[Thermo_pw-forum] The free energy of the adsorbed molecule

[Andrea Dal Corso]

I do not know which is the reason for these negative
frequencies. Maybe you are fixing some atoms during the
relaxation, or simply your system is unstable.

Thermo_pw cannot deal with this situation. Maybe you can
extract the information that you need from the positive
frequencies, but you have to do it yourself, it is not
implemented in thermo_pw.

Andrea

Quoting Yun Yang <yy9702 at outlook.com>:

> I tried again to improve the relax convergence accuracy, for  
> forc_conv_thr=1.0d-05, but there still 3N imaginary frequencies,  
> which I though was unreasonable.
>
> Here are the vibrational frequencies of a carbon monoxide molecule  
> adsorbed over a surface.
>      freq (   1-   1) =       -235.7  [cm-1]   --> A               I+R
>      freq (   2-   2) =       -199.4  [cm-1]   --> A               I+R
>      freq (   3-   3) =       -185.2  [cm-1]   --> A               I+R
>      freq (   4-   4) =        -58.0   [cm-1]   --> A               I+R
>      freq (   5-   5) =        -49.5   [cm-1]   --> A               I+R
>      freq (   6-   6) =        -29.6   [cm-1]   --> A               I+R
>      freq (  94-  94) =        68.8   [cm-1]   --> A               I+R
>      freq (  95-  95) =        74.5   [cm-1]   --> A               I+R
>      freq (  96-  96) =      410.0   [cm-1]   --> A               I+R
>      freq (  97-  97) =      433.5   [cm-1]   --> A               I+R
>      freq (  98-  98) =      457.0   [cm-1]   --> A               I+R
>      freq (  99-  99) =    1993.1   [cm-1]   --> A               I+R
> --
> Postgraduate Yun Yang
> School of Chemical Science and Technology
> Yunnan University
> 2 North Road of Green Lake, Kunming 650091, Yunnan, China
> Tel.:+86-871-65033723, Fax: +86-871-65033679, E-mail: yy9702 at mail.ynu.edu.cn
> From: Yun Yang<mailto:yy9702 at outlook.com>
> Sent: 2021年6月30日 23:27
> To:  
> thermo_pw-forum at lists.quantum-espresso.org<mailto:thermo_pw-forum at lists.quantum-espresso.org>
> Subject: 回复: The free energy of the adsorbed molecule
>
> Yes, there are several smaller imaginary frequencies. I haven’t seen  
> anyone use thermo_pw to calculate the free energy of  
> electrocatalysis, and I suspect that thermos_pw can’t calculate the  
> energy. I will calculate it again after relax the intermediates,  
> thank you very much!
>
> --
> Postgraduate Yun Yang
> School of Chemical Science and Technology
> Yunnan University
> 2 North Road of Green Lake, Kunming 650091, Yunnan, China
> Tel.:+86-871-65033723, Fax: +86-871-65033679, E-mail: yy9702 at mail.ynu.edu.cn
> 发件人: Yun Yang<mailto:yy9702 at outlook.com>
> 发送时间: 2021年6月30日 22:00
> 收件人:  
> thermo_pw-forum at lists.quantum-espresso.org<mailto:thermo_pw-forum at lists.quantum-espresso.org>
> 主题: The free energy of the adsorbed molecule
>
> Dear thermo_pw user
>
> I am try to calculate electrocatalytic reduction of carbon dioxide  
> with thermos_pw.1.4.1, but when I calculate the free energy of the  
> adsorbed molecule, the contribution of vibration entropy is nearly  
> 10 times larger than that calculated by other software and the Zero  
> point vibration energy is similar. My calculation flow is first  
> relax the intermediates with high convergence accuracy, than perform  
> thermos_pw.x for calculate the free energy of adsorbed molecules  
> with fixed the slab. My question is does thermos_pw support this and  
> why does the calculation make such a big difference. Here are the  
> ph_control and thermo_control:
>
> &INPUTPH
>   tr2_ph=1.0d-16,
>   prefix='CoN4-CO',
>   fildyn='CoN4-CO.dyn',
>   ldisp=.TRUE.,
>   trans=.TRUE.,
>   nat_todo=2,
>   nq1=1,
>   nq2=1,
>   nq3=1,
> /
> 32 33
>
> &INPUT_THERMO
>   what='scf_disp',
>   nq1_d=192,
>   nq2_d=192,
>   nq3_d=192,
>   ltherm_dos=.FALSE.,
>   ltherm_freq=.TRUE.
> /
>
> Thank you very much in advance for your time
>
> Sincerely yours
>
> --
> Postgraduate Yun Yang
> School of Chemical Science and Technology
> Yunnan University
> 2 North Road of Green Lake, Kunming 650091, Yunnan, China
> Tel.:+86-871-65033723, Fax: +86-871-65033679, E-mail: yy9702 at mail.ynu.edu.cn