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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@16001 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2017-01-09 18:26:52 +00:00
parent c093ec15a5
commit f9f2c96d17
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1
doc/src/Section_commands.txt
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@ -583,6 +583,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"lineforce"_fix_lineforce.html,
"momentum (k)"_fix_momentum.html,
"move"_fix_move.html,
"mscg"_fix_mscg.html,
"msst"_fix_msst.html,
"neb"_fix_neb.html,
"nph (ko)"_fix_nh.html,

120
doc/src/fix_mscg.txt
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@ -21,7 +21,7 @@ keyword = {range} or {name} or {max} :l
{on} = range finding functionality is performed
{off} = force matching functionality is performed
{name} args = name1 ... nameN
name1,...,nameN = string names for all atom types (1-N)
name1,...,nameN = string names for each atom type (1-Ntype)
{max} args = maxb maxa maxd
maxb,maxa,maxd = maximum bonds/angles/dihedrals per atom :pre
:ule
@ -34,69 +34,91 @@ fix 1 all mscg 1 max 4 8 20 :pre
[Description:]
This fix applies the Multi-Scale Coarse-Graining (MSCG) package to snapshots
from a dump file to generates potentials for coarse-grained simulations from
all-atom simulations using a force-matching technique ("Izvekov"_#Izvekov,
"Noid"_#Noid).
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 ("Izvekov"_#Izvekov, "Noid"_#Noid).
The general workflow for the MSCG package is as follows: (1) Perform all-atom
simulations on the system to be coarse grianed. (2) Generate a trajectory
mapped to the coarse-grained model. (3) Create input files for the MSCG code.
(4) Run the range finder functionality of the MSCG package. (5) Run the force
matching functionality of the MSCG package. (6) Check the results of the force
matching. (7) Run coarse-grained simulations using the generated coarse-grained
potentials.
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.
This fix is set up to run the range finding and force matching functions
(steps 4 and 5) of the above workflow using the "rerun"_rerun.html command.
The dump file provided for the rerun should contain the positions and forces
of the coarse-grained beads mapped from an all-atom trajectory. An additional
input file (control.in) is needed by the MSCG package to set the parameters
for the range finding and force matching functionalities. See the documentation
provided with the MSCG package for more info.
An example script using this fix is provided the examples/mscg
directory.
The MSCG package also provides additional output files when using this fix.
The range finder functionality outputs files defining pair and bonded
interaction ranges. The force matching functionality outputs tabulated force
files for every interaction in the system. Other diagnostic files can also be
output depending on the paramters in the input script. See the documentation
provided with the MSCG package for more info.
The general workflow for using LAMMPS in conjunction with the MS-CG
library to create a coarse-grained model and run coarse-grained
simulations is as follows:
This fix makes use of the MSCG library, which is maintained by Gregory Voth's
group at the University of Chicago. See instructions on obtaining and installing
the MSCG library in the src/USER-MSCG/README file.
Perform all-atom simulations on the system to be coarse grained.
Generate a trajectory mapped to the coarse-grained model.
Create input files for the MS-CG library.
Run the range finder functionality of the MS-CG library.
Run the force matching functionality of the MS-CG library.
Check the results of the force matching.
Run coarse-grained simulations using the new coarse-grained potentials. :ol
This fix can perform the range finding and force matching steps 4 and
5 of the above workflow when used in conjunction with the
"rerun"_rerun.html 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.
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
functionalities. See the examples/mscg/control.in file as an example.
And see the documentation provided with the MS-CG library for more
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 paramters in the MS-CG library input
script. Again, see the documentation provided with the MS-CG library
for more info.
:line
The {range} keyword specifies which MSCG functionality should be performed. If
{on}, the range finder functionality is performed. If {off}, the force matching
functionality is performed.
The {range} keyword specifies which MS-CG library functionality should
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. A list of space separated names should be
provided for each atom type (1-N).
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).
The {max} keyword specifies the maximum number of bonds, angles, and dihedrals
a bead can have in the current coarse-grained model.
The {max} keyword specifies the maximum number of bonds, angles, and
dihedrals a bead can have in the coarse-grained model.
[Restrictions:]
This fix is part of the USER-MSCG package. It is only enabled if LAMMPS was
built with that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
This fix is part of the MSCG package. It is only enabled if LAMMPS was
built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
The MSCG library uses C++11, which may not be supported by older compilers. The
MSCG library also has some dependencies, which are describd in the documentation
included with that package.
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 describd in its documentation.
Currently, the MSCG library is not set up to run with mpi, so this fix can only
be used with serial runs.
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.
[Related commands:]
[Related commands:] none
none
[Default:]
[Default:] {range} off, {max} 4 12 36
The default keyword settings are range off, max 4 12 36.
:line
@ -104,5 +126,5 @@ none
[(Izvekov)] Izvekov, Voth, J Chem Phys 123, 134105 (2005).
:link(Noid)
[(Noid)] Noid, Chu, Ayton, Krishna, Izvekov, Voth, Das, Andersen, J Chem Phys
128, 134105 (2008).
[(Noid)] Noid, Chu, Ayton, Krishna, Izvekov, Voth, Das, Andersen, J
Chem Phys 128, 134105 (2008).