Re: [QE-users] visualising vibrations from the results of phonon calculations
On Mon, 2019-09-30 at 15:59 +0200, Yohei Uemura wrote:
> Dear users,
>
> As someone discussed before, XCrysDen did not work to show the
> motions of atoms.("[Pw_forum] Phonon axsf does not move in XCrysden")
xcrysden shows normal modes with arrows (to this end, either press "f"
or use Display-->Forces menu).
Best regards, Tone
--
Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
(tel: +386-1-477-3523 // fax: +386-1-251-9385)
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Re: [QE-users] visualising vibrations from the results of phonon calculations
Dear Yohei,
There is a very nice visualization tool for phonons on the Materials Cloud:
https://www.materialscloud.org/work/tools/interactivephonon
Greetings,
Iurii
--
Dr. Iurii Timrov
Postdoctoral Researcher
STI - IMX - THEOS and NCCR - MARVEL
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334
From: users on behalf of Yohei
Uemura
Sent: Monday, September 30, 2019 3:59:50 PM
To: users@lists.quantum-espresso.org
Subject: [QE-users] visualising vibrations from the results of phonon
calculations
Dear users,
I'm new for quantum espresso (phonon.x).
I calculated the vibrations of CO2 or CH4.
I would like to visualise the motion of atoms in CO2 or CH4.
As someone discussed before, XCrysDen did not work to show the motions of
atoms.("[Pw_forum] Phonon axsf does not move in XCrysden")
Does anyone know how to visualise the motions of atoms?
I have the output file from dynmat.x.
Best regards,
Yohei
--
Yohei Uemura (Ph.D)
Affiliation : Paul Scherrer Institut (PSI),
Laboratory for Environmental Chemistry (LUC)
Address : OFLB 106 (PSI Ost), PSI, Forschungsstrasse 111,
5232 Villigen, Switzerland
Phone: +41 (0)5-6310-4571
上村洋平
所属 : Paul Scherrer Institut (PSI),
Laboratory for Environmental Chemistry (LUC)
住所 : OFLB 106 (PSI Ost), PSI, Forschungsstrasse 111,
5232 Villigen, Switzerland
電話 : +41 (0)5-6310-4571
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Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
users mailing list users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] visualising vibrations from the results of phonon calculations
Dear users,
I'm new for quantum espresso (phonon.x).
I calculated the vibrations of CO2 or CH4.
I would like to visualise the motion of atoms in CO2 or CH4.
As someone discussed before, XCrysDen did not work to show the motions of
atoms.("[Pw_forum] Phonon axsf does not move in XCrysden")
Does anyone know how to visualise the motions of atoms?
I have the output file from dynmat.x.
Best regards,
Yohei
--
Yohei Uemura (Ph.D)
Affiliation : Paul Scherrer Institut (PSI),
Laboratory for Environmental Chemistry (LUC)
Address : OFLB 106 (PSI Ost), PSI, Forschungsstrasse 111,
5232 Villigen, Switzerland
Phone: +41 (0)5-6310-4571
上村洋平
所属 : Paul Scherrer Institut (PSI),
Laboratory for Environmental Chemistry (LUC)
住所 : OFLB 106 (PSI Ost), PSI, Forschungsstrasse 111,
5232 Villigen, Switzerland
電話 : +41 (0)5-6310-4571
___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
users mailing list users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Ce19O32 cluster does not convergence
Dear Andrey I see that you are trying to relax your cluster. I suppose that the Ce f electrons require some correction to delocalization, as suggested by José. But this is not enough in the case of EXX, because the first scf step in the inner EXX loop is a GGA step and may fail. You can try by using diagonalization='cg', which is more stable than 'david', but my advice is to try with scf_must_converge=.false. This is useful in the case of GGA or DFT+U, because it forces the geometry step even with an unconverged wavefunction. This can help you to cross your system over to structures easier to converge. This is also useful in the case of EXX, because you can enter the first EXX calculation with an unconverged wavefunction, localize it and improve it through smoother inner-loop iterations. HTH Giuseppe "José C. Conesa" ha scritto: Dear Andrey, This type of system usually needs a DFT+U or hybrid functional treatment, otherwise the electrons are too delocalized. Perhaps this is the reason for lack of convergence. Hope this helps, José Carlos Conesa El 29/09/2019 a las 16:08, Andrey Chibisov escribió: Hello. I study Ce19O32 cluster, but I can't get the total energy convergence. My input file is: calculation ='relax', restart_mode='from_scratch', !restart_mode='restart', wf_collect = .TRUE., verbosity='high' pseudo_dir='/home/achibisov/CeO2/PBEsol', outdir='/home/achibisov/CeO2/Ce19O32/temp', forc_conv_thr = 0.01 / ibrav=0, celldm(1)=47.2431531141d0, nat=51, ntyp=2, ecutwfc = 80.0, ecutrho = 800 nbnd = 216, nspin = 2, tot_magnetization = 0, !occupations='smearing', smearing='gaussian', degauss=0.001 !occupations='fixed', occupations='from_input', !input_dft='gaup', nqx1=3, nqx2=3, nqx3=3, !exxdiv_treatment='none' !x_gamma_extrapolation = .false. / conv_thr = 1.D-3, mixing_beta = 0.1, / ion_dynamics = 'bfgs', / cell_dynamics = 'bfgs', cell_dofree = 'all' / ATOMIC_SPECIES Ce 140.116000d0 Ce.UPF O 15.999400d0 O.UPF ATOMIC_POSITIONS (crystal) Ce 0.4868629311d0 0.3815474927d0 0.3558657432d0 Ce 0.3771040218d0 0.490420d0 0.3549706445d0 Ce 0.6997754464d0 0.490420d0 0.4702201205d0 Ce 0.4817073780d0 0.490420d0 0.6789561145d0 Ce 0.5929365462d0 0.490420d0 0.5766024711d0 Ce 0.4856620596d0 0.490420d0 0.4648645351d0 Ce 0.5970259661d0 0.490420d0 0.3568597695d0 Ce 0.4878552272d0 0.490420d0 0.2520196160d0 Ce 0.3758834729d0 0.3812732135d0 0.4636105009d0 Ce 0.5946046648d0 0.5992001660d0 0.4665465423d0 Ce 0.4834909260d0 0.5989686798d0 0.5739788312d0 Ce 0.4852252352d0 0.7025437161d0 0.4644374565d0 Ce 0.3742294968d0 0.490420d0 0.5727685260d0 Ce 0.4868629311d0 0.5992925073d0 0.3558657432d0 Ce 0.3758834729d0 0.5995667865d0 0.4636105009d0 Ce 0.2710982326d0 0.490420d0 0.4624561301d0 Ce 0.4852252352d0 0.2782962839d0 0.4644374565d0 Ce 0.4834909260d0 0.3818713202d0 0.5739788312d0 Ce 0.5946046648d0 0.3816398340d0 0.4665465423d0 O 0.4284190778d0 0.6603888564d0 0.4068385834d0 O 0.4284190778d0 0.3204511436d0 0.4068385834d0 O 0.4303395760d0 0.4335412916d0 0.2944091083d0 O 0.5406516600d0 0.3208219210d0 0.5230927952d0 O 0.4268663193d0 0.3204747807d0 0.5205121157d0 O 0.4252404411d0 0.4334727625d0 0.6353234695d0 O 0.4274621721d0 0.4342213819d0 0.5206566174d0 O 0.4294662094d0 0.4340081656d0 0.4077237855d0 O 0.5453391746d0 0.4338342959d0 0.2948938831d0 O 0.5436599091d0 0.3208116404d0 0.4083172133d0 O 0.5435957226d0 0.4343203087d0 0.4082928771d0 O 0.6574624760d0 0.4339635776d0 0.4125821189d0 O 0.3132683540d0 0.4337662653d0 0.5196972618d0
Re: [QE-users] Ce19O32 cluster does not convergence
Dear Andrey, This type of system usually needs a DFT+U or hybrid functional treatment, otherwise the electrons are too delocalized. Perhaps this is the reason for lack of convergence. Hope this helps, José Carlos Conesa El 29/09/2019 a las 16:08, Andrey Chibisov escribió: Hello. I study Ce19O32 cluster, but I can't get the total energy convergence. My input file is: calculation ='relax', restart_mode='from_scratch', !restart_mode='restart', wf_collect = .TRUE., verbosity='high' pseudo_dir='/home/achibisov/CeO2/PBEsol', outdir='/home/achibisov/CeO2/Ce19O32/temp', forc_conv_thr = 0.01 / ibrav=0, celldm(1)=47.2431531141d0, nat=51, ntyp=2, ecutwfc = 80.0, ecutrho = 800 nbnd = 216, nspin = 2, tot_magnetization = 0, !occupations='smearing', smearing='gaussian', degauss=0.001 !occupations='fixed', occupations='from_input', !input_dft='gaup', nqx1=3, nqx2=3, nqx3=3, !exxdiv_treatment='none' !x_gamma_extrapolation = .false. / conv_thr = 1.D-3, mixing_beta = 0.1, / ion_dynamics = 'bfgs', / cell_dynamics = 'bfgs', cell_dofree = 'all' / ATOMIC_SPECIES Ce 140.116000d0 Ce.UPF O 15.999400d0 O.UPF ATOMIC_POSITIONS (crystal) Ce 0.4868629311d0 0.3815474927d0 0.3558657432d0 Ce 0.3771040218d0 0.490420d0 0.3549706445d0 Ce 0.6997754464d0 0.490420d0 0.4702201205d0 Ce 0.4817073780d0 0.490420d0 0.6789561145d0 Ce 0.5929365462d0 0.490420d0 0.5766024711d0 Ce 0.4856620596d0 0.490420d0 0.4648645351d0 Ce 0.5970259661d0 0.490420d0 0.3568597695d0 Ce 0.4878552272d0 0.490420d0 0.2520196160d0 Ce 0.3758834729d0 0.3812732135d0 0.4636105009d0 Ce 0.5946046648d0 0.5992001660d0 0.4665465423d0 Ce 0.4834909260d0 0.5989686798d0 0.5739788312d0 Ce 0.4852252352d0 0.7025437161d0 0.4644374565d0 Ce 0.3742294968d0 0.490420d0 0.5727685260d0 Ce 0.4868629311d0 0.5992925073d0 0.3558657432d0 Ce 0.3758834729d0 0.5995667865d0 0.4636105009d0 Ce 0.2710982326d0 0.490420d0 0.4624561301d0 Ce 0.4852252352d0 0.2782962839d0 0.4644374565d0 Ce 0.4834909260d0 0.3818713202d0 0.5739788312d0 Ce 0.5946046648d0 0.3816398340d0 0.4665465423d0 O 0.4284190778d0 0.6603888564d0 0.4068385834d0 O 0.4284190778d0 0.3204511436d0 0.4068385834d0 O 0.4303395760d0 0.4335412916d0 0.2944091083d0 O 0.5406516600d0 0.3208219210d0 0.5230927952d0 O 0.4268663193d0 0.3204747807d0 0.5205121157d0 O 0.4252404411d0 0.4334727625d0 0.6353234695d0 O 0.4274621721d0 0.4342213819d0 0.5206566174d0 O 0.4294662094d0 0.4340081656d0 0.4077237855d0 O 0.5453391746d0 0.4338342959d0 0.2948938831d0 O 0.5436599091d0 0.3208116404d0 0.4083172133d0 O 0.5435957226d0 0.4343203087d0 0.4082928771d0 O 0.6574624760d0 0.4339635776d0 0.4125821189d0 O 0.3132683540d0 0.4337662653d0 0.5196972618d0 O 0.4303395760d0 0.5472987084d0 0.2944091083d0 O 0.3146749157d0 0.4334990899d0 0.4063334249d0 O 0.6564105394d0 0.5474457199d0 0.5266229596d0 O 0.4268663193d0 0.6603652193d0 0.5205121157d0 O 0.4252404411d0 0.5473672375d0 0.6353234695d0 O 0.3132683540d0 0.5470737347d0 0.5196972618d0
