Changeset 9a5bcd for src/config.cpp

Timestamp:

Oct 17, 2008, 1:20:42 PM (17 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, Candidate_v1.7.0, 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:

4ee3df

Parents:

f00693

Message:

config::Save() and config::SaveMPQC() now take string for filename, instead of opened ofstream.

This was necessary, as config::SaveMPQC() now writes to files: One with hessian calc enabled, the other not. As it is a pendant of config::Save(), this file was changed accordingly. Both are called from builder.cpp (ParseFromParamters() and main()) and moleculelist.cpp (MoleculeListClass::OutputConfigForListOfFragments()), hence these were changed,too.

File:

• src/config.cpp (modified) (5 diffs)

src/config.cpp

@@ -971 +971 @@
 
 /** Stores all elements of config structure from which they can be re-read.
- * \param output open output *file stream to write to
+ * \param *filename name of file
  * \param *periode pointer to a periodentafel class with all elements
  * \param *mol pointer to molecule containing all atoms of the molecule 
  */
-bool config::Save(ofstream *output, periodentafel *periode, molecule *mol) const
+bool config::Save(const char *filename, periodentafel *periode, molecule *mol) const
 {
   bool result = true;
         // bring MaxTypes up to date
         mol->CountElements();
+  ofstream *output = NULL;
+  output = new ofstream(filename, ios::out);
   if (output != NULL) {
     *output << "# ParallelCarParinello - main configuration file - created with molecuilder" << endl;
@@ -1067 +1069 @@
     else
       result = result && mol->OutputTrajectories(output);
+    output->close();
+    output->clear();
+    delete(output);
     return result;
   } else
@@ -1074 +1079 @@
 /** Stores all elements in a MPQC input file.
  * Note that this format cannot be parsed again.
- * \param output open output *file stream to write to
+ * \param *filename name of file (without ".in" suffix!)
  * \param *mol pointer to molecule containing all atoms of the molecule 
  */
-bool config::SaveMPQC(ofstream *output, molecule *mol) const
+bool config::SaveMPQC(const char *filename, molecule *mol) const
 {
   int ElementNo = 0;
   int AtomNo;
   atom *Walker = NULL;
-  element *runner = mol->elemente->start;
+  element *runner = NULL;
   Vector *center = NULL;
-
+  ofstream *output = NULL;
+  stringstream *fname = NULL;
+  
+  // first without hessian
+  fname = new stringstream;
+  *fname << filename << ".in";
+  output = new ofstream(fname->str().c_str(), ios::out);
   *output << "% Created by MoleCuilder" << endl;
   *output << "mpqc: (" << endl;
@@ -1100 +1111 @@
   center = mol->DetermineCenterOfAll(output);
   // output of atoms
+  runner = mol->elemente->start;
   while (runner->next != mol->elemente->end) { // go through every element
     runner = runner->next;
@@ -1122 +1134 @@
   *output << "\tmolecule = $:molecule" << endl;
   *output << ")" << endl;
+  output->close();
+  delete(output);
+  delete(fname);
+
+  // second with hessian
+  fname = new stringstream;
+  *fname << filename << ".hess.in";
+  output = new ofstream(fname->str().c_str(), ios::out);
+  *output << "% Created by MoleCuilder" << endl;
+  *output << "mpqc: (" << endl;
+  *output << "\tsavestate = no" << endl;
+  *output << "\tdo_gradient = yes" << endl;
+  *output << "\tmole<CLHF>: (" << endl;
+  *output << "\t\tmaxiter = 200" << endl;
+  *output << "\t\tbasis = $:basis" << endl;
+  *output << "\t\tmolecule = $:molecule" << endl;
+  *output << "\t)" << endl;
+  *output << "\tfreq<MolecularFrequencies>: (" << endl;
+  *output << "\t\tmolecule=$:molecule" << endl;
+  *output << "\t)" << endl;
+  *output << ")" << endl;
+  *output << "molecule<Molecule>: (" << endl;
+  *output << "\tunit = " << (IsAngstroem ? "angstrom" : "bohr" ) << endl;
+  *output << "\t{ atoms geometry } = {" << endl;
+  center = mol->DetermineCenterOfAll(output);
+  // output of atoms
+  runner = mol->elemente->start;
+  while (runner->next != mol->elemente->end) { // go through every element
+    runner = runner->next;
+    if (mol->ElementsInMolecule[runner->Z]) { // if this element got atoms
+      ElementNo++;
+      AtomNo = 0;
+      Walker = mol->start;
+      while (Walker->next != mol->end) { // go through every atom of this element
+        Walker = Walker->next;
+        if (Walker->type == runner) { // if this atom fits to element
+          AtomNo++;
+          *output << "\t\t" << Walker->type->symbol << " [ " << Walker->x.x[0]-center->x[0] << "\t" << Walker->x.x[1]-center->x[1] << "\t" << Walker->x.x[2]-center->x[2] << " ]" << endl;
+        }
+      }
+    }
+  }
+  delete(center);
+  *output << "\t}" << endl;
+  *output << ")" << endl;
+  *output << "basis<GaussianBasisSet>: (" << endl;
+  *output << "\tname = \"3-21G\"" << endl;
+  *output << "\tmolecule = $:molecule" << endl;
+  *output << ")" << endl;
+  output->close();
+  delete(output);
+  delete(fname);
+  
   return true;
 };