[CP2K-user] [CP2K:20187] Re: Vibrational Analysis
Gustavo Cervi
gustavo at iq.usp.br
Tue May 7 14:07:17 UTC 2024
I think you may follow this tutorial to calculate vibrational spectroscopy
with molecular dynamics: https://brehm-research.de/spectroscopy.php
it is not so simple as just a vibrational analysis of a static
conformation, but it's possible.
I hope it helps you.
Em domingo, 5 de maio de 2024 às 07:23:06 UTC-3, Muhammad Rafiq escreveu:
> 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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>>>>>> <https://groups.google.com/d/msgid/cp2k/60f3a959-3150-421a-b591-4538d437b6b6n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>>>>> .
>>>>>>
>>>>>
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