[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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