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From: Michel Sassi <michel.sassi@cu...>  20121119 08:21:47
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Dear All, I am using Phonopy v1.2.1 and VASP to get the phonon spectra. For that I generated a FORCE_SET file from the different vasprun.xml files. Then I asked Phonopy to calculate the force constants for the band structure by giving a band.conf as input file. I have the following error message: Band structure mode Settings: Supercell: [3 3 2] Spacegroup: I4/mmm (139) Calculating force constants... Phonopy enconters symmetry problem. Phonopy enconters symmetry problem. Phonopy enconters symmetry problem. Phonopy enconters symmetry problem. Phonopy enconters symmetry problem. Phonopy enconters symmetry problem. Phonopy enconters symmetry problem. etc.... I never had this kind of messages before and surprizingly, the determination of the space group works very well. So I am not sure where does this come from. Thank you very much for your your help or advices regarding this issue. Best Regards, Michel. 
From: Atsushi Togo <atz.togo@gm...>  20121119 08:38:48

Hi, Symmetry finder used to determine space group type and the symmetry handling for the force constants are differently implemented. The crystal symmetry finder used in phonopy is spglib. This is carefully implemented with respect to geometric tolerance in Cartesian distance. But symmetry handling with tolerance in phonopy is not very carefully coded. I expect users use symmetrically clean enough crystal structure as their input structures. I guess your crystal structure is distorted. This problem would be tentatively solved by increasing symmetry search tolerance (i.e., tolerance=1e3). But my recommendation is that first refine your unit cell by % phonopy symmetry to obtain the symmetrically clean crystal structure as BPOSCAR. Then calculate phonons. Togo On Mon, Nov 19, 2012 at 5:06 PM, Michel Sassi <michel.sassi@...> wrote: > Dear All, > > I am using Phonopy v1.2.1 and VASP to get the phonon spectra. > For that I generated a FORCE_SET file from the different vasprun.xml > files. Then I asked Phonopy to calculate the force constants for the > band structure by giving a band.conf as input file. I have the following > error message: > > Band structure mode > Settings: > Supercell: [3 3 2] > Spacegroup: I4/mmm (139) > Calculating force constants... > Phonopy enconters symmetry problem. > Phonopy enconters symmetry problem. > Phonopy enconters symmetry problem. > Phonopy enconters symmetry problem. > Phonopy enconters symmetry problem. > Phonopy enconters symmetry problem. > Phonopy enconters symmetry problem. > > etc.... > > > I never had this kind of messages before and surprizingly, the determination > of the space group works very well. So I am not sure where does this > come from. > > Thank you very much for your your help or advices regarding this issue. > > Best Regards, > Michel. > > > >  > Monitor your physical, virtual and cloud infrastructure from a single > web console. Get indepth insight into apps, servers, databases, vmware, > SAP, cloud infrastructure, etc. Download 30day Free Trial. > Pricing starts from $795 for 25 servers or applications! > http://p.sf.net/sfu/zoho_dev2dev_nov > _______________________________________________ > Phonopyusers mailing list > Phonopyusers@... > https://lists.sourceforge.net/lists/listinfo/phonopyusers >  Atsushi Togo http://atztogo.users.sourceforge.net/ atz.togo@... 
From: Michel Sassi <michel.sassi@cu...>  20121119 09:06:56

Hi, Thank you for your reply. In fact, I used the primitive cell (PPOSCAR) generated by % phonopy symmetry then I did a supercell of this primitive cell on which I calculate the phonons. All along, the symmetry tolerance is 1e5 and I still keep the good space group. As a double check, the BPOSCAR file generated from the previously obtained PPOSCAR file contains the same numerical value than my original relaxed structure with a tolerance of 1e8. For obtain the band structures without any error message, I have to set a tolerance of 1e1. Maybe the problem can come from the forces themselves. Maybe they are not consistent with the symmetry of the structure. Ultimately, I can send you my POSCAR and the FORCE_SET files. Best, Michel. On 19/11/2012, at 4:38 PM, Atsushi Togo wrote: > Hi, > > Symmetry finder used to determine space group type and the symmetry > handling for the force constants are differently implemented. The > crystal symmetry finder used in phonopy is spglib. This is carefully > implemented with respect to geometric tolerance in Cartesian distance. > But symmetry handling with tolerance in phonopy is not very carefully > coded. I expect users use symmetrically clean enough crystal structure > as their input structures. > > I guess your crystal structure is distorted. This problem would be > tentatively solved by increasing symmetry search tolerance (i.e., > tolerance=1e3). But my recommendation is that first refine your > unit cell by > > % phonopy symmetry > > to obtain the symmetrically clean crystal structure as BPOSCAR. Then > calculate phonons. > > > Togo > > On Mon, Nov 19, 2012 at 5:06 PM, Michel Sassi > <michel.sassi@...> wrote: >> Dear All, >> >> I am using Phonopy v1.2.1 and VASP to get the phonon spectra. >> For that I generated a FORCE_SET file from the different vasprun.xml >> files. Then I asked Phonopy to calculate the force constants for the >> band structure by giving a band.conf as input file. I have the following >> error message: >> >> Band structure mode >> Settings: >> Supercell: [3 3 2] >> Spacegroup: I4/mmm (139) >> Calculating force constants... >> Phonopy enconters symmetry problem. >> Phonopy enconters symmetry problem. >> Phonopy enconters symmetry problem. >> Phonopy enconters symmetry problem. >> Phonopy enconters symmetry problem. >> Phonopy enconters symmetry problem. >> Phonopy enconters symmetry problem. >> >> etc.... >> >> >> I never had this kind of messages before and surprizingly, the determination >> of the space group works very well. So I am not sure where does this >> come from. >> >> Thank you very much for your your help or advices regarding this issue. >> >> Best Regards, >> Michel. >> >> >> >>  >> Monitor your physical, virtual and cloud infrastructure from a single >> web console. Get indepth insight into apps, servers, databases, vmware, >> SAP, cloud infrastructure, etc. Download 30day Free Trial. >> Pricing starts from $795 for 25 servers or applications! >> http://p.sf.net/sfu/zoho_dev2dev_nov >> _______________________________________________ >> Phonopyusers mailing list >> Phonopyusers@... >> https://lists.sourceforge.net/lists/listinfo/phonopyusers >> > > > >  > Atsushi Togo > http://atztogo.users.sourceforge.net/ > atz.togo@... > 
From: Atsushi Togo <atz.togo@gm...>  20121119 11:48:13

Hi, PPOSCAR is not symmetrized. If your double check is correct, phonopy may have an unknown problem(s). If you want to show your files to me, you can send your files to me. The message, "Phonopy enconters symmetry problem.", appears when checking the sitesymmetry from the atomic positions failed. Forces are not checked at all in phonopy. Togo On Mon, Nov 19, 2012 at 6:05 PM, Michel Sassi <michel.sassi@...> wrote: > Hi, > > Thank you for your reply. > > In fact, I used the primitive cell (PPOSCAR) generated by > > % phonopy symmetry > > then I did a supercell of this primitive cell on which I calculate > the phonons. All along, the symmetry tolerance is 1e5 and I still > keep the good space group. As a double check, the BPOSCAR file > generated from the previously obtained PPOSCAR file contains > the same numerical value than my original relaxed structure with > a tolerance of 1e8. > > For obtain the band structures without any error message, I have to > set a tolerance of 1e1. > > Maybe the problem can come from the forces themselves. Maybe they > are not consistent with the symmetry of the structure. > > Ultimately, I can send you my POSCAR and the FORCE_SET files. > > Best, > Michel. > > > On 19/11/2012, at 4:38 PM, Atsushi Togo wrote: > >> Hi, >> >> Symmetry finder used to determine space group type and the symmetry >> handling for the force constants are differently implemented. The >> crystal symmetry finder used in phonopy is spglib. This is carefully >> implemented with respect to geometric tolerance in Cartesian distance. >> But symmetry handling with tolerance in phonopy is not very carefully >> coded. I expect users use symmetrically clean enough crystal structure >> as their input structures. >> >> I guess your crystal structure is distorted. This problem would be >> tentatively solved by increasing symmetry search tolerance (i.e., >> tolerance=1e3). But my recommendation is that first refine your >> unit cell by >> >> % phonopy symmetry >> >> to obtain the symmetrically clean crystal structure as BPOSCAR. Then >> calculate phonons. >> >> >> Togo >> >> On Mon, Nov 19, 2012 at 5:06 PM, Michel Sassi >> <michel.sassi@...> wrote: >>> Dear All, >>> >>> I am using Phonopy v1.2.1 and VASP to get the phonon spectra. >>> For that I generated a FORCE_SET file from the different vasprun.xml >>> files. Then I asked Phonopy to calculate the force constants for the >>> band structure by giving a band.conf as input file. I have the following >>> error message: >>> >>> Band structure mode >>> Settings: >>> Supercell: [3 3 2] >>> Spacegroup: I4/mmm (139) >>> Calculating force constants... >>> Phonopy enconters symmetry problem. >>> Phonopy enconters symmetry problem. >>> Phonopy enconters symmetry problem. >>> Phonopy enconters symmetry problem. >>> Phonopy enconters symmetry problem. >>> Phonopy enconters symmetry problem. >>> Phonopy enconters symmetry problem. >>> >>> etc.... >>> >>> >>> I never had this kind of messages before and surprizingly, the determination >>> of the space group works very well. So I am not sure where does this >>> come from. >>> >>> Thank you very much for your your help or advices regarding this issue. >>> >>> Best Regards, >>> Michel. >>> >>> >>> >>>  >>> Monitor your physical, virtual and cloud infrastructure from a single >>> web console. Get indepth insight into apps, servers, databases, vmware, >>> SAP, cloud infrastructure, etc. Download 30day Free Trial. >>> Pricing starts from $795 for 25 servers or applications! >>> http://p.sf.net/sfu/zoho_dev2dev_nov >>> _______________________________________________ >>> Phonopyusers mailing list >>> Phonopyusers@... >>> https://lists.sourceforge.net/lists/listinfo/phonopyusers >>> >> >> >> >>  >> Atsushi Togo >> http://atztogo.users.sourceforge.net/ >> atz.togo@... >> > >  Atsushi Togo http://atztogo.users.sourceforge.net/ atz.togo@... 
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