Re: [Wien] Phonopy
Additionally I would suggest having a look at an introduction into phonons and phonontheory, which is eg available by A. Togo: http://icms3.weebly.com/uploads/3/5/9/0/3590130/version2.pdf In this slides both phonon theory and the workflow of phonopy (including the creation of the supercells) are well explained. Hope that helps! Kind regards Magdalena Am 08.05.2016 um 19:26 schrieb Gavin Abo: I want to calculate the Phonon spectra of A2BB'O6, which has the Fm3m space group whose atomic position are A (0.25 0.25 0.25) B (0 0 0.5) B' (0 0 0) O (0 0 0.2376) when i create the super cell and make the displacement on that atom then it gives like this Number of non-equivalent atoms in BP.structS-001: 80 Number of non-equivalent atoms in BP.structS-002: 80 Number of non-equivalent atoms in BP.structS-003: 52 Number of non-equivalent atoms in BP.structS-004: 52 Number of non-equivalent atoms in BP.structS-005: 80 Number of non-equivalent atoms in BP.structS-006: 52 Number of non-equivalent atoms in BP.structS-007: 80 Number of non-equivalent atoms in BP.structS-008: 52 Number of non-equivalent atoms in BP.structS-009: 80 Number of non-equivalent atoms in BP.structS-010: 80 Number of non-equivalent atoms in BP.structS-011: 52 Number of non-equivalent atoms in BP.structS-012: 52 Number of non-equivalent atoms in BP.structS-013: 80 Number of non-equivalent atoms in BP.structS-014: 80 Number of non-equivalent atoms in BP.structS-015: 80 Number of non-equivalent atoms in BP.structS-016: 80 Number of non-equivalent atoms in BP.structS-017: 80 Number of non-equivalent atoms in BP.structS-018: 80 So is it required to run the scf of all the 18 structS file? The phonopy documentation [ http://atztogo.github.io/phonopy/wien2k.html ] says: /case.structS and case.structS-xxx (xxx are numbers) are the perfect supercell and the supercells with displacements, respectively. Perhaps these are renamed to case-xxx.struct and stored in case-xxx directories, then to be calculated using Wien2k./ My understanding from the above two sentences is: Yes, the scf needs to be ran for all structS-xxx files. In the case of NaCl only two structS file generate after the crating the displacement and also the same case happens in the SrTiO3. So please suggest me whether I am doing something is wrong? The 18 structS-xxx above look like they still might have been generated from the spacegroup C2/m (12) seen in the terminal output from phonopy [ http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg14199.html ] . Implied from what I said before [ http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg14200.html , http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg14219.html ], I suspect that the BP.struct that you provided as input to phonopy might not be correct. which theory used to generate the structS file? I currently don't know. However, you should be able to check the structS files, phonopy source code [ https://sourceforge.net/projects/phonopy/files/ ], or ask the phonopy users/developers [ https://lists.sourceforge.net/lists/listinfo/phonopy-users ] to determine how the displacements are made. At least in one case (i.e., LiH), I read that the atoms might just be displaced by 0.01 angstrom: http://dft-blog.natanzon.eu/2010/06/using-phonopy-with-wien2k.html Why these 18 strcutS generate in my case? While i have only four different atom. All I can currently say about that is: You gave phonopy BP.struct as input and that is what the program determined that you needed as output. Though, it could be because of GIGO [ https://en.wikipedia.org/wiki/Garbage_in,_garbage_out ]. I don't know what you used for lattice parameters, A, B, and B', but phonopy gave 5 structS-xxx for Ba2ZnWO6: A2BB'O6, where A = Ba, B = Zn, and B' = W [ http://dx.doi.org/10.1016/j.commatsci.2013.04.053 ]. username@computername:~/wiendata$ mkdir Ba2ZnWO6 username@computername:~/wiendata$ cd Ba2ZnWO6/ username@computername:~/wiendata/Ba2ZnWO6$ makestruct ... TITLE :Ba2ZnWO6 ... Would you like to enter Spacegroup or Lattice (S/L)(def=S)? S ... give SPACE GROUP as SYMBOL or NUMBER: 225 ... Units of lattice parameters (Bohr/Angstrom) (b/A) (def=ANG):A Lattice PARAMETERS as a b c (3 numbers):8.11 8.11 8.11 ANGLES BETWEEN lattice vectors, as alpha beta gamma (def=90.0 90.0 90.0):90 90 90 NUMBER INEQUEVALENT ATOMS :4 ATOM 1 (ELEMENT): Ba POSITION OF ATOM Ba as X,Y,Z (def=0 0 0) :0.25 0.25 0.25 ATOM 2 (ELEMENT): Zn POSITION OF ATOM Zn as X,Y,Z (def=0 0 0) :0 0 0 ATOM 3 (ELEMENT): W POSITION OF ATOM W as X,Y,Z (def=0 0 0) :0.5 0.5 0.5 ATOM 4 (ELEMENT): O POSITION OF ATOM O as X,Y,Z (def=0 0 0) :0.262 0 0 ... SPECIFY possible REDUCTION of SPHERE RADII in % (def=0) 2 ... rerun setrmt ?(y,N) (def=N): N ... username@computername:~/wiendata/Ba2ZnWO6$ cp init.struct Ba2ZnWO6.struct username@computername:~/wiendata/Ba2ZnWO6$ init_lapw -b ... username@computername:~/wiendata/Ba2ZnWO6$
Re: [Wien] Phonopy
I want to calculate the Phonon spectra of A2BB'O6, which has the Fm3m space group whose atomic position are A (0.25 0.25 0.25) B (0 0 0.5) B' (0 0 0) O (0 0 0.2376) when i create the super cell and make the displacement on that atom then it gives like this Number of non-equivalent atoms in BP.structS-001: 80 Number of non-equivalent atoms in BP.structS-002: 80 Number of non-equivalent atoms in BP.structS-003: 52 Number of non-equivalent atoms in BP.structS-004: 52 Number of non-equivalent atoms in BP.structS-005: 80 Number of non-equivalent atoms in BP.structS-006: 52 Number of non-equivalent atoms in BP.structS-007: 80 Number of non-equivalent atoms in BP.structS-008: 52 Number of non-equivalent atoms in BP.structS-009: 80 Number of non-equivalent atoms in BP.structS-010: 80 Number of non-equivalent atoms in BP.structS-011: 52 Number of non-equivalent atoms in BP.structS-012: 52 Number of non-equivalent atoms in BP.structS-013: 80 Number of non-equivalent atoms in BP.structS-014: 80 Number of non-equivalent atoms in BP.structS-015: 80 Number of non-equivalent atoms in BP.structS-016: 80 Number of non-equivalent atoms in BP.structS-017: 80 Number of non-equivalent atoms in BP.structS-018: 80 So is it required to run the scf of all the 18 structS file? The phonopy documentation [ http://atztogo.github.io/phonopy/wien2k.html ] says: /case.structS and case.structS-xxx (xxx are numbers) are the perfect supercell and the supercells with displacements, respectively. Perhaps these are renamed to case-xxx.struct and stored in case-xxx directories, then to be calculated using Wien2k./ My understanding from the above two sentences is: Yes, the scf needs to be ran for all structS-xxx files. In the case of NaCl only two structS file generate after the crating the displacement and also the same case happens in the SrTiO3. So please suggest me whether I am doing something is wrong? The 18 structS-xxx above look like they still might have been generated from the spacegroup C2/m (12) seen in the terminal output from phonopy [ http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg14199.html ] . Implied from what I said before [ http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg14200.html , http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg14219.html ], I suspect that the BP.struct that you provided as input to phonopy might not be correct. which theory used to generate the structS file? I currently don't know. However, you should be able to check the structS files, phonopy source code [ https://sourceforge.net/projects/phonopy/files/ ], or ask the phonopy users/developers [ https://lists.sourceforge.net/lists/listinfo/phonopy-users ] to determine how the displacements are made. At least in one case (i.e., LiH), I read that the atoms might just be displaced by 0.01 angstrom: http://dft-blog.natanzon.eu/2010/06/using-phonopy-with-wien2k.html Why these 18 strcutS generate in my case? While i have only four different atom. All I can currently say about that is: You gave phonopy BP.struct as input and that is what the program determined that you needed as output. Though, it could be because of GIGO [ https://en.wikipedia.org/wiki/Garbage_in,_garbage_out ]. I don't know what you used for lattice parameters, A, B, and B', but phonopy gave 5 structS-xxx for Ba2ZnWO6: A2BB'O6, where A = Ba, B = Zn, and B' = W [ http://dx.doi.org/10.1016/j.commatsci.2013.04.053 ]. username@computername:~/wiendata$ mkdir Ba2ZnWO6 username@computername:~/wiendata$ cd Ba2ZnWO6/ username@computername:~/wiendata/Ba2ZnWO6$ makestruct ... TITLE :Ba2ZnWO6 ... Would you like to enter Spacegroup or Lattice (S/L)(def=S)? S ... give SPACE GROUP as SYMBOL or NUMBER: 225 ... Units of lattice parameters (Bohr/Angstrom) (b/A) (def=ANG):A Lattice PARAMETERS as a b c (3 numbers):8.11 8.11 8.11 ANGLES BETWEEN lattice vectors, as alpha beta gamma (def=90.0 90.0 90.0):90 90 90 NUMBER INEQUEVALENT ATOMS :4 ATOM 1 (ELEMENT): Ba POSITION OF ATOM Ba as X,Y,Z (def=0 0 0) :0.25 0.25 0.25 ATOM 2 (ELEMENT): Zn POSITION OF ATOM Zn as X,Y,Z (def=0 0 0) :0 0 0 ATOM 3 (ELEMENT): W POSITION OF ATOM W as X,Y,Z (def=0 0 0) :0.5 0.5 0.5 ATOM 4 (ELEMENT): O POSITION OF ATOM O as X,Y,Z (def=0 0 0) :0.262 0 0 ... SPECIFY possible REDUCTION of SPHERE RADII in % (def=0) 2 ... rerun setrmt ?(y,N) (def=N): N ... username@computername:~/wiendata/Ba2ZnWO6$ cp init.struct Ba2ZnWO6.struct username@computername:~/wiendata/Ba2ZnWO6$ init_lapw -b ... username@computername:~/wiendata/Ba2ZnWO6$ x supercell Program generates supercell from a WIEN struct file. Filename of struct file: Ba2ZnWO6.struct Number of cells in x direction: 1 Number of cells in y direction: 1 Number of cells in z direction: 1 Optional shift all atoms by the same amount (fractional coordinates). Please enter x shift: 0 Please enter y shift: 0 Please enter z shift: 0 Current structure has lattice type F En
Re: [Wien] Phonopy
Dear Wien2k Users, I want to calculate the Phonon spectra of A2BB'O6, which has the Fm3m space group whose atomic position are A (0.25 0.25 0.25) B (0 0 0.5) B' (0 0 0) O (0 0 0.2376) when i create the super cell and make the displacement on that atom then it gives like this Number of non-equivalent atoms in BP.structS-001: 80 Number of non-equivalent atoms in BP.structS-002: 80 Number of non-equivalent atoms in BP.structS-003: 52 Number of non-equivalent atoms in BP.structS-004: 52 Number of non-equivalent atoms in BP.structS-005: 80 Number of non-equivalent atoms in BP.structS-006: 52 Number of non-equivalent atoms in BP.structS-007: 80 Number of non-equivalent atoms in BP.structS-008: 52 Number of non-equivalent atoms in BP.structS-009: 80 Number of non-equivalent atoms in BP.structS-010: 80 Number of non-equivalent atoms in BP.structS-011: 52 Number of non-equivalent atoms in BP.structS-012: 52 Number of non-equivalent atoms in BP.structS-013: 80 Number of non-equivalent atoms in BP.structS-014: 80 Number of non-equivalent atoms in BP.structS-015: 80 Number of non-equivalent atoms in BP.structS-016: 80 Number of non-equivalent atoms in BP.structS-017: 80 Number of non-equivalent atoms in BP.structS-018: 80 So is it required to run the scf of all the 18 structS file? In the case of NaCl only two structS file generate after the crating the displacement and also the same case happens in the SrTiO3. So please suggest me whether I am doing something is wrong? which theory used to generate the structS file? Why these 18 strcutS generate in my case? While i have only four different atom. Thank You On Sun, May 1, 2016 at 1:11 PM, Rajneesh Chaurasiya wrote: > Dear Gavin, > Are you sure that after changing the space group of material it will not > effect the phonon calculation. > because after changing the space group of crystal structure all the atom > position changes and calculate forces on that atoms will not be same as the > previous one space group. > I have verified this problem in your given examples of NaCl and SrTiO3. > > So can you explain this problem in more details??? > > Thank you > > On Wed, Apr 27, 2016 at 2:29 PM, Rajneesh Chaurasiya < > rajnano2...@gmail.com> wrote: > >> Dear Sir, >> >> I have computed the phonon spectrum of example of NaCl and SrTiO3 >> successfully now when i started the new calculation. in that calculation i >> construct the case.struct file and after initialization i make a supercell >> (2 2 2) and create a displacement then it change change the space group. >> initially my space group is Fm3m and after creating the displacement it >> become C2/m. I thing some thing is happening in a unusual way so any one >> can help? >> >> The procedure which i follow. >> >> makestruct.. >> cp init.struct BP.struct >> init_lapw >> phonopy --wien2k -c BP.struct -d --dim="2 2 2" >> at this steps the erorrs looks like... >> >> >> _ __ | |__ ___ _ __ ___ _ __ _ _ >> | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | | >> | |_) | | | | (_) | | | | (_) || |_) | |_| | >> | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | >> |_||_||___/ >> 1.10.0 >> >> Python version 2.7.11 >> Creating displacements >> Settings: >> Supercell: [2 2 2] >> Spacegroup: C2/m (12) >> Number of non-equivalent atoms in BP.structS-001: 80 >> Number of non-equivalent atoms in BP.structS-002: 80 >> Number of non-equivalent atoms in BP.structS-003: 52 >> Number of non-equivalent atoms in BP.structS-004: 52 >> Number of non-equivalent atoms in BP.structS-005: 80 >> Number of non-equivalent atoms in BP.structS-006: 52 >> Number of non-equivalent atoms in BP.structS-007: 80 >> Number of non-equivalent atoms in BP.structS-008: 52 >> Number of non-equivalent atoms in BP.structS-009: 80 >> Number of non-equivalent atoms in BP.structS-010: 80 >> Number of non-equivalent atoms in BP.structS-011: 52 >> Number of non-equivalent atoms in BP.structS-012: 52 >> Number of non-equivalent atoms in BP.structS-013: 80 >> Number of non-equivalent atoms in BP.structS-014: 80 >> Number of non-equivalent atoms in BP.structS-015: 80 >> Number of non-equivalent atoms in BP.structS-016: 80 >> Number of non-equivalent atoms in BP.structS-017: 80 >> Number of non-equivalent atoms in BP.structS-018: 80 >> >> disp.yaml and supercells have been created. >> _ >>___ _ __ __| | >> / _ \ '_ \ / _` | >> | __/ | | | (_| | >> \___|_| |_|\__,_| >> >> >> >> -- >> Thanks & Regards >> Rajneesh Chaurasiya >> Junior Research Fellow >> IIT,Jodhpur, India >> Mob. No. +91-9584499697 >> +91-7610950803 >> > > > > -- > Thanks & Regards > Rajneesh Chaurasiya > Junior Research Fellow > IIT,Jodhpur, India > Mob. No. +91-9584499697 > +91-7610950803 > -- Thanks & Regards Rajneesh Chaurasiya Junior Research Fellow IIT,Jodhpur, India Mob. No. +91-9584499697 +91-7610950803 ___ Wien m
Re: [Wien] Phonopy
Take NaCl for example. Its cubic unit cell (alpha = beta = gamma = 90 deg) has space group 225, a lattice constant (a = b = c) of about 5.6 ang, and two nonequivalent positions (Cl: 0, 0, 0; Na: 0.5, 0.5, 0.5) [ http://www.ilpi.com/inorganic/structures/nacl/ ]. First, do it the wrong way using the NaCl unit cell struct file having the spacegroup 225 with F lattice as the input for phonopy. You expect phonopy to give spacegroup 225 as output in the terminal. However, the wrong input (F lattice) was used for phonopy, so it gives spacegroup 221 as the output: username@computername:~/wiendata/NaCl$ sed -n 2p NaCl.struct F LATTICE,NONEQUIV.ATOMS: 2 225_Fm-3m username@computername:~/wiendata/NaCl$ phonopy --wien2k -c NaCl.struct -d --dim="2 2 2" ... Spacegroup: Pm-3m (221) Number of non-equivalent atoms in NaCl.structS-001: 8 Number of non-equivalent atoms in NaCl.structS-002: 8 ... Spacegroups can have atomic positions where atoms are free to move and others where atoms cannot move as they are fixed. The atomic positions for NaCl in the spacegroup 225 are fixed [ http://www.wien2k.at/reg_user/textbooks/WIEN2k_lecture-notes_2013/WIEN2k-getting_started.pdf (slide 36) ]. Thus, it is not possible to displace the NaCl atomic positions in the spacegroup 225 [ http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg00119.html ]. Now, do it correctly by following the instructions in phonopy documentation [ http://atztogo.github.io/phonopy/wien2k.html#wien2k-interface ]. Convert NaCl having spacegroup 225 (F lattice) to its equivalent representation in the general P lattice: username@computername:~/wiendata/NaCl$ sed -n 2p NaCl.struct F LATTICE,NONEQUIV.ATOMS: 2 225_Fm-3m username@computername:~/wiendata/NaCl$ x supercell Program generates supercell from a WIEN struct file. Filename of struct file: NaCl.struct Number of cells in x direction: 1 Number of cells in y direction: 1 Number of cells in z direction: 1 Optional shift all atoms by the same amount (fractional coordinates). Please enter x shift: 0 Please enter y shift: 0 Please enter z shift: 0 Current structure has lattice type F Enter your target lattice type: (P,B,F) P Target lattice type will be P Add vacuum in x-direction for surface-slab [bohr]: 0 Add vacuum in y-direction for surface-slab [bohr]: 0 Add vacuum in z-direction for surface slab [bohr]: 0 Supercell generated sucessfully. Stored in struct file: NaCl_super.struct You may need to replace an atom by an impurity or distort the positions, 0.0u 0.0s 0:19.31 0.0% 0+0k 0+16io 0pf+0w username@computername:~/wiendata/NaCl$ cp NaCl_super.struct NaCl.struct username@computername:~/wiendata/NaCl$ sed -n 2p NaCl.struct P LATTICE,NONEQUIV. ATOMS 8 Unlike NaCl with spacegroup 225, the 1x1x1 supercell representation of NaCl with P lattice has no spacegroup associated with it [ http://www.wien2k.at/reg_user/faq/supercells.html ]. Since the P lattice has no spacegroup, there is no longer the restriction of the 225 spacegroup that the NaCl positions are fixed. Thus, the NaCl positions are free and can be displaced in the P lattice. The initial NaCl.struct with P lattice has no displacement. Therefore, the symmetry of the supercell can be expected to reduce to the spacegroup 225. In WIEN2k, there is "x sgroup" for determining the spacegroup. However, phonopy has its own way of determining the spacegroup (note: it has a built-in symmetry finder [ https://sourceforge.net/p/phonopy/mailman/message/25001819/ ]), and it detects the expected spacegroup 225 when NaCl.struct is given in the P lattice format as input: username@computername:~/wiendata/NaCl$ phonopy --wien2k -c NaCl.struct -d --dim="2 2 2" ... Creating displacements Settings: Supercell: [2 2 2] Spacegroup: Fm-3m (225) Number of non-equivalent atoms in NaCl.structS-001: 24 Number of non-equivalent atoms in NaCl.structS-002: 24 ... Togo mentioned another reason why the spacegroup 225 case.struct file cannot be used for phonopy [ https://sourceforge.net/p/phonopy/mailman/message/26200243/ ]: /I didn't want to implement a full Wien2k structure parser, so I just decided to implement only for P1./ The files with the displacements (NaCl.structS-001 and NaCl.structS-002) of the atomic positions have the P lattice, not the spacegroup 225, as expected: username@computername:~/wiendata/NaCl$ sed -n 2p NaCl.structS-001 P LATTICE,NONEQUIV.ATOMS: 64 username@computername:~/wiendata/NaCl$ sed -n 2p NaCl.structS-002 P LATTICE,NONEQUIV.ATOMS: 64 So that looks fine. Of course, if the atomic position of an atom is displaced, that could change the forces on atoms in the structure [ https://en.wikipedia.org/wiki/Coulomb%27s_law ] and the spacegroup of the structure. Indeed, if you check NaCl.structS-001 and NaCl.structS-002, it looks like they will have spacegroup 99 (P4mm) from the output of "x sgroup". On 5/1/2016 1:41 AM, Rajneesh Chaurasiya wrote
Re: [Wien] Phonopy
Dear Gavin, Are you sure that after changing the space group of material it will not effect the phonon calculation. because after changing the space group of crystal structure all the atom position changes and calculate forces on that atoms will not be same as the previous one space group. I have verified this problem in your given examples of NaCl and SrTiO3. So can you explain this problem in more details??? Thank you On Wed, Apr 27, 2016 at 2:29 PM, Rajneesh Chaurasiya wrote: > Dear Sir, > > I have computed the phonon spectrum of example of NaCl and SrTiO3 > successfully now when i started the new calculation. in that calculation i > construct the case.struct file and after initialization i make a supercell > (2 2 2) and create a displacement then it change change the space group. > initially my space group is Fm3m and after creating the displacement it > become C2/m. I thing some thing is happening in a unusual way so any one > can help? > > The procedure which i follow. > > makestruct.. > cp init.struct BP.struct > init_lapw > phonopy --wien2k -c BP.struct -d --dim="2 2 2" > at this steps the erorrs looks like... > > > _ __ | |__ ___ _ __ ___ _ __ _ _ > | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | | > | |_) | | | | (_) | | | | (_) || |_) | |_| | > | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | > |_||_||___/ > 1.10.0 > > Python version 2.7.11 > Creating displacements > Settings: > Supercell: [2 2 2] > Spacegroup: C2/m (12) > Number of non-equivalent atoms in BP.structS-001: 80 > Number of non-equivalent atoms in BP.structS-002: 80 > Number of non-equivalent atoms in BP.structS-003: 52 > Number of non-equivalent atoms in BP.structS-004: 52 > Number of non-equivalent atoms in BP.structS-005: 80 > Number of non-equivalent atoms in BP.structS-006: 52 > Number of non-equivalent atoms in BP.structS-007: 80 > Number of non-equivalent atoms in BP.structS-008: 52 > Number of non-equivalent atoms in BP.structS-009: 80 > Number of non-equivalent atoms in BP.structS-010: 80 > Number of non-equivalent atoms in BP.structS-011: 52 > Number of non-equivalent atoms in BP.structS-012: 52 > Number of non-equivalent atoms in BP.structS-013: 80 > Number of non-equivalent atoms in BP.structS-014: 80 > Number of non-equivalent atoms in BP.structS-015: 80 > Number of non-equivalent atoms in BP.structS-016: 80 > Number of non-equivalent atoms in BP.structS-017: 80 > Number of non-equivalent atoms in BP.structS-018: 80 > > disp.yaml and supercells have been created. > _ >___ _ __ __| | > / _ \ '_ \ / _` | > | __/ | | | (_| | > \___|_| |_|\__,_| > > > > -- > Thanks & Regards > Rajneesh Chaurasiya > Junior Research Fellow > IIT,Jodhpur, India > Mob. No. +91-9584499697 > +91-7610950803 > -- Thanks & Regards Rajneesh Chaurasiya Junior Research Fellow IIT,Jodhpur, India Mob. No. +91-9584499697 +91-7610950803 ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Phonopy
initially my space group is Fm3m => Phonopy needs case.struct with P lattice to work correctly [1, 2]. [1] https://sourceforge.net/p/phonopy/mailman/message/25001819/ [2] http://atztogo.github.io/phonopy/wien2k.html On 4/27/2016 2:59 AM, Rajneesh Chaurasiya wrote: Dear Sir, I have computed the phonon spectrum of example of NaCl and SrTiO3 successfully now when i started the new calculation. in that calculation i construct the case.struct file and after initialization i make a supercell (2 2 2) and create a displacement then it change change the space group. initially my space group is Fm3m and after creating the displacement it become C2/m. I thing some thing is happening in a unusual way so any one can help? The procedure which i follow. makestruct.. cp init.struct BP.struct init_lapw phonopy --wien2k -c BP.struct -d --dim="2 2 2" at this steps the erorrs looks like... _ __ | |__ ___ _ __ ___ _ __ _ _ | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | | | |_) | | | | (_) | | | | (_) || |_) | |_| | | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | |_||_||___/ 1.10.0 Python version 2.7.11 Creating displacements Settings: Supercell: [2 2 2] Spacegroup: C2/m (12) Number of non-equivalent atoms in BP.structS-001: 80 Number of non-equivalent atoms in BP.structS-002: 80 Number of non-equivalent atoms in BP.structS-003: 52 Number of non-equivalent atoms in BP.structS-004: 52 Number of non-equivalent atoms in BP.structS-005: 80 Number of non-equivalent atoms in BP.structS-006: 52 Number of non-equivalent atoms in BP.structS-007: 80 Number of non-equivalent atoms in BP.structS-008: 52 Number of non-equivalent atoms in BP.structS-009: 80 Number of non-equivalent atoms in BP.structS-010: 80 Number of non-equivalent atoms in BP.structS-011: 52 Number of non-equivalent atoms in BP.structS-012: 52 Number of non-equivalent atoms in BP.structS-013: 80 Number of non-equivalent atoms in BP.structS-014: 80 Number of non-equivalent atoms in BP.structS-015: 80 Number of non-equivalent atoms in BP.structS-016: 80 Number of non-equivalent atoms in BP.structS-017: 80 Number of non-equivalent atoms in BP.structS-018: 80 disp.yaml and supercells have been created. _ ___ _ __ __| | / _ \ '_ \ / _` | | __/ | | | (_| | \___|_| |_|\__,_| -- Thanks & Regards Rajneesh Chaurasiya Junior Research Fellow IIT,Jodhpur, India Mob. No. +91-9584499697 +91-7610950803 ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] Phonopy
Dear Sir, I have computed the phonon spectrum of example of NaCl and SrTiO3 successfully now when i started the new calculation. in that calculation i construct the case.struct file and after initialization i make a supercell (2 2 2) and create a displacement then it change change the space group. initially my space group is Fm3m and after creating the displacement it become C2/m. I thing some thing is happening in a unusual way so any one can help? The procedure which i follow. makestruct.. cp init.struct BP.struct init_lapw phonopy --wien2k -c BP.struct -d --dim="2 2 2" at this steps the erorrs looks like... _ __ | |__ ___ _ __ ___ _ __ _ _ | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | | | |_) | | | | (_) | | | | (_) || |_) | |_| | | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | |_||_||___/ 1.10.0 Python version 2.7.11 Creating displacements Settings: Supercell: [2 2 2] Spacegroup: C2/m (12) Number of non-equivalent atoms in BP.structS-001: 80 Number of non-equivalent atoms in BP.structS-002: 80 Number of non-equivalent atoms in BP.structS-003: 52 Number of non-equivalent atoms in BP.structS-004: 52 Number of non-equivalent atoms in BP.structS-005: 80 Number of non-equivalent atoms in BP.structS-006: 52 Number of non-equivalent atoms in BP.structS-007: 80 Number of non-equivalent atoms in BP.structS-008: 52 Number of non-equivalent atoms in BP.structS-009: 80 Number of non-equivalent atoms in BP.structS-010: 80 Number of non-equivalent atoms in BP.structS-011: 52 Number of non-equivalent atoms in BP.structS-012: 52 Number of non-equivalent atoms in BP.structS-013: 80 Number of non-equivalent atoms in BP.structS-014: 80 Number of non-equivalent atoms in BP.structS-015: 80 Number of non-equivalent atoms in BP.structS-016: 80 Number of non-equivalent atoms in BP.structS-017: 80 Number of non-equivalent atoms in BP.structS-018: 80 disp.yaml and supercells have been created. _ ___ _ __ __| | / _ \ '_ \ / _` | | __/ | | | (_| | \___|_| |_|\__,_| -- Thanks & Regards Rajneesh Chaurasiya Junior Research Fellow IIT,Jodhpur, India Mob. No. +91-9584499697 +91-7610950803 ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] Phonopy
Dear Sir, I have computed the phonon spectrum of example of NaCl and SrTiO3 successfully now when i started the new calculation. in that calculation i construct the case.struct file and after initialization i make a supercell (2 2 2) and create a displacement then it change change the space group. initially my space group is Fm3m and after creating the displacement it become C2/m. I thing some thing is happening in a unusual way so any one can help? The procedure which i follow. makestruct.. cp init.struct BP.struct init_lapw phonopy --wien2k -c BP.struct -d --dim="2 2 2" at this steps the erorrs looks like... -- Thanks & Regards Rajneesh Chaurasiya Junior Research Fellow IIT,Jodhpur, India Mob. No. +91-9584499697 +91-7610950803 ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] phonopy
Dear gavin, I have modified the .bashrc file, which i am attaching through this mail and also the some one image file which contains the file inside the python folder. please find the attached files and give your suggestions.. bashrc Description: Binary data ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] PHONOPY and symmetry
Dear WIEN2k community, I am trying to use PHONOPY to calculate phonon dispersion curves for InP in the zincblend phase as a test. I used an optimized structural parameter to build a 3x3x3 supercell using the "supercell" utility program. After that, PHONOPY built two other supercells displacing atoms 1 and 109 by 0.02 Bohr along x direction. Now, it is important to say that PHONOPY works with P1 symmetry, what means I can use the new cell suggested by "nn", but not the one suggested by "sgroup" during initialization. Everything went smoothly when I initialized the calculation for the first supercell (that one with displacement for atom 1) accepting twice the cell generated by "nn", but I got the following error message for the second cell (that one with displacement for atom 109). Finally, I would like to mention that if I accept the cell suggested by "sgroup", everything goes fine for the second cell, but this is not suitable for PHONOPY as mentioned above. I would appreciate any help with this issue. The case.struct is too big for the mailing list (64 KB), but I can send it to the personal e-mail of anyone interested in. The error message is at the end of this message. All the best, Luis -- ERROR -- ERROR: (multiplicity of atom 31 )*(number of pointgroup-operations) ERROR: is NOT = (number of spacegroup-operations) ERROR: MULT: 2 ISYM: 1 NSYM 4 ERROR: Check your struct file withx sgroup -- ERROR -- -- ERROR -- ERROR: (multiplicity of atom 32 )*(number of pointgroup-operations) ERROR: is NOT = (number of spacegroup-operations) ERROR: MULT: 2 ISYM: 1 NSYM 4 ERROR: Check your struct file withx sgroup -- ERROR -- -- ERROR -- ERROR: (multiplicity of atom 33 )*(number of pointgroup-operations) ERROR: is NOT = (number of spacegroup-operations) ERROR: MULT: 2 ISYM: 1 NSYM 4 ERROR: Check your struct file withx sgroup -- ERROR -- -- ERROR -- ERROR: (multiplicity of atom 37 )*(number of pointgroup-operations) ERROR: is NOT = (number of spacegroup-operations) ERROR: MULT: 1 ISYM: 2 NSYM 4 ERROR: Check your struct file withx sgroup -- ERROR -- -- ERROR -- ERROR: (multiplicity of atom 38 )*(number of pointgroup-operations) ERROR: is NOT = (number of spacegroup-operations) ERROR: MULT: 1 ISYM: 2 NSYM 4 ERROR: Check your struct file withx sgroup -- ERROR -- -- ERROR -- ERROR: (multiplicity of atom 39 )*(number of pointgroup-operations) ERROR: is NOT = (number of spacegroup-operations) ERROR: MULT: 1 ISYM: 2 NSYM 4 ERROR: Check your struct file withx sgroup -- ERROR -- -- ERROR -- ERROR: (multiplicity of atom 52 )*(number of pointgroup-operations) ERROR: is NOT = (number of spacegroup-operations) ERROR: MULT: 2 ISYM: 1 NSYM 4 ERROR: Check your struct file withx sgroup -- ERROR -- -- ERROR -- ERROR: (multiplicity of atom 53 )*(number of pointgroup-operations) ERROR: is NOT = (number of spacegroup-operations) ERROR: MULT: 2 ISYM: 1 NSYM 4 ERROR: Check your struct file withx sgroup -- ERROR -- -- ERROR -- ERROR: (multiplicity of atom 54 )*(number of pointgroup-operations) ERROR: is NOT = (number of spacegroup-operations) ERROR: MULT: 2 ISYM: 1 NSYM 4 ERROR: Check your struct file withx sgroup -- ERROR -- -- ERROR -- ERROR: (multiplicity of atom 63 )*(number of pointgroup-operations) ERROR: is NOT = (number of spacegroup-operations) ERROR: MULT: 1 ISYM: 2 NSYM 4 ERROR: Check your struct file withx sgroup -- ERROR -- -- ERROR -- ERROR: (multiplicity of atom 64 )*(number of pointgroup-operations) ERROR: is NOT = (number of spacegroup-operations) ERROR: MULT: 1 ISYM: 2 NSYM 4 ERROR: Check your struct file withx sgroup -- ERROR -- -- ERROR -- ERROR: (multiplicity of atom 65 )*(number of pointgroup-operations) ERROR: is NOT = (number of spacegroup-operations) ERROR: