Changeset aa8ef2

Timestamp:

Feb 7, 2011, 10:27:23 AM (14 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

9cff8b

Parents:

f31edc

git-author:

Frederik Heber <heber@…> (02/02/11 20:39:54)

git-committer:

Frederik Heber <heber@…> (02/07/11 10:27:23)

Message:

Implemented MpqcParser::load().

• extended ParserMpqcUnitTest to check minimal functionality of load.

Location:

src/Parser

Files:

• MpqcParser.cpp (modified) (3 diffs)
• unittests/ParserMpqcUnitTest.cpp (modified) (1 diff)
• unittests/ParserMpqcUnitTest.hpp (modified) (2 diffs)

src/Parser/MpqcParser.cpp

@@ -18 +18 @@
 #endif
 
+#include <iostream>
+#include <boost/tokenizer.hpp>
+#include <string>
+
 #include "CodePatterns/MemDebug.hpp"
 
@@ -25 +29 @@
 #include "config.hpp"
 #include "element.hpp"
+#include "molecule.hpp"
 #include "CodePatterns/Log.hpp"
+#include "CodePatterns/toString.hpp"
 #include "CodePatterns/Verbose.hpp"
 #include "LinearAlgebra/Vector.hpp"
@@ -51 +57 @@
 void MpqcParser::load(istream *file)
 {
-  // TODO: MpqcParser::load implementation
-  ASSERT(false, "Not implemented yet");
+  bool GeometryFollows = false;
+  char line[MAXSTRINGSIZE];
+  typedef boost::tokenizer<boost::char_separator<char> > tokenizer;
+  boost::char_separator<char> sep("[]");
+  boost::char_separator<char> whitesep(" \t");
+  ConvertTo<double> toDouble;
+
+  molecule *newmol = World::getInstance().createMolecule();
+  newmol->ActiveFlag = true;
+  while (file->good()) {
+    file->getline(line, MAXSTRINGSIZE-1);
+    std::string linestring(line);
+    if ((linestring.find("atoms geometry") == string::npos) && (linestring.find("}") != string::npos)) {
+      GeometryFollows = false;
+    }
+    if (GeometryFollows) { // we have an atom
+      tokenizer tokens(linestring, sep);
+//      if (tokens.size() != 2)
+//        throw MpqcParseException;
+      tokenizer::iterator tok_iter = tokens.begin();
+      std::stringstream whitespacefilter(*tok_iter++);
+      std::string element;
+      whitespacefilter >> element;
+      std::string vector = *tok_iter;
+      tokenizer vectorcomponents(vector, whitesep);
+      Vector X;
+//      if (vectorcomponents.size() != NDIM)
+//        throw MpqcParseException;
+      tok_iter = vectorcomponents.begin();
+      for (int i=0; i<NDIM; ++i) {
+        X[i] = toDouble(*tok_iter++);
+      }
+      // create atom
+      atom *newAtom = World::getInstance().createAtom();
+      newAtom->setType(World::getInstance().getPeriode()->FindElement(element));
+      newAtom->setPosition(X);
+      newmol->AddAtom(newAtom);
+      DoLog(1) && (Log() << Verbose(1) << "Adding atom " << *newAtom << std::endl);
+    }
+    // set some scan flags
+    if (linestring.find("atoms geometry") != string::npos) {
+      GeometryFollows = true;
+    }
+  }
 }
 

src/Parser/unittests/ParserMpqcUnitTest.cpp

@@ -166 +166 @@
 
 /************************************ tests ***********************************/
+
+void ParserMpqcUnitTest::readMpqcTest() {
+  stringstream input(waterMpqc_CLHF);
+  MpqcParser* testParser = new MpqcParser();
+  testParser->setTheory(MpqcParser::CLHF);
+  testParser->load(&input);
+
+  CPPUNIT_ASSERT_EQUAL(3, World::getInstance().numAtoms());
+}
 
 void ParserMpqcUnitTest::writeMpqcTest() {

src/Parser/unittests/ParserMpqcUnitTest.hpp

@@ -21 +21 @@
   CPPUNIT_TEST_SUITE( ParserMpqcUnitTest ) ;
   CPPUNIT_TEST ( writeMpqcTest );
+  CPPUNIT_TEST ( readMpqcTest );
   CPPUNIT_TEST_SUITE_END();
 
@@ -27 +28 @@
   void tearDown();
 
+  void readMpqcTest();
   void writeMpqcTest();
 };