Changeset 0c83d8 for utils/boxmaker.py

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:

32bc47

Parents:

5735ba

git-author:

Gregor Bollerhey <bollerhe@…> (10/17/11 11:03:12)

git-committer:

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

Message:

Less ugly advanced version

• Class (struct) based global options
• Minor bugfixes
• Feature: Cubic cell
• Feature: Skip unit conversion
• Feature: Options via cmd line
• Feature: More settings

TODO:

• Output postprocessing (INPUTCONVs)
• Auto-rotate to minimum BBox
• Documentation

File:

• utils/boxmaker.py (modified) (4 diffs)

utils/boxmaker.py

@@ -1 +1 @@
 import re, os, os.path, sys, operator
 
-def ReadSettings():
+class c_opt():
+    basename = None
+    tremofiledir = './'
+    potentialsfiledir = './'
+    outfilename = 'out'
+
+    source = None
+    molarmass = None
+    density = None
+    temp = None
+
+    number = '1000'
+    
+    cubicdomain = 'on'
+    cubiccell = 'off'
+    autorotate = 'off' # Not implemented yet
+    autodim = 'on'
+
+    def update(self, name, value):
+        if name in dir(self):
+            exec('self.%s = "%s"' % (name, value))
+        else:
+            print 'Warning: Unknown option:', name
+
+
+def ReadSettings(opt):
+    # Obtain basename
     if len(sys.argv) >= 2:
-        global opt_basename
-        opt_basename = sys.argv[1]
-    else:
-        print 'usage: boxmaker.py <basename>'
+        opt.basename = sys.argv[1]
+    else:
+        print 'Usage: boxmaker.py <basename> [options]'
         exit()
-    
-    with open('boxmaker.'+opt_basename) as f:
+
+    # Read settings file
+    with open('boxmaker.' + opt.basename) as f:
         for line in f:
             if len(line) > 0 and line[0] != '#':
                 L, S, R = line.partition('=')
-                varname = 'opt_' + L.strip()
-                
-                exec('global %s\n%s="%s"' % (varname, varname, R.strip()))
-                
-    # IT'S A HACK
-    global opt_number
-    
-    if len(sys.argv) == 3:
-        opt_number = sys.argv[2]
-    
-    
-def ReadUnits():    
-    lines = []
-    with open(opt_tremofiledir+opt_basename+'.tremolo') as f:
+                opt.update(L.strip(), R.strip())
+
+    # Parse parameters
+    i = 2
+    while i < len(sys.argv):
+        L = sys.argv[i]
+
+        if L[0] in '+-':
+            LN = L[1:]
+
+            if L[0] == '+':
+                R = 'on'
+            else:
+                R = 'off'
+        else:
+            LN = L
+            i += 1
+            R = sys.argv[i]
+        
+        opt.update(LN, R)
+        i += 1
+
+
+def ReadUnits(opt):
+    lines = [] # The file needs to be processed twice, so we save the lines in the first run
+
+    with open(opt.tremofiledir + opt.basename + '.tremolo') as f:
         for line in f:
             if len(line) > 0 and line[0] != '#':
                 line = line.strip()
-                lines.append(line.strip())
-                
+                lines.append(line)
+
                 if 'systemofunits' in line:
                     L, S, SOU = line.partition('=')
-                    SOU = SOU.strip()[:-1]
-                    
+                    SOU = SOU.strip()[:-1] # Remove semicolon
+
     if SOU == 'custom':
         units = {}
         quantities = ['length', 'mass']
-        
+
         for quantity in quantities:
-            units[quantity] = [None, None] # scaling factor and unit.
-        
+            units[quantity] = [None, None] # Init with scaling factor and unit 'None'.
+
         for line in lines:
             for quantity in quantities:
                 if quantity in line:
                     L, S, R = line.partition('=')
-                    R = R.strip()[:-1] # remove semicolon
-                    
+                    R = R.strip()[:-1] # Remove semicolon
+
                     if 'scalingfactor' in line:
                         units[quantity][0] = R
                     else:
                         units[quantity][1] = R
-                        
+
     elif SOU == 'kcalpermole':
         units = {'length': ['1', 'angstrom'], 'mass': ['1', 'u']}
-    
+
     elif SOU == 'evolt':
         units = {'length': ['1', 'angstrom'], 'mass': ['1', 'u']}
-        
+
     else: # SI
         units = {'length': ['1', 'm'], 'mass': ['1', 'kg']}
-                                         
+
     return units
-    
-    
+
+
 def ConvertUnits(have, want):
-    # redo with pipes?
+    # Redo with pipes?
     ret = os.system("units '%s' '%s' > temp_units_output" % (have, want))
-    
+
     if ret == 0:
         with open('temp_units_output') as f:
             line = f.readline()
+
+        os.system('rm temp_units_output')
+
+        return float(line[3:-1])
+    else:
+        raise NameError('UnitError')
+
+
+def UpdateSettings(opt):
+    # Map boolean values
+    for name in ['cubicdomain', 'cubiccell', 'autorotate', 'autodim']:
+        value = eval('opt.' + name)
+        
+        if value == 'on':
+            value = True
+        elif value == 'off':
+            value = False
+        else:
+            print 'Not a boolean value:', value
+            exit()
             
-        os.system('rm temp_units_output')
-            
-        return float(line[3:-1])
-    else:
-        raise NameError('UnitError')
-    
-    
-def UpdateSettings():
-    global opt_molarmass, opt_density, opt_number
-    
-    units = ReadUnits()
-    
-    have = opt_molarmass
-    want = '%s*%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'])
-    opt_density = ConvertUnits(have, want)
-    
-    nvec = opt_number.split()
+        exec('opt.' + name + '= value')
+
+    # Convert dimensions
+    if opt.autodim:
+        units = ReadUnits(opt)
+
+        have = opt.molarmass
+        want = '%s*%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'])
+        opt.density = ConvertUnits(have, want)
+    else:
+        opt.molarmass = float(opt.molarmass)
+        opt.density = float(opt.density)
+
+    # Number might be an integer or a 3-vector
+    nvec = opt.number.split()
     if len(nvec) == 3:
-        opt_number = [0]*3
-        
+        opt.number = [0]*3
+
         for i in range(3):
-            opt_number[i] = int(nvec[i])
-    else:
-        opt_number = int(opt_number)
-        
-        
-def FindNearestCube(n):
-    global opt_number
-    
-    newroot = round(opt_number**(1./3))
-    
-    opt_number = int(newroot**3)
-    print 'warning: number changed to %d' % opt_number
-    
-    return [int(newroot)] * 3
-        
-        
-def FindBestCuboid(n):
-    # prime factors of n
-    # taken from http://www.hsg-kl.de/faecher/inf/python/listen/index.php, "Beispiel 2"
-    
-    F = []
-
-    while n%2 == 0:
-        F.append(2)
-        n = n/2
-    while n%3 == 0:
-        F.append(3)
-        n = n/3
-    
+            opt.number[i] = int(nvec[i])
+    else:
+        opt.number = int(opt.number)
+
+
+def FindBestCube(opt):
+    newroot = int( round(opt.number**(1./3)) )
+    newnumber = newroot**3
+
+    if newnumber != opt.number:
+        print 'Warning: Number changed to %d.' % newnumber
+
+    return [newroot] * 3
+
+
+def FindBestCuboid(opt):
+    n = opt.number
+
+    # Prime factors of n
+    factors = []
+
+    for i in [2, 3]:
+        while n % i == 0:
+            factors.append(i)
+            n /= 2
+
     t = 5
     diff = 2
-    
+
     while t*t <= n:
-        while n%t == 0:
-            F.append(t)
-            n = n/t
+        while n % t == 0:
+            factors.append(t)
+            n /= t
+
         t = t + diff
         diff = 6 - diff
+
     if n > 1:
-        F.append(n)
-        
-    # even distribution of current biggest prime to each vector -> similar sizes
-    if len(F) < 3:
-        print 'warning: not enough prime factors - falling back to cubic placement'
-        return FindNearestCube(n, mlen)
-    
-    F.sort()
+        factors.append(n)
+
+    # Even distribution of current biggest prime to each vector -> similar sizes
+    if len(factors) < 3:
+        print 'Warning: Not enough prime factors - falling back to cubic placement'
+        return FindBestCube(opt)
+
+    factors.sort()
     distri = [[],[],[]]
     current = 0
-    
-    for primfaktor in F:
-        distri[current].append(primfaktor)
+
+    for factor in factors:
+        distri[current].append(factor)
         current += 1
         if current == 3:
             current = 0
-            
-    result = []
-    
-    print 'box used:',
-    
+
+    result = [0]*3
+
+    print '======== CUBOID USED:',
+
     for i in range(3):
-        a = reduce(operator.mul, distri[i])
-        print a,
-        result.append(int(a))
-        
-    print
+        result[i] = int( reduce(operator.mul, distri[i]) )
+
+    print result
     return result
-    
-    
-def GetSourceBBabs():
+
+
+def GetSourceBBabs(opt):
     bbmax = [0.0]*3
-    bbmin = [0.0]*3
-    
-    s_name_ext = os.path.basename(opt_source).rsplit('.',1)
+    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[0])> 1:
+
+    if len(s_name_ext) > 1:
         s_ext = s_name_ext[1]
     else:
         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))
-        
+
+    # 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:
         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]))
@@ -196 +251 @@
 
     bb = [0.0]*3
-    
+
     for i in range(3):
-        bb[i] = bbmax[i] - bbmin[i]
-        
-    
+        bb[i] = abs(bbmax[i] - bbmin[i])
+
     os.system('rm temp_source.*')
     return bb
 
-
-ReadSettings()
-UpdateSettings()
-
-
-if type(opt_number) == type([]):
-    nbox = opt_number
+# Global options with sensible default parameters
+opt = c_opt()
+
+ReadSettings(opt)
+UpdateSettings(opt)
+
+if type(opt.number) == type([]):
+    # Number is a vector - use it without any modification
+    nbox = opt.number
 else:
-    if opt_constraint == 'cube':
-        nbox = FindNearestCube(opt_number)
-    else:
-        nbox = FindBestCuboid(opt_number)
+    if opt.cubicdomain:
+        nbox = FindBestCube(opt)
+    else:
+        nbox = FindBestCuboid(opt)
 
 avogadro =  6.022143e23
-VolumePerMolecule = opt_molarmass / (avogadro * opt_density)
-
-try:
-    bb = GetSourceBBabs()
-    print '======== BBOX:', bb
-    s = (VolumePerMolecule / (bb[0]*bb[1]*bb[2])) ** (1./3)
-    
-    if s < 0:
-        print 'warning: molecular cells will overlap'
-    
-    for i in range(3):
-        bb[i] = bb[i]*s
+VolumePerMolecule = opt.molarmass / (avogadro * opt.density)
+cell = [VolumePerMolecule**(1./3)] * 3
+
+if not opt.cubiccell:
+    try:
+        bb = GetSourceBBabs(opt)
+        print '======== BBOX:', bb
+        # Scaling factor - the molecules bounding box is scaled to fit the volume suiting the density
+        s = (VolumePerMolecule / (bb[0]*bb[1]*bb[2])) ** (1./3)
+
+        if s < 1:
+            print 'Warning: Molecular cells will overlap.'
+
+        for i in range(3):
+            cell[i] = bb[i]*s
+    except ZeroDivisionError:
+        print 'Warning:  Singularity in bounding box, falling back to cubic cell.'
         
-    cell = bb
-except ZeroDivisionError:
-    print 'warning:  singularity in bounding box, using cubic cell'
-    cell = [VolumePerMolecule**(1./3)] * 3
-    
+
 print '======== CELL: ', cell
 
@@ -241 +298 @@
 
 mol.CommandVerbose('0')
-mol.ParserParseTremoloPotentials(opt_potentialsfiledir+opt_basename+'.potentials')
-mol.WorldInput(opt_source)
+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))
-mol.WorldOutput('out.data')
-mol.WorldOutput('out.xyz')
+mol.WorldOutput(opt.outfilename + '.data')
+mol.WorldOutput(opt.outfilename + '.xyz')
 
 domain = [0.0]*3
@@ -252 +309 @@
 for i in range(3):
     domain[i] = cell[i]*nbox[i]
-    
+
 print  '======== DOMAIN: ', domain