source: src/ConfigFileBuffer.cpp@ ba9f5b

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Last change on this file since ba9f5b was 1b2d30, checked in by Frederik Heber <heber@…>, 15 years ago

Extended PcpParser, completed MpqcParser.

  • BUGFIX: ConfigFileBuffer::InitFileBuffer() did not clear istream before re-use.
  • class PcpParser
    • operator== - compares every variable by ASSERTs.
    • constructor initializes variables all to sensible values.
  • class MpqcParser
    • new function save() - calls either SaveHessian() or Save() according to flag HessianPresent.
    • new functions SaveHessian() and Save() which contain both parts of config::SaveMPQC().
    • no function load() - this functionality has not been present and is not needed right away.
  • Extended ParserUnitTest
    • new test case readwritePcpTest() - load from static string, store, load again and compare both.
    • new test case writeMpqcTest() - write a state of the world and compare to one from static string.
    • all static strings have been made static and set before all functions.
    • new string containing an example pcp config file.
    • we check whether hydrogen and oxygen are known to the world as we test with these two elements.
  • atom::OutputMPQCLine() - now takes ostream instead of ofstream.
  • config::SaveMPQC() - adapted accordingly (cast is necessary)
  • Property mode set to 100644
File size: 5.3 KB
Line 
1/*
2 * ConfigFileBuffer.cpp
3 *
4 * Created on: 12.06.2010
5 * Author: heber
6 */
7
8#include "ConfigFileBuffer.hpp"
9#include "helpers.hpp"
10#include "lists.hpp"
11#include "log.hpp"
12#include "World.hpp"
13
14/******************************** Functions for class ConfigFileBuffer **********************/
15
16/** Structure containing compare function for Ion_Type sorting.
17 */
18struct IonTypeCompare {
19 bool operator()(const char* s1, const char *s2) const {
20 char number1[8];
21 char number2[8];
22 const char *dummy1, *dummy2;
23 //Log() << Verbose(0) << s1 << " " << s2 << endl;
24 dummy1 = strchr(s1, '_')+sizeof(char)*5; // go just after "Ion_Type"
25 dummy2 = strchr(dummy1, '_');
26 strncpy(number1, dummy1, dummy2-dummy1); // copy the number
27 number1[dummy2-dummy1]='\0';
28 dummy1 = strchr(s2, '_')+sizeof(char)*5; // go just after "Ion_Type"
29 dummy2 = strchr(dummy1, '_');
30 strncpy(number2, dummy1, dummy2-dummy1); // copy the number
31 number2[dummy2-dummy1]='\0';
32 if (atoi(number1) != atoi(number2))
33 return (atoi(number1) < atoi(number2));
34 else {
35 dummy1 = strchr(s1, '_')+sizeof(char);
36 dummy1 = strchr(dummy1, '_')+sizeof(char);
37 dummy2 = strchr(dummy1, ' ') < strchr(dummy1, '\t') ? strchr(dummy1, ' ') : strchr(dummy1, '\t');
38 strncpy(number1, dummy1, dummy2-dummy1); // copy the number
39 number1[dummy2-dummy1]='\0';
40 dummy1 = strchr(s2, '_')+sizeof(char);
41 dummy1 = strchr(dummy1, '_')+sizeof(char);
42 dummy2 = strchr(dummy1, ' ') < strchr(dummy1, '\t') ? strchr(dummy1, ' ') : strchr(dummy1, '\t');
43 strncpy(number2, dummy1, dummy2-dummy1); // copy the number
44 number2[dummy2-dummy1]='\0';
45 return (atoi(number1) < atoi(number2));
46 }
47 }
48};
49
50/** Constructor for ConfigFileBuffer class.
51 */
52ConfigFileBuffer::ConfigFileBuffer() : buffer(NULL), LineMapping(NULL), CurrentLine(0), NoLines(0)
53{
54};
55
56/** Constructor for ConfigFileBuffer class with filename to be parsed.
57 * \param *filename file name
58 */
59ConfigFileBuffer::ConfigFileBuffer(const char * const filename) : buffer(NULL), LineMapping(NULL), CurrentLine(0), NoLines(0)
60{
61 InitFileBuffer(filename);
62}
63
64void ConfigFileBuffer::InitFileBuffer(const char * const filename)
65{
66 ifstream *file= new ifstream(filename);
67 InitFileBuffer(file);
68}
69
70void ConfigFileBuffer::InitFileBuffer(istream *file)
71{
72 char line[MAXSTRINGSIZE];
73
74 RemoveMapping();
75
76 // prescan number of lines
77 if (file->fail()) {
78 DoeLog(1) && (eLog()<< Verbose(1) << "config file missing!" << endl);
79 return;
80 }
81 NoLines = 0; // we're overcounting by one
82 long file_position = file->tellg(); // mark current position
83 do {
84 file->getline(line, MAXSTRINGSIZE-1);
85 NoLines++;
86 } while (!file->eof());
87 file->clear();
88 file->seekg(file_position, ios::beg);
89 DoLog(1) && (Log() << Verbose(1) << NoLines-1 << " lines were recognized." << endl);
90
91 // allocate buffer's 1st dimension
92 if (buffer != NULL) {
93 DoeLog(1) && (eLog()<< Verbose(1) << "FileBuffer->buffer is not NULL!" << endl);
94 return;
95 } else
96 buffer = new char *[NoLines];
97
98 // scan each line and put into buffer
99 int lines=0;
100 int i;
101 do {
102 buffer[lines] = new char[MAXSTRINGSIZE];
103 file->getline(buffer[lines], MAXSTRINGSIZE-1);
104 i = strlen(buffer[lines]);
105 buffer[lines][i] = '\n';
106 buffer[lines][i+1] = '\0';
107 lines++;
108 } while((!file->eof()) && (lines < NoLines));
109 DoLog(1) && (Log() << Verbose(1) << lines-1 << " lines were read into the buffer." << endl);
110 file->clear();
111 file->seekg(file_position, ios::beg);
112
113 InitMapping();
114}
115
116/** Destructor for ConfigFileBuffer class.
117 */
118ConfigFileBuffer::~ConfigFileBuffer()
119{
120 RemoveBuffer();
121 RemoveMapping();
122}
123
124
125/** Create trivial mapping.
126 */
127void ConfigFileBuffer::InitMapping()
128{
129 LineMapping = new int[NoLines];
130 for (int i=0;i<NoLines;i++)
131 LineMapping[i] = i;
132 MappingAllocated = true;
133}
134
135/** Remove allocated mapping.
136 */
137void ConfigFileBuffer::RemoveMapping()
138{
139 delete[](LineMapping);
140 MappingAllocated = false;
141}
142
143/** Remove allocated mapping.
144 */
145void ConfigFileBuffer::RemoveBuffer()
146{
147 for(int i=0;i<NoLines;++i)
148 delete[](buffer[i]);
149 delete[](buffer);
150}
151
152
153/** Creates a mapping for the \a *FileBuffer's lines containing the Ion_Type keyword such that they are sorted.
154 * \a *map on return contains a list of NoAtom entries such that going through the list, yields indices to the
155 * lines in \a *FileBuffer in a sorted manner of the Ion_Type?_? keywords. We assume that ConfigFileBuffer::CurrentLine
156 * points to first Ion_Type entry.
157 * \param *FileBuffer pointer to buffer structure
158 * \param NoAtoms of subsequent lines to look at
159 */
160void ConfigFileBuffer::MapIonTypesInBuffer(const int NoAtoms)
161{
162 map<const char *, int, IonTypeCompare> IonTypeLineMap;
163 if (!MappingAllocated) {
164 InitMapping();
165 }
166
167 // put all into hashed map
168 for (int i=0; i<NoAtoms; ++i) {
169 IonTypeLineMap.insert(pair<const char *, int> (buffer[CurrentLine+i], CurrentLine+i));
170 }
171
172 // fill map
173 int nr=0;
174 for (map<const char *, int, IonTypeCompare>::iterator runner = IonTypeLineMap.begin(); runner != IonTypeLineMap.end(); ++runner) {
175 if (CurrentLine+nr < NoLines)
176 LineMapping[CurrentLine+(nr++)] = runner->second;
177 else {
178 DoeLog(0) && (eLog()<< Verbose(0) << "config::MapIonTypesInBuffer - NoAtoms is wrong: We are past the end of the file!" << endl);
179 performCriticalExit();
180 }
181 }
182}
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