Fix more typos in tools

tools/i-pi/drivers/driver.f90

@@ -67,7 +67,7 @@
       INTEGER i
 
       ! parse the command line parameters
-      ! intialize defaults
+      ! initialize defaults
       ccmd = 0
       inet = 1
       host = "localhost"//achar(0)

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

@@ -120,7 +120,7 @@ class Atoms(dobject):
 
       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
-      the initialisation so that they always agree with each other.
+      the initialization so that they always agree with each other.
 
       Args:
          natoms: An integer giving the number of atoms.

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

@@ -460,7 +460,7 @@ class Properties(dobject):
          key: A string contained in property_dict.
 
       Returns:
-         The property labelled by the keyword key, along with its unit
+         The property labeled by the keyword key, along with its unit
          keyword, and the argument lists for the function used to calculate
          the property specified by the keyword key.
       """
@@ -1216,7 +1216,7 @@ class Trajectories(dobject):
          key: A string contained in trajectory_dict.
 
       Returns:
-         The trajectory labelled by the keyword key, along with its unit
+         The trajectory labeled by the keyword key, along with its unit
          keyword, and the argument lists for the function used to calculate
          the trajectory specified by the keyword key.
       """

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

@@ -49,7 +49,7 @@ class Simulation(dobject):
    """Main simulation object.
 
    Contains all the references and the main dynamics loop. Also handles the
-   initialisation and output.
+   initialization and output.
 
    Attributes:
       beads: A beads object giving the atom positions.

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

@@ -243,7 +243,7 @@ class DriverSocket(socket.socket):
          return np.fromstring(self._buf[0:blen], dest.dtype).reshape(dest.shape)
 
    def initialize(self, rid, pars):
-      """Sends the initialisation string to the driver.
+      """Sends the initialization string to the driver.
 
       Args:
          rid: The index of the request, i.e. the replica that
@@ -456,13 +456,13 @@ class InterfaceSocket(object):
       """Adds a request.
 
       Note that the pars dictionary need to be sent as a string of a
-      standard format so that the initialisation of the driver can be done.
+      standard format so that the initialization of the driver can be done.
 
       Args:
          atoms: An Atoms object giving the atom positions.
          cell: A Cell object giving the system box.
          pars: An optional dictionary giving the parameters to be sent to the
-            driver for initialisation. Defaults to {}.
+            driver for initialization. Defaults to {}.
          reqid: An optional integer that identifies requests of the same type,
             e.g. the bead index
 

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

@@ -115,7 +115,7 @@ class depend_base(object):
    def __init__(self, name, synchro=None, func=None, dependants=None, dependencies=None, tainted=None):
       """Initialises depend_base.
 
-      An unusual initialisation routine, as it has to be able to deal with the
+      An unusual initialization routine, as it has to be able to deal with the
       depend array mechanism for returning slices as new depend arrays.
 
       This is the reason for the penultimate if statement; it automatically

tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README.TXT

@@ -2,7 +2,7 @@ The simulation consists of a mixture of isobutane and water.
 Over time (less than 1 ns), the two molecules phase-separate.
 
 The GAFF parameters are applied only to the isobutane molecule.
-(The water molecule paramters are defined explicitly in
+(The water molecule parameters are defined explicitly in
  src/moltemplate_force_fields/tip3p_2004.lt)
 
 WARNING: THIS IS A PRELIMINARY EXAMPLE WHICH USES AMBER'S GAFF FORCE FIELD.

tools/moltemplate/src/bonds_by_type.py

@@ -315,7 +315,7 @@ if __name__ == "__main__":
 
             elif argv[i][0] == '-':
                 raise ttree_lex.InputError('Error('+g_program_name+'):\n'
-                                 'Unrecogized command line argument \"'+argv[i]+'\"\n')
+                                 'Unrecognized command line argument \"'+argv[i]+'\"\n')
             else:
                 i += 1
 

tools/moltemplate/src/chargepairs_by_type.py

@@ -328,7 +328,7 @@ if __name__ == "__main__":
 
             elif argv[i][0] == '-':
                 raise ttree_lex.InputError('Error('+g_program_name+'):\n'
-                                 'Unrecogized command line argument \"'+argv[i]+'\"\n')
+                                 'Unrecognized command line argument \"'+argv[i]+'\"\n')
             else:
                 i += 1
 

tools/moltemplate/src/dump2data.py

@@ -458,7 +458,7 @@ def ParseArgs(argv,
             del(argv[i:i+2])
 
         elif ((argv[i][0] == '-') and (__name__ == "__main__")):
-            raise InputError('Error(dump2data): Unrecogized command line argument \"'+argv[i]+'\"\n')
+            raise InputError('Error(dump2data): Unrecognized command line argument \"'+argv[i]+'\"\n')
         else:
             i += 1
 

tools/moltemplate/src/lttree.py

@@ -165,7 +165,7 @@ def LttreeParseArgs(argv, settings):
         elif ((argv[i][0] == '-') and (__name__ == "__main__")):
             #elif (__name__ == "__main__"):
             raise InputError('Error('+g_program_name+'):\n'
-                             'Unrecogized command line argument \"'+argv[i]+'\"\n')
+                             'Unrecognized command line argument \"'+argv[i]+'\"\n')
         else:
             i += 1
 

tools/moltemplate/src/moltemplate.sh

@@ -57,7 +57,7 @@ ERR_INTERNAL()
   echo "    !!!!!!   Possible internal error  !!!!!!" >&2
   echo "This could be a bug in moltemplate." >&2
   echo "Please report this error." >&2
-  echo "(And please include the last few lines of moltemplate output preceeding this.)" >&2
+  echo "(And please include the last few lines of moltemplate output preceding this.)" >&2
   echo "  Thank you." >&2
   exit 100
 }

tools/moltemplate/src/moltemplate_force_fields/oplsaa/README.TXT

@@ -5,7 +5,7 @@ NOTE: THE "oplsaa_moltemplate.py" SCRIPT HAS MOVED TO THE "../src/" DIRECTORY.
 Description:
 
 Unfortunately, moltemplate does not come with a file containing OPLSAA 
-paramters which is ready to use.  You must build it yourself.
+parameters which is ready to use.  You must build it yourself.
 This directory has tools and instructions to explain how to do this.
 
 -----------------------------

tools/moltemplate/src/moltemplate_scripts_depreciated/oplsaa_moltemplate.py

@@ -109,7 +109,7 @@ atom_lookup={} #this dictionary contains all the atom ffid's as a key and the nu
 #atom=[[10000,10000] for i in range(906)]  <- don't assume there are 906 atoms
 atom=[[-10000,-10000] for i in range(0,max_atomType+1)]
 #charge_by_type={} # lookup charge by atom type
-#vdw_by_type={}    # lookup epsilon & sigma paramters by atom type
+#vdw_by_type={}    # lookup epsilon & sigma parameters by atom type
 charge_by_type=[0.0 for i in range(0,max_atomType+1)]    # lookup charge by atom
 vdw_by_type=[(0.0,0.0) for i in range(0,max_atomType+1)] # lookup epsilon & sigma
 

tools/moltemplate/src/nbody_by_type.py

@@ -524,7 +524,7 @@ if __name__ == "__main__":
 
             elif argv[i][0] == '-':
                 raise InputError('Error('+g_program_name+'):\n'
-                                 'Unrecogized command line argument \"'+argv[i]+'\"\n')
+                                 'Unrecognized command line argument \"'+argv[i]+'\"\n')
             else:
                 i += 1
 

tools/moltemplate/src/ttree.py

@@ -2489,7 +2489,7 @@ class StaticObj(object):
                             raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
                                              '      Error near '+lex.error_leader()+'\n'
                                              '      new '+class_name_str+'\n'
-                                             'Bracketed number should be preceeded by a class name.')
+                                             'Bracketed number should be preceded by a class name.')
                         class_names = []
                         weights = []
                         num_by_type = []
@@ -2979,7 +2979,7 @@ class StaticObj(object):
         # Dots in class names can appear for 2 reasons:
         #   1) as part of a path like "../" describing the location 
         #      where this class was defined relative to the caller.
-        #      In that case it will be preceeded or followed by
+        #      In that case it will be preceded or followed by
         #      either another dot '.', or a slash '/'
         #   2) as part of a "suffix" which appears after the name
         #      containing instructions which modify how to
@@ -4434,7 +4434,7 @@ def ExtractFormattingCommands(suffix):
     if suffix[-1] != ')': # Format functions are always followed by parens
         return None, None
     else:
-        idot = suffix.find('.') # Format functions usually preceeded by '.'
+        idot = suffix.find('.') # Format functions usually preceded by '.'
         ioparen = suffix.find('(')
         icparen = suffix.find(')')
         format_fname = suffix[idot+1:ioparen]
@@ -5113,7 +5113,7 @@ def BasicUIParseArgs(argv, settings):
         elif ((argv[i][0] == '-') and (__name__ == "__main__")):
             #elif (__name__ == "__main__"):
             raise InputError('Error('+g_filename+'):\n'
-                             'Unrecogized command line argument \"'+argv[i]+'\"\n')
+                             'Unrecognized command line argument \"'+argv[i]+'\"\n')
         else:
             i += 1
 

tools/moltemplate/src/ttree_lex.py

@@ -1107,7 +1107,7 @@ def _DeleteLineFromTemplate(tmpl_list,
     tmpl_list is an alternating list of VarRefs and TextBlocks.
     To identify the line, the index corresponding to one of the
     entries in the tmpl_list is used. (Usually it is a VarRef)
-    The text after the preceeding newline, and the text up to the next newline 
+    The text after the preceding newline, and the text up to the next newline 
        (starting from the beginning of the current entry, if a TextBlock)
     is deleted, including any VarRef (variables) located in between.
 
@@ -1505,7 +1505,7 @@ class TemplateLexer(TtreeShlex):
     new member function (ReadTemplate()), which can read in a block of raw text,
     (halting at an (non-escaped) terminal character), and split the text into
     alternating blocks of text and variables.  (As far as this lexer is 
-    concerned, "variables" are simply tokens preceeded by $ or @ characters,
+    concerned, "variables" are simply tokens preceded by $ or @ characters,
     and surrounded by optional curly-brackets {}.)
 
     """
@@ -1652,7 +1652,7 @@ class TemplateLexer(TtreeShlex):
         (for example, '}' in "\}" does not cause terminate parsing).
         In that case, the text is considered normal text.  (However the 
         '\' character is also stripped out.  It is also stripped out if it
-        preceeds any characters in "other_esc_chars", which is 
+        precedes any characters in "other_esc_chars", which is 
         the second argument.  Otherwise it is left in the text block.)
 
         """

tools/msi2lmp/frc_files/cvff_aug.frc

@@ -209,7 +209,7 @@
 
 #define cvff_aug
 
-> This specifes the use of the ionic parameter types    
+> This specifies the use of the ionic parameter types    
 
 !Ver  Ref               Function                Label
 !---- ---   ---------------------------------   ------

tools/msi2lmp/src/msi2lmp.h

@@ -172,7 +172,7 @@ extern int    periodic;      /* 0= nonperiodic 1= 3-D periodic */
 extern int    TriclinicFlag; /* 0= Orthogonal  1= Triclinic */
 extern int    forcefield;    /* BitMask: the value FF_TYPE_COMMON is set for common components of the options below,
                               * FF_TYPE_CLASS1 = ClassI,  FF_TYPE_CLASS2 = ClassII, FF_TYPE_OPLSAA = OPLS-AA*/
-extern int    ljtypeflag;    /* how LJ paramters are stored: 0 = A-B, 1 = r-eps */
+extern int    ljtypeflag;    /* how LJ parameters are stored: 0 = A-B, 1 = r-eps */
 extern int    centerflag;    /* 1= center box  0= keep box */
 extern int    hintflag;      /* 1= print style hint comments  0= no hints */
 extern int    pflag;         /* print level: 0, 1, 2, 3 */

tools/phonon/dynmat.cpp

@@ -3,7 +3,7 @@
 #include "version.h"
 #include "global.h"
 
-// to intialize the class
+// to initialize the class
 DynMat::DynMat(int narg, char **arg)
 {
   attyp = NULL;

tools/pymol_asphere/src/cartesian.cpp

@@ -4,7 +4,7 @@
  *		Also contains quaternion structures and operations
  *
  *    Cartesian point of doubles: cPt
- *    Cartesian point of intergers: iPt
+ *    Cartesian point of integers: iPt
  *    Vector of doubles: vectorPt
  *    Color of doubles:   colorPt
  *    Quaternion: Quaternion

tools/pymol_asphere/src/cartesian.h

@@ -4,7 +4,7 @@
  *		Also contains quaternion structures and operations
  *
  *    Cartesian point of doubles: cPt
- *    Cartesian point of intergers: iPt
+ *    Cartesian point of integers: iPt
  *    Vector of doubles: vectorPt
  *    Color of doubles:   colorPt
  *    Quaternion: Quaternion

tools/python/pizza/dump.py

@@ -448,7 +448,7 @@ class dump:
 
   # --------------------------------------------------------------------
   # scale coords to 0-1 for all snapshots or just one
-  # use 6 params as h-matrix to treat orthongonal or triclinic boxes
+  # use 6 params as h-matrix to treat orthogonal or triclinic boxes
 
   def scale(self,*list):
     if len(list) == 0:
@@ -512,7 +512,7 @@ class dump:
         
   # --------------------------------------------------------------------
   # unscale coords from 0-1 to box size for all snapshots or just one
-  # use 6 params as h-matrix to treat orthongonal or triclinic boxes
+  # use 6 params as h-matrix to treat orthogonal or triclinic boxes
 
   def unscale(self,*list):
     if len(list) == 0: