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

[Andrea Dal Corso]

dft-D is something I never used, I do not know if the phonon works with
it. Then I would use occupations='mp'. If this does not solve your
problem, it means that for some reason the system is unstable. 
In this case I do not think thermo_pw can compute the thermodynamic
quantities. What happens if you compute the frequencies with ph.x.
Are they still imaginary? 

Andrea




On Thu, 2021-07-01 at 14:10 +0000, Yun Yang wrote:
> No, I didn’t fixed the atoms for relax, attached is my input file.
> Please help me, thanks 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
> From: Yun Yang<mailto:yy9702 at outlook.com>
> Sent: 2021年7月1日 20:50
> To: thermo_pw-forum at lists.quantum-espresso.org<mailto:
> thermo_pw-forum at lists.quantum-espresso.org>
> Subject: RE: The free energy of the adsorbed molecule
> 
> 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
> 
> 
> 
> 
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-- 
Andrea Dal Corso                    Tel. 0039-040-3787428
SISSA, Via Bonomea 265              Fax. 0039-040-3787249
I-34136 Trieste (Italy)             e-mail: dalcorso at sissa.it