[CP2K-user] [CP2K:13894] Need advice on bulk metal system calculations
Krack Matthias (PSI)
matthi... at psi.ch
Tue Sep 15 16:40:26 UTC 2020
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<mailto: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<mailto: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<mailto:c... at googlegroups.com> <c... at googlegroups.com<mailto:c... at googlegroups.com>> On Behalf Of Stephen
Sent: Montag, 14. September 2020 14:54
To: cp2k <c... at googlegroups.com<mailto: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<mailto: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
<mailto:svi... at g.clemson.edu>
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