## Using multiple softwares for performing a simulation

### Re: Using multiple softwares for performing a simulation

https://askubuntu.com/questions/500647/ ... hard-drive

The Programming Languages Beacon

Thermal conductivity of fluids with nanoparticles

1. Enhancing the thermal conductivity of fluids with nanoparticles

2. https://www.sciencedirect.com/science/a ... 7X99000673

3. https://www.sciencedirect.com/science/a ... 1009001069

4. https://www.crcpress.com/Heat-Transfer- ... 1138749481

5. https://pubs.acs.org/doi/abs/10.1021/ie403712f

6. https://engineering.purdue.edu/NanoLab/ ... ixture.pdf

7. https://www.sciencedirect.com/science/a ... 1114004542

8. https://www.sciencedirect.com/science/a ... 0217301431

9. PhD dissertation on nanoscale heat transfer process in nanostructures by Jihong Ma (2017)

Research works in Biology and Environment

1. https://cbd.vib.be/research/groups/

2.Finite element modeling on welding phenomena

3. https://eco.pusan.ac.kr/eco/index..do

4. https://wiki.aalto.fi/display/AEEproject/Smart-bike

The Programming Languages Beacon

Thermal conductivity of fluids with nanoparticles

1. Enhancing the thermal conductivity of fluids with nanoparticles

2. https://www.sciencedirect.com/science/a ... 7X99000673

3. https://www.sciencedirect.com/science/a ... 1009001069

4. https://www.crcpress.com/Heat-Transfer- ... 1138749481

5. https://pubs.acs.org/doi/abs/10.1021/ie403712f

6. https://engineering.purdue.edu/NanoLab/ ... ixture.pdf

7. https://www.sciencedirect.com/science/a ... 1114004542

8. https://www.sciencedirect.com/science/a ... 0217301431

9. PhD dissertation on nanoscale heat transfer process in nanostructures by Jihong Ma (2017)

Research works in Biology and Environment

1. https://cbd.vib.be/research/groups/

2.Finite element modeling on welding phenomena

3. https://eco.pusan.ac.kr/eco/index..do

4. https://wiki.aalto.fi/display/AEEproject/Smart-bike

Last edited by annier on 21 Sep 2018, 01:32, edited 2 times in total.

Anil Kunwar

Department of Materials Engineering, KU Leuven, Belgium

Department of Materials Engineering, KU Leuven, Belgium

### Re: Using multiple softwares for performing a simulation

Crystallography general softwares available at github:

1. Advanced Simulation Library (ASL)

2. https://github.com/AvtechScientific/ASL ... mples/flow

3. Computational Crystallography Toolbox (cctbx)

4. https://github.com/cctbx/cctbx_project

5.https://en.wikipedia.org/wiki/OpenCL

6. https://askubuntu.com/questions/796770/ ... -on-ubuntu

Tutorials on Phase Field Method with Fluid Flow

1. http://www.lorentzcenter.nl/lc/web/2010 ... derson.pdf

2. https://link.springer.com/article/10.10 ... 009-3924-7

3. https://www.math.ust.hk/~mawang/researc ... -shiyi.pdf

4. https://www.sciencedirect.com/science/a ... via%3Dihub

5. https://math.nist.gov/~GMcFadden/solder.html

1. Advanced Simulation Library (ASL)

2. https://github.com/AvtechScientific/ASL ... mples/flow

3. Computational Crystallography Toolbox (cctbx)

4. https://github.com/cctbx/cctbx_project

5.https://en.wikipedia.org/wiki/OpenCL

6. https://askubuntu.com/questions/796770/ ... -on-ubuntu

Tutorials on Phase Field Method with Fluid Flow

1. http://www.lorentzcenter.nl/lc/web/2010 ... derson.pdf

2. https://link.springer.com/article/10.10 ... 009-3924-7

3. https://www.math.ust.hk/~mawang/researc ... -shiyi.pdf

4. https://www.sciencedirect.com/science/a ... via%3Dihub

5. https://math.nist.gov/~GMcFadden/solder.html

Anil Kunwar

Department of Materials Engineering, KU Leuven, Belgium

Department of Materials Engineering, KU Leuven, Belgium

### Re: Using multiple softwares for performing a simulation

Wetting boundary conditions for Phase Field Models

1. https://onlinelibrary.wiley.com/doi/abs ... 2/fld.3975

2. https://link.springer.com/article/10.10 ... 015-9551-2

Additive Layer Manufacturing (ALM) of Aluminum

1. https://www.farinia.com/additive-manufa ... ufacturing

2. Y.S. Hwang's dissertation on multiphysics PFM for melting and superheating of Al nanolayer and nanoparticles

Solid Mechanics and Tensor Mechanics of Cu6Sn5 IMC

1. Stress analysis on intermetallics compounds S.F. Choudhary, 2016

2. https://www.sciencedirect.com/science/a ... via%3Dihub

3. https://link.springer.com/content/pdf/1 ... 0911-3.pdf

4. https://www.sciencedirect.com/science/a ... 5416300933

Conversion of bibliography from ris format to bibtex format

1. https://www.bruot.org/ris2bib/

Research group of Professor Ying Sun

Complex fluid and multiphase transport laboratory

Research works and scientific contributions from Professor Nestler's Laboratory and University

https://www.iam.kit.edu/cms/english/Ver ... hungen.php

Tensorlab and Matlab Works

1. https://www.tensorlab.net/

2. http://pajarito.materials.cmu.edu/rolle ... 4Feb16.pdf

3. http://mtex-toolbox.github.io/

4. http://prism.mit.edu/xray/documents/7%2 ... igures.pdf

5. https://groups.google.com/forum/?fromgr ... m/mtexmail

Bioinformatics

1. Software (Opensource) for bioinformatics (for leukemia treatment) developed primarily in INRIA

2. Bonsai project

3. Role of bioinformatics in fighting leukemia

4. https://cs.wmich.edu/elise/courses/cs60 ... ation3.pdf

5. https://www.novusbio.com/diseases/leukemia

6. http://neuron.mefst.hr/docs/katedre/fiz ... ology).pdf

Python language for data analysis

1. Analytics vidhya

Phase field modeling of welding and precipitation/dissolution

1. PFM of welding and numerical optimization

2. https://aip.scitation.org/doi/pdf/10.1063/1.2948949

http://pubs.rsc.org/en/Content/ArticleH ... c6ra28628c

https://www.sciencedirect.com/science/a ... 5495002359

Dissertation by Hai Fu

https://aip.scitation.org/doi/abs/10.1063/1.2102907

Basics of Ternary Phase Diagram

Research works on complex fluids & Multiphase transport laboratory

Parallel MD simualtions of oxidation dynamics and reactive wetting in metal/ceramic systems

Dissertation phase field model for surface energy driven processes by Klara Asp Gronhagen

Gantt Charts in Latex

1. http://www.martin-kumm.de/wiki/doku.php ... antt_plots

2. http://texdoc.net/texmf-dist/doc/latex/ ... fgantt.pdf

tutorials from stack-exchanges

1. https://tex.stackexchange.com/questions ... antt-chart

2. https://tex.stackexchange.com/questions ... -left-side

3. https://tex.stackexchange.com/questions ... chart?rq=1

4. https://tex.stackexchange.com/questions ... bar-labels

5. https://tex.stackexchange.com/questions ... recognised

latex template for KU Leuven presentation slides

Research Portal

1. Professor Nele Moelans

2. Dr. David Seveno

3. Dr. Muxing Guo

4. Professor Bart Blanpain

5. Professor Patrick Wollants

Latex templates for CV

1. https://www.quora.com/What-are-some-ele ... cademic-CV

2. http://www.tjansson.dk/2009/03/writing-a-cv-in-latex/

Aluminides in turbine blades

1. http://www.phase-trans.msm.cam.ac.uk/20 ... index.html

1. https://onlinelibrary.wiley.com/doi/abs ... 2/fld.3975

2. https://link.springer.com/article/10.10 ... 015-9551-2

Additive Layer Manufacturing (ALM) of Aluminum

1. https://www.farinia.com/additive-manufa ... ufacturing

2. Y.S. Hwang's dissertation on multiphysics PFM for melting and superheating of Al nanolayer and nanoparticles

Solid Mechanics and Tensor Mechanics of Cu6Sn5 IMC

1. Stress analysis on intermetallics compounds S.F. Choudhary, 2016

2. https://www.sciencedirect.com/science/a ... via%3Dihub

3. https://link.springer.com/content/pdf/1 ... 0911-3.pdf

4. https://www.sciencedirect.com/science/a ... 5416300933

Conversion of bibliography from ris format to bibtex format

1. https://www.bruot.org/ris2bib/

Research group of Professor Ying Sun

Complex fluid and multiphase transport laboratory

Research works and scientific contributions from Professor Nestler's Laboratory and University

https://www.iam.kit.edu/cms/english/Ver ... hungen.php

Tensorlab and Matlab Works

1. https://www.tensorlab.net/

2. http://pajarito.materials.cmu.edu/rolle ... 4Feb16.pdf

3. http://mtex-toolbox.github.io/

4. http://prism.mit.edu/xray/documents/7%2 ... igures.pdf

5. https://groups.google.com/forum/?fromgr ... m/mtexmail

Bioinformatics

1. Software (Opensource) for bioinformatics (for leukemia treatment) developed primarily in INRIA

2. Bonsai project

3. Role of bioinformatics in fighting leukemia

4. https://cs.wmich.edu/elise/courses/cs60 ... ation3.pdf

5. https://www.novusbio.com/diseases/leukemia

6. http://neuron.mefst.hr/docs/katedre/fiz ... ology).pdf

Python language for data analysis

1. Analytics vidhya

Phase field modeling of welding and precipitation/dissolution

1. PFM of welding and numerical optimization

2. https://aip.scitation.org/doi/pdf/10.1063/1.2948949

http://pubs.rsc.org/en/Content/ArticleH ... c6ra28628c

https://www.sciencedirect.com/science/a ... 5495002359

Dissertation by Hai Fu

https://aip.scitation.org/doi/abs/10.1063/1.2102907

Basics of Ternary Phase Diagram

Research works on complex fluids & Multiphase transport laboratory

Parallel MD simualtions of oxidation dynamics and reactive wetting in metal/ceramic systems

Dissertation phase field model for surface energy driven processes by Klara Asp Gronhagen

Gantt Charts in Latex

1. http://www.martin-kumm.de/wiki/doku.php ... antt_plots

2. http://texdoc.net/texmf-dist/doc/latex/ ... fgantt.pdf

tutorials from stack-exchanges

1. https://tex.stackexchange.com/questions ... antt-chart

2. https://tex.stackexchange.com/questions ... -left-side

3. https://tex.stackexchange.com/questions ... chart?rq=1

4. https://tex.stackexchange.com/questions ... bar-labels

5. https://tex.stackexchange.com/questions ... recognised

latex template for KU Leuven presentation slides

Research Portal

1. Professor Nele Moelans

2. Dr. David Seveno

3. Dr. Muxing Guo

4. Professor Bart Blanpain

5. Professor Patrick Wollants

Latex templates for CV

1. https://www.quora.com/What-are-some-ele ... cademic-CV

2. http://www.tjansson.dk/2009/03/writing-a-cv-in-latex/

Aluminides in turbine blades

1. http://www.phase-trans.msm.cam.ac.uk/20 ... index.html

Anil Kunwar

Department of Materials Engineering, KU Leuven, Belgium

Department of Materials Engineering, KU Leuven, Belgium

### Re: Using multiple softwares for performing a simulation

Notes on non-linearity of Navier-Stokes equations:

1. Reynold's number and turbulence

2. https://math.unice.fr/~musacchi/tesi/node5.html

Multiphysics simulations of hotspot cooling:

1. https://www.comsol.com/paper/download/2 ... _paper.pdf

2. http://forum.notebookreview.com/threads ... ks.800890/

3. https://link.springer.com/content/pdf/1 ... 060049.pdf

4. https://pubs.acs.org/doi/abs/10.1021/acsami.5b10769

Langevin Noise

1.documentation on langevin noise

2. Langevin noise for electrodeposits

3. Discussion on langevin noise

4. Kernel for Langevin noise

5. Discrete nucleation theory description

6. More discussion on steps 2

1. Reynold's number and turbulence

2. https://math.unice.fr/~musacchi/tesi/node5.html

Multiphysics simulations of hotspot cooling:

1. https://www.comsol.com/paper/download/2 ... _paper.pdf

2. http://forum.notebookreview.com/threads ... ks.800890/

3. https://link.springer.com/content/pdf/1 ... 060049.pdf

4. https://pubs.acs.org/doi/abs/10.1021/acsami.5b10769

Langevin Noise

1.documentation on langevin noise

2. Langevin noise for electrodeposits

3. Discussion on langevin noise

4. Kernel for Langevin noise

5. Discrete nucleation theory description

6. More discussion on steps 2

Last edited by annier on 20 Sep 2018, 05:19, edited 6 times in total.

Anil Kunwar

Department of Materials Engineering, KU Leuven, Belgium

Department of Materials Engineering, KU Leuven, Belgium

### Re: Using multiple softwares for performing a simulation

Windows subsystem for linux (WSL)

1. Installation of VcXsrv followed by installation of nautilus and grsync
2. Transfer of files from Windows to Ubuntu , and vice-versa

a. Windows to Ubuntu file transfers

Reference: https://stackoverflow.com/questions/425 ... -subsystem
b. Ubuntu to Windows file transfers

Reference: https://superuser.com/questions/1110974 ... ows-10-wsl
3. Conda environment and python versions

Reference: https://conda.io/docs/user-guide/tasks/ ... ython.html

and,

https://www.digitalocean.com/community/ ... quickstart

If conda is installed with python3, then conda environment for python 2.7 can be utilized via:
For activation of python2 environment
For deactivating the active environment
Notes: For newer versions of Anaconda,

If your shell is Bash or a Bourne variant, enable conda for the current user with

or, for all users, enable conda with

The above options replace the following task:

4. Alias of paraFoam as builtin in Ubuntu (WSL)

https://www.cfd-online.com/Forums/openf ... linux.html

1. Installation of VcXsrv followed by installation of nautilus and grsync

Code: Select all

`$ sudo apt install nautilus && sudo apt install grsync`

a. Windows to Ubuntu file transfers

Reference: https://stackoverflow.com/questions/425 ... -subsystem

Code: Select all

`$ cd /mnt/c/Users/<ubuntu.username>/Pictures`

Reference: https://superuser.com/questions/1110974 ... ows-10-wsl

Code: Select all

`C:\Users\<ubuntu.username>\AppData\Local\lxss`

Reference: https://conda.io/docs/user-guide/tasks/ ... ython.html

and,

https://www.digitalocean.com/community/ ... quickstart

If conda is installed with python3, then conda environment for python 2.7 can be utilized via:

Code: Select all

`$ conda create -n py27 python=2.7 anaconda`

Code: Select all

` $ source activate py27`

Code: Select all

` (py27) ...$ source deactivate `

If your shell is Bash or a Bourne variant, enable conda for the current user with

Code: Select all

` $ echo ". /home/romagurung/anaconda3/etc/profile.d/conda.sh" >> ~/.bashrc`

Code: Select all

` $ sudo ln -s /home/romagurung/anaconda3/etc/profile.d/conda.sh /etc/profile.d/conda.sh`

Code: Select all

` $ echo "export PATH="/home/romagurung/anaconda3/bin:$PATH" " >> ~/.bashrc`

4. Alias of paraFoam as builtin in Ubuntu (WSL)

https://www.cfd-online.com/Forums/openf ... linux.html

Anil Kunwar

Department of Materials Engineering, KU Leuven, Belgium

Department of Materials Engineering, KU Leuven, Belgium

### Re: Using multiple softwares for performing a simulation

Tutorials on using github repository

1. on git username and emails

2. https://stackoverflow.com/questions/847 ... cked-files

3. https://confluence.atlassian.com/bitbuc ... 20876.html

4. beginners tutorial

5. http://www.mooseframework.org/old/create-an-app/

6. How to get the local files from online repository when they are deleted locally ($ git checkout -f HEAD)

Website of crossref for finding data of research works

1. https://search.crossref.org/

Computing Jacobian Matrix of Finite Element

1.0 https://scicomp.stackexchange.com/quest ... te-element

Lattice Boltzmann Method in Fluid Mechanics

1. https://pypi.org/project/pyLBM/0.2.1/

2. pyLBM software

3. http://www.palabos.org/forum/read.php?9,5783

4. http://wiki.palabos.org/numerics:codes

5. https://scicomp.stackexchange.com/quest ... nn-solvers

6. https://www.sciencedirect.com/science/a ... 5517301017

1. on git username and emails

2. https://stackoverflow.com/questions/847 ... cked-files

3. https://confluence.atlassian.com/bitbuc ... 20876.html

4. beginners tutorial

5. http://www.mooseframework.org/old/create-an-app/

6. How to get the local files from online repository when they are deleted locally ($ git checkout -f HEAD)

Website of crossref for finding data of research works

1. https://search.crossref.org/

Computing Jacobian Matrix of Finite Element

1.0 https://scicomp.stackexchange.com/quest ... te-element

Lattice Boltzmann Method in Fluid Mechanics

1. https://pypi.org/project/pyLBM/0.2.1/

2. pyLBM software

3. http://www.palabos.org/forum/read.php?9,5783

4. http://wiki.palabos.org/numerics:codes

5. https://scicomp.stackexchange.com/quest ... nn-solvers

6. https://www.sciencedirect.com/science/a ... 5517301017

Last edited by annier on 09 Oct 2019, 18:56, edited 1 time in total.

Anil Kunwar

Department of Materials Engineering, KU Leuven, Belgium

Department of Materials Engineering, KU Leuven, Belgium

### Re: Using multiple softwares for performing a simulation

PRISMS-PF software

1. An opensource framework for PFM

2. Opensource finite element library

3. https://prisms-center.github.io/phaseFi ... ereqs.html

4. https://github.com/prisms-center/phaseField

5. http://www.prisms-center.org/#/ctools/software

6. Installation of cmake in ubuntu

7. docker for software installations

8. https://groups.google.com/forum/#!topic ... l7uZ1Exw5o

Software installation guide in HPC cluster

1. general method

Research Profiles

1. Professor Qing Peng and his research works

Research group on rechargeable Li ion battery

1. https://cmtl.uic.edu/research4.html

Language and literature arts

1. dutch grammar in forum word reference

2. dutch grammar noun and articles

HPC introduction

1. https://hpcc.usc.edu/gettingstarted/

2. https://lammps.sandia.gov/workshops/Aug17/pdf/moore.pdf

3. http://www.afs.enea.it/software/lammps/ ... ml#start_6

4. https://linuxcluster.wordpress.com/2016 ... i-and-gnu/

Machine Learning some useful concepts

1. https://stackoverflow.com/questions/185 ... ation-gain

2. https://en.wikipedia.org/wiki/Truth_table

3. https://medium.com/swlh/shannon-entropy ... aee2709e32

4. https://en.wikipedia.org/wiki/List_of_logic_symbols

5. http://www.math.unipd.it/~aiolli/corsi/ ... /Lez12.pdf

6. https://www3.nd.edu/~rjohns15/cse40647. ... es%202.pdf

7. https://en.wikipedia.org/wiki/Information_gain_ratio

8. https://developers.google.com/machine-l ... oc-and-auc

9. https://www.medcalc.org/manual/roc-curves.php

10. https://medium.com/datadriveninvestor/u ... 706fb710cb

11. https://docs.eyesopen.com/toolkits/cook ... g/roc.html

12. http://gim.unmc.edu/dxtests/roc2.htm

13. Lecture slides on inductive logic programming (ILP)

14. Leture slides in ILP

15.Neural networks and backpropagation

Grand potential

1. Phase diagram

Machine Learning

1. Convex hull for ROC curves

2. Probability approximately correct (PAC) learning

3. Interactive tutorials on numerical optimization by Ben Frederickson

4. Lecture notes on loss functions and numerical optimization

ThermoCALC and computational thermodynamics

1. Thermodynamic description of Cu-Bi system

2. Thermodynamic description of Cu-Sn system

3. Presentation on DICTRA software

4. Documentation on ThermoCALC software

5. Princples and methods on elementary phase diagrams

6. Notes on thermodynqmic modeling and calphad

7. Introduction to CALPHAD method and CEF (Compound Energy Formalism)

8. CALPHAD method and its roles in materials model and process developments (U.R. Kattner)

9. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4912057/

10. Thermodynamic description of Ni-Al-O system

11. Thermodynamics of Ni-Al-O by Elrefaie1981

12. Oxidation of Ni-Cr-Al study by Mueller2007

13. NIST repository for thermodynamic database

14. Thermodynamic description of reactive kinetics in Ni-Al nanolayers

15. Lecture on thermodynamics and statistical mechanics

16. Research profile of Professor Olga Fabrichnaya

17. Yue Li's work on computational thermodynamics

18. Composition of co-existing phases and common-tangent

19. TEA and calculation of thermochemical equilibrium advances

20. Gibbs free energy of multiphase mixtures at equilibrium

21. Common tangent function in python

22. Common tangent construction using MATLAB

23. Using markers during using plot command in MATLAB

The plot command is used for general plot , whereas fplot (and, ezplot) commands are used for plotting functions using symbolic expressions.

pdf to word converter and other tools

1. https://pdf2doc.com/

2. https://www.duplichecker.com/

Fluid flow in electrochemical systems

1. Dissertation in 2012 by G. Bauer

2. Poster on coupled fluid flow and electrochemistry by Bauer et al, 2009

https://www.desmos.com/calculator

Opensource Softwares for Renewable Energy Systems

1 .https://sam.nrel.gov/

2. https://openmod-initiative.org/

3. Questions and reply at research gate

mechanoChem project

Thermo-Calc and thermodynamic database

1. Kyle Deane's masteral dissertation

2. Introduction for thermodynamic modeling

3. https://sites.ualberta.ca/~ccwj/teachin ... hermocalc/

4. http://www.dema.ufscar.br/wjbotta/posgr ... amples.pdf

5. http://www.crct.polymtl.ca/thermo_databases.html

6. http://www.materials.ucsb.edu/~nsf/pape ... Al-PRB.pdf

7. T.R. Elliot 2012 Dissertation on gibbs energy modeling for binary and ternary systems

8. chemical potential of a species i as the partial molar gibbs free energy of i

pycalphad and related database

1. Marker2017-Dissertation

2. Discussions on chemical potential with pycalphad

Polynomial Fitting of CALPHAD expressions

1. parabolic fitting in dissertation of A.N. Choudhury 2012

2. least square method and fsolve method to find common tangent of curves

Finite element method in electrochemistry

1. Relation betweed diffusivity and chemical potential

2. Relation between mobility and diffusivity

3. Nernst-Planck Equation

4. Elmer wiki page for Nernst Planck equation

Dielectric properties of biological tissues

1. compilation of dielectric properties by Gabriel and Gabriel

2. Calculator of dielectric properties at several frequencies

Thermodynamic database and CALPHAD literature

1. The fundamentals of thermodynamic database

2. Thermodynamic description of ternary Sn Ag Cu system

a. Sn, Ag and Cu phase can be considered as regular solutions.

b. Ag3Sn treated as line compounds

c. Cu3Sn and Cu6Sn5 treated as stoichiometric compounds.

Reference: Doi et al, Materials Transactions, 45 (2004)

Phase Diagrams and Gibbs Free Energy in Metallurgy

1. Beginner's tutorial in phase diagram and gibbs free energy

Python Tutorials

Kitchin's work in python for computational science and engineering

basic tutorials in using conda environment

https://realpython.com/python3-object-o ... ogramming/

Neural Network literatures \Neural network with autograd

1. http://kitchingroup.cheme.cmu.edu/blog/ ... /python/3/

2. http://neuralnetworksanddeeplearning.com/chap4.html

3. https://www.analyticsvidhya.com/blog/20 ... -learning/

4. https://skymind.ai/wiki/neural-network

5. neural network with numpy

6. https://www.kdnuggets.com/2018/10/simpl ... ython.html

7. https://towardsdatascience.com/how-to-b ... 998a08e4f6

8. neural network in eleven lines of python

9. https://www.programiz.com/python-programming/array

10. Samay's tutorial on neural network and machine learning

11. Terms and definitions in neural network

12. Mukul's tutorial on neural networks

13. Supervised learning and activation functions f(z) for neural networks

14. works of Alex Krizhevsky

15. Neural networks in python

16. a good tutorial for neural networks in python

17. Definition of bias in neural networks

18. zip() function in python

19. zip and unzip in python

20. a simple neural network tutorial in tensorflow

21. Install scikit tool in anaconda environment

22. Alan Turing's work on artificial neural network

23. Efficient BackPropagation

24. Data normalization and standardisation methods or procedures in neural networks

25. Illustration of neural network with backpropagation

26. Implementation of back propagation in neural networks

27. Cost function and gradient descent method in machine learning

28. a Tensors and machine learning

b. Implementation of backpropagation algorithm i n machine learning using python

29. Creating a neural network with python

30. Bias and variance in neural network calculation

31. The bias variables in neural networks - illustration

32. Mathematical optimization using scipy

33. Multiple rows and columns selection using Pandas

34. seacas software

35. pandas documentation

36. https://medium.com/dunder-data/selectin ... cd0170be9c

37. https://www.geeksforgeeks.org/how-to-se ... dataframe/

38. Boolean commands for panda

39. Documentation of Panda for Boolean indexing

40. https://medium.com/dunder-data/selectin ... e811c81a0c

41. https://www.geeksforgeeks.org/boolean-i ... in-pandas/

42. https://pandas.pydata.org/pandas-docs/s ... o_csv.html

43. Neural network with structured datasets

Concepts of dropout technique in neural networks

44. https://iamtrask.github.io/2015/07/28/dropout/

45. http://iamtrask.github.io/2015/07/27/py ... ork-part2/

46. https://www.python-course.eu/neural_net ... ropout.php

47. https://visualstudiomagazine.com/articl ... opout.aspx

48. https://wiseodd.github.io/techblog/2016/06/25/dropout/

Neural networks in melanoma research

49. Using neural networks in classification of lesions

50. Derivative of ReLU function

Mean Square Error (MSE) in Neural Networks

1. Definition of MSE in feedforward neural network with backward propagation

2. Illustration of figure for MSE in neural network

3. http://neuralnetworksanddeeplearning.com/chap2.html

4. Tutorial on multilayer feed-forward neural networks

5. Improving the performance of neural network

Video Splitter in Linux

1. https://itsfoss.com/best-video-editing-software-linux/

2. https://jliljebl.github.io/flowblade/webhelp/help.html

3. https://itsfoss.com/losslesscut-video-cutter/

4. https://itsfoss.com/vidcutter-video-editor-linux/

Crystal Plasticity in MOOSE Framework

Bachelor's Thesis by Viktor Hultgren 2018

1. An opensource framework for PFM

2. Opensource finite element library

3. https://prisms-center.github.io/phaseFi ... ereqs.html

4. https://github.com/prisms-center/phaseField

5. http://www.prisms-center.org/#/ctools/software

6. Installation of cmake in ubuntu

7. docker for software installations

8. https://groups.google.com/forum/#!topic ... l7uZ1Exw5o

Software installation guide in HPC cluster

1. general method

Research Profiles

1. Professor Qing Peng and his research works

Research group on rechargeable Li ion battery

1. https://cmtl.uic.edu/research4.html

Language and literature arts

1. dutch grammar in forum word reference

2. dutch grammar noun and articles

HPC introduction

1. https://hpcc.usc.edu/gettingstarted/

2. https://lammps.sandia.gov/workshops/Aug17/pdf/moore.pdf

3. http://www.afs.enea.it/software/lammps/ ... ml#start_6

4. https://linuxcluster.wordpress.com/2016 ... i-and-gnu/

Machine Learning some useful concepts

1. https://stackoverflow.com/questions/185 ... ation-gain

2. https://en.wikipedia.org/wiki/Truth_table

3. https://medium.com/swlh/shannon-entropy ... aee2709e32

4. https://en.wikipedia.org/wiki/List_of_logic_symbols

5. http://www.math.unipd.it/~aiolli/corsi/ ... /Lez12.pdf

6. https://www3.nd.edu/~rjohns15/cse40647. ... es%202.pdf

7. https://en.wikipedia.org/wiki/Information_gain_ratio

8. https://developers.google.com/machine-l ... oc-and-auc

9. https://www.medcalc.org/manual/roc-curves.php

10. https://medium.com/datadriveninvestor/u ... 706fb710cb

11. https://docs.eyesopen.com/toolkits/cook ... g/roc.html

12. http://gim.unmc.edu/dxtests/roc2.htm

13. Lecture slides on inductive logic programming (ILP)

14. Leture slides in ILP

15.Neural networks and backpropagation

Grand potential

1. Phase diagram

Machine Learning

1. Convex hull for ROC curves

2. Probability approximately correct (PAC) learning

3. Interactive tutorials on numerical optimization by Ben Frederickson

4. Lecture notes on loss functions and numerical optimization

ThermoCALC and computational thermodynamics

1. Thermodynamic description of Cu-Bi system

2. Thermodynamic description of Cu-Sn system

3. Presentation on DICTRA software

4. Documentation on ThermoCALC software

5. Princples and methods on elementary phase diagrams

6. Notes on thermodynqmic modeling and calphad

7. Introduction to CALPHAD method and CEF (Compound Energy Formalism)

8. CALPHAD method and its roles in materials model and process developments (U.R. Kattner)

9. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4912057/

10. Thermodynamic description of Ni-Al-O system

11. Thermodynamics of Ni-Al-O by Elrefaie1981

12. Oxidation of Ni-Cr-Al study by Mueller2007

13. NIST repository for thermodynamic database

14. Thermodynamic description of reactive kinetics in Ni-Al nanolayers

15. Lecture on thermodynamics and statistical mechanics

16. Research profile of Professor Olga Fabrichnaya

17. Yue Li's work on computational thermodynamics

18. Composition of co-existing phases and common-tangent

19. TEA and calculation of thermochemical equilibrium advances

20. Gibbs free energy of multiphase mixtures at equilibrium

21. Common tangent function in python

22. Common tangent construction using MATLAB

23. Using markers during using plot command in MATLAB

The plot command is used for general plot , whereas fplot (and, ezplot) commands are used for plotting functions using symbolic expressions.

pdf to word converter and other tools

1. https://pdf2doc.com/

2. https://www.duplichecker.com/

Fluid flow in electrochemical systems

1. Dissertation in 2012 by G. Bauer

2. Poster on coupled fluid flow and electrochemistry by Bauer et al, 2009

https://www.desmos.com/calculator

Opensource Softwares for Renewable Energy Systems

1 .https://sam.nrel.gov/

2. https://openmod-initiative.org/

3. Questions and reply at research gate

mechanoChem project

Thermo-Calc and thermodynamic database

1. Kyle Deane's masteral dissertation

2. Introduction for thermodynamic modeling

3. https://sites.ualberta.ca/~ccwj/teachin ... hermocalc/

4. http://www.dema.ufscar.br/wjbotta/posgr ... amples.pdf

5. http://www.crct.polymtl.ca/thermo_databases.html

6. http://www.materials.ucsb.edu/~nsf/pape ... Al-PRB.pdf

7. T.R. Elliot 2012 Dissertation on gibbs energy modeling for binary and ternary systems

8. chemical potential of a species i as the partial molar gibbs free energy of i

pycalphad and related database

1. Marker2017-Dissertation

2. Discussions on chemical potential with pycalphad

Polynomial Fitting of CALPHAD expressions

1. parabolic fitting in dissertation of A.N. Choudhury 2012

2. least square method and fsolve method to find common tangent of curves

Finite element method in electrochemistry

1. Relation betweed diffusivity and chemical potential

2. Relation between mobility and diffusivity

3. Nernst-Planck Equation

4. Elmer wiki page for Nernst Planck equation

Dielectric properties of biological tissues

1. compilation of dielectric properties by Gabriel and Gabriel

2. Calculator of dielectric properties at several frequencies

Thermodynamic database and CALPHAD literature

1. The fundamentals of thermodynamic database

2. Thermodynamic description of ternary Sn Ag Cu system

a. Sn, Ag and Cu phase can be considered as regular solutions.

b. Ag3Sn treated as line compounds

c. Cu3Sn and Cu6Sn5 treated as stoichiometric compounds.

Reference: Doi et al, Materials Transactions, 45 (2004)

Phase Diagrams and Gibbs Free Energy in Metallurgy

1. Beginner's tutorial in phase diagram and gibbs free energy

Python Tutorials

Kitchin's work in python for computational science and engineering

basic tutorials in using conda environment

https://realpython.com/python3-object-o ... ogramming/

Neural Network literatures \Neural network with autograd

1. http://kitchingroup.cheme.cmu.edu/blog/ ... /python/3/

2. http://neuralnetworksanddeeplearning.com/chap4.html

3. https://www.analyticsvidhya.com/blog/20 ... -learning/

4. https://skymind.ai/wiki/neural-network

5. neural network with numpy

6. https://www.kdnuggets.com/2018/10/simpl ... ython.html

7. https://towardsdatascience.com/how-to-b ... 998a08e4f6

8. neural network in eleven lines of python

9. https://www.programiz.com/python-programming/array

10. Samay's tutorial on neural network and machine learning

11. Terms and definitions in neural network

12. Mukul's tutorial on neural networks

13. Supervised learning and activation functions f(z) for neural networks

14. works of Alex Krizhevsky

15. Neural networks in python

16. a good tutorial for neural networks in python

17. Definition of bias in neural networks

18. zip() function in python

19. zip and unzip in python

20. a simple neural network tutorial in tensorflow

21. Install scikit tool in anaconda environment

22. Alan Turing's work on artificial neural network

23. Efficient BackPropagation

24. Data normalization and standardisation methods or procedures in neural networks

25. Illustration of neural network with backpropagation

26. Implementation of back propagation in neural networks

27. Cost function and gradient descent method in machine learning

28. a Tensors and machine learning

b. Implementation of backpropagation algorithm i n machine learning using python

29. Creating a neural network with python

30. Bias and variance in neural network calculation

31. The bias variables in neural networks - illustration

32. Mathematical optimization using scipy

**Pandas and SEACAS for reading data**33. Multiple rows and columns selection using Pandas

34. seacas software

35. pandas documentation

36. https://medium.com/dunder-data/selectin ... cd0170be9c

37. https://www.geeksforgeeks.org/how-to-se ... dataframe/

38. Boolean commands for panda

39. Documentation of Panda for Boolean indexing

40. https://medium.com/dunder-data/selectin ... e811c81a0c

41. https://www.geeksforgeeks.org/boolean-i ... in-pandas/

42. https://pandas.pydata.org/pandas-docs/s ... o_csv.html

43. Neural network with structured datasets

Concepts of dropout technique in neural networks

44. https://iamtrask.github.io/2015/07/28/dropout/

45. http://iamtrask.github.io/2015/07/27/py ... ork-part2/

46. https://www.python-course.eu/neural_net ... ropout.php

47. https://visualstudiomagazine.com/articl ... opout.aspx

48. https://wiseodd.github.io/techblog/2016/06/25/dropout/

Neural networks in melanoma research

49. Using neural networks in classification of lesions

50. Derivative of ReLU function

Mean Square Error (MSE) in Neural Networks

1. Definition of MSE in feedforward neural network with backward propagation

2. Illustration of figure for MSE in neural network

3. http://neuralnetworksanddeeplearning.com/chap2.html

4. Tutorial on multilayer feed-forward neural networks

5. Improving the performance of neural network

Video Splitter in Linux

1. https://itsfoss.com/best-video-editing-software-linux/

2. https://jliljebl.github.io/flowblade/webhelp/help.html

3. https://itsfoss.com/losslesscut-video-cutter/

4. https://itsfoss.com/vidcutter-video-editor-linux/

Crystal Plasticity in MOOSE Framework

Bachelor's Thesis by Viktor Hultgren 2018

Last edited by annier on 03 Jul 2019, 21:24, edited 9 times in total.

Anil Kunwar

Department of Materials Engineering, KU Leuven, Belgium

Department of Materials Engineering, KU Leuven, Belgium

### Re: Using multiple softwares for performing a simulation

Image to video conversion and vice versa in linux using ffmpeg command

1. Video to image conversion (sequential images)
Here,

r is the framerate (4 images per 1 second)

2. Image to video conversion (sequential images)
Here,

r is the framerate (5 images per 1 second)

References:

1. https://superuser.com/questions/135117/ ... -to-images

2. https://choreonoid.org/en/manuals/lates ... image.html

3. https://linuxhint.com/ffmpeg_images_to_video_tutorial/

4. https://unix.stackexchange.com/question ... video-file

Refreshing frozen ubuntu operating system

https://askubuntu.com/questions/574090/ ... er-locking

Embedding videos in latex beamer presentation

1. https://tex.stackexchange.com/questions ... media-pack

Google research football based on reinforcement learning

1. blog

2. https://github.com/google-research/football

Hamiltonian Neural Network

1.a. explanation

b. paper

2. source code

Handling data in python for list without commas

1. https://stackoverflow.com/questions/320 ... y/32026649

2. saving numpy arrays using numpy as text file

3. https://stackoverflow.com/questions/109 ... ith-python

4. https://physics.nyu.edu/pine/pymanual/h ... rrays.html

5. Numpy and convolutional neural networks

tensorflow-cpu and tensorflow-gpu with keras

1. Installation of tensorflow cpu using conda

2. Tutorialspoint website for tutorials on tensorflow

3. Simple tutorial on tensorflow and keras for neural networks

4. https://machinelearningmastery.com/adam ... -learning/

5. http://ruder.io/optimizing-gradient-descent/

6. https://machinelearningmastery.com/tuto ... hon-keras/

7. https://keras.io/getting-started/sequen ... del-guide/

8. https://keras.io/layers/core/

9. https://keras.io/activations/

10. https://keras.io/datasets/

11. Regression analysis with keras + tensorflow

12. Switching between keras and tensoorflow backend in keras

13. Neural network with numpy

14. Piotr Skalski's github page for machine learning

Machine Learning

1. https://www.ritchieng.com/neural-networ ... sentation/

2. https://towardsdatascience.com/an-overv ... 72ba552dee

3. https://towardsdatascience.com/super-si ... 7800e8b624

4. https://www.kdnuggets.com/2017/04/build ... rflow.html

5.Differences between greedy layer learning and backpropagation

6. Sarkar et al, 2018 - Practical Machine Learning with Python

7. Github repository of Sarkar on machine learning

Autoencoders in machine learning

1. An introduction to autoencoders

2. (a) lstm autoencoders

(b) Samples, timesteps and features as 3D input for lstm-autoencoders

3. https://keras.io/getting-started/functional-api-guide/

4. https://www.quora.com/How-do-I-train-an ... Vi%C3%B1as

5. https://blog.keras.io/building-autoenco ... keras.html

6. https://tiao.io/post/tutorial-on-variat ... mentation/

7. Dissertation work related to pretraining and finetuning of data in neural networks

8. Greedy layerwise pre-training of data

Regression based neural networks

1. Example using keras and tensorflow

2. Machine learning tutorials and codes

3. Fuel efficiency tutorial in tensorflow with keras frontend

4. Source code for tutorial on point 3

5. seaborn statistical data visualization toolkit

6. Feed-forward neural network for regression

Phase Field Methods for Materials Discovery

1. Journal article on phase field method for materials discovery by Tonks and Aagesen, 2019

Metal anodes for Batteries

1. Doctoral dissertation by Greca Garcia, 2016

1. Video to image conversion (sequential images)

Code: Select all

`$ ffmpeg -i inputfile.avi -r 0.25 image_%04d.png`

r is the framerate (4 images per 1 second)

2. Image to video conversion (sequential images)

Code: Select all

`$ ffmpeg -r 5 -i image_%04d.png -r 5 outputtfile.avi`

r is the framerate (5 images per 1 second)

References:

1. https://superuser.com/questions/135117/ ... -to-images

2. https://choreonoid.org/en/manuals/lates ... image.html

3. https://linuxhint.com/ffmpeg_images_to_video_tutorial/

4. https://unix.stackexchange.com/question ... video-file

Refreshing frozen ubuntu operating system

https://askubuntu.com/questions/574090/ ... er-locking

Embedding videos in latex beamer presentation

1. https://tex.stackexchange.com/questions ... media-pack

Google research football based on reinforcement learning

1. blog

2. https://github.com/google-research/football

Hamiltonian Neural Network

1.a. explanation

b. paper

2. source code

Handling data in python for list without commas

1. https://stackoverflow.com/questions/320 ... y/32026649

2. saving numpy arrays using numpy as text file

3. https://stackoverflow.com/questions/109 ... ith-python

4. https://physics.nyu.edu/pine/pymanual/h ... rrays.html

5. Numpy and convolutional neural networks

tensorflow-cpu and tensorflow-gpu with keras

1. Installation of tensorflow cpu using conda

2. Tutorialspoint website for tutorials on tensorflow

3. Simple tutorial on tensorflow and keras for neural networks

4. https://machinelearningmastery.com/adam ... -learning/

5. http://ruder.io/optimizing-gradient-descent/

6. https://machinelearningmastery.com/tuto ... hon-keras/

7. https://keras.io/getting-started/sequen ... del-guide/

8. https://keras.io/layers/core/

9. https://keras.io/activations/

10. https://keras.io/datasets/

11. Regression analysis with keras + tensorflow

12. Switching between keras and tensoorflow backend in keras

13. Neural network with numpy

14. Piotr Skalski's github page for machine learning

Machine Learning

1. https://www.ritchieng.com/neural-networ ... sentation/

2. https://towardsdatascience.com/an-overv ... 72ba552dee

3. https://towardsdatascience.com/super-si ... 7800e8b624

4. https://www.kdnuggets.com/2017/04/build ... rflow.html

5.Differences between greedy layer learning and backpropagation

6. Sarkar et al, 2018 - Practical Machine Learning with Python

7. Github repository of Sarkar on machine learning

Autoencoders in machine learning

1. An introduction to autoencoders

2. (a) lstm autoencoders

(b) Samples, timesteps and features as 3D input for lstm-autoencoders

3. https://keras.io/getting-started/functional-api-guide/

4. https://www.quora.com/How-do-I-train-an ... Vi%C3%B1as

5. https://blog.keras.io/building-autoenco ... keras.html

6. https://tiao.io/post/tutorial-on-variat ... mentation/

7. Dissertation work related to pretraining and finetuning of data in neural networks

8. Greedy layerwise pre-training of data

Regression based neural networks

1. Example using keras and tensorflow

2. Machine learning tutorials and codes

3. Fuel efficiency tutorial in tensorflow with keras frontend

4. Source code for tutorial on point 3

5. seaborn statistical data visualization toolkit

6. Feed-forward neural network for regression

Phase Field Methods for Materials Discovery

1. Journal article on phase field method for materials discovery by Tonks and Aagesen, 2019

Metal anodes for Batteries

1. Doctoral dissertation by Greca Garcia, 2016

Last edited by annier on 14 Sep 2019, 03:32, edited 8 times in total.

Anil Kunwar

Department of Materials Engineering, KU Leuven, Belgium

Department of Materials Engineering, KU Leuven, Belgium

### Re: Using multiple softwares for performing a simulation

Deep Learning for Scientific Computing

1. Github repository for DeepXDE software

2. Paper on DEEPXDE by Lu et al, 2019

Lecture notes on machine learning by Saptashwa Bhattacharyya

1. https://towardsdatascience.com/dive-int ... ded13ead21

2. https://towardsdatascience.com/ridge-an ... 0e34bcbf0b

Notes on Deep Learning

1.Theory on Deep Learning

Solar PV Cells and Panels

1. PV ribbon

2. Building a solar panel

3. An article on quantitative analysis of PV modules

4. Electrical resistivity of Ag

5. Temperature coefficient of electrical resistivity

6. Temperature coefficient of resistance of tin

7. Electrical resistivity of tin and silver

8. PV ribbon dimensions and measurements

Velocity (u) Boundary conditions in Fluid Mechanics

1. Lecture notes on boundary conditions at rigid boundaries

1. Github repository for DeepXDE software

2. Paper on DEEPXDE by Lu et al, 2019

Lecture notes on machine learning by Saptashwa Bhattacharyya

1. https://towardsdatascience.com/dive-int ... ded13ead21

2. https://towardsdatascience.com/ridge-an ... 0e34bcbf0b

Notes on Deep Learning

1.Theory on Deep Learning

Solar PV Cells and Panels

1. PV ribbon

2. Building a solar panel

3. An article on quantitative analysis of PV modules

4. Electrical resistivity of Ag

5. Temperature coefficient of electrical resistivity

6. Temperature coefficient of resistance of tin

7. Electrical resistivity of tin and silver

8. PV ribbon dimensions and measurements

Velocity (u) Boundary conditions in Fluid Mechanics

1. Lecture notes on boundary conditions at rigid boundaries

Last edited by annier on 07 Dec 2019, 18:10, edited 1 time in total.

Anil Kunwar

Department of Materials Engineering, KU Leuven, Belgium

Department of Materials Engineering, KU Leuven, Belgium

### Re: Using multiple softwares for performing a simulation

Anil Kunwar

Department of Materials Engineering, KU Leuven, Belgium

Department of Materials Engineering, KU Leuven, Belgium