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README.txt
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README.txt
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!%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
!
! Felix
!
! Richard Beanland, Keith Evans & Rudolf A Roemer
!
! (C) 2013-17, all rights reserved
!
! Version: :VERSION:
! Date: :DATE:
! Time: :TIME:
! Status: :RLSTATUS:
! Build: :BUILD:
! Author: :AUTHOR:
!
!%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
!
! Felix is free software: you can redistribute it and/or modify
! it under the terms of the GNU General Public License as published by
! the Free Software Foundation, either version 3 of the License, or
! (at your option) any later version.
!
! Felix is distributed in the hope that it will be useful,
! but WITHOUT ANY WARRANTY; without even the implied warranty of
! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
! GNU General Public License for more details.
!
! You should have received a copy of the GNU General Public License
! along with Felix. If not, see <http://www.gnu.org/licenses/>.
!
!%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
!
! Contributors: Alex Hubert, Jacob Richardson
!
!%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
README.txt file for felixsim bloch wave method diffraction pattern simulation software.
Input File:
IWriteFlag: Controls the amount of information printed to the screen or
logfile during simulation, values 0-11 increase amount with 0 resulting in no
information being printed appart from start and stop messages. More output
allows for easier debugging but will slow the execution.
IImageFLAG: Determines what images will be produced by the software :
0 Montages of Diffraction patterns one per thickness in .bin file format
1 Individual reflections saved in .bin file format, Reflections
will be bundled into seperate folders for each thickness.
2 Amplitude and phase images will be saved, phase and
amplitude images will be saved individually for each reflection and labelled
-A or -P respectively
Any combination (in any order) of up to three of these options can be specified to suit the users requirements
IOutputFLAG: Determines the amount of calculated Variables which are saved
for later use by felixdraw.
0 Nothing is saved (Fastest)
1 Ug Matrix will be saved in binary format
2 Eigenspectra is saved in binary format
3 Wavefunctions are saved in binary format
Any combination (in any order) of up to three of these options can be specified to suit the users requirements
IBinorTextFLAG: Select binary or text output files, binary are smaller and faster to read/write however text files are easier to import into other programs for later use
0 Binary
1 Text
IScatteringFactorMethod: Determines which method by which to calculate potentials
0 Kirkands Method (103 Elements)
1 Peng (98 Elements)
2 Doyle and Turner (only works for 68 elements)
IZolzFLAG: Choose to limit the simulation to the zeroth order laue zone.
0 No (Includes HOLZ, slower)
1 Yes (ZOLZ only, faster)
ICentralBeamFlag: Exclude the [000] beam from the final images which improves
relative intensity
0 No central beam
1 Central beam included
IMaskFLAG: Chooses between a circular or square input beam
0 Circular
1 Square
IAbsorbFLAG: Choose to include absorption in simulation
0 no
1 Proportional Model
2 Einstein Model (Perturbative approach)
3 Einstein Model (Exact Approach)
IAnisotropicDebyeWallerFLAG: Choose to use anisotropic debye waller factors if
available
0 no
1 yes
IBeamConvergence: Not Yet Implemented
IPseudoCubicFLAG: Indicate whether given directions are expressed in PseudoCubic
or Orthorhombic notation
0 Orthorhomnic
1 PseudoCubic
IXDirectionFLAG : If set to 0 the program will ignore any specified X Direction and take the shortest G Vector as the X direction
0 Ignore X Direction
1 Use X Direction
IPixelCount: Pixel Radius of images, simulation scales as the square of this
number but primary parallelisation is over pixels (more pixels, more cores
can be used effectively) 64 is a good for images, 128+ better for
quantitative analysis
IMinReflectionPool : Controls the size of the reflection pool accessible
during diagonalisation
IMinStrongBeams : This paramater sets the minimum number of beams overwhich the
diagonisation is preformed, increasing it will result in greater accuracy
but will slow simultion
IMinWeakBeams: Minimum number of weak beams with which to perturb the Strong beams
RBSBmax : Maximum weak beam purturbation strength before the beam is
considered strong
RBSPmax : Maximum weak beam purturbation of a prior weak beam
RConvergenceTolerance (%) : Not yet implemented
RDebyeWallerConstant: If no Debye waller factor is found in the .cif
file this value will be used for all atomic species missing the factor, note
this is the B factor not U
RAbsorptionPer: Defines the percentage of absorption applied to the
potentials when using the propotional model, this values is used for all atomic species
RConvergenceAngle: Defines the convergence angle of the beam in units of half
the minimum gvector magnitude, at a value of 1 all beams will touch at
tjtheir edges, values greater than 1 would (experimentally) cause beams to
overlap, in the simulation this will not occur
IIncidentBeamDirectionX: X Component of the incident beam direction (Zone
axis) expressed in the crystal reference frame in real space
IIncidentBeamDirectionY: Y Component of the incident beam direction (Zone
axis) expressed in the crystal reference frame in real space
IIncidentBeamDirectionZ: Z Component of the incident beam direction (Zone
axis) expressed in the crystal reference frame in real space
IXDirectionX: X component of the chosen X-axis expressed in the crystal
reference frame in reciprocal space
IXDirectionY: Y component of the chosen X-axis expressed in the crystal
reference frame in reciprocal space
IXDirectionZ: Z component of the chosen X-axis expressed in the crystal
reference frame in reciprocal space
INormalDirectionX: X component of the plane normal to the surface of crystal
in real space
INormalDirectionY: Y component of the plane normal to the surface of crystal
in real space
INormalDirectionZ: Z component of the plane normal to the surface of crystal
in real space
RAccelerationVoltage: Acceleration voltage of the microscope expressed in KV
RInitialThickness: Lower bound thickness to be applied (Angstroms)
RFinalThickness: Upper Bound Thickness to be Appliced (Angstroms)
RDeltaThickness: Step between thickness (Angstroms)
IReflectOut: The number of the reflections to be included in the final
image(s)
The Remainder of the options apply to FelixRefine only
IImageOutputFLAG: Choose whether FelixRefine will output images at the conclusion of the refinement
0 No
1 Yes
IDevFLAG: Unused awaiting Removal
IRefineModeFLAG: Choose the refinement variable(s)
0 Refine Debye-waller Factor
1 Refine Structure Factors (UGs)
2 Refine Thickness
This options