Changeset cabb46 for src

Timestamp:

Dec 5, 2010, 12:20:07 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:

001f8a, ca03c7

Parents:

4fbca9c

git-author:

Frederik Heber <heber@…> (12/04/10 21:23:07)

git-committer:

Frederik Heber <heber@…> (12/05/10 00:20:07)

Message:

Extended LoadXyz and SaveXyz to any format.

• renamed ParserAction/LoadXyz -> MoleculeAction/Load (same with Save).
• also changed .def for both.
• LoadAction then uses stuff from InputAction but without output name setting.
• new function FormatParserStorage::put() which is opposite to get and stores world to a given ofstream with type from suffix.
• SaveAction uses new FormatParserStorage::put().
• short form of LodAction is "l" not "p"
• short form of SaveAction is "s", ScaleBox has no short form anymore

Testchanges:

• copied all from Simple_configuration/2/pre to ./post.
• changes to test.conf:

MaxPsiStep (if 0 given, then 3 is set).
MaxMinGapStopStep (if 0 given, then 1 is set).
InitMaxMinGapStopStep (if 0 given, then 1 is set).

• changes to test.pdb:

segName is tes (from _tes_t.pdb) not non.
Obtaining molecule names from pdb file's segName is not implemented yet.

• ParserCommonUnitTest::rewriteAnXyzTest(), we don't check for string equality but parse the output stream again and check whether first and second half of all atoms are equal with respect to position and element.
• all regression test that diff an xyz file now use -I '.*Created by....*'
• changed regression tests with respect to changed short forms.

Location:

src

Files:

• Actions/Makefile.am (modified) (3 diffs)
• Actions/MoleculeAction/LoadAction.cpp (added)
• Actions/MoleculeAction/LoadAction.def (moved) (moved from src/Actions/ParserAction/LoadXyzAction.def ) (3 diffs)
• Actions/MoleculeAction/LoadAction.hpp (moved) (moved from src/Actions/ParserAction/LoadXyzAction.hpp ) (1 diff)
• Actions/MoleculeAction/SaveAction.cpp (moved) (moved from src/Actions/ParserAction/SaveXyzAction.cpp ) (4 diffs)
• Actions/MoleculeAction/SaveAction.def (moved) (moved from src/Actions/ParserAction/SaveXyzAction.def ) (3 diffs)
• Actions/MoleculeAction/SaveAction.hpp (moved) (moved from src/Actions/ParserAction/SaveXyzAction.hpp ) (1 diff)
• Actions/ParserAction/LoadXyzAction.cpp (deleted)
• Actions/WorldAction/InputAction.cpp (modified) (1 diff)
• Actions/WorldAction/ScaleBoxAction.def (modified) (1 diff)
• Parser/FormatParserStorage.cpp (modified) (1 diff)
• Parser/FormatParserStorage.hpp (modified) (1 diff)
• Parser/XyzParser.cpp (modified) (2 diffs)
• unittests/ParserCommonUnitTest.cpp (modified) (1 diff)

src/Actions/Makefile.am

@@ -96 +96 @@
   MoleculeAction/FillVoidWithMoleculeAction.cpp \
   MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp \
+  MoleculeAction/LoadAction.cpp \
   MoleculeAction/RotateAroundSelfByAngleAction.cpp \
   MoleculeAction/RotateToPrincipalAxisSystemAction.cpp \
+  MoleculeAction/SaveAction.cpp \
   MoleculeAction/SaveAdjacencyAction.cpp \
   MoleculeAction/SaveBondsAction.cpp \
@@ -110 +112 @@
   MoleculeAction/FillVoidWithMoleculeAction.hpp \
   MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp \
+  MoleculeAction/LoadAction.cpp \
   MoleculeAction/RotateAroundSelfByAngleAction.hpp \
   MoleculeAction/RotateToPrincipalAxisSystemAction.hpp \
+  MoleculeAction/SaveAction.hpp \
   MoleculeAction/SaveAdjacencyAction.hpp \
   MoleculeAction/SaveBondsAction.hpp \
@@ -118 +122 @@
   MoleculeAction/VerletIntegrationAction.hpp
                  
-PARSERACTIONSOURCE = \
-  ParserAction/LoadXyzAction.cpp \
-  ParserAction/SaveXyzAction.cpp       
-PARSERACTIONHEADER = \
-  ParserAction/LoadXyzAction.hpp \
-  ParserAction/SaveXyzAction.hpp
-
 SELECTIONACTIONSOURCE = \
         SelectionAction/AllAtomsAction.cpp \

src/Actions/MoleculeAction/LoadAction.def

@@ -1 +1 @@
 /*
- * LoadXyzAction.def
+ * LoadAction.def
  *
  *  Created on: Aug 26, 2010
@@ -13 +13 @@
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
 #define paramtypes (boost::filesystem::path)
-#define paramtokens ("parse-xyz")
-#define paramdescriptions ("name of xyz file")
+#define paramtokens ("load")
+#define paramdescriptions ("name of molecule file")
 #undef paramdefaults
 #define paramreferences (filename)
@@ -22 +22 @@
 
 // some defines for all the names, you may use ACTION, STATE and PARAMS
-#define CATEGORY Parser
-#define MENUNAME "parser"
+#define CATEGORY Molecule
+#define MENUNAME "molecule"
 #define MENUPOSITION 1
-#define ACTIONNAME LoadXyz
-#define TOKEN "parse-xyz"
+#define ACTIONNAME Load
+#define TOKEN "load"
 
 
 // finally the information stored in the ActionTrait specialization
-#define DESCRIPTION "parse xyz file into World"
-#define SHORTFORM "p"
+#define DESCRIPTION "parse file with molecule into World"
+#define SHORTFORM "l"

src/Actions/MoleculeAction/LoadAction.hpp

@@ -11 +11 @@
 #include "Actions/Action.hpp"
 
-#include "LoadXyzAction.def"
+#include "LoadAction.def"
 #include "Action_impl_header.hpp"
 

src/Actions/MoleculeAction/SaveAction.cpp

@@ -7 +7 @@
 
 /*
- * SaveXyzAction.cpp
+ * SaveAction.cpp
  *
  *  Created on: May 8, 2010
@@ -22 +22 @@
 #include "Helpers/Log.hpp"
 #include "Helpers/Verbose.hpp"
-#include "Parser/XyzParser.hpp"
+#include "Parser/FormatParserStorage.hpp"
 
 #include <iostream>
 #include <string>
 
+#include <boost/filesystem/fstream.hpp>
+
 using namespace std;
 
-#include "Actions/ParserAction/SaveXyzAction.hpp"
+#include "SaveAction.hpp"
 
 // and construct the stuff
-#include "SaveXyzAction.def"
+#include "SaveAction.def"
 #include "Action_impl_pre.hpp"
 /** =========== define the function ====================== */
-Action::state_ptr ParserSaveXyzAction::performCall() {
-  XyzParser parser;
-
+Action::state_ptr MoleculeSaveAction::performCall() {
   // obtain information
   getParametersfromValueStorage();
 
-  DoLog(1) && (Log() << Verbose(1) << "Storing xyz file " << params.filename << "." << endl);
-  // store xyz file
-  ofstream output;
-  output.open(params.filename.string().c_str());
+  DoLog(1) && (Log() << Verbose(1) << "Storing world to file " << params.filename << "." << endl);
+
+  // extract suffix
+  std::string FilenameSuffix;
+  std::string FilenamePrefix;
+  if (params.filename.has_filename()) {
+    // get suffix
+    FilenameSuffix = params.filename.extension().substr(1); // remove the prefixed "."
+    FilenamePrefix = params.filename.stem();
+  } else {
+    DoeLog(1) && (eLog() << Verbose(1) << "Output file does not have a suffix, cannot recognize format." << endl);
+    return Action::failure;
+  }
+
+  // store file
+  // parse the file
+  boost::filesystem::ofstream output;
+  output.open(params.filename);
   if (!output.fail()) {
-    parser.save(&output);
+    FormatParserStorage::getInstance().put(output, FilenameSuffix);
   } else {
     DoeLog(1) && (eLog() << Verbose(1) << "Could not open file " << params.filename << "." << endl);
   }
   output.close();
+
   return Action::failure;
 }
 
-Action::state_ptr ParserSaveXyzAction::performUndo(Action::state_ptr _state) {
+Action::state_ptr MoleculeSaveAction::performUndo(Action::state_ptr _state) {
 //  ParserSaveXyzState *state = assert_cast<ParserSaveXyzState*>(_state.get());
 
@@ -64 +79 @@
 }
 
-Action::state_ptr ParserSaveXyzAction::performRedo(Action::state_ptr _state){
+Action::state_ptr MoleculeSaveAction::performRedo(Action::state_ptr _state){
   return Action::failure;
 //  // Undo and redo have to do the same for this action
@@ -70 +85 @@
 }
 
-bool ParserSaveXyzAction::canUndo() {
+bool MoleculeSaveAction::canUndo() {
   return false;
 }
 
-bool ParserSaveXyzAction::shouldUndo() {
+bool MoleculeSaveAction::shouldUndo() {
   return false;
 }

src/Actions/MoleculeAction/SaveAction.def

@@ -1 +1 @@
 /*
- * SaveXyzAction.def
+ * SaveAction.def
  *
  *  Created on: Aug 26, 2010
@@ -13 +13 @@
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
 #define paramtypes (boost::filesystem::path)
-#define paramtokens ("store-xyz")
-#define paramdescriptions ("file name of xyz file")
+#define paramtokens ("save")
+#define paramdescriptions ("file name of file")
 #undef paramdefaults
 #define paramreferences (filename)
@@ -22 +22 @@
 
 // some defines for all the names, you may use ACTION, STATE and PARAMS
-#define CATEGORY Parser
-#define MENUNAME "parser"
+#define CATEGORY Molecule
+#define MENUNAME "molecule"
 #define MENUPOSITION 2
-#define ACTIONNAME SaveXyz
-#define TOKEN "store-xyz"
+#define ACTIONNAME Save
+#define TOKEN "save"
 
 
 // finally the information stored in the ActionTrait specialization
-#define DESCRIPTION "save world as xyz file"
-#undef SHORTFORM
+#define DESCRIPTION "save world as file of certain type"
+#define SHORTFORM "s"

src/Actions/MoleculeAction/SaveAction.hpp

@@ -11 +11 @@
 #include "Actions/Action.hpp"
 
-#include "SaveXyzAction.def"
+#include "SaveAction.def"
 #include "Action_impl_header.hpp"
 

src/Actions/WorldAction/InputAction.cpp

@@ -23 +23 @@
 #include "molecule.hpp"
 #include "Parser/FormatParserStorage.hpp"
-#include "Parser/PcpParser.hpp"
 #include "Helpers/Verbose.hpp"
 #include "World.hpp"

src/Actions/WorldAction/ScaleBoxAction.def

@@ -32 +32 @@
 // finally the information stored in the ActionTrait specialization
 #define DESCRIPTION "scale box and atomic positions inside"
-#define SHORTFORM "s"
+#undef SHORTFORM

src/Parser/FormatParserStorage.cpp

@@ -243 +243 @@
 }
 
+
+/** Stores world in an ostream depending on its suffix
+ * \param &output output stream
+ * \param suffix
+ * \return true - storing ok, false - suffix unknown
+ */
+bool FormatParserStorage::put(std::ostream &output, std::string suffix)
+{
+  if (suffix == ParserSuffixes[mpqc]) {
+    getMpqc().save(&output);
+  } else if (suffix == ParserSuffixes[pcp]) {
+    getPcp().save(&output);
+  } else if (suffix == ParserSuffixes[pdb]) {
+    getPdb().save(&output);
+  } else if (suffix == ParserSuffixes[tremolo]) {
+    getTremolo().save(&output);
+  } else if (suffix == ParserSuffixes[xyz]) {
+    getXyz().save(&output);
+  } else {
+    DoeLog(1) && (eLog() << Verbose(1) << "Unknown suffix " << suffix << " to for FormatParserStorage::put()." << endl);
+    return false;
+  }
+  return true;
+}
+
 /** Returns reference to the output MpqcParser, adds if not present.
  * \return reference to the output MpqcParser

src/Parser/FormatParserStorage.hpp

@@ -46 +46 @@
 
   bool get(std::istream &input, std::string suffix);
+  bool put(std::ostream &output, std::string suffix);
   MpqcParser &getMpqc();
   PcpParser &getPcp();

src/Parser/XyzParser.cpp

@@ -84 +84 @@
 void XyzParser::save(ostream* file) {
   DoLog(0) && (Log() << Verbose(0) << "Saving changes to xyz." << std::endl);
-  if (comment == "") {
+  //if (comment == "") {
     time_t now = time((time_t *)NULL);   // Get the system time and put it into 'now' as 'calender time'
     comment = "Created by molecuilder on ";
@@ -94 +94 @@
     else
       comment += time;
-  }
+  //}
   *file << World::getInstance().numAtoms() << endl << "\t" << comment << endl;
 

src/unittests/ParserCommonUnitTest.cpp

@@ -187 +187 @@
   input << waterXyz;
   testParser->load(&input);
+  input.clear();
 
   CPPUNIT_ASSERT_EQUAL(3, World::getInstance().numAtoms());
 
-  string newWaterXyz = "";
-  stringstream output;
-  testParser->save(&output);
-  newWaterXyz = output.str();
-
-  CPPUNIT_ASSERT(waterXyz == newWaterXyz);
+  // store and parse in again
+  stringstream output;
+  testParser->save(&output);
+  input << output.str();
+  testParser->load(&input);
+
+  // now twice as many
+  CPPUNIT_ASSERT_EQUAL(6, World::getInstance().numAtoms());
+
+  // check every atom
+  World::AtomComposite atoms = World::getInstance().getAllAtoms();
+  World::AtomComposite::const_iterator firstiter = atoms.begin();
+  World::AtomComposite::const_iterator seconditer = atoms.begin();
+  for (size_t i=0;i<3;i++)
+    ++seconditer;
+  for (;
+      seconditer != atoms.end();
+      ++firstiter,++seconditer) {
+    // check position and type (only stuff xyz stores)
+    CPPUNIT_ASSERT_EQUAL((*firstiter)->getPosition(),(*seconditer)->getPosition());
+    CPPUNIT_ASSERT_EQUAL((*firstiter)->getType(),(*seconditer)->getType());
+  }
 }