Using multiple softwares for performing a simulation

Discussion about building and installing Elmer

Using multiple softwares for performing a simulation

Postby annier » 22 May 2014, 11:11

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 (
In Linux
The guidelines for installation of cantera in Ubuntu 12.04 is given in the following website:
website of charlesmartinreid where installation of cantera and combination use of cantera with FiPy is explained as well as illustrated clearly
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:

In Windows
The guidelines for installation of Cantera in windows is given in the following website:

A useful link for phase-field-model and CALPHAD

Molecular Weight and Thermodynamic Calculators
At. % and wt. % conversions
Excel file for interconversion between at % and wt % k

Relation between Gibbs Free Energy, Electrochemical Potential and Equilibrium Constant dictionary and electromigration)
mechanical properties of intermetallic compounds

Gibbs Free Energy and Phase Diagram

Length Scales and Time Scales in Advection-Diffusion Equation


hyperbolic functions

Diffusion in Bioengineering

Libraries in Computational Materials Science

Python based thermodynamics modules

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
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

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. ... 120706.pdf
2. ... ps_tut.pdf
3. ... basic.html

Database for Interatomic Potentials
NIST Database
NIST Database-New Requests
Potential Database for Potfit Software
MEAM for Mg-X binary alloys -CALPHAD
Database through website of Wolverton research group

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

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

which will eventually produce the executable lmp-serial within the same directory.
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

2. Go to lammps-master/lib/meam directory and type
Code: Select all
$make -f Makefile.gfortran

3. Return to the lammps-master/src/ directory and type
Code: Select all
$make serial

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:
Code: Select all

LAMMPS how to input commands

MAKE UBUNTU (For ubuntu machine in parallel -->> ./lmp_ubuntu)
LAMMPS making way for Ubuntu
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

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
Code: Select all
$ sudo apt-get install build-essential gfortran

2.Jump into the lammps-master/src directory and do "make yes-libname" to meam and manybody potentials (including external libraries for LAMMPS).
Code: Select all
$ make yes-meam

Code: Select all
$ make yes-manybody

Then, proceed to the lammps-master/lib/meam/ directory and compile the lammps/meam potential library for gfortran
Code: Select all
$ make -f Makefile.gfortran

3. Return to the lammps-master/src/ directory and compile lammps for Ubuntu(LAMMPS executable built up process)
Code: Select all
$ make clean-all

Code: Select all
$ make ubuntu

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.
Code: Select all
$ sudo cp -r ~/PROJECT/lammps-master/src/lmp_ubuntu /usr/local/bin

Then, open the terminal, jump into the directory of input file in.inputfile and run lammps in ubuntu as:
Code: Select all
$ lmp_ubuntu<in.inputfile

For parallel run , the following code can be types:
Code: Select all
$ mpirun -np 4 lmp_ubuntu -in in.inputfile

LAMMPS how to input commands

On the installation of pre/postprocessing tools of LAMMPS

a. xmovies
about x11/XAW/Form.h
b. VMD
VMD tool
g. PizzaPy

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

Extended Fem (XFEM) softwares

Multiphase Flow

Android emulation in Ubuntu
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

bubble formation in liquid

numerical values of convection heat transfer coefficient

ICEPT_2014 ... 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
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

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. ... uTherm.pdf
3. ... AlZnMg.pdf
4. MinKin software
5. Cantera for CVD simulation
6. SOFC modeling using Cantera
7. DENIS software for modeling of SOFC
9.quantum wise and virtual nanolab GUI
10. VNL as gui for quantum espresso

Type in Nepali Fonts

paper titles in icept-2016, Wuhan, 16-19 August 2016
Basic requirements of letter of motivation
Tips for letter of motivation in DAAD application ... vation.pdf ... ion-letter ... 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 -
2. ia32 libs for setting up teamviewer -
3. ... 4-04-64bit
6. ... untu-1404/
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 16.04
    Code: Select all
    $ sudo dpkg --add-architecture i386

    Code: Select all
    $ sudo apt-get update

    Code: Select all
    sudo gdebi teamviewer_12.0.71510_i386.deb

    In order to uninstall teamviewer, please follow the following step
    Code: Select all
    $ sudo apt-get remove teamviewer*
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
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. ... y-precise/
2. ... 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)

2. Install Pymatgen using Conda (recommended)
Thank you

Anil Kunwar
Last edited by annier on 12 Sep 2017, 17:22, edited 216 times in total.
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Joined: 27 Aug 2013, 13:51

Re: Using multiple softwares for performing a simulation

Postby annier » 15 Jul 2014, 21:38

Regarding the installation of python and python related tools , the following websites might be useful: on fipy software)
solution for -->>.python-eggs is writable by group/others and vulnerable …
Crank-Nicolson Method in Python (intuitive notes on python)
concepts of diagonals in numpy
examples and illustrations in numpy
matrix calculation in numpy alt-install instead of make install for installing python from source in Ubuntu) python tkinter module)

For working in isolated python environment, virtual environment seems to be helpful. The following posts discuss about setting up the virtual environment. another version of python in home directory for running virtual environment with this module) for solving the error related to installation of another version of python module in home directory) that the configuration option as:
Code: Select all
$SVNVERSION=not-found ./configure
, will resolve
Code: Select all
gcc: error: directory": No such file or directory make: *** [Modules/getbuildinfo.o] Error 1

anil kunwar
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Joined: 27 Aug 2013, 13:51

Re: Using multiple softwares for performing a simulation

Postby annier » 09 Oct 2014, 10:06

Installation of Virtual Box in Ubuntu14.04 is discussed in the following link:

Anil Kunwar
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Joined: 27 Aug 2013, 13:51

Re: Using multiple softwares for performing a simulation

Postby annier » 10 Oct 2014, 09:59

Installation of OpenFOAM in Ubuntu 14.04
The instructions for installation of OpenFOAM in ubuntu 14.04 are given in :

Anil Kunwar
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Joined: 27 Aug 2013, 13:51

Re: Using multiple softwares for performing a simulation

Postby annier » 10 Oct 2014, 10:27

List of Some Softwares
A. For multiphysics numerical computations using finite element method, some of the softwares are listed below:

B. For multiphysics numerical computations using finite volume method, some of the softwares are listed below:
The installation of FiPy has been described in
Most of the python packages (except PySparse and FiPy) required for FiPy Installation are available in

C. For calculation of Thermodynamics, Chemical Kinetics and Transport Properties, the following softwares can be used:

D.For numerical computations in biology and physiology

For more names of the softwares

Anil Kunwar
Last edited by annier on 11 Apr 2015, 10:26, edited 16 times in total.
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Joined: 27 Aug 2013, 13:51

Re: Using multiple softwares for performing a simulation

Postby annier » 10 Oct 2014, 11:17

List of Some Useful Library and Toolkits for Numerical Computation
    1. LibMesh

    2. Portable, Extensible Toolkit for Scientific Computation (PETSc)
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Re: Using multiple softwares for performing a simulation

Postby annier » 20 Oct 2014, 17:00

1.Gnuplot can be utilized in plotting the data related with experiments and simulations.
Some Useful Links for Gnuplot (tutorials) (tutorials) (tutorials) (tutorials) (tutorials)
colored lines in gnuplot many tutorials about basic gnuplot) (bar chart in gnuplot) ... r-category (tutorials on histogram in gnuplot) ... 00%29.aspx
plotting data from csv file in gnuplot
gnuplot working with dot_dat and dot_csv(comma_separated_variable) files
more on barchart and histogram
clustered barchart in gnuplot
grouping multiple bars in gnuplot
easy guide for plotting histogram ... in-gnuplot

2. Gimp (GNU Image Manipulation Program)
For input of Greek Symbols in GIMP
1. Table containing unicode characters for the Greek Symbols
2. How to make Greek Symbols using GIMP software
3. Graphic edition using GIMP software
4. Grimpusers forum
5. ... characters
7. ... -gimp.html
8. ... -gimp.html

3. Mattplotlib

4. OpenMPI installation in Ubuntu

5. ImageJ Software in Ubuntu/Windows and other OS
5.1. ... d-diameter
5.2. Website of IMAGEJ software
5.3. Download of imageJ software
5.4. basics of imagej software
5.5.Example illustration for imageJ software
5.6. ImageJ software user guide
5.7 Cellprofiler software similar to image J software
5.8 An essay on image analysis softwares
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Re: Using multiple softwares for performing a simulation

Postby annier » 06 Nov 2014, 16:14

Links Related to Phase-Field Simulation Tools in Python volume fraction of 2nd phase in FiPy) and Coordinates in FiPy) Group in FiPy) or shape mismatch)
frequently asked questions on FiPy
fipy manual
information related to fipy variables coefficient for convection term in fipy) coefficient for convection term in fipy) (metal ion diffusion equation)
source term in vector representation (FiPy)

femlego software
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Re: Using multiple softwares for performing a simulation

Postby annier » 06 Nov 2014, 16:49

Environment Variables
They are the way for implementing the behaviour of software on the system and thus, consist of nomenclatures having values assigned to them. more
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Re: Using multiple softwares for performing a simulation

Postby annier » 07 Nov 2014, 11:39

Building and Installing FiPy (software for Phase Field Simulation) in Ubuntu 14.04
The details instructions for these are provided here.
1. Install gmsh, linsuperlu3 and python-sparse
Code: Select all
$sudo apt-get install gmsh libsuperlu3 python-sparse

2. Download the python-central package from Ubuntu 10.04 package center and install it via dpkg command'
Code: Select all
$sudo -s

Code: Select all
#dpkg -i python-central_0.6.15ubuntu1_all.deb

3. Download the python-fipy_3.1-1_all.deb or any available later versions( dependencies of fipy software) from here and install it.
Code: Select all
$sudo -s

Code: Select all
#dpkg -i python-fipy_3.1-1_all.deb

4.Now, as all dependencies(required and optional packages) for fipy are configured in Ubuntu, download the FiPy software and ez_set up software; then copy them into a FiPy_Installation Directory
(It is assumed that FiPy_Installation directory is in HOME)
a. ez_set python package
    ii.tar it
    Code: Select all
    tar xzvf ez_setup-0.9.tar.gz
    iii.Build and install it as a root user
    Code: Select all
    #cd ~/FiPy_Installation/ez_setup-0.9/

    Code: Select all
    #python build

    Code: Select all
    #python install

b. FiPy-3.1 FiPy-3.1.tar.gz or later versions from here)
    ii.tar it
    Code: Select all
    tar xzvf FiPy-3.1.tar.gz
    iii.Build and install it as a root user
    Code: Select all
    #cd ~/FiPy_Installation/FiPy-3.1

    Code: Select all
    #python build

    Code: Select all
    #python install

1.The $ indicates that the things has to be typed in the terminal and # indicates the user has typed the things in the terminal as a root user.
2. For running the level set solver: LSMLIB and SKFMM needs to be in the python path and so they need to be installed from the following links:

Copying the script codes in python from examples of FiPy to Users Project to create a working template
Code: Select all
$ python copy_script --From --To

Reference:FiPy website

Using conda to install FiPy software ... nvironment

Electrodeposition Study in FiPy
Module for metalIonDiffusionEquation
python code for metalIonDiffusionEquation
python code for metalIonSourceEquation
extensionVelocityVariable in FiPy
cfl number for convection in FiPy
Updated syntax for Boundary conditions in FiPy
Superconformal electrodeposition in FiPy
Phase field model of a chemical reaction
Benchmarks for multicomponent diffusion and electrochemical migration

Reactive Wetting in FiPy ... Warren.pdf ... -field.pdf ... GM-L08.pdf ... iPy_v9.pdf

Thermotransport in FiPy ... 05_PhD.pdf ... newest&f=1 ... 03060.html

The flow solver of fipy uses dolfyn codes.

Virtual box in Ubuntu Linux
1. ... box-linux/
2. ... irtual-box

Anil Kunwar
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