Re: [Wien] opticcpara crashed for mstar

[Dr. K. C. Bhamu]

I believe I have figured it out.
Will update you.

Thank you
Bhamu

On Thu, Mar 11, 2021 at 4:26 AM Rubel, Oleg  wrote:

> I am glad Si worked out. Sorry, Bhamu. You need to figure it out even if
> it takes more time. When searching through eigenvalues, keep in mind the
> number of digits. For instance, 0.383706 from case.scf can appear as
> 0.3837058 in the eigenvalue file.
>
> All the best
> Oleg
>
> 
> From: Wien  on behalf of Dr. K.
> C. Bhamu 
> Sent: Wednesday, March 10, 2021 11:50
> To: A Mailing list for WIEN2k users
> Subject: Re: [Wien] opticcpara crashed for mstar
>
> Dear Prof. Oleg
> I tried to follow your advice and it worked for Si case. I found VBM at
> #KP1 and CBM at #KP15. The band index edges were matched with the
> particular KP in case.energyso.
>
> But In my case, I could not find the VBM/CBM edges either in case.eneryso
> or in case.bands.agr/spagetti_ene.
>
> I finished two different calculations (with shifted k-mesh and unshifted
> k-mesh) and both can be downloaded from [1].
> [1] https://we.tl/t-Mhv6nv4Zlf
>
> I would be grateful to you, if you can suggest me #KP's with respect to
> VBM/CBM.
> CBM is not exactly on high-symmetry  k-point.
>
>
> Thank you
> Bhamu
>
>
> On Tue, Mar 9, 2021 at 11:13 PM Rubel, Oleg  rub...@mcmaster.ca>> wrote:
> Dear Bhamu,
>
> to get a VBM k-point index, you would need to look for "0.383706" in your
> case.energyso and see which k-point this eigenvalue belongs to. For CBE,
> look for "0.401998" (it can be a different k-point).
>
> In Si VBM is at Gamma, and CBM is far away from Gamma. Thus we have two
> different k-points. After some trials, I found that 7x7x7 unshifted k-mesh
> "hits" CBM of Si quite precisely.
>
> Of course you need to be confident that the selected k-mesh "hits" the
> relevant extremum (extrema) of your band structure. For instance if you
> need Gamma, do not select a shifted mesh. When the extremum is away from
> the high-symmetry points and coordinates are known, it might be easier to
> use case.klist_band and target the point(s) of interest.
>
> I hope it helps
> Oleg
>
> 
> From: Wien  wien-boun...@zeus.theochem.tuwien.ac.at>> on behalf of Dr. K. C. Bhamu <
> kcbham...@gmail.com>
> Sent: Tuesday, March 9, 2021 08:15
> To: A Mailing list for WIEN2k users
> Subject: Re: [Wien] opticcpara crashed for mstar
>
> Dear Prof. Oleg
> Sorry for the late reply. As we have the opposite time zone so I am
> replying according to your office time.
>
> My previous information was from pbe.spaghetti_ene.
>
> Here is the relevant part from case.scf.
>
>  Bandranges (emin - emax) and occupancy:
> :BAN00066:  660.2189000.284902  1.
> :BAN00067:  670.2817550.322256  1.
> :BAN00068:  680.2817550.322256  1.
> :BAN00069:  690.2879140.335582  1.
> :BAN00070:  700.2879140.335582  1.
> :BAN00071:  710.2941570.351734  1.
> :BAN00072:  720.2941570.351734  1.
> :BAN00073:  730.3010710.368987  1.
> :BAN00074:  740.3010710.368987  1.
> :BAN00075:  750.3400590.383706  1.
> :BAN00076:  760.3400590.383706  1.  VBM
> :BAN00077:  770.4019980.551266  0.  CBM
> :BAN00078:  780.4019980.551266  0.
> :BAN00079:  790.4728340.603663  0.
> :BAN00080:  800.4728340.603663  0.
> :BAN00081:  810.5567370.634231  0.
> Energy to separate low and high energystates:   -0.57035
>
> Just above this part, I see
> :KPT   :  NUMBER OF K-POINTS: 40
>0.0   0.0 angle (M,z), angle (M,x) deg
>
> SPIN-ORBIT EIGENVALUES:
>  K=   0.14286   0.14286   0.14286 1  (In case of "Si" it is 0 0 0
> so you took KP =1?)
>   MATRIX SIZE=  552   WEIGHT= 8.00
>
> Does it mean that I should look for #KP 1? and then of course, bandinxed
> 75,76 for VBM and CBM, respectively.
> But in case of Si, you took #KP =1 for VBM and #KP=15 for CBM.
> So now the band index is clear to me.
>
> My next query is, how can I know #KP for VBM and CBM?
>
> Sorry for the long conversation.
>
> Thank you
> Bhamu
>
> On Mon, Mar 8, 2021 at 8:48 PM Rubel, Oleg  rub...@mcmaster.ca>>>
> wrote:
> Dear Bhamu,
>
> it seems you have k-point index=38, band index=653. To be on a safe side,
> I would look for band ranges (":BANXXX") in case.scf (last iteration). The
> occupancies are written down in the same table. If you have questions about
> interpretation of :BANXXX, it will be better if you list this section for
> your SCF file.
>
> Thanks
> Oleg
>
> 
> From: Wien  wien-boun...@zeus.theochem.tuwien.ac.at> wien-boun...@zeus.theochem.tuwien.ac.at wien-boun...@zeus.theochem.tuwien.ac.at>>> on behalf of Dr. K. C. Bhamu <
> 

Re: [Wien] opticcpara crashed for mstar

[Dr. K. C. Bhamu]

Dear Prof. Oleg,
Before sending my last email to the mailing list, I checked with the digits
too.
Also, a simple grep command can grep the nearest number from all the files
present in the working directory and I used this trick too.

I don't really don't know where is the mistake.

Regards
Bhamu




On Thu, Mar 11, 2021, 07:56 Rubel, Oleg  wrote:

> I am glad Si worked out. Sorry, Bhamu. You need to figure it out even if
> it takes more time. When searching through eigenvalues, keep in mind the
> number of digits. For instance, 0.383706 from case.scf can appear as
> 0.3837058 in the eigenvalue file.
>
> All the best
> Oleg
>
> 
> From: Wien  on behalf of Dr. K.
> C. Bhamu 
> Sent: Wednesday, March 10, 2021 11:50
> To: A Mailing list for WIEN2k users
> Subject: Re: [Wien] opticcpara crashed for mstar
>
> Dear Prof. Oleg
> I tried to follow your advice and it worked for Si case. I found VBM at
> #KP1 and CBM at #KP15. The band index edges were matched with the
> particular KP in case.energyso.
>
> But In my case, I could not find the VBM/CBM edges either in case.eneryso
> or in case.bands.agr/spagetti_ene.
>
> I finished two different calculations (with shifted k-mesh and unshifted
> k-mesh) and both can be downloaded from [1].
> [1] https://we.tl/t-Mhv6nv4Zlf
>
> I would be grateful to you, if you can suggest me #KP's with respect to
> VBM/CBM.
> CBM is not exactly on high-symmetry  k-point.
>
>
> Thank you
> Bhamu
>
>
> On Tue, Mar 9, 2021 at 11:13 PM Rubel, Oleg  rub...@mcmaster.ca>> wrote:
> Dear Bhamu,
>
> to get a VBM k-point index, you would need to look for "0.383706" in your
> case.energyso and see which k-point this eigenvalue belongs to. For CBE,
> look for "0.401998" (it can be a different k-point).
>
> In Si VBM is at Gamma, and CBM is far away from Gamma. Thus we have two
> different k-points. After some trials, I found that 7x7x7 unshifted k-mesh
> "hits" CBM of Si quite precisely.
>
> Of course you need to be confident that the selected k-mesh "hits" the
> relevant extremum (extrema) of your band structure. For instance if you
> need Gamma, do not select a shifted mesh. When the extremum is away from
> the high-symmetry points and coordinates are known, it might be easier to
> use case.klist_band and target the point(s) of interest.
>
> I hope it helps
> Oleg
>
> 
> From: Wien  wien-boun...@zeus.theochem.tuwien.ac.at>> on behalf of Dr. K. C. Bhamu <
> kcbham...@gmail.com>
> Sent: Tuesday, March 9, 2021 08:15
> To: A Mailing list for WIEN2k users
> Subject: Re: [Wien] opticcpara crashed for mstar
>
> Dear Prof. Oleg
> Sorry for the late reply. As we have the opposite time zone so I am
> replying according to your office time.
>
> My previous information was from pbe.spaghetti_ene.
>
> Here is the relevant part from case.scf.
>
>  Bandranges (emin - emax) and occupancy:
> :BAN00066:  660.2189000.284902  1.
> :BAN00067:  670.2817550.322256  1.
> :BAN00068:  680.2817550.322256  1.
> :BAN00069:  690.2879140.335582  1.
> :BAN00070:  700.2879140.335582  1.
> :BAN00071:  710.2941570.351734  1.
> :BAN00072:  720.2941570.351734  1.
> :BAN00073:  730.3010710.368987  1.
> :BAN00074:  740.3010710.368987  1.
> :BAN00075:  750.3400590.383706  1.
> :BAN00076:  760.3400590.383706  1.  VBM
> :BAN00077:  770.4019980.551266  0.  CBM
> :BAN00078:  780.4019980.551266  0.
> :BAN00079:  790.4728340.603663  0.
> :BAN00080:  800.4728340.603663  0.
> :BAN00081:  810.5567370.634231  0.
> Energy to separate low and high energystates:   -0.57035
>
> Just above this part, I see
> :KPT   :  NUMBER OF K-POINTS: 40
>0.0   0.0 angle (M,z), angle (M,x) deg
>
> SPIN-ORBIT EIGENVALUES:
>  K=   0.14286   0.14286   0.14286 1  (In case of "Si" it is 0 0 0
> so you took KP =1?)
>   MATRIX SIZE=  552   WEIGHT= 8.00
>
> Does it mean that I should look for #KP 1? and then of course, bandinxed
> 75,76 for VBM and CBM, respectively.
> But in case of Si, you took #KP =1 for VBM and #KP=15 for CBM.
> So now the band index is clear to me.
>
> My next query is, how can I know #KP for VBM and CBM?
>
> Sorry for the long conversation.
>
> Thank you
> Bhamu
>
> On Mon, Mar 8, 2021 at 8:48 PM Rubel, Oleg  rub...@mcmaster.ca>>>
> wrote:
> Dear Bhamu,
>
> it seems you have k-point index=38, band index=653. To be on a safe side,
> I would look for band ranges (":BANXXX") in case.scf (last iteration). The
> occupancies are written down in the same table. If you have questions about
> interpretation of :BANXXX, it will be better if you list this section for
> your SCF file.
>
> Thanks
> 

Re: [Wien] opticcpara crashed for mstar

[Rubel, Oleg]

I am glad Si worked out. Sorry, Bhamu. You need to figure it out even if it 
takes more time. When searching through eigenvalues, keep in mind the number of 
digits. For instance, 0.383706 from case.scf can appear as 0.3837058 in the 
eigenvalue file.

All the best
Oleg


From: Wien  on behalf of Dr. K. C. 
Bhamu 
Sent: Wednesday, March 10, 2021 11:50
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] opticcpara crashed for mstar

Dear Prof. Oleg
I tried to follow your advice and it worked for Si case. I found VBM at  #KP1 
and CBM at #KP15. The band index edges were matched with the particular KP in 
case.energyso.

But In my case, I could not find the VBM/CBM edges either in case.eneryso or in 
case.bands.agr/spagetti_ene.

I finished two different calculations (with shifted k-mesh and unshifted 
k-mesh) and both can be downloaded from [1].
[1] https://we.tl/t-Mhv6nv4Zlf

I would be grateful to you, if you can suggest me #KP's with respect to VBM/CBM.
CBM is not exactly on high-symmetry  k-point.


Thank you
Bhamu


On Tue, Mar 9, 2021 at 11:13 PM Rubel, Oleg 
mailto:rub...@mcmaster.ca>> wrote:
Dear Bhamu,

to get a VBM k-point index, you would need to look for "0.383706" in your 
case.energyso and see which k-point this eigenvalue belongs to. For CBE, look 
for "0.401998" (it can be a different k-point).

In Si VBM is at Gamma, and CBM is far away from Gamma. Thus we have two 
different k-points. After some trials, I found that 7x7x7 unshifted k-mesh 
"hits" CBM of Si quite precisely.

Of course you need to be confident that the selected k-mesh "hits" the relevant 
extremum (extrema) of your band structure. For instance if you need Gamma, do 
not select a shifted mesh. When the extremum is away from the high-symmetry 
points and coordinates are known, it might be easier to use case.klist_band and 
target the point(s) of interest.

I hope it helps
Oleg


From: Wien 
mailto:wien-boun...@zeus.theochem.tuwien.ac.at>>
 on behalf of Dr. K. C. Bhamu mailto:kcbham...@gmail.com>>
Sent: Tuesday, March 9, 2021 08:15
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] opticcpara crashed for mstar

Dear Prof. Oleg
Sorry for the late reply. As we have the opposite time zone so I am replying 
according to your office time.

My previous information was from pbe.spaghetti_ene.

Here is the relevant part from case.scf.

 Bandranges (emin - emax) and occupancy:
:BAN00066:  660.2189000.284902  1.
:BAN00067:  670.2817550.322256  1.
:BAN00068:  680.2817550.322256  1.
:BAN00069:  690.2879140.335582  1.
:BAN00070:  700.2879140.335582  1.
:BAN00071:  710.2941570.351734  1.
:BAN00072:  720.2941570.351734  1.
:BAN00073:  730.3010710.368987  1.
:BAN00074:  740.3010710.368987  1.
:BAN00075:  750.3400590.383706  1.
:BAN00076:  760.3400590.383706  1.  VBM
:BAN00077:  770.4019980.551266  0.  CBM
:BAN00078:  780.4019980.551266  0.
:BAN00079:  790.4728340.603663  0.
:BAN00080:  800.4728340.603663  0.
:BAN00081:  810.5567370.634231  0.
Energy to separate low and high energystates:   -0.57035

Just above this part, I see
:KPT   :  NUMBER OF K-POINTS: 40
   0.0   0.0 angle (M,z), angle (M,x) deg

SPIN-ORBIT EIGENVALUES:
 K=   0.14286   0.14286   0.14286 1  (In case of "Si" it is 0 0 0 so 
you took KP =1?)
  MATRIX SIZE=  552   WEIGHT= 8.00

Does it mean that I should look for #KP 1? and then of course, bandinxed 75,76 
for VBM and CBM, respectively.
But in case of Si, you took #KP =1 for VBM and #KP=15 for CBM.
So now the band index is clear to me.

My next query is, how can I know #KP for VBM and CBM?

Sorry for the long conversation.

Thank you
Bhamu

On Mon, Mar 8, 2021 at 8:48 PM Rubel, Oleg 
mailto:rub...@mcmaster.ca>>>
 wrote:
Dear Bhamu,

it seems you have k-point index=38, band index=653. To be on a safe side, I 
would look for band ranges (":BANXXX") in case.scf (last iteration). The 
occupancies are written down in the same table. If you have questions about 
interpretation of :BANXXX, it will be better if you list this section for your 
SCF file.

Thanks
Oleg


From: Wien 
mailto:wien-boun...@zeus.theochem.tuwien.ac.at>>>
 on behalf of Dr. K. C. Bhamu 
mailto:kcbham...@gmail.com>>>
Sent: Sunday, March 7, 2021 08:09
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] opticcpara crashed for mstar

Dear Prof. Oleg
Sorry to interrupt you.
Earlier I was looking for the wrong file.
My case.klist has 40 

Re: [Wien] mBJ crash

[Peter Blaha]

But it seems that you still have   MSR1a   in case.inm
(Most likely the previous runsp -min was not finishing successfully).

restore the previous PBE calculation (your atomic positions have been 
"destroyed"); edit case.inm and make sure you do not have MSR1a but only 
MSR1. Then:

runsp 



Am 10.03.2021 um 21:12 schrieb delamora:
Thanks for your reply, I did a "min", but after that I did a normal mBJ 
and after mBJ iniciation I ran;

nohup runsp -orb -so -p -NI -i 100 &

Pablo


Normally the "infeasible step" occurs in MSR1a. Are you doing -min 
(dubious for mBJ) or PRATTO ? Just guessing.


---
Prof Laurence Marks
"Research is to see what everyone else has seen, and to think what 
nobody else has thought", Albert Szent-Györgyi

www.numis.northwestern.edu 

On Wed, Mar 10, 2021, 13:40 delamora > wrote:


Dear WIEN2k comunity;
I am doping Dy3TaO7 with Sc, so I have a large cell with 44 atoms.
I put
RxK = 7
500 k points

This system is an insulator, so after converging I did a mBJ, but
the calculation stoped at cycle 18;
in cycle 15    ETEST: .13247691   CTEST: .0181758
in cycle 16    ETEST: .02511053   CTEST: .0179594
in cycle 17    ETEST: .050679725000   CTEST: .0143033
in cycle 18    ETEST: .055618435000   CTEST: .0130839

the last lines in the nohup.out were;
  SUMPARA END
  CORE  END
  CORE  END
Mixer - Error. no feasible step small enough, check RMT and model
grep: No existe correspondencia. (there is no correspondence)

I tried to continue the calculation and it stoped again after one cycle.

What can I do?

Pablo


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--
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
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Re: [Wien] mBJ crash

[delamora]

Thanks for your reply, I did a "min", but after that I did a normal mBJ and 
after mBJ iniciation I ran;
nohup runsp -orb -so -p -NI -i 100 &

Pablo



Normally the "infeasible step" occurs in MSR1a. Are you doing -min (dubious for 
mBJ) or PRATTO ? Just guessing.

---
Prof Laurence Marks
"Research is to see what everyone else has seen, and to think what nobody else 
has thought", Albert Szent-Györgyi
www.numis.northwestern.edu

On Wed, Mar 10, 2021, 13:40 delamora 
mailto:delam...@unam.mx>> wrote:
Dear WIEN2k comunity;
I am doping Dy3TaO7 with Sc, so I have a large cell with 44 atoms.
I put
RxK = 7
500 k points

This system is an insulator, so after converging I did a mBJ, but the 
calculation stoped at cycle 18;
in cycle 15ETEST: .13247691   CTEST: .0181758
in cycle 16ETEST: .02511053   CTEST: .0179594
in cycle 17ETEST: .050679725000   CTEST: .0143033
in cycle 18ETEST: .055618435000   CTEST: .0130839

the last lines in the nohup.out were;
 SUMPARA END
 CORE  END
 CORE  END
Mixer - Error. no feasible step small enough, check RMT and model
grep: No existe correspondencia. (there is no correspondence)

I tried to continue the calculation and it stoped again after one cycle.

What can I do?

Pablo


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Re: [Wien] mBJ crash

[Laurence Marks]

Normally the "infeasible step" occurs in MSR1a. Are you doing -min (dubious
for mBJ) or PRATTO ? Just guessing.

---
Prof Laurence Marks
"Research is to see what everyone else has seen, and to think what nobody
else has thought", Albert Szent-Györgyi
www.numis.northwestern.edu

On Wed, Mar 10, 2021, 13:40 delamora  wrote:

> Dear WIEN2k comunity;
> I am doping Dy3TaO7 with Sc, so I have a large cell with 44 atoms.
> I put
> RxK = 7
> 500 k points
>
> This system is an insulator, so after converging I did a mBJ, but the
> calculation stoped at cycle 18;
> in cycle 15ETEST: .13247691   CTEST: .0181758
> in cycle 16ETEST: .02511053   CTEST: .0179594
> in cycle 17ETEST: .050679725000   CTEST: .0143033
> in cycle 18ETEST: .055618435000   CTEST: .0130839
>
> the last lines in the nohup.out were;
>  SUMPARA END
>  CORE  END
>  CORE  END
> Mixer - Error. no feasible step small enough, check RMT and model
> grep: No existe correspondencia. (there is no correspondence)
>
> I tried to continue the calculation and it stoped again after one cycle.
>
> What can I do?
>
> Pablo
>
>
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[Wien] mBJ crash

[delamora]

Dear WIEN2k comunity;
I am doping Dy3TaO7 with Sc, so I have a large cell with 44 atoms.
I put
RxK = 7
500 k points

This system is an insulator, so after converging I did a mBJ, but the 
calculation stoped at cycle 18;
in cycle 15ETEST: .13247691   CTEST: .0181758
in cycle 16ETEST: .02511053   CTEST: .0179594
in cycle 17ETEST: .050679725000   CTEST: .0143033
in cycle 18ETEST: .055618435000   CTEST: .0130839

the last lines in the nohup.out were;
 SUMPARA END
 CORE  END
 CORE  END
Mixer - Error. no feasible step small enough, check RMT and model
grep: No existe correspondencia. (there is no correspondence)

I tried to continue the calculation and it stoped again after one cycle.

What can I do?

Pablo


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Re: [Wien] opticcpara crashed for mstar

[Dr. K. C. Bhamu]

Dear Prof. Oleg
I tried to follow your advice and it worked for Si case. I found VBM at
#KP1 and CBM at #KP15. The band index edges were matched with the
particular KP in case.energyso.

But In my case, I could not find the VBM/CBM edges either in case.eneryso
or in case.bands.agr/spagetti_ene.

I finished two different calculations (with shifted k-mesh and unshifted
k-mesh) and both can be downloaded from [1].
[1] https://we.tl/t-Mhv6nv4Zlf

I would be grateful to you, if you can suggest me #KP's with respect to
VBM/CBM.
CBM is not exactly on high-symmetry  k-point.


Thank you
Bhamu


On Tue, Mar 9, 2021 at 11:13 PM Rubel, Oleg  wrote:

> Dear Bhamu,
>
> to get a VBM k-point index, you would need to look for "0.383706" in your
> case.energyso and see which k-point this eigenvalue belongs to. For CBE,
> look for "0.401998" (it can be a different k-point).
>
> In Si VBM is at Gamma, and CBM is far away from Gamma. Thus we have two
> different k-points. After some trials, I found that 7x7x7 unshifted k-mesh
> "hits" CBM of Si quite precisely.
>
> Of course you need to be confident that the selected k-mesh "hits" the
> relevant extremum (extrema) of your band structure. For instance if you
> need Gamma, do not select a shifted mesh. When the extremum is away from
> the high-symmetry points and coordinates are known, it might be easier to
> use case.klist_band and target the point(s) of interest.
>
> I hope it helps
> Oleg
>
> 
> From: Wien  on behalf of Dr. K.
> C. Bhamu 
> Sent: Tuesday, March 9, 2021 08:15
> To: A Mailing list for WIEN2k users
> Subject: Re: [Wien] opticcpara crashed for mstar
>
> Dear Prof. Oleg
> Sorry for the late reply. As we have the opposite time zone so I am
> replying according to your office time.
>
> My previous information was from pbe.spaghetti_ene.
>
> Here is the relevant part from case.scf.
>
>  Bandranges (emin - emax) and occupancy:
> :BAN00066:  660.2189000.284902  1.
> :BAN00067:  670.2817550.322256  1.
> :BAN00068:  680.2817550.322256  1.
> :BAN00069:  690.2879140.335582  1.
> :BAN00070:  700.2879140.335582  1.
> :BAN00071:  710.2941570.351734  1.
> :BAN00072:  720.2941570.351734  1.
> :BAN00073:  730.3010710.368987  1.
> :BAN00074:  740.3010710.368987  1.
> :BAN00075:  750.3400590.383706  1.
> :BAN00076:  760.3400590.383706  1.  VBM
> :BAN00077:  770.4019980.551266  0.  CBM
> :BAN00078:  780.4019980.551266  0.
> :BAN00079:  790.4728340.603663  0.
> :BAN00080:  800.4728340.603663  0.
> :BAN00081:  810.5567370.634231  0.
> Energy to separate low and high energystates:   -0.57035
>
> Just above this part, I see
> :KPT   :  NUMBER OF K-POINTS: 40
>0.0   0.0 angle (M,z), angle (M,x) deg
>
> SPIN-ORBIT EIGENVALUES:
>  K=   0.14286   0.14286   0.14286 1  (In case of "Si" it is 0 0 0
> so you took KP =1?)
>   MATRIX SIZE=  552   WEIGHT= 8.00
>
> Does it mean that I should look for #KP 1? and then of course, bandinxed
> 75,76 for VBM and CBM, respectively.
> But in case of Si, you took #KP =1 for VBM and #KP=15 for CBM.
> So now the band index is clear to me.
>
> My next query is, how can I know #KP for VBM and CBM?
>
> Sorry for the long conversation.
>
> Thank you
> Bhamu
>
> On Mon, Mar 8, 2021 at 8:48 PM Rubel, Oleg  rub...@mcmaster.ca>> wrote:
> Dear Bhamu,
>
> it seems you have k-point index=38, band index=653. To be on a safe side,
> I would look for band ranges (":BANXXX") in case.scf (last iteration). The
> occupancies are written down in the same table. If you have questions about
> interpretation of :BANXXX, it will be better if you list this section for
> your SCF file.
>
> Thanks
> Oleg
>
> 
> From: Wien  wien-boun...@zeus.theochem.tuwien.ac.at>> on behalf of Dr. K. C. Bhamu <
> kcbham...@gmail.com>
> Sent: Sunday, March 7, 2021 08:09
> To: A Mailing list for WIEN2k users
> Subject: Re: [Wien] opticcpara crashed for mstar
>
> Dear Prof. Oleg
> Sorry to interrupt you.
> Earlier I was looking for the wrong file.
> My case.klist has 40 k-points and thus #KP also varies upto 40.
> From my eigenvalue file, my VBM lies on band index=38 (XX)
> row number   KP(YY)  ENE
> 6531.08800-0.04699
> So according to your hint, I should look for #KP 653 and then index number
> 38.
> But I have #KP upto 40.
> You also mentioned occupancy, but I could not understand it.
>
> Could you please correct me?
>
> Thank you in advance.
> Regards
> Bhamu
>
>
>
>
>
>
> On Thu, Mar 4, 2021 at 10:51 PM Rubel, Oleg  rub...@mcmaster.ca>>>
> wrote:
> Oh, sorry about the misunderstanding. In your previous correspondence it
> 

Re: [Wien] DFT in biomedical research

[Fabiana Da Pieve]

 In reference to the email from Suxing, some attention should be paid to
the words "energetic particles"

It is actually more the speed of the particle, rather than the energy, that
counts for the relevance of the applicability of electronic structure
methods in the field of ion irradiation.

For energetic light ions (from few tenths of Mev to higher) impacting on
biomaterials, one absolutely does NOT need DFT, as the impacting particle
will not be sensitive to the electronic structure details of the target.
If the light ion is slow (so, the speed is low, and energy is below some
few MeV), then the electronic and geometrical details of the target maye
play a role (I would say starting from few hundreds keV, even less)

If the "energetic particle" is a heavy ion, then its energy may be mostly
due to the mass. It could  actually be a slow big ion. In the case of such
a low speed big ion, with high energy, then one would indeed be sensitive
again to the details of the target. If the heavy ion is very energetic also
because it has high speed, then again DFT methods are not of relevance.





Il giorno mer 10 mar 2021 alle ore 15:44 Michael Sluydts <
michael.sluy...@ugent.be> ha scritto:

> Hey Laurence,
>
> Not sure if you're specifically thinking of solid-state, but typical
> biochemistry applications are common.
>
> For instance DFT and AI for drug discovery:
>
> https://www.technologyreview.com/10-breakthrough-technologies/2020/#ai-discovered-molecules
>
> Studies of initial polymer reactions, functional groups of proteins and so
> on also spring to mind or to try and get dynamic properties/spectroscopy of
> (parts of) very small proteins.
>
> In the end also DFT components to make forcefields or machine learning
> potentials for all kinds of applications are also very relevant nowadays
> (by sampling subsystems of larger ones).
> Colleague of mine used to study oxygen transport in lipid membranes with
> the NIH, not ab initio MD, but i can imagine the ML potential approach may
> be interesting.
>
> https://molmod.ugent.be/publications/permeability-membranes-liquid-ordered-and-liquid-disordered-phases
>
> Just some quick thoughts though. ;)
>
> Kind regards,
>
> Michael Sluydts
>
> On 3/10/2021 2:45 PM, Laurence Marks wrote:
>
> I realize this is not really a W2k question, but anyway: is anyone aware
> of much use of DFT in biomedical research?
>
> _
> Professor Laurence Marks
> "Research is to see what everybody else has seen, and to think what nobody
> else has thought", Albert Szent-Györgyi
> www.numis.northwestern.edu
>
> ___
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> SEARCH the MAILING-LIST at:  
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>
>
> --
> dr. ir. Michael Sluydts
> Center for Molecular Modeling
> Ghent University
> Technologiepark 903
> 9052 Zwijnaarde, Belgium
> tel. +32 (0)9 264 66 19https://molmod.ugent.be
>
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Re: [Wien] DFT in biomedical research

[Michael Sluydts]

Hey Laurence,

Not sure if you're specifically thinking of solid-state, but typical 
biochemistry applications are common.


For instance DFT and AI for drug discovery:
https://www.technologyreview.com/10-breakthrough-technologies/2020/#ai-discovered-molecules

Studies of initial polymer reactions, functional groups of proteins and 
so on also spring to mind or to try and get dynamic 
properties/spectroscopy of (parts of) very small proteins.


In the end also DFT components to make forcefields or machine learning 
potentials for all kinds of applications are also very relevant nowadays 
(by sampling subsystems of larger ones).
Colleague of mine used to study oxygen transport in lipid membranes with 
the NIH, not ab initio MD, but i can imagine the ML potential approach 
may be interesting.

https://molmod.ugent.be/publications/permeability-membranes-liquid-ordered-and-liquid-disordered-phases

Just some quick thoughts though. ;)

Kind regards,

Michael Sluydts

On 3/10/2021 2:45 PM, Laurence Marks wrote:
I realize this is not really a W2k question, but anyway: is anyone 
aware of much use of DFT in biomedical research?


_
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what 
nobody else has thought", Albert Szent-Györgyi

www.numis.northwestern.edu 

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--
dr. ir. Michael Sluydts
Center for Molecular Modeling
Ghent University
Technologiepark 903
9052 Zwijnaarde, Belgium
tel. +32 (0)9 264 66 19
https://molmod.ugent.be

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Re: [Wien] [EXT] Re: DFT in biomedical research

[Suxing Hu]

Here I list two recent papers in whcih we used TD-DFT to study stopping 
power of ions in warm-dense matter. I think one can use the same way to 
look at how energetic particles damage bio-materials.


https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.121.145001

https://journals.aps.org/prb/abstract/10.1103/PhysRevB.98.144302

Best,

Suxing

===
Suxing Hu (胡素兴), PhD  Email: s...@lle.rochester.edu
Distinguished Scientist Tel: (585)273-3794
Group Leader of Theoretical HEDP Group
Laboratory for Laser Energetics
University of Rochester
250 E. River Rd
Rochester, NY 14623, USA
https://www.lle.rochester.edu/index.php/education/research-areas/high-energy-density-physics-hedp-theory-group/
http://scholar.google.com/citations?user=MZP-8HEJ=en=ao
http://www.researchgate.net/profile/Suxing_Hu
http://www.researcherid.com/rid/A-1265-2007
===

On 3/10/2021 9:04 AM, Fabiana Da Pieve wrote:

Dear Prof. Marks

I am coordinating an European project where we are using DFT/TDDFT to 
study the impact of ions in biological matter, of importance for 
radiation biology and biomedical research. But we are *NOT* studying 
any particular material of practical use in biomedical research.


Fabiana





Il giorno mer 10 mar 2021 alle ore 14:45 Laurence Marks 
mailto:laurence.ma...@gmail.com>> ha scritto:


I realize this is not really a W2k question, but anyway: is anyone
aware of much use of DFT in biomedical research?

_
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think
what nobody else has thought", Albert Szent-Györgyi
www.numis.northwestern.edu


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Re: [Wien] DFT in biomedical research

[Laurence Marks]

Dear Fabiana,

Thanks, that is exactly the type of information I am interested in; all I
am looking for is biomedical relevance. Hopefully other people know of
other projects.

_
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody
else has thought", Albert Szent-Györgyi
www.numis.northwestern.edu

On Wed, Mar 10, 2021, 08:05 Fabiana Da Pieve 
wrote:

> Dear Prof. Marks
>
> I am coordinating an European project where we are using DFT/TDDFT to
> study the impact of ions in biological matter, of importance for radiation
> biology and biomedical research. But we are *NOT* studying any particular
> material of practical use in biomedical research.
>
> Fabiana
>
>
>
>
>
> Il giorno mer 10 mar 2021 alle ore 14:45 Laurence Marks <
> laurence.ma...@gmail.com> ha scritto:
>
>> I realize this is not really a W2k question, but anyway: is anyone aware
>> of much use of DFT in biomedical research?
>>
>> _
>> Professor Laurence Marks
>> "Research is to see what everybody else has seen, and to think what
>> nobody else has thought", Albert Szent-Györgyi
>> www.numis.northwestern.edu
>> ___
>> Wien mailing list
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>> 
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>>
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Re: [Wien] DFT in biomedical research

[Fabiana Da Pieve]

Dear Prof. Marks

I am coordinating an European project where we are using DFT/TDDFT to study
the impact of ions in biological matter, of importance for radiation
biology and biomedical research. But we are *NOT* studying any particular
material of practical use in biomedical research.

Fabiana





Il giorno mer 10 mar 2021 alle ore 14:45 Laurence Marks <
laurence.ma...@gmail.com> ha scritto:

> I realize this is not really a W2k question, but anyway: is anyone aware
> of much use of DFT in biomedical research?
>
> _
> Professor Laurence Marks
> "Research is to see what everybody else has seen, and to think what nobody
> else has thought", Albert Szent-Györgyi
> www.numis.northwestern.edu
> ___
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>
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[Wien] DFT in biomedical research

[Laurence Marks]

I realize this is not really a W2k question, but anyway: is anyone aware of
much use of DFT in biomedical research?

_
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody
else has thought", Albert Szent-Györgyi
www.numis.northwestern.edu
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