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 abinit code.

Content of the file : alphabetical list of structure optimization variables.


A. adpimd   adpimd_gamma   amu  
B. bmass  
C. 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
Characteristic:
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
Characteristic:
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
Characteristic: EVOLVING
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
Characteristic:
Variable type: real
Default is 10

bmass is the mass of the barostat when ionmov=13 (constant pressure molecular dynamics)





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cineb_start
Mnemonics: Climbing-Image Nudged Elastic Band: STARTing iteration
Characteristic:
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
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.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
Characteristic:
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: DILATation : MaXimal value
Characteristic:
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). 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 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.





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dtion
Mnemonics: Delta Time for IONs
Characteristic:
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
Characteristic:
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
Characteristic: ENERGY
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
Characteristic:
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
Characteristic:
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 selection
Characteristic:
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
Characteristic:
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
Characteristic:
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
Characteristic:
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
Characteristic:
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 ...
Characteristic:
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 ...
Characteristic:
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 ...
Characteristic:
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 ...
Characteristic:
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
Characteristic:
Variable type: integer
Default is 0

Set the kind of preconditioner to be used for Geometry Optimization
(Note : Under development now (2011.05.20))






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goprecprm
Mnemonics: Geometry Optimization PREconditioner PaRaMeters equations
Characteristic:
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
Characteristic: NO_MULTI, INPUT_ONLY
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)





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iatfix
Mnemonics: Indices of AToms that are FIXed
Characteristic:
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 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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iatfixx
Mnemonics: Indices of AToms that are FIXed along the X direction
Characteristic: INPUT_ONLY
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.





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iatfixy
Mnemonics: Indices of AToms that are FIXed along the Y direction
Characteristic: INPUT_ONLY
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.





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iatfixz
Mnemonics: Indices of AToms that are FIXed along the Z direction
Characteristic: INPUT_ONLY
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.





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imgmov
Mnemonics: IMaGe MOVEs
Characteristic:
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

No meaning for RF calculations.





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ionmov
Mnemonics: IONic MOVEs
Characteristic:
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.


No meaning for RF calculations.





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istatimg
Mnemonics: Integer governing the computation of STATic IMaGes
Characteristic:
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.





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mdtemp
Mnemonics: Molecular Dynamics Temperatures
Characteristic:
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.





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mdwall
Mnemonics: Molecular Dynamics WALL location
Characteristic:
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.





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mep_mxstep
Mnemonics: Minimal Energy Path search: MaXimum allowed STEP size
Characteristic: LENGTH
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.





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mep_solver
Mnemonics: Minimal Energy Path ordinary differential equation SOLVER
Characteristic:
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:

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).





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natcon
Mnemonics: Number of AToms in CONstraint equations
Characteristic: NO_MULTI, INPUT_ONLY
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).





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natfix
Mnemonics: Number of Atoms that are FIXed
Characteristic: INPUT_ONLY
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 .





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natfixx
Mnemonics: Number of Atoms that are FIXed along the X direction
Characteristic: INPUT_ONLY
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.





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natfixy
Mnemonics: Number of Atoms that are FIXed along the Y direction
Characteristic: INPUT_ONLY
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





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natfixz
Mnemonics: Number of Atoms that are FIXed along the Z direction
Characteristic: INPUT_ONLY
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.





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nconeq
Mnemonics: Number of CONstraint EQuations
Characteristic: NO_MULTI
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).





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neb_algo
Mnemonics: Nudged Elastic Band ALGOrithm
Characteristic:
Variable type: integer
Default is 1

Only relevant if imgmov==5

Gives the variant of the NEB method used.
Possible values can be:

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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neb_spring
Mnemonics: Nudged Elastic Band: SPRING constant
Characteristic:
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).





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nimage
Mnemonics: Number of IMAGEs
Characteristic:
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. : 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 : 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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nnos
Mnemonics: Number of nose masses
Characteristic:
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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noseinert
Mnemonics: NOSE thermostat INERTia factor
Characteristic:
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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ntime
Mnemonics: Number of TIME steps
Characteristic:
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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ntimimage
Mnemonics: Number of TIME steps for IMAGE propagation
Characteristic:
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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optcell
Mnemonics: OPTimize the CELL shape and dimensions
Characteristic:
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.

A few details require attention when performing unit cell optimisation : 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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pimass
Mnemonics: Path Integral fictitious MASSes
Characteristic:
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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pimd_constraint
Mnemonics: Path-Integral Molecular Dynamics: CONSTRAINT to be applied on a reaction coordinate
Characteristic:
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:





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pitransform
Mnemonics: Path Integral coordinate TRANSFORMation
Characteristic:
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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prtatlist
Mnemonics: PRinT by ATom LIST of ATom
Characteristic: NO_MULTI
Variable type: integer
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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qmass
Mnemonics: Q thermostat mass
Characteristic:
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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random_atpos
Mnemonics: RANDOM ATomic POSitions
Characteristic:
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 completly 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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restartxf
Mnemonics: RESTART from (X,F) history
Characteristic:
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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signperm
Mnemonics: SIGN of PERMutation potential
Characteristic:
Variable type: integer
Default is 1

+1 favors alternation of species -1 favors segregation



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strfact
Mnemonics: STRess FACTor
Characteristic:
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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string_algo
Mnemonics: STRING method ALGOrithm
Characteristic:
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:





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strprecon
Mnemonics: STRess PRECONditioner
Characteristic:
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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strtarget
Mnemonics: STRess TARGET
Characteristic:
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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tolimg
Mnemonics: TOLerance on the mean total energy for IMaGes
Characteristic: ENERGY
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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tolmxde
Mnemonics: TOLerance on the MaXimal Difference in Energy
Characteristic: ENERGY
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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tolmxf
Mnemonics: TOLerance on the MaXimal Force
Characteristic:
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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vel
Mnemonics: VELocity
Characteristic: EVOLVING
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 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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vel_cell
Mnemonics: VELocity of the CELL parameters
Characteristic: EVOLVING
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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vis
Mnemonics: VIScosity
Characteristic:
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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wtatcon
Mnemonics: WeighTs for AToms in CONstraint equations
Characteristic: NO_MULTI
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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