In this talk I will discuss different approximations in DFT: pseduo-potentials, exchange correlation functions.
The presentation can be downloaded here:
http://www.attaccalite.com/wp-content/uploads/2022/03/dft_approximations.odp
In this talk I will discuss different approximations in DFT: pseduo-potentials, exchange correlation functions.
The presentation can be downloaded here:
http://www.attaccalite.com/wp-content/uploads/2022/03/dft_approximations.odp
SCF methods, basis sets, and integrals part IIIAkefAfaneh2
Some DFT implementations (such as Octopus) attempt to describe the molecular
Kohn–Sham orbitals on a real-space grid.
• A 3D simulation box is chosen together with a grid spacing, for example 0.5 a0. Then,
a grid in 3D is constructed and the SCF equations are solved on the grid.
• This is different from an MO-LCAO expansion in numerical AOs!
• Pseudopotentials are inevitable for real-space grid methods, but they are not required
when numerical AOs are used.
• A great advantage of the use of numerical AOs as in DMol3 is that the method is free
of the basis-set superposition error (BSSE).
• Because exact atomic orbitals are used, the atoms in a molecule cannot improve
their orbitals artificially using basis functions from other atoms.
Recent developments for the quantum chemical investigation of molecular syste...Stephan Irle
The structural complexity of molecular clusters increases with size due to the associated, rapidly growing configuration space. Two examples are realized in i) the transition from molecular to bulk systems, and ii) in the subsequent chemical functionalization of nanomaterials. In such systems, traditional quantum chemical approaches of investigations are hampered by the vastly increasing computational cost, even considering ever-growing supercomputer capabilities. Computationally inexpensive, yet accurate schemes such as the density-functional tight-binding (DFTB) method promise here a significant advantage.
We have recently engaged in developing novel methodologies for systems with increasing structural complexity, driven by motivation from experimental studies. In this presentation, we will briefly review a) our advances in the automatic parameterization of DFTB, and b) the Kick-fragment-based “CrazyLego” conformationally aware approach for studying molecular and ionic liquid clusters with increasing size.
Basic intro to running Siesta, a code written to simulate multi atomic material using Density functional Theory (DFT). It covers how to create an input file, simulation command and analysing the output file, i.e. to make sense of the data dumped in .out file.
Gamry’s eQCM 10M™ is a rapid, impedance-scanning electrochemical quartz crystal microbalance (EQCM) that adds a valuable tool in the analytical toolbox of anyone investigating interfacial processes.
NMR Random Coil Index & Protein Dynamics. Presentation is related to: biochemistry, bioinformatics, biology, biophysics, Mark Berjanskii, molecular biology, molecular dynamics, molecular modeling, nmr spectroscopy, protein nmr, public speaking, python programming, sparse data, structural biology, structure determination, teaching, web design, web development, web programming, web server, Wishart group, protein dynamics, NMR dynamics, protein flexibility, accessible surface area, RCI, random coil index, order parameter, bruker, jeol
This presentation is about the emerging and future possible trends of the exciting field of nanotechnology. Scientists and engineers are working on a smaller scale day-by-day to increase portability and smaller devices, and to change the way we see the world and live in!
Francesca Gottschalk - How can education support child empowerment.pptxEduSkills OECD
Francesca Gottschalk from the OECD’s Centre for Educational Research and Innovation presents at the Ask an Expert Webinar: How can education support child empowerment?
June 3, 2024 Anti-Semitism Letter Sent to MIT President Kornbluth and MIT Cor...Levi Shapiro
Letter from the Congress of the United States regarding Anti-Semitism sent June 3rd to MIT President Sally Kornbluth, MIT Corp Chair, Mark Gorenberg
Dear Dr. Kornbluth and Mr. Gorenberg,
The US House of Representatives is deeply concerned by ongoing and pervasive acts of antisemitic
harassment and intimidation at the Massachusetts Institute of Technology (MIT). Failing to act decisively to ensure a safe learning environment for all students would be a grave dereliction of your responsibilities as President of MIT and Chair of the MIT Corporation.
This Congress will not stand idly by and allow an environment hostile to Jewish students to persist. The House believes that your institution is in violation of Title VI of the Civil Rights Act, and the inability or
unwillingness to rectify this violation through action requires accountability.
Postsecondary education is a unique opportunity for students to learn and have their ideas and beliefs challenged. However, universities receiving hundreds of millions of federal funds annually have denied
students that opportunity and have been hijacked to become venues for the promotion of terrorism, antisemitic harassment and intimidation, unlawful encampments, and in some cases, assaults and riots.
The House of Representatives will not countenance the use of federal funds to indoctrinate students into hateful, antisemitic, anti-American supporters of terrorism. Investigations into campus antisemitism by the Committee on Education and the Workforce and the Committee on Ways and Means have been expanded into a Congress-wide probe across all relevant jurisdictions to address this national crisis. The undersigned Committees will conduct oversight into the use of federal funds at MIT and its learning environment under authorities granted to each Committee.
• The Committee on Education and the Workforce has been investigating your institution since December 7, 2023. The Committee has broad jurisdiction over postsecondary education, including its compliance with Title VI of the Civil Rights Act, campus safety concerns over disruptions to the learning environment, and the awarding of federal student aid under the Higher Education Act.
• The Committee on Oversight and Accountability is investigating the sources of funding and other support flowing to groups espousing pro-Hamas propaganda and engaged in antisemitic harassment and intimidation of students. The Committee on Oversight and Accountability is the principal oversight committee of the US House of Representatives and has broad authority to investigate “any matter” at “any time” under House Rule X.
• The Committee on Ways and Means has been investigating several universities since November 15, 2023, when the Committee held a hearing entitled From Ivory Towers to Dark Corners: Investigating the Nexus Between Antisemitism, Tax-Exempt Universities, and Terror Financing. The Committee followed the hearing with letters to those institutions on January 10, 202
The French Revolution, which began in 1789, was a period of radical social and political upheaval in France. It marked the decline of absolute monarchies, the rise of secular and democratic republics, and the eventual rise of Napoleon Bonaparte. This revolutionary period is crucial in understanding the transition from feudalism to modernity in Europe.
For more information, visit-www.vavaclasses.com
Safalta Digital marketing institute in Noida, provide complete applications that encompass a huge range of virtual advertising and marketing additives, which includes search engine optimization, virtual communication advertising, pay-per-click on marketing, content material advertising, internet analytics, and greater. These university courses are designed for students who possess a comprehensive understanding of virtual marketing strategies and attributes.Safalta Digital Marketing Institute in Noida is a first choice for young individuals or students who are looking to start their careers in the field of digital advertising. The institute gives specialized courses designed and certification.
for beginners, providing thorough training in areas such as SEO, digital communication marketing, and PPC training in Noida. After finishing the program, students receive the certifications recognised by top different universitie, setting a strong foundation for a successful career in digital marketing.
Read| The latest issue of The Challenger is here! We are thrilled to announce that our school paper has qualified for the NATIONAL SCHOOLS PRESS CONFERENCE (NSPC) 2024. Thank you for your unwavering support and trust. Dive into the stories that made us stand out!
Acetabularia Information For Class 9 .docxvaibhavrinwa19
Acetabularia acetabulum is a single-celled green alga that in its vegetative state is morphologically differentiated into a basal rhizoid and an axially elongated stalk, which bears whorls of branching hairs. The single diploid nucleus resides in the rhizoid.
Macroeconomics- Movie Location
This will be used as part of your Personal Professional Portfolio once graded.
Objective:
Prepare a presentation or a paper using research, basic comparative analysis, data organization and application of economic information. You will make an informed assessment of an economic climate outside of the United States to accomplish an entertainment industry objective.
A Strategic Approach: GenAI in EducationPeter Windle
Artificial Intelligence (AI) technologies such as Generative AI, Image Generators and Large Language Models have had a dramatic impact on teaching, learning and assessment over the past 18 months. The most immediate threat AI posed was to Academic Integrity with Higher Education Institutes (HEIs) focusing their efforts on combating the use of GenAI in assessment. Guidelines were developed for staff and students, policies put in place too. Innovative educators have forged paths in the use of Generative AI for teaching, learning and assessments leading to pockets of transformation springing up across HEIs, often with little or no top-down guidance, support or direction.
This Gasta posits a strategic approach to integrating AI into HEIs to prepare staff, students and the curriculum for an evolving world and workplace. We will highlight the advantages of working with these technologies beyond the realm of teaching, learning and assessment by considering prompt engineering skills, industry impact, curriculum changes, and the need for staff upskilling. In contrast, not engaging strategically with Generative AI poses risks, including falling behind peers, missed opportunities and failing to ensure our graduates remain employable. The rapid evolution of AI technologies necessitates a proactive and strategic approach if we are to remain relevant.
Unit 8 - Information and Communication Technology (Paper I).pdfThiyagu K
This slides describes the basic concepts of ICT, basics of Email, Emerging Technology and Digital Initiatives in Education. This presentations aligns with the UGC Paper I syllabus.
2024.06.01 Introducing a competency framework for languag learning materials ...Sandy Millin
http://sandymillin.wordpress.com/iateflwebinar2024
Published classroom materials form the basis of syllabuses, drive teacher professional development, and have a potentially huge influence on learners, teachers and education systems. All teachers also create their own materials, whether a few sentences on a blackboard, a highly-structured fully-realised online course, or anything in between. Despite this, the knowledge and skills needed to create effective language learning materials are rarely part of teacher training, and are mostly learnt by trial and error.
Knowledge and skills frameworks, generally called competency frameworks, for ELT teachers, trainers and managers have existed for a few years now. However, until I created one for my MA dissertation, there wasn’t one drawing together what we need to know and do to be able to effectively produce language learning materials.
This webinar will introduce you to my framework, highlighting the key competencies I identified from my research. It will also show how anybody involved in language teaching (any language, not just English!), teacher training, managing schools or developing language learning materials can benefit from using the framework.
3. Themes
• Interoperability
• Reinvent the wheel
• Tools add value
• Libraries spread the work, and increase the
reach
• Cross-platform
• Python where possible
www.ccdc.cam.ac.uk
4. Python is the dominant scripting language in
chemistry
• Cheminformatics
– OpenBabel, RDKit, OEChem, Daylight, Cambios Molecular
Toolkit, Frowns, PyBabel
• Computational chemistry
– OpenBabel, PyQuante, NWChem, Maestro/Jaguar, MMTK
• Visualisation
– CCP1GUI, PyMOL, Zeobuilder
• Scientific programming
– numpy (interface to ATLAS, LAPACK), can interface to C/C++,
FORTRAN, matplotlib, VTK
www.ccdc.cam.ac.uk
5. GaussSum
• GUI written in Python
• Enables comparisons of calculated properties
with experimental results
– orbitals and molecular structure
• HOMO is 40% Ligand 1, 20% Ligand 2, etc.
– vibrational frequencies and IR spectrum
• scale frequencies individually or generally
– electronic transitions and UV-vis, CD spectra
– electronic transitions and molecular structure
• lowest energy transition involves change in ‘charge density’
on Ligand 1 from 0% to 80%
NM O’Boyle, AL Tenderholt, KM Langner. J. Comp. Chem.
2008, 29, 839. http://gausssum.sf.net
www.ccdc.cam.ac.uk
6.
7. GaussSum
• Simple features that make life easier for
modellers
– ‘grep’ for lines containing particular expressions
• can store up to four expressions
– plot convergence of geometry or SCF
• early warning of problems (unlike plotting of energy)
– spectra and extracted data are written to files suitable
for Excel
• GaussSum is popular...
– 3300 downloads last 12 months - referenced 23 times
in 2007
• …but is a simple program
– Mulliken analysis and convolution of spectra
www.ccdc.cam.ac.uk
8. Some questions
• Why is it so easy to add value to QM
calculations?
– developers not familiar with needs of users?
• Why don’t QM software developers list
compatible tools on their website?
– Good for the QM software, good for the tool
• Why don’t QM software developers make it
easier for tool developers?
– API, documentation describing output, XML,
interoperability
• Why not open source?
– Could fix these problems myself.
www.ccdc.cam.ac.uk
9. cclib - a Python library for package-
independent computational chemistry
algorithms
• In Jan 2005, Adam Tenderholt started writing PyMOlyze (now
QMForge)
– some overlap with GaussSum
– we decided to collaborate on a common framework for extracting data from
QM log files
• Karol Langner joined in Jan 2007
• cclib now extracts and standardises data from ADF, GAMESS,
GAMESS-UK, Gaussian, PC GAMESS, Jaguar, Molpro, ORCA...
(someone offered this week to help with ACES, Dalton, NWChem, and
PSI too)
NM O’Boyle, AL Tenderholt, KM Langner. J. Comp. Chem.
2008, 29, 839. http://cclib.sf.net
www.ccdc.cam.ac.uk
10. Why is cclib needed?
• Analysis methods are available only to users of
certain packages
– Morokuma energy decomposition (implemented in
GAMESS)
– Charge Decomposition Analysis (Frenking's code
only reads Gaussian output files)
• Keeps up to date with new versions of packages
• Allows chemists to focus on algorithms
• Makes implementation of algorithms
independent of proprietary software
www.ccdc.cam.ac.uk
12. Attribute
Description Units Datatype
Name
aonames atomic orbital names List
aooverlaps atomic orbital overlap matrix array of rank 2
atomcoords atom coordinates Å array of rank 3
atomnos atomic numbers array of rank 1
coreelectrons number of core electrons in an atom's pseudopotential array of rank 1
-1
etenergies energies of electronic transitions cm array of rank 1
etoscs oscillator strengths of electronic transitions array of rank 1
etrotats rotatory strengths of electronic transitions array of rank 1
etsecs singly-excited configurations for electronic transitions list of lists
etsyms symmetries of electronic transitions List
fonames fragment molecular orbital names List
fooverlaps fragment molecular orbital overlap matrix array of rank 2
gbasis coefficients and exponents of Gaussian basis functions PyQuante format
geotargets criteria target values for geometry convergence array of rank 1
geovalues criteria values for geometry convergence array of rank 2
homos molecular orbital index of the HOMO(s) array of rank 1
mocoeffs molecular orbital coefficients list of arrays of rank 2
moenergies molecular orbital energies eV list of arrays of rank 1
mosyms molecular orbital symmetries list of lists
mpenergies Möller-Plesset corrected electronic energies eV array of rank 2
natom number of atoms Integer
nbasis number of basis functions Integer
nmo number of molecular orbitals Integer
scfenergies electronic energy of the molecule eV array of rank 1
scftargets criteria target values for SCF convergence array of rank 2
scfvalues criteria values for SCF convergence list of arrays of rank 2
vibdisps Cartesian displacement vectors ΔÅ array of rank 3
-1
vibfreqs vibrational frequencies cm array of rank 1
-1
vibirs IR intensities km mol array of rank 1
4 -1
vibramans Raman intensities A amu array of rank 1
vibsyms Symmetries of vibrations List
www.ccdc.cam.ac.uk
14. **** testGeoOpt: GAMESS-UK geometry optimization unittest. ****
Are the indices in atombasis the right amount and unique? ... ok
Are atomcoords consistent with natom and Angstroms? ... ok
Are the atomnos correct? ... ok
Are the charge and multiplicity correct? ... ok
Are the coreelectrons all 0? ... ok
Are the dimensions of mocoeffs equal to 1 x (homo+5) x nbasis? ... ok
Do the geo targets have the right dimensions? ... ok
Are atomcoords consistent with geovalues? ... ok
Are scfvalues consistent with geovalues? ... ok
Is the index of the HOMO equal to 34? ... ok
Is the number of evalues equal to nmo? ... ok
Is the number of atoms equal to 20? ... ok
Is the number of basis set functions correct? ... ok
Did this subclass overwrite normalisesym? ... ok
Is the SCF energy within 40eV of target? ... ok
Do the scf targets have the right dimensions? ... ok
Are scfvalues and its elements the right type? ... ok
Are all the symmetry labels either Ag/u or Bg/u? ... ok
Is moenergies a list containing one numpy array? ... ok
----------------------------------------------------------------------
Ran 19 tests in 0.016s
********* SUMMARY PER PACKAGE ****************
Total Passed Failed Errors Skipped
ADF2007.01 48 46 0 0 2
GAMESS-UK 58 58 0 0 0
GAMESS-US 75 71 2 0 2
Gaussian03 92 88 1 0 3
Jaguar7.0 54 47 0 0 7
Molpro2006 63 59 0 0 4
ORCA2.6 54 44 5 3 2
PCGAMESS 75 74 0 0 1
********* SUMMARY OF EVERYTHING **************
TOTAL: 519 PASSED: 487 FAILED: 8 ERRORS: 3 SKIPPED: 21
15. But it’s Python! I only code C, FORTRAN, etc.
• Use cclib to convert the log file to JSON
• JSON libraries are available for
– C, C++, Java, Javascript, Perl, PHP, Python, Ruby
• Could easily write convertor to some type of FORTRAN
format
www.ccdc.cam.ac.uk
16. Some questions
• Why don’t QM software developers list compatible tools
on their website?
– Good for the QM software, good for the tool
• Why don’t QM software developers make it easier for
tool developers?
– API, documentation describing output, XML, interoperability
• Why not open source?
– Could fix these problems myself
• Why can’t I mix and match calculation methods from
different programs?
• Why do academics restrict usage of their sophisticated
routines to a single proprietary code?
www.ccdc.cam.ac.uk
17. OpenBabel - “Not just file conversion”
• A C++ library for…
• Cheminformatics
– SMARTS searching, InChI, SMILES, molecular fingerprints, group-
contribution based descriptors, determination of SSSR, bond order
perception, hydrogen addition, Gasteiger charge calculation
• Computational chemistry
– AMBER, DMol3, Gaussian, GAMESS, GROMOS96, HyperChem,
Jaguar, MOPAC, Q-Chem, Turbomole, ZINDO
• varying levels of support
– forcefield minimisation (UFF, MMFF94, Ghemical)
– symmetrisation of almost symmetric molecules (coming soon)
http://openbabel.org
www.ccdc.cam.ac.uk
18. Language bindings…and wrappers
• OpenBabel is a C++ library
• SWIG allows access to OpenBabel from
– Java, Perl, Python, Ruby (and many more if we wish)
• SWIG bindings are direct 1-to-1 translation of C++ API
and objects to a Python API and objects
• Pybel is a Pythonic wrapper around the SWIG bindings
– Makes it easy to carry out common tasks
– Allows idiomatic Python, e.g. using iterators, direct access to
attribute values rather than Get/Set, reduces verbosity
NM O’Boyle, C Morley, GR Hutchison. Chem. Cent. J. 2008,
2, 5. http://openbabel.org/wiki/Python
www.ccdc.cam.ac.uk
19. Let’s read a MOL file and optimise the geometry with
the UFF forcefield
SWIG bindings
import openbabel as ob
obconv = ob.OBConversion()
obconv.SetInFormat(“mol")
obmol = ob.OBMol()
obconv.ReadFile(obmol, “caffeine.mol")
obff = ob.OBForceField.FindForceField("UFF")
obff.Setup(obmol)
obff.ConjugateGradients(1000)
obff.UpdateCoordinates(obmol)
Pybel
import pybel
mol = pybel.readfile(“mol”, “caffeine.mol”).next()
mol.optimise(“UFF”) # Coming soon!
www.ccdc.cam.ac.uk
20. Some questions
• Why do some visualisation packages use their
own parsing routines instead of adding them to
libraries like OpenBabel or cclib?
• Why don’t QM packages donate code or
contract developers to improve support in
libraries like OpenBabel or cclib?
– ADF is doing this
• How can we coordinate interoperability?
…
www.ccdc.cam.ac.uk
23. Make it work on Windows!
• Most users use Windows, and even Linux users
want the option of jumping between OSs
• You restrict the reach of your software (and
hasten its replacement)
• Case study cclib-0.8 (Nov 07):
– cclib-0.8.tar.gz 63
– cclib-0.8.zip 58
– cclib-0.8-py2.4.exe 26
– cclib-0.8-py2.5.exe 45
• For every Linux user, there are 2 Windows
users
www.ccdc.cam.ac.uk
24. Make it easy to install on Windows!
• No dependencies
• Case study: GaussSum 2.1.4 (Nov 2007)
– GaussSum-2.1.4.tar.gz 143 (Linux)
– GaussSum-2.1.4.zip 206 (Windows, requires Python, Numpy
and Python Imaging Library)
– GaussSumexe-2.1.4.zip 396 (Windows, no dependencies)
• Lower the barrier to installation
– A one-click installer > a .zip file >> a .tar.gz file
– Make the installation instructions easy
• Case study: OpenBabel
– OB 2.0.1 Linux:Windows 5:4
– OB 2.1.1 Linux:Windows 5:7.5
www.ccdc.cam.ac.uk
25. Thanks!
• The OpenBabel development team and particularly
Geoff Hutchison and Chris Morley
• cclib: Adam Tenderholt and Karol Langner
• SourceForge
• Email: baoilleach@gmail.com, oboyle@ccdc.cam.ac.uk
• Blog: http://baoilleach.blogspot.com
• Website: http://www.redbrick.dcu.ie/~noel
www.ccdc.cam.ac.uk