[CP2K-user] [CP2K:13894] Need advice on bulk metal system calculations

[Stephen Vicchio]

>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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