[CP2K:4024] Energy conservation NVT/NVE simulation
alber... at virgilio.it
alber... at virgilio.it
Mon Sep 17 09:52:58 UTC 2012
Hi,
I have solved my problems either by using PBE functional or using BLYP with
the smoothing parameters suggested by Garold.
BLYP seeems indeed numerically quite difficult and delicate while PBE is
better from this point of view.
Concerning the other parameters, in particular in &QS section, I used those
suggested above by Juerg.
Thank you all for your suggestions,
Alberto
Il giorno mercoledì 12 settembre 2012 12:38:09 UTC+2, garold ha scritto:
>
> Hi Alberto,
>
> May I suggest use of smoothing, i.e., including a section:
>
> &XC_GRID
> XC_SMOOTH_RHO NN10 ! (or NN50)
> XC_DERIV SPLINE2_SMOOTH
> &END XC_GRID
>
> You can also see the previous discussion on this forum:
>
> https://groups.google.com/forum/?hl=it&fromgroups=#!topic/cp2k/dc4kzNqNw-8
>
> where a similar discussion occurred.
>
> Best,
> Garold
>
>
>
> On Tuesday, September 11, 2012 12:35:42 PM UTC+3, alber... at virgilio.itwrote:
>>
>> Hi,
>>
>> for the restart I used the last restart file of the previous run,
>> modifying the parameters in $QS or $SCF to test the new ones.
>> I observed a drift also for NVE even if most of the tests have been done
>> for NVT.
>> I will carry out more tests for NVE to reduce the number of variables and
>> avoid also the problem of thermostat setting.
>>
>> About the drift, after few ps it is about 10^-3 au, depending on the
>> simulations.
>> Changing the parameters to increase the accuracy, in some cases I
>> observed no drift but sudden jumps in the total energy.
>>
>> I will keep you updated about further NVE tests.
>> Thanks
>>
>> alberto
>>
>> Il giorno martedì 11 settembre 2012 11:04:00 UTC+2, jgh ha scritto:
>>>
>>> Hi
>>>
>>> it is difficult to give good advice without more information.
>>>
>>> Possible problems might be:
>>>
>>> - Restarts: do you correctly restart all variables
>>> - Thermostat: I don't know if the setting you have is reasonable
>>> and adequate for this timestep.
>>> Do you see a drift also for NVE?
>>> - How big is the drift and how long is your trajectory?
>>>
>>> regards
>>>
>>> Juerg
>>>
>>> --------------------------------------------------------------
>>> Juerg Hutter Phone : ++41 44 635 4491
>>> Physical Chemistry Institute FAX : ++41 44 635 6838
>>> University of Zurich E-mail: hut... at pci.uzh.ch
>>> Winterthurerstrasse 190
>>> CH-8057 Zurich, Switzerland
>>> ---------------------------------------------------------------
>>>
>>> -----cp... at googlegroups.com wrote: -----
>>> To: cp... at googlegroups.com
>>> From: "albe... at virgilio.it"
>>> Sent by: cp... at googlegroups.com
>>> Date: 09/11/2012 10:06AM
>>> Subject: Re: [CP2K:4024] Energy conservation NVT/NVE simulation
>>>
>>> Dear Juerg,
>>>
>>> thank you very much.
>>>
>>> I changed the functional to BLYP and I used ASPC interpolator.
>>> I carried out different tests where I tried different values of the
>>> EXTRAPOLATION_ORDER (up to 6), I increased the EPS_SCF and used defaults
>>> for most of the other parameters.
>>> Unfortunately, I still observe either drifts or jumps in the total
>>> energy.
>>>
>>> I think that there is still a problem in the input, reported below.
>>>
>>> Many thanks for your help.
>>>
>>> Alberto
>>>
>>> ************
>>>
>>> &FORCE_EVAL
>>> METHOD QS
>>> &DFT
>>> BASIS_SET_FILE_NAME GTH_BASIS_SETS
>>> POTENTIAL_FILE_NAME GTH_POTENTIALS
>>> &MGRID
>>> CUTOFF 300
>>> REL_CUTOFF 40
>>> &END MGRID
>>> &QS
>>> EPS_DEFAULT 1.0E-12
>>> WF_INTERPOLATION ASPC
>>> EXTRAPOLATION_ORDER 3
>>> &END QS
>>> &SCF
>>> SCF_GUESS ATOMIC
>>> EPS_SCF 1.0E-6
>>> &OT T
>>> &END OT
>>> &PRINT
>>> &RESTART OFF
>>> &END
>>> &END
>>> &END SCF
>>> &XC
>>> &XC_FUNCTIONAL BLYP
>>> &END XC_FUNCTIONAL
>>> &END XC
>>> &PRINT
>>> &MOMENTS MEDIUM
>>> &END
>>> &END PRINT
>>> &END DFT
>>> &SUBSYS
>>> &CELL
>>> ABC 9.8528 9.8528 9.8528
>>> &END CELL
>>> # 32 H2O (TIP5P,1bar,300K) a = 9.8528
>>> &COORD
>>> O 2.280398 9.146539 5.088696
>>> O 1.251703 2.406261 7.769908
>>> O 1.596302 6.920128 0.656695
>>> O 2.957518 3.771868 1.877387
>>> O 0.228972 5.884026 6.532308
>>> O 9.023431 6.119654 0.092451
>>> O 7.256289 8.493641 5.772041
>>> O 5.090422 9.467016 0.743177
>>> O 6.330888 7.363471 3.747750
>>> O 7.763819 8.349367 9.279457
>>> O 8.280798 3.837153 5.799282
>>> O 8.878250 2.025797 1.664102
>>> O 9.160372 0.285100 6.871004
>>> O 4.962043 4.134437 0.173376
>>> O 2.802896 8.690383 2.435952
>>> O 9.123223 3.549232 8.876721
>>> O 1.453702 1.402538 2.358278
>>> O 6.536550 1.146790 7.609732
>>> O 2.766709 0.881503 9.544263
>>> O 0.856426 2.075964 5.010625
>>> O 6.386036 1.918950 0.242690
>>> O 2.733023 4.452756 5.850203
>>> O 4.600039 9.254314 6.575944
>>> O 3.665373 6.210561 3.158420
>>> O 3.371648 6.925594 7.476036
>>> O 5.287920 3.270653 6.155080
>>> O 5.225237 6.959594 9.582991
>>> O 0.846293 5.595877 3.820630
>>> O 9.785620 8.164617 3.657879
>>> O 8.509982 4.430362 2.679946
>>> O 1.337625 8.580920 8.272484
>>> O 8.054437 9.221335 1.991376
>>> H 1.762019 9.820429 5.528454
>>> H 3.095987 9.107088 5.588186
>>> H 0.554129 2.982634 8.082024
>>> H 1.771257 2.954779 7.182181
>>> H 2.112148 6.126321 0.798136
>>> H 1.776389 7.463264 1.424030
>>> H 3.754249 3.824017 1.349436
>>> H 3.010580 4.524142 2.466878
>>> H 0.939475 5.243834 6.571945
>>> H 0.515723 6.520548 5.877445
>>> H 9.852960 6.490366 0.393593
>>> H 8.556008 6.860063 -0.294256
>>> H 7.886607 7.941321 6.234506
>>> H 7.793855 9.141028 5.315813
>>> H 4.467366 9.971162 0.219851
>>> H 5.758685 10.102795 0.998994
>>> H 6.652693 7.917443 3.036562
>>> H 6.711966 7.743594 4.539279
>>> H 7.751955 8.745180 10.150905
>>> H 7.829208 9.092212 8.679343
>>> H 8.312540 3.218330 6.528858
>>> H 8.508855 4.680699 6.189990
>>> H 9.742249 1.704975 1.922581
>>> H 8.799060 2.876412 2.095861
>>> H 9.505360 1.161677 6.701213
>>> H 9.920117 -0.219794 7.161006
>>> H 4.749903 4.186003 -0.758595
>>> H 5.248010 5.018415 0.403676
>>> H 3.576065 9.078451 2.026264
>>> H 2.720238 9.146974 3.273164
>>> H 9.085561 4.493058 9.031660
>>> H 9.215391 3.166305 9.749133
>>> H 1.999705 2.060411 1.927796
>>> H 1.824184 0.564565 2.081195
>>> H 7.430334 0.849764 7.438978
>>> H 6.576029 1.537017 8.482885
>>> H 2.415851 1.576460 8.987338
>>> H 2.276957 0.099537 9.289499
>>> H 1.160987 1.818023 4.140602
>>> H 0.350256 2.874437 4.860741
>>> H 5.768804 2.638450 0.375264
>>> H 7.221823 2.257514 0.563730
>>> H 3.260797 5.243390 5.962382
>>> H 3.347848 3.732214 5.988196
>>> H 5.328688 9.073059 5.982269
>>> H 5.007063 9.672150 7.334875
>>> H 4.566850 6.413356 3.408312
>>> H 3.273115 7.061666 2.963521
>>> H 3.878372 7.435003 6.843607
>>> H 3.884673 6.966316 8.283117
>>> H 5.918240 3.116802 5.451335
>>> H 5.355924 2.495093 6.711958
>>> H 5.071858 7.687254 10.185667
>>> H 6.106394 7.112302 9.241707
>>> H 1.637363 5.184910 4.169264
>>> H 0.427645 4.908936 3.301903
>>> H 9.971698 7.227076 3.709104
>>> H 10.647901 8.579244 3.629806
>>> H 8.046808 5.126383 2.213838
>>> H 7.995317 4.290074 3.474723
>>> H 1.872601 7.864672 7.930401
>>> H 0.837635 8.186808 8.987268
>>> H 8.314696 10.115534 2.212519
>>> H 8.687134 8.667252 2.448452
>>> &END COORD
>>> &KIND H
>>> BASIS_SET TZV2P-GTH
>>> POTENTIAL GTH-BLYP-q1
>>> &END KIND
>>> &KIND O
>>> BASIS_SET TZV2P-GTH
>>> POTENTIAL GTH-BLYP-q6
>>> &END KIND
>>> &END SUBSYS
>>> &END FORCE_EVAL
>>> &GLOBAL
>>> PROJECT H2O-32
>>> RUN_TYPE MD
>>> PRINT_LEVEL MEDIUM
>>> &TIMINGS
>>> THRESHOLD 0.000001
>>> &END
>>> &END GLOBAL
>>> &MOTION
>>> &MD
>>> ENSEMBLE NVT
>>> STEPS 30000
>>> TIMESTEP 0.5
>>> TEMPERATURE 300.0
>>> &THERMOSTAT
>>> TYPE CSVR
>>> &CSVR
>>> TIMECON 100.0
>>> &END CSVR
>>> &END THERMOSTAT
>>> &END MD
>>> &PRINT
>>> &VELOCITIES LOW
>>> &END
>>> &END PRINT
>>> &END MOTION
>>>
>>> **************
>>>
>>>
>>> Il giorno mercoledì 5 settembre 2012 09:56:16 UTC+2, jgh ha scritto:Hi
>>>
>>> the main problem is
>>>
>>> &QS
>>> EPS_DEFAULT 1.0E-12
>>> WF_INTERPOLATION PS
>>> EXTRAPOLATION_ORDER 3
>>> &END QS
>>>
>>> change to WF_INTERPOLATION ASPC (the default) and maybe
>>> increase the EXTRAPOLATION_ORDER slightly.
>>> See
>>> J. Hutter, Car-Parrinello molecular dynamics
>>> Wiley Interdisciplinary Reviews: Computational Molecular Science 2 (4) ,
>>> pp. 604-612
>>> for an explanation.
>>>
>>> You should also change to a more reasonable DFT functional.
>>> LDA (PADE) will lead to an extremly overstructured system.
>>> See
>>> J. Schmidt et al.,
>>> Isobaric-isothermal molecular dynamics simulations utilizing density
>>> functional theory: An assessment of the structure and density of water at
>>> near-ambient conditions
>>> Journal of Physical Chemistry B Volume 113, Issue 35, 3 September 2009,
>>> Pages 11959-11964
>>>
>>> regards
>>>
>>> Juerg
>>>
>>> --------------------------------------------------------------
>>> Juerg Hutter Phone : ++41 44 635 4491
>>> Physical Chemistry Institute FAX : ++41 44 635 6838
>>> University of Zurich E-mail: hut... at pci.uzh.ch
>>> Winterthurerstrasse 190
>>> CH-8057 Zurich, Switzerland
>>> ---------------------------------------------------------------
>>>
>>> -----cp... at googlegroups.com wrote: -----
>>> To: cp... at googlegroups.com
>>> From: "albe... at virgilio.it"
>>> Sent by: cp... at googlegroups.com
>>> Date: 09/05/2012 09:44AM
>>> Subject: [CP2K:4010] Energy conservation NVT/NVE simulation
>>>
>>> Dear all,
>>>
>>> I'm carrying out some tests to reproduce the VDOS of water and I used as
>>> starting points the input files 'H2O-32.inp' and 'H2O-64.inp' in
>>> tests/QS/benchmark directory.
>>>
>>> In both cases I ran a NVT simulation at 300K for 15 ps followed by an
>>> NVE
>>> simulation on the equilibrated system.
>>>
>>> I'm puzzled about the results in the energies: in both NVT and NVE the
>>> plot of
>>> "Cons Qty" show a constant and linear drift while temperature, kinetic
>>> and
>>> potential energy are equilibrated and stable.
>>>
>>> Since "Cons Qty" should be conserved and this is not the case I think
>>> that
>>> there are some problems in the setup of the simulation.
>>> I did not modify the parameters of the benchmark inputs but I just added
>>> the
>>> thermostat section in NVT and I modified only the printing option.
>>>
>>> Thank you very much for your help and suggestions,
>>>
>>> Alberto
>>>
>>>
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>>
>>
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