Using multiple softwares for performing a simulation

Discussion about building and installing Elmer

Re: Using multiple softwares for performing a simulation

Postby annier » 29 Jun 2016, 12:35

Last edited by annier on 15 Jul 2016, 21:24, edited 3 times in total.
Posts: 1034
Joined: 27 Aug 2013, 13:51

Re: Using multiple softwares for performing a simulation

Postby annier » 01 Jul 2016, 12:14

ABINIT - A DFT based software for computational chemistry
Presentation on ABINIT software
forum for ABINIT software
developers of abinit software
A brief introduction of abinit software package
Computational materials science - ABINIT software
VESTA software for visualization
VESTA - citation articles and downloads
Presentation on ABINIT by xavier gonze
Density functional theory in the abinit code By Matteo Giantomassi
Discussions on ABINIT, Gaussian and Quantum Espresso softwares for DFT calculations
Quantum theory of solids - ABINIT codes
Amorphous TiO2 as a photocatalyst for Hydrogen production

Quantum Espresso - DFT code and AB-INITIO MD code
2. ... ndouts.pdf
3. DFT simulations of anatase TiO2
4. Tutorial on using module
5. Atomic simulation environment - python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations
6. ... _unit_cell
7. Structural, optical and electronic properties of TiO2 clusters
8. Questionnaire on energy band gap of TiO2
9. Tutorials on Quantum Espresso
10. Installation procedure of Quantum espresso
11. Installation of Quantum Espresso in Ubuntu 14.04
12. Karibe's experience with Quantum Espresso in Ubuntu 14.04
13. Nnemec github repository of quantum espresso
14. Setting up and testing Quantum Espresso in Ubuntu 14.04 in UNIST, Energy Conversion Lab
15.Online tutorial for Quantum Espresso Installation
16. Step by Step procedures for using VNL (Virtual Nano Lab ) gui for QE (Quantum Espresso) Software
(i) Install Quantum Espresso from Ubuntu Software Centre or "
Code: Select all
sudo apt-get update
Code: Select all
sudo apt-get install quantum-espresso
" command.
(ii) Download VNL from here or there.
(iii) The step by step installation procedure are give here.
Code: Select all
$ chmod a+x VNL-ATK-2015.2-linux64.bin

Code: Select all

(iv) In ubuntu the license file is kept at $HOME directory and VNL can find it when it loads.
(v) The tutorial with VNL as GUI for QE is given in this link: ... m-espresso
or ... s_dos.html
17. Notes on Quantum Wise
18. Density of states calculation tutorial
19. Fundamentals of Quantumwise - VNL tutorials
20. QE tutorials on carbon-nanotubes with hydrogen defects
21. Simple calculations with Quantum Espresso
22. Introduction to DFT via QE
23. First step tutorial of CO adsorption on Pt Surface
24. Modeling materials using DFT theory
25. Computational studies of functionalized ZnO
26. Computational studies on functionalized SnO2
27. Dissertation using DFT and qe

Quantumwise and virtual nanolab
1. Tutorials on benzene adsorption on Au - VNL preprocessing for creating QE input file
2. [url]Building LUMO water in vnl[/url]
3. Interface builder in vnl
4. DFT for metal-semiconductor (Ag-Si) interface
5. Thermal conductivity of interface in polycrystal Silicon
6. Thermal conductivity of Boron nitride

Literature on Electronic Structure
1. Electronic structure and psuedopotentials of rutile TiO2
2. Advanced courses on Electronic Structure

Energy and Environment Science
1. Research works on energy and environment studies(Team of C. Yang and C.P. Wong)
2. Solvothermal synthesis of Sno2/graphene as electrode materials of supercapacitors
3. Overview of supercapacitors Mitre
4. Supercapacitor modeling in Comsol
5. Electrodes of ternary nanocomposites
6. Thermal analysis on stackable supercapacitor
7. Low order mathematical modeling of electrical double layer supercapacitors
8. Batteries , Fuel Cells and SuperCapacitors
9. Graphene based nanocomposites for energy storage and conversion
10. Application of nanocomposites for Supercapacitors
11. Review article for SnO2 based nanomaterials for Lithium ion battery and Supercapacitors
12. Mesoporous Carbon/SnO2 nanocomposites for Supercapacitors

13. Nuclear Energy as Clean Energy
a. Is Nuclear Energy Renewable Energy

DFT methods for modeling electrode materials in the supercapacitors
1. Quantum capacitance performance analysis
2. Design strategies
3. interfacial microstructure and graphene capacitance
4. Codoped graphenes
5. Large area few layer graphene
6. Electronic structures and quantum capacitance
7. Relation between electrode and electrolyte in supercapacitor
Last edited by annier on 10 Jun 2017, 08:16, edited 26 times in total.
Posts: 1034
Joined: 27 Aug 2013, 13:51

Re: Using multiple softwares for performing a simulation

Postby annier » 15 Jul 2016, 10:45

annier wrote: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 (
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

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
A good lecture in density functional theory

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

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)
citation machine


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

Thank you

Anil Kunwar
Posts: 1034
Joined: 27 Aug 2013, 13:51

Re: Using multiple softwares for performing a simulation

Postby annier » 19 Jul 2016, 11:33

Poly(LacticAcid) - Literature Review
1. ... 5812029414
2. ... sertations
3. ... 2106a.html
4. Impact behaviour of Polylactic Acid reinforced with Mg
5. Mechanical characterization and finite element modeling of Polylactic acid
6. Computational modeling of polylactic acid - calcium phosphate glass scaffold
7. Biodegradable poly-lactic acid reinforced with high-strength magnesium alloys
8. Atomistic modeling of CNT - Master's thesis
9. Electrospun polylactic acid and characterization
10. Degradability of poly(lacticacid) containing nanoparticles
11. Magnetite Polylactic acid core-shell nanoparticles by Ring opening polymerization via microwave irradiation
12. Polylactic acid in drug delivery system
13. Crystallinity of Polylactic acid and TiO2 nanocomposite
14. Structural stability of polylactic acid , pe and TiO2
15. On the dissolution of Polylactic acid
16. Biodegradability and biodegradation of polylactide
17. Polylactide degradation by kA
18. Dissertation on FEM of 3D Printed Polymer
19. Mg reinforced Polylactic Acid Composite for Orthopedic Application
Book/literatures on renewable energy and particle technology
1. ... /index.htm
2. Particle characterization in pharmaceutical engineering
4. Crop drying using solar air heating
5. Design of solar thermal dryers for crop heating
6. CFD analysis of solar air dryer
7. Drying of agricultural crops by solar heating
8. Analysing and modeling solar dryer in comsol (Heat transfer)
9. Solar air heater with pcm
10. Thermal analysis of solar air heater with PCM for thermal energy storage
11. Heat transfer enhancement of paraffin wax as PCM
12. Paraffin and palygorskite as composite PCM
13. Using aluminum/paraffin wax composite as a solar thermal air heater composite
14. Natural convection in cavities
15. Natural convection in rectangular enclosures
16. Surface modification of polylactic acid using laser
Last edited by annier on 03 Oct 2016, 12:56, edited 15 times in total.
Posts: 1034
Joined: 27 Aug 2013, 13:51

Re: Using multiple softwares for performing a simulation

Postby annier » 27 Jul 2016, 11:46

Installation of electrochemistry toolkit (ECTk) in Ubuntu14.04
Reference: 1.
2. ... nstall.pdf
1. Install the build essentials libraries: tcl/tk, tcl-readline and libcomedi
Code: Select all
$ sudo apt-get install tcl8.5-dev tk8.5-dev tcl-tclreadline libcomedi-dev

The unavailability of these libraries will produce the following errors
a. fatal error: tk.h: No such file or directory
b. fatal error:tcl.h no such file or directory
c. fatal error:tclreadline.h no such file or directory
d. fatal error:comedilib.h no such file or directory

2. Download ECTK source files from here.

3. Extract or untar the source file ECTK.

4. Jump into the location $path_to_ECTK/v1/src/ and type the following:
Code: Select all
$ sudo make install

ECTK software is installed now.

5. In order to run the Electrochemistry Toolkit software, type in terminal
Code: Select all
$ ectk

6. Add your computer user name in the iocard
Code: Select all
$sudo adduser your_user_name iocard

Yours Sincerely,
Anil Kunwar
Posts: 1034
Joined: 27 Aug 2013, 13:51

Re: Using multiple softwares for performing a simulation

Postby annier » 03 Aug 2016, 11:54

Laser welding.soldering of materials
1. Effect of scanning speed on coating properties
2. Investigation on the effects of laser power and scanning speed on polypropylene diode transmission welds
3. laser forming process a scientific view
4. Numerical modeling of scanning laser induced melting of metals
5. Implicit enthalpy method for modeling laser induced melting in Silicon
6. Pulsed laser induced melting and solidification of Silicon
7. Thermal analysis during laser sintering
8. Modeling of laser welding in keyhole formation
9. Keyhole laser welding modeling in Ansys/FLUENT
10. Notes on laser soldering
11. Optimization of uncertainty parameters in laser welding
12. temperature field in the melting of metals by laser
13. Modeling of temperature field in selective laser melting
14. FEM for direct laser melting
15. Thermal evolution for laser based microsintering in metals alloys
16. Dispensing of solder paste for laser soldering SMTM July 2016 Vol 31 Issue 7 pp. 102-113
17. Specifications of thermal imaging camera 1
18. Specifications of thermal imaging camera 2
19. Viscosity and electrical conductivity of SAC alloys
20. Experiments and numerical analysis on melting and solidification of SnAgCu solder joints, IEEE2016August-September
21. Modeling surface ablation and melting of plasma
22. How laser scanning works
23. Abaqus UDF code for moving laser source
24. laser heating source in a rotating cylinder
25. The plasma simulation code project
27. Heat conduction of a moving heat source
28.Preparation of solder pads by selective laser scanning
29. Experimental and numerical analyses of laser remelted Sn0.7wtCu Solder Surfaces by B.L. Silva et al (2015)
30. Reflectance and absorptance on metal surface for incident laser beam
31. Laser beam soldering behaviour of Eutectic Sn-Ag solder 1995
32. Solar absorptance and reflectance properties of 12 Metals from 300 to 500 K
33. Optical absorption aspects of laser soldering for high density interconnects Michael Greenstein, Applied Optics, 1989
34. Fiber optic contact microsoldering device
35. Impact strength of SAC processed by laser soldering
36. Article on laser parameter for soldering
37. Good discussions on timestep size and timestep interval
38. Correct use of heat transfer coefficients for casting and solidification process
39. MOOSE software and laser processing of sheet metals
40. A good concept on adaptive timestepping strategy within FEM
41. Elmer thread on Adaptive timestepping
42. ... g_2015.pdf
43. Ph.D. dissertation on simulation of laser welding by Bon Sueng Koo (January 2013)
44. Elmer Optimization solvers - find optimum and elmer param notes by Peter Raback

45. Literature on heat and mass transfer during laser soldering (Advances on Heat Transfer Chapter 4)

IOE graduate conference website
Last edited by annier on 07 Mar 2017, 13:43, edited 6 times in total.
Posts: 1034
Joined: 27 Aug 2013, 13:51


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