Changeset 39cbae 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:

0ad49c

Parents:

751d7f1

git-author:

Gregor Bollerhey <bollerhe@…> (10/19/11 11:30:16)

git-committer:

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

Message:

Update: Unit handling

• temp might have a dimension now
• Leading "!" skips processing by tool 'units' so already converted numbers can be used without specifying 'autodim off' resp. '-autodim'.
• Scaling factor in unit-dictionary is float now, proper typing is GOOD.

File:

• utils/boxmaker.py (modified) (5 diffs)

utils/boxmaker.py

@@ -86 +86 @@
     if SOU == 'custom':
         units = {}
-        quantities = ['length', 'mass']
+        quantities = ['length', 'mass', 'temperature']
 
         for quantity in quantities:
@@ -98 +98 @@
 
                     if 'scalingfactor' in line:
-                        units[quantity][0] = R
+                        units[quantity][0] = float(R)
                     else:
                         units[quantity][1] = R
 
     elif SOU == 'kcalpermole':
-        units = {'length': ['1', 'angstrom'], 'mass': ['1', 'u']}
+        units = {'length': [1.0, 'angstrom'], 'mass': [1.0, 'u'], 'temperature': [503.556, 'K']}
 
     elif SOU == 'evolt':
-        units = {'length': ['1', 'angstrom'], 'mass': ['1', 'u']}
+        units = {'length': [1.0, 'angstrom'], 'mass': [1.0, 'u'], 'temperature': [11604.0, 'K']}
 
     else: # SI
-        units = {'length': ['1', 'm'], 'mass': ['1', 'kg']}
+        units = {'length': [1.0, 'm'], 'mass': [1.0, 'kg'], 'temperature': [1.0, 'K']}
 
     return units
@@ -115 +115 @@
 
 def ConvertUnits(have, want):
+    if have[0] == '!':
+        return float(have[1:])
+    
     # Redo with pipes?
     ret = os.system("units '%s' '%s' > temp_units_output" % (have, want))
@@ -149 +152 @@
 
         have = opt.molarmass
-        want = '%s*%s / mol' % tuple(units['mass'])
+        want = '%f*%s / mol' % tuple(units['mass'])
         opt.molarmass = ConvertUnits(have, want)
 
         have = opt.density
-        want = '(%s*%s) ' % tuple(units['mass']) + '/ (%s*%s)**3' % tuple(units['length'])
+        want = '(%f*%s) ' % tuple(units['mass']) + '/ (%f*%s)**3' % tuple(units['length'])
         opt.density = ConvertUnits(have, want)
+        
+        if opt.temp:
+            have = opt.temp
+            want = '%f*%s' % tuple(units['temperature'])
+            opt.temp = ConvertUnits(have, want)
     else:
         opt.molarmass = float(opt.molarmass)
@@ -168 +176 @@
     else:
         opt.number = int(opt.number)
-        
-    # Temp should be float or None
-    if opt.temp:
-        opt.temp = float(opt.temp)