Changes in / [d26fb7:6a922b]

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(0);
+    double typical_distance = _atom->getType()->getHBondDistance(1);
     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 Bounce Ignore'")
+#define paramdescriptions ("new boundary conditions as list of three strings, e.g. 'wrap wrap 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] = -1.;
-  for (size_t i =0; i<3;++i)
-    HBondAngle[i] = -1.;
+    HBondDistance[i] = 0.;
+  for (size_t i =0; i<3;++i)
+    HBondAngle[i] = 0.;
 };
 

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       0.741283  -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\
+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\
 ";
 
@@ -303 +280 @@
 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( -1., testelement->getHBondDistance(i) );
+    CPPUNIT_ASSERT_EQUAL( 0., testelement->getHBondDistance(i) );
   for (size_t i = 0; i < 3; ++i)
-    CPPUNIT_ASSERT_EQUAL( -1., testelement->getHBondAngle(i) );
+    CPPUNIT_ASSERT_EQUAL( 0., 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 for "
-      +saturated_atom.getElement().getName());
+      "SaturatedBond::SaturatedBond() - negative bond distance");
   const double HydrogenAngle =
       saturated_atom.getElement().getHBondAngle(saturated_bond.getDegree()-1);
   ASSERT( HydrogenAngle >= 0.,
-      "SaturatedBond::SaturatedBond() - negative bond angle for "
-      +saturated_atom.getElement().getName());
+      "SaturatedBond::SaturatedBond() - negative bond angle");
   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"
 
@@ -47 +45 @@
 static const element * FindElementByString(const std::string &_value)
 {
-  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;
+  static ConvertTo<atomicNumber_t> converter;
+  const element * _element =
+      World::getInstance().getPeriode()->FindElement(converter(_value));
+  return _element;
 }
 

src/Parameters/Specifics/Value_elements.cpp

@@ -57 +57 @@
   for(tokenizer::iterator beg=tok.begin();
       beg != tok.end();++beg) {
-    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,
+    const int tempvalue = boost::lexical_cast<atomicNumber_t>(*beg);
+    const element * _element =
+        World::getInstance().getPeriode()->FindElement(tempvalue);
+    ASSERT( _element != NULL,
         "FindElementsByString() - cannnot find element "
-        +toString(*beg)+" in periodentafel.");
-    elements.push_back(elem);
+        +toString(tempvalue)+" in periodentafel.");
+    elements.push_back(_element);
   }
   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;
@@ -375 +374 @@
       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 +86 @@
   }
   //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
@@ -191 +177 @@
 }
 
-/** 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
 
@@ -70 +69 @@
     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
   };
 
@@ -103 +93 @@
   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;
 
@@ -110 +99 @@
   //!> 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\
@@ -87 +86 @@
 static string waterMpqc_CLKS ="% Created by MoleCuilder\n\
 mpqc: (\n\
-\tcheckpoint = no\n\
 \tsavestate = no\n\
 \tdo_gradient = yes\n\
@@ -112 +110 @@
 static string waterMpqc_MBPT2 ="% Created by MoleCuilder\n\
 mpqc: (\n\
-\tcheckpoint = no\n\
 \tsavestate = no\n\
 \tdo_gradient = yes\n\
@@ -141 +138 @@
 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 < std::string >(),
+                  po::value < int >(),
                   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<std::string> >()->multitoken(),
+                  po::value < std::vector<int> >()->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"
@@ -56 +54 @@
   // 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 {
-      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);
-      }
+      Z = CommandLineParser::getInstance().vm[getTitle()].as< int >();
     } 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"
@@ -53 +51 @@
 {}
 
-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 {
-      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;
-        }
-      }
+      AllElements = CommandLineParser::getInstance().vm[getTitle()].as< vector<int> >();
     } catch(boost::bad_any_cast &e) {
+      AllElements.clear();
       return false;
     }
-    if (temp.empty())
-      return false;
-    else
-      return true;
+    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;
   }
   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 Sep 30 19:50:39 2015, time step 0
+        Created by molecuilder on Wed Jan 28 20:57:11 2015, time step 0
 C       10      10      10
-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
+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

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

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