Re: [QE-users] pw.x Segmentation failed with libxc
It compiles and works normally, thanks again. -原始邮件- 发件人:"Paolo Giannozzi" 发送时间:2018-12-19 21:15:37 (星期三) 收件人: "Quantum Espresso users Forum" 抄送: 主题: Re: [QE-users] pw.x Segmentation failed with libxc That is? it "compiles and works" and "compiles but still does not work"? On Wed, Dec 19, 2018 at 2:14 PM 魏亚东 wrote: Thanks a lot, with reinstalling libxc-4.2.3, pw.x has been compiled normally. -Original Messages- From:"Paolo Giannozzi" Sent Time:2018-12-19 00:00:44 (Wednesday) To: "Quantum Espresso users Forum" Cc: Subject: Re: [QE-users] pw.x Segmentation failed with libxc On Tue, Dec 18, 2018 at 1:39 PM 魏亚东 wrote: forrtl: severe (174): SIGSEGV, segmentation fault occurred pw.x 009973E8 date_and_tim_ 23 date_and_tim.f90 It seems that libxcf90 were implemented in wrong way. maybe, but it is hard to see the link between compilation with libxc and a routine that just prints the date and time Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] SCF energy tolerance of GGA+U for Er2O3
Dear Lorenzo,My system is an output of optimized experimental primitive structure of Er2O3. Since I know it has a gap, I used a small smearing instead of occupation=fixed for better convergence of SCF. However, you know that using large smearing produces wrong results. I use your comment to change mixing mode. I know that SCF convergence in f-series with hubbard parameter is difficult. I will post new results. Regards David On Monday, December 17, 2018, 2:30:14 PM GMT+3:30, Lorenzo Paulatto wrote: You're using a very large value of U in a large system, with little symmetry, a very small smearing and no initial guess on the final state (starting_ns, mixing_fixed_eigenvalues, magnetization,..) it's going to take a lot of sweat, tears and possibly blood to converge it. I see no magic solution. Maybe try to use a different mixing_mode. Cheers -- Lorenzo Paulatto Written on a virtual keyboard with real fingers On Mon, 17 Dec 2018, 08:41 David Foster https://lists.quantum-espresso.org/mailman/listinfo/users ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] pw.x Segmentation failed with libxc
That is? it "compiles and works" and "compiles but still does not work"? On Wed, Dec 19, 2018 at 2:14 PM 魏亚东 wrote: > Thanks a lot, with reinstalling libxc-4.2.3, pw.x has been compiled > normally. > > > -Original Messages- > *From:*"Paolo Giannozzi" > *Sent Time:*2018-12-19 00:00:44 (Wednesday) > *To:* "Quantum Espresso users Forum" > *Cc:* > *Subject:* Re: [QE-users] pw.x Segmentation failed with libxc > > On Tue, Dec 18, 2018 at 1:39 PM 魏亚东 wrote: > > forrtl: severe (174): SIGSEGV, segmentation fault occurred >> >> pw.x 009973E8 date_and_tim_ 23 >> date_and_tim.f90 >> > It seems that libxcf90 were implemented in wrong way. >> > maybe, but it is hard to see the link between compilation with libxc and a > routine that just prints the date and time > > Paolo > > -- > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > ___ > users mailing list > users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] 答复: 答复: DFT+U can not converge
Thanks very much. Both cases I will try with and without saturation.
发件人: users 代表 Giuseppe Mattioli
发送时间: 2018年12月19日 21:11
收件人: users@lists.quantum-espresso.org
主题: Re: [QE-users] 答复: DFT+U can not converge
Yes, I suppose so, but it is not easy to say exactly how it has to be
done in this case (H or OH saturation? surface reconstruction?). If
you are lucky, you may find something in literature...
Best
Giuseppe
LEUNG Clarence ha scritto:
> Dear Giuseppe,
>
> Thanks for your suggest.
>
> My structure is (3 1 0) surface of Co3(PO4)2 with 15 angstrom
> vacuum. You mean that the unsaturated bond should be passivated by H
> or something？
>
> LIANG Xiongyi
>
> 发件人: users 代表 Giuseppe
> Mattioli
> 发送时间: 2018年12月19日 19:30
> 收件人: users@lists.quantum-espresso.org
> 主题: Re: [QE-users] DFT+U can not converge
>
>
> Dear Liang Xiongyi
>
> In my opinion, your initial structure is possibly wrong or missing
> necessary saturation (i.e. twofold-coordinated P atoms on the surface
> and P=O free terminations, which are likely unstable in gas phase).
> However, and generally speaking, if your calculation is going
> somewhere not so far from convergence, you can overcome a difficult
> initial step by using this very useful switch:
>
> scf_must_converge=.false.
>
> Coupled with a suitable electron_maxstep variable, it will calculate
> forces and move atoms when scf ends. If the structure is meaningful
> and not wrong (and this may not be the case) in a few steps you should
> recover an acceptably smooth convergence.
> HTH
> Giuseppe
>
> LEUNG Clarence ha scritto:
>
>> Dear QEusers,
>>
>> When I use QE6.3 to perform DFT+U to relax a slab, it is very
>> difficult to converge and even can not converge (more than 300 scf
>> steps). Thanks for your suggestion in advances.
>>
>> The input file is:
>>
>>
>> calculation='relax',
>> nstep = 200 ,
>> wf_collect = .true. ,
>> etot_conv_thr = 3.5D-6 ,
>> forc_conv_thr = 4.0D-4,
>> /
>>
>>
>> ibrav=0,
>> celldm(1)=9.6431795847d0,
>> nat=109,
>> ntyp=3,
>> ecutwfc=60,
>> ecutrho=480,
>> input_dft='PBE',
>> occupations='smearing',
>> smearing = 'gaussian' ,
>> degauss = 0.01 ,
>> nspin = 2 ,
>> starting_magnetization(1) = 0.5 ,
>> lda_plus_u = .true. ,
>> Hubbard_U(1) = 3.32 ,
>> vdw_corr = dft-d3 ,
>> /
>>
>> conv_thr=1d-05,
>> mixing_beta=0.3d0,
>> mixing_mode ='local-TF',
>> electron_maxstep = 600 ,
>> /
>>
>> /
>>
>> /
>>
>> ATOMIC_SPECIES
>> Co 58.933200d0 Co.pbe-spn-rrkjus_psl.0.3.1.UPF
>> O 15.999400d0 O.pbe-n-rrkjus_psl.1.0.0.UPF
>> P 30.973800d0 P.pbe-n-rrkjus_psl.1.0.0.UPF
>>
>> ATOMIC_POSITIONS {crystal}
>> O0.175510868 0.823201091 0.0040419020 0 0
>> Co 0.752963028 0.655948399 0.0043135660 0 0
>> O0.301125723 0.416151961 0.0048799970 0 0
>> Co 0.846799898 0.775755648 0.0052751820 0 0
>> Co 0.346800351 0.275755641 0.0052752040 0 0
>> O0.392474471 0.135359341 0.0056702340 0 0
>> Co 0.940637166 0.895562903 0.006230 0 0
>> O0.518089326 0.728310212 0.0065083300 0 0
>> O0.902313840 0.059368885 0.0179593930 0 0
>> O0.807187857 0.964594997 0.0204575570 0 0
>> O0.036878250 0.705581722 0.0238905990 0 0
>> P0.893919682 0.538810250 0.0262428490 0 0
>> Co 0.451343782 0.481124665 0.0337500410 0 0
>> O0.028914218 0.314809876 0.0343233470 0 0
>> P0.323165643 0.700374526 0.0446558860 0 0
>> O0.412931350 0.644218586 0.0452437970 0 0
>> O0.180081232 0.532598515 0.0466851490 0 0
>> O0.551818853 0.324973894 0.0622826950 0 0
>> O0.318968869 0.213353805 0.0637240070 0 0
>> P0.408734429 0.157197863 0.0643119200 0 0
>> O0.702985853 0.542762514 0.0746444590 0 0
>> Co 0.280556437 0.376447725 0.0752177630 0 0
>> P0.837980537 0.318762141 0.0827249540 0 0
>> O0.695021832 0.151990660 0.0850772360 0 0
>> O0.924712372 0.892977386 0.0885102760 0 0
>> O0.829586379 0.798203506 0.0910084100 0 0
>> O0.213810893 0.129262179 0.1024594740 0 0
>> Co 0.791263053 0.962009487 0.1027311380 0 0
>> O0.339425748 0.722213050 0.1032975690 0 0
>> Co 0.885099923 0.081816736 0.1036927540 0 0
>> Co 0.385100377 0.581816730 0.1036927760 0 0
>> O0.430774496 0.441420429 0.1040878070 0 0
>> Co 0.978937191 0.201623991 0.1046542380 0 0
>> O0.556389351 0.034371300 0.1049259020 0 0
>> O0.940613865 0.365429972 0.1163769650 0 0
>> O
Re: [QE-users] pw.x Segmentation failed with libxc
Thanks a lot, with reinstalling libxc-4.2.3, pw.x has been compiled normally. -Original Messages- From:"Paolo Giannozzi" Sent Time:2018-12-19 00:00:44 (Wednesday) To: "Quantum Espresso users Forum" Cc: Subject: Re: [QE-users] pw.x Segmentation failed with libxc On Tue, Dec 18, 2018 at 1:39 PM 魏亚东 wrote: forrtl: severe (174): SIGSEGV, segmentation fault occurred pw.x 009973E8 date_and_tim_ 23 date_and_tim.f90 It seems that libxcf90 were implemented in wrong way. maybe, but it is hard to see the link between compilation with libxc and a routine that just prints the date and time Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] 答复: DFT+U can not converge
Yes, I suppose so, but it is not easy to say exactly how it has to be
done in this case (H or OH saturation? surface reconstruction?). If
you are lucky, you may find something in literature...
Best
Giuseppe
LEUNG Clarence ha scritto:
Dear Giuseppe,
Thanks for your suggest.
My structure is (3 1 0) surface of Co3(PO4)2 with 15 angstrom
vacuum. You mean that the unsaturated bond should be passivated by H
or something？
LIANG Xiongyi
发件人: users 代表 Giuseppe
Mattioli
发送时间: 2018年12月19日 19:30
收件人: users@lists.quantum-espresso.org
主题: Re: [QE-users] DFT+U can not converge
Dear Liang Xiongyi
In my opinion, your initial structure is possibly wrong or missing
necessary saturation (i.e. twofold-coordinated P atoms on the surface
and P=O free terminations, which are likely unstable in gas phase).
However, and generally speaking, if your calculation is going
somewhere not so far from convergence, you can overcome a difficult
initial step by using this very useful switch:
scf_must_converge=.false.
Coupled with a suitable electron_maxstep variable, it will calculate
forces and move atoms when scf ends. If the structure is meaningful
and not wrong (and this may not be the case) in a few steps you should
recover an acceptably smooth convergence.
HTH
Giuseppe
LEUNG Clarence ha scritto:
Dear QEusers,
When I use QE6.3 to perform DFT+U to relax a slab, it is very
difficult to converge and even can not converge (more than 300 scf
steps). Thanks for your suggestion in advances.
The input file is:
calculation='relax',
nstep = 200 ,
wf_collect = .true. ,
etot_conv_thr = 3.5D-6 ,
forc_conv_thr = 4.0D-4,
/
ibrav=0,
celldm(1)=9.6431795847d0,
nat=109,
ntyp=3,
ecutwfc=60,
ecutrho=480,
input_dft='PBE',
occupations='smearing',
smearing = 'gaussian' ,
degauss = 0.01 ,
nspin = 2 ,
starting_magnetization(1) = 0.5 ,
lda_plus_u = .true. ,
Hubbard_U(1) = 3.32 ,
vdw_corr = dft-d3 ,
/
conv_thr=1d-05,
mixing_beta=0.3d0,
mixing_mode ='local-TF',
electron_maxstep = 600 ,
/
/
/
ATOMIC_SPECIES
Co 58.933200d0 Co.pbe-spn-rrkjus_psl.0.3.1.UPF
O 15.999400d0 O.pbe-n-rrkjus_psl.1.0.0.UPF
P 30.973800d0 P.pbe-n-rrkjus_psl.1.0.0.UPF
ATOMIC_POSITIONS {crystal}
O0.175510868 0.823201091 0.0040419020 0 0
Co 0.752963028 0.655948399 0.0043135660 0 0
O0.301125723 0.416151961 0.0048799970 0 0
Co 0.846799898 0.775755648 0.0052751820 0 0
Co 0.346800351 0.275755641 0.0052752040 0 0
O0.392474471 0.135359341 0.0056702340 0 0
Co 0.940637166 0.895562903 0.006230 0 0
O0.518089326 0.728310212 0.0065083300 0 0
O0.902313840 0.059368885 0.0179593930 0 0
O0.807187857 0.964594997 0.0204575570 0 0
O0.036878250 0.705581722 0.0238905990 0 0
P0.893919682 0.538810250 0.0262428490 0 0
Co 0.451343782 0.481124665 0.0337500410 0 0
O0.028914218 0.314809876 0.0343233470 0 0
P0.323165643 0.700374526 0.0446558860 0 0
O0.412931350 0.644218586 0.0452437970 0 0
O0.180081232 0.532598515 0.0466851490 0 0
O0.551818853 0.324973894 0.0622826950 0 0
O0.318968869 0.213353805 0.0637240070 0 0
P0.408734429 0.157197863 0.0643119200 0 0
O0.702985853 0.542762514 0.0746444590 0 0
Co 0.280556437 0.376447725 0.0752177630 0 0
P0.837980537 0.318762141 0.0827249540 0 0
O0.695021832 0.151990660 0.0850772360 0 0
O0.924712372 0.892977386 0.0885102760 0 0
O0.829586379 0.798203506 0.0910084100 0 0
O0.213810893 0.129262179 0.1024594740 0 0
Co 0.791263053 0.962009487 0.1027311380 0 0
O0.339425748 0.722213050 0.1032975690 0 0
Co 0.885099923 0.081816736 0.1036927540 0 0
Co 0.385100377 0.581816730 0.1036927760 0 0
O0.430774496 0.441420429 0.1040878070 0 0
Co 0.978937191 0.201623991 0.1046542380 0 0
O0.556389351 0.034371300 0.1049259020 0 0
O0.940613865 0.365429972 0.1163769650 0 0
O0.845487883 0.270656085 0.1188751290 0 0
O0.075178275 0.011642810 0.1223081710 0 0
P0.932219708 0.844871338 0.1246604210 0 0
Co 0.489643808 0.787185753 0.1321676130 0 0
O0.067214244 0.620870964 0.1327409190 0 0
P0.361354279 0.006083789 0.142115621
O0.446802131 0.950135511 0.145110715
O0.214381915 0.837791409 0.146887224
O0.593110221 0.629859448 0.161855388
O0.355569602 0.519337757
[QE-users] 答复: DFT+U can not converge
Dear Giuseppe,
Thanks for your suggest.
My structure is (3 1 0) surface of Co3(PO4)2 with 15 angstrom vacuum. You mean
that the unsaturated bond should be passivated by H or something？
LIANG Xiongyi
发件人: users 代表 Giuseppe Mattioli
发送时间: 2018年12月19日 19:30
收件人: users@lists.quantum-espresso.org
主题: Re: [QE-users] DFT+U can not converge
Dear Liang Xiongyi
In my opinion, your initial structure is possibly wrong or missing
necessary saturation (i.e. twofold-coordinated P atoms on the surface
and P=O free terminations, which are likely unstable in gas phase).
However, and generally speaking, if your calculation is going
somewhere not so far from convergence, you can overcome a difficult
initial step by using this very useful switch:
scf_must_converge=.false.
Coupled with a suitable electron_maxstep variable, it will calculate
forces and move atoms when scf ends. If the structure is meaningful
and not wrong (and this may not be the case) in a few steps you should
recover an acceptably smooth convergence.
HTH
Giuseppe
LEUNG Clarence ha scritto:
> Dear QEusers,
>
> When I use QE6.3 to perform DFT+U to relax a slab, it is very
> difficult to converge and even can not converge (more than 300 scf
> steps). Thanks for your suggestion in advances.
>
> The input file is:
>
>
> calculation='relax',
> nstep = 200 ,
> wf_collect = .true. ,
> etot_conv_thr = 3.5D-6 ,
> forc_conv_thr = 4.0D-4,
> /
>
>
> ibrav=0,
> celldm(1)=9.6431795847d0,
> nat=109,
> ntyp=3,
> ecutwfc=60,
> ecutrho=480,
> input_dft='PBE',
> occupations='smearing',
> smearing = 'gaussian' ,
> degauss = 0.01 ,
> nspin = 2 ,
> starting_magnetization(1) = 0.5 ,
> lda_plus_u = .true. ,
> Hubbard_U(1) = 3.32 ,
> vdw_corr = dft-d3 ,
> /
>
> conv_thr=1d-05,
> mixing_beta=0.3d0,
> mixing_mode ='local-TF',
> electron_maxstep = 600 ,
> /
>
> /
>
> /
>
> ATOMIC_SPECIES
> Co 58.933200d0 Co.pbe-spn-rrkjus_psl.0.3.1.UPF
> O 15.999400d0 O.pbe-n-rrkjus_psl.1.0.0.UPF
> P 30.973800d0 P.pbe-n-rrkjus_psl.1.0.0.UPF
>
> ATOMIC_POSITIONS {crystal}
> O0.175510868 0.823201091 0.0040419020 0 0
> Co 0.752963028 0.655948399 0.0043135660 0 0
> O0.301125723 0.416151961 0.0048799970 0 0
> Co 0.846799898 0.775755648 0.0052751820 0 0
> Co 0.346800351 0.275755641 0.0052752040 0 0
> O0.392474471 0.135359341 0.0056702340 0 0
> Co 0.940637166 0.895562903 0.006230 0 0
> O0.518089326 0.728310212 0.0065083300 0 0
> O0.902313840 0.059368885 0.0179593930 0 0
> O0.807187857 0.964594997 0.0204575570 0 0
> O0.036878250 0.705581722 0.0238905990 0 0
> P0.893919682 0.538810250 0.0262428490 0 0
> Co 0.451343782 0.481124665 0.0337500410 0 0
> O0.028914218 0.314809876 0.0343233470 0 0
> P0.323165643 0.700374526 0.0446558860 0 0
> O0.412931350 0.644218586 0.0452437970 0 0
> O0.180081232 0.532598515 0.0466851490 0 0
> O0.551818853 0.324973894 0.0622826950 0 0
> O0.318968869 0.213353805 0.0637240070 0 0
> P0.408734429 0.157197863 0.0643119200 0 0
> O0.702985853 0.542762514 0.0746444590 0 0
> Co 0.280556437 0.376447725 0.0752177630 0 0
> P0.837980537 0.318762141 0.0827249540 0 0
> O0.695021832 0.151990660 0.0850772360 0 0
> O0.924712372 0.892977386 0.0885102760 0 0
> O0.829586379 0.798203506 0.0910084100 0 0
> O0.213810893 0.129262179 0.1024594740 0 0
> Co 0.791263053 0.962009487 0.1027311380 0 0
> O0.339425748 0.722213050 0.1032975690 0 0
> Co 0.885099923 0.081816736 0.1036927540 0 0
> Co 0.385100377 0.581816730 0.1036927760 0 0
> O0.430774496 0.441420429 0.1040878070 0 0
> Co 0.978937191 0.201623991 0.1046542380 0 0
> O0.556389351 0.034371300 0.1049259020 0 0
> O0.940613865 0.365429972 0.1163769650 0 0
> O0.845487883 0.270656085 0.1188751290 0 0
> O0.075178275 0.011642810 0.1223081710 0 0
> P0.932219708 0.844871338 0.1246604210 0 0
> Co 0.489643808 0.787185753 0.1321676130 0 0
> O0.067214244 0.620870964 0.1327409190 0 0
> P0.361354279 0.006083789 0.142115621
> O0.446802131 0.950135511 0.145110715
> O0.214381915 0.837791409 0.146887224
> O0.593110221 0.629859448 0.161855388
> O0.355569602 0.519337757 0.162613913
> P0.444333889 0.463046511 0.162481449
> O
Re: [QE-users] DFT+U can not converge
Dear Liang Xiongyi
In my opinion, your initial structure is possibly wrong or missing
necessary saturation (i.e. twofold-coordinated P atoms on the surface
and P=O free terminations, which are likely unstable in gas phase).
However, and generally speaking, if your calculation is going
somewhere not so far from convergence, you can overcome a difficult
initial step by using this very useful switch:
scf_must_converge=.false.
Coupled with a suitable electron_maxstep variable, it will calculate
forces and move atoms when scf ends. If the structure is meaningful
and not wrong (and this may not be the case) in a few steps you should
recover an acceptably smooth convergence.
HTH
Giuseppe
LEUNG Clarence ha scritto:
Dear QEusers,
When I use QE6.3 to perform DFT+U to relax a slab, it is very
difficult to converge and even can not converge (more than 300 scf
steps). Thanks for your suggestion in advances.
The input file is:
calculation='relax',
nstep = 200 ,
wf_collect = .true. ,
etot_conv_thr = 3.5D-6 ,
forc_conv_thr = 4.0D-4,
/
ibrav=0,
celldm(1)=9.6431795847d0,
nat=109,
ntyp=3,
ecutwfc=60,
ecutrho=480,
input_dft='PBE',
occupations='smearing',
smearing = 'gaussian' ,
degauss = 0.01 ,
nspin = 2 ,
starting_magnetization(1) = 0.5 ,
lda_plus_u = .true. ,
Hubbard_U(1) = 3.32 ,
vdw_corr = dft-d3 ,
/
conv_thr=1d-05,
mixing_beta=0.3d0,
mixing_mode ='local-TF',
electron_maxstep = 600 ,
/
/
/
ATOMIC_SPECIES
Co 58.933200d0 Co.pbe-spn-rrkjus_psl.0.3.1.UPF
O 15.999400d0 O.pbe-n-rrkjus_psl.1.0.0.UPF
P 30.973800d0 P.pbe-n-rrkjus_psl.1.0.0.UPF
ATOMIC_POSITIONS {crystal}
O0.175510868 0.823201091 0.0040419020 0 0
Co 0.752963028 0.655948399 0.0043135660 0 0
O0.301125723 0.416151961 0.0048799970 0 0
Co 0.846799898 0.775755648 0.0052751820 0 0
Co 0.346800351 0.275755641 0.0052752040 0 0
O0.392474471 0.135359341 0.0056702340 0 0
Co 0.940637166 0.895562903 0.006230 0 0
O0.518089326 0.728310212 0.0065083300 0 0
O0.902313840 0.059368885 0.0179593930 0 0
O0.807187857 0.964594997 0.0204575570 0 0
O0.036878250 0.705581722 0.0238905990 0 0
P0.893919682 0.538810250 0.0262428490 0 0
Co 0.451343782 0.481124665 0.0337500410 0 0
O0.028914218 0.314809876 0.0343233470 0 0
P0.323165643 0.700374526 0.0446558860 0 0
O0.412931350 0.644218586 0.0452437970 0 0
O0.180081232 0.532598515 0.0466851490 0 0
O0.551818853 0.324973894 0.0622826950 0 0
O0.318968869 0.213353805 0.0637240070 0 0
P0.408734429 0.157197863 0.0643119200 0 0
O0.702985853 0.542762514 0.0746444590 0 0
Co 0.280556437 0.376447725 0.0752177630 0 0
P0.837980537 0.318762141 0.0827249540 0 0
O0.695021832 0.151990660 0.0850772360 0 0
O0.924712372 0.892977386 0.0885102760 0 0
O0.829586379 0.798203506 0.0910084100 0 0
O0.213810893 0.129262179 0.1024594740 0 0
Co 0.791263053 0.962009487 0.1027311380 0 0
O0.339425748 0.722213050 0.1032975690 0 0
Co 0.885099923 0.081816736 0.1036927540 0 0
Co 0.385100377 0.581816730 0.1036927760 0 0
O0.430774496 0.441420429 0.1040878070 0 0
Co 0.978937191 0.201623991 0.1046542380 0 0
O0.556389351 0.034371300 0.1049259020 0 0
O0.940613865 0.365429972 0.1163769650 0 0
O0.845487883 0.270656085 0.1188751290 0 0
O0.075178275 0.011642810 0.1223081710 0 0
P0.932219708 0.844871338 0.1246604210 0 0
Co 0.489643808 0.787185753 0.1321676130 0 0
O0.067214244 0.620870964 0.1327409190 0 0
P0.361354279 0.006083789 0.142115621
O0.446802131 0.950135511 0.145110715
O0.214381915 0.837791409 0.146887224
O0.593110221 0.629859448 0.161855388
O0.355569602 0.519337757 0.162613913
P0.444333889 0.463046511 0.162481449
O0.733915313 0.849462282 0.171314557
Co 0.331397450 0.684149370 0.17454
P0.880835007 0.624048906 0.181575275
O0.729016571 0.457586972 0.184340848
O0.943694570 0.199413194 0.185888622
O0.842699539 0.103890146 0.188690045
O0.246376254 0.435621465 0.201025875
Co 0.819907469 0.267437250 0.200281311
O0.371654672 0.028624679 0.201597106
Co 0.919293748 0.386217687 0.198228118
Co 0.408991643 0.881622266 0.208931455
O
Re: [QE-users] Unexpected adsorption energy
Dear Mohamed
I'm afraid that I cannot help you more than this without seeing your
input files. If you want, you can send them in private.
HTH
Giuseppe
Mohamed Safy ha scritto:
Dear Giuseppe
I took your advice but the E[cation+anion] system was very difficult to be
converged.
I tried to reduce the mixing_beta and conv_thr with no results.
Thanks
On Sun, 9 Dec 2018 at 14:37, Mohamed Safy wrote:
Dear Giuseppe
Many thanks for your response.
I will try with your advice and give you the response
Thanks
On Thu, 6 Dec 2018 at 12:24, Giuseppe Mattioli <
giuseppe.matti...@ism.cnr.it> wrote:
Dear Mohamed
charged ions are tricky in DFT for multiple reasons. The excess and
well localized charge can suffer a very strong delocalization error
which may lead to unbound electronic states. Moreover, charged ions
are generally not stable in gas phase. They often require a polar
solvent to exist. Finally, in periodic boundary conditions a
distribution of charge (aka "jellium") is required to compensate the
positive/negative charge in a supercell, and the reference potential
is affected by the insertion of such charge, so that for example you
cannot calculate the ionization energy of a molecule as
E[q=+1]-E[q=0], as you do when you use GTO codes.
This said, it is not impossible to calculate the adsorption energy of
charged ions on a given substrate, provided that:
1) You use a hybrid EXX-GGA functional. This is not mandatory, but it
is recommended because it generally avoids the accommodation of excess
electrons in unbound states.
2) You embed your system in an implicit dielectric medium (maybe
"water", in your case). In QE this is easily provided by the
QUANTUM-ENVIRON plug-in.
Then you can calculate the adsorption energy in two ways:
A) you can start from the interacting configuration of your system and
progressively remove the ion in several snapshots (or a few snapshot,
depending on the computational resources you can afford). Then you
build an interaction potential curve and yiu try to estimate its
asymptotic value. It requires also a large supercell, of course.
B) you can use a little trick (which however requires 1 and 2 above).
Put a cation in a part of your supercell where the interaction energy
with you polymer+anion system is negligible. Then calculate the energy
of your cation+anion system in a neutral supercell where their charge
is exactly compensated. The energy difference between three neutral
supercells E[polymer+anion+cation]-E[polymer]-E[cation+anion] should
be a sensible estimate of the anion adsorption energy
HTH
Giuseppe
Mohamed Safy ha scritto:
> Thanks for your valuable information but I have experimental results
which
> indicate the presence of adsorption. is this can be considered a
> conflict?. I tried to validate the method using a smaller system. I
> studied the adsorption of H2 on Graphene.
> The adsorption energy was 17.17 kcal/mol.
> the systems are below
> Complex
>
> calculation = "scf"
> forc_conv_thr = 1.0e-03
> max_seconds = 1.72800e+05
> nstep = 1000
> verbosity='high'
> restart_mode='from_scratch'
> iprint=1
> tprnfor=.true.
> pseudo_dir = '/lfs01/workdirs/val/Test/pseudo',
> outdir='/lfs01/workdirs/val/Test/Out/C',
> /
>
>
> a = 7.40525e+00
> c = 9.99906e+00
> ibrav = 4
> nat = 19
> ntyp = 2
> ecutwfc = 45.0 ,
> ecutrho = 450.0 ,
> input_DFT = 'PBE-D2' ,
> occupations = 'smearing' ,
> degauss = 1.0d-4 ,
> vdw_corr = 'Grimme-D2'
> assume_isolated = 'mt'
> smearing = 'marzari-vanderbilt' ,
> /
>
>
> conv_thr = 1.0d-7 ,
> electron_maxstep = 1000
> mixing_mode = 'plain' ,
> mixing_beta = 0.3d0 ,
> /
>
>
> ion_dynamics='bfgs'
> upscale=20.0
> /
>
>
> /
>
> K_POINTS {automatic}
> 3 3 3 0 0 0
>
> ATOMIC_SPECIES
> C 12.01070 C.pbe-n-kjpaw_psl.1.0.0.UPF
> H 1.00794 H.pbe-kjpaw_psl.1.0.0.UPF
> ATOMIC_POSITIONS {angstrom}
> C1.280642168 0.685951341 -0.000431048
> C -1.236653977 3.539880413 -0.001566184
> C -0.000377617 2.903279130 -0.002911997
> C -2.489554615 5.710262290 -0.000852594
> C -1.229721248 4.990709007 -0.000338911
> C2.449440629 1.438897112 0.002319254
> C3.702198081 0.707454065 -0.001265064
> C1.236237242 3.539760579 0.000958837
> C2.478517989 2.856386275 0.004841971
> C -0.000246038 5.700684987 -0.000997560
> C1.229347070 4.990770096 -0.000716604
> C4.955272233 1.438694069 -0.002138838
> C6.124721243 0.686321393 0.000987763
> C3.702044434 3.562937903 0.001926384
> C4.925831271 2.856536000 -0.00173
> C2.489209922 5.710445901 -0.000342579
> C3.702309214 4.976078918 -0.48704
> H3.360489134 2.350036356 -3.014528460
> H2.719672863 2.741584163 -3.037540110
>
>
> Graphen
>
> calculation = "scf"
> forc_conv_thr = 1.0e-03
>
[QE-users] DFT+U can not converge
Dear QEusers,
When I use QE6.3 to perform DFT+U to relax a slab, it is very difficult to
converge and even can not converge (more than 300 scf steps). Thanks for your
suggestion in advances.
The input file is:
calculation='relax',
nstep = 200 ,
wf_collect = .true. ,
etot_conv_thr = 3.5D-6 ,
forc_conv_thr = 4.0D-4,
/
ibrav=0,
celldm(1)=9.6431795847d0,
nat=109,
ntyp=3,
ecutwfc=60,
ecutrho=480,
input_dft='PBE',
occupations='smearing',
smearing = 'gaussian' ,
degauss = 0.01 ,
nspin = 2 ,
starting_magnetization(1) = 0.5 ,
lda_plus_u = .true. ,
Hubbard_U(1) = 3.32 ,
vdw_corr = dft-d3 ,
/
conv_thr=1d-05,
mixing_beta=0.3d0,
mixing_mode ='local-TF',
electron_maxstep = 600 ,
/
/
/
ATOMIC_SPECIES
Co 58.933200d0 Co.pbe-spn-rrkjus_psl.0.3.1.UPF
O 15.999400d0 O.pbe-n-rrkjus_psl.1.0.0.UPF
P 30.973800d0 P.pbe-n-rrkjus_psl.1.0.0.UPF
ATOMIC_POSITIONS {crystal}
O0.175510868 0.823201091 0.0040419020 0 0
Co 0.752963028 0.655948399 0.0043135660 0 0
O0.301125723 0.416151961 0.0048799970 0 0
Co 0.846799898 0.775755648 0.0052751820 0 0
Co 0.346800351 0.275755641 0.0052752040 0 0
O0.392474471 0.135359341 0.0056702340 0 0
Co 0.940637166 0.895562903 0.006230 0 0
O0.518089326 0.728310212 0.0065083300 0 0
O0.902313840 0.059368885 0.0179593930 0 0
O0.807187857 0.964594997 0.0204575570 0 0
O0.036878250 0.705581722 0.0238905990 0 0
P0.893919682 0.538810250 0.0262428490 0 0
Co 0.451343782 0.481124665 0.0337500410 0 0
O0.028914218 0.314809876 0.0343233470 0 0
P0.323165643 0.700374526 0.0446558860 0 0
O0.412931350 0.644218586 0.0452437970 0 0
O0.180081232 0.532598515 0.0466851490 0 0
O0.551818853 0.324973894 0.0622826950 0 0
O0.318968869 0.213353805 0.0637240070 0 0
P0.408734429 0.157197863 0.0643119200 0 0
O0.702985853 0.542762514 0.0746444590 0 0
Co 0.280556437 0.376447725 0.0752177630 0 0
P0.837980537 0.318762141 0.0827249540 0 0
O0.695021832 0.151990660 0.0850772360 0 0
O0.924712372 0.892977386 0.0885102760 0 0
O0.829586379 0.798203506 0.0910084100 0 0
O0.213810893 0.129262179 0.1024594740 0 0
Co 0.791263053 0.962009487 0.1027311380 0 0
O0.339425748 0.722213050 0.1032975690 0 0
Co 0.885099923 0.081816736 0.1036927540 0 0
Co 0.385100377 0.581816730 0.1036927760 0 0
O0.430774496 0.441420429 0.1040878070 0 0
Co 0.978937191 0.201623991 0.1046542380 0 0
O0.556389351 0.034371300 0.1049259020 0 0
O0.940613865 0.365429972 0.1163769650 0 0
O0.845487883 0.270656085 0.1188751290 0 0
O0.075178275 0.011642810 0.1223081710 0 0
P0.932219708 0.844871338 0.1246604210 0 0
Co 0.489643808 0.787185753 0.1321676130 0 0
O0.067214244 0.620870964 0.1327409190 0 0
P0.361354279 0.006083789 0.142115621
O0.446802131 0.950135511 0.145110715
O0.214381915 0.837791409 0.146887224
O0.593110221 0.629859448 0.161855388
O0.355569602 0.519337757 0.162613913
P0.444333889 0.463046511 0.162481449
O0.733915313 0.849462282 0.171314557
Co 0.331397450 0.684149370 0.17454
P0.880835007 0.624048906 0.181575275
O0.729016571 0.457586972 0.184340848
O0.943694570 0.199413194 0.185888622
O0.842699539 0.103890146 0.188690045
O0.246376254 0.435621465 0.201025875
Co 0.819907469 0.267437250 0.200281311
O0.371654672 0.028624679 0.201597106
Co 0.919293748 0.386217687 0.198228118
Co 0.408991643 0.881622266 0.208931455
O0.502982285 0.747275057 0.201700410
Co 0.015942502 0.506736170 0.203798000
O0.581988259 0.338815157 0.205761317
O0.989082264 0.670263393 0.214923633
O0.891588821 0.575388161 0.217463006
O0.102116329 0.316952504 0.225311380
P0.946018990 0.150667428 0.220957196
Co 0.509889754 0.092572883 0.231027714
O0.087929910 0.910622245 0.254736182
P0.390071467 0.310008795 0.243522265
O0.475452219 0.253683339 0.241349488
O0.235229551 0.143749020 0.238654386
O0.612387032 0.940393783 0.254302766
O0.441611912 0.82770 0.264038723
P0.540200975 0.770461487 0.260363655
O0.761099937
