ABINIT, structural optimization input variables:
List and description.
This document lists and provides the description
of the name (keywords) of the "structural optimization" input
variables to be used in the main input file of the abinit code.
Copyright (C) 1998-2017 ABINIT group (DCA,XG,RC,YG,FJ)
Content of the file : alphabetical list of "structural optimization" variables.
A.
adpimd
adpimd_gamma
amu
B.
bmass
C.
chkdilatmx
cineb_start
D.
delayperm
diismemory
dilatmx
dtion
dynimage
E.
ecutsm
F.
friction
fxcartfactor
G.
ga_algor
ga_fitness
ga_n_rules
ga_opt_percent
ga_rules
getcell
getvel
getxcart
getxred
goprecon
goprecprm
H.
I.
iatcon
iatfix
iatfixx
iatfixy
iatfixz
imgmov
ionmov
istatimg
J.
K.
L.
M.
mdtemp
mdwall
mep_mxstep
mep_solver
N.
natcon
natfix
natfixx
natfixy
natfixz
nconeq
neb_algo
neb_spring
nimage
nnos
noseinert
ntime
ntimimage
O.
optcell
P.
pimass
pimd_constraint
pitransform
prtatlist
Q.
qmass
R.
random_atpos
restartxf
S.
signperm
strfact
string_algo
strprecon
strtarget
T.
tolimg
tolmxde
tolmxf
U.
V.
vel
vel_cell
vis
W.
wtatcon
adpimd
Mnemonics: ADiabatic Path-Integral Molecular Dynamics
Executable: abinit
Mentioned in topic: PIMD.
Rarely used: [1/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v7:[08]}.
Variable type: integer
Default is 0
Only relevant if imgmov==9 or imgmov==13
Controls whether adiabatic Path-Integral Molecular Dynamics is performed or not.
The corresponding adiabaticity parameter is given by adpimd_gamma.
If equal to 0, no adiabatic Path-Integral Molecular Dynamics (standard PIMD) is performed.
If equal to 1, adiabatic Path-Integral Molecular Dynamics is activated.
Only relevant with pitransform=1 (normal mode transformation). In that case,
- the mass associated with to the zero-frequency mode is the true mass amu,
- the mass associated to the other higher frequency modes of the polymer chains is equal to the normal mode mass divided by
adpimd_gamma (adiabaticity parameter),
- the equation of motion on the zero-frequency mode is not thermostated.
NOT YET USABLE
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adpimd_gamma
Mnemonics: ADiabatic Path-Integral Molecular Dynamics: GAMMA factor
Executable: abinit
Mentioned in topic: PIMD.
Rarely used: [1/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v7:[08]}.
Variable type: real
Default is 1
Only relevant if adpimd==1 and imgmov in [9,13]
Adiabaticity parameter to be used in adiabatic Path-Integral Molecular Dynamics.
NOT YET USABLE
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amu
Mnemonics: Atomic Mass Units
Executable: abinit
Characteristic: EVOLVING
Mentioned in topics: PIMD, Phonons, AtomTypes, Artificial.
Moderately used: [67/907] in abinit tests, [2/136] in tuto abinit tests. Tuto test list: {tutorespfn:[optic_1,optic_3]}.
Variable type: real(ntypat)
No default (Comment: 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.
They are also used in phonon calculations, in the diagonalization of the dynamical matrix.
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 occurrence 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 mixing
coefficients mixalch
In most cases, the use of amu
will be as a static (non-evolving) variable. However, the possibility to have
different values of amu for different images has been coded. A population of
cells with different atomic characteristics can thus be considered,
and can be made to evolve, e.g. with a genetic algorithm (not coded in v7.0.0 though).
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bmass
Mnemonics: Barostat MASS
Executable: abinit
Mentioned in topic: MolecularDynamics.
Rarely used: [1/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v5:[01]}.
Variable type: real
Default is 10
bmass is the mass of the barostat when
ionmov=13 (constant pressure molecular dynamics)
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chkdilatmx
Mnemonics: CHecK DILATMX
Executable: abinit
Mentioned in topic: GeoOpt.
Rarely used: [1/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v3:[42]}.
Variable type: integer
Default is 1
If 0, will not stop the execution if the dilatmx threshold is exceeded, but simply issue a warning. There will be no rescaling.
If 1, after tentative rescalings as described in dilatmx, will stop the execution.
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cineb_start
Mnemonics: Climbing-Image Nudged Elastic Band: STARTing iteration
Executable: abinit
Mentioned in topic: TransPath.
Rarely used: [1/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v6:[24]}.
Variable type: integer
Default is 7
Only relevant if imgmov== 5 and neb_algo==2
Gives the index of the first CI-NEB iteration..
The CI-NEB method constitutes a small modification to the NEB method allowing a rigorous
convergence to the saddle point. As the image with the highest energy has to be identified,
the calculation begins with several iterations of the standard NEB algorithm.
The effective CI-NEB begins at the cineb_start iteration.
See: J. Chem. Phys. 113, 9901 (2000).
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delayperm
Mnemonics: DELAY between trials to PERMUTE atoms
Executable: abinit
Mentioned in topic: MolecularDynamics.
Rarely used: [2/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v2:[87,88]}.
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.F90. See also signperm.
When delayperm is zero, there is not permutation trials.
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diismemory
Mnemonics: Direct Inversion in the Iterative Subspace MEMORY
Executable: abinit
Mentioned in topic: MolecularDynamics.
Rarely used: [0/907] in abinit tests, [0/136] in tuto abinit tests.
Variable type: integer
Default is 8
Gives the maximum number of "time" steps for which the
forces and stresses are stored, and taken into account in the
DIIS algorithm (ionmov=20)
to find zero-force and stress configurations.
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dilatmx
Mnemonics: lattice DILATation : MaXimal value
Executable: abinit
Mentioned in topic: GeoOpt.
Moderately used: [82/907] in abinit tests, [21/136] in tuto abinit tests. Too many tests to report (>10).
Variable type: real
Default is 1.0
Gives the maximal permitted scaling of
the lattice parameters when the cell shape and
dimension is varied (see variable optcell). Accordingly defines the plane wave basis set for this purpose. The dilatmx threshold might be exceeded if chkdilatmx=0, otherwise ABINIT exits after three tentative rescalings, as described below.
dilatmx 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 dilatmx
2
(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.
When the dilatmx threshold is exceeded, ABINIT will rescale uniformly the tentative new primitive vectors to a value that leads at most to 90% of the maximal allowed dilatmx deviation from 1. It will do this three times (to forbid the geometry optimization algorithms to have take a too large trial step), but afterwards will exit. Setting chkdilatmx==0 allows the definition of an appropriate planewave basis, but will not lead to an exit when the threshold is exceeded.
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dtion
Mnemonics: Delta Time for IONs
Executable: abinit
Mentioned in topics: PIMD, MolecularDynamics.
Moderately used: [26/907] in abinit tests, [7/136] in tuto abinit tests. Tuto test list: {tutoparal:[moldyn_01,moldyn_02,moldyn_03,moldyn_04,moldyn_05,moldyn_06,moldyn_07]}.
Variable type: real
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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dynimage
Mnemonics: DYNamics of the IMAGE
Executable: abinit
Mentioned in topics: PIMD, TransPath.
Rarely used: [8/907] in abinit tests, [2/136] in tuto abinit tests. Test list: {paral:[08],tutoparal:[string_03,string_04],v6:[22,24,25],v7:[08],v8:[05]}.
Variable type: integer(nimage)
Default is *1 (Comment: if imgmov in [2,5] (String Method, NEB), dynimage(1)=0 and dynimage(nimage)=0.)
This input variable is relevant when sets of images are activated (see
imgmov). Not all images might be required to evolve from one time step to the other.
Indeed, in the String Method or the Nudged Elastic Band, one might impose that the extremal configurations of the string are fixed.
In case the dynimage(iimage)=0, the image with index "iimage" will be consider as fixed.
Thus, there is no need to compute forces and stresses for this image at each time step. The purpose of defining extremal images is to make the input/output easier.
In order to save CPU time, the computation of properties of static images (dynimage(iimage)=0)
can be avoided: see istatimg keyword.
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ecutsm
Mnemonics: Energy CUToff SMearing
Executable: abinit
Characteristic: ENERGY
Mentioned in topic: Planewaves.
Moderately used: [127/907] in abinit tests, [30/136] in tuto abinit tests. Too many tests to report (>10).
Variable type: real
Default is 0.0
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 / ( x
2
(3+x-6x
2
+3x
3
))
where x = (ecut - kinetic_energy)/ecutsm
Note that x
2
( 3+x-6x
2
+3x
3
) 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.
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friction
Mnemonics: internal FRICTION coefficient
Executable: abinit
Mentioned in topic: MolecularDynamics.
Rarely used: [2/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v2:[87,88]}.
Variable type: real
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 :
M
I
d
2
R
I
/dt
2
= F
I
- friction M
I
dR
I
/dt - F_random
I
where F_random
I
is a Gaussian random force with average
zero,
and variance 2 friction M
I
kT.
The atomic unit of friction is
hartrees*electronic mass*(atomic time units)/Bohr
2
. See J.
Chelikowsky, J. Phys. D : Appl Phys. 33(2000)R33.
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fxcartfactor
Mnemonics: Forces to (X) CARTesian coordinates FACTOR
Executable: abinit
Mentioned in topics: TransPath, GeoOpt.
Rarely used: [6/907] in abinit tests, [2/136] in tuto abinit tests. Test list: {paral:[08],tutoparal:[string_03,string_04],v6:[21,24,25]}.
Variable type: real
Default is 1 (Bohr^2)/Hartree
The forces multiplied
by fxcartfactor will be treated like difference in cartesian coordinates in the
process of optimization. This is a simple preconditioner.
TO BE UPDATED See (ionmov=2,
non-zero
optcell).
For example, the stopping criterion defined by
tolmxf relates to these scaled
stresses.
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ga_algor
Mnemonics: Genetic Algorithm - ALGOrithm selection
Executable: abinit
Mentioned in topic: GeoOpt.
Rarely used: [0/907] in abinit tests, [0/136] in tuto abinit tests.
Variable type: integer
Default is 1
Choosing method to make the structure selection. Only the enthalpy is used now but we
plan to include, energy, electronic band gap and alchemical potentials. Right now only value of 1 (enthalpy)
works.
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ga_fitness
Mnemonics: Genetic Algorithm FITNESS function selection
Executable: abinit
Mentioned in topic: GeoOpt.
Rarely used: [1/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v6:[27]}.
Variable type: integer
Default is 1
Different methodologies to perform the roulette-wheel selection of parents. Even though, the
objective function is the crystalline enthalpy (H_i), the weight of the population elements to be chosen from
in a roulette-wheel selection can be given through different functions. We consider the following cases.
1. F = H_i / Sum H_i
2. F = exp(-(H_i-H_min)) / Sum exp(-(H_i-H_min))
3. F = (1/n_i) / Sum (1/n_i). Where n_i is the position in the ordered list of enthalpies
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ga_n_rules
Mnemonics: Genetic Algorithm Number of RULES
Executable: abinit
Mentioned in topic: GeoOpt.
Rarely used: [1/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v6:[27]}.
Variable type: integer
Default is 1
Different genetic rules have been implemented and the user has the change to choose between any of them.
Right now we have 4 rules. See
ga_rules
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ga_opt_percent
Mnemonics: Genetic Algorithm OPTimal PERCENT
Executable: abinit
Mentioned in topic: GeoOpt.
Rarely used: [1/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v6:[27]}.
Variable type: real
Default is 0.2
Percentage of the population that according to the fitness function passes
to the following iteration.
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ga_rules
Mnemonics: Genetic Algorithm RULES
Executable: abinit
Mentioned in topic: GeoOpt.
Rarely used: [1/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v6:[27]}.
Variable type: integer
Default is 1
Different genetic rules have been implemented and the user has the change to choose between any of them.
The chosen number of rules have been defined in
ga_n_rules
Implemented rules are
1) crossover. Two parents are randomly chosen and two springs are mixed from the two by (a) choosing randomly (through
Fitness function) two parents and then randomly rotating and shifting the coordinates withing that particular cell.
(b) Slice every one of the unit cell of the parents along a random direction and creating the spring offs from the
pieces of the two parents.
2) Vector flip mutation. From the coordinates from a given parent, a piece of it is inverted.
3) random strain. A random anisotropic deformation is given to the unit cell.
4) Coordinates mutation of 1/4 of the whole coordinates.
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getcell
Mnemonics: GET CELL parameters from ...
Executable: abinit
Mentioned in topic: multidtset.
Rarely used: [4/907] in abinit tests, [1/136] in tuto abinit tests. Test list: {gpu:[04],tutorespfn:[elast_6],v1:[78,80]}.
Variable type: integer
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 occurring 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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getvel
Mnemonics: GET VEL from ...
Executable: abinit
Mentioned in topic: multidtset.
Rarely used: [1/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v5:[04]}.
Variable type: integer
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 occurring 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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getxcart
Mnemonics: GET XCART from ...
Executable: abinit
Mentioned in topic: multidtset.
Rarely used: [9/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v1:[61,64,65,66,74,75],v3:[80],v5:[04],v6:[68]}.
Variable type: integer
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 occurring 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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getxred
Mnemonics: GET XRED from ...
Executable: abinit
Mentioned in topic: multidtset.
Rarely used: [9/907] in abinit tests, [1/136] in tuto abinit tests. Test list: {libxc:[68,69,70,71],tutorespfn:[elast_1],v1:[60,80],v2:[44],v6:[22]}.
Variable type: integer
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 occurring 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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goprecon
Mnemonics: Geometry Optimization PRECONditioner equations
Executable: abinit
Mentioned in topic: GeoOpt.
Rarely used: [1/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v5:[02]}.
Variable type: integer
Default is 0
Set the kind of preconditioner to be used for Geometry Optimization
(Note : Under development now (2011.05.20))
-
goprecon=0 : No preconditioner
-
goprecon=[1-9] : Linear preconditioner
-
goprecon=[11-19] : Non-linear preconditioner
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goprecprm
Mnemonics: Geometry Optimization PREconditioner PaRaMeters equations
Executable: abinit
Mentioned in topic: GeoOpt.
Rarely used: [1/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v5:[02]}.
Variable type: real(3)
Default is 0
Set the paramenters use by the preconditioner to be
used for Geometry Optimization
(Note : Under development now (2011.06.06))
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iatcon
Mnemonics: Indices of AToms in CONstraint equations
Executable: abinit
Characteristic: NO_MULTI, INPUT_ONLY
Mentioned in topic: GeoConstraints.
Rarely used: [3/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v3:[40],v6:[22],v8:[05]}.
Variable type: integer(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)
Go to the top
| Complete list of input variables
iatfix
Mnemonics: Indices of AToms that are FIXed
Executable: abinit
Mentioned in topic: GeoConstraints.
Moderately used: [22/907] in abinit tests, [5/136] in tuto abinit tests. Tuto test list: {tutoparal:[string_01,string_02,string_03,string_04],tutorespfn:[elast_1]}.
Variable type: integer(natfix)
No default
Only relevant if natfix > 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 variables iatfixx, iatfixy, and iatfixz, 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 atom manipulator is used, iatfix will be related
to the preprocessed set of atoms, generated by the
atom manipulator. The user must thus foresee the effect
of this atom manipulator (see objarf).
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| Complete list of input variables
iatfixx
Mnemonics: Indices of AToms that are FIXed along the X direction
Executable: abinit
Characteristic: INPUT_ONLY
Mentioned in topic: GeoConstraints.
Rarely used: [2/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v1:[85],v6:[25]}.
Variable type: integer(natfixx)
No default
Only relevant if natfixx > 0
Give the index (in the range 1 to
natom )
of each atom which is to
be held fixed ALONG THE X direction for structural optimization or molecular dynamics.
The variable iatfix lists those fixed in the three directions,
while the variables iatfixx, iatfixy, and iatfixz, allow to fix some atoms along
x, y or z directions, or a combination of these.
See the variable iatfix for more information.
Go to the top
| Complete list of input variables
iatfixy
Mnemonics: Indices of AToms that are FIXed along the Y direction
Executable: abinit
Characteristic: INPUT_ONLY
Mentioned in topic: GeoConstraints.
Rarely used: [2/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v1:[85,86]}.
Variable type: integer(natfixy)
No default
Only relevant if natfixy > 0
Give the index (in the range 1 to
natom )
of each atom which is to
be held fixed ALONG THE Y direction for structural optimization or molecular dynamics.
The variable iatfix lists those fixed in the three directions,
while the variables iatfixx, iatfixy, and iatfixz, allow to fix some atoms along
x, y or z directions, or a combination of these.
See the variable iatfix for more information.
Go to the top
| Complete list of input variables
iatfixz
Mnemonics: Indices of AToms that are FIXed along the Z direction
Executable: abinit
Characteristic: INPUT_ONLY
Mentioned in topic: GeoConstraints.
Rarely used: [2/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v1:[85,86]}.
Variable type: integer(natfixz)
No default
Only relevant if natfixz > 0
Give the index (in the range 1 to
natom )
of each atom which is to
be held fixed ALONG THE Z direction for structural optimization or molecular dynamics.
The variable iatfix lists those fixed in the three directions,
while the variables iatfixx, iatfixy, and iatfixz, allow to fix some atoms along
x, y or z directions, or a combination of these.
See the variable iatfix for more information.
Go to the top
| Complete list of input variables
imgmov
Mnemonics: IMaGe MOVEs
Executable: abinit
Mentioned in topics: PIMD, TransPath.
Moderately used: [10/907] in abinit tests, [2/136] in tuto abinit tests. Tuto test list: {tutoparal:[string_03,string_04]}.
Variable type: integer
Default is 0
Control the collective changes of images (see nimage,npimage, dynimage,
ntimimage, tolimg, istatimg, prtvolimg).
Similar to ionmov in spirit, although here, a population
of self-consistent calculations for different geometries is managed, while with ionmov,
only one geometry for self-consistent calculation is managed.
In this respect the maximal number of time step for image propagation is ntimimage,
corresponding to the input variable ntime of the single geometry case.
Also, the stopping criterion is governed by tolimg, corresponding to the
input variable toldfe of the single geometry case.
The stopping condition is crude: the image propagation is stopped when the mean value (over dynamic images)
of the absolute difference of total energy (previous and current time step) is less than tolimg.
Actually, there might be combinations of ionmov and imgmov
in which the two mechanisms are at work.
Usually, however, only one mechanism will be activated
(so, usually, either ntimimage is bigger than one OR ntime is bigger than one).
In order for the user to acquire a mental representation of the interplay between ionmov and imgmov,
here is a F90 pseudo-code presenting the interplay between the different above-mentioned input variables,
as well as with the parallelism (see input variable npimage).
do itimimage=1,ntimimage
do iimage=1,nimage
(possibly, parallelisation over images)
do itime=1,ntime
Compute the forces and stresses for image(iimage)
Examine whether the stopping criterion defined by tolmxf is fulfilled
Predict the next geometry for image(iimage) using ionmov
enddo
enddo
Examine whether the stopping criterion defined by tolimg is fulfilled
Predict the next geometries for all images using imgmov
enddo
- = 0 => simply copy images from previous timimage step.
- = 1 => move images according to Steepest Descent
following the (scaled) forces, the scaling factor being fxcartfactor.
- = 2 => String Method for finding Minimal Energy Path (MEP)
connecting to minima (see PRB 66, 052301 (2002));
the algorithm variant can be selected with the string_algo keyword
(Simplified String Method by default).
The solver for the Ordinary Differential Equation (ODE) can be selected with mep_solver
(steepest-descent by default). See also mep_mxstep keyword.
- = 3 => (tentatively, not yet coded) Metadynamics .
- = 4 => (tentatively, not yet coded) Genetic Algorithm.
- = 5 => Nudged Elastic Band (NEB) for finding Minimal Energy Path (MEP)
connecting two minima;
the algorithm variant can be selected with the neb_algo keyword
(NEB+improved tangent by default).
The solver for the Ordinary Differential Equation (ODE) can be selected with mep_solver
(steepest-descent by default).
The spring constant connecting images along the path is defined by neb_spring.
See also mep_mxstep keyword.
- = 9 or 13 => Path-Integral Molecular Dynamics
(see e.g. [D. Marx and M. Parrinello, J. Chem. Phys. 104, 4077 (1996)]).
Will use 9 for Langevin thermostat (associated friction coefficient given by vis)
and 13 for Nose-Hoover thermostat chains
(associated input variables are the number of thermostats in the chains, nnos,
and the masses of these thermostats qmass).
nimage is the Trotter number (no use of dynimage);
possible transformations of coordinates are defined by pitransform;
Fictitious masses of the atoms (possibly different from the true masses given by amu)
can be specified by pimass.
At present, it is only possible to perform calculations in the (N,V,T) ensemble (optcell=0).
No meaning for RF calculations.
Go to the top
| Complete list of input variables
ionmov
Mnemonics: IONic MOVEs
Executable: abinit
Mentioned in topics: MolecularDynamics, GeoOpt.
Moderately used: [138/907] in abinit tests, [28/136] in tuto abinit tests. Too many tests to report (>10).
Variable type: integer
Default is 0
Choice of algorithm to 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.
Purpose:
Molecular dynamics (if vis=0), Structural optimization (if vis>0)
Cell optimization:
No (Use optcell=0 only)
Related variables:
Viscous parameter vis, time step dtion, index of atoms fixed iatfix
-
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
about 10 degrees of freedom to optimize.
Purpose:
Structural optimization
Cell optimization:
Yes (if optcell/=0)
Related variables:
-
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). Can be very unstable - use with caution!
Purpose:
Structural optimization
Cell optimization:
Yes (if optcell/=0)
Related variables:
-
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).
Purpose:
Structural optimization
Cell optimization:
No (Use optcell=0 only)
Related variables:
-
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.
Purpose:
Structural optimization
Cell optimization:
No (Use optcell=0 only)
Related variables:
-
6=> Molecular dynamics using the Verlet algorithm, see [Allen & Tildesley "Computer simulation of liquids" 1987, p 81].
The only related parameter is the time step (dtion).
Purpose:
Molecular dynamics
Cell optimization:
No (Use optcell=0 only)
Related variables:
time step dtion, index of atoms fixed iatfix
-
7=> Quenched Molecular dynamics using the Verlet algorithm, and stopping each atom for which the scalar product
of velocity and force is negative. 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).
Purpose:
Structural optimization
Cell optimization:
No (Use optcell=0 only)
Related variables:
time step dtion, index of atoms fixed iatfix
-
8=> Molecular dynamics with Nose-Hoover thermostat, using the Verlet algorithm.
Purpose:
Molecular dynamics
Cell optimization:
No (Use optcell=0 only)
Related variables:
time step (dtion), Temperatures (mdtemp), and thermostat mass (noseinert).
-
9=> Langevin molecular dynamics.
Purpose:
Molecular dynamics
Cell optimization:
No (Use optcell=0 only)
Related variables:
time step (dtion), temperatures (mdtemp) and friction coefficient (friction).
-
10=> Delocalized internal coordinates. with BFGS simple
Purpose:
Structural optimization
Cell optimization:
No (Use optcell=0 only)
Related variables:
-
11=> Delocalized internal coordinates. with BFGS using total energy
Purpose:
Structural optimization
Cell optimization:
No (Use optcell=0 only)
Related variables:
-
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.
Related parameters : the time step (dtion), the temperatures (mdtemp), and the friction coefficient (friction).
Purpose:
Molecular dynamics
Cell optimization:
No (Use optcell=0 only)
Related variables:
-
13=> Isothermal/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].
If optcell=1 or 2, the mass of the barostat (bmass) must be given in addition.
Purpose:
Molecular dynamics
Cell optimization:
Yes (if optcell/=0)
Related variables:
The time step (dtion), the temperatures (mdtemp), the number of thermostats (nnos), and the masses of thermostats (qmass).
-
14=> Simple molecular dynamics with a symplectic algorithm proposed
by S.Blanes and P.C.Moans [called SRKNa14 in Practical symplectic partitioned
Runge--Kutta and Runge--Kutta--Nyström methods, Journal of Computational
and Applied Mathematics archive, volume 142, issue 2 (May 2002), pages 313 - 330]
of the kind first published by H. Yoshida [Construction of higher order symplectic
integrators, Physics Letters A, volume 150, number 5 to 7, pages 262 - 268].
This algorithm requires at least 14 evaluation of the forces (actually 15 are done
within Abinit) per time step. At this cost it usually gives much better
energy conservation than the verlet algorithm (ionmov 6) for a 30 times bigger
value of dtion. Notice that the potential energy of the initial atomic configuration is never evaluated using this algorithm.
Purpose:
Molecular dynamics
Cell optimization:
No (Use optcell=0 only)
Related variables:
-
20=> Direct inversion of the iterative subspace.
Given a starting point xred that is a vector of length 3*natom
(reduced nuclei coordinates), and unit cell parameters (rprimd)
this routine uses the DIIS (direct inversion of the iterative
subspace) to minimize the gradient (forces) on atoms. The preconditioning
used to compute errors from gradients is using an inverse hessian matrix obtained by a BFGS algorithm.
This method is known to converge to the nearest point where gradients
vanish. This is efficient to refine positions around a saddle point for instance.
Purpose:
Structural optimization
Cell optimization:
No (Use optcell=0 only)
Related variables:
DIIS memory diismemory
-
22=> Conduct structural optimization using the Limited-memory Broyden-Fletcher-Goldfarb-Shanno minimization (L-BFGS).
The working routines were based on the original implementation of J. Nocera available on netlib.org.
This algorithm can be much better than the native implementation of BFGS in ABINIT (ionmov=2)
when one approaches convergence, perhaps because of better treatment of numerical details.
Purpose:
Structural optimization
Cell optimization:
Yes (if optcell/=0)
Related variables:
-
23=> Use of Learn on The Fly method (LOTF) for Molecular Dynamics.
In the framework of isokinetic MD, the atomic forces and positions are computed
by using LOTF interpolation. A SCF computation is performed only any lotf_nitex
steps. The results of the SCF are used to compute the parameters of a
short range classical potential (for the moment only the glue potential for gold is implemented).
Then these parameters are continuously tuned to compute atomic trajectories.
LOTF has to be enabled at configure time. If LOTF is not enabled and ionmov=23,
abinit will set automatically ionmov=12.
The LOTF cycle is divided in the following steps:
a) Initialization (SFC at t=0) and computation of potential parameters.
b) Extrapolation of the atomic forces and positions for lotf_nitex time step.
To perform this extrapolation, the potential computed in a) is used (Verlet algorithm).
c) SFC at t=lotf_nitex. Computation of the potential parameters.
d) LOTF interpolation, linear interpolation of the potential parameters and computation of the atomic
forces and positions between t=0 and t=lotf_nitex.
Purpose:
Molecular Dynamics
Cell optimization:
No (Use optcell=0 only)
Related variables:
dtion, lotf_classic, lotf_nitex, lotf_nneigx, lotf_version.
-
24=> Simple constant energy molecular dynamics using the velocity Verlet symplectic algorithm (second order), see e.g. [E. Hairer et al. Acta Numerica. 12, 399 (2003)].
The only related parameter is the time step (dtion).
Purpose:
Molecular dynamics
Cell optimization:
No (Use optcell=0 only)
Related variables:
time step dtion
-
25=> Hybrid Monte Carlo sampling of the ionic positions at fixed temperature and unit cell geometry (NVT ensemle). The underlying molecular dynamics corresponds to ionmov=24.
The related parameters are the time step (dtion) and thermostat temperature (mdtemp).
Purpose:
Monte Carlo sampling
Cell optimization:
No (Use optcell=0 only)
Related variables:
time step dtion, thermostat temperature mdtemp,
-
30=> Using a supercell, calculate a self consistent phonon structure
as in PRL 100 095901 (2008). The initial phonon eigenvectors and
eigenvalues are read in, and then atoms are displaced according
to the normal modes populated at a given temperature until
convergence of the vibrational free energy (or so I hope)
Purpose:
Phonon structure
Cell optimization:
No (Use optcell=0 only)
Related variables:
No meaning for RF calculations.
Go to the top
| Complete list of input variables
istatimg
Mnemonics: Integer governing the computation of STATic IMaGes
Executable: abinit
Mentioned in topic: PIMD.
Rarely used: [2/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v6:[24,25]}.
Variable type: integer
Default is 1
This input variable is relevant when sets of images are activated (see
imgmov).
Not all images might be required to evolve from one time step to the other
(seedynimage): these are static images.
If istatimg=0, the total energy of static images is not computed (but static images are
used to make the dynamic images evolve). This can be useful to save CPU time.
If istatimg=1, the total energy of static images is computed.
Go to the top
| Complete list of input variables
mdtemp
Mnemonics: Molecular Dynamics TEMPeratures
Executable: abinit
Mentioned in topics: PIMD, MolecularDynamics.
Moderately used: [17/907] in abinit tests, [7/136] in tuto abinit tests. Tuto test list: {tutoparal:[moldyn_01,moldyn_02,moldyn_03,moldyn_04,moldyn_05,moldyn_06,moldyn_07]}.
Variable type: real(2)
Default is [300, 300]
Give the initial and final temperature
of the Nose-Hoover thermostat (ionmov=8)
and Langevin dynamics (ionmov=9), in
Kelvin.
This temperature will change linearly from the initial temperature
mdtemp(1)
at itime=1 to
the final temperature
mdtemp(2)
at the end of the
ntime timesteps.
Go to the top
| Complete list of input variables
mdwall
Mnemonics: Molecular Dynamics WALL location
Executable: abinit
Mentioned in topic: MolecularDynamics.
Rarely used: [1/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v2:[87]}.
Variable type: real
Default is 10000.0 (Comment: 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.
Go to the top
| Complete list of input variables
mep_mxstep
Mnemonics: Minimal Energy Path search: MaXimum allowed STEP size
Executable: abinit
Characteristic: LENGTH
Mentioned in topic: TransPath.
Rarely used: [1/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v6:[24]}.
Variable type: real
Default is 0.4 if imgmov==5,
100.0 otherwise.
Relevant only when imgmov=1 (Steepest-Descent), 2 (String Method) or 5 (Nudged Elastic Band).
The optimizer used to solve the Ordinary Differential Equation (ODE) can be constrained with a maximum allowed step size for each image. By default this feature is only activated for Nudged Elastic Band (NEB) and the value is inspired by
J. Chem. Phys. 128, 134106 (2008)
.
Note that the step size is defined for each image as
step = SQRT[SUM(R_i dot R_i)]
where the
R_i
are the positions of
the atoms in the cell.
Go to the top
| Complete list of input variables
mep_solver
Mnemonics: Minimal Energy Path ordinary differential equation SOLVER
Executable: abinit
Mentioned in topic: TransPath.
Rarely used: [1/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v6:[24]}.
Variable type: integer
No default
Relevant only when imgmov=2 (String Method) or 5 (Nudged Elastic Band).
Gives the algorithm used to solve the Ordinary Differential Equation (ODE) when searching for
a Minimal Energy Path (MEP).
Possible values can be:
-
0=>
Steepest-Descent algorithm
following the (scaled) forces,
the scaling factor being fxcartfactor
(forward Euler method).
Compatible with all MEP search methods.
-
1=>
Quick-min optimizer
following the (scaled) forces,
the scaling factor being fxcartfactor.
The "quick minimizer" improves upon the steepest-descent method by
accelerating the system in the direction of the forces. The velocity (of the image) is
projected long the force and cancelled if antiparallel to it.
Compatible only with Nudged Elastic Band (imgmov=5).
See, for instance: J. Chem. Phys. 128, 134106 (2008).
-
2=>
Local Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) algorithm
; each image along the
band is minimized with a different instance of the BFGS optimizer.
Compatible only with Nudged Elastic Band (imgmov=5).
See, for instance: J. Chem. Phys. 128, 134106 (2008).
IN DEVELOPPMENT - NOT RELIABLE
-
3=>
Global Broyden-Fletcher-Goldfarb-Shanno (GL-BFGS) algorithm
; all images along the
band are minimized with a single instance of the BFGS optimizer.
Compatible only with Nudged Elastic Band (imgmov=5).
See, for instance: J. Chem. Phys. 128, 134106 (2008).
IN DEVELOPPMENT - NOT RELIABLE
-
4=>
Fourth-order Runge-Kutta method
; the images along the band are moved
every four steps (1<=istep<=ntimimage)
following the Runge-Kutta algorithm,
the time step being fxcartfactor.
Compatible only with Simplified String Method (imgmov=2
and string_algo=1 or 2).
See: J. Chem. Phys. 126, 164103 (2007).
All of the optimizers can be constrained with a maximum allowed step size for each image; see mep_mxstep. This is by default the case of the Nudged Elastic Band (imgmov=5).
Go to the top
| Complete list of input variables
natcon
Mnemonics: Number of AToms in CONstraint equations
Executable: abinit
Characteristic: NO_MULTI, INPUT_ONLY
Mentioned in topic: GeoConstraints.
Rarely used: [3/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v3:[40],v6:[22],v8:[05]}.
Variable type: integer(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).
Go to the top
| Complete list of input variables
natfix
Mnemonics: Number of Atoms that are FIXed
Executable: abinit
Characteristic: INPUT_ONLY
Mentioned in topic: GeoConstraints.
Moderately used: [22/907] in abinit tests, [5/136] in tuto abinit tests. Tuto test list: {tutoparal:[string_01,string_02,string_03,string_04],tutorespfn:[elast_1]}.
Variable type: integer
Default is 0 (Comment: (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
.
Go to the top
| Complete list of input variables
natfixx
Mnemonics: Number of Atoms that are FIXed along the X direction
Executable: abinit
Characteristic: INPUT_ONLY
Mentioned in topic: GeoConstraints.
Rarely used: [2/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v1:[85],v6:[25]}.
Variable type: integer
Default is 0
Gives the number of atoms (not to exceed
natom) which are to be held fixed along the X direction
during a structural
optimization or molecular dynamics.
When natfixx > 0, natfixx entries should be provided
in array iatfixx.
Go to the top
| Complete list of input variables
natfixy
Mnemonics: Number of Atoms that are FIXed along the Y direction
Executable: abinit
Characteristic: INPUT_ONLY
Mentioned in topic: GeoConstraints.
Rarely used: [2/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v1:[85,86]}.
Variable type: integer
Default is 0
Gives the number of atoms (not to exceed
natom) which are to be held fixed along the Y direction
during a structural
optimization or molecular dynamics.
When natfixy > 0, natfixy entries should be provided in array iatfixy
Go to the top
| Complete list of input variables
natfixz
Mnemonics: Number of Atoms that are FIXed along the Z direction
Executable: abinit
Characteristic: INPUT_ONLY
Mentioned in topic: GeoConstraints.
Rarely used: [2/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v1:[85,86]}.
Variable type: integer
Default is 0
Gives the number of atoms (not to exceed
natom) which are to be held fixed along the Z direction
during a structural
optimization or molecular dynamics.
When natfixz > 0, natfixz entries should be provided in array iatfixz.
Go to the top
| Complete list of input variables
nconeq
Mnemonics: Number of CONstraint EQuations
Executable: abinit
Characteristic: NO_MULTI
Mentioned in topic: GeoConstraints.
Rarely used: [3/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v3:[40],v6:[22],v8:[05]}.
Variable type: integer
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).
Go to the top
| Complete list of input variables
neb_algo
Mnemonics: Nudged Elastic Band ALGOrithm
Executable: abinit
Mentioned in topic: TransPath.
Rarely used: [1/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v6:[24]}.
Variable type: integer
Default is 1
Only relevant if imgmov==5
Gives the variant of the NEB method used.
Possible values can be:
-
0=>
Original NEB method
.
See: Classical and Quantum Dynamics in Condensed Phase Simulations, edited by
Berne, Ciccotti, Coker (World Scientific, Singapore, 1998), pp. 385-404
-
1=>
NEB + improved tangent
.
The Improved Tangent Method builds on the NEB with an improved estimate of the
tangent direction and a resulting change of the component of the spring force acting
on the images.
See: J. Chem. Phys. 113, 9978 (2000).
-
2=>
Climbing-Image NEB (CI-NEB)
.
The CI-NEB method constitutes a small modification to the NEB method.
Information about the shape of the MEP is retained, but a rigorous
convergence to a saddle point is also obtained.
By default the spring constants are variable (see neb_spring).
As the image with the highest energy has to be identified,
the calculation begins with several iterations of the standard NEB
algorithm. The effective CI-NEB begins at the cineb_start iteration.
See: J. Chem. Phys. 113, 9901 (2000).
Note that, in all cases, it is possible to define the value of the spring constant connecting images with
neb_spring, keeping it constant or allowing it
to vary between 2 values (to have higher resolution close to the saddle point).
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| Complete list of input variables
neb_spring
Mnemonics: Nudged Elastic Band: SPRING constant
Executable: abinit
Mentioned in topic: TransPath.
Rarely used: [1/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v6:[24]}.
Variable type: real(2)
Default is [0.02, 0.15] if neb_algo==2,
[0.05, 0.05] otherwise.
Only relevant if imgmov==5
Gives the minimal and maximal values of the spring constant connecting images for the NEB method.
In the standard "Nudged Elastic Band" method, the spring constant is constant along the path,
but, in order to have higher resolution close to the saddle point, it can be better
to have stronger springs close to it.
See: J. Chem. Phys. 113, 9901 (2000).
Go to the top
| Complete list of input variables
nimage
Mnemonics: Number of IMAGEs
Executable: abinit
Mentioned in topics: PIMD, TransPath.
Moderately used: [11/907] in abinit tests, [2/136] in tuto abinit tests. Tuto test list: {tutoparal:[string_03,string_04]}.
Variable type: integer
Default is 1
Give the number of images (or replicas) of the system,
for which the forces and stresses might be computed independently,
in the context of the string method, the genetic algorithm, hyperdynamics or Path-Integral Molecular Dynamics
depending on the value of imgmov).
Related input variables : dynimage,
npimage, ntimimage
and prtvolimg.
Images might differ by the position of atoms in the unit cell, their
velocity, as well as by their cell geometry. The following input variables might be used to define
the images :
These input variables, non-modified, will be used to define the image with index 1.
For the image with the last index, the input file might specify the values
of such input variables, appended with "_lastimg", e.g. :
-
acell_lastimg
-
rprim_lastimg
-
xcart_lastimg
-
...
By default, these values will be interpolated linearly to define values for the other images, unless
there exist specific values for some images, for which the string "last" has to be replaced by the
index of the image, e.g. for the image number 4 :
-
acell_4img
-
rprim_4img
-
xcart_4img
-
...
It is notably possible to specify the starting point and the end point of the path (of images), while specifying intermediate points.
It usually happen that the images do not have the same symmetries and space group.
ABINIT has not been designed to use different set of symmetries for different images.
ABINIT will use the symmetry and space group of the image number 2, that
is expected to have a low number of symmetries.
This might lead to erroneous calculations, in case some image has even less
symmetry. By contrast, there is no problem if some other image has more symmetries
than those of the second image.
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| Complete list of input variables
nnos
Mnemonics: Number of NOSe masses
Executable: abinit
Mentioned in topics: PIMD, MolecularDynamics.
Rarely used: [2/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v5:[01],v7:[08]}.
Variable type: integer
Default is 0
Gives the number of thermostats in the Martyna et al. chain of oscillators thermostats.
The thermostat chains can be used either to perform Molecular Dynamics (MD) (ionmov=13) or to perform Path Integral Molecular Dynamics (PIMD) (imgmov=13).
The mass of these thermostats is given by qmass.
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| Complete list of input variables
noseinert
Mnemonics: NOSE thermostat INERTia factor
Executable: abinit
Mentioned in topic: MolecularDynamics.
Rarely used: [1/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v2:[87]}.
Variable type: real
Default is 100000
Only relevant if ionmov==8
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 mdtemp).
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| Complete list of input variables
ntime
Mnemonics: Number of TIME steps
Executable: abinit
Mentioned in topics: MolecularDynamics, GeoOpt.
Moderately used: [147/907] in abinit tests, [28/136] in tuto abinit tests. Too many tests to report (>10).
Variable type: integer
Default is 0
Gives the number of molecular dynamics time steps or
Broyden
structural optimization steps to be done if
ionmov
is non-zero.
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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| Complete list of input variables
ntimimage
Mnemonics: Number of TIME steps for IMAGE propagation
Executable: abinit
Mentioned in topics: PIMD, TransPath.
Moderately used: [10/907] in abinit tests, [2/136] in tuto abinit tests. Tuto test list: {tutoparal:[string_03,string_04]}.
Variable type: integer
Default is 1
Gives the maximal number of molecular dynamics time steps or
structural optimization steps to be done
for the set of images, referred to as 'image-timesteps'. At each image-timestep,
all the images are propagated simultaneously, each according to the algorithm
determined by imgmov and the usual accompanying
input variables, and then the next positions and velocities for each image
are determined from the set of results obtained for all images.
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| Complete list of input variables
optcell
Mnemonics: OPTimize the CELL shape and dimensions
Executable: abinit
Mentioned in topics: PIMD, GeoOpt.
Moderately used: [69/907] in abinit tests, [11/136] in tuto abinit tests. Too many tests to report (>10).
Variable type: integer
Default is 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 or 3, 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).
A few details require attention when performing unit cell optimisation :
- one has to get rid of the discontinuities 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)
It is STRONGLY suggested first to optimize the ionic positions without cell shape and size optimization (optcell=0), then start the cell shape and size optimization from the cell with relaxed ionic positions.
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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| Complete list of input variables
pimass
Mnemonics: Path Integral fictitious MASSes
Executable: abinit
Mentioned in topic: PIMD.
Rarely used: [2/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v6:[26],v7:[08]}.
Variable type: real(ntypat)
Default is ntypat
Only relevant if imgmov=9 or 13
Only relevant if imgmov=9 or 13 (Path-Integral Molecular Dynamics).
Gives the fictitious masses (
D. Marx and M. Parrinello, J. Chem. Phys. 104, 4077 (1996)
)
in atomic mass units for each kind of atom in cell. These masses are the inertial masses used
in performing Path Integral Molecular Dynamics (PIMD), they are different from the true masses (amu) used to define the quantum spring that relates the different beads in PIMD. They can be chosen arbitrarily, but an appropriate choice will lead the different variables to move on the same time scale in order to optimize the sampling efficiency of the PIMD trajectory.
If pitransform=1 (normal mode transformation), or pitransform=2 (staging transformation), pimass is automatically set to its optimal value.
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| Complete list of input variables
pimd_constraint
Mnemonics: Path-Integral Molecular Dynamics: CONSTRAINT to be applied on a reaction coordinate
Executable: abinit
Mentioned in topic: PIMD.
Rarely used: [1/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v8:[05]}.
Variable type: integer
Default is 0
Only relevant if imgmov=9 or 13
Only relevant for Path-Integral Molecular Dynamics.
Selects a constraint to be applied during the PIMD trajectory. The constraint is holonomic (it is a relation between the position variables).In practice, the total forces applied to the atomic positions are modified so as to respect the constraint.
To date, the available constraints are:
- 0: no constraint
- 1: "Blue Moon Ensemble" method.
The constraint is a linear combination of the positions of atomic centroids (this linear combination is kept constant during the simulation).
Sum[W_i * X_i]=constant
The X_i are the coordinates of the atomic centroids. The weights W_i have to be specified with the wtatcon(3,natcon,nconeq), iatcon(natcon) and natcon input parameters (where nconeq is fixed to 1).
More details on the implementation in: Y. Komeiji,Chem-Bio Informatics Journal 7, 12-23 (2007).
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| Complete list of input variables
pitransform
Mnemonics: Path Integral coordinate TRANSFORMation
Executable: abinit
Mentioned in topic: PIMD.
Rarely used: [3/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v6:[26],v7:[08],v8:[05]}.
Variable type: integer
Default is 0
Only relevant if imgmov=9 or 13 (Path-Integral Molecular Dynamics).
Coordinate transformation used in the integration of the Path Integral Molecular Dynamics equations of motion. The transformation, with an appropriate choice of fictitious masses (pimass), is used to force the different modes to move on the same time scale, and thus optimize the efficiency of the statistical sampling in the corresponding statistical ensemble.
Available with a Langevin thermostat (imgmov=9) or with Nose-Hoover chains (imgmov=13).
See M. Tuckerman et al, J. Chem. Phys. 104, 5579 (1996).
If equal to 0, no transformation is applied (primitive coordinates).
If equal to 1, normal mode transformation (in that case, nimage must be absolutely EVEN).
If equal to 2, staging transformation.
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| Complete list of input variables
prtatlist
Mnemonics: PRinT by ATom LIST of ATom
Executable: abinit
Characteristic: NO_MULTI
Mentioned in topics: printing, Output.
Rarely used: [1/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v4:[97]}.
Variable type: integer(natom)
Default is 0
This is an array of the numbers associated to the index atoms that
the user want to print in the output or log files, this is useful when
you have a large number of atoms and you are only interested to
follow specific atoms, the numbers associated should be consistent
with the list in xcart or xred.
This input varible does not affect the contents of the "OUT.nc" or
"HIST.nc", those are NetCDF files containing the information about
all the atoms.
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| Complete list of input variables
qmass
Mnemonics: Q thermostat MASS
Executable: abinit
Mentioned in topics: PIMD, MolecularDynamics.
Rarely used: [2/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v5:[01],v7:[08]}.
Variable type: real(nnos)
Default is *10.0
This are the masses of the chains of nnos thermostats to be used when ionmov=13 (Molecular Dynamics) or imgmov=13 (Path Integral Molecular Dynamics).
If ionmov=13 (Molecular Dynamics),
this temperature control can be used with
optcell =0, 1 (homogeneous cell deformation) or 2 (full cell deformation).
If imgmov=13 (Path Integral Molecular Dynamics),
this temperature control can be used with
optcell =0 (NVT ensemble) or 2 (fully flexible NPT ensemble).
In that case, optcell=2 iS NOT USABLE yet.
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| Complete list of input variables
random_atpos
Mnemonics: RANDOM ATomic POSitions
Executable: abinit
Mentioned in topics: crystal, GeoOpt.
Rarely used: [1/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v6:[27]}.
Variable type: integer
Default is 0
Control the inner coordinates, which can be generated randomly by using 4 different methods depending
ont its value
(0) if zero, no random generation and xred are taken as they have been introduced by the user
(1) if one, particles are generated completely random within the unit cell.
(2) if two, particles are generated randomly but the inner particle distance is always larger than a factor of the
sum of the covalent bonds between the atoms (note : this is incompatible with the definition of alchemical mixing, in which
ntypat differs from npsp)
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| Complete list of input variables
restartxf
Mnemonics: RESTART from (X,F) history
Executable: abinit
Mentioned in topics: PIMD, MolecularDynamics, GeoOpt.
Rarely used: [3/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v1:[75,80],v8:[05]}.
Variable type: integer
Default is 0
Control the restart of a molecular dynamics or structural
optimization job.
restartxf>0 (Deprecated)
: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.
Works only for ionmov=2 (Broyden) and
when an input wavefunction file is specified, thanks to the
appropriate values of irdwfk or getwfk.
NOTES :
* 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.
* 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. Starting a non-zero optcell
run from a zero
optcell run should work.
* Deprecated, the use of the new options (-1 and -2) is preferred.
restartxf=0 (Default)
: No restart procedure is enable
and will start a Molecular dynamics or structural optimization
from scratch.
restartxf=-1 (New)
: Use the HIST file to reconstruct
a partial calculation. It will reconstruct the different configurations
using the forces and stress store in the HIST file, instead of calling
the SCF procedure.
Enable
restartxf=-1
from the beginning is harmless.
The only condition is to keep the input file the same in such a way
that the same predictor is used and it will predict the same structure
recorded in the HIST file.
This option will always compute extra ntime
iterations independent of the number of iterations recovered previously.
restartxf=-2 (New)
:Read the HIST file and select the atomic
positions and cell parameters with the lowest energy. Forget all the
history and start the calculation using those values. The original
atomic coordinates and cell parameters are irrelevant in that case.
NOTES:
* You can use
restartxf=-1 or -2
for all predictiors that
make no use of random numbers.
* You can use
restartxf=-1 or -2
to restart a calculation
that was not completed. The HIST file is written on each iteration. So
you always have something to recover from.
* You can take advantage of the appropriate values
of irdwfk or getwfk
to get a good wave function
to continue your job.
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| Complete list of input variables
signperm
Mnemonics: SIGN of PERMutation potential
Executable: abinit
Mentioned in topic: MolecularDynamics.
Rarely used: [2/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v2:[87,88]}.
Variable type: integer
Default is 1
+1 favors alternation of species
-1 favors segregation
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| Complete list of input variables
strfact
Mnemonics: STRess FACTor
Executable: abinit
Mentioned in topic: GeoOpt.
Rarely used: [5/907] in abinit tests, [2/136] in tuto abinit tests. Test list: {tutorespfn:[elast_1,elast_6],v1:[78],v5:[79],v6:[121]}.
Variable type: real
Default is 100
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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| Complete list of input variables
string_algo
Mnemonics: STRING method ALGOrithm
Executable: abinit
Mentioned in topic: TransPath.
Rarely used: [1/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v6:[24]}.
Variable type: integer
Default is 1
Relevant only when imgmov=2 (String Method).
Gives the variant of the String Method method used.
Possible values can be:
-
0=>
Original String Method
.
NOT YET IMPLEMENTED
See: Phys. Rev. B 66, 052301 (2002)
-
1=>
Simplified String Method
with parametrization by
equal arc length
.
Instead of using the normal force (wr the band), the full force is used; the
reparametrization is enforced by keeping the points of the string equally spaced.
See: J. Chem. Phys. 126, 164103 (2007)
-
2=>
Simplified String Method
with parametrization by
energy-weighted arc length
.
A variant of the Simplified String Method (like 2-); the reparametrization is done by using
energy-weight arc-lengths, giving a finer distribution near the saddle point..
See: J. Chem. Phys. 126, 164103 (2007) and J. Chem. Phys. 130, 244108 (2009)
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| Complete list of input variables
strprecon
Mnemonics: STRess PRECONditioner
Executable: abinit
Mentioned in topics: ForcesStresses, GeoOpt.
Rarely used: [3/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {bigdft:[14],v5:[77],v6:[18]}.
Variable type: real
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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| Complete list of input variables
strtarget
Mnemonics: STRess TARGET
Executable: abinit
Mentioned in topics: ForcesStresses, GeoOpt.
Rarely used: [3/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v1:[80],v5:[01],v6:[18]}.
Variable type: real(6)
Default is [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
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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| Complete list of input variables
tolimg
Mnemonics: TOLerance on the mean total energy for IMaGes
Executable: abinit
Characteristic: ENERGY
Mentioned in topic: TransPath.
Rarely used: [6/907] in abinit tests, [2/136] in tuto abinit tests. Test list: {paral:[08],tutoparal:[string_03,string_04],v6:[21,24,25]}.
Variable type: real
Default is 5e-05
Sets a maximal absolute energy tolerance (in hartree, averaged over dynamic images)
below which iterations on images (the one governed by the ntimimage
input variable) will stop.
This is to be used when trying to optimize a
population of structures to their lowest energy configuration,
taking into account the particular algorithm defined by imgmov
A value of about 5.0d-5 hartree or smaller
is suggested (this corresponds to about 3.7d-7 eV).
No meaning for RF calculations.
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| Complete list of input variables
tolmxde
Mnemonics: TOLerance on the MaXimal Difference in Energy
Executable: abinit
Characteristic: ENERGY
Mentioned in topic: GeoOpt.
Rarely used: [1/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v7:[15]}.
Variable type: real
Default is 0.0
Sets a maximal difference in energy with respect to the
two previous steps below which
BFGS structural relaxation iterations will stop.
A value of about 0.0005 eV/atom or smaller is suggested.
In order to use tolmxde, you should explicitly set tolmxf to 0.0.
No meaning for RF calculations.
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| Complete list of input variables
tolmxf
Mnemonics: TOLerance on the MaXimal Force
Executable: abinit
Mentioned in topic: GeoOpt.
Moderately used: [94/907] in abinit tests, [16/136] in tuto abinit tests. Too many tests to report (>10).
Variable type: real
Default is 5e-05
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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| Complete list of input variables
vel
Mnemonics: VELocity
Executable: abinit
Characteristic: EVOLVING
Mentioned in topics: PIMD, MolecularDynamics.
Rarely used: [2/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v4:[97],v5:[03]}.
Variable type: real(3,natom) (Comment: It is represented internally as vel(3,natom,nimage))
Default is *0
Only relevant if ionmov > 0
Gives the starting velocities
of atoms, in cartesian coordinates, in Bohr/atomic time
units (atomic time units given where dtion
is described).
For ionmov=8 (Nose thermostat),
if vel is not initialized, a random initial
velocity giving the right kinetic energy will be generated.
If the atom manipulator is used, vel will be related
to the preprocessed set of atoms, generated by the
atom manipulator. The user must thus foresee the effect
of this atom manipulator (see objarf).
Velocities evolve is ionmov==1.
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| Complete list of input variables
vel_cell
Mnemonics: VELocity of the CELL parameters
Executable: abinit
Characteristic: EVOLVING
Mentioned in topic: PIMD.
Rarely used: [1/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v6:[26]}.
Variable type: real(3,3) (Comment: It is represented internally as vel_cell(3,3,nimage) )
Default is *3
Only relevant if imgmov in [9,13] and optcell > 0
(Path-Integral Molecular Dynamics
with NPT algorithm)
Irrelevant unless imgmov=9 or 13
and optcell>0 (Path-Integral Molecular Dynamics
with NPT algorithm).
Gives the starting velocities of the dimensional cell parameters in Bohr/atomic time
units (atomic time units given where dtion
is described).
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| Complete list of input variables
vis
Mnemonics: VIScosity
Executable: abinit
Mentioned in topics: PIMD, MolecularDynamics.
Rarely used: [6/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {fast:[21,29],v2:[88],v3:[40],v7:[08],v8:[05]}.
Variable type: real
Default is 100
The equation of motion is :
M
I
d
2
R
I
/dt
2
= F
I
- vis dR
I
/dt
The atomic unit of viscosity is hartrees*(atomic time units)/Bohr
2
.
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.
In the case of Path-Integral Molecular Dynamics using the Langevin Thermostat (imgmov=9), vis defines the friction coefficient, in atomic units. Typical value range is 0.00001-0.001.
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| Complete list of input variables
wtatcon
Mnemonics: WeighTs for AToms in CONstraint equations
Executable: abinit
Characteristic: NO_MULTI
Mentioned in topic: GeoConstraints.
Rarely used: [3/907] in abinit tests, [0/136] in tuto abinit tests. Test list: {v3:[40],v6:[22],v8:[05]}.
Variable type: real(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, W
I
,
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, F
I
,
are
replaced by projected forces, F'
I
, which satisfy the set of
constraint equations
Sum
mu=x,y,z; I=1,natcon
: W
mu,I
* F'
mu,I
= 0 for each of the nconeq arrays W
I
.
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 z
1
- z
2
= constant.
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