ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

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

Browse Source 
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
Download Patch File Download Diff File Expand all files Collapse all files

21
doc/src/Howto_tip4p.rst
View File

@ -193,11 +193,14 @@ file changed):
write_data tip4p-implicit.data nocoeff write_data tip4p-implicit.data nocoeff
Below is the code for a LAMMPS input file using the explicit method and 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 <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 to be reserved for them, but we need to either switch to atom style full
:doc:`fix property/atom mol <fix_property_atom>` so that fix or use :doc:`fix property/atom mol <fix_property_atom>` so that fix
rigid/nvt/small can identify rigid bodies by their molecule ID: 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 .. 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 2 2 0.0 1.0
pair_coeff 3 3 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 molecule water tip4p.mol
create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33 create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
neigh_modify exclude molecule/intra all
timestep 0.5 timestep 0.5
fix integrate all rigid/nvt/small molecule temp 300.0 300.0 100.0 fix integrate all rigid/small molecule langevin 300.0 300.0 100.0 2345634
velocity all create 300.0 5463576
thermo_style custom step temp press etotal density pe ke thermo_style custom step temp press etotal density pe ke
thermo 1000 thermo 2000
run 20000 run 40000
write_data tip4p-explicit.data nocoeff write_data tip4p-explicit.data nocoeff
.. _tip4p_molecule: .. _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 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 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 rigid/small <fix_rigid>` no bonds need to be defined and thus no extra
extra storage needs to be reserved for them, but we need to switch to 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>` 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 so that fix rigid/small can identify rigid bodies by their molecule ID.
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 .. code-block:: LAMMPS
@ -107,11 +109,11 @@ ID:
fix mol all property/atom mol fix mol all property/atom mol
molecule water tip5p.mol molecule water tip5p.mol
create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33 create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
neigh_modify exclude molecule/intra all
timestep 0.5 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 reset_timestep 0
velocity all create 300.0 5463576
thermo_style custom step temp press etotal density pe ke thermo_style custom step temp press etotal density pe ke
thermo 1000 thermo 1000