Using multiple softwares for performing a simulation
Posted: 22 May 2014, 11:11
Hi,
Sometimes a simulation requires more than one softwares for computational works.
For an example, the boundary variable or constants required by Elmer may be calculated using other softwares. As an example, the specific heat of a multicomponent mixture , if cannot be determined from an experiment, needs to be calculated from some softwares on kinetics or thermodynamics by creating databases. Cantera is an example of an opensource software for that (http://www.cantera.org/docs/sphinx/html/index.html).
In Linux
The guidelines for installation of cantera in Ubuntu 12.04 is given in the following website:
http://bryanwweber.com/writing/personal ... compilers/
http://bryanwweber.github.io/CanSen/htm ... ation.html
http://www.stanford.edu/group/ihmegroup ... ion-guide/
http://page.mi.fu-berlin.de/pberndt/cantera/install/
website of charlesmartinreid where installation of cantera and combination use of cantera with FiPy is explained as well as illustrated clearly
https://aandreasen.files.wordpress.com/ ... 39_m_2.pdf
couple cantera with openfoam interface
lecture notes on reactor design with cantera
Theory for CFD simulation of catalytic reactions in OpenFOAM and Cantera
Cantera 2.1.2 Packages are available for Ubuntu 12.04 and Ubuntu 14.04. and the installation steps are given in:
http://cantera.github.io/docs/sphinx/ht ... all-ubuntu
In Windows
The guidelines for installation of Cantera in windows is given in the following website:
http://code.google.com/p/cantera/wiki/W ... stallation
http://stuff.mit.edu/afs/athena/course/ ... stall.html
A useful link for phase-field-model and CALPHAD
http://www.kumarankitresearch.com/
https://nanohub.org/resources/gibbs
https://github.com/JunOu/phaseFieldGrainGrowth
http://imechanica.org/node/1282
https://github.com/mesoscale/mmsp
http://matforge.org/cmu/wiki/mmsp
http://matforge.org/cmu/wiki/mmsp/users-guide
http://www.opencalphad.com/index.html
Molecular Weight and Thermodynamic Calculators
http://www.shodor.org/UNChem/advanced/t ... ocalc.html
http://www.webqc.org/mmcalc.php
At. % and wt. % conversions
Excel file for interconversion between at % and wt % k
Relation between Gibbs Free Energy, Electrochemical Potential and Equilibrium Constant
http://chemwiki.ucdavis.edu/Analytical_ ... modynamics
http://www.hobbyprojects.com/computer-t ... ration.htm(general dictionary and electromigration)
mechanical properties of intermetallic compounds
Gibbs Free Energy and Phase Diagram
http://oregonstate.edu/instruct/me581/H ... Hmwk3.html
http://chemed.chem.purdue.edu/genchem/t ... /gibbs.php
Length Scales and Time Scales in Advection-Diffusion Equation
http://www.enigmatic-consulting.com/sem ... ength.html
Electrochemistry
http://matdl.org/matdlwiki/index.php/elecchem:Main_Page
Mathematics
hyperbolic functions
Diffusion in Bioengineering
http://www.labome.org/expert/usa/harvar ... 52981.html
Libraries in Computational Materials Science
http://matforge.org/
http://matforge.org/redmine/projects/mmsp
http://magnetserver.cmpe.ubc.ca/wiki/in ... Field_Code
http://magnetserver.cmpe.ubc.ca/wiki/in ... _CMPE_Code
https://github.com/SinaShahandeh/MultiP ... /2D_circle
Python based thermodynamics modules
http://thermopynamics.sourceforge.net/
https://pypi.python.org/pypi/thermopy#downloads
https://pythonhosted.org/thermopy/
ab-initio methods a.k.a. density functional theory
Thesis on bond order potentials for group IV elements
A thesis on Improved atomic scale simulations of Si
AMULET code
Quantum Espresso software website
user guide of quantum espresso software
VASP software
Running a dft tutorial in vasp sofware
siesta software
Computational platform for VASP software
Installation of Quantum Espresso in Ubuntu
Molecular Dynamics
LAMMPS software
commands used in the LAMMPS software
Repositories for MEAM Interatomic Potentials
Installing and Running LAMMPS software for MD run
Nuwan's website
Research directions using LAMMPS software
Discrete element modeling using LAMMPS software
MEAM potentials in MD Simulation
MEAM Potentials for Cubic Materials and Impurities
equilibrium and thermodynamic properties of tin for MD simulation
MEAM potential in LAMMPS documentation
MEAM potential illustration with Al-Mg system(icme_hpc_msstate_edu_LAMMPS_software)
shear strain and shear strain rate definition in LAMMPS software
MD simulation of viscoplaticity of beta-tin (beta_sn)
Effect of Ni solute on the GB diffusion of tin
Atomistic modeling of surface energies on beta tin
Solute effects on GB OF BETA TIN and shear stress
Lattice strains/ vibrations due to atomic vacancy
diffusivity of Cu and Sn in Cu3Sn
MD study on micro-spallation of single crystal tin
A book on MD Simulation of Intechopen
shear stress and strain behavior of beta tin
Data for Ag3Sn for LAMMPS software (MEAM potential)
CHARMM software
DL_POLY UserManual4.07
DL_POLY Software
stfc & daresbury laboratory
Microstructure Database available in CAMS , UFL
MD simulation of solid liquid beta tin by Shaon Yasmin
Structure,energetics,dynamics of cu_sn interface by JFAguilar
question-answers on lammps tutorial beginning
create atoms for lammps input file
DLPOLY and LAMMPS softwares
Some notes on LAMMPS usage
1. http://scent.gist.ac.kr/downloads/tutor ... 120706.pdf
2. http://www.utdallas.edu/~bxw109120/lj17 ... ps_tut.pdf
3. https://acf.ku.edu/~pregier/guides/lamm ... basic.html
4. http://lammps.sandia.gov/user.html
5. Getting started with the theory and methods or steps of Molecular Dynamics simulations
6. https://icme.hpc.msstate.edu/mediawiki/ ... _tutorials
Database for Interatomic Potentials
NIST Database
NIST Database-New Requests
Potential Database for Potfit Software
MEAM for Mg-X binary alloys -CALPHAD
Database J_M_D_LANE_UTEXAS
Database through website of Wolverton research group
Openkim Database
Opensource software to build molecular inputs for LAMMPS/softwares related with LAMMPS software
1. Avogadro - an advanced molecular editor
2. How to cite the AVOGADRO - Molecular Editor Software
3. OCTA and J-OCTA software
4. ATOMSK software
5. Packmol
6. Moltemplate
7. VMD-topotools
8. Enhanced Monte Carlo(EMC)
9. LIGGHTS-cfdem
10. PLUMED software
11. HOOMD-BLUE
Methods of Installation of LAMMPS in Ubuntu 14.04
A. MAKE SERIAL (basic installation -->> ./lmp_serial)
Installation of LAMMPS in serial in Ubuntu 14.04(For Preliminary learnings about this software)
1. Download the software from github source and unzip it.
2. Jump into the directory lammps-master/src and type
which will eventually produce the executable lmp-serial within the same directory.
Note:
The package using MEAM potential pair style uses external libraries and should be compiled before making lammps.
Another note on MEAM library.
LAMMPS in serial along with the MEAM libraries
1. Jump into the lammps-master/src/ directory and type
2. Go to lammps-master/lib/meam directory and type
3. Return to the lammps-master/src/ directory and type
This will lead to the built up of lmp-serial executive able to work with the external meam library.
4. To run an example with meam library , copy the example lammps-master/examples/meam/ into a given directory and copy-paste therein the lmp-serial executive. Then, type within the directory:
LAMMPS how to input commands
MAKE UBUNTU (For ubuntu machine in parallel -->> ./lmp_ubuntu)
LAMMPS making way for Ubuntu
Steps:
1. Installation of Essential Ubuntu Packages (Pre-installtion)
We must install the following packages: g++ mpi-default-bin mpi-default-dev libfftw3-dev libjpeg-dev libpng12-dev.
Also, to make sure gfortran is there, as it will not affect even if there is an existing one, gfortran is installed via build essential
2.Jump into the lammps-master/src directory and do "make yes-libname" to meam and manybody potentials (including external libraries for LAMMPS).
Then, proceed to the lammps-master/lib/meam/ directory and compile the lammps/meam potential library for gfortran
3. Return to the lammps-master/src/ directory and compile lammps for Ubuntu(LAMMPS executable built up process)
This procedure will creat a lmp_ubuntu executable in ~/PROJECT/lammps-master/src/ directory.
4. Running lammps from ubuntu path ==>> /usr/local/bin/
Copy the executable/binary ./lmp_ubuntu to the /usr/local/bin/ directory.
Then, open the terminal, jump into the directory of input file in.inputfile and run lammps in ubuntu as:
For parallel run , the following code can be types:
LAMMPS how to input commands
Ubuntu executables installation of Lammps
On the installation of pre/postprocessing tools of LAMMPS
a. xmovies
about x11/XAW/Form.h
b. VMD
VMD tool
c. RASMOL
http://www.bernstein-plus-sons.com/software/rasmol/
d. ATOMEYE
http://li.mit.edu/Archive/Graphics/A/
e.OVITO
http://www.ovito.org/
f. PYMOL
http://www.pymol.org/
g. PizzaPy
http://pizza.sandia.gov/
Notes on running Lammps software
How to Run LAMMPS
Thesis on MD simulation of SN crystal and liquid (2010)
Thesis on microstructure and transport properties of lead-free solders using atomistic simulations(2010)
free energy calculations of cu-sn interfaces
Data for MEAM_Si which also contains information about beta tin and different structures
LAMMPS-an object oriented scientific application
MEAM potential
1. MEAM potential data file for SiC system
2. MEAM potential Ag3Sn by Michael Sellers
3. Twist grain boundaries and ideal shear stresses in Ni
4. M.S.Seller Atomistic Simulation in 2010
5. Work by L.T.S. Norman
6. Melting point and phase diagram modeling of SAC nanoparticles
7. LAMMPS software description in materialsdesigndotcom
8. Tutorial on nanoindentation in LAMMPS software
Crystallography Softwares
Uspex-Software for prediction of crystal structure
1. Homepage of USPEX software
PTCLab Software
1. Website for phase transformation crystallography lab (PTClab) software
2. User Manual of PTCLab software
List of Crystallography Softwares
1. http://www.iucr.org/resources/other-dir ... ult_page=P
Wulff net
1. https://www.doitpoms.ac.uk/tlplib/stere ... struct.php
2. http://jcrystal.com/products/winwulff/index.htm
Extended Fem (XFEM) softwares
GetFEM++
OpenXfem++
xfem++
Multiphase Flow
http://wins.engr.wisc.edu/teaching/mpfBook/main.html
Android emulation in Ubuntu
http://ubuntuforums.org/showthread.php?t=2183444
http://ubuntuguide.org/wiki/Android_emulation
http://veronicawrites.com/page/2/
health tips
food for good health
Natural Beauty
type in nepali fonts
research topic assessment and consolidating
latex templates for chinese universities and dlut
world clock
meaningful_geometries
bubble formation in liquid
numerical values of convection heat transfer coefficient
ICEPT_2014
http://www.farm.net/~mason/materials/th ... ivity.html
how to write an erratum to an article and also illustration about how that is cited
Schematic representation of BL13W1 of SSRF
modeling hydrogen bubble growth model in melt aluminum
weight percent to atomic percent and vice versa
principle of the conversion
the atomic percent to weight percent and vice versa calculator
Explanation of the conversion between atomic to weight percent
GRE-psychology_test_model
Journal of the Institute of Engineering
adiabatic flame temperature theory
mercury wifi router installation or setup procedures
Notes on references and citations
Solar Thermal Pasteurization System for Purification of Water
solar thermal energy transport
David A. Hodgson MS Thesis 2005 on Density Driven System
Passive solar water heating system
solar energy pasteurization system
simulation of natural convection flow in a rectangular loop using finite elements
Natural convection flow simulation in OpenFOAM
Natural convection in a horizontal cylinder in OpenFOAM
Liquid metal MHD flows using OpenFOAM
Analysis of natural convection in heated pools system
Overview Manual of apricus ETC collectors
Installation Manual of apricus ETC collectors
Sanitation by R. Feachem et al (1983)
International Research Center for Renewable Energy
citation machine
novoresume
Microsoft security essential user guide and use procedures
Linux equivalents of windows software
Second Annual Academic Forum For Chinese and International PhD Students “HUMAN HEALTH AND THE GREEN EARTH”
13th International Conference on Quasi-crystals, Kathmandu, Nepal (18-23 September(9), 2016
quasicrystal application by Y.J. Chen et al (2015)
Precipitation Kinetics
1. http://www.nist.gov/mml/msed/thermodyna ... uTherm.pdf
2. http://jes.ecsdl.org/content/142/8/2823.short
3. http://rommet.com/remco/NAPOM/Precipita ... AlZnMg.pdf
4. MinKin software
5. Cantera for CVD simulation
6. SOFC modeling using Cantera
7. DENIS software for modeling of SOFC
8. http://arc.aiaa.org/doi/pdf/10.2514/6.2012-1488
9.quantum wise and virtual nanolab GUI
10. VNL as gui for quantum espresso
Type in Nepali Fonts
1. http://www.easynepalityping.com/
2. http://v2.unicodenepali.com/convert/index.html
paper titles in icept-2016, Wuhan, 16-19 August 2016
Basic requirements of letter of motivation
Tips for letter of motivation in DAAD application
http://www.daad.tj/how_to_write_a_lette ... vation.pdf
http://ecs.ihu.edu.gr/co/employment-bus ... ion-letter
http://www.cmc.iit.edu/JobSearchTips/Re ... etters.pdf
E-vision 2009 - Mechanical Engineering Journal Published at Tribhuvan University, Institute of Engineering, Pulchowk Campus, Lalitpur
1. scribd website
2. documents website
Remote accessing a computer
1. Teamviewer - https://www.teamviewer.com/en/download/linux/
2. ia32 libs for setting up teamviewer -http://stackoverflow.com/questions/2318 ... rusty-tahr
3. http://askubuntu.com/questions/578172/c ... 4-04-64bit
4. https://packages.debian.org/wheezy/ia32-libs
5. https://ubuntuforums.org/showthread.php?t=2182653
6. http://ubuntuhandbook.org/index.php/201 ... untu-1404/
7. https://ubuntuforums.org/showthread.php?t=2181680
8. https://answers.launchpad.net/ubuntu/+question/234339
9. Installation of teamviewer in Ubuntu 16.04
http://emojipedia.org/flag-for-nepal/
Writing the circle accent over letter as in the name of Peter Raback in latex
Emotional Management
Researchers also have to go along with emotional management to persevere with their long-term research objectives.
1. letting go
2. Getting rid of the feeling of attachment
3. How to practice non-attachment
4. How healthy people handle touch times
5. http://jodiegale.com/
6. 5 ways to maintain boundaries with difficult people
7. Cutting ties - a simple way to free you from emotional baggage
8. 10-life changing facts about attachment
9. Ashley - Slug in webpage notes
Solving hash sum mismatch in ubuntu computer
1. https://blog.packagecloud.io/eng/2016/1 ... y-precise/
2. http://unix.stackexchange.com/questions ... m-mismatch
The Materials Genome Project
Materials Genome Project for materials innovation
Fireworks in Material Genome Project
pymatgen in Materials Genome Project
Contributing in pymatgen project
Materials Virtual Lab of Prof Ong
mategenie and pymatgen in prof ong's lab
Kristine Persson's research group
Installation of Pymatgen Libraries:
1. Install Conda (Miniconda) Libraries in Ubuntu/Linux
(Installation of Conda on the System which has other Python installations or Packages)
https://conda.io/docs/user-guide/install/linux.html
2. Install Pymatgen using Conda (recommended)
http://pymatgen.org/installation.html
Wolfram Project
1. http://demonstrations.wolfram.com/Solvi ... ngFiniteD/
2. http://demonstrations.wolfram.com/SomeS ... llography/
Thank you
Research Funding
1. Horizon 2020 programme and guidelines
2. Marie Sklodowska-Curie Actions
Sample of teaching portfolio for applications
Latex template for research proposal and additional ideas on msca applications
CV
1. https://aubert.perso.math.cnrs.fr/
2. https://github.com/auino/europasscv-template
3. https://ctan.org/tex-archive/macros/lat ... cv?lang=en
4. https://impatti.sostenibilita.enea.it/s ... rcea_0.pdf
5. http://sandamirskaya.eu/resources/IEF_PartB_3.tex
6. http://rainnic.altervista.org/en/conten ... _entity=en
7. https://texblog.org/2012/04/25/writing-a-cv-in-latex/
Blog and writings of Binita
https://www.explorer-cafe.com/
Yours
Anil Kunwar
Sometimes a simulation requires more than one softwares for computational works.
For an example, the boundary variable or constants required by Elmer may be calculated using other softwares. As an example, the specific heat of a multicomponent mixture , if cannot be determined from an experiment, needs to be calculated from some softwares on kinetics or thermodynamics by creating databases. Cantera is an example of an opensource software for that (http://www.cantera.org/docs/sphinx/html/index.html).
In Linux
The guidelines for installation of cantera in Ubuntu 12.04 is given in the following website:
http://bryanwweber.com/writing/personal ... compilers/
http://bryanwweber.github.io/CanSen/htm ... ation.html
http://www.stanford.edu/group/ihmegroup ... ion-guide/
http://page.mi.fu-berlin.de/pberndt/cantera/install/
website of charlesmartinreid where installation of cantera and combination use of cantera with FiPy is explained as well as illustrated clearly
https://aandreasen.files.wordpress.com/ ... 39_m_2.pdf
couple cantera with openfoam interface
lecture notes on reactor design with cantera
Theory for CFD simulation of catalytic reactions in OpenFOAM and Cantera
Cantera 2.1.2 Packages are available for Ubuntu 12.04 and Ubuntu 14.04. and the installation steps are given in:
http://cantera.github.io/docs/sphinx/ht ... all-ubuntu
In Windows
The guidelines for installation of Cantera in windows is given in the following website:
http://code.google.com/p/cantera/wiki/W ... stallation
http://stuff.mit.edu/afs/athena/course/ ... stall.html
A useful link for phase-field-model and CALPHAD
http://www.kumarankitresearch.com/
https://nanohub.org/resources/gibbs
https://github.com/JunOu/phaseFieldGrainGrowth
http://imechanica.org/node/1282
https://github.com/mesoscale/mmsp
http://matforge.org/cmu/wiki/mmsp
http://matforge.org/cmu/wiki/mmsp/users-guide
http://www.opencalphad.com/index.html
Molecular Weight and Thermodynamic Calculators
http://www.shodor.org/UNChem/advanced/t ... ocalc.html
http://www.webqc.org/mmcalc.php
At. % and wt. % conversions
Excel file for interconversion between at % and wt % k
Relation between Gibbs Free Energy, Electrochemical Potential and Equilibrium Constant
http://chemwiki.ucdavis.edu/Analytical_ ... modynamics
http://www.hobbyprojects.com/computer-t ... ration.htm(general dictionary and electromigration)
mechanical properties of intermetallic compounds
Gibbs Free Energy and Phase Diagram
http://oregonstate.edu/instruct/me581/H ... Hmwk3.html
http://chemed.chem.purdue.edu/genchem/t ... /gibbs.php
Length Scales and Time Scales in Advection-Diffusion Equation
http://www.enigmatic-consulting.com/sem ... ength.html
Electrochemistry
http://matdl.org/matdlwiki/index.php/elecchem:Main_Page
Mathematics
hyperbolic functions
Diffusion in Bioengineering
http://www.labome.org/expert/usa/harvar ... 52981.html
Libraries in Computational Materials Science
http://matforge.org/
http://matforge.org/redmine/projects/mmsp
http://magnetserver.cmpe.ubc.ca/wiki/in ... Field_Code
http://magnetserver.cmpe.ubc.ca/wiki/in ... _CMPE_Code
https://github.com/SinaShahandeh/MultiP ... /2D_circle
Python based thermodynamics modules
http://thermopynamics.sourceforge.net/
https://pypi.python.org/pypi/thermopy#downloads
https://pythonhosted.org/thermopy/
ab-initio methods a.k.a. density functional theory
Thesis on bond order potentials for group IV elements
A thesis on Improved atomic scale simulations of Si
AMULET code
Quantum Espresso software website
user guide of quantum espresso software
VASP software
Running a dft tutorial in vasp sofware
siesta software
Computational platform for VASP software
Installation of Quantum Espresso in Ubuntu
Molecular Dynamics
LAMMPS software
commands used in the LAMMPS software
Repositories for MEAM Interatomic Potentials
Installing and Running LAMMPS software for MD run
Nuwan's website
Research directions using LAMMPS software
Discrete element modeling using LAMMPS software
MEAM potentials in MD Simulation
MEAM Potentials for Cubic Materials and Impurities
equilibrium and thermodynamic properties of tin for MD simulation
MEAM potential in LAMMPS documentation
MEAM potential illustration with Al-Mg system(icme_hpc_msstate_edu_LAMMPS_software)
shear strain and shear strain rate definition in LAMMPS software
MD simulation of viscoplaticity of beta-tin (beta_sn)
Effect of Ni solute on the GB diffusion of tin
Atomistic modeling of surface energies on beta tin
Solute effects on GB OF BETA TIN and shear stress
Lattice strains/ vibrations due to atomic vacancy
diffusivity of Cu and Sn in Cu3Sn
MD study on micro-spallation of single crystal tin
A book on MD Simulation of Intechopen
shear stress and strain behavior of beta tin
Data for Ag3Sn for LAMMPS software (MEAM potential)
CHARMM software
DL_POLY UserManual4.07
DL_POLY Software
stfc & daresbury laboratory
Microstructure Database available in CAMS , UFL
MD simulation of solid liquid beta tin by Shaon Yasmin
Structure,energetics,dynamics of cu_sn interface by JFAguilar
question-answers on lammps tutorial beginning
create atoms for lammps input file
DLPOLY and LAMMPS softwares
Some notes on LAMMPS usage
1. http://scent.gist.ac.kr/downloads/tutor ... 120706.pdf
2. http://www.utdallas.edu/~bxw109120/lj17 ... ps_tut.pdf
3. https://acf.ku.edu/~pregier/guides/lamm ... basic.html
4. http://lammps.sandia.gov/user.html
5. Getting started with the theory and methods or steps of Molecular Dynamics simulations
6. https://icme.hpc.msstate.edu/mediawiki/ ... _tutorials
Database for Interatomic Potentials
NIST Database
NIST Database-New Requests
Potential Database for Potfit Software
MEAM for Mg-X binary alloys -CALPHAD
Database J_M_D_LANE_UTEXAS
Database through website of Wolverton research group
Openkim Database
Opensource software to build molecular inputs for LAMMPS/softwares related with LAMMPS software
1. Avogadro - an advanced molecular editor
2. How to cite the AVOGADRO - Molecular Editor Software
3. OCTA and J-OCTA software
4. ATOMSK software
5. Packmol
6. Moltemplate
7. VMD-topotools
8. Enhanced Monte Carlo(EMC)
9. LIGGHTS-cfdem
10. PLUMED software
11. HOOMD-BLUE
Methods of Installation of LAMMPS in Ubuntu 14.04
A. MAKE SERIAL (basic installation -->> ./lmp_serial)
Installation of LAMMPS in serial in Ubuntu 14.04(For Preliminary learnings about this software)
1. Download the software from github source and unzip it.
2. Jump into the directory lammps-master/src and type
Code: Select all
$ make serial
Note:
The package using MEAM potential pair style uses external libraries and should be compiled before making lammps.
Another note on MEAM library.
LAMMPS in serial along with the MEAM libraries
1. Jump into the lammps-master/src/ directory and type
Code: Select all
$make yes-meam
Code: Select all
$make -f Makefile.gfortran
Code: Select all
$make serial
4. To run an example with meam library , copy the example lammps-master/examples/meam/ into a given directory and copy-paste therein the lmp-serial executive. Then, type within the directory:
Code: Select all
$./lmp-serial<in.meam
MAKE UBUNTU (For ubuntu machine in parallel -->> ./lmp_ubuntu)
LAMMPS making way for Ubuntu
Steps:
1. Installation of Essential Ubuntu Packages (Pre-installtion)
We must install the following packages: g++ mpi-default-bin mpi-default-dev libfftw3-dev libjpeg-dev libpng12-dev.
Code: Select all
$ sudo apt-get install g++
$ sudo apt-get install mpi-default-bin mpi-default-dev # openmpi
$ sudo apt-get install libfftw3-dev # fftw3 (instead of fftw)
$ sudo apt-get install libjpeg-dev libpng12-dev
Code: Select all
$ sudo apt-get install build-essential gfortran
Code: Select all
$ make yes-meam
Code: Select all
$ make yes-manybody
Code: Select all
$ make -f Makefile.gfortran
Code: Select all
$ make clean-all
Code: Select all
$ make ubuntu
4. Running lammps from ubuntu path ==>> /usr/local/bin/
Copy the executable/binary ./lmp_ubuntu to the /usr/local/bin/ directory.
Code: Select all
$ sudo cp -r ~/PROJECT/lammps-master/src/lmp_ubuntu /usr/local/bin
Code: Select all
$ lmp_ubuntu<in.inputfile
Code: Select all
$ mpirun -np 4 lmp_ubuntu -in in.inputfile
Ubuntu executables installation of Lammps
On the installation of pre/postprocessing tools of LAMMPS
a. xmovies
about x11/XAW/Form.h
b. VMD
VMD tool
c. RASMOL
http://www.bernstein-plus-sons.com/software/rasmol/
d. ATOMEYE
http://li.mit.edu/Archive/Graphics/A/
e.OVITO
http://www.ovito.org/
f. PYMOL
http://www.pymol.org/
g. PizzaPy
http://pizza.sandia.gov/
Notes on running Lammps software
How to Run LAMMPS
Thesis on MD simulation of SN crystal and liquid (2010)
Thesis on microstructure and transport properties of lead-free solders using atomistic simulations(2010)
free energy calculations of cu-sn interfaces
Data for MEAM_Si which also contains information about beta tin and different structures
LAMMPS-an object oriented scientific application
MEAM potential
1. MEAM potential data file for SiC system
2. MEAM potential Ag3Sn by Michael Sellers
3. Twist grain boundaries and ideal shear stresses in Ni
4. M.S.Seller Atomistic Simulation in 2010
5. Work by L.T.S. Norman
6. Melting point and phase diagram modeling of SAC nanoparticles
7. LAMMPS software description in materialsdesigndotcom
8. Tutorial on nanoindentation in LAMMPS software
Crystallography Softwares
Uspex-Software for prediction of crystal structure
1. Homepage of USPEX software
PTCLab Software
1. Website for phase transformation crystallography lab (PTClab) software
2. User Manual of PTCLab software
List of Crystallography Softwares
1. http://www.iucr.org/resources/other-dir ... ult_page=P
Wulff net
1. https://www.doitpoms.ac.uk/tlplib/stere ... struct.php
2. http://jcrystal.com/products/winwulff/index.htm
Extended Fem (XFEM) softwares
GetFEM++
OpenXfem++
xfem++
Multiphase Flow
http://wins.engr.wisc.edu/teaching/mpfBook/main.html
Android emulation in Ubuntu
http://ubuntuforums.org/showthread.php?t=2183444
http://ubuntuguide.org/wiki/Android_emulation
http://veronicawrites.com/page/2/
health tips
food for good health
Natural Beauty
type in nepali fonts
research topic assessment and consolidating
latex templates for chinese universities and dlut
world clock
meaningful_geometries
bubble formation in liquid
numerical values of convection heat transfer coefficient
ICEPT_2014
http://www.farm.net/~mason/materials/th ... ivity.html
how to write an erratum to an article and also illustration about how that is cited
Schematic representation of BL13W1 of SSRF
modeling hydrogen bubble growth model in melt aluminum
weight percent to atomic percent and vice versa
principle of the conversion
the atomic percent to weight percent and vice versa calculator
Explanation of the conversion between atomic to weight percent
GRE-psychology_test_model
Journal of the Institute of Engineering
adiabatic flame temperature theory
mercury wifi router installation or setup procedures
Notes on references and citations
Solar Thermal Pasteurization System for Purification of Water
solar thermal energy transport
David A. Hodgson MS Thesis 2005 on Density Driven System
Passive solar water heating system
solar energy pasteurization system
simulation of natural convection flow in a rectangular loop using finite elements
Natural convection flow simulation in OpenFOAM
Natural convection in a horizontal cylinder in OpenFOAM
Liquid metal MHD flows using OpenFOAM
Analysis of natural convection in heated pools system
Overview Manual of apricus ETC collectors
Installation Manual of apricus ETC collectors
Sanitation by R. Feachem et al (1983)
International Research Center for Renewable Energy
citation machine
novoresume
Microsoft security essential user guide and use procedures
Linux equivalents of windows software
Second Annual Academic Forum For Chinese and International PhD Students “HUMAN HEALTH AND THE GREEN EARTH”
13th International Conference on Quasi-crystals, Kathmandu, Nepal (18-23 September(9), 2016
quasicrystal application by Y.J. Chen et al (2015)
Precipitation Kinetics
1. http://www.nist.gov/mml/msed/thermodyna ... uTherm.pdf
2. http://jes.ecsdl.org/content/142/8/2823.short
3. http://rommet.com/remco/NAPOM/Precipita ... AlZnMg.pdf
4. MinKin software
5. Cantera for CVD simulation
6. SOFC modeling using Cantera
7. DENIS software for modeling of SOFC
8. http://arc.aiaa.org/doi/pdf/10.2514/6.2012-1488
9.quantum wise and virtual nanolab GUI
10. VNL as gui for quantum espresso
Type in Nepali Fonts
1. http://www.easynepalityping.com/
2. http://v2.unicodenepali.com/convert/index.html
paper titles in icept-2016, Wuhan, 16-19 August 2016
Basic requirements of letter of motivation
Tips for letter of motivation in DAAD application
http://www.daad.tj/how_to_write_a_lette ... vation.pdf
http://ecs.ihu.edu.gr/co/employment-bus ... ion-letter
http://www.cmc.iit.edu/JobSearchTips/Re ... etters.pdf
E-vision 2009 - Mechanical Engineering Journal Published at Tribhuvan University, Institute of Engineering, Pulchowk Campus, Lalitpur
1. scribd website
2. documents website
Remote accessing a computer
1. Teamviewer - https://www.teamviewer.com/en/download/linux/
2. ia32 libs for setting up teamviewer -http://stackoverflow.com/questions/2318 ... rusty-tahr
3. http://askubuntu.com/questions/578172/c ... 4-04-64bit
4. https://packages.debian.org/wheezy/ia32-libs
5. https://ubuntuforums.org/showthread.php?t=2182653
6. http://ubuntuhandbook.org/index.php/201 ... untu-1404/
7. https://ubuntuforums.org/showthread.php?t=2181680
8. https://answers.launchpad.net/ubuntu/+question/234339
9. Installation of teamviewer in Ubuntu 16.04
- (a) Download teamviewer (teamviewer_12.0.71510_i386.deb) for 32 bit (i386) even for 64 bit computer from the teamviewer website
(b) Install the teamviewer using gdebi feature of Ubuntu 16.04Code: Select all
$ sudo dpkg --add-architecture i386
Code: Select all
$ sudo apt-get update
In order to uninstall teamviewer, please follow the following stepCode: Select all
sudo gdebi teamviewer_12.0.71510_i386.deb
Code: Select all
$ sudo apt-get remove teamviewer*
http://emojipedia.org/flag-for-nepal/
Writing the circle accent over letter as in the name of Peter Raback in latex
Emotional Management
Researchers also have to go along with emotional management to persevere with their long-term research objectives.
1. letting go
2. Getting rid of the feeling of attachment
3. How to practice non-attachment
4. How healthy people handle touch times
5. http://jodiegale.com/
6. 5 ways to maintain boundaries with difficult people
7. Cutting ties - a simple way to free you from emotional baggage
8. 10-life changing facts about attachment
9. Ashley - Slug in webpage notes
Solving hash sum mismatch in ubuntu computer
1. https://blog.packagecloud.io/eng/2016/1 ... y-precise/
2. http://unix.stackexchange.com/questions ... m-mismatch
The Materials Genome Project
Materials Genome Project for materials innovation
Fireworks in Material Genome Project
pymatgen in Materials Genome Project
Contributing in pymatgen project
Materials Virtual Lab of Prof Ong
mategenie and pymatgen in prof ong's lab
Kristine Persson's research group
Installation of Pymatgen Libraries:
1. Install Conda (Miniconda) Libraries in Ubuntu/Linux
(Installation of Conda on the System which has other Python installations or Packages)
https://conda.io/docs/user-guide/install/linux.html
2. Install Pymatgen using Conda (recommended)
http://pymatgen.org/installation.html
Wolfram Project
1. http://demonstrations.wolfram.com/Solvi ... ngFiniteD/
2. http://demonstrations.wolfram.com/SomeS ... llography/
Thank you
Research Funding
1. Horizon 2020 programme and guidelines
2. Marie Sklodowska-Curie Actions
Sample of teaching portfolio for applications
Latex template for research proposal and additional ideas on msca applications
CV
1. https://aubert.perso.math.cnrs.fr/
2. https://github.com/auino/europasscv-template
3. https://ctan.org/tex-archive/macros/lat ... cv?lang=en
4. https://impatti.sostenibilita.enea.it/s ... rcea_0.pdf
5. http://sandamirskaya.eu/resources/IEF_PartB_3.tex
6. http://rainnic.altervista.org/en/conten ... _entity=en
7. https://texblog.org/2012/04/25/writing-a-cv-in-latex/
Blog and writings of Binita
https://www.explorer-cafe.com/
Yours
Anil Kunwar