spglib-users — Mailing list for the spglib users

Re: [Spglib-users] Issue with pyspglib

[Éric G. <ger...@sj...>]

Hey,

I  think it's from atoms module.
Something has changed in the way to use it but I don't know what.
I also forgot why I needed this module actually.
I'm really wondering how do people do this thing now, it's maybe not 
require anymore.
Thanks,

                   Éric.

On 07/06/2015 03:02 PM, Atsushi Togo wrote:
> Hi,
>
> Where is your Atoms class installed?
>
> Togo
>
> On Mon, Jul 6, 2015 at 8:34 AM, Éric Germaneau <ger...@sj...> wrote:
>> Dear all,
>>
>> I use to use pyspglib two years ago but recently got an issue.
>> The following simple script doesn't work anymore:
>>
>> #!/usr/bin/python
>>
>> from numpy import *
>> from pyspglib import spglib
>> from atoms import *
>>
>> lattice = array([[4.,0.,0.], [0.,4.,0.], [0.,0.,3.]])
>> position = array([
>>      [0.0, 0.0, 0.0],
>>      [0.5, 0.5, 0.5],
>>      [0.3, 0.3, 0.0],
>>      [0.7, 0.7, 0.0],
>>      [0.2, 0.8, 0.5],
>>      [0.8, 0.2, 0.5]
>>      ])
>> atom_type = array([1,1,2,2,2,2])
>> atom_symbols = ['H', 'H', 'He', 'He', 'He', 'He']
>> atoms = Atoms( cell=lattice, scaled_positions=position, symbols=atom_symbols
>> )
>> print atoms.symbols
>> print atoms.numbers
>> print spglib.get_spacegroup(atoms, 1e-5)
>>
>> Here is the error I get:
>>
>> Traceback (most recent call last):
>>    File "./example2.py", line 18, in <module>
>>      atoms = Atoms( cell=lattice, scaled_positions=position,
>> symbols=atom_symbols )
>> NameError: name 'Atoms' is not defined
>>
>> I've installed atoms 0.1 and pyspglib 1.6.0.13 via pip.
>>
>> Can someone tell what changed and how to run this script now?
>>
>> Thanks.
>>
>> --
>> Éric Germaneau (艾海克), Specialist
>> Center for High Performance Computing
>> Shanghai Jiao Tong University
>> Room 205 Network Center, 800 Dongchuan Road, Shanghai 200240 China
>> Email:ger...@sj... Mobi:+86-136-4161-6480 http://hpc.sjtu.edu.cn
>>
>> Chinese (Simplified) - detected
>> English
>> Chinese (Simplified)
>>
>> English
>> Chinese (Simplified)
>>
>>
>> ------------------------------------------------------------------------------
>> Don't Limit Your Business. Reach for the Cloud.
>> GigeNET's Cloud Solutions provide you with the tools and support that
>> you need to offload your IT needs and focus on growing your business.
>> Configured For All Businesses. Start Your Cloud Today.
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>> _______________________________________________
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>> Spg...@li...
>> https://lists.sourceforge.net/lists/listinfo/spglib-users
>>
>
>

-- 
Éric Germaneau (艾海克), Specialist
Center for High Performance Computing
Shanghai Jiao Tong University
Room 205 Network Center, 800 Dongchuan Road, Shanghai 200240 China
Email:ger...@sj... Mobi:+86-136-4161-6480 http://hpc.sjtu.edu.cn

Re: [Spglib-users] Issue with pyspglib

[Atsushi T. <atz...@gm...>]

Hi,

Where is your Atoms class installed?

Togo

On Mon, Jul 6, 2015 at 8:34 AM, Éric Germaneau <ger...@sj...> wrote:
> Dear all,
>
> I use to use pyspglib two years ago but recently got an issue.
> The following simple script doesn't work anymore:
>
> #!/usr/bin/python
>
> from numpy import *
> from pyspglib import spglib
> from atoms import *
>
> lattice = array([[4.,0.,0.], [0.,4.,0.], [0.,0.,3.]])
> position = array([
>     [0.0, 0.0, 0.0],
>     [0.5, 0.5, 0.5],
>     [0.3, 0.3, 0.0],
>     [0.7, 0.7, 0.0],
>     [0.2, 0.8, 0.5],
>     [0.8, 0.2, 0.5]
>     ])
> atom_type = array([1,1,2,2,2,2])
> atom_symbols = ['H', 'H', 'He', 'He', 'He', 'He']
> atoms = Atoms( cell=lattice, scaled_positions=position, symbols=atom_symbols
> )
> print atoms.symbols
> print atoms.numbers
> print spglib.get_spacegroup(atoms, 1e-5)
>
> Here is the error I get:
>
> Traceback (most recent call last):
>   File "./example2.py", line 18, in <module>
>     atoms = Atoms( cell=lattice, scaled_positions=position,
> symbols=atom_symbols )
> NameError: name 'Atoms' is not defined
>
> I've installed atoms 0.1 and pyspglib 1.6.0.13 via pip.
>
> Can someone tell what changed and how to run this script now?
>
> Thanks.
>
> --
> Éric Germaneau (艾海克), Specialist
> Center for High Performance Computing
> Shanghai Jiao Tong University
> Room 205 Network Center, 800 Dongchuan Road, Shanghai 200240 China
> Email:ger...@sj... Mobi:+86-136-4161-6480 http://hpc.sjtu.edu.cn
>
> Chinese (Simplified) - detected
> English
> Chinese (Simplified)
>
> English
> Chinese (Simplified)
>
>
> ------------------------------------------------------------------------------
> Don't Limit Your Business. Reach for the Cloud.
> GigeNET's Cloud Solutions provide you with the tools and support that
> you need to offload your IT needs and focus on growing your business.
> Configured For All Businesses. Start Your Cloud Today.
> https://www.gigenetcloud.com/
> _______________________________________________
> Spglib-users mailing list
> Spg...@li...
> https://lists.sourceforge.net/lists/listinfo/spglib-users
>



-- 
Atsushi Togo
http://atztogo.github.com/
atz...@gm...

[Spglib-users] Issue with pyspglib

[Éric G. <ger...@sj...>]

Dear all,

I use to use pyspglib two years ago but recently got an issue.
The following simple script doesn't work anymore:

    #!/usr/bin/python

    from numpy import *
    from pyspglib import spglib
    from atoms import *

    lattice = array([[4.,0.,0.], [0.,4.,0.], [0.,0.,3.]])
    position = array([
         [0.0, 0.0, 0.0],
         [0.5, 0.5, 0.5],
         [0.3, 0.3, 0.0],
         [0.7, 0.7, 0.0],
         [0.2, 0.8, 0.5],
         [0.8, 0.2, 0.5]
         ])
    atom_type = array([1,1,2,2,2,2])
    atom_symbols = ['H', 'H', 'He', 'He', 'He', 'He']
    atoms = Atoms( cell=lattice, scaled_positions=position,
    symbols=atom_symbols )
    print atoms.symbols
    print atoms.numbers
    print spglib.get_spacegroup(atoms, 1e-5)

Here is the error I get:

    Traceback (most recent call last):
       File "./example2.py", line 18, in <module>
         atoms = Atoms( cell=lattice, scaled_positions=position,
    symbols=atom_symbols )
    *NameError: name 'Atoms' is not defined*

I've installed atoms 0.1 and pyspglib 1.6.0.13 via pip.

Can someone tell what changed and how to run this script now?

Thanks.

-- 
Éric Germaneau (艾海克), Specialist
Center for High Performance Computing
Shanghai Jiao Tong University
Room 205 Network Center, 800 Dongchuan Road, Shanghai 200240 China
Email:ger...@sj... Mobi:+86-136-4161-6480 http://hpc.sjtu.edu.cn

  * Chinese (Simplified) - detected
  * English
  * Chinese (Simplified)

  * English
  * Chinese (Simplified)

<javascript:void(0);><#>

[Spglib-users] Spglib 1.8 released

[Atsushi T. <atz...@gm...>]

Dear spglib users,

I have released spglib-1.8. Relatively large code refactoring was made
for the future development and maintenance, but almost no new feature
was added. Therefore spglib-1.7.4 may be more stable than spglib-1.8.

Summary of changes can be found at

https://github.com/atztogo/spglib/blob/master/ChangeLog

More details may be found in the commit log,

https://github.com/atztogo/spglib/commits/master

Best regards,

Togo

-- 
Atsushi Togo
http://atztogo.github.com/
atz...@gm...

Re: [Spglib-users] Algorithm for refine_cell

[Andrius M. <and...@gm...>]

Dear Atsushi Togo,

thank you very much for the information and the reference.

Best wishes,
Andrius Merkys

2015-03-09 12:10 GMT+01:00 Atsushi Togo <atz...@gm...>:
> Hi,
>
> I read the below for the spglib implementation.
>
> Algorithms for deriving crystallographic space-group information. II.
> Treatment of special positions
> R. W. Grosse-Kunstleve and P. D. Adams
> http://scripts.iucr.org/cgi-bin/paper?au0265
>
> Togo
>
> On Mon, Mar 9, 2015 at 7:42 PM, Andrius Merkys <and...@gm...> wrote:
>> Dear all,
>>
>> I am using pyspglib's refine_cell() to convert the results of quantum
>> simulations to unit cells of the crystal. I would like to know what
>> algorithms are performed by refine_cell() procedure? As far as I know
>> the symmetry reduction, as by Grosse-Kunstleve (1999), is performed,
>> but I am unable to identify the unit cell reduction algorithm (is the
>> Krivy & Gruber (1976) or Grosse-Kunstleve et al. (2003) algorithm
>> employed?). I would be very grateful to find the details on this
>> issue.
>>
>> Best wishes,
>> Andrius Merkys
>>
>> ------------------------------------------------------------------------------
>> Dive into the World of Parallel Programming The Go Parallel Website, sponsored
>> by Intel and developed in partnership with Slashdot Media, is your hub for all
>> things parallel software development, from weekly thought leadership blogs to
>> news, videos, case studies, tutorials and more. Take a look and join the
>> conversation now. http://goparallel.sourceforge.net/
>> _______________________________________________
>> Spglib-users mailing list
>> Spg...@li...
>> https://lists.sourceforge.net/lists/listinfo/spglib-users
>
>
>
> --
> Atsushi Togo
> http://atztogo.github.com/
> atz...@gm...

Re: [Spglib-users] Algorithm for refine_cell

[Atsushi T. <atz...@gm...>]

Hi,

I read the below for the spglib implementation.

Algorithms for deriving crystallographic space-group information. II.
Treatment of special positions
R. W. Grosse-Kunstleve and P. D. Adams
http://scripts.iucr.org/cgi-bin/paper?au0265

Togo

On Mon, Mar 9, 2015 at 7:42 PM, Andrius Merkys <and...@gm...> wrote:
> Dear all,
>
> I am using pyspglib's refine_cell() to convert the results of quantum
> simulations to unit cells of the crystal. I would like to know what
> algorithms are performed by refine_cell() procedure? As far as I know
> the symmetry reduction, as by Grosse-Kunstleve (1999), is performed,
> but I am unable to identify the unit cell reduction algorithm (is the
> Krivy & Gruber (1976) or Grosse-Kunstleve et al. (2003) algorithm
> employed?). I would be very grateful to find the details on this
> issue.
>
> Best wishes,
> Andrius Merkys
>
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming The Go Parallel Website, sponsored
> by Intel and developed in partnership with Slashdot Media, is your hub for all
> things parallel software development, from weekly thought leadership blogs to
> news, videos, case studies, tutorials and more. Take a look and join the
> conversation now. http://goparallel.sourceforge.net/
> _______________________________________________
> Spglib-users mailing list
> Spg...@li...
> https://lists.sourceforge.net/lists/listinfo/spglib-users



-- 
Atsushi Togo
http://atztogo.github.com/
atz...@gm...

[Spglib-users] Algorithm for refine_cell

[Andrius M. <and...@gm...>]

Dear all,

I am using pyspglib's refine_cell() to convert the results of quantum
simulations to unit cells of the crystal. I would like to know what
algorithms are performed by refine_cell() procedure? As far as I know
the symmetry reduction, as by Grosse-Kunstleve (1999), is performed,
but I am unable to identify the unit cell reduction algorithm (is the
Krivy & Gruber (1976) or Grosse-Kunstleve et al. (2003) algorithm
employed?). I would be very grateful to find the details on this
issue.

Best wishes,
Andrius Merkys

Re: [Spglib-users] Segmentation Fault with Fortran interface

[Navaneetha K. <nav...@ca...>]

Hi Atsushi Togo,

Thanks for the prompt action. That resolved the issue.

-Navaneeth

On Sun, Dec 14, 2014 at 9:49 PM, Atsushi Togo <atz...@gm...> wrote:
>
> Hi Navaneeth,
>
> Thank you for your report. Probably this happened because I changed
> the C-structure SpglibDataset. I updated the fortran wrapper and
> example to follow this change as attached.
>
> Best regards,
>
> Togo
>
> On Mon, Dec 15, 2014 at 5:17 AM, Navaneetha Krishnan
> <nav...@ca...> wrote:
> > Hi everyone,
> >
> > I am trying to use spglib library; I am unable to execute the Fortran
> > example in the example folder.
> >
> > I have been getting segmentation faults and they point to line 403 in
> > spglib_f08.f90 in the debugger.
> >
> > "dset % wyckoffs         = wyckoffs"
> >
> > If I comment out lines 393, 394, 398, 399, 403 and 404 (all lines
> involving
> > assignment and reassignments of pointers wyckoffs and equivalent_atoms)
> in
> > the file spglib_f08.f90, the code seems to execute completely without
> error.
> > However, since I don't know a lot about the algorithm and the
> > implementation, I don't want to risk using this interface by commenting
> out
> > those lines.
> >
> > I executed the ruby script in tests folder and that worked fine. I am
> using
> > gcc 4.9.2 and gfortran 4.9.2 to compile the library and the example
> code. I
> > have tried using this library with ubuntu and redhat systems with
> different
> > gcc compilers and they all seem to fail with this example.
> >
> > Since the problem seems to be with a pointer assignment, I wondering if
> > there is any major memory leak/wrong memory access that I am unable to
> see.
> > It would be great if someone can address this issue soon.
> >
> > Thanks,
> > -
> > Navaneeth
> > Caltech
> >
> >
> ------------------------------------------------------------------------------
> > Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> > from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> > with Interactivity, Sharing, Native Excel Exports, App Integration & more
> > Get technology previously reserved for billion-dollar corporations, FREE
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
> > _______________________________________________
> > Spglib-users mailing list
> > Spg...@li...
> > https://lists.sourceforge.net/lists/listinfo/spglib-users
> >
>
>
>
> --
> Atsushi Togo
> http://atztogo.github.com/
> atz...@gm...
>


-- 
Navaneetha Krishnan Ravichandran,
Graduate Student,
Mechanical Engineering,
Caltech.

Re: [Spglib-users] Segmentation Fault with Fortran interface

[Atsushi T. <atz...@gm...>]

Hi Navaneeth,

Thank you for your report. Probably this happened because I changed
the C-structure SpglibDataset. I updated the fortran wrapper and
example to follow this change as attached.

Best regards,

Togo

On Mon, Dec 15, 2014 at 5:17 AM, Navaneetha Krishnan
<nav...@ca...> wrote:
> Hi everyone,
>
> I am trying to use spglib library; I am unable to execute the Fortran
> example in the example folder.
>
> I have been getting segmentation faults and they point to line 403 in
> spglib_f08.f90 in the debugger.
>
> "dset % wyckoffs         = wyckoffs"
>
> If I comment out lines 393, 394, 398, 399, 403 and 404 (all lines involving
> assignment and reassignments of pointers wyckoffs and equivalent_atoms) in
> the file spglib_f08.f90, the code seems to execute completely without error.
> However, since I don't know a lot about the algorithm and the
> implementation, I don't want to risk using this interface by commenting out
> those lines.
>
> I executed the ruby script in tests folder and that worked fine. I am using
> gcc 4.9.2 and gfortran 4.9.2 to compile the library and the example code. I
> have tried using this library with ubuntu and redhat systems with different
> gcc compilers and they all seem to fail with this example.
>
> Since the problem seems to be with a pointer assignment, I wondering if
> there is any major memory leak/wrong memory access that I am unable to see.
> It would be great if someone can address this issue soon.
>
> Thanks,
> -
> Navaneeth
> Caltech
>
> ------------------------------------------------------------------------------
> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> with Interactivity, Sharing, Native Excel Exports, App Integration & more
> Get technology previously reserved for billion-dollar corporations, FREE
> http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
> _______________________________________________
> Spglib-users mailing list
> Spg...@li...
> https://lists.sourceforge.net/lists/listinfo/spglib-users
>



-- 
Atsushi Togo
http://atztogo.github.com/
atz...@gm...

[Spglib-users] Segmentation Fault with Fortran interface

[Navaneetha K. <nav...@ca...>]

Hi everyone,

I am trying to use spglib library; I am unable to execute the Fortran
example in the example folder.

I have been getting segmentation faults and they point to line 403 in
spglib_f08.f90 in the debugger.

"dset % wyckoffs         = wyckoffs"

If I comment out lines 393, 394, 398, 399, 403 and 404 (all lines involving
assignment and reassignments of pointers wyckoffs and equivalent_atoms) in
the file spglib_f08.f90, the code seems to execute completely without
error. However, since I don't know a lot about the algorithm and the
implementation, I don't want to risk using this interface by commenting out
those lines.

I executed the ruby script in tests folder and that worked fine. I am using
gcc 4.9.2 and gfortran 4.9.2 to compile the library and the example code. I
have tried using this library with ubuntu and redhat systems with different
gcc compilers and they all seem to fail with this example.

Since the problem seems to be with a pointer assignment, I wondering if
there is any major memory leak/wrong memory access that I am unable to see.
It would be great if someone can address this issue soon.

Thanks,
-
Navaneeth
Caltech

Re: [Spglib-users] spglib and cubic silicon

[Atsushi T. <atz...@gm...>]

Hi,

You have these lines:

dataset = spg_get_dataset(lattice,
                          positions,
                          types,
                          num_atom,
                              1e-5);

But they should be like this:

dataset = spg_get_dataset(lattice,
                          positions,
                          types,
                          num_atom_prim,
                              1e-5);


Togo

On Mon, Nov 10, 2014 at 11:22 PM, SAYEDE ADLANE
<say...@ho...> wrote:
> Dear spglib devlopper and users,
>
> I wanted a clarification on the use of spglib in the case of cubic silicon,
> I want to find the primitive cell of the following structure
>
> Lattice:
> 4.000000 0.000000 0.000000
> 0.000000 4.000000 0.000000
> 0.000000 0.000000 4.000000
>
> Positions :
> 0.000000 0.000000 0.000000
> 0.250000 0.750000 0.750000
> 0.000000 0.500000 0.500000
> 0.250000 0.250000 0.250000
> 0.500000 0.000000 0.500000
> 0.750000 0.750000 0.250000
> 0.500000 0.500000 0.000000
> 0.750000 0.250000 0.750000
>
> spg_find_primitive give me :
>
> Lattice:
> 2.000000 -2.000000 2.000000
> -2.000000 -0.000000 2.000000
> 0.000000 -2.000000 0.000000
>
> Positions :
> 0.000000 0.000000 0.000000
> -0.250000 -0.500000 0.250000
>
> When I use the obtained structure spg_get_dataset indicate that structure
> has  Cm (8) symmetry !!
>
> The code :
> ######################################################################################
> #include "spglib.h"
> #include <stdio.h>
>
> int main()
> {
>   double lattice[3][3] = { {4, 0, 0}, {0, 4, 0}, {0, 0, 4} };
>   double positions[32][3];
>   double pos_orig[][3] = {
>     {0, 0, 0},
>     {0.0, 0.5, 0.5},
>     {0.5, 0.5, 0.0},
>     {0.5, 0.0, 0.5},
>     {0.75, 0.25, 0.75},
>     {0.25, 0.25, 0.25},
>     {0.25, 0.75, 0.75},
>     {0.75, 0.75, 0.25}
>   };
>   int types[32];
>   int i, num_atom = 8, num_atom_prim, num_atom_bravais;
>   double symprec = 1e-5;
>
>   for (i = 0; i < num_atom; i++) {
>     positions[i][0] = pos_orig[i][0];
>     positions[i][1] = pos_orig[i][1];
>     positions[i][2] = pos_orig[i][2];
>     types[i] = 1;
>   }
>
>   num_atom_bravais = spg_refine_cell(lattice,
>                                      positions,
>                                      types,
>                                      num_atom,
>                                      symprec);
>  num_atom_prim = spg_find_primitive(lattice, positions, types,
> num_atom_bravais, symprec);
>
>   for (i = 0; i < 3; i++) {
>     printf("%f %f %f\n", lattice[i][0], lattice[i][1], lattice[i][2]);
>   }
>
> for (i = 0; i < num_atom_prim; i++) {
>     printf("%f %f %f\n",  positions[i][0], positions[i][1],
> positions[i][2]);
>   }
>
> SpglibDataset *dataset;
> const char *wl = "abcdefghijklmnopqrstuvwxyz";
> char symbol[11];
> spg_get_schoenflies(symbol, lattice, positions, types, num_atom, 1e-5);
> dataset = spg_get_dataset(lattice,
>                           positions,
>                           types,
>                           num_atom,
>                               1e-5);
>
> printf("International: %s (%d)\n", dataset->international_symbol,
> dataset->spacegroup_number );
> printf("Hall symbol:   %s\n", dataset->hall_symbol );
> printf("Number o f symmetry operations: %d\n", dataset->n_operations);
> }
> ######################################################################################
> Can someone tell me  what going wrong ?
>
> Thank you in advance ,
> Adlane
>
>
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Spglib-users mailing list
> Spg...@li...
> https://lists.sourceforge.net/lists/listinfo/spglib-users
>



-- 
Atsushi Togo
http://atztogo.github.com/
atz...@gm...

[Spglib-users] spglib and cubic silicon

[SAYEDE A. <say...@ho...>]

Dear spglib devlopper and users,
I wanted a clarification on the use of spglib in the case of cubic silicon, I want to find the primitive cell of the following structure 
Lattice:4.000000 0.000000 0.0000000.000000 4.000000 0.0000000.000000 0.000000 4.000000
Positions :0.000000 0.000000 0.0000000.250000 0.750000 0.7500000.000000 0.500000 0.5000000.250000 0.250000 0.2500000.500000 0.000000 0.5000000.750000 0.750000 0.2500000.500000 0.500000 0.0000000.750000 0.250000 0.750000
spg_find_primitive give me :
Lattice:2.000000 -2.000000 2.000000-2.000000 -0.000000 2.0000000.000000 -2.000000 0.000000
Positions :0.000000 0.000000 0.000000-0.250000 -0.500000 0.250000
When I use the obtained structure spg_get_dataset indicate that structure has  Cm (8) symmetry !!
The code : #######################################################################################include "spglib.h"#include <stdio.h>
int main(){  double lattice[3][3] = { {4, 0, 0}, {0, 4, 0}, {0, 0, 4} };  double positions[32][3];  double pos_orig[][3] = {    {0, 0, 0},    {0.0, 0.5, 0.5},    {0.5, 0.5, 0.0},    {0.5, 0.0, 0.5},    {0.75, 0.25, 0.75},    {0.25, 0.25, 0.25},    {0.25, 0.75, 0.75},    {0.75, 0.75, 0.25}  };  int types[32];  int i, num_atom = 8, num_atom_prim, num_atom_bravais;  double symprec = 1e-5;
  for (i = 0; i < num_atom; i++) {    positions[i][0] = pos_orig[i][0];    positions[i][1] = pos_orig[i][1];    positions[i][2] = pos_orig[i][2];    types[i] = 1;  }
  num_atom_bravais = spg_refine_cell(lattice,                                     positions,                                     types,                                     num_atom,                                     symprec); num_atom_prim = spg_find_primitive(lattice, positions, types,num_atom_bravais, symprec);
  for (i = 0; i < 3; i++) {    printf("%f %f %f\n", lattice[i][0], lattice[i][1], lattice[i][2]);  }  for (i = 0; i < num_atom_prim; i++) {    printf("%f %f %f\n",  positions[i][0], positions[i][1], positions[i][2]);  }
SpglibDataset *dataset;const char *wl = "abcdefghijklmnopqrstuvwxyz";char symbol[11];spg_get_schoenflies(symbol, lattice, positions, types, num_atom, 1e-5);dataset = spg_get_dataset(lattice,                          positions,                          types,                          num_atom,                              1e-5);
printf("International: %s (%d)\n", dataset->international_symbol, dataset->spacegroup_number );printf("Hall symbol:   %s\n", dataset->hall_symbol );printf("Number o f symmetry operations: %d\n", dataset->n_operations);}######################################################################################Can someone tell me  what going wrong ? 
Thank you in advance ,Adlane

 
 		 	   		  

[Spglib-users] spglib version 1.6.1 released

[Atsushi T. <atz...@gm...>]

Dear spglib users,

I released spglib version 1.6.1. This is a maintenance release that
includes collection of bug fixes. The below is the changelog.

2014-08-04  Atsushi Togo  <atz...@gm...>

        * Version 1.6.1:

        * src/{refinement.*,primitive.*,spglib.c}

        Fix symmetry finding bug for supercell that has lower point group
        than the primitive cell.

        * src/spglib.*

        New functions of spg_get_spacegroup_type and
        spg_get_grid_point. The former offers difrect access to space
        group type database using hall symbol number. The later perfoms
        converting grid address to grid point index on the reciprocal
        mesh.

        * pyspglib update.

Best regards,

Togo

-- 
Atsushi Togo
http://atztogo.github.com/
atz...@gm...

Re: [Spglib-users] spglib_f08.f90 fails to compile with gfortran earlier than 4.7

[Atsushi T. <atz...@gm...>]

Hi Keith,

Thanks for your patch. I'm not familiar with Fortran. So I just put
the link to this post from the top page of spglib web site,
http://spglib.sourceforge.net/#fortran-interface
which will be helpful for spglib users.

Togo


On Thu, Apr 3, 2014 at 6:13 PM, Keith Refson <kr...@gm...> wrote:
> I found that the Fortran interface spglib_f08.f90 fails to compile using
> gfortran 4.6.x or earlier.
>
> Source/Utility/spglib_f08.f90:360.34:
>
>             import SpglibDataset_c
>                                   1
> Error: Cannot IMPORT 'spglibdataset_c' from host scoping unit at (1) - does
> not exist.
>
> ...
>
> This appears to be a bug in the compiler, and later versions work fine.
> However there is a simple workaround - move the definition of the
> SpglibDataset_c type to the top level of the module.  Then it works as far
> back as gfortran 4.3.
>
> I hope this is useful.
>
> Keith Refson
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Spglib-users mailing list
> Spg...@li...
> https://lists.sourceforge.net/lists/listinfo/spglib-users
>



-- 
Atsushi Togo
http://atztogo.github.com/
atz...@gm...

[Spglib-users] spglib_f08.f90 fails to compile with gfortran earlier than 4.7

[Keith R. <kr...@gm...>]

I found that the Fortran interface spglib_f08.f90 fails to compile using 
gfortran 4.6.x or earlier.

Source/Utility/spglib_f08.f90:360.34:

             import SpglibDataset_c
                                   1
Error: Cannot IMPORT 'spglibdataset_c' from host scoping unit at (1) - 
does not exist.

...

This appears to be a bug in the compiler, and later versions work fine. 
  However there is a simple workaround - move the definition of the
SpglibDataset_c type to the top level of the module.  Then it works as 
far back as gfortran 4.3.

I hope this is useful.

Keith Refson

Re: [Spglib-users] Case where symmetry displacements are wrong.

[Keith R. <kr...@gm...>]

Dear Togo,

Aha, that was it! The rotation matrices were transposed which 
effectively switched the translations making them inconsistent.

Thank you for the hint!

sincerely

Keith Refson

On 28/03/14 12:08, Atsushi Togo wrote:
> I can't see if it is wrong or not from your files. What is the K290?
> The definition of rotation matrix is the same (could be trasposed)?
>
> Togo
>
> On Fri, Mar 28, 2014 at 8:45 PM, Keith Refson <kr...@gm...> wrote:
>> My tests of spglib have turned up a case where it seems that spglib is
>> returning an incorrect result.  In the attached case, spglib returns an
>> identical set of symmetry rotations to the old K290 symmetry analysis.
>> However the non-symmorphic translations are different and, I believe wrong
>> for all of the 3-fold axes in the attached example.  In particular any
>> attempt to construct an atom-atom map for the 3-fold and -3 operations
>> fails.
>>
>> Do you agree that this is a bug in spglib?
>>
>> Keith
>>
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> Spglib-users mailing list
>> Spg...@li...
>> https://lists.sourceforge.net/lists/listinfo/spglib-users
>>
>
>
>

Re: [Spglib-users] Case where symmetry displacements are wrong.

[Atsushi T. <atz...@gm...>]

I can't see if it is wrong or not from your files. What is the K290?
The definition of rotation matrix is the same (could be trasposed)?

Togo

On Fri, Mar 28, 2014 at 8:45 PM, Keith Refson <kr...@gm...> wrote:
> My tests of spglib have turned up a case where it seems that spglib is
> returning an incorrect result.  In the attached case, spglib returns an
> identical set of symmetry rotations to the old K290 symmetry analysis.
> However the non-symmorphic translations are different and, I believe wrong
> for all of the 3-fold axes in the attached example.  In particular any
> attempt to construct an atom-atom map for the 3-fold and -3 operations
> fails.
>
> Do you agree that this is a bug in spglib?
>
> Keith
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Spglib-users mailing list
> Spg...@li...
> https://lists.sourceforge.net/lists/listinfo/spglib-users
>



-- 
Atsushi Togo
http://atztogo.github.com/
atz...@gm...

[Spglib-users] Case where symmetry displacements are wrong.

[Keith R. <kr...@gm...>]

My tests of spglib have turned up a case where it seems that spglib is 
returning an incorrect result.  In the attached case, spglib returns an 
identical set of symmetry rotations to the old K290 symmetry analysis.
However the non-symmorphic translations are different and, I believe 
wrong for all of the 3-fold axes in the attached example.  In particular 
any attempt to construct an atom-atom map for the 3-fold and -3 
operations fails.

Do you agree that this is a bug in spglib?

Keith

Re: [Spglib-users] Introduction and CASTEP

[Atsushi T. <atz...@gm...>]

Hello,

I'm a developer of spglib.

1) I think it's not a very hard work. lattice parameters are necessary
to be supplied for hal_get_hall_symbol, but for this purpose, just
dummy lattice parameters should be OK.
2) If I understand correctly, what usually obtained as symmetry
operations are not a space group, but coset representatives, which may
not form a group in the case of non-symmorphic crystals. For an lxmxn
supercell, spglib returns the coset representatives (or symmetry
operations) x a set of pure translations of lxmxn. In addition, the
point group of the lattice parameters given for the supercell is not
the same as that of primitive cell, then the symmetry is given lower,
i.e. 2x1x1 of cubic is not treated as cubic symmetry x pure
translations, but tetragonal symmetry x pure translations.
3) The symmetry operations are internally compared with database of
space group types, and if the operations can be a space group type,
the tolerance parameter to be used for symmetry operation search is
adjusted (usually only reduced) until the symmetry operations will be
OK.

Best regards,

Togo

On Wed, Mar 26, 2014 at 10:37 PM, Keith Refson <kr...@gm...> wrote:
> Hello,
>
> I would like to introduce myself as one of the developers of the CASTEP
> DFT materials modelling code.   We plan to replace some old space group
> symmetry analysis code with spglib.
>
> My initial tests are proving very positive about the capabilities of
> spglib for this purpose.
>
> 1) There is one piece of missing functionality we need.  This would be
>     a routine similar to spg_get_dataset() but which takes as input a
>     list of symmetry operations, not the lattice and co-ordinates. This
>     would be to analyse a pre-supplied set of operations (rotation
>     matrices and translations).  How hard would it be to add this?
>
> 2) May I ask how spglib handles non-primitive supercells. If,
>     for example you were to pass a lxmxn block of primitive cells would
>     spglib return the complete product group of the translation and
>     rotation groups?  This is important because if only the rotation
>     subset were specified the set of operations do not form a complete
>     group. (As atoms can be mapped between different primitive cells).
>
> 3) Is there any built-in test whether the symmetry operations form a
>     group?
>
> sincerely
>
> Keith Refson
>
> ------------------------------------------------------------------------------
> Learn Graph Databases - Download FREE O'Reilly Book
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> this first edition is now available. Download your free book today!
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> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/spglib-users



-- 
Atsushi Togo
http://atztogo.github.com/
atz...@gm...

[Spglib-users] Introduction and CASTEP

[Keith R. <kr...@gm...>]

Hello,

I would like to introduce myself as one of the developers of the CASTEP 
DFT materials modelling code.   We plan to replace some old space group 
symmetry analysis code with spglib.

My initial tests are proving very positive about the capabilities of 
spglib for this purpose.

1) There is one piece of missing functionality we need.  This would be
    a routine similar to spg_get_dataset() but which takes as input a
    list of symmetry operations, not the lattice and co-ordinates. This
    would be to analyse a pre-supplied set of operations (rotation
    matrices and translations).  How hard would it be to add this?

2) May I ask how spglib handles non-primitive supercells. If,
    for example you were to pass a lxmxn block of primitive cells would
    spglib return the complete product group of the translation and
    rotation groups?  This is important because if only the rotation
    subset were specified the set of operations do not form a complete
    group. (As atoms can be mapped between different primitive cells).

3) Is there any built-in test whether the symmetry operations form a
    group?

sincerely

Keith Refson

[Spglib-users] No module named phonopy

[Dang, S. <s....@fz...>]

Hi everyone,

I have tried to install phonopy on my local workstation:

python setup.py install --home=/home/siaufung/lib/python/

Then I included this PATH in .bashrc by doing export PYTHONPATH.

But when I try to run an example like Al2O3.py I get the message:

siaufung@iwv2901:~/phonopy-1.7.2/example/Al2O3$ python Al2O3.py
Traceback (most recent call last):
  File "Al2O3.py", line 1, in <module>
    from phonopy import Phonopy
ImportError: No module named phonopy
siaufung@iwv2901:~/phonopy-1.7.2/example/Al2O3$

However I have already set my Pythonpath to the directory where the script phonopy lies in.
Have I missed anything?

Many thanks.


------------------------------------------------------------------------------------------------
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Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
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Prof. Dr. Sebastian M. Schmidt
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Re: [Spglib-users] Tolerances differ in get_int and get_sym?

[Michael R. <mjr...@gm...>]

Dear Togo,

Thanks for your prompt and clear reply. As you say, not a bug, a feature.

Regards,

Michael

Re: [Spglib-users] Tolerances differ in get_int and get_sym?

[Atsushi T. <atz...@gm...>]

Hello,

I guess this is not a bug.

spg_get_symmetry just searches symmetry operations by trying possible
operations and checking overlapping of atoms within tolerance
distance.
spg_get_international uses symmetry operations found by
spg_get_symmetry as the starting point. Then it compares with the
database of space groups. In this database matching, tolerance is also
used. The ways that tolerance used for symmetry operation search and
database matching are not exactly same. So they can make different
results in crystal symmetry sense.

You can also obtain symmetry operations from spg_get_dataset, which
are consistent with the space group that is found, because the
symmetry operations in spg_get_dataset are those recovered from the
space group database.  So I recommend to use this and I consider this
set of symmetry operations used as return values of spg_get_symmetry
in the future. There is another problem of spg_get_symmetry. In some
case, the symmetry operations obtained by spg_get_symmetry don't form
group (when the obtained symmetry operations are considered as coset
representatives in the terminology of group theory).

Togo

> I am, in general, very impressed with spglib. It does a difficult and
> tedious task well.
>
> However, one point confuses me. It seems that the symmetry operations
> returned by spg_get_symmetry are not always consistent with the
> international symbol found by spg_get_international when the same
> tolerance is used for both. The attached example prints
>
> Symprec=1e-05, int symbol is Cmc2_1
> Symprec=2e-05, int symbol is Cmc2_1
> Symprec=0.0001, int symbol is Cmc2_1
>
> Symprec=1e-05, 4 symmetry operations
> Symprec=2e-05, 4 symmetry operations
> Symprec=0.0001, 8 symmetry operations
>
> whereas I would expect Cmc2_1 to have 8 symmetry operations always.
>
> Am I confused, or is this a slight bug in spglib? (I am using version
> 1.3 from Sourceforge.)
>
> Regards,
>
> Michael
>
> ------------------------------------------------------------------------------
> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
> MVPs and experts. ON SALE this month only -- learn more at:
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> _______________________________________________
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>



-- 
Atsushi Togo
http://atztogo.users.sourceforge.net/
atz...@gm...

[Spglib-users] Tolerances differ in get_int and get_sym?

[Michael R. <mjr...@gm...>]

I am, in general, very impressed with spglib. It does a difficult and
tedious task well.

However, one point confuses me. It seems that the symmetry operations
returned by spg_get_symmetry are not always consistent with the
international symbol found by spg_get_international when the same
tolerance is used for both. The attached example prints

Symprec=1e-05, int symbol is Cmc2_1
Symprec=2e-05, int symbol is Cmc2_1
Symprec=0.0001, int symbol is Cmc2_1

Symprec=1e-05, 4 symmetry operations
Symprec=2e-05, 4 symmetry operations
Symprec=0.0001, 8 symmetry operations

whereas I would expect Cmc2_1 to have 8 symmetry operations always.

Am I confused, or is this a slight bug in spglib? (I am using version
1.3 from Sourceforge.)

Regards,

Michael

Re: [Spglib-users] A comparison of FINDSYM and Spglib symmetry finders

[Atsushi T. <atz...@gm...>]

Hi Evgeny,

Thank you for your reply. I'm happy to know that no mismatching
between spglib and FINDSYM on your test.

There is no preference how the axes of orthorhombic are chosen in
spglib. So the determined space group type name can be different from
FINDSYM.
On tolerance (accuracy), I think it is very dependent on
implementations. For example, only one value tolerance, there may be
many ways to implement angle tolerance between two lattice vectors. So
the same tolerance value may not result in the same symmetry in naive
cases.
On magnetic moments, collinear spin symmetry operations can be
searched in spglib, but magnetic space group type determination is not
implemented.

Thank you again for your test.

Togo

On Wed, Aug 15, 2012 at 5:26 PM, Evgeny Blokhin <ja...@ya...> wrote:
> Dear Dr. Togo san,
>
> I have figured out the reasons of my mismatches. They were non-tuned
> accuracies and skipping of magnetic moments (in my Spglib wrapper test
> class, in particular), exactly as i thought. I noted that you have a
> function spg_get_symmetry_with_collinear_spin in Spglib C API, which
> is inaccessible from python extension. Now I removed magmoms
> consideration (comparing only the "pure structural space groups") and
> made 1e-04 accuracy for both programs. And so the new results do not
> contain any group numbers mismatching at all. There are still some
> cases where group settings do not match though. Most of them belong to
> orthorhombic space groups (the most frequent case in my tests was Pnma
> / Pbnm, the cyclic transposition of basic translation vectors a, b, c
> to c, a, b with Wyckoff position change c(z, x, 1/4) to d(z, x, y), an
> example can be found in spglib tests folder).
>
> Regards,
> Evgeny Blokhin



-- 
Atsushi Togo
http://atztogo.users.sourceforge.net/
atz...@gm...