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Re: [lammps-users] Rigid
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Re: [lammps-users] Rigid


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Mon, 13 Nov 2017 06:14:50 -0500



On Mon, Nov 13, 2017 at 4:28 AM, Zohreh Ahadi <zohreh.ahadi@...24...> wrote:
Dear all,
I have simulated a system consist of nanotube which it was filled by water inside( SPCE model), my question is:
I used rigid command for nanotube and I expect that nanotube's atom don't move , but it didn't happen..my input is following. what can I do for fix this problem?

​there are multiple problems here:
- you are confusing "rigid" with "immobile". a rigid object can still translate and rotate, only it does it as a whole (i.e. rigid) object.
- as stated in the documentation, fix rigid is not active during minimization
- you are applying time integration to some atoms multiple times in the script segment after the minimization
- there are two common ways to immobilize atoms: 1) do not include them in time integration 2) initialize their velocities to zero and set forces to zero
- you should not need to override the neighbor list settings for "one" and "page", if your system is set up correctly

​axel.​

 
Thanks, for your attention,


echo            both
boundary        p p p
units           metal
atom_style      full
bond_style      harmonic
angle_style     harmonic
read_data       16_202_water2.data
group           water type 3 4
group           nanotube type 1 2
#neighbor        2.0 bin
neigh_modify    every 1 one 10000 page 200000 #include all  binsize 2.0 #delay 10 check yes exclude all  
fix 1 nanotube rigid molecule
#potential===================================================================================================
pair_style      lj/charmm/coul/long    10    20
 
pair_coeff       3  3            0.0            0.0    0      2.5  
pair_coeff       4  4          0.1553         3.166   0.25   7.9     
pair_coeff       3  4          0.0            1.583   0.0     2.5

#pair_coeff       1  1          0.115918        4.43     0.2     11.075
#pair_coeff       2  2          0.498327        3.34     0.6      8.35
#pair_coeff       1  2          0.240344        3.885    0.36      9.75


pair_coeff       1  4         0.134172        3.798    0.195   9.475
pair_coeff       2  4        0.278191         3.253     0.40  8.1325
pair_coeff       1  3         0.0              2.215     0   5.5375
pair_coeff       2  3         0.0               1.67     0   4.175
kspace_style    pppm 1e-4
delete_atoms    overlap 1.5   water nanotube mol yes
#=====================================================================================================================
minimize          0.001 0.001 1000 10000
fix             22 water shake 1e-6 500 0 m 1.0 a 1
fix        2 all  npt temp 300 300 0.1 iso 1 1 1
timestep         0.001

.........

Regards,
Zohreh

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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.