Using multiple softwares for performing a simulation

Discussion about building and installing Elmer


annier
Posts: 1109
Joined: 27 Aug 2013, 13:51
Antispam: Yes

Re: Using multiple softwares for performing a simulation

Post by annier » 04 Jun 2018, 02:51

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
Anil Kunwar
Department of Materials Engineering, KU Leuven, Belgium


annier
Posts: 1109
Joined: 27 Aug 2013, 13:51
Antispam: Yes

Re: Using multiple softwares for performing a simulation

Post by annier » 17 Sep 2018, 00:44

Windows subsystem for linux (WSL)
1. Installation of VcXsrv followed by installation of nautilus and grsync

Code: Select all

$ sudo apt install nautilus && sudo apt install 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

Code: Select all

$ cd /mnt/c/Users/<ubuntu.username>/Pictures
b. Ubuntu to Windows file transfers
Reference: https://superuser.com/questions/1110974 ... ows-10-wsl

Code: Select all

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

Code: Select all

$ conda create -n py27 python=2.7 anaconda
For activation of python2 environment

Code: Select all

 $ source activate py27
For deactivating the active environment

Code: Select all

 (py27) ...$ source deactivate 
Notes: For newer versions of Anaconda,
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
or, for all users, enable conda with

Code: Select all

 $ sudo ln -s /home/romagurung/anaconda3/etc/profile.d/conda.sh /etc/profile.d/conda.sh
The above options replace the following task:

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


annier
Posts: 1109
Joined: 27 Aug 2013, 13:51
Antispam: Yes

Re: Using multiple softwares for performing a simulation

Post by annier » 04 Oct 2018, 01:33

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

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

Crystal Plasticity in MOOSE Framework
Bachelor's Thesis by Viktor Hultgren 2018
Anil Kunwar
Department of Materials Engineering, KU Leuven, Belgium

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