source: src/Parser/XyzParser.cpp@ fa1830

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Last change on this file since fa1830 was b5c53d, checked in by Frederik Heber <heber@…>, 15 years ago

Merge branch 'StructureRefactoring' into stable

Conflicts:

src/Actions/AtomAction/AddAction.cpp
src/Actions/AtomAction/ChangeElementAction.cpp
src/Parser/XyzParser.cpp
src/analysis_correlation.cpp
src/atom.cpp
src/config.cpp
src/molecule.cpp

  • AtomInfo::element were privatized in stable and element::symbol, ::name in StructureRefactoring (overlapped in various lines).
  • Property mode set to 100644
File size: 2.2 KB
Line 
1/*
2 * XyzParser.cpp
3 *
4 * Created on: Mar 2, 2010
5 * Author: metzler
6 */
7
8#include "Helpers/MemDebug.hpp"
9
10#include "Helpers/Log.hpp"
11#include "Helpers/Verbose.hpp"
12#include "XyzParser.hpp"
13#include "World.hpp"
14#include "atom.hpp"
15#include "molecule.hpp"
16#include "element.hpp"
17#include "periodentafel.hpp"
18
19using namespace std;
20
21/**
22 * Constructor.
23 */
24XyzParser::XyzParser() :
25 comment("")
26{}
27
28/**
29 * Destructor.
30 */
31XyzParser::~XyzParser() {
32}
33
34/**
35 * Loads an XYZ file into the World.
36 *
37 * \param XYZ file
38 */
39void XyzParser::load(istream* file) {
40 atom* newAtom = NULL;
41 molecule* newmol = NULL;
42 int numberOfAtoms;
43 char commentBuffer[512], type[3];
44 double tmp;
45
46 // the first line tells number of atoms, the second line is always a comment
47 *file >> numberOfAtoms >> ws;
48 file->getline(commentBuffer, 512);
49 comment = commentBuffer;
50
51 newmol = World::getInstance().createMolecule();
52 newmol->ActiveFlag = true;
53 World::getInstance().getMolecules()->insert(newmol);
54 for (int i = 0; i < numberOfAtoms; i++) {
55 newAtom = World::getInstance().createAtom();
56 *file >> type;
57 for (int j=0;j<NDIM;j++) {
58 *file >> tmp;
59 newAtom->set(j, tmp);
60 }
61 newAtom->setType(World::getInstance().getPeriode()->FindElement(type));
62 newmol->AddAtom(newAtom);
63 }
64}
65
66/**
67 * Saves the current state of the World into the given XYZ file.
68 *
69 * \param XYZ file
70 */
71void XyzParser::save(ostream* file) {
72 DoLog(0) && (Log() << Verbose(0) << "Saving changes to xyz." << std::endl);
73 if (comment == "") {
74 time_t now = time((time_t *)NULL); // Get the system time and put it into 'now' as 'calender time'
75 comment = "Created by molecuilder on ";
76 // ctime ends in \n\0, we have to cut away the newline
77 std::string time(ctime(&now));
78 size_t pos = time.find('\n');
79 if (pos != 0)
80 comment += time.substr(0,pos);
81 else
82 comment += time;
83 }
84 *file << World::getInstance().numAtoms() << endl << "\t" << comment << endl;
85
86 vector<atom*> atoms = World::getInstance().getAllAtoms();
87 for(vector<atom*>::iterator it = atoms.begin(); it != atoms.end(); it++) {
88 *file << noshowpoint << (*it)->getType()->getSymbol() << "\t" << (*it)->at(0) << "\t" << (*it)->at(1) << "\t" << (*it)->at(2) << endl;
89 }
90}
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