Changeset d26fb7

Timestamp:

Jan 31, 2016, 12:47:12 PM (9 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:

e38750

Parents:

6a922b (diff), 2f429e (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 'Better_HBondDistances' into Candidate_v1.5.1

Files:

• src/Actions/AtomAction/SaturateAction.cpp (modified) (1 diff)
• src/Actions/WorldAction/SetBoundaryConditionsAction.def (modified) (1 diff)
• src/Element/element.cpp (modified) (1 diff)
• src/Element/elements_db.cpp (modified) (2 diffs)
• src/Element/unittests/ElementUnitTest.cpp (modified) (1 diff)
• src/Fragmentation/Exporters/SaturatedBond.cpp (modified) (1 diff)
• src/Parameters/Specifics/Value_element.cpp (modified) (2 diffs)
• src/Parameters/Specifics/Value_elements.cpp (modified) (1 diff)
• src/Parser/MpqcParser.cpp (modified) (2 diffs)
• src/Parser/MpqcParser_Parameters.cpp (modified) (3 diffs)
• src/Parser/MpqcParser_Parameters.hpp (modified) (4 diffs)
• src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) (4 diffs)
• src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) (2 diffs)
• src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) (2 diffs)
• src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) (2 diffs)
• tests/regression/Atoms/Add/post/test.in (modified) (1 diff)
• tests/regression/Atoms/Remove/post/test.in (modified) (1 diff)
• tests/regression/Atoms/Saturate/post/saturated_carbon.xyz (modified) (1 diff)
• tests/regression/Atoms/Saturate/post/saturated_nitrogen.xyz (modified) (1 diff)
• tests/regression/Parser/Mpqc/post/doublewater.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/post/empty.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/post/test.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/post/testCLHF.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/post/testCLKS.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/post/testMBPT2.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/post/testMBPT2_R12.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/pre/testCLHF.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/pre/testCLHF_n.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/pre/testCLHF_n_ascend_ids.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/pre/testCLHF_n_mixed_ids.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/pre/testCLKS.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/pre/testMBPT2.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/pre/testMBPT2_R12.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/pre/water.in (modified) (1 diff)
• tests/regression/Parser/SetParameters/Mpqc/post/testCLHF.in (modified) (1 diff)
• tests/regression/Parser/SetParameters/Mpqc/pre/testCLHF.in (modified) (1 diff)

src/Actions/AtomAction/SaturateAction.cpp

@@ -79 +79 @@
     // add the hydrogens
     const Vector AtomsPosition = _atom->getPosition();
-    double typical_distance = _atom->getType()->getHBondDistance(1);
+    double typical_distance = _atom->getType()->getHBondDistance(0);
     if (typical_distance == -1.)
       typical_distance = 1.;

src/Actions/WorldAction/SetBoundaryConditionsAction.def

@@ -18 +18 @@
 #define paramtypes (std::vector< std::string >)
 #define paramtokens ("set-boundary-conditions")
-#define paramdescriptions ("new boundary conditions as list of three strings, e.g. 'wrap wrap ignore'")
+#define paramdescriptions ("new boundary conditions as list of three strings, e.g. 'Wrap Bounce Ignore'")
 #undef paramdefaults
 #define paramreferences (newconditions)

src/Element/element.cpp

@@ -64 +64 @@
     color[i] = (unsigned char)0;
   for (size_t i =0; i<3;++i)
-    HBondDistance[i] = 0.;
-  for (size_t i =0; i<3;++i)
-    HBondAngle[i] = 0.;
+    HBondDistance[i] = -1.;
+  for (size_t i =0; i<3;++i)
+    HBondAngle[i] = -1.;
 };
 

src/Element/elements_db.cpp

@@ -258 +258 @@
 const char *HbonddistanceDB =\
 "#atomic number bond distances for single, double and triple bond (-1 no bond)\n\
-1       0.74    -1      -1\n\
-2       0.77429209      -1      -1\n\
-5       1.23    1.19    1.18\n\
-6       1.09    1.076   1.06\n\
-7       1.04    1.02    1.01\n\
-8       0.96    0.957   -1\n\
-14      1.48    1.48    1.48\n\
-15      1.42    -1      -1\n\
-16      1.35    -1      -1\n\
-17      1.29    -1      -1\n\
-20      1.09    1.09    -1\n\
-34      1.47    -1      -1\n\
-35      1.44    -1      -1\n\
+1       0.741283  -1. -1.\n\
+2       0  -1. -1.\n\
+3       1.65217  -1. -1.\n\
+4       1.3455  -1. -1.\n\
+5       1.1962  1.19 1.18\n\
+6       1.09234  1.076 1.06\n\
+7       1.00154  1.02 1.01\n\
+8       0.941566  0.957 -1.\n\
+9       0.958865  -1. -1.\n\
+10      0  -1. -1.\n\
+11      1.9426  -1. -1.\n\
+12      1.73705  -1. -1.\n\
+13      1.60991  -1. -1.\n\
+14      1.49796  1.48 1.48\n\
+15      1.39145  -1. -1.\n\
+16      1.32987  -1. -1.\n\
+17      1.31403  -1. -1.\n\
+18      0  -1. -1.\n\
+19      2.38168  -1. -1.\n\
+20      2.39602  -1. -1.\n\
+21      1.69169  -1. -1.\n\
+22      1.69817  -1. -1.\n\
+23      1.75022  -1. -1.\n\
+24      1.79185  -1. -1.\n\
+25      1.49581  -1. -1.\n\
+26      1.76215  -1. -1.\n\
+27      1.4284  -1. -1.\n\
+28      1.56442  -1. -1.\n\
+29      2.00512  -1. -1.\n\
+30      1.55672  -1. -1.\n\
+31      1.58872  -1. -1.\n\
+32      1.5484  -1. -1.\n\
+33      1.47208  -1. -1.\n\
+34      1.43322  -1. -1.\n\
+35      1.45079  -1. -1.\n\
+36      0  -1. -1.\n\
 ";
 
@@ -280 +303 @@
 7       0       110     106.67\n\
 8       0       104.5   -1\n\
+11  0 -1 -1\n\
 14      0       120     109.47\n\
 15      0       -1      -1\n\

src/Element/unittests/ElementUnitTest.cpp

@@ -110 +110 @@
   CPPUNIT_ASSERT_EQUAL( 0, testelement->getNoValenceOrbitals() );
   for (size_t i = 0; i < 3; ++i)
-    CPPUNIT_ASSERT_EQUAL( 0., testelement->getHBondDistance(i) );
+    CPPUNIT_ASSERT_EQUAL( -1., testelement->getHBondDistance(i) );
   for (size_t i = 0; i < 3; ++i)
-    CPPUNIT_ASSERT_EQUAL( 0., testelement->getHBondAngle(i) );
+    CPPUNIT_ASSERT_EQUAL( -1., testelement->getHBondAngle(i) );
 }
 

src/Fragmentation/Exporters/SaturatedBond.cpp

@@ -64 +64 @@
       saturated_atom.getElement().getHBondDistance(saturated_bond.getDegree()-1);
   ASSERT( HydrogenDistance > 0.,
-      "SaturatedBond::SaturatedBond() - negative bond distance");
+      "SaturatedBond::SaturatedBond() - negative bond distance for "
+      +saturated_atom.getElement().getName());
   const double HydrogenAngle =
       saturated_atom.getElement().getHBondAngle(saturated_bond.getDegree()-1);
   ASSERT( HydrogenAngle >= 0.,
-      "SaturatedBond::SaturatedBond() - negative bond angle");
+      "SaturatedBond::SaturatedBond() - negative bond angle for "
+      +saturated_atom.getElement().getName());
   LOG(5, "DEBUG: Hydrogen distance is " << HydrogenDistance
       << ", angle is " << HydrogenAngle);

src/Parameters/Specifics/Value_element.cpp

@@ -35 +35 @@
 #include "CodePatterns/MemDebug.hpp"
 
+#include <boost/lexical_cast.hpp>
+
 #include "Value_element.hpp"
 
@@ -45 +47 @@
 static const element * FindElementByString(const std::string &_value)
 {
-  static ConvertTo<atomicNumber_t> converter;
-  const element * _element =
-      World::getInstance().getPeriode()->FindElement(converter(_value));
-  return _element;
+  const element * elem = NULL;
+  try {
+    const int tempvalue = boost::lexical_cast<atomicNumber_t>(_value);
+    elem = World::getInstance().getPeriode()->FindElement(tempvalue);
+  } catch( boost::bad_lexical_cast &e) {
+    elem = World::getInstance().getPeriode()->FindElement(_value);
+  }
+  return elem;
 }
 

src/Parameters/Specifics/Value_elements.cpp

@@ -57 +57 @@
   for(tokenizer::iterator beg=tok.begin();
       beg != tok.end();++beg) {
-    const int tempvalue = boost::lexical_cast<atomicNumber_t>(*beg);
-    const element * _element =
-        World::getInstance().getPeriode()->FindElement(tempvalue);
-    ASSERT( _element != NULL,
+    const element * elem = NULL;
+    try {
+      const int tempvalue = boost::lexical_cast<atomicNumber_t>(*beg);
+      elem = World::getInstance().getPeriode()->FindElement(tempvalue);
+    } catch( boost::bad_lexical_cast &e) {
+      elem = World::getInstance().getPeriode()->FindElement(*beg);
+    }
+    ASSERT( elem != NULL,
         "FindElementsByString() - cannnot find element "
-        +toString(tempvalue)+" in periodentafel.");
-    elements.push_back(_element);
+        +toString(*beg)+" in periodentafel.");
+    elements.push_back(elem);
   }
   return elements;

src/Parser/MpqcParser.cpp

@@ -309 +309 @@
     *file << "% Created by MoleCuilder" << endl;
     *file << "mpqc: (" << endl;
+    *file << "\tcheckpoint = no" << endl;
     *file << "\tsavestate = " << getParams().getParameter(MpqcParser_Parameters::savestateParam) << endl;
     *file << "\tdo_gradient = " << getParams().getParameter(MpqcParser_Parameters::do_gradientParam) << endl;
@@ -374 +375 @@
       ELOG(0, "Unknown level of theory requested for MPQC output file.");
     }
+    const std::string jobtype = getParams().getParameter(MpqcParser_Parameters::jobtypeParam);
+    if (jobtype == getParams().getJobtypeName(MpqcParser_Parameters::Optimization)) {
+      *file << "\t% optimizer object for the molecular geometry" << endl;
+      *file << "\topt<QNewtonOpt>: (" << endl;
+      *file << "\t\tfunction = $..:mole" << endl;
+      *file << "\t\tupdate<BFGSUpdate>: ()" << endl;
+      *file << "\t\tconvergence<MolEnergyConvergence>: (" << endl;
+      *file << "\t\t\tcartesian = yes" << endl;
+      *file << "\t\t\tenergy = $..:..:mole" << endl;
+      *file << "\t\t)" << endl;
+      *file << "\t)" << endl;
+    }
     *file << ")" << endl;
     *file << "molecule<Molecule>: (" << endl;

src/Parser/MpqcParser_Parameters.cpp

@@ -69 +69 @@
     ParamNames[integrationParam] = "integration";
     ParamNames[theoryParam] = "theory";
+    ParamNames[jobtypeParam] = "jobtype";
   }
 
@@ -87 +88 @@
   //InvertMap<TheoryNamesType,TheoryLookupType>(TheoryNames,TheoryLookup);
 
+  // create Jobs parameter
+  {
+    ValidJobtypes.clear();
+    ValidJobtypes.resize(unknownJob);
+    ValidJobtypes[Default]="Default";
+    ValidJobtypes[Optimization]="Optimization";
+    appendParameter(
+        new Parameter<std::string>(
+            ParamNames[jobtypeParam],
+            ValidJobtypes,
+            ValidJobtypes[Default]));
+  }
+
   // create integration parameter
   {
@@ -177 +191 @@
 }
 
+/** Getter for name of a specific Parameter.
+ *
+ * @param param index among enum Jobtype
+ * @return name of the desired Jobtype
+ */
+const std::string &MpqcParser_Parameters::getJobtypeName(const enum Jobtype jobtype) const
+{
+  return ValidJobtypes[jobtype];
+}
+
 /** Getter for the name of specific of IntegrationMethod.
  *

src/Parser/MpqcParser_Parameters.hpp

@@ -58 +58 @@
     integrationParam,//!< integrationParam, integration method to use in MBPT2 R12
     theoryParam,     //!< theoryParam, level of theory to use
+    jobtypeParam,    //!< jobtypeParam, job type to use
     unknownParam};   //!< unknownParam, designates an unknown parameter
 
@@ -69 +70 @@
     MBPT2_R12,  //!< Moeller Plesset Perturbation Theory second order with R12 integral
     unknownTheory //!< designates an unknown theory
+  };
+
+  /** Enumeration of all known jobtypes.
+   *
+   */
+  enum Jobtype {
+    Default,       //!< standard energy and force calculation
+    Optimization,       //!< additional optimization of geometry
+    unknownJob //!< designates an unknown job
   };
 
@@ -93 +103 @@
   const std::string &getParameterName(const enum Parameters param) const;
   const std::string &getTheoryName(const enum Theory theory) const;
+  const std::string &getJobtypeName(const enum Jobtype jobtype) const;
   const std::string &getIntegrationMethodName(const enum IntegrationMethod integration) const;
 
@@ -99 +110 @@
   //!> vector with all available theories in same order as enum Theory.
   std::vector<std::string> ValidTheories;
+
+  //!> vector with all available jobtypes in same order as enum Jobs.
+  std::vector<std::string> ValidJobtypes;
 
   //!> vector with all available integration methods in same order as enum IntegrationMethod.

src/Parser/unittests/ParserMpqcUnitTest.cpp

@@ -63 +63 @@
 static string waterMpqc_CLHF ="% Created by MoleCuilder\n\
 mpqc: (\n\
+\tcheckpoint = no\n\
 \tsavestate = no\n\
 \tdo_gradient = yes\n\
@@ -86 +87 @@
 static string waterMpqc_CLKS ="% Created by MoleCuilder\n\
 mpqc: (\n\
+\tcheckpoint = no\n\
 \tsavestate = no\n\
 \tdo_gradient = yes\n\
@@ -110 +112 @@
 static string waterMpqc_MBPT2 ="% Created by MoleCuilder\n\
 mpqc: (\n\
+\tcheckpoint = no\n\
 \tsavestate = no\n\
 \tdo_gradient = yes\n\
@@ -138 +141 @@
 static string waterMpqc_MBPT2_R12 ="% Created by MoleCuilder\n\
 mpqc: (\n\
+\tcheckpoint = no\n\
 \tsavestate = no\n\
 \tdo_gradient = yes\n\

src/UIElements/CommandLineUI/CommandLineParser.cpp

@@ -390 +390 @@
 //            currentOption->hasDefaultValue() ?
 //                  po::value < const element * >()->default_value(boost::lexical_cast<const element *>(currentOption->getDefaultValue().c_str())) :
-                  po::value < int >(),
+                  po::value < std::string >(),
                   currentOption->getDescription().c_str())
         ;
@@ -399 +399 @@
 //            currentOption->hasDefaultValue() ?
 //                  po::value < std::vector<const element *> >()->default_value(boost::lexical_cast< std::vector<const element *> >(currentOption->getDefaultValue().c_str())) :
-                  po::value < std::vector<int> >()->multitoken(),
+                  po::value < std::vector<std::string> >()->multitoken(),
                   currentOption->getDescription().c_str())
         ;

src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp

@@ -36 +36 @@
 #include "CodePatterns/MemDebug.hpp"
 
+#include <string>
+
 #include "CommandLineUI/Query/CommandLineQuery.hpp"
 #include "CommandLineUI/CommandLineParser.hpp"
@@ -54 +56 @@
   // TODO: vector of ints and removing first is not correctly implemented yet. How to remove from a vector?
   periodentafel *periode = World::getInstance().getPeriode();
-  int Z = -1;
   if (CommandLineParser::getInstance().vm.count(getTitle())) {
+    std::string argument("none");
     try {
-      Z = CommandLineParser::getInstance().vm[getTitle()].as< int >();
+      argument = CommandLineParser::getInstance().vm[getTitle()].as< std::string >();
+      try {
+        int Z = -1;
+        Z = boost::lexical_cast<int>(argument);
+        temp = periode->FindElement(Z);
+      } catch(boost::bad_lexical_cast &e) {
+        temp = periode->FindElement(argument);
+      }
     } catch(boost::bad_any_cast &e) {
-      Z = -1;
       return false;
     }
-    temp = periode->FindElement(Z);
     ASSERT(temp != NULL, "Invalid element specified in ElementCommandLineQuery");
     return true;

src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp

@@ -36 +36 @@
 #include "CodePatterns/MemDebug.hpp"
 
+#include <string>
+
 #include "CommandLineUI/Query/CommandLineQuery.hpp"
 #include "CommandLineUI/CommandLineParser.hpp"
@@ -51 +53 @@
 {}
 
+template <typename T>
+std::vector<const element *> getElementsFromInput(const std::vector<std::string> &_input)
+{
+  periodentafel *periode = World::getInstance().getPeriode();
+  std::vector<const element *> result;
+  const element *temp_element;
+  for (typename std::vector<std::string>::const_iterator ZRunner = _input.begin(); ZRunner != _input.end(); ++ZRunner) {
+    const T argument = boost::lexical_cast<T>(*ZRunner);
+    temp_element = periode->FindElement(argument);
+    ASSERT(temp_element != NULL, "Invalid element specified in ElementCommandLineQuery");
+    result.push_back(temp_element);
+  }
+  return result;
+}
+
 bool CommandLineDialog::ElementsCommandLineQuery::handle() {
   // TODO: vector of ints and removing first is not correctly implemented yet. How to remove from a vector?
-  periodentafel *periode = World::getInstance().getPeriode();
-  std::vector<int> AllElements;
   if (CommandLineParser::getInstance().vm.count(getTitle())) {
     try {
-      AllElements = CommandLineParser::getInstance().vm[getTitle()].as< vector<int> >();
+      std::vector<std::string> AllArguments;
+      AllArguments = CommandLineParser::getInstance().vm[getTitle()].as< vector<std::string> >();
+      try {
+        temp = getElementsFromInput<int>(AllArguments);
+      } catch(boost::bad_lexical_cast &e) {
+        try {
+        temp = getElementsFromInput<std::string>(AllArguments);
+        } catch(boost::bad_lexical_cast &e) {
+          return false;
+        }
+      }
     } catch(boost::bad_any_cast &e) {
-      AllElements.clear();
       return false;
     }
-    const element *temp_element;
-    for (vector<int>::iterator ZRunner = AllElements.begin(); ZRunner != AllElements.end(); ++ZRunner) {
-      temp_element = periode->FindElement(*ZRunner);
-      ASSERT(temp_element != NULL, "Invalid element specified in ElementCommandLineQuery");
-      temp.push_back(temp_element);
-    }
-    return true;
+    if (temp.empty())
+      return false;
+    else
+      return true;
   }
   return false;

tests/regression/Atoms/Add/post/test.in

@@ -1 +1 @@
 % Created by MoleCuilder
 mpqc: (
+        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Atoms/Remove/post/test.in

@@ -1 +1 @@
 % Created by MoleCuilder
 mpqc: (
+        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Atoms/Saturate/post/saturated_carbon.xyz

@@ -1 +1 @@
 5
-        Created by molecuilder on Wed Jan 28 20:57:11 2015, time step 0
+        Created by molecuilder on Wed Sep 30 19:50:39 2015, time step 0
 C       10      10      10
-H       11.076  10      10
-H       9.64133 11.0145 10
-H       9.64133 9.49277 10.8786
-H       9.64133 9.49277 9.12145
+H       11.0923 10      10
+H       9.63589 11.0299 10
+H       9.63589 9.48507 10.8919
+H       9.63589 9.48507 9.10811

tests/regression/Atoms/Saturate/post/saturated_nitrogen.xyz

@@ -1 +1 @@
 4
-        Created by molecuilder on Wed Jan 28 21:41:39 2015, time step 0
+        Created by molecuilder on Wed Sep 30 19:50:40 2015, time step 0
 N       10      10      10
-H       11.02   10      10
-H       9.49    10.866  10
-H       9.49    9.13397 10
+H       11.0015 10      10
+H       9.49923 10.866  10
+H       9.49923 9.13397 10

tests/regression/Parser/Mpqc/post/doublewater.in

@@ -1 +1 @@
 % Created by MoleCuilder
 mpqc: (
+        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/post/empty.in

@@ -1 +1 @@
 % Created by MoleCuilder
 mpqc: (
+        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/post/test.in

@@ -1 +1 @@
 % Created by MoleCuilder
 mpqc: (
+        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/post/testCLHF.in

@@ -1 +1 @@
 mpqc: (
+        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/post/testCLKS.in

@@ -1 +1 @@
 mpqc: (
+        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/post/testMBPT2.in

@@ -1 +1 @@
 mpqc: (
+        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/post/testMBPT2_R12.in

@@ -1 +1 @@
 mpqc: (
+        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/pre/testCLHF.in

@@ -1 +1 @@
 mpqc: (
+        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/pre/testCLHF_n.in

@@ -1 +1 @@
 mpqc: (
+        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/pre/testCLHF_n_ascend_ids.in

@@ -1 +1 @@
 mpqc: (
+        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/pre/testCLHF_n_mixed_ids.in

@@ -1 +1 @@
 mpqc: (
+        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/pre/testCLKS.in

@@ -1 +1 @@
 mpqc: (
+        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/pre/testMBPT2.in

@@ -1 +1 @@
 mpqc: (
+        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/pre/testMBPT2_R12.in

@@ -1 +1 @@
 mpqc: (
+        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/pre/water.in

@@ -1 +1 @@
 % Created by MoleCuilder
 mpqc: (
+        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/SetParameters/Mpqc/post/testCLHF.in

@@ -1 +1 @@
 mpqc: (
+        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/SetParameters/Mpqc/pre/testCLHF.in

@@ -1 +1 @@
 mpqc: (
+        checkpoint = no
         savestate = no
         do_gradient = yes