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- builtins.object
-
- BavFile
- Density
- Fdmnes
- FdmnesAnalysis
- FdmnesCompare
- Reflection
- Spherical
- Xanes
class BavFile(builtins.object) |
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BavFile(text)
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Methods defined here:
- __init__(self, text)
- Initialize self. See help(type(self)) for accurate signature.
- charge_str(self)
- returns final cycle ion charge
:return: str
- cycle_energy(self)
- Return array of total energy per atom for each cycle
- cycles(self)
- Returns the number of cycles completed
:return:
- edge(self)
- Returns the resoant edge used in calculation
:return: str
- fdmnes_version(self)
- Returns the version date of FDMNES used in the calculation
:return: str
- header(self)
- Returns the top part of the file
:return:
- plot_cycle_energy(self)
- Plot progress of energy during SCF cycles
- potrmt_str(self)
- Return final cycle "Potrmt" string
:return: str
- radius(self)
- Returns the radius used for the calculation
:return: float
- reflections(self)
- Return list of reflections specified in the header
:return: list
- time(self)
- Returns the date and time the calculation was run on
:return: str
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
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class Density(builtins.object) |
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Density(file)
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Methods defined here:
- __init__(self, file)
- Load Density of states file from FDMNES calculations '..._sd0.txt'
:param file: filename
- __repr__(self)
- Return repr(self).
- plot(self)
- Creates a plot of the DOS spectra, with all d states in one plot
:return: None
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
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class Fdmnes(builtins.object) |
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Fdmnes(xtl=Crystal with 1 atomic positions, 1 symmetries)
FDMNES class: Create input files for the FDMNES software and run the program inside a python console
FDMNES (Finite Difference Method for Near Edge Structure) is an abinitio DFT program for
simulating x-ray absorption spectra and resonant diffraction.
FDMNES is developed by Yves Joly at CNRS and can be freely downloaded from here:
www.fdmnes.neel.cnrs.fr
In case of publication, please include the following citation:
O. Bunau and Y. Joly "Self-consistent aspects of x-ray absorption calculations"
J. Phys.: Condens. Matter 21, 345501 (2009)
This class creates a simple wrapper to automatically generate input files from Dans_Diffraction
Crystal structures. The output files from the calculation can also be automatically plotted.
E.G.
xtl = Crystal('Co.cif')
fdm = Fdmnes(xtl)
fdm.setup(folder_name='New_Calculation',
comment='Test',
absorber='Co',
edge='K'
azi_ref=[0,0,1],
hkl_reflections=[[1,0,0],[0,1,0],[1,1,0]]
fdm.create_files()
fdm.write_fdmfile()
fdm.run_fdmnes()
###Wait for program completion###
analysis = fdm.analyse()
print(analysis)
analysis.xanes.plot()
analysis.density.plot()
for ref in analysis:
ref.plot3D()
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Methods defined here:
- __init__(self, xtl=Crystal with 1 atomic positions, 1 symmetries)
- Initialize self. See help(type(self)) for accurate signature.
- __repr__(self)
- Return repr(self).
- __str__(self)
- Return str(self).
- analyse(self, folder_name=None)
- Analyse the completed calculation
:param folder_name: str name or directory of calculation (None to use current calculation)
:return: FdmnesAnalysis Object
- azimuthal_reference(self, hkl=(1, 0, 0))
- Generate the azimuthal reference
:param hkl: (1*3) array [h,k,l]
:return: None
- create_directory(self)
- Create a directory in the FDMNES/Sim folder
:return: None
- create_files(self, param_string=None)
- Create FDMNES calculation directory and files
- creates new directory
- writes the input file to that directory
:param param_string: str text to add to indata file (None will generate)
:return: None
- find_fdmnes_exe(self, initial_dir=None, fdmnes_filename='fdmnes_win64.exe', reset=False)
- Find fdmnes executable
- generate_input_path(self)
- Returns the input file pathname
E.G. 'c:\FDMNES\Sim\Fe2O3\FDMNES_Fe2O3.txt'
:return: filepath
- generate_output_path(self, folder_name=None, overwrite=False)
- Creates an automatic output path in the FDMNES/Sim directory
If overwrite is False and the directory already exists, a number will be appended to the name
:param folder_name: str or None, if None xtl.name will be used
:param overwrite: True/False
:return: str directory E.G. 'c:\FDMNES\Sim\Fe2O3'
- generate_parameters_string(self)
- Create the string of parameters and comments for the input file
:return: str
- info(self)
- Print setup info
:return: str
- run_fdmnes(self)
- Run the fdmnes code, waits until the program completes
Remember to use self.create_files and self.write_fdmfile first!
:return: subprocess.call output
- setup(self, exe_path=None, output_path=None, output_name=None, folder_name=None, input_name=None, comment=None, energy_range=None, radius=None, edge=None, absorber=None, green=None, scf=None, quadrupole=None, azi_ref=None, correct_azi=None, hkl_reflections=None)
- Set FDMNES Parameters
:param exe_path: Location of FDMNES executable, e.g. 'c:\FDMNES dmnes_win64.exe'
:param output_path: Specify the output path
:param folder_name: Specify output folder name (replaces output_path)
:param output_name: Name of FDMNES output files
:param input_name: Name of FDMNES input file
:param comment: A comment written in the input file
:param energy_range: str energy range in eV relative to Fermi energy
:param radius: calculation radius
:param edge: absorptin edge, 'K', 'L3', 'L2'
:param absorber: absorbing element, 'Co'
:param green: Green's function (muffin-tin potential)
:param scf: True/False, Self consistent solution
:param quadrupole: False/True, E1E2 terms allowed
:param azi_ref: azimuthal reference, [1,0,0]
:param correct_azi: if True, correct azimuthal reference for real cell (use in hexagonal systems)
:param hkl_reflections: list of hkl reflections [[1,0,0],[0,1,0]]
:return: None
- write_fdmfile(self, file_list=None)
- Create fdmfile with list of calculations
:param file_list: list of parameter file names for fdmfile, or None to only calculate current parameters
:return: None
- write_runfile(self, param_string=None)
- Write FDMNES input data to a file
:param param_string: str text to add to indata file (None will generate)
:return: None
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
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class FdmnesAnalysis(builtins.object) |
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FdmnesAnalysis(output_path, output_name='out', calc_name=None)
Create fdmnes object from *_scan_conv.txt file
Usage:
fdm = FdmnesAnalysis(output_path, output_name)
fdm contains all calculated reflections and xanes spectra, as well as spherical tensors
Automated plotting of azimuths, spectra and density of states.
fdm.xanes.plot()
fdm.density.plot()
fdm.I100sp.plot3D()
fdm.sph_I100sp.plot()
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Methods defined here:
- __add__(self, other)
- __getitem__(self, item)
- Return Reflection
- __init__(self, output_path, output_name='out', calc_name=None)
- Loads data from an FDMNES calculation, allowing plotting and data cuts
E.G.
fdm = FdmnesAnalysis('c:\FDMNES\Fe2O3','out')
fdm.xanes.plot()
plt.show()
:param output_path: directory of the calculation to be loaded
:param output_name: base output name for the calculation (default='out')
- __repr__(self)
- Return repr(self).
- __str__(self)
- Return str(self).
- info(self)
- Returns header of calculation output fipe (*_bav.txt)
:return: str
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
Data and other attributes defined here:
- angle = array([0])
- energy = array([0])
- refkeys = []
- reflections = {}
- reflist = []
- sphkeys = []
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class FdmnesCompare(builtins.object) |
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FdmnesCompare(fdm_objects)
Compare FDMNES Calculations
Method of joining sevearl FdmnesAnalysis objects to plot spectra on the same plot for comparison.
Usage:
fd1 = FdmnesAnalysis('calc_dir/calc1')
fd2 = FdmnesAnalysis('calc_dir/calc2')
fd3 = FdmnesAnalysis('calc_dir/calc3')
fdms = FdmnesCompare([fd1, fd2, fd3])
*or*
fdms = fd1 + fd2 + fd3
*or*
fdms = load_fdmnes_files('calc_dir') # loads all calculations ind calc_dir
fdms.plot_xanes()
fdms.plot_reflection_spectra('I003sp', 0) # specify azimuthal angle in deg
fdms.plot_reflection_azimuth('I003sp', 2838) # specify energy in eV
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Methods defined here:
- __add__(self, other)
- __init__(self, fdm_objects)
- Initialize self. See help(type(self)) for accurate signature.
- __repr__(self)
- Return repr(self).
- info(self)
- load(self, bav_files=())
- Load a series of calculation files
- plot_all_azimuth(self, energy=0, normalise=False, new_figure=True)
- Plot all available azimuths across calculations
:param energy: point at which to cut energy
:param normalise: normalise each spectra by max point
:return:
- plot_all_spectra(self, psi=0, normalise=False)
- Plot all available spectra across calculations
:param psi: azimuthal angle [Deg]
:param normalise: normalise each spectra by max point
:return:
- plot_reflection_azimuth(self, refkey, energy=0, normalise=False, new_figure=True)
- Plot all energy spectra for a reflection
:param refkey: str, reflection key as in name_conv.txt
:param energy: float, energy [eV]
:param normalise: normalise each spectra by max point
:param new_figure: create a new figure if True, otherwise plot on the current axis
:return: None
- plot_reflection_spectra(self, refkey, psi=0, normalise=False, new_figure=True)
- Plot all energy spectra for a reflection
:param refkey: str, reflection key as in name_conv.txt
:param psi: float, azimuthal angle
:param normalise: normalise each spectra by max point
:param new_figure: create a new figure if True, otherwise plot on the current axis
:return: None
- plot_xanes(self, normalise=False, new_figure=True)
- Plot XANES spectra for each calculation
:param normalise: normalise each spectra by max point
:param new_figure: create a new figure if True, otherwise plot on the current axis
:return: None
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
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class Reflection(builtins.object) |
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Reflection(energy, angle, intensity, refname, calc_name)
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Methods defined here:
- __init__(self, energy, angle, intensity, refname, calc_name)
- Container for FDMNES RXS calculations for each reflection
:param energy: array of energy values [1xm]
:param angle: array of angle values [1xn]
:param intensity: array of intensity values [mxn]
:param refname: reflection name, for plot title
:param calc_name: calculation name, for plot title
- __repr__(self)
- Return repr(self).
- azi_cut(self, cutenergy=None)
- Returns the array of intensitiy values at a particular energy
:param cutenergy: energy of cut (eV)
:return: array of intensities
- eng_cut(self, cutangle=None)
- Returns the array of intensitiy values at a particular angle
:param cutangle: angle of cut (deg)
:return: array of intensities
- plot3D(self)
- Generate a 3D figure of energy vs angle vs intensity
:return: None
- plot_azi(self, cutenergy='max')
- Generate a plot of azimuthal dependence at a particular energy
:param cutenergy: 'max' to use the maximum height energy, or an energy in eV
:return: None
- plot_eng(self, cutangle='max')
- Generate a plot of energy dependence at a particular azimuth
:param cutangle: 'max' to use the maximum intensity height angle, or an angle in deg
:return: None
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
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class Spherical(builtins.object) |
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Spherical(data, refname, calc_name)
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Methods defined here:
- __init__(self, data, refname, calc_name)
- Load contribution from spherical harmonics from out_sph_signal_rxs1.txt
:param data: data array from read_spherical()
:param refname: reflection name for plot title
:param calc_name: calculation name for plot title
- __repr__(self)
- Return repr(self).
- plot(self)
- Plot the spherical components
:return: None
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
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class Xanes(builtins.object) |
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Xanes(energy, intensity, calc_name)
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Methods defined here:
- __init__(self, energy, intensity, calc_name)
- Container for XANES spectra from FDMNES
:param energy: array of energy values
:param intensity: array of intensity values
:param calc_name: calculation name for plot title
- __repr__(self)
- Return repr(self).
- plot(self)
- Plot the Xanes spectra
:return: None
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
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