Re: [QE-users] (no subject)

[Fariba Nazari]

Hi 
I have run the in put on my mac with no problem.
The only change was the introducing the path for out directory.
outdir = '/Users/./tmp' ,

regards
Fariba
IASBS


On Fri, 24/08/2018 08:00 PM, Dan Gil  wrote:
> 
Hi, 
> 

> 
I am using pwscf v6.3, and running into some issues that I could not resolve.

> 
I first ran simulations with hydroxylated sapphire (0001) surface with only 42 
atoms successfully. Now I am trying to run an identical simulation with the 
same surface with 168 atoms (2x2 supercell) and here is where I am running into 
issues.

> 
I've tried various settings, and I've gotten a variety of error messages. With 
the input format shown below, I get the following error from the HPC.

> 
- - - - -
/tmp/slurm/job8327489/slurm_script: line 11: 111713 Killed  
pw.x < sapphire.pw.in > sapphire.pw.out
> slurmstepd: error: Exceeded step memory limit at some point.
- - - - -

> 
When I run it on my personal computer, I get this error:

> 
- - - - -
 task # 0
>  from diropn : error #10
>  error opening sapphire/pwscf.wfc1
> 
- - - - -

> 
And indeed, there is no pwscf.wfc1 to be seen.

> 
Here is the input:

> 
- - - - - 
> 
&control
> calculation='relax',
> wf_collect = .true. ,
> outdir = 'sapphire' ,
> restart_mode = 'from_scratch' ,
> pseudo_dir = 'pseudo' ,
> disk_io = 'low' ,
> verbosity = 'low' ,
> max_seconds = 72000 ,
>  /
>  &system
> ibrav = 4 ,
> celldm(1)=17.99085377,
> celldm(3)=10,
> nat = 168 ,
> ntyp = 3 ,
> ecutwfc =50,
> ecutrho =400,
> smearing='mp',
> occupations='smearing',
> degauss=0.03,
>  /
>  &electrons
> diagonalization='david',
> conv_thr = 1.d-9,
> mixing_mode = 'plain',
>  /
>  &ions
>  /
> ATOMIC_SPECIES
> Al   26.981539   Al.pbe-n-rrkjus_psl.0.1.UPF
> O15.999000   O.pbe-n-rrkjus_psl.0.1.UPF
> H 1.000800   H.pbe-rrkjus_psl.0.1.UPF
> ATOMIC_POSITIONS crystal
> Al   0.0   0.0   0.095697893
> Al   0.0   0.0   0.177259148
> Al   0.0   0.0   0.040053860
> Al   0.0   0.0   0.232903158
> Al   0.33311   0.16621   0.187801968
> Al   0.33311   0.16621   0.270721823
> Al   0.33311   0.16621   0.131337383
> Al   0.33311   0.16621   0.045832216
> Al   0.16682   0.33364   0.002235215
> Al   0.16682   0.33364   0.085155073
> Al   0.16682   0.33364   0.227124825
> Al   0.16682   0.33364   0.141619636
> Al   0.5   0.0   0.095697893
> Al   0.5   0.0   0.177259148
> Al   0.5   0.0   0.040053860
> Al   0.5   0.0   0.232903158
> Al   0.83311   0.16621   0.187801968
> Al   0.83311   0.16621   0.270721823
> Al   0.83311   0.16621   0.131337383
> Al   0.83311   0.16621   0.045832216
> Al   0.66682   0.33364   0.002235215
> Al   0.66682   0.33364   0.085155073
> Al   0.66682   0.33364   0.227124825
> Al   0.66682   0.33364   0.141619636
> Al   0.5   0.5   0.095697893
> Al   0.5   0.5   0.177259148
> Al   0.5   0.5   0.040053860
> Al   0.5   0.5   0.232903158
> Al   0.83311   0.66621   0.187801968
> Al   0.83311   0.66621   0.270721823
> Al   0.83311   0.66621   0.131337383
> Al   0.83311   0.66621   0.045832216
> Al   0.66682   0.83364   0.002235215
> Al   0.66682   0.83364   0.085155073
> Al   0.66682   0.83364   0.227124825
> Al   0.66682   0.83364   0.141619636
> Al   0.0   0.5   0.095697893
> Al   0.0   0.5   0.177259148
> Al   0.0   0.5   0.040053860
> Al   0.0   0.5   0.232903158
> Al   0.33311   0.66621   0.187801968
> Al   0.33311   0.66621   0.270721823
> Al   0.33311   0.66621   0.131337383
> Al   0.33311   0.66621   0.045832216
> Al   0.16682   0.83364   0.002235215
> Al   0.16682   0.83364   0.085155073
> Al   0.16682   0.83364   0.227124825
> Al   0.16682   0.83364   0.141619636
> O0.155404208   0.001886947   0.067662578
> O0.344595898  -0.001886947   0.205294440
> O   -0.001886987   0.153517181   0.06766257

[QE-users] (no subject)

[Dan Gil]

Hi,

I am using pwscf v6.3, and running into some issues that I could not
resolve.

I first ran simulations with hydroxylated sapphire (0001) surface with only
42 atoms successfully. Now I am trying to run an identical simulation with
the same surface with 168 atoms (2x2 supercell) and here is where I am
running into issues.

I've tried various settings, and I've gotten a variety of error messages.
With the input format shown below, I get the following error from the HPC.

- - - - -
/tmp/slurm/job8327489/slurm_script: line 11: 111713 Killed
pw.x < sapphire.pw.in > sapphire.pw.out
slurmstepd: error: Exceeded step memory limit at some point.
- - - - -

When I run it on my personal computer, I get this error:

- - - - -
 task # 0
 from diropn : error #10
 error opening sapphire/pwscf.wfc1
- - - - -

And indeed, there is no pwscf.wfc1 to be seen.

Here is the input:

- - - - -
&control
calculation='relax',
wf_collect = .true. ,
outdir = 'sapphire' ,
restart_mode = 'from_scratch' ,
pseudo_dir = 'pseudo' ,
disk_io = 'low' ,
verbosity = 'low' ,
max_seconds = 72000 ,
 /
 &system
ibrav = 4 ,
celldm(1)=17.99085377,
celldm(3)=10,
nat = 168 ,
ntyp = 3 ,
ecutwfc =50,
ecutrho =400,
smearing='mp',
occupations='smearing',
degauss=0.03,
 /
 &electrons
diagonalization='david',
conv_thr = 1.d-9,
mixing_mode = 'plain',
 /
 &ions
 /
ATOMIC_SPECIES
Al   26.981539   Al.pbe-n-rrkjus_psl.0.1.UPF
O15.999000   O.pbe-n-rrkjus_psl.0.1.UPF
H 1.000800   H.pbe-rrkjus_psl.0.1.UPF
ATOMIC_POSITIONS crystal
Al   0.0   0.0   0.095697893
Al   0.0   0.0   0.177259148
Al   0.0   0.0   0.040053860
Al   0.0   0.0   0.232903158
Al   0.33311   0.16621   0.187801968
Al   0.33311   0.16621   0.270721823
Al   0.33311   0.16621   0.131337383
Al   0.33311   0.16621   0.045832216
Al   0.16682   0.33364   0.002235215
Al   0.16682   0.33364   0.085155073
Al   0.16682   0.33364   0.227124825
Al   0.16682   0.33364   0.141619636
Al   0.5   0.0   0.095697893
Al   0.5   0.0   0.177259148
Al   0.5   0.0   0.040053860
Al   0.5   0.0   0.232903158
Al   0.83311   0.16621   0.187801968
Al   0.83311   0.16621   0.270721823
Al   0.83311   0.16621   0.131337383
Al   0.83311   0.16621   0.045832216
Al   0.66682   0.33364   0.002235215
Al   0.66682   0.33364   0.085155073
Al   0.66682   0.33364   0.227124825
Al   0.66682   0.33364   0.141619636
Al   0.5   0.5   0.095697893
Al   0.5   0.5   0.177259148
Al   0.5   0.5   0.040053860
Al   0.5   0.5   0.232903158
Al   0.83311   0.66621   0.187801968
Al   0.83311   0.66621   0.270721823
Al   0.83311   0.66621   0.131337383
Al   0.83311   0.66621   0.045832216
Al   0.66682   0.83364   0.002235215
Al   0.66682   0.83364   0.085155073
Al   0.66682   0.83364   0.227124825
Al   0.66682   0.83364   0.141619636
Al   0.0   0.5   0.095697893
Al   0.0   0.5   0.177259148
Al   0.0   0.5   0.040053860
Al   0.0   0.5   0.232903158
Al   0.33311   0.66621   0.187801968
Al   0.33311   0.66621   0.270721823
Al   0.33311   0.66621   0.131337383
Al   0.33311   0.66621   0.045832216
Al   0.16682   0.83364   0.002235215
Al   0.16682   0.83364   0.085155073
Al   0.16682   0.83364   0.227124825
Al   0.16682   0.83364   0.141619636
O0.155404208   0.001886947   0.067662578
O0.344595898  -0.001886947   0.205294440
O   -0.001886987   0.153517181   0.067662578
O0.001886979   0.346482804   0.205294440
O0.346482772   0.344595857   0.067662578
O0.153517221   0.155404128   0.205294440
O0.171949672   0.170609214   0.023055667
O0.333498557   0.320107131   0.159438914
O0.329390758   0.001340470   0.023055667
O0.179892883   0.013391458   0.159438914
O0.328050321   0.329390771   0.249901352
O0.01339143

[QE-users] About electron-phonon coupling matrix elements

[Han Yang]

Dear all,

I have been using Phonon package ( version 6.1) to compute electron-phonon 
coupling matrix elements. Following example 3 in Phonon package, I computed the 
elements of Al(bcc) and the elements are written in 
_ph0/al.phsave/elph.*.*.xml. According to phonon user’s guide and developer’s 
manual, the elements in these files are coupling matrix in the basis of normal 
mode, ie g_{q nu} and it has been scaled to phonon frequencies and masses. 
However, if I manually change masses in Phonon input file, the elements do not 
change. So, are you sure the elements are in normal mode basis and are scaled 
to masses? Also, what is the unit for the elements written in those files? I 
assume it is Rydberg?

Another question is about the elements at k=gamma and q=gamma. Because the 
el-ph coupling matrix elements are computed with < psi_mk+q | dvscf | psi_nk >. 
At k=gamma and q=gamma, I believe these quantities should be real numbers, 
right? However, I get complex numbers for Al at k=gamma, q=gamma. Here are 
first several elements:

 
 
0.000E+000  0.000E+000  0.000E+000
 
 
1.173453794238444E-007, 5.551115123125783E-017
   -2.279566019787527E-002, 3.586239646544477E-001
   -4.862786020311256E-001, 2.450200129592524E-001
3.623894552425257E+000,-5.173393946467373E-001
   -6.097101185043030E-009, 1.009496251869191E-008
2.988349845356453E-010, 9.034043582656359E-010
2.767334139619493E-010, 1.470082250376592E-010

Do I make any mistake in computing or interpreting the results? 

Here’s my input file for phonon calculation:
 &inputph
  tr2_ph=1.0d-10,
  prefix='al',
  fildvscf='aldv',
  amass(1)=26.98,
  fildyn='./_ph0/al.dyn',
  outdir='./',
  electron_phonon='yambo',
  el_ph_sigma=0.005,
 el_ph_nsigma=10,
 asr = .true.
 zue = .false.
 epsil = .false.
 trans=.true.,
 ldisp=.true.
 nq1=5, nq2=5, nq3=5
  /

Thank you very much!

Han.
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Re: [QE-users] Question on Initial and final energies in NEB

[Stefano Baroni]

Sounds like something wrong is going on. You may want to post your input files 
and some relevant snapshots of the output, although I am afraid that at that 
point others may be more knowledgeable than me … SB

> On 24 Aug 2018, at 13:57, Stella, Martina  wrote:
> 
> Dear Prof. Baroni,
> 
> thanks for prompt reply. 
> 
> So yes I am using NEB to find a barrier between two states.
> 
> Before starting the NEB I have separately relaxed the geometries associated 
> with my two configurations (initial and final). Hence now I have two relaxed 
> geometries.
> 
> I start the NEB using the relaxed geometries for these states as first and 
> last image and I use the option to freeze these configurations. 
> 
> When I start my NEB and I check for the absolute energies of these two images 
> (which supposedly are kept frozen so probably they just go through a SCF 
> cycle?), these energies are quite different from the ones I have from my 
> separate relaxations of the aforementioned geometries . So I was wondering if 
> this is what I should expect. 
>  
> But maybe I am missing something or thinking about it in the wrong way, I 
> will think about what you said. 
> 
> Thank again. 
> 
> Cheers. 
> 
> 
> 
> Martina Stella
> Post-Doctoral researcher
> Physics Department, King's College London
> Strand,London WC2R 2LS UK
> 
> From: users  > on behalf of Stefano 
> Baroni mailto:bar...@sissa.it>>
> Sent: 24 August 2018 12:24:14
> To: Quantum Espresso users Forum
> Subject: Re: [QE-users] Question on Initial and final energies in NEB
>  
> Dear M., I do not quite get what the problem is. The solution may just be a 
> matter of definition. The “Minimum Energy Path” that the NEB is alleged to 
> find is the path in configuration space which *connects two minima* (hence 
> the answer to your question, I guess) and whose maximum energy (along the 
> path) is minimum (with respect to other paths). Put in a different way. What 
> are you using the NEB for? Finding an energy barrier, right? Between what? 
> Stable molecular configurations, right? (hence energy minima).  Does this 
> help? SB
> 
>> On 24 Aug 2018, at 13:12, Stella, Martina > > wrote:
>> 
>> Hi,
>>  
>> I am new to NEBs calculations and I am getting familiar with the method. I 
>> have a couple of questions, maybe trivial, but for which I don't have an 
>> answer yet. Hopefully someone can help.  
>> 
>> 1) How is the energy for the Initial and final structure estimated when I 
>> keep the two configurations frozen? 
>> 2)Should it be exactly the same as the final relaxed energies that I would 
>> get from completely separate calculations with the same simulation 
>> conditions and same geometries? 
>> 3) If they are not expected to be exactly the same which factors does the 
>> difference I may see depend on? 
>> 
>> Thanks. 
>> 
>> 
>> M. Stella
>> Post-Doctoral researcher
>> Physics Department, King's College London
>> Strand,London WC2R 2LS UK
>> 
>> ___
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>> users@lists.quantum-espresso.org 
>> https://lists.quantum-espresso.org/mailman/listinfo/users 
>> 
> — 
> Stefano Baroni -  SISSA, Trieste - http://stefano.baroni.me 
> ,
>  stefanobaroni (Skype) 
> 
> I believe in the despotism of human life and happiness against the liberty of 
> money and possessions - John Steinbeck
> 
> 
> 
> 
> 
> 
> ___
> users mailing list
> users@lists.quantum-espresso.org 
> https://lists.quantum-espresso.org/mailman/listinfo/users 
> 
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Re: [QE-users] Question on Initial and final energies in NEB

[Stella, Martina]

Dear Prof. Baroni,

thanks for prompt reply.

So yes I am using NEB to find a barrier between two states.

Before starting the NEB I have separately relaxed the geometries associated 
with my two configurations (initial and final). Hence now I have two relaxed 
geometries.

I start the NEB using the relaxed geometries for these states as first and last 
image and I use the option to freeze these configurations.

When I start my NEB and I check for the absolute energies of these two images 
(which supposedly are kept frozen so probably they just go through a SCF 
cycle?), these energies are quite different from the ones I have from my 
separate relaxations of the aforementioned geometries . So I was wondering if 
this is what I should expect.

But maybe I am missing something or thinking about it in the wrong way, I will 
think about what you said.

Thank again.

Cheers.




Martina Stella

Post-Doctoral researcher

Physics Department, King's College London

Strand,London WC2R 2LS UK



From: users  on behalf of Stefano 
Baroni 
Sent: 24 August 2018 12:24:14
To: Quantum Espresso users Forum
Subject: Re: [QE-users] Question on Initial and final energies in NEB

Dear M., I do not quite get what the problem is. The solution may just be a 
matter of definition. The “Minimum Energy Path” that the NEB is alleged to find 
is the path in configuration space which *connects two minima* (hence the 
answer to your question, I guess) and whose maximum energy (along the path) is 
minimum (with respect to other paths). Put in a different way. What are you 
using the NEB for? Finding an energy barrier, right? Between what? Stable 
molecular configurations, right? (hence energy minima).  Does this help? SB

On 24 Aug 2018, at 13:12, Stella, Martina 
mailto:martina.ste...@kcl.ac.uk>> wrote:


Hi,

I am new to NEBs calculations and I am getting familiar with the method. I have 
a couple of questions, maybe trivial, but for which I don't have an answer yet. 
Hopefully someone can help.

1) How is the energy for the Initial and final structure estimated when I keep 
the two configurations frozen?
2)Should it be exactly the same as the final relaxed energies that I would get 
from completely separate calculations with the same simulation conditions and 
same geometries?
3) If they are not expected to be exactly the same which factors does the 
difference I may see depend on?

Thanks.


M. Stella
Post-Doctoral researcher

Physics Department, King's College London
Strand,London WC2R 2LS UK


___
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—
Stefano Baroni -  SISSA, Trieste - 
http://stefano.baroni.me,
 stefanobaroni (Skype)

I believe in the despotism of human life and happiness against the liberty of 
money and possessions - John Steinbeck






___
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Re: [QE-users] Question on Initial and final energies in NEB

[Stefano Baroni]

Dear M., I do not quite get what the problem is. The solution may just be a 
matter of definition. The “Minimum Energy Path” that the NEB is alleged to find 
is the path in configuration space which *connects two minima* (hence the 
answer to your question, I guess) and whose maximum energy (along the path) is 
minimum (with respect to other paths). Put in a different way. What are you 
using the NEB for? Finding an energy barrier, right? Between what? Stable 
molecular configurations, right? (hence energy minima).  Does this help? SB

> On 24 Aug 2018, at 13:12, Stella, Martina  wrote:
> 
> Hi,
>  
> I am new to NEBs calculations and I am getting familiar with the method. I 
> have a couple of questions, maybe trivial, but for which I don't have an 
> answer yet. Hopefully someone can help.  
> 
> 1) How is the energy for the Initial and final structure estimated when I 
> keep the two configurations frozen? 
> 2)Should it be exactly the same as the final relaxed energies that I would 
> get from completely separate calculations with the same simulation conditions 
> and same geometries? 
> 3) If they are not expected to be exactly the same which factors does the 
> difference I may see depend on? 
> 
> Thanks. 
> 
> 
> M. Stella
> Post-Doctoral researcher
> Physics Department, King's College London
> Strand,London WC2R 2LS UK
> 
> ___
> users mailing list
> users@lists.quantum-espresso.org 
> https://lists.quantum-espresso.org/mailman/listinfo/users 
> 
— 
Stefano Baroni -  SISSA, Trieste - http://stefano.baroni.me 
, stefanobaroni (Skype) 

I believe in the despotism of human life and happiness against the liberty of 
money and possessions - John Steinbeck






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[QE-users] Question on Initial and final energies in NEB

[Stella, Martina]

Hi,

I am new to NEBs calculations and I am getting familiar with the method. I have 
a couple of questions, maybe trivial, but for which I don't have an answer yet. 
Hopefully someone can help.

1) How is the energy for the Initial and final structure estimated when I keep 
the two configurations frozen?
2)Should it be exactly the same as the final relaxed energies that I would get 
from completely separate calculations with the same simulation conditions and 
same geometries?
3) If they are not expected to be exactly the same which factors does the 
difference I may see depend on?

Thanks.



M. Stella

Post-Doctoral researcher

Physics Department, King's College London

Strand,London WC2R 2LS UK

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[QE-users] A problem of parallel excuting pwcond.x(SOC)

[Hamideh Kahnouji]

Dear all,
I tried to calculate conduction of  WS2 single layer without and with
spin-orbit coupling (SOC) by "pwcond".Calculation without SOC had been done
successfully by 32  cores.But for calculation with SOC I  used 16 and  32
cores I saw this error.
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 13838 RUNNING AT node588
=   EXIT CODE: 9
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES

I think I need more RAM ,Therefore,  I used  64 and 128 cores, the
code will stop at  line
" ngper, shell number =  804  82
ngper, n2d =  804 391
---  E-Ef =0.000  k =0.500   0.500
---  ie =  1  ik =  1"
and showed

"forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image  PCRoutineLine
Source

pwcond.x   025AD7C9  Unknown   Unknown  Unknown
pwcond.x   025AC140  Unknown   Unknown  Unknown
pwcond.x   0255DBC2  Unknown   Unknown  Unknown
pwcond.x   024F15F3  Unknown   Unknown  Unknown
pwcond.x   024F753B  Unknown   Unknown  Unknown
libpthread.so.0003F2280F710  Unknown   Unknown  Unknown
pwcond.x   004F9B35  scatter_forw_ 444
scatter_forw.
f90
pwcond.x   004ADD66  do_cond_  518
do_cond.f90
pwcond.x   004A8B42  MAIN__ 22  co

So could you tell me how can I  fix this error so that I can using
more cores to excute pwcond.x? I met this problem in both 6.2.1 and
6.3.

The input for PWSCF:
&control
calculation='scf'
restart_mode='from_scratch',
pseudo_dir = '/homes/hp0330/pseudo',
outdir='./TMP'
prefix='center'
tprnfor = .true.
verbosity='high'
/
&system
  ibrav = 8, celldm(1) =10.425257341,celldm(2)= 5.4437266180503983,
celldm(3)=6.927332448884853, nat=144, ntyp= 3,
ecutwfc = 50, ecutrho = 400.0
occupations='smearing',   smearing='methfessel-paxton', degauss=0.005
vdw_corr= 'Grimme-D2'
noncolin= .true.
   lspinorb=.true.


/
&electrons
diagonalization='david'
mixing_beta = 0.2
   electron_maxstep =1000
/
&ions
/
ATOMIC_SPECIES
W  183.84   W.rel-pbe-spn-rrkjus_psl.0.2.3.UPF
S  32.064  S.rel-pbe-n-rrkjus_psl.0.1.UPF
Zr  91.224  Zr.rel-pbe-spn-rrkjus_psl.0.2.3.UPF
ATOMIC_POSITIONS {crystal}
W0.973739000   0.5   0.0001740000   0   0
W0.973739000   0.5   0.0835080000   0   0
W0.973739000   0.5   0.1668410000   0   0
W0.973739000   0.5   0.2501740000   0   0
W0.973739000   0.5   0.3335080000   0   0
W0.973739000   0.5   0.4168410000   0   0
W0.973739000   0.5   0.5001740000   0   0
W0.973739000   0.5   0.5835070000   0   0
W0.973739000   0.5   0.6668410000   0   0
W0.973739000   0.5   0.7501740000   0   0
W0.973739000   0.5   0.8335070000   0   0
W0.973739000   0.5   0.9168410000   0   0
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S0.14149   0.447273000   0.2081410000   0   0
S0.14149   0.447273000   0.2914750000   0   0
S0.14149   0.447273000   0.3748080000   0   0
S0.14149   0.447273000   0.4581410000   0   0
S0.14149   0.447273000   0.5414750000   0   0
S0.14149   0.447273000   0.6248080000   0   0
S0.14149   0.447273000   0.7081410000   0   0
S0.14149   0.447273000   0.7914750000   0   0
S0.14149   0.447273000   0.8748080000   0   0
S0.14149   0.447273000   0.9581410000   0   0
S0.141662000   0.552021000   0.0420160000   0   0
S0.141662000   0.552021000   0.1253490000   0   0
S0.141662000   0.552021000   0.2086830000   0   0
S0.141662000   0.552021000   0.2920160000   0   0
S0.141662000   0.552021000   0.3753490000   0   0
S0.141662000   0.552021000   0.4586830000   0   0
S0.141662000   0.552021000   0.5420160000   0   0
S0.141662000   0.552021000   0.6253490000   0   0
S0.141662000   0.552021000   0.7086830000   0   0
S0.141662000   0.552021000   0.7920160000   0   0
S0.141662000   0.552021000   0.8753490000   0   0
S0.141662000   0.552021000   0.9586830000   0   0
W0.474891000   0.499624000   0.0415590000   0   0
W0.474891000   0.499624000   0.1248920000   0   0
W0.474891000   0.499624000   0.2082260000   0   0
W0.474891000   0.499624000   0.2915590000   0   0
W0.474891000   0.499624

[QE-users] Monte carlo simulations

[Amreen Bano]

Deal all,

I am interested in studying the magneto-caloric effect of some manganite
based systems. For this,  can someone guide me how we can perform monte
carlo calculations.
Any information will be helpful.

Regards,
Amreen.
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