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Re: [lammps-users] Temperature and Energy increases with "nve/limit" command
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Re: [lammps-users] Temperature and Energy increases with "nve/limit" command


From: surendra jain <jainsk.iitkgp@...24...>
Date: Tue, 8 Aug 2017 10:19:36 +0530

Dear Axel,

 Many thanks for your reply. I found that the some atoms were
experiencing large forces during the simulation. So, I tried using a
soft potential. Below is shown part of my input script :

pair_style   lj/cut/coul/long/soft 2.0 0.5 10.0 10.0 12.0

read_data       lammps_data.dat

pair_coeff      * *  0.0      0.0    0.95
pair_coeff      1 8  0.0546   3.08   0.95
pair_coeff      2 8  0.00     1.4    0.95
pair_coeff      3 8  0.0744   3.275  0.95
pair_coeff      4 8  0.00     1.4    0.95
pair_coeff      5 8  0.106    2.88   0.95
pair_coeff      6 8  0.0955   2.9    0.95
pair_coeff      7 8  0.04     2.610  0.95

pair_coeff      1 9  0.0934   3.205  0.95
pair_coeff      2 9  0.00     1.525  0.95
pair_coeff      3 9  0.127    3.4    0.95
pair_coeff      4 9  0.00     1.525  0.95
pair_coeff      5 9  0.181    3.005  0.95
pair_coeff      6 9  0.163    3.025  0.95
pair_coeff      7 9  0.0685   2.735  0.95

pair_coeff      8 8  0.053654  2.8   0.95
pair_coeff      8 9  0.0917    2.925 0.95
pair_coeff      9 9  0.1569    3.05  095

This  is working fine. When I switch to full strength of the potential
 from 0.95 to 1.0, I get an error

----------------------------------------------------------
Step c_mytemp PotEng KinEng Fmax E_vdwl E_coul E_pair E_bond E_angle
E_long E_tail

  100000    302.94912   -28974.945    1914.4316    202.90136
-2193.2657   -1299.8602   -29793.114    401.92992    416.23932
-26299.988            0

  100100    306.07354   -28993.423    1934.1758    193.19966
-1846.9499   -1704.2272   -29852.518    412.88093    446.21454
-26301.341            0

ERROR on proc 0: Bond atoms 6303 6305 missing on proc 0 at step 100130
(../ntopo_bond_all.cpp:63)
---------------------------------------------------------------------------------------------------------

My question is after equilibration using (lamda = 0.95) I switch back
to full potential (lambda = 1) and got this error. I will appreciate
your help.

Best Regards,
Surendra

On 8/8/17, Kohlmeyer <akohlmey@...1086...> wrot
> On Sat, Aug 5, 2017 at 1:40 AM, surendra jain <jainsk.iitkgp@...24...>
> wrot
l

>> Dear Lammps users,>>   I am working on dynamics of fluids in carbon models. The carbon
>> model remains fixed during simulation. I am using "NVE/limit 0.05" for
>>  the fluid molecules for equilibration and to remove any high energy
>> configurations. However, the temperature and energy (both KE and PE)
>> increase during the simulation.
>>
>
> ​there is no reason why this should not happen. nve/limit only applies
> restrictions when atoms reach the threshold. otherwise it will behave just
> like fix nve.
> a more effective way to remove initial high potential energy spots would be
> to run a minimization first.
>
> ​axel.​
>
>
>
>>
>> I am attaching the input script . Any help will be appreciated.
>>
>> ------------------------------------------------------------
>> -----------------------
>>
>> dimension       3
>> units           real
>> boundary        p p p
>>
>> kspace_style    pppm 1.0e-4
>> kspace_modify   order 3
>> atom_style      full
>> pair_style      lj/cut/coul/long 10.0 12.0
>> bond_style      harmonic
>> angle_style     harmonic
>> pair_modify     mix arithmetic
>>
>>
>> read_data       lammps_data.dat
>>
>> pair_coeff      * *  0.0      0.0
>> pair_coeff      1 8  0.0546   3.08
>> pair_coeff      2 8  0.00     1.4
>> pair_coeff      3 8  0.0744   3.275
>> pair_coeff      4 8  0.00     1.4
>> pair_coeff      5 8  0.106    2.88
>> pair_coeff      6 8  0.0955   2.9
>> pair_coeff      7 8  0.04     2.610
>>
>> pair_coeff      1 9  0.0934   3.205
>> pair_coeff      2 9  0.00     1.525
>> pair_coeff      3 9  0.127    3.4
>> pair_coeff      4 9  0.00     1.525
>> pair_coeff      5 9  0.181    3.005
>> pair_coeff      6 9  0.163    3.025
>> pair_coeff      7 9  0.0685   2.735
>>
>> pair_coeff      8 8  0.053654  2.8
>> pair_coeff      8 9  0.0917    2.925
>> pair_coeff      9 9  0.1569    3.05
>>
>>
>> group   matrix type 1 2 3 4 5 6 7
>> group   fluid type 8 9
>>
>>
>> neighbor   2.0  bin
>> neigh_modify    delay 0 every 1 check yes
>> neigh_modify   exclude molecule fluid
>>
>> fix             11 matrix setforce 0.0 0.0 0.0
>> fix             1 fluid nve/limit 0.05
>> compute          mytemp fluid temp
>>
>> timestep        0.050
>>
>> thermo_style    custom  step c_mytemp pe ke fmax evdwl ecoul  epair
>> ebond eangle elong etail
>> thermo          10
>> run             100000
>> unfix 1
>>
>> fix             22 fluid nve
>> fix             2  fluid langevin 100.0 100.0 100.0 498094
>>
>> thermo      10
>> run         100000
>>
>> unfix 2
>> fix             29  fluid langevin 300.0 300.0 100.0 498094
>>
>> reset_timestep  0
>>
>> compute     2 fluid vacf
>> fix        14 fluid ave/time 1 1 1 c_2[4] file tmp.vacf
>> fix         5 fluid vector 1 c_2[4]
>> variable    diff equal dt*trap(f_5)
>>
>> compute          CCRDF all rdf 200  8 8
>> fix              3 all ave/time 100 1 1000 c_CCRDF[*] file cc.rdf mode
>> vector
>> compute          CMRDF all rdf 200  1 8
>> fix             32 all ave/time 100 1 1000 c_CMRDF[*] file cm.rdf mode
>> vector
>>
>> compute         13 fluid msd com yes
>> variable        twopoint equal c_13[4]/4/(step*dt+1.0e-6)
>> fix             9 all vector 10 c_13[4]
>> variable        fitslope equal slope(f_9)/4/(10*dt)
>>
>>
>> thermo_style    custom step temp pe ke etotal fmax c_13[4] c_mytemp
>> evdwl ecoul  epair ebond eangle elong etail
>>
>> restart         10000 temp.restart
>>
>> dump            108 all xyz 10 tmp.xyz
>> dump            109 fluid custom 10 tmp5.xyz id mol type xu yu zu ix iy
>> iz
>> dump            110 fluid custom 10 tmp6.xyz id mol type x y z
>> dump            311 fluid custom 10 tmp7.xyz id mol type xu yu zu
>>
>> timestep        0.05
>>
>> thermo          10
>> run             100000
>>
>> ------------------------------------------------------------
>> -----------------------
>>
>> Best Regards,
>> Surendra
>>
>> ------------------------------------------------------------
>> ------------------
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>>
>
>
>
> --
> 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.
>