[CP2K-user] [CP2K:11972] THERMOCHEMISTRY

SUNG-SIK toda... at gmail.com
Tue Jul 16 11:02:29 CET 2019


Hi. 

in my experience, (local minima case)

[1] the negative frequencies may be occured by the loose EPS_SCF value. 
smaller EPS_SCF value will be helpful.

[2] the scf should be converged in a given MAX_SCF. you can find the scf 
results in each raplica output files.

[3] sometimes, very small negative value frequencies (~ 0) will bother you. 
in that case,

  1) adjust atomic positions slightly associated with the negative 
frequency normal mode.
  2) (rarely) To adjust the DX value in VIBRATIONAL_ANALYSIS section will 
be a solution. 


sincerely.
SEONGSIK LEE


2019년 7월 15일 월요일 오후 11시 37분 29초 UTC+9, Gerard pareras niell 님의 말:
>
> Hi Juerg,
>
> Thank you for your answer.
> Yes, it has some negative frequencies. 
> Please find attached the output file below.
>
>
>
> El lunes, 15 de julio de 2019, 12:54:53 (UTC+2), jgh escribió:
>>
>> Hi 
>>
>> making a wild guess: something went wrong before the calculation 
>> of Thermodynamic properties. That is why you get NaN's for 
>> the Entropy. Maybe you have negative vib. frequencies? 
>>
>> Without the output or other information we can only guess. 
>>
>> regards 
>>
>> Juerg Hutter 
>> -------------------------------------------------------------- 
>> Juerg Hutter                         Phone : ++41 44 635 4491 
>> Institut für Chemie C                FAX   : ++41 44 635 6838 
>> Universität Zürich                   E-mail: h... at chem.uzh.ch 
>> Winterthurerstrasse 190 
>> CH-8057 Zürich, Switzerland 
>> --------------------------------------------------------------- 
>>
>> -----c... at googlegroups.com wrote: ----- 
>> To: "cp2k" <c... at googlegroups.com> 
>> From: "Gerard pareras niell" 
>> Sent by: c... at googlegroups.com 
>> Date: 07/15/2019 12:05PM 
>> Subject: [CP2K:11972] THERMOCHEMISTRY 
>>
>> Dear colleagues, 
>>
>> I'm trying to obtain thermochemistry data, like enthalpy, entropy and 
>> Gibbs energies correction, same analysis as gaussian does on the Freq 
>> calculation. 
>> I tried with VIBRATIONAL_ANALYSIS using THERMOCHEMISTRY, however I'm not 
>> able to obtain the entropic contribution and the final Gibbs energy. 
>>
>> Is some information missing on the input? 
>>
>> Please find attached below the input: 
>> &GLOBAL 
>>   PROJECT $SLURM_JOB_NAME 
>>   RUN_TYPE VIBRATIONAL_ANALYSIS 
>> &END GLOBAL 
>> &FORCE_EVAL 
>>   METHOD Quickstep 
>>   STRESS_TENSOR ANALYTICAL 
>>   &DFT 
>>     &PRINT 
>>      &MOMENTS 
>>      &END 
>>     &END 
>>   WFN_RESTART_FILE_NAME $SLURM_JOB_NAME-RESTART.wfn 
>>     BASIS_SET_FILE_NAME $HOME/scr/cp2k/data/BASIS_MOLOPT 
>>     POTENTIAL_FILE_NAME $HOME/scr/cp2k/data/GTH_POTENTIALS   
>>     CHARGE 0 
>>     MULTIPLICITY 1 
>>     &MGRID 
>>        CUTOFF [Ry] 500 
>>     &END 
>>     &QS 
>>        METHOD GPW 
>>        EPS_DEFAULT 1.0E-10 
>>     &END 
>>     &POISSON 
>>        PERIODIC NONE 
>>        POISSON_SOLVER MULTIPOLE 
>>     &END 
>>     &SCF                               
>>     SCF_GUESS RESTART 
>>       MAX_SCF 30 
>>       EPS_SCF 1.0E-5 
>>       !!CHOLESKY OFF 
>>        &OT 
>>         PRECONDITIONER FULL_ALL 
>>         ENERGY_GAP 2E-03 
>>         MINIMIZER DIIS 
>>        &END OT 
>>       &OUTER_SCF 
>>         MAX_SCF 30 
>>         EPS_SCF 1.0E-5 ! must match the above 
>>       &END 
>>     &END SCF 
>>     &XC 
>>      &XC_FUNCTIONAL 
>>          &PBE 
>> !!         PARAMETRIZATION PBESOL 
>>          &END 
>>      &END XC_FUNCTIONAL 
>>     &END XC 
>>   &END DFT 
>>   &SUBSYS 
>>     &CELL 
>>       ABC [angstrom] 15. 15. 15. 
>>       ALPHA_BETA_GAMMA 90. 90. 90. 
>>       SYMMETRY NONE 
>>       PERIODIC NONE 
>>     &END CELL 
>>   &TOPOLOGY 
>>     COORD_FILE_NAME $SLURM_JOB_NAME.xyz 
>>     COORD_FILE_FORMAT XYZ 
>>   &END 
>>     
>>     &KIND   H 
>>       BASIS_SET DZVP-MOLOPT-SR-GTH 
>>       POTENTIAL GTH-PBE 
>>     &END KIND 
>>
>>     &KIND   C 
>>       BASIS_SET DZVP-MOLOPT-SR-GTH 
>>       POTENTIAL GTH-PBE 
>>     &END KIND 
>>
>>     &KIND   N 
>>       BASIS_SET DZVP-MOLOPT-SR-GTH 
>>       POTENTIAL GTH-PBE 
>>     &END KIND 
>>
>>     &KIND   O 
>>       BASIS_SET DZVP-MOLOPT-SR-GTH 
>>       POTENTIAL GTH-PBE 
>>     &END KIND 
>>
>>     &KIND   P 
>>       BASIS_SET DZVP-MOLOPT-SR-GTH 
>>       POTENTIAL GTH-PBE 
>>     &END KIND 
>>
>>     &KIND  Co 
>>       BASIS_SET DZVP-MOLOPT-SR-GTH 
>>       POTENTIAL GTH-PBE 
>>     &END KIND 
>>
>>     &KIND   I 
>>       BASIS_SET DZVP-MOLOPT-SR-GTH 
>>       POTENTIAL GTH-PBE 
>>     &END KIND 
>>
>>     &KIND  Ni 
>>       BASIS_SET DZVP-MOLOPT-SR-GTH 
>>       POTENTIAL GTH-PBE 
>>     &END KIND 
>>
>>   &END SUBSYS 
>> &END FORCE_EVAL 
>>
>> &VIBRATIONAL_ANALYSIS 
>>   FULLY_PERIODIC 
>>   INTENSITIES 
>>   THERMOCHEMISTRY 
>>   TC_TEMPERATURE 298.15 
>>   TC_PRESSURE 1.01325000E+005 
>>   NPROC_REP 12 
>> !!   &MODE_SELECTIVE 
>> !!     ATOMS 1..46 
>> !!    &INVOLVED_ATOMS 
>> !!      INVOLVED_ATOMS 1..46 
>> !!    &END 
>> !!   INITIAL_GUESS ATOMIC 
>> !!  EPS_NORM 1.0E-04 
>> !!   EPS_MAX_VAL 1.0E-05 
>> !!  &END 
>> &END     
>>
>> And the output information: 
>>
>>  VIB|                        NORMAL MODES - THERMOCHEMICAL DATA 
>>  VIB| 
>>  VIB|              Symmetry number:                                       
>>           1 
>>  VIB|              Temperature [K]:                                       
>>      298.15 
>>  VIB|              Pressure [Pa]:                                         
>>   101325.00 
>>
>>
>>  VIB|              Electronic energy (U) [kJ/mol]:                 
>>  -1023152.20665924 
>>  VIB|              Zero-point correction [kJ/mol]:                       
>> 956.45314459 
>>  VIB|              Entropy [kJ/(mol K)]:                                 
>>             Nan 
>>  VIB|              Enthalpy correction (H-U) [kJ/mol]:                 
>>  1009.07755543 
>>  VIB|              Gibbs energy correction [kJ/mol]:                     
>>     Nan 
>>  VIB|              Heat capacity [kJ/(mol*K)]:                           
>>   0.38550655 
>>
>> Thank you. 
>> Gerard.   
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>
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