From 9a625b715aa822af3ec96a9928089e425e74d582 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 10 Dec 2023 09:43:39 -0500 Subject: [PATCH] use Langevin thermostat with fix rigid/small instead of fix rigid/nvt/small also intra-molecular non-bonded interactions are excluded now --- doc/src/Howto_tip4p.rst | 21 ++++++++++++--------- doc/src/Howto_tip5p.rst | 14 ++++++++------ 2 files changed, 20 insertions(+), 15 deletions(-) diff --git a/doc/src/Howto_tip4p.rst b/doc/src/Howto_tip4p.rst index 4d9b514e0d..bc6e91b6b0 100644 --- a/doc/src/Howto_tip4p.rst +++ b/doc/src/Howto_tip4p.rst @@ -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 ` 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 ` 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 ` so that fix +rigid/small can identify rigid bodies by their molecule ID. Also a +:doc:`neigh_modify exclude ` 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: diff --git a/doc/src/Howto_tip5p.rst b/doc/src/Howto_tip5p.rst index 10674a04b6..4bb9754875 100644 --- a/doc/src/Howto_tip5p.rst +++ b/doc/src/Howto_tip5p.rst @@ -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 ` 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 ` 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 ` -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 ` 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