Re: [Phonopy-users] Phonon dispersion of graphene From: Atsushi Togo - 2013-09-01 12:30:33 ```Hi, Without watching your band structure, it is difficult to guess what your problem is. Togo On Sun, Sep 1, 2013 at 6:32 PM, Yang Ming wrote: > Dear All, > > > > I am new in Phonopy. I was just using Phonopy to calculate phonon dispersion > of graphene for testing, but the results are incorrect (negative frequencies > were found). Could anyone there help to check my inputs below? > > > > > > Basically, I followed the Phonopy tutorial for VASP step by step: > > > > 1. Generate a 6×6×1 supercell from below bulk by using the commad: > phonopy –d –dim="6 6 1". > > > > C > > 1.00000000000000 > > 2.1304215583187101 -1.2299994601826900 0.0000000000000000 > > 0.0000000000000000 2.4599989203653800 0.0000000000000000 > > 0.0000000000000000 0.0000000000000000 12.0000000000000000 > > 2 > > Direct > > 0.0000000000000000 0.0000000000000000 0.5000000000000000 > > 0.6666666699999979 0.3333333300000021 0.5000000000000000 > > > > 2. Calculate the force using the generated structure POSCAR-001 and > standard VASP setting: > > > > ENCUT = 400 > > ISMEAR = 0; SIGMA = 0.01 > > PREC = A > > > > EDIFF = 1.0E-8 > > NELM = 400 > > > > IDIPOL = 3 > > > > LWAVE = .F. > > LCHARG = .F. > > LREAL = .F. > > NPAR = 2 > > NELMDL = -5 > > LPLANE = .T. > > > > The KPOINTS for VASP calculation were set to 3×3×1. > > > > 3. Create the FORCE_SETS by using: phonopy –f disp-001/vasprun.xml > > 4. > > 5. Phonon band structure was calculated by using the band.conf like > below: > > > > ATOM_NAME = C > > DIM = 6 6 1 > > BAND = 0.0 0.5 0.0 0.0 0.0 0.0 -0.3333 0.6667 0.0 0.0 0.5 0.0 > > 6. Plot the band structure by using: phonopy –p band.conf > > > > After all these steps, I found some negative frequencies and the values of > the related frequencies are not consistent with those of previous results > also. I doule-checked the calculation processes, but don’t know the problem. > > > > Thank you a lot for your time, and any comments are appreciated. > > > > Best regards, > > Yang Ming > > ****** > > Computational Condensed-Matter Physics Lab > > Department of Physics > > National University of Singapore > > Singapore 117542 > > Email: phyym@...; ming_young@... > > Tel: +65 6516 4335 (office) > > > > > ------------------------------------------------------------------------------ > Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! > Discover the easy way to master current and previous Microsoft technologies > and advance your career. Get an incredible 1,500+ hours of step-by-step > tutorial videos with LearnDevNow. Subscribe today and save! > http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.clktrk > _______________________________________________ > Phonopy-users mailing list > Phonopy-users@... > https://lists.sourceforge.net/lists/listinfo/phonopy-users > -- Atsushi Togo http://atztogo.github.com/ atz.togo@... ```
 Re: [Phonopy-users] Phonon dispersion of graphene From: Atsushi Togo - 2013-09-01 13:43:49 Attachments: band-graphene-small.jpg ```Hi, Your band structure is really broken. I doubt your setting of ISMEAR = 0; SIGMA = 0.01, and few k-points though I don't know how much it affect to phonons. So I recommend you to check carefully about VASP setting, e.g. by drawing electronic band structure. If you don't know well about electronic structure calculations, you may ask it to your colleagues. Togo On Sun, Sep 1, 2013 at 10:21 PM, Yang Ming wrote: > Dear Dr. Togo, > > Thanks a lot for the prompt reply. > > Please find the attached data and calculated eigenvalue. > > Thanks. > > Best regards, > Yang Ming > ****** > Computational Condensed-Matter Physics Lab > Department of Physics > National University of Singapore > Singapore 117542 > Email: phyym@...; ming_young@... > Tel: +65 6516 4335 (office) > > -----Original Message----- > From: Atsushi Togo [mailto:atz.togo@...] > Sent: Sunday, 1 September, 2013 8:30 PM > To: Yang Ming > Cc: phonopy-users@... > Subject: Re: [Phonopy-users] Phonon dispersion of graphene > > Hi, > > Without watching your band structure, it is difficult to guess what your problem is. > > Togo > > On Sun, Sep 1, 2013 at 6:32 PM, Yang Ming wrote: >> Dear All, >> >> >> >> I am new in Phonopy. I was just using Phonopy to calculate phonon >> dispersion of graphene for testing, but the results are incorrect >> (negative frequencies were found). Could anyone there help to check my inputs below? >> >> >> >> >> >> Basically, I followed the Phonopy tutorial for VASP step by step: >> >> >> >> 1. Generate a 6×6×1 supercell from below bulk by using the commad: >> phonopy -d -dim="6 6 1". >> >> >> >> C >> >> 1.00000000000000 >> >> 2.1304215583187101 -1.2299994601826900 0.0000000000000000 >> >> 0.0000000000000000 2.4599989203653800 0.0000000000000000 >> >> 0.0000000000000000 0.0000000000000000 12.0000000000000000 >> >> 2 >> >> Direct >> >> 0.0000000000000000 0.0000000000000000 0.5000000000000000 >> >> 0.6666666699999979 0.3333333300000021 0.5000000000000000 >> >> >> >> 2. Calculate the force using the generated structure POSCAR-001 and >> standard VASP setting: >> >> >> >> ENCUT = 400 >> >> ISMEAR = 0; SIGMA = 0.01 >> >> PREC = A >> >> >> >> EDIFF = 1.0E-8 >> >> NELM = 400 >> >> >> >> IDIPOL = 3 >> >> >> >> LWAVE = .F. >> >> LCHARG = .F. >> >> LREAL = .F. >> >> NPAR = 2 >> >> NELMDL = -5 >> >> LPLANE = .T. >> >> >> >> The KPOINTS for VASP calculation were set to 3×3×1. >> >> >> >> 3. Create the FORCE_SETS by using: phonopy -f disp-001/vasprun.xml >> >> 4. >> >> 5. Phonon band structure was calculated by using the band.conf like >> below: >> >> >> >> ATOM_NAME = C >> >> DIM = 6 6 1 >> >> BAND = 0.0 0.5 0.0 0.0 0.0 0.0 -0.3333 0.6667 0.0 0.0 0.5 0.0 >> >> 6. Plot the band structure by using: phonopy -p band.conf >> >> >> >> After all these steps, I found some negative frequencies and the >> values of the related frequencies are not consistent with those of >> previous results also. I doule-checked the calculation processes, but don't know the problem. >> >> >> >> Thank you a lot for your time, and any comments are appreciated. >> >> >> >> Best regards, >> >> Yang Ming >> >> ****** >> >> Computational Condensed-Matter Physics Lab >> >> Department of Physics >> >> National University of Singapore >> >> Singapore 117542 >> >> Email: phyym@...; ming_young@... >> >> Tel: +65 6516 4335 (office) >> >> >> >> >> ---------------------------------------------------------------------- >> -------- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL >> 2012, more! >> Discover the easy way to master current and previous Microsoft >> technologies and advance your career. Get an incredible 1,500+ hours >> of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! >> http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.c >> lktrk _______________________________________________ >> Phonopy-users mailing list >> Phonopy-users@... >> https://lists.sourceforge.net/lists/listinfo/phonopy-users >> > > > > -- > Atsushi Togo > http://atztogo.github.com/ > atz.togo@... -- Atsushi Togo http://atztogo.github.com/ atz.togo@... ```
 Re: [Phonopy-users] Phonon dispersion of graphene From: Yang Ming - 2013-09-03 03:03:06 Attachments: band strucutre of graphene.opj ```Dear Prof. Togo, Thank you so much for the kind reply. I just checked the KPOINTS and the INCAR setting, which are correct for the electronic structure (see the band structure attached). Actually, I also increased denser k-point meshes (18×18×1), and also changed the INCAR setting (ENCUT =500, ISMEAR=-5, EDIFF=1.0E-8, and ADDGRID = .True) , but still got negative frequencies. Let me show you my calculation processes again below, and please help me to check the problems and let me know if the settings are incorrect: 1. Generate a 6×6×1 supercell from below bulk by using the commad: phonopy -d -dim="6 6 1". 2. Calculate the force using the generated structure POSCAR-001 and standard VASP setting. 3. Create the FORCE_SETS by using: phonopy -f disp-001/vasprun.xml 4 Phonon band structure was calculated by using the band.conf like below: ATOM_NAME = C DIM = 6 6 1 BAND = 0.0 0.5 0.0 0.0 0.0 0.0 -0.3333 0.6667 0.0 0.0 0.5 0.0 5. Plot the band structure by using: phonopy -p band.conf Thanks a lot. Best regards, Yang Ming ****** Computational Condensed-Matter Physics Lab Department of Physics National University of Singapore Singapore 117542 Email: phyym@...; ming_young@... Tel: +65 6516 4335 (office) -----Original Message----- From: Yang Ming Sent: Sunday, 1 September, 2013 9:22 PM To: 'Atsushi Togo' Subject: RE: [Phonopy-users] Phonon dispersion of graphene Dear Dr. Togo, Thanks a lot for the prompt reply. Please find the attached data and calculated eigenvalue. Thanks. Best regards, Yang Ming ****** Computational Condensed-Matter Physics Lab Department of Physics National University of Singapore Singapore 117542 Email: phyym@...; ming_young@... Tel: +65 6516 4335 (office) -----Original Message----- From: Atsushi Togo [mailto:atz.togo@...] Sent: Sunday, 1 September, 2013 8:30 PM To: Yang Ming Cc: phonopy-users@... Subject: Re: [Phonopy-users] Phonon dispersion of graphene Hi, Without watching your band structure, it is difficult to guess what your problem is. Togo On Sun, Sep 1, 2013 at 6:32 PM, Yang Ming wrote: > Dear All, > > > > I am new in Phonopy. I was just using Phonopy to calculate phonon > dispersion of graphene for testing, but the results are incorrect > (negative frequencies were found). Could anyone there help to check my inputs below? > > > > > > Basically, I followed the Phonopy tutorial for VASP step by step: > > > > 1. Generate a 6×6×1 supercell from below bulk by using the commad: > phonopy -d -dim="6 6 1". > > > > C > > 1.00000000000000 > > 2.1304215583187101 -1.2299994601826900 0.0000000000000000 > > 0.0000000000000000 2.4599989203653800 0.0000000000000000 > > 0.0000000000000000 0.0000000000000000 12.0000000000000000 > > 2 > > Direct > > 0.0000000000000000 0.0000000000000000 0.5000000000000000 > > 0.6666666699999979 0.3333333300000021 0.5000000000000000 > > > > 2. Calculate the force using the generated structure POSCAR-001 and > standard VASP setting: > > > > ENCUT = 400 > > ISMEAR = 0; SIGMA = 0.01 > > PREC = A > > > > EDIFF = 1.0E-8 > > NELM = 400 > > > > IDIPOL = 3 > > > > LWAVE = .F. > > LCHARG = .F. > > LREAL = .F. > > NPAR = 2 > > NELMDL = -5 > > LPLANE = .T. > > > > The KPOINTS for VASP calculation were set to 3×3×1. > > > > 3. Create the FORCE_SETS by using: phonopy -f disp-001/vasprun.xml > > 4. > > 5. Phonon band structure was calculated by using the band.conf like > below: > > > > ATOM_NAME = C > > DIM = 6 6 1 > > BAND = 0.0 0.5 0.0 0.0 0.0 0.0 -0.3333 0.6667 0.0 0.0 0.5 0.0 > > 6. Plot the band structure by using: phonopy -p band.conf > > > > After all these steps, I found some negative frequencies and the > values of the related frequencies are not consistent with those of > previous results also. I doule-checked the calculation processes, but don't know the problem. > > > > Thank you a lot for your time, and any comments are appreciated. > > > > Best regards, > > Yang Ming > > ****** > > Computational Condensed-Matter Physics Lab > > Department of Physics > > National University of Singapore > > Singapore 117542 > > Email: phyym@...; ming_young@... > > Tel: +65 6516 4335 (office) > > > > > ---------------------------------------------------------------------- > -------- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL > 2012, more! > Discover the easy way to master current and previous Microsoft > technologies and advance your career. Get an incredible 1,500+ hours > of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! > http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.c > lktrk _______________________________________________ > Phonopy-users mailing list > Phonopy-users@... > https://lists.sourceforge.net/lists/listinfo/phonopy-users > -- Atsushi Togo http://atztogo.github.com/ atz.togo@... ```
 Re: [Phonopy-users] Phonon dispersion of graphene From: Atsushi Togo - 2013-09-03 05:04:57 ```Hi, Now I think your problem is not in phonopy but VASP. From vasp web site, For the calculation of the total energy in bulk materials we recommend the tetrahedron method with Blöchl corrections (ISMEAR=-5). This method also gives a smooth nice electronic density of states (DOS). The only drawback is that the methods is not variational with respect to the partial occupancies, therefore the calculated forces might be wrong by a few percent for metals. For the calculation of phonon frequencies based on forces we recommend the method of Methfessel-Paxton (ISMEAR>0). For semiconductors and insulators the forces are always correct, because partial occupancies do not vary! So you can read VASP manual carefully before asking VASP questions to the phonopy mailing list or you can ask them at the VASP forum. Togo On Tue, Sep 3, 2013 at 12:02 PM, Yang Ming wrote: > Dear Prof. Togo, > > Thank you so much for the kind reply. > > I just checked the KPOINTS and the INCAR setting, which are correct for the electronic structure (see the band structure attached). > > Actually, I also increased denser k-point meshes (18×18×1), and also changed the INCAR setting (ENCUT =500, ISMEAR=-5, EDIFF=1.0E-8, and ADDGRID = .True) , but still got negative frequencies. > > Let me show you my calculation processes again below, and please help me to check the problems and let me know if the settings are incorrect: > > 1. Generate a 6×6×1 supercell from below bulk by using the commad: phonopy -d -dim="6 6 1". > > 2. Calculate the force using the generated structure POSCAR-001 and standard VASP setting. > > 3. Create the FORCE_SETS by using: phonopy -f disp-001/vasprun.xml > > 4 Phonon band structure was calculated by using the band.conf like below: > > ATOM_NAME = C > DIM = 6 6 1 > BAND = 0.0 0.5 0.0 0.0 0.0 0.0 -0.3333 0.6667 0.0 0.0 0.5 0.0 > > 5. Plot the band structure by using: phonopy -p band.conf > > > Thanks a lot. > Best regards, > Yang Ming > ****** > Computational Condensed-Matter Physics Lab > Department of Physics > National University of Singapore > Singapore 117542 > Email: phyym@...; ming_young@... > Tel: +65 6516 4335 (office) > > > -----Original Message----- > From: Yang Ming > Sent: Sunday, 1 September, 2013 9:22 PM > To: 'Atsushi Togo' > Subject: RE: [Phonopy-users] Phonon dispersion of graphene > > Dear Dr. Togo, > > Thanks a lot for the prompt reply. > > Please find the attached data and calculated eigenvalue. > > Thanks. > > Best regards, > Yang Ming > ****** > Computational Condensed-Matter Physics Lab Department of Physics National University of Singapore Singapore 117542 > Email: phyym@...; ming_young@... > Tel: +65 6516 4335 (office) > > -----Original Message----- > From: Atsushi Togo [mailto:atz.togo@...] > Sent: Sunday, 1 September, 2013 8:30 PM > To: Yang Ming > Cc: phonopy-users@... > Subject: Re: [Phonopy-users] Phonon dispersion of graphene > > Hi, > > Without watching your band structure, it is difficult to guess what your problem is. > > Togo > > On Sun, Sep 1, 2013 at 6:32 PM, Yang Ming wrote: >> Dear All, >> >> >> >> I am new in Phonopy. I was just using Phonopy to calculate phonon >> dispersion of graphene for testing, but the results are incorrect >> (negative frequencies were found). Could anyone there help to check my inputs below? >> >> >> >> >> >> Basically, I followed the Phonopy tutorial for VASP step by step: >> >> >> >> 1. Generate a 6×6×1 supercell from below bulk by using the commad: >> phonopy -d -dim="6 6 1". >> >> >> >> C >> >> 1.00000000000000 >> >> 2.1304215583187101 -1.2299994601826900 0.0000000000000000 >> >> 0.0000000000000000 2.4599989203653800 0.0000000000000000 >> >> 0.0000000000000000 0.0000000000000000 12.0000000000000000 >> >> 2 >> >> Direct >> >> 0.0000000000000000 0.0000000000000000 0.5000000000000000 >> >> 0.6666666699999979 0.3333333300000021 0.5000000000000000 >> >> >> >> 2. Calculate the force using the generated structure POSCAR-001 and >> standard VASP setting: >> >> >> >> ENCUT = 400 >> >> ISMEAR = 0; SIGMA = 0.01 >> >> PREC = A >> >> >> >> EDIFF = 1.0E-8 >> >> NELM = 400 >> >> >> >> IDIPOL = 3 >> >> >> >> LWAVE = .F. >> >> LCHARG = .F. >> >> LREAL = .F. >> >> NPAR = 2 >> >> NELMDL = -5 >> >> LPLANE = .T. >> >> >> >> The KPOINTS for VASP calculation were set to 3×3×1. >> >> >> >> 3. Create the FORCE_SETS by using: phonopy -f disp-001/vasprun.xml >> >> 4. >> >> 5. Phonon band structure was calculated by using the band.conf like >> below: >> >> >> >> ATOM_NAME = C >> >> DIM = 6 6 1 >> >> BAND = 0.0 0.5 0.0 0.0 0.0 0.0 -0.3333 0.6667 0.0 0.0 0.5 0.0 >> >> 6. Plot the band structure by using: phonopy -p band.conf >> >> >> >> After all these steps, I found some negative frequencies and the >> values of the related frequencies are not consistent with those of >> previous results also. I doule-checked the calculation processes, but don't know the problem. >> >> >> >> Thank you a lot for your time, and any comments are appreciated. >> >> >> >> Best regards, >> >> Yang Ming >> >> ****** >> >> Computational Condensed-Matter Physics Lab >> >> Department of Physics >> >> National University of Singapore >> >> Singapore 117542 >> >> Email: phyym@...; ming_young@... >> >> Tel: +65 6516 4335 (office) >> >> >> >> >> ---------------------------------------------------------------------- >> -------- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL >> 2012, more! >> Discover the easy way to master current and previous Microsoft >> technologies and advance your career. Get an incredible 1,500+ hours >> of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! >> http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.c >> lktrk _______________________________________________ >> Phonopy-users mailing list >> Phonopy-users@... >> https://lists.sourceforge.net/lists/listinfo/phonopy-users >> > > > > -- > Atsushi Togo > http://atztogo.github.com/ > atz.togo@... -- Atsushi Togo http://atztogo.github.com/ atz.togo@... ```
 Re: [Phonopy-users] Phonon dispersion of graphene From: Atsushi Togo - 2013-09-03 07:26:24 Attachments: graphene.jpg ```And just as an example, I attach a graphene band structure that I calculated just now. As we can see, the acoustic modes are very soft, in this case the structure optimization is better to be done by the supercell though I didn't in this calculation. Then, I don't (can't) describe all about my VASP settings (please don't ask me about VASP), but some are shown as follows: For the structure optimization of theunit cell, INCAR: PREC = Accurate IBRION = 2 NSW = 20 NELMIN = 5 ISIF = 3 ENCUT = 500 EDIFF = 1.000000e-08 EDIFFG = -1.000000e-08 ISMEAR = 1 SIGMA = 2.000000e-01 IALGO = 38 LREAL = .FALSE. ADDGRID = .TRUE. LWAVE = .FALSE. LCHARG = .FALSE. KPOINTS: Automatic mesh 0 Monkhorst-pack 12 12 1 0.500 0.500 0.000 For force calculations of supercells, INCAR: PREC = Accurate IBRION = -1 NELMIN = 5 ENCUT = 500 EDIFF = 1.000000e-08 ISMEAR = 1 SIGMA = 2.000000e-01 IALGO = 38 LREAL = .FALSE. ADDGRID = .TRUE. LWAVE = .FALSE. LCHARG = .FALSE. NPAR = 4 KPOINTS: Automatic mesh 0 Monkhorst-pack 2 2 1 0.500 0.500 0.000 phonopy: % phonopy --dim="6 6 1" --band="0 1/2 0 0 0 0 -1/3 2/3 0 0 1/2 0" -p -c POSCAR-unitcell Togo On Tue, Sep 3, 2013 at 2:04 PM, Atsushi Togo wrote: > Hi, > > Now I think your problem is not in phonopy but VASP. From vasp web site, > > For the calculation of the total energy in bulk materials we recommend > the tetrahedron method with Blöchl corrections (ISMEAR=-5). This > method also gives a smooth nice electronic density of states (DOS). > The only drawback is that the methods is not variational with respect > to the partial occupancies, therefore the calculated forces might be > wrong by a few percent for metals. For the calculation of phonon > frequencies based on forces we recommend the method of > Methfessel-Paxton (ISMEAR>0). For semiconductors and insulators the > forces are always correct, because partial occupancies do not vary! > > So you can read VASP manual carefully before asking VASP questions to > the phonopy mailing list or you can ask them at the VASP forum. > > Togo > > On Tue, Sep 3, 2013 at 12:02 PM, Yang Ming wrote: >> Dear Prof. Togo, >> >> Thank you so much for the kind reply. >> >> I just checked the KPOINTS and the INCAR setting, which are correct for the electronic structure (see the band structure attached). >> >> Actually, I also increased denser k-point meshes (18×18×1), and also changed the INCAR setting (ENCUT =500, ISMEAR=-5, EDIFF=1.0E-8, and ADDGRID = .True) , but still got negative frequencies. >> >> Let me show you my calculation processes again below, and please help me to check the problems and let me know if the settings are incorrect: >> >> 1. Generate a 6×6×1 supercell from below bulk by using the commad: phonopy -d -dim="6 6 1". >> >> 2. Calculate the force using the generated structure POSCAR-001 and standard VASP setting. >> >> 3. Create the FORCE_SETS by using: phonopy -f disp-001/vasprun.xml >> >> 4 Phonon band structure was calculated by using the band.conf like below: >> >> ATOM_NAME = C >> DIM = 6 6 1 >> BAND = 0.0 0.5 0.0 0.0 0.0 0.0 -0.3333 0.6667 0.0 0.0 0.5 0.0 >> >> 5. Plot the band structure by using: phonopy -p band.conf >> >> >> Thanks a lot. >> Best regards, >> Yang Ming >> ****** >> Computational Condensed-Matter Physics Lab >> Department of Physics >> National University of Singapore >> Singapore 117542 >> Email: phyym@...; ming_young@... >> Tel: +65 6516 4335 (office) >> >> >> -----Original Message----- >> From: Yang Ming >> Sent: Sunday, 1 September, 2013 9:22 PM >> To: 'Atsushi Togo' >> Subject: RE: [Phonopy-users] Phonon dispersion of graphene >> >> Dear Dr. Togo, >> >> Thanks a lot for the prompt reply. >> >> Please find the attached data and calculated eigenvalue. >> >> Thanks. >> >> Best regards, >> Yang Ming >> ****** >> Computational Condensed-Matter Physics Lab Department of Physics National University of Singapore Singapore 117542 >> Email: phyym@...; ming_young@... >> Tel: +65 6516 4335 (office) >> >> -----Original Message----- >> From: Atsushi Togo [mailto:atz.togo@...] >> Sent: Sunday, 1 September, 2013 8:30 PM >> To: Yang Ming >> Cc: phonopy-users@... >> Subject: Re: [Phonopy-users] Phonon dispersion of graphene >> >> Hi, >> >> Without watching your band structure, it is difficult to guess what your problem is. >> >> Togo >> >> On Sun, Sep 1, 2013 at 6:32 PM, Yang Ming wrote: >>> Dear All, >>> >>> >>> >>> I am new in Phonopy. I was just using Phonopy to calculate phonon >>> dispersion of graphene for testing, but the results are incorrect >>> (negative frequencies were found). Could anyone there help to check my inputs below? >>> >>> >>> >>> >>> >>> Basically, I followed the Phonopy tutorial for VASP step by step: >>> >>> >>> >>> 1. Generate a 6×6×1 supercell from below bulk by using the commad: >>> phonopy -d -dim="6 6 1". >>> >>> >>> >>> C >>> >>> 1.00000000000000 >>> >>> 2.1304215583187101 -1.2299994601826900 0.0000000000000000 >>> >>> 0.0000000000000000 2.4599989203653800 0.0000000000000000 >>> >>> 0.0000000000000000 0.0000000000000000 12.0000000000000000 >>> >>> 2 >>> >>> Direct >>> >>> 0.0000000000000000 0.0000000000000000 0.5000000000000000 >>> >>> 0.6666666699999979 0.3333333300000021 0.5000000000000000 >>> >>> >>> >>> 2. Calculate the force using the generated structure POSCAR-001 and >>> standard VASP setting: >>> >>> >>> >>> ENCUT = 400 >>> >>> ISMEAR = 0; SIGMA = 0.01 >>> >>> PREC = A >>> >>> >>> >>> EDIFF = 1.0E-8 >>> >>> NELM = 400 >>> >>> >>> >>> IDIPOL = 3 >>> >>> >>> >>> LWAVE = .F. >>> >>> LCHARG = .F. >>> >>> LREAL = .F. >>> >>> NPAR = 2 >>> >>> NELMDL = -5 >>> >>> LPLANE = .T. >>> >>> >>> >>> The KPOINTS for VASP calculation were set to 3×3×1. >>> >>> >>> >>> 3. Create the FORCE_SETS by using: phonopy -f disp-001/vasprun.xml >>> >>> 4. >>> >>> 5. Phonon band structure was calculated by using the band.conf like >>> below: >>> >>> >>> >>> ATOM_NAME = C >>> >>> DIM = 6 6 1 >>> >>> BAND = 0.0 0.5 0.0 0.0 0.0 0.0 -0.3333 0.6667 0.0 0.0 0.5 0.0 >>> >>> 6. Plot the band structure by using: phonopy -p band.conf >>> >>> >>> >>> After all these steps, I found some negative frequencies and the >>> values of the related frequencies are not consistent with those of >>> previous results also. I doule-checked the calculation processes, but don't know the problem. >>> >>> >>> >>> Thank you a lot for your time, and any comments are appreciated. >>> >>> >>> >>> Best regards, >>> >>> Yang Ming >>> >>> ****** >>> >>> Computational Condensed-Matter Physics Lab >>> >>> Department of Physics >>> >>> National University of Singapore >>> >>> Singapore 117542 >>> >>> Email: phyym@...; ming_young@... >>> >>> Tel: +65 6516 4335 (office) >>> >>> >>> >>> >>> ---------------------------------------------------------------------- >>> -------- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL >>> 2012, more! >>> Discover the easy way to master current and previous Microsoft >>> technologies and advance your career. Get an incredible 1,500+ hours >>> of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! >>> http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.c >>> lktrk _______________________________________________ >>> Phonopy-users mailing list >>> Phonopy-users@... >>> https://lists.sourceforge.net/lists/listinfo/phonopy-users >>> >> >> >> >> -- >> Atsushi Togo >> http://atztogo.github.com/ >> atz.togo@... > > > > -- > Atsushi Togo > http://atztogo.github.com/ > atz.togo@... -- Atsushi Togo http://atztogo.github.com/ atz.togo@... ```