Fix typo

tools/i-pi/drivers/LJ.f90

@@ -182,7 +182,7 @@
             start = 1
 
             DO i = 1, natoms - 1
-               ! Only loops over the neigbour list, not all the atoms.
+               ! Only loops over the neighbour list, not all the atoms.
                DO j = start, index_list(i)
                   CALL vector_separation(cell_h, cell_ih, atoms(i,:), atoms(n_list(j),:), rij, r2)
                   IF (r2 < rc*rc) THEN ! Only calculates contributions between neighbouring particles.

tools/i-pi/drivers/SG.f90

@@ -250,7 +250,7 @@
             start = 1
 
             DO i = 1, natoms - 1
-               ! Only loops over the neigbour list, not all the atoms.
+               ! Only loops over the neighbour list, not all the atoms.
                DO j = start, index_list(i)
                   CALL vector_separation(cell_h, cell_ih, atoms(i,:), atoms(n_list(j),:), rij, r2)
                   IF (r2 < rc*rc) THEN ! Only calculates contributions between neighbouring particles.

tools/i-pi/ipi/engine/ensembles.py

@@ -104,7 +104,7 @@ class Ensemble(dobject):
       conserved quantity the dependencies are defined in bind.
 
       Args:
-         beads: The beads object from whcih the bead positions are taken.
+         beads: The beads object from which the bead positions are taken.
          nm: A normal modes object used to do the normal modes transformation.
          cell: The cell object from which the system box is taken.
          bforce: The forcefield object from which the force and virial are
@@ -303,7 +303,7 @@ class NVTEnsemble(NVEEnsemble):
       higher simulation temperature, as is appropriate.
 
       Args:
-         beads: The beads object from whcih the bead positions are taken.
+         beads: The beads object from which the bead positions are taken.
          nm: A normal modes object used to do the normal modes transformation.
          cell: The cell object from which the system box is taken.
          bforce: The forcefield object from which the force and virial are
@@ -422,7 +422,7 @@ class NPTEnsemble(NVTEnsemble):
       higher simulation temperature, as is appropriate.
 
       Args:
-         beads: The beads object from whcih the bead positions are taken.
+         beads: The beads object from which the bead positions are taken.
          nm: A normal modes object used to do the normal modes transformation.
          cell: The cell object from which the system box is taken.
          bforce: The forcefield object from which the force and virial are

tools/i-pi/ipi/engine/outputs.py

@@ -85,7 +85,7 @@ class PropertyOutput(dobject):
       self.simul = simul
 
       # Checks as soon as possible if some asked-for properties are
-      # missing or mispelled
+      # missing or misspelled
       for what in self.outlist:
          key = getkey(what)
          if not key in self.simul.properties.property_dict.keys():
@@ -218,7 +218,7 @@ class TrajectoryOutput(dobject):
 
       self.simul = simul
 
-      # Checks as soon as possible if some asked-for trajs are missing or mispelled
+      # Checks as soon as possible if some asked-for trajs are missing or misspelled
       key = getkey(self.what)
       if not key in self.simul.trajs.traj_dict.keys():
          print "Computable trajectories list: ", self.simul.trajs.traj_dict.keys()

tools/i-pi/ipi/engine/properties.py

@@ -141,7 +141,7 @@ def help_latex(idict, standalone=True):
 }
 """
       rstr += "\n\\begin{document}\n"
-      rstr += "The following are the different allowable ouputs:\n\\par"
+      rstr += "The following are the different allowable outputs:\n\\par"
 
    for out in sorted(idict):
       rstr += "\\ipiitem{" + out + "}"

tools/i-pi/ipi/engine/simulation.py

@@ -172,7 +172,7 @@ class Simulation(dobject):
 
       self.forces.run()
 
-      # prints inital configuration -- only if we are not restarting
+      # prints initial configuration -- only if we are not restarting
       if (self.step == 0):
          self.step = -1
          for o in self.outputs:

tools/i-pi/ipi/engine/thermostats.py

@@ -532,9 +532,9 @@ class ThermoGLE(Thermostat):
    J. Chem. Phys. 134, 084104 (2011)).
 
    Attributes:
-      ns: The number of auxilliary degrees of freedom.
+      ns: The number of auxiliary degrees of freedom.
       s: An array holding all the momenta, including the ones for the
-         auxilliary degrees of freedom.
+         auxiliary degrees of freedom.
 
    Depend objects:
       A: Drift matrix giving the damping time scales for all the different
@@ -560,7 +560,7 @@ class ThermoGLE(Thermostat):
 
       SST = Constants.kb*(self.C - np.dot(self.T,np.dot(self.C,self.T.T)))
 
-      # Uses a symetric decomposition rather than Cholesky, since it is more stable
+      # Uses a symmetric decomposition rather than Cholesky, since it is more stable
       return root_herm(SST)
 
    def get_C(self):
@@ -675,10 +675,10 @@ class ThermoNMGLE(Thermostat):
    GLE for each normal mode
 
    Attributes:
-      ns: The number of auxilliary degrees of freedom.
+      ns: The number of auxiliary degrees of freedom.
       nb: The number of beads.
       s: An array holding all the momenta, including the ones for the
-         auxilliary degrees of freedom.
+         auxiliary degrees of freedom.
 
    Depend objects:
       A: Drift matrix giving the damping time scales for all the different

tools/i-pi/ipi/tests/README

@@ -3,7 +3,7 @@
  * This is the directory containing the tests that can be run with nosetests.
 
  * Files:
-   - common.py: Common helper funtions for use in the tests.
+   - common.py: Common helper functions for use in the tests.
    - datest.py: Tests the dependency utility and some of the numpy
       facilities.
    - test_*.py: The actual tests for at least some of the code basis.

tools/i-pi/ipi/utils/depend.py

@@ -209,7 +209,7 @@ class depend_base(object):
       further down the dependency tree until either all objects have been
       tainted, or it reaches only objects that have already been tainted. Note
       that in the case of a dependency loop the initial setting of _tainted to
-      True prevents an infinite loop occuring.
+      True prevents an infinite loop occurring.
 
       Also, in the case of a synchro object, the manually set quantity is not
       tainted, as it is assumed that synchro objects only depend on each other.

tools/i-pi/ipi/utils/inputvalue.py

@@ -252,7 +252,7 @@ class Input(object):
       called, so that their tags are written between the start and end tags
       of this object, as is required for the xml format.
 
-      This also adds an indent to the lower levels of the xml heirarchy,
+      This also adds an indent to the lower levels of the xml hierarchy,
       so that it is easy to see which tags contain other tags.
 
       Args:

tools/i-pi/ipi/utils/io/io_xml.py

@@ -119,7 +119,7 @@ class xml_handler(ContentHandler):
 
       Adds the opening tag to the list of open tags, adds a new space in the
       buffer, reads the appropriate attributes and adds a new level to the 
-      heirarchy.
+      hierarchy.
 
       Args:
          name: The tag_name.
@@ -139,7 +139,7 @@ class xml_handler(ContentHandler):
    def characters(self, data):
       """Reads data.
 
-      Adds the data to the buffer of the current level of the heirarchy.
+      Adds the data to the buffer of the current level of the hierarchy.
       Data is read as a string, and needs to be converted to the required
       type later.