Changeset 0ad49c

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:

b82ede

Parents:

39cbae

git-author:

Gregor Bollerhey <bollerhe@…> (10/19/11 14:39:35)

git-committer:

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

Message:

Update: Automatic mass calculation

Also:

• Shortcut for every option

File:

• utils/boxmaker.py (modified) (7 diffs)

utils/boxmaker.py

@@ -1 +1 @@
 import re, os, os.path, sys, operator
+
+avogadro =  6.022143e23
 
 class c_opt():
@@ -19 +21 @@
     autodim = 'on'
     postprocess = 'on'
+    automass = 'on'
 
     def update(self, name, value):
-        shortcuts = {'o': 'outfilename', 'i': 'source', 'm': 'molarmass', 'rho': 'density', 'n': 'number', 'cd': 'cubicdomain', 'cc': 'cubiccell', 'pp': 'postprocess'}
+        shortcuts = {'tf': 'temofiledir', 'pf': 'potentialsfiledir', 'o': 'outfilename',
+        'i': 'source', 'm': 'molarmass', 'rho': 'density',
+        't': 'temp', 'n': 'number', 'cd': 'cubicdomain',
+        'cc': 'cubiccell', 'ar': 'autorotate', 'ad': 'autodim',
+        'pp': 'postprocess', 'am': 'automass'}
         
         if name in shortcuts:
@@ -130 +137 @@
     else:
         raise NameError('UnitError')
+        
+        
+def GetSourcMolareMass(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])
+    
+    # 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
+    
+    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]
+            
+    os.system('rm temp_source*')     
+    return mass_sum*avogadro
 
 
 def UpdateSettings(opt):
     # Map boolean values
-    for name in ['cubicdomain', 'cubiccell', 'autorotate', 'autodim', 'postprocess']:
+    for name in ['cubicdomain', 'cubiccell', 'autorotate', 'autodim', 'postprocess', 'automass']:
         value = eval('opt.' + name)
         
@@ -151 +184 @@
         units = ReadUnits(opt)
 
-        have = opt.molarmass
-        want = '%f*%s / mol' % tuple(units['mass'])
-        opt.molarmass = ConvertUnits(have, want)
+        if not opt.automass:
+            have = opt.molarmass
+            want = '%f*%s / mol' % tuple(units['mass'])
+            opt.molarmass = ConvertUnits(have, want)
 
         have = opt.density
@@ -164 +198 @@
             opt.temp = ConvertUnits(have, want)
     else:
-        opt.molarmass = float(opt.molarmass)
+        if not opt.automass:
+            opt.molarmass = float(opt.molarmass)
+        
         opt.density = float(opt.density)
+        
+        if opt.temp:
+            opt.temp = float(opt.temp)
 
     # Number might be an integer or a 3-vector
@@ -176 +215 @@
     else:
         opt.number = int(opt.number)
+        
+    # Automatic source mass
+    if opt.automass:
+        opt.molarmass = GetSourcMolareMass(opt)
+        print '======== MOLAR MASS:', opt.molarmass
 
 
@@ -295 +339 @@
     opt.source = 'rotated_temp_source.data'
 
-avogadro =  6.022143e23
 VolumePerMolecule = opt.molarmass / (avogadro * opt.density)
 cell = [VolumePerMolecule**(1./3)] * 3