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doc/src/Manual.txt

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<!-- HTML_ONLY -->

<HEAD>

<TITLE>LAMMPS Users Manual</TITLE>

<META NAME="docnumber" CONTENT="22 Feb 2018 version">

<META NAME="docnumber" CONTENT="16 Mar 2018 version">

<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">

<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">

</HEAD>
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<H1></H1>



LAMMPS Documentation :c,h3

22 Feb 2018 version :c,h4

16 Mar 2018 version :c,h4



Version info: :h4

doc/src/PDF/colvars-refman-lammps.pdf

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doc/src/Section_start.txt

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@@ -803,6 +803,10 @@ currently installed. For those that are installed, it will list any 
files that are different in the src directory and package

sub-directory.



Typing "make package-installed" or "make pi" will list which packages are

currently installed, without listing the status of packages that are not

installed.



Typing "make package-update" or "make pu" will overwrite src files

with files from the package sub-directories if the package is

installed.  It should be used after a patch has been applied, since

doc/src/pair_meam.txt

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@@ -77,7 +77,7 @@ See the "pair_coeff"_pair_coeff.html doc page for alternate ways 
to specify the path for the potential files.



As an example, the potentials/library.meam file has generic MEAM

settings for a variety of elements.  The potentials/sic.meam file has

settings for a variety of elements.  The potentials/SiC.meam file has

specific parameter settings for a Si and C alloy system.  If your

LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si,

and the 4th to be C, you would use the following pair_coeff command:
@@ -105,6 +105,15 @@ This can be used when a {meam} potential is used as part of the 
{hybrid} pair style.  The NULL values are placeholders for atom types

that will be used with other potentials.



NOTE: If the 2nd filename is NULL, the element names between the two

filenames can appear in any order, e.g. "Si C" or "C Si" in the

example above.  However, if the 2nd filename is not NULL (as in the

example above), it contains settings that are Fortran-indexed for the

elements that preceed it.  Thus you need to insure you list the

elements between the filenames in an order consistent with how the

values in the 2nd filename are indexed.  See details below on the

syntax for settings in the 2nd file.



The MEAM library file provided with LAMMPS has the name

potentials/library.meam.  It is the "meamf" file used by other MD

codes.  Aside from blank and comment lines (start with #) which can
@@ -164,7 +173,15 @@ keyword(I) = value 
keyword(I,J) = value

keyword(I,J,K) = value :pre



The recognized keywords are as follows:

The indices I, J, K correspond to the elements selected from the

MEAM library file numbered in the order of how those elements were

selected starting from 1. Thus for the example given below



pair_coeff * * library.meam Si C sic.meam Si Si Si C :pre



an index of 1 would refer to Si and an index of 2 to C. 



The recognized keywords for the parameter file are as follows:



Ec, alpha, rho0, delta, lattce, attrac, repuls, nn2, Cmin, Cmax, rc, delr,

augt1, gsmooth_factor, re

doc/src/read_data.txt

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@@ -15,10 +15,11 @@ read_data file keyword args ... :pre 
file = name of data file to read in :ulb,l

zero or more keyword/arg pairs may be appended :l

keyword = {add} or {offset} or {shift} or {extra/atom/types} or {extra/bond/types} or {extra/angle/types} or {extra/dihedral/types} or {extra/improper/types} or {extra/bond/per/atom} or {extra/angle/per/atom} or {extra/dihedral/per/atom} or {extra/improper/per/atom} or {group} or {nocoeff} or {fix} :l

  {add} arg = {append} or {Nstart} or {merge}

    append = add new atoms with IDs appended to current IDs

    Nstart = add new atoms with IDs starting with Nstart

    merge = add new atoms with their IDs unchanged

  {add} arg = {append} or {IDoffset} or {IDoffset MOLoffset} or {merge}

    append = add new atoms with atom IDs appended to current IDs

    IDoffset = add new atoms with atom IDs having IDoffset added

    MOLoffset = add new atoms with molecule IDs having MOLoffset added (only when molecule IDs are enabled)

    merge = add new atoms with their atom IDs (and molecule IDs) unchanged

  {offset} args = toff boff aoff doff ioff

    toff = offset to add to atom types

    boff = offset to add to bond types
@@ -120,20 +121,26 @@ boundary, then the atoms may become far apart if the box size grows. 
This will separate the atoms in the bond, which can lead to "lost"

bond atoms or bad dynamics.



The three choices for the {add} argument affect how the IDs of atoms

in the data file are treated.  If {append} is specified, atoms in the

data file are added to the current system, with their atom IDs reset

so that an atomID = M in the data file becomes atomID = N+M, where N

is the largest atom ID in the current system.  This rule is applied to

all occurrences of atom IDs in the data file, e.g. in the Velocity or

Bonds section.  If {Nstart} is specified, then {Nstart} is a numeric

value is given, e.g. 1000, so that an atomID = M in the data file

becomes atomID = 1000+M.  If {merge} is specified, the data file atoms

The three choices for the {add} argument affect how the atom IDs and

molecule IDs of atoms in the data file are treated.  If {append} is

specified, atoms in the data file are added to the current system,

with their atom IDs reset so that an atomID = M in the data file

becomes atomID = N+M, where N is the largest atom ID in the current

system.  This rule is applied to all occurrences of atom IDs in the

data file, e.g. in the Velocity or Bonds section. This is also done

for molecule IDs, if the atom style does support molecule IDs or

they are enabled via fix property/atom. If {IDoffset} is specified,

then {IDoffset} is a numeric value is given, e.g. 1000, so that an

atomID = M in the data file becomes atomID = 1000+M. For systems

with enabled molecule IDs, another numerical argument {MOLoffset}

is required representing the equivalent offset for molecule IDs.

If {merge} is specified, the data file atoms

are added to the current system without changing their IDs.  They are

assumed to merge (without duplication) with the currently defined

atoms.  It is up to you to insure there are no multiply defined atom

IDs, as LAMMPS only performs an incomplete check that this is the case

by insuring the resulting max atomID >= the number of atoms.

by insuring the resulting max atomID >= the number of atoms. For

molecule IDs, there is no check done at all.



The {offset} and {shift} keywords can only be used if the {add}

keyword is also specified.

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