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use Langevin thermostat with fix rigid/small instead of fix rigid/nvt/small

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also intra-molecular non-bonded interactions are excluded now
This commit is contained in:
Axel Kohlmeyer
2023-12-10 09:43:39 -05:00
parent 010a7a4d44
commit 9a625b715a
2 changed files with 20 additions and 15 deletions
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21
doc/src/Howto_tip4p.rst
View File

@ -193,11 +193,14 @@ file changed):
write_data tip4p-implicit.data nocoeff
Below is the code for a LAMMPS input file using the explicit method and
a TIP4P molecule file. Because of using :doc:`fix rigid/nvt/small
a TIP4P molecule file. Because of using :doc:`fix rigid/small
<fix_rigid>` no bonds need to be defined and thus no extra storage needs
to be reserved for them, but we need to switch to atom style full or use
:doc:`fix property/atom mol <fix_property_atom>` so that fix
rigid/nvt/small can identify rigid bodies by their molecule ID:
to be reserved for them, but we need to either switch to atom style full
or use :doc:`fix property/atom mol <fix_property_atom>` so that fix
rigid/small can identify rigid bodies by their molecule ID. Also a
:doc:`neigh_modify exclude <neigh_modify>` command is added to exclude
computing intramolecular non-bonded interactions, since those are
removed by the rigid fix anyway:
.. code-block:: LAMMPS
@ -216,17 +219,17 @@ rigid/nvt/small can identify rigid bodies by their molecule ID:
pair_coeff 2 2 0.0 1.0
pair_coeff 3 3 0.0 1.0
fix mol all property/atom mol
fix mol all property/atom mol ghost yes
molecule water tip4p.mol
create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
neigh_modify exclude molecule/intra all
timestep 0.5
fix integrate all rigid/nvt/small molecule temp 300.0 300.0 100.0
velocity all create 300.0 5463576
fix integrate all rigid/small molecule langevin 300.0 300.0 100.0 2345634
thermo_style custom step temp press etotal density pe ke
thermo 1000
run 20000
thermo 2000
run 40000
write_data tip4p-explicit.data nocoeff
.. _tip4p_molecule:

14
doc/src/Howto_tip5p.rst
View File

@ -81,11 +81,13 @@ long-range Coulombic solver (e.g. Ewald or PPPM in LAMMPS).
Below is the code for a LAMMPS input file for setting up a simulation of
TIP5P water with a molecule file. Because of using :doc:`fix
rigid/nvt/small <fix_rigid>` no bonds need to be defined and thus no
extra storage needs to be reserved for them, but we need to switch to
rigid/small <fix_rigid>` no bonds need to be defined and thus no extra
storage needs to be reserved for them, but we need to either switch to
atom style full or use :doc:`fix property/atom mol <fix_property_atom>`
so that fix rigid/nvt/small can identify rigid bodies by their molecule
ID:
so that fix rigid/small can identify rigid bodies by their molecule ID.
Also a :doc:`neigh_modify exclude <neigh_modify>` command is added to
exclude computing intramolecular non-bonded interactions, since those
are removed by the rigid fix anyway:
.. code-block:: LAMMPS
@ -107,11 +109,11 @@ ID:
fix mol all property/atom mol
molecule water tip5p.mol
create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
neigh_modify exclude molecule/intra all
timestep 0.5
fix integrate all rigid/nvt/small molecule temp 300.0 300.0 100.0
fix integrate all rigid/small molecule langevin 300.0 300.0 50.0 235664
reset_timestep 0
velocity all create 300.0 5463576
thermo_style custom step temp press etotal density pe ke
thermo 1000