Changeset c0c85f for utils

Timestamp:

Nov 7, 2011, 4:12:25 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:

bfbb62

Parents:

b82ede

git-author:

Gregor Bollerhey <bollerhe@…> (10/20/11 13:16:38)

git-committer:

Frederik Heber <heber@…> (11/07/11 16:12:25)

Message:

Restructured Code

• temp_source.xyz is created only once
• boolean mapping with dict rather than if-tree

File:

• utils/boxmaker.py (modified) (9 diffs)

utils/boxmaker.py

@@ -139 +139 @@
         
         
-def GetSourcMolareMass(opt):
+def GetSourceMolareMass(opt):
     with open(opt.potentialsfiledir+opt.basename+'.potentials') as f:
         potfile = f.read()
@@ -147 +147 @@
     for key in elementmasses:
         elementmasses[key] = float(elementmasses[key])
-    
-    # Convert from any format to xyz
-    os.system('molecuilder -o xyz --parse-tremolo-potentials %s -i temp_source.xyz -l %s' % (opt.potentialsfiledir+opt.basename+'.potentials', opt.source))
     
     mass_sum = 0.0
@@ -160 +157 @@
             elem = f.readline().split(None, 1)[0].strip()
             mass_sum += elementmasses[elem]
-            
-    os.system('rm temp_source*')     
+
     return mass_sum*avogadro
 
 
-def UpdateSettings(opt):
+def UpdateSettingsAndSource(opt):
     # Map boolean values
+    boolmap = {'on': True, 'off': False}
+    
     for name in ['cubicdomain', 'cubiccell', 'autorotate', 'autodim', 'postprocess', 'automass']:
         value = eval('opt.' + name)
         
-        if value == 'on':
-            value = True
-        elif value == 'off':
-            value = False
+        if value in boolmap:
+            value = boolmap[value]
         else:
             print 'Not a boolean value:', value
@@ -216 +212 @@
         opt.number = int(opt.number)
         
+    UpdateSource(opt)
+        
     # Automatic source mass
     if opt.automass:
-        opt.molarmass = GetSourcMolareMass(opt)
+        opt.molarmass = GetSourceMolareMass(opt)
         print '======== MOLAR MASS:', opt.molarmass
 
@@ -295 +293 @@
         s_ext = ''
 
-    # Convert from any format to xyz
-    os.system('molecuilder -o xyz --parse-tremolo-potentials %s -i temp_source.xyz -l %s' % (opt.potentialsfiledir+opt.basename+'.potentials', opt.source))
-
     # Calculate bounding box from xyz-file
     with open('temp_source.xyz') as f:
@@ -316 +311 @@
         bb[i] = abs(bbmax[i] - bbmin[i])
 
-    os.system('rm temp_source.*')
     return bb
+    
+    
+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)
+    
+    if opt.autorotate:
+        cmd += ' --select-all-atoms --rotate-to-principal-axis-system "0, 1, 0"'
+        
+    os.system(cmd)
+        
+    opt.source = 'temp_source.data'
+
 
 # Global options with sensible default parameters
@@ -323 +331 @@
 
 ReadSettings(opt)
-UpdateSettings(opt)
+UpdateSettingsAndSource(opt)
 
 if type(opt.number) == type([]):
@@ -333 +341 @@
     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'
 
 VolumePerMolecule = opt.molarmass / (avogadro * opt.density)
@@ -390 +393 @@
         f.write(ofile)
         
-if opt.autorotate:
-    os.system('rm ' + opt.source)
+os.system('rm temp_source.data temp_source.xyz')