[CP2K-user] [CP2K:20171] Re: Vibrational Analysis
Muhammad Rafiq
rafiq789.ra at gmail.com
Sun May 5 09:54:23 UTC 2024
(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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