Applied PEP-8 script...

bin/i-pi

@@ -23,7 +23,7 @@ import os
 
 # Check that we have the import path for this i-PI set and if not, add it.
 dir_root = os.path.realpath(
-               os.path.join(os.path.dirname(os.path.realpath(__file__)), '..'))
+    os.path.join(os.path.dirname(os.path.realpath(__file__)), '..'))
 if not dir_root in sys.path:
     sys.path.insert(0, dir_root)
 
@@ -36,13 +36,13 @@ def main(fn_input, do_yappi=False):
 
     # optionally profile this run - set up
     #~ if do_yappi:
-        #~ try:
-            #~ import yappi
-            #~ yappi.start(builtins=True, profile_threads=True)
-        #~ except ImportError:
-            #~ print 'Profiling with yappi was enabled but could not be imported.'
-            #~ print "Profiling with yappi was enabled but could not be imported."
-            #~ sys.exit(1)
+    #~ try:
+    #~ import yappi
+    #~ yappi.start(builtins=True, profile_threads=True)
+    #~ except ImportError:
+    #~ print 'Profiling with yappi was enabled but could not be imported.'
+    #~ print "Profiling with yappi was enabled but could not be imported."
+    #~ sys.exit(1)
 
     # construct simulation based on input file
     simulation = Simulation.load_from_xml(fn_input, request_banner=True)
@@ -79,7 +79,7 @@ if __name__ == '__main__':
     parser = OptionParser(usage='%prog [options] <input file>',
                           description='The main i-PI executable used to run '
                                       'a simulation, given an XML input file.'
-                         )
+                          )
 
     parser.add_option('-p', '--profile',
                       action='store_true', dest='do_yappi', default=False,

doc/create_man.py

@@ -25,10 +25,10 @@
 
 
 if not os.path.exists("input_docs"):
-   os.mkdir("input_docs")
+    os.mkdir("input_docs")
 
 help(xml=True, prefix="manual")
 for opt in objects:
-   help(latex=True, levels=1, option=opt, prefix=("input_docs/" + opt), standalone=False)
+    help(latex=True, levels=1, option=opt, prefix=("input_docs/" + opt), standalone=False)
 for opt in list_objects:
-   help_list(option=opt, prefix=("input_docs/" + opt), standalone=False)
+    help_list(option=opt, prefix=("input_docs/" + opt), standalone=False)

doc/help.py

@@ -31,92 +31,92 @@
 sys.path.append(src_dir)
 
 from ipi.inputs import barostats, cell, simulation, paratemp, system, \
-             ensembles, thermostats, forcefields, forces, atoms, beads, \
-             prng, initializer, normalmodes, outputs, motion
-
+    ensembles, thermostats, forcefields, forces, atoms, beads, \
+    prng, initializer, normalmodes, outputs, motion
 
 
 time.sleep(1)
 __all__ = ['help', 'objects']
 
-objects = { 'barostats': barostats.InputBaro(),
-            'cell': cell.InputCell(),
-            'simulation': simulation.InputSimulation(),
-            # 'paratemp': paratemp.InputParaTemp(),
-            'system': system.InputSystem(),
-            'ensembles': ensembles.InputEnsemble(),
-            'motion': motion.motion.InputMotion(),
-            'dynamics': motion.dynamics.InputDynamics(),
-            'thermostats': thermostats.InputThermo(),
-            'forcefield' : forcefields.InputForceField(),
-            'ffsocket': forcefields.InputFFSocket(),
-            'fflj': forcefields.InputFFLennardJones(),
-            'forcecomponent' : forces.InputForceComponent(),
-            'forces': forces.InputForces(),
-            'atoms': atoms.InputAtoms(),
-            'beads': beads.InputBeads(),
-            'prng': prng.InputRandom(),
-            'normal_modes': normalmodes.InputNormalModes(),
-            'init_file': initializer.InputInitFile(),
-            'init_pos': initializer.InputInitPositions(),
-            'init_mom': initializer.InputInitMomenta(),
-            'init_lab': initializer.InputInitLabels(),
-            'init_mass': initializer.InputInitMasses(),
-            'init_vel': initializer.InputInitVelocities(),
-            'init_cell': initializer.InputInitCell(),
-            'init_therm': initializer.InputInitThermo(),
-            'initializer': initializer.InputInitializer(),
-            'output': outputs.InputOutputs(),
-            'properties': outputs.InputProperties(),
-            'checkpoint': outputs.InputCheckpoint(),
-            'trajectory': outputs.InputTrajectory() }
+objects = {'barostats': barostats.InputBaro(),
+           'cell': cell.InputCell(),
+           'simulation': simulation.InputSimulation(),
+           # 'paratemp': paratemp.InputParaTemp(),
+           'system': system.InputSystem(),
+           'ensembles': ensembles.InputEnsemble(),
+           'motion': motion.motion.InputMotion(),
+           'dynamics': motion.dynamics.InputDynamics(),
+           'thermostats': thermostats.InputThermo(),
+           'forcefield': forcefields.InputForceField(),
+           'ffsocket': forcefields.InputFFSocket(),
+           'fflj': forcefields.InputFFLennardJones(),
+           'forcecomponent': forces.InputForceComponent(),
+           'forces': forces.InputForces(),
+           'atoms': atoms.InputAtoms(),
+           'beads': beads.InputBeads(),
+           'prng': prng.InputRandom(),
+           'normal_modes': normalmodes.InputNormalModes(),
+           'init_file': initializer.InputInitFile(),
+           'init_pos': initializer.InputInitPositions(),
+           'init_mom': initializer.InputInitMomenta(),
+           'init_lab': initializer.InputInitLabels(),
+           'init_mass': initializer.InputInitMasses(),
+           'init_vel': initializer.InputInitVelocities(),
+           'init_cell': initializer.InputInitCell(),
+           'init_therm': initializer.InputInitThermo(),
+           'initializer': initializer.InputInitializer(),
+           'output': outputs.InputOutputs(),
+           'properties': outputs.InputProperties(),
+           'checkpoint': outputs.InputCheckpoint(),
+           'trajectory': outputs.InputTrajectory()}
 
 usage = "usage: python %prog [options]"
 parser = OptionParser(usage=usage)
-parser.add_option("-x", action="store_true", dest = "xml", default=False, help="write an xml help file")
-parser.add_option("-l", action="store_true", dest = "latex", default=False, help="write a latex help file")
+parser.add_option("-x", action="store_true", dest="xml", default=False, help="write an xml help file")
+parser.add_option("-l", action="store_true", dest="latex", default=False, help="write a latex help file")
 parser.add_option("-n", action="store", type="int", dest="levels", help="number of levels depth to which data is printed out")
 parser.add_option("-o", action="store", dest="prefix", help="Prefix for the output files", default="help")
 parser.add_option("-i", action="store", dest="opt", help="Root object for the help files. Options: ['barostats', 'cell', 'simulation', 'ensembles', 'thermostats', 'interface', 'forces', 'atoms', 'beads', 'prng', 'output', 'trajectory', 'properties', 'checkpoint']", default='simulation')
-parser.add_option("-r", action="store_true", dest = "ref", default=False, help="add references to a latex help file. Ignored if -l is not present")
+parser.add_option("-r", action="store_true", dest="ref", default=False, help="add references to a latex help file. Ignored if -l is not present")
 (options, args) = parser.parse_args()
 
 if options.opt not in objects:
-   raise ValueError("Option " + options.opt + " is not a viable tag name")
-
-def help(latex=False, xml=False, levels = None, option='simulation', prefix="help", standalone=True):
-   """Writes the help file.
-
-   Will write an xml file 'prefix.xml' if xml=True and a latex file 'prefix.tex'
-   if latex=True. Will write out tags to a depth equal to the value of levels,
-   if it is specified, and will print using a root tag as specified by
-   the value of option. The output will be given by prefix.tex and/or
-   prefix.xml, if latex and/or xml is True respectively. Can also print out
-   sections of latex documents with cross-references rather than entire
-   documents, so that we can input them into other latex documents, such as
-   the manual.
-
-   Args:
-      latex: Boolean specifying whether a latex file will be printed.
-      xml: Boolean specifying whether an xml file will be printed.
-      levels: An integer specifying how many layers of the hierarchy will be
-         printed. If not given, all layers will be printed.
-      option: A string specifying which object will be used as the root object
-         for the latex and xml files. Defaults to 'simulation'.
-      prefix: File prefix for the output files. Defaults to 'help'.
-      standalone: Boolean specifying whether the latex file will be a stand-alone
-         document, or will instead be intended to be used in a larger document
-         with cross references between the different objects.
-   """
-
-   simrestart = objects[option]
-
-   if xml:
-      xml_output = open(prefix + ".xml","w")
-      xml_output.write(simrestart.help_xml(name=option, stop_level=levels))
-   if latex:
-      latex_output = open(prefix + ".tex","w")
-      latex_output.write(simrestart.help_latex(stop_level=levels, standalone=standalone))
+    raise ValueError("Option " + options.opt + " is not a viable tag name")
+
+
+def help(latex=False, xml=False, levels=None, option='simulation', prefix="help", standalone=True):
+    """Writes the help file.
+
+    Will write an xml file 'prefix.xml' if xml=True and a latex file 'prefix.tex'
+    if latex=True. Will write out tags to a depth equal to the value of levels,
+    if it is specified, and will print using a root tag as specified by
+    the value of option. The output will be given by prefix.tex and/or
+    prefix.xml, if latex and/or xml is True respectively. Can also print out
+    sections of latex documents with cross-references rather than entire
+    documents, so that we can input them into other latex documents, such as
+    the manual.
+
+    Args:
+       latex: Boolean specifying whether a latex file will be printed.
+       xml: Boolean specifying whether an xml file will be printed.
+       levels: An integer specifying how many layers of the hierarchy will be
+          printed. If not given, all layers will be printed.
+       option: A string specifying which object will be used as the root object
+          for the latex and xml files. Defaults to 'simulation'.
+       prefix: File prefix for the output files. Defaults to 'help'.
+       standalone: Boolean specifying whether the latex file will be a stand-alone
+          document, or will instead be intended to be used in a larger document
+          with cross references between the different objects.
+    """
+
+    simrestart = objects[option]
+
+    if xml:
+        xml_output = open(prefix + ".xml", "w")
+        xml_output.write(simrestart.help_xml(name=option, stop_level=levels))
+    if latex:
+        latex_output = open(prefix + ".tex", "w")
+        latex_output.write(simrestart.help_latex(stop_level=levels, standalone=standalone))
 
 if __name__ == '__main__':
-   help(options.latex, options.xml, options.levels, options.opt, options.prefix, not options.ref)
+    help(options.latex, options.xml, options.levels, options.opt, options.prefix, not options.ref)

doc/help_list.py

@@ -26,46 +26,47 @@
 __all__ = ['help_list', 'list_objects']
 
 
-list_objects = { 'property_list': Properties(),
-            'trajectory_list': Trajectories()}
+list_objects = {'property_list': Properties(),
+                'trajectory_list': Trajectories()}
 
 usage = "usage: python %prog [options]"
 parser = OptionParser(usage=usage)
 parser.add_option("-o", action="store", dest="prefix", help="Prefix for the output files", default="help")
 parser.add_option("-i", action="store", dest="opt", help="Root object for the help files. Options: ['property_list', 'trajectory_list']", default='property_list')
-parser.add_option("-r", action="store_true", dest = "ref", default=False, help="If false, this creates a stand-alone document.")
+parser.add_option("-r", action="store_true", dest="ref", default=False, help="If false, this creates a stand-alone document.")
 (options, args) = parser.parse_args()
 
 if options.opt not in list_objects:
-   raise ValueError("Option " + options.opt + " is not a viable tag name")
+    raise ValueError("Option " + options.opt + " is not a viable tag name")
+
 
 def help_list(option='property_list', prefix="help", standalone=True):
-   """Writes the help file.
-
-   Will write a latex file 'prefix.tex'. Can also print out
-   sections of latex documents rather than entire
-   documents, so that we can input them into other latex documents, such as
-   the manual.
-
-   Args:
-      option: A string specifying which object will be used as the root object
-         for the latex and xml files. Defaults to 'property_list'.
-      prefix: File prefix for the output files. Defaults to 'help'.
-      standalone: Boolean specifying whether the latex file will be a stand-alone
-         document, or will instead be intended to be used in a larger document
-         with cross references between the different objects.
-   """
-
-   simrestart = list_objects[option]
-   if option == "property_list":
-      idict = simrestart.property_dict
-   elif option == "trajectory_list":
-      idict = simrestart.traj_dict
-   else:
-      raise ValueError("Incorrect option specified.")
-
-   latex_output = open(prefix + ".tex","w")
-   latex_output.write(help_latex(idict, standalone=standalone))
+    """Writes the help file.
+
+    Will write a latex file 'prefix.tex'. Can also print out
+    sections of latex documents rather than entire
+    documents, so that we can input them into other latex documents, such as
+    the manual.
+
+    Args:
+       option: A string specifying which object will be used as the root object
+          for the latex and xml files. Defaults to 'property_list'.
+       prefix: File prefix for the output files. Defaults to 'help'.
+       standalone: Boolean specifying whether the latex file will be a stand-alone
+          document, or will instead be intended to be used in a larger document
+          with cross references between the different objects.
+    """
+
+    simrestart = list_objects[option]
+    if option == "property_list":
+        idict = simrestart.property_dict
+    elif option == "trajectory_list":
+        idict = simrestart.traj_dict
+    else:
+        raise ValueError("Incorrect option specified.")
+
+    latex_output = open(prefix + ".tex", "w")
+    latex_output.write(help_latex(idict, standalone=standalone))
 
 if __name__ == '__main__':
-   help_list(options.opt, options.prefix, not options.ref)
+    help_list(options.opt, options.prefix, not options.ref)

examples/ASE/W2-PIMD-MP2/run-ase.py

@@ -33,13 +33,13 @@
 atoms = ase.io.read('init.xyz')
 atoms.set_calculator(
     Gaussian(
-        method = 'MP2',
+        method='MP2',
         # Note that 6-31G is for faster testing only, not a good basis set
         # for gas-phase W2. Use the bigger one instead.
-        basis = '6-31G',
+        basis='6-31G',
         #basis = '6-311++G**',
-        nproc = nthreads,
-        label = dir_calc + '/calculator'
+        nproc=nthreads,
+        label=dir_calc + '/calculator'
     )
 )
 

examples/cp2k/nvt-cl/idtau_plot.py

@@ -1,7 +1,7 @@
 from pylab import *
 
 idtdata = []
-#output is a standard output from i-pi
+# output is a standard output from i-pi
 for line in open("output"):
     llist = line.split()
     if llist:
@@ -10,10 +10,10 @@
 
 nsteps = len(idtdata)
 maxt = nsteps * 0.1
-print("Mean IDTAU for " + str(maxt*0.5) + "<t<" + str(maxt) + " fs: "+str(mean(idtdata[nsteps//2:nsteps])))
-    
+print("Mean IDTAU for " + str(maxt * 0.5) + "<t<" + str(maxt) + " fs: " + str(mean(idtdata[nsteps // 2:nsteps])))
+
 fig = figure()
 ax = fig.add_subplot(111)
-ax.plot(linspace(0,maxt,num=nsteps), idtdata)
-ax.set(title="Automatic IDTAU Parameter Adjustment",xlabel="Time [fs]", ylabel="IDTAU [a.u.]",xlim=(0,maxt))
+ax.plot(linspace(0, maxt, num=nsteps), idtdata)
+ax.set(title="Automatic IDTAU Parameter Adjustment", xlabel="Time [fs]", ylabel="IDTAU [a.u.]", xlim=(0, maxt))
 show()

examples/hswfqmc/FixWF_1Bead/intau_plot.py

@@ -9,10 +9,10 @@
 
 nsteps = len(invdata)
 maxt = nsteps * 0.1
-print("Mean INTAU for " + str(maxt*0.5) + "<t<" + str(maxt) + " fs: "+str(mean(invdata[nsteps//2:nsteps])))
-    
+print("Mean INTAU for " + str(maxt * 0.5) + "<t<" + str(maxt) + " fs: " + str(mean(invdata[nsteps // 2:nsteps])))
+
 fig = figure()
 ax = fig.add_subplot(111)
-ax.plot(linspace(0,maxt,num=nsteps), invdata)
-ax.set(title="Automatic INTAU Parameter Adjustment",xlabel="Time [fs]", ylabel="INTAU [a.u.]",xlim=(0,maxt))
+ax.plot(linspace(0, maxt, num=nsteps), invdata)
+ax.set(title="Automatic INTAU Parameter Adjustment", xlabel="Time [fs]", ylabel="INTAU [a.u.]", xlim=(0, maxt))
 show()

examples/hswfqmc/WFOpt_2Bead/intau_plot.py

@@ -9,10 +9,10 @@
 
 nsteps = len(invdata)
 maxt = nsteps * 0.1
-print("Mean INTAU for " + str(maxt*0.5) + "<t<" + str(maxt) + " fs: "+str(mean(invdata[nsteps//2:nsteps])))
-    
+print("Mean INTAU for " + str(maxt * 0.5) + "<t<" + str(maxt) + " fs: " + str(mean(invdata[nsteps // 2:nsteps])))
+
 fig = figure()
 ax = fig.add_subplot(111)
-ax.plot(linspace(0,maxt,num=nsteps), invdata)
-ax.set(title="Automatic INTAU Parameter Adjustment",xlabel="Time [fs]", ylabel="INTAU [a.u.]",xlim=(0,maxt))
+ax.plot(linspace(0, maxt, num=nsteps), invdata)
+ax.set(title="Automatic INTAU Parameter Adjustment", xlabel="Time [fs]", ylabel="INTAU [a.u.]", xlim=(0, maxt))
 show()