CDTK.Tools.Utils module

Some miscellaneous tools

CDTK.Tools.Utils.ReverseArray(array)

Reverse array.

Parameters:

array1D array_like

array to be reversed

rtype:

Reversed array

CDTK.Tools.Utils.ShiftArray(array, shift, **option)

Shift array.

Parameters:

array1D array_like

array to be shifted

shiftint

amount of shifting, positive integer will shift the array to the right, negative integer will shift the array to the left.

periodicBool, optional, default: True

if True, use the periodic boudary condition on the array edge (the right most array element which is right shifted will appear on the left most, and vice versa). If False, the new array element which enter the array as the right most or the left most elements will be set 0.0.

Returns:

Shifted array

CDTK.Tools.Utils.atomicCoordinatesFromRlog(Rlog)

Sort the entries of an Rlog file on a per atom basis

Rlog:

t0 X01 Y01 Z01 X02 Y02 Z02 …… X0N Y0N Z0N t1 X11 Y11 Z11 X12 Y12 Z12 …… X1N Y1N Z1N … tf Xf1 Yf1 Zf1 Xf2 Yf2 Zf2 …… XfN YfN ZfN

Returns as array

[ [ [X01 Y01 Z01 ], [X02 Y02 Z02], …. [X0N Y0N Z0N] ],

[ [Xf1 Yf1 Zf1 ], [Xf2 Yf2 Zf2], …. [XfN YfN ZfN] ]

]

CDTK.Tools.Utils.changeIsotopeSymbols(listin)

CDTK.Tools.Utils.fileLineParser(path, regexp, functions=[])

Parse a file line by line using a regexp to find matching values

path – path to the file being parsed regexp – a valid regexp with one or more parenthesis to catch matching

values

functions – list of transformation functions to be applied to the matching

strings, e.g. “float” if provided should have as many elements as the number of elements to be matched from every matching line

output:

List of lists, one list per matching line. Empty list if no matches.

CDTK.Tools.Utils.getDataFromLog(log)

CDTK.Tools.Utils.getDateString()

CDTK.Tools.Utils.getDenTable(finput, dof, **args)

Return the next grid reduced density in table form

Input:

finput - file object with the gden file dof - degree of freedom to look for

Returns:

found - True/False, whether still data to be returned table - list of lists with x,y,z data

CDTK.Tools.Utils.getDirectoryList(folder='./', file_name=None)

Get trj_ subfolders in a given folder. If a file name is given, only trj_ subfolders are returned that contain a file with that name. The returned list is sorted.

Parameters:

• folder (string, optional, default: './') – Folder to search for trj_ subfolders.

• file_name (string, optional, default: None) – If given, only trj_ subfolders are returned that contain a file with that name.

Returns:

dirs – Sorted list of trj_ subfolders.

Return type:

list of string

CDTK.Tools.Utils.getNextTime(finput)

Return next time in data file

Input:

finput - file object with the gpop file

Returns:

time - time (float) or None if EOF is reached

CDTK.Tools.Utils.getPopTable(finput, dof)

Return the next grid population in table form

Input:

finput - file object with the gpop file dof - degree of freedom to look for

Returns:

found - True/False, whether still data to be returned table - list of lists with x,y data

CDTK.Tools.Utils.getTrajectoryTimeSteps(Rlog)

CDTK.Tools.Utils.getUniqueID(idlength=12)

CDTK.Tools.Utils.listToFile(mylist, fname)

CDTK.Tools.Utils.loadDataStruct(fname)

Load a data structure from a file

The data structure must have been saved as a string, for example by saveDataStruct

fname – path to the file with the data structure

CDTK.Tools.Utils.readAuto(fname, **opts)

Read an autocorrelation file into a complex array fname – path to file to be read or file object Options:

skip – integer, dafault 0. New row read every <skip> rows.

CDTK.Tools.Utils.readColumnFile(fname, col_ix=0)

CDTK.Tools.Utils.readFile(path)

return a string with the contents of a file

path - path to the file to be read

CDTK.Tools.Utils.readRlogRestricted(rlog, col0=0, coln=1)

Read log file and return array with vals starting at col0, ending at col0 + coln

CDTK.Tools.Utils.readTableFile(fname, **opts)

read a file with data organized in table form and return a l[i,j] list

fname – path to file to be read or file object Options:

mode – text string: “rows” (default) or “cols”

• in “rows” mode the first index runs over the rows of the table

• in “cols” mode the first index runs over the columns of the table

skip – integer, dafault 0. New row read every <skip> rows.

CDTK.Tools.Utils.readTag(tag, string)

In a string look for XML tag “tag” and return its content

tag - string containing the tag whose contents are to be retrieved string - text string

returns the contents between <tag> and </tag> or None if <tag> is not present.

CDTK.Tools.Utils.readTagFromFile(tag, path)

return a string with the contents between <tag> and </tag>

CDTK.Tools.Utils.saveDataStruct(fname, obj)

Store the string representation of a data structure to a file

The repr() function is used, this function is intended only for rather simple data structures made for example of nested lists and dictionaries.

obj – object to store fname – path to the file where to store the string

CDTK.Tools.Utils.traj2vtf(atomlist, Rlog, vtfname='traj', mmlist=None, disp_n_atoms=None)

Generate a trajectory in .vtf format

Useful for plots with VMD

Point charges represented by “X”

Input arguments:

atomlist – path to atomlist file Rlog – path to R.log file vtfname – vtf filename mmlist – path to MM region atomlist file disp_n_atoms – int; number of atoms to output (truncation for large systems)

CDTK.Tools.Utils.traj2xyz(atomlist, geoms, filename='traj.xyz', comment='CDTK-generated traj file', timesteps=None)

Generate a trajectory in .xyz format Useful for plots with VMD

Parameters:

• atomlist (list of strings) – list of atom symbols

• geoms (numpy array [step, atoms, 3 ]) – geometries

• filename (str, optional) – output filename. Defaults to ‘traj.xyz’.

• comment (str, optional) – comment line. Defaults to ‘CDTK-generated traj file’.

• timesteps (array of floats, optional) – time step information. Defaults to None.