[CP2K-user] [CP2K:20173] Re: Vibrational Analysis
Marcella Iannuzzi
marci.akira at gmail.com
Sun May 5 10:02:40 UTC 2024
It is not possible to calculate this property with this method for your
system with cp2k!
On Sunday, May 5, 2024 at 11:54:24 AM UTC+2 rafiq... at gmail.com wrote:
> (Please check my input file, when i remove the pbc then my system will not
> treat as periodic) so what should i change in my input please consider my
> input , thanks for your response
>
> &GLOBAL
> PROJECT MoP100-44-pos-1
> PRINT_LEVEL LOW
> RUN_TYPE VIBRATIONAL_ANALYSIS
> &END GLOBAL
>
> &FORCE_EVAL
> METHOD Quickstep
> &SUBSYS
> &CELL
> A 12.87500000 0.00000000 0.00000000
> B 6.43800000 11.15094310 0.00000000
> C 0.00000000 0.00000000 31.10900000
> PERIODIC XYZ
> &END CELL
> &COORD
> Mo 3.21900000 1.85900000 1.58700000
> Mo 3.21900000 1.85900000 4.76100000
> Mo 3.21900000 1.85900000 7.93500000
> Mo 3.21900000 1.85900000 11.00400000
> P 0.00000000 0.00000000 0.00000000
> P 0.00000000 0.00000000 3.17400000
> P 0.00000000 0.00000000 6.34800000
> P 12.87500000 0.00000000 9.58600000
> Mo 6.43800000 1.85900000 1.58700000
> Mo 6.43800000 1.85900000 4.76100000
> Mo 6.43800000 1.85900000 7.93500000
> Mo 6.43800000 1.85900000 11.00400000
> P 3.21900000 0.00000000 0.00000000
> P 3.21900000 0.00000000 3.17400000
> P 3.21900000 0.00000000 6.34800000
> P 3.21900000 0.00000000 9.58600000
> Mo 9.65600000 1.85900000 1.58700000
> Mo 9.65600000 1.85900000 4.76100000
> Mo 9.65600000 1.85900000 7.93500000
> Mo 9.65600000 1.85900000 11.00400000
> P 6.43800000 0.00000000 0.00000000
> P 6.43800000 0.00000000 3.17400000
> P 6.43800000 0.00000000 6.34800000
> P 6.43800000 0.00000000 9.58600000
> Mo 12.87500000 1.85900000 1.58700000
> Mo 12.87500000 1.85900000 4.76100000
> Mo 12.87500000 1.85900000 7.93500000
> Mo 12.87500000 1.85900000 11.00400000
> P 9.65600000 0.00000000 0.00000000
> P 9.65600000 0.00000000 3.17400000
> P 9.65600000 0.00000000 6.34800000
> P 9.65600000 0.00000000 9.58600000
> Mo 4.82800000 4.64600000 1.58700000
> Mo 4.82800000 4.64600000 4.76100000
> Mo 4.82800000 4.64600000 7.93500000
> Mo 4.82800000 4.64600000 11.00400000
> P 1.60900000 2.78800000 0.00000000
> P 1.60900000 2.78800000 3.17400000
> P 1.60900000 2.78800000 6.34800000
> P 14.48500000 2.78800000 9.58600000
> Mo 8.04700000 4.64600000 1.58700000
> Mo 8.04700000 4.64600000 4.76100000
> Mo 8.04700000 4.64600000 7.93500000
> Mo 8.04700000 4.64600000 11.00400000
> P 4.82800000 2.78800000 0.00000000
> P 4.82800000 2.78800000 3.17400000
> P 4.82800000 2.78800000 6.34800000
> P 4.82800000 2.78800000 9.58600000
> Mo 11.26600000 4.64600000 1.58700000
> Mo 11.26600000 4.64600000 4.76100000
> Mo 11.26600000 4.64600000 7.93500000
> Mo 11.26600000 4.64600000 11.00400000
> P 8.04700000 2.78800000 0.00000000
> P 8.04700000 2.78800000 3.17400000
> P 8.04700000 2.78800000 6.34800000
> P 8.04700000 2.78800000 9.58600000
> Mo 14.48500000 4.64600000 1.58700000
> Mo 14.48500000 4.64600000 4.76100000
> Mo 14.48500000 4.64600000 7.93500000
> Mo 14.48500000 4.64600000 11.00400000
> P 11.26600000 2.78800000 0.00000000
> P 11.26600000 2.78800000 3.17400000
> P 11.26600000 2.78800000 6.34800000
> P 11.26600000 2.78800000 9.58600000
> Mo 6.43800000 7.43400000 1.58700000
> Mo 6.43800000 7.43400000 4.76100000
> Mo 6.43800000 7.43400000 7.93500000
> Mo 6.43800000 7.43400000 11.00400000
> P 3.21900000 5.57600000 0.00000000
> P 3.21900000 5.57600000 3.17400000
> P 3.21900000 5.57600000 6.34800000
> P 3.21900000 5.57600000 9.58600000
> Mo 9.65600000 7.43400000 1.58700000
> Mo 9.65600000 7.43400000 4.76100000
> Mo 9.65600000 7.43400000 7.93500000
> Mo 9.65600000 7.43400000 11.00400000
> P 6.43800000 5.57600000 0.00000000
> P 6.43800000 5.57600000 3.17400000
> P 6.43800000 5.57600000 6.34800000
> P 6.43800000 5.57600000 9.58600000
> Mo 12.87500000 7.43400000 1.58700000
> Mo 12.87500000 7.43400000 4.76100000
> Mo 12.87500000 7.43400000 7.93500000
> Mo 12.87500000 7.43400000 11.00400000
> P 9.65600000 5.57600000 0.00000000
> P 9.65600000 5.57600000 3.17400000
> P 9.65600000 5.57600000 6.34800000
> P 9.65600000 5.57600000 9.58600000
> Mo 16.09400000 7.43400000 1.58700000
> Mo 16.09400000 7.43400000 4.76100000
> Mo 16.09400000 7.43400000 7.93500000
> Mo 16.09400000 7.43400000 11.00400000
> P 12.87500000 5.57600000 0.00000000
> P 12.87500000 5.57600000 3.17400000
> P 12.87500000 5.57600000 6.34800000
> P 12.87500000 5.57600000 9.58600000
> Mo 8.04700000 10.22200000 1.58700000
> Mo 8.04700000 10.22200000 4.76100000
> Mo 8.04700000 10.22200000 7.93500000
> Mo 8.04700000 10.22200000 11.00400000
> P 4.82800000 8.36300000 0.00000000
> P 17.70300000 8.36300000 3.17400000
> P 17.70300000 8.36300000 6.34800000
> P 4.82800000 8.36300000 9.58600000
> Mo 11.26600000 10.22200000 1.58700000
> Mo 11.26600000 10.22200000 4.76100000
> Mo 11.26600000 10.22200000 7.93500000
> Mo 11.26600000 10.22200000 11.00400000
> P 8.04700000 8.36300000 0.00000000
> P 8.04700000 8.36300000 3.17400000
> P 8.04700000 8.36300000 6.34800000
> P 8.04700000 8.36300000 9.58600000
> Mo 14.48500000 10.22200000 1.58700000
> Mo 14.48500000 10.22200000 4.76100000
> Mo 14.48500000 10.22200000 7.93500000
> Mo 14.48500000 10.22200000 11.00400000
> P 11.26600000 8.36300000 0.00000000
> P 11.26600000 8.36300000 3.17400000
> P 11.26600000 8.36300000 6.34800000
> P 11.26600000 8.36300000 9.58600000
> Mo 17.70300000 10.22200000 1.58700000
> Mo 17.70300000 10.22200000 4.76100000
> Mo 17.70300000 10.22200000 7.93500000
> Mo 17.70300000 10.22200000 11.00400000
> P 14.48500000 8.36300000 0.00000000
> P 14.48500000 8.36300000 3.17400000
> P 14.48500000 8.36300000 6.34800000
> P 14.48500000 8.36300000 9.58600000
> &END COORD
> &KIND Mo
> ELEMENT Mo
> BASIS_SET DZVP-MOLOPT-SR-GTH-q14
> POTENTIAL GTH-PBE
> &END KIND
> &KIND P
> ELEMENT P
> BASIS_SET DZVP-MOLOPT-SR-GTH-q5
> POTENTIAL GTH-PBE
> &END KIND
> &END SUBSYS
>
> &DFT
> BASIS_SET_FILE_NAME BASIS_MOLOPT
> POTENTIAL_FILE_NAME POTENTIAL
> # WFN_RESTART_FILE_NAME MoP100-44-pos-1-RESTART.kp
> CHARGE 0
> MULTIPLICITY 1
> &KPOINTS
> SCHEME MONKHORST-PACK 3 3 1
> &END KPOINTS
> &QS
> EPS_DEFAULT 1.0E-12
> # EXTRAPOLATION USE_PREV_P
> &END QS
> &POISSON
> PERIODIC XYZ
> PSOLVER PERIODIC
> &END POISSON
> &XC
> &XC_FUNCTIONAL PBE
> &END XC_FUNCTIONAL
> &VDW_POTENTIAL
> POTENTIAL_TYPE PAIR_POTENTIAL
> &PAIR_POTENTIAL
> PARAMETER_FILE_NAME dftd3.dat
> TYPE DFTD3(BJ)
> REFERENCE_FUNCTIONAL PBE
> #CALCULATE_C9_TERM T
> &END PAIR_POTENTIAL
> &END VDW_POTENTIAL
> &END XC
> &MGRID
> CUTOFF 500
> REL_CUTOFF 65
> &END MGRID
> &SCF
> MAX_SCF 300
> EPS_SCF 1.0E-8
> # SCF_GUESS RESTART
> # IGNORE_CONVERGENCE_FAILURE
> &DIAGONALIZATION
> ALGORITHM STANDARD
> &END DIAGONALIZATION
> &MIXING
> METHOD BROYDEN_MIXING
> ALPHA 0.4
> NBROYDEN 8
> &END MIXING
> &SMEAR
> METHOD FERMI_DIRAC
> ELECTRONIC_TEMPERATURE 300
> &END SMEAR
> ADDED_MOS 64
> &PRINT
> &RESTART
> BACKUP_COPIES 0
> &END RESTART
> &END PRINT
> &END SCF
> &END DFT
> &END FORCE_EVAL
>
> &MOTION
> &CONSTRAINT
> &FIXED_ATOMS
> COMPONENTS_TO_FIX XYZ
> LIST 1 2 3 5 6 7 9 10 11 13 14 15 17 18 19 21 22 23 25 26 27 29 30
> 31 33 34 35 37 38 39 41 42 43 45 46 47 49 50 51 53 54 55 57 58 59 61 62 63
> 65 66 67 69 70 71 73 74 75 77 78 79 81 82 83 85 86 87 89 90 91 93 94 95 97
> 98 99 101 102 103 105 106 107 109 110 111 113 114 115 117 118 119 121 122
> 123 125 126 127
> &END FIXED_ATOMS
> &END CONSTRAINT
> &PRINT
> &RESTART
> BACKUP_COPIES 0
> &END RESTART
> &END PRINT
> &END MOTION
> &VIBRATIONAL_ANALYSIS
> DX 0.1
> NPROC_REP 60
> TC_PRESSURE 101325
> TC_TEMPERATURE 298.15
> THERMOCHEMISTRY T
> INTENSITIES T
> FULLY_PERIODIC T
> &PRINT
> &MOLDEN_VIB
> &END MOLDEN_VIB
> &END PRINT
> &END VIBRATIONAL_ANALYSIS
>
> On Sunday, May 5, 2024 at 5:18:00 PM UTC+8 Marcella Iannuzzi wrote:
>
>> Hi ....
>>
>> This property is calculated only for molecule in gas phase, and not when
>> PBC are used
>> Regards
>> Marcella
>>
>> On Saturday, May 4, 2024 at 4:27:07 PM UTC+2 rafiq... at gmail.com wrote:
>>
>>> Like what should I write in input file for thermochemistry calculation?
>>>
>>> On Sat, 4 May 2024, 9:32 pm Marcella Iannuzzi, <marci... at gmail.com>
>>> wrote:
>>>
>>>> Hi...
>>>>
>>>>
>>>> THERMOCHEMISTRY*: logical**= F*
>>>> <https://manual.cp2k.org/trunk/CP2K_INPUT/VIBRATIONAL_ANALYSIS.html#CP2K_INPUT.VIBRATIONAL_ANALYSIS.THERMOCHEMISTRY>
>>>>
>>>> *Lone keyword:* T
>>>>
>>>> Calculation of the thermochemical data. *Valid for molecules in the
>>>> gas phase.*
>>>>
>>>>
>>>> Regards
>>>>
>>>> Marcella
>>>> On Friday, May 3, 2024 at 2:23:20 PM UTC+2 rafiq... at gmail.com wrote:
>>>>
>>>>> &VIBRATIONAL_ANALYSIS
>>>>> DX 0.1
>>>>> NPROC_REP 48
>>>>> TC_PRESSURE 101325
>>>>> TC_TEMPERATURE 298.15
>>>>> THERMOCHEMISTRY T
>>>>> FULLY_PERIODIC T
>>>>> &END VIBRATIONAL_ANALYSIS
>>>>>
>>>>> Why in output file no thermochemistry? See my output file.
>>>>>
>>>>> VIB| 142 143
>>>>> 144
>>>>> VIB|Frequency (cm^-1) 439.322414 439.460912
>>>>> 445.868786
>>>>> VIB|Red.Masses (a.u.) 34.271393 34.269852
>>>>> 34.289785
>>>>> VIB|Frc consts (a.u.) 0.003268 0.003272
>>>>> 0.003469
>>>>> ATOM EL X Y Z X Y Z X
>>>>> Y Z
>>>>> 3 Mo 0.01 -0.00 0.02 -0.00 0.00 0.03 -0.00
>>>>> -0.00 -0.03
>>>>> 4 Mo 0.02 -0.00 -0.03 -0.00 0.01 -0.07 0.00
>>>>> 0.00 -0.05
>>>>> 8 P -0.28 0.04 0.00 0.08 -0.17 0.00 0.00
>>>>> 0.00 0.24
>>>>> 11 Mo -0.01 -0.00 -0.00 0.00 -0.00 -0.03 -0.00
>>>>> -0.00 -0.03
>>>>> 12 Mo -0.02 -0.01 0.00 0.00 -0.01 0.07 0.00
>>>>> 0.00 -0.05
>>>>> 16 P 0.28 0.12 0.00 -0.08 0.17 -0.00 0.00
>>>>> 0.00 0.24
>>>>> 19 Mo 0.01 -0.00 0.02 -0.00 0.00 0.03 0.00
>>>>> -0.00 -0.03
>>>>> 20 Mo 0.02 -0.00 -0.03 -0.00 0.01 -0.07 -0.00
>>>>> 0.00 -0.05
>>>>> 24 P -0.28 0.04 0.00 0.08 -0.16 0.00 0.00
>>>>> -0.00 0.24
>>>>> 27 Mo -0.01 -0.00 -0.00 0.00 -0.00 -0.03 0.00
>>>>> -0.00 -0.03
>>>>> 28 Mo -0.02 -0.01 0.00 0.00 -0.01 0.07 -0.00
>>>>> 0.00 -0.05
>>>>> 32 P 0.28 0.12 -0.00 -0.08 0.16 -0.01 -0.00
>>>>> -0.00 0.24
>>>>> 35 Mo -0.00 -0.00 -0.04 -0.01 0.00 0.01 0.00
>>>>> 0.00 -0.03
>>>>> 36 Mo -0.00 -0.00 0.08 -0.02 0.00 -0.02 -0.00
>>>>> -0.00 -0.05
>>>>> 40 P 0.07 0.08 -0.01 0.29 -0.04 0.00 0.00
>>>>> -0.00 0.24
>>>>> 43 Mo 0.00 0.00 0.02 0.01 -0.00 -0.01 0.00
>>>>> 0.00 -0.03
>>>>> 44 Mo 0.00 0.01 -0.05 0.02 -0.00 0.02 -0.00
>>>>> -0.00 -0.05
>>>>> 48 P -0.07 -0.24 0.00 -0.29 0.04 0.00 -0.00
>>>>> -0.00 0.24
>>>>> 51 Mo -0.00 -0.00 -0.04 -0.01 0.00 0.01 0.00
>>>>> 0.00 -0.03
>>>>> 52 Mo -0.00 -0.00 0.08 -0.02 0.00 -0.02 0.00
>>>>> -0.00 -0.05
>>>>> 56 P 0.07 0.08 -0.01 0.29 -0.04 0.00 0.00
>>>>> -0.00 0.25
>>>>> 59 Mo 0.00 0.00 0.02 0.01 -0.00 -0.01 -0.00
>>>>> 0.00 -0.03
>>>>> 60 Mo 0.00 0.01 -0.05 0.02 -0.00 0.02 0.00
>>>>> -0.00 -0.05
>>>>> 64 P -0.07 -0.24 0.00 -0.29 0.04 -0.00 0.00
>>>>> 0.00 0.24
>>>>> 67 Mo 0.01 -0.00 0.02 -0.00 0.00 0.03 -0.00
>>>>> -0.00 -0.03
>>>>> 68 Mo 0.02 -0.00 -0.03 -0.00 0.01 -0.07 0.00
>>>>> -0.00 -0.05
>>>>> 72 P -0.27 0.04 0.00 0.07 -0.17 0.00 0.00
>>>>> 0.00 0.24
>>>>> 75 Mo -0.01 -0.00 -0.00 0.00 -0.00 -0.03 0.00
>>>>> -0.00 -0.03
>>>>> 76 Mo -0.02 -0.01 0.00 0.00 -0.01 0.07 -0.00
>>>>> -0.00 -0.05
>>>>> 80 P 0.27 0.12 0.00 -0.07 0.17 -0.00 0.00
>>>>> 0.00 0.24
>>>>> 83 Mo 0.01 -0.00 0.02 -0.00 0.00 0.03 -0.00
>>>>> -0.00 -0.03
>>>>> 84 Mo 0.02 -0.00 -0.03 -0.00 0.01 -0.07 -0.00
>>>>> -0.00 -0.05
>>>>> 88 P -0.27 0.04 0.00 0.07 -0.17 0.00 -0.00
>>>>> 0.00 0.24
>>>>> 91 Mo -0.01 -0.00 -0.00 0.00 -0.00 -0.03 0.00
>>>>> 0.00 -0.03
>>>>> 92 Mo -0.02 -0.01 0.00 0.00 -0.01 0.07 0.00
>>>>> -0.00 -0.05
>>>>> 96 P 0.27 0.12 -0.00 -0.07 0.17 -0.00 -0.00
>>>>> 0.00 0.24
>>>>> 99 Mo -0.00 -0.00 -0.04 -0.01 0.00 0.01 -0.00
>>>>> 0.00 -0.03
>>>>> 100 Mo -0.00 -0.00 0.08 -0.02 0.00 -0.02 -0.00
>>>>> 0.00 -0.05
>>>>> 104 P 0.07 0.08 -0.01 0.29 -0.04 -0.00 -0.00
>>>>> -0.00 0.24
>>>>> 107 Mo 0.00 0.01 0.02 0.01 -0.00 -0.01 0.00
>>>>> 0.00 -0.03
>>>>> 108 Mo 0.00 0.01 -0.05 0.02 -0.00 0.02 -0.00
>>>>> 0.00 -0.05
>>>>> 112 P -0.07 -0.24 0.00 -0.29 0.04 -0.00 -0.00
>>>>> -0.00 0.24
>>>>> 115 Mo -0.00 -0.00 -0.04 -0.01 0.00 0.01 -0.00
>>>>> -0.00 -0.03
>>>>> 116 Mo -0.00 -0.00 0.08 -0.02 0.00 -0.02 0.00
>>>>> 0.00 -0.05
>>>>> 120 P 0.07 0.08 -0.00 0.29 -0.05 0.00 0.00
>>>>> -0.00 0.24
>>>>> 123 Mo 0.00 0.01 0.02 0.01 -0.00 -0.01 0.00
>>>>> 0.00 -0.03
>>>>> 124 Mo 0.00 0.01 -0.05 0.02 -0.00 0.02 -0.00
>>>>> -0.00 -0.05
>>>>> 128 P -0.07 -0.24 0.00 -0.29 0.05 -0.00 0.00
>>>>> -0.00 0.24
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> -------------------------------------------------------------------------------
>>>>> -
>>>>> -
>>>>> - DBCSR STATISTICS
>>>>> -
>>>>> -
>>>>> -
>>>>>
>>>>> -------------------------------------------------------------------------------
>>>>> COUNTER TOTAL BLAS SMM
>>>>> ACC
>>>>> flops inhomo. stacks 0 0.0% 0.0%
>>>>> 0.0%
>>>>> flops total 0.000000E+00 0.0% 0.0%
>>>>> 0.0%
>>>>> flops max/rank 0.000000E+00 0.0% 0.0%
>>>>> 0.0%
>>>>> matmuls inhomo. stacks 0 0.0% 0.0%
>>>>> 0.0%
>>>>> matmuls total 0 0.0% 0.0%
>>>>> 0.0%
>>>>> number of processed stacks 0 0.0% 0.0%
>>>>> 0.0%
>>>>> average stack size 0.0 0.0
>>>>> 0.0
>>>>> marketing flops 0.000000E+00
>>>>>
>>>>> -------------------------------------------------------------------------------
>>>>> -
>>>>> -
>>>>> - DBCSR MESSAGE PASSING PERFORMANCE
>>>>> -
>>>>> -
>>>>> -
>>>>>
>>>>> -------------------------------------------------------------------------------
>>>>> ROUTINE CALLS AVE VOLUME [Bytes]
>>>>> MP_Bcast 1 12.
>>>>> MP_Allreduce 1316782 8.
>>>>> MP_Alltoall 12045666 733641.
>>>>>
>>>>> -------------------------------------------------------------------------------
>>>>>
>>>>> --
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