forked from lijiext/lammps
131 lines
4.7 KiB
Plaintext
131 lines
4.7 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Commands_all.html)
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:line
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fix mscg command :h3
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[Syntax:]
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fix ID group-ID mscg N keyword args ... :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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mscg = style name of this fix command :l
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N = envoke this fix every this many timesteps :l
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zero or more keyword/value pairs may be appended :l
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keyword = {range} or {name} or {max} :l
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{range} arg = {on} or {off}
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{on} = range finding functionality is performed
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{off} = force matching functionality is performed
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{name} args = name1 ... nameN
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name1,...,nameN = string names for each atom type (1-Ntype)
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{max} args = maxb maxa maxd
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maxb,maxa,maxd = maximum bonds/angles/dihedrals per atom :pre
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:ule
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[Examples:]
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fix 1 all mscg 1
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fix 1 all mscg 1 range name A B
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fix 1 all mscg 1 max 4 8 20 :pre
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[Description:]
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This fix applies the Multi-Scale Coarse-Graining (MSCG) method to
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snapshots from a dump file to generate potentials for coarse-grained
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simulations from all-atom simulations, using a force-matching
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technique ("Izvekov"_#Izvekov, "Noid"_#Noid).
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It makes use of the MS-CG library, written and maintained by Greg
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Voth's group at the University of Chicago, which is freely available
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on their "MS-CG GitHub
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site"_https://github.com/uchicago-voth/MSCG-release. See instructions
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on obtaining and installing the MS-CG library in the src/MSCG/README
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file, which must be done before you build LAMMPS with this fix command
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and use the command in a LAMMPS input script.
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An example script using this fix is provided the examples/mscg
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directory.
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The general workflow for using LAMMPS in conjunction with the MS-CG
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library to create a coarse-grained model and run coarse-grained
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simulations is as follows:
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Perform all-atom simulations on the system to be coarse grained.
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Generate a trajectory mapped to the coarse-grained model.
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Create input files for the MS-CG library.
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Run the range finder functionality of the MS-CG library.
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Run the force matching functionality of the MS-CG library.
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Check the results of the force matching.
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Run coarse-grained simulations using the new coarse-grained potentials. :ol
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This fix can perform the range finding and force matching steps 4 and
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5 of the above workflow when used in conjunction with the
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"rerun"_rerun.html command. It does not perform steps 1-3 and 6-7.
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Step 2 can be performed using a Python script (what is the name?)
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provided with the MS-CG library which defines the coarse-grained model
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and converts a standard LAMMPS dump file for an all-atom simulation
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(step 1) into a LAMMPS dump file which has the positions of and forces
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on the coarse-grained beads.
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In step 3, an input file named "control.in" is needed by the MS-CG
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library which sets parameters for the range finding and force matching
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functionalities. See the examples/mscg/control.in file as an example.
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And see the documentation provided with the MS-CG library for more
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info on this file.
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When this fix is used to perform steps 4 and 5, the MS-CG library also
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produces additional output files. The range finder functionality
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(step 4) outputs files defining pair and bonded interaction ranges.
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The force matching functionality (step 5) outputs tabulated force
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files for every interaction in the system. Other diagnostic files can
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also be output depending on the parameters in the MS-CG library input
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script. Again, see the documentation provided with the MS-CG library
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for more info.
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:line
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The {range} keyword specifies which MS-CG library functionality should
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be invoked. If {on}, the step 4 range finder functionality is invoked.
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{off}, the step 5 force matching functionality is invoked.
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If the {name} keyword is used, string names are defined to associate
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with the integer atom types in LAMMPS. {Ntype} names must be
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provided, one for each atom type (1-Ntype).
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The {max} keyword specifies the maximum number of bonds, angles, and
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dihedrals a bead can have in the coarse-grained model.
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[Restrictions:]
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This fix is part of the MSCG package. It is only enabled if LAMMPS was
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built with that package. See the "Build package"_Build_package.html
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doc page for more info.
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The MS-CG library uses C++11, which may not be supported by older
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compilers. The MS-CG library also has some additional numeric library
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dependencies, which are described in its documentation.
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Currently, the MS-CG library is not setup to run in parallel with MPI,
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so this fix can only be used in a serial LAMMPS build and run
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on a single processor.
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[Related commands:] none
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[Default:]
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The default keyword settings are range off, max 4 12 36.
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:line
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:link(Izvekov)
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[(Izvekov)] Izvekov, Voth, J Chem Phys 123, 134105 (2005).
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:link(Noid)
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[(Noid)] Noid, Chu, Ayton, Krishna, Izvekov, Voth, Das, Andersen, J
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Chem Phys 128, 134105 (2008).
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