Phonons & Phonopy: Pro Tips (2015)

1. Phonons & Phonopy: “Pro Tips” J. M. Skelton Bath CompChem 14th April 2015 [Version 2.0]

2. Phonons and La*ce Dynamics Crystallography is generally concerned with the sta3c proper3es of crystals, describing features such as the average posi3ons of atoms and the symmetry of a crystal. Solid state physics takes a similar line as far as elementary electronic proper3es are concerned. We know, however, that atoms actually move around inside the crystal structure, since it is these mo3ons that give the concept of temperature […]. The sta3c laBce model, which is only concerned with the average posi3ons of atoms and neglects their mo3ons, can explain a large number of material features […]. There are, however, a number of proper3es that cannot be explained by a sta3c model… MarEn Dove, “IntroducEon to LaNce Dynamics” Bath CompChem, April 2015 | Slide 2

3. What Can Phonopy Do? “Anharmonicity” Proper:es phonopy phonopy-gruneisen phonopy-qha phono3py Bath CompChem, April 2015 | Slide 3

4. Overview •  “PracEcal” Theory •  phonopy §  Workflow/setup §  CalculaEng forces: opEons and “gotchas” §  Post processing §  Input/output files; using phonopy with other force-‐constant calculators •  phonopy-qha §  Workflow and post-‐processing §  Example applicaEons: which DFT funcEonal? •  phono3py §  Workflow, setup and post processing §  Examples •  Some current developments •  Summary Bath CompChem, April 2015 | Slide 4

5. “Prac:cal” Theory Bath CompChem, April 2015 | Slide 5 Force-‐constant matrix: From ﬁnite diﬀerences: Dynamical matrix: A_er diagonalisaEon:

6. “Prac:cal” Theory Bath CompChem, April 2015 | Slide 6

7. phonopy: Workﬂow Input Structure Create Displacements Calculate Forces Extract Forces Post-‐Process phonopy -d [--dim=“1 1 1”] phonopy -f vasprun-{001..XXX}.xml phonopy --fc vasprun.xml phonopy [-t] [-p] [-s] Settings.conf Bath CompChem, April 2015 | Slide 7

8. phonopy: Setup phonopy -d [--dim=“1 1 1”] [--tolerance=1e-5] [-c POSCAR] Set up the calculaEons on an XxYxZ supercell PosiEon tolerance for symmetry detecEon Path to POSCAR-‐format structure (“cell”), if not “POSCAR” disp.yaml POSCAR-001 POSCAR-002 POSCAR-003 ... SPOSCAR POSCAR ﬁles containing single atomic displacements “Unperturbed” supercell for DFPT phonon calculaEon InformaEon about the structure, supercell and displaced atoms Bath CompChem, April 2015 | Slide 8

9. phonopy: Calcula:ng Forces ADDGRID = .TRUE. EDIFF = 1E-8 ENCUT = 500-800 eV LREAL = .FALSE. PREC = High | Accurate ADDGRID = .TRUE. EDIFF = 1E-8 ENCUT = 500-800 eV IBRION = 5|6|7|8 LREAL = .FALSE. NSW = 1 PREC = High | Accurate •  Accurate forces are essenEal -‐> crank the standard seNngs right up •  LREAL = .FALSE. is essenEal, unless you manually adjust ROPT •  ADDGRID = .TRUE. doesn’t seem to be essenEal, but doesn’t cost much either •  For finite-‐difference/DFPT phonon calculaEons in VASP, set NSW = 1 Sample finite-‐displacement INCAR: Sample VASP force-‐constants INCAR: Bath CompChem, April 2015 | Slide 9

10. phonopy: Calcula:ng Forces (PbTe) ADDGRID=.FALSE. LREAL=Auto ADDGRID=.FALSE. LREAL=.FALSE. ADDGRID=.TRUE. LREAL=Auto ADDGRID=.TRUE. LREAL=.FALSE. Bath CompChem, April 2015 | Slide 10

11. phonopy: Calcula:ng Forces (ZnS) Bath CompChem, April 2015 | Slide 11

12. phonopy: Calcula:ng Forces (ZnS) Bath CompChem, April 2015 | Slide 12 •  Symmetrising the force constants during the post processing with phonopy corrects the PBE dispersion •  SymmetrisaEon enforces the acousEc-‐sum rule in the TPSS dispersion, but does not remove the artefacts away from Γ •  Symmetrising within phonopy gives the same result as calcula3ng the force constants with the VASP internal DFPT/ﬁnite-‐ displacement rou3nes -‐ as with most codes, VASP enforces symmetry by default

13. phonopy: Calcula:ng Forces (ZnS) Bath CompChem, April 2015 | Slide 13

14. phonopy: Calcula:ng Forces Bath CompChem, April 2015 | Slide 14

15. phonopy: Calcula:ng Forces Bath CompChem, April 2015 | Slide 15

16. phonopy: A Few “Top Tips” If using VASP FD/DFPT, set NWRITE = 3 in the INCAR file, and you can run this bash script on the OUTCAR to obtain a simulated IR spectrum “for free”: hrp://homepage.univie.ac.at/david.karhanek/downloads.html#Entry02 If using DFPT with an LDA/GGA funcEonal, set LEPSILON = .TRUE. in the INCAR file to obtain the staEc dielectric constant, in parEcular the ionic-‐ relaxaEon part, for a small added cost When using FD/DFPT, VASP tries to change the k-‐point set internally, which requires NPAR = #Cores to be set in the INCAR file; seNng ISYM = -1 avoids this, and although the number of displacements which need to be evaluated may increase, the performance gained by using band parallelism can quite easily offset this for low-‐symmetry systems (!) Bath CompChem, April 2015 | Slide 16

17. phonopy: Post Processing phonopy -p -s Settings.conf “Plot” “Save” SeNngs ﬁle DIM = 4 4 4 MP = 48 48 48 GAMMA_CENTER = .TRUE. Sample phonon DOS se*ngs ﬁle: PbTe Bath CompChem, April 2015 | Slide 17

18. phonopy: Post Processing phonopy -p -s Settings.conf “Plot” “Save” SeNngs ﬁle DIM = 4 4 4 MP = 48 48 48 GAMMA_CENTER = .TRUE. EIGENVECTORS = .TRUE. PDOS = 1, 2 Sample phonon DOS se*ngs ﬁle: PbTe Bath CompChem, April 2015 | Slide 18

19. phonopy: Post Processing “[Calculate] thermal properEes” DIM = 4 4 4 MP = 48 48 48 GAMMA_CENTER = .TRUE. Sample phonon DOS se*ngs ﬁle: phonopy -p -s -t Settings.conf “Plot” “Save” SeNngs ﬁle PbTe Bath CompChem, April 2015 | Slide 19

20. phonopy: Post Processing phonopy -p -s Settings.conf “Plot” “Save” SeNngs ﬁle DIM = 4 4 4 BAND = 0.0 0.0 0.0 0.5 0.25 0.75 0.5 0.0 0.5 0.0 0.0 0.0 0.5 0.5 0.5 BAND_POINTS = 101 BAND_LABELS = Gamma W X Gamma L [EIGENVECTORS = .TRUE.] Sample phonon band structure se*ngs ﬁle: PbTe Bath CompChem, April 2015 | Slide 20

21. phonopy: Post Processing phonopy -p -s Settings.conf “Plot” “Save” SeNngs ﬁle DIM = 4 4 4 BAND = 0.0 0.0 0.0 0.5 0.25 0.75 0.5 0.0 0.5 0.0 0.0 0.0 0.5 0.5 0.5 BAND_POINTS = 101 BAND_LABELS = Gamma W X Gamma L BAND_CONNECTION = .TRUE. Sample phonon band structure se*ngs ﬁle: PbTe Bath CompChem, April 2015 | Slide 21

22. phonopy: Non-‐Analy:cal Correc:ons EDIFF = 1E-8 ENCUT = 500-800 eV LEPSILON = .TRUE. LREAL = .FALSE. NSW = 0 PREC = High | Accurate INCAR for Born charges using DFPT: EDIFF = 1E-8 ENCUT = 500-800 eV LCALCEPS = .TRUE. LREAL = .FALSE. NSW = 0 PREC = High | Accurate [EFIELD_PEAD = Ex Ey Ez] INCAR for Born charges using LCALCEPS: •  To apply a non-‐analyEcal correcEon (LO/TO spliNng) to the phonon frequencies, phonopy needs the Born eﬀecEve charges and electronic-‐polarisaEon contribuEon to the macroscopic dielectric constant •  In VASP, for LDA/GGA funcEonals these can be computed using DFPT; for others, they need to be computed from the response to an electric ﬁeld Bath CompChem, April 2015 | Slide 22

23. phonopy: Non-‐Analy:cal Correc:ons outcar-born > BORN <Conversion Factor> εxx εxy εxz εyx εyy εyz εzx εzy εzz Zxx Zxy Zxz Zyx Zyy Zyz Zzx Zzy Zzz Zxx Zxy Zxz Zyx Zyy Zyz Zzx Zzy Zzz Dielectric tensor Born charge tensors for unique atoms Sample BORN file: •  CorrecEons are enabled by seNng NAC = .TRUE. in the configuraEon file, or passing --nac as a command-‐line argument •  When this opEon is used, phonopy expects to find a BORN file in the working directory Bath CompChem, April 2015 | Slide 23

24. phonopy: Non-‐Analy:cal Correc:ons PbTe NAC = .FALSE. NAC = .TRUE. Bath CompChem, April 2015 | Slide 24

25. phonopy: Force-‐Constant Symmetrisa:on FC_SYMMETRY = 0 FC_SYMMETRY = 1 •  Force-‐constant symmetrisaEon is enabled by seNng FC_SYMMETRY = > 0 in the conﬁguraEon ﬁle ZnS Bath CompChem, April 2015 | Slide 25

26. phonopy: Output Files mesh: [ mx, my, mz ] nqpoint: 32000 natom: 8 phonon: - q-position: [ qx, qy, qz ] weight: w1 band: - # 1 frequency: ω1 ... Sample mesh.yaml file: nqpoint: 808 npath: 8 natom: 8 phonon: - q-position: [ qx, qy, qz ] distance: d1 band: - # 1 frequency: ω1 ... Sample band.yaml file: •  If EIGENVECTORS = .TRUE. is set in the configuraEon file, the mode eigenvectors will also appear in these files •  With BAND_CONNECTION = .TRUE., the frequencies for each band in band.yaml are ordered so that they connect across the band structure Bath CompChem, April 2015 | Slide 26

27. phonopy: Output Files # Sigma = 0.053821 -0.5372... 0.0000... -0.5103... 0.0000... -0.4834... 0.0000... -0.4564... 0.0000... -0.4295... 0.0000... -0.4026... 0.0000... -0.3757... 0.0000... -0.3488... 0.0000... -0.3219... 0.0000... ... Sample total_dos.dat file: unit: temperature: K ... natom: 8 zero_point_energy: 18.9108676 high_T_entropy: 847.3220815 thermal_properties: - temperature: 0.0000000 - free_energy: 18.9108676 - entropy: 0.0000000 - heat_capacity: 0.0000000 - energy: 18.9108676 ... Sample thermal_proper:es.yaml file: •  The “parEal_dos.dat” file generated with EIGENVECTORS = .TRUE. contains one column for each atom in the primiEve cell Bath CompChem, April 2015 | Slide 27

28. phonopy: Force-‐Constant Calculators 128 2 1 d1x d1y d1z F1x F1y F1z F2x F2y F2z ... 2 d2x d2y d2z F1x F1y F1z F2x F2y F2z ... Sample FORCE_SETS ﬁle: 128 1 1 Φxx Φxy Φxz Φyx Φyy Φyz Φzx Φzy Φzz 1 2 Φxx Φxy Φxz Φyx Φyy Φyz Φzx Φzy Φzz ... Sample FORCE_CONSTANTS ﬁle: Bath CompChem, April 2015 | Slide 28

29. IRMOF-‐10 Bath CompChem, April 2015 | Slide 29 phonopy: Force-‐Constant Calculators *Tinker calculaEons by J. K. Bristow and D. Tiana

30. phonopy-qha: Workﬂow EoS Curve Harmonic Phonopy Thermal ProperEes Post-‐Process phonopy -d --dim=“...” phonopy -f vasprun-{001..XXX}.xml phonopy -t -p -s Settings.conf E/V curve -‐> “e-‐v.dat” phonopy-qha e-v.dat thermal_properties-{001..XXX}.yaml --tmax=980 [--tstep=10] [--pressure=<p/GPa>] [-p] [-s] Needs to be two points smaller than the maximum temperature in the YAML ﬁles Bath CompChem, April 2015 | Slide 30

31. phonopy-qha: Output Bath CompChem, April 2015 | Slide 31 *J. M. Skelton et al., Phys. Rev. B 89, 205203 (2014)

32. phonopy-qha: Output bulk_modulus-‐temperature.dat Cp-‐temperature.dat Cp-‐temperature_polyﬁt.dat Cv-‐volume.dat dsdv-‐temperature.dat entropy-‐volume.dat gibbs-‐temperature.dat gruneisen-‐temperature.dat helmholtz-‐volume.dat thermal_expansion.dat volume_expansion.dat volume-‐temperature.dat <-‐ B is temperature dependent(!) <-‐ CV at each volume, at each temperature <-‐ SV at each volume, at each temperature <-‐ Average Gruneisen parameter (?) <-‐ A at each volume, at each temperature Bath CompChem, April 2015 | Slide 32

33. phonopy-qha: Examples Bath CompChem, April 2015 | Slide 33 *J. M. Skelton et al., in preparaEon

36. phonopy-qha: Examples Bath CompChem, April 2015 | Slide 36 ~4 K ~105 K ~150 K 300-‐310 K 450-‐475 K 550-‐600 K *J. M. Skelton et al., Phys. Rev. B 89, 205203 (2014)

37. phonopy-qha: Examples SnS: 10 K -‐ 350 K PbTe: 0 K -‐ 600 K Bath CompChem, April 2015 | Slide 37 *PbTe: J. M. Skelton et al., Phys. Rev. B 89, 205203 (2014)

38. phono3py: Workﬂow Input Structure Create Displacements Calculate Forces Extract Forces Post-‐Process phono3py -d --dim=“2 2 2” phono3py --cf3 vasprun-{001..XXX}.xml phono3py --tmax=1000 --tstep=10 --fc2 --fc3 --dim=“2 2 2” -v --mesh=“24 24 24” --br --sigma=“0.1” phono3py --dim=“2 2 2” Bath CompChem, April 2015 | Slide 38

39. phono3py: Setup phono3py -d --dim=“...” [--cutoff_pair=4] [--dim_fc2=“4 4 4”] phono3py --cf3 vasprun-{001..XXX}.xml phono3py --dim=“...” [--dim_fc2...] Extract forces from VASP output The --cutoff_pair tag uses the same numbering for the displaced POSCAR ﬁles as the full calculaEon; this means the cutoﬀ can be increased, and the extra displacements added, systemaEcally, to converge w.r.t. the interacEon range Bath CompChem, April 2015 | Slide 39

40. phono3py: Post Processing phono3py --tmax=1000 --tstep=10 --fc2 --fc3 --dim=“...” -v --mesh=“24 24 24” --br --sigma=“0.1” [--nac] [--dim2=“...”/--dim_fc2=“...”] •  The post-‐processing (mainly the phonon-‐lifeEme calculaEons) takes a very long Eme for large supercells/large or low-‐symmetry structures •  It is possible to run the calculaEon on (ranges of) q-‐points separately, and then combine them a_erwards •  Various post-‐processing tags can be applied, e.g. to incorporate isotope eﬀects Read in pre-‐calculated force constants # of interacEons per q-‐point becomes larger with mesh size; cannot easily “max out” as for DOS calculaEons, but needs to be converged Bath CompChem, April 2015 | Slide 40

41. phono3py: Examples Bath CompChem, April 2015 | Slide 41 *J. M. Skelton et al., APL Materials 3, 041102 (2015)

42. phono3py: Examples Bath CompChem, April 2015 | Slide 42 Simulated IR/Raman spectra with… • 10 K linewidths • 300 K linewidths … and an instrument broadening of 3.5 cm-‐1, compared to expt. *J. M. Skelton et al., APL Materials 3, 041102 (2015)

43. Some Current Developments Bath CompChem, April 2015 | Slide 43 *E. L. da Silva et al., Phys. Rev. B 91, 144107 (2015)

44. A Few Closing Remarks Bath CompChem, April 2015 | Slide 44

Phonons & Phonopy: Pro Tips (2015)

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Phonons & Phonopy: Pro Tips (2015)

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