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ABINIT developer workshop 2009
ABINIT &
V_Sim
AUTRANS - F RANCE
Parser
Objectives
Status
Implementation
API
Outlooks
V_Sim
Parser and visualisation: how to link ABINIT
and V_Sim?
News
Damien Caliste
L_Sim - CEA Grenoble
25th March 2009
Laboratoire de Simulation Atomistique
inac.cea.fr/sp2m/L_Sim
Why do I want to touch the parser of ABINIT?
ABINIT &
V_Sim
Parser
Objectives
Status
Implementation
API
Outlooks
V_Sim
News
I’ve got a ’foo.in’ file and I’m wondering. . .
. . . how many datasets in this file?
. . . what is the XC functional used in the second
one?
This means isolating the parser code from ABINIT and
add some ’write’ statements.
Laboratoire de Simulation Atomistique
inac.cea.fr/sp2m/L_Sim
Why do I want to touch the parser of ABINIT?
I’ve got a ’foo.in’ file and I’m wondering. . .
ABINIT &
V_Sim
Parser
Objectives
Status
. . . how many datasets in this file?
. . . what is the XC functional used in the second
one?
Implementation
API
Outlooks
V_Sim
This means isolating the parser code from ABINIT and
add some ’write’ statements.
News
What about a more complex action like: “find all files in
/home/caliste/2008Runs dealing with silicon in
PBE approximation where Ecut > 15Ht?”
Laboratoire de Simulation Atomistique
inac.cea.fr/sp2m/L_Sim
Why do I want to touch the parser of ABINIT?
I’ve got a ’foo.in’ file and I’m wondering. . .
. . . how many datasets in this file?
ABINIT &
V_Sim
Parser
Objectives
Status
Implementation
API
. . . what is the XC functional used in the second
one?
This means isolating the parser code from ABINIT and
add some ’write’ statements.
Outlooks
V_Sim
News
What about a more complex action like: “find all files in
/home/caliste/2008Runs dealing with silicon in
PBE approximation where Ecut > 15Ht?”
objective
This means having a multi-language library.
Laboratoire de Simulation Atomistique
inac.cea.fr/sp2m/L_Sim
Pre 5.6 status of the parser
Main routines
ABINIT &
V_Sim
Parser
Objectives
Status
12parser: generic Fortran tokenification and
analysing routines ;
13iovars: allocation, default values, set up and
memory check of dtset.
Implementation
API
Outlooks
V_Sim
News
Based on: 01manage_mpi, 11util, 12geometry,
13recipspace and 13xml.
Existing drawbacks for a library
all major steps are called from abinit.F90;
error are reported through human-readable
messages;
program is stoped on error.
Laboratoire de Simulation Atomistique
inac.cea.fr/sp2m/L_Sim
Pre 5.6 status of the parser
Main routines
ABINIT &
V_Sim
Parser
Objectives
Status
12parser: generic Fortran tokenification and
analysing routines ;
13iovars: allocation, default values, set up and
memory check of dtset.
Implementation
API
Outlooks
V_Sim
News
Based on: 01manage_mpi, 11util, 12geometry,
13recipspace and 13xml.
Existing drawbacks for a library
4 all major steps are called from abinit.F90;
8 error are reported through human-readable
messages;
8 program is stoped on error.
Laboratoire de Simulation Atomistique
inac.cea.fr/sp2m/L_Sim
Main ideas about the implementation
Input / output
ABINIT &
V_Sim
Parser
Objectives
IN: a file name or a string.
OUT: a dtsets object (dictionnary-like) with querying
methods:
keys defined as ab_dtset_<varname> ;
Status
Implementation
API
Outlooks
_get() methods retrieving integer/double as
scalar/arrays.
V_Sim
News
Internals:
Fortran90 implementation ;
private ab_dtset_load() routine gathering the
calls from abinit.F90 ;
identification of new parsed dtsets structure with a
unique integer and internaly stored in a private
Fortran90 linked list.
Laboratoire de Simulation Atomistique
inac.cea.fr/sp2m/L_Sim
The API in Fortran90
ABINIT &
V_Sim
module a b _ d t s e t
! E r r o r codes
integer , parameter ,
integer , parameter ,
integer , parameter ,
integer , parameter ,
integer , parameter ,
public
public
public
public
public
::
::
::
::
::
AB_NO_ERROR
AB_ERROR_DTSET_OBJ
AB_ERROR_DTSET_ATT
AB_ERROR_DTSET_ID
AB_ERROR_DTSET_SIZE
=
=
=
=
=
0
1
2
3
4
Parser
Objectives
! Key d e f i n i t i o n s
integer , parameter , public : : a b _ d t s e t _ i s c f
= 150
integer , parameter , public : : a b _ d t s e t _ i x c
= 151
integer , parameter , public : : ab_dtset_delayperm = 152
Status
Implementation
API
Outlooks
V_Sim
News
! Main
public
public
public
public
public
public
public
public
public
routines
: : ab_dtset_new
: : ab_dtset_new_from_string
: : ab_dtset_free
: : ab_dtset_get_ndtset
: : ab_dtset_get_integer
: : ab_dtset_get_real
: : ab_dtset_get_shape
: : ab_dtset_get_integer_array
: : ab_dtset_get_real_array
Laboratoire de Simulation Atomistique
inac.cea.fr/sp2m/L_Sim
The API in Fortran90
ABINIT &
V_Sim
Parser
Objectives
Status
Implementation
subroutine ab_dtset_new ( d t s e t s I d , f i l e n a m e , n )
integer , i n t e n t ( out ) : : d t s e t s I d
integer , i n t e n t ( i n ) : : n
character ( len = n ) , i n t e n t ( i n ) : : f i l e n a m e
dtsetsId: an identifier to later address these
datasets ;
API
Outlooks
V_Sim
News
filename: a filename ;
n: the length of the string (for binding reasons).
Remember to call ab_dtset_free() after use.
Recovering tricks
ab_dtset_new() on failure calls wrtout() and then
leave_new().
Laboratoire de Simulation Atomistique
inac.cea.fr/sp2m/L_Sim
The API in Fortran90
ABINIT &
V_Sim
Parser
Objectives
subroutine a b _ d t s e t _ g e t _ i n t e g e r ( d t s e t s I d , &
& value , i d , i d t s e t , e r r n o )
integer , i n t e n t ( i n ) : : d t s e t s I d
integer , i n t e n t ( i n ) : : i d , i d t s e t
integer , i n t e n t ( out ) : : v a l u e
integer , i n t e n t ( out ) : : e r r n o
Status
Implementation
API
Outlooks
V_Sim
News
dtsetsId: the identifier returned by
ab_dtset_new() ;
value: the returned value ;
id: the variable identifier ;
idtset: the dataset number (0 is default like in
ABINIT) ;
errno: an error code. value is correct only if
errno is AB_NO_ERROR.
Laboratoire de Simulation Atomistique
inac.cea.fr/sp2m/L_Sim
The API in C
ABINIT &
V_Sim
Parser
typedef enum {
_INT_SCALAR , _INT_ARRAY ,
_DOUBLE_SCALAR, _DOUBLE_ARRAY,
_OTHER
} AbDtsetTypes ;
AbDtsetTypes a b _ d t s e t _ g e t _ t y p e _ f r o m _ i d ( A b D t s e t I d s i d ) ;
# define AB_DTSET_TYPE( A ) a b _ d t s e t _ g e t _ t y p e _ f r o m _ i d ( A )
Objectives
Status
Implementation
API
Outlooks
AbDtsets ∗ ab_dtset_new ( const char ∗ f i l e n a m e ) ;
AbDtsets ∗ a b _ d t s e t _ n e w _ f r o m _ s t r i n g ( const char ∗ s t r i n g ) ;
void a b _ d t s e t _ f r e e ( AbDtsets ∗ d t ) ;
V_Sim
News
AbError a b _ d t s e t _ g e t _ n d t s e t ( AbDtsets ∗ dt , i n t ∗ n d t s e t ) ;
AbError a b _ d t s e t _ g e t _ i n t e g e r ( AbDtsets ∗ dt , A b D t s e t I d s i d ,
i n t i d t s e t , i n t ∗ value ) ;
AbError ab_dtset_get_shape
( AbDtsets ∗ dt , i n t ∗n , i n t dims [ 7 ] ,
AbDtsetIds id , i n t i d t s e t ) ;
AbError a b _ d t s e t _ g e t _ i n t e g e r _ a r r a y
( AbDtsets ∗ dt , i n t ∗ values , s i z e _ t n ,
AbDtsetIds id , i n t i d t s e t ) ;
Laboratoire de Simulation Atomistique
inac.cea.fr/sp2m/L_Sim
The API in Python
import a b i n i t
ABINIT &
V_Sim
Parser
Objectives
Status
Implementation
API
Outlooks
V_Sim
# Create a new d a t a s e t .
d t = a b i n i t . dtsets_new ( f i l e n a m e = " f o o . i n " )
# Get t h e number o f data s e t s .
ndtset = dt . dtsets_get_ndtset ( )
# Get t h e v a l u e o f v a r i a b l e ’ i x c ’ f o r d a t a s e t 2
dt . dtsets_get ( " i x c " , 2)
News
Additional information
One can get the list of available variables using
abinit.dtsets_get_ids().
The arrays are implemented using numarray.
Laboratoire de Simulation Atomistique
inac.cea.fr/sp2m/L_Sim
Example in Python
ABINIT &
V_Sim
Parser
Objectives
Status
Implementation
API
Outlooks
V_Sim
News
Laboratoire de Simulation Atomistique
inac.cea.fr/sp2m/L_Sim
Outlooks
ABINIT &
V_Sim
Parser
Objectives
Issues
Difficult to build ;
Tricks to handle errors.
Status
Implementation
API
Outlooks
V_Sim
What next, open propositions. . .
a proper error handler ;
News
a possible write API (?) ;
do the same for the symetry routines.
Laboratoire de Simulation Atomistique
inac.cea.fr/sp2m/L_Sim
V_Sim, a visualisation software
Interactive, 3D, visualisation software.
isolated / periodic systems ;
ABINIT &
V_Sim
balls and sticks (and more) ;
Parser
cutting planes ;
Objectives
Status
isosurfaces ;
Implementation
API
spin / forces representation ;
Outlooks
V_Sim
...
News
Resources:
Home page
http://inac.cea.fr/L_Sim/V_Sim
Debian package
http://packages.debian.org/sid/v-sim
Laboratoire de Simulation Atomistique
inac.cea.fr/sp2m/L_Sim
New features since Liège (not so complete list)
Input/output formats
Native ABINIT input files ;
ABINIT &
V_Sim
Parser
XCrysden structure and forces ;
SVG output for schemes ;
Objectives
Status
Implementation
API
Outlooks
Capabilities
Coloured maps with isolines ;
V_Sim
News
Smooth periodic duplication ;
Full customisation of pairs.
Geometry modifications (the road to a builder)
Single / group node moving with
interactive update of pairs ;
removal / addition of nodes.
Laboratoire de Simulation Atomistique
inac.cea.fr/sp2m/L_Sim