ABINIT, structural optimization input variables:
List and description.
This document lists and provides the description of the name (keywords) of structural optimization input variables to be used in the main input file of the abinis code.
The new user is advised to read first the new user's guide, before reading the present file. It will be easier to discover the present file with the help of the tutorial.
When the user is sufficiently familiarized with ABINIT, the reading of the ~abinit/doc/users/tuning file might be useful. For response-function calculations using abinis, please read the response function help file
Copyright (C) 1998-2007
ABINIT group (DCA, XG, RC)
This file is distributed under the terms of the GNU General Public
License, see
~abinit/COPYING or
http://www.gnu.org/copyleft/gpl.txt . For the initials of
contributors, see ~abinit/doc/developers/contributors.txt .
Goto : ABINIT home Page | Suggested acknowledgments | List of input variables | Tutorial home page | Bibliography
Help files : New user's guide | Abinis (main) | Abinis (respfn) | Mrgddb | Anaddb | AIM (Bader) | Cut3D | Optic | Mrgscr
Files that describe other input variables:
- Basic variables, VARBAS
- Developper variables, VARDEV
- File handling variables, VARFIL
- Geometry builder + symmetry related variables, VARGEO
- Ground-state calculation variables, VARGS
- GW variables, VARGW
- Internal variables, VARINT
- Parallelisation variables, VARPAR
- Projector-Augmented Wave variables, VARPAW
- Response Function variables, VARRF
- Wannier90 interface variables, VARW90
Content of the file : alphabetical list of variables.
A. amu
B. bmass
C.
D. delayperm dilatmx dtion
E. ecutsm
F. friction
G. getcell getxcart getxred
H.
I. iatcon iatfix iatfixx iatfixy iatfixz ionmov
J.
K.
L.
M. mdftemp mditemp mdwall
N. natfix natfixx natfixy natfixz natcon nconeq nnos ntime
O. optcell
P.
Q.
qmass R. restartxf
S. signperm strfact strprecon strtarget
T. tolmxf
U.
V. vel vis vmass
W. wtatcon
X.
Y.
Z.
amu
Mnemonics: Atomic Mass Units
Characteristic:
Variable type: real array amu(ntypat)
Default is provided by a database of atomic masses.
Gives the masses in atomic mass units for each kind of atom in cell. These masses are used in performing molecular dynamical atomic motion if ionmov=1, 6, 7 or 8. Note that one may set all masses to 1 for certain cases in which merely structural relaxation is desired and not actual molecular dynamics.
Using 1986 recommended values, 1 atomic mass unit = 1.6605402e-27 kg. In this unit the mass of Carbon 12 is exactly 12.
A database of atomic masses is provided, giving
default values.
Note that the default database uses mixed isotope masses (for Carbon
the natural occurence of Carbon 13 is taken into account).
The values are those recommended by the commission on Atomic Weights
and
Isotopic Abundances, Inorganic Chemistry Division, IUPAC, in
Pure Appl. Chem. 60, 841 (1988).
For Tc, Pm, Po to Ac, Pa and beyond U,
none of the isotopes has a half-life greater than 3.0d10 years, and
the values provided in the database do not come from that source.
For alchemical pseudoatoms, the masses of the constituents
atoms are mixed, according to the alchemical miwing
coefficients mixalch
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| Complete list of input variables
delayperm
Mnemonics: DELAY between trials to PERMUTE atoms
Characteristic:
Variable type: integer
Default is 0.
Delay (number of time steps) between trials to permute two atoms, in view of accelerated search of minima. Still in development. See the routine moldyn.f. See also signperm. When delayperm is zero, there is not permutation trials.
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dilatmx
Mnemonics: DILATation : MaXimal value
Characteristic:
Variable type: real parameter
Default is 1.0 .
Gives the maximal permitted scaling of the lattice parameters when the cell shape and dimension is varied (see variable optcell). It is used to define the sphere of plane waves and FFT box coherent with the possible modifications of the cell (ionmov==2 and optcell/=0). For these definitions, it is equivalent to changing ecut by multiplying it by dilatmx2 (the result is an "effective ecut", called internally "ecut_eff", other uses of ecut being not modified when dilatmx>1.0 .
Using dilatmx<1.0 is equivalent to changing ecut in all its uses. This is allowed, although its meaning is no longer related to a maximal expected scaling.
Setting dilatmx to a large value leads to waste of CPU time and memory. Supposing you think that the optimized acell values might be 10% larger than your input values, use simply dilatmx 1.1 . This will already lead to an increase of the number of planewaves by a factor (1.1)3=1.331 , and a corresponding increase in CPU time and memory.
It is possible to use dilatmx when optcell=0, but a value larger than 1.0 will be a waste.
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dtion
Mnemonics: Delta Time for IONs
Characteristic:
Variable type: real parameter
Default is 100.
Used for controlling ion time steps. If ionmov is set to 1, 6 or 7, then molecular dynamics is used to update atomic positions in response to forces. The parameter dtion is a time step in atomic units of time. (One atomic time unit is 2.418884e-17 seconds, which is the value of Planck's constant in hartree*sec.) In this case the atomic masses, in amu (given in array "amu"), are used in Newton's equation and the viscosity (for ionmov=1) and number of time steps are provided to the code using input variables "vis" and "ntime". The code actually converts from masses in amu to masses in atomic units (in units of electron masses) but the user enters masses in amu. (The conversion from amu to atomic units (electron masses) is 1822.88851 electron masses/amu.)
A typical good value for dtion is about 100. The user must try several values for dtion in order to establish the stable and efficient choice for the accompanying amu, atom types and positions, and vis (viscosity).
For quenched dynamics (ionmov=7), a larger time step might be taken, for example 200.
No meaning for RF calculations.
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ecutsm
Mnemonics: Energy CUToff SMearing
Characteristic: ENERGY
Variable type: real parameter (in Hartree)
Default is 0.d0
This input variable is important when performing relaxation of unit cell size and shape (non-zero optcell). Using a non-zero ecutsm, the total energy curves as a function of ecut, or acell, can be smoothed, keeping consistency with the stress (and automatically including the Pulay stress). The recommended value is 0.5 Ha. Actually, when optcell/=0, ABINIT requires ecutsm to be larger than zero. If you want to optimize cell shape and size without smoothing the total energy curve (a dangerous thing to do), use a very small ecutsm, on the order of one microHartree.
Technical information :
See Bernasconi et al, J. Phys. Chem. Solids 56, 501 (1995)
for a related method.
ecutsm allows to define an effective kinetic energy for plane
waves, close to, but
lower than the
maximal kinetic energy ecut. For
kinetic
energies less than ecut-ecutsm,
nothing is modified,
while between ecut-ecutsm and ecut,
the kinetic energy is multiplied by:
1.0 / ( x2 (3+x-6x2+3x3))
where x = (ecut - kinetic_energy)/ecutsm
Note that x2 ( 3+x-6x2+3x3) is 0 at
x=0, with vanishing derivative,
and that at x=1 , it is 1, with also vanishing derivative.
If ecutsm is zero, the unmodified kinetic energy is used.
ecutsm can be specified in Ha (the default), Ry, eV or Kelvin,
since
ecutsm has the
'ENERGY'
characteristics.
(1 Ha=27.2113845 eV).
A few test for Silicon (diamond structure, 2 k-points) have
shown 0.5 Ha to be largely enough for ecut
between 2Ha and 6Ha,
to get smooth curves. It is likely that this value is OK
as soon as ecut is larger than 4Ha.
Note that prior to v4.4 (in v4.3 and older versions), the smoothing
function was
1.0 / ( x2 ( 3-2*x) )
However, the second derivative was not continuous at the cut-off
energy. This
leads to problems for elastic constant calculations using response
functions.
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friction
Mnemonics: internal FRICTION coefficient
Characteristic:
Variable type: real parameter
Default is 0.001
Gives the internal friction coefficient (atomic units) for Langevin dynamics (when ionmov=9): fixed temperature simulations with random forces.
The equation of motion is :
MI d2RI/dt2= FI
- friction MI dRI/dt - F_randomI
where F_randomI is a Gaussian random force with average
zero,
and variance 2 friction MI kT.
The atomic unit of friction is
hartrees*electronic mass*(atomic time units)/Bohr2. See J.
Chelikowsky, J. Phys. D : Appl Phys. 33(2000)R33.
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getcell
Mnemonics: GET CELL parameters from ...
Characteristic:
Variable type: integer parameter, an instance of a 'get' variable.
Default is 0.
This variable is typically used to chain the calculations, in the multi-dataset mode (ndtset>0), since it describes from which dataset acell and rprim are to be taken, as input of the present dataset. The cell parameters are EVOLVING variables, for which such a chain of calculations is useful.
If ==0, no use of previously computed values must occur.
If it is positive, its value gives the index of the dataset from which the data are to be used as input data. It must be the index of a dataset already computed in the SAME run.
If equal to -1, the output data of the previous dataset must be taken, which is a frequently occuring case. However, if the first dataset is treated, -1 is equivalent to 0, since no dataset has yet been computed in the same run.
If another negative number, it indicates the number of datasets to go backward to find the needed data (once again, going back beyond the first dataset is equivalent to using a null get variable).
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getxcart
Mnemonics: GET XCART from ...
getxred
Mnemonics: GET XRED from ...
getvel
Mnemonics: GET VEL from ...
Characteristic:
Variable type: integer parameters, instances of
'get' variables
Default is 0.
These variables are typically used to chain the
calculations,
in the multi-dataset mode (ndtset>0)
since they describe from which dataset the corresponding
output variables are to be taken, as input of the present
dataset. The atomic positions and velocities are EVOLVING variables,
for which such a chain of calculation is useful.
Note that the use of getxcart and getxred differs when
acell and rprim
are different from one dataset
to the other.
If ==0, no use of previously computed values must occur.
If it is positive, its value gives the index of the dataset
from which the data are to be used as input data.
It must be the index of a dataset already computed in the
SAME run.
If equal to -1, the output data of the previous dataset
must be taken, which is a frequently occuring case.
However, if the first dataset is treated, -1 is equivalent
to 0, since no dataset has yet been computed in the same run.
If another negative number, it indicates the number
of datasets to go backward to find the needed data
(once again, going back beyond the first dataset is equivalent
to using a null get variable).
Note : getxred and getxcart cannot be simultaneously
non-zero for the same dataset. On the other hand the use of
getvel with getxred is allowed, despite the different
coordinate system.
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iatcon
Mnemonics: Indices of AToms in CONstraint equations
Characteristic: NO MULTI, NOT INTERNAL
Variable type: integer array iatcon(natcon,nconeq)
Default is 0
Gives the indices of the atoms appearing in each of the nconeq independent equations constraining the motion of atoms during structural optimization or molecular dynamics (see nconeq, natcon, and wtatcon).
(Note : combined with wtatcon to give internal representation of the latter - this should be described)
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iatfix
Mnemonics: Indices of AToms that are FIXed
iatfixx
Mnemonics: Indices of AToms that are FIXed along
the X direction
iatfixy
Mnemonics: Indices of AToms that are FIXed along
the Y direction
iatfixz
Mnemonics: Indices of AToms that are FIXed along
the Z direction
Characteristic: iatfixx,iatfixy and iatfixz
are NOT INTERNAL
Variable type: integer arrays of length natfix,
natfixx, natfixy or
natfixz
Default is No Default (ignored unless natfix,
natfixx, natfixy or
natfixz > 0).
Give the index (in the range 1 to natom)
of each atom which is to
be held fixed for structural optimization or molecular dynamics.
The variable iatfix lists those fixed in the three directions,
while the other variables allow to fix some atoms along
x, y or z directions, or a combination of these.
WARNING : The implementation is inconsistent !! For ionmov==1, the fixing of directions was done in cartesian coordinates, while for the other values of ionmov, it was done in reduced coordinates. Sorry for this.
There is no harm in fixing one atom in the three
directions
using iatfix, then fixing it again in other directions
by mentioning it in iatfixx, iatfixy or iatfixz.
The internal representation of these input data is done
by the mean of one variable iatfix(3,natom),
defined
for each direction and each atom, being 0 if the atom is
not fixed along the direction, and 1 if the atom is fixed
along the direction.
When some atoms are fixed along 1 or 2 directions, the
use of symmetries is restricted to symmetry operations
whose (3x3) matrices symrel are
diagonal.
If the geometry builder is used, iatfix will be related
to the preprocessed set of atoms, generated by the
geometry builder. The user must thus foresee the effect
of this geometry builder (see objarf).
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ionmov
Mnemonics: IONic MOVEs
Characteristic:
Variable type: integer parameter
Default is 0.
Control the displacements of ions, and eventually (see optcell) changes of cell shape and size.
- 0=> do not move ions;
- 1=> move atoms using molecular dynamics with optional viscous damping (friction linearly proportional to velocity). The viscous damping is controlled by the parameter "vis". If actual undamped molecular dynamics is desired, set vis to 0. The implemented algorithm is the generalisation of the Numerov technique (6th order), but is NOT invariant upon time-reversal, so that the energy is not conserved. The value ionmov=6 will usually be preferred, although the algorithm that is implemented is lower-order. The time step is governed by dtion. opcell/=0 is not available
- 2=> conduct structural optimization using the Broyden-Fletcher-Goldfarb-Shanno minimization (BFGS). This is much more efficient for structural optimization than viscous damping, when there are less than let's say 10 degrees of freedom to optimize.
- 3=> conduct structural optimization using the
Broyden-Fletcher-Goldfarb-Shanno minimization (BFGS),
modified to take into account the total energy as well as
the gradients (as in usual BFGS).
See the paper by Schlegel, J. Comp. Chem. 3, 214 (1982). Might be better than ionmov=2 for few degrees of freedom (less than 3 or 4) - 4=> conjugate gradient algorithm for simultaneous optimization of potential and ionic degrees of freedom. It can be used with iscf=2 and iscf=5 or 6 (WARNING : this is under development, and does not work very well in many cases). optcell/=0 is not available.
- 5=> Simple relaxation of ionic positions according to (converged) forces. Equivalent to ionmov=1 with zero masses, albeit the relaxation coefficient is not vis, but iprcfc. optcell/=0 is not available.
- 6=> Molecular dynamics using the Verlet algorithm, see Allen & Tildesley "Computer simulation of liquids" 1987, p 81. Although partly coded, optcell/=0 is not available. The only related parameter is the time step (dtion).
- 7=> Quenched Molecular dynamics using the Verlet algorithm, and stopping each atom for which the scalar product of velocity and force is negative. Although partly coded, optcell/=0 is not available. The only related parameter is the time step (dtion). The goal is not to produce a realistic dynamics, but to go as fast as possible to the minimum. For this purpose, it is advised to set all the masses to the same value (for example, use the Carbon mass, i.e. set amu to 12 for all type of atoms).
- 8=> Molecular dynamics with Nose-Hoover thermostat, using the Verlet algorithm. Although partly coded, optcell/=0 is not available. Related parameters : the time step (dtion), the initial temperature (mditemp), the final temperature (mdftemp), and the thermostat mass (noseinert).
- 9=> Langevin molecular dynamics. Although partly coded, optcell/=0 is not available. Related parameters : the time step (dtion), the initial temperature (mditemp), the final temperature (mdftemp), and the friction coefficient (friction).
- 12=> Isokinetic ensemble molecular dynamics.
The equation of motion of the ions in contact with a thermostat
are solved with the algorithm proposed by Zhang [J. Chem. Phys. 106,
6102 (1997)],
as worked out by Minary et al [J. Chem. Phys. 188, 2510 (2003)].
The conservation of the kinetic energy is obtained within machine
precision,
at each step.
Although partly coded, optcell/=0 is not available. Related parameters : the time step (dtion), the initial temperature (mditemp), the final temperature (mdftemp), and the friction coefficient (friction). - 13=> Iosthermal/isenthalpic ensemble.
The equation of motion of the ions in contact with a thermostat
and a barostat are solved with the algorithm proposed by Martyna,
Tuckermann Tobias and Klein [Mol. Phys., 1996, p. 1117].
optcell/=0 is available. Related parameters : the time step (dtion), the initial temperature (mditemp), the final temperature (mdftemp), the number of thermostats (nnos), and the masses of thermostats (qmass). If optcell=1 or 2, the mass of the barostat (bmass or vmass) must be given in addition.
No meaning for RF calculations.
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mdftemp
Mnemonics: Molecular Dynamics Final Temperature
Characteristic:
Variable type: real mdftemp
Default is mdftemp=mditemp
Give the final temperature (for itime=ntime) of the Nose-Hoover thermostat (ionmov=8) and Langevin dynamics (ionmov=9), in Kelvin. This temperature will change linearly from mditemp at itime=1 to the final temperature mdftemp at the end of the ntime timesteps.
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mditemp
Mnemonics: Molecular Dynamics Initial Temperature
Characteristic:
Variable type: real mditemp
Default is 300
Give the initial temperature (for itime=1) of the Nose-Hoover thermostat (ionmov=8) and Langevin dynamics (ionmov=9), in Kelvin. This temperature will change linearly to reach the temperature mdftemp at the end of the ntime timesteps.
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mdwall
Mnemonics: Molecular Dynamics WALL location
Characteristic:
Variable type: real parameter
Default is 10000.0 Bohr (the walls are extremely far away).
Gives the location (atomic units) of walls on which the atoms will bounce back. when ionmov=6, 7, 8 or 9. For each cartesian direction idir=1, 2 or 3, there is a pair of walls with coordinates xcart(idir)=-wall and xcart(idir)=rprimd(idir,idir)+wall . Supposing the particle will cross the wall, its velocity normal to the wall is reversed, so that it bounces back.
By default, given in Bohr atomic units (1 Bohr=0.5291772108 Angstroms), although Angstrom can be specified, if preferred, since mdwall has the 'LENGTH' characteristics.
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natcon
Mnemonics: Number of AToms in CONstraint equations
Characteristic: NO MULTI
Variable type: integer array of length nconeq
Default is 0
Gives the number of atoms appearing in each of the nconeq independent equations constraining the motion of atoms during structural optimization or molecular dynamics (see nconeq, iatcon, and wtatcon).
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natfix
Mnemonics: Number of Atoms that are FIXed
natfixx
Mnemonics: Number of Atoms that are FIXed along
the X direction
natfixy
Mnemonics: Number of Atoms that are FIXed along
the Y direction
natfixz
Mnemonics: Number of Atoms that are FIXed along
the Z direction
Characteristic: NOT INTERNAL
Variable type: integer parameter
Default is 0 (no atoms held fixed).
Gives the number of atoms (not to exceed
natom) which are to be held fixed
during a structural
optimization or molecular dynamics.
When natfix > 0,
natfix entries should be provided in array iatfix.
When natfixx > 0, natfixx entries should be provided
in array iatfixx, and so on ...
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nconeq
Mnemonics: Number of CONstraint EQuations
Characteristic: NO MULTI
Variable type: integer parameter
Default is 0
Gives the number of independent equations constraining the motion of atoms during structural optimization or molecular dynamics (see natcon, iatcon, and wtatcon).
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noseinert
Mnemonics: NOSE INERTia factor
Characteristic:
Variable type: real noseinert
Default is 1.0d5
Give the inertia factor WT of the Nose-Hoover thermostat (when ionmov=8), in atomic units of weight*length2, that is (electron mass)*(Bohr)2. The equations of motion are :
MI d2RI/dt2= FI - dX/dt MI dRI/dt
and
WT d2X/dt2= Sum(I) MI (dRI/dt)2 - 3NkBT
where I represent each nucleus, MI is the mass of each nucleus (see amu), RI is the coordinate of each nucleus (see xcart), dX/dt is a dynamical friction coefficient, and T is the temperature of the thermostat (see mditemp and mdftemp).
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nnos
Mnemonics: Number of nose masses
Characteristic:
Variable type: integer nnos
Default is 0
Give the number of oscillators in the Martyna et al. chain of oscillators thermostats (when ionmov=13). The mass of these oscillators is given by qmass (similar to noseinert)
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ntime
Mnemonics: Number of TIME steps
Characteristic:
Variable type: integer parameter
Default is 0.
Gives the number of molecular dynamics time steps or Broyden structural optimization steps to be done if ionmov=1 or 2 respectively.
Note that at the present the option ionmov=1 is initialized with four Runge-Kutta steps which costs some overhead in the startup. By contrast, the initialisation of other ionmov values is only one SCF call.
ntime is ignored if ionmov=0.
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ntypat
Mnemonics: Number of TYPEs of atoms
Characteristic: NO MULTI
Variable type: integer parameter
Default is 1.
Gives the number of types of atoms. E.g. for a homopolar system (e.g. pure Si) ntypat is 1.
The code tries to read the same number pseudopotential files.
The first pseudopotential is assigned type number 1, and so on ...
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optcell
Mnemonics: OPTimize the CELL shape and dimensions
Characteristic:
Variable type: integer parameter
The Default is optcell=0
Allows to optimize the unit cell shape and dimensions, when ionmov=2 or 3. The configuration for which the stress almost vanishes is iteratively determined, by using the same algorithms as for the nuclei positions. Will eventually modify acell and/or rprim. The ionic positions are ALWAYS updated, according to the forces. A target stress tensor might be defined, see strtarget
- optcell=0 : modify nuclear positions, since ionmov=2, but no cell shape and dimension optimisation.
- optcell=1 : optimisation of volume only (do not modify rprim, and allow an homogeneous dilatation of the three components of acell)
- optcell=2 : full optimization of cell geometry (modify acell and rprim - normalize the vectors of rprim to generate the acell). This is the usual mode for cell shape and volume optimization. It takes into account the symmetry of the system, so that only the effectively relevant degrees of freedom are optimized.
- optcell=3 : constant-volume optimization of cell geometry (modify acell and rprim under constraint - normalize the vectors of rprim to generate the acell)
- optcell=4,5 or 6 : optimize acell(1), acell(2) or acell(3), respectively (only works if the two other vectors are orthogonal to the optimized one, the latter being along its cartesian axis).
- optcell=7,8 or 9 : optimize the cell geometry while keeping the first, second or third vector unchanged (only works if the two other vectors are orthogonal to the one left unchanged, the latter being along its cartesian axis).
- one has to get rid of the discontinuites due to discrete changes of plane wave number with cell size, by using a suitable value of ecutsm;
- one has to allow for the possibility of a larger sphere of plane waves, by using dilatmx;
- one might have to adjust the scale of stresses to the scale of forces, by using strfact.
- if all the reduced coordinates of atoms are fixed by symmetry, one cannot use toldff to stop the SCF cycle. (Suggestion : use toldfe with a small value, like 1.0d-10)
Presently (v3.1), one cannot restart (restartxf)
a calculation with a non-zero optcell value from the
(x,f) history of another run with a different non-zero optcell
value. There
are still a few problems at that level.
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restartxf
Mnemonics: RESTART from (X,F) history
Characteristic:
Variable type: integer parameter
Default is 0.
Control the restart of broyden minimisation.
Works only for ionmov=2 (Broyden) and when an input wavefunction file is specified, thanks to the appropriate values of irdwfk or getwfk.
If positive, the code reads from the input wf file, the previous history of atomic coordinates and corresponding forces, in order to continue the work done by the job that produced this wf file. If optcell/=0, the history of acell and rprim variables is also taken into account. The code will take into consideration the whole history (if restartxf==1), or discard the few first (x,f) pairs, and begin only at the pair whose number corresponds to restartxf.
If zero, the Broyden minimization is done from scratch.
NOTE : the input wf file must have been produced by a run that exited cleanly. It cannot be one of the temporary wf files that exist when a job crashed.
Presently (v3.1), one cannot restart a calculation
with a non-zero optcell value from
the
(x,f) history of another run with a different non-zero optcell value. There
are still a few problems at that level. Starting a non-zero optcell
run from a zero optcell run should
work.
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rfasr
Mnemonics: Response Function : Acoustic Sum Rule
Characteristic: RESPFN
Variable type: integer parameter
Default is 0.
Control the evaluation of the acoustic sum rule in effective charge calculations within a response function calculation.
- 0 => no acoustic sum rule imposed
- 1 => acoustic sum rule imposed with extra charge evenly distributed among atoms
- 2 => acoustic sum rule imposed with extra charge given proportionally to those atoms with the largest effective charge.
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signperm
Mnemonics: SIGN of PERMutation potential
Characteristic:
Variable type: integer
Default is 1.
In development. See the routine moldyn.f. See also delayperm.
+1 favors alternation of species
-1 favors segregation
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strfact
Mnemonics: STRess FACTor
Characteristic:
Variable type: real parameter
Default is 100.0 (Bohr^2)
The stresses multiplied by strfact will be treated like forces in the process of optimization (ionmov=2, non-zero optcell).
For example, the stopping criterion defined by tolmxf relates to these scaled stresses.
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strprecon
Mnemonics: STRess PRECONditioner
Characteristic:
Variable type: real parameter
Default is 1.0
This is a scaling factor to initialize the part of the Hessian related to the treatment of the stresses (optimisation of the unit cell). In case there is an instability, decrease the default value, e.g. set it to 0.1 .
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strtarget
Mnemonics: STRess TARGET
Characteristic:
Variable type: real array strtarget(6)
Default is 6*0.0 (Ha/Bohr**3)
The optimization of cell size and shape, as might be asked through optcell, will target the stress tensor defined by by strtarget, or part thereof (if restricted optimizations are asked, like fixed shape). Presently, this required target stress is not taken into account for the determination of the symmetries. If it breaks the symmetries of the input unit cell, so that symrel disagrees with strtarget, the result will be unreliable. Also, presently, the thermodynamical potential to be used in this situation (the free energy) does not replace the total energy, so that, for exemple, ionmov=3 cannot be used, since this algorithm is taking into account the total energy.
The components of the stress tensor must be stored
according to :
(1,1)->1 ; (2,2)->2 ; (3,3)->3 ; (2,3)->4 ; (3,1)->5 ;
(1,2)->6.
The conversion factor
between Ha/Bohr**3 and GPa is : 1 Ha/Bohr**3 = 29421.033d0 GPa.
Not used if optcell==0.
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qmass
Mnemonics: Q thermostat mass
Characteristic:
Variable type: real array qmass(nnos)
Default is nnos*10.0
This are the masses of the chains of nnos thermostats to be used when ionmov=13.
This temperature control can be used with optcell==0, 1 (homogeneous cell
deformation) or 2 (full cell deformation)
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bmass,vmass
Mnemonics: Barostat mass
Characteristic:
Variable type: real parameter
Default is 10.
vmass is the mass of the barostat when ionmov=13 (constant pressure), and optcell=1 full cell fluctuations.
bmass is the mass of the barostat when ionmov=13 (constant pressure), and optcell=2 full cell fluctuations.
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tolmxf
Mnemonics: TOLerance on the MaXimal Force
Characteristic:
Variable type: real parameter
Default is 5.0d-5 hartree/Bohr.
Sets a maximal absolute force tolerance (in hartree/Bohr) below which BFGS structural relaxation iterations will stop.
Can also control tolerance on stresses, when optcell/=0, using the conversion factor strfact. This tolerance applies to any particular cartesian component of any atom, excluding fixed ones. See the parameter ionmov.
This is to be used when trying to equilibrate a structure to its lowest energy configuration (ionmov=2).
A value of about 5.0d-5 hartree/Bohr or smaller is suggested (this corresponds to about 2.5d-3 eV/Angstrom).
No meaning for RF calculations.
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vel
Mnemonics: VELocity
Characteristic: EVOLVING
Variable type: real array vel(3,natom)
Default is 3*natom 0's.
Gives the starting velocities of atoms, in cartesian coordinates, in Bohr/atomic time units (atomic time units given where dtion is described).
Irrelevant unless ionmov > 0.
For ionmov=8 (Nose thermostat), if vel is not initialized, a random initial velocity giving the right kinetic energy will be generated.
If the geometry builder is used, vel will be related to the preprocessed set of atoms, generated by the geometry builder. The user must thus foresee the effect of this geometry builder (see objarf).
Velocities evolve is ionmov==1.
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vis
Mnemonics: VIScosity
Characteristic:
Variable type: real parameter
Default is 100.
Gives the viscosity (atomic units) for linear frictional damping term applied to molecular dynamics when ionmov=1. Used for eventual relaxation of structure (however, ionmov=2 is in general more efficient).
The equation of motion is :
MI d2RI/dt2= FI
- vis dRI/dt
The atomic unit of viscosity is hartrees*(atomic time units)/Bohr2.
Units are not
critical as this is a fictitious damping used to relax
structures. A typical value for silicon is 400 with
dtion of 350 and atomic mass 28 amu. Critical
damping is most desirable and is found only by
optimizing vis for a given situation.
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| Complete list of input variables
wtatcon
Mnemonics: WeighTs for AToms in CONstraint equations
Characteristic: NO MULTI
Variable type: real array wtatcon(3,natcon,nconeq)
Default is 0.
Gives the weights determining how the motion of atoms is constrained during structural optimization or molecular dynamics (see nconeq, natcon, and iatcon). For each of the nconeq independent constraint equations, wtatcon is a 3*natcon array giving weights, WI, for the x, y, and z components of each of the atoms (labeled by I) in the list of indices iatcon. Prior to taking an atomic step, the calculated forces, FI, are replaced by projected forces, F'I, which satisfy the set of constraint equations
Summu=x,y,z; I=1,natcon: Wmu,I * F'mu,I = 0 for each of the nconeq arrays WI.
Different types of motion constraints can be implemented this way. For example,
nconeq 1 natcon 2 iatcon 1 2 wtatcon 0 0 +1 0 0 -1
could be used to constrain the relative height difference of two adsorbate atoms on a surface (assuming their masses are equal), since F'z,1 - F'z,2 = 0 implies z1 - z2 = constant.
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