R: Re: Per atom energy of rigid water

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1

Maybe I understood. It's because in the TIP3P one puts:

pair_coeff * 2 0.0000 0.0000

so no-one interacts with hydrogens?

          Aris

----Messaggio originale----
Da: [email protected]...
Data: 06/05/2014 13.58
A: <[email protected]>
Cc: "Lammps-users"<[email protected]>
Ogg: R: Re: [lammps-users] Per atom energy of rigid water

Ok thanks, but it should remain the contribution of pair potentials or not?

Here is my setting:

---------------------------------------------------
# SPC/E water box benchmark

units real
atom_style full

read_data system_chosen

pair_style lj/cut 6.0

pair_coeff 1 1 0.1521 3.1507
pair_coeff * 2 0.0000 0.0000

bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none

bond_coeff 1 450 0.9572
angle_coeff 1 55 104.52

special_bonds lj 0.0 0.0 0.5

neighbor 2.0 bin
neigh_modify every 1 delay 10 check yes

fix NVT all nvt temp 300.0 300.0 100.0

velocity all create 300 432567 dist uniform

fix 1 all shake 0.0001 20 0 b 1 a 1

timestep 2.0

thermo 10

run 100000

unfix NVT

fix NVE all nve

reset_timestep 0

velocity all zero linear

#
compute myKE all ke/atom
#
#
compute myPE all pe/atom
#
#
thermo 1

dump mydump all custom 1 energy.file c_myPE c_myKE

run 500000
-----------------------

and the file system_chosen begins like this:

LAMMPS Description

    192 atoms
    128 bonds
    64 angles
    0 dihedrals
    0 impropers

    2 atom types
    1 bond types
    1 angle types

0.0 12.448 xlo xhi
0.0 12.448 ylo yhi
0.0 12.448 zlo zhi

Masses

   1 15.9994
   2 1.008

Atoms

1 1 1 -0.834 0.0 0.0 0.0
2 1 2 0.417 0.577345898614 0.577345898614 0.577359
3 1 2 0.417 -0.577345898614 -0.577345898614 0.577359
4 2 1 -0.834 0.0 0.0 3.112
5 2 2 0.417 0.577345898614 0.577345898614 3.689359

------------------------------------------------------------

DId I do something wrong?

----Messaggio originale----
Da: [email protected]
Data: 06/05/2014 12.28
A: "[email protected]..."<[email protected]...>
Cc: "Lammps-users"<[email protected]>
Ogg: Re: [lammps-users] Per atom energy of rigid water

Hello,

    I tried to print per atom energy using TIP3P parameters of the
documentation per both flexible and rigid water. I used a

compute myPE all pe/atom

In the case of rigid water several atoms seem to have zero potential

energy