pdielec - PDielec Version 8.2.0 Powder and Single Crystal Infrared Calculations

The Python package PDielec calculates the infrared and terahertz absorption characteristics of crystalline materials by post-processing the output of solid-state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. For crystalline samples (thin films or thick slabs) the program use generalized transfer and scattering matrix approaches to calculate the transmission, absorption and reflection. For powdered systems, the package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach for small crystallites is published in the Journal of Computational Chemistry, DOI: 10.1002/jcc.24344 .

Changes in version 8.2.0 A -threads or --threads option has been added to pdgui. Added QT6 support by including the qtpy module Changed the use of scipy.interpolate.trapz to np.trapz Introduced a pyproject.toml file Added version number to the pyproject.toml file and modified the setup.py file accordingly Removed setup.cfg file. setup.py no longer sets the version number. Updated the requirements.txt file using pipreq Updated the condainstalls.txt file Removed the need for the mkl package. But this means the number of processors used for threading is set by the environment variables. It is best to NOT use threading and have the number of processors set to the number of cores. The number of threads used by each core should be 1. To force the BLAS routines to use threads it is best to use environment variables to control the The exporting of these variables is now performed automatically at runtime from App.py, before numpy is loaded pdmake.py has been modified to allow -cpus and -threads to be passed to pdgui during benchmarking Added additional escape characters to pdmake.py - to remove SyntaxWarning errors Added additional escape characters to Mie.py - to remove SyntaxWarning errors Added additional escape characters to CastepOutputReader.py - to remove SyntaxWarning errors Added additional escape characters to CrystalOutputReader.py - to remove SyntaxWarning errors Added a -style default in the creation of the App. Default style is "fusion" Fixed a bug in the save cif file (ViewerTab) Added xml readers to VaspOutputReader and QEOutputReader Added a new example to QE/Urea which tests the xml reader Added a new example to Vasp/Urea which test the xml reader GenericOutputReader: Created a new routine to find the frequencies and normal modes from the mass-weighted hessian QEOutputReader: Added a code to read pwscf.xml and tensors.xml PhonopyOutputReader: PDGui now reads the conversion factor store by Phonopy to scale the Hessian Utilities: Altered the logic in the "findprogramfromroutine". The routine now recognises pwscf.xml and vasprun.xml files. If an OUTCAR (Vasp) or a QE .log/.out is specified on the command line the old method of analysing the output is used and the xml files are not read. If vasprun.xml (Vasp) or a .dynG file is given on the command line then the xml will be read if it is there. Changed the GTMCore.py use of clongdouble to cdouble. Added a .nojekyll file into the docs/ directory to stop git hub pages over processing things Changed the name PDielec to pdielec in setup.py to help with Windows install on conda-forge Changed the findprogramfrom_name() function to return (program,qmprogram). Affected routines are; - Utilities.py, HelperRoutines.py p1reader.py, preader.py, vibanalysis,py, App.py, NoteBook.py, - MainTab.py, p2cif.py. - Also changes in Helper/ and Jupyter/ Example directories. Removed the slicing capability as it is no longer needed Added new code for handling Phonopy DFT programs other than Vasp The materials database is now cached to improve performance The materials database is now kept open, instead of repeated opening and closing Added support for AbInit v10 files, changed the AlAs abinit example to a version 10 example Added support for Crystal 23: modified file extension handling to include .log as a crystal output file. - Added a Crystal23 example in Examples/Crystal/Quartz - Added an AbInit 10.0 example in Examples/Abinit/AlAs - Added an QE 7.3.1 example in Examples/QE/Na2SO42-v7 - Added support for Phonopy-Crystal calculations: example in Examples/Phonopy/Crystal Revamped the README.md files in the Examples directories Modified the jupyter lab notebooks to use os.path.join for all directory access Removed linked directories in Examples/Helper/Jupyter/..

Changes in version 8.1.1 The documentation has been revamped. An API description is now generated from each class and routine. The examples of Jupyter notebooks has been added to. Static routines have been created in the FitterTab to allow their use in notebooks The UnitCell and SuperCell classes have been enhance to use a units specifier Added new routines to the Materials and DielectricFunction classes to allow sigmas, oscillator strengths and frequencies to be changed The write_cif() routine in UnitCell has been modified slightly to allow files to be written Update of setup.py to reflect deprecation of naming of sklearn Development of helper functions to aid future use of notebooks

Changes in version 8.1.0 Modifications to the plotter tab to allow the use of wavelength and frequency units Redesign of the single crystal scenario tab. The new design means that scripts are not backwards compatible. The method of calculation for single crystals can now be 'Transfer matrix' or 'Scattering matrix' The default method is 'Scattering matrix' Other changes to the Single Crystal options:

Thick slab is now an option for an individual layer and has been termed 'Incoherent (non-reflective)' Other incoherent options have been added for a layer, using either intensities or phase matching the pygtm module has been modified so that subclasses are used for coherent and incoherent layers and 'Transfer matrix' and 'Scattering matrix' classes are subclasses of the pygtm 'System' class removed the need to have specific super- and sub-strate entries in the singleCrystalTab superstrate is the top of the material list and substrate is at the bottom. the old 'Thick slab' option is still available if the dielectric layer is the last in the list of materials Updated the progress bar algorithms Fixed a bug in the specification of the support matrix for the powder case Fixed a bug in the reporting of absorptance, s- and p- were reported the wrong way round Fixed a bug in the powder scenario tab, the super- and sub-matrix dielectric functions, were not being set properly for frequency dependent permittivities Fixed a bug in the plotting tab when writing to the spread-sheet a scalar permittivity The option to use slicing has been removed The option to do partial incoherence has been removed from the GUI but left in the code There are compatibility issues with the previous version, so some scripts may not be compatible.

- Python
Published by JohnKendrick over 1 year ago

pdielec - PDielec Version 8.1.1

PDielec Version 8.1.1 - Powder and Single Crystal Infrared Calculations

The Python package PDielec calculates the infrared and terahertz absorption characteristics of crystalline materials by post-processing the output of solid-state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. For crystalline samples (thin films or thick slabs) the program use generalized transfer and scattering matrix approaches to calculate the transmission, absorption and reflection. For powdered systems, the package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach for small crystallites is published in the Journal of Computational Chemistry, DOI: 10.1002/jcc.24344 .

Changes in version 8.1.1 The documentation has been revamped. An API description is now generated from each class and routine. The examples of Jupyter notebooks has been added to. Static routines have been created in the FitterTab to allow their use in notebooks The UnitCell and SuperCell classes have been enhance to use a units specifier Added new routines to the Materials and DielectricFunction classes to allow sigmas, oscillator strengths and frequencies to be changed The write_cif() routine in UnitCell has been modified slightly to allow files to be written Update of setup.py to reflect deprecation of naming of sklearn Development of helper functions to aid future use of notebooks

Changes in version 8.1.0 Modifications to the plotter tab to allow the use of wavelength and frequency units Redesign of the single crystal scenario tab. The new design means that scripts are not backwards compatible. The method of calculation for single crystals can now be 'Transfer matrix' or 'Scattering matrix' The default method is 'Scattering matrix' Other changes to the Single Crystal options:

Thick slab is now an option for an individual layer and has been termed 'Incoherent (non-reflective)' Other incoherent options have been added for a layer, using either intensities or phase matching the pygtm module has been modified so that subclasses are used for coherent and incoherent layers and 'Transfer matrix' and 'Scattering matrix' classes are subclasses of the pygtm 'System' class removed the need to have specific super- and sub-strate entries in the singleCrystalTab superstrate is the top of the material list and substrate is at the bottom. the old 'Thick slab' option is still available if the dielectric layer is the last in the list of materials Updated the progress bar algorithms Fixed a bug in the specification of the support matrix for the powder case Fixed a bug in the reporting of absorptance, s- and p- were reported the wrong way round Fixed a bug in the powder scenario tab, the super- and sub-matrix dielectric functions, were not being set properly for frequency dependent permittivities Fixed a bug in the plotting tab when writing to the spread-sheet a scalar permittivity The option to use slicing has been removed The option to do partial incoherence has been removed from the GUI but left in the code There are compatibility issues with the previous version, so some scripts may not be compatible.

- Python
Published by ADBurnett almost 2 years ago

pdielec - PDielec Version 8.1.0 - Powder and Single Crystal Infrared Calculations

The Python package PDielec calculates the infrared and terahertz absorption characteristics of crystalline materials by post-processing the output of solid-state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. For crystalline samples (thin films or thick slabs) the program use generalized transfer and scattering matrix approaches to calculate the transmission, absorption and reflection. For powdered systems, the package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach for small crystallites is published in the Journal of Computational Chemistry, DOI: 10.1002/jcc.24344 .

Changes in version 8.1.0 Modifications to the plotter tab to allow the use of wavelength and frequency units Redesign of the single crystal scenario tab. The new design means that scripts are not backwards compatible. The method of calculation for single crystals can now be 'Transfer matrix' or 'Scattering matrix' The default method is 'Scattering matrix' Other changes to the Single Crystal options: - Thick slab is now an option for an individual layer and has been termed 'Incoherent (non-reflective)' - Other incoherent options have been added for a layer, using either intensities or phase matching - the pygtm module has been modified so that subclasses are used for coherent and incoherent layers and 'Transfer matrix' and 'Scattering matrix' classes are subclasses of the pygtm 'System' class - removed the need to have specific super- and sub-strate entries in the singleCrystalTab superstrate is the top of the material list and substrate is at the bottom. - the old 'Thick slab' option is still available if the dielectric layer is the last in the list of materials Updated the progress bar algorithms Fixed a bug in the specification of the support matrix for the powder case Fixed a bug in the reporting of absorptance, s- and p- were reported the wrong way round Fixed a bug in the powder scenario tab, the super- and sub-matrix dielectric functions, were not being set properly for frequency dependent permittivities Fixed a bug in the plotting tab when writing to the spread-sheet a scalar permittivity The option to use slicing has been removed The option to do partial incoherence has been removed from the GUI but left in the code There are compatibility issues with the previous version, so some scripts may not be compatible.

- Python
Published by JohnKendrick about 2 years ago

pdielec - Version 8.0.0

PDielec Version 8.0.0 - Powder and Single Crystal Infrared Calculations Latest

The Python package PDielec calculates the infrared and terahertz absorption characteristics of crystalline materials by post-processing the output of solid-state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. For crystalline samples (thin films or thick slabs) the program uses a generalized transfer matrix approach to calculate the transmission, absorption and reflection. For powdered systems, the package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach for small crystallites is published in the Journal of Computational Chemistry, DOI: 10.1002/jcc.24344 .

version 8.0.0 - Introduced various changes to handle the difference between Windows and Linux. The mainTab settings now has a compatibility mode option which can be 'Linux' or 'Windows' - Modified the AlN test case to use Windows compatibility mode - Added a slicing option in the single crystal case to address issues with exponential overflow - Added frequency-dependent support matrix capability to the powder simulation - Added complex permittivity to the support matrix - Added incoherent light to the single-crystal simulation - Added both partially incoherent thin film mode and incoherent thin film mode - Included smoothing for the partially incoherent case - Modified the handling of changing the legend in a scenario so a recalculation is not needed - Updated the documentation to reflect the new options for incoherent light - Added a range of units to handle crystal thickness - Changed the complex matrices in pyGTM to clongdouble - Modified pyGTM to improve its numerical stability - Added the concept of slicing to the single-crystal scenario, again attempting to improve numerical stability - Modified the reading of scripts as updates to Python seem to have changed the exec() command, now read the whole file at once. - Added the concept of layers in the single-crystal scenarios. This allows multiple layers to be treated between the superstrate and substrate - Added a materials library which can be used to store material properties - The materials library can be used for powder and single-crystal calculations - There are compatibility issues with the previous version, so some scripts may not be compatible.

- Python
Published by JohnKendrick over 2 years ago

pdielec - PDielec Release Version 7.2.2

PDielec Version 7.2.2 - Powder and Single Crystal Infrared Calculations Latest

The Python package PDielec calculates the infrared and terahertz absorption characteristics of crystalline materials by post processing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. For crystalline samples (thin films or thick slabs) the program uses a generalized transfer matrix approach to calculate the transmission, absorption and reflection. For powdered systems, the package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach for small crystallites is published in Journal of Computational Chemistry, DOI: 10.1002/jcc.24344 .

Version 7.2.2/7.2.1 Changes to accommodate some numpy deprecated syntax

version 7.1.1 Release of a new testing suite

version 7.0.2 Bug fix - when executing a script chdir to the directory of the script

version 7.0.1 Added a single crystal tab to show transmission and reflectance at a single crystal surface The method used is that described by Passler et al Rewrote the calculation of dielectric permittivity so that it would be much more general. There is now a class which looks after dielectric permittivity information The sign convention for the imaginary component of the permittivity has changed - e(real)-e(imag)j Moved the CrystalPermittivity to the SettingsTab Modified the scripting, scripts written before version 7 may not work. Modified the way masses are handled, so if the gui modifies the masses they are written out to the script. Changed the communication between tabs, it was completed before and it still is unfortunately Stopped setting the requestRefresh variable directly - now use a subroutine to do it. Added a lot of debugging information to the tabs so it is much clearer what the flow is through the code Two new input file type has been added 'experimental' and 'pdgui'. 'experimental' allows an experimental dieletric to be specified this includes a lorentz type spectrum 'pdgui' allows a script to be read in and executed 'experimental' and 'pdgui'. The mainTab gui no longer needs to have specified the 'program' name (eg. castep, or vasp). This is determined from the name of the file. Added a new example of using the fitter and the fitting tab Revised all the documentation Added the Mie module from PyMieScatt as there were some issues about crossover Major changes to the parallel methods used by the code. Now using 'partial' from functools also removed sending the whole crystal_permittivity array at once. also create the pool in the notebook and keep reusing it. also switch back to multiprocessing MKL threads are no longer changed by the code

version 6.4.5 Fixed a couple of problems when switching molecule using the GUI. The sigmas array and the mode fitting flags are now reset when a new molecule/crystal is read in. Modified the ViewerTab to display super-cells Added a new VibAnalysis module based on the work of filipe teixeira https://github.com/teixeirafilipe/vibAnalysis Example output in Examples/Castep/AsparticAcid/phonon.nm (generated with 'vibanalysis phonon) Examples/Vasp/Na2SO42/OUTCAR.nma (generated with 'vibanalysis OUTCAR) Added sklearn to the list of required packages

version 6.4.4 (Internal release only) Added an option in viewerTab to write the vibrating molecule as a cif file. Modified the cif output format so it is more like that of Mercury Introduced psutil.cpucount as this will give the number of physical processors Switched the multiprocessing module to the multiprocess module (pickling is better) Overrode the mkl environment variable for the number of threads. PDgui now uses mkl threading, unless it is in multiprocessing mode. Used dill for the pickling itself. In preader added an option to pickle each of the readers that are created and store them in a file Added a script, pickledreader which can read the pickled file. The script is just an example of how the readers can be read in and the contents accessed. Modified UnitCell.py to use print_info instead of printInfo New set of pyhton packages are needed for the above; dill,multiprocess,psutil Added new test for p2cif Removed redundant imports from all files

version 6.4.3 Modified p2cif so that it becomes a windows executable Modified p2cif and preader to be more robust when reading phonopy output Re-introduced fitting the frequency scaling in the fitter tab

version 6.4.2 Modified the plotting in fitter so that scaling is always applied Removed the tick box in the Fitter tab that switches scaling on/off Only store the optical permittivity in a script if it has been altered in the GUI This means that older scripts will not be compatible with the newer defaults.

version 6.4.1 Fixed a packaging problem on pypi and conda-forge No changes to source code

version 6.4.0 Removed the imageio-ffmpeg download code added pip install dependence instead Updated the installation instructions on the documentation to reflect conda-forge installation Added environment variables to control threading and number of cpus Made the refractiveindexmedium variable real (not complex) to remove the warning message from PyMieScatt

Assets 2 Source code (zip) Source code (tar.gz) 05 Dec 2021 @JohnKendrick JohnKendrick v7.0.1 https://github.com/JohnKendrick/PDielec/commit/d77f934c0f35aa51faf64135a7e2352676e95d2f PDielec Version 7.0.1 - Powder and Single Crystal Infrared Calculations The Python package PDielec calculates the infrared and terahertz absorption characteristics of crystalline materials by post processing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. For crystalline samples (thin films or thick slabs) the program uses a generalized transfer matrix approach to calculate the transmission, absorption and reflection. For powdered systems, the package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach for small crystallites is published in Journal of Computational Chemistry, DOI: 10.1002/jcc.24344 .

version 7.0.1 Added a single crystal tab to show transmission and reflectance at a single crystal surface The method used is that described by Passler et al Rewrote the calculation of dielectric permittivity so that it would be much more general. There is now a class which looks after dielectric permittivity information The sign convention for the imaginary component of the permittivity has changed - e(real)-e(imag)j Moved the CrystalPermittivity to the SettingsTab Modified the scripting, scripts written before version 7 may not work. Modified the way masses are handled, so if the gui modifies the masses they are written out to the script. Changed the communication between tabs, it was completed before and it still is unfortunately Stopped setting the requestRefresh variable directly - now use a subroutine to do it. Added a lot of debugging information to the tabs so it is much clearer what the flow is through the code Two new input file type has been added 'experimental' and 'pdgui'. 'experimental' allows an experimental dieletric to be specified this includes a lorentz type spectrum 'pdgui' allows a script to be read in and executed 'experimental' and 'pdgui'. The mainTab gui no longer needs to have specified the 'program' name (eg. castep, or vasp). This is determined from the name of the file. Added a new example of using the fitter and the fitting tab Revised all the documentation Added the Mie module from PyMieScatt as there were some issues about crossover Major changes to the parallel methods used by the code. Now using 'partial' from functools also removed sending the whole crystal_permittivity array at once. also create the pool in the notebook and keep reusing it. also switch back to multiprocessing MKL threads are no longer changed by the code

version 6.4.5 Fixed a couple of problems when switching molecule using the GUI. The sigmas array and the mode fitting flags are now reset when a new molecule/crystal is read in. Modified the ViewerTab to display super-cells Added a new VibAnalysis module based on the work of filipe teixeira https://github.com/teixeirafilipe/vibAnalysis Example output in Examples/Castep/AsparticAcid/phonon.nm (generated with 'vibanalysis phonon) Examples/Vasp/Na2SO42/OUTCAR.nma (generated with 'vibanalysis OUTCAR) Added sklearn to the list of required packages

version 6.4.4 (Internal release only) Added an option in viewerTab to write the vibrating molecule as a cif file. Modified the cif output format so it is more like that of Mercury Introduced psutil.cpucount as this will give the number of physical processors Switched the multiprocessing module to the multiprocess module (pickling is better) Overrode the mkl environment variable for the number of threads. PDgui now uses mkl threading, unless it is in multiprocessing mode. Used dill for the pickling itself. In preader added an option to pickle each of the readers that are created and store them in a file Added a script, pickledreader which can read the pickled file. The script is just an example of how the readers can be read in and the contents accessed. Modified UnitCell.py to use print_info instead of printInfo New set of pyhton packages are needed for the above; dill,multiprocess,psutil Added new test for p2cif Removed redundant imports from all files

version 6.4.3 Modified p2cif so that it becomes a windows executable Modified p2cif and preader to be more robust when reading phonopy output Re-introduced fitting the frequency scaling in the fitter tab

- Python
Published by JohnKendrick almost 3 years ago

pdielec - PDielec Version 7.1.1 - Powder and Single Crystal Infrared Calculations

The Python package PDielec calculates the infrared and terahertz absorption characteristics of crystalline materials by post processing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. For crystalline samples (thin films or thick slabs) the program uses a generalized transfer matrix approach to calculate the transmission, absorption and reflection. For powdered systems, the package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach for small crystallites is published in Journal of Computational Chemistry, DOI: 10.1002/jcc.24344 .

version 7.1.1 Release of a new testing suite

version 7.0.2 Bug fix - when executing a script chdir to the directory of the script

version 7.0.1 Added a single crystal tab to show transmission and reflectance at a single crystal surface The method used is that described by Passler et al Rewrote the calculation of dielectric permittivity so that it would be much more general. There is now a class which looks after dielectric permittivity information The sign convention for the imaginary component of the permittivity has changed - e(real)-e(imag)j Moved the CrystalPermittivity to the SettingsTab Modified the scripting, scripts written before version 7 may not work. Modified the way masses are handled, so if the gui modifies the masses they are written out to the script. Changed the communication between tabs, it was completed before and it still is unfortunately Stopped setting the requestRefresh variable directly - now use a subroutine to do it. Added a lot of debugging information to the tabs so it is much clearer what the flow is through the code Two new input file type has been added 'experimental' and 'pdgui'. 'experimental' allows an experimental dieletric to be specified this includes a lorentz type spectrum 'pdgui' allows a script to be read in and executed 'experimental' and 'pdgui'. The mainTab gui no longer needs to have specified the 'program' name (eg. castep, or vasp). This is determined from the name of the file. Added a new example of using the fitter and the fitting tab Revised all the documentation Added the Mie module from PyMieScatt as there were some issues about crossover Major changes to the parallel methods used by the code. Now using 'partial' from functools also removed sending the whole crystal_permittivity array at once. also create the pool in the notebook and keep reusing it. also switch back to multiprocessing MKL threads are no longer changed by the code

version 6.4.5 Fixed a couple of problems when switching molecule using the GUI. The sigmas array and the mode fitting flags are now reset when a new molecule/crystal is read in. Modified the ViewerTab to display super-cells Added a new VibAnalysis module based on the work of filipe teixeira https://github.com/teixeirafilipe/vibAnalysis Example output in Examples/Castep/AsparticAcid/phonon.nm (generated with 'vibanalysis phonon) Examples/Vasp/Na2SO42/OUTCAR.nma (generated with 'vibanalysis OUTCAR) Added sklearn to the list of required packages

version 6.4.4 (Internal release only) Added an option in viewerTab to write the vibrating molecule as a cif file. Modified the cif output format so it is more like that of Mercury Introduced psutil.cpucount as this will give the number of physical processors Switched the multiprocessing module to the multiprocess module (pickling is better) Overrode the mkl environment variable for the number of threads. PDgui now uses mkl threading, unless it is in multiprocessing mode. Used dill for the pickling itself. In preader added an option to pickle each of the readers that are created and store them in a file Added a script, pickledreader which can read the pickled file. The script is just an example of how the readers can be read in and the contents accessed. Modified UnitCell.py to use print_info instead of printInfo New set of pyhton packages are needed for the above; dill,multiprocess,psutil Added new test for p2cif Removed redundant imports from all files

version 6.4.3 Modified p2cif so that it becomes a windows executable Modified p2cif and preader to be more robust when reading phonopy output Re-introduced fitting the frequency scaling in the fitter tab

version 6.4.2 Modified the plotting in fitter so that scaling is always applied Removed the tick box in the Fitter tab that switches scaling on/off Only store the optical permittivity in a script if it has been altered in the GUI This means that older scripts will not be compatible with the newer defaults.

version 6.4.1 Fixed a packaging problem on pypi and conda-forge No changes to source code

version 6.4.0 Removed the imageio-ffmpeg download code added pip install dependence instead Updated the installation instructions on the documentation to reflect conda-forge installation Added environment variables to control threading and number of cpus Made the refractiveindexmedium variable real (not complex) to remove the warning message from PyMieScatt

Assets 2 Source code (zip) Source code (tar.gz) 05 Dec 2021 @JohnKendrick JohnKendrick v7.0.1 d77f934 PDielec Version 7.0.1 - Powder and Single Crystal Infrared Calculations The Python package PDielec calculates the infrared and terahertz absorption characteristics of crystalline materials by post processing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. For crystalline samples (thin films or thick slabs) the program uses a generalized transfer matrix approach to calculate the transmission, absorption and reflection. For powdered systems, the package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach for small crystallites is published in Journal of Computational Chemistry, DOI: 10.1002/jcc.24344 .

version 7.0.1 Added a single crystal tab to show transmission and reflectance at a single crystal surface The method used is that described by Passler et al Rewrote the calculation of dielectric permittivity so that it would be much more general. There is now a class which looks after dielectric permittivity information The sign convention for the imaginary component of the permittivity has changed - e(real)-e(imag)j Moved the CrystalPermittivity to the SettingsTab Modified the scripting, scripts written before version 7 may not work. Modified the way masses are handled, so if the gui modifies the masses they are written out to the script. Changed the communication between tabs, it was completed before and it still is unfortunately Stopped setting the requestRefresh variable directly - now use a subroutine to do it. Added a lot of debugging information to the tabs so it is much clearer what the flow is through the code Two new input file type has been added 'experimental' and 'pdgui'. 'experimental' allows an experimental dieletric to be specified this includes a lorentz type spectrum 'pdgui' allows a script to be read in and executed 'experimental' and 'pdgui'. The mainTab gui no longer needs to have specified the 'program' name (eg. castep, or vasp). This is determined from the name of the file. Added a new example of using the fitter and the fitting tab Revised all the documentation Added the Mie module from PyMieScatt as there were some issues about crossover Major changes to the parallel methods used by the code. Now using 'partial' from functools also removed sending the whole crystal_permittivity array at once. also create the pool in the notebook and keep reusing it. also switch back to multiprocessing MKL threads are no longer changed by the code

version 6.4.5 Fixed a couple of problems when switching molecule using the GUI. The sigmas array and the mode fitting flags are now reset when a new molecule/crystal is read in. Modified the ViewerTab to display super-cells Added a new VibAnalysis module based on the work of filipe teixeira https://github.com/teixeirafilipe/vibAnalysis Example output in Examples/Castep/AsparticAcid/phonon.nm (generated with 'vibanalysis phonon) Examples/Vasp/Na2SO42/OUTCAR.nma (generated with 'vibanalysis OUTCAR) Added sklearn to the list of required packages

version 6.4.4 (Internal release only) Added an option in viewerTab to write the vibrating molecule as a cif file. Modified the cif output format so it is more like that of Mercury Introduced psutil.cpucount as this will give the number of physical processors Switched the multiprocessing module to the multiprocess module (pickling is better) Overrode the mkl environment variable for the number of threads. PDgui now uses mkl threading, unless it is in multiprocessing mode. Used dill for the pickling itself. In preader added an option to pickle each of the readers that are created and store them in a file Added a script, pickledreader which can read the pickled file. The script is just an example of how the readers can be read in and the contents accessed. Modified UnitCell.py to use print_info instead of printInfo New set of pyhton packages are needed for the above; dill,multiprocess,psutil Added new test for p2cif Removed redundant imports from all files

version 6.4.3 Modified p2cif so that it becomes a windows executable Modified p2cif and preader to be more robust when reading phonopy output Re-introduced fitting the frequency scaling in the fitter tab

version 6.4.2 Modified the plotting in fitter so that scaling is always applied Removed the tick box in the Fitter tab that switches scaling on/off Only store the optical permittivity in a script if it has been altered in the GUI This means that older scripts will not be compatible with the newer defaults.

version 6.4.1 Fixed a packaging problem on pypi and conda-forge No changes to source code

version 6.4.0 Removed the imageio-ffmpeg download code added pip install dependence instead Updated the installation instructions on the documentation to reflect conda-forge installation Added environment variables to control threading and number of cpus Made the refractiveindexmedium variable real (not complex) to remove the warning message from PyMieScatt

- Python
Published by JohnKendrick about 4 years ago

pdielec - PDielec Version 7.0.2 - Powder and Single Crystal Infrared Calculations

The Python package PDielec calculates the infrared and terahertz absorption characteristics of crystalline materials by post processing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. For crystalline samples (thin films or thick slabs) the program uses a generalized transfer matrix approach to calculate the transmission, absorption and reflection. For powdered systems, the package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach for small crystallites is published in Journal of Computational Chemistry, DOI: 10.1002/jcc.24344 .

version 7.0.2 Bug fix - when executing a script chdir to the directory of the script

version 7.0.1 Added a single crystal tab to show transmission and reflectance at a single crystal surface The method used is that described by Passler et al Rewrote the calculation of dielectric permittivity so that it would be much more general. There is now a class which looks after dielectric permittivity information The sign convention for the imaginary component of the permittivity has changed - e(real)-e(imag)j Moved the CrystalPermittivity to the SettingsTab Modified the scripting, scripts written before version 7 may not work. Modified the way masses are handled, so if the gui modifies the masses they are written out to the script. Changed the communication between tabs, it was completed before and it still is unfortunately Stopped setting the requestRefresh variable directly - now use a subroutine to do it. Added a lot of debugging information to the tabs so it is much clearer what the flow is through the code Two new input file type has been added 'experimental' and 'pdgui'. 'experimental' allows an experimental dieletric to be specified this includes a lorentz type spectrum 'pdgui' allows a script to be read in and executed 'experimental' and 'pdgui'. The mainTab gui no longer needs to have specified the 'program' name (eg. castep, or vasp). This is determined from the name of the file. Added a new example of using the fitter and the fitting tab Revised all the documentation Added the Mie module from PyMieScatt as there were some issues about crossover Major changes to the parallel methods used by the code. Now using 'partial' from functools also removed sending the whole crystal_permittivity array at once. also create the pool in the notebook and keep reusing it. also switch back to multiprocessing MKL threads are no longer changed by the code

version 6.4.5 Fixed a couple of problems when switching molecule using the GUI. The sigmas array and the mode fitting flags are now reset when a new molecule/crystal is read in. Modified the ViewerTab to display super-cells Added a new VibAnalysis module based on the work of filipe teixeira https://github.com/teixeirafilipe/vibAnalysis Example output in Examples/Castep/AsparticAcid/phonon.nm (generated with 'vibanalysis phonon) Examples/Vasp/Na2SO42/OUTCAR.nma (generated with 'vibanalysis OUTCAR) Added sklearn to the list of required packages

version 6.4.4 (Internal release only) Added an option in viewerTab to write the vibrating molecule as a cif file. Modified the cif output format so it is more like that of Mercury Introduced psutil.cpucount as this will give the number of physical processors Switched the multiprocessing module to the multiprocess module (pickling is better) Overrode the mkl environment variable for the number of threads. PDgui now uses mkl threading, unless it is in multiprocessing mode. Used dill for the pickling itself. In preader added an option to pickle each of the readers that are created and store them in a file Added a script, pickledreader which can read the pickled file. The script is just an example of how the readers can be read in and the contents accessed. Modified UnitCell.py to use print_info instead of printInfo New set of pyhton packages are needed for the above; dill,multiprocess,psutil Added new test for p2cif Removed redundant imports from all files

version 6.4.3 Modified p2cif so that it becomes a windows executable Modified p2cif and preader to be more robust when reading phonopy output Re-introduced fitting the frequency scaling in the fitter tab

version 6.4.2 Modified the plotting in fitter so that scaling is always applied Removed the tick box in the Fitter tab that switches scaling on/off Only store the optical permittivity in a script if it has been altered in the GUI This means that older scripts will not be compatible with the newer defaults.

version 6.4.1 Fixed a packaging problem on pypi and conda-forge No changes to source code

version 6.4.0 Removed the imageio-ffmpeg download code added pip install dependence instead Updated the installation instructions on the documentation to reflect conda-forge installation Added environment variables to control threading and number of cpus Made the refractiveindexmedium variable real (not complex) to remove the warning message from PyMieScatt

- Python
Published by JohnKendrick over 4 years ago

pdielec - PDielec Version 7.0.1 - Powder and Single Crystal Infrared Calculations

The Python package PDielec calculates the infrared and terahertz absorption characteristics of crystalline materials by post processing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. For crystalline samples (thin films or thick slabs) the program uses a generalized transfer matrix approach to calculate the transmission, absorption and reflection. For powdered systems, the package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach for small crystallites is published in Journal of Computational Chemistry, DOI: 10.1002/jcc.24344 .

version 7.0.1 Added a single crystal tab to show transmission and reflectance at a single crystal surface The method used is that described by Passler et al Rewrote the calculation of dielectric permittivity so that it would be much more general. There is now a class which looks after dielectric permittivity information The sign convention for the imaginary component of the permittivity has changed - e(real)-e(imag)j Moved the CrystalPermittivity to the SettingsTab Modified the scripting, scripts written before version 7 may not work. Modified the way masses are handled, so if the gui modifies the masses they are written out to the script. Changed the communication between tabs, it was completed before and it still is unfortunately Stopped setting the requestRefresh variable directly - now use a subroutine to do it. Added a lot of debugging information to the tabs so it is much clearer what the flow is through the code Two new input file type has been added 'experimental' and 'pdgui'. 'experimental' allows an experimental dieletric to be specified this includes a lorentz type spectrum 'pdgui' allows a script to be read in and executed 'experimental' and 'pdgui'. The mainTab gui no longer needs to have specified the 'program' name (eg. castep, or vasp). This is determined from the name of the file. Added a new example of using the fitter and the fitting tab Revised all the documentation Added the Mie module from PyMieScatt as there were some issues about crossover Major changes to the parallel methods used by the code. Now using 'partial' from functools also removed sending the whole crystal_permittivity array at once. also create the pool in the notebook and keep reusing it. also switch back to multiprocessing MKL threads are no longer changed by the code

version 6.4.5 Fixed a couple of problems when switching molecule using the GUI. The sigmas array and the mode fitting flags are now reset when a new molecule/crystal is read in. Modified the ViewerTab to display super-cells Added a new VibAnalysis module based on the work of filipe teixeira https://github.com/teixeirafilipe/vibAnalysis Example output in Examples/Castep/AsparticAcid/phonon.nm (generated with 'vibanalysis phonon) Examples/Vasp/Na2SO42/OUTCAR.nma (generated with 'vibanalysis OUTCAR) Added sklearn to the list of required packages

version 6.4.4 (Internal release only) Added an option in viewerTab to write the vibrating molecule as a cif file. Modified the cif output format so it is more like that of Mercury Introduced psutil.cpucount as this will give the number of physical processors Switched the multiprocessing module to the multiprocess module (pickling is better) Overrode the mkl environment variable for the number of threads. PDgui now uses mkl threading, unless it is in multiprocessing mode. Used dill for the pickling itself. In preader added an option to pickle each of the readers that are created and store them in a file Added a script, pickledreader which can read the pickled file. The script is just an example of how the readers can be read in and the contents accessed. Modified UnitCell.py to use print_info instead of printInfo New set of pyhton packages are needed for the above; dill,multiprocess,psutil Added new test for p2cif Removed redundant imports from all files

version 6.4.3 Modified p2cif so that it becomes a windows executable Modified p2cif and preader to be more robust when reading phonopy output Re-introduced fitting the frequency scaling in the fitter tab

version 6.4.2 Modified the plotting in fitter so that scaling is always applied Removed the tick box in the Fitter tab that switches scaling on/off Only store the optical permittivity in a script if it has been altered in the GUI This means that older scripts will not be compatible with the newer defaults.

version 6.4.1 Fixed a packaging problem on pypi and conda-forge No changes to source code

version 6.4.0 Removed the imageio-ffmpeg download code added pip install dependence instead Updated the installation instructions on the documentation to reflect conda-forge installation Added environment variables to control threading and number of cpus Made the refractiveindexmedium variable real (not complex) to remove the warning message from PyMieScatt

- Python
Published by JohnKendrick over 4 years ago

pdielec - PDielec - 6.4.5 New molecular vibrational analysis and super-cell visualisation

version 6.4.5 Fixed a couple of problems when switching molecule using the GUI. The sigmas array and the mode fitting flags are now reset when a new molecule/crystal is read in. Modified the ViewerTab to display super-cells Added a new VibAnalysis module based on the work of filipe teixeira https://github.com/teixeirafilipe/vibAnalysis Example output in Examples/Castep/AsparticAcid/phonon.nm (generated with 'vibanalysis phonon) Examples/Vasp/Na2SO42/OUTCAR.nma (generated with 'vibanalysis OUTCAR) Added sklearn to the list of required packages

version 6.4.4 (Internal release only) Added an option in viewerTab to write the vibrating molecule as a cif file. Modified the cif output format so it is more like that of Mercury Introduced psutil.cpucount as this will give the number of physical processors Switched the multiprocessing module to the multiprocess module (pickling is better) Overrode the mkl environment variable for the number of threads. PDgui now uses mkl threading, unless it is in multiprocessing mode. Used dill for the pickling itself. In preader added an option to pickle each of the readers that are created and store them in a file Added a script, pickledreader which can read the pickled file. The script is just an example of how the readers can be read in and the contents accessed. Modified UnitCell.py to use print_info instead of printInfo New set of pyhton packages are needed for the above; dill,multiprocess,psutil Added new test for p2cif Removed redundant imports from all files

version 6.4.3 Modified p2cif so that it becomes a windows executable Modified p2cif and preader to be more robust when reading phonopy output Re-introduced fitting the frequency scaling in the fitter tab

version 6.4.2 Modified the plotting in fitter so that scaling is always applied Removed the tick box in the Fitter tab that switches scaling on/off Only store the optical permittivity in a script if it has been altered in the GUI This means that older scripts will not be compatible with the newer defaults.

version 6.4.1 Fixed a packaging problem on pypi and conda-forge No changes to source code

version 6.4.0 Removed the imageio-ffmpeg download code added pip install dependence instead Updated the installation instructions on the documentation to reflect conda-forge installation Added environment variables to control threading and number of cpus Made the refractiveindexmedium variable real (not complex) to remove the warning message from PyMieScatt

- Python
Published by JohnKendrick almost 5 years ago

pdielec - PDielec - 6.4.3 - minor updates

The Python package PDielec calculates the infrared absorption characteristics of a crystalline material supported in a non absorbing medium by post processing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. The package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach is published in Journal of Computational Chemistry, DOI: 10.1002/jcc.24344 .

Version 6.4.3 Modified p2cif so that it becomes a windows executable Modified p2cif and preader to be more robust when reading phonopy output Re-introduced fitting the frequency scaling in the fitter tab

version 6.4.2 Modified the plotting in fitter so that scaling is always applied Removed the tick box in the Fitter tab that switches scaling on/off Only store the optical permittivity in a script if it has been altered in the GUI This means that older scripts will not be compatible with the newer defaults.

version 6.4.1 Fixed a packaging problem on pypi and conda-forge No changes to source code

version 6.4.0 Removed the imageio-ffmpeg download code added pip install dependence instead Updated the installation instructions on the documentation to reflect conda-forge installation Added environment variables to control threading and number of cpus Made the refractiveindexmedium variable real (not complex) to remove the warning message from PyMieScatt

- Python
Published by JohnKendrick almost 6 years ago

pdielec - PDielec - 6.4.2 - minor updates

The Python package PDielec calculates the infrared absorption characteristics of a crystalline material supported in a non absorbing medium by post processing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. The package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach is published in Journal of Computational Chemistry, DOI: 10.1002/jcc.24344 .

version 6.4.2 Modified the plotting in fitter so that scaling is always applied Removed the tick box in the Fitter tab that switches scaling on/off Only store the optical permittivity in a script if it has been altered in the GUI This means that older scripts will not be compatible with the newer defaults.

version 6.4.1 Fixed a packaging problem on pypi and conda-forge No changes to source code

version 6.4.0 Removed the imageio-ffmpeg download code added pip install dependence instead Updated the installation instructions on the documentation to reflect conda-forge installation Added environment variables to control threading and number of cpus Made the refractiveindexmedium variable real (not complex) to remove the warning message from PyMieScatt

- Python
Published by JohnKendrick almost 6 years ago

pdielec - PDielec - Release on conda-forge - new setup.py

The Python package PDielec calculates the infrared absorption characteristics of a crystalline material supported in a non absorbing medium by post processing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. The package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach is published in Journal of Computational Chemistry, DOI: 10.1002/jcc.24344 .

version 6.4.1 There were packaging problems on pypi and conda-forge.
The source code has not changed since 6.4.0

version 6.4.0 Removed the imageio-ffmpeg download code added pip install dependence instead Updated the installation instructions on the documentation to reflect conda-forge installation Added environment variables to control threading and number of cpus Made the refractiveindexmedium variable real (not complex) to remove the warning message from PyMieScatt

Version 6.3.1 Solved packaging issues ready for release on PyPi

Version 6.3.0 Added ability to request fewer cpus for parallel computation. Also can now switch to threading model if necessary. Restructured directory structure to be consistent with setup.py. Changed the spreadsheet checking so that 'Settings' is not included - problems with checking degenerate systems. Changed the threshold in checkcsv to 3E-2. All tests now pass. Created commands in the root directory which should be similar to those created by a pip installation - pdgui, preader

Version 6.2 Treats the case of a support matrix with spherical inclusions. The scattering from the inclusions is accounted for by Mie theory. The resulting effective permittivity is used in the calculation of the effective permittivity of the active dielectric in the matrix. In addition the following features have been added;

• the sign of the imaginary component of the Mie permittivity is now consistent with Bruggeman and Maxwell-Garnett methods
• a Hodrick-Prescott filter performs a baseline correction to the experimental spectrum in the Fitter tab. saving a script has been modified to improve the scripts robustness various other minor bugs have been fixed

Version 6.1 sees the release of new Mie routines which allow a more robust treatment of anisotropic crystals. A few other issues have also been addressed. The mass and volume fractions can be edited more easily. The spreadsheet is now written out at the end of the calculation (on exiting the program). There are several changes to the fitter tab. All the options are now in their own settings tab, which gives more space for listing the frequencies. A new fitting algorithm has been provided, which minimises the root means squared error between the experimental and calculated spectra.

Version 6.0.1 is a minor bug-fix release to Version v6.0. Version6.0 adds the ability to alter the Lorentzian widths of the phonon transitions and compare the results interactively with an experimental spectrum.

Version v5.0 sees the removal of the command line interface. All calculations are now performed by PDGui. Calculation of ATR spectra has now been incorporated into the package.

Version v4.0 Sees the release of a version of PDielec with a graphical user interface. PDGui allows access to nearly all of the functionality of PDielec. In addition there is a visualiser which allows the normal modes to be shown using an arrow to describe the atomic displacements, or as an animation. There is also the ability to break down each phonon mode into inter and intra-molecular contributions. Included in this release is a Windows compatible installation executable, which installs a version of PDielec/PDGui onto a Windows machine.

A major change in this v3.0 is the support of Phonopy (using its VASP interface). An internal set of atomic masses has been introduced, making the code independent of the masses used in the QM/MM program being analysed.

v3.0.1 Has updates to the PReader helper program. PReader now has an interface which is consistent with PDielec. PReader reads output files from the supported QM/MM packages and summarises the output in a format which can be read easily into a spreadsheet.

v3.1.0 now runs in parallel on multicore machines. Changes to the examples and the example testing routines mean that the tests are less sensitive to change in the machine/BLAS libraries.

Packages supported are; Abinit, Castep, Crystal, Gulp, Quantum Espresso, Phonopy and VASP.

v6.0 8c125d4 PDielec - Comparing calculation and experiment @JohnKendrick JohnKendrick released this on 29 Oct · 13 commits to master since this release

Assets 3 PDGuiv6.0windows_setup.exe 193 MB Source code (zip) Source code (tar.gz) The Python package PDielec calculates the infrared absorption characteristics of a crystalline material supported in a non absorbing medium by post processing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. The package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach is published in Journal of Computational Chemistry, DOI: 10.1002/jcc.24344 .

Version v6.0 adds the ability to alter the Lorentzian widths of the phonon transitions and compare the results interactively with an experimental spectrum.

Version v5.0 sees the removal of the command line interface. All calculations are now performed by PDGui. Calculation of ATR spectra has now been incorporated into the package.

Version v4.0 Sees the release of a version of PDielec with a graphical user interface. PDGui allows access to nearly all of the functionality of PDielec. In addition there is a visualiser which allows the normal modes to be shown using an arrow to describe the atomic displacements, or as an animation. There is also the ability to break down each phonon mode into inter and intra-molecular contributions. Included in this release is a Windows compatible installation executable, which installs a version of PDielec/PDGui onto a Windows machine.

A major change in this v3.0 is the support of Phonopy (using its VASP interface). An internal set of atomic masses has been introduced, making the code independent of the masses used in the QM/MM program being analysed.

v3.0.1 Has updates to the PReader helper program. PReader now has an interface which is consistent with PDielec. PReader reads output files from the supported QM/MM packages and summarises the output in a format which can be read easily into a spreadsheet.

v3.1.0 now runs in parallel on multicore machines. Changes to the examples and the example testing routines mean that the tests are less sensitive to change in the machine/BLAS libraries.

Packages supported are; Abinit, Castep, Crystal, Gulp, Quantum Espresso, Phonopy and VASP. Assets 2 Source code (zip) Source code (tar.gz)

v6.2 d1c5962

PDielec Scattering from air inclusions

@JohnKendrick JohnKendrick released this on Dec 30, 2018 · 62 commits to master since this release

The Python package PDielec calculates the infrared absorption characteristics of a crystalline material supported in a non absorbing medium by post processing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. The package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach is published in Journal of Computational Chemistry, DOI: 10.1002/jcc.24344 .

Version 6.2 treats the case of a support matrix with spherical inclusions. The scattering from the inclusions is accounted for by Mie theory. The resulting effective permittivity is used in the calculation of the effective permittivity of the active dielectric in the matrix. In addition the following features have been added;

the sign of the imaginary component of the Mie permittivity is now consistent with Bruggeman and Maxwell-Garnett methods
a Hodrick-Prescott filter performs a baseline correction to the experimental spectrum in the Fitter tab.
saving a script has been modified to improve the scripts robustness
various other minor bugs have been fixed

Version 6.1 sees the release of new Mie routines which allow a more robust treatment of anisotropic crystals. A few other issues have also been addressed. The mass and volume fractions can be edited more easily. The spreadsheet is now written out at the end of the calculation (on exiting the program). There are several changes to the fitter tab. All the options are now in their own settings tab, which gives more space for listing the frequencies. A new fitting algorithm has been provided, which minimises the root means squared error between the experimental and calculated spectra.

Version 6.0.1 is a minor bug-fix release to Version v6.0.

Version6.0 adds the ability to alter the Lorentzian widths of the phonon transitions and compare the results interactively with an experimental spectrum.

Version v5.0 sees the removal of the command line interface. All calculations are now performed by PDGui. Calculation of ATR spectra has now been incorporated into the package.

Version v4.0 Sees the release of a version of PDielec with a graphical user interface. PDGui allows access to nearly all of the functionality of PDielec. In addition there is a visualiser which allows the normal modes to be shown using an arrow to describe the atomic displacements, or as an animation. There is also the ability to break down each phonon mode into inter and intra-molecular contributions. Included in this release is a Windows compatible installation executable, which installs a version of PDielec/PDGui onto a Windows machine.

A major change in this v3.0 is the support of Phonopy (using its VASP interface). An internal set of atomic masses has been introduced, making the code independent of the masses used in the QM/MM program being analysed.

v3.0.1 Has updates to the PReader helper program. PReader now has an interface which is consistent with PDielec. PReader reads output files from the supported QM/MM packages and summarises the output in a format which can be read easily into a spreadsheet.

v3.1.0 now runs in parallel on multicore machines. Changes to the examples and the example testing routines mean that the tests are less sensitive to change in the machine/BLAS libraries.

Packages supported are; Abinit, Castep, Crystal, Gulp, Quantum Espresso, Phonopy and VASP.

- Python
Published by JohnKendrick almost 6 years ago

pdielec - PDielec - Release on conda-forge

The Python package PDielec calculates the infrared absorption characteristics of a crystalline material supported in a non absorbing medium by post processing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. The package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach is published in Journal of Computational Chemistry, DOI: 10.1002/jcc.24344 .

version 6.4.0 Removed the imageio-ffmpeg download code added pip install dependence instead Updated the installation instructions on the documentation to reflect conda-forge installation Added environment variables to control threading and number of cpus Made the refractiveindexmedium variable real (not complex) to remove the warning message from PyMieScatt

Version 6.3.1 Solved packaging issues ready for release on PyPi

Version 6.3.0 Added ability to request fewer cpus for parallel computation. Also can now switch to threading model if necessary. Restructured directory structure to be consistent with setup.py. Changed the spreadsheet checking so that 'Settings' is not included - problems with checking degenerate systems. Changed the threshold in checkcsv to 3E-2. All tests now pass. Created commands in the root directory which should be similar to those created by a pip installation - pdgui, preader

Version 6.2 Treats the case of a support matrix with spherical inclusions. The scattering from the inclusions is accounted for by Mie theory. The resulting effective permittivity is used in the calculation of the effective permittivity of the active dielectric in the matrix. In addition the following features have been added;

- the sign of the imaginary component of the Mie permittivity is now consistent with Bruggeman and Maxwell-Garnett methods
- a Hodrick-Prescott filter performs a baseline correction to the experimental spectrum in the Fitter tab.
saving a script has been modified to improve the scripts robustness
various other minor bugs have been fixed

Version 6.1 sees the release of new Mie routines which allow a more robust treatment of anisotropic crystals. A few other issues have also been addressed. The mass and volume fractions can be edited more easily. The spreadsheet is now written out at the end of the calculation (on exiting the program). There are several changes to the fitter tab. All the options are now in their own settings tab, which gives more space for listing the frequencies. A new fitting algorithm has been provided, which minimises the root means squared error between the experimental and calculated spectra.

Version 6.0.1 is a minor bug-fix release to Version v6.0. Version6.0 adds the ability to alter the Lorentzian widths of the phonon transitions and compare the results interactively with an experimental spectrum.

Version v5.0 sees the removal of the command line interface. All calculations are now performed by PDGui. Calculation of ATR spectra has now been incorporated into the package.

Version v4.0 Sees the release of a version of PDielec with a graphical user interface. PDGui allows access to nearly all of the functionality of PDielec. In addition there is a visualiser which allows the normal modes to be shown using an arrow to describe the atomic displacements, or as an animation. There is also the ability to break down each phonon mode into inter and intra-molecular contributions. Included in this release is a Windows compatible installation executable, which installs a version of PDielec/PDGui onto a Windows machine.

A major change in this v3.0 is the support of Phonopy (using its VASP interface). An internal set of atomic masses has been introduced, making the code independent of the masses used in the QM/MM program being analysed.

v3.0.1 Has updates to the PReader helper program. PReader now has an interface which is consistent with PDielec. PReader reads output files from the supported QM/MM packages and summarises the output in a format which can be read easily into a spreadsheet.

v3.1.0 now runs in parallel on multicore machines. Changes to the examples and the example testing routines mean that the tests are less sensitive to change in the machine/BLAS libraries.

Packages supported are; Abinit, Castep, Crystal, Gulp, Quantum Espresso, Phonopy and VASP.

v6.0 8c125d4 PDielec - Comparing calculation and experiment @JohnKendrick JohnKendrick released this on 29 Oct · 13 commits to master since this release

Assets 3 PDGuiv6.0windows_setup.exe 193 MB Source code (zip) Source code (tar.gz) The Python package PDielec calculates the infrared absorption characteristics of a crystalline material supported in a non absorbing medium by post processing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. The package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach is published in Journal of Computational Chemistry, DOI: 10.1002/jcc.24344 .

Version v6.0 adds the ability to alter the Lorentzian widths of the phonon transitions and compare the results interactively with an experimental spectrum.

Version v5.0 sees the removal of the command line interface. All calculations are now performed by PDGui. Calculation of ATR spectra has now been incorporated into the package.

Version v4.0 Sees the release of a version of PDielec with a graphical user interface. PDGui allows access to nearly all of the functionality of PDielec. In addition there is a visualiser which allows the normal modes to be shown using an arrow to describe the atomic displacements, or as an animation. There is also the ability to break down each phonon mode into inter and intra-molecular contributions. Included in this release is a Windows compatible installation executable, which installs a version of PDielec/PDGui onto a Windows machine.

A major change in this v3.0 is the support of Phonopy (using its VASP interface). An internal set of atomic masses has been introduced, making the code independent of the masses used in the QM/MM program being analysed.

v3.0.1 Has updates to the PReader helper program. PReader now has an interface which is consistent with PDielec. PReader reads output files from the supported QM/MM packages and summarises the output in a format which can be read easily into a spreadsheet.

v3.1.0 now runs in parallel on multicore machines. Changes to the examples and the example testing routines mean that the tests are less sensitive to change in the machine/BLAS libraries.

Packages supported are; Abinit, Castep, Crystal, Gulp, Quantum Espresso, Phonopy and VASP.

- Python
Published by JohnKendrick almost 6 years ago

pdielec - PDielec Scattering from air inclusions

The Python package PDielec calculates the infrared absorption characteristics of a crystalline material supported in a non absorbing medium by post processing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. The package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach is published in Journal of Computational Chemistry, DOI: 10.1002/jcc.24344 .

Version 6.2 treats the case of a support matrix with spherical inclusions. The scattering from the inclusions is accounted for by Mie theory. The resulting effective permittivity is used in the calculation of the effective permittivity of the active dielectric in the matrix. In addition the following features have been added; - the sign of the imaginary component of the Mie permittivity is now consistent with Bruggeman and Maxwell-Garnett methods - a Hodrick-Prescott filter performs a baseline correction to the experimental spectrum in the Fitter tab. - saving a script has been modified to improve the scripts robustness - various other minor bugs have been fixed

Version 6.1 sees the release of new Mie routines which allow a more robust treatment of anisotropic crystals. A few other issues have also been addressed. The mass and volume fractions can be edited more easily. The spreadsheet is now written out at the end of the calculation (on exiting the program). There are several changes to the fitter tab. All the options are now in their own settings tab, which gives more space for listing the frequencies. A new fitting algorithm has been provided, which minimises the root means squared error between the experimental and calculated spectra.

Version 6.0.1 is a minor bug-fix release to Version v6.0.

Version6.0 adds the ability to alter the Lorentzian widths of the phonon transitions and compare the results interactively with an experimental spectrum.

Version v5.0 sees the removal of the command line interface. All calculations are now performed by PDGui. Calculation of ATR spectra has now been incorporated into the package.

Version v4.0 Sees the release of a version of PDielec with a graphical user interface. PDGui allows access to nearly all of the functionality of PDielec. In addition there is a visualiser which allows the normal modes to be shown using an arrow to describe the atomic displacements, or as an animation. There is also the ability to break down each phonon mode into inter and intra-molecular contributions. Included in this release is a Windows compatible installation executable, which installs a version of PDielec/PDGui onto a Windows machine.

A major change in this v3.0 is the support of Phonopy (using its VASP interface). An internal set of atomic masses has been introduced, making the code independent of the masses used in the QM/MM program being analysed.

v3.0.1 Has updates to the PReader helper program. PReader now has an interface which is consistent with PDielec. PReader reads output files from the supported QM/MM packages and summarises the output in a format which can be read easily into a spreadsheet.

v3.1.0 now runs in parallel on multicore machines. Changes to the examples and the example testing routines mean that the tests are less sensitive to change in the machine/BLAS libraries.

Packages supported are; Abinit, Castep, Crystal, Gulp, Quantum Espresso, Phonopy and VASP.

- Python
Published by JohnKendrick over 7 years ago

pdielec - PDGui - minor bug fix release to v6.0

The Python package PDielec calculates the infrared absorption characteristics of a crystalline material supported in a non absorbing medium by post processing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. The package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach is published in Journal of Computational Chemistry, DOI: 10.1002/jcc.24344 .

Version 6.0.1 is a minor bug-fix release to Version v6.0. Version6.0 adds the ability to alter the Lorentzian widths of the phonon transitions and compare the results interactively with an experimental spectrum.

Version v5.0 sees the removal of the command line interface. All calculations are now performed by PDGui. Calculation of ATR spectra has now been incorporated into the package.

Version v4.0 Sees the release of a version of PDielec with a graphical user interface. PDGui allows access to nearly all of the functionality of PDielec. In addition there is a visualiser which allows the normal modes to be shown using an arrow to describe the atomic displacements, or as an animation. There is also the ability to break down each phonon mode into inter and intra-molecular contributions. Included in this release is a Windows compatible installation executable, which installs a version of PDielec/PDGui onto a Windows machine.

A major change in this v3.0 is the support of Phonopy (using its VASP interface). An internal set of atomic masses has been introduced, making the code independent of the masses used in the QM/MM program being analysed.

v3.0.1 Has updates to the PReader helper program. PReader now has an interface which is consistent with PDielec. PReader reads output files from the supported QM/MM packages and summarises the output in a format which can be read easily into a spreadsheet.

v3.1.0 now runs in parallel on multicore machines. Changes to the examples and the example testing routines mean that the tests are less sensitive to change in the machine/BLAS libraries.

Packages supported are; Abinit, Castep, Crystal, Gulp, Quantum Espresso, Phonopy and VASP.

- Python
Published by JohnKendrick over 7 years ago

pdielec - PDielec - Comparing calculation and experiment

The Python package PDielec calculates the infrared absorption characteristics of a crystalline material supported in a non absorbing medium by post processing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. The package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach is published in Journal of Computational Chemistry, DOI: 10.1002/jcc.24344 .

Version v6.0 adds the ability to alter the Lorentzian widths of the phonon transitions and compare the results interactively with an experimental spectrum.

Version v5.0 sees the removal of the command line interface. All calculations are now performed by PDGui. Calculation of ATR spectra has now been incorporated into the package.

Version v4.0 Sees the release of a version of PDielec with a graphical user interface. PDGui allows access to nearly all of the functionality of PDielec. In addition there is a visualiser which allows the normal modes to be shown using an arrow to describe the atomic displacements, or as an animation. There is also the ability to break down each phonon mode into inter and intra-molecular contributions. Included in this release is a Windows compatible installation executable, which installs a version of PDielec/PDGui onto a Windows machine.

A major change in this v3.0 is the support of Phonopy (using its VASP interface). An internal set of atomic masses has been introduced, making the code independent of the masses used in the QM/MM program being analysed.

v3.0.1 Has updates to the PReader helper program. PReader now has an interface which is consistent with PDielec. PReader reads output files from the supported QM/MM packages and summarises the output in a format which can be read easily into a spreadsheet.

v3.1.0 now runs in parallel on multicore machines. Changes to the examples and the example testing routines mean that the tests are less sensitive to change in the machine/BLAS libraries.

Packages supported are; Abinit, Castep, Crystal, Gulp, Quantum Espresso, Phonopy and VASP.

- Python
Published by JohnKendrick over 7 years ago

pdielec - PDielec - ATR support

The Python package PDielec calculates the infrared absorption characteristics of a crystalline material supported in a non absorbing medium by post processing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. The package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach is published in Journal of Computational Chemistry, DOI: 10.1002/jcc.24344 .

Version v5.0 sees the removal of the command line interface. All calculations are now performed by PDGui. Calculation of ATR spectra has now been incorporated into the package.

Version v4.0 Sees the release of a version of PDielec with a graphical user interface. PDGui allows access to nearly all of the functionality of PDielec. In addition there is a visualiser which allows the normal modes to be shown using an arrow to describe the atomic displacements, or as an animation. There is also the ability to break down each phonon mode into inter and intra-molecular contributions. Included in this release is a Windows compatible installation executable, which installs a version of PDielec/PDGui onto a Windows machine.

A major change in this v3.0 is the support of Phonopy (using its VASP interface). An internal set of atomic masses has been introduced, making the code independent of the masses used in the QM/MM program being analysed.

v3.0.1 Has updates to the PReader helper program. PReader now has an interface which is consistent with PDielec. PReader reads output files from the supported QM/MM packages and summarises the output in a format which can be read easily into a spreadsheet.

v3.1.0 now runs in parallel on multicore machines. Changes to the examples and the example testing routines mean that the tests are less sensitive to change in the machine/BLAS libraries.

Packages supported are; Abinit, Castep, Crystal, Gulp, Quantum Espresso, Phonopy and VASP.

- Python
Published by JohnKendrick over 7 years ago

pdielec - PDielec - A Graphical User Interface

The Python package PDielec calculates the infrared absorption characteristics of a crystalline material supported in a non absorbing medium by post processing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. The package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach is published in Journal of Computational Chemistry, DOI: 10.1002/jcc.24344 .

Version v4.0 Sees the release of a version of PDielec with a graphical user interface. PDGui allows access to nearly all of the functionality of PDielec. In addition there is a visualiser which allows the normal modes to be shown using an arrow to describe the atomic displacements, or as an animation. There is also the ability to break down each phonon mode into inter and intra-molecular contributions. Included in this release is a Windows compatible installation executable, which installs a version of PDielec/PDGui onto a Windows machine.

A major change in this v3.0 is the support of Phonopy (using its VASP interface). An internal set of atomic masses has been introduced, making the code independent of the masses used in the QM/MM program being analysed.

v3.0.1 Has updates to the PReader helper program. PReader now has an interface which is consistent with PDielec. PReader reads output files from the supported QM/MM packages and summarises the output in a format which can be read easily into a spreadsheet.

v3.1.0 now runs in parallel on multicore machines. Changes to the examples and the example testing routines mean that the tests are less sensitive to change in the machine/BLAS libraries.

Packages supported are; Abinit, Castep, Crystal, Gulp, Quantum Espresso, Phonopy and VASP.

- Python
Published by JohnKendrick about 8 years ago

pdielec - PDielec - parallelisation

The Python package PDielec calculates the infrared absorption characteristics of a crystalline material supported in a non absorbing medium by post processesing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. The package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach is published in Journal of Computational Chemistry, DOI: 10.1002/jcc.24344 .

A major change in this v3.0 is the support of Phonopy (using its VASP interface). An internal set of atomic masses has been introduced, making the code independent of the masses used in the QM/MM program being analysed.

v3.0.1 Has updates to the PReader helper program. PReader now has an interface which is consistent with PDielec. PReader reads output files from the supported QM/MM packages and summarises the output in a format which can be read easily into a spreadsheet.

v3.1.0 now runs in parallel on multicore machines. Changes to the examples and the example testing routines mean that the tests are less sensitive to change in the machine/BLAS libraries.

Packages supported are; Abinit, Castep, Crystal, Gulp, Quantum Espresso, Phonopy and VASP.

- Python
Published by JohnKendrick over 8 years ago

pdielec - PDielec 3.0.1

The Python package PDielec calculates the infrared absorption characteristics of a crystalline material supported in a non absorbing medium by post processesing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. The package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach is published in Journal of Computational Chemistry, DOI: 10.1002/jcc.24344 .

A major change in this v3.0 is the support of Phonopy (using its VASP interface). An internal set of atomic masses has been introduced, making the code independent of the masses used in the QM/MM program being analysed.

v3.0.1 Has updates to the PReader helper program. PReader no has an interface which is consist with PDielec. PReader reads output files from the supported QM/MM packages and summarises the output in a format which can be read easily into a spreadsheet.

Packages supported are; Abinit, Castep, Crystal, Gulp, Quantum Espresso, Phonopy and VASP.

- Python
Published by JohnKendrick almost 9 years ago

pdielec - PDielec 3.0

The Python package PDielec calculates the infrared absorption characteristics of a crystalline material supported in a non absorbing medium by post processesing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. The package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach is published in Journal of Computational Chemistry, DOI: 10.1002/jcc.24344 .

A major change in this v3.0 is the support of Phonopy (using its VASP interface). An internal set of atomic masses has been introduced, making the code independent of the masses used in the QM/MM program being analysed.

Packages supported are; Abinit, Castep, Crystal, Gulp, Quantum Espresso, Phonopy and VASP.

- Python
Published by JohnKendrick almost 9 years ago

pdielec - PDielec, minor bug fixes for version 2.0

The Python package PDielec calculates the infrared absorption characteristics of a crystalline material supported in a non absorbing medium by post processesing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. The package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach is accepted for publication in Journal of Computational Chemistry.

The major change in this v2.0 is that the code should be compatible with Python 2 or Python 3 interpreters. The code output has been modified extensively to make it easier to read. v2.0.1 is a minor bug release.

Packages supported are; Abinit, Castep, Crystal, Gulp, Quantum Espresso and VASP.

- Python
Published by JohnKendrick almost 10 years ago

pdielec - Python 2/3 Compatibility

The Python package PDielec calculates the infrared absorption characteristics of a crystalline material supported in a non absorbing medium by post processesing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. The package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach is accepted for publication in Journal of Computational Chemistry.

The major change in this release is that the code should run with Python 2 or Python 3 interpreters. The code output has been modified extensively to make it easier to read.

Packages supported are; Abinit, Castep, Crystal, Gulp, Quantum Espresso and VASP.

- Python
Published by JohnKendrick almost 10 years ago

pdielec - Release adding support for Abinit and Quantum Espresso

The Python package PDielec calculates the infrared absorption characteristics of a crystalline material supported in a non absorbing medium by post processesing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. The package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach is accepted for publication in Journal of Computational Chemistry.

The major changes in this release is the addition of an interfaces to Abinit and Quantum Espresso.

Packages supported are; Abinit, Castep, Crystal, Gulp, Quantum Espresso and VASP.

- Python
Published by JohnKendrick almost 10 years ago

pdielec - Release with CRYSTAL14 interface

The Python package PDielec calculates the infrared absorption characteristics of a crystalline material supported in a non absorbing medium by post processesing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. The package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach is accepted for publication in Journal of Computational Chemistry.

The major changes in this release is the addition of an interface to Crystal14

- Python
Published by JohnKendrick almost 10 years ago

pdielec - Version used in submission to Journal of Computational Chemistry

The Python package PDielec calculates the infrared absorption characteristics of a crystalline material supported in a non absorbing medium by post processesing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. The package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach is accepted for publication in Journal of Computational Chemistry.

The major changes in this release is the calculation of longitudinal optic modes frequencies

- Python
Published by JohnKendrick about 10 years ago

pdielec - Release for publication to Zenodo

No modifications to the code from version 1.0 This release is simply to trigger storage in Zonodo.

- Python
Published by JohnKendrick over 10 years ago

pdielec - Initial Release of PDielec

The Python package PDielec calculates the infrared absorption characteristics of a crystalline material supported in a non absorbing medium by post processesing the output of solid state quantum mechanical and molecular mechanical calculations of the phonons or dielectric response of the crystalline material. The package calculates the internal electric field arising from different particle morphologies and calculates the resulting shift in absorption frequency and intensity arising from the coupling between a phonon and the internal field. The theory of the approach is about to be submitted for publication.

- Python
Published by JohnKendrick over 10 years ago