[CP2K:4043] Re: MC-QS-NPT calculations
Matt McGrath
obfis... at gmail.com
Sat Sep 22 01:33:06 UTC 2012
Hello Riping.
1. There is no evolution of the angles. The NpT moves in CP2K-MC only
sample the boxlengths, so the cell has to be cubic (though rectangular
might work too). Therefore, all the angles are constant at 90 degrees.
2. There pressure and temperature are not calculated from the simulation.
Since MC has no kinetic energy, the temperature cannot be calculated. The
pressure can be calculated, but it's an expensive calculation so it's not
done. The code has been validated against an independent code not written
by me and by literature comparisons, so you can have some faith in the
results (though of course you can also run your own tests).
3. Yes, this is a bit difficult to understand. I will try to find a
tutorial that I wrote for a CP2K workshop last year and send that to you.
That should help you with some of your questions.
4. This is a difficult question to answer. I suggest you look at some of
my previous articles on using CP2K with water, methane, and methanol, and
see what parameters I address specifically in those papers. That's
probably the best starting place. You can, for example, ignore anything
with AVBMC, so long as PMAVBMC is set to 0.0 (then no AVBMC moves will be
attempted, so the values of those parameters are not used).
Cheers, Matt
On Thursday, September 20, 2012 1:27:18 AM UTC-5, Northstar wrote:
>
> Hi, Matt,
>
> Thank you very much for reply.
> Following your instruction, I finally make the MC_QS_NPT runing without
> error reported.
>
> I paste the box1 of input file in Appendix.
>
> But there are some questions:
> 1. I find the evolution of cell length in mc_cell_length. However, I can
> not find alpha_beta_gamma evolution, even in output file. Where are they?
> 2. I set the pressure and temperature in input file. But I can not find
> evolution pressure and temperature anywhere. Where are they?
> 3. There are so many parameter in MC section to set. I use all the
> parameters from the example file cp2k/tests/MC/canonical.inp, except that I
> changed
> PMVOLUME from 0 to be 1. The on-line input reference is so concise
> that I can not well understand the physical meaning of many parameters.
> So, Is there any better reference material about how to use MC in
> cp2k.
> 4. For NPT ensemble wit MC, which parameters need more careful attention?
>
> Thank you very much.
> WANG Riping
> 2012.9.20
>
> Appendix:
> '''
> #CPQA INCLUDE MC_QS_molec_box1.inp
> #CPQA DEPENDS MC_QS_molec_box2.inp
> # this dependency rule is fake: the reason is that MC is the only
> module as of Today that writes
> # hard-coded output files, which are then read in the subsequent
> steps. Once modernized, these
> # dependencies for CPQA can be deleted.
>
>
> &GLOBAL
> PROJECT H2OAr
> RUN_TYPE MC
> PRINT_LEVEL HIGH
> &END GLOBAL
>
>
> &FORCE_EVAL
> METHOD Quickstep
> &DFT
> BASIS_SET_FILE_NAME ../../QS/BASIS_SET
> POTENTIAL_FILE_NAME ../../QS/POTENTIAL
> &MGRID
> CUTOFF 100
> &END MGRID
> &QS
> EXTRAPOLATION USE_PREV_WF
> &END QS
> &SCF
> SCF_GUESS ATOMIC
> &END SCF
> &XC
> &XC_FUNCTIONAL Pade
> &END XC_FUNCTIONAL
> &XC_GRID
> XC_DERIV SPLINE2
> XC_SMOOTH_RHO NONE
> &END XC_GRID
> &END XC
> &END DFT
>
> &SUBSYS
> &CELL
> ABC 13.5 13.5 13.5
> ALPHA_BETA_GAMMA 90 90 90
> &END CELL
> &COORD
> O 11.667599837210 7.964352234664 0.059453614019
> H 10.873359634781 8.005423314626 0.665667823055
> H 11.364979095795 7.770411108906 -0.873716837951
> O 2.314161441602 5.011228167767 2.784706973673
> H 1.663128370368 5.686998340596 3.130381117447
> H 2.659721328394 5.306531429441 1.893985965664
> O 10.262864742466 5.548805003571 11.360725453725
> H 10.424041748648 4.666485986338 11.802918991113
> H 9.436479204754 5.494708086386 10.800225647804
> O 5.937092785694 12.752770338234 7.554822749656
> H 6.459679552548 12.731874699056 8.407152758147
> H 6.560379344025 12.890048310674 6.784973290144
> O 1.052476316752 3.192494253568 0.284763135867
> H 1.009686510209 3.892635795528 0.997483876183
> H 1.385134340137 3.601676794269 -0.564888471374
> O 11.621014134223 7.899470257763 6.835708666826
> H 10.723243819476 8.290315257093 7.038806299646
> H 12.107936378358 8.496446358905 6.198114886544
> O 3.255054397643 5.532098285916 13.500752220167
> H 3.169785700155 4.860242146843 12.764995074351
> H 3.889107504717 6.253294143532 13.221731148935
> Ar 1.43 3.54 6.24
> Ar 4.43 10.54 9.24
> Ar 11.43 3.54 6.24
> Ar 11.43 3.54 2.24
> Ar 2.43 5.54 6.24
> Ar 10.43 5.54 5.24
> &END COORD
>
> &KIND H
> BASIS_SET DZVP-GTH-Pade
> POTENTIAL GTH-BLYP-q1
> &END KIND
> &KIND O
> BASIS_SET DZVP-GTH-Pade
> POTENTIAL GTH-BLYP-q6
> &END KIND
> &KIND Ar
> BASIS_SET DZVP-GTH-PADE
> POTENTIAL GTH-BLYP-q8
> &END KIND
> &TOPOLOGY
> CONNECTIVITY MOL_SET
> &MOL_SET
> &MOLECULE
> NMOL 7
> CONN_FILE_NAME topology_fist_WAT.psf
> &END
> &MOLECULE
> NMOL 6
> CONN_FILE_NAME topology_fist_ARG.psf
> &END
> &END
> &END
> &END SUBSYS
> &END FORCE_EVAL
>
>
> &MOTION
> &MC
> ! IUPTRANS 100
> ! IUPVOLUME 100
> ! LBIAS no
> ! LSTOP no
> ! NMOVES 1
> NSTEP 100
> ! PMSWAP 0.0
> PMSWAP_MOL 0.5 1.0
> PMTRAION 0.33
> PMTRAION_MOL 1.0 1.0
> PMTRANS 0.67
> PMTRANS_MOL 0.5 1.0
> PMROT_MOL 1.0 1.0
> ! PMVOLUME 0.0
> PMVOLUME 1.0
> ! PMVOL_BOX 1.0
> PMHMC 0.0
> PMHMC_BOX 1.0
> PRESSURE 1.013
> ENSEMBLE GEMC_NPT
> RESTART no
> BOX2_FILE_NAME MC_QS_box2.inp
> RESTART_FILE_NAME mc_restart_1
> RMDIHEDRAL 3.0 1.0
> RMANGLE 10.0 5.0
> RMBOND 0.074 0.07
> RMROT 26.0 16.0
> RMTRANS 0.58 0.55
> RMVOLUME 500.0
> TEMPERATURE 298.0
> IPRINT 1
> AVBMC_ATOM 1 1
> PMAVBMC 0.0
> PMAVBMC_MOL 0.5 1.0
> AVBMC_RMIN 1.0 1.0
> AVBMC_RMAX 5.0 5.0
> PBIAS 0.5 0.5
> ETA 0.0 0.0
> VIRIAL_TEMPS 300.0
> &END MC
> &END MOTION
> '''
>
>
>
>
>
> On 19 September 2012 07:50, Matt McGrath <obfi... at gmail.com <javascript:>
> > wrote:
>
>> Hello Riping. This error is due to the Gibbs phase rule, which says
>> F=C-P+2, where F is the total number of degrees of freedom in the system, C
>> is the number of components, and P is the number of phases. In a system of
>> pure water with a liquid and vapor phase, C=1 and P=2, so F=1. That is,
>> you can only have a single degree of freedom where both phases coexist.
>> This is generally the temperature, so for a single component system with
>> two phases, you have to use the NVT Gibbs ensemble. If you want to use NpT
>> (which has two degrees of freedom, the temperature and the pressure), and
>> you have two phases (two simulation boxes), you have to have at least two
>> components in your system.
>>
>> Cheers, Matt
>>
>>
>> On Tuesday, September 18, 2012 8:29:47 PM UTC-5, Northstar wrote:
>>>
>>> Dear matt,
>>>
>>> I concern on change A defined above.
>>> I follow your instruction to make the second box.
>>> box1 and box2 have BOX2_FILE_NAME linked to each other.
>>>
>>> It comes the following error.
>>> '''
>>> ************************************************************
>>> *** ERROR in mc_input_parameters_check (MODULE mc_types) ***
>>> ************************************************************
>>>
>>> *** Cannot have GEMC-NPT simulation with only one molecule type ***
>>>
>>> *** Program stopped at line number 2068 of MODULE mc_types ***
>>>
>>> ===== Routine Calling Stack =====
>>>
>>> 1 CP2K
>>> CP2K| Abnormal program termination, stopped by process number 0
>>> '''
>>>
>>>
>>> And then I adjust
>>> AVBMC_ATOM 1 to be
>>> AVBMC_ATOM 3
>>> in both input files.
>>> The following error comes.
>>> '''
>>> ************************************************************
>>> *** ERROR in mc_input_parameters_check (MODULE mc_types) ***
>>> ************************************************************
>>>
>>> *** Cannot have GEMC-NPT simulation with only one molecule type ***
>>>
>>> *** Program stopped at line number 2068 of MODULE mc_types ***
>>>
>>> ===== Routine Calling Stack =====
>>>
>>> 1 CP2K
>>> CP2K| Abnormal program termination, stopped by process number 0
>>> '''
>>>
>>> Is it any help for me?
>>> Thank you very much.
>>>
>>> WANG Riping
>>> 2012.9.19
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> --
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>
>
>
> --
>
> ******************************************************************************
> WANG Riping
> Ph.D student,
> Institute for Study of the Earth's Interior,Okayama University,
> 827 Yamada, Misasa, Tottori-ken 682-0193, Japan
> Tel: +81-858-43-3739(Office), +81-858-43-1215(Inst)
> E-mail: wang.... at gmail.com <javascript:>
>
> ******************************************************************************
>
>
>
>
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