Change arrangement of electrons in POTENTIALS file
226 views
Skip to first unread message
Daniele Ongari
Jan 4, 2021, 5:36:20 AM1/4/21
to cp2k
Dear all,
for some high-throughput calculation on Metal Organic Frameworks I need to specify the MAGNETIZATION in order to impose the highest ferromagnetic state at a given oxidation state. It is an assumption to treat all the metals in a coherent way.
The problem I'm facing is that, when the electrons of the potential are arranges such as:
- all the orbitals are filled
or
- more than one orbital is partially filled
CP2K fails with the error *******************************************************************************
for some high-throughput calculation on Metal Organic Frameworks I need to specify the MAGNETIZATION in order to impose the highest ferromagnetic state at a given oxidation state. It is an assumption to treat all the metals in a coherent way.
The problem I'm facing is that, when the electrons of the potential are arranges such as:
- all the orbitals are filled
or
- more than one orbital is partially filled
CP2K fails with the error *******************************************************************************
* ___ *
* / \ *
* [ABORT] *
* \___/ Magnetization value cannot be imposed for this atom type *
* | *
* O/| *
* /| | *
* / \ qs_kind_types.F:2790 *
*******************************************************************************
because, I think, MAGNETIZATION can not decide which electrons to unpair.
I could use the section &BS but it gets too complicate, so the question is: am I allowed to change the original ordering in the POTENTIAL file?
To explain better, let's take the elements of the 10th column that lead to failure, Pt and Pd:
(row 3) Ni is arranged "4 6 8", and it is fine as magnetization will unpair electrons form the partially occupied d orbitals
(row 4) Pd is arranged as "3 6 9" and fails because both s and d orbitals are partially occupied. Am I allowed to modify it as "4 6 8"?
(row 5) Pt is arranged as "2 6 10" and fails because all orbitals are fully occupied. Am I allowed to modify it as "4 6 8"?
Technically this trick works and the CP2K calculation starts an even converges, but do you see any theoretical problem in doing this?
Thanks for your attention.
Daniele
because, I think, MAGNETIZATION can not decide which electrons to unpair.
I could use the section &BS but it gets too complicate, so the question is: am I allowed to change the original ordering in the POTENTIAL file?
To explain better, let's take the elements of the 10th column that lead to failure, Pt and Pd:
(row 3) Ni is arranged "4 6 8", and it is fine as magnetization will unpair electrons form the partially occupied d orbitals
(row 4) Pd is arranged as "3 6 9" and fails because both s and d orbitals are partially occupied. Am I allowed to modify it as "4 6 8"?
(row 5) Pt is arranged as "2 6 10" and fails because all orbitals are fully occupied. Am I allowed to modify it as "4 6 8"?
Technically this trick works and the CP2K calculation starts an even converges, but do you see any theoretical problem in doing this?
Thanks for your attention.
Daniele
hut...@chem.uzh.ch
Jan 4, 2021, 6:15:11 AM1/4/21
to cp...@googlegroups.com
Hi Daniele
the electron counts in the POTENTIAL files are just for the
initial guess. You can change them without any problem. The definition
of the potential does not change.
Maybe we should have this as an input option.
best
Juerg
--------------------------------------------------------------
Juerg Hutter Phone : ++41 44 635 4491
Institut für Chemie C FAX : ++41 44 635 6838
Universität Zürich E-mail: hut...@chem.uzh.ch
Winterthurerstrasse 190
CH-8057 Zürich, Switzerland
---------------------------------------------------------------
-----cp...@googlegroups.com wrote: -----
To: "cp2k" <cp...@googlegroups.com>
From: "Daniele Ongari"
Sent by: cp...@googlegroups.com
Date: 01/04/2021 11:45AM
Subject: [CP2K:14465] Change arrangement of electrons in POTENTIALS file
--
You received this message because you are subscribed to the Google Groups "cp2k" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/9dbd45d2-b990-41c4-b964-79ad84843f2en%40googlegroups.com.
the electron counts in the POTENTIAL files are just for the
initial guess. You can change them without any problem. The definition
of the potential does not change.
Maybe we should have this as an input option.
best
Juerg
--------------------------------------------------------------
Juerg Hutter Phone : ++41 44 635 4491
Institut für Chemie C FAX : ++41 44 635 6838
Universität Zürich E-mail: hut...@chem.uzh.ch
Winterthurerstrasse 190
CH-8057 Zürich, Switzerland
---------------------------------------------------------------
-----cp...@googlegroups.com wrote: -----
To: "cp2k" <cp...@googlegroups.com>
From: "Daniele Ongari"
Sent by: cp...@googlegroups.com
Date: 01/04/2021 11:45AM
Subject: [CP2K:14465] Change arrangement of electrons in POTENTIALS file
You received this message because you are subscribed to the Google Groups "cp2k" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/9dbd45d2-b990-41c4-b964-79ad84843f2en%40googlegroups.com.
Daniele Ongari
Jan 4, 2021, 6:19:18 AM1/4/21
to cp2k
Dear Juerg,
thanks for your quick reply: then I will adjust it conveniently.
Daniele
thanks for your quick reply: then I will adjust it conveniently.
Daniele
Daniele Ongari
Jan 4, 2021, 9:24:21 AM1/4/21
to cp2k
Dear Juerg,
I think you may refer to the keyword https://manual.cp2k.org/cp2k-5_1-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/KIND.html#ELEC_CONF
I think you may refer to the keyword https://manual.cp2k.org/cp2k-5_1-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/KIND.html#ELEC_CONF
for adjusting the electronic configuration form the input file.
However, I just tested it (e.g., ELEC_CONF 4 6 8) and it is not working: the program seems to simply skip this information and use the configuration read from POTENTIALS.
I'm using CP2K 5.1
I wonder if I'm missing something or it is a bug.
Thanks,
Daniele
However, I just tested it (e.g., ELEC_CONF 4 6 8) and it is not working: the program seems to simply skip this information and use the configuration read from POTENTIALS.
I'm using CP2K 5.1
I wonder if I'm missing something or it is a bug.
Thanks,
Daniele
hut...@chem.uzh.ch
Jan 5, 2021, 11:38:59 AM1/5/21
to cp...@googlegroups.com
Dear Daniele
Thank you for pointing this out. I fixed this in the current
version and added some more tests to avoid job failures.
It will now stop with an (meaningful) error message.
Subject: Re: [CP2K:14470] Change arrangement of electrons in POTENTIALS file
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/ceeb0a05-e78e-480b-8f67-72c0721f29abn%40googlegroups.com.
Thank you for pointing this out. I fixed this in the current
version and added some more tests to avoid job failures.
It will now stop with an (meaningful) error message.
Juerg
--------------------------------------------------------------
Juerg Hutter Phone : ++41 44 635 4491
Institut für Chemie C FAX : ++41 44 635 6838
Universität Zürich E-mail: hut...@chem.uzh.ch
Winterthurerstrasse 190
CH-8057 Zürich, Switzerland
---------------------------------------------------------------
-----cp...@googlegroups.com wrote: -----
To: "cp2k" <cp...@googlegroups.com>
From: "Daniele Ongari"
Sent by: cp...@googlegroups.com
Date: 01/04/2021 03:24PM
--------------------------------------------------------------
Juerg Hutter Phone : ++41 44 635 4491
Institut für Chemie C FAX : ++41 44 635 6838
Universität Zürich E-mail: hut...@chem.uzh.ch
Winterthurerstrasse 190
CH-8057 Zürich, Switzerland
---------------------------------------------------------------
-----cp...@googlegroups.com wrote: -----
To: "cp2k" <cp...@googlegroups.com>
From: "Daniele Ongari"
Sent by: cp...@googlegroups.com
Subject: Re: [CP2K:14470] Change arrangement of electrons in POTENTIALS file
Daniele Ongari
Jan 5, 2021, 12:19:06 PM1/5/21
to cp2k
Dear Juerg,
thanks for your action. I have another concern.
When I modify e.g., Pd from "3 6 9" to "4 6 8", I'm basically expecting to move on valence electron from the D orbital to the S orbital,
to have only one orbital partially occupied (D) and make the MAGNETIZATION 2 work.
However, what CP2K prints out is the following. I'm concerned with the core "[ 5.00 1.00]" configuration of the D orbital, as it looks like the program assumes some weird configuration for the pseudo.
I was expecting indeed to read "[ 5.00 ] 5.00" for Alpha and "[ 5.00 ] 3.00" for Beta.
thanks for your action. I have another concern.
When I modify e.g., Pd from "3 6 9" to "4 6 8", I'm basically expecting to move on valence electron from the D orbital to the S orbital,
to have only one orbital partially occupied (D) and make the MAGNETIZATION 2 work.
However, what CP2K prints out is the following. I'm concerned with the core "[ 5.00 1.00]" configuration of the D orbital, as it looks like the program assumes some weird configuration for the pseudo.
I was expecting indeed to read "[ 5.00 ] 5.00" for Alpha and "[ 5.00 ] 3.00" for Beta.
Guess for atomic kind: Pd
Electronic structure
Total number of core electrons 28.00
Total number of valence electrons 18.00
Total number of electrons 46.00
Multiplicity triplet
Alpha Electrons
S [ 1.00 1.00] 1.00 1.00
P [ 3.00 3.00] 3.00
D [ 5.00 1.00] 5.00
Beta Electrons
S [ 1.00 1.00] 1.00 1.00
P [ 3.00 3.00] 3.00
D [ 5.00 1.00] 3.00
What is your opinion about it?
What I want to achieve, at the end, is the corresponding of:
&BS
What I want to achieve, at the end, is the corresponding of:
&BS
&ALPHA
NEL 1 1
N 5 4
L 0 3
&BETA
NEL 1 -3
N 5 4
L 0 3
starting with the default ELEC_CONF 3 6 9
Thanks for your kind attention,
Daniele
Thanks for your kind attention,
Daniele
hut...@chem.uzh.ch
Jan 14, 2021, 4:46:13 PM1/14/21
to cp...@googlegroups.com
Hi
I changed the method of initialization of the atom wfn.
It now tries to guess the core states first and then adds
the electronic configuration. I hope this adds flexibility.
regards
Juerg
--------------------------------------------------------------
Juerg Hutter Phone : ++41 44 635 4491
Institut für Chemie C FAX : ++41 44 635 6838
Universität Zürich E-mail: hut...@chem.uzh.ch
Winterthurerstrasse 190
CH-8057 Zürich, Switzerland
---------------------------------------------------------------
-----cp...@googlegroups.com wrote: -----
To: "cp2k" <cp...@googlegroups.com>
From: "Daniele Ongari"
Sent by: cp...@googlegroups.com
Date: 01/05/2021 06:19PM
Subject: Re: [CP2K:14488] Change arrangement of electrons in POTENTIALS file
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/c2e6be8c-1239-48a8-a7f2-6544626d5550n%40googlegroups.com.
I changed the method of initialization of the atom wfn.
It now tries to guess the core states first and then adds
the electronic configuration. I hope this adds flexibility.
regards
Juerg
--------------------------------------------------------------
Juerg Hutter Phone : ++41 44 635 4491
Institut für Chemie C FAX : ++41 44 635 6838
Universität Zürich E-mail: hut...@chem.uzh.ch
Winterthurerstrasse 190
CH-8057 Zürich, Switzerland
---------------------------------------------------------------
-----cp...@googlegroups.com wrote: -----
To: "cp2k" <cp...@googlegroups.com>
From: "Daniele Ongari"
Sent by: cp...@googlegroups.com
Subject: Re: [CP2K:14488] Change arrangement of electrons in POTENTIALS file
Message has been deleted
Václav Havel
May 17, 2021, 11:42:44 PM5/17/21
to cp2k
Dear all
I am confused about how to set the keyword ELEC_CONF (FORCE_EVAL / SUBSYS / KIND/ELEC_CONF ) . How to do with the cation Al3+ in aluminum chloride aqueous solution. Could I set ELEC_CONF 0 0 0 because the electron configuration of cation Al3+ is 1s2 2s2 2p6 ,which different from the Al atom's configuration 1s2 2s2 2p6 3s2 3p1 .
Thanks
Vaclav
Reply all
Reply to author
Forward
0 new messages