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Resources

Created Friday 21 October 2016

Books

Computer Science

• UNIX

http://docstore.mik.ua/orelly/index.html

• Introduction to High-Performance Scientific Computing

http://tacc-web.austin.utexas.edu/veijkhout/public_html/istc/istc.html

• What is heap and stack?

http://www.maxi-pedia.com/what+is+heap+and+stack

• OpenMP Tutorial

https://computing.llnl.gov/tutorials/openMP/
http://docs.oracle.com/cd/E19059-01/stud.10/819-0501/index.html

• OpenMP examples

http://people.sc.fsu.edu/~jburkardt/f_src/openmp/openmp.html
http://openmp.org/wp/resources/

• Debugging BGP

http://www.alcf.anl.gov/resource-guides/debugging
http://www.yolinux.com/TUTORIALS/GDB-Commands.html
http://stackoverflow.com/questions/329259/how-do-i-debug-an-mpi-program

FORTRAN

• Introduction to Object-Oriented Concepts using Fortran90

http://www.cs.rpi.edu/~szymansk/OOF90/F90_Objects.html

• Fortran resources

http://www.star.le.ac.uk/~cgp/fortran.htm

• Fortran77 IO

http://www.amath.unc.edu/sysadmin/DOC4.0/fortran/f77rm/5_io.doc.html

• Advanced Fortran90

http://www.sdsc.edu/~tkaiser/f90.html

• Fortran90 for Fortran77 Programmers

http://www.star.le.ac.uk/~cgp/f90course/f90.html

• Mistakes in Fortran 90 Programs That Might Surprise You

http://www.cs.rpi.edu/~szymansk/OOF90/bugs.html

Preprocessor

C Preprocessor
https://gcc.gnu.org/onlinedocs/cpp/index.html#Top

Compilers and building tools

• Autotools

http://www.linuxselfhelp.com/gnu/automake/html_chapter/automake_9.html

• Libtool

http://www.gnu.org/software/libtool/manual/html_node/index.html#Top
IBM AIX compiler information center
http://publib.boulder.ibm.com/infocenter/comphelp/v7v91/index.jsp

• Git Guide

http://rogerdudler.github.io/git-guide/

• Cheat Sheets

VIM editor
https://www.cfa.harvard.edu/~jbattat/computer/python/science/idl-numpy.html
alterative

• Python NumPy

https://www.cfa.harvard.edu/~jbattat/computer/python/science/idl-numpy.html
aternative

Chemistry

• Encyclopedia of Computational Chemistry

http://onlinelibrary.wiley.com/book/10.1002/0470845015

• Electron Scattering

Book Chapter: Atomic Confinement
http://www.springerlink.com/content/h771145771601408/

• Some notes in Parameters for Molecular Mechanics

http://www.bmb.uga.edu/wampler/8200/parameters/index.htm

• Density Functional Perturbation Theory

http://link.springer.com/chapter/10.1007/978-3-319-08320-9_3

• Modeling Marvels

Computational Anticipation of Novel Molecules

14. Lewars

http://www.springerlink.com/content/l2008l

• Linear-Scaling Techniques in Computational Chemistry and Physics

http://link.springer.com/book/10.1007%2F978-90-481-2853-2

• Springer Book Series: Progress in Theoretical Chemistry and Physics

http://www.springerlink.com/content/1567-7354/

• Techniques and Applications of Quantum Monte Carlo

http://web.ornl.gov/~pk7/thesis/Thesis.html

• DFT Lectures

http://institute.loni.org/dft2011/schedule.php

• MOLECULAR MODELING Jay Ponder

http://dasher.wustl.edu/chem478/

• Molecular optimization

http://www3.nd.edu/~gezelter/Teaching/650/exercises/discover3/#homework

• Resonance Raman Theory

http://www.personal.dundee.ac.uk/~tjdines/Raman/RRTHEORY.HTM

• Cartesian-to-internal

http://www.ccl.net/cca/documents/cartesian-to-internal.shtml

• Einstein coefficients, cross sections, f values, dipole moments, and all that

http://arxiv.org/abs/physics/0202029v1

• Comparing Solid State DFT Codes, Basis Sets and Potentials

http://molmod.ugent.be/DeltaCodesDFT

• Mike tutorial

http://www.tcm.phy.cam.ac.uk/~mdt26/tmo/page18.html

• Engel's web page Normconserving Pseudopotentials

http://th.physik.uni-frankfurt.de/~engel/ncpp.html

• Hartree-Fock equations

http://www.theoretical-physics.net/dev/index.html

• Modeling materials using density functional theory

http://kitchingroup.cheme.cmu.edu/dft-book/dft.html

• Dissertations form Dirac program

http://dirac.chem.sdu.dk/thesis/index.shtml
Federal Office of Research Integrity
http://ori.hhs.gov/general-resources-0

Writing manuals

• Chicago Manual of Style

http://www.chicagomanualofstyle.org/home.html

• Grammar resources

http://writing-program.uchicago.edu/resources/grammar.htm

• Verb Tense Tutorial

http://www.englishpage.com/verbpage/verbtenseintro.html

• Sentence Types

https://owl.english.purdue.edu/owl/resource/573/02/

• Verb Tense Quiz

http://a4esl.org/q/h/vm/verbtense.html

Job marketing

• GCM-HERC webinar on networking

http://www.hercjobs.org/jobseeker_tools/webinars/
http://vimeo.com/33371649

Mathematics

• Abramowitz and Stegun.

Handbook of Mathematical Functions.
http://people.math.sfu.ca/~cbm/aands/page_302.htm

Public speaking

http://speakermix.com
http://en.wikipedia.org/wiki/Public_speaker
https://www.ted.com/
http://www.cs.berkeley.edu/~jrs/speaking.html

Journals

• List of scientific journals

http://www.tcm.phy.cam.ac.uk/~mdt26/science_journals.html

Tutorials

Chemistry

• Computational Chemistry of Complexes of Lanthanides

MOPAC tutorials
http://www.sparkle.pro.br/

• Hands-on Workshop on Density Functional Theory and Beyond: Computational Materials Science for Real Materials

http://cdsagenda5.ictp.it/full_display.php?ida=a12198

• Graduate course on open quantum systems.

A.J. Fisher et al.
http://www.cmmp.ucl.ac.uk/~ajf/course_notes/course_notes.html

• Adresses constructeurs et formations PIR (Proche Infra rouge, Infra rouge, Raman)

http://nte-serveur.univ-lyon1.fr/nte/spectroscopie/docspedagogiques.html

• Car-Parrinello summer school

http://www.impmc.jussieu.fr/~seitsonen/Science/Presentations/Taiwan-juillet-2005/exercises.html

• Quantum chemistry using Quantum-ESPRESSO

http://www.stanford.edu/~hkulik/www/Tutorials/Tutorials.html

• Tutorials in GAMESS

http://www.msg.ameslab.gov/tutorials/tutorials.html

• Tutorials in PCGAMESS

http://www.angelfire.com/pro/riturajkalita/PCGAMESS_Inputs.htm

• Quantum Espresso Manual

http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html
http://www.quantum-espresso.org/wp-content/uploads/Doc/pw_user_guide/

• CP-Quantum Espresso Manual

http://www.quantum-espresso.org/wp-content/uploads/Doc/cp_user_guide/user_guide.html
http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_cp.html

Computer Science

• Using the Massively Parallel Quantum Chemistry Program Version 2.2

http://www.mpqc.org/talks/user/text0.html

• Free book – Optimizing HPC Applications with Intel Cluster Tools

http://www.techenablement.com/free-ebook-optimizing-hpc-applications-intel-cluster-tools/

• Valgrind Quick Start

http://valgrind.org/docs/manual/quick-start.html
/usr/local/mpich-install/bin/mpirun -np 8 valgrind --tool=callgrind ./tubinarioexecutable parameter_filke.in

Notes In IBM/Q

• Portable Hardware Locality (hwloc) Documentation: v1.1

http://www.open-mpi.org/projects/hwloc/doc/v1.1/index.php

• Compilers for IBM/Q manual

http://pic.dhe.ibm.com/infocenter/compbg/v121v141/index.jsp

• Advanced Scientific Computing

http://www.mcs.anl.gov/~hzhang/teach/cs595/

Machine Learning

• Practical machine learning: methods and algorithmics

http://www.cbcb.umd.edu/~hcorrada/PracticalML/
http://statweb.stanford.edu/~tibs/ElemStatLearn/

• Machine Learning for Many-Particle Systems - IPAM Workshop Feb 2015

https://www.ipam.ucla.edu/programs/workshops/machine-learning-for-many-particle-systems/?tab=schedule

Lectures

• The Feynman Lectures on Physics, Volume I

http://www.feynmanlectures.caltech.edu/I_toc.html

• 2007 Summer School on Computational Materials Science

Quantum Monte Carlo from Minerals and Materials to Molecules
http://www.mcc.uiuc.edu/summerschool/2007/qmc/

• Computational Chemistry (CHEM 4021/8021) Chris Cramer

http://pollux.chem.umn.edu/8021/Lectures/

• Introduction to Computer Science and Programming

http://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-00-introduction-to-computer-science-and-programming-fall-2008/

• 2014 Summer School on Electronic Structure Theory

http://www.ipam.ucla.edu/programs/summer-schools/hands-on-summer-school-electronic-structure-theory-for-materials-and-biomolecules/?tab=schedule

• ATPESC Lectures

http://extremecomputingtraining.anl.gov/

General

• The Universal Digital Library

http://www.ulib.org/index.html

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