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restore changes to read_data docs, that would have been lost due to merging an outdated version

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This commit is contained in:
Axel Kohlmeyer
2017-08-23 00:01:19 -04:00
parent 79d5ca669d
commit b80752a40c
1 changed files with 30 additions and 18 deletions
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48
doc/src/read_data.txt
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@ -14,7 +14,7 @@ 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 {group} or {nocoeff} or {fix} :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
@ -32,6 +32,11 @@ keyword = {add} or {offset} or {shift} or {extra/atom/types} or {extra/bond/type
{extra/angle/types} arg = # of extra angle types
{extra/dihedral/types} arg = # of extra dihedral types
{extra/improper/types} arg = # of extra improper types
{extra/bond/per/atom} arg = leave space for this many new bonds per atom
{extra/angle/per/atom} arg = leave space for this many new angles per atom
{extra/dihedral/per/atom} arg = leave space for this many new dihedrals per atom
{extra/improper/per/atom} arg = leave space for this many new impropers per atom
{extra/special/per/atom} arg = leave space for extra 1-2,1-3,1-4 interactions per atom
{group} args = groupID
groupID = add atoms in data file to this group
{nocoeff} = ignore force field parameters
@ -57,7 +62,7 @@ simulation. The file can be ASCII text or a gzipped text file
atom coordinates; see the "read_restart"_read_restart.html and
"create_atoms"_create_atoms.html commands for alternative methods.
Also see the explanation of the "-restart command-line
switch"_Section_start.html#start_7 which can convert a restart file to
switch"_Section_start.html#start_6 which can convert a restart file to
a data file.
This command can be used multiple times to add new atoms and their
@ -264,11 +269,11 @@ is different than the default.
{angle types} = # of angle types in system
{dihedral types} = # of dihedral types in system
{improper types} = # of improper types in system
{extra bond per atom} = leave space for this many new bonds per atom
{extra angle per atom} = leave space for this many new angles per atom
{extra dihedral per atom} = leave space for this many new dihedrals per atom
{extra improper per atom} = leave space for this many new impropers per atom
{extra special per atom} = leave space for this many new special bonds per atom
{extra bond per atom} = leave space for this many new bonds per atom (deprecated, use extra/bond/per/atom keyword)
{extra angle per atom} = leave space for this many new angles per atom (deprecated, use extra/angle/per/atom keyword)
{extra dihedral per atom} = leave space for this many new dihedrals per atom (deprecated, use extra/dihedral/per/atom keyword)
{extra improper per atom} = leave space for this many new impropers per atom (deprecated, use extra/improper/per/atom keyword)
{extra special per atom} = leave space for this many new special bonds per atom (deprecated, use extra/special/per/atom keyword)
{ellipsoids} = # of ellipsoids in system
{lines} = # of line segments in system
{triangles} = # of triangles in system
@ -367,25 +372,32 @@ read_data command will generate an error in this case.
The "extra bond per atom" setting (angle, dihedral, improper) is only
needed if new bonds (angles, dihedrals, impropers) will be added to
the system when a simulation runs, e.g. by using the "fix
bond/create"_fix_bond_create.html command. This will pre-allocate
space in LAMMPS data structures for storing the new bonds (angles,
bond/create"_fix_bond_create.html command. Using this header flag
is deprecated; please use the {extra/bond/per/atom} keyword (and
correspondingly for angles, dihedrals and impropers) in the
read_data command instead. Either will pre-allocate space in LAMMPS
data structures for storing the new bonds (angles,
dihedrals, impropers).
The "extra special per atom" setting is typically only needed if new
bonds/angles/etc will be added to the system, e.g. by using the "fix
bond/create"_fix_bond_create.html command. Or if entire new molecules
will be added to the system, e.g. by using the "fix
deposit"_fix_deposit.html or "fix pour"_fix_pour.html commands, which
will have more special 1-2,1-3,1-4 neighbors than any other molecules
defined in the data file. Using this setting will pre-allocate space
in the LAMMPS data structures for storing these neighbors. See the
will be added to the system, e.g. by using the
"fix deposit"_fix_deposit.html or "fix pour"_fix_pour.html commands,
which will have more special 1-2,1-3,1-4 neighbors than any other
molecules defined in the data file. Using this header flag is
deprecated; please use the {extra/special/per/atom} keyword instead.
Using this setting will pre-allocate space in the LAMMPS data
structures for storing these neighbors. See the
"special_bonds"_special_bonds.html and "molecule"_molecule.html doc
pages for more discussion of 1-2,1-3,1-4 neighbors.
NOTE: All of the "extra" settings are only used if they appear in the
first data file read; see the description of the {add} keyword above
for reading multiple data files. If they appear in later data files,
they are ignored.
NOTE: All of the "extra" settings are only applied in the first data
file read and when no simulation box has yet been created; as soon as
the simulation box is created (and read_data implies that), these
settings are {locked} and cannot be changed anymore. Please see the
description of the {add} keyword above for reading multiple data files.
If they appear in later data files, they are ignored.
The "ellipsoids" and "lines" and "triangles" and "bodies" settings are
only used with "atom_style ellipsoid or line or tri or