Changeset 6b8b57 for src

Timestamp:

Aug 29, 2008, 10:12:00 AM (16 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:

c1fc22

Parents:

ab3a0e

Message:

new function SaveMPQC(), bugfixes in ParseForParameter()

ParseForParameter(): first while loop tested dummy[0] although it might occur that dummy = NULL, this is now checked beforehand. On stepping through the values in the keyword line, the end marker (dummy) was shifted to the start of the next value, hence included the tabs. This lead to strings being stored with tabs at the end and on consecutive loading&storing in an MD run to an accumulation of tabs till MD step 152, where the config file could not be parsed anymore due to the size of the string value. This is fixed (the shifthing further is removed, as unnecessary).
SaveMPQC(): molecuilder now stores input files for MPQC directly, i.e. they don't have to be converted from the ESPACK format externally. This saves a lot of time during BOSSANOVA MD.

File:

• src/config.cpp (modified) (6 diffs)

src/config.cpp

@@ -652 +652 @@
     atom *neues = NULL;
     while (status) {
+      cout << "Currently parsing MD step " << repetition << "." << endl;
       for (int i=0; i < config::MaxTypes; i++) {
         sprintf(name,"Ion_Type%i",i+1);
@@ -1060 +1061 @@
 };
 
+/** 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 *mol pointer to molecule containing all atoms of the molecule 
+ */
+bool config::SaveMPQC(ofstream *output, molecule *mol) const
+{
+  int ElementNo;
+  int AtomNo;
+  atom *Walker = NULL;
+  element *runner;
+  Vector center;
+
+  *output << "% Created by MoleCuilder" << endl;
+  *output << "mpqc: (" << endl;
+  *output << "\tsavestate = no" << endl;
+  *output << "\tdo_gradient = yes" << endl;
+  *output << "\tmole<CLHF>: (" << endl;
+  *output << "\t\tmolecule<Molecule>: (" << endl;
+  *output << "\t\t\tunit = " << (IsAngstroem ? "angstrom" : "bohr" ) << endl;
+  *output << "\t\t\t{ atoms geometry } = {" << endl;
+  mol->DetermineCenter(center);
+  // output of atoms
+  ElementNo = 0;
+  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\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;
+        }
+      }
+    }
+  }
+  *output << "\t\t\t}" << endl;
+  *output << "\t\t)" << endl;
+  *output << "\t\tbasis<GaussianBasisSet>: (" << endl;
+  *output << "\t\t\tname = \"STO-3G\"" << endl;
+  *output << "\t\t\tmolecule = $:mpqc:mole:molecule" << endl;
+  *output << "\t\t)" << endl;
+  *output << "\t)" << endl;
+  *output << ")" << endl;
+  return true;
+};
+
 /** Reads parameter from a parsed file.
  * The file is either parsed for a certain keyword or if null is given for
@@ -1103 +1155 @@
           Free((void **)&free_dummy, "config::ParseForParameter: *free_dummy");
           //Error(InitReading, name);
-          fprintf(stderr,"Error:InitReading, critical %s not found\n", name);
+          //fprintf(stderr,"Error:InitReading, critical %s not found\n", name);
           exit(255);
         } else {
@@ -1114 +1166 @@
       }
       line++;
-    } while (((dummy1[0] == '#') || (dummy1[0] == '\n')) && dummy != NULL); // skip commentary and empty lines
+    } while (dummy != NULL && dummy1 != NULL && ((dummy1[0] == '#') || (dummy1[0] == '\0'))); // skip commentary and empty lines
     
     // C++ getline removes newline at end, thus re-add
@@ -1122 +1174 @@
       dummy1[i+1] = '\0';
     }
-    //fprintf(stderr,"line ends at %i, newline at %i\n", strlen(dummy1), strchr(dummy1,'\n')-free_dummy);
+    //fprintf(stderr,"line %i ends at %i, newline at %i\n", line, strlen(dummy1), strchr(dummy1,'\n')-free_dummy);
+
     if (dummy1 == NULL) {
       if (verbose) fprintf(stderr,"Error reading line %i\n",line);
     } else {
-      //fprintf(stderr,"Reading next line %i: %s\n", line, dummy1);
+      //fprintf(stderr,"Now parsing the line %i: %s\n", line, dummy1);
     }
     // Seek for possible end of keyword on line if given ...
@@ -1204 +1257 @@
               if (dummy == NULL)
                 dummy = strchr(dummy1, ' ');  // if not found seek for space
-              while ((dummy != NULL) && ((*dummy == '\t') || (*dummy == ' ')))    // skip some more tabs and spaces if necessary
-                dummy++;
-/*              while ((dummy != NULL) && ((*dummy == '\t') || (*dummy == ' ')))    // skip some more tabs and spaces if necessary
-                dummy++;*/
               if (dummy == NULL) { // if still zero returned ...
                 dummy = strchr(dummy1, '\n');  // ... at line end then