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Re: [lammps-users] Region instead of group


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Tue, 8 May 2018 01:37:06 -0400

On Sun, May 6, 2018 at 11:45 AM, Zohreh Ahadi <zohreh.ahadi@...24...> wrote:
> Dear Dr axel
>
> Thanks for your attention.
> Yes, the thermal conductivity of our nanotube (MoS2) according our result in
> this article  https://aip.scitation.org/doi/10.1063/1.5001383 is very much
> lower than carbon nanotubes.
> I thought my details are annoyed you, as you said  "my description is too
> vague to give specific advice"

while your initial post was too vague, this input is too complex to
debug it and give advice on it.
could you try to build a much simpler system (less atoms, shorter
trajectory, less regions/groups), so it is easier to study faster what
is going on (even if it would not be physically very meaningful)?

also can you give a description with more details of what you want to
achieve and what you want to learn from the simulation.
please also clarify, if it is your intention to simulate a rigid or a
flexible water potential.

axel.

> I should mention them:
>
> # Created by charmm2lammps v1.8.3 on
> echo            both
> boundary        p p p
> units           metal
>
> atom_style      full
> bond_style      harmonic
> angle_style     harmonic
> neigh_modify    delay 2 every 1
>
> read_data      water_2_1550.data
> #read_restart    eq.restart.300000
>
> group           water type 1 2
> group           oxy   type 2
> group           nanotube type 3 4
>
>
> neighbor        2.0 bin
> #neigh_modify    every 2 one 10000 page 200000 #include all  binsize 2.0
> #delay 10 check yes exclude all
>
> #fix 1 nanotube rigid molecule
> #==================================================================================================
> #0.00058595          epsilon_MM
> #0.01386             epsilon_SS
> #4.200               sigma_MM
> #3.130               sigma_SS
>
> pair_style     hybrid rebomos  lj/cut/tip4p/long 2 1 1 1 0.1546  8.5
> pair_coeff     *  *  rebomos  MoS.REBO.set5b  NULL  NULL  M  S
>
> pair_coeff   2   2     lj/cut/tip4p/long  0.008031034   3.1589
> pair_coeff   1   1     lj/cut/tip4p/long  0.0   0.0
> pair_coeff   1   2     lj/cut/tip4p/long  0.0   0.0
> pair_coeff   1   3     lj/cut/tip4p/long  0.0   0.0
> pair_coeff   1   4     lj/cut/tip4p/long  0.0   0.0
> pair_coeff   2   3     lj/cut/tip4p/long  0.002169  3.67945
> pair_coeff   2   4     lj/cut/tip4p/long  0.01055   3.14445
>
> kspace_style  pppm/tip4p 1e-4
> delete_atoms    overlap 1.0   water nanotube mol yes
>
>  # region
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> region        coldl  block  INF INF  INF INF  INF 6.32  units box
> group          coldl region coldl
>
> region          1 block    INF INF  INF INF  6.32  12.64   units box
> group           1 region 1
>
> region          2 block   INF INF  INF INF   12.64  18.96   units box
> group           2 region 2
>
> region          3 block   INF INF  INF INF   18.96  25.28  units box
> group           3 region 3
>
> region          4 block    INF INF  INF INF  25.28  31.6  units box
> group           4 region 4
>
> region          5 block   INF INF  INF INF  31.6  37.92    units box
> group           5 region 5
>
> region          6 block  INF INF  INF INF   37.92  44.24   units box
> group           6 region 6
>
> region          hot block   INF INF  INF INF  44.24  56.88   units box
> group           hot  region hot
>
> region          7  block   INF INF  INF INF  56.88  63.2    units box
> group           7 region 7
>
> region          8  block  INF INF  INF INF     63.2  69.52   units box
> group           8 region 8
>
> region          9  block    INF INF  INF INF   69.52  75.84   units box
> group           9 region 9
>
> region          10   block   INF INF  INF INF   75.84  82.16   units box
> group           10 region 10
>
> region          11 block   INF INF  INF INF    82.16  88.48    units box
> group           11 region 11
>
> region          12 block   INF INF  INF INF   88.4  94.8  units box
> group           12 region 12
>
>
> region         coldr block   INF INF  INF INF  94.8  INF units box
> group           coldr region coldr
>
> group           middle subtract all hot coldl coldr
>
> #===============================================================================================
>  region          inc cylinder z 100 100  12.035  0.7  100.34  units box side
> in
> group           inc region inc
>
> variable     natoms equal count(inc)
> variable        nmass equal mass(inc)
>
> variable        A32cm3 equal 1e-24 # Angstrom^3 in cm^3
> variable        volInCNT equal 99.64*3.14*11.9*11.9
> variable DensityIn equal (v_nmass/6.02e23)/(v_volInCNT*${A32cm3})
> print    ${DensityIn}
>
> #................................................................................................
>
>  compute MSDwat water msd com yes
>  #compute MSDeq all msd com yes
>  variable Temp equal  temp
>   variable Atoms equal atoms
>   variable Ke equal ke
>   variable Pe equal pe
>   variable Enthalpy equal enthalpy
>   variable Press equal press
>   variable Etotal equal etotal
>   variable Eperatom equal etotal/atoms
>   variable Ebond equal ebond
>   variable Density equal density
>   variable  ncoldl equal count(coldl)
>   variable n1 equal count(1)
>   variable n2 equal count(2)
>   variable n3 equal count(3)
>   variable n4 equal count(4)
>   variable n5 equal count(5)
>   variable n6 equal count(6)
>   variable  nhot equal count(hot)
>   variable n7 equal count(7)
>   variable n8 equal count(8)
>   variable n9 equal count(9)
>   variable n10 equal count(10)
>   variable n11 equal count(11)
>   variable n12 equal count(12)
>   variable  ncoldr equal count(coldr)
> compute Tcoldl coldl temp
> compute T1 1 temp
> compute T2 2 temp
> compute T3 3 temp
> compute T4 4 temp
> compute T5 5 temp
> compute T6 6 temp
> compute Thot hot temp
> compute T7 7 temp
> compute T8 8 temp
> compute T9 9 temp
> compute T10 10 temp
> compute T11 11 temp
> compute T12 12 temp
> compute Tcoldr coldr temp
>
> #kinetik Energy
> profile============================================================================================
>
> compute kecoldl coldl ke
> compute ke1 1 ke
> compute ke2 2 ke
> compute ke3 3 ke
> compute ke4 4 ke
> compute ke5 5 ke
> compute ke6 6 ke
> compute kehot hot ke
> compute ke7 7 ke
> compute ke8 8 ke
> compute ke9 9 ke
> compute ke10 10 ke
> compute ke11 11 ke
> compute ke12 12 ke
> compute kecoldr coldr ke
>
> #================================================================================================================
>
> compute percoldl coldl pe/atom
> compute         pe_coldl  coldl reduce sum c_percoldl
> compute per1 1 pe/atom
> compute         pe_1 1 reduce sum c_per1
> compute per2 2 pe/atom
> compute         pe_2 2 reduce sum c_per2
> compute per3 3 pe/atom
> compute         pe_3 3 reduce sum c_per3
> compute per4 4 pe/atom
> compute         pe_4 4 reduce sum c_per4
> compute per5 5 pe/atom
> compute         pe_5 5 reduce sum c_per5
> compute per6 6 pe/atom
> compute         pe_6 6 reduce sum c_per6
> compute perhot hot pe/atom
> compute         pe_hot hot reduce sum c_perhot
> compute per7 7 pe/atom
> compute         pe_7 7 reduce sum c_per7
> compute per8 8 pe/atom
> compute         pe_8 8 reduce sum c_per8
> compute per9 9 pe/atom
> compute         pe_9 9 reduce sum c_per9
> compute per10 10 pe/atom
> compute         pe_10 10 reduce sum c_per10
> compute per11 11 pe/atom
> compute         pe_11 11 reduce sum c_per11
> compute per12 12 pe/atom
> compute         pe_12 12 reduce sum c_per12
> compute percoldr coldr pe/atom
> compute         pe_coldr  coldr reduce sum c_percoldr
>   variable  Etcoldl equal c_kecoldl+c_pe_coldl
>   variable  Et1 equal c_ke1+c_pe_1
>   variable  Et2 equal c_ke2+c_pe_2
>   variable  Et3 equal c_ke3+c_pe_3
>   variable  Et4 equal c_ke4+c_pe_4
>   variable  Et5 equal c_ke5+c_pe_5
>   variable  Et6 equal c_ke6+c_pe_6
>   variable    Ethot equal c_kehot+c_pe_hot
>   variable Et7 equal c_ke7+c_pe_7
>   variable Et8 equal c_ke8+c_pe_8
>   variable Et9 equal c_ke9+c_pe_9
>   variable Et10 equal c_ke10+c_pe_10
>   variable Et11 equal c_ke11+c_pe_11
>   variable Et12 equal c_ke12+c_pe_12
>   variable  Etcoldr equal c_kecoldr+c_pe_coldr
>
> #++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++=
> compute         MSDcoldl coldl msd com yes
> compute         msd1 1 msd com yes
> compute         msd2 2 msd com yes
> compute         msd3 3 msd com yes
> compute         msd4 4 msd com yes
> compute         msd5 5 msd com yes
> compute         msd6 6 msd com yes
> compute         msdhot hot msd com yes
> compute         msd7 7 msd com yes
> compute         msd8 8 msd com yes
> compute         msd9 9 msd com yes
> compute         msd10 10 msd com yes
> compute         msd11 11 msd com yes
> compute         msd12 12 msd com yes
> compute         MSDcoldr coldr msd com yes
>
> #relaxation
> ==================================================================================================
> minimize          0.001 0.001 1000 10000
> fix               2 all nvt temp 300 300 0.1
>  timestep          0.001
> thermo  1000
> dump            1 all atom 1000  equi.lammpstrj
> thermo_style    custom step temp etotal enthalpy press pe v_DensityIn
> fix  3  all ave/time 1 1000 1000 c_Tcoldl c_T1 c_T2 c_T3 c_T4 c_T5 c_T6
> c_T7 c_Thot c_T8 c_T9 c_T10 c_T11 c_T12 c_Tcoldr v_Etcoldl v_Et1 v_Et2 v_Et3
> v_Et4 v_Et5 v_Et6 v_Ethot v_Et7 v_Et8 v_Et9 v_Et10 v_Et11 v_Et12  v_Etcoldr
> v_ncoldl v_n1 v_n2 v_n3 v_n4 v_n5 v_n6 v_nhot v_n7 v_n8 v_n9 v_n10 v_n11
> v_n12  v_ncoldr file avequi.txt
>
> restart 100000  equi.restart
> run  300000
> unfix  2
> unfix  3
> #=======================================================================================================================
> fix 4 hot  nvt temp 350 350 0.1
> fix 5 coldl nvt temp 200 130 0.1
> fix 6 coldr nvt temp 200 130 0.1
> fix             7 middle nve
> #Result========================================================================================================================
>
> thermo_style    custom step temp etotal enthalpy press pe
> timestep          0.001
> dump             2 all atom 1000  gradian.lammpstrj
> dump             2dcd  all dcd 2000  gradian.dcd
>  dump_modify     2dcd  unwrap yes
>
> fix  8  all ave/time 1 1000 1000 c_Tcoldl c_T1 c_T2 c_T3 c_T4 c_T5 c_T6
> c_T7 c_Thot c_T8 c_T9 c_T10 c_T11 c_T12  c_Tcoldr v_Etcoldl v_Et1 v_Et2
> v_Et3 v_Et4 v_Et5 v_Et6 v_Ethot v_Et7 v_Et8 v_Et9 v_Et10 v_Et11 v_Et12
> v_Etcoldr v_ncoldl v_n1 v_n2 v_n3 v_n4 v_n5 v_n6  v_nhot v_n7 v_n8 v_n9
> v_n10 v_n11 v_n12 v_ncoldr v_Pe v_Press v_Enthalpy v_Etotal v_Eperatom
> v_DensityIn c_MSDwat[1] c_MSDwat[2] c_MSDwat[3] c_MSDwat[4]  file
> avfreez.txt
>
> fix   9 all  ave/time 1 1000 1000 c_MSDcoldl[4] c_msd1[4] c_msd2[4]
> c_msd3[4] c_msd4[4] c_msd5[4] c_msd6[4] c_msdhot[4] c_msd7[4] c_msd8[4]
> c_msd9[4] c_msd10[4] c_msd11[4] c_msd12[4] c_MSDcoldr[4] file aveMSd.txt
> thermo  1000
>
> restart 100000  grad.restart
>
> run  2500000
>
>
> I ask my question in other words: as clear in input I considered 15 regions
> along of axis of MoS2 nanotube, 12 middles, two ends are cold , one center
> is hot.
> my question all of them did not reach to temp which I want. of course in my
> previous article without water, when we calculated the thermal conductivity
> of Mos2, we could reach the desire temp. but MoS2 nanotube with filled water
> it didn't happen.
> when water and Mos2nanotube  around water considered as a cold or hot group,
> after steady state didn't reach appropriate temp, I send the temp of each
> region.
> of course before the inducing temp gradient I relax my system( MoS2 nanotube
> and water inside it) and checked the energy of system and  density which I
> send my pic.
>
> I hope I clear my question.
> Sincerely yours.
> Thanks.
>
>
>
> On Sun, May 6, 2018 at 6:49 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:
>>
>> On Sun, May 6, 2018 at 6:26 AM, Zohreh Ahadi <zohreh.ahadi@...24...>
>> wrote:
>> > Dear all lammps user
>> >
>> > Thanks with your regarding , I have one question about the regions, It
>> > maybe
>> > considered easy but stop my project.
>> > I simulated the nanotube which filled water, the two end of nanotube are
>> > considered cold groups and the center of nanotube is hot group by NVT at
>> > specific temperature.
>> > I tested two strategy: Firstly , I considered the two end of nanotube
>> > with
>> > water, as cold group , after running  the  temp  result didn't match
>> > with
>> > the NVT temp which I set, and the cold group were very colder, and hot,
>> > was
>> > very hotter than I am set in NVT.
>> > Secondly:  I considered the two end of nanotube, without water as one
>> > group...again the result temp was not match.( The nanotube has low
>> > thermal
>> > conductivity)
>>
>> actually, nanotubes have high thermal conductivity due to their
>> rigidity, but along the axis.
>>
>> >
>> > Question:I would like to Know, Is it possible instead of one group,
>> > (cold or
>> > hot) the region set as NVT?( untill water moleculars when come or exit
>> > from
>> > this region feel the NVT)
>> >
>> > I am eager to know your advise for solving this problem.
>>
>> your description is too vague to give specific advice. it looks from
>> your description, that you are not considering time scales (and
>> possibly also length scales) well enough and that you are looking at a
>> slow process. if that is the case, there is no use to accelerating
>> this process with a thermostat. you will replace computer simulation
>> with computer animation and the scientific value of your results will
>> approach zero.
>>
>> axel.
>>
>> >
>> > sincerely yours,
>> > Zohreh
>> > PhD student nano physics
>> >
>> >
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Check out the vibrant tech community on one of the world's most
>> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> > _______________________________________________
>> > lammps-users mailing list
>> > lammps-users@lists.sourceforge.net
>> > https://lists.sourceforge.net/lists/listinfo/lammps-users
>> >
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>
>



-- 
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.