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consolidate and update error message and read_data documentation for the updated read_data command

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This commit is contained in:
Axel Kohlmeyer
2017-06-29 16:30:49 -04:00
parent aa3f4b7690
commit d5921e9fb9
3 changed files with 39 additions and 34 deletions
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18
doc/src/Section_errors.txt
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@ -9686,25 +9686,23 @@ Self-explanatory. :dd
{Subsequent read data induced too many angles per atom} :dt {Subsequent read data induced too many angles per atom} :dt
See the read_data or create_box commands for info on using the See the extra/angle/per/atom keyword for the create_box
"extra/angle/per/atom" keyword to allow for additional angles to be formed :dd or the read_data command to set this limit larger :dd
{Subsequent read data induced too many bonds per atom} :dt {Subsequent read data induced too many bonds per atom} :dt
See the read_data or create_box commands for info on using the See the extra/bond/per/atom keyword for the create_box
"extra/bond/per/atom" keyword to allow for additional bonds to be formed :dd or the read_data command to set this limit larger :dd
{Subsequent read data induced too many dihedrals per atom} :dt {Subsequent read data induced too many dihedrals per atom} :dt
See the read_data or create_box commands for info on using the See the extra/dihedral/per/atom keyword for the create_box
"extra/dihedral/per/atom" keyword to allow for additional or the read_data command to set this limit larger :dd
dihedrals to be formed :dd
{Subsequent read data induced too many impropers per atom} :dt {Subsequent read data induced too many impropers per atom} :dt
See the read_data or create_box commands for info on using the See the extra/improper/per/atom keyword for the create_box
"extra/improper/per/atom" keyword to allow for additional or the read_data command to set this limit larger :dd
impropers to be formed :dd
{Substitution for illegal variable} :dt {Substitution for illegal variable} :dt

39
doc/src/read_data.txt
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@ -269,11 +269,11 @@ is different than the default.
{angle types} = # of angle types in system {angle types} = # of angle types in system
{dihedral types} = # of dihedral types in system {dihedral types} = # of dihedral types in system
{improper types} = # of improper types in system {improper types} = # of improper types in system
{extra bond per atom} = leave space for this many new 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 {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 {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 {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 {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 {ellipsoids} = # of ellipsoids in system
{lines} = # of line segments in system {lines} = # of line segments in system
{triangles} = # of triangles in system {triangles} = # of triangles in system
@ -372,25 +372,32 @@ read_data command will generate an error in this case.
The "extra bond per atom" setting (angle, dihedral, improper) is only The "extra bond per atom" setting (angle, dihedral, improper) is only
needed if new bonds (angles, dihedrals, impropers) will be added to needed if new bonds (angles, dihedrals, impropers) will be added to
the system when a simulation runs, e.g. by using the "fix the system when a simulation runs, e.g. by using the "fix
bond/create"_fix_bond_create.html command. This will pre-allocate bond/create"_fix_bond_create.html command. Using this header flag
space in LAMMPS data structures for storing the new bonds (angles, 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). dihedrals, impropers).
The "extra special per atom" setting is typically only needed if new 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 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 bond/create"_fix_bond_create.html command. Or if entire new molecules
will be added to the system, e.g. by using the "fix will be added to the system, e.g. by using the
deposit"_fix_deposit.html or "fix pour"_fix_pour.html commands, which "fix deposit"_fix_deposit.html or "fix pour"_fix_pour.html commands,
will have more special 1-2,1-3,1-4 neighbors than any other molecules which will have more special 1-2,1-3,1-4 neighbors than any other
defined in the data file. Using this setting will pre-allocate space molecules defined in the data file. Using this header flag is
in the LAMMPS data structures for storing these neighbors. See the 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 "special_bonds"_special_bonds.html and "molecule"_molecule.html doc
pages for more discussion of 1-2,1-3,1-4 neighbors. 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 NOTE: All of the "extra" settings are only applied in the first data
first data file read; see the description of the {add} keyword above file read and when no simulation box has yet been created; as soon as
for reading multiple data files. If they appear in later data files, the simulation box is created (and read_data implies that), these
they are ignored. 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 The "ellipsoids" and "lines" and "triangles" and "bodies" settings are
only used with "atom_style ellipsoid or line or tri or only used with "atom_style ellipsoid or line or tri or

16
src/read_data.h
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@ -472,8 +472,8 @@ outside a non-periodic simulation box.
E: Subsequent read data induced too many bonds per atom E: Subsequent read data induced too many bonds per atom
See the create_box extra/bond/per/atom or the read_data See the extra/bond/per/atom keyword for the create_box
extra/bond/per/atom keyword to set this limit larger. or the read_data command to set this limit larger.
E: Bonds assigned incorrectly E: Bonds assigned incorrectly
@ -482,8 +482,8 @@ This means there is something invalid about the topology definitions.
E: Subsequent read data induced too many angles per atom E: Subsequent read data induced too many angles per atom
See the create_box extra/angle/per/atom or the read_data See the extra/angle/per/atom keyword for the create_box
extra/angle/per/atom keyword to set this limit larger. or the read_data command to set this limit larger.
E: Angles assigned incorrectly E: Angles assigned incorrectly
@ -493,8 +493,8 @@ definitions.
E: Subsequent read data induced too many dihedrals per atom E: Subsequent read data induced too many dihedrals per atom
See the create_box extra/dihedral/per/atom or the read_data See the extra/dihedral/per/atom keyword for the create_box
extra/dihedral/per/atom keyword to set this limit larger. or the read_data command to set this limit larger.
E: Dihedrals assigned incorrectly E: Dihedrals assigned incorrectly
@ -504,8 +504,8 @@ definitions.
E: Subsequent read data induced too many impropers per atom E: Subsequent read data induced too many impropers per atom
See the create_box extra/improper/per/atom or the read_data See the extra/improper/per/atom keyword for the create_box
extra/improper/per/atom keyword to set this limit larger. or the read_data command to set this limit larger.
E: Impropers assigned incorrectly E: Impropers assigned incorrectly