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better align with docs bundled with the MSCG library

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This commit is contained in:
Axel Kohlmeyer
2023-03-01 20:41:36 -05:00
parent 04d3032914
commit c5c787ca5c
1 changed files with 33 additions and 33 deletions
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doc/src/fix_mscg.rst
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@ -40,15 +40,15 @@ Description
This fix applies the Multi-Scale Coarse-Graining (MSCG) method to
snapshots from a dump file to generate potentials for coarse-grained
simulations from all-atom simulations, using a force-matching
technique (:ref:`Izvekov <Izvekov>`, :ref:`Noid <Noid>`).
simulations from all-atom simulations, using a force-matching technique
(:ref:`Izvekov <Izvekov>`, :ref:`Noid <Noid>`).
It makes use of the MS-CG library, written and maintained by Greg
Voth's group at the University of Chicago, which is freely available
on their `MS-CG GitHub site <https://github.com/uchicago-voth/MSCG-release>`_. See instructions
on obtaining and installing the MS-CG library in the src/MSCG/README
file, which must be done before you build LAMMPS with this fix command
and use the command in a LAMMPS input script.
It makes use of the MS-CG library, written and maintained by Greg Voth's
group at the University of Chicago, which is freely available on their
`MS-CG GitHub site <https://github.com/uchicago-voth/MSCG-release>`_.
See instructions on obtaining and installing the MS-CG library in the
src/MSCG/README file, which must be done before you build LAMMPS with
this fix command and use the command in a LAMMPS input script.
An example script using this fix is provided the examples/mscg
directory.
@ -65,15 +65,18 @@ simulations is as follows:
6. Check the results of the force matching.
7. Run coarse-grained simulations using the new coarse-grained potentials.
This fix can perform the range finding and force matching steps 4 and
5 of the above workflow when used in conjunction with the
:doc:`rerun <rerun>` command. It does not perform steps 1-3 and 6-7.
This fix can perform the range finding and force matching steps 4 and 5
of the above workflow when used in conjunction with the :doc:`rerun
<rerun>` command. It does not perform steps 1-3 and 6-7.
Step 2 can be performed using a Python script (what is the name?)
provided with the MS-CG library which defines the coarse-grained model
and converts a standard LAMMPS dump file for an all-atom simulation
(step 1) into a LAMMPS dump file which has the positions of and forces
on the coarse-grained beads.
Step 2 can be performed using a Python script (cgmap), which defines the
coarse-grained model and converts a standard LAMMPS dump file for an
all-atom simulation (step 1) into a LAMMPS dump file which has the
positions of and forces on the coarse-grained beads. To use cgmap the
following repositories need to be downloaded and installed.
#. The custom lammpsdata branch of mdtraj from https://github.com/hockyg/mdtraj/tree/lammpsdata
#. The master branch of cgmap from https://github.com/uchicago-voth/cgmap
In step 3, an input file named "control.in" is needed by the MS-CG
library which sets parameters for the range finding and force matching
@ -83,12 +86,12 @@ info on this file.
When this fix is used to perform steps 4 and 5, the MS-CG library also
produces additional output files. The range finder functionality
(step 4) outputs files defining pair and bonded interaction ranges.
The force matching functionality (step 5) outputs tabulated force
files for every interaction in the system. Other diagnostic files can
also be output depending on the parameters in the MS-CG library input
script. Again, see the documentation provided with the MS-CG library
for more info.
(step 4) outputs files defining pair and bonded interaction ranges. The
force matching functionality (step 5) outputs tabulated force files for
every interaction in the system. Other diagnostic files can also be
output depending on the parameters in the MS-CG library input script.
Again, see the documentation provided with the MS-CG library for more
info.
----------
@ -97,8 +100,8 @@ be invoked. If *on*, the step 4 range finder functionality is invoked.
*off*, the step 5 force matching functionality is invoked.
If the *name* keyword is used, string names are defined to associate
with the integer atom types in LAMMPS. *Ntype* names must be
provided, one for each atom type (1-Ntype).
with the integer atom types in LAMMPS. *Ntype* names must be provided,
one for each atom type (1-Ntype).
The *max* keyword specifies the maximum number of bonds, angles, and
dihedrals a bead can have in the coarse-grained model.
@ -107,16 +110,13 @@ Restrictions
""""""""""""
This fix is part of the MSCG package. It is only enabled if LAMMPS was
built with that package. See the :doc:`Build package <Build_package>`
doc page for more info.
built with that package. Building the MSCG package also requires
external libraries. See the :doc:`Build_package` and :doc:`Build_extras`
pages for more info.
The MS-CG library uses C++11, which may not be supported by older
compilers. The MS-CG library also has some additional numeric library
dependencies, which are described in its documentation.
Currently, the MS-CG library is not setup to run in parallel with MPI,
so this fix can only be used in a serial LAMMPS build and run
on a single processor.
Currently, the MS-CG library is not set up to run in parallel with MPI,
so this fix can only be used in a serial LAMMPS build and run on a
single processor.
Related commands
""""""""""""""""