From d5921e9fb9e8d231edefcab5b5cdbc9f413c47c7 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 29 Jun 2017 16:30:49 -0400
Subject: [PATCH] consolidate and update error message and read_data
documentation for the updated read_data command
---
doc/src/Section_errors.txt | 18 ++++++++----------
doc/src/read_data.txt | 39 ++++++++++++++++++++++----------------
src/read_data.h | 16 ++++++++--------
3 files changed, 39 insertions(+), 34 deletions(-)
diff --git a/doc/src/Section_errors.txt b/doc/src/Section_errors.txt
index 4fe6766d12..40e61a248e 100644
--- a/doc/src/Section_errors.txt
+++ b/doc/src/Section_errors.txt
@@ -9686,25 +9686,23 @@ Self-explanatory. :dd
{Subsequent read data induced too many angles per atom} :dt
-See the read_data or create_box commands for info on using the
-"extra/angle/per/atom" keyword to allow for additional angles to be formed :dd
+See the extra/angle/per/atom keyword for the create_box
+or the read_data command to set this limit larger :dd
{Subsequent read data induced too many bonds per atom} :dt
-See the read_data or create_box commands for info on using the
-"extra/bond/per/atom" keyword to allow for additional bonds to be formed :dd
+See the extra/bond/per/atom keyword for the create_box
+or the read_data command to set this limit larger :dd
{Subsequent read data induced too many dihedrals per atom} :dt
-See the read_data or create_box commands for info on using the
-"extra/dihedral/per/atom" keyword to allow for additional
-dihedrals to be formed :dd
+See the extra/dihedral/per/atom keyword for the create_box
+or the read_data command to set this limit larger :dd
{Subsequent read data induced too many impropers per atom} :dt
-See the read_data or create_box commands for info on using the
-"extra/improper/per/atom" keyword to allow for additional
-impropers to be formed :dd
+See the extra/improper/per/atom keyword for the create_box
+or the read_data command to set this limit larger :dd
{Substitution for illegal variable} :dt
diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt
index 732578b9f4..bd602eee5a 100644
--- a/doc/src/read_data.txt
+++ b/doc/src/read_data.txt
@@ -269,11 +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
@@ -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
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
diff --git a/src/read_data.h b/src/read_data.h
index 5f83b78c61..730229c722 100644
--- a/src/read_data.h
+++ b/src/read_data.h
@@ -472,8 +472,8 @@ outside a non-periodic simulation box.
E: Subsequent read data induced too many bonds per atom
-See the create_box extra/bond/per/atom or the read_data
-extra/bond/per/atom keyword to set this limit larger.
+See the extra/bond/per/atom keyword for the create_box
+or the read_data command to set this limit larger.
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
-See the create_box extra/angle/per/atom or the read_data
-extra/angle/per/atom keyword to set this limit larger.
+See the extra/angle/per/atom keyword for the create_box
+or the read_data command to set this limit larger.
E: Angles assigned incorrectly
@@ -493,8 +493,8 @@ definitions.
E: Subsequent read data induced too many dihedrals per atom
-See the create_box extra/dihedral/per/atom or the read_data
-extra/dihedral/per/atom keyword to set this limit larger.
+See the extra/dihedral/per/atom keyword for the create_box
+or the read_data command to set this limit larger.
E: Dihedrals assigned incorrectly
@@ -504,8 +504,8 @@ definitions.
E: Subsequent read data induced too many impropers per atom
-See the create_box extra/improper/per/atom or the read_data
-extra/improper/per/atom keyword to set this limit larger.
+See the extra/improper/per/atom keyword for the create_box
+or the read_data command to set this limit larger.
E: Impropers assigned incorrectly
--
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