[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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