Dynamics, Control and Energy Transfer at Terahertz Frequencies.

Lead Research Organisation: University of Leeds
Department Name: Sch of Chemistry

Abstract

Chemical and biological reactions are governed by the coupling of ultrafast chemical events to dynamics on much slower timescales. These ultrafast chemical events often occur at THz frequencies and there is a range of indirect experimental and theoretical evidence to suggest that the coupling of vibrational motion at these frequencies governs the dynamics of a range of reactions across chemistry and biology. In this proposal, enabled by recent technological developments, I will develop a THz multidimensional spectrometer that will be able to measure directly the coupling between these modes on an ultrafast timescale. This will enable me to measure energy transfer between THz frequency modes and the timescales involved therein. Once demonstrated this will be a new, powerful analytical technique with many possible applications. Initial measurements will be performed on two very different material types, the first being energetic materials, and the second, materials that show a dramatic structural change upon illumination by light (a photo-induced phase transition or PIPT). In both materials there is strong indirect experimental and theoretical evidence that the coupling between THz frequency vibrations governs the reaction pathways in these materials. THz multidimensional spectroscopic measurements of these materials will provide the first direct experimental evidence that the coupling between these THz vibrations directly governs the pathway, and dynamics, of a reaction. Once this has been demonstrated, in these two diverse sets of materials, this new analytical technique can be applied to many chemical or biological questions, providing an understanding of reaction dynamics on ultrafast timescales - essentially enabling us to watch chemistry happen. This underlying understanding of reactions dynamics will also underpin the future rational design of materials with tailored physical and chemical properties.
Following on from measuring the coupling between THz modes using THz multidimensional spectroscopy, specifically designed intense THz pulses will then be used to interact directly with this vibrational motion, essentially controlling and steering the chemical dynamics. This control, coupled with the understanding of reaction dynamics and the associated timescales provided directly by THz multidimensional spectroscopy, leads to a method where reactions can be steered and controlled - with huge potential applications. This fellowship will concentrate on three possible applications for THz-driven dynamics, namely (a) the control of enzymatic reactions, (b) the control of solid state phase transformations (concentrating of pharmaceutically relevant polymorphs) and (c) the control of catalytic reactions.

Planned Impact

Beneficiaries of this work over the short term (3-5 years) will be mainly academic in nature, which is a necessary step in moving towards non-academic beneficiaries. In particular, the new spectroscopic techniques that I will develop will have a significant impact on the terahertz (THz) and wider ultrafast/multidimensional spectroscopy communities, which are particularly strong within the UK. As the fellowship progresses, the techniques developed and the associated results will be relevant to a cross-disciplinary selection of fields including analytical chemistry, biophysics, reaction dynamics, and free electron laser science. The aim of my impact activities throughout this fellowship will therefore be to disseminate my results to the widest possible audience. To do this the main dissemination route for this proposal will be publication in primary refereed journals with a significant cross-disciplinary readership and by presentations at conferences and workshops that are well attended by a range of academics, SMEs, large companies and government employees.
Industrial beneficiaries in the medium term (5-10 years) will include companies that are interested in the understanding of the initiation and dynamics of reactions involving energetic materials such as the Atomic Weapons Establishment (AWE). In particular the results gained from this fellowship will directly influence the future rational design of more stable, safe energetic materials through control of energy transfer in these materials. I have a track record of working closely with government agencies who are major stakeholders in AWE and would be well placed to increase my impact in this area.
In the longer term (10-25 years), the technology and understanding I will develop as part of this fellowship, and continue to develop beyond the tenure of this programme, has the potential to provide a paradigm shift in the understanding of reaction dynamics in chemistry and biology. Three important areas that I have identified are:
(a) The control and understanding of catalytic reactions;
(b) The control of the formation of pharmaceutical polymorphs;
(c) The development of smart materials.
The areas I have identified are diverse, but a greater understanding of the dynamics of these reactions, coupled with the ability to control them directly, will provide the experimental data needed to design the next generation of such materials. The beneficiaries of such impact would be very broad. It is thought that as much as 90% of all commercially produced chemical products involve catalysts at some stage in the process of their manufacture, thus any information that leads to more efficient, specific catalysts has the potential to improve production and reduce energy consumption across the entire chemical processing industry. In the pharmaceutical industry the development of novel polymorphs and co-crystals is now crucial to the development of new pharmaceutics with the patent landscape of pharmaceutical co-crystals developing rapidly over the previous decade. The potential for new drug discovery by companies such as AstraZeneca and GSK would be significantly increased by the demonstration of control of polymorph formation. Finally, the development of smart materials whose properties can be significantly altered by external stimuli is crucial to the development of new technologies that are interactable, with companies such as Apple, Google and Samsung, along with small technology focussed SMEs all looking for the next technique that provides them with the designing edge in this competitive market.
These are certainly not the only areas where this new technology has the potential to have an impact, however, the connections with academics and industry that I will develop via the network meetings and conferences that I will attend will help me to confirm and develop these areas, while also allowing me to evaluate other high potential and high likelihood impact areas.

Publications

10 25 50
 
Description Work has concentrated on the development of the best combination of high-field THz sources and detection schemes to develop a practical spectrometer. This means having a range of schemes that are easily inter-changed that provide a range of THz fields and bandwidths depending on the properties of the material under test. As such we have developed a range of THz sources including photoconductive arrays, air plasma and Electro-optic sources that produce fields > 300 kV/cm with bandwidths in excess of 20 THz with the development of this instrument continuing through additional funding.

We have for the first time demonstrated a 2D-THz signal on an instrument in the UK noting that a 2D-THz instrument had not been demonstrated before the grant was submitted. The instrument will now be used for a range of different samples which will aid its future development. Measurements have been performed on Arsenic doped Germanium where the T2 lifetimes of several states have been determined for the first time, these measurements have also showed a number of cross-peaks linked to the coupling between states. Additionally, measurements have been performed on powdered lactose monohydrate. These measurements show both 2nd and 3rd order effects within the lowest frequency phonon mode at 520 GHz. The field strength of the sources we have developed needs to be improved to be able to measure these non-linear effects in a larger number of crystalline organic materials.

Our work in this area has led to the groups involvement in both national and international discussions to combined these THz sources with X-ray free electron lasers to explore the control of materials through phononics.
Exploitation Route The main outcome of this fellowship is the UK's first 2D-THz spectrometer. This technique has the potential to provide a new insight into the dynamics of a range of range of materials from photovoltaics through to pharmaceuticals and energetic materials.
Sectors Aerospace

Defence and Marine

Chemicals

Electronics

Energy

Environment

Healthcare

Manufacturing

including Industrial Biotechology

Pharmaceuticals and Medical Biotechnology

 
Description Contributions to the Science Case for a UKFEL as part of the chemical sciences team - the Science Case was positively endorsed by the expert Review Committee in November 2020
Geographic Reach National 
Policy Influence Type Contribution to a national consultation/review
URL https://www.clf.stfc.ac.uk/Pages/UK-XFEL-science-case.aspx
 
Description Applications of 1-D and 2-D Spectroscopy at THz and IR Frequencies
Amount £54,000 (GBP)
Funding ID 2107312 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 09/2018 
End 03/2022
 
Description CEOI THz Facilities Upgrade
Amount £172,123 (GBP)
Organisation National Centre for Earth Observation 
Sector Academic/University
Country United Kingdom
Start 01/2023 
End 03/2023
 
Description Capital Award Support for Early Career Researchers at the University of Leeds
Amount £225,000 (GBP)
Funding ID EP/S01764X/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 11/2018 
End 04/2020
 
Description Functional Hydrogen-Bonded Self-Sorting Networks
Amount £454,258 (GBP)
Funding ID EP/T011726/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 05/2020 
End 02/2023
 
Description Spin-Crossover Lattice Effects
Amount £371,315 (GBP)
Organisation The Leverhulme Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 09/2022 
End 09/2026
 
Description Terahertz calibration targets
Amount £47,917 (GBP)
Funding ID RS04299 
Organisation ESA - ESTEC 
Sector Public
Country Netherlands
Start 03/2022 
End 06/2023
 
Description Understanding complex materials using THz spectral measurements
Amount £6,000 (GBP)
Funding ID IES\R1\201157 
Organisation The Royal Society 
Sector Charity/Non Profit
Country United Kingdom
Start 06/2020 
End 12/2021
 
Title Data associated with 'Increasing the sensitivity of terahertz split ring resonator metamaterials for dielectric sensing by localized substrate etching' 
Description Data relevant to the design and measurement of split ring resonator metamaterials for dielectric sensing 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact none currently 
URL https://doi.org/10.5518/546
 
Title Data associated with Exploring the Reliability of DFT Calculations of the Infrared and Terahertz Spectra of Sodium Peroxodisulfate. 
Description The data included in this dataset has been generated by A number of DFT programs with various combinations of pseudo-potentials and van der Waals' dispersive corrections have been used to optimize the structure of sodium peroxodisulfate and to calculate the infra-red, attenuated total reflectance and terahertz absorption spectra of the powdered crystal. Comparison of the results from the different methods highlights the problems of calculating the absorption spectrum reliably. In particular the low frequency phonon modes are especially sensitive to the choice of grids to represent the wavefunction or the charge distribution, k-point integration grid and the energy cutoff. A comparison is made between the Maxwell-Garnett (MG) and Bruggeman effective medium methods used to account for the effect of crystal shape on the predicted spectrum. Possible scattering of light by air inclusions in the sample and by larger particles sodium peroxodisulfate of is also considered using the Mie method. The results of the calculations are compared with experimental measurements of the transmission and attenuated total reflection spectra. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact Only recently been released 
URL https://doi.org/10.5518/606
 
Title Data to Support Photoconductive Arrays on Insulating Substrates for High-Field Terahertz Generation 
Description The data included in this repository supports our work on the design, fabrication and characterisation of large-area photoconductive THz array structures, consisting of a thin LT-GaAs active region transferred to an insulating substrate using a wafer-scale bonding process. The electrically insulating, transparent substrate reduces the parasitic currents in the devices, allowing peak THz-fields as high as 140 kV cm-1 to be generated over a bandwidth >5 THz. These results are achieved using lower pulse energies than demanded by conventional photoconductive arrays and other popular methods of generating high-field THz radiation. Two device sizes are fully characterised and the emission properties are compared to generation by optical rectification in ZnTe. The device can be operated in an optically saturated regime in order to suppress laser noise. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
URL http://archive.researchdata.leeds.ac.uk/682/
 
Title Dataset associated with "All-electronic phase-resolved THz microscopy using the self-mixing effect in a semiconductor laser" 
Description This dataset relates to data presented in the work, "All-electronic phase-resolved THz microscopy using the self-mixing effect in a semiconductor laser". In this work we report all-electronic coherent scattering-type scanning near-field microscopy (s-SNOM) using a terahertz-frequency quantum cascade laser. By exploiting the coherent self-mixing effect in these lasers, in conjunction with electronic frequency tuning of the laser, we demonstrate spatial mapping of both the amplitude and phase of the scattered field with deeply sub-wavelength resolution. We apply our technique for coherent microscopy of a phonon-resonant crystal. The extracted amplitude and phase parameters reveal clear contrast when compared to both metallic and non-resonant dielectric materials, and show excellent agreement with those calculated using a finite-dipole model of the near-field interaction between the s-SNOM tip and the resonant sample in the Reststrahlen band. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
URL http://archive.researchdata.leeds.ac.uk/835/
 
Title Dataset associated with "Terahertz Dielectric Property Characterization of Photopolymers for Additive Manufacturing" 
Description Figures and source data for the paper '0.2 - 1.4-THz Dielectric Property Characterization of Photopolymers for Additive Manufacturing': In this paper, resin-based photocurable polymer materials for stereolithography (SLA), digital-light-processing (DLP) and polymer-jetting (PolyJet) additive manufacturing techniques were characterized from 0.2 - 1.4 terahertz (THz) for their comprehensive dielectric properties, e.g. reflective index, absorption coefficient, dielectric constant and loss tangent, by using laser-based time-domain spectroscopy (TDS). Fourteen photocurable 3D-printing polymers were chosen due to their suitability, in terms of printing resolution, material characteristics and etc., for millimeter-wave (mm-wave) and THz applications. The propagation loss mechanism and other electrical/optical properties of the chosen photopolymers for terahertz radiation were determined by correlating absorption coefficients and loss tangents obtained from the measurements. To demonstrate the utilization of the selected photopolymers at THz spectrum, an asymptotically quasi-single-mode Bragg fiber microfabricated by DLP micromanufacturing technique using HTM140-V2 photopolymer was prototyped and characterized at the nominal frequencies from 0.246 to 0.276 THz. The measurement results show that the average propagation loss of the asymptotically single-mode THz Bragg fiber is less than 5dB/m for the whole band, which is the lowest propagation loss reported to date for asymptotically single-mode all-dielectric fiber at this frequency band. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact Data will be useful when designing and developing new microwave/terahertz devices based on Additive Manufacturing techniques 
URL https://doi.org/10.5518/440
 
Title Dataset associated with "Tunable broadband terahertz polarizer using graphene-metal hybrid metasurface" 
Description An electrically tunable polarizer for terahertz frequency electromagnetic waves formed from a hybrid graphene-metal metasurface is demonstrated. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
 
Title Dataset associated with Effects of Structural Ordering on IR Active Vibrations Within Bi2(Te?1???Se?)3 
Description This is the dataset associated with the materials study performed on the IR active E1u phonon within the Bi2(Te?1???Se?)3 alloy system. It contains THz and DC conductivity data that show the change in phonon dynamics over a wide range of temperatures and stoichiometries. 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
Impact This dataset includes spectral measurements of a range TI materials along with supporting DFT based calculations. In particular the calculated data can be sued by other research groups to further there understanding of these materials without wasting time and energy performing the same calculations again 
URL https://archive.researchdata.leeds.ac.uk/1047/
 
Title Dataset associated with Liquid-crystal-based controllable attenuators for terahertz-frequency quantum-cascade lasers 
Description This archive contains the dataset associated with the publication entitled ''Liquid-crystal-based controllable attenuators for terahertz-frequency quantum-cascade lasers". There has been considerable progress in the development of terahertz-frequency (THz) radiation source and detectors, along with their potential applications in recent years. However, there remains a lack of adaptive optical components to manipulate, modulate and control THz radiation. Here, we demonstrate liquid-crystal devices (LCDs), made with a commercially available material (E7), with unbiased birefringence values of 0.14-0.18 in the 0.3-4 THz band. The LCDs were used to modulate the THz radiation generated from a 3.4-THz quantum cascade laser by up to 40%, dependent upon both the liquid crystal layer thickness and bias voltage applied. Data included are the raw time-domain data used to calculate the refractive indices and absorption coefficients shown in Figure 1, the raw time-domain data used to calculate the change in THz transmission shown in Figure 2, and an example .json file used to provide the calculation parameters to the Nelly open-access THz spectroscopy package which is available on GitHub. Also included are the raw data for Figure 3. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
URL https://archive.researchdata.leeds.ac.uk/1140/
 
Title Dataset exploring the use of quasi-harmonic approximation to understand the thermal properties of Bi2Se3 
Description This data set contains input and output files for DFT calculations on Bi2Se3 for a number of different fixed unit cells with calculations performed using VASP and Phonopy. At each fixed volume, optimisations and phonon calculations have been performed. These have been used to understand the thermal properties of the material using the quasi-harmonic approximation. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
URL https://zenodo.org/record/8199623
 
Title Static and Dynamic DFT Data Sets for Polymorphs of l-Cysteine - Stability and Terahertz Spectra 
Description Data sets associated with static and dynamic density functional calculations are reported for the four known polymorphs of l-cysteine and for models associated with the known disorder in Form I.. Static calculations are used to explore the relative free energies (within the harmonic approximation) of the polymorphs as a function of pressure. The energetics for dihedral angle rotation are explored and the barriers for rotation between the hydrogen bonding motifs have been calculated for each polymorph. Molecular dynamics calculations are reported for each polymorph and for models of hydrogen bond disorder which are known to exist at higher temperatures. Finally static and dynamic calculations of the infrared and terahertz spectra are performed. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
URL https://zenodo.org/record/7752765
 
Description P2D - Polarised 2D spectroscopy for probing spin systems 
Organisation University of Hamburg
Country Germany 
Sector Academic/University 
PI Contribution This project is jointly funded through the University of Leeds and University of Hamburg's joint call as part of a new strategic partnership. From the Leeds side we will produce topological insulator samples and develop THz/IR measurement systems in Hamburg for characterisation of these samples. We will also provide THz training to Hamburg staff
Collaborator Contribution Hamburg will host Visits from Leeds researchers and provide guidance in the setup of the IR side of the instrument. We will also jointly host a THz workshop in Hamburg. Hamburg Staff will also visit Leeds to perform THz measurements on there own samples
Impact This is a multi-disciplinary collaboration across, chemistry, physics and biology to develop instrumentation for a range of applications across both sites and is currently ongoing
Start Year 2022
 
Title JohnKendrick/PDielec: PDielec Release Version 7.2.1 
Description PDielec Version 7.2.1 - 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 7.2.1 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.cpu_count 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, pickled_reader 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 refractive_index_medium 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.cpu_count 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, pickled_reader 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 a... 
Type Of Technology Software 
Year Produced 2023 
Open Source License? Yes  
Impact first extension to single crystalline samples to increase reach of software for other users 
URL https://zenodo.org/record/8113796
 
Title JohnKendrick/PDielec: Version 8.0.0 
Description 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. 
Type Of Technology Software 
Year Produced 2023 
Open Source License? Yes  
Impact significant rewrite of the software base to increase the applicability of crystalline samples. Additional material database which allows access to functionality around effective medium approximation without the need for DFT calculations that will be used as part of future grant funding 
URL https://zenodo.org/doi/10.5281/zenodo.10411259
 
Title PDielec (v6.4.5) 
Description 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. In this release significant changes were made to the GUI including fixing issues with displaying molecules and adding a supercell functionality. The package now includes a modified version of the VibAnalysis module based on the work of filipe teixeira (https://github.com/teixeirafilipe/vibAnalysis) which can now be applied to solid-sate calculations 
Type Of Technology Software 
Year Produced 2021 
Open Source License? Yes  
Impact regularly used by a number of groups across Chemistry/Physics and Earth sciences. 
URL https://github.com/JohnKendrick/PDielec
 
Title PDielec V 6.2 
Description 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 about to be submitted for publication. 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. 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact This Version of the software is described in detail in 10.1007/s10762-019-00643-8 
URL https://github.com/JohnKendrick/PDielec
 
Title PDielec v5.0 
Description 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 about to be submitted for publication. 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. 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact Two papers explaining the use of PDielec for IR and THz calculations are currently in preparation and the work has been presented at a castep training workshop by Calum Towler (current PhD student) and was presented by myself at the first Castep User Meeting 
URL https://github.com/JohnKendrick/PDielec
 
Title PDielec(7.1.1) 
Description 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. In this particular version large changes have been made to the working of the code, increasing the parallel efficiency and improving the ability to use the scripting system included. There is now additional functionality to calculate the reflected and transmitted radiation from a crystal surface to expand the use of the code to include single crystals. Additionally a new testing suite has been included. 
Type Of Technology Software 
Year Produced 2022 
Open Source License? Yes  
Impact The code is now used by a number of groups across chemistry, physics and earth sciences. The code has been download > 9000 times since we made the code avaliable on conda-forge (https://anaconda.org/conda-forge/pdielec) 
URL https://github.com/JohnKendrick/PDielec
 
Title Pdielec V 6.0 
Description 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 about to be submitted for publication. Version v6.0 adds the ability to alter the Lorentzian widths of the phonon transitions and compare the results interactively with an experimental spectrum. 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact Continued development of a number of publications based on the use of PDielec 
 
Title Pdielec V4.0 
Description 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 about to be submitted for publication. 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. 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact none at the moment