Convert British spelling to American

doc/src/Build_development.rst

@@ -44,7 +44,7 @@ usually faster than using tools like Valgrind.
 .. code-block:: bash
 
    -D ENABLE_SANITIZE_ADDRESS=value    # enable Address Sanitizer, value = no (default) or yes
-   -D ENABLE_SANITIZE_UNDEFINED=value  # enable Undefined Behaviour Sanitizer, value = no (default) or yes
+   -D ENABLE_SANITIZE_UNDEFINED=value  # enable Undefined Behavior Sanitizer, value = no (default) or yes
    -D ENABLE_SANITIZE_THREAD=value     # enable Thread Sanitizer, value = no (default) or yes
 
 ----------

examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py

@@ -373,7 +373,7 @@ def generate_strand(bp, sequence=None, start_pos=np.array([0, 0, 0]), \
     # if not provided switch off random orientation
     if perp is None or perp is False:
         v1 = np.random.random_sample(3)
-        # comment in to suppress randomised base vector
+        # comment in to suppress randomized base vector
         v1 = [1,0,0]
         v1 -= dir * (np.dot(dir, v1))
         v1 /= np.sqrt(sum(v1*v1))
@@ -644,12 +644,12 @@ def read_strands(filename):
 
             # generate random position of the first nucleotide
             com = box_offset + np.random.random_sample(3) * box
-            # comment out to randomise
+            # comment out to randomize
             com = [0,0,0]
 
             # generate the random direction of the helix 
             axis = np.random.random_sample(3)
-            # comment out to randomise
+            # comment out to randomize
             axis = [0,0,1]
             axis /= np.sqrt(np.dot(axis, axis))
 
@@ -702,12 +702,12 @@ def read_strands(filename):
 
 	    # generate random position of the first nucleotide
             com = box_offset + np.random.random_sample(3) * box
-            # comment out to randomise
+            # comment out to randomize
             com = [-30,0,0]
 
             # generate the random direction of the helix 
             axis = np.random.random_sample(3)
-            # comment out to randomise
+            # comment out to randomize
             axis = [0,0,1]
             axis /= np.sqrt(np.dot(axis, axis))
 

examples/USER/manifold/diffusion/plot_msd.gpl

@@ -47,7 +47,7 @@ set object 1 rectangle from graph 0,0 to graph 1,1 fillcolor rgb "white" behind
 unset key
 set grid front
 
-set title 'Short time behaviour' offset 0,-0.8
+set title 'Short time behavior' offset 0,-0.8
 set ylabel ''
 set xrange[0:10]
 set yrange[0:40]

python/examples/pylammps/montecarlo/mc.ipynb

@@ -822,7 +822,7 @@
        "}\n",
        "\n",
        "mpl.figure.prototype._key_event_extra = function(event, name) {\n",
-       "    // Handle any extra behaviour associated with a key event\n",
+       "    // Handle any extra behavior associated with a key event\n",
        "}\n",
        "\n",
        "mpl.figure.prototype.key_event = function(event, name) {\n",
@@ -1053,7 +1053,7 @@
        "mpl.find_output_cell = function(html_output) {\n",
        "    // Return the cell and output element which can be found *uniquely* in the notebook.\n",
        "    // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n",
-       "    // IPython event is triggered only after the cells have been serialised, which for\n",
+       "    // IPython event is triggered only after the cells have been serialized, which for\n",
        "    // our purposes (turning an active figure into a static one), is too late.\n",
        "    var cells = IPython.notebook.get_cells();\n",
        "    var ncells = cells.length;\n",

src/RIGID/fix_rattle.cpp

@@ -119,7 +119,7 @@ int FixRattle::setmask()
 
 void FixRattle::init() {
 
-  // initialise SHAKE first
+  // initialize SHAKE first
 
   FixShake::init();
 

src/RIGID/fix_shake.cpp

@@ -3059,7 +3059,7 @@ void FixShake::correct_velocities() {}
 void FixShake::correct_coordinates(int vflag) {
 
   // save current forces and velocities so that you
-  // initialise them to zero such that FixShake::unconstrained_coordinate_update has no effect
+  // initialize them to zero such that FixShake::unconstrained_coordinate_update has no effect
 
   for (int j=0; j<nlocal; j++) {
     for (int k=0; k<3; k++) {

src/USER-MANIFOLD/README

@@ -31,7 +31,7 @@ To add a new manifold, do the following in the "USER-MANIFOLD" directory:
    c. In namespace LAMMPS_NS, add a new class that inherits publicly from manifold
      and protectedly from Pointers.
    d. The constructor has to take ( LAMMPS*, int, char ** ) as arguments,
-     and should initialise Pointers.
+     and should initialize Pointers.
    e. The header file has to contain somewhere the macro ManifoldStyle with as
      first argument the name of the manifold and as second argument the name
      of the class implementing this manifold. The macro expands into some code
@@ -45,7 +45,7 @@ To add a new manifold, do the following in the "USER-MANIFOLD" directory:
 +====================================+=========================================+
 |  destructor                        | Free space (can be empty)               |
 |  constructor                       | Has to take (LAMMPS *lmp, int, char **) |
-|                                    | as arguments and has to initialise      |
+|                                    | as arguments and has to initialize      |
 |                                    | Pointers with lmp.                      |
 |  double g( double *x )             | A function that is 0 if the 3-vector    |
 |                                    | x is on the manifold.                   |

src/USER-MANIFOLD/fix_manifoldforce.h

@@ -21,7 +21,7 @@
    This file is part of the user-manifold package written by
    Stefan Paquay at the Eindhoven University of Technology.
    This module makes it possible to do MD with particles constrained
-   to pretty arbitrary manifolds characterised by some constraint function
+   to pretty arbitrary manifolds characterized by some constraint function
    g(x,y,z) = 0 and its normal grad(g). The number of manifolds available
    right now is limited but can be extended straightforwardly by making
    a new class that inherits from manifold and implements all pure virtual

src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp

@@ -21,7 +21,7 @@
    This file is part of the user-manifold package written by
    Stefan Paquay at the Eindhoven University of Technology.
    This module makes it possible to do MD with particles constrained
-   to pretty arbitrary manifolds characterised by some constraint function
+   to pretty arbitrary manifolds characterized by some constraint function
    g(x,y,z) = 0 and its normal grad(g). The number of manifolds available
    right now is limited but can be extended straightforwardly by making
    a new class that inherits from manifold and implements all pure virtual

src/USER-MANIFOLD/fix_nve_manifold_rattle.h

@@ -21,7 +21,7 @@
    This file is part of the user-manifold package written by
    Stefan Paquay at the Eindhoven University of Technology.
    This module makes it possible to do MD with particles constrained
-   to pretty arbitrary manifolds characterised by some constraint function
+   to pretty arbitrary manifolds characterized by some constraint function
    g(x,y,z) = 0 and its normal grad(g). The number of manifolds available
    right now is limited but can be extended straightforwardly by making
    a new class that inherits from manifold and implements all pure virtual

src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp

@@ -21,7 +21,7 @@
    This file is part of the user-manifold package written by
    Stefan Paquay at the Eindhoven University of Technology.
    This module makes it possible to do MD with particles constrained
-   to pretty arbitrary manifolds characterised by some constraint function
+   to pretty arbitrary manifolds characterized by some constraint function
    g(x,y,z) = 0 and its normal grad(g). The number of manifolds available
    right now is limited but can be extended straightforwardly by making
    a new class that inherits from manifold and implements all pure virtual

src/USER-MANIFOLD/fix_nvt_manifold_rattle.h

@@ -21,7 +21,7 @@
    This file is part of the user-manifold package written by
    Stefan Paquay at the Eindhoven University of Technology.
    This module makes it possible to do MD with particles constrained
-   to pretty arbitrary manifolds characterised by some constraint function
+   to pretty arbitrary manifolds characterized by some constraint function
    g(x,y,z) = 0 and its normal grad(g). The number of manifolds available
    right now is limited but can be extended straightforwardly by making
    a new class that inherits from manifold and implements all pure virtual

src/USER-MANIFOLD/manifold_factory.cpp

@@ -21,7 +21,7 @@
    This file is part of the user-manifold package written by
    Stefan Paquay at the Eindhoven University of Technology.
    This module makes it possible to do MD with particles constrained
-   to pretty arbitrary manifolds characterised by some constraint function
+   to pretty arbitrary manifolds characterized by some constraint function
    g(x,y,z) = 0 and its normal grad(g). The number of manifolds available
    right now is limited but can be extended straightforwardly by making
    a new class that inherits from manifold and implements all pure virtual

src/USER-MANIFOLD/manifold_factory.h

@@ -21,7 +21,7 @@
    This file is part of the user-manifold package written by
    Stefan Paquay at the Eindhoven University of Technology.
    This module makes it possible to do MD with particles constrained
-   to pretty arbitrary manifolds characterised by some constraint function
+   to pretty arbitrary manifolds characterized by some constraint function
    g(x,y,z) = 0 and its normal grad(g). The number of manifolds available
    right now is limited but can be extended straightforwardly by making
    a new class that inherits from manifold and implements all pure virtual

src/USER-QUIP/pair_quip.cpp

@@ -298,8 +298,8 @@ void PairQUIP::coeff(int narg, char **arg)
   if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
 
   // Initialise potential
-  // First call initialises potential via the fortran code in memory, and returns the necessary size
-  // of quip_potential. This behaviour is invoked by setting n_potential_quip to 0.
+  // First call initializes potential via the fortran code in memory, and returns the necessary size
+  // of quip_potential. This behavior is invoked by setting n_potential_quip to 0.
   n_quip_potential = 0;
   quip_potential = new int[0];
   quip_lammps_potential_initialise(quip_potential,&n_quip_potential,&cutoff,quip_file,&n_quip_file,quip_string,&n_quip_string);

tools/amber2lmp/amber2lammps.py

@@ -175,7 +175,7 @@ class Lammps:
 
 class Amber:
     def __init__(self):
-        'Initialise the Amber class'
+        'Initialize the Amber class'
         self.CRD_is_read = 0
         self.TOP_is_read = 0
 

tools/amber2lmp/dump2trj.py

@@ -70,7 +70,7 @@ def Find_dump_files():
 
 class Snapshot:
     def __init__(self, The_trajectory):
-        'Initialise the Snapshot class'
+        'Initialize the Snapshot class'
         
         self.timestep = The_trajectory.timestep
         self.atoms = The_trajectory.atoms

tools/amber2lmp/dump2trj99.py

@@ -68,7 +68,7 @@ def Find_dump_files():
 
 class Snapshot:
     def __init__(self, The_trajectory):
-        'Initialise the Snapshot class'
+        'Initialize the Snapshot class'
         
         self.atoms = The_trajectory.atoms
         self.xlo = The_trajectory.xlo

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

@@ -51,7 +51,7 @@ class Atom(dobject):
    """
 
    def __init__(self, system, index):
-      """Initialises Atom.
+      """Initializes Atom.
 
       Args:
          system: An Atoms object containing the required atom.
@@ -116,7 +116,7 @@ class Atoms(dobject):
 
 
    def __init__(self, natoms, _prebind=None):
-      """Initialises Atoms.
+      """Initializes Atoms.
 
       Each replica and the centroid coordinate are all held as Atoms objects,
       and so slices of the global position and momentum arrays must be used in

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

@@ -70,7 +70,7 @@ class Barostat(dobject):
    """
 
    def __init__(self, dt=None, temp=None, pext=None, tau=None, ebaro=None, thermostat=None):
-      """Initialises base barostat class.
+      """Initializes base barostat class.
 
       Note that the external stress and the external pressure are synchronized.
       This makes most sense going from the stress to the pressure, but if you

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

@@ -71,7 +71,7 @@ class Beads(dobject):
    """
 
    def __init__(self, natoms, nbeads):
-      """Initialises Beads.
+      """Initializes Beads.
 
       Args:
          natoms: Number of atoms.

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

@@ -44,7 +44,7 @@ class Cell(dobject):
    """
 
    def __init__(self, h=None):
-      """Initialises base cell class.
+      """Initializes base cell class.
 
       Args:
          h: Optional array giving the initial lattice vector matrix. The

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

@@ -78,7 +78,7 @@ class Ensemble(dobject):
    """
 
    def __init__(self, dt, temp, fixcom=False):
-      """Initialises Ensemble.
+      """Initializes Ensemble.
 
       Args:
          dt: The timestep of the simulation algorithms.
@@ -177,7 +177,7 @@ class NVEEnsemble(Ensemble):
    """
 
    def __init__(self, dt, temp, fixcom=False):
-      """Initialises NVEEnsemble.
+      """Initializes NVEEnsemble.
 
       Args:
          dt: The simulation timestep.
@@ -273,7 +273,7 @@ class NVTEnsemble(NVEEnsemble):
    """
 
    def __init__(self, dt, temp, thermostat=None, fixcom=False):
-      """Initialises NVTEnsemble.
+      """Initializes NVTEnsemble.
 
       Args:
          dt: The simulation timestep.
@@ -384,7 +384,7 @@ class NPTEnsemble(NVTEnsemble):
    """
 
    def __init__(self, dt, temp, pext, thermostat=None, barostat=None, fixcom=False):
-      """Initialises NPTEnsemble.
+      """Initializes NPTEnsemble.
 
       Args:
          dt: The simulation timestep.
@@ -508,7 +508,7 @@ class ReplayEnsemble(Ensemble):
    """
 
    def __init__(self, dt, temp, fixcom=False, intraj=None):
-      """Initialises ReplayEnsemble.
+      """Initializes ReplayEnsemble.
 
       Args:
          dt: The simulation timestep.

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

@@ -66,7 +66,7 @@ class ForceField(dobject):
    """
 
    def __init__(self):
-      """Initialises ForceField."""
+      """Initializes ForceField."""
 
       # ufvx is a list [ u, f, vir, extra ]  which stores the results of the force
       #calculation
@@ -217,7 +217,7 @@ class FFSocket(ForceField):
    """
 
    def __init__(self, pars=None, interface=None):
-      """Initialises FFSocket.
+      """Initializes FFSocket.
 
       Args:
          pars: Optional dictionary, giving the parameters needed by the driver.

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

@@ -493,7 +493,7 @@ class Initializer(dobject):
             rv *= np.sqrt(self.nbeads/nbeads)
             set_vector(v, simul.beads.p, rv)
             fmom = True
-         elif k == "thermostat": pass   # thermostats must be initialised in a second stage
+         elif k == "thermostat": pass   # thermostats must be initialized in a second stage
 
       if simul.beads.natoms == 0:
          raise ValueError("Initializer could not initialize the atomic positions")

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

@@ -349,7 +349,7 @@ class CheckpointOutput(dobject):
       """Writes out the required trajectories.
 
       Used for both the checkpoint files and the soft-exit restart file.
-      We have slightly different behaviour for these two different types of
+      We have slightly different behavior for these two different types of
       checkpoint file, as the soft-exit files have their store() function
       called automatically, and we do not want this to be updated as the
       status of the simulation after a soft-exit call is unlikely to be in

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

@@ -212,7 +212,7 @@ class Properties(dobject):
    _DEFAULT_MINFID = 1e-12
 
    def __init__(self):
-      """Initialises Properties."""
+      """Initializes Properties."""
 
       self.property_dict = {
       "step": {       "dimension" : "number",
@@ -1094,7 +1094,7 @@ class Trajectories(dobject):
    """
 
    def __init__(self):
-      """Initialises a Trajectories object."""
+      """Initializes a Trajectories object."""
 
       self.traj_dict = {
       # Note that here we want to return COPIES of the different arrays, so we make sure to make an operation in order not to return a reference.

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

@@ -20,7 +20,7 @@ along with this program. If not, see <http.//www.gnu.org/licenses/>.
 The root class for the whole simulation. Contains references to all the top
 level objects used in the simulation, and controls all the steps that are
 not inherently system dependent, like the running of each time step,
-choosing which properties to initialise, and which properties to output.
+choosing which properties to initialize, and which properties to output.
 
 Classes:
    Simulation: Deals with running the simulation and outputting the results.
@@ -81,7 +81,7 @@ class Simulation(dobject):
    """
 
    def __init__(self, beads, cell, forces, ensemble, prng, outputs, nm, init, step=0, tsteps=1000, ttime=0):
-      """Initialises Simulation class.
+      """Initializes Simulation class.
 
       Args:
          beads: A beads object giving the atom positions.

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

@@ -31,11 +31,11 @@ Classes:
       the entire system.
    ThermoSVR: Holds the algorithms for a stochastic velocity rescaling
       thermostat.
-   ThermoGLE: Holds the algorithms for a generalised langevin equation
+   ThermoGLE: Holds the algorithms for a generalized langevin equation
       thermostat.
-   ThermoNMGLE: Holds the algorithms for a generalised langevin equation
+   ThermoNMGLE: Holds the algorithms for a generalized langevin equation
       thermostat in the normal mode representation.
-   ThermoNMGLEG: Holds the algorithms for a generalised langevin equation
+   ThermoNMGLEG: Holds the algorithms for a generalized langevin equation
       thermostat in the normal mode representation, with kinetic energy as
       well as potential energy sampling optimization.
 """
@@ -75,14 +75,14 @@ class Thermostat(dobject):
    """
 
    def __init__(self, temp = 1.0, dt = 1.0, ethermo=0.0):
-      """Initialises Thermostat.
+      """Initializes Thermostat.
 
       Args:
          temp: The simulation temperature. Defaults to 1.0.
          dt: The simulation time step. Defaults to 1.0.
          ethermo: The initial heat energy transferred to the bath.
             Defaults to 0.0. Will be non-zero if the thermostat is
-            initialised from a checkpoint file.
+            initialized from a checkpoint file.
       """
 
       dset(self,"temp",   depend_value(name='temp', value=temp))
@@ -181,7 +181,7 @@ class ThermoLangevin(Thermostat):
       return np.sqrt(Constants.kb*self.temp*(1 - self.T**2))
 
    def __init__(self, temp = 1.0, dt = 1.0, tau = 1.0, ethermo=0.0):
-      """Initialises ThermoLangevin.
+      """Initializes ThermoLangevin.
 
       Args:
          temp: The simulation temperature. Defaults to 1.0.
@@ -189,7 +189,7 @@ class ThermoLangevin(Thermostat):
          tau: The thermostat damping timescale. Defaults to 1.0.
          ethermo: The initial heat energy transferred to the bath.
             Defaults to 0.0. Will be non-zero if the thermostat is
-            initialised from a checkpoint file.
+            initialized from a checkpoint file.
       """
 
       super(ThermoLangevin,self).__init__(temp, dt, ethermo)
@@ -241,14 +241,14 @@ class ThermoPILE_L(Thermostat):
    """
 
    def __init__(self, temp = 1.0, dt = 1.0, tau = 1.0, ethermo=0.0, scale=1.0):
-      """Initialises ThermoPILE_L.
+      """Initializes ThermoPILE_L.
 
       Args:
          temp: The simulation temperature. Defaults to 1.0.
          dt: The simulation time step. Defaults to 1.0.
          tau: The centroid thermostat damping timescale. Defaults to 1.0.
          ethermo: The initial conserved energy quantity. Defaults to 0.0. Will
-            be non-zero if the thermostat is initialised from a checkpoint file.
+            be non-zero if the thermostat is initialized from a checkpoint file.
          scale: A float used to reduce the intensity of the PILE thermostat if
             required.
 
@@ -404,14 +404,14 @@ class ThermoSVR(Thermostat):
       return Constants.kb*self.temp*0.5
 
    def __init__(self, temp = 1.0, dt = 1.0, tau = 1.0, ethermo=0.0):
-      """Initialises ThermoSVR.
+      """Initializes ThermoSVR.
 
       Args:
          temp: The simulation temperature. Defaults to 1.0.
          dt: The simulation time step. Defaults to 1.0.
          tau: The thermostat damping timescale. Defaults to 1.0.
          ethermo: The initial conserved energy quantity. Defaults to 0.0. Will
-            be non-zero if the thermostat is initialised from a checkpoint file.
+            be non-zero if the thermostat is initialized from a checkpoint file.
       """
 
       super(ThermoSVR,self).__init__(temp,dt,ethermo)
@@ -459,14 +459,14 @@ class ThermoPILE_G(ThermoPILE_L):
    """
 
    def __init__(self, temp = 1.0, dt = 1.0, tau = 1.0, ethermo=0.0, scale = 1.0):
-      """Initialises ThermoPILE_G.
+      """Initializes ThermoPILE_G.
 
       Args:
          temp: The simulation temperature. Defaults to 1.0.
          dt: The simulation time step. Defaults to 1.0.
          tau: The centroid thermostat damping timescale. Defaults to 1.0.
          ethermo: The initial conserved energy quantity. Defaults to 0.0. Will
-            be non-zero if the thermostat is initialised from a checkpoint file.
+            be non-zero if the thermostat is initialized from a checkpoint file.
          scale: A float used to reduce the intensity of the PILE thermostat if
             required.
       """
@@ -556,7 +556,7 @@ class ThermoGLE(Thermostat):
       return matrix_exp(-0.5*self.dt*self.A)
 
    def get_S(self):
-      """Calculates the matrix for the coloured noise."""
+      """Calculates the matrix for the colored noise."""
 
       SST = Constants.kb*(self.C - np.dot(self.T,np.dot(self.C,self.T.T)))
 
@@ -570,7 +570,7 @@ class ThermoGLE(Thermostat):
       return rC[:]
 
    def __init__(self, temp = 1.0, dt = 1.0, A = None, C = None, ethermo=0.0):
-      """Initialises ThermoGLE.
+      """Initializes ThermoGLE.
 
       Args:
          temp: The simulation temperature. Defaults to 1.0.
@@ -582,7 +582,7 @@ class ThermoGLE(Thermostat):
             total number of degrees of freedom in the system.
          ethermo: The initial heat energy transferred to the bath.
             Defaults to 0.0. Will be non-zero if the thermostat is
-            initialised from a checkpoint file.
+            initialized from a checkpoint file.
       """
 
       super(ThermoGLE,self).__init__(temp,dt,ethermo)
@@ -643,15 +643,15 @@ class ThermoGLE(Thermostat):
       # allocates, initializes or restarts an array of s's
       if self.s.shape != (self.ns + 1, len(dget(self,"m"))):
          if len(self.s) > 0:
-            warning("Mismatch in GLE s array size on restart, will reinitialise to free particle.", verbosity.low)
+            warning("Mismatch in GLE s array size on restart, will reinitialize to free particle.", verbosity.low)
          self.s = np.zeros((self.ns + 1, len(dget(self,"m"))))
 
          # Initializes the s vector in the free-particle limit
-         info(" GLE additional DOFs initialised to the free-particle limit.", verbosity.low)
+         info(" GLE additional DOFs initialized to the free-particle limit.", verbosity.low)
          SC = stab_cholesky(self.C*Constants.kb)
          self.s[:] = np.dot(SC, self.prng.gvec(self.s.shape))
       else:
-         info("GLE additional DOFs initialised from input.", verbosity.medium)
+         info("GLE additional DOFs initialized from input.", verbosity.medium)
 
    def step(self):
       """Updates the bound momentum vector with a GLE thermostat"""
@@ -699,7 +699,7 @@ class ThermoNMGLE(Thermostat):
       return rv[:]
 
    def __init__(self, temp = 1.0, dt = 1.0, A = None, C = None, ethermo=0.0):
-      """Initialises ThermoGLE.
+      """Initializes ThermoGLE.
 
       Args:
          temp: The simulation temperature. Defaults to 1.0.
@@ -711,7 +711,7 @@ class ThermoNMGLE(Thermostat):
             total number of degrees of freedom in the system.
          ethermo: The initial heat energy transferred to the bath.
             Defaults to 0.0. Will be non-zero if the thermostat is
-            initialised from a checkpoint file.
+            initialized from a checkpoint file.
       """
 
       super(ThermoNMGLE,self).__init__(temp,dt,ethermo)
@@ -767,16 +767,16 @@ class ThermoNMGLE(Thermostat):
       # allocates, initializes or restarts an array of s's
       if self.s.shape != (self.nb, self.ns + 1, nm.natoms *3) :
          if len(self.s) > 0:
-            warning("Mismatch in GLE s array size on restart, will reinitialise to free particle.", verbosity.low)
+            warning("Mismatch in GLE s array size on restart, will reinitialize to free particle.", verbosity.low)
          self.s = np.zeros((self.nb, self.ns + 1, nm.natoms*3))
 
          # Initializes the s vector in the free-particle limit
-         info(" GLE additional DOFs initialised to the free-particle limit.", verbosity.low)
+         info(" GLE additional DOFs initialized to the free-particle limit.", verbosity.low)
          for b in range(self.nb):
             SC = stab_cholesky(self.C[b]*Constants.kb)
             self.s[b] = np.dot(SC, self.prng.gvec(self.s[b].shape))
       else:
-         info("GLE additional DOFs initialised from input.", verbosity.medium)
+         info("GLE additional DOFs initialized from input.", verbosity.medium)
 
       prev_ethermo = self.ethermo
 

tools/i-pi/ipi/inputs/atoms.py

@@ -78,7 +78,7 @@ class InputAtoms(Input):
       """Takes an Atoms instance and stores a minimal representation of it.
 
       Args:
-         atoms: An Atoms object from which to initialise from.
+         atoms: An Atoms object from which to initialize from.
          filename: An optional string giving a filename to take the atom
             positions from. Defaults to ''.
       """

tools/i-pi/ipi/inputs/beads.py

@@ -82,7 +82,7 @@ class InputBeads(Input):
       """Takes a Beads instance and stores a minimal representation of it.
 
       Args:
-         beads: A Beads object from which to initialise from.
+         beads: A Beads object from which to initialize from.
       """
 
       super(InputBeads,self).store()

tools/i-pi/ipi/inputs/prng.py

@@ -38,7 +38,7 @@ class InputRandom(Input):
    instance of the object.
 
    Attributes:
-      seed: An optional integer giving a seed to initialise the random number
+      seed: An optional integer giving a seed to initialize the random number
          generator from. Defaults to 123456.
       state: An optional array giving the state of the random number generator.
          Defaults to an empty array.
@@ -74,7 +74,7 @@ class InputRandom(Input):
       representation of it.
 
       Args:
-         prng: A random number object from which to initialise from.
+         prng: A random number object from which to initialize from.
       """
 
       super(InputRandom,self).store(prng)

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

@@ -56,7 +56,7 @@ class InputThermo(Input):
 
    attribs = { "mode": (InputAttribute, { "dtype"   : str,
                                       "options" : [ "", "langevin", "svr", "pile_l", "pile_g", "gle", "nm_gle", "nm_gle_g" ],
-                                      "help"    : "The style of thermostatting. 'langevin' specifies a white noise langevin equation to be attached to the cartesian representation of the momenta. 'svr' attaches a velocity rescaling thermostat to the cartesian representation of the momenta. Both 'pile_l' and 'pile_g' attaches a white noise langevin thermostat to the normal mode representation, with 'pile_l' attaching a local langevin thermostat to the centroid mode and 'pile_g' instead attaching a global velocity rescaling thermostat. 'gle' attaches a coloured noise langevin thermostat to the cartesian representation of the momenta, 'nm_gle' attaches a coloured noise langevin thermostat to the normal mode representation of the momenta and a langevin thermostat to the centroid and 'nm_gle_g' attaches a gle thermostat to the normal modes and a svr thermostat to the centroid."
+                                      "help"    : "The style of thermostatting. 'langevin' specifies a white noise langevin equation to be attached to the cartesian representation of the momenta. 'svr' attaches a velocity rescaling thermostat to the cartesian representation of the momenta. Both 'pile_l' and 'pile_g' attaches a white noise langevin thermostat to the normal mode representation, with 'pile_l' attaching a local langevin thermostat to the centroid mode and 'pile_g' instead attaching a global velocity rescaling thermostat. 'gle' attaches a colored noise langevin thermostat to the cartesian representation of the momenta, 'nm_gle' attaches a colored noise langevin thermostat to the normal mode representation of the momenta and a langevin thermostat to the centroid and 'nm_gle_g' attaches a gle thermostat to the normal modes and a svr thermostat to the centroid."
                                          }) }
    fields = { "ethermo" : (InputValue, {  "dtype"     : float,
                                           "default"   : 0.0,

tools/i-pi/ipi/interfaces/sockets.py

@@ -108,7 +108,7 @@ class DriverSocket(socket.socket):
    """Deals with communication between the client and driver code.
 
    Deals with sending and receiving the data from the driver code. Keeps track
-   of the status of the driver. Initialises the driver forcefield, sends the
+   of the status of the driver. Initializes the driver forcefield, sends the
    position and cell data, and receives the force data.
 
    Attributes:
@@ -119,7 +119,7 @@ class DriverSocket(socket.socket):
    """
 
    def __init__(self, socket):
-      """Initialises DriverSocket.
+      """Initializes DriverSocket.
 
       Args:
          socket: A socket through which the communication should be done.
@@ -378,7 +378,7 @@ class InterfaceSocket(object):
    """
 
    def __init__(self, address="localhost", port=31415, slots=4, mode="unix", latency=1e-3, timeout=1.0, dopbc=True):
-      """Initialises interface.
+      """Initializes interface.
 
       Args:
          address: An optional string giving the name of the host server.
@@ -556,7 +556,7 @@ class InterfaceSocket(object):
 
       Deals with maintaining the jobs list. Gets data from drivers that have
       finished their calculation and removes that job from the list of running
-      jobs, adds jobs to free clients and initialises the forcefields of new
+      jobs, adds jobs to free clients and initializes the forcefields of new
       clients.
       """
 

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

@@ -73,7 +73,7 @@ class synchronizer(object):
    """
 
    def __init__(self, deps=None):
-      """Initialises synchronizer.
+      """Initializes synchronizer.
 
       Args:
          deps: Optional dictionary giving the synched objects of the form
@@ -113,7 +113,7 @@ class depend_base(object):
    """
 
    def __init__(self, name, synchro=None, func=None, dependants=None, dependencies=None, tainted=None):
-      """Initialises depend_base.
+      """Initializes depend_base.
 
       An unusual initialization routine, as it has to be able to deal with the
       depend array mechanism for returning slices as new depend arrays.
@@ -291,7 +291,7 @@ class depend_value(depend_base):
    """
 
    def __init__(self, name, value=None, synchro=None, func=None, dependants=None, dependencies=None, tainted=None):
-      """Initialises depend_value.
+      """Initializes depend_value.
 
       Args:
          name: A string giving the name of self.
@@ -375,7 +375,7 @@ class depend_array(np.ndarray, depend_base):
       return obj
 
    def __init__(self, value, name, synchro=None, func=None, dependants=None, dependencies=None, tainted=None, base=None):
-      """Initialises depend_array.
+      """Initializes depend_array.
 
       Note that this is only called when a new array is created by an
       explicit constructor.

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

@@ -22,7 +22,7 @@ attributes dictionary, which are filled with the tags and attributes that
 are allowed to be present, along with their default values and data type.
 
 These are then filled with the data from the xml file when the program
-is initialised, and are filled by the values calculated in the program which
+is initialized, and are filled by the values calculated in the program which
 are then output to the checkpoint file when a restart file is required.
 
 Also deals with checking for user input errors, of the form of misspelt tags,
@@ -65,14 +65,14 @@ class input_default(object):
    """
 
    def __init__(self, factory, args = None, kwargs = None):
-      """Initialises input_default.
+      """Initializes input_default.
 
       Args:
          type: The class or function to be used to create the default object.
-         args: A tuple giving the arguments to be used to initialise
+         args: A tuple giving the arguments to be used to initialize
             the default value.
          kwargs: A dictionary giving the key word arguments to be used
-            to initialise the default value.
+            to initialize the default value.
       """
 
       if args is None:
@@ -147,10 +147,10 @@ class Input(object):
                       #hyperlinks
 
    def __init__(self, help=None, default=None):
-      """Initialises Input.
+      """Initializes Input.
 
       Automatically adds all the fields and attribs names to the input object's
-      dictionary, then initialises all the appropriate input objects
+      dictionary, then initializes all the appropriate input objects
       as the corresponding values.
 
       Args:
@@ -676,7 +676,7 @@ class InputAttribute(Input):
    """
 
    def __init__(self,  help=None, default=None, dtype=None, options=None):
-      """Initialises InputAttribute.
+      """Initializes InputAttribute.
 
       Args:
          help: A help string.
@@ -773,7 +773,7 @@ class InputValue(InputAttribute):
    attribs= { "units" : ( InputAttribute, { "dtype" : str, "help" : "The units the input data is given in.", "default" : default_units } ) }
 
    def __init__(self,  help=None, default=None, dtype=None, options=None, dimension=None):
-      """Initialises InputValue.
+      """Initializes InputValue.
 
       Args:
          help: A help string.
@@ -874,7 +874,7 @@ class InputArray(InputValue):
    attribs["shape"] = (InputAttribute,  {"dtype": tuple,  "help": "The shape of the array.", "default": (0,)})
 
    def __init__(self,  help=None, default=None, dtype=None, dimension=None):
-      """Initialises InputArray.
+      """Initializes InputArray.
 
       Args:
          help: A help string.

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

@@ -63,7 +63,7 @@ class xml_node(object):
    """
 
    def __init__(self, attribs=None, name="", fields=None):
-      """Initialises xml_node.
+      """Initializes xml_node.
 
       Args:
          attribs: An optional dictionary giving attribute data. Defaults to {}.
@@ -101,7 +101,7 @@ class xml_handler(ContentHandler):
    """
 
    def __init__(self):
-      """Initialises xml_handler."""
+      """Initializes xml_handler."""
 
       #root xml node with all the data
       self.root = xml_node(name="root", fields=[])

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

@@ -34,7 +34,7 @@ import math
 class Random(object):
    """Class to interface with the standard pseudo-random number generator.
 
-   Initialises the standard numpy pseudo-random number generator from a seed
+   Initializes the standard numpy pseudo-random number generator from a seed
    at the beginning of the simulation, and keeps track of the state so that
    it can be output to the checkpoint files throughout the simulation.
 
@@ -51,11 +51,11 @@ class Random(object):
    """
 
    def __init__(self, seed=12345, state=None):
-      """Initialises Random.
+      """Initializes Random.
 
       Args:
-         seed: An optional seed giving an integer to initialise the state with.
-         state: An optional state tuple to initialise the state with.
+         seed: An optional seed giving an integer to initialize the state with.
+         state: An optional state tuple to initialize the state with.
       """
 
       self.rng = np.random.mtrand.RandomState(seed=seed)

tools/polybond/lmpsdata.py

@@ -881,7 +881,7 @@ class Lmpsdata:
 class booleanarray:
 	"""A class that stores boolean values in a list of lists."""	
 	def __init__(self,rownum, colnum, initval): 		
-		""" initialise a list of lists (array) with
+		""" initialize a list of lists (array) with
 		rownum correspondinig to the number of lists in the list and 
 		colnum corresponding to the number of elements in the list's list.
 		initval is the value the list of lists will be initialized with.

tools/replica/reorder_remd_traj.py

@@ -53,7 +53,7 @@ except ImportError:
 
 
 
-#### INITIALISE MPI ####
+#### INITIALIZE MPI ####
 # (note that all output on screen will be printed only on the ROOT proc)
 ROOT = 0
 comm = MPI.COMM_WORLD