[Pw_forum] Pw_forum Digest, Vol 27, Issue 47

[Stefano Baroni]

>> >iflag = 3
>> >   output_format = 5,
>> >  /
>> >
>> > with regards,
>> > Dev Sharma,
>> > University of Delhi,
>> >  
>> --- 
>> -
>> >
>> > ___
>> > Pw_forum mailing list
>> > Pw_forum at pwscf.org
>> > http://www.democritos.it/mailman/listinfo/pw_forum
>> >
>>
>>
>>
>> --
>>
>> Message: 2
>> Date: Fri, 11 Sep 2009 13:42:19 +0200
>> From: Gabriele Sclauzero 
>> Subject: [Pw_forum] [Fwd: Re:  problem with charge density with
>> xcrysden]
>> To: PWscf Mailing List 
>> Message-ID: <4AAA379B.4070804 at sissa.it>
>> Content-Type: text/plain; charset=iso-8859-1; format=flowed
>>
>> Forwarding e-mail from Emine. So I guess it may be a compatibility  
>> issue.
>>
>> GS
>>
>>  Original Message 
>> Subject:Re: [Pw_forum] problem with charge density with  
>> xcrysden
>> Date:   Fri, 11 Sep 2009 03:50:17 -0700 (PDT)
>> From:   e kb 
>> To: sclauzer at sissa.it
>>
>>
>>
>>
>> The old version of xcrysden that i had didnt work with this line :
>>   > DATAGRID_3D_UNKNOWN
>> but with this one:
>>   > BEGIN_DATAGRID_3D_UNKNOWN
>>
>> I am not up to date on this but you can check it.
>> emine kucukbenli, SISSA, Italy
>>
>>
>>
>> --
>>
>>
>> o  o
>> | Gabriele Sclauzero, PhD Student  |
>> | c/o:   SISSA & CNR-INFM Democritos,  |
>> |via Beirut 2-4, 34014 Trieste (Italy) |
>> | email: sclauzer at sissa.it |
>> | phone: +39 040 3787 511  |
>> | skype: gurlonotturno |
>> o  o
>>
>>
>> --
>>
>> Message: 3
>> Date: Fri, 11 Sep 2009 13:44:13 +0200
>> From: Paolo Giannozzi 
>> Subject: Re: [Pw_forum] input file for isolated atom
>> To: PWSCF Forum 
>> Message-ID: <8F9E43BE-144C-4B5B-B984-327C99F59649 at democritos.it>
>> Content-Type: text/plain; charset=US-ASCII; format=flowed
>>
>>
>> On Sep 11, 2009, at 10:36 , Prasenjit Ghosh wrote:
>>
>> > (a) while doing calculations for any zero dimensions
>> > you should always set nosym =.true.
>>
>> for Gamma-point calculations it shouldn't make any
>> difference
>>
>> P.
>> ---
>> Paolo Giannozzi, Dept of Physics, University of Udine
>> via delle Scienze 208, 33100 Udine, Italy
>> Phone +39-0432-558216, fax +39-0432-558222
>>
>>
>>
>>
>>
>> --
>>
>> Message: 4
>> Date: Fri, 11 Sep 2009 12:45:43 +0100
>> From: Shaptrishi Sharma 
>> Subject: [Pw_forum] K Points and Band structures
>> To: pw_forum at pwscf.org
>> Message-ID:
>> 
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi QEs users,
>>
>> Can anybody please help me in understanding what are the k  
>> points ?? I have
>> read books a lot but its difficult to understand.
>>
>> And also  how do we choose k points while performing a band structure
>> calculation in quantum espresso when we are having 330 atoms.
>>
>> Thanks
>>
>> S
>> -- next part --
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>> http://www.democritos.it/pipermail/pw_forum/attachments/20090911/54396d57/attachment-0001.htm
>>
>> --
>>
>> Message: 5
>> Date: Fri, 11 Sep 2009 13:58:19 +0200
>> From: "Lorenzo Paulatto" 
>> Subject: Re: [Pw_forum] K Points and Band structures
>> To: "PWSCF Forum" 
>> Message-ID: 
>> Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes
>>
>> In data 11 settembre 2009 alle ore 13:45:43, Shaptrishi Sharma
>>  ha scritto:
>>
>> > Can anybody please help me in understanding what are the k  
>> points ?? I
>> > have read books a lot but its difficult to understand.
>>
>> They are eigenvalues of the translation operator, T(R) where
>> R=n1*a1+n2*a2+n3*a3; a1,a2,a3 are the cell basis vectors and n1,n2,n3
>> integer numb

[Pw_forum] K Points and Band structures

[Stefano Baroni]

On Sep 11, 2009, at 9:00 PM, dev sharma wrote:

> And also Dear, recently, Summer school on Materials modeling from  
> first principles: theory and practice, ICMR, University of  
> California at Santa Barbara, July 19-31, 2009 was held for Quantum  
> Espresso, and the slides and video lectures are given at link
> http://www.quantum-espresso.org/wiki/index.php/QESB09
>
> My advise is that please have a look on the slides, as they are very  
> useful.

thank you, Dev Sharma ;-)

also, Davatri Sharma, do not forget textbooks
I know ... they are hard to study, but this is only to teach you that  
"life is hard" (if it was not, it would not be as interesting)

>  Take Care.

Stefano B

---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center -  
Trieste
http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) /  
stefanobaroni (skype)

La morale est une logique de l'action comme la logique est une morale  
de la pens?e - Jean Piaget

Please, if possible, don't  send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html







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[Pw_forum] Pw_forum Digest, Vol 27, Issue 47

[Stefano Baroni]

Pw_forum] problem with charge density with  
> xcrysden
> Date:   Fri, 11 Sep 2009 03:50:17 -0700 (PDT)
> From:   e kb 
> To: sclauzer at sissa.it
>
>
>
>
> The old version of xcrysden that i had didnt work with this line :
>   > DATAGRID_3D_UNKNOWN
> but with this one:
>   > BEGIN_DATAGRID_3D_UNKNOWN
>
> I am not up to date on this but you can check it.
> emine kucukbenli, SISSA, Italy
>
>
>
> --
>
>
> o  o
> | Gabriele Sclauzero, PhD Student  |
> | c/o:   SISSA & CNR-INFM Democritos,  |
> |via Beirut 2-4, 34014 Trieste (Italy) |
> | email: sclauzer at sissa.it |
> | phone: +39 040 3787 511  |
> | skype: gurlonotturno |
> o  o
>
>
> --
>
> Message: 3
> Date: Fri, 11 Sep 2009 13:44:13 +0200
> From: Paolo Giannozzi 
> Subject: Re: [Pw_forum] input file for isolated atom
> To: PWSCF Forum 
> Message-ID: <8F9E43BE-144C-4B5B-B984-327C99F59649 at democritos.it>
> Content-Type: text/plain; charset=US-ASCII; format=flowed
>
>
> On Sep 11, 2009, at 10:36 , Prasenjit Ghosh wrote:
>
> > (a) while doing calculations for any zero dimensions
> > you should always set nosym =.true.
>
> for Gamma-point calculations it shouldn't make any
> difference
>
> P.
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
>
> --
>
> Message: 4
> Date: Fri, 11 Sep 2009 12:45:43 +0100
> From: Shaptrishi Sharma 
> Subject: [Pw_forum] K Points and Band structures
> To: pw_forum at pwscf.org
> Message-ID:
> 
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi QEs users,
>
> Can anybody please help me in understanding what are the k points ??  
> I have
> read books a lot but its difficult to understand.
>
> And also  how do we choose k points while performing a band structure
> calculation in quantum espresso when we are having 330 atoms.
>
> Thanks
>
> S
> -- next part --
> An HTML attachment was scrubbed...
> URL: 
> http://www.democritos.it/pipermail/pw_forum/attachments/20090911/54396d57/attachment-0001.htm
>
> --
>
> Message: 5
> Date: Fri, 11 Sep 2009 13:58:19 +0200
> From: "Lorenzo Paulatto" 
> Subject: Re: [Pw_forum] K Points and Band structures
> To: "PWSCF Forum" 
> Message-ID: 
> Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes
>
> In data 11 settembre 2009 alle ore 13:45:43, Shaptrishi Sharma
>  ha scritto:
>
> > Can anybody please help me in understanding what are the k  
> points ?? I
> > have read books a lot but its difficult to understand.
>
> They are eigenvalues of the translation operator, T(R) where
> R=n1*a1+n2*a2+n3*a3; a1,a2,a3 are the cell basis vectors and n1,n2,n3
> integer numbers. The eigenvectors are, of course, the Bloch  
> wavefunctions.
>
> Because the hamiltonian is periodic it commutes with the translation
> operator, you can diagonalize both the hamiltonian and the translation
> operator at the same time. As a consequence each Bloch wavefunction  
> has a
> well-defined energy (hamiltonian's eigenvalue) and k-point  
> (translation
> eigenvalue). Using both eigenvalues you can classify the states  
> without
> ambiguity, except where the bands cross.
>
> > And also  how do we choose k points while performing a band  
> structure
> > calculation in quantum espresso when we are having 330 atoms.
>
> It does not depend on the number of atoms.
>
> You have to test the convergence at fixed smearing. E.g. you choose a
> smearing that's small enough for you, than you increase the number of
> k-points until total energy converges. You may then try again for a
> smaller/larger smearing and see if the results are consistent.
>
> I would advise starting with a smaller system, it would take ages to  
> do it
> on 330 atoms. Keep in mind that the number of k-points needed for an
> accurate sampling is directly proportional to the size of the  
> Brillouin
> zone, hence inversely proportional to the size of the cell.
>
> E.g. if you estimate that 6x6x6 k-points converge a certain  
> calculation
> than 3x3x3 k-points will be converge a 2x2x2 supercell to exactly  
> the same
> level.
>
> Best regards
>
>
> --
> Lorenzo Paulatto
> SISSA  &  DEMOCRITOS (Trieste

[Pw_forum] The low usage of CUPs

[wangqj1]

Dear pwscf users
 I use 16 CPUs to run a job,but the usage of CPUs is very slow ,it as like:
 
Tasks: 179 total,   1 running, 178 sleeping,   0 stopped,   0 zombie
Cpu0  :  0.0%us,  4.8%sy,  0.0%ni, 90.3%id,  0.3%wa,  0.0%hi,  4.5%si,  0.0%st
Cpu1  :  0.0%us,  1.0%sy,  0.0%ni, 95.8%id,  3.3%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu2  :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu3  :  0.7%us,  0.0%sy,  0.0%ni, 99.0%id,  0.3%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu4  :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu5  :  0.0%us,  0.3%sy,  0.0%ni, 99.7%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu6  :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu7  :  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Mem:   8048812k total,  7995856k used,52956k free,   283692k buffers
Swap:  4192956k total,  124k used,  4192832k free,  7492420k cached
  PID USER  PR  NI  VIRT  RES  SHR S %CPU %MEMTIME+  COMMAND
 4522 root  15  -5 000 S5  0.0  17:59.16 nfsd   
 2012 root  15  -5 000 S1  0.0   6:29.01 kjournald  
 4404 root  20   0  104m  17m 5044 S0  0.2  55:07.93 X  
 4519 root  15  -5 000 S0  0.0  18:05.58 nfsd   
 4521 root  15  -5 000 S0  0.0  16:55.33 nfsd   
 5023 gdm   20   0  235m  31m  11m S0  0.4  13:39.99 gdm-simple-gree
1 root  20   0  1064  408  348 S0  0.0   0:02.90 init   
2 root  15  -5 000 S0  0.0   0:00.02 kthreadd   
3 root  RT  -5 000 S0  0.0   0:00.00 migration/0
4 root  15  -5 000 S0  0.0   0:00.22 ksoftirqd/0

The ifort ,MKL,and mpi I used is :
INTFC=/opt/intel/Compiler/11.0/081
INTMKL=/opt/intel/mkl/10.1.1.019
/opt/mpich2/bin/mpd
My machine model is as following :
processor   : 0
vendor_id   : GenuineIntel
cpu family  : 6
model   : 23
model name  : Intel(R) Xeon(R) CPU   E5410  @ 2.33GHz
stepping: 10
cpu MHz : 2327.489
cache size  : 6144 KB
physical id : 0
siblings: 4
core id : 0
cpu cores   : 4
apicid  : 0
initial apicid  : 0
fpu : yes
fpu_exception   : yes
cpuid level : 13
wp  : yes
flags   : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov 
pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm constant
_tsc arch_perfmon pebs bts rep_good nopl pni monitor ds_cpl vmx est tm2 ssse3 cx
16 xtpr dca sse4_1 lahf_lm
bogomips: 4654.97
...
The pwscf version is espresso-4.0.3 .
 
So , I want to know why the usage is so slow ?
How can I solve this problem ? Anybody who meet the same problem ?
Your kind help will be appreciated !
Best regards
Q.J.Wang
XiangTan University 


 
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[Pw_forum] problem with charge density with xcrysden

[shypirate]

it definitely can not be used as input file for  xcrysden.
try to use the data included in "BLOCK_DATAGRID_3D" section



2009-09-11 



shypirate 



 dev sharma 
? 2009-09-11  16:53:38 
 PWSCF Forum 
??? 
??? Re: [Pw_forum] problem with charge density with xcrysden 
 
Dear sir, my.xsf file is below 

Program POST-PROC v.4.0.2  starts ...
 Today is 11Sep2009 at 12:54:29 

 Check: negative/imaginary core charge=   -0.090.00

 negative rho (up, down):  0.188E+00 0.000E+00

 Calling punch_plot, plot_num =   0
 Writing data to file  yvocharge
 Reading data from file  yvocharge
 CRYSTAL
 PRIMVEC
7.1183005140.00.0
0.07.1183005140.0
0.00.06.289300454
 PRIMCOORD
  24   1
Y 0.05.3387253560.786162553
/
/
O 1.3111908685.3387253562.835216639
BEGIN_BLOCK_DATAGRID_3D
3D_PWSCF
DATAGRID_3D_UNKNOWN
  61  61  49
  0.00  0.00  0.00
  7.118301  0.00  0.00
  0.00  7.118301  0.00
  0.00  0.00  6.289300
  0.19131E-01  0.18756E-01  0.17478E-01  0.15613E-01  0.13484E-01  0.11234E-01
/
/
 0.93736E-02  0.11234E-01  0.13484E-01  0.15613E-01  0.17478E-01  0.18756E-01
  0.19131E-01
END_DATAGRID_3D
END_BLOCK_DATAGRID_3D
 Plot Type: 3D Output format: XCrySDen 

thanks.


On Fri, Sep 11, 2009 at 2:14 PM, Gabriele Sclauzero  
wrote:

Dear Dev,


dev sharma wrote:
> hi 2 all,
>  I am trying to plot the charge density with the XCrysden, but when i am
> opening's XSF(file--> open structure--> open XSF(xcryden structure
> file)) file , generated by my calculations, it is showing the structure
> of my system. And i am not getting the   option tools--> DATA GRID as
> ready. Please help or advice ?? Thankful to all of you. What i did is
> listed below.


Have you had a look inside your .xsf file? How does it look? Does it actually 
contain the
DATAGRID block? Is it complete? Please supply more information!

Regards,

GS



> I run my input file with command
> /home/physics/espresso-4.0.2/bin/pp.x   density.xsf

> and inputs of density.in <http://density.in> are

>  
>   prefix  = 'yvo'
>  outdir  = '/home/physics/work/yvo/temp/',
> filplot = 'yvocharge'
>   plot_num= 0
>  /
>  
>   nfile = 1
>  filepp(1) = 'yvocharge'
>   weight(1) = 1.0
>iflag = 3
>   output_format = 5,
>  /
>
> with regards,
> Dev Sharma,
> University of Delhi,
>
>

> 
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

--


o  o
| Gabriele Sclauzero, PhD Student  |
| c/o:   SISSA & CNR-INFM Democritos,  |
|via Beirut 2-4, 34014 Trieste (Italy) |
| email: sclauzer at sissa.it |
| phone: +39 040 3787 511  |
| skype: gurlonotturno |
o  o
___
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Pw_forum at pwscf.org
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[Pw_forum] resp_mat.f90

[Matteo Cococcioni]

Dear Duy,

I have no experience with hexagonal systems. but the first three results 
seem reasonable.
maybe some array is not big enough to contain your system? in my 
experience it's usually a problem of this kind
causing errors.

Matteo



Duy Le wrote:
> Dear Matteo and all,
>
> I am trying to calculated the U with resp_mat.f90 code for colbalt.
>
> The primitive cell has 16 Co.
> The code extrapolated to 2x2x2, 3x3x3 super cell successfully.
>
> However, when it came to 4x4x4 super cell, the code was initially 
> doing pretty fine, and in the end it gave an U1, but the code did not 
> finish normally. Then error came (see below).
>
> The worse thing is that the value of U1 given in 4x4x4 extrapolation 
> is nonsense.
>
> 16 3.30938654705739
> 128 3.59144217433734
> 432 3.61280367128581
> 1024 -0.703549684908895
>
> I did a quick search and found that you have mentioned the error of 
> resp_mat.f90 code with hexagonal lattice (which my system is). Are the 
> error you was talking about and the error I am facing with identical? 
> Do you have the resp_mat.f90 fixed?
>
> Thank you.
>
> *---ERROR*
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image  PCRoutineLine
> Source
> libpthread.so.000397480DE80  Unknown   Unknown  
> Unknown
> libc.so.6  003973C71083  Unknown   Unknown  
> Unknown
> libc.so.6  003973C74CCC  Unknown   Unknown  
> Unknown
> r.x006496CD  Unknown   Unknown  
> Unknown
> r.x004C  Unknown   Unknown  
> Unknown
> r.x004065C2  Unknown   Unknown  
> Unknown
> libc.so.6  003973C1D8B4  Unknown   Unknown  
> Unknown
> r.x004064E9  Unknown   Unknown  
> Unknown
>
>
> *---OLD 
> MESSAGE
> Matteo Cococcioni* matteo at umn.edu 
> 
> /Fri Dec 5 16:56:00 CET 2008/
>
> * Previous message: [Pw_forum] Strange things when calculating
>   bands using pw.x
>   
> * Next message: [Pw_forum] Scf can converge, But Band can not
>   converge
>   
> * *Messages sorted by:* [ date ]
>   
> 
>   [ thread ]
>   
> 
>   [ subject ]
>   
> 
>   [ author ]
>   
> 
>
>
> Dear all,
>
> I have recently realized that the code resp_mat.f90, contained in some 
> tutorials on LDA+U calculations (e.g.,
> from http://vlab.msi.umn.edu/events/lecture.shtml) and used to compute 
>
>
> U, has some problems and doesn't work as expected.
> I have realized this on a hexagonal system but I'm not sure yet if the 
> problem manifests itself also with other crystal structures.
>
> Hoping that not many people were using it I apologize for the 
>
>
> inconvenient. I also hope to provide a fix in short time.
>
> regards,
>
> Matteo
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>  
>
>
>   
>
> 
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


-- 
%%%
Matteo Cococcioni
Department of Chemical Engineering and Materials Science,
University of Minnesota
421 Washington Av. SE
Minneapolis, MN 55455
Tel. +1 612 624 9056Fax +1 612 626 7246
%%%

[Pw_forum] How to control number of slabs in pwcond calculation？

[xirainbow]

Dear all:  I find the following content at
"/espresso-4.0.4/examples/example12/results/al.cond.out" file.
*" nrz  =   21*
*.*
*k slabz(k)  z(k+1) crossing(iorb=1,norb)*
*1   0. 0.0673 0.0673   *
*.*
*   20   1.2793 1.3467 0.0673   0111*
*   21   1.3467 1.4140 0.0673     "*

 I want to know, at *.cond.in input file, how to control the number of
slabs along z direction in left, right lead and scattering region,
respectively.
 By the way, what is the meaning of "crossing(iorb=1,norb)"?

 Thanks in advance ??



Hui Wang
School of physics, Nankai University, Tianjin, China
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[Pw_forum] Pw_forum Digest, Vol 27, Issue 47

[Stefano de Gironcoli]

Dear Shaptrishi Sharma,
  I'm a bit confused...
  How many electrons your system has ? not 21 for sure since you have 66 
atoms... so why are you focusing on the 21 Hydrogen atoms ? If you 
forget about spin polarization and perform a simple non-magnetic 
calculation...does it converge?
  try to face one difficulty at a time...
  Have you checked that your structure is reasonable ? if some of your 
atoms end up to be unrealistically close to each other the 
diagonalization routine gets crazy but the calculation would be useless 
anyway. check your structure by xcrysden.

   stefano

Shaptrishi Sharma wrote:
> Hi Stefano,
>
> My nband value is 122 as my total number of atoms are 66 .of which 21 
> Hydrogen.And if I remove the option nelup and neldw, I got it as "too 
> many bands are not converged" thus I increased my vaccum, however it 
> still remains the same.
>
> Thanks
> S

[Pw_forum] Pw_forum Digest, Vol 27, Issue 47

[Duy Le]

pwscf.org
>> > http://www.democritos.it/mailman/listinfo/pw_forum
>> >
>>
>>
>>
>> --
>>
>> Message: 2
>> Date: Fri, 11 Sep 2009 13:42:19 +0200
>> From: Gabriele Sclauzero 
>> Subject: [Pw_forum] [Fwd: Re:  problem with charge density with
>> xcrysden]
>> To: PWscf Mailing List 
>> Message-ID: <4AAA379B.4070804 at sissa.it>
>> Content-Type: text/plain; charset=iso-8859-1; format=flowed
>>
>> Forwarding e-mail from Emine. So I guess it may be a compatibility issue.
>>
>> GS
>>
>>  Original Message 
>> Subject:Re: [Pw_forum] problem with charge density with xcrysden
>> Date:   Fri, 11 Sep 2009 03:50:17 -0700 (PDT)
>> From:   e kb 
>> To: sclauzer at sissa.it
>>
>>
>>
>>
>> The old version of xcrysden that i had didnt work with this line :
>>   > DATAGRID_3D_UNKNOWN
>> but with this one:
>>   > BEGIN_DATAGRID_3D_UNKNOWN
>>
>> I am not up to date on this but you can check it.
>> emine kucukbenli, SISSA, Italy
>>
>>
>>
>> --
>>
>>
>> o  o
>> | Gabriele Sclauzero, PhD Student  |
>> | c/o:   SISSA & CNR-INFM Democritos,  |
>> |via Beirut 2-4, 34014 Trieste (Italy) |
>> | email: sclauzer at sissa.it |
>> | phone: +39 040 3787 511  |
>> | skype: gurlonotturno |
>> o  o
>>
>>
>> --
>>
>> Message: 3
>> Date: Fri, 11 Sep 2009 13:44:13 +0200
>> From: Paolo Giannozzi 
>> Subject: Re: [Pw_forum] input file for isolated atom
>> To: PWSCF Forum 
>> Message-ID: <8F9E43BE-144C-4B5B-B984-327C99F59649 at democritos.it>
>> Content-Type: text/plain; charset=US-ASCII; format=flowed
>>
>>
>> On Sep 11, 2009, at 10:36 , Prasenjit Ghosh wrote:
>>
>> > (a) while doing calculations for any zero dimensions
>> > you should always set nosym =.true.
>>
>> for Gamma-point calculations it shouldn't make any
>> difference
>>
>> P.
>> ---
>> Paolo Giannozzi, Dept of Physics, University of Udine
>> via delle Scienze 208, 33100 Udine, Italy
>> Phone +39-0432-558216, fax +39-0432-558222
>>
>>
>>
>>
>>
>> --
>>
>> Message: 4
>> Date: Fri, 11 Sep 2009 12:45:43 +0100
>> From: Shaptrishi Sharma 
>> Subject: [Pw_forum] K Points and Band structures
>> To: pw_forum at pwscf.org
>> Message-ID:
>> 
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi QEs users,
>>
>> Can anybody please help me in understanding what are the k points ?? I
>> have
>> read books a lot but its difficult to understand.
>>
>> And also  how do we choose k points while performing a band structure
>> calculation in quantum espresso when we are having 330 atoms.
>>
>> Thanks
>>
>> S
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>>
>> --
>>
>> Message: 5
>> Date: Fri, 11 Sep 2009 13:58:19 +0200
>> From: "Lorenzo Paulatto" 
>> Subject: Re: [Pw_forum] K Points and Band structures
>> To: "PWSCF Forum" 
>> Message-ID: 
>> Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes
>>
>> In data 11 settembre 2009 alle ore 13:45:43, Shaptrishi Sharma
>>  ha scritto:
>>
>> > Can anybody please help me in understanding what are the k points ?? I
>> > have read books a lot but its difficult to understand.
>>
>> They are eigenvalues of the translation operator, T(R) where
>> R=n1*a1+n2*a2+n3*a3; a1,a2,a3 are the cell basis vectors and n1,n2,n3
>> integer numbers. The eigenvectors are, of course, the Bloch wavefunctions.
>>
>> Because the hamiltonian is periodic it commutes with the translation
>> operator, you can diagonalize both the hamiltonian and the translation
>> operator at the same time. As a consequence each Bloch wavefunction has a
>> well-defined energy (hamiltonian's eigenvalue) and k-point (translation
>> eigenvalue). Using both eigenvalues you can classify the states without
>> ambiguity, except wher

[Pw_forum] resp_mat.f90

[Duy Le]

Dear Matteo and all,

I am trying to calculated the U with resp_mat.f90 code for colbalt.

The primitive cell has 16 Co.
The code extrapolated to 2x2x2, 3x3x3 super cell successfully.

However, when it came to 4x4x4 super cell, the code was initially doing
pretty fine, and in the end it gave an U1, but the code did not finish
normally. Then error came (see below).

The worse thing is that the value of U1 given in 4x4x4 extrapolation is
nonsense.

16 3.30938654705739
128 3.59144217433734
432 3.61280367128581
1024 -0.703549684908895

I did a quick search and found that you have mentioned the error of
resp_mat.f90 code with hexagonal lattice (which my system is). Are the error
you was talking about and the error I am facing with identical? Do you have
the resp_mat.f90 fixed?

Thank you.

*---ERROR*
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image  PCRoutineLine
Source
libpthread.so.000397480DE80  Unknown   Unknown  Unknown
libc.so.6  003973C71083  Unknown   Unknown  Unknown
libc.so.6  003973C74CCC  Unknown   Unknown  Unknown
r.x006496CD  Unknown   Unknown  Unknown
r.x004C  Unknown   Unknown  Unknown
r.x004065C2  Unknown   Unknown  Unknown
libc.so.6  003973C1D8B4  Unknown   Unknown  Unknown
r.x004064E9  Unknown   Unknown  Unknown


*---OLD MESSAGE
Matteo Cococcioni* matteo at umn.edu
<pw_forum%40pwscf.org?Subject=%5BPw_forum%5D%20resp_mat.f90=>
*Fri Dec 5 16:56:00 CET 2008*

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--

Dear all,

I have recently realized that the code resp_mat.f90, contained in some
tutorials on LDA+U calculations (e.g.,
from http://vlab.msi.umn.edu/events/lecture.shtml) and used to compute

U, has some problems and doesn't work as expected.
I have realized this on a hexagonal system but I'm not sure yet if the
problem manifests itself also with other crystal structures.

Hoping that not many people were using it I apologize for the

inconvenient. I also hope to provide a fix in short time.

regards,

Matteo
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[Pw_forum] Pw_forum Digest, Vol 27, Issue 47

[Lorenzo Paulatto]

In data 11 settembre 2009 alle ore 15:23:39, Shaptrishi Sharma  
 ha scritto:
> My nband value is 122 as my total number of atoms are 66 .of which 21
> Hydrogen.And if I remove the option nelup and neldw, I got it as "too  
> many bands are not converged" thus I increased my vaccum, however it  
> still
> remains the same.

Dear Shaptrishi,
 from the file Doc/INPUT_PW.txt

Variable:   nelec

Type:   REAL
Default:the same as ionic charge (neutral cell)
Description:number of electron in the unit cell
(may be noninteger if you wish)

as you see, nelec is the total number of electrons, not only the ones from  
hydrogen. Accordingly, a few lines later you should have found:

Variables:  nelup, neldw

Type:   REAL
Description:number of spin-up and spin-down electrons, respectively
Note that this fixes the final value of the  
magnetization.
The sum must yield nelec that must also be specified
explicitly in this case. Not valid for spin-unpolarized
or noncollinear calculations, only for LSDA.  
Obsolescent:
use multiplicity or tot_magnetization instead.

it says quite clearly that nelec=nelup+neldw, again nelec is the total  
number of electrons.

best regards




-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/

 *** save italian brains ***
  http://saveitalianbrains.wordpress.com/

[Pw_forum] The low usage of CUPs

[Giovanni Cantele]

wangqj1 wrote:
> Dear pwscf users
> I use 16 CPUs to run a job,but the usage of CPUs is very slow ,it as like:
> Tasks: 179 total, 1 running, 178 sleeping, 0 stopped, 0 zombie
> Cpu0 : 0.0%us, 4.8%sy, 0.0%ni, 90.3%id, 0.3%wa, 0.0%hi, 4.5%si, 0.0%st
> Cpu1 : 0.0%us, 1.0%sy, 0.0%ni, 95.8%id, 3.3%wa, 0.0%hi, 0.0%si, 0.0%st
> Cpu2 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st
> Cpu3 : 0.7%us, 0.0%sy, 0.0%ni, 99.0%id, 0.3%wa, 0.0%hi, 0.0%si, 0.0%st
> Cpu4 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st
> Cpu5 : 0.0%us, 0.3%sy, 0.0%ni, 99.7%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st
> Cpu6 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st
> Cpu7 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st
> Mem: 8048812k total, 7995856k used, 52956k free, 283692k buffers
> Swap: 4192956k total, 124k used, 4192832k free, 7492420k cached
> PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
> 4522 root 15 -5 0 0 0 S 5 0.0 17:59.16 nfsd
> 2012 root 15 -5 0 0 0 S 1 0.0 6:29.01 kjournald
> 4404 root 20 0 104m 17m 5044 S 0 0.2 55:07.93 X
> 4519 root 15 -5 0 0 0 S 0 0.0 18:05.58 nfsd
> 4521 root 15 -5 0 0 0 S 0 0.0 16:55.33 nfsd
> 5023 gdm 20 0 235m 31m 11m S 0 0.4 13:39.99 gdm-simple-gree
> 1 root 20 0 1064 408 348 S 0 0.0 0:02.90 init
> 2 root 15 -5 0 0 0 S 0 0.0 0:00.02 kthreadd
> 3 root RT -5 0 0 0 S 0 0.0 0:00.00 migration/0
> 4 root 15 -5 0 0 0 S 0 0.0 0:00.22 ksoftirqd/0
>
> The ifort ,MKL,and mpi I used is :
> INTFC=/opt/intel/Compiler/11.0/081
> INTMKL=/opt/intel/mkl/10.1.1.019
> /opt/mpich2/bin/mpd
> My machine model is as following :
> processor : 0
> vendor_id : GenuineIntel
> cpu family : 6
> model : 23
> model name : Intel(R) Xeon(R) CPU E5410 @ 2.33GHz
> stepping : 10
> cpu MHz : 2327.489
> cache size : 6144 KB
> physical id : 0
> siblings : 4
> core id : 0
> cpu cores : 4
> apicid : 0
> initial apicid : 0
> fpu : yes
> fpu_exception : yes
> cpuid level : 13
> wp : yes
> flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov
> pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx 
> lm constant
> _tsc arch_perfmon pebs bts rep_good nopl pni monitor ds_cpl vmx est 
> tm2 ssse3 cx
> 16 xtpr dca sse4_1 lahf_lm
> bogomips : 4654.97
> ...
> The pwscf version is espresso-4.0.3 .
> So , I want to know why the usage is so slow ?
> How can I solve this problem ? Anybody who meet the same problem ?
> Your kind help will be appreciated !
> Best regards
> Q.J.Wang
> XiangTan University
>
Some possibilities are:

1) 
http://www.quantum-espresso.org/wiki/index.php/Frequently_Asked_Questions#Why_is_my_parallel_job_running_in_such_a_lousy_way.3F
2) you are running a job over a very slow network (interconnecting the 
different nodes)
3) you are trying to force a node to write on a disk which is local to 
other nodes and connected to it
through a very-low performance network
4) your job requests much more resources than you have, e.g. RAM memory 
(causing a node to swap). From
your data it seems you are using all the 8Gb mem, actually the same test 
should be done on every node.


How are distributed the 16 CPU? Over more than one node?

Giovanni

-- 



Dr. Giovanni Cantele
Coherentia CNR-INFM and Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario di Monte S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910
Fax:   +39 081 676346
E-mail: giovanni.cantele at cnr.it
giovanni.cantele at na.infn.it
Web: http://people.na.infn.it/~cantele
Research Group: http://www.nanomat.unina.it
Skype contact: giocan74

[Pw_forum] The low usage of CUPs

[Lorenzo Paulatto]

In data 11 settembre 2009 alle ore 14:29:34, wangqj1  ha  
scritto:
> So , I want to know why the usage is so slow ?

Dear Q.J.
it is the same issue you were asking the last time. As you have not  
provided any further detail (network connection speed, details on the job  
and on how you're running it) my answer is the same as the last time.

best regards

-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/

 *** save italian brains ***
  http://saveitalianbrains.wordpress.com/

[Pw_forum] problem with charge density with xcrysden

[dev sharma]

 advice ?? Thankful to all of you. What
> > i did is
> >  > listed below.
> >
> > Have you had a look inside your .xsf file? How does it look?
> > Does it actually contain the
> > DATAGRID block? Is it complete? Please supply more information!
> >
> > Regards,
> >
> > GS
> >
> >
> >  > I run my input file with command
> >  > /home/physics/espresso-4.0.2/bin/pp.x  
> density.xsf
> >  > and inputs of density.in <http://density.in>
> > <http://density.in> are
> >  >  
> >  >   prefix  = 'yvo'
> >  >  outdir  = '/home/physics/work/yvo/temp/',
> >  > filplot = 'yvocharge'
> >  >   plot_num= 0
> >  >  /
> >  >  
> >  >   nfile = 1
> >  >  filepp(1) = 'yvocharge'
> >  >   weight(1) = 1.0
> >  >iflag = 3
> >  >   output_format = 5,
> >  >  /
> >  >
> >  > with regards,
> >  > Dev Sharma,
> >  > University of Delhi,
> >  >
> >  >
> >  >
> >
> 
> >  >
> >  > ___
> >  > Pw_forum mailing list
> >  > Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
> >  > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> > --
> >
> >
> > o  o
> > | Gabriele Sclauzero, PhD Student  |
> > | c/o:   SISSA & CNR-INFM Democritos,  |
> > |via Beirut 2-4, 34014 Trieste (Italy) |
> > | email: sclauzer at sissa.it <mailto:sclauzer at sissa.it>
> >   |
> > | phone: +39 040 3787 511  |
> > | skype: gurlonotturno |
> > o  o
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> >
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> >
> >
> > --
> > PRASENJIT GHOSH,
> > POST-DOC,
> > ROOM NO: 265, MAIN BUILDING,
> > CM SECTION, ICTP,
> > STRADA COSTERIA 11,
> > TRIESTE, 34104,
> > ITALY
> > PHONE: +39 040 2240 369 (O)
> >  +39 3807528672 (M)
> >
> >
> > 
> >
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
>
> --
>
>
> o  o
> | Gabriele Sclauzero, PhD Student  |
> | c/o:   SISSA & CNR-INFM Democritos,  |
> |via Beirut 2-4, 34014 Trieste (Italy) |
> | email: sclauzer at sissa.it |
> | phone: +39 040 3787 511  |
> | skype: gurlonotturno |
> o  o
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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[Pw_forum] input file for isolated atom

[udayagiri sai babu]

>>>> K_POINTS GAMMA
>>>>
>>>> --
>>>> U.Saibabu
>>>> PhD student,
>>>> Deformation mechanisms modeling group,
>>>> Materials engineering department,
>>>> IISc Bangalore,
>>>> India.
>>>>
>>>>
>>>> ___
>>>> Pw_forum mailing list
>>>> Pw_forum at pwscf.org
>>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>>
>>>>
>>>
>>>
>>> --
>>> PRASENJIT GHOSH,
>>> POST-DOC,
>>> ROOM NO: 265, MAIN BUILDING,
>>> CM SECTION, ICTP,
>>> STRADA COSTERIA 11,
>>> TRIESTE, 34104,
>>> ITALY
>>> PHONE: +39 040 2240 369 (O)
>>>  +39 3807528672 (M)
>>>
>>> ___
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>
>>>
>>
>>
>> --
>> U.Saibabu
>> PhD student,
>> Deformation mechanisms modeling group,
>> Materials engineering department,
>> IISc Bangalore,
>> India.
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
> PRASENJIT GHOSH,
> POST-DOC,
> ROOM NO: 265, MAIN BUILDING,
> CM SECTION, ICTP,
> STRADA COSTERIA 11,
> TRIESTE, 34104,
> ITALY
> PHONE: +39 040 2240 369 (O)
>  +39 3807528672 (M)
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
U.Saibabu
PhD student,
Deformation mechanisms modeling group,
Materials engineering department,
IISc Bangalore,
India.
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[Pw_forum] Problem in spin polarisation

[Paolo Giannozzi]

On Sep 11, 2009, at 14:24 , Stefano de Gironcoli wrote:

> It should be fixed

or even better, removed, since there are alternative
and simpler methods to specify occupancies

P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222

[Pw_forum] Problem in spin polarisation

[Stefano de Gironcoli]

I think that in this case you need to explicitly specify also the value 
for nelec  because a test that 0<=nelup< =nelec
is performed before the default for nelec is calculated.
It should be fixed but it is not so straightforward as the default value 
is presently defined much later.
stefano

Shaptrishi Sharma wrote:
> Hi QE users,
>
> In one of my previous mail, I have asked about the spin polarisation 
> in a sytem having odd number of electrons , (I have 21 hydrogen atoms 
> in my system ).
>
> As suggested I used nelup =11 and neldw = 10, however, it is showing 
> me the same error, as
>
> nelp out of range.
> so what shall I do now??
>
> Thanks
>
> SS
>
>
> 
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   

[Pw_forum] Pw_forum Digest, Vol 27, Issue 47

[Shaptrishi Sharma]

NR-INFM Democritos,  |
> |via Beirut 2-4, 34014 Trieste (Italy) |
> | email: sclauzer at sissa.it |
> | phone: +39 040 3787 511  |
> | skype: gurlonotturno |
> o  o
>
>
> --
>
> Message: 3
> Date: Fri, 11 Sep 2009 13:44:13 +0200
> From: Paolo Giannozzi 
> Subject: Re: [Pw_forum] input file for isolated atom
> To: PWSCF Forum 
> Message-ID: <8F9E43BE-144C-4B5B-B984-327C99F59649 at democritos.it>
> Content-Type: text/plain; charset=US-ASCII; format=flowed
>
>
> On Sep 11, 2009, at 10:36 , Prasenjit Ghosh wrote:
>
> > (a) while doing calculations for any zero dimensions
> > you should always set nosym =.true.
>
> for Gamma-point calculations it shouldn't make any
> difference
>
> P.
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
>
> --
>
> Message: 4
> Date: Fri, 11 Sep 2009 12:45:43 +0100
> From: Shaptrishi Sharma 
> Subject: [Pw_forum] K Points and Band structures
> To: pw_forum at pwscf.org
> Message-ID:
> 
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi QEs users,
>
> Can anybody please help me in understanding what are the k points ?? I have
> read books a lot but its difficult to understand.
>
> And also  how do we choose k points while performing a band structure
> calculation in quantum espresso when we are having 330 atoms.
>
> Thanks
>
> S
> -- next part --
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> URL:
> http://www.democritos.it/pipermail/pw_forum/attachments/20090911/54396d57/attachment-0001.htm
>
> --
>
> Message: 5
> Date: Fri, 11 Sep 2009 13:58:19 +0200
> From: "Lorenzo Paulatto" 
> Subject: Re: [Pw_forum] K Points and Band structures
> To: "PWSCF Forum" 
> Message-ID: 
> Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes
>
> In data 11 settembre 2009 alle ore 13:45:43, Shaptrishi Sharma
>  ha scritto:
>
> > Can anybody please help me in understanding what are the k points ?? I
> > have read books a lot but its difficult to understand.
>
> They are eigenvalues of the translation operator, T(R) where
> R=n1*a1+n2*a2+n3*a3; a1,a2,a3 are the cell basis vectors and n1,n2,n3
> integer numbers. The eigenvectors are, of course, the Bloch wavefunctions.
>
> Because the hamiltonian is periodic it commutes with the translation
> operator, you can diagonalize both the hamiltonian and the translation
> operator at the same time. As a consequence each Bloch wavefunction has a
> well-defined energy (hamiltonian's eigenvalue) and k-point (translation
> eigenvalue). Using both eigenvalues you can classify the states without
> ambiguity, except where the bands cross.
>
> > And also  how do we choose k points while performing a band structure
> > calculation in quantum espresso when we are having 330 atoms.
>
> It does not depend on the number of atoms.
>
> You have to test the convergence at fixed smearing. E.g. you choose a
> smearing that's small enough for you, than you increase the number of
> k-points until total energy converges. You may then try again for a
> smaller/larger smearing and see if the results are consistent.
>
> I would advise starting with a smaller system, it would take ages to do it
> on 330 atoms. Keep in mind that the number of k-points needed for an
> accurate sampling is directly proportional to the size of the Brillouin
> zone, hence inversely proportional to the size of the cell.
>
> E.g. if you estimate that 6x6x6 k-points converge a certain calculation
> than 3x3x3 k-points will be converge a 2x2x2 supercell to exactly the same
> level.
>
> Best regards
>
>
> --
> Lorenzo Paulatto
> SISSA  &  DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www:   http://people.sissa.it/~paulatto/
>
>  *** save italian brains ***
>   http://saveitalianbrains.wordpress.com/
>
>
> --
>
> Message: 6
> Date: Fri, 11 Sep 2009 13:59:05 +0200
> From: Stefano de Gironcoli 
> Subject: Re: [Pw_forum] K Points and Band structures
> To: PWSCF Forum 
> Message-ID: <4AAA3B89.9020002 at sissa.it>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Shaptrishi Sharma wrote:
> > Hi QEs users,
> >
> > Can anybody please help me in understanding what are the k points ?? I
> > have read books a

[Pw_forum] How to control number of slabs in pwcond calculation？

[Manoj Srivastava]

Dear Hui Wang, 
 I dont think there is a straight forward way of doing this, at least not
that I know of. (Community members are most welcome to correct me on
this).changing the number of slabs along z direction is determined using
the unit cell length along z direction. Here is what I found upon some
grep. I tried to show here only when we have only one region present, lets
say left lead.
 from cond_out.f90
 do k=1, nrzl
   write(stdout,'(2x,i3,2x,3f7.4,3x,80i1)')   &
 k,zl(k),zl(k+1),zl(k+1)-zl(k),(crosl(iorb,k),iorb=1,norbl)
 enddo
so if you wish to change the number of slabs along z direction, you need
to change nrzl and so on 
 from init_cond.f90
line 211 
 nrzl = nrzreg(1)
line 86
nrz1=0.0
do iz = 2, 5
 naux=(dwid(iz)+dz1*0.5d0)/dz1-nrz1
 nrzreg(iz-1) = naux
  ...
   
 we have two options, dz1 and dwid(2)
line 44
 nrztot = nr3s
  if(nrztot/2*2.eq.nrztot) nrztot = nrztot+1
  zlen = at(3,3)
  dz1 = zlen/nrztot 
 zlen=z component of a_3 lattice vector. nr3s=
smooth fft dimension in z direction, so if you could change nr3s, you
might be able to change nrzl. 
 now, dwid(2)- line 80
 dwid(2) = bd2
line 60 
 if(flag.eq.'l') then
bd2 = bdl
 from the input file description - 
bdl: right boundary of the left lead (left one is supposed to be at 0)

I dont know how one can change smooth fft dimesion in z direction. I
believe its done in SCF part not in PWCOND. 

Regards, 
Manoj

On Fri, 11 Sep 2009, xirainbow wrote:

> Dear all:  I find the following content at
> "/espresso-4.0.4/examples/example12/results/al.cond.out" file.
> *" nrz  =   21*
> *.*
> *k slabz(k)  z(k+1) crossing(iorb=1,norb)*
> *1   0. 0.0673 0.0673   *
> *.*
> *   20   1.2793 1.3467 0.0673   0111*
> *   21   1.3467 1.4140 0.0673     "*
> 
>  I want to know, at *.cond.in input file, how to control the number of
> slabs along z direction in left, right lead and scattering region,
> respectively.
>  By the way, what is the meaning of "crossing(iorb=1,norb)"?
> 
>  Thanks in advance ??
> 
> 
> 
> Hui Wang
> School of physics, Nankai University, Tianjin, China
> 

[Pw_forum] problem with charge density with xcrysden

[dev sharma]

Dear sir, my.xsf file is below

Program POST-PROC v.4.0.2  starts ...
 Today is 11Sep2009 at 12:54:29

 Check: negative/imaginary core charge=   -0.090.00

 negative rho (up, down):  0.188E+00 0.000E+00

 Calling punch_plot, plot_num =   0
 Writing data to file  yvocharge
 Reading data from file  yvocharge
 CRYSTAL
 PRIMVEC
7.1183005140.00.0
0.07.1183005140.0
0.00.06.289300454
 PRIMCOORD
  24   1
Y 0.05.3387253560.786162553
/
/
O 1.3111908685.3387253562.835216639
BEGIN_BLOCK_DATAGRID_3D
3D_PWSCF
DATAGRID_3D_UNKNOWN
  61  61  49
  0.00  0.00  0.00
  7.118301  0.00  0.00
  0.00  7.118301  0.00
  0.00  0.00  6.289300
  0.19131E-01  0.18756E-01  0.17478E-01  0.15613E-01  0.13484E-01
0.11234E-01
/
/
 0.93736E-02  0.11234E-01  0.13484E-01  0.15613E-01  0.17478E-01
0.18756E-01
  0.19131E-01
END_DATAGRID_3D
END_BLOCK_DATAGRID_3D
 Plot Type: 3D Output format: XCrySDen

thanks.

On Fri, Sep 11, 2009 at 2:14 PM, Gabriele Sclauzero wrote:

> Dear Dev,
>
> dev sharma wrote:
> > hi 2 all,
> >  I am trying to plot the charge density with the XCrysden, but when i am
> > opening's XSF(file--> open structure--> open XSF(xcryden structure
> > file)) file , generated by my calculations, it is showing the structure
> > of my system. And i am not getting the   option tools--> DATA GRID as
> > ready. Please help or advice ?? Thankful to all of you. What i did is
> > listed below.
>
> Have you had a look inside your .xsf file? How does it look? Does it
> actually contain the
> DATAGRID block? Is it complete? Please supply more information!
>
> Regards,
>
> GS
>
>
> > I run my input file with command
> > /home/physics/espresso-4.0.2/bin/pp.x   density.xsf
> > and inputs of density.in <http://density.in> are
> >  
> >   prefix  = 'yvo'
> >  outdir  = '/home/physics/work/yvo/temp/',
> > filplot = 'yvocharge'
> >   plot_num= 0
> >  /
> >  
> >   nfile = 1
> >  filepp(1) = 'yvocharge'
> >   weight(1) = 1.0
> >iflag = 3
> >   output_format = 5,
> >  /
> >
> > with regards,
> > Dev Sharma,
> > University of Delhi,
> >
> >
> > 
> >
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
>
> --
>
>
> o  o
> | Gabriele Sclauzero, PhD Student  |
> | c/o:   SISSA & CNR-INFM Democritos,  |
> |via Beirut 2-4, 34014 Trieste (Italy) |
> | email: sclauzer at sissa.it |
> | phone: +39 040 3787 511  |
> | skype: gurlonotturno |
> o ---- o
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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[Pw_forum] input file for isolated atom

[udayagiri sai babu]

Dear prasenajit this is the part of my output for the posted input file.
(smearing contribution is there! though it is small ) is the degauss value
too high for isolated atom or it is high for bulk calculation also? because
i use around 0.01 Ry value for all my calculations. Does the mixing beta
value effect the energy of the system?

one-electron contribution =  -155.91791626 Ry
 hartree contribution  =74.49216944 Ry
 xc contribution   =   -14.37611953 Ry
 ewald contribution=   -20.42854186 Ry
 smearing contrib. (-TS)   =-0.00972779 Ry

 total magnetization   = 3.24 Bohr mag/cell
 absolute magnetization= 3.24 Bohr mag/cell

 convergence has been achieved in  34 iterations

On Fri, Sep 11, 2009 at 2:06 PM, Prasenjit Ghosh wrote:

> Dear Udayagiri,
>
> First of all it's not clear whether you have any question other than
> whether your input file is correct.
>
> Now some comments about your input file:
>
> (a) while doing calculations for any zero dimensions you should always set
> nosym =.true.
> (b) Your value of degauss is too high.you should use some value around
> 0.001 Ry. According to my experience, doing cal. for a single atom is
> tricky, specially when you are using a smearing. Even that doesn't confirm
> you will get the correct ground state for the atom. So what you should do is
> at the end of the calculation check the values of the total magnetization,
> absolute magnetization and the smearing contribution. The last term should
> be exactly zero.
> (c) You don't need to set tstress and tprnfor true.
> (c) mixing_beta= 0.7 too large.I would put something smaller0.3
> (d) I hope you have checked the convergence of ecut rho & ecutwfc.
>
> Prasenjit.
>
> 2009/9/11 udayagiri sai babu 
>
>> Hi everybody
>> I want to calculate the cohesive energy of Titanium for that i need to
>> calculate the energy of an isolated atom previously in the forum somebody
>> has suggested me to do spin polarisation calculation for the isolated atom.
>> I have written an input file accordingly some one can see and tell me if my
>> input script is true. I have read the forum archives on this topic but they
>> are not exactly answering my question. Can somebody please help me.
>> *
>> Input file for isolated atom *
>>
>> 
>> calculation = 'scf',
>> restart_mode='from_scratch',
>> outdir='/home/sai/temp',
>> prefix='titanium'
>> pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/',
>> tstress = .TRUE.,
>> tprnfor = .TRUE.,
>> /
>> 
>> ibrav=1
>> celldm(1)=20,
>> nat=1,
>> ntyp=1
>> ecutwfc=25,
>> ecutrho=250,
>> occupations='smearing',
>> smearing='mv',
>> degauss=0.01
>> nspin=2
>> starting_magnetization(1)=0.2
>> /
>> 
>> conv_thr=1.D-8,
>> diagonalization='david',
>> mixing_mode='plain',
>> mixing_beta= 0.7,
>> /
>> ATOMIC_SPECIES
>> Ti  47.867  Ti.pbe-sp-van_ak.UPF
>> ATOMIC_POSITIONS (crystal)
>> Ti 0.0.0.
>> K_POINTS GAMMA
>>
>> --
>> U.Saibabu
>> PhD student,
>> Deformation mechanisms modeling group,
>> Materials engineering department,
>> IISc Bangalore,
>> India.
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
> PRASENJIT GHOSH,
> POST-DOC,
> ROOM NO: 265, MAIN BUILDING,
> CM SECTION, ICTP,
> STRADA COSTERIA 11,
> TRIESTE, 34104,
> ITALY
> PHONE: +39 040 2240 369 (O)
>  +39 3807528672 (M)
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
U.Saibabu
PhD student,
Deformation mechanisms modeling group,
Materials engineering department,
IISc Bangalore,
India.
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[Pw_forum] Problem in spin polarisation

[Stefano de Gironcoli]

what is your value for nbnd ?
stefano

Shaptrishi Sharma wrote:
> Hi QE users,
>
> In one of my previous mail, I have asked about the spin polarisation 
> in a sytem having odd number of electrons , (I have 21 hydrogen atoms 
> in my system ).
>
> As suggested I used nelup =11 and neldw = 10, however, it is showing 
> me the same error, as
>
> nelp out of range.
> so what shall I do now??
>
> Thanks
>
> SS
>
>
> 
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   

[Pw_forum] K Points and Band structures

[Stefano de Gironcoli]

Shaptrishi Sharma wrote:
> Hi QEs users,
>
> Can anybody please help me in understanding what are the k points ?? I 
> have read books a lot but its difficult to understand.
Please ask to any solid state physicist nearby.

> And also  how do we choose k points while performing a band structure 
> calculation in quantum espresso when we are having 330 atoms.
If you still have QE specific doubts after you have understood Bloch 
theorem, Real and Reciprocal Space lattices, Brilloun Zone and the like 
please  formulate them again, trying to be specific.
> Thanks
> S
Please provide your affilaition.

Best regards,

Stefano de Gironcoli - SISSA and DEMOCRITOS

> 
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   

[Pw_forum] K Points and Band structures

[Lorenzo Paulatto]

In data 11 settembre 2009 alle ore 13:45:43, Shaptrishi Sharma  
 ha scritto:

> Can anybody please help me in understanding what are the k points ?? I  
> have read books a lot but its difficult to understand.

They are eigenvalues of the translation operator, T(R) where  
R=n1*a1+n2*a2+n3*a3; a1,a2,a3 are the cell basis vectors and n1,n2,n3  
integer numbers. The eigenvectors are, of course, the Bloch wavefunctions.

Because the hamiltonian is periodic it commutes with the translation  
operator, you can diagonalize both the hamiltonian and the translation  
operator at the same time. As a consequence each Bloch wavefunction has a  
well-defined energy (hamiltonian's eigenvalue) and k-point (translation  
eigenvalue). Using both eigenvalues you can classify the states without  
ambiguity, except where the bands cross.

> And also  how do we choose k points while performing a band structure
> calculation in quantum espresso when we are having 330 atoms.

It does not depend on the number of atoms.

You have to test the convergence at fixed smearing. E.g. you choose a  
smearing that's small enough for you, than you increase the number of  
k-points until total energy converges. You may then try again for a  
smaller/larger smearing and see if the results are consistent.

I would advise starting with a smaller system, it would take ages to do it  
on 330 atoms. Keep in mind that the number of k-points needed for an  
accurate sampling is directly proportional to the size of the Brillouin  
zone, hence inversely proportional to the size of the cell.

E.g. if you estimate that 6x6x6 k-points converge a certain calculation  
than 3x3x3 k-points will be converge a 2x2x2 supercell to exactly the same  
level.

Best regards


-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/

 *** save italian brains ***
  http://saveitalianbrains.wordpress.com/

[Pw_forum] input file for isolated atom

[Paolo Giannozzi]

On Sep 11, 2009, at 10:36 , Prasenjit Ghosh wrote:

> (a) while doing calculations for any zero dimensions
> you should always set nosym =.true.

for Gamma-point calculations it shouldn't make any
difference

P.
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222

[Pw_forum] [Fwd: Re: problem with charge density with xcrysden]

[Gabriele Sclauzero]

Forwarding e-mail from Emine. So I guess it may be a compatibility issue.

GS

 Original Message 
Subject:Re: [Pw_forum] problem with charge density with xcrysden
Date:   Fri, 11 Sep 2009 03:50:17 -0700 (PDT)
From:   e kb 
To: sclauzer at sissa.it




The old version of xcrysden that i had didnt work with this line :
  > DATAGRID_3D_UNKNOWN
but with this one:
  > BEGIN_DATAGRID_3D_UNKNOWN

I am not up to date on this but you can check it.
emine kucukbenli, SISSA, Italy



-- 


o  o
| Gabriele Sclauzero, PhD Student  |
| c/o:   SISSA & CNR-INFM Democritos,  |
|via Beirut 2-4, 34014 Trieste (Italy) |
| email: sclauzer at sissa.it |
| phone: +39 040 3787 511  |
| skype: gurlonotturno |
o  o

[Pw_forum] problem with charge density with xcrysden

[dev sharma]

hi 2 all,
 I am trying to plot the charge density with the XCrysden, but when i am
opening's XSF(file--> open structure--> open XSF(xcryden structure file))
file , generated by my calculations, it is showing the structure of my
system. And i am not getting the   option tools--> DATA GRID as ready.
Please help or advice ?? Thankful to all of you. What i did is listed below.
I run my input file with command
/home/physics/espresso-4.0.2/bin/pp.x   density.xsf
and inputs of density.in are
 
  prefix  = 'yvo'
 outdir  = '/home/physics/work/yvo/temp/',
filplot = 'yvocharge'
  plot_num= 0
 /
 
  nfile = 1
 filepp(1) = 'yvocharge'
  weight(1) = 1.0
   iflag = 3
  output_format = 5,
 /

with regards,
Dev Sharma,
University of Delhi,
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[Pw_forum] Problem in spin polarisation

[Shaptrishi Sharma]

Hi QE users,

In one of my previous mail, I have asked about the spin polarisation in a
sytem having odd number of electrons , (I have 21 hydrogen atoms in my
system ).

As suggested I used nelup =11 and neldw = 10, however, it is showing me the
same error, as

nelp out of range.
so what shall I do now??

Thanks

SS
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[Pw_forum] K Points and Band structures

[Shaptrishi Sharma]

Hi QEs users,

Can anybody please help me in understanding what are the k points ?? I have
read books a lot but its difficult to understand.

And also  how do we choose k points while performing a band structure
calculation in quantum espresso when we are having 330 atoms.

Thanks

S
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[Pw_forum] problem with charge density with xcrysden

[Stefano de Gironcoli]

dear Dev Sharma
  the xsf file with the DATAGRID field IS NOT the output of pp.x!  
Rather its name needs to be specified in variable fileout in the  
namelist of your density.in input
  Please read the documentation of pp.x code for the meaning of the 
other variables.
  HTH

   Stefano de Gironcoli - SISSA and DEMOCRITOS

dev sharma wrote:
> hi 2 all,
>  I am trying to plot the charge density with the XCrysden, but when i 
> am opening's XSF(file--> open structure--> open XSF(xcryden structure 
> file)) file , generated by my calculations, it is showing the 
> structure of my system. And i am not getting the   option tools--> 
> DATA GRID as ready. Please help or advice ?? Thankful to all of you. 
> What i did is listed below.
> I run my input file with command
> /home/physics/espresso-4.0.2/bin/pp.x   density.xsf
> and inputs of density.in  are
>  
>   prefix  = 'yvo'
>  outdir  = '/home/physics/work/yvo/temp/',
> filplot = 'yvocharge'
>   plot_num= 0
>  /
>  
>   nfile = 1
>  filepp(1) = 'yvocharge'
>   weight(1) = 1.0
>iflag = 3
>   output_format = 5,
>  /
>
> with regards,
> Dev Sharma,
> University of Delhi,
> 
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   

[Pw_forum] input file for isolated atom

[Gabriele Sclauzero]

udayagiri sai babu wrote:
> Dear prasenajit
> thank you for your valuable inputs 
> 
> On Fri, Sep 11, 2009 at 2:43 PM, Prasenjit Ghosh 
> mailto:prasenjit.jnc at gmail.com>> wrote:
> 
> For Ti atom, the electronic configuration is  [*Ar*].*3d*^2 .*4s*^2
> . So the magnetization should be 2.0 Bohr magneton due to the two
> electrons in the d-orbital, which is not what you are getting from
> your calculation.
> 
> Also your smearing contribution is -0.00972779 Ry (about 0.1 eV),
> which I would say very high. If you would have find the correct
> magnetic ground state, then this should have been 0.0 Ry.
> 
> As far as the bulk system is concerned, I'm not sure. It depends how
> Ti bulk behaves. You can search in the literature to find out what
> values of degauss other people have used.

If you want to obtain the correct ground state and magnetization for the 
isolated Ti atom, 
I suggest you to use either occupations=fixed and tot_magnetization=2 (but this 
calculation will not converge, probably), or better to use 
occupations='from_input' and 
use the OCCUPATIONS card to specify the correct electronic configuration.
Another solution could be to use smearing and the constrained-magnetization 
method, though 
I never used it for isolated atoms.

HTH

GS



> 
> Mixing beta doesn't effect the energy of the system. It just helps
> you in convergence.
> 
> 
> Prasenjit.
> 
> 2009/9/11 udayagiri sai babu  >
> 
> Dear prasenajit this is the part of my output for the posted
> input file. (smearing contribution is there! though it is small
> ) is the degauss value too high for isolated atom or it is high
> for bulk calculation also? because i use around 0.01 Ry value
> for all my calculations. Does the mixing beta value effect the
> energy of the system?
> 
> one-electron contribution =  -155.91791626 Ry
>  hartree contribution  =74.49216944 Ry
>  xc contribution   =   -14.37611953 Ry
>  ewald contribution=   -20.42854186 Ry
>  smearing contrib. (-TS)   =-0.00972779 Ry
> 
>  total magnetization   = 3.24 Bohr mag/cell
>  absolute magnetization= 3.24 Bohr mag/cell
> 
>  convergence has been achieved in  34 iterations
> 
> 
> On Fri, Sep 11, 2009 at 2:06 PM, Prasenjit Ghosh
> mailto:prasenjit.jnc at gmail.com>> 
> wrote:
> 
> Dear Udayagiri,
> 
> First of all it's not clear whether you have any question
> other than whether your input file is correct.
> 
> Now some comments about your input file:
> 
> (a) while doing calculations for any zero dimensions you
> should always set nosym =.true.
> (b) Your value of degauss is too high.you should use
> some value around 0.001 Ry. According to my experience,
> doing cal. for a single atom is tricky, specially when you
> are using a smearing. Even that doesn't confirm you will get
> the correct ground state for the atom. So what you should do
> is at the end of the calculation check the values of the
> total magnetization, absolute magnetization and the smearing
> contribution. The last term should be exactly zero.
> (c) You don't need to set tstress and tprnfor true.
> (c) mixing_beta= 0.7 too large.I would put something
> smaller0.3
> (d) I hope you have checked the convergence of ecut rho &
> ecutwfc.
> 
> Prasenjit.
> 
> 2009/9/11 udayagiri sai babu  >
> 
> Hi everybody
> I want to calculate the cohesive energy of Titanium for
> that i need to calculate the energy of an isolated atom
> previously in the forum somebody has suggested me to do
> spin polarisation calculation for the isolated atom. I
> have written an input file accordingly some one can see
> and tell me if my input script is true. I have read the
> forum archives on this topic but they are not exactly
> answering my question. Can somebody please help me.
> *
> Input file for isolated atom *
> 
> 
> calculation = 'scf',
> restart_mode='from_scratch',
> outdir='/home/sai/temp',
> prefix='titanium'
> pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/',
> tstress = .TRUE.,
> tprnfor = .TRUE.,
> /
> 
> ibrav=1
> celldm(1)=20,
> nat=1,
>  

[Pw_forum] problem with charge density with xcrysden

[Gabriele Sclauzero]

Prasenjit Ghosh wrote:
> You remove the following lines & try seeing it in xcrysden:
> 
> Program POST-PROC v.4.0.2  starts ...
>  Today is 11Sep2009 at 12:54:29
> 
>  Check: negative/imaginary core charge=   -0.090.00
> 
>  negative rho (up, down):  0.188E+00 0.000E+00
> 
>  Calling punch_plot, plot_num =   0
>  Writing data to file  yvocharge
>  Reading data from file  yvocharge

I think these lines are not the problem. In my version of Xcrysden (1.5.17) I 
could read 
successfully an XSF file including the pp.x information shown here above.
I could also visualize the 3D data contained in a file produced with the same 
options of Dev,
 >  >  
 >  >   nfile = 1
 >  >  filepp(1) = 'yvocharge'
 >  >   weight(1) = 1.0
 >  >iflag = 3
 >  >   output_format = 5,
 >  >  /

so I think he has a problem with his installation of pw.x or xcrysden.

GS


> 
> 2009/9/11 shypirate mailto:shypirate at gmail.com>>
> 
> it definitely can not be used as input file for  xcrysden.
> try to use the data included in "BLOCK_DATAGRID_3D" section
>  
>  
> 2009-09-11
> 
> shypirate
> 
> ** dev sharma
> *?* 2009-09-11  16:53:38
> ** PWSCF Forum
> *???*
> *???* Re: [Pw_forum] problem with charge density with xcrysden
> Dear sir, my.xsf file is below
> 
> Program POST-PROC v.4.0.2  starts ...
>  Today is 11Sep2009 at 12:54:29
> 
>  Check: negative/imaginary core charge=   -0.090.00
> 
>  negative rho (up, down):  0.188E+00 0.000E+00
> 
>  Calling punch_plot, plot_num =   0
>  Writing data to file  yvocharge
>  Reading data from file  yvocharge
>  CRYSTAL
>  PRIMVEC
> 7.1183005140.00.0
> 0.07.1183005140.0
> 0.00.06.289300454
>  PRIMCOORD
>   24   1
> Y 0.05.3387253560.786162553
> /
> /
> O 1.3111908685.3387253562.835216639
> BEGIN_BLOCK_DATAGRID_3D
> 3D_PWSCF
> DATAGRID_3D_UNKNOWN
>   61  61  49
>   0.00  0.00  0.00
>   7.118301  0.00  0.00
>   0.00  7.118301  0.00
>   0.00  0.00  6.289300
>   0.19131E-01  0.18756E-01  0.17478E-01  0.15613E-01  0.13484E-01 
> 0.11234E-01
> /
> /
>  0.93736E-02  0.11234E-01  0.13484E-01  0.15613E-01  0.17478E-01 
> 0.18756E-01
>   0.19131E-01
> END_DATAGRID_3D
> END_BLOCK_DATAGRID_3D
>  Plot Type: 3D Output format: XCrySDen
> 
> thanks.
> 
> On Fri, Sep 11, 2009 at 2:14 PM, Gabriele Sclauzero
> mailto:sclauzer at sissa.it>> wrote:
> 
> Dear Dev,
> 
> dev sharma wrote:
>  > hi 2 all,
>  >  I am trying to plot the charge density with the XCrysden,
> but when i am
>  > opening's XSF(file--> open structure--> open XSF(xcryden
> structure
>  > file)) file , generated by my calculations, it is showing the
> structure
>  > of my system. And i am not getting the   option tools--> DATA
> GRID as
>  > ready. Please help or advice ?? Thankful to all of you. What
> i did is
>  > listed below.
> 
> Have you had a look inside your .xsf file? How does it look?
> Does it actually contain the
> DATAGRID block? Is it complete? Please supply more information!
> 
> Regards,
> 
> GS
> 
> 
>  > I run my input file with command
>  > /home/physics/espresso-4.0.2/bin/pp.x   density.xsf
>  > and inputs of density.in 
>  are
>  >  
>  >   prefix  = 'yvo'
>  >  outdir  = '/home/physics/work/yvo/temp/',
>  > filplot = 'yvocharge'
>  >   plot_num= 0
>  >  /
>  >  
>  >   nfile = 1
>  >  filepp(1) = 'yvocharge'
>  >   weight(1) = 1.0
>  >iflag = 3
>  >   output_format = 5,
>  >  /
>  >
>  > with regards,
>  > Dev Sharma,
>  > University of Delhi,
>  >
>  >
>  >
> 
> 
>  >
>  > ___
>  > Pw_forum mailing list
>  > Pw_forum at pwscf.org 
>  > http://www.democritos.it/mailman/listinfo/pw_forum
> 
> --
> 
> 
> o  o
> | Gabriele Sclauzero, PhD Student  |
> | 

[Pw_forum] input file for isolated atom

[Prasenjit Ghosh]

 BUILDING,
>> CM SECTION, ICTP,
>> STRADA COSTERIA 11,
>> TRIESTE, 34104,
>> ITALY
>> PHONE: +39 040 2240 369 (O)
>>  +39 3807528672 (M)
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
> U.Saibabu
> PhD student,
> Deformation mechanisms modeling group,
> Materials engineering department,
> IISc Bangalore,
> India.
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
PRASENJIT GHOSH,
POST-DOC,
ROOM NO: 265, MAIN BUILDING,
CM SECTION, ICTP,
STRADA COSTERIA 11,
TRIESTE, 34104,
ITALY
PHONE: +39 040 2240 369 (O)
 +39 3807528672 (M)
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[Pw_forum] problem with charge density with xcrysden

[Prasenjit Ghosh]

You remove the following lines & try seeing it in xcrysden:

Program POST-PROC v.4.0.2  starts ...
 Today is 11Sep2009 at 12:54:29

 Check: negative/imaginary core charge=   -0.090.00

 negative rho (up, down):  0.188E+00 0.000E+00

 Calling punch_plot, plot_num =   0
 Writing data to file  yvocharge
 Reading data from file  yvocharge

2009/9/11 shypirate 

>  it definitely can not be used as input file for  xcrysden.
> try to use the data included in "BLOCK_DATAGRID_3D" section
>
>
> 2009-09-11
> --
>  shypirate
> --
> ** dev sharma
> *?* 2009-09-11  16:53:38
> ** PWSCF Forum
> *???*
> *???* Re: [Pw_forum] problem with charge density with xcrysden
>  Dear sir, my.xsf file is below
>
> Program POST-PROC v.4.0.2  starts ...
>  Today is 11Sep2009 at 12:54:29
>
>  Check: negative/imaginary core charge=   -0.090.00
>
>  negative rho (up, down):  0.188E+00 0.000E+00
>
>  Calling punch_plot, plot_num =   0
>  Writing data to file  yvocharge
>  Reading data from file  yvocharge
>  CRYSTAL
>  PRIMVEC
> 7.1183005140.00.0
> 0.07.1183005140.0
> 0.00.06.289300454
>  PRIMCOORD
>   24   1
> Y 0.05.3387253560.786162553
> /
> /
> O 1.3111908685.3387253562.835216639
> BEGIN_BLOCK_DATAGRID_3D
> 3D_PWSCF
> DATAGRID_3D_UNKNOWN
>   61  61  49
>   0.00  0.00  0.00
>   7.118301  0.00  0.00
>   0.00  7.118301  0.00
>   0.00  0.00  6.289300
>   0.19131E-01  0.18756E-01  0.17478E-01  0.15613E-01  0.13484E-01
> 0.11234E-01
> /
> /
>  0.93736E-02  0.11234E-01  0.13484E-01  0.15613E-01  0.17478E-01
> 0.18756E-01
>   0.19131E-01
> END_DATAGRID_3D
> END_BLOCK_DATAGRID_3D
>  Plot Type: 3D Output format: XCrySDen
>
> thanks.
>
> On Fri, Sep 11, 2009 at 2:14 PM, Gabriele Sclauzero  sissa.it>wrote:
>
>> Dear Dev,
>>
>> dev sharma wrote:
>> > hi 2 all,
>> >  I am trying to plot the charge density with the XCrysden, but when i am
>> > opening's XSF(file--> open structure--> open XSF(xcryden structure
>> > file)) file , generated by my calculations, it is showing the structure
>> > of my system. And i am not getting the   option tools--> DATA GRID as
>> > ready. Please help or advice ?? Thankful to all of you. What i did is
>> > listed below.
>>
>> Have you had a look inside your .xsf file? How does it look? Does it
>> actually contain the
>> DATAGRID block? Is it complete? Please supply more information!
>>
>> Regards,
>>
>> GS
>>
>>
>> > I run my input file with command
>> > /home/physics/espresso-4.0.2/bin/pp.x   density.xsf
>> > and inputs of density.in <http://density.in> are
>> >  
>> >   prefix  = 'yvo'
>> >  outdir  = '/home/physics/work/yvo/temp/',
>> > filplot = 'yvocharge'
>> >   plot_num= 0
>> >  /
>> >  
>> >   nfile = 1
>> >  filepp(1) = 'yvocharge'
>> >   weight(1) = 1.0
>> >iflag = 3
>> >   output_format = 5,
>> >  /
>> >
>> > with regards,
>> > Dev Sharma,
>> > University of Delhi,
>> >
>> >
>> > 
>> >
>> > ___
>> > Pw_forum mailing list
>> > Pw_forum at pwscf.org
>> > http://www.democritos.it/mailman/listinfo/pw_forum
>>
>> --
>>
>>
>> o  o
>> | Gabriele Sclauzero, PhD Student  |
>> | c/o:   SISSA & CNR-INFM Democritos,  |
>> |via Beirut 2-4, 34014 Trieste (Italy) |
>> | email: sclauzer at sissa.it |
>> | phone: +39 040 3787 511  |
>> | skype: gurlonotturno |
>> o ---- o
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
PRASENJIT GHOSH,
POST-DOC,
ROOM NO: 265, MAIN BUILDING,
CM SECTION, ICTP,
STRADA COSTERIA 11,
TRIESTE, 34104,
ITALY
PHONE: +39 040 2240 369 (O)
 +39 3807528672 (M)
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[Pw_forum] input file for isolated atom

[udayagiri sai babu]

Hi everybody
I want to calculate the cohesive energy of Titanium for that i need to
calculate the energy of an isolated atom previously in the forum somebody
has suggested me to do spin polarisation calculation for the isolated atom.
I have written an input file accordingly some one can see and tell me if my
input script is true. I have read the forum archives on this topic but they
are not exactly answering my question. Can somebody please help me.
*
Input file for isolated atom *


calculation = 'scf',
restart_mode='from_scratch',
outdir='/home/sai/temp',
prefix='titanium'
pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/',
tstress = .TRUE.,
tprnfor = .TRUE.,
/

ibrav=1
celldm(1)=20,
nat=1,
ntyp=1
ecutwfc=25,
ecutrho=250,
occupations='smearing',
smearing='mv',
degauss=0.01
nspin=2
starting_magnetization(1)=0.2
/

conv_thr=1.D-8,
diagonalization='david',
mixing_mode='plain',
mixing_beta= 0.7,
/
ATOMIC_SPECIES
Ti  47.867  Ti.pbe-sp-van_ak.UPF
ATOMIC_POSITIONS (crystal)
Ti 0.0.0.
K_POINTS GAMMA

-- 
U.Saibabu
PhD student,
Deformation mechanisms modeling group,
Materials engineering department,
IISc Bangalore,
India.
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[Pw_forum] problem with charge density with xcrysden

[Gabriele Sclauzero]

Dear Dev,

dev sharma wrote:
> hi 2 all,
>  I am trying to plot the charge density with the XCrysden, but when i am 
> opening's XSF(file--> open structure--> open XSF(xcryden structure 
> file)) file , generated by my calculations, it is showing the structure 
> of my system. And i am not getting the   option tools--> DATA GRID as 
> ready. Please help or advice ?? Thankful to all of you. What i did is 
> listed below.

Have you had a look inside your .xsf file? How does it look? Does it actually 
contain the 
DATAGRID block? Is it complete? Please supply more information!

Regards,

GS


> I run my input file with command
> /home/physics/espresso-4.0.2/bin/pp.x   density.xsf
> and inputs of density.in  are
>  
>   prefix  = 'yvo'
>  outdir  = '/home/physics/work/yvo/temp/',
> filplot = 'yvocharge'
>   plot_num= 0
>  /
>  
>   nfile = 1
>  filepp(1) = 'yvocharge'
>   weight(1) = 1.0
>iflag = 3
>   output_format = 5,
>  /
> 
> with regards,
> Dev Sharma,
> University of Delhi,
> 
> 
> 
> 
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

-- 


o  o
| Gabriele Sclauzero, PhD Student  |
| c/o:   SISSA & CNR-INFM Democritos,  |
|via Beirut 2-4, 34014 Trieste (Italy) |
| email: sclauzer at sissa.it |
| phone: +39 040 3787 511  |
| skype: gurlonotturno |
o  o

[Pw_forum] input file for isolated atom

[Prasenjit Ghosh]

Dear Udayagiri,

First of all it's not clear whether you have any question other than whether
your input file is correct.

Now some comments about your input file:

(a) while doing calculations for any zero dimensions you should always set
nosym =.true.
(b) Your value of degauss is too high.you should use some value around
0.001 Ry. According to my experience, doing cal. for a single atom is
tricky, specially when you are using a smearing. Even that doesn't confirm
you will get the correct ground state for the atom. So what you should do is
at the end of the calculation check the values of the total magnetization,
absolute magnetization and the smearing contribution. The last term should
be exactly zero.
(c) You don't need to set tstress and tprnfor true.
(c) mixing_beta= 0.7 too large.I would put something smaller0.3
(d) I hope you have checked the convergence of ecut rho & ecutwfc.

Prasenjit.

2009/9/11 udayagiri sai babu 

> Hi everybody
> I want to calculate the cohesive energy of Titanium for that i need to
> calculate the energy of an isolated atom previously in the forum somebody
> has suggested me to do spin polarisation calculation for the isolated atom.
> I have written an input file accordingly some one can see and tell me if my
> input script is true. I have read the forum archives on this topic but they
> are not exactly answering my question. Can somebody please help me.
> *
> Input file for isolated atom *
>
> 
> calculation = 'scf',
> restart_mode='from_scratch',
> outdir='/home/sai/temp',
> prefix='titanium'
> pseudo_dir='/home/sai/softwares/espresso-4.0.1/pseudo/',
> tstress = .TRUE.,
> tprnfor = .TRUE.,
> /
> 
> ibrav=1
> celldm(1)=20,
> nat=1,
> ntyp=1
> ecutwfc=25,
> ecutrho=250,
> occupations='smearing',
> smearing='mv',
> degauss=0.01
> nspin=2
> starting_magnetization(1)=0.2
> /
> 
> conv_thr=1.D-8,
> diagonalization='david',
> mixing_mode='plain',
> mixing_beta= 0.7,
> /
> ATOMIC_SPECIES
> Ti  47.867  Ti.pbe-sp-van_ak.UPF
> ATOMIC_POSITIONS (crystal)
> Ti 0.0.0.
> K_POINTS GAMMA
>
> --
> U.Saibabu
> PhD student,
> Deformation mechanisms modeling group,
> Materials engineering department,
> IISc Bangalore,
> India.
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
PRASENJIT GHOSH,
POST-DOC,
ROOM NO: 265, MAIN BUILDING,
CM SECTION, ICTP,
STRADA COSTERIA 11,
TRIESTE, 34104,
ITALY
PHONE: +39 040 2240 369 (O)
 +39 3807528672 (M)
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[Pw_forum] Problem in spin polarisation

[Duy Le]

Add nelec to input
Please just reply instead of creating a new email starting with "In one of
my previous mail" so that all your emails and communications are ordered in
the same thread.

:-)

On Fri, Sep 11, 2009 at 8:05 AM, Stefano de Gironcoli wrote:

> what is your value for nbnd ?
> stefano
>
> Shaptrishi Sharma wrote:
> > Hi QE users,
> >
> > In one of my previous mail, I have asked about the spin polarisation
> > in a sytem having odd number of electrons , (I have 21 hydrogen atoms
> > in my system ).
> >
> > As suggested I used nelup =11 and neldw = 10, however, it is showing
> > me the same error, as
> >
> > nelp out of range.
> > so what shall I do now??
> >
> > Thanks
> >
> > SS
> >
> >
> > 
> >
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.
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