Changeset 2aa9ef for utils/boxmaker.py.in

Timestamp:

Nov 7, 2011, 4:13:18 PM (13 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:

6c61a9

Parents:

dfef3f

git-author:

Frederik Heber <heber@…> (11/01/11 23:53:28)

git-committer:

Frederik Heber <heber@…> (11/07/11 16:13:18)

Message:

UpdateSource function of boxmaker.py is not an external call to molecuilder anymore.

• this is unusable in a test and was contradictory to the intention of a script. As now we may safely reinit() the pyMoleCuilder module, we may use it to do the same as the external call did.

File:

• utils/boxmaker.py.in (modified) (3 diffs)

utils/boxmaker.py.in

@@ -8 +8 @@
 
 import re, os, os.path, sys, operator
+import pyMoleCuilder as mol
 
 avogadro =  6.022143e23
@@ -324 +325 @@
 def UpdateSource(opt):
     potfilepath = opt.potentialsfiledir + opt.basename + '.potentials'
-    
-    cmd = 'molecuilder -o xyz tremolo --parse-tremolo-potentials %s -i temp_source.xyz -l %s' % (potfilepath, opt.source)
+    mol.ParserSetOutputFormats("xyz tremolo")
+    mol.ParserParseTremoloPotentials(potfilepath)
+    mol.MoleculeLoad(opt.source)
+    
+    #cmd = 'molecuilder -o xyz tremolo --parse-tremolo-potentials %s -i temp_source.xyz -l %s' % (potfilepath, opt.source)
     
     if opt.autorotate:
-        cmd += ' --select-all-atoms --rotate-to-principal-axis-system "0, 1, 0"'
-        
-    os.system(cmd)
+        mol.SelectAllAtoms()
+        mol.RotateToPrincipalAxisSystem("0 1 0")
+        #cmd += ' --select-all-atoms --rotate-to-principal-axis-system "0, 1, 0"'
+    mol.WorldOutput('temp_source' + '.data')
+    mol.WorldOutput('temp_source' + '.xyz')
+        
+    #os.system(cmd)
+    mol.reinit()
         
     opt.source = 'temp_source.data'
@@ -371 +380 @@
 print '======== CELL: ', cell
 
-import pyMoleCuilder as mol
 mol.CommandVerbose('0')
 mol.ParserParseTremoloPotentials(opt.potentialsfiledir + opt.basename + '.potentials')