Install
Requirements
Preferables
- gnuplot (version 4.2 or higher)
- Ruby (version 1.8.6 or higher)
- autoconf (version 2.61 or higher)
- automake (version 1.10 higher)
Quick compilation
$ tar zxf feram-X.YY.ZZ.tar.gz
$ cd feram-X.YY.ZZ
$ mkdir Linux-i686-gfortran-4.2.2
$ cd Linux-i686-gfortran-4.2.2
$ ../configure --help
$ ../configure
$ cd src
$ make
$ ls -l feram
$ cp -r ../../src/01example-BaTiO3-epit-hysteresis-loop .
$ cd 01example-BaTiO3-epit-hysteresis-loop
$ ./externalE.sh # test run
$ gnuplot hysteresis.gp # plot a hysteresis loop
$ gv hysteresis.gp # preview
Available platforms and compilers
HITACHI SR11000 with xf90 (super1 in IMR)
feram runs on 1 node (16 CPUs) of SR11000 effectively.
% tar zxf feram-X.YY.ZZ.tar.gz
% cd feram-X.YY.ZZ
% mkdir SR11000-xf90
% cd SR11000-xf90
% env FC=xf90 ../configure --host=SR11000
% make
Because SR11000 and its Fortran compiler cannot treat command arguments,
you have to specify input file(s) in FILES file. For example,
3
foo
bar
baz
1st line: number of input file(s). 2nd- line filename(s).
x86_64 GNU/Linux
On x86_64, i.e. AMD64 and Intel 64, feram may be compiled with gfortran,
Intel Fortran (ifort), and PGI Fortran (pgf95). For example,
$ FC=gfortran ../configure
If FFTW3 was installed other than in /usr/lib and /usr/include or /usr/local/lib
and /usr/local/include, you have to specify the directories with LDFLAGS and CPPFLAGS
environment variables.
$ FC=ifort LDFLAGS=-L/home/t-nissie/x86_64-Linux/lib CPPFLAGS=-I/home/t-nissie/x86_64-Linux/include ../configure
rupc05
$ FC=pgf95 LDFLAGS=-L/home/takeshi/x86_64-Linux/fftw3-pgcc-pgcpp-pgf77/lib CPPFLAGS=-I/home/takeshi/x86_64-Linux/fftw3-pgcc-pgcpp-pgf77/include ../configure
$ make
$ cd examples/BaTiO3-bulk-16x16x16-local.field-new-format/
$ OMP_NUM_THREADS=6 ../../pgf95/src/feram foo123 > feram.log
IA-64 GNU/Linux (appc in IMR)
On IA-64, feram may be compiled with gfortran or Intel Fortran (ifort). For example:
% tar zxf feram-X.YY.ZZ.tar.gz
% cd feram-X.YY.ZZ
% mkdir appc-FFTW3/
% cd appc-FFTW3/
% env FC=ifort LDFLAGS=-L/home/t-nissie/ia64-Linux/lib CPPFLAGS=-I/home/t-nissie/ia64-Linux/include ../configure
% cd src
% make
x86 32-bit GNU/Linux
On x86 32-bit GNU/Linux, feram may be compiled with gfortran and Intel Fortran (ifort),
and PGI Fortran (pgf95).
Input files
parameter file
The parameter file for feram is a text file consisting of
comment lines and 'tag = value(s)' lines. Filenames for
parameter files are arbitrary.
How to determine the parameters is described in parameters/parameters.html.
Comment
Lines beginning with '#' are ignored.
Blank lines are also ignored.
# This is a comment line.
# Here are two more
# comment lines.
Tags
You must put ' = ', space-equal-space, between tag and value(s) as:
tag = 1.0
tag = -2.0 -3.0 -4.0
tag = 5.0 6.0 7.0
Followings are currently available tags alphabetically ordered.
method
method = 'md'
'md' is for a molecular-dynamics simulation in the canonical ensemble using the Nosé-Poincaré thermostat.
method = 'lf'
'lf' is for a molecular-dynamics simulation in the microcanonical ensemble using the leap-frog method.
method = 'mc'
'mc' is for a Monte Carlo simulation, but it is NOT IMPLEMENTED YET.
method = 'hl'
'hl' is for a simulation of hysteresis loop. In this case, tags of n_average and external_E_field have special meanings.
foo.hl file will be created.
See the directory of src/11example-BaTiO3-new-hysteresis-loop/.
GPa
Pressure in GPa unit.
GPa = -5.0
kelvin
Temperature in Kelvin.
kelvin = 100
Q_Nose
Q_Nose for Nose-Poincare thermostat.
Q_Nose = 14.4
bulk_or_film
Specifies the structure of the system.
'bulk' for infinitely periodic bulk
'film' for free standing thin film.
'epit' for epitaxially strained thin film.
bulk_or_film = 'epit'
L
System size, L_x, L_y and L_z. They must be equal or larger than 4.
L = 32 32 4
gap
Gap for the thin film.
gap = 1
a0
Lattice constant for the perovskite ferroelectrics in Angstrom unit.
a0 = 3.99
epi_strain
epi_strain = -0.01
dt
Time step in pico second.
dt = 0.002
n_thermalize, n_average, n_coord_freq
The number of time steps of thermalizing, averaging, and frequency
of taking snapshots. If n_thermalize+n_average=n_coord_freq, a
snapshot is taken at the end of the MD at each temperature.
n_thermalize = 40000
n_average = 10000
n_coord_freq = 50000
external_E_field
Vector of the external electric field in the unit of [V/Angstrom].
external_E_field = 0.00 0.00 -0.01
P_kappa2, P_alpha, P_gamma
Coefficients for the 4-th order polynomial.
P_kappa2 = 5.502 [eV/Angstrom^2] # P_4(u) = kappa2*u^2 + alpha*u^4
P_alpha = 110.4 [eV/Angstrom^4] # + gamma*(u_y*u_z+u_z*u_x+u_x*u_y),
P_gamma = -163.1 [eV/Angstrom^4] # where u^2 = u_x^2 + u_y^2 + u_z^2
P_k1, P_k2, P_k3
Coefficients for the 6-th order part
j
Short-range inter-site interaction coefficients
j = -2.648 3.894 0.898 -0.789 0.562 0.358 0.179 j(i) [eV/Angstrom^2]
B11, B12, B44
Elastic Constants
B11 = 126.
B12 = 44.9
B44 = 50.3 [eV]
B1xx, B1yy, B4yz
Elastic Coupling
B1xx = -211. [eV/Angstrom^2]
B1yy = -19.3 [eV/Angstrom^2]
B4yz = -7.75 [eV/Angstrom^2]
init_dipo_avg, init_dipo_dev
Initial dipole settings
init_dipo_avg = 0.00 0.00 0.00 [Angstrom] # Average of initial dipole displacements
init_dipo_dev = 0.02 0.02 0.02 [Angstrom] # Deviation of initial dipole displacements
Z_star
Effective charge per site.
Z_star = 9.956
epsilon_inf
epsilon_inf = 5.24
kappa
This is for debug. You do not have to set this tag.
Arbitrary kappa for Ewald summation in src/dipole-dipole-long-range.F.
kappa = 0.15
plot_dispersion
If
plot_dispersion = .true.
data files for plotting dispersion relation will be written. Default is .false..
defect_position, defect_u
Position and u of a defect.
defect_position = 16 16 16
defect_u = 0.0 0.0 0.0
ionic.configuration file
(Not implemented yet.)
This file is required for the calculation of the local field.
0.0 0.0 0.0 +3.0
0.5 0.0 0.0 -2.0
0.0 0.5 0.0 -2.0
0.0 0.0 0.5 -2.0
:
:
position_x position_y position_z effective_charge_of_the_ion
:
:
Position must be given in the unit of a0.
local.field input file
0 0 0 0.1 -0.1 0.7
1 0 0 0.1 0.1 0.7
2 0 0 0.1 0.2 0.7
:
:
position_x position_y position_z E_local_x E_local_y E_local_z [V/Angstrom]
:
:
Lx Ly Lz 0.1 0.2 0.7
If feram cannot find both ionic.configuration and local.field,
it will set local.field to ZERO.
Output files
If you execute the feram like `feram foo123`,
filenames of output files are starting from 'foo123',
e.g. foo123.avg, foo123.320K0050000.coord,
foo123.dipole-dipole-long.dat, etc.
Standard output (stdout)
To stdout, feram reports the energies of every iterations.
src/plot.gp can plot the energies:
$ feram foo123 > feram.log
$ gnuplot plot.gp
foo123.avg
Averages for each temperature.
foo123.hl
In the case of method = 'hl', a simulation of hysteresis loop, one .hl file will be created instead of a .avg file.
foo123.tttKnnnnnnn.coord
Snapshot of dipoles at ttt Kelvin and nnnnnnn-th iteration.
This file can be visualized with slice.rb (Ruby script) and
cross-section-q.sh, cross-section-p.sh, and cross-section-dVddi.sh
(Bourne Shell scripts). cross-section-p.sh and cross-section-dVddi.sh
are symbolic links or copy of cross-section-q.sh.
foo123.dipole-dipole-long+short.dat
foo123.dipole-dipole-long.dat
foo123.dipole-dipole-short.dat
foo123.inhomo-K.dat
local.field output file
The calculated local field from the given ionic configuration (ionic.configuration
file) is stored in this file. This file will be reloaded in consequent temperature
calculations and the other calculations.
Copying
feram
Copyright © 2007-2009 by Takeshi Nishimatsu
feram is distributed in the hope that
it will be useful, but WITHOUT ANY WARRANTY.
You can copy, modify and redistribute feram,
but only under the conditions described in
the GNU General Public License (the "GPL").
For more detail, see COPYING.
You can make a DONATION to Takeshi Nishimatsu through
Tohoku University http://www.rpip.tohoku.ac.jp/kensui/kifukin.html (in Japanese).
The author is grateful if you would kindly refer the
name of this program and cite our articles,
[Takeshi Nishimatsu, Umesh V. Waghmare, Yoshiyuki Kawazoe, and
David Vanderbilt: Phys. Rev. B 78 (2008) 104104] and [Jaita Paul,
Takeshi Nishimatsu, Yoshiyuki Kawazoe, and Umesh V. Waghmare:
Phys. Rev. Lett. 99 (2007) 077601] in your papers.
BLAS and LAPACK
Files under the directory libblaslapack are coming from BLAS and LAPACK
packages http://www.netlib.org/lapack/ . See libblaslapack/COPYING.
Cited figures
Authors and/or publishers of the papers have their copyrights for the following cited figures.
- doc/figures/BaTiO3-abc-T-dependence.eps and doc/figures/BaTiO3-abc-T-dependence.jpg
are cited from [H. E. Kay and P. Vousden: Philos. Mag. 40, 1019 (1949)].
- doc/figures/Fong.jpg and doc/figures/FongScience.eps are cited from
[Dillon D. Fong et al.: Science 304, 1650 (2004)].
- doc/figures/J.F.Scott.Fig.1.1.a.eps, doc/figures/J.F.Scott.Fig.1.1.ae.eps
doc/figures/J.F.Scott.Fig.1.1.ae.jpg, doc/figures/J.F.Scott.Fig.1.1.e.eps are
cited from [J. F. Scott: Ferroelectric Memories (Springer-Verlag,
Berlin Heidelberg, 2000)].
- doc/figures/MC-vs-MD.eps, doc/figures/MC-vs-MD.jpg, doc/figures/MC-vs-MD.obj, and
doc/figures/PRBv52p6301-FIG3.jpg are cited from [W. Zhong, D. Vanderbilt, and
K. M. Rabe: Phys. Rev. B 52, 6301 (1995)].
- doc/figures/PbTiO3ShiraneHoshinoSuzuki.eps and doc/figures/PbTiO3ShiraneHoshinoSuzuki.jpg
are cited from [Gen Shirane, Sadao Hoshino, and Kazuo Suzuki: Phys. Rev. 80, 1105 (1950)]
- doc/figures/RandallBhallaFig3.jpg and doc/figures/RandallBhallaFig8.jpg are
cited from [C. A. Randall and A. S. Bhalla: Jpn. J. Appl. Phys. 29, 327 (1990)].
- doc/figures/SilviaFig1.jpg is cited from [Silvia Tinte, B. P. Burton,
Eric Cockayne and U. V. Waghmare: Phys. Rev. Lett. 97, 137601 (2006)].
- doc/figures/TsurumiFig3.eps and doc/figures/TsurumiFig3.jpg are cited from
[Takaaki Tsurumi, Kouji Soejima, Toshio Kamiya. and Masaki Daimon:
Jpn. J. Appl. Phys. 33, 1959 (1994)].
pseudopotentials
Four Teter's "extended norm-conserving" LDA pseudopotential files are downloaded from
http://www.abinit.org/Psps/?text=../Psps/LDA_EX/lda . They are distributed under GPL.
56ba.psp.mod
82pb.960808c.mod
22ti.psp.mod
8o.phoney.mod
