[CP2K-user] [CP2K:13897] Need advice on bulk metal system calculations
Stephen Vicchio
svi... at g.clemson.edu
Wed Sep 16 01:40:56 UTC 2020
Hi Matthias,
Thank you so much for the information! From your suggestions, I was able to
set up the input file for my bulk Cu metal systems. For other metal
systems, do you recommend a similar set of parameters? Specifically, the
mixing, smearing, and kpoints? My previous CP2K calculations were on
metal-organic frameworks so my computational parameters were set up for
these porous structures.
With much appreciation,
Stephen
On Tue, Sep 15, 2020 at 12:40 PM Krack Matthias (PSI) <matthi... at psi.ch>
wrote:
> Hi Stephen
>
>
>
> For bulk Cu you will need to apply
>
> - k point sampling (e.g. MP 8 8 8)
>
> - diagonalization (with Broyden mixing)
>
> - smearing (e.g. T(elec) = 2000 K)
>
>
>
> Moreover, you should use the conventional (cubic) unit cell with 4 Cu
> atoms instead of the primitive one with one Cu atom. CP2K is slower for
> non-orthorhombic cells.
>
> Plane wave (PW) codes are fast for small unit cells as they scale with the
> size of the cell which has to be filled with PWs. That’s not the case for
> CP2K using atomic basis functions which requires to calculate the
> interactions with the image Cu atoms in neighboring cells. So it can make
> sense to use multiple unit cells, e.g. a 2x2x2 supercell, and to reduce the
> k point mesh correspondingly (e.g. from 8x8x8 to 4x4x4).
>
>
>
> Below you will find a CP2K input for bulk Cu in which I have considered
> the suggestions above. No guarantee, of course, that it will work properly.
>
>
>
> Matthias
>
>
>
> &GLOBAL
>
> PRINT_LEVEL low
>
> PROJECT_NAME Cu
>
> RUN_TYPE cell_opt
>
> &END GLOBAL
>
>
>
> &MOTION
>
> &CELL_OPT
>
> EXTERNAL_PRESSURE [bar] 1.0
>
> MAX_DR 0.001
>
> MAX_FORCE 0.0001
>
> MAX_ITER 400
>
> OPTIMIZER BFGS
>
> PRESSURE_TOLERANCE [bar] 10.0
>
> RMS_DR 0.0003
>
> RMS_FORCE 0.00003
>
> TYPE direct_cell_opt
>
> &BFGS
>
> TRUST_RADIUS 0.1
>
> USE_MODEL_HESSIAN off
>
> USE_RAT_FUN_OPT on
>
> &END BFGS
>
> &END CELL_OPT
>
> &END MOTION
>
>
>
> &FORCE_EVAL
>
> METHOD QS
>
> STRESS_TENSOR analytical
>
> &DFT
>
> BASIS_SET_FILE_NAME BASIS_MOLOPT
>
> POTENTIAL_FILE_NAME GTH_POTENTIALS
>
> &KPOINTS
>
> SCHEME MONKHORST-PACK 2 2 2
>
> FULL_GRID yes
>
> SYMMETRY yes
>
> VERBOSE yes
>
> PARALLEL_GROUP_SIZE -1
>
> &END KPOINTS
>
> &MGRID
>
> NGRIDS 5
>
> CUTOFF 400.0
>
> REL_CUTOFF 60.0
>
> &END MGRID
>
> &QS
>
> EPS_DEFAULT 1.0E-12
>
> EXTRAPOLATION use_prev_p
>
> &END QS
>
> &SCF
>
> ADDED_MOS 60
>
> EPS_SCF 1.0E-8
>
> MAX_SCF 300
>
> SCF_GUESS restart
>
> &DIAGONALIZATION yes
>
> ALGORITHM STANDARD
>
> &END DIAGONALIZATION
>
> &MIXING yes
>
> ALPHA 0.4
>
> BETA 1.0
>
> METHOD broyden_mixing
>
> NBROYDEN 8
>
> &END MIXING
>
> &SMEAR on
>
> METHOD FERMI_DIRAC
>
> ELECTRONIC_TEMPERATURE [K] 2000.0
>
> &END SMEAR
>
> &END SCF
>
> &XC
>
> &XC_FUNCTIONAL PBE
>
> &END XC_FUNCTIONAL
>
> &VDW_POTENTIAL
>
> POTENTIAL_TYPE pair_potential
>
> &PAIR_POTENTIAL
>
> TYPE DFTD3(BJ)
>
> PARAMETER_FILE_NAME dftd3.dat
>
> REFERENCE_FUNCTIONAL PBE
>
> &END PAIR_POTENTIAL
>
> &END VDW_POTENTIAL
>
> &END XC
>
> &END DFT
>
> &SUBSYS
>
> &CELL
>
> ABC 3.62 3.62 3.62
>
> MULTIPLE_UNIT_CELL 2 2 2
>
> &END CELL
>
> &COORD
>
> SCALED
>
> Cu 0 0 0
>
> Cu 0 1/2 1/2
>
> Cu 1/2 0 1/2
>
> Cu 1/2 1/2 0
>
> &END COORD
>
> &KIND Cu
>
> BASIS_SET DZVP-MOLOPT-SR-GTH-q11
>
> POTENTIAL GTH-PBE-q11
>
> &END KIND
>
> &TOPOLOGY
>
> MULTIPLE_UNIT_CELL 2 2 2
>
> &END TOPOLOGY
>
> &END SUBSYS
>
> &END FORCE_EVAL
>
>
>
> *From:* cp... at googlegroups.com <cp... at googlegroups.com> *On Behalf Of *Stephen
> Vicchio
> *Sent:* Dienstag, 15. September 2020 17:06
> *To:* cp... at googlegroups.com
> *Subject:* Re: [CP2K:13894] Need advice on bulk metal system calculations
>
>
>
> From materials project, the .cif file I'm using for bulk Cu has unit cell
> dimensions of 2.24 2.24 2.24 and 60 60 60. Do you think that might explain
> what's happening? The error message I'm receiving isn't located in the out
> file from CP2K, but the out file from the cluster:
>
>
>
> Error termination. Backtrace:
> At line 470 of file
> /tmp/spack/spack-stage/spack-stage-cp2k-7.1-h7ky2rvmv3fvzjrtpbqv2rr3fie3l6zy/spack-src/src/cell_methods.F
> Fortran runtime error: Bad real number in item 1 of list input
>
>
>
> The example scripts run fines, but it my current .inp that is giving me
> issues.
>
>
> Stephen
>
>
>
> On Tue, Sep 15, 2020 at 11:01 AM Marcella Iannuzzi <marci... at gmail.com>
> wrote:
>
> Dear Stephen
>
>
>
> Are you sure about
>
> ALPHA_BETA_GAMMA 60 60 60
>
>
>
> Best regards
>
> Marcella
>
> On Tuesday, September 15, 2020 at 4:22:21 PM UTC+2 Stephen wrote:
>
> Hi Matthias,
>
>
>
> Thanks for your input! Using the CP2K example 'Getting the band structure
> of graphene' (
> https://www.cp2k.org/exercises:2016_uzh_cmest:band_structure_calculation),
> I was able to add the KPOINT section into my current input shown above.
> I've been altering the parameters and playing around with the input file,
> but I'm having issues troubleshooting why my new input isn't working
> properly. The CP2K example was able to run, but my job isn't which makes
> me think there is an issue with some of the other flags I've set in my .inp
> file for bulk Cu.
>
>
>
> Below you can find the new .inp file that I've been using. Thanks for
> taking a look!
>
>
>
> With much appreciation,
>
> Stephen
>
> &GLOBAL
> PRINT_LEVEL MEDIUM
> PROJECT_NAME bulk-Cu-CELL_DIMA
> RUN_TYPE ENERGY_FORCE
> WALLTIME 23:40:00
> &END GLOBAL
> &FORCE_EVAL
> METHOD QS
> STRESS_TENSOR ANALYTICAL
>
>
> &DFT
> BASIS_SET_FILE_NAME BASIS_file
> POTENTIAL_FILE_NAME POTENTIALS_file
> UKS T
> MULTIPLICITY 2
> CHARGE 0
> &SCF
> MAX_SCF 1000
> EPS_SCF 9.9999999999999995E-07
> SCF_GUESS ATOMIC
> &OT T
> MINIMIZER CG
> PRECONDITIONER FULL_ALL
> ENERGY_GAP 1.0000000000000000E-03
> &END OT
> &OUTER_SCF T
> EPS_SCF 9.9999999999999995E-07
> MAX_SCF 50
> &END OUTER_SCF
> &END SCF
> &QS
> EPS_DEFAULT 1.0000000000000000E-10
> METHOD GPW
>
> EXTRAPOLATION USE_GUESS
>
>
> &END QS
> &MGRID
> NGRIDS 5
> CUTOFF 3.6000000000000000E+02
> REL_CUTOFF 8.0000000000000000E+01
> &END MGRID
> &XC
> DENSITY_CUTOFF 1.0000000000000000E-10
> GRADIENT_CUTOFF 1.0000000000000000E-10
> TAU_CUTOFF 1.0000000000000000E-10
> &XC_FUNCTIONAL NO_SHORTCUT
> &PBE T
> &END PBE
> &END XC_FUNCTIONAL
> &VDW_POTENTIAL
> POTENTIAL_TYPE PAIR_POTENTIAL
> &PAIR_POTENTIAL
> TYPE DFTD3(BJ)
> PARAMETER_FILE_NAME dftd3.dat
> REFERENCE_FUNCTIONAL PBE
> CALCULATE_C9_TERM F
> &END PAIR_POTENTIAL
> &END VDW_POTENTIAL
> &END XC
>
> &KPOINTS
> SCHEME MONKHORST-PACK 1 1 1
> SYMMETRY OFF
> WAVEFUNCTIONS REAL
> FULL_GRID .TRUE.
> PARALLEL_GROUP_SIZE 0
> &END KPOINTS
> &END DFT
> &SUBSYS
> &CELL
> ABC 2.24 2.24 2.24
> ALPHA_BETA_GAMMA 60 60 60
> MULTIPLE_UNIT_CELL 1 1 1
> &END CELL
> &TOPOLOGY
> COORD_FILE_FORMAT CIF
> COORD_FILE_NAME bulk-Cu.cif
> NUMBER_OF_ATOMS 1
> MULTIPLE_UNIT_CELL 1 1 1
> &END TOPOLOGY
> &KIND Cu
> BASIS_SET DZVP-MOLOPT-SR-GTH-q11
> POTENTIAL GTH-PBE-q11
> &END KIND
> &END SUBSYS
> &PRINT
> &FORCES ON
> &END FORCES
> &END PRINT
> &END FORCE_EVAL
>
>
>
>
>
> On Mon, Sep 14, 2020 at 11:27 AM Krack Matthias (PSI) <mat... at psi.ch>
> wrote:
>
> Hi Stephen
>
>
>
> For the description of metallic bulk systems, you will need Brillouin zone
> sampling with an appropriate k point mesh. It seems this is missing in your
> input.
>
>
>
> HTH
>
>
>
> Matthias
>
>
>
> *From:* c... at googlegroups.com <c... at googlegroups.com> *On Behalf Of *
> Stephen
> *Sent:* Montag, 14. September 2020 14:54
> *To:* cp2k <c... at googlegroups.com>
> *Subject:* [CP2K:13869] Need advice on bulk metal system calculations
>
>
>
> Hi All,
>
>
>
> I was wondering if anyone has tips for computing bulk metallic system in
> CP2K (specifically for bulk Cu and bulk Ni system). I need the electronic
> energy for bulk Cu and bulk Ni for some modeling on NP thermodynamic
> stability.
>
>
>
> I've optimized the unit cell parameters for both Cu and Ni systems by
> varying the unit cell dimensions found on Materials Project
> <https://materialsproject.org/materials/mp-30/> with the same level of
> theory as my CP2K on metal-organic frameworks. When I try to compute
> different metallic properties though such as atomization and bulk Cu + O2
> (g) --> bulk CuO my energies are way off..
>
> From Web Elements for Ni
> <https://www.webelements.com/copper/thermochemistry.html>, the
> atomization energy was determined:
>
> bulk Cu (s) --> Cu(0) (g) w/ deltaH=338 kJ/mol
>
>
> Now using DFT, the follow atomisation energy was determined to be:
>
> bulk Cu (s) --> Cu(0) (g) w/ deltaE=1658.2 kJ/mol
>
>
>
> Either my bulk system is too stable, or my atomized Cu is too unstable.
> Here is my DFT section for the bulk Cu calculations.
>
>
>
> &DFT
>
> BASIS_SET_FILE_NAME BASIS_file
>
> POTENTIAL_FILE_NAME POTENTIALS_file
>
> UKS T
>
> MULTIPLICITY 2
>
> CHARGE 0
>
> &SCF
>
> MAX_SCF 1000
>
> EPS_SCF 9.9999999999999995E-07
>
> SCF_GUESS ATOMIC
>
> &OT T
>
> MINIMIZER CG
>
> PRECONDITIONER FULL_ALL
>
> ENERGY_GAP 1.0000000000000000E-03
>
> &END OT
>
> &OUTER_SCF T
>
> EPS_SCF 9.9999999999999995E-07
>
> MAX_SCF 50
>
> &END OUTER_SCF
>
> &END SCF
>
> &QS
>
> EPS_DEFAULT 1.0000000000000000E-10
>
> METHOD GPW
>
> &END QS
>
> &MGRID
>
> NGRIDS 5
>
> CUTOFF 3.6000000000000000E+02
>
> REL_CUTOFF 8.0000000000000000E+01
>
> &END MGRID
>
> &XC
>
> DENSITY_CUTOFF 1.0000000000000000E-10
>
> GRADIENT_CUTOFF 1.0000000000000000E-10
>
> TAU_CUTOFF 1.0000000000000000E-10
>
> &XC_FUNCTIONAL NO_SHORTCUT
>
> &PBE T
>
> &END PBE
>
> &END XC_FUNCTIONAL
>
> &VDW_POTENTIAL
>
> POTENTIAL_TYPE PAIR_POTENTIAL
>
> &PAIR_POTENTIAL
>
> TYPE DFTD3(BJ)
>
> PARAMETER_FILE_NAME dftd3.dat
>
> REFERENCE_FUNCTIONAL PBE
>
> CALCULATE_C9_TERM F
>
> &END PAIR_POTENTIAL
>
> &END VDW_POTENTIAL
>
> &END XC
>
> &END DFT
>
>
>
> Sample .inp and .out files are attached.
>
>
>
> Any feedback would be much appreciated! Thanks for taking a look at my
> issues.
>
>
>
> With much appreciation,
>
> Stephen
>
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>
> --
>
> *Stephen P. Vicchio*
>
> PhD Candidate | Getman Research Group
>
> Dept. of Education GAANN Fellow
>
> Department of Chemical & Biomolecular Engineering
> <https://www.clemson.edu/cecas/departments/chbe/>
>
> 105 Earle Hall | Clemson, SC 29634-0909
>
> s... at g.clemson.edu
>
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> .
>
>
>
>
> --
>
> *Stephen P. Vicchio*
>
> PhD Candidate | Getman Research Group
>
> Dept. of Education GAANN Fellow
>
> Department of Chemical & Biomolecular Engineering
> <https://www.clemson.edu/cecas/departments/chbe/>
>
> 105 Earle Hall | Clemson, SC 29634-0909
>
> svi... at g.clemson.edu
>
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--
*Stephen P. Vicchio*
PhD Candidate | Getman Research Group
Dept. of Education GAANN Fellow
Department of Chemical & Biomolecular Engineering
<https://www.clemson.edu/cecas/departments/chbe/>
105 Earle Hall | Clemson, SC 29634-0909
svi... at g.clemson.edu
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