diff --git a/tools/i-pi/drivers/driver.f90 b/tools/i-pi/drivers/driver.f90 index 9ff992dab3..646f1e9add 100644 --- a/tools/i-pi/drivers/driver.f90 +++ b/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) diff --git a/tools/i-pi/ipi/engine/atoms.py b/tools/i-pi/ipi/engine/atoms.py index 02ffcd7551..fd52ccf96b 100644 --- a/tools/i-pi/ipi/engine/atoms.py +++ b/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. diff --git a/tools/i-pi/ipi/engine/properties.py b/tools/i-pi/ipi/engine/properties.py index 1ea07bda87..a76aca1faf 100644 --- a/tools/i-pi/ipi/engine/properties.py +++ b/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. """ diff --git a/tools/i-pi/ipi/engine/simulation.py b/tools/i-pi/ipi/engine/simulation.py index 42645939ee..3c16a99621 100644 --- a/tools/i-pi/ipi/engine/simulation.py +++ b/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. diff --git a/tools/i-pi/ipi/interfaces/sockets.py b/tools/i-pi/ipi/interfaces/sockets.py index 998a87d113..2783d31e06 100644 --- a/tools/i-pi/ipi/interfaces/sockets.py +++ b/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 diff --git a/tools/i-pi/ipi/utils/depend.py b/tools/i-pi/ipi/utils/depend.py index 1ca361f781..4b87323533 100644 --- a/tools/i-pi/ipi/utils/depend.py +++ b/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 diff --git a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README.TXT b/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README.TXT index b57d0e76c8..6ec463efab 100644 --- a/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README.TXT +++ b/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. diff --git a/tools/moltemplate/src/bonds_by_type.py b/tools/moltemplate/src/bonds_by_type.py index 786a6a8a86..919cfa51af 100644 --- a/tools/moltemplate/src/bonds_by_type.py +++ b/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 diff --git a/tools/moltemplate/src/chargepairs_by_type.py b/tools/moltemplate/src/chargepairs_by_type.py index 0d006abd5a..3de8131141 100644 --- a/tools/moltemplate/src/chargepairs_by_type.py +++ b/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 diff --git a/tools/moltemplate/src/dump2data.py b/tools/moltemplate/src/dump2data.py index adcb5a0369..25c73219dd 100644 --- a/tools/moltemplate/src/dump2data.py +++ b/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 diff --git a/tools/moltemplate/src/lttree.py b/tools/moltemplate/src/lttree.py index c77d820434..743419eb2b 100644 --- a/tools/moltemplate/src/lttree.py +++ b/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 diff --git a/tools/moltemplate/src/moltemplate.sh b/tools/moltemplate/src/moltemplate.sh index 3a8d17bcd6..d6f76a2483 100755 --- a/tools/moltemplate/src/moltemplate.sh +++ b/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 } diff --git a/tools/moltemplate/src/moltemplate_force_fields/oplsaa/README.TXT b/tools/moltemplate/src/moltemplate_force_fields/oplsaa/README.TXT index 3bb903968a..ab7c32530a 100644 --- a/tools/moltemplate/src/moltemplate_force_fields/oplsaa/README.TXT +++ b/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. ----------------------------- diff --git a/tools/moltemplate/src/moltemplate_scripts_depreciated/oplsaa_moltemplate.py b/tools/moltemplate/src/moltemplate_scripts_depreciated/oplsaa_moltemplate.py index 059aacaafb..5a2ce05c4a 100755 --- a/tools/moltemplate/src/moltemplate_scripts_depreciated/oplsaa_moltemplate.py +++ b/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 diff --git a/tools/moltemplate/src/nbody_by_type.py b/tools/moltemplate/src/nbody_by_type.py index ee9884302b..13fc012015 100644 --- a/tools/moltemplate/src/nbody_by_type.py +++ b/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 diff --git a/tools/moltemplate/src/ttree.py b/tools/moltemplate/src/ttree.py index cddc9b8ac6..dda1880c1d 100644 --- a/tools/moltemplate/src/ttree.py +++ b/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 diff --git a/tools/moltemplate/src/ttree_lex.py b/tools/moltemplate/src/ttree_lex.py index a8bb10a73c..d0938047c7 100644 --- a/tools/moltemplate/src/ttree_lex.py +++ b/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.) """ diff --git a/tools/msi2lmp/frc_files/cvff_aug.frc b/tools/msi2lmp/frc_files/cvff_aug.frc index 9fcdd30068..75af9ace24 100644 --- a/tools/msi2lmp/frc_files/cvff_aug.frc +++ b/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 !---- --- --------------------------------- ------ diff --git a/tools/msi2lmp/src/msi2lmp.h b/tools/msi2lmp/src/msi2lmp.h index e07a4486db..377ab1a6c3 100644 --- a/tools/msi2lmp/src/msi2lmp.h +++ b/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 */ diff --git a/tools/phonon/dynmat.cpp b/tools/phonon/dynmat.cpp index eb91647ed2..e82f473130 100644 --- a/tools/phonon/dynmat.cpp +++ b/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; diff --git a/tools/pymol_asphere/src/cartesian.cpp b/tools/pymol_asphere/src/cartesian.cpp index 38550db0e7..a244d07dac 100644 --- a/tools/pymol_asphere/src/cartesian.cpp +++ b/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 diff --git a/tools/pymol_asphere/src/cartesian.h b/tools/pymol_asphere/src/cartesian.h index a486b5163e..a5acd70b33 100644 --- a/tools/pymol_asphere/src/cartesian.h +++ b/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 diff --git a/tools/python/pizza/dump.py b/tools/python/pizza/dump.py index 3b7e7c46c7..36a24dcd39 100644 --- a/tools/python/pizza/dump.py +++ b/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: