def inputFileRead(filename):
"""
read and process an input file
"""
keywords = [
'trajectory', 'output_files', 'title', 'time_info', 'time_steps',
'frequency_points', 'q_vector_set', 'deuter', 'projection_vector',
'reference', 'rotation_coefficients', 'ft_window', 'groups', 'weights',
'atoms', 'units_length', 'units_frequency', 'log_file', 'groups_code',
'atoms_code', 'filter_window', 'results_file', 'atoms_pdb',
'differentiation', 'verbose', 'symbols', 'ar_order', 'ar_precision'
]
newvars = {}
file_text = Utility.readURL(filename)
exec file_text in vars(sys.modules['__builtin__']), newvars
input = Quidam()
for key in keywords:
if newvars.has_key(key): setattr(input, key, newvars[key])
else: setattr(input, key, None)
import os
print os.getcwd()
print input.trajectory
#
# general settings
#
if input.trajectory:
if len(input.trajectory) == 1:
traj = Trajectory(None, input.trajectory[0], 'r')
if traj.variables().count('quaternion') > 0:
traj = qTrajectory(None, input.trajectory[0], 'r')
elif len(input.trajectory) > 1:
traj = TrajectorySet(None, input.trajectory)
if not input.units_length: input.units_length = Units.nm
if not input.units_frequency:
input.units_frequency = Units.tera * Units.Hz
types = getTypes(traj.universe)
if input.q_vector_set is None:
input.q_vector_set = (N.arange(0., 100., 2.), 1., 50) # default
if input.time_info is None: input.time_info = (0, len(traj), 1)
qVectors = qVectorGenerator(input.q_vector_set, traj)
#
# Substitute Hydrogen atoms with Deuter?
#
if input.deuter:
collection = Collection()
for i in input.deuter.keys():
for ia in input.deuter[i]:
gj = getChemicalObjects({i: types[i]}, {i: ia})
collection.addObject(gj)
h2d = collection.atomList()
print 'number of Deuter atoms: ', len(h2d)
#
# Atom selection related keywords
# atoms selected in a different way are stored together
# and filtered at the end (if there're repetitions only
# atoms which occur many times are stored and passed to
# further calculations, else all atoms are passed)
#
if input.atoms:
print 'processing atom selection:\n\t', input.atoms
collection = []
for i in input.atoms.keys():
for ia in input.atoms[i]:
typs = {}
typs[i] = types[i]
vlst = {}
vlst[i] = ia
gj = getChemicalObjects(typs, vlst)
collection = collection + gj.atomList()
input.atoms = collection
print '\t...done\n\tstored ', len(input.atoms), ' atoms\n'
if input.atoms_pdb:
print 'processing atom selection from a PDB file\n\t(',
print input.atoms_pdb, '):'
atoms_add = parsePDBAtomSelection(input.atoms_pdb, traj)
print '\t...done\n\tstored ', len(atoms_add.atomList()), ' atoms\n'
if input.atoms: input.atoms = input.atoms + atoms_add.atomList()
else: input.atoms = atoms_add.atomList()
if input.atoms_code:
print 'processing atom selection hardcoded in Python'
# syntax:
# def atoms_code(traj,nothing,dummy_a='gj')
# # a python code here
# return Collection(atom_list)
#
# atoms_code is a function object whose first argument is
# a Trajectory object and which returns a Collection object.
print '...done\n\tstored ', len(input.atoms_code(traj).atomList()),
print ' atoms'
if input.atoms:
input.atoms = input.atoms + input.atoms_code(traj).atomList()
else:
input.atoms = input.atoms_code(traj).atomList()
if not input.atoms:
print ' No atom selection found, taking everything... just in case'
input.atoms = traj.universe
else:
input.atoms = Collection(input.atoms)
input.atoms = ghostBusters(input.atoms)
print ' # atoms in selection: ', len(input.atoms.atomList())
#
# Group selection
#
if input.groups:
input.groups, input.reference = parseGroupSelection(
types, input.groups, input.reference, verbose=input.verbose)
if input.groups_code:
# previous def (if any) overwritten
# the result returned by groups_code should be consistent
# with that one from misc.paresGroupSelection
input.groups, input.reference = input.groups_code(traj)
#
# Another piece of general settings
#
if input.weights == 'mass':
weightsList = MassList(traj.universe, input.atoms)
elif input.weights == 'incoherent':
if input.deuter:
weightsList = BincohList(traj.universe, input.atoms, h2d)
else:
weightsList = BincohList(traj.universe, input.atoms)
elif input.weights == 'coherent':
if input.deuter:
weightsList = BcohList(traj.universe, input.atoms, h2d)
else:
weightsList = BcohList(traj.universe, input.atoms)
else:
weightsList = None
# input.trajectory = (traj, input.trajectory)
input.trajectory = traj
input.q_vector_set = qVectors
input.weights = weightsList
return input
def body(self, master):
"""Create dialog body. Return widget that should have initial focus.
"""
# The frame that will contain the widgets whose the analysis dialog is built up.
widgetsFrame = LabelFrame(master, text='Setup', bd=2, relief=GROOVE)
widgetsFrame.grid(row=0, column=0, padx=3, pady=3, sticky=EW)
widgetsFrame.grid_columnconfigure(0, weight=1)
self.widgets = {}
for widget in self.db_parameternames:
widget = widget.lower()
if widget == 'angminmax':
self.widgets[widget] = ComboStringEntry(widgetsFrame,\
frameLabel = "HB angle min:max values (in deg)",\
tagName = 'angle_min_max',\
contents = "150.0:180.0")
elif widget == 'armodelorder':
self.widgets[widget] = ComboIntegerEntry(widgetsFrame,\
frameLabel = "Model order", \
tagName = 'model_order',\
contents = 50)
elif widget == 'atomorder':
self.widgets[widget] = ComboButton(widgetsFrame,\
frameLabel = "Atom order",\
tagName = 'atom_selection',\
contents = "Select",\
withEntry = '')
t = Trajectory(None, self.trajectory, 'r')
self.widgets[widget].command = lambda s=self, n=sorted(
set([at.name for at in t.universe.atomList()])
): AtomOrderDialog(s, n)
t.close()
elif widget == 'truebreakstep':
self.widgets[widget] = ComboIntegerEntry(widgetsFrame,\
frameLabel = "True break step", \
tagName = 'true_break_step',\
contents = 1)
elif widget == 'comselection':
self.widgets[widget] = ComboButton(widgetsFrame,\
frameLabel = "Center of mass selection",\
tagName = 'center_of_mass_selection',\
contents = "Select",\
withEntry = 'all')
self.widgets[
widget].command = lambda s=self, t='subset', c=self.chemicalObjectInfo, w=self.widgets[
widget]: SelectionDialog(s, t, c, w)
elif widget == 'deuteration':
self.widgets[widget] = ComboButton(widgetsFrame,\
frameLabel = "Deuteration selection",\
tagName = 'deuteration_selection',\
contents = "Select",\
withEntry = 'no')
self.widgets[
widget].command = lambda s=self, t='deuteration', c=self.chemicalObjectInfo, w=self.widgets[
widget]: SelectionDialog(s, t, c, w)
elif widget == 'differentiation':
t = Trajectory(None, GVAR['current_traj'], 'r')
if 'velocities' in t.variables():
diffOrder = (0, 1, 2, 3, 4, 5)
else:
diffOrder = (1, 2, 3, 4, 5)
t.close()
self.widgets[widget] = ComboSpinbox(widgetsFrame,\
frameLabel = "Differentiation order",\
tagName = 'differentiation_order',\
contents = diffOrder)
elif widget == 'direction':
self.widgets[widget] = ComboRadiobutton(widgetsFrame,\
frameLabel = "Direction",\
tagName = 'direction',\
contents = ["X", "Y", "Z"],\
layout = (1,3))
elif widget == 'disminmax':
self.widgets[widget] = ComboStringEntry(widgetsFrame,\
frameLabel = "HB distance min:max values",\
tagName = 'dis_min_max',\
contents = "0.0:0.35")
elif widget == 'distanceunits':
self.widgets[widget] = ComboRadiobutton(widgetsFrame,\
frameLabel = "Distance units",\
tagName = 'distanceunits',\
contents = ["nm", "ang", "fm"],\
layout = (1,3))
elif widget == 'filter':
self.widgets[widget] = ComboStringEntry(widgetsFrame,\
frameLabel = "Pass-Band filter (in tHz)",\
tagName = 'pass_band_filer',\
contents = "0.0:1000.0")
elif widget == 'frequencyunits':
self.widgets[widget] = ComboRadiobutton(widgetsFrame,\
frameLabel = "Frequency units",\
tagName = 'frequencyunits',\
contents = ["THz", "rad s^-1", "cm^-1", "meV", "ueV"],\
layout = (1,5))
elif widget == 'group':
self.widgets[widget] = ComboButton(widgetsFrame,\
frameLabel = "Group selection",\
tagName = 'group_selection',\
contents = "Select",\
withEntry = 'all')
self.widgets[
widget].command = lambda s=self, t='group', c=self.chemicalObjectInfo, w=self.widgets[
widget]: SelectionDialog(s, t, c, w)
elif widget == 'normalize':
self.widgets[widget] = ComboCheckbutton(widgetsFrame,\
frameLabel = "Normalize",\
tagName = 'normalize',\
onvalue = "yes",\
offvalue = "no")
elif widget == 'output':
# The basename of the input trajectory name.
baseName = self.db_shortname.upper() + '_' + os.path.basename(
self.trajectory)
try:
outputFilename = os.path.join(
PREFERENCES['outputfile_path'], baseName)
except TypeError:
outputFilename = baseName
self.widgets[widget] = ComboFileBrowser(widgetsFrame,\
frameLabel = "Output file",\
tagName= "output_file",\
contents = outputFilename,\
save = True,\
filetypes = [("NetCDF file", ".nc"),])
elif widget == 'phivalues':
self.widgets[widget] = ComboStringEntry(widgetsFrame,\
frameLabel = "Phi values (in deg)",\
tagName = 'phi_values',\
contents = "-180.0:180.0:10.0")
elif widget == 'projection':
self.widgets[widget] = ComboStringEntry(widgetsFrame,\
frameLabel = "Project displacement on",\
tagName = 'project_displacement_on',\
contents = "no")
elif widget == 'pyroserver':
self.widgets[widget] = ComboButton(widgetsFrame,\
frameLabel = "Pyro server",\
tagName = 'pyro_server',\
contents = "Select",\
withEntry = 'monoprocessor')
self.widgets[widget].command = lambda s=self, w=self.widgets[
widget]: PyroServerDialog(s, w)
elif widget == 'qshellvalues':
self.widgets[widget] = ComboStringEntry(widgetsFrame,\
frameLabel = "Q values (in nm-1)",\
tagName = 'qshell_values',\
contents = "0.0:100.0:1.0")
elif widget == 'qshellwidth':
self.widgets[widget] = ComboFloatEntry(widgetsFrame,\
frameLabel = "Q shell width (in nm-1)",\
tagName = 'qshell_width',\
contents = 1.0)
elif widget == 'qunits':
self.widgets[widget] = ComboRadiobutton(widgetsFrame,\
frameLabel = "Q units",\
tagName = 'qunits',\
contents = ["nm^-1", "ang^-1"],\
layout = (1,2))
elif widget == 'qvectors':
self.widgets[widget] = ComboButton(widgetsFrame,\
frameLabel = "Q vectors",\
tagName = 'qvectors',\
contents = "Setup",\
withEntry = {'qgeometry': 'spatial', \
'qshellwidth': 1.0, \
'qshellvalues': '0.0:10.0:1.0', \
'qvectorspershell': 50,\
'hkls' : None})
self.widgets[widget].command = lambda s=self, w=self.widgets[
widget]: QVectorsDialog(s, w)
elif widget == 'qvectorsdirection':
self.widgets[widget] = ComboStringEntry(widgetsFrame,\
frameLabel = "Q vectors direction",\
tagName = 'qvectors_direction',\
contents = "no")
elif widget == 'qvectorsgenerator':
self.widgets[widget] = ComboRadiobutton(widgetsFrame,\
frameLabel = "Q vectors generator",\
tagName = 'qvectors_generator',\
contents = ["3D isotropic", "2D isotropic", "anisotropic"],\
layout = (1,3))
elif widget == 'qvectorspershell':
self.widgets[widget] = ComboIntegerEntry(widgetsFrame,\
frameLabel = "Q vectors per shell",\
tagName= 'qvectors_per_shell',\
contents = 50)
elif widget == 'referencedirection':
self.widgets[widget] = ComboStringEntry(widgetsFrame,\
frameLabel = "Reference direction",\
tagName = 'reference_direction',\
contents = "0.0,0.0,1.0")
elif widget == 'referenceframe':
self.widgets[widget] = ComboIntegerEntry(widgetsFrame,\
frameLabel = "Reference frame",\
tagName= 'reference_frame',\
contents = 1)
elif widget == 'removetranslation':
self.widgets[widget] = ComboCheckbutton(widgetsFrame,\
frameLabel = "Remove translation",\
tagName = 'remove_translation',\
onvalue = "yes",\
offvalue = "no")
elif widget == 'resolution':
self.widgets[widget] = ComboFloatEntry(widgetsFrame,\
frameLabel = "Resolution (FWHM meV)",\
tagName = 'resolution',\
contents = 10.0)
self.updateResolution()
self.widgets[widget].entry.variable.trace_vdelete(
'w', self.widgets[widget].entry.cbname)
self.widgets[widget].entry.variable.trace_variable(
'w', self.updateResolution)
self.widgets[widget].entry.variable.trace_variable(
'w', self.widgets[widget].entry._callback)
elif widget == 'rvalues':
self.widgets[widget] = ComboStringEntry(widgetsFrame,\
frameLabel = "Distances (in nm)",\
tagName = 'distances',\
contents = "0.0:1.0:0.1")
elif widget == 'stepwiserbt':
self.widgets[widget] = ComboCheckbutton(widgetsFrame,\
frameLabel = "Stepwise RBT",\
tagName = 'stepwise_rbt',\
onvalue = "yes",\
offvalue = "no")
elif widget == 'storerbtdetails':
self.widgets[widget] = ComboCheckbutton(widgetsFrame,\
frameLabel = "Store RBT details",\
tagName = 'store_rbt_details',\
onvalue = "yes",\
offvalue = "no")
elif widget in ['subset', 'subset1', 'subset2']:
self.widgets[widget] = ComboButton(widgetsFrame,\
frameLabel = "%s selection" % widget.capitalize(),\
tagName = 'subset_selection',\
contents = "Select",\
withEntry = 'all')
self.widgets[
widget].command = lambda s=self, t='subset', c=self.chemicalObjectInfo, w=self.widgets[
widget]: SelectionDialog(s, t, c, w)
elif widget == 'target':
self.widgets[widget] = ComboButton(widgetsFrame,\
frameLabel = "Target selection",\
tagName = 'target_selection',\
contents = "Select",\
withEntry = 'all')
if self.db_shortname == "GMFT":
self.widgets[
widget].command = lambda s=self, t='subset', c=self.chemicalObjectInfo, w=self.widgets[
widget]: SelectionDialog(s, t, c, w)
else:
self.widgets[
widget].command = lambda s=self, t='group', c=self.chemicalObjectInfo, w=self.widgets[
widget]: SelectionDialog(s, t, c, w)
elif widget == 'temperature':
self.widgets[widget] = ComboFloatEntry(widgetsFrame,\
frameLabel = "Temperature (in K)",\
tagName = 'temperature',\
contents = 1.0)
elif widget == 'thetavalues':
self.widgets[widget] = ComboStringEntry(widgetsFrame,\
frameLabel = "Theta values (in deg)",\
tagName = 'theta_values',\
contents = "0.0:180.0:10.0")
elif widget == 'thickness':
self.widgets[widget] = ComboFloatEntry(widgetsFrame,\
frameLabel = "Thickness (in nm)",\
tagName = 'thickness',\
contents = 0.05)
elif widget == 'timeinfo':
t = load_trajectory_file(self.trajectory)
timeInfo = '%d:%d:%d' % (1, len(t), 1)
self.widgets[widget] = ComboStringEntry(widgetsFrame,\
frameLabel = "Frame selection",\
tagName = 'frame_selection',\
contents = timeInfo)
self.updateTimeInfo(t)
self.widgets[widget].entry.variable.trace_variable(
'w', lambda: self.updateTimeInfo(t))
elif widget == 'timeunits':
self.widgets[widget] = ComboRadiobutton(widgetsFrame,\
frameLabel = "Time units",\
tagName = 'timeunits',\
contents = ["ps", "ns", "fs"],\
layout = (1,3))
elif widget == 'trajectory':
self.widgets[widget] = ComboLabel(widgetsFrame,\
frameLabel = "Trajectory file",\
tagName = 'tajectory_file',\
contents = self.trajectory)
elif widget == 'weights':
self.widgets[widget] = ComboRadiobutton(widgetsFrame,\
frameLabel = "Weights",\
tagName = 'weights',\
contents = ["equal", "mass", "coherent", "incoherent", "atomicNumber"],\
layout = (2,3))
elif widget == 'wignerindexes':
self.widgets[widget] = ComboStringEntry(widgetsFrame,\
frameLabel = "Wigner indexes",\
tagName = 'wigner_indexes',\
contents = "0,0,0")
# The tagName for the combo widget is set.
setattr(
self.widgets[widget], 'tagName',
'%s_%s' % (self.db_shortname.lower(),
self.widgets[widget].tagName.lower()))
# And displayed into the analysis dialog.
self.widgets[widget].grid(column=0, sticky=EW, padx=2, pady=2)
self.widgets[widget].grid_columnconfigure(0, weight=1)
if hasattr(self, 'db_modulator'):
for k, v in self.db_modulator.items():
k = k.lower()
if k == 'weights':
self.widgets[k].setValue(v)
elif k == 'differentiation':
self.widgets[k].spinbox.config(values=v)
return None
x2 += a2.beadPositions()[bead][x] * a2.mass()
y2 += a2.beadPositions()[bead][y] * a2.mass()
z2 += a2.beadPositions()[bead][z] * a2.mass()
return sqrt(((x1/m1) - (x2/m2))**2 + ((y1/m1) - (y2/m2))**2 + ((z1/m1) - (z2/m2))**2)
####################################################################################################################################################################
print '.....Performing Analysis........................................................'
#Read in trajectory from file
trajectory = Trajectory(None, dir + '//' + dir + '_prod.nc')
#Output the variables stored in the trajectory
print 'The available variables in the trajectory are:', trajectory.variables()
universe = trajectory.universe
natoms = universe.numberOfAtoms()
P = universe[0].atomList()[0].numberOfPoints()
print 'There are', natoms, 'atoms and', P, 'beads per atom present in the trajectory'
#Output files to write centre of masses to.
com_out = open(dir + '//' + dir + '_centroid_com_distance.txt','w')
bead_com_out = open(dir + '//' + dir + '_bead_com_distance.txt','w')
for step in trajectory:
#set the configuration to each new step
universe.setConfiguration(step['configuration'])
for object1 in universe.objectList():
for object2 in universe.objectList():
y2 += a2.beadPositions()[bead][y] * a2.mass()
z2 += a2.beadPositions()[bead][z] * a2.mass()
return sqrt(((x1 / m1) - (x2 / m2))**2 + ((y1 / m1) - (y2 / m2))**2 +
((z1 / m1) - (z2 / m2))**2)
####################################################################################################################################################################
print '.....Performing Analysis........................................................'
#Read in trajectory from file
trajectory = Trajectory(None, dir + '//' + dir + '_prod.nc')
#Output the variables stored in the trajectory
print 'The available variables in the trajectory are:', trajectory.variables()
universe = trajectory.universe
natoms = universe.numberOfAtoms()
P = universe[0].atomList()[0].numberOfPoints()
print 'There are', natoms, 'atoms and', P, 'beads per atom present in the trajectory'
#Output files to write centre of masses to.
com_out = open(dir + '//' + dir + '_centroid_com_distance.txt', 'w')
bead_com_out = open(dir + '//' + dir + '_bead_com_distance.txt', 'w')
for step in trajectory:
#set the configuration to each new step
universe.setConfiguration(step['configuration'])
for object1 in universe.objectList():
for object2 in universe.objectList():
