feram: molecular dynamics simulator for bulk and thin-film ferroelectrics and relaxors
The parameter file for feram is a text file consisting of comment lines and 'tag = value(s)' lines. Filenames of parameter files may be foo123 or foo123.feram. In these cases, filenames of output files will be foo123.*, e.g. foo123.log, foo123.coord, etc.
How to determine the parameters is described in parameters/parameters.html.
Lines beginning with '#' are ignored. Blank lines are also ignored.
# This is a comment line. # Here are two more # comment lines.
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.
verbose tag determines how much messages will be written to the .log file. (Details of .log file is described below.)
verbose = 0
(NOT IMPLEMENTED YET) .log file will not be created.
verbose = 1
1 is the default value for verbose tag. Minimum messages will be written to the .log file.
verbose = 2
When 2 is given for verbose tag, messages will be written to .log file in every iterations.
method = 'md'
'md' is for a molecular-dynamics simulation in the canonical ensemble using the Nosé-Poincaré thermostat.
method = 'vs'
'vs' is for a molecular-dynamics simulation in the canonical ensemble using the velocity scaling 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 (see Fig:external). .hl file,e.g. foo123.hl, will be created. See the directory of src/11example-BaTiO3-new-hysteresis-loop/.
Pressure in GPa unit.
GPa = -5.0
Temperature in Kelvin.
kelvin = 100
Effective mass of u(R), the length of dipole on the unit cell R. In atomic mass unit.
If acoustic_mass_amu is not set, acoustic displacements, i.e. inhomogeneous strains, are optimized according to the {u(R)}. If it is set to the effective mass of acoustic displacements
acoustic_mass_amu = 46.44
molecular dynamics is performed on acoustic displacements. Its unit is atomic mass unit. Generally, it is average of mass of 5 atoms. You cannot use method = 'md' nor 'lf' togeter with acoustic_mass_amu, currently.
Q_Nose for Nose-Poincare thermostat. For large system and high temperature, use large value. For Small system and low temperature, use small value.
Q_Nose = 14.4
Specifies the structure of the system. 'bulk' for infinitely periodic bulk 'film' for free standing thin film. 'epit' for epitaxially strained thin film. See epi_strain tag.
bulk_or_film = 'epit'
System size, L_x, L_y and L_z. They must be equal or larger than 4.
L = 32 32 4
0: There is no dead layer. 1: Single dead layer is on the bottom electrode. 2: There are dead layers both on the bottom and top electrodes.
gap_id = 1
Thickness of dead layer is always 1 unit cell.
Polarization of dead layer(s) in Angstrom unit.
gap_dipole_u = 0.0 0.0 0.16
Lattice constant for the perovskite ferroelectrics in Angstrom unit.
a0 = 3.99
Epitaxial strain.
epi_strain = -0.01
Note that epi_strain is effective only when bulk_or_film = 'epit'. See src/optimize-homo-strain.F for more details.
Time step in pico second.
dt = 0.002
The number of time steps of thermalizing, averaging, frequency of taking snapshots, and frequency of writing to .hl file.
n_thermalize = 40000 n_average = 10000 n_coord_freq = 50000 n_hl_freq = 5000
You can restart and continue a hysteresis-loop calculation from the n_hysteresis_loop_continue-th iteration.
n_hysteresis_loop_continue = 20000
If this tag is set as
coord_directory = 'coord_files'
.coord file will be written into coord_files/foo123.0000020000.coord . For example, use this tag to store huge .coord files into a local HDD.
If you do not want to get any .coord files, set it as
coord_directory = 'never'
If this tag is set as
distribution_directory = 'distribution_files'
.distribution and .distribution3d files will be written into distribution_files/foo123.distribution and distribution_files/foo123.distribution3d . For example, use this tag to store the huge .distribution3d file into a local HDD.
If you do not want to get any .distribution and .distribution3d files, set it as
distribution_directory = 'never'
This can also reduce computational time.
Vector of the external electric field in the unit of [V/Angstrom].
external_E_field = 0.00 0.00 -0.01
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
Coefficients for the 6-th order part
Coefficient for u^8
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]
Elastic Constants
B11 = 126. B12 = 44.9 B44 = 50.3 [eV]
Elastic Coupling
B1xx = -211. [eV/Angstrom^2] B1yy = -19.3 [eV/Angstrom^2] B4yz = -7.75 [eV/Angstrom^2]
Two integers for Marsaglia-Tsang 64-bit uiniversal RNG (random number generator).
seed = 123384 8984847
Its default values are 123456789 987654321. It may be a good idea to generate the seed with jot(1) command.
$ jot -r 2 1 2147483648 639779840 1297280417
Values for initial random setting of dipoles. The normal-distributed random number generator N(mu,sigma^2) is used.
For example, if you only have four dipoles and
init_dipo_avg = 0.10 0.00 0.00 [Angstrom] # Average (mu) of initial dipole displacements init_dipo_dev = 0.02 0.02 0.02 [Angstrom] # Deviation (sigma) of initial dipole displacements,
the dipoles may be
0.09 0.01 0.02 0.11 -0.02 0.01 0.08 0.02 -0.03 0.12 -0.01 0.00 .
If there is a .restart file in the same directory, there values are not used and the .restart file will be read.
Effective charge per site.
Z_star = 9.956
epsilon_inf = 5.24
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
If
plot_dispersion = .true.
data files for plotting dispersion relation will be written. Default is .false..
If you executed feram with a parameter file "foo123.feram" as
$ feram foo123.feram
feram searches for the "foo123.restart" file as an initial configurations. If there is no such file, feram starts from a random configurations.
Qudratic inter-atomic force constant (IFC) matrices can be read from .quadratic file. Set all j1-j7 to ZERO. Use P_kappa2 for *elevation*. (Lx/2+1)*Ly*Lz 3x3 matrices are required. See src/25example-BaTiO3-read-quadratic/ for more details.
If you executed feram with a parameter file "foo123.feram" as
$ feram foo123.feram
feram searches for the "foo123.defects" file as information of defects. If there is no such file, feram do not introduce defects.
The .defects input file gives positions and fixed dipole moments u for simulations of defects in ferroelectrics.
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 fixed_u_x fixed_u_y fixed_u_z [Angstrom] :
Use src/defects-maker.rb to make this .defects file.
If you executed feram with a parameter file "foo123.feram" as
$ feram foo123.feram
feram searches for the "foo123.localfield" file as information of local electric field. Format of .localfield file is:
4 6 13 0.00 0.00 0.10 : ix iy iz Ex Ey Ez :
The unit of local field is V/Angstrom. If feram cannot find both ionic.configuration and .localfield, it will set the local field to ZERO for all sites.
(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.
By preparing an FFTW wisdom file in your current directory, you can reduce initial computational time, i.e. computational time before the "Ready for simulation!!!" message. You can generate an FFTW wisdom file with `fft_check` command, which will be built in the src/ directory besides `feram` command. In the src/18example-benchmark/ directory, for example, you can generate an FFTW wisdom file of system size Lx*Ly*Lz=32*32*243 for the forward.feram input file,
$ w # Before executing fft_check, confirm that load average is zero and there is no background job.
$ OMP_NUM_THREADS=6 ../fft_check 1000 32 32 243
:
It takes a few minutes or a few hours depending on the system size.
'1000' in the command line arguments is the number of iterations of
FFT benchmarks. So, do not set a large number for it.
:
$ mv wisdom_new wisdom
$ OMP_NUM_THREADS=6 ../feram forward.feram
$ grep FFTW_WISDOM forward.log
feram_common.F: 47: FFTW_WISDOM: Successfully imported FFTW wisdom in current directory.
$ w
$ OMP_NUM_THREADS=6 ../fft_check 100 300 300 300
$ sudo cp wisdom_new /etc/fftw/wisdom
$ rm wisdom wisdom_new
$ OMP_NUM_THREADS=6 ../feram epit300x300x300.feram &
$ grep FFTW_WISDOM epit300x300x300.log
feram_common.F: 52: FFTW_WISDOM: FFTW wisdom is not in current directory.
feram_common.F: 55: FFTW_WISDOM: Successfully imported FFTW system wisdom, /etc/fftw/wisdom.
Here, /etc/fftw/wisdom is the system wisdom. In this case, you can use this /etc/fftw/wisdom for both Lx*Ly*Lz=32*32*243 and Lx*Ly*Lz=300*300*300 in the OMP_NUM_THREADS=6 environment.
See src/fft_check.html for more details on fft_check.
Check http://www.fftw.org/doc/Other-Important-Topics.html for more details on FFTW wisdom.
If you are not using the FFTW library but other FFT libraries such as MKL, MATRIX/MPP, SSL II, ACML, etc., you do not have to prepare the wisdom file.
You can find input files and their simulated results in following directories in the software package.
feram-X.YY.ZZ/src/03example-BaTiO3-bulk-phase-transition/ feram-X.YY.ZZ/src/17example-PbTiO3-100-900K/ feram-X.YY.ZZ/src/20example-BaTiO3-new-param-pyro/ feram-X.YY.ZZ/src/21example-KNbO3/ feram-X.YY.ZZ/src/22example-BaTiO3-new-param-hl/
This project is/was partially supported by:
http://loto.sourceforge.net/feram/ is hosted by
.
