[CP2K-user] NEGF calculation

Dmitry Ryndyk dary... at googlemail.com
Thu Nov 26 13:42:02 UTC 2020


And add 
NEGF%EPS_GEO       1e-4
your coordinates are not very good periodic.

Best to continue!
Dmitry Ryndyk schrieb am Donnerstag, 26. November 2020 um 13:18:57 UTC+1:

> Hi,
>
> coordinates 9.438804   16.348399    8.899098 are in Bohr, it means in 
> Angstrom
> Au      4.994800    8.651200    4.709200 L3
>
> lim... at outlook.com schrieb am Donnerstag, 26. November 2020 um 
> 03:25:18 UTC+1:
>
>> Hello,
>>
>> I tried to use cp2k to reproduce previous group member's NEGF calculation 
>> who used ATK. I encountered the error  ''Unable to map the atom onto the 
>> atom (Au    9.438804   16.348399    8.899098) from the corresponding 
>> FORCE_EVAL section". What I found strange is that the Au atom mentioned 
>> above didn't appear in my input file. Please find attached my input and 
>> output. 
>>
>> Thank you for your help.
>>
>> Here is my input file.
>>
>> @SET project      Au-4TPA-C60-Au
>> @SET fermi_level  0.38
>> @SET v_bias_volt  0
>> @SET temperature  293.0
>>
>> @SET basis_set_path BASIS_MOLOPT
>> @SET potential_path GTH_POTENTIALS
>>
>> @SET xc_functional  PBE
>>
>> @SET cutoff         500
>> @SET added_mos      10000
>> @SET max_scf        300
>> @SET eps_scf        1e-7
>>
>> &GLOBAL
>>    PROJECT              ${project}
>>    RUN_TYPE             negf
>>    PRINT_LEVEL          low
>>    EXTENDED_FFT_LENGTHS .true.
>> &END GLOBAL
>>
>> &MULTIPLE_FORCE_EVALS
>>    # Order in which the input file parser should store force environments.
>>    #
>>    # 'FORCE_EVAL_ORDER a b c' means that the a-th force environment --
>>    # which holds the entire system -- will have the internal index '0',
>>    # while the b-th and c-th force environments -- which correspond to the
>>    # 1st and 2nd semi-infinite electrodes respectively -- will have
>>    # the internal indices '1' and '2'. Note that internal indices start 
>> from 0.
>>    #
>>    FORCE_EVAL_ORDER 1 2 3
>>
>>    # Different force environments contain non-identical molecular 
>> structures.
>>    # By default, the input parser ignores 'subsys' sections from all but 
>> the force
>>    # environment with the internal index '0'.
>>    MULTIPLE_SUBSYS .true.
>> &END
>>
>> &NEGF
>>    &CONTACT
>>       FORCE_EVAL_SECTION 1
>>
>>       &BULK_REGION
>>          MOLNAME  L2 L3
>>       &END
>>       &SCREENING_REGION
>>          MOLNAME L1
>>       &END
>>
>>       # comment the next line to recompute Fermi level for this (bulk) 
>> contact from scratch
>>       #FERMI_LEVEL  ${fermi_level}
>>       TEMPERATURE [K] ${temperature}
>>       ELECTRIC_POTENTIAL [eV] ${v_bias_volt}/2
>>    &END CONTACT
>>
>>    &CONTACT
>>       FORCE_EVAL_SECTION 2
>>
>>       &BULK_REGION
>>          MOLNAME R2 R3
>>       &END
>>       &SCREENING_REGION
>>          MOLNAME R1
>>       &END
>>
>>       # comment the next line to recompute Fermi level for this (bulk) 
>> contact from scratch.
>>       # Alternatively the keyword REFINE_FERMI_LEVEL can be given, so the 
>> next line will be
>>       # interpreted as an initial guess
>>       #FERMI_LEVEL  ${fermi_level}
>>       TEMPERATURE [K] ${temperature}
>>       ELECTRIC_POTENTIAL [eV] -${v_bias_volt}/2
>>    &END CONTACT
>>
>>    &SCATTERING_REGION
>>       MOLNAME L0 S R0
>>    &END SCATTERING_REGION
>>
>>    &MIXING
>>       ALPHA   0.03
>>       METHOD  broyden_mixing
>>       NBUFFER 4
>>    &END MIXING
>>
>>    INTEGRATION_MIN_POINTS 64
>>    INTEGRATION_MAX_POINTS 768
>>
>>    ENERGY_LBOUND -3.0
>>    EPS_DENSITY   1e-4
>>    EPS_SCF       1e-3
>>    MAX_SCF        500
>>
>>    #V_SHIFT           0.07621247
>>    V_SHIFT_MAX_ITERS   30
>>
>>    # split available MPI processes into a number of groups with 12 
>> processes per group;
>>    # each group will then compute lesser Green's functions at its own set 
>> of energy points
>>    #NPROC_POINT 12
>>
>>    # recompute retarded surface Green's function at every NEGF 
>> self-consistent iteration.
>>    # In case of NEGF calculations with applied bias, it may be worth to 
>> disable caching,
>>    # so adaptive integration routines will prefer points that minimised 
>> overall error
>>    # in best possible way to ones that have precomputed Green's functions.
>>    DISABLE_CACHE true
>> &END NEGF
>>
>> &FORCE_EVAL
>>    METHOD Quickstep
>>
>>    &DFT
>>       BASIS_SET_FILE_NAME ${basis_set_path}
>>       POTENTIAL_FILE_NAME ${potential_path}
>>       WFN_RESTART_FILE_NAME Au-4TPA-C60-Au.wfn
>>
>>       &MGRID
>>          CUTOFF ${cutoff}
>>       &END MGRID
>>
>>       &SCF
>>          MAX_SCF   ${max_scf}
>>          EPS_SCF   ${eps_scf}
>>          SCF_GUESS restart
>>          ADDED_MOS ${added_mos}
>>
>>          &SMEAR
>>             ELECTRONIC_TEMPERATURE [K] ${temperature}
>>             METHOD fermi_dirac
>>          &END SMEAR
>>
>>          &MIXING
>>             ALPHA   0.1
>>             METHOD  broyden_mixing
>>             NBUFFER 4
>>          &END MIXING
>>       &END SCF
>>
>>       &POISSON
>>          PERIODIC xyz
>>       &END POISSON
>>
>>       &XC
>>          &XC_FUNCTIONAL ${xc_functional}
>>          &END XC_FUNCTIONAL
>>       &END XC
>>    &END DFT
>>
>>    &SUBSYS
>>       &CELL
>>          # Lattice constant = 2.920 Angstroms
>>          # Lattice constant = 2.920 Angstroms
>>          A 9.9896000000 <(989)%20600-0000>        0.0000000000      
>>  0.0000000000
>>          B 4.9948000000        8.6512000000 <(651)%20200-0000>      
>>  0.0000000000
>>          C 0.0000000000        0.0000000000       76.801904000
>>
>>          PERIODIC xyz
>>       &END CELL
>>
>>       &COORD
>> Au      6.659699    8.651200    0.000000 L3
>> Au      11.654600    8.651200    0.000000 L3
>> Au      4.162300    1.441900    0.000000 L3
>> Au      9.157201    1.441900    0.000000 L3
>> Au      6.659800    2.883800    0.000000 L3
>> Au      1.665000    2.883800    0.000000 L3
>> Au      4.162300    4.325600    0.000000 L3
>> Au      9.157200    4.325600    0.000000 L3
>> Au      6.659800    5.767500    0.000000 L3
>> Au      11.654600    5.767500    0.000000 L3
>> Au      9.157200    7.209401    0.000000 L3
>> Au      4.162400    7.209401    0.000000 L3
>> Au      8.324699    8.651200    2.354600 L3
>> Au      13.319500    8.651200    2.354600 L3
>> Au      5.827300    1.441900    2.354600 L3
>> Au      0.832500    1.441900    2.354600 L3
>> Au      8.324700    2.883800    2.354600 L3
>> Au      3.329900    2.883800    2.354600 L3
>> Au      5.827300    4.325600    2.354600 L3
>> Au      10.822100    4.325600    2.354600 L3
>> Au      8.324699    5.767500    2.354600 L3
>> Au      3.329900    5.767500    2.354600 L3
>> Au      10.822100    7.209401    2.354600 L3
>> Au      5.827300    7.209401    2.354600 L3
>> Au      4.994800    8.651200    4.709200 L3
>> Au      9.989599    8.651200    4.709200 L3
>> Au      2.497400    1.441900    4.709200 L3
>> Au      7.492200    1.441900    4.709200 L3
>> Au      4.994800    2.883800    4.709200 L3
>> Au      9.989600    2.883800    4.709200 L3
>> Au      2.497400    4.325600    4.709200 L3
>> Au      7.492199    4.325600    4.709200 L3
>> Au      4.994800    5.767500    4.709200 L3
>> Au      9.989600    5.767500    4.709200 L3
>> Au      7.492200    7.209401    4.709200 L3
>> Au      12.487000    7.209401    4.709200 L3
>> Au      6.659699    8.651200    7.063800 L2
>> Au      11.654600    8.651200    7.063800 L2
>> Au      4.162300    1.441900    7.063800 L2
>> Au      9.157201    1.441900    7.063800 L2
>> Au      6.659800    2.883800    7.063800 L2
>> Au      1.665000    2.883800    7.063800 L2
>> Au      4.162300    4.325600    7.063800 L2
>> Au      9.157200    4.325600    7.063800 L2
>> Au      6.659800    5.767500    7.063800 L2
>> Au      11.654600    5.767500    7.063800 L2
>> Au      9.157200    7.209401    7.063800 L2
>> Au      4.162400    7.209401    7.063800 L2
>> Au      8.324699    8.651200    9.418400 L2
>> Au      13.319500    8.651200    9.418400 L2
>> Au      5.827300    1.441900    9.418400 L2
>> Au      0.832500    1.441900    9.418400 L2
>> Au      8.324700    2.883800    9.418400 L2
>> Au      3.329900    2.883800    9.418400 L2
>> Au      5.827300    4.325600    9.418400 L2
>> Au      10.822100    4.325600    9.418400 L2
>> Au      8.324699    5.767500    9.418400 L2
>> Au      3.329900    5.767500    9.418400 L2
>> Au      10.822100    7.209401    9.418400 L2
>> Au      5.827300    7.209401    9.418400 L2
>> Au      4.994800    8.651200    11.772900 L2
>> Au      9.989599    8.651200    11.772900 L2
>> Au      2.497400    1.441900    11.772900 L2
>> Au      7.492200    1.441900    11.772900 L2
>> Au      4.994800    2.883800    11.772900 L2
>> Au      9.989600    2.883800    11.772900 L2
>> Au      2.497400    4.325600    11.772900 L2
>> Au      7.492199    4.325600    11.772900 L2
>> Au      4.994800    5.767500    11.772900 L2
>> Au      9.989600    5.767500    11.772900 L2
>> Au      7.492200    7.209401    11.772900 L2
>> Au      12.487000    7.209401    11.772900 L2
>> Au      6.659699    8.651200    14.127601 L1
>> Au      11.654600    8.651200    14.127601 L1
>> Au      4.162300    1.441900    14.127601 L1
>> Au      9.157201    1.441900    14.127601 L1
>> Au      6.659800    2.883800    14.127601 L1
>> Au      1.665000    2.883800    14.127601 L1
>> Au      4.162300    4.325600    14.127601 L1
>> Au      9.157200    4.325600    14.127601 L1
>> Au      6.659800    5.767500    14.127601 L1
>> Au      11.654600    5.767500    14.127601 L1
>> Au      9.157200    7.209401    14.127601 L1
>> Au      4.162400    7.209401    14.127601 L1
>> Au      8.324699    8.651200    16.482201 L1
>> Au      13.319500    8.651200    16.482201 L1
>> Au      5.827300    1.441900    16.482201 L1
>> Au      0.832500    1.441900    16.482201 L1
>> Au      8.324700    2.883800    16.482201 L1
>> Au      3.329900    2.883800    16.482201 L1
>> Au      5.827300    4.325600    16.482201 L1
>> Au      10.822100    4.325600    16.482201 L1
>> Au      8.324699    5.767500    16.482201 L1
>> Au      3.329900    5.767500    16.482201 L1
>> Au      10.822100    7.209401    16.482201 L1
>> Au      5.827300    7.209401    16.482201 L1
>> Au      4.994800    8.651200    18.836800 L1
>> Au      9.989599    8.651200    18.836800 L1
>> Au      2.497400    1.441900    18.836800 L1
>> Au      7.492200    1.441900    18.836800 L1
>> Au      4.994800    2.883800    18.836800 L1
>> Au      9.989600    2.883800    18.836800 L1
>> Au      2.497400    4.325600    18.836800 L1
>> Au      7.492199    4.325600    18.836800 L1
>> Au      4.994800    5.767500    18.836800 L1
>> Au      9.989600    5.767500    18.836800 L1
>> Au      7.492200    7.209401    18.836800 L1
>> Au      12.487000    7.209401    18.836800 L1
>> Au      6.659699    8.651200    21.191401 L0
>> Au      11.654600    8.651200    21.191401 L0
>> Au      4.162300    1.441900    21.191401 L0
>> Au      9.157201    1.441900    21.191401 L0
>> Au      6.659800    2.883800    21.191401 L0
>> Au      1.665000    2.883800    21.191401 L0
>> Au      4.162300    4.325600    21.191401 L0
>> Au      9.157200    4.325600    21.191401 L0
>> Au      6.659800    5.767500    21.191401 L0
>> Au      11.654600    5.767500    21.191401 L0
>> Au      9.157200    7.209401    21.191401 L0
>> Au      4.162400    7.209401    21.191401 L0
>> Au      8.324699    8.651200    23.546001 L0
>> Au      13.319500    8.651200    23.546001 L0
>> Au      5.827300    1.441900    23.546001 L0
>> Au      0.832500    1.441900    23.546001 L0
>> Au      8.324700    2.883800    23.546001 L0
>> Au      3.329900    2.883800    23.546001 L0
>> Au      5.827300    4.325600    23.546001 L0
>> Au      10.822100    4.325600    23.546001 L0
>> Au      8.324699    5.767500    23.546001 L0
>> Au      3.329900    5.767500    23.546001 L0
>> Au      10.822100    7.209401    23.546001 L0
>> Au      5.827300    7.209401    23.546001 L0
>> Au      4.994800    8.651200    25.900501 L0
>> Au      9.989599    8.651200    25.900501 L0
>> Au      2.497400    1.441900    25.900501 L0
>> Au      7.492200    1.441900    25.900501 L0
>> Au      4.994800    2.883800    25.900501 L0
>> Au      9.989600    2.883800    25.900501 L0
>> Au      2.497400    4.325600    25.900501 L0
>> Au      7.492199    4.325600    25.900501 L0
>> Au      4.994800    5.767500    25.900501 L0
>> Au      9.989600    5.767500    25.900501 L0
>> Au      7.492200    7.209401    25.900501 L0
>> Au      12.487000    7.209401    25.900501 L0
>> H      6.135220    6.365897    30.845380999999996    S
>> C      7.017228    6.097746    31.434368    S
>> C      6.994224    6.248103    32.813154    S
>> H      6.098742    6.637346    33.306813    S
>> C      8.133347    5.918045    33.593515    S
>> N      8.135972    6.121728    34.96992    S
>> C      9.283717    5.416500    32.931788    S
>> H      10.170585    5.157507    33.518111    S
>> C      9.297813    5.276695    31.552042    S
>> H      10.197830    4.902434    31.055082999999996    S
>> C      8.171635    5.619315    30.740966    S
>> S      8.223920    5.494425    29.018895999999998    S
>> C      4.827984    7.907365    39.047452    S
>> C      5.691122    8.980087    39.492661    S
>> C      6.628941    9.260723    38.420794    S
>> C      6.346789    8.379585    37.315127    S
>> C      5.223137    7.544895    37.696557999999996    S
>> C      5.220366    6.198122    37.315154    S
>> C      6.239676    5.692897    36.430504    S
>> C      7.092373    6.615593    35.800297    S
>> C      7.360399    7.879104    36.473791    S
>> C      8.772153    8.153042    36.806324    S
>> C      9.024763    9.018179    37.907789    S
>> C      7.951706    9.593769    38.702919    S
>> C      8.381148    9.686503    40.093328    S
>> C      7.479693    9.418714    41.134721    S
>> C      6.108102    9.053539    40.827678    S
>> C      5.689614    8.032401    41.773621    S
>> C      6.801672    7.769768    42.6741    S
>> C      7.907322    8.630513    42.28236    S
>> C      9.226157    8.154264    42.355087    S
>> C      10.160555    8.448496    41.281264    S
>> C      9.736751    9.192084    40.166714999999996    S
>> C      10.133673    8.797588    38.823617    S
>> C      10.959517    7.690608    38.654945    S
>> C      10.718543    6.796197    37.553504    S
>> C      9.705500    7.029899    36.600597    S
>> C      9.170635    5.864939    35.912309    S
>> C      9.176350    4.631827    36.588797    S
>> C      7.974382    3.869325    36.984809999999996    S
>> C      6.636718    4.350097    36.912766    S
>> C      5.722062    4.033425    38.021296    S
>> C      6.118268    3.261915    39.123129    S
>> C      7.471094    2.771700    39.195458    S
>> C      8.368667    3.078451    38.165104    S
>> C      9.732238    3.407868    38.52316    S
>> C      10.194160    4.399479    37.583352    S
>> C      11.009902    5.450755    38.01226    S
>> C      11.415622    5.521570    39.404651    S
>> C      11.400043    6.915571    39.80163    S
>> C      11.005926    7.282449    41.091696    S
>> C      10.591882    6.259820    42.041101    S
>> C      9.488309    6.797750    42.821909    S
>> C      8.419827    5.964579    43.192257    S
>> C      7.052556    6.459408    43.115365    S
>> C      6.203670    5.365352    42.670165    S
>> C      7.043674    4.195483    42.462704    S
>> C      8.412519    4.565039    42.791239    S
>> C      9.474857    4.049382    42.034903    S
>> C      10.585765    4.909800    41.655689    S
>> C      11.001566    4.536764    40.312818    S
>> C      10.142125    3.460559    39.861482    S
>> C      9.204899    3.153182    40.922586    S
>> C      7.890094    2.807836    40.592369    S
>> C      6.790913    3.334067    41.381336    S
>> C      5.690549    3.607614    40.471871    S
>> C      4.871910    4.720446    40.6883    S
>> C      5.134144    5.619621    41.797615    S
>> C      4.874011    6.976134    41.341005    S
>> C      4.443619    6.911500    39.955932    S
>> C      4.449165    5.516640    39.551786    S
>> C      4.856629    5.169441    38.259973    S
>> Au      8.324699    5.767500    46.192200 R0
>> Au      6.659699    8.651200    48.546803 R0
>> Au      11.654600    8.651200    48.546803 R0
>> Au      4.162300    1.441900    48.546803 R0
>> Au      9.157201    1.441900    48.546803 R0
>> Au      6.659800    2.883800    48.546803 R0
>> Au      1.665000    2.883800    48.546803 R0
>> Au      4.162300    4.325600    48.546803 R0
>> Au      9.157200    4.325600    48.546803 R0
>> Au      6.659800    5.767500    48.546803 R0
>> Au      11.654600    5.767500    48.546803 R0
>> Au      9.157200    7.209401    48.546803 R0
>> Au      4.162400    7.209401    48.546803 R0
>> Au      8.324699    8.651200    50.901405 R0
>> Au      13.319500    8.651200    50.901405 R0
>> Au      5.827300    1.441900    50.901405 R0
>> Au      0.832500    1.441900    50.901405 R0
>> Au      8.324700    2.883800    50.901405 R0
>> Au      3.329900    2.883800    50.901405 R0
>> Au      5.827300    4.325600    50.901405 R0
>> Au      10.822100    4.325600    50.901405 R0
>> Au      8.324699    5.767500    50.901405 R0
>> Au      3.329900    5.767500    50.901405 R0
>> Au      10.822100    7.209401    50.901405 R0
>> Au      5.827300    7.209401    50.901405 R0
>> Au      4.994800    8.651200    53.255802 R0
>> Au      9.989599    8.651200    53.256001 R0
>> Au      2.497400    1.441900    53.256001 R0
>> Au      7.492200    1.441900    53.256001 R0
>> Au      4.994800    2.883800    53.256001 R0
>> Au      9.989600    2.883800    53.256001 R0
>> Au      2.497400    4.325600    53.256001 R0
>> Au      7.492199    4.325600    53.256001 R0
>> Au      4.994800    5.767500    53.256001 R0
>> Au      9.989600    5.767500    53.256001 R0
>> Au      7.492200    7.209401    53.256001 R0
>> Au      12.487000    7.209401    53.256001 R0
>> Au      6.659699    8.651200    55.610504 R1
>> Au      11.654600    8.651200    55.610504 R1
>> Au      4.162300    1.441900    55.610504 R1
>> Au      9.157201    1.441900    55.610504 R1
>> Au      6.659800    2.883800    55.610504 R1
>> Au      1.665000    2.883800    55.610504 R1
>> Au      4.162300    4.325600    55.610504 R1
>> Au      9.157200    4.325600    55.610504 R1
>> Au      6.659800    5.767500    55.610504 R1
>> Au      11.654600    5.767500    55.610504 R1
>> Au      9.157200    7.209401    55.610504 R1
>> Au      4.162400    7.209401    55.610504 R1
>> Au      8.324699    8.651200    57.965103 R1
>> Au      13.319500    8.651200    57.965103 R1
>> Au      5.827300    1.441900    57.965103 R1
>> Au      0.832500    1.441900    57.965103 R1
>> Au      8.324700    2.883800    57.965103 R1
>> Au      3.329900    2.883800    57.965103 R1
>> Au      5.827300    4.325600    57.965103 R1
>> Au      10.822100    4.325600    57.965103 R1
>> Au      8.324699    5.767500    57.965103 R1
>> Au      3.329900    5.767500    57.965103 R1
>> Au      10.822100    7.209401    57.965103 R1
>> Au      5.827300    7.209401    57.965103 R1
>> Au      4.994800    8.651200    60.319698 R1
>> Au      9.989599    8.651200    60.319698 R1
>> Au      2.497400    1.441900    60.319698 R1
>> Au      7.492200    1.441900    60.319698 R1
>> Au      4.994800    2.883800    60.319698 R1
>> Au      9.989600    2.883800    60.319698 R1
>> Au      2.497400    4.325600    60.319698 R1
>> Au      7.492199    4.325600    60.319698 R1
>> Au      4.994800    5.767500    60.319698 R1
>> Au      9.989600    5.767500    60.319698 R1
>> Au      7.492200    7.209401    60.319698 R1
>> Au      12.487000    7.209401    60.319698 R1
>> Au      6.659699    8.651200    62.674404 R2
>> Au      11.654600    8.651200    62.674404 R2
>> Au      4.162300    1.441900    62.674404 R2
>> Au      9.157201    1.441900    62.674404 R2
>> Au      6.659800    2.883800    62.674404 R2
>> Au      1.665000    2.883800    62.674404 R2
>> Au      4.162300    4.325600    62.674404 R2
>> Au      9.157200    4.325600    62.674404 R2
>> Au      6.659800    5.767500    62.674404 R2
>> Au      11.654600    5.767500    62.674404 R2
>> Au      9.157200    7.209401    62.674404 R2
>> Au      4.162400    7.209401    62.674404 R2
>> Au      8.324699    8.651200    65.028999 R2
>> Au      13.319500    8.651200    65.028999 R2
>> Au      5.827300    1.441900    65.028999 R2
>> Au      0.832500    1.441900    65.028999 R2
>> Au      8.324700    2.883800    65.028999 R2
>> Au      3.329900    2.883800    65.028999 R2
>> Au      5.827300    4.325600    65.028999 R2
>> Au      10.822100    4.325600    65.028999 R2
>> Au      8.324699    5.767500    65.028999 R2
>> Au      3.329900    5.767500    65.028999 R2
>> Au      10.822100    7.209401    65.028999 R2
>> Au      5.827300    7.209401    65.028999 R2
>> Au      4.994800    8.651200    67.383400 R2
>> Au      9.989599    8.651200    67.383606 R2
>> Au      2.497400    1.441900    67.383606 R2
>> Au      7.492200    1.441900    67.383606 R2
>> Au      4.994800    2.883800    67.383606 R2
>> Au      9.989600    2.883800    67.383606 R2
>> Au      2.497400    4.325600    67.383606 R2
>> Au      7.492199    4.325600    67.383606 R2
>> Au      4.994800    5.767500    67.383606 R2
>> Au      9.989600    5.767500    67.383606 R2
>> Au      7.492200    7.209401    67.383606 R2
>> Au      12.487000    7.209401    67.383606 R2
>> Au      6.659699    8.651200    69.738098 R3
>> Au      11.654600    8.651200    69.738098 R3
>> Au      4.162300    1.441900    69.738098 R3
>> Au      9.157201    1.441900    69.738098 R3
>> Au      6.659800    2.883800    69.738098 R3
>> Au      1.665000    2.883800    69.738098 R3
>> Au      4.162300    4.325600    69.738098 R3
>> Au      9.157200    4.325600    69.738098 R3
>> Au      6.659800    5.767500    69.738098 R3
>> Au      11.654600    5.767500    69.738098 R3
>> Au      9.157200    7.209401    69.738098 R3
>> Au      4.162400    7.209401    69.738098 R3
>> Au      8.324699    8.651200    72.092697 R3
>> Au      13.319500    8.651200    72.092697 R3
>> Au      5.827300    1.441900    72.092697 R3
>> Au      0.832500    1.441900    72.092697 R3
>> Au      8.324700    2.883800    72.092697 R3
>> Au      3.329900    2.883800    72.092697 R3
>> Au      5.827300    4.325600    72.092697 R3
>> Au      10.822100    4.325600    72.092697 R3
>> Au      8.324699    5.767500    72.092697 R3
>> Au      3.329900    5.767500    72.092697 R3
>> Au      10.822100    7.209401    72.092697 R3
>> Au      5.827300    7.209401    72.092697 R3
>> Au      4.994800    8.651200    74.447304 R3
>> Au      9.989599    8.651200    74.447304 R3
>> Au      2.497400    1.441900    74.447304 R3
>> Au      7.492200    1.441900    74.447304 R3
>> Au      4.994800    2.883800    74.447304 R3
>> Au      9.989600    2.883800    74.447304 R3
>> Au      2.497400    4.325600    74.447304 R3
>> Au      7.492199    4.325600    74.447304 R3
>> Au      4.994800    5.767500    74.447304 R3
>> Au      9.989600    5.767500    74.447304 R3
>> Au      7.492200    7.209401    74.447304 R3
>> Au      12.487000    7.209401    74.447304 R3
>>
>>      &END COORD
>>
>>      &KIND Au
>>         BASIS_SET SZV-MOLOPT-SR-GTH
>>         POTENTIAL GTH-PBE-q11
>>      &END KIND
>>      &KIND C
>>         BASIS_SET TZVP-MOLOPT-GTH
>>         POTENTIAL GTH-PBE-q4
>>      &END KIND
>>      &KIND S
>>         BASIS_SET TZVP-MOLOPT-GTH
>>         POTENTIAL GTH-PBE-q6
>>      &END KIND
>>      &KIND H
>>         BASIS_SET TZVP-MOLOPT-GTH
>>         POTENTIAL GTH-PBE-q1
>>      &END KIND
>>      &KIND N
>>         BASIS_SET TZVP-MOLOPT-GTH
>>         POTENTIAL GTH-PBE-q5
>>      &END KIND
>>   &END SUBSYS
>> &END FORCE_EVAL
>>
>> &FORCE_EVAL
>>    METHOD Quickstep
>>
>>    &DFT
>>       BASIS_SET_FILE_NAME ${basis_set_path}
>>       POTENTIAL_FILE_NAME ${potential_path}
>>       WFN_RESTART_FILE_NAME Au-4TPA-C60-Au-lead1.kp
>>
>>       &MGRID
>>          CUTOFF ${cutoff}
>>       &END MGRID
>>
>>       &SCF
>>          MAX_SCF   ${max_scf}
>>          EPS_SCF   ${eps_scf}
>>          SCF_GUESS restart
>>          ADDED_MOS ${added_mos}
>>
>>          &SMEAR
>>             ELECTRONIC_TEMPERATURE [K] ${temperature}
>>             METHOD fermi_dirac
>>          &END SMEAR
>>
>>          &MIXING
>>             ALPHA   0.1
>>             METHOD  broyden_mixing
>>             NBUFFER 4
>>          &END MIXING
>>
>>          &PRINT
>>             &RESTART
>>                FILENAME lead1-RESTART
>>             &END RESTART
>>          &END PRINT
>>       &END SCF
>>
>>       &POISSON
>>          PERIODIC xyz
>>       &END POISSON
>>
>>       &XC
>>         &XC_FUNCTIONAL ${xc_functional}
>>         &END XC_FUNCTIONAL
>>       &END XC
>>
>>       &KPOINTS
>>          SCHEME  MONKHORST-PACK  6 6 6
>>          SYMMETRY OFF
>>          EPS_GEO 1.e-3
>>          FULL_GRID ON
>>       &END KPOINTS
>>    &END DFT
>>
>>    &SUBSYS
>>       &CELL
>>          # Lattice constant = 2.920 Angstroms
>>          A 9.9896000000 <(989)%20600-0000>        0.0000000000      
>>  0.0000000000
>>          B 4.9948000000        8.6512000000 <(651)%20200-0000>      
>>  0.0000000000
>>          C 0.0000000000        0.0000000000       7.0638000000
>>          #PERIODIC xyz
>>       &END CELL
>>
>>       &COORD
>> Au      6.659699    8.651200    7.063800 L2
>> Au      11.654600    8.651200    7.063800 L2
>> Au      4.162300    1.441900    7.063800 L2
>> Au      9.157201    1.441900    7.063800 L2
>> Au      6.659800    2.883800    7.063800 L2
>> Au      1.665000    2.883800    7.063800 L2
>> Au      4.162300    4.325600    7.063800 L2
>> Au      9.157200    4.325600    7.063800 L2
>> Au      6.659800    5.767500    7.063800 L2
>> Au      11.654600    5.767500    7.063800 L2
>> Au      9.157200    7.209401    7.063800 L2
>> Au      4.162400    7.209401    7.063800 L2
>> Au      8.324699    8.651200    9.418400 L2
>> Au      13.319500    8.651200    9.418400 L2
>> Au      5.827300    1.441900    9.418400 L2
>> Au      0.832500    1.441900    9.418400 L2
>> Au      8.324700    2.883800    9.418400 L2
>> Au      3.329900    2.883800    9.418400 L2
>> Au      5.827300    4.325600    9.418400 L2
>> Au      10.822100    4.325600    9.418400 L2
>> Au      8.324699    5.767500    9.418400 L2
>> Au      3.329900    5.767500    9.418400 L2
>> Au      10.822100    7.209401    9.418400 L2
>> Au      5.827300    7.209401    9.418400 L2
>> Au      4.994800    8.651200    11.772900 L2
>> Au      9.989599    8.651200    11.772900 L2
>> Au      2.497400    1.441900    11.772900 L2
>> Au      7.492200    1.441900    11.772900 L2
>> Au      4.994800    2.883800    11.772900 L2
>> Au      9.989600    2.883800    11.772900 L2
>> Au      2.497400    4.325600    11.772900 L2
>> Au      7.492199    4.325600    11.772900 L2
>> Au      4.994800    5.767500    11.772900 L2
>> Au      9.989600    5.767500    11.772900 L2
>> Au      7.492200    7.209401    11.772900 L2
>> Au      12.487000    7.209401    11.772900 L2
>>       &END COORD
>>
>>       &KIND Au
>>          BASIS_SET SZV-MOLOPT-SR-GTH
>>          POTENTIAL GTH-PBE-q11
>>       &END KIND
>>    &END SUBSYS
>> &END FORCE_EVAL
>>
>> &FORCE_EVAL
>>    METHOD Quickstep
>>
>>    &DFT
>>       BASIS_SET_FILE_NAME ${basis_set_path}
>>       POTENTIAL_FILE_NAME ${potential_path}
>>       WFN_RESTART_FILE_NAME Au-4TPA-C60-Au-lead2.kp
>>
>>       &MGRID
>>          CUTOFF ${cutoff}
>>       &END MGRID
>>
>>       &SCF
>>          MAX_SCF   ${max_scf}
>>          EPS_SCF   ${eps_scf}
>>          SCF_GUESS restart
>>          ADDED_MOS ${added_mos}
>>
>>          &SMEAR
>>             ELECTRONIC_TEMPERATURE [K] ${temperature}
>>             METHOD fermi_dirac
>>          &END SMEAR
>>
>>          &MIXING
>>             ALPHA   0.1
>>             METHOD  broyden_mixing
>>             NBUFFER 4
>>          &END MIXING
>>
>>          &PRINT
>>             &RESTART
>>                FILENAME lead2-RESTART
>>             &END RESTART
>>          &END PRINT
>>       &END SCF
>>
>>       &POISSON
>>          PERIODIC xyz
>>       &END POISSON
>>
>>       &XC
>>          &XC_FUNCTIONAL ${xc_functional}
>>          &END XC_FUNCTIONAL
>>       &END XC
>>
>>       &KPOINTS
>>          SCHEME  MONKHORST-PACK  6 6 6
>>          SYMMETRY OFF
>>          EPS_GEO 1.e-3
>>          FULL_GRID ON
>>        &END KPOINTS
>>    &END DFT
>>
>>    &SUBSYS
>>       &CELL
>>          # Lattice constant = 2.920 Angstroms
>>          A 9.9896000000 <(989)%20600-0000>        0.0000000000      
>>  0.0000000000
>>          B 4.9948000000        8.6512000000 <(651)%20200-0000>      
>>  0.0000000000
>>          C 0.0000000000        0.0000000000       7.0638000000
>>          PERIODIC xyz
>>       &END CELL
>>
>>       &COORD
>> Au      6.659699    8.651200    62.674404 R2
>> Au      11.654600    8.651200    62.674404 R2
>> Au      4.162300    1.441900    62.674404 R2
>> Au      9.157201    1.441900    62.674404 R2
>> Au      6.659800    2.883800    62.674404 R2
>> Au      1.665000    2.883800    62.674404 R2
>> Au      4.162300    4.325600    62.674404 R2
>> Au      9.157200    4.325600    62.674404 R2
>> Au      6.659800    5.767500    62.674404 R2
>> Au      11.654600    5.767500    62.674404 R2
>> Au      9.157200    7.209401    62.674404 R2
>> Au      4.162400    7.209401    62.674404 R2
>> Au      8.324699    8.651200    65.028999 R2
>> Au      13.319500    8.651200    65.028999 R2
>> Au      5.827300    1.441900    65.028999 R2
>> Au      0.832500    1.441900    65.028999 R2
>> Au      8.324700    2.883800    65.028999 R2
>> Au      3.329900    2.883800    65.028999 R2
>> Au      5.827300    4.325600    65.028999 R2
>> Au      10.822100    4.325600    65.028999 R2
>> Au      8.324699    5.767500    65.028999 R2
>> Au      3.329900    5.767500    65.028999 R2
>> Au      10.822100    7.209401    65.028999 R2
>> Au      5.827300    7.209401    65.028999 R2
>> Au      4.994800    8.651200    67.383400 R2
>> Au      9.989599    8.651200    67.383606 R2
>> Au      2.497400    1.441900    67.383606 R2
>> Au      7.492200    1.441900    67.383606 R2
>> Au      4.994800    2.883800    67.383606 R2
>> Au      9.989600    2.883800    67.383606 R2
>> Au      2.497400    4.325600    67.383606 R2
>> Au      7.492199    4.325600    67.383606 R2
>> Au      4.994800    5.767500    67.383606 R2
>> Au      9.989600    5.767500    67.383606 R2
>> Au      7.492200    7.209401    67.383606 R2
>> Au      12.487000    7.209401    67.383606 R2
>>       &END COORD
>>
>>       &KIND Au
>>          BASIS_SET SZV-MOLOPT-SR-GTH
>>          POTENTIAL GTH-PBE-q11
>>       &END KIND
>>    &END SUBSYS
>> &END FORCE_EVAL
>>
>>
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