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[lammps-users] periodic molecule COM moving with fix momentum
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[lammps-users] periodic molecule COM moving with fix momentum


From: Ali Shomali <ali.shomali111@...24...>
Date: Wed, 20 Sep 2017 12:57:13 +0330

Hello all Dear lammps useres

I'm facing an odd problem with my simulation. I'm modeling an infinite CNT and another modified-functionalized CNT  that are  co-centered , thus the outer CNT is moving on the inner one with smaller diameter. the problem is no matter how many time steps I eliminate my infinite cnt center of mass momentum using fix momentum command, it moves! I managed to solve this problem by fix recenter but I'm not sure why this happened in fix momentum command, I've checked the control parameters and log file and every thing seems normal. 
by the way I've used OPLS forcefield so I defined the extra angles and bonds and dihedrals which across the boundaries in data file.
Thanks for your kind help


this is my input file:
#processors 1 1 10
units                    real
dimension                3
boundary                 p p p
atom_style               full
read_data                pucnthimproper.data extra/atom/types 1 extra/bond/types 1 extra/angle/types 1 extra/dihedral/types 1
read_data                innerperiodic.data add append offset 2 2 2 3 1 
neighbor                 2.0 bin
neigh_modify             delay 2 every 1
region bottom block INF INF INF INF INF 5
region top block INF INF INF INF 355 INF 
group pucnt type 1 2
group                    nanotube type 3
group                    cm id 536
#********************************************************** force-field *********************************************

pair_style               lj/cut/coul/cut 10 10
bond_style               harmonic
angle_style              harmonic
dihedral_style           opls
improper_style           harmonic
special_bonds            lj/coul 0.0 0.0 0.5

################set parameters#####################

## argon and PUCNTH  opls

pair_coeff               1 1 0.070    3.55000
pair_coeff               2 2 0.030000 2.4200 
pair_coeff     3 3 0.070    3.55000 # carbon 2 = nanotube inner
pair_modify              mix geometric
bond_coeff               1 469.00     1.4000 
bond_coeff               2 367.00     1.0800
bond_coeff               3 469.00     1.4000 
angle_coeff              1  63.00     120.00 
angle_coeff              2  35.00     120.00
angle_coeff              3  63.00     120.00 

dihedral_coeff           1 0.0 7.250 0.0 0.0
dihedral_coeff           2 0.0 7.250 0.0 0.0
dihedral_coeff           3 0.0 7.250 0.0 0.0
dihedral_coeff           4 0.0 7.250 0.0 0.0
improper_coeff            1 0.55 180

################simualtion#####################
#kspace_style            pppm 1e-4
compute                  com pucnt com
timestep                 1
minimize                 0.001 0.001 1000 10000
velocity                 pucnt create 300 1234 dist gaussian 
velocity                 nanotube create 300 1234 dist gaussian
#delete_atoms             overlap 1 argon nanotube mol yes
fix                      1 nanotube nvt temp 300 300 100
fix                      2 pucnt nve 
compute                  1 pucnt chunk/atom molecule
compute                  msd pucnt msd/chunk 1
fix                      3 pucnt ave/time 1000 1 1000 c_msd file msd.out mode vector
dump                     t all xyz 1000 dumpt.xyz
thermo_style             custom step temp press ke pe etotal c_com[1] c_com[2] c_com[3] 
thermo                   1000
fix      momcnt nanotube momentum 100 linear 0 0 0 angular 
run                      1000000
undump t
write_data               cocenterrealxed.data
dump                     1 all xyz 1000 dump.xyz
dump                     2 pucnt xyz 1000 dump_pucnt.xyz
dump                     3 cm xyz 10000 dumpcm_pucnt.xyz
restart 1000000 poly.restart
run                      10000000
write_data               final.data