Changeset b21a64

Timestamp:

Oct 30, 2009, 3:49:38 PM (15 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:

34e0013

Parents:

b70721

git-author:

Frederik Heber <heber@…> (10/30/09 15:33:51)

git-committer:

Frederik Heber <heber@…> (10/30/09 15:49:38)

Message:

BondGraph is parsed if command line switch '-g' is given.

• builder.cpp: case 'g' which gives a bond length table file which is parsed after the configuration and before other command line options.
• BondGraph::BondLengthMatrixMinMaxDistance() falls back to CovalentMinMaxDistance() if no table parsed.
• Bond Length Table was changed to have first row _and_ column each enlist all the elements and does not have a "#" in front anymore.
• The unit test has been changed accordingly.

Signed-off-by: Frederik Heber <heber@…>

Location:

src

Files:

• bondgraph.cpp (modified) (2 diffs)
• builder.cpp (modified) (6 diffs)
• config.cpp (modified) (1 diff)
• config.hpp (modified) (2 diffs)
• unittests/bondgraphunittest.cpp (modified) (1 diff)

src/bondgraph.cpp

@@ -49 +49 @@
 
   // parse in matrix
-  BondLengthMatrix->ParseMatrix(filename.c_str(), 0, 0, 0);
+  BondLengthMatrix->ParseMatrix(filename.c_str(), 0, 1, 0);
 
   // find greatest distance
@@ -113 +113 @@
 void BondGraph::BondLengthMatrixMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem)
 {
-  MinDistance = GetBondLength(Walker->type->Z-1, OtherWalker->type->Z-1);
-  MinDistance *= (IsAngstroem) ? 1. : 1. / AtomicLengthToAngstroem;
-  MaxDistance = MinDistance + BONDTHRESHOLD;
-  MinDistance -= BONDTHRESHOLD;
+  if (BondLengthMatrix->Matrix == NULL) {// safety measure if no matrix has been parsed yet
+    cerr << Verbose(1) << "WARNING:  BondLengthMatrixMinMaxDistance() called without having parsed the bond length matrix yet!" << endl;
+    CovalentMinMaxDistance(Walker, OtherWalker, MinDistance, MaxDistance, IsAngstroem);
+  } else {
+    MinDistance = GetBondLength(Walker->type->Z-1, OtherWalker->type->Z-1);
+    MinDistance *= (IsAngstroem) ? 1. : 1. / AtomicLengthToAngstroem;
+    MaxDistance = MinDistance + BONDTHRESHOLD;
+    MinDistance -= BONDTHRESHOLD;
+  }
 };
 

src/builder.cpp

@@ -1357 +1357 @@
   int argptr;
   molecule *mol = NULL;
+  string BondGraphFileName("");
   strncpy(configuration.databasepath, LocalPath, MAXSTRINGSIZE-1);
 
@@ -1384 +1385 @@
             cout << "\t-E <id> <Z>\tChange atom <id>'s element to <Z>, <id> begins at 0." << endl;
             cout << "\t-f/F <dist> <order>\tFragments the molecule in BOSSANOVA manner (with/out rings compressed) and stores config files in same dir as config (return code 0 - fragmented, 2 - no fragmentation necessary)." << endl;
+            cout << "\t-g <file>\tParses a bond length table from the given file." << endl;
             cout << "\t-h/-H/-?\tGive this help screen." << endl;
             cout << "\t-L <step0> <step1> <prefix>\tStore a linear interpolation between two configurations <step0> and <step1> into single config files with prefix <prefix> and as Trajectories into the current config file." << endl;
@@ -1420 +1422 @@
             }
             break;
+          case 'g':
+            if ((argptr >= argc) || (argv[argptr][0] == '-')) {
+              cerr << "Not enough or invalid arguments for specifying bond length table: -g <table file>" << endl;
+            } else {
+              BondGraphFileName = argv[argptr];
+              cout << "Using " << BondGraphFileName << " as bond length table." << endl;
+              argptr+=1;
+            }
+            break;
           case 'n':
             cout << "I won't parse trajectories." << endl;
@@ -1432 +1443 @@
     } while (argptr < argc);
 
-    // 2. Parse the element database
+    // 3a. Parse the element database
     if (periode->LoadPeriodentafel(configuration.databasepath)) {
       cout << Verbose(0) << "Element list loaded successfully." << endl;
@@ -1440 +1451 @@
       return 1;
     }
-    // 3. Find config file name and parse if possible
+    // 3b. Find config file name and parse if possible
     if (argv[1][0] != '-') {
       // simply create a new molecule, wherein the config file is loaded and the manipulation takes place
@@ -1483 +1494 @@
     } else
       configPresent = absent;
+    // 3c. parse the bond graph file if given
+    configuration.BG = new BondGraph(configuration.GetIsAngstroem());
+    if (configuration.BG->LoadBondLengthTable((ofstream *)&cout, BondGraphFileName)) {
+      cout << Verbose(0) << "Bond length table loaded successfully." << endl;
+    } else {
+      cout << Verbose(0) << "Bond length table loading failed." << endl;
+      return 1;
+    }
     // 4. parse again through options, now for those depending on elements db and config presence
     argptr = 1;

src/config.cpp

@@ -160 +160 @@
 /** Constructor for config file class.
  */
-config::config() : PsiType(0), MaxPsiDouble(0), PsiMaxNoUp(0), PsiMaxNoDown(0), MaxMinStopStep(1), InitMaxMinStopStep(1), ProcPEGamma(8), ProcPEPsi(1), configpath(NULL),
+config::config() : BG(NULL), PsiType(0), MaxPsiDouble(0), PsiMaxNoUp(0), PsiMaxNoDown(0), MaxMinStopStep(1), InitMaxMinStopStep(1), ProcPEGamma(8), ProcPEPsi(1), configpath(NULL),
     configname(NULL), FastParsing(false), Deltat(0.01), basis(""), databasepath(NULL), DoConstrainedMD(0), MaxOuterStep(0), Thermostat(4), ThermostatImplemented(NULL),
     ThermostatNames(NULL), TempFrequency(2.5), alpha(0.), HooverMass(0.), TargetTemp(0.00095004455), ScaleTempStep(25),  mainname(NULL), defaultpath(NULL), pseudopotpath(NULL),

src/config.hpp

@@ -19 +19 @@
 
 #include <string>
+
+#include "bondgraph.hpp"
 
 /****************************************** forward declarations *****************************/
@@ -47 +49 @@
 class config {
   public:
+    class BondGraph *BG;
+
     int PsiType;
     int MaxPsiDouble;

src/unittests/bondgraphunittest.cpp

@@ -79 +79 @@
   filename = new string("test.dat");
   ofstream test(filename->c_str());
-  test << "# Hydrogen\tCarbon\n1.\t1.2\n1.2\t1.5" << endl;
+  test << ".\tH\tC\n";
+  test << "H\t1.\t1.2\n";
+  test << "C\t1.2\t1.5\n";
   BG = new BondGraph(true);
 };