpenMDException(ss.str());
92 //}
93 int lineNo = startingLine;
94 os << "#line " << lineNo << " \"" << filename << "\"\n";
95 const int bufferSize = 8192;
96 char buffer[bufferSize];
97 while(myStream.getline(buffer, bufferSize)) {
98 ++lineNo;
99 std::string line = Utils::trimLeftCopy(buffer);
100 if (!line.empty() && line[0] == '#') {
101 StringTokenizer tokenizer(line.substr(1, line.length()));
102 std::vector<std::string> tokens = tokenizer.getAllTokens();
103 if (tokens.empty()) {
104 return false;
105 }
106 if (tokens[0] == "endif") {
107 ifStates.pop();
108 if (ifStates.empty()) {
109 std::cout << "Error in preprocessing: endif \n";
110 return false;
111 }
112 os << std::endl;
113 } else if (tokens.size() == 2) {
114 if (tokens[0] == "include") {
115 SimplePreprocessor subPreprocessor;
116 std::string includeFilename = tokens[1];
117 includeFilename = includeFilename.substr(1, includeFilename.length() -2);
118 std::ifstream includeStream(includeFilename.c_str());
119 if (!includeStream.is_open()) {
120 std::stringstream ss;
121 ss << "Can not open " << includeFilename << " for preprocessing\n";
122 throw OpenMDException(ss.str());
123 }
124
125 bool ret = subPreprocessor.doPreprocess(includeStream, includeFilename, 1, os, defineSet, ifStates);
126 if (!ret) {
127 std::cout << "Error in preprocessing\n";
128 return false;
129 }
130 os << "#line " << lineNo << " \"" << filename << "\"\n";
131 } else if (tokens[0] == "define") {
132 defineSet.insert(tokens[1]);
133 os << std::endl;
134 } else if (tokens[0] == "undef") {
135 defineSet.erase(tokens[1]);
136 os << std::endl;
137 } else if (tokens[0] == "ifdef") {
138 if (defineSet.find(tokens[1]) != defineSet.end() ) {
139 ifStates.push(true);
140 } else {
141 ifStates.push(false);
142 }
143 os << std::endl;
144 } else if (tokens[0] == "ifndef") {
145 if (defineSet.find(tokens[1]) == defineSet.end() ) {
146 ifStates.push(true);
147 } else {
148 ifStates.push(false);
149 }
150 os << std::endl;
151 } else {
152 std::cout << tokens[0] << " is not supported (yet)." << std::endl;
153 return false;
154 }
155 }else {
156 return false;
157 }
158
159 }else if (ifStates.top()){
160 os << buffer << std::endl;
161 }
162
163 }
164
165 return true;
166 }
167 private:
168
169};
170
171}
172#endif
The string tokenizer class allows an application to break a string into tokens The set of delimiters ...
std::vector< std::string > getAllTokens()
Returns all of the tokens.
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.