source: src/Parser/Psi3Parser.cpp@ 1bef07

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Last change on this file since 1bef07 was 1bef07, checked in by Frederik Heber <heber@…>, 13 years ago

Added first working version of a Psi3Parser.

  • is so far mostly copy&paste from MpqcParser.
  • important parameters all are in (including valid ranges).
  • also added unit tests.
  • Property mode set to 100644
File size: 15.3 KB
RevLine 
[1bef07]1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
4 * Copyright (C) 2010 University of Bonn. All rights reserved.
5 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
6 */
7
8/*
9 * Psi3Parser.cpp
10 *
11 * Created on: Oct 04, 2011
12 * Author: heber
13 */
14
15// include config.h
16#ifdef HAVE_CONFIG_H
17#include <config.h>
18#endif
19
20#include <iostream>
21#include <boost/tokenizer.hpp>
22#include <string>
23
24#include "CodePatterns/MemDebug.hpp"
25
26#include "Psi3Parser.hpp"
27#include "Psi3Parser_Parameters.hpp"
28
29#include "atom.hpp"
30#include "config.hpp"
31#include "element.hpp"
32#include "molecule.hpp"
33#include "CodePatterns/Log.hpp"
34#include "CodePatterns/toString.hpp"
35#include "CodePatterns/Verbose.hpp"
36#include "LinearAlgebra/Vector.hpp"
37#include "periodentafel.hpp"
38#include "World.hpp"
39
40// declare specialized static variables
41const std::string FormatParserTrait<psi3>::name = "psi3";
42const std::string FormatParserTrait<psi3>::suffix = "in";
43const ParserTypes FormatParserTrait<psi3>::type = psi3;
44
45// a converter we often need
46ConvertTo<bool> FormatParser<psi3>::Converter;
47
48/** Constructor of Psi3Parser.
49 *
50 */
51FormatParser< psi3 >::FormatParser() :
52 FormatParser_common(new Psi3Parser_Parameters())
53{}
54
55/** Destructor of Psi3Parser.
56 *
57 */
58FormatParser< psi3 >::~FormatParser()
59{}
60
61/** Load an MPQC config file into the World.
62 * \param *file input stream
63 */
64void FormatParser< psi3 >::load(istream *file)
65{
66// bool Psi3Section = false;
67// bool MoleculeSection = false;
68// bool GeometrySection = false;
69// bool BasisSection = false;
70// bool AuxBasisSection = false;
71// char line[MAXSTRINGSIZE];
72// typedef boost::tokenizer<boost::char_separator<char> > tokenizer;
73// boost::char_separator<char> sep("[]");
74// boost::char_separator<char> angularsep("<>");
75// boost::char_separator<char> equalitysep(" =");
76// boost::char_separator<char> whitesep(" \t");
77// ConvertTo<double> toDouble;
78//
79// molecule *newmol = World::getInstance().createMolecule();
80// newmol->ActiveFlag = true;
81// // TODO: Remove the insertion into molecule when saving does not depend on them anymore. Also, remove molecule.hpp include
82// World::getInstance().getMolecules()->insert(newmol);
83// while (file->good()) {
84// file->getline(line, MAXSTRINGSIZE-1);
85// std::string linestring(line);
86// if ((linestring.find("atoms geometry") == string::npos) && (linestring.find("}") != string::npos)) {
87// GeometrySection = false;
88// }
89// if ((linestring.find(")") != string::npos)) { // ends a section which do not overlap
90// Psi3Section = false;
91// MoleculeSection = false;
92// BasisSection = false;
93// AuxBasisSection = false;
94// }
95// if (MoleculeSection) {
96// if (GeometrySection) { // we have an atom
97// tokenizer tokens(linestring, sep);
98// // if (tokens.size() != 2)
99// // throw Psi3ParseException;
100// tokenizer::iterator tok_iter = tokens.begin();
101// ASSERT(tok_iter != tokens.end(),
102// "FormatParser< psi3 >::load() - missing token for MoleculeSection in line "+linestring+"!");
103// std::stringstream whitespacefilter(*tok_iter++);
104// std::string element;
105// whitespacefilter >> ws >> element;
106// ASSERT(tok_iter != tokens.end(),
107// "FormatParser< psi3 >::load() - missing token for MoleculeSection in line "+linestring+"!");
108// std::string vector = *tok_iter;
109// tokenizer vectorcomponents(vector, whitesep);
110// Vector X;
111// // if (vectorcomponents.size() != NDIM)
112// // throw Psi3ParseException;
113// tok_iter = vectorcomponents.begin();
114// for (int i=0; i<NDIM; ++i) {
115// X[i] = toDouble(*tok_iter++);
116// }
117// // create atom
118// atom *newAtom = World::getInstance().createAtom();
119// newAtom->setType(World::getInstance().getPeriode()->FindElement(element));
120// newAtom->setPosition(X);
121// newmol->AddAtom(newAtom);
122// DoLog(1) && (Log() << Verbose(1) << "Adding atom " << *newAtom << std::endl);
123// }
124// }
125// if (Psi3Section) {
126// if (linestring.find("mole<") != string::npos) { // get theory
127// tokenizer tokens(linestring, angularsep);
128// tokenizer::iterator tok_iter = tokens.begin();
129// ++tok_iter;
130// ASSERT(tok_iter != tokens.end(),
131// "FormatParser< psi3 >::load() - missing token in brackets<> for mole< in line "+linestring+"!");
132// std::string value(*tok_iter);
133// std::stringstream linestream("theory = "+value);
134// linestream >> getParams();
135// } else if (linestring.find("integrals<") != string::npos) { // get theory
136// tokenizer tokens(linestring, angularsep);
137// tokenizer::iterator tok_iter = tokens.begin();
138// ++tok_iter;
139// ASSERT(tok_iter != tokens.end(),
140// "FormatParser< psi3 >::load() - missing token in brackets<> for integrals< in line "+linestring+"!");
141// std::string value(*tok_iter);
142// std::stringstream linestream("integration = "+value);
143// linestream >> getParams();
144// } else if ((linestring.find("molecule") == string::npos) && (linestring.find("basis") == string::npos)){
145// // molecule and basis must not be parsed in this section
146// tokenizer tokens(linestring, equalitysep);
147// tokenizer::iterator tok_iter = tokens.begin();
148// ASSERT(tok_iter != tokens.end(),
149// "FormatParser< psi3 >::load() - missing token before '=' for Psi3Section in line "+linestring+"!");
150// std::stringstream whitespacefilter(*tok_iter);
151// std::string key;
152// whitespacefilter >> ws >> key;
153// if (getParams().haveParameter(key)) {
154// std::stringstream linestream(linestring);
155// linestream >> getParams();
156// } else { // unknown keys are simply ignored as long as parser is incomplete
157// DoLog(2) && (Log() << Verbose(2) << "INFO: '"+key+"' is unknown and ignored." << std::endl);
158// }
159// }
160// }
161// if (BasisSection) {
162// tokenizer tokens(linestring, equalitysep);
163// tokenizer::iterator tok_iter = tokens.begin();
164// ASSERT(tok_iter != tokens.end(),
165// "FormatParser< psi3 >::load() - missing token for BasisSection in line "+linestring+"!");
166// std::string key(*tok_iter++);
167// ASSERT(tok_iter != tokens.end(),
168// "FormatParser< psi3 >::load() - missing value for BasisSection after key "+key+" in line "+linestring+"!");
169// std::string value(*tok_iter);
170// tok_iter++;
171// // TODO: use exception instead of ASSERT
172// ASSERT(tok_iter == tokens.end(),
173// "FormatParser< psi3 >::load() - more than (key = value) on line "+linestring+".");
174// if (key == "name") {
175// std::stringstream linestream("basis = "+value);
176// linestream >> getParams();
177// }
178// }
179// if (AuxBasisSection) {
180// tokenizer tokens(linestring, equalitysep);
181// tokenizer::iterator tok_iter = tokens.begin();
182// ASSERT(tok_iter != tokens.end(),
183// "FormatParser< psi3 >::load() - missing token for AuxBasisSection in line "+linestring+"!");
184// std::string key(*tok_iter++);
185// ASSERT(tok_iter != tokens.end(),
186// "FormatParser< psi3 >::load() - missing value for BasisSection after key "+key+" in line "+linestring+"!");
187// std::string value(*tok_iter);
188// tok_iter++;
189// // TODO: use exception instead of ASSERT
190// ASSERT(tok_iter == tokens.end(),
191// "FormatParser< psi3 >::load() - more than (key = value) on line "+linestring+".");
192// if (key == "name") {
193// std::stringstream linestream("aux_basis = "+value);
194// linestream >> getParams();
195// }
196// }
197// // set some scan flags
198// if (linestring.find("psi3:") != string::npos) {
199// Psi3Section = true;
200// }
201// if (linestring.find("molecule<Molecule>:") != string::npos) {
202// MoleculeSection = true;
203// }
204// if (linestring.find("atoms geometry") != string::npos) {
205// GeometrySection = true;
206// }
207// if ((linestring.find("basis<GaussianBasisSet>:") != string::npos) && ((linestring.find("abasis<") == string::npos))) {
208// BasisSection = true;
209// }
210// if (linestring.find("abasis<") != string::npos) {
211// AuxBasisSection = true;
212// }
213// }
214// // refresh atom::nr and atom::name
215// newmol->getAtomCount();
216}
217
218/** Saves all atoms and data into a MPQC config file.
219 * \param *file output stream
220 * \param atoms atoms to store
221 */
222void FormatParser< psi3 >::save(ostream *file, const std::vector<atom *> &atoms)
223{
224// Vector center;
225//// vector<atom *> allatoms = World::getInstance().getAllAtoms();
226//
227// // calculate center
228// for (std::vector<atom *>::const_iterator runner = atoms.begin();runner != atoms.end(); ++runner)
229// center += (*runner)->getPosition();
230// center.Scale(1./(double)atoms.size());
231//
232// // first without hessian
233// if (file->fail()) {
234// DoeLog(1) && (eLog()<< Verbose(1) << "Cannot open psi3 output file." << endl);
235// } else {
236// *file << "% Created by MoleCuilder" << endl;
237// *file << "psi3: (" << endl;
238// *file << "\tsavestate = " << getParams().getParameter(Psi3Parser_Parameters::savestateParam) << endl;
239// *file << "\tdo_gradient = " << getParams().getParameter(Psi3Parser_Parameters::do_gradientParam) << endl;
240// if (Converter(getParams().getParameter(Psi3Parser_Parameters::hessianParam))) {
241// *file << "\tfreq<MolecularFrequencies>: (" << endl;
242// *file << "\t\tmolecule=$:molecule" << endl;
243// *file << "\t)" << endl;
244// }
245// const std::string theory = getParams().getParameter(Psi3Parser_Parameters::theoryParam);
246// if (theory == getParams().getTheoryName(Psi3Parser_Parameters::CLHF)) {
247// *file << "\tmole<" << getParams().getParameter(Psi3Parser_Parameters::theoryParam) << ">: (" << endl;
248// *file << "\t\tmolecule = $:molecule" << endl;
249// *file << "\t\t" << getParams().getParameterName(Psi3Parser_Parameters::basisParam) << " = $:basis" << endl;
250// *file << "\t\t" << getParams().getParameterName(Psi3Parser_Parameters::maxiterParam)
251// << " = " << getParams().getParameter(Psi3Parser_Parameters::maxiterParam)<< endl;
252// *file << "\t\t" << getParams().getParameterName(Psi3Parser_Parameters::memoryParam)
253// << " = " << getParams().getParameter(Psi3Parser_Parameters::memoryParam) << endl;
254// *file << "\t)" << endl;
255// } else if (theory == getParams().getTheoryName(Psi3Parser_Parameters::CLKS)) {
256// *file << "\tmole<" << getParams().getParameter(Psi3Parser_Parameters::theoryParam) << ">: (" << endl;
257// *file << "\t\tfunctional<StdDenFunctional>:(name=B3LYP)" << endl;
258// *file << "\t\tmolecule = $:molecule" << endl;
259// *file << "\t\t" << getParams().getParameterName(Psi3Parser_Parameters::basisParam) << " = $:basis" << endl;
260// *file << "\t\t" << getParams().getParameterName(Psi3Parser_Parameters::maxiterParam)
261// << " = " << getParams().getParameter(Psi3Parser_Parameters::maxiterParam)<< endl;
262// *file << "\t\t" << getParams().getParameterName(Psi3Parser_Parameters::memoryParam)
263// << " = " << getParams().getParameter(Psi3Parser_Parameters::memoryParam) << endl;
264// *file << "\t)" << endl;
265// } else if (theory == getParams().getTheoryName(Psi3Parser_Parameters::MBPT2)) {
266// *file << "\tmole<" << getParams().getParameter(Psi3Parser_Parameters::theoryParam) << ">: (" << endl;
267// *file << "\t\t" << getParams().getParameterName(Psi3Parser_Parameters::basisParam) << " = $:basis" << endl;
268// *file << "\t\tmolecule = $:molecule" << endl;
269// *file << "\t\t" << getParams().getParameterName(Psi3Parser_Parameters::memoryParam)
270// << " = " << getParams().getParameter(Psi3Parser_Parameters::memoryParam) << endl;
271// *file << "\t\treference<CLHF>: (" << endl;
272// *file << "\t\t\t" << getParams().getParameterName(Psi3Parser_Parameters::maxiterParam)
273// << " = " << getParams().getParameter(Psi3Parser_Parameters::maxiterParam)<< endl;
274// *file << "\t\t\t" << getParams().getParameterName(Psi3Parser_Parameters::basisParam) << " = $:basis" << endl;
275// *file << "\t\t\tmolecule = $:molecule" << endl;
276// *file << "\t\t\t" << getParams().getParameterName(Psi3Parser_Parameters::memoryParam)
277// << " = " << getParams().getParameter(Psi3Parser_Parameters::memoryParam) << endl;
278// *file << "\t\t)" << endl;
279// *file << "\t)" << endl;
280// } else if (theory == getParams().getTheoryName(Psi3Parser_Parameters::MBPT2_R12)) {
281// *file << "\tmole<" << getParams().getParameter(Psi3Parser_Parameters::theoryParam) << ">: (" << endl;
282// *file << "\t\tmolecule = $:molecule" << endl;
283// *file << "\t\t" << getParams().getParameterName(Psi3Parser_Parameters::basisParam) << " = $:basis" << endl;
284// *file << "\t\t" << getParams().getParameterName(Psi3Parser_Parameters::aux_basisParam) << " = $:abasis" << endl;
285// *file << "\t\t" << getParams().getParameterName(Psi3Parser_Parameters::stdapproxParam)
286// << " = \"" << getParams().getParameter(Psi3Parser_Parameters::stdapproxParam) << "\"" << endl;
287// *file << "\t\t" << getParams().getParameterName(Psi3Parser_Parameters::nfzcParam)
288// << " = " << getParams().getParameter(Psi3Parser_Parameters::nfzcParam) << endl;
289// *file << "\t\t" << getParams().getParameterName(Psi3Parser_Parameters::memoryParam)
290// << " = " << getParams().getParameter(Psi3Parser_Parameters::memoryParam) << endl;
291// *file << "\t\tintegrals<IntegralCints>:()" << endl;
292// *file << "\t\treference<CLHF>: (" << endl;
293// *file << "\t\t\tmolecule = $:molecule" << endl;
294// *file << "\t\t\t" << getParams().getParameterName(Psi3Parser_Parameters::basisParam) << " = $:basis" << endl;
295// *file << "\t\t\tmaxiter = " << getParams().getParameter(Psi3Parser_Parameters::maxiterParam) << endl;
296// *file << "\t\t\tmemory = " << getParams().getParameter(Psi3Parser_Parameters::memoryParam) << endl;
297// *file << "\t\t\tintegrals<" << getParams().getParameter(Psi3Parser_Parameters::integrationParam) << ">:()" << endl;
298// *file << "\t\t)" << endl;
299// *file << "\t)" << endl;
300// } else {
301// DoeLog(0) && (eLog() << Verbose(0)
302// << "Unknown level of theory requested for MPQC output file." << std::endl);
303// }
304// *file << ")" << endl;
305// *file << "molecule<Molecule>: (" << endl;
306// *file << "\tunit = " << (World::getInstance().getConfig()->GetIsAngstroem() ? "angstrom" : "bohr" ) << endl;
307// *file << "\t{ atoms geometry } = {" << endl;
308// // output of atoms
309// for (std::vector<atom *>::const_iterator AtomRunner = atoms.begin(); AtomRunner != atoms.end(); ++AtomRunner) {
310// (*AtomRunner)->OutputMPQCLine(file, &center);
311// }
312// *file << "\t}" << endl;
313// *file << ")" << endl;
314// *file << "basis<GaussianBasisSet>: (" << endl;
315// *file << "\tname = \"" << getParams().getParameter(Psi3Parser_Parameters::basisParam) << "\"" << endl;
316// *file << "\tmolecule = $:molecule" << endl;
317// *file << ")" << endl;
318// if (theory == getParams().getTheoryName(Psi3Parser_Parameters::MBPT2_R12)) {
319// *file << "% auxiliary basis set specification" << endl;
320// *file << "\tabasis<GaussianBasisSet>: (" << endl;
321// *file << "\tname = \"" << getParams().getParameter(Psi3Parser_Parameters::aux_basisParam) << "\"" << endl;
322// *file << "\tmolecule = $:molecule" << endl;
323// *file << ")" << endl;
324// }
325// }
326}
327
328
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