[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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