Command line flags
-addpathonly
flag: -addpathonly
description: does nothing except adding all nanodcal-paths which are needed for a nanodcal calculation.
-autotest
flag: -autotest
description: test the installation of nanodcal. Usage: nanodcal -autotest [-parallel].
-basis
flag: -basis
description: display a periodic table containing elements whose basis are available. If it is followed by an element name or a list of element names, all available basis of those elements will be displayed. e.g. “nanodcal -basis” “nanodcal -basis C” “nanodcal -basis Mg O Fe”
-doexit
flag: -doexit
description: used when want to exit the matlab session after the calculation being finished.
-help
flag: -help
description: display some on-line help information.
-install
flag: -install
description: used for installation of nanodcal. Usage: nanodcal -install
-parallel
flag: -parallel
description: used to run a parallel calculation. The input parameter calculation.control.parallel will be automatically set to true.
-parameter
flag: -parameter
description: display information of all input parameters which are organized into several categories.
If used with no other arguments, i.e., “nanodcal -parameter”, all category names will be displayed.
If a number follows, i.e., “nanodcal -parameter #”, all parameter names in the category of that number will be displayed.
If another number follows (two numbers maximum), i.e., “nanodcal -parameter #1 #2”, the description of the parameter of the second number in the category of the first number will be displayed.
If a question mark follows, i.e., “nanodcal -parameter ?”, all parameter names, grouped in the categories, will be displayed.
If a string follows the question mark, e.g., “nanodcal -parameter ? control”, all parameters whose names contain the given string will be displayed. If there is only one parameter found, its description will be directly displayed.
-plot
flag: -plot
description: used to plot or re-plot a calculated result.
Usage:
nanodcal -plot name [datafile]
where the name is the calculation name, e.g., bandStructure, densityOfStates, ect. The datafile is the file name of the calculated results, e.g., BandStructure.mat, DensityOfStates.mat, ect. If it is missing, the default name for the corresponding calculation will be used.
The structure can also be re-ploted by using the Atoms.mat file:
nanodcal -plot structure dfile [parameter/value pairs]
where the dfile is a file name of the Atoms.mat, the parameter/value pairs are optional, and they are same as those used in -structure calculation.
-resume
flag: -resume
description: used in self-consistent field calculation, to resume an interrupted calculation or an intentionally stopped calculation for changing some calculation parameters.
-rmpathonly
flag: -rmpathonly
description: does nothing except removing all the nanodcal-paths.
-structure or -struct
flag: -structure or -struct
description: do structure check only. used to get the atomic structure only, mainly for checking the correctness of the atomic structure set up before the self-consistent field calculation which might take a long time.
After the calculation, a file Atoms.xyz will be generated for the user to check the structure set up. A figure and the corresponding file Atoms.fig are also generated.
Usage:
nanodcal -structure [parameter/value pairs] inputfile
where the inputfile is the input file the user prepared for the calculation. The parameter/value pairs are optional, to specify some properties of the figure. Possible parameters are listed bellow:
bondLength: atoms form bonds if their distance <= bondLength. a double number or a number-unit string, e.g. 2.5ang, or 3.5, or 3.5au. (The default value is 4 Bohr.) showAtomLabel: 0: don’t show; 1: show atom label; 2: show region labels, i.e. “L” for lead and “C” for central 3: show both atom and region labels (The default value is 0.) repFactors: replicated factors. the system will be replicated by the factors before plot. 1 x 3 integer array. (The default value is [1,1,1].) bondType: a string of 3 characters made from the characters listed under the matlab PLOT command, to specify the line type and color used for the bonds and the symbol type used for the atoms. (The default value is ‘b-o’, and see the help information of the matlab function plot for other possibilities.) bondWidth: an integer, to specify the line width used for the bonds. (The default value is 3.) atomColor: a character chosen from the characters listed under the matlab PLOT command, to specify the symbol color used for the atoms. (The default value is ‘b’, and see the help information of the matlab function plot for other possibilities.) atomSize: an integer, to specify the symbol size used for the atoms. (The default value is 8.)
-version
flag: -version
description: display the current version of the nanodcal.