[CP2K-user] NEGF calculation

Li Mengxuan limeng... at outlook.com
Fri Nov 27 23:20:54 UTC 2020


Dear Dmitry Ryndyk,

Thank you very much! I got the calculation running.

在2020年11月26日星期四 UTC 下午1:42:02<Dmitry Ryndyk> 写道:

> 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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