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add a Howto demonstrating how to convert a bulk molecular system to a slab

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Axel Kohlmeyer
2025-03-22 04:41:34 -04:00
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Howto_walls
Howto_nemd
Howto_dispersion
Howto_bulk2slab
Analysis howto
==============

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======================================
Convert a bulk system to a slab system
======================================
A regularly encountered simulation problem is how to convert a bulk
system that has been run for a while into a slab system with some vacuum
space. The challenge here is that one cannot just change the box
dimensions with the :doc:`change_box command <change_box>` because some
atoms will have non-zero image flags. Changing the box dimensions
results in an undesired displacement of those atoms, since the image
flags indicate how many times the box length in x-, y-, or z-direction
needs to be added or subtracted to get the "unwrapped" coordinates.
Below is a suggested workflow that can be applied to the :doc:`Rhodo
benchmark input <Speed_bench>`. The modifications to the ``in.rhodo``
input file are discussed below. The first lines up to and including the
:doc:`read_data command <read_data>` remain unchanged. Then we insert
the following lines to add vacuum to the z direction above and below
the system:
.. code-block:: LAMMPS
variable delta index 10.0
reset_atoms image all
write_dump all custom rhodo-unwrap.lammpstrj id xu yu zu
change_box all z final $(zlo-2.0*v_delta) $(zhi+2.0*v_delta)
set atom * image NULL NULL 0
read_dump rhodo-unwrap.lammpstrj 0 x y z box no replace yes
change_box all boundary p p f
kspace_modify slab 3.0
The :doc:`variable delta <variable>` (set to :math:`10 \AA`) represents
a distance that determines the amount of vacuum added: we add twice its
value in each direction to the z-dimension so in total :math:`40 \AA`
get added. The :doc:`reset_atoms image all <reset_atoms>` command shall
reset any image flags to become either 0 or :math:`\pm 1`.
The :doc:`write_dump command <write_dump>` then writes out the resulting
"unwrapped" coordinates of the system. After expanding the box, coordinates
that were outside the box should now be inside.
The first :doc:`change_box command <change_box>` adds the desired
distance to the low and high box boundary in z-direction as thus will
create an undesired displacement for the atoms with non-zero image
flags. With the :doc:`set command <set>` the image flags in z-direction
will be set to zero while preserving the values in x- and y-direction.
With the :doc:`read_dump command <read_dump>` we read back and replace
partially incorrect coordinates with the previously saved, unwrapped
coordinates. It is important to ignore the box dimensions stored in the
dump file. We want to preserve the expanded box. At this point it is
also possible to change the periodicity in z-direction with the second
:doc:`change_box command <change_box>` and turn on the slab correction
to the PPPM long-range solver with the :doc:`kspace_modify command
<kspace_modify>`.
Next we replace the :doc:`fix npt command <fix_nh>` with:
.. code-block:: LAMMPS
fix 2 nvt temp 300.0 300.0 10.0
We now have an open system and thus the adjustment of the cell in
z-direction is no longer required. Since the splitting of the bulk
system where the vacuum is inserted, we reduce the thermostat time
constant from 100.0 to 10.0 to remove excess kinetic energy resulting
from that change faster.
Since atoms and molecules at the interface will experience a large
change in potential energy due to the box expansion, and thus it is
possible that some of them will be ejected from the slab. In order to
suppress that, we add soft harmonic walls to push back any atoms that
want to leave the slab. To determine the position of the wall, we
first need to to determine the extent of the atoms in z-direction
and then place the harmonic walls based on that information:
.. code-block:: LAMMPS
compute zmin all reduce min z
compute zmax all reduce max z
thermo_style custom zlo c_zmin zhi c_zmax
run 0 post no
fix 3 all wall/harmonic zhi $(c_zmax+v_delta) 10.0 0.0 ${delta} &
zlo $(c_zmin-v_delta) 10.0 0.0 ${delta}
The two :doc:`compute reduce <compute_reduce>` command determine the
minimum and maximum z-coordinate across all atoms. In order to trigger
the compute commands we need to "consume" them. This is done with the
:doc:`thermo_style custom <thermo_style>` command followed by the
:doc:`run 0 <run>` command. This enables using the min/max values
determined by the compute commands to compute the location of the wall
in lower and upper direction. This uses the previously defined *delta*
variable to determine the distance of the wall from the extent of the
system and the cutoff for the wall interaction. This way only atoms
that move beyond the min/max values in z-direction will experience a
restoring force. The force constant of :math:`10.0
\frac{\mathrm{kcal/mol}}{\AA}` was determined empirically.
Finally, we replace the :doc:`run 100 <run>` of the original input with:
.. code-block:: LAMMPS
run 1000 post no
unfix 3
fix 2 all nvt temp 300.0 300.0 100.0
run 1000 post no
write_data data.rhodo-slab
This runs the system converted to a slab first for 1000 MD steps using
the walls and stronger Nose-Hoover thermostat. Then the walls are
removed and the thermostat time constant reset to 100.0 and the system
run for another 1000 steps. Finally the resulting slab geometry is
written to a new data file ``data.rhodo-slab`` with a :doc:`write_data
command <write_data>`. The number of MD steps required to reach a
proper equilibrium state is very likely larger. The number of 1000
steps (corresponding to 2 picoseconds) was chosen for demonstration
purposes, so that the procedure can be easily and quickly tested.