Changeset be97a8 for src/Parser

Timestamp:

Jul 20, 2010, 1:01:11 PM (15 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:

3d078d, 4b6777, c644a5

Parents:

ba9f5b (diff), 818eda (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'StructureRefactoring' into stable

Conflicts:

test_all.sh

• test_all.sh was modified by Till in StructureRefactoring (these changes taken over).
• World::setDomain() was missing OBSERVE macro.
• MapOfActions: "molecule-by-name" needs String not Molecule.
• TESTFIX: Tesselations/defs.in - paths changed such that @srcdir@ may be absolute.
• TESTFIX: Tesselations/heptan/1.5/NonConvexEnvelope.dat - exchanged due to same surface but different polygon triangulation.
• TESTFIX: Domain/4 molecule-by-id changed from 208 to 207 due to different handling of molecule ids.

Location:

src/Parser

Files:

• MpqcParser.hpp (modified) (1 diff)
• PcpParser.cpp (modified) (6 diffs)
• PcpParser.hpp (modified) (1 diff)

src/Parser/MpqcParser.hpp

@@ -11 +11 @@
 #include "FormatParser.hpp"
 
-#include <iostream>
+#include <iosfwd>
 
 /**

src/Parser/PcpParser.cpp

@@ -7 +7 @@
 
 #include <iostream>
+#include <iomanip>
 
 #include "atom.hpp"
@@ -20 +21 @@
 #include "verbose.hpp"
 #include "World.hpp"
+#include "Matrix.hpp"
+#include "Box.hpp"
 
 /** Constructor of PcpParser.
@@ -210 +213 @@
   // Unit cell and magnetic field
   ParseForParameter(verbose,FileBuffer, "BoxLength", 0, 3, 3, lower_trigrid, BoxLength, 1, critical); /* Lattice->RealBasis */
-  double * const cell_size = World::getInstance().getDomain();
+  double *cell_size = new double[6];
   cell_size[0] = BoxLength[0];
   cell_size[1] = BoxLength[3];
@@ -217 +220 @@
   cell_size[4] = BoxLength[7];
   cell_size[5] = BoxLength[8];
+  World::getInstance().setDomain(cell_size);
+  delete[] cell_size;
   //if (1) fprintf(stderr,"\n");
 
@@ -327 +332 @@
 void PcpParser::save(std::ostream* file)
 {
-  const double * const cell_size = World::getInstance().getDomain();
+  const Matrix &domain = World::getInstance().getDomain().getM();
   class ThermoStatContainer *Thermostats = World::getInstance().getThermostats();
   if (!file->fail()) {
@@ -412 +417 @@
     *file << endl;
     *file << "BoxLength\t\t\t# (Length of a unit cell)" << endl;
-    *file << cell_size[0] << "\t" << endl;
-    *file << cell_size[1] << "\t" << cell_size[2] << "\t" << endl;
-    *file << cell_size[3] << "\t" << cell_size[4] << "\t" << cell_size[5] << "\t" << endl;
+    *file << domain.at(0,0) << "\t" << endl;
+    *file << domain.at(1,0) << "\t" << domain.at(1,1) << "\t" << endl;
+    *file << domain.at(2,0) << "\t" << domain.at(2,1) << "\t" << domain.at(2,2) << "\t" << endl;
     // FIXME
     *file << endl;

src/Parser/PcpParser.hpp

@@ -9 +9 @@
 #define PCPPARSER_HPP_
 
-#include <iostream>
+#include <iosfwd>
 #include "Parser/FormatParser.hpp"