JETSPIN is a specific-purpose open-source software for electrospinning simulations of nanofibers.
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README.md

README.md

The JETSPIN README File
Version 1.21 (July 2016)

JETSPIN is a specific-purpose open-source software for electrospinning
simulations of nanofibers. The code was originally written by
Marco Lauricella at Applicazioni del Calcolo "Mauro Picone" -
Consiglio Nazionale delle Ricerche with contributions from:
Ivan Coluzza University of Vienna Austria
Dario Pisignano University of Salento Italy
Giuseppe Pontrelli IAC-CNR, Rome Italy
Sauro Succi IAC-CNR, Rome Italy

The software development process has received funding from the
European Research Council under the European Union's Seventh Framework
Programme (FP/2007-2013)/ERC Grant Agreement n. 306357 (NANO-JETS).

This is an experimental code. The authors accept no responsibility
for the performance of the code or for the correctness of the results.

The code is licensed under Open Software License v. 3.0 (OSL-3.0).

If results obtained with this code are published, an appropriate
citation would be:

Marco Lauricella, Giuseppe Pontrelli, Ivan Coluzza, Dario Pisignano,
Sauro Succi, JETSPIN: A specific-purpose open-source software for
electrospinning simulations of nanofibers, Computer Physics
Communications, 197 (2015), pp. 227-238.

Structure

JETSPIN is supplied as a main UNIX directory with 4 subdirectories.
All the source code files are contained in the source sub-directory.
The examples sub-directory contains different test cases that can help
the user to edit new input files. For further details on the input
directives the reader is referred to the article:

Marco Lauricella, Giuseppe Pontrelli, Ivan Coluzza, Dario Pisignano,
Sauro Succi, JETSPIN: A specific-purpose open-source software for
electrospinning simulations of nanofibers, Computer Physics
Communications, 197 (2015), pp. 227-238.

Compiling JETSPIN

The build sub-directory stores a UNIX makefile that assembles the
executable versions of the code both in serial and parallel version
with different compilers. Note that JETSPIN may be compiled on any
UNIX platform. The makefile should be copied (and eventually modified
for several common workstations and parallel computers) into the
source sub-directory, where the code is compiled and linked. Finally,
the binary executable file can be run in the execute sub-directory,
which isintended to be the 'working' directory from which jobs are
submitted for execution and the data files manipulated. A list of
targets for several common workstations and parallel computers can be
used by the command "make target", where target is one of the
following options:
gfortran ---> compile in serial mode using the GFortran compiler.
gfortran-mpi ---> compile in serial mode using the GFortran compiler
under the command-line interface Cygwin for Windows. cygwin ---> compile in serial mode using the GFortran compiler
under the command-line interface Cygwin for Windows. cygwin-mpi ---> compile in parallel mode using the GFortran compiler and the Open Mpi library under the command-line
interface Cygwin for Windows (note a precompiled
package of the Open Mpi library is already available on Cygwin).
intel ---> compile in serial mode using the Intel compiler.
intel-mpi ---> compile in parallel mode using the Intel compiler
and the Intel Mpi library.
intel-openmpi ---> compile in parallel mode using the Intel compiler
and the Open Mpi library.
help ---> return the list of possible target choices.
On Windows system we advice the user to compile JETSPIN under the
command-line interface Cygwin. Note that a Message Passing Interface
Implementation is necessary to compile and run JETSPIN in parallel
mode.

Executing JETSPIN

To run JETSPIN, it is necessary first to ensure that the program is
compiled (from the source sub-directory) and that the file input.dat
is present in the execute subdirectory.
All output data files will be returned to the execute sub-directory.
Remember that the input file HAS TO BE NAMED 'input.dat' and put in
the 'execute' Sub-directory. Few example input files are contained in
the examples sub-directory which can be used as test cases.

Example command to run JETSPIN in serial mode:

./main.x

Example command to run JETSPIN in parallel mode on 4 CPUs:

mpirun -np 4 ./main.x

New features in JETSPIN Version 1.21

  • The dynamic refinement method was implemented.

  • It was implemented a multiple step algorithm for the long-range
    Coulomb forces.

  • The rheological Kelvin–Voigt model was added.

  • Example 6 was added modelling a Kelvin–Voigt fluid.

  • JETSPIN can write PDB formatted file with a PSF file containing the structure of the jet (defining a bond for each pair of consecutive
    jet beads).

  • The manual was updated.