57 lines
2.9 KiB
Plaintext
57 lines
2.9 KiB
Plaintext
Three examples inputs for pair styles threebody/table (in.spce and
|
|
in.spce2) and sw/angle/table (in.spce_sw). All inputs are for the
|
|
simulation of coarse-grained SPC/E water.
|
|
|
|
A water molecule is represented by one coarse-grained (CG) bead.
|
|
|
|
For the two threebody/table examples the three-body (force) tables are
|
|
in the files 1-1-1.table and 1-1-2.table. These have been parametrized
|
|
with the kernel-based machine learning (ML) with the VOTCA package
|
|
(https://gitlab.mpcdf.mpg.de/votca/votca). For a example on the
|
|
parametrization, have a look at
|
|
https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/guide
|
|
and
|
|
https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/ml.
|
|
|
|
In both cases, the parametrization is done according to a sample system,
|
|
using the three-body forces of a Stillinger-Weber potential with
|
|
tabulated angular forces (sw/angle/table) (see in.spce_sw). These then
|
|
are learned with the covariant meshing technique with the settings files
|
|
used in
|
|
https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/ml/3body/with_binning.
|
|
|
|
The first example, in.spce uses the LAMMPS data file (data.spce) with
|
|
the starting configuration of 1000 CG water molecules, and a threebody
|
|
file (spce.3b) which loads the 1-1-1.table file.
|
|
|
|
A hybrid/overlay pair style is used to sum a tabulated pairwise
|
|
interaction (table_CG_CG.txt) with the tabulated threebody interactions.
|
|
The tabulated pair interaction is the effectively the same as in the
|
|
what is used by the in.spce_sw input using sw/angle/table pair style.
|
|
|
|
IMPORTANT NOTE: The threebody tables are parameterized without storing
|
|
energies (the last column of the threebody table files is zero). This
|
|
is due to a current limitation of the paramerization procedure.
|
|
|
|
This in.spce2 example uses the data.spce2 file and the threebody input
|
|
spce2.3b. This is essentially the same simulation as in in.spce only
|
|
the atom type of the first 100 CG water molecules has been changed from
|
|
1 to 2. This is done to demonstrate how to run a simulation with
|
|
different atom types.
|
|
|
|
For this (artificial) two-element simulation, the threebody file now
|
|
contain 8 entries for: type1 type1 type1, type1 type1 type2, type1 type2
|
|
type1, type1 type2 type2, type2 type1 type1, type2 type1 type2, type2
|
|
type2 type1, type2 type2 type2. Each entry has the same structure as
|
|
above. However, entries where the second and the third element are
|
|
different require a different force table (1-1-2.table) instead of
|
|
(1-1-1.table). 1-1-2.table contains exactly the force constants as
|
|
1-1-1.table. However it has to have the asymmetric structure where both
|
|
interparticle distances (r_ij and r_ik) are varied from rmin to rmax and
|
|
therefore contains "M = 2 * N * N * N" (2 * 12 * 12 * 12 = 3456)
|
|
entries.
|
|
|
|
The third example, in.spce_sw, contains the analytical twobody interactions
|
|
and replaces the threebody term of the Stillinger-Weber potential with an
|
|
angle/table style potential which is stored in the table_CG_CG_CG.txt file.
|