ABINIT, file handling input variables:

Complete list and description.


This document lists and provides the description of the name (keywords) of "file handling" input variables to be used in the main input file of the abinis code.

The new user is advised to read first the new user's guide, before reading the present file. It will be easier to discover the present file with the help of the tutorial.

When the user is sufficiently familiarized with ABINIT, the reading of the ~ABINIT/Infos/tuning file might be useful. For response-function calculations using abinis, the complementary file ~ABINIT/Infos/respfn_help is needed.

Copyright (C) 1998-2004 ABINIT group (DCA, XG, RC)
This file is distributed under the terms of the GNU General Public License, see ~ABINIT/Infos/copyright or http://www.gnu.org/copyleft/gpl.txt .
For the initials of contributors, see ~ABINIT/Infos/contributors .

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Files that describe other input variables:

Content of the file : alphabetical list of "file handling" variables.


A.
B.
C. cmlfile  
D.
E.
F.
G. getddk   getden   getkss   getocc   getscr   getwfk   getwfq   get1den   get1wf   get1wfden  
H.
I. irdddk   irdkss   irdscr   irdwfk   irdwfq   ird1wf  
J.
K. kssform  
L.
M. mffmem   mkmem  
N.
O.
P. prtcml   prtden   prtdos   prteig   prtfsurf   prtgeo   prtkpt   prtpot   prtstm   prtvha   prtvhxc   prtvol   prtvxc   prtwf   prt1dm  
Q.
R.
S.
T.
U.
V.
W.
X.
Y.
Z.




cmlfile
Mnemonics: Chemical Markup Language FILE
Characteristic: NO INTERNAL
Variable type: character string
Default is no file.

Used to import some of the data from one or more Chemical Markup Language 2 (CML2) file(s) (one per dataset). Unlike most of the other input variables, it refers to a character string, e.g. :
 cmlfile ../t67.in_CML.xml
The file is preprocessed, and the relevant information is translated in order to be used as an alternative to the usual input variables. Note that the input variables directly defined in the usual input file have precedence over the CML data : the latter are used only when there is no occurence of the corresponding keyword in the input file...
The ABINIT CML parser is still quite primitive. The mechanism followed to parse the CML file is described afterwards.
The ABINIT CML parser will localize in the CML file the first occurence of a 'molecule' markup section. It will ignore all other occurences of 'molecule'. Inside this 'molecule' section, it will localize the first occurences of the 'crystal', 'symmetry' and 'atomArray' sections. All other occurences, and all other sections, are ignored.
The following ABINIT input variables will be extracted from these sections of the CML file (if the data is available) :
These limited parsing capabilities are enough for ABINIT to read the CML files it has created thanks to the use of the prtcml input variable.




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getden
Mnemonics: GET the DENsity from ...
Characteristic:
Variable type: integer parameter
Default is 0.

Eventually used when ndtset>0 (multi-dataset mode) and, in the case of a ground-state calculation, if iscf<0 (non-SCF calculation), to indicate that the starting density is to be taken from the output of a previous dataset. It is used to chain the calculations, since it describes from which dataset the OUTPUT density are to be taken, as INPUT density of the present dataset.
If getden==0, no such use of previously computed output density file is done.
If getden is positive, its value gives the index of the dataset from which the output density is to be used as input.
If getden is -1, the output density of the previous dataset must be taken, which is a frequently occuring case.
If getden is a negative number, it indicates the number of datasets to go backward to find the needed file. In this case, if one refers to a non existant data set (prior to the first), the density is not initialised from a disk file, so that it is as if getden=0 for that initialisation. Thanks to this rule, the use of getden -1 is rather straightforward : except for the first density, that is not initialized by reading a disk file, the output density of one dataset is input of the next one.
Be careful : the output density file of a run with non-zero ionmov does not have the proper name (it has a "TIM" indication) for use as an input of an iscf<0 calculation.
One should use the output density of a ionmov==0 run.




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getkss
Mnemonics: GET Kohn-Sham Structure from ...
Characteristic: GW
Variable type: integer parameter
Default is 0.

Used when ndtset>0 (multi-dataset mode) and optdriver=3 or 4 (a GW calculation), to indicate that the KSS wavefunction file is to be taken from the output of a previous dataset. It is used to chain the calculations, since it describes from which dataset the OUTPUT wavefunctions are to be taken, as INPUT of the present dataset.
If getkss==0, no such use of previously computed output KSS file is done.
If getkss is positive, its value gives the index of the dataset from which the output KSS file is to be used as input.
If getkss is -1, the output KSS file of the previous dataset must be taken, which is a frequently occuring case.
If getkss is a negative number, it indicates the number of datasets to go backward to find the needed file. In this case, if one refers to a non existent data set (prior to the first), the KSS file is not initialised from a disk file, so that it is as if getkss=0 for that initialisation.




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getocc
Mnemonics: GET OCC parameters from ...
Characteristic:
Variable type: integer parameter, an instance of a 'get' variable
Default is 0.

This variable is typically used to chain the calculations, in the multi-dataset mode (ndtset>0), since it describes from which dataset the array occ is to be taken, as input of the present dataset. The occupation numbers are EVOLVING variables, for which such a chain of calculations is useful.
If ==0, no use of previously computed values must occur.
If it is positive, its value gives the index of the dataset from which the data are to be used as input data. It must be the index of a dataset already computed in the SAME run.
If equal to -1, the output data of the previous dataset must be taken, which is a frequently occuring case. However, if the first dataset is treated, -1 is equivalent to 0, since no dataset has yet been computed in the same run.
If another negative number, it indicates the number of datasets to go backward to find the needed data (once again, going back beyond the first dataset is equivalent to using a null get variable).
NOTE that a non-zero getocc MUST be used with occopt==2, so that the number of bands has to be initialized for each k point. Of course, these numbers of bands must be identical with the numbers of bands of the dataset from which occ will be copied. The same is true for the number of k points.




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getscr
Mnemonics: GET SCReening (the inverse dielectric matrix) from ...
Characteristic: GW
Variable type: integer parameter
Default is 0.

Used when ndtset>0 (multi-dataset mode) and optdriver=4 (sigma step of a GW calculation), to indicate that the dielectric matrix (EPS file) is to be taken from the output of a previous dataset. It is used to chain the calculations, since it describes from which dataset the OUTPUT dielectric matrix are to be taken, as INPUT of the present dataset.
If getscr==0, no such use of previously computed output EPS file is done.
If getscr is positive, its value gives the index of the dataset from which the output EPS file is to be used as input.
If getscr is -1, the output EPS file of the previous dataset must be taken, which is a frequently occuring case.
If getscr is a negative number, it indicates the number of datasets to go backward to find the needed file. In this case, if one refers to a non existent data set (prior to the first), the EPS file is not initialised from a disk file, so that it is as if getscr=0 for that initialisation.




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getwfk
Mnemonics: GET the wavefunctions from _WFK file

getwfq
Mnemonics: GET the wavefunctions from _WFQ file

get1wf
Mnemonics: GET the first-order wavefunctions from _1WF file

getddk
Mnemonics: GET the ddk wavefunctions from _1WF file
Characteristic:
Variable type: integer parameter
Default is 0.

Eventually used when ndtset>0 (in the multi-dataset mode), to indicate starting wavefunctions, as an alternative to irdwfk, irdwfq, ird1wf, or irdddk. One should first read the explanations given for these latter variables.
The getwfk, getwfq, get1wf and getddk variables are typically used to chain the calculations in the multi-dataset mode, since they describe from which dataset the OUTPUT wavefunctions are to be taken, as INPUT wavefunctions of the present dataset.

We now focus on the getwfk input variable (the only one used in ground-state calculations), but the rules for getwfq and get1wf are similar, with _WFK replaced by _WFQ or _1WF.
If getwfk==0, no use of previously computed output wavefunction file appended with _DSx_WFK is done.
If getwfk is positive, its value gives the index of the dataset for which the output wavefunction file appended with _WFK must be used.
If getwfk is -1, the output wf file with _WFK of the previous dataset must be taken, which is a frequently occuring case.
If getwfk is a negative number, it indicates the number of datasets to go backward to find the needed wavefunction file. In this case, if one refers to a non existent data set (prior to the first), the wavefunctions are not initialised from a disk file, so that it is as if getwfk=0 for that initialisation. Thanks to this rule, the use of getwfk -1 is rather straightforward : except for the first wavefunctions, that are not initialized by reading a disk file, the output wavefunction of one dataset is input of the next one.
In the case of a ddk calculation in a multidataset run, in order to compute correctly the localisation tensor, it is mandatory to declare give getddk the value of the current dataset (i.e. getddk3 3 ) - this is a bit strange and should be changed in the future.




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get1den
Mnemonics: GET the wavefunctions from _WFK file, DenSIFied ?? (to be completed)



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get1wfden
Mnemonics: GET the wavefunctions from _WFK file, DenSIFied ?? (to be completed)



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irdkss
Mnemonics: Integer that governs the ReaDing of KSS file
Characteristic: GW
Variable type: integer parameter
Default is 0.

Relevant only when optdriver=3 or 4. Indicate the file from which the dielectric matrix must be obtained. As alternative, one can use the input variable getkss.
When optdriver=3 or 4, at least one of irdkss or getscr must be non-zero.

A non-zero value of irdkss is treated in the same way as other "ird" variables, see the section 4 of abinis_help.



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irdscr
Mnemonics: Integer that governs the ReaDing of EPSilon
Characteristic: GW
Variable type: integer parameter
Default is 0.

Relevant only when optdriver=4. Indicate the file from which the dielectric matrix must be obtained. As alternative, one can use the input variable getscr.
When optdriver=4, at least one of irdscr or getscr must be non-zero.

A non-zero value of irdscr is treated in the same way as other "ird" variables, see the section 4 of abinis_help.



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irdwfk
Mnemonics: Integer that governs the ReaDing of _WFK files

irdwfq
Mnemonics: Integer that governs the ReaDing of _WFQ files

ird1wf
Mnemonics: Integer that governs the ReaDing of _1WF files

irdddk
Mnemonics: Integer that governs the ReaDing of DDK wavefunctions, in _1WF files
Characteristic:
Variable type: integer parameter
Default is 0.

Indicates eventual starting wavefunctions. As alternative, one can use the input variables getwfk, getwfq, get1wf or getddk.

Ground-state calculation :

Response-function calculation :



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kssform
Mnemonics: Kohn Sham Structure file FORMat
Characteristic:
Variable type: integer parameter
Default is 1, i.e. the KSS format

Governs the choice of the format for the file that contains the Kohn-Sham electronic structure information, for use in GW calculations, see the input variables optdriver and nbandkss.



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mffmem
Mnemonics: Maximum number of FFt grids in MEMory
Characteristic:
Variable type: integer parameter
Default is 1, i.e. an in-core solution.

Governs the choice of number of FFT arrays that will be kept permanently in core memory.
The allowed values are 0, in which case maximal use is made of disk space, saving core memory at the expense of execution time (not much, usually), or 1, in which case everything is kept in core memory.
More detailed explanations : if mffmem==0, some arrays of size
double precision :: xx(nfft,nsppol)
will be saved on disk when the wavefunctions are optimized or when the Hartree and xc potential is computed (which can require some sizeable memory space also).
The number of these arrays is 10 if iscf==5, 5 if iscf==1, and 4 if iscf==2 or 3. The saving of memory can be appreciable especially when iscf==5 and nsppol=2.




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mkmem
Mnemonics: Maximum number of K - points in MEMory
Characteristic:
Variable type: integer parameter
Default is nkpt, i.e. in-core solution.

Sets the maximum number of k points for which the ground state wavefunctions are kept in core memory at one time.
This value should either be 0, in which case an out-of-core solution will be used, or else nkpt, in which case an in-core solution will be used.
Internal representation as mkmems(1)




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prtcml
Mnemonics: PRinT CML file
Characteristic:
Variable type: integer parameter
Default is 0.

If set to 1 or a larger value, provide output of geometrical parameters using CML (the Chemical Markup Language, see papers by P. Murray-Rust and H. Rzepa, especially J. Chem. Inf. Comput. Sci. 39, 928-942 (1998) and the Web site http://www.xml-cml.org). Such file can be treated automatically by tools developed to handle XML formatted files.
Such a CML file contains :
If ionmov==0, the name of the CML file will be the root output name, followed by _CML.xml .
If ionmov==1 or 2, the CML file will be output at each time step, with the name being made of
No output is provided by prtcml lower or equal to 0.




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prtden
Mnemonics: PRinT the DENsity
Characteristic:
Variable type: integer parameter
Default is 0.

If set to 1 or a larger value , provide output of electron density in real space rho(r), in units of electrons/bohr^3.
If ionmov==0, the name of the density file will be the root output name, followed by _DEN .
If ionmov==1 or 2, density files will be output at each time step, with the name being made of The file structure of the unformatted output file is described below, see section 6).
No output is provided by prtden lower or equal to 0.




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prtdos
Mnemonics: PRinT the Density Of States
Characteristic:
Variable type: integer parameter
Default is 0.

Provide output of Density of States if set to 1, 2 or 3. Can either use a smearing technique (prtdos=1), or the tetrahedron method (prtdos=2). If prtdos=3, provide output of Local Density of States inside a sphere centered on an atom, as well as the angular-momentum projected DOS, in the same sphere. The resolution of the linear grid of energies for which the DOS is computed can be tuned thanks to dosdeltae.

If prtdos=1, the smeared density of states is obtained from the eigenvalues, properly weighted at each k point using wtk, and smeared according to occopt and tsmear. All levels that are present in the calculation are taken into account (occupied and unoccupied). Note that occopt must be between 3 and 7 .
In order to compute the DOS of an insulator with prtdos=1, compute its density thanks to a self-consistent calculation (with a non-metallic occopt value, 0, 1 or 2), then use prtdos=1, together with iscf=-3, and a metallic occopt, between 3 and 7, providing the needed smearing. If prtdos=1, the name of the DOS file is the root name for the output files, followed by "_DOS" .

If prtdos=2, the DOS is computed using the tetrahedron method. As in the case of prtdos=1, all levels that are present in the calculation are taken into account (occupied and unoccupied). In this case, the k-points must have been defined using the input variable ngkpt or the input variable kptrlatt. There must be at least two non-equivalent points in the Irreducible Brillouin Zone to use prtdos=2. There is no need to take care of the occopt or tsmear input variables, and there is no subtlety to be taken into account for insulators. The computation can be done in the self-consistent case as well as in the non-self-consistent case, using iscf=-3. This allows to refine the DOS at fixed starting density.
In that case, if ionmov==0, the name of the potential file will be the root output name, followed by _DOS (like in the prtdos=1 case).
However, if ionmov==1 or 2, potential files will be output at each time step, with the name being made of

If prtdos=3, the same tetrahedron method as for prtdos=2 is used, but the DOS inside a sphere centered on some atom is delivered, as well as the angular-momentum projected (l=0,1,2,3,4) DOS in the same sphere. The preparation of this case, the parameters under which the computation is to be done, and the file denomination is similar to the prtdos=2 case. However, three additional input variables might be provided, describing the atoms that are the center of the sphere (input variables natsph and iatsph), as well as the radius of this sphere (input variable ratsph).



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prteig
Mnemonics: PRinT EIGenenergies
Characteristic:
Variable type: integer parameter
Default is 0 or 1 ?????.

(Not yet active)



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prtfsurf
Mnemonics: PRinT Fermi SURFace file
Characteristic:
Variable type: integer parameter
Default is 0.

If set to 1, print Fermi surface file. For the time being, under development.



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prtgeo
Mnemonics:PRinT the GEOmetry analysis
Characteristic:
Variable type: integer parameter
Default is 0.

If set to 1 or a larger value, provide output of geometrical analysis (bond lengths and bond angles). The value of prtgeo is taken by the code to be the maximum coordination number of atoms in the system.
It will deduce a maximum number of "nearest" and "next-nearest" neighbors accordingly , and compute corresponding bond lengths.
It will compute bond angles for the "nearest" neighbours only.
If ionmov==0, the name of the file will be the root output name, followed by _GEO .
If ionmov==1 or 2, one file will be output at each time step, with the name being made of The content of the file should be rather self-explanatory.
No output is provided by prtgeo is lower than or equal to 0.
If prtgeo>0, the maximum number of atoms (natom) is 9999.




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prtkpt
Mnemonics:PRinT the K-PoinTs sets
Characteristic:
Variable type: integer parameter
Default is 0.

If set /= 0 , proceeds to a detailed analysis of different k point grids. Works only if kptopt is positive, and neither kptrlatt nor ngkpt are defined. ABINIT will stop after this analysis.

Different sets of k point grids are defined, with common values of shiftk. In each set, ABINIT increases the length of vectors of the supercell (see kptrlatt) by integer steps. The different sets are labelled by "iset". For each k point grid, kptrlen and nkpt are computed (the latter always invoking kptopt=1, that is, full use of symmetries). A series is finished when the computed kptrlen is twice larger than the input variable kptrlen. After the examination of the different sets, ABINIT summarizes, for each nkpt, the best possible grid, that is, the one with the largest computed kptrlen.

Note that this analysis is also performed when prtkpt=0, as soon as neither kptrlatt nor ngkpt are defined. But, in this case, no analysis report is given, and the code selects the grid with the smaller ngkpt for the desired kptrlen. However, this analysis takes some times (well sometimes, it is only a few seconds - it depends on the value of the input kptrlen), and it is better to examine the full analysis for a given cell and set of symmetries, shiftk for all the production runs.



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prtpot
Mnemonics: PRinT the iotal (kohn-sham)POTential

prtvha
Mnemonics: PRinT V_HArtree

prtvhxc
Mnemonics: PRinT V_(Hartree+XC)

prtvxc
Mnemonics: PRinT V_XC
Characteristic:
Variable type: integer parameter
Default is 0.

If set >=1 , provide output of different potentials.
For prtpot, output the total (Kohn-Sham) potential, sum of local pseudo-potential, Hartree potential, and xc potential.
For prtvha, output the Hartree potential.
For prtvhxc, output the sum of Hartree potential and xc potential.
For prtvxc, output the exchange-correlation potential.

If ionmov==0, the name of the potential file will be the root output name, followed by _POT, _VHA, _VHXC, or _VXC .
If ionmov==1 or 2, potential files will be output at each time step, with the name being made of

The file structure of this unformatted output file is described in section 6.6 of abinis_help. No output is provided by a negative value of these variables.



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prtstm
Mnemonics: PRinT the STM density
Characteristic:
Variable type: integer parameter
Default is 0.

If set to 1 or a larger value, provide output of the electron density in real space rho(r), made only from the electrons close to the Fermi energy, in a range of energy (positive or negative), determined by the (positive or negative, but non-zero) value of the STM bias stmbias.
This is a very approximate way to obtain STM profiles : one can choose an equidensity surface, and consider that the STM tip will follow this surface. Such equidensity surface might be determined with the help of Cut3D, and further post-processing of it (to be implemented). The big approximations of this technique are : neglect of the finite size of the tip, and position-independent transfer matrix elements between the tip and the surface.
The charge density is provided in units of electrons/bohr^3. The name of the STM density file will be the root output name, followed by _STM . Like a _DEN file, it can be analyzed by cut3d. The file structure of this unformatted output file is described in section 6.5 of abinis_help.
For the STM charge density to be generated, one must give, as an input file, the converged wavefunctions obtained from a previous run, at exactly the same k-points and cut-off energy, self-consistently determined, using the occupation numbers from occopt=7.
In the run with positive prtstm, one has to use :
Note that you might have to adjust the value of nband as well, for the treatment of unoccupied states, because the automatic determination of nband will often not include enough unoccupied states.
When prtstm is non-zero, the stress tensor is set to zero.
No output of _STM file is provided by prtstm lower or equal to 0.




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prtvol
Mnemonics: PRinT VOLume
Characteristic:
Variable type: integer parameter
Default is 0.

Control the volume of printed output.
Standard choice is 0. Positive values print more in the output and log files, while negative values are for debugging (or preprocessing only), and cause the code to stop at some point. Debugging options : This debugging feature is not yet activated in the RF routines. Note that fftalg offers another option for debugging.




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prtwf
Mnemonics: PRinT the WaveFunction
Characteristic:
Variable type: integer parameter
Default is 1.

If set >=1 , provide output of wavefunction and eigenvalue file, as described in section 6.7 of the main abinis help file.
For a standard ground-state calculation, the name of the wavefunction file will be the root output name, followed by _WFK. If nqpt=1, the root name will be followed by _WFQ. For response-function calculations, the root name will be followed by _1WFx, where x is the number of the perturbation. The dataset information will be added as well, if relevant.
No wavefunction output is provided by prtwf=0.




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prt1dm
Mnemonics: PRinT 1-DiMensional potential and density
Characteristic:
Variable type: integer parameter
Default is 0.

If set >= 1, provide one-dimensional projection of potential and density, for each of the three axis. This corresponds to averaging the potential or the density on bi-dimensional slices of the FFT grid.



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