[CP2K-user] [CP2K:20174] Re: Vibrational Analysis
Muhammad Rafiq
rafiq789.ra at gmail.com
Sun May 5 10:23:06 UTC 2024
so what should i do, which method i use
On Sunday, May 5, 2024 at 6:02:40 PM UTC+8 Marcella Iannuzzi wrote:
> 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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>>>>> .
>>>>>
>>>>
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