[Pw_forum] "Lanczos.x with k-point algorithm"
Iurii Timrov
itimrov at sissa.it
Mon Jan 25 10:28:06 CET 2016
Dear Sajid Ali,
On 2016-01-23 01:53, Sajid Ali wrote:
> Dear,
> Iurii
> Thanks, i am providing hereby the input for turbo_davidson.x and
> turbo_spectrum.x
> For turbo_davidson.x
> &lr_input
> prefix = 'BN',
> outdir = './',
> /
> &lr_dav
> num_eign = 35,
> num_init = 70,
> num_basis_max = 200,
> start = 0.0d0
> finish = 3.5d0
> step = 0.001d0
> broadening = 0.005d0,
> p_nbnd_occ = 50
> p_nbnd_virt = 50
> /
The input for the turbo_davidson.x code seems OK. Actually, this code
produces two files, namely in your case they are BN.eigen (contains the
eigenvalues and corresponding intensities) and BN.plot (contains the
absorption spectrum computed from the eigenvalues). So, in order to plot
the spectrum you just need to use the BN.plot file, and you do not need
the post-processing program turbo_spectrum.x.
The turbo_spectrum.x can be useful in these cases:
- when one wants to obtain the absorption spectrum with a different
value of the Lorentzian smearing from the BN.eigen file (without
re-running the turbo_davidson.x program);
- when one performed several independent calculations with the
turbo_davidson.x code in different energy windows, and wants to compute
the resulting absorption spectrum (in this case those eigenvalues must
be manually collected in one file BN.eigen).
> For turbo_spectrum.x
> &lr_input
> prefix='BN',
> outdir='./',
> itermax=500
> itermax0=100
> end=3.50d0
> extrapolation='osc'
> increment=0.0001d0
> start=0.0d0
> td= 'davidson',
> eign_file = 'BN.eigen',
> /
>
In order to use the turbo_spectrum.x post-processing program after the
turbo_davidson.x program, the keywords 'itermax', 'itermax0', and
'extrapolation' are not needed (these keywords are meaningful only when
turbo_spectrum.x is used after turbo_lanczos.x).
You should provide a value for the Lorentzian smearing 'epsil' (which
has the same meaning as 'broadening' in the turbo_davidson.x program).
If you don't specify it, then the default value of 0.02 Ry will be used.
The parameter 'increment' has the same meaning as 'step' in the
turbo_davidson.x program.
The turbo_spectrum.x program actually uses only one core, so it is
meaningless to run it in parallel.
All in all, I don't see a reason why you obtain "NaN" in your
calculation. Could you report also the output of "BN.eigen" and the
output produced after the turbo_spectrum.x calculation?
> Cheers
>
> SAJID ALI
> Cell#+61449764974
> Ph.D. Scholar
> School of Mathematical and Physical Sciences
> University of Technology, Sydney
> Australia
>
>
P.S.: The subject of the discussions has deviated from the original one
"Lanczos.x with k-point algorithm". It is better to write a new question
to the pw_forum with the appropriate subject. This would help for other
users to perform search on the pw_forum in the future.
HTH
Best regards,
Iurii
--
Dr. Iurii TIMROV
Postdoctoral Researcher
SISSA - International School for Advanced Studies
Condensed Matter Sector
Via Bonomea n. 265,
Trieste 34151, Italy
> ________________________________________
> From: Iurii Timrov <itimrov at sissa.it>
> Sent: 22 January 2016 14:01
> To: Sajid Ali
> Cc: PWSCF Forum
> Subject: Re: [Pw_forum] "Lanczos.x with k-point algorithm"
>
> Dear Sajid Ali,
>
> Could you provide the input for the turbo_spectrum.x program? This
> post-processing program can be used both after turbo_lanczos.x and
> turbo_davidson.x.
>
> The input parameters for the turbo_spectrum.x program are described in
> TDDFPT/Doc/INPUT_Spectrum.txt. In particular, see the parameter "td"
> which can be either "lanczos" or "davidson". It seems that the error
> which you have below is due to the fact that you have td="davidson",
> but
> before you performed the Lanczos calculation (I presume). Please check.
>
> You may have a look in this paper: X. Ge et al., Comput. Phys. Commun.
> 185, 2080 (2014).
>
> HTH
>
> Best regards,
> Iurii
>
>
> Dr. Iurii TIMROV
> Postdoctoral Researcher
> SISSA - International School for Advanced Studies
> Condensed Matter Sector
> Via Bonomea n. 265, Trieste, Italy
>
>
>
> On 2016-01-22 06:19, Sajid Ali wrote:
>> Hi,
>> Iurii Timrov
>> I was able to get rid of the error i was getting while trying to
>> implement the k-point algorithm in Lanczos.x programme of TDDFPT(by
>> correctly linking the scalapack libraries during the compilation of
>> QE). Thanks
>> Now i have another problem the output of turbo_spectrum.x gives me a
>> *.plot file which looks like the one pasted below..Any ideas?
>> I am able to have polarizability tensor but not the spectrum....Any
>> help will be greatly appreciated.
>>
>> # Energy(Ry) total X Y Z
>> # Broadening is: 0.0050000 Ry
>> 0.00000000E+00 NaN NaN
>> NaN NaN
>> 0.10000000E-02 NaN NaN
>> NaN NaN
>> 0.20000000E-02 NaN NaN
>> NaN NaN
>> 0.30000000E-02 NaN NaN
>> NaN NaN
>> 0.40000000E-02 NaN NaN
>> NaN NaN
>> 0.50000000E-02 NaN NaN
>> NaN NaN
>> 0.60000000E-02 NaN NaN
>> NaN NaN
>> 0.70000000E-02 NaN NaN
>> NaN NaN
>> 0.80000000E-02 NaN NaN
>> NaN NaN
>> 0.90000000E-02 NaN NaN
>> NaN NaN
>> 0.10000000E-01 NaN NaN
>> NaN NaN
>> 0.11000000E-01 NaN NaN
>> NaN NaN
>> 0.12000000E-01 NaN NaN
>> NaN NaN
>> 0.13000000E-01 NaN NaN
>> NaN NaN
>> 0.14000000E-01 NaN NaN
>> NaN NaN
>> 0.15000000E-01 NaN NaN
>> NaN NaN
>> 0.16000000E-01 NaN NaN
>> NaN NaN
>> 0.17000000E-01 NaN NaN
>> NaN NaN
>> 0.18000000E-01 NaN NaN
>> NaN NaN
>> 0.19000000E-01 NaN NaN
>> NaN NaN
>> 0.20000000E-01 NaN NaN
>> NaN NaN
>> 0.21000000E-01 NaN NaN
>> NaN NaN
>> 0.22000000E-01 NaN NaN
>> NaN NaN
>> 0.23000000E-01 NaN NaN
>> NaN NaN
>>
>>
>>
>> SAJID ALI
>> Cell#+61449764974
>> Ph.D. Scholar
>> School of Mathematical and Physical Sciences
>> University of Technology, Sydney
>> Australia
>>
>>
>> ________________________________________
>> From: Sajid Ali
>> Sent: 18 January 2016 05:05
>> To: Iurii Timrov
>> Cc: PWSCF Forum
>> Subject: Re: [Pw_forum] "Lanczos.x with k-point algorithm"
>>
>> Dear,
>> Iurii Timrov
>> i am Sorry, It was a typo, i meant QE-5.3.0.
>>
>>
>> SAJID ALI
>> Cell#+61449764974
>> Ph.D. Scholar
>> School of Mathematical and Physical Sciences
>> University of Technology, Sydney
>> Australia
>>
>>
>> ________________________________________
>> From: Iurii Timrov <itimrov at sissa.it>
>> Sent: 17 January 2016 20:43
>> To: Sajid Ali
>> Cc: PWSCF Forum
>> Subject: Re: [Pw_forum] "Lanczos.x with k-point algorithm"
>>
>> Dear Sajid Ali,
>>
>> On 2016-01-17 00:40, Sajid Ali wrote:
>>> Dear,
>>> Iurii Timrov
>>> I have tried using QE-5.5.0 for both SCF and TDDFPT
>>
>> This version does not exist...
>>
>>> But i recieived
>>> similar kind of error in lanczos.x output
>>> i.e. "mpirun noticed that process rank 1 with PID 1046 on node
>>> ermdc06
>>> exited on signal 11 (Segmentation fault)".
>>> Cant find a way out of it....?
>>>
>>
>> Do you perform a calculation for CH4 without any modifications? In
>> your
>> test do you use gamma_only case or general k points algorithm?
>>
>> Do you run your calculation on a cluster using some script? How many
>> cores did you use? How did you install QE? Could you ask your system
>> administrator to help you? Try to run the code on a local workstation
>> and see if it crashes.
>>
>> Please provide more details (every step you do), because otherwise I
>> cannot help you.
>>
>>> SAJID ALI
>>> Cell#+61449764974
>>> Ph.D. Scholar
>>> School of Mathematical and Physical Sciences
>>> University of Technology, Sydney
>>> Australia
>>>
>>>
>>
>> Iurii Timrov
>> Postdoctoral Researcher
>> SISSA - International School for Advanced Studies
>> Condensed Matter Sector
>> Via Bonomea n. 265,
>> Trieste 34151, Italy
>>
>>
>>> ________________________________________
>>> From: Iurii Timrov <itimrov at sissa.it>
>>> Sent: 16 January 2016 14:01
>>> To: Sajid Ali
>>> Cc: PWSCF Forum
>>> Subject: Re: [Pw_forum] "Lanczos.x with k-point algorithm"
>>>
>>> Dear Sajid Ali,
>>>
>>> Why do you use now QE-5.2.1? Before you used QE-5.2.0. First of all,
>>> you
>>> should stick to one version, otherwise it is not possible to solve
>>> the
>>> problem. I suggest to use the latest official release, i.e. QE-5.3.0.
>>>
>>> On 2016-01-16 00:09, Sajid Ali wrote:
>>>> Dear,
>>>> Iurii Timrov
>>>> Thanks for your reply. I tried running default tests provided
>>>> with
>>>> the
>>>> TDDFPT code by command 'make', but did not succeed. I was returned
>>>> with the error message
>>>
>>> Try to run just one test:
>>>
>>> cd TDDFPT/Examples/CH4
>>> make
>>>
>>> Does this work for you?
>>>
>>>> "make[1]: Entering directory
>>>> `/panfs/panspermia/12108332/Programs/QE/espresso-5.2.1/TDDFPT/Examples/CH4'
>>>> Error reading bands from output file
>>>
>>> Do this:
>>>
>>> cd TDDFPT/Examples/CH4
>>> make clean
>>> make
>>>
>>> Does it work now?
>>>
>>>> Checking CH4.pw-out using CH4.pw-ref : make[1]: *** [small_test]
>>>> Error
>>>> 5
>>>> make[1]: Leaving directory
>>>> `/panfs/panspermia/12108332/Programs/QE/espresso-5.2.1/TDDFPT/Examples/CH4'
>>>> make[1]: Entering directory
>>>> `/panfs/panspermia/12108332/Programs/QE/espresso-5.2.1/TDDFPT/Examples/SiH4'
>>>> mpirun -np 48 "../../../bin/turbo_lanczos.x" < SiH4.tddfpt-st-in >
>>>> SiH4.tddfpt-st-out
>>>
>>> 48 cores are too many. Try to use just 1 or 2 cores for testing.
>>>
>>>> /bin/sh: mpirun: command not found
>>>> make[1]: *** [SiH4.tddfpt-st-out] Error 127
>>>> make[1]: Leaving directory
>>>> `/panfs/panspermia/12108332/Programs/QE/espresso-5.2.1/TDDFPT/Examples/SiH4'
>>>> make[1]: Entering directory
>>>> `/panfs/panspermia/12108332/Programs/QE/espresso-5.2.1/TDDFPT/Examples/Benzene'
>>>> Checking Benzene.pw-out using Benzene.pw-ref : [OK]
>>>> Checking Benzene.tddfpt-st-out using Benzene.tddfpt-st-ref : [NOT
>>>> OK]
>>>> Different number of norms in files
>>>> make[1]: *** [small_test] Error 5
>>>> make[1]: Leaving directory
>>>> `/panfs/panspermia/12108332/Programs/QE/espresso-5.2.1/TDDFPT/Examples/Benzene'
>>>> make: *** [small_test] Error 2
>>>> -bash-4.1$ Different number of norms in files
>>>> -bash: Different: command not found
>>>> -bash-4.1$ make[1]: *** [small_test] Error 5
>>>> -bash: make[1]:: command not found"
>>>>
>>>> As you suggested me to provide the input files for PWscf and TDDFPT
>>>> for my own calculations. so i am pasting them here respectively, I
>>>> will be thankful for any help you can provide to me as it is really
>>>> important for me....
>>>> For SCF input file is
>>>> "&CONTROL
>>>> calculation = 'scf'
>>>> prefix='BN'
>>>> pseudo_dir = './'
>>>> outdir='./'
>>>> tstress=.true.
>>>> tprnfor = .true.
>>>> forc_conv_thr=1.0d-4
>>>> nstep=200
>>>> /
>>>
>>> For 'scf' you don't need 'forc_conv_thr' and 'nstep'.
>>>
>>>> &SYSTEM
>>>> ibrav=0
>>>> celldm(1)=1.889726
>>>> nat=2
>>>> ntyp=2
>>>> ecutwfc=50.0
>>>> nosym = .true.,
>>>> nosym_evc= .true.,
>>>> /
>>>
>>> Are you sure that you need to set 'nosym = .true.' and 'nosym_evc=
>>> .true.'? For HGH norm-conserving pseudopotentials the cutoff of 50 Ry
>>> is
>>> probably too low (others probably can comment more on this issue).
>>> Check
>>> the convergence wrt ecutwfc.
>>>
>>>> &ELECTRONS
>>>> mixing_beta=0.7
>>>> conv_thr = 1.0d-8
>>>> electron_maxstep=200
>>>> /
>>>
>>> The default value for 'electron_maxstep' should be fine.
>>>
>>>> &IONS
>>>> trust_radius_max=0.2
>>>> /
>>>> &CELL
>>>> cell_dynamics='bfgs'
>>>> /
>>>
>>> The cards "ions" and "cell" are not needed for the SCF calculation.
>>>
>>>> ATOMIC_SPECIES
>>>> N 14.0067 N.pbe-hgh.UPF
>>>> B 10.8110 B.pbe-hgh.UPF
>>>>
>>>> CELL_PARAMETERS (alat= 1.88972600)
>>>> 2.509073557 -0.002024330 0.000000000
>>>> 1.252797201 2.173934109 0.000000000
>>>> -0.000000000 -0.000000000 29.979498417
>>>>
>>>> ATOMIC_POSITIONS (crystal)
>>>> B -0.000266196 -0.000266358 -0.000000000
>>>> N 0.333599496 0.333599658 0.000000000
>>>>
>>>> K_POINTS {automatic}
>>>> 4 4 1 0 0 0 "
>>>> For Lanczos the input file is
>>>> "&lr_input
>>>> prefix = 'BN',
>>>> outdir = './',
>>>> restart=.false.,
>>>> restart_step=500
>>>> /
>>>> &lr_control
>>>> itermax = 500,
>>>> ipol = 1,
>>>> /
>>>> [ &lr_post
>>>> epsil = 0.0004d0
>>>> ]
>>>> /"
>>>>
>>>
>>> The input for the turbo_lanczos.x code seems to be fine.
>>>
>>>> SAJID ALI
>>>> Cell#+61449764974
>>>> Ph.D. Scholar
>>>> School of Mathematical and Physical Sciences
>>>> University of Technology, Sydney
>>>> Australia
>>>>
>>>
>>> HTH
>>>
>>> Iurii Timrov
>>> Postdoctoral Researcher
>>> SISSA - International School for Advanced Studies
>>> Condensed Matter Sector
>>> Via Bonomea n. 265,
>>> Trieste, Italy
>>>
>>>
>>>>
>>>> ________________________________________
>>>> From: Iurii Timrov <itimrov at sissa.it>
>>>> Sent: 15 January 2016 17:10
>>>> To: PWSCF Forum
>>>> Cc: Sajid Ali
>>>> Subject: Re: [Pw_forum] "Lanczos.x with k-point algorithm"
>>>>
>>>> Dear Sajid Ali,
>>>>
>>>> I made a test using QE-5.3.0 (the latest release) and QE-5.2.0 (the
>>>> one
>>>> which you use apparently) for the example TDDFPT/Examples/CH4 using
>>>> the
>>>> general k-points implementation of TDDFPT. My calculations didn't
>>>> crash
>>>> (neither in serial nor in parallel). Could you repeat these tests
>>>> too?
>>>>
>>>> In order to understand what is the problem with your calculations,
>>>> you
>>>> should provide here the input data for PWscf and TDDFPT. Otherwise
>>>> we
>>>> cannot help you. But before that try the default tests provided with
>>>> the
>>>> TDDFPT code, which I mentioned above.
>>>>
>>>> Please note, even if you solve your problem, remember that the
>>>> general
>>>> k-points implementation of TDDFPT was not benchmarked, and hence it
>>>> can
>>>> give completely wrong results. This is why it is disabled in the
>>>> code.
>>>>
>>>> HTH
>>>>
>>>> Iurii Timrov
>>>>
>>>>
>>>> On 2016-01-15 00:52, Sajid Ali wrote:
>>>>> Dear,
>>>>>
>>>>> All,
>>>>>
>>>>> i am trying to do some TDDFPT calculations with K-point algorithm.
>>>>> I
>>>>> did comment the line ''IF ( .NOT. gamma_only ) && CALL errore('
>>>>> iosys', 'k-point algorithm is not tested yet',1)" in
>>>>> espresso/TDDFPT/src/lr_readin.f90 as was suggested by "Iurii
>>>>> Timrov".
>>>>> K point algorithm is implemented. But still i am returned the
>>>>> following error message in Lanczos.x output.[i am pasting the
>>>>> entire
>>>>> output file]..Can somebody help me out of this? It will be greatly
>>>>> appreciated.
>>>>>
>>>>> Program turboTDDFT v.5.2.0 starts on 15Jan2016 at 10:32:10
>>>>> This program is part of the open-source Quantum ESPRESSO suite
>>>>> for quantum simulation of materials; please cite
>>>>> "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
>>>>> URL http://www.quantum-espresso.org",
>>>>> in publications or presentations arising from this work. More
>>>>> details
>>>>> at
>>>>> http://www.quantum-espresso.org/quote
>>>>>
>>>>> Parallel version (MPI), running on 24 processors
>>>>> R & G space division: proc/nbgrp/npool/nimage = 24
>>>>> Reading data from directory:
>>>>> ./BN.save
>>>>> Info: using nr1, nr2, nr3 values from input
>>>>> Info: using nr1, nr2, nr3 values from input
>>>>> IMPORTANT: XC functional enforced from input :
>>>>> Exchange-correlation = SLA-PW-PBX-PBC ( 1 4 3 4 0 0)
>>>>> Any further DFT definition will be discarded
>>>>> Please, verify this is what you really want
>>>>> Parallelization info
>>>>> --------------------
>>>>> sticks: dense smooth PW G-vecs: dense smooth PW
>>>>> Min 13 13 3 2189 2189 339
>>>>> Max 14 14 4 2219 2219 394
>>>>> Sum 313 313 91 52939 52939 8919
>>>>> Subspace diagonalization in iterative solution of the eigenvalue
>>>>> problem:
>>>>> a serial algorithm will be used
>>>>> Normal read
>>>>> WARNING: Generalised k-points algorithm
>>>>> LANCZOS LINEAR-RESPONSE SPECTRUM CALCULATION
>>>>> Number of Lanczos iterations = 1500
>>>>> Starting Lanczos loop 2
>>>>> Lanczos iteration: 1 Pol:1
>>>>> lr_apply_liouvillian: not applying interaction
>>>>> alpha(00000001)= 0.000000
>>>>> beta (00000001)= 2.374383
>>>>> gamma(00000001)= 2.374383
>>>>> z1= 1 0.000000000000000E+00 0.000000000000000E+00
>>>>> Lanczos iteration: 2 Pol:1
>>>>> --------------------------------------------------------------------------
>>>>>
>>>>> mpirun noticed that process rank 20 with PID 62359 on node c3node01
>>>>> exited on signal 11 (Segmentation fault).
>>>>> --------------------------------------------------------------------------
>>>>>
>>>>>
>>>>> SAJID ALI
>>>>>
>>>>> Cell#+61449764974
>>>>>
>>>>> Ph.D. Scholar
>>>>>
>>>>> School of Mathematical and Physical Sciences
>>>>>
>>>>> University of Technology, Sydney
>>>>>
>>>>> Australia
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Pw_forum mailing list
>>>>> Pw_forum at pwscf.org
>>>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>>
>>>> --
>>>> Dr. Iurii TIMROV
>>>> Postdoctoral Researcher
>>>> SISSA - International School for Advanced Studies
>>>> Condensed Matter Sector
>>>> Via Bonomea n. 265,
>>>> Trieste 34151, Italy
>
> --
> Dr. Iurii TIMROV
> Postdoctoral Researcher
> SISSA - International School for Advanced Studies
> Condensed Matter Sector
> Via Bonomea n. 265,
> Trieste 34151, Italy
> (+39) 04 03 78 74 77
> http://people.sissa.it/~itimrov/
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