Changeset 698b04 for src

Timestamp:

Sep 9, 2008, 8:37:07 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:

2985c8

Parents:

bd3e55

Message:

new function: molecule::OutputTemperatureFromTrajectories() stores velocities as temperature

In order to use VibrAlyzer we need a temperature file, which we don't have anymore as we do the M
D in molecuilder now. Hence, there is a new command line switch (-L) and a menu item in MeasureAt
oms() in order to print temperature or to store it to a given file.

Location:

src

Files:

• builder.cpp (modified) (5 diffs)
• defs.hpp (modified) (1 diff)
• molecules.cpp (modified) (1 diff)
• molecules.hpp (modified) (1 diff)

src/builder.cpp

@@ -499 +499 @@
   cout << Verbose(0) << " d - calculate principal axis of the system" << endl;
   cout << Verbose(0) << " e - calculate volume of the convex envelope" << endl;
+  cout << Verbose(0) << " f - calculate temperature from current velocity" << endl;
+  cout << Verbose(0) << " g - output all temperatures per step from velocities" << endl;
   cout << Verbose(0) << "all else - go back" << endl;
   cout << Verbose(0) << "===============================================" << endl;
@@ -569 +571 @@
         VolumeOfConvexEnvelope((ofstream *)&cout, configuration, NULL, mol);
         break;
+    case 'f':
+      mol->OutputTemperatureFromTrajectories((ofstream *)&cout, mol->MDSteps-1, mol->MDSteps, (ofstream *)&cout);
+      break;
+    case 'g':
+      {
+        char filename[255];
+        cout << "Please enter filename: " << endl;
+        cin >> filename;
+        cout << Verbose(1) << "Storing temperatures in " << filename << "." << endl;
+        ofstream *output = new ofstream(filename, ios::trunc);
+        if (!mol->OutputTemperatureFromTrajectories((ofstream *)&cout, 0, mol->MDSteps, output))
+          cout << Verbose(2) << "File could not be written." << endl;
+        else
+          cout << Verbose(2) << "File stored." << endl;
+        output->close();
+        delete(output);
+      }
+      break;
   }
 };
@@ -801 +821 @@
             cout << "\t-r\t\tConvert file from an old pcp syntax." << endl;
             cout << "\t-t x1 x2 x3\tTranslate all atoms by this vector (x1,x2,x3)." << endl;
+            cout << "\t-T <file> Store temperatures from the config file in <file>." << endl; 
             cout << "\t-s x1 x2 x3\tScale all atom coordinates by this vector (x1,x2,x3)." << endl;
             cout << "\t-u rho\tsuspend in water solution and output necessary cell lengths, average density rho and repetition." << endl; 
@@ -931 +952 @@
                 MoleculeLeafClass *Subgraphs = NULL;      // list of subgraphs from DFS analysis
                 int *MinimumRingSize = NULL;
-                mol->CreateAdjacencyList((ofstream *)&cout, atof(argv[argptr++]), configuration.GetIsAngstroem());
+                mol->CreateAdjacencyList((ofstream *)&cout, atof(argv[argptr]), configuration.GetIsAngstroem());
                 mol->CreateListOfBondsPerAtom((ofstream *)&cout);
                 Subgraphs = mol->DepthFirstSearchAnalysis((ofstream *)&cout, MinimumRingSize);
@@ -942 +963 @@
                   delete(Subgraphs);
                 }
+              }
+              argptr+=1;
+              break;
+            case 'L':
+              ExitFlag = 1;
+              {
+                cout << Verbose(1) << "Storing temperatures in " << argv[argptr] << "." << endl;
+                ofstream *output = new ofstream(argv[argptr], ios::trunc);
+                if (!mol->OutputTemperatureFromTrajectories((ofstream *)&cout, 0, mol->MDSteps, output))
+                  cout << Verbose(2) << "File could not be written." << endl;
+                else
+                  cout << Verbose(2) << "File stored." << endl;
+                output->close();
+                delete(output);
               }
               argptr+=1;

src/defs.hpp

@@ -15 +15 @@
 #define AtomicLengthToAngstroem  0.52917721 //!< conversion factor from atomic length/bohrradius to angstroem
 #define BONDTHRESHOLD 0.5   //!< CSD threshold in bond check which is the width of the interval whose center is the sum of the covalent radii 
-
+#define AtomicEnergyToKelvin 315774.67  //!< conversion factor from atomic energy to kelvin via boltzmann factor
 #define VERSIONSTRING "v1.0"
 

src/molecules.cpp

@@ -4664 +4664 @@
 };
 
+/** Stores the temperature evaluated from velocities in molecule::Trajectories.
+ * We simply use the formula equivaleting temperature and kinetic energy:
+ * \f$k_B T = \sum_i m_i v_i^2\f$
+ * \param *out output stream for debugging
+ * \param startstep first MD step in molecule::Trajectories
+ * \param endstep last plus one MD step in molecule::Trajectories
+ * \param *output output stream of temperature file
+ * \return file written (true), failure on writing file (false)
+ */ 
+bool molecule::OutputTemperatureFromTrajectories(ofstream *out, int startstep, int endstep, ofstream *output)
+{
+  double temperature;
+  atom *Walker = NULL;
+  // test stream
+  if (output == NULL)
+    return false;
+  else 
+    *output << "# Step Temperature [K] Temperature [a.u.]" << endl;
+  for (int step=startstep;step < endstep; step++) { // loop over all time steps
+    temperature = 0.;
+    Walker = start;
+    while (Walker->next != end) {
+      Walker = Walker->next;
+      for (int i=NDIM;i--;)
+        temperature += Walker->type->mass * Trajectories[Walker].U.at(step).x[i]* Trajectories[Walker].U.at(step).x[i];
+    }
+    *output << step << "\t" << temperature*AtomicEnergyToKelvin << "\t" << temperature << endl;
+  }
+  return true;
+};

src/molecules.hpp

@@ -316 +316 @@
   bool OutputTrajectoriesXYZ(ofstream *out);
   bool Checkout(ofstream *out) const;
+  bool OutputTemperatureFromTrajectories(ofstream *out, int startstep, int endstep, ofstream *output);
 
   private: