Changeset 32bc47 for utils

Timestamp:

Nov 7, 2011, 4:12:24 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:

751d7f1

Parents:

0c83d8

git-author:

Gregor Bollerhey <bollerhe@…> (10/17/11 12:08:19)

git-committer:

Frederik Heber <heber@…> (11/07/11 16:12:24)

Message:

Update: autorotate

Not tested yet, but it seems like it does *something* (means: paths etc. are correctly handled).

File:

• utils/boxmaker.py (modified) (6 diffs)

utils/boxmaker.py

@@ -16 +16 @@
     cubicdomain = 'on'
     cubiccell = 'off'
-    autorotate = 'off' # Not implemented yet
+    autorotate = 'off'
     autodim = 'on'
+    postprocess = 'on'
 
     def update(self, name, value):
@@ -122 +123 @@
 def UpdateSettings(opt):
     # Map boolean values
-    for name in ['cubicdomain', 'cubiccell', 'autorotate', 'autodim']:
+    for name in ['cubicdomain', 'cubiccell', 'autorotate', 'autodim', 'postprocess']:
         value = eval('opt.' + name)
         
@@ -159 +160 @@
     else:
         opt.number = int(opt.number)
+        
+    # Temp should be float or None
+    if opt.temp:
+        opt.temp = float(opt.temp)
 
 
@@ -272 +277 @@
     else:
         nbox = FindBestCuboid(opt)
+        
+# Autorotate
+if opt.autorotate:
+    os.system('molecuilder --parse-tremolo-potentials %s -i rotated_temp_source.data -l %s --rotate-to-principal-axis-system "1, 0, 0"' % (opt.potentialsfiledir+opt.basename+'.potentials', opt.source))
+    opt.source = 'rotated_temp_source.data'
 
 avogadro =  6.022143e23
@@ -296 +306 @@
 
 import pyMoleCuilder as mol
-
 mol.CommandVerbose('0')
 mol.ParserParseTremoloPotentials(opt.potentialsfiledir + opt.basename + '.potentials')
@@ -311 +320 @@
 
 print  '======== DOMAIN: ', domain
+
+# Postprocessing
+
+if opt.postprocess:
+    with open(opt.outfilename + '.data') as f:
+        ofile = f.read()
+    
+    with open(opt.outfilename + '.data', 'w') as f:
+        f.write('# INPUTCONV shift center\n')
+        
+        if opt.temp:
+            f.write('# INPUTCONV temp %.4f\n' % opt.temp)
+            
+        f.write(ofile)
+        
+if opt.autorotate:
+    os.system('rm ' + opt.source)