[Pw_forum] "Lanczos.x with k-point algorithm"
Iurii Timrov
itimrov at sissa.it
Fri Jan 22 10:01:53 CET 2016
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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