Changeset f894fe 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:

5ab796

Parents:

f89b45

git-author:

Frederik Heber <heber@…> (11/02/11 01:17:53)

git-committer:

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

Message:

Changed GetSourceMolareMass() and GetSourceBBabs() of boxmaker.py.

• now all is done in a single molecuilder run, there are no more temporary files.
• also renamed UpdateSource -> InitialiseSource.

File:

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

utils/boxmaker.py.in

@@ -135 +135 @@
     
     # Redo with pipes?
+    #sys.stdout.write("units '%s' '%s'\n" % (have, want))
     ret = os.system("units '%s' '%s' > temp_units_output" % (have, want))
 
@@ -148 +149 @@
         
         
-def GetSourceMolareMass(opt):
-    with open(opt.potentialsfiledir+opt.basename+'.potentials') as f:
-        potfile = f.read()
-        
-    elementmasses = dict(re.findall(r'element_name=(\w{1,2}).*?mass=([0-9.]*)', potfile))
-    
-    for key in elementmasses:
-        elementmasses[key] = float(elementmasses[key])
-    
-    mass_sum = 0.0
-    
-    with open('temp_source.xyz') as f:
-        N = int(f.readline())
-        comment = f.readline()
-        
-        for i in range(N):
-            elem = f.readline().split(None, 1)[0].strip()
-            mass_sum += elementmasses[elem]
-
-    return mass_sum*avogadro
+def GetSourceMolareMass(opt, units):
+    mol.SelectionAllAtoms()
+    mass_sum = mol.AnalysisCalculateMolarMass()
+    have = ("%f atomicmassunit" % mass_sum)
+    want = ("%f*%s" % tuple(units['mass']))
+    return ConvertUnits(have, want)*avogadro
 
 
@@ -221 +208 @@
         opt.number = int(opt.number)
         
-    UpdateSource(opt)
+    InitialiseSource(opt)
         
     # Automatic source mass
     if opt.automass:
-        opt.molarmass = GetSourceMolareMass(opt)
+        opt.molarmass = GetSourceMolareMass(opt, units)
         print '======== MOLAR MASS:', opt.molarmass
 
@@ -291 +278 @@
 
 def GetSourceBBabs(opt):
-    bbmax = [0.0]*3
-    bbmin = [float('inf')]*3
-
-    s_name_ext = os.path.basename(opt.source).rsplit('.', 1)
-    s_namepart = s_name_ext[0]
-
-    if len(s_name_ext) > 1:
-        s_ext = s_name_ext[1]
-    else:
-        s_ext = ''
-
-    # Calculate bounding box from xyz-file
-    with open('temp_source.xyz') as f:
-        N = int(f.readline())
-        comment = f.readline()
-
-        for i in xrange(N):
-            buf = f.readline()
-            xyz = buf.split()[1:]
-
-            for i in range(3):
-                bbmax[i] = max(bbmax[i], float(xyz[i]))
-                bbmin[i] = min(bbmin[i], float(xyz[i]))
+    mol.WorldCenterOnEdge()
+    bb = mol.AnalysisCalculateBoundingBox()
+    bbmin = [bb[0], bb[2], bb[4]]
+    bbmax = [bb[1], bb[3], bb[5]]
 
     bb = [0.0]*3
@@ -323 +291 @@
     
     
-def UpdateSource(opt):
+def InitialiseSource(opt):
     potfilepath = opt.potentialsfiledir + opt.basename + '.potentials'
-    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:
         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'
-
 
 # Global options with sensible default parameters
@@ -381 +337 @@
 
 mol.CommandVerbose('0')
-mol.ParserParseTremoloPotentials(opt.potentialsfiledir + opt.basename + '.potentials')
-mol.WorldInput(opt.source)
 mol.WorldCenterInBox('%f 0 0 %f 0 %f' % tuple(cell))
 mol.WorldRepeatBox('%d %d %d' % tuple(nbox))