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# Conflicts:
#	doc/Manual.html
#	doc/Manual.txt
#	doc/read_restart.txt
#	src/atom.cpp
#	src/read_data.cpp
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4
doc/Manual.html
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@ -1,7 +1,7 @@
<HTML>
<HEAD>
<TITLE>LAMMPS-ICMS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="17 Jul 2015 version">
<META NAME="docnumber" CONTENT="18 Jul 2015 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>
@ -22,7 +22,7 @@
<CENTER><H3>LAMMPS-ICMS Documentation
</H3></CENTER>
<CENTER><H4>17 Jul 2015 version
<CENTER><H4>18 Jul 2015 version
</H4></CENTER>
<H4>Version info:
</H4>

4
doc/Manual.txt
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@ -1,6 +1,6 @@
<HEAD>
<TITLE>LAMMPS-ICMS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="17 Jul 2015 version">
<META NAME="docnumber" CONTENT="18 Jul 2015 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>
@ -18,7 +18,7 @@
<H1></H1>
LAMMPS-ICMS Documentation :c,h3
17 Jul 2015 version :c,h4
18 Jul 2015 version :c,h4
Version info: :h4

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doc/atom_modify.html
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@ -46,16 +46,18 @@ simulation box is defined; other keywords can be specified any time.
to each atom. If the value is <I>yes</I>, which is the default, IDs are
assigned, whether you use the <A HREF = "create_atoms.html">create atoms</A> or
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands to initialize atoms. If atom IDs are used, they must all be
positive integers. They should also be unique, though LAMMPS does not
check for this. Typically they should also be consecutively numbered
(from 1 to Natoms), though this is not required. Molecular <A HREF = "atom_style.html">atom
styles</A> are those that store bond topology information
(styles bond, angle, molecular, full). These styles require atom IDs
since the IDs are used to encode the topology. Some other LAMMPS
commands also require the use of atom IDs. E.g. some many-body pair
styles use them to avoid double computation of the I-J interaction
between two atoms.
commands to initialize atoms. If the value is <I>no</I> the IDs for all
atoms are assumed to be 0.
</P>
<P>If atom IDs are used, they must all be positive integers. They should
also be unique, though LAMMPS does not check for this. Typically they
should also be consecutively numbered (from 1 to Natoms), though this
is not required. Molecular <A HREF = "atom_style.html">atom styles</A> are those
that store bond topology information (styles bond, angle, molecular,
full). These styles require atom IDs since the IDs are used to encode
the topology. Some other LAMMPS commands also require the use of atom
IDs. E.g. some many-body pair styles use them to avoid double
computation of the I-J interaction between two atoms.
</P>
<P>The only reason not to use atom IDs is if you are running an atomic
simulation so large that IDs cannot be uniquely assigned. For a

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doc/atom_modify.txt
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@ -40,16 +40,18 @@ The {id} keyword determines whether non-zero atom IDs can be assigned
to each atom. If the value is {yes}, which is the default, IDs are
assigned, whether you use the "create atoms"_create_atoms.html or
"read_data"_read_data.html or "read_restart"_read_restart.html
commands to initialize atoms. If atom IDs are used, they must all be
positive integers. They should also be unique, though LAMMPS does not
check for this. Typically they should also be consecutively numbered
(from 1 to Natoms), though this is not required. Molecular "atom
styles"_atom_style.html are those that store bond topology information
(styles bond, angle, molecular, full). These styles require atom IDs
since the IDs are used to encode the topology. Some other LAMMPS
commands also require the use of atom IDs. E.g. some many-body pair
styles use them to avoid double computation of the I-J interaction
between two atoms.
commands to initialize atoms. If the value is {no} the IDs for all
atoms are assumed to be 0.
If atom IDs are used, they must all be positive integers. They should
also be unique, though LAMMPS does not check for this. Typically they
should also be consecutively numbered (from 1 to Natoms), though this
is not required. Molecular "atom styles"_atom_style.html are those
that store bond topology information (styles bond, angle, molecular,
full). These styles require atom IDs since the IDs are used to encode
the topology. Some other LAMMPS commands also require the use of atom
IDs. E.g. some many-body pair styles use them to avoid double
computation of the I-J interaction between two atoms.
The only reason not to use atom IDs is if you are running an atomic
simulation so large that IDs cannot be uniquely assigned. For a

24
doc/info.html
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@ -15,20 +15,30 @@
</P>
<PRE>info args
</PRE>
<UL><LI>args = one or more of the following keywords: <I>system</I>, <I>computes</I>, <I>dumps</I>, <I>fixes</I>, <I>groups</I>, <I>regions</I>, <I>variables</I>, <I>time</I>, or <I>configuration</I>
</UL>
<P>args = one or more of the following keywords: <I>out</I>, <I>all</I>, <I>system</I>, <I>computes</I>, <I>dumps</I>, <I>fixes</I>, <I>groups</I>, <I>regions</I>, <I>variables</I>, <I>time</I>, or <I>configuration</I>
<I>out</I> values = <I>screen</I>, <I>log</I>, <I>append</I> filename, <I>overwrite</I> filename:ul
</P>
<P><B>Examples:</B>
</P>
<PRE>info system
info groups computes variables
info groups computes variables
info all out log
info all out append info.txt
</PRE>
<P><B>Description:</B>
</P>
<P>Print out information about the current internal state of the running
LAMMPS process. This can be helpful when debugging or validating
complex input scripts. Several output categories are available and
one or more output category may be requested. Output is only sent to
the screen, provided screen output is enabled.
one or more output category may be requested.
</P>
<P>The <I>out</I> flag controls where the output is sent. It can only be sent
to one target. By default this is the screen, if it is active. The
<I>log</I> argument selects the log file instead. With the <I>append</I> and
<I>overwrite</I> option, followed by a filename, the output is written
to that file, which is either appended to or overwritten, respectively.
</P>
<P>The <I>all</I> flag activates printing all categories listed below.
</P>
<P>The <I>system</I> category prints a general system overview listing. This
includes the unit style, atom style, number of atoms, bonds, angles,
@ -68,6 +78,8 @@ reported.
</P>
<P><A HREF = "print.html">print</A>
</P>
<P><B>Default:</B> none
<P><B>Default:</B>
</P>
<P>The <I>out</I> option has the default <I>screen</I>.
</P>
</HTML>

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doc/read_data.html
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@ -19,9 +19,28 @@
<LI>zero or more keyword/arg pairs may be appended
<LI>keyword = <I>fix</I>
<LI>keyword = <I>add</I> or <I>offset</I> or <I>shift</I> or <I>extra/atom/types</I> or <I>extra/bond/types</I> or <I>extra/angle/types</I> or <I>extra/dihedral/types</I> or <I>extra/improper/types</I> or <I>group</I> or <I>fix</I>
<PRE> <I>fix</I> args = fix-ID header-string section-string
<PRE> <I>add</I> arg = <I>append</I> or <I>Nstart</I> or <I>merge</I>
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
<I>offset</I> args = toff boff aoff doff ioff
toff = offset to add to atom types
boff = offset to add to bond types
aoff = offset to add to angle types
doff = offset to add to dihedral types
ioff = offset to add to improper types
<I>shift</I> args = Sx Sy Sz
Sx,Sy,Sz = distance to shift atoms when adding to system (distance units)
<I>extra/atom/types</I> arg = # of extra atom types
<I>extra/bond/types</I> arg = # of extra bond types
<I>extra/angle/types</I> arg = # of extra angle types
<I>extra/dihedral/types</I> arg = # of extra dihedral types
<I>extra/improper/types</I> arg = # of extra improper types
<I>group</I> args = groupID
groupID = add atoms in data file to this group
<I>fix</I> args = fix-ID header-string section-string
fix-ID = ID of fix to process header lines and sections of data file
header-string = header lines containing this string will be passed to fix
section-string = section names with this string will be passed to fix
@ -33,6 +52,8 @@
<PRE>read_data data.lj
read_data ../run7/data.polymer.gz
read_data data.protein fix mycmap crossterm CMAP
read_data data.water add append offset 3 1 1 1 1 shift 0.0 0.0 50.0
read_data data.water add merge 1 group solvent
</PRE>
<P><B>Description:</B>
</P>
@ -45,6 +66,140 @@ Also see the explanation of the <A HREF = "Section_start.html#start_7">-restart
switch</A> which can convert a restart file to
a data file.
</P>
<P>This command can be used multiple times to add new atoms and their
properties to an existing system by using the <I>add</I>, <I>offset</I>, and
<I>shift</I> keywords. See more details below, which includes the use case
for the <I>extra</I> keywords.
</P>
<P>The <I>group</I> keyword adds all the atoms in the data file to the
specified group-ID. The group will be created if it does not already
exist. This is useful if you are reading multiple data files and wish
to put sets of atoms into different groups so they can be operated on
later. E.g. a group of added atoms can be moved to new positions via
the <A HREF = "displace_atoms.html">displace_atoms</A> command. Note that atoms
read from the data file are also always added to the "all" group. The
<A HREF = "group.html">group</A> command discusses atom groups, as used in LAMMPS.
</P>
<P>The use of the <I>fix</I> keyword is discussed below.
</P>
<HR>
<P><B>Reading multiple data files</B>
</P>
<P>The read_data command can be used multiple times with the same or
different data files to build up a complex system from components
contained in individual data files. For example one data file could
contain fluid in a confined domain; a second could contain wall atoms,
and the second file could be read a third time to create a wall on the
other side of the fluid. The third set of atoms could be rotated to
an opposing direction using the <A HREF = "displace_atoms.html">displace_atoms</A>
command, after the third read_data command is used.
</P>
<P>The <I>add</I>, <I>offset</I>, <I>shift</I>, <I>extra</I>, and <I>group</I> keywords are
useful in this context.
</P>
<P>If a simulation box does not yet exist, the <I>add</I> keyword
cannot be used; the read_data command is being used for the first
time. If a simulation box does exist, due to using the
<A HREF = "create_box.html">create_box</A> command, or a previous read_data command,
then the <I>add</I> keyword must be used.
</P>
<P>IMPORTANT NOTE: The simulation box size (xlo to xhi, ylo to yhi, zlo
to zhi) in the new data file will be merged with the existing
simulation box to create a large enough box in each dimension to
contain both the existing and new atoms. Each box dimension never
shrinks due to this merge operation, it only stays the same or
grows. Care must be used if you are growing the existing simulation
box in a periodic dimension. If there are existing atoms with bonds
that straddle that periodic 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.
</P>
<P>The three choices for the <I>add</I> argument affect how the IDs of atoms
in the data file are treated. If <I>append</I> 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 <I>Nstart</I> is specified, then <I>Nstart</I> is a numeric
value is given, e.g. 1000, so that an atomID = M in the data file
becomes atomID = 1000+M. If <I>merge</I> 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.
</P>
<P>The <I>offset</I> and <I>shift</I> keywords can only be used if the <I>add</I>
keyword is also specified.
</P>
<P>The <I>offset</I> keyword adds the specified offset values to the atom
types, bond types, angle types, dihedral types, and improper types as
they are read from the data file. E.g. if <I>toff</I> = 2, and the file
uses atom types 1,2,3, then the added atoms will have atom types
3,4,5. These offsets apply to all occurrences of types in the data
file, e.g. for the Atoms or Masses or Pair Coeffs or Bond Coeffs
sections. This makes it easy to use atoms and molecules and their
attributes from a data file in different simulations, where you want
their types (atom, bond, angle, etc) to be different depending on what
other types already exist. All five offset values must be specified,
but individual values will be ignored if the data file does not use
that attribute (e.g. no bonds).
</P>
<P>The <I>shift</I> keyword can be used to specify an (Sx, Sy, Sz)
displacement applied to the coordinates of each atom. Sz must be 0.0
for a 2d simulation. This is a mechanism for adding structured
collections of atoms at different locations within the simulation box,
to build up a complex geometry. It is up to you to insure atoms do
not end up overlapping unphysically which would lead to bad dynamics.
Note that the <A HREF = "displace_atoms.html">displace_atoms</A> command can be used
to move a subset of atoms after they have been read from a data file.
Likewise, the <A HREF = "delete_atoms.html">delete_atoms</A> command can be used to
remove overlapping atoms. Note that the shift values (Sx, Sy, Sz) are
also added to the simulation box information (xlo, xhi, ylo, yhi, zlo,
zhi) in the data file to shift its boundaries. E.g. xlo_new = xlo +
Sx, xhi_new = xhi + Sx.
</P>
<P>The <I>extra</I> keywords can only be used the first time the read_data
command is used. They are useful if you intend to add new atom, bond,
angle, etc types later with additional read_data commands. This is
because the maximum number of allowed atom, bond, angle, etc types is
set by LAMMPS when the system is first initialized. If you do not use
the <I>extra</I> keywords, then the number of these types will be limited
to what appears in the first data file you read. For example, if the
first data file is a solid substrate of Si, it will likely specify a
single atom type. If you read a second data file with a different
material (water molecules) that sit on top of the substrate, you will
want to use different atom types for those atoms. You can only do
this if you set the <I>extra/atom/types</I> keyword to a sufficiently large
value when reading the substrate data file. Note that use of the
<I>extra</I> keywords also allows each data file to contain sections like
Masses or Pair Coeffs or Bond Coeffs which are sized appropriately for
the number of types in that data file. If the <I>offset</I> keyword is
used appropriately when each data file is read, the values in those
sections will be stored correctly in the larger data structures
allocated by the use of the <I>extra</I> keywords. E.g. the substrate file
can list mass and pair coefficients for type 1 silicon atoms. The
water file can list mass and pair coeffcients for type 1 and type 2
hydrogen and oxygen atoms. Use of the <I>extra</I> and <I>offset</I> keywords
will store those mass and pair coefficient values appropriately in
data structures that allow for 3 atom types (Si, H, O). Of course,
you would still need to specify coefficients for H/Si and O/Si
interactions in your input script to have a complete pairwise
interaction model.
</P>
<P>An alternative to using the <I>extra</I> keywords with the read_data
command, is to use the <A HREF = "create_box.html">create_box</A> command to
initialize the simulation box and all the various type limits you need
via its <I>extra</I> keywords. Then use the read_data command one or more
times to populate the system with atoms, bonds, angles, etc, using the
<I>offset</I> keyword if desired to alter types used in the various data
files you read.
</P>
<HR>
<P><B>Format of a data file</B>
</P>
<P>The structure of the data file is important, though many settings and
sections are optional or can come in any order. See the examples
directory for sample data files for different problems.
@ -88,6 +243,8 @@ the 2 words in "Bond Coeffs", is not valid.
</P>
<HR>
<P><B>Format of the header of a data file</B>
</P>
<P>These are the recognized header keywords. Header lines can come in
any order. The value(s) are read from the beginning of the line.
Thus the keyword <I>atoms</I> should be in a line like "1000 atoms"; the
@ -183,7 +340,11 @@ and yz tilt factors must be 0.0.
</P>
<P>If the system is periodic (in a dimension), then atom coordinates can
be outside the bounds (in that dimension); they will be remapped (in a
periodic sense) back inside the box.
periodic sense) back inside the box. Note that if the <I>add</I> option is
being used to add atoms to a simulation box that already exists, this
periodic remapping will be performed using simulation box bounds that
are the union of the existing box and the box boundaries in the new
data file.
</P>
<P>IMPORTANT NOTE: If the system is non-periodic (in a dimension), then
all atoms in the data file must have coordinates (in that dimension)
@ -222,6 +383,11 @@ in the LAMMPS data structures for storing these neighbors. See the
<A HREF = "special_bonds.html">special_bonds</A> and <A HREF = "molecule.html">molecule</A> doc
pages for more discussion of 1-2,1-3,1-4 neighbors.
</P>
<P>IMPORTANT NOTE: All of the "extra" settings are only used if they
appear in the first data file read; see the description of the <I>add</I>
keyword above for reading multiple data files. If they appear in
later data files, they are ignored.
</P>
<P>The "ellipsoids" and "lines" and "triangles" and "bodies" settings are
only used with <A HREF = "atom_style.html">atom_style ellipsoid or line or tri or
body</A> and specify how many of the atoms are
@ -243,6 +409,8 @@ the maximum values defined in any of the template molecules.
</P>
<HR>
<P><B>Format of the body of a data file</B>
</P>
<P>These are the section keywords for the body of the file.
</P>
<UL><LI><I>Atoms, Velocities, Masses, Ellipsoids, Lines, Triangles, Bodies</I> = atom-property sections
@ -1056,6 +1224,8 @@ LAMMPS</A> section of the documentation.
<P><A HREF = "read_dump.html">read_dump</A>, <A HREF = "read_restart.html">read_restart</A>,
<A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "write_data.html">write_data</A>
</P>
<P><B>Default:</B> none
<P><B>Default:</B>
</P>
<P>The default for all the <I>extra</I> keywords is 0.
</P>
</HTML>

179
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@ -14,19 +14,39 @@ 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 = {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 {group} 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
{offset} args = toff boff aoff doff ioff
toff = offset to add to atom types
boff = offset to add to bond types
aoff = offset to add to angle types
doff = offset to add to dihedral types
ioff = offset to add to improper types
{shift} args = Sx Sy Sz
Sx,Sy,Sz = distance to shift atoms when adding to system (distance units)
{extra/atom/types} arg = # of extra atom types
{extra/bond/types} arg = # of extra bond types
{extra/angle/types} arg = # of extra angle types
{extra/dihedral/types} arg = # of extra dihedral types
{extra/improper/types} arg = # of extra improper types
{group} args = groupID
groupID = add atoms in data file to this group
{fix} args = fix-ID header-string section-string
fix-ID = ID of fix to process header lines and sections of data file
header-string = header lines containing this string will be passed to fix
section-string = section names with this string will be passed to fix :pre
:ule
[Examples:]
read_data data.lj
read_data ../run7/data.polymer.gz
read_data data.protein fix mycmap crossterm CMAP :pre
read_data data.protein fix mycmap crossterm CMAP
read_data data.water add append offset 3 1 1 1 1 shift 0.0 0.0 50.0
read_data data.water add merge 1 group solvent :pre
[Description:]
@ -39,6 +59,140 @@ Also see the explanation of the "-restart command-line
switch"_Section_start.html#start_7 which can convert a restart file to
a data file.
This command can be used multiple times to add new atoms and their
properties to an existing system by using the {add}, {offset}, and
{shift} keywords. See more details below, which includes the use case
for the {extra} keywords.
The {group} keyword adds all the atoms in the data file to the
specified group-ID. The group will be created if it does not already
exist. This is useful if you are reading multiple data files and wish
to put sets of atoms into different groups so they can be operated on
later. E.g. a group of added atoms can be moved to new positions via
the "displace_atoms"_displace_atoms.html command. Note that atoms
read from the data file are also always added to the "all" group. The
"group"_group.html command discusses atom groups, as used in LAMMPS.
The use of the {fix} keyword is discussed below.
:line
[Reading multiple data files]
The read_data command can be used multiple times with the same or
different data files to build up a complex system from components
contained in individual data files. For example one data file could
contain fluid in a confined domain; a second could contain wall atoms,
and the second file could be read a third time to create a wall on the
other side of the fluid. The third set of atoms could be rotated to
an opposing direction using the "displace_atoms"_displace_atoms.html
command, after the third read_data command is used.
The {add}, {offset}, {shift}, {extra}, and {group} keywords are
useful in this context.
If a simulation box does not yet exist, the {add} keyword
cannot be used; the read_data command is being used for the first
time. If a simulation box does exist, due to using the
"create_box"_create_box.html command, or a previous read_data command,
then the {add} keyword must be used.
IMPORTANT NOTE: The simulation box size (xlo to xhi, ylo to yhi, zlo
to zhi) in the new data file will be merged with the existing
simulation box to create a large enough box in each dimension to
contain both the existing and new atoms. Each box dimension never
shrinks due to this merge operation, it only stays the same or
grows. Care must be used if you are growing the existing simulation
box in a periodic dimension. If there are existing atoms with bonds
that straddle that periodic 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
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.
The {offset} and {shift} keywords can only be used if the {add}
keyword is also specified.
The {offset} keyword adds the specified offset values to the atom
types, bond types, angle types, dihedral types, and improper types as
they are read from the data file. E.g. if {toff} = 2, and the file
uses atom types 1,2,3, then the added atoms will have atom types
3,4,5. These offsets apply to all occurrences of types in the data
file, e.g. for the Atoms or Masses or Pair Coeffs or Bond Coeffs
sections. This makes it easy to use atoms and molecules and their
attributes from a data file in different simulations, where you want
their types (atom, bond, angle, etc) to be different depending on what
other types already exist. All five offset values must be specified,
but individual values will be ignored if the data file does not use
that attribute (e.g. no bonds).
The {shift} keyword can be used to specify an (Sx, Sy, Sz)
displacement applied to the coordinates of each atom. Sz must be 0.0
for a 2d simulation. This is a mechanism for adding structured
collections of atoms at different locations within the simulation box,
to build up a complex geometry. It is up to you to insure atoms do
not end up overlapping unphysically which would lead to bad dynamics.
Note that the "displace_atoms"_displace_atoms.html command can be used
to move a subset of atoms after they have been read from a data file.
Likewise, the "delete_atoms"_delete_atoms.html command can be used to
remove overlapping atoms. Note that the shift values (Sx, Sy, Sz) are
also added to the simulation box information (xlo, xhi, ylo, yhi, zlo,
zhi) in the data file to shift its boundaries. E.g. xlo_new = xlo +
Sx, xhi_new = xhi + Sx.
The {extra} keywords can only be used the first time the read_data
command is used. They are useful if you intend to add new atom, bond,
angle, etc types later with additional read_data commands. This is
because the maximum number of allowed atom, bond, angle, etc types is
set by LAMMPS when the system is first initialized. If you do not use
the {extra} keywords, then the number of these types will be limited
to what appears in the first data file you read. For example, if the
first data file is a solid substrate of Si, it will likely specify a
single atom type. If you read a second data file with a different
material (water molecules) that sit on top of the substrate, you will
want to use different atom types for those atoms. You can only do
this if you set the {extra/atom/types} keyword to a sufficiently large
value when reading the substrate data file. Note that use of the
{extra} keywords also allows each data file to contain sections like
Masses or Pair Coeffs or Bond Coeffs which are sized appropriately for
the number of types in that data file. If the {offset} keyword is
used appropriately when each data file is read, the values in those
sections will be stored correctly in the larger data structures
allocated by the use of the {extra} keywords. E.g. the substrate file
can list mass and pair coefficients for type 1 silicon atoms. The
water file can list mass and pair coeffcients for type 1 and type 2
hydrogen and oxygen atoms. Use of the {extra} and {offset} keywords
will store those mass and pair coefficient values appropriately in
data structures that allow for 3 atom types (Si, H, O). Of course,
you would still need to specify coefficients for H/Si and O/Si
interactions in your input script to have a complete pairwise
interaction model.
An alternative to using the {extra} keywords with the read_data
command, is to use the "create_box"_create_box.html command to
initialize the simulation box and all the various type limits you need
via its {extra} keywords. Then use the read_data command one or more
times to populate the system with atoms, bonds, angles, etc, using the
{offset} keyword if desired to alter types used in the various data
files you read.
:line
[Format of a data file]
The structure of the data file is important, though many settings and
sections are optional or can come in any order. See the examples
directory for sample data files for different problems.
@ -82,6 +236,8 @@ the 2 words in "Bond Coeffs", is not valid.
:line
[Format of the header of a data file]
These are the recognized header keywords. Header lines can come in
any order. The value(s) are read from the beginning of the line.
Thus the keyword {atoms} should be in a line like "1000 atoms"; the
@ -177,7 +333,11 @@ and yz tilt factors must be 0.0.
If the system is periodic (in a dimension), then atom coordinates can
be outside the bounds (in that dimension); they will be remapped (in a
periodic sense) back inside the box.
periodic sense) back inside the box. Note that if the {add} option is
being used to add atoms to a simulation box that already exists, this
periodic remapping will be performed using simulation box bounds that
are the union of the existing box and the box boundaries in the new
data file.
IMPORTANT NOTE: If the system is non-periodic (in a dimension), then
all atoms in the data file must have coordinates (in that dimension)
@ -216,6 +376,11 @@ 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.
IMPORTANT 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.
The "ellipsoids" and "lines" and "triangles" and "bodies" settings are
only used with "atom_style ellipsoid or line or tri or
body"_atom_style.html and specify how many of the atoms are
@ -237,6 +402,8 @@ the maximum values defined in any of the template molecules.
:line
[Format of the body of a data file]
These are the section keywords for the body of the file.
{Atoms, Velocities, Masses, Ellipsoids, Lines, Triangles, Bodies} = atom-property sections
@ -946,4 +1113,6 @@ LAMMPS"_Section_start.html#start_2 section of the documentation.
"read_dump"_read_dump.html, "read_restart"_read_restart.html,
"create_atoms"_create_atoms.html, "write_data"_write_data.html
[Default:] none
[Default:]
The default for all the {extra} keywords is 0.

34
doc/read_restart.html
View File

@ -30,12 +30,13 @@ read_restart poly.*.% remap
</PRE>
<P><B>Description:</B>
</P>
<P>Read in a previously saved simulation from a restart file. This
allows continuation of a previous run. Information about what is
stored in a restart file is given below. Basically this operation
will re-create the simulation box with all its atoms and their
attributes, at the point in time it was written to the restart file by
a previous simluation. The simulation box will be partitioned into a
<P>Read in a previously saved system configuration from a restart file.
This allows continuation of a previous run. Details about what
information is stored (and not stored) in a restart file is given
below. Basically this operation will re-create the simulation box
with all its atoms and their attributes as well as some related global
settings, at the point in time it was written to the restart file by a
previous simluation. The simulation box will be partitioned into a
regular 3d grid of rectangular bricks, one per processor, based on the
number of processors in the current simulation and the settings of the
<A HREF = "processors.html">processors</A> command. The partitioning can later be
@ -137,22 +138,25 @@ written and read using MPI-IO.
<HR>
<P>A restart file stores the following information about a simulation:
units and atom style, simulation box size and shape and boundary
settings, group definitions, per-type atom settings such as mass,
per-atom attributes including their group assignments and molecular
topology attributes, force field styles and coefficients, and
units, atom style and atom style related settings (<I>id</I>, <I>map</I>,
<I>sort</I>), communication settings (<I>mode</I>, <I>cutoff</I>, <I>vel</I>), timestep,
simulation box size and shape and boundary settings, group
definitions, per-type atom settings such as mass, per-atom attributes
including their group assignments and molecular topology attributes,
force field styles and - in most cases - force field coefficients, and
<A HREF = "special_bonds.html">special_bonds</A> settings. This means that commands
for these quantities do not need to be re-specified in the input
script that reads the restart file, though you can redefine settings
after the restart file is read.
</P>
<P>One exception is that some pair styles do not store their info in
restart files. Typically these are many-body potentials which read
their parameters from separate files; you need to re-specify the <A HREF = "pair_style.html">pair
<P>One exception is that some force styles (pair, bond, angle, etc) do
not store their coefficient info in restart files. Typically these
are many-body or tabulated potentials which read their parameters from
separate files; you may need to re-specify the <A HREF = "pair_style.html">pair
style</A> and <A HREF = "pair_coeff.html">pair coeff</A> commands in
your restart input script. The doc pages for individual pair styles
note if this is the case. This is also true of bond_style hybrid (and
angle_style, dihedral_style, improper_style hybrid).
mention if this is the case. This is also true of bond_style hybrid
(and angle_style, dihedral_style, improper_style hybrid).
</P>
<P>All settings made by the <A HREF = "pair_modify.html">pair_modify</A> command, such
as the shift and tail settings, are stored in the restart file with

33
doc/read_restart.txt
View File

@ -28,15 +28,14 @@ read_restart poly.*.% remap :pre
[Description:]
Read in a previously saved system configuration from a restart file.
This allows continuation of a previous run. However, not the entire
state of a simulation can be saved and read back. Details about what
information is stored in a restart file is given below. Basically
this operation will re-create the simulation box with all its atoms
and their attributes as well as some related global settings, at the
point in time it was written to the restart file by a previous
simluation. The simulation box will be partitioned into a regular 3d
grid of rectangular bricks, one per processor, based on the number of
processors in the current simulation and the settings of the
This allows continuation of a previous run. Details about what
information is stored (and not stored) in a restart file is given
below. Basically this operation will re-create the simulation box
with all its atoms and their attributes as well as some related global
settings, at the point in time it was written to the restart file by a
previous simluation. The simulation box will be partitioned into a
regular 3d grid of rectangular bricks, one per processor, based on the
number of processors in the current simulation and the settings of the
"processors"_processors.html command. The partitioning can later be
changed by the "balance"_balance.html or "fix
balance"_fix_balance.html commands.
@ -147,14 +146,14 @@ for these quantities do not need to be re-specified in the input
script that reads the restart file, though you can redefine settings
after the restart file is read.
One exception is that some force styles do not store their coefficient
info in restart files. Typically these are many-body or tabulated
potentials which read their parameters from separate files;
you may need to re-specify the "pair style"_pair_style.html and
"pair coeff"_pair_coeff.html commands in your restart input script.
The doc pages for individual pair styles mention if this is the case.
This is also true of bond_style hybrid (and angle_style, dihedral_style,
improper_style hybrid).
One exception is that some force styles (pair, bond, angle, etc) do
not store their coefficient info in restart files. Typically these
are many-body or tabulated potentials which read their parameters from
separate files; you may need to re-specify the "pair
style"_pair_style.html and "pair coeff"_pair_coeff.html commands in
your restart input script. The doc pages for individual pair styles
mention if this is the case. This is also true of bond_style hybrid
(and angle_style, dihedral_style, improper_style hybrid).
All settings made by the "pair_modify"_pair_modify.html command, such
as the shift and tail settings, are stored in the restart file with

15
doc/restart.html
View File

@ -47,13 +47,14 @@ restart v_mystep poly.restart
</PRE>
<P><B>Description:</B>
</P>
<P>Write out a binary restart file every so many timesteps, in either or
both of two modes, as a run proceeds. A value of 0 means do not write
out any restart files. The two modes are as follows. If one filename
is specified, a series of filenames will be created which include the
timestep in the filename. If two filenames are specified, only 2
restart files will be created, with those names. LAMMPS will toggle
between the 2 names as it writes successive restart files.
<P>Write out a binary restart file with the current state of the
simulation every so many timesteps, in either or both of two modes, as
a run proceeds. A value of 0 means do not write out any restart
files. The two modes are as follows. If one filename is specified, a
series of filenames will be created which include the timestep in the
filename. If two filenames are specified, only 2 restart files will
be created, with those names. LAMMPS will toggle between the 2 names
as it writes successive restart files.
</P>
<P>Note that you can specify the restart command twice, once with a
single filename and once with two filenames. This would allow you,

7
doc/write_restart.html
View File

@ -83,9 +83,10 @@ fixes that were specified during the initial run is not stored, which
means the new input script must specify any fixes you want to use.
Even when restart information is stored in the file, as it is for some
fixes, commands may need to be re-specified in the new input script,
in order to re-use that information. See the
<A HREF = "read_restart.html">read_restart</A> command for information about what is
stored in a restart file.
in order to re-use that information. Details are usually given in
the documentation of the respective command. Also, see the
<A HREF = "read_restart.html">read_restart</A> command for general information
about what is stored in a restart file.
</P>
<HR>

185
lib/kokkos/config/nvcc_wrapper Executable file
View File

@ -0,0 +1,185 @@
#!/bin/bash
#
# This shell script (nvcc_wrapper) wraps both the host compiler and
# NVCC, if you are building Trilinos with CUDA enabled. The script
# remedies some differences between the interface of NVCC and that of
# the host compiler, in particular for linking. It also means that
# Trilinos doesn't need separate .cu files; it can just use .cpp
# files.
#
# Hopefully, at some point, NVIDIA may fix NVCC so as to make this
# script obsolete. For now, this script exists and if you want to
# build Trilinos with CUDA enabled, you must use this script as your
# compiler.
# Default settings: change those according to your machine. For
# example, you may have have two different wrappers with either icpc
# or g++ as their back-end compiler. The defaults can be overwritten
# by using the usual arguments (e.g., -arch=sm_30 -ccbin icpc).
default_arch="sm_35"
#default_arch="sm_50"
#
# The default C++ compiler.
#
default_compiler=${NVCC_WRAPPER_DEFAULT_COMPILER:-"g++"}
#default_compiler="icpc"
#default_compiler="/usr/local/gcc/4.8.3/bin/g++"
#default_compiler="/usr/local/gcc/4.9.1/bin/g++"
#
# Internal variables
#
cpp_files=""
xcompiler_args=""
cuda_arg=""
xlinker_args=""
object_files=""
object_files_xlinker=""
first_host_option=1
arch_set=0
ccbin_set=0
nvcc_error_code=0
dry_run=0
replace_pragma_ident=0
#echo "Arguments: $# $@"
while [ $# -gt 0 ]
do
case $1 in
#show the executed command
--show)
dry_run=1
;;
#replace '#pragma ident' with '#ident' this is needed to compile OpenMPI due to a configure script bug and a non standardized behaviour of pragma with macros
--replace-pragma-ident)
replace_pragma_ident=1
;;
#handle source files to be compiled as cuda files
*.cpp|*.cxx|*.cc|*.C|*.c++|*.cu)
cpp_files="$cpp_files $1"
;;
#Handle known nvcc args
-O*|-D*|-gencode*|-c|-I*|-L*|-l*|-g|--help|--version|--dryrun|--verbose|--keep-dir|-E|-M|-G|--relocatable-device-code*|-shared|-lineinfo|-expt-extended-lambda|--resource-usage)
cuda_args="$cuda_args $1"
;;
#Handle c++11 setting
--std=c++11|-std=c++11)
cuda_args="$cuda_args $1"
;;
#strip of -std=c++98 due to nvcc warnings and Tribits will place both -std=c++11 and -std=c++98
-std=c++98|--std=c++98)
;;
#Handle known nvcc args that have an argument
-o|-rdc|-maxrregcount|--default-stream)
cuda_args="$cuda_args $1 $2"
shift
;;
#strip of pedantic because it produces endless warnings about #LINE added by the preprocessor
-pedantic|-Wpedantic|-ansi)
;;
#strip -Xcompiler because we add it
-Xcompiler)
;;
#strip of "-x cu" because we add that
-x)
if [[ $2 != "cu" ]]; then
xcompiler_args="$xcompiler_args,-x,$2"
fi
shift
;;
#Handle -ccbin (if its not set we can set it to a default value)
-ccbin)
cuda_args="$cuda_args $1 $2"
ccbin_set=1
shift
;;
#Handle -arch argument (if its not set use a default
-arch*)
cuda_args="$cuda_args $1"
arch_set=1
;;
#Handle -Xcudafe argument
-Xcudafe)
cuda_args="$cuda_args -Xcudafe $2"
shift
;;
#Handle args that should be sent to the linker
-Wl*)
xlinker_args="$xlinker_args -Xlinker ${1:4:${#1}}"
;;
#Handle object files: -x cu applies to all input files, so give them to linker, except if only linking
*.a|*.so|*.o|*.obj)
object_files="$object_files $1"
object_files_xlinker="$object_files_xlinker -Xlinker $1"
;;
#Handle object files: -x cu applies to all input files, so give them to linker, except if only linking
*.so.*|*.dylib)
object_files_xlinker="$object_files_xlinker -Xlinker $1"
object_files="$object_files -Xlinker $1"
;;
#All other args are sent to the host compiler
*)
if [ $first_host_option -eq 0 ]; then
xcompiler_args="$xcompiler_args,$1"
else
xcompiler_args="-Xcompiler $1"
first_host_option=0
fi
;;
esac
shift
done
#Add default host compiler if necessary
if [ $ccbin_set -ne 1 ]; then
cuda_args="$cuda_args -ccbin $default_compiler"
fi
#Add architecture command
if [ $arch_set -ne 1 ]; then
cuda_args="$cuda_args -arch=$default_arch"
fi
#Compose compilation command
command="nvcc $cuda_args $xlinker_args $xcompiler_args"
#nvcc does not accept '#pragma ident SOME_MACRO_STRING' but it does accept '#ident SOME_MACRO_STRING'
if [ $replace_pragma_ident -eq 1 ]; then
cpp_files2=""
for file in $cpp_files
do
var=`grep pragma ${file} | grep ident | grep "#"`
if [ "${#var}" -gt 0 ]
then
sed 's/#[\ \t]*pragma[\ \t]*ident/#ident/g' $file > /tmp/nvcc_wrapper_tmp_$file
cpp_files2="$cpp_files2 /tmp/nvcc_wrapper_tmp_$file"
else
cpp_files2="$cpp_files2 $file"
fi
done
cpp_files=$cpp_files2
echo $cpp_files
fi
if [ "$cpp_files" ]; then
command="$command $object_files_xlinker -x cu $cpp_files"
else
command="$command $object_files"
fi
#Print command for dryrun
if [ $dry_run -eq 1 ]; then
echo $command
exit 0
fi
#Run compilation command
$command
nvcc_error_code=$?
#Report error code
exit $nvcc_error_code

4
src/KOKKOS/neighbor_kokkos.cpp
View File

@ -396,9 +396,9 @@ void NeighborKokkos::operator()(TagNeighborCheckDistance<DeviceType>, const int
void NeighborKokkos::build(int topoflag)
{
if (nlist_device)
this->template build_kokkos<LMPDeviceType>(topoflag);
build_kokkos<LMPDeviceType>(topoflag);
else
this->template build_kokkos<LMPHostType>(topoflag);
build_kokkos<LMPHostType>(topoflag);
}
template<class DeviceType>

2
src/KOKKOS/pair_buck_coul_cut_kokkos.h
View File

@ -74,7 +74,7 @@ class PairBuckCoulCutKokkos : public PairBuckCoulCut {
Kokkos::DualView<params_buck_coul**,Kokkos::LayoutRight,DeviceType> k_params;
typename Kokkos::DualView<params_buck_coul**,
Kokkos::LayoutRight,DeviceType>::t_dev_const params;
Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
// hardwired to space for 15 atom types
params_buck_coul m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];

2
src/KOKKOS/pair_buck_coul_long_kokkos.h
View File

@ -75,7 +75,7 @@ class PairBuckCoulLongKokkos : public PairBuckCoulLong {
Kokkos::DualView<params_buck_coul**,Kokkos::LayoutRight,DeviceType> k_params;
typename Kokkos::DualView<params_buck_coul**,
Kokkos::LayoutRight,DeviceType>::t_dev_const params;
Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
// hardwired to space for 15 atom types
params_buck_coul m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];

2
src/KOKKOS/pair_buck_kokkos.h
View File

@ -67,7 +67,7 @@ class PairBuckKokkos : public PairBuck {
Kokkos::DualView<params_buck**,Kokkos::LayoutRight,DeviceType> k_params;
typename Kokkos::DualView<params_buck**,Kokkos::LayoutRight,DeviceType>::t_dev_const params;
typename Kokkos::DualView<params_buck**,Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
params_buck m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1]; // hardwired to space for 15 atom types
F_FLOAT m_cutsq[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
typename ArrayTypes<DeviceType>::t_x_array_randomread x;

2
src/KOKKOS/pair_coul_cut_kokkos.h
View File

@ -80,7 +80,7 @@ class PairCoulCutKokkos : public PairCoulCut {
Kokkos::DualView<params_coul**,Kokkos::LayoutRight,DeviceType> k_params;
typename Kokkos::DualView<params_coul**,
Kokkos::LayoutRight,DeviceType>::t_dev_const params;
Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
// hardwired to space for 15 atom types
params_coul m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];

2
src/KOKKOS/pair_coul_debye_kokkos.h
View File

@ -78,7 +78,7 @@ class PairCoulDebyeKokkos : public PairCoulDebye {
Kokkos::DualView<params_coul**,Kokkos::LayoutRight,DeviceType> k_params;
typename Kokkos::DualView<params_coul**,
Kokkos::LayoutRight,DeviceType>::t_dev_const params;
Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
// hardwired to space for 15 atom types
params_coul m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];

2
src/KOKKOS/pair_coul_long_kokkos.h
View File

@ -79,7 +79,7 @@ class PairCoulLongKokkos : public PairCoulLong {
Kokkos::DualView<params_coul**,Kokkos::LayoutRight,DeviceType> k_params;
typename Kokkos::DualView<params_coul**,
Kokkos::LayoutRight,DeviceType>::t_dev_const params;
Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
// hardwired to space for 15 atom types
params_coul m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];

2
src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.h
View File

@ -75,7 +75,7 @@ class PairLJCharmmCoulCharmmImplicitKokkos : public PairLJCharmmCoulCharmmImplic
Kokkos::DualView<params_lj_coul**,Kokkos::LayoutRight,DeviceType> k_params;
typename Kokkos::DualView<params_lj_coul**,
Kokkos::LayoutRight,DeviceType>::t_dev_const params;
Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
// hardwired to space for 15 atom types
params_lj_coul m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];

2
src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.h
View File

@ -75,7 +75,7 @@ class PairLJCharmmCoulCharmmKokkos : public PairLJCharmmCoulCharmm {
Kokkos::DualView<params_lj_coul**,Kokkos::LayoutRight,DeviceType> k_params;
typename Kokkos::DualView<params_lj_coul**,
Kokkos::LayoutRight,DeviceType>::t_dev_const params;
Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
// hardwired to space for 15 atom types
params_lj_coul m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];

2
src/KOKKOS/pair_lj_charmm_coul_long_kokkos.h
View File

@ -75,7 +75,7 @@ class PairLJCharmmCoulLongKokkos : public PairLJCharmmCoulLong {
Kokkos::DualView<params_lj_coul**,Kokkos::LayoutRight,DeviceType> k_params;
typename Kokkos::DualView<params_lj_coul**,
Kokkos::LayoutRight,DeviceType>::t_dev_const params;
Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
// hardwired to space for 15 atom types
params_lj_coul m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];

2
src/KOKKOS/pair_lj_class2_coul_cut_kokkos.h
View File

@ -74,7 +74,7 @@ class PairLJClass2CoulCutKokkos : public PairLJClass2CoulCut {
Kokkos::DualView<params_lj_coul**,Kokkos::LayoutRight,DeviceType> k_params;
typename Kokkos::DualView<params_lj_coul**,
Kokkos::LayoutRight,DeviceType>::t_dev_const params;
Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
// hardwired to space for 15 atom types
params_lj_coul m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];

2
src/KOKKOS/pair_lj_class2_coul_long_kokkos.h
View File

@ -75,7 +75,7 @@ class PairLJClass2CoulLongKokkos : public PairLJClass2CoulLong {
Kokkos::DualView<params_lj_coul**,Kokkos::LayoutRight,DeviceType> k_params;
typename Kokkos::DualView<params_lj_coul**,
Kokkos::LayoutRight,DeviceType>::t_dev_const params;
Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
// hardwired to space for 15 atom types
params_lj_coul m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];

2
src/KOKKOS/pair_lj_class2_kokkos.h
View File

@ -74,7 +74,7 @@ class PairLJClass2Kokkos : public PairLJClass2 {
}
Kokkos::DualView<params_lj**,Kokkos::LayoutRight,DeviceType> k_params;
typename Kokkos::DualView<params_lj**,Kokkos::LayoutRight,DeviceType>::t_dev_const params;
typename Kokkos::DualView<params_lj**,Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
params_lj m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1]; // hardwired to space for 15 atom types
F_FLOAT m_cutsq[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
typename ArrayTypes<DeviceType>::t_x_array_randomread x;

2
src/KOKKOS/pair_lj_cut_coul_cut_kokkos.h
View File

@ -76,7 +76,7 @@ class PairLJCutCoulCutKokkos : public PairLJCutCoulCut {
Kokkos::DualView<params_lj_coul**,Kokkos::LayoutRight,DeviceType> k_params;
typename Kokkos::DualView<params_lj_coul**,
Kokkos::LayoutRight,DeviceType>::t_dev_const params;
Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
// hardwired to space for 15 atom types
params_lj_coul m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];

2
src/KOKKOS/pair_lj_cut_coul_debye_kokkos.h
View File

@ -74,7 +74,7 @@ class PairLJCutCoulDebyeKokkos : public PairLJCutCoulDebye {
Kokkos::DualView<params_lj_coul**,Kokkos::LayoutRight,DeviceType> k_params;
typename Kokkos::DualView<params_lj_coul**,
Kokkos::LayoutRight,DeviceType>::t_dev_const params;
Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
// hardwired to space for 15 atom types
params_lj_coul m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];

2
src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.h
View File

@ -73,7 +73,7 @@ class PairLJCutCoulDSFKokkos : public PairLJCutCoulDSF {
Kokkos::DualView<params_lj_coul**,Kokkos::LayoutRight,DeviceType> k_params;
typename Kokkos::DualView<params_lj_coul**,
Kokkos::LayoutRight,DeviceType>::t_dev_const params;
Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
// hardwired to space for 15 atom types
params_lj_coul m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];

2
src/KOKKOS/pair_lj_cut_coul_long_kokkos.h
View File

@ -75,7 +75,7 @@ class PairLJCutCoulLongKokkos : public PairLJCutCoulLong {
Kokkos::DualView<params_lj_coul**,Kokkos::LayoutRight,DeviceType> k_params;
typename Kokkos::DualView<params_lj_coul**,
Kokkos::LayoutRight,DeviceType>::t_dev_const params;
Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
// hardwired to space for 15 atom types
params_lj_coul m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];

2
src/KOKKOS/pair_lj_cut_kokkos.h
View File

@ -70,7 +70,7 @@ class PairLJCutKokkos : public PairLJCut {
Kokkos::DualView<params_lj**,Kokkos::LayoutRight,DeviceType> k_params;
typename Kokkos::DualView<params_lj**,Kokkos::LayoutRight,DeviceType>::t_dev_const params;
typename Kokkos::DualView<params_lj**,Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
params_lj m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1]; // hardwired to space for 15 atom types
F_FLOAT m_cutsq[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
typename ArrayTypes<DeviceType>::t_x_array_randomread x;

2
src/KOKKOS/pair_lj_expand_kokkos.h
View File

@ -74,7 +74,7 @@ class PairLJExpandKokkos : public PairLJExpand {
}
Kokkos::DualView<params_lj**,Kokkos::LayoutRight,DeviceType> k_params;
typename Kokkos::DualView<params_lj**,Kokkos::LayoutRight,DeviceType>::t_dev_const params;
typename Kokkos::DualView<params_lj**,Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
params_lj m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1]; // hardwired to space for 15 atom types
F_FLOAT m_cutsq[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
typename ArrayTypes<DeviceType>::t_x_array_randomread x;

2
src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.h
View File

@ -75,7 +75,7 @@ class PairLJGromacsCoulGromacsKokkos : public PairLJGromacsCoulGromacs {
Kokkos::DualView<params_lj_coul**,Kokkos::LayoutRight,DeviceType> k_params;
typename Kokkos::DualView<params_lj_coul**,
Kokkos::LayoutRight,DeviceType>::t_dev_const params;
Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
// hardwired to space for 15 atom types
params_lj_coul m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];

2
src/KOKKOS/pair_lj_gromacs_kokkos.h
View File

@ -78,7 +78,7 @@ class PairLJGromacsKokkos : public PairLJGromacs {
Kokkos::DualView<params_lj**,Kokkos::LayoutRight,DeviceType> k_params;
typename Kokkos::DualView<params_lj**,
Kokkos::LayoutRight,DeviceType>::t_dev_const params;
Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
// hardwired to space for 15 atom types
params_lj m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];

2
src/KOKKOS/pair_lj_sdk_kokkos.h
View File

@ -71,7 +71,7 @@ class PairLJSDKKokkos : public PairLJSDK {
Kokkos::DualView<params_lj**,Kokkos::LayoutRight,DeviceType> k_params;
typename Kokkos::DualView<params_lj**,Kokkos::LayoutRight,DeviceType>::t_dev_const params;
typename Kokkos::DualView<params_lj**,Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
params_lj m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1]; // hardwired to space for 15 atom types
F_FLOAT m_cutsq[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
typename ArrayTypes<DeviceType>::t_x_array_randomread x;

2
src/KOKKOS/pair_tersoff_kokkos.h
View File

@ -180,7 +180,7 @@ class PairTersoffKokkos : public PairTersoff {
typedef Kokkos::DualView<int***,DeviceType> tdual_int_3d;
Kokkos::DualView<params_ters***,Kokkos::LayoutRight,DeviceType> k_params;
typename Kokkos::DualView<params_ters***,
Kokkos::LayoutRight,DeviceType>::t_dev_const paramskk;
Kokkos::LayoutRight,DeviceType>::t_dev_const_um paramskk;
// hardwired to space for 15 atom types
//params_ters m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];

2
src/KOKKOS/pair_tersoff_mod_kokkos.h
View File

@ -180,7 +180,7 @@ class PairTersoffMODKokkos : public PairTersoffMOD {
typedef Kokkos::DualView<int***,DeviceType> tdual_int_3d;
Kokkos::DualView<params_ters***,Kokkos::LayoutRight,DeviceType> k_params;
typename Kokkos::DualView<params_ters***,
Kokkos::LayoutRight,DeviceType>::t_dev_const paramskk;
Kokkos::LayoutRight,DeviceType>::t_dev_const_um paramskk;
// hardwired to space for 15 atom types
//params_ters m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];

2
src/KOKKOS/pair_tersoff_zbl_kokkos.h
View File

@ -186,7 +186,7 @@ class PairTersoffZBLKokkos : public PairTersoffZBL {
typedef Kokkos::DualView<int***,DeviceType> tdual_int_3d;
Kokkos::DualView<params_ters***,Kokkos::LayoutRight,DeviceType> k_params;
typename Kokkos::DualView<params_ters***,
Kokkos::LayoutRight,DeviceType>::t_dev_const paramskk;
Kokkos::LayoutRight,DeviceType>::t_dev_const_um paramskk;
// hardwired to space for 15 atom types
//params_ters m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];

10
src/MAKE/OPTIONS/Makefile.kokkos_cuda
View File

@ -1,17 +1,20 @@
# kokkos_cuda = KOKKOS package with CUDA support, nvcc/mpicxx compiler
# kokkos_cuda = KOKKOS package with CUDA support, OpenMPI, nvcc/mpicxx compiler
SHELL = /bin/sh
KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = nvcc -ccbin=mpicxx
CC = mpicxx
CCFLAGS = -g -O3
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = nvcc -ccbin=mpicxx
LINK = mpicxx
LINKFLAGS = -g -O
LIB =
SIZE = size
@ -21,7 +24,6 @@ ARFLAGS = -rc
SHLIBFLAGS = -shared
KOKKOS_DEVICES = Cuda, OpenMP
KOKKOS_ARCH = Kepler35
CUDA_PATH = /usr/local/cuda
# ---------------------------------------------------------------------
# LAMMPS-specific settings, all OPTIONAL

6
src/MAKE/OPTIONS/Makefile.kokkos_phi
View File

@ -1,4 +1,4 @@
# kokkos_phi = KOKKOS package with PHI support, MPI compiler, default MPI
# kokkos_phi = KOKKOS package with PHI support, Intel compiler, default MPI
SHELL = /bin/sh
@ -6,12 +6,12 @@ SHELL = /bin/sh
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = mpicxx
CC = mpiicpc
CCFLAGS = -g -O3
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = mpicxx
LINK = mpiicpc
LINKFLAGS = -g -O
LIB =
SIZE = size

94
src/atom.cpp
View File

@ -516,7 +516,7 @@ void Atom::modify_params(int narg, char **arg)
error->all(FLERR,
"Atom_modify id command after simulation box is defined");
if (strcmp(arg[iarg+1],"yes") == 0) tag_enable = 1;
else if (strcmp(arg[iarg+1],"no") == 0) tag_enable = 2;
else if (strcmp(arg[iarg+1],"no") == 0) tag_enable = 0;
else error->all(FLERR,"Illegal atom_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"map") == 0) {
@ -559,9 +559,11 @@ void Atom::modify_params(int narg, char **arg)
check that atom IDs are valid
error if any atom ID < 0 or atom ID = MAXTAGINT
if any atom ID > 0, error if any atom ID == 0
if any atom ID > 0, error if tag_enable = 0
if all atom IDs = 0, tag_enable must be 0
OK if atom IDs > natoms
NOTE: not checking that atom IDs are unique
if max atom IDs < natoms, must be duplicates
OK if max atom IDs > natoms
NOTE: not fully checking that atom IDs are unique
------------------------------------------------------------------------- */
void Atom::tag_check()
@ -578,12 +580,16 @@ void Atom::tag_check()
MPI_Allreduce(&min,&minall,1,MPI_LMP_TAGINT,MPI_MIN,world);
MPI_Allreduce(&max,&maxall,1,MPI_LMP_TAGINT,MPI_MAX,world);
if (minall < 0) error->all(FLERR,"Atom ID is negative");
if (maxall >= MAXTAGINT) error->all(FLERR,"Atom ID is too big");
if (maxall > 0 && minall == 0) error->all(FLERR,"Atom ID is zero");
// this last message is wrong
if (maxall == 0 && tag_enable && natoms)
error->all(FLERR,"Not all atom IDs are 0");
if (minall < 0) error->all(FLERR,"One or more Atom IDs is negative");
if (maxall >= MAXTAGINT) error->all(FLERR,"One or more atom IDs is too big");
if (maxall > 0 && minall == 0)
error->all(FLERR,"One or more atom IDs is zero");
if (maxall > 0 && tag_enable == 0)
error->all(FLERR,"Non-zero atom IDs with atom_modify id = no");
if (maxall == 0 && natoms && tag_enable)
error->all(FLERR,"All atom IDs = 0 but atom_modify id = yes");
if (tag_enable && maxall < natoms)
error->all(FLERR,"Duplicate atom IDs exist");
}
/* ----------------------------------------------------------------------
@ -725,7 +731,8 @@ void Atom::deallocate_topology()
call style-specific routine to parse line
------------------------------------------------------------------------- */
void Atom::data_atoms(int n, char *buf)
void Atom::data_atoms(int n, char *buf, tagint id_offset, int type_offset,
int shiftflag, double *shift)
{
int m,xptr,iptr;
imageint imagedata;
@ -833,6 +840,12 @@ void Atom::data_atoms(int n, char *buf)
xdata[0] = atof(values[xptr]);
xdata[1] = atof(values[xptr+1]);
xdata[2] = atof(values[xptr+2]);
if (shiftflag) {
xdata[0] += shift[0];
xdata[1] += shift[1];
xdata[2] += shift[2];
}
domain->remap(xdata,imagedata);
if (triclinic) {
domain->x2lamda(xdata,lamda);
@ -841,8 +854,15 @@ void Atom::data_atoms(int n, char *buf)
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1] &&
coord[2] >= sublo[2] && coord[2] < subhi[2])
coord[2] >= sublo[2] && coord[2] < subhi[2]) {
avec->data_atom(xdata,imagedata,values);
if (id_offset) tag[nlocal-1] += id_offset;
if (type_offset) {
type[nlocal-1] += type_offset;
if (type[nlocal-1] > ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
}
}
buf = next + 1;
}
@ -856,7 +876,7 @@ void Atom::data_atoms(int n, char *buf)
call style-specific routine to parse line
------------------------------------------------------------------------- */
void Atom::data_vels(int n, char *buf)
void Atom::data_vels(int n, char *buf, tagint id_offset)
{
int j,m;
tagint tagdata;
@ -883,7 +903,7 @@ void Atom::data_vels(int n, char *buf)
for (j = 1; j < nwords; j++)
values[j] = strtok(NULL," \t\n\r\f");
tagdata = ATOTAGINT(values[0]);
tagdata = ATOTAGINT(values[0]) + id_offset;
if (tagdata <= 0 || tagdata > map_tag_max)
error->one(FLERR,"Invalid atom ID in Velocities section of data file");
if ((m = map(tagdata)) >= 0) avec->data_vel(m,&values[1]);
@ -901,7 +921,7 @@ void Atom::data_vels(int n, char *buf)
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
void Atom::data_bonds(int n, char *buf, int *count)
void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset)
{
int m,tmp,itype;
tagint atom1,atom2;
@ -913,6 +933,11 @@ void Atom::data_bonds(int n, char *buf, int *count)
*next = '\0';
sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2);
if (id_offset) {
atom1 += id_offset;
atom2 += id_offset;
}
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max)
error->one(FLERR,"Invalid atom ID in Bonds section of data file");
@ -947,7 +972,7 @@ void Atom::data_bonds(int n, char *buf, int *count)
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
void Atom::data_angles(int n, char *buf, int *count)
void Atom::data_angles(int n, char *buf, int *count, tagint id_offset)
{
int m,tmp,itype;
tagint atom1,atom2,atom3;
@ -959,6 +984,12 @@ void Atom::data_angles(int n, char *buf, int *count)
*next = '\0';
sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2,&atom3);
if (id_offset) {
atom1 += id_offset;
atom2 += id_offset;
atom3 += id_offset;
}
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max ||
atom3 <= 0 || atom3 > map_tag_max)
@ -1008,7 +1039,7 @@ void Atom::data_angles(int n, char *buf, int *count)
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
void Atom::data_dihedrals(int n, char *buf, int *count)
void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset)
{
int m,tmp,itype;
tagint atom1,atom2,atom3,atom4;
@ -1021,6 +1052,13 @@ void Atom::data_dihedrals(int n, char *buf, int *count)
sscanf(buf,"%d %d "
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
if (id_offset) {
atom1 += id_offset;
atom2 += id_offset;
atom3 += id_offset;
atom4 += id_offset;
}
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max ||
atom3 <= 0 || atom3 > map_tag_max ||
@ -1086,7 +1124,7 @@ void Atom::data_dihedrals(int n, char *buf, int *count)
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
void Atom::data_impropers(int n, char *buf, int *count)
void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset)
{
int m,tmp,itype;
tagint atom1,atom2,atom3,atom4;
@ -1099,6 +1137,13 @@ void Atom::data_impropers(int n, char *buf, int *count)
sscanf(buf,"%d %d "
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
if (id_offset) {
atom1 += id_offset;
atom2 += id_offset;
atom3 += id_offset;
atom4 += id_offset;
}
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max ||
atom3 <= 0 || atom3 > map_tag_max ||
@ -1163,7 +1208,7 @@ void Atom::data_impropers(int n, char *buf, int *count)
call style-specific routine to parse line
------------------------------------------------------------------------- */
void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus)
void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus, tagint id_offset)
{
int j,m,tagdata;
char *next;
@ -1189,7 +1234,7 @@ void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus)
for (j = 1; j < nwords; j++)
values[j] = strtok(NULL," \t\n\r\f");
tagdata = ATOTAGINT(values[0]);
tagdata = ATOTAGINT(values[0]) + id_offset;
if (tagdata <= 0 || tagdata > map_tag_max)
error->one(FLERR,"Invalid atom ID in Bonus section of data file");
@ -1210,7 +1255,8 @@ void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus)
call style-specific routine to parse line
------------------------------------------------------------------------- */
void Atom::data_bodies(int n, char *buf, AtomVecBody *avec_body)
void Atom::data_bodies(int n, char *buf, AtomVecBody *avec_body,
tagint id_offset)
{
int j,m,tagdata,ninteger,ndouble;
@ -1222,8 +1268,8 @@ void Atom::data_bodies(int n, char *buf, AtomVecBody *avec_body)
// if I own atom tag, unpack its values
for (int i = 0; i < n; i++) {
if (i == 0) tagdata = ATOTAGINT(strtok(buf," \t\n\r\f"));
else tagdata = ATOTAGINT(strtok(NULL," \t\n\r\f"));
if (i == 0) tagdata = ATOTAGINT(strtok(buf," \t\n\r\f")) + id_offset;
else tagdata = ATOTAGINT(strtok(NULL," \t\n\r\f")) + id_offset;
ninteger = atoi(strtok(NULL," \t\n\r\f"));
ndouble = atoi(strtok(NULL," \t\n\r\f"));
@ -1260,9 +1306,10 @@ void Atom::allocate_type_arrays()
/* ----------------------------------------------------------------------
set a mass and flag it as set
called from reading of data file
type_offset may be used when reading multiple data files
------------------------------------------------------------------------- */
void Atom::set_mass(const char *str)
void Atom::set_mass(const char *str, int type_offset)
{
if (mass == NULL) error->all(FLERR,"Cannot set mass for this atom style");
@ -1270,6 +1317,7 @@ void Atom::set_mass(const char *str)
double mass_one;
int n = sscanf(str,"%d %lg",&itype,&mass_one);
if (n != 2) error->all(FLERR,"Invalid mass line in data file");
itype += type_offset;
if (itype < 1 || itype > ntypes)
error->all(FLERR,"Invalid type for mass set");

18
src/atom.h
View File

@ -188,19 +188,19 @@ class Atom : protected Pointers {
void deallocate_topology();
void data_atoms(int, char *);
void data_vels(int, char *);
void data_atoms(int, char *, tagint, int, int, double *);
void data_vels(int, char *, tagint);
void data_bonds(int, char *, int *);
void data_angles(int, char *, int *);
void data_dihedrals(int, char *, int *);
void data_impropers(int, char *, int *);
void data_bonds(int, char *, int *, tagint);
void data_angles(int, char *, int *, tagint);
void data_dihedrals(int, char *, int *, tagint);
void data_impropers(int, char *, int *, tagint);
void data_bonus(int, char *, class AtomVec *);
void data_bodies(int, char *, class AtomVecBody *);
void data_bonus(int, char *, class AtomVec *, tagint);
void data_bodies(int, char *, class AtomVecBody *, tagint);
virtual void allocate_type_arrays();
void set_mass(const char *);
void set_mass(const char *, int);
void set_mass(int, double);
void set_mass(int, char **);
void set_mass(double *);

2
src/fix.h
View File

@ -182,7 +182,7 @@ class Fix : protected Pointers {
virtual void reset_dt() {}
virtual void read_data_header(char *) {}
virtual void read_data_section(char *, int, char *) {}
virtual void read_data_section(char *, int, char *, tagint) {}
virtual bigint read_data_skip_lines(char *) {return 0;}
virtual void write_data_header(FILE *, int) {}

6
src/fix_property_atom.cpp
View File

@ -182,9 +182,11 @@ void FixPropertyAtom::init()
/* ----------------------------------------------------------------------
unpack N lines in buf from section of data file labeled by keyword
id_offset is applied to first atomID field if multiple data files are read
------------------------------------------------------------------------- */
void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf)
void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf,
tagint id_offset)
{
int j,m;
tagint itag;
@ -223,7 +225,7 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf)
for (j = 1; j < nwords; j++)
values[j] = strtok(NULL," \t\n\r\f");
itag = ATOTAGINT(values[0]);
itag = ATOTAGINT(values[0]) + id_offset;
if (itag <= 0 || itag > map_tag_max) {
char str[128];
sprintf(str,"Invalid atom ID in %s section of data file",keyword);

2
src/fix_property_atom.h
View File

@ -31,7 +31,7 @@ class FixPropertyAtom : public Fix {
int setmask();
void init();
void read_data_section(char *, int, char *);
void read_data_section(char *, int, char *, tagint);
bigint read_data_skip_lines(char *);
void write_data_section_size(int, int &, int &);
void write_data_section_pack(int, double **);

20
src/group.cpp
View File

@ -587,6 +587,26 @@ int Group::find(const char *name)
return -1;
}
/* ----------------------------------------------------------------------
find group with name or create group if it doesn't exist
return group index
------------------------------------------------------------------------- */
int Group::find_or_create(const char *name)
{
int igroup = find(name);
if (igroup >= 0) return igroup;
if (ngroup == MAX_GROUP) error->all(FLERR,"Too many groups");
igroup = find_unused();
int n = strlen(name) + 1;
names[igroup] = new char[n];
strcpy(names[igroup],name);
ngroup++;
return igroup;
}
/* ----------------------------------------------------------------------
return index of first available group
should never be called when group limit has been reached

1
src/group.h
View File

@ -33,6 +33,7 @@ class Group : protected Pointers {
void assign(int, char **); // assign atoms to a group
void create(char *, int *); // add flagged atoms to a group
int find(const char *); // lookup name in list of groups
int find_or_create(const char *); // lookup name or create new group
void write_restart(FILE *);
void read_restart(FILE *);

490
src/read_data.cpp
View File

@ -29,6 +29,7 @@
#include "atom_vec_tri.h"
#include "force.h"
#include "molecule.h"
#include "group.h"
#include "comm.h"
#include "update.h"
#include "modify.h"
@ -41,6 +42,7 @@
#include "dihedral.h"
#include "improper.h"
#include "special.h"
#include "irregular.h"
#include "error.h"
#include "memory.h"
@ -55,6 +57,8 @@ using namespace LAMMPS_NS;
// customize for new sections
#define NSECTIONS 25 // change when add to header::section_keywords
enum{NONE,APPEND,VALUE,MERGE};
// pair style suffixes to ignore
// when matching Pair Coeffs comment to currently-defined pair style
@ -115,8 +119,16 @@ void ReadData::command(int narg, char **arg)
// optional args
addflag = mergeflag = 0;
offset[0] = offset[1] = offset[2] = 0.0;
addflag = NONE;
id_offset = 0;
offsetflag = shiftflag = 0;
toffset = boffset = aoffset = doffset = ioffset = 0;
shift[0] = shift[1] = shift[2] = 0.0;
extra_atom_types = extra_bond_types = extra_angle_types =
extra_dihedral_types = extra_improper_types = 0;
groupbit = 0;
nfix = 0;
fix_index = NULL;
fix_header = NULL;
@ -125,18 +137,81 @@ void ReadData::command(int narg, char **arg)
int iarg = 1;
while (iarg < narg) {
if (strcmp(arg[iarg],"add") == 0) {
addflag = 1;
iarg++;
} else if (strcmp(arg[iarg],"merge") == 0) {
mergeflag = 1;
iarg++;
if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
if (strcmp(arg[iarg+1],"append") == 0) addflag = APPEND;
else if (strcmp(arg[iarg+1],"merge") == 0) addflag = MERGE;
else {
addflag = VALUE;
bigint offset = force->bnumeric(FLERR,arg[iarg+1]);
if (offset > MAXTAGINT)
error->all(FLERR,"Read data add offset is too big");
id_offset = offset;
}
iarg += 2;
} else if (strcmp(arg[iarg],"offset") == 0) {
if (iarg+4 > narg)
if (iarg+6 > narg) error->all(FLERR,"Illegal read_data command");
offsetflag = 1;
toffset = force->inumeric(FLERR,arg[iarg+1]);
boffset = force->inumeric(FLERR,arg[iarg+2]);
aoffset = force->inumeric(FLERR,arg[iarg+3]);
doffset = force->inumeric(FLERR,arg[iarg+4]);
ioffset = force->inumeric(FLERR,arg[iarg+5]);
if (toffset < 0 || boffset < 0 || aoffset < 0 ||
doffset < 0 || ioffset < 0)
error->all(FLERR,"Illegal read_data command");
offset[0] = force->numeric(FLERR,arg[iarg+1]);
offset[1] = force->numeric(FLERR,arg[iarg+2]);
offset[2] = force->numeric(FLERR,arg[iarg+3]);
iarg += 6;
} else if (strcmp(arg[iarg],"shift") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal read_data command");
shiftflag = 1;
shift[0] = force->numeric(FLERR,arg[iarg+1]);
shift[1] = force->numeric(FLERR,arg[iarg+2]);
shift[2] = force->numeric(FLERR,arg[iarg+3]);
if (domain->dimension == 2 && shift[2] != 0.0)
error->all(FLERR,"Non-zero read_data shift z value for 2d simulation");
iarg += 4;
} else if (strcmp(arg[iarg],"extra/atom/types") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
extra_atom_types = force->inumeric(FLERR,arg[iarg+1]);
if (extra_atom_types < 0) error->all(FLERR,"Illegal read_data command");
iarg += 2;
} else if (strcmp(arg[iarg],"extra/bond/types") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
if (!atom->avec->bonds_allow)
error->all(FLERR,"No bonds allowed with this atom style");
extra_bond_types = force->inumeric(FLERR,arg[iarg+1]);
if (extra_bond_types < 0) error->all(FLERR,"Illegal read_data command");
iarg += 2;
} else if (strcmp(arg[iarg],"extra/angle/types") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
if (!atom->avec->angles_allow)
error->all(FLERR,"No angles allowed with this atom style");
extra_angle_types = force->inumeric(FLERR,arg[iarg+1]);
if (extra_angle_types < 0) error->all(FLERR,"Illegal read_data command");
iarg += 2;
} else if (strcmp(arg[iarg],"extra/dihedral/types") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
if (!atom->avec->dihedrals_allow)
error->all(FLERR,"No dihedrals allowed with this atom style");
extra_dihedral_types = force->inumeric(FLERR,arg[iarg+1]);
if (extra_dihedral_types < 0)
error->all(FLERR,"Illegal read_data command");
iarg += 2;
} else if (strcmp(arg[iarg],"extra/improper/types") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
if (!atom->avec->impropers_allow)
error->all(FLERR,"No impropers allowed with this atom style");
extra_improper_types = force->inumeric(FLERR,arg[iarg+1]);
if (extra_improper_types < 0)
error->all(FLERR,"Illegal read_data command");
iarg += 2;
} else if (strcmp(arg[iarg],"group") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
int igroup = group->find_or_create(arg[iarg+1]);
groupbit = group->bitmask[igroup];
iarg += 2;
} else if (strcmp(arg[iarg],"fix") == 0) {
if (iarg+4 > narg)
error->all(FLERR,"Illegal read_data command");
@ -161,25 +236,54 @@ void ReadData::command(int narg, char **arg)
strcpy(fix_section[nfix],arg[iarg+3]);
nfix++;
iarg += 4;
} else error->all(FLERR,"Illegal read_data command");
}
// error checks
if (domain->box_exist && !addflag && !mergeflag)
error->all(FLERR,"Cannot read_data after simulation box is defined");
if (addflag && mergeflag) error->all(FLERR,"Cannot read_data add and merge");
if (domain->dimension == 2 && offset[2] != 0.0)
error->all(FLERR,"Cannot use non-zero z offset in read_data "
"for 2d simulation");
if (domain->dimension == 2 && domain->zperiodic == 0)
error->all(FLERR,"Cannot run 2d simulation with nonperiodic Z dimension");
if (domain->box_exist && !addflag)
error->all(FLERR,"Cannot read_data without add keyword "
"after simulation box is defined");
if (!domain->box_exist && addflag)
error->all(FLERR,"Cannot use read_data add before "
"simulation box is defined");
if (offsetflag && addflag == NONE)
error->all(FLERR,"Cannot use read_data offset without add flag");
if (shiftflag && addflag == NONE)
error->all(FLERR,"Cannot use read_data shift without add flag");
if (addflag != NONE &&
(extra_atom_types || extra_bond_types || extra_angle_types ||
extra_dihedral_types || extra_improper_types))
error->all(FLERR,"Cannot use read_data extra with add flag");
// first time system initialization
if (addflag == NONE) {
domain->box_exist = 1;
update->ntimestep = 0;
}
// compute atomID offset for addflag = MERGE
if (addflag == APPEND) {
tagint *tag = atom->tag;
int nlocal = atom->nlocal;
tagint max = 0;
for (int i = 0; i < nlocal; i++) max = MAX(max,tag[i]);
MPI_Allreduce(&max,&id_offset,1,MPI_LMP_TAGINT,MPI_MAX,world);
}
// -----------------------------------------------------------------
// perform 1-pass read if no molecular topoogy in file
// perform 2-pass read if molecular topology,
// first pass calculates max topology/atom
// flags for this data file
int atomflag,topoflag;
int bondflag,angleflag,dihedralflag,improperflag;
int ellipsoidflag,lineflag,triflag,bodyflag;
@ -188,6 +292,14 @@ void ReadData::command(int narg, char **arg)
bondflag = angleflag = dihedralflag = improperflag = 0;
ellipsoidflag = lineflag = triflag = bodyflag = 0;
// values in this data file
natoms = ntypes = 0;
nbonds = nangles = ndihedrals = nimpropers = 0;
nbondtypes = nangletypes = ndihedraltypes = nimpropertypes = 0;
triclinic = 0;
int nlocal_previous = atom->nlocal;
int firstpass = 1;
while (1) {
@ -204,16 +316,12 @@ void ReadData::command(int narg, char **arg)
header();
// problem setup using info from header
// 1st pass only
if (firstpass) {
domain->box_exist = 1;
update->ntimestep = 0;
// apply extra settings before grow(), even if no topology in file
// deallocate() insures new settings are used for topology arrays
// if per-atom topology is in file, another grow() is done below
// only done once, if firstpass and first data file
// apply extra settings before grow(), even if no topology in file
// deallocate() insures new settings are used for topology arrays
// if per-atom topology is in file, another grow() is done below
if (firstpass && addflag == NONE) {
atom->bond_per_atom = atom->extra_bond_per_atom;
atom->angle_per_atom = atom->extra_angle_per_atom;
atom->dihedral_per_atom = atom->extra_dihedral_per_atom;
@ -227,6 +335,37 @@ void ReadData::command(int narg, char **arg)
atom->deallocate_topology();
atom->avec->grow(n);
domain->boxlo[0] = boxlo[0]; domain->boxhi[0] = boxhi[0];
domain->boxlo[1] = boxlo[1]; domain->boxhi[1] = boxhi[1];
domain->boxlo[2] = boxlo[2]; domain->boxhi[2] = boxhi[2];
if (triclinic) {
domain->xy = xy; domain->xz = xz; domain->yz = yz;
}
domain->print_box(" ");
domain->set_initial_box();
domain->set_global_box();
comm->set_proc_grid();
domain->set_local_box();
}
// change simulation box to be union of existing box and new box + shift
// only done if firstpass and not first data file
if (firstpass && addflag != NONE) {
domain->boxlo[0] = MIN(domain->boxlo[0],boxlo[0]+shift[0]);
domain->boxhi[0] = MAX(domain->boxhi[0],boxhi[0]+shift[0]);
domain->boxlo[1] = MIN(domain->boxlo[1],boxlo[1]+shift[1]);
domain->boxhi[1] = MAX(domain->boxhi[1],boxhi[1]+shift[1]);
domain->boxlo[2] = MIN(domain->boxlo[2],boxlo[2]+shift[2]);
domain->boxhi[2] = MAX(domain->boxhi[2],boxhi[2]+shift[2]);
// NOTE: not sure what to do about tilt value in subsequent data files
//if (triclinic) {
// domain->xy = xy; domain->xz = xz; domain->yz = yz;
// }
domain->print_box(" ");
domain->set_initial_box();
domain->set_global_box();
@ -261,34 +400,34 @@ void ReadData::command(int narg, char **arg)
error->warning(FLERR,"Atom style in data file differs "
"from currently defined atom style");
atoms();
} else skip_lines(atom->natoms);
} else skip_lines(natoms);
} else if (strcmp(keyword,"Velocities") == 0) {
if (atomflag == 0)
error->all(FLERR,"Must read Atoms before Velocities");
if (firstpass) velocities();
else skip_lines(atom->natoms);
else skip_lines(natoms);
} else if (strcmp(keyword,"Bonds") == 0) {
topoflag = bondflag = 1;
if (atom->nbonds == 0)
if (nbonds == 0)
error->all(FLERR,"Invalid data file section: Bonds");
if (atomflag == 0) error->all(FLERR,"Must read Atoms before Bonds");
bonds(firstpass);
} else if (strcmp(keyword,"Angles") == 0) {
topoflag = angleflag = 1;
if (atom->nangles == 0)
if (nangles == 0)
error->all(FLERR,"Invalid data file section: Angles");
if (atomflag == 0) error->all(FLERR,"Must read Atoms before Angles");
angles(firstpass);
} else if (strcmp(keyword,"Dihedrals") == 0) {
topoflag = dihedralflag = 1;
if (atom->ndihedrals == 0)
if (ndihedrals == 0)
error->all(FLERR,"Invalid data file section: Dihedrals");
if (atomflag == 0) error->all(FLERR,"Must read Atoms before Dihedrals");
dihedrals(firstpass);
} else if (strcmp(keyword,"Impropers") == 0) {
topoflag = improperflag = 1;
if (atom->nimpropers == 0)
if (nimpropers == 0)
error->all(FLERR,"Invalid data file section: Impropers");
if (atomflag == 0) error->all(FLERR,"Must read Atoms before Impropers");
impropers(firstpass);
@ -325,7 +464,7 @@ void ReadData::command(int narg, char **arg)
} else if (strcmp(keyword,"Masses") == 0) {
if (firstpass) mass();
else skip_lines(atom->ntypes);
else skip_lines(ntypes);
} else if (strcmp(keyword,"Pair Coeffs") == 0) {
if (force->pair == NULL)
error->all(FLERR,"Must define pair_style before Pair Coeffs");
@ -334,7 +473,7 @@ void ReadData::command(int narg, char **arg)
error->warning(FLERR,"Pair style in data file differs "
"from currently defined pair style");
paircoeffs();
} else skip_lines(atom->ntypes);
} else skip_lines(ntypes);
} else if (strcmp(keyword,"PairIJ Coeffs") == 0) {
if (force->pair == NULL)
error->all(FLERR,"Must define pair_style before PairIJ Coeffs");
@ -343,7 +482,7 @@ void ReadData::command(int narg, char **arg)
error->warning(FLERR,"Pair style in data file differs "
"from currently defined pair style");
pairIJcoeffs();
} else skip_lines(atom->ntypes*(atom->ntypes+1)/2);
} else skip_lines(ntypes*(ntypes+1)/2);
} else if (strcmp(keyword,"Bond Coeffs") == 0) {
if (atom->avec->bonds_allow == 0)
error->all(FLERR,"Invalid data file section: Bond Coeffs");
@ -354,7 +493,7 @@ void ReadData::command(int narg, char **arg)
error->warning(FLERR,"Bond style in data file differs "
"from currently defined bond style");
bondcoeffs();
} else skip_lines(atom->nbondtypes);
} else skip_lines(nbondtypes);
} else if (strcmp(keyword,"Angle Coeffs") == 0) {
if (atom->avec->angles_allow == 0)
error->all(FLERR,"Invalid data file section: Angle Coeffs");
@ -365,7 +504,7 @@ void ReadData::command(int narg, char **arg)
error->warning(FLERR,"Angle style in data file differs "
"from currently defined angle style");
anglecoeffs(0);
} else skip_lines(atom->nangletypes);
} else skip_lines(nangletypes);
} else if (strcmp(keyword,"Dihedral Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all(FLERR,"Invalid data file section: Dihedral Coeffs");
@ -376,7 +515,7 @@ void ReadData::command(int narg, char **arg)
error->warning(FLERR,"Dihedral style in data file differs "
"from currently defined dihedral style");
dihedralcoeffs(0);
} else skip_lines(atom->ndihedraltypes);
} else skip_lines(ndihedraltypes);
} else if (strcmp(keyword,"Improper Coeffs") == 0) {
if (atom->avec->impropers_allow == 0)
error->all(FLERR,"Invalid data file section: Improper Coeffs");
@ -387,7 +526,7 @@ void ReadData::command(int narg, char **arg)
error->warning(FLERR,"Improper style in data file differs "
"from currently defined improper style");
impropercoeffs(0);
} else skip_lines(atom->nimpropertypes);
} else skip_lines(nimpropertypes);
} else if (strcmp(keyword,"BondBond Coeffs") == 0) {
if (atom->avec->angles_allow == 0)
@ -395,14 +534,14 @@ void ReadData::command(int narg, char **arg)
if (force->angle == NULL)
error->all(FLERR,"Must define angle_style before BondBond Coeffs");
if (firstpass) anglecoeffs(1);
else skip_lines(atom->nangletypes);
else skip_lines(nangletypes);
} else if (strcmp(keyword,"BondAngle Coeffs") == 0) {
if (atom->avec->angles_allow == 0)
error->all(FLERR,"Invalid data file section: BondAngle Coeffs");
if (force->angle == NULL)
error->all(FLERR,"Must define angle_style before BondAngle Coeffs");
if (firstpass) anglecoeffs(2);
else skip_lines(atom->nangletypes);
else skip_lines(nangletypes);
} else if (strcmp(keyword,"MiddleBondTorsion Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
@ -413,7 +552,7 @@ void ReadData::command(int narg, char **arg)
"Must define dihedral_style before "
"MiddleBondTorsion Coeffs");
if (firstpass) dihedralcoeffs(1);
else skip_lines(atom->ndihedraltypes);
else skip_lines(ndihedraltypes);
} else if (strcmp(keyword,"EndBondTorsion Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all(FLERR,"Invalid data file section: EndBondTorsion Coeffs");
@ -421,7 +560,7 @@ void ReadData::command(int narg, char **arg)
error->all(FLERR,
"Must define dihedral_style before EndBondTorsion Coeffs");
if (firstpass) dihedralcoeffs(2);
else skip_lines(atom->ndihedraltypes);
else skip_lines(ndihedraltypes);
} else if (strcmp(keyword,"AngleTorsion Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all(FLERR,"Invalid data file section: AngleTorsion Coeffs");
@ -429,7 +568,7 @@ void ReadData::command(int narg, char **arg)
error->all(FLERR,
"Must define dihedral_style before AngleTorsion Coeffs");
if (firstpass) dihedralcoeffs(3);
else skip_lines(atom->ndihedraltypes);
else skip_lines(ndihedraltypes);
} else if (strcmp(keyword,"AngleAngleTorsion Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all(FLERR,
@ -439,7 +578,7 @@ void ReadData::command(int narg, char **arg)
"Must define dihedral_style before "
"AngleAngleTorsion Coeffs");
if (firstpass) dihedralcoeffs(4);
else skip_lines(atom->ndihedraltypes);
else skip_lines(ndihedraltypes);
} else if (strcmp(keyword,"BondBond13 Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all(FLERR,"Invalid data file section: BondBond13 Coeffs");
@ -447,7 +586,7 @@ void ReadData::command(int narg, char **arg)
error->all(FLERR,
"Must define dihedral_style before BondBond13 Coeffs");
if (firstpass) dihedralcoeffs(5);
else skip_lines(atom->ndihedraltypes);
else skip_lines(ndihedraltypes);
} else if (strcmp(keyword,"AngleAngle Coeffs") == 0) {
if (atom->avec->impropers_allow == 0)
@ -456,7 +595,7 @@ void ReadData::command(int narg, char **arg)
error->all(FLERR,
"Must define improper_style before AngleAngle Coeffs");
if (firstpass) impropercoeffs(1);
else skip_lines(atom->nimpropertypes);
else skip_lines(nimpropertypes);
} else {
char str[128];
@ -469,7 +608,7 @@ void ReadData::command(int narg, char **arg)
// error if natoms > 0 yet no atoms were read
if (atom->natoms > 0 && atomflag == 0)
if (natoms > 0 && atomflag == 0)
error->all(FLERR,"No atoms in data file");
// close file
@ -486,9 +625,8 @@ void ReadData::command(int narg, char **arg)
// at end of 1st pass, error check for required sections
// customize for new sections
if ((atom->nbonds && !bondflag) || (atom->nangles && !angleflag) ||
(atom->ndihedrals && !dihedralflag) ||
(atom->nimpropers && !improperflag))
if ((nbonds && !bondflag) || (nangles && !angleflag) ||
(ndihedrals && !dihedralflag) || (nimpropers && !improperflag))
error->one(FLERR,"Needed molecular topology not in data file");
if ((nellipsoids && !ellipsoidflag) || (nlines && !lineflag) ||
@ -510,6 +648,15 @@ void ReadData::command(int narg, char **arg)
atom->avec->grow(atom->nmax);
}
// assign atoms added by this data file to specified group
if (groupbit) {
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = nlocal_previous; i < nlocal; i++)
mask[i] |= groupbit;
}
// create special bond lists for molecular systems
if (atom->molecular == 1) {
@ -590,6 +737,19 @@ void ReadData::command(int narg, char **arg)
if (atom->molecular == 2) atom->avec->onemols[0]->check_attributes(1);
// if adding atoms, migrate atoms to new processors
// use irregular() b/c box size could have changed dramaticaly
// resulting in procs now owning very different subboxes
// with their previously owned atoms now far outside the subbox
if (addflag != NONE) {
if (domain->triclinic) domain->x2lamda(atom->nlocal);
Irregular *irregular = new Irregular(lmp);
irregular->migrate_atoms(1);
delete irregular;
if (domain->triclinic) domain->lamda2x(atom->nlocal);
}
// shrink-wrap the box if necessary and move atoms to new procs
// if atoms are lost is b/c data file box was far from shrink-wrapped
// do not use irregular() comm, which would not lose atoms,
@ -621,6 +781,7 @@ void ReadData::command(int narg, char **arg)
header ends with EOF or non-blank line containing no header keyword
if EOF, line is set to blank line
else line has first keyword line for rest of file
some logic differs if adding atoms
------------------------------------------------------------------------- */
void ReadData::header()
@ -648,7 +809,7 @@ void ReadData::header()
while (1) {
// read a line and bcast length if flag is set
// read a line and bcast length
if (me == 0) {
if (fgets(line,MAXLINE,fp) == NULL) n = 0;
@ -689,7 +850,9 @@ void ReadData::header()
// customize for new header lines
if (strstr(line,"atoms")) {
sscanf(line,BIGINT_FORMAT,&atom->natoms);
sscanf(line,BIGINT_FORMAT,&natoms);
if (addflag == NONE) atom->natoms = natoms;
else atom->natoms += natoms;
// check for these first
// otherwise "triangles" will be matched as "angles"
@ -710,52 +873,70 @@ void ReadData::header()
if (!avec_body)
error->all(FLERR,"No bodies allowed with this atom style");
sscanf(line,BIGINT_FORMAT,&nbodies);
}
else if (strstr(line,"bonds")) sscanf(line,BIGINT_FORMAT,&atom->nbonds);
else if (strstr(line,"angles")) sscanf(line,BIGINT_FORMAT,&atom->nangles);
else if (strstr(line,"dihedrals")) sscanf(line,BIGINT_FORMAT,
&atom->ndihedrals);
else if (strstr(line,"impropers")) sscanf(line,BIGINT_FORMAT,
&atom->nimpropers);
} else if (strstr(line,"bonds")) {
sscanf(line,BIGINT_FORMAT,&nbonds);
if (addflag == NONE) atom->nbonds = nbonds;
else atom->nbonds += nbonds;
} else if (strstr(line,"angles")) {
sscanf(line,BIGINT_FORMAT,&nangles);
if (addflag == NONE) atom->nangles = nangles;
else atom->nangles += nangles;
} else if (strstr(line,"dihedrals")) {
sscanf(line,BIGINT_FORMAT,&ndihedrals);
if (addflag == NONE) atom->ndihedrals = ndihedrals;
else atom->ndihedrals += natoms;
} else if (strstr(line,"impropers")) {
sscanf(line,BIGINT_FORMAT,&nimpropers);
if (addflag == NONE) atom->nimpropers = nimpropers;
else atom->nimpropers += nimpropers;
// Atom class type settings are only set by first data file
else if (strstr(line,"atom types")) sscanf(line,"%d",&atom->ntypes);
else if (strstr(line,"bond types")) sscanf(line,"%d",&atom->nbondtypes);
else if (strstr(line,"angle types")) sscanf(line,"%d",&atom->nangletypes);
else if (strstr(line,"dihedral types"))
sscanf(line,"%d",&atom->ndihedraltypes);
else if (strstr(line,"improper types"))
sscanf(line,"%d",&atom->nimpropertypes);
} else if (strstr(line,"atom types")) {
sscanf(line,"%d",&ntypes);
if (addflag == NONE) atom->ntypes = ntypes + extra_atom_types;
} else if (strstr(line,"bond types")) {
sscanf(line,"%d",&nbondtypes);
if (addflag == NONE) atom->nbondtypes = nbondtypes + extra_bond_types;
} else if (strstr(line,"angle types")) {
sscanf(line,"%d",&nangletypes);
if (addflag == NONE) atom->nangletypes = nangletypes + extra_angle_types;
} else if (strstr(line,"dihedral types")) {
sscanf(line,"%d",&ndihedraltypes);
if (addflag == NONE)
atom->ndihedraltypes = ndihedraltypes + extra_dihedral_types;
} else if (strstr(line,"improper types")) {
sscanf(line,"%d",&nimpropertypes);
if (addflag == NONE)
atom->nimpropertypes = nimpropertypes + extra_improper_types;
else if (strstr(line,"extra bond per atom"))
sscanf(line,"%d",&atom->extra_bond_per_atom);
else if (strstr(line,"extra angle per atom"))
sscanf(line,"%d",&atom->extra_angle_per_atom);
else if (strstr(line,"extra dihedral per atom"))
sscanf(line,"%d",&atom->extra_dihedral_per_atom);
else if (strstr(line,"extra improper per atom"))
sscanf(line,"%d",&atom->extra_improper_per_atom);
else if (strstr(line,"extra special per atom"))
sscanf(line,"%d",&force->special_extra);
// these settings only used by first data file
else if (strstr(line,"extra bonds per atom"))
sscanf(line,"%d",&atom->extra_bond_per_atom);
else if (strstr(line,"extra angles per atom"))
sscanf(line,"%d",&atom->extra_angle_per_atom);
else if (strstr(line,"extra dihedrals per atom"))
sscanf(line,"%d",&atom->extra_dihedral_per_atom);
else if (strstr(line,"extra impropers per atom"))
sscanf(line,"%d",&atom->extra_improper_per_atom);
} else if (strstr(line,"extra bond per atom")) {
if (addflag == NONE) sscanf(line,"%d",&atom->extra_bond_per_atom);
} else if (strstr(line,"extra angle per atom")) {
if (addflag == NONE) sscanf(line,"%d",&atom->extra_angle_per_atom);
} else if (strstr(line,"extra dihedral per atom")) {
if (addflag == NONE) sscanf(line,"%d",&atom->extra_dihedral_per_atom);
} else if (strstr(line,"extra improper per atom")) {
if (addflag == NONE) sscanf(line,"%d",&atom->extra_improper_per_atom);
} else if (strstr(line,"extra special per atom")) {
if (addflag == NONE) sscanf(line,"%d",&force->special_extra);
// local copy of box info
// so can treat differently for first vs subsequent data files
} else if (strstr(line,"xlo xhi")) {
sscanf(line,"%lg %lg",&boxlo[0],&boxhi[0]);
} else if (strstr(line,"ylo yhi")) {
sscanf(line,"%lg %lg",&boxlo[1],&boxhi[1]);
} else if (strstr(line,"zlo zhi")) {
sscanf(line,"%lg %lg",&boxlo[2],&boxhi[2]);
} else if (strstr(line,"xy xz yz")) {
triclinic = 1;
sscanf(line,"%lg %lg %lg",&xy,&xz,&yz);
else if (strstr(line,"xlo xhi"))
sscanf(line,"%lg %lg",&domain->boxlo[0],&domain->boxhi[0]);
else if (strstr(line,"ylo yhi"))
sscanf(line,"%lg %lg",&domain->boxlo[1],&domain->boxhi[1]);
else if (strstr(line,"zlo zhi"))
sscanf(line,"%lg %lg",&domain->boxlo[2],&domain->boxhi[2]);
else if (strstr(line,"xy xz yz")) {
domain->triclinic = 1;
sscanf(line,"%lg %lg %lg",&domain->xy,&domain->xz,&domain->yz);
} else break;
}
@ -824,27 +1005,28 @@ void ReadData::atoms()
}
bigint nread = 0;
bigint natoms = atom->natoms;
while (nread < natoms) {
nchunk = MIN(natoms-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
atom->data_atoms(nchunk,buffer);
atom->data_atoms(nchunk,buffer,id_offset,toffset,shiftflag,shift);
nread += nchunk;
}
// check that all atoms were assigned correctly
bigint tmp = atom->nlocal;
MPI_Allreduce(&tmp,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
bigint n = atom->nlocal;
bigint sum;
MPI_Allreduce(&n,&sum,1,MPI_LMP_BIGINT,MPI_SUM,world);
bigint nassign = sum - (atom->natoms - natoms);
if (me == 0) {
if (screen) fprintf(screen," " BIGINT_FORMAT " atoms\n",natoms);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " atoms\n",natoms);
if (screen) fprintf(screen," " BIGINT_FORMAT " atoms\n",nassign);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " atoms\n",nassign);
}
if (natoms != atom->natoms)
if (sum != atom->natoms)
error->all(FLERR,"Did not assign all atoms correctly");
// check that atom IDs are valid
@ -881,13 +1063,12 @@ void ReadData::velocities()
}
bigint nread = 0;
bigint natoms = atom->natoms;
while (nread < natoms) {
nchunk = MIN(natoms-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
atom->data_vels(nchunk,buffer);
atom->data_vels(nchunk,buffer,id_offset);
nread += nchunk;
}
@ -937,7 +1118,7 @@ void ReadData::bonds(int firstpass)
nchunk = MIN(nbonds-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
atom->data_bonds(nchunk,buffer,count);
atom->data_bonds(nchunk,buffer,count,id_offset);
nread += nchunk;
}
@ -1012,7 +1193,7 @@ void ReadData::angles(int firstpass)
nchunk = MIN(nangles-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
atom->data_angles(nchunk,buffer,count);
atom->data_angles(nchunk,buffer,count,id_offset);
nread += nchunk;
}
@ -1087,7 +1268,7 @@ void ReadData::dihedrals(int firstpass)
nchunk = MIN(ndihedrals-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
atom->data_dihedrals(nchunk,buffer,count);
atom->data_dihedrals(nchunk,buffer,count,id_offset);
nread += nchunk;
}
@ -1162,7 +1343,7 @@ void ReadData::impropers(int firstpass)
nchunk = MIN(nimpropers-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
atom->data_impropers(nchunk,buffer,count);
atom->data_impropers(nchunk,buffer,count,id_offset);
nread += nchunk;
}
@ -1225,7 +1406,7 @@ void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
nchunk = MIN(natoms-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
atom->data_bonus(nchunk,buffer,ptr);
atom->data_bonus(nchunk,buffer,ptr,id_offset);
nread += nchunk;
}
@ -1305,7 +1486,7 @@ void ReadData::bodies(int firstpass)
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
if (firstpass) atom->data_bodies(nchunk,buffer,avec_body);
if (firstpass) atom->data_bodies(nchunk,buffer,avec_body,id_offset);
nread += nchunk;
}
@ -1325,16 +1506,16 @@ void ReadData::bodies(int firstpass)
void ReadData::mass()
{
char *next;
char *buf = new char[atom->ntypes*MAXLINE];
char *buf = new char[ntypes*MAXLINE];
int eof = comm->read_lines_from_file(fp,atom->ntypes,MAXLINE,buf);
int eof = comm->read_lines_from_file(fp,ntypes,MAXLINE,buf);
if (eof) error->all(FLERR,"Unexpected end of data file");
char *original = buf;
for (int i = 0; i < atom->ntypes; i++) {
for (int i = 0; i < ntypes; i++) {
next = strchr(buf,'\n');
*next = '\0';
atom->set_mass(buf);
atom->set_mass(buf,toffset);
buf = next + 1;
}
delete [] original;
@ -1345,16 +1526,16 @@ void ReadData::mass()
void ReadData::paircoeffs()
{
char *next;
char *buf = new char[atom->ntypes*MAXLINE];
char *buf = new char[ntypes*MAXLINE];
int eof = comm->read_lines_from_file(fp,atom->ntypes,MAXLINE,buf);
int eof = comm->read_lines_from_file(fp,ntypes,MAXLINE,buf);
if (eof) error->all(FLERR,"Unexpected end of data file");
char *original = buf;
for (int i = 0; i < atom->ntypes; i++) {
for (int i = 0; i < ntypes; i++) {
next = strchr(buf,'\n');
*next = '\0';
parse_coeffs(buf,NULL,1);
parse_coeffs(buf,NULL,1,2,toffset);
if (narg == 0) error->all(FLERR,"Unexpected end of PairCoeffs section");
force->pair->coeff(narg,arg);
buf = next + 1;
@ -1369,18 +1550,18 @@ void ReadData::pairIJcoeffs()
int i,j;
char *next;
int nsq = atom->ntypes* (atom->ntypes+1) / 2;
int nsq = ntypes * (ntypes+1) / 2;
char *buf = new char[nsq * MAXLINE];
int eof = comm->read_lines_from_file(fp,nsq,MAXLINE,buf);
if (eof) error->all(FLERR,"Unexpected end of data file");
char *original = buf;
for (i = 0; i < atom->ntypes; i++)
for (j = i; j < atom->ntypes; j++) {
for (i = 0; i < ntypes; i++)
for (j = i; j < ntypes; j++) {
next = strchr(buf,'\n');
*next = '\0';
parse_coeffs(buf,NULL,0);
parse_coeffs(buf,NULL,0,2,toffset);
if (narg == 0) error->all(FLERR,"Unexpected end of PairCoeffs section");
force->pair->coeff(narg,arg);
buf = next + 1;
@ -1393,16 +1574,16 @@ void ReadData::pairIJcoeffs()
void ReadData::bondcoeffs()
{
char *next;
char *buf = new char[atom->nbondtypes*MAXLINE];
char *buf = new char[nbondtypes*MAXLINE];
int eof = comm->read_lines_from_file(fp,atom->nbondtypes,MAXLINE,buf);
int eof = comm->read_lines_from_file(fp,nbondtypes,MAXLINE,buf);
if (eof) error->all(FLERR,"Unexpected end of data file");
char *original = buf;
for (int i = 0; i < atom->nbondtypes; i++) {
for (int i = 0; i < nbondtypes; i++) {
next = strchr(buf,'\n');
*next = '\0';
parse_coeffs(buf,NULL,0);
parse_coeffs(buf,NULL,0,1,boffset);
if (narg == 0) error->all(FLERR,"Unexpected end of BondCoeffs section");
force->bond->coeff(narg,arg);
buf = next + 1;
@ -1415,18 +1596,18 @@ void ReadData::bondcoeffs()
void ReadData::anglecoeffs(int which)
{
char *next;
char *buf = new char[atom->nangletypes*MAXLINE];
char *buf = new char[nangletypes*MAXLINE];
int eof = comm->read_lines_from_file(fp,atom->nangletypes,MAXLINE,buf);
int eof = comm->read_lines_from_file(fp,nangletypes,MAXLINE,buf);
if (eof) error->all(FLERR,"Unexpected end of data file");
char *original = buf;
for (int i = 0; i < atom->nangletypes; i++) {
for (int i = 0; i < nangletypes; i++) {
next = strchr(buf,'\n');
*next = '\0';
if (which == 0) parse_coeffs(buf,NULL,0);
else if (which == 1) parse_coeffs(buf,"bb",0);
else if (which == 2) parse_coeffs(buf,"ba",0);
if (which == 0) parse_coeffs(buf,NULL,0,1,aoffset);
else if (which == 1) parse_coeffs(buf,"bb",0,1,aoffset);
else if (which == 2) parse_coeffs(buf,"ba",0,1,aoffset);
if (narg == 0) error->all(FLERR,"Unexpected end of AngleCoeffs section");
force->angle->coeff(narg,arg);
buf = next + 1;
@ -1439,21 +1620,21 @@ void ReadData::anglecoeffs(int which)
void ReadData::dihedralcoeffs(int which)
{
char *next;
char *buf = new char[atom->ndihedraltypes*MAXLINE];
char *buf = new char[ndihedraltypes*MAXLINE];
int eof = comm->read_lines_from_file(fp,atom->ndihedraltypes,MAXLINE,buf);
int eof = comm->read_lines_from_file(fp,ndihedraltypes,MAXLINE,buf);
if (eof) error->all(FLERR,"Unexpected end of data file");
char *original = buf;
for (int i = 0; i < atom->ndihedraltypes; i++) {
for (int i = 0; i < ndihedraltypes; i++) {
next = strchr(buf,'\n');
*next = '\0';
if (which == 0) parse_coeffs(buf,NULL,0);
else if (which == 1) parse_coeffs(buf,"mbt",0);
else if (which == 2) parse_coeffs(buf,"ebt",0);
else if (which == 3) parse_coeffs(buf,"at",0);
else if (which == 4) parse_coeffs(buf,"aat",0);
else if (which == 5) parse_coeffs(buf,"bb13",0);
if (which == 0) parse_coeffs(buf,NULL,0,1,doffset);
else if (which == 1) parse_coeffs(buf,"mbt",0,1,doffset);
else if (which == 2) parse_coeffs(buf,"ebt",0,1,doffset);
else if (which == 3) parse_coeffs(buf,"at",0,1,doffset);
else if (which == 4) parse_coeffs(buf,"aat",0,1,doffset);
else if (which == 5) parse_coeffs(buf,"bb13",0,1,doffset);
if (narg == 0) error->all(FLERR,"Unexpected end of DihedralCoeffs section");
force->dihedral->coeff(narg,arg);
buf = next + 1;
@ -1466,17 +1647,17 @@ void ReadData::dihedralcoeffs(int which)
void ReadData::impropercoeffs(int which)
{
char *next;
char *buf = new char[atom->nimpropertypes*MAXLINE];
char *buf = new char[nimpropertypes*MAXLINE];
int eof = comm->read_lines_from_file(fp,atom->nimpropertypes,MAXLINE,buf);
int eof = comm->read_lines_from_file(fp,nimpropertypes,MAXLINE,buf);
if (eof) error->all(FLERR,"Unexpected end of data file");
char *original = buf;
for (int i = 0; i < atom->nimpropertypes; i++) {
for (int i = 0; i < nimpropertypes; i++) {
next = strchr(buf,'\n');
*next = '\0';
if (which == 0) parse_coeffs(buf,NULL,0);
else if (which == 1) parse_coeffs(buf,"aa",0);
if (which == 0) parse_coeffs(buf,NULL,0,1,ioffset);
else if (which == 1) parse_coeffs(buf,"aa",0,1,ioffset);
if (narg == 0) error->all(FLERR,"Unexpected end of ImproperCoeffs section");
force->improper->coeff(narg,arg);
buf = next + 1;
@ -1500,7 +1681,7 @@ void ReadData::fix(int ifix, char *keyword)
nchunk = MIN(nline-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
modify->fix[ifix]->read_data_section(keyword,nchunk,buffer);
modify->fix[ifix]->read_data_section(keyword,nchunk,buffer,id_offset);
nread += nchunk;
}
}
@ -1643,9 +1824,11 @@ void ReadData::skip_lines(bigint n)
if 2nd word starts with letter, then is hybrid style, add addstr after it
else add addstr before 2nd word
if dupflag, duplicate 1st word, so pair_coeff "2" becomes "2 2"
if noffset, add offset to first noffset args, which are atom/bond/etc types
------------------------------------------------------------------------- */
void ReadData::parse_coeffs(char *line, const char *addstr, int dupflag)
void ReadData::parse_coeffs(char *line, const char *addstr,
int dupflag, int noffset, int offset)
{
char *ptr;
if ((ptr = strchr(line,'#'))) *ptr = '\0';
@ -1664,6 +1847,17 @@ void ReadData::parse_coeffs(char *line, const char *addstr, int dupflag)
if (dupflag && narg == 1) arg[narg++] = word;
word = strtok(NULL," \t\n\r\f");
}
if (noffset) {
int value = force->inumeric(FLERR,arg[0]);
sprintf(argoffset1,"%d",value+offset);
arg[0] = argoffset1;
if (noffset == 2) {
value = force->inumeric(FLERR,arg[1]);
sprintf(argoffset2,"%d",value+offset);
arg[1] = argoffset2;
}
}
}
/* ----------------------------------------------------------------------

41
src/read_data.h
View File

@ -32,19 +32,19 @@ class ReadData : protected Pointers {
void command(int, char **);
private:
int me,compressed;
char *line,*keyword,*buffer,*style;
FILE *fp;
char **arg;
int me,narg,maxarg,compressed;
int narg,maxarg;
char argoffset1[8],argoffset2[8];
// optional args
bigint id_offset;
int addflag,mergeflag;
double offset[3];
int nfix;
int *fix_index;
char **fix_header;
char **fix_section;
bigint natoms;
bigint nbonds,nangles,ndihedrals,nimpropers;
int ntypes;
int nbondtypes,nangletypes,ndihedraltypes,nimpropertypes;
bigint nellipsoids;
class AtomVecEllipsoid *avec_ellipsoid;
@ -55,13 +55,36 @@ class ReadData : protected Pointers {
bigint nbodies;
class AtomVecBody *avec_body;
// box info
double boxlo[3],boxhi[3];
double xy,xz,yz;
int triclinic;
// optional args
int addflag,offsetflag,shiftflag;
tagint addvalue;
int toffset,boffset,aoffset,doffset,ioffset;
double shift[3];
int extra_atom_types,extra_bond_types,extra_angle_types;
int extra_dihedral_types,extra_improper_types;
int groupbit;
int nfix;
int *fix_index;
char **fix_header;
char **fix_section;
// methods
void open(char *);
void scan(int &, int &, int &, int &);
int reallocate(int **, int, int);
void header();
void parse_keyword(int);
void skip_lines(bigint);
void parse_coeffs(char *, const char *, int);
void parse_coeffs(char *, const char *, int, int, int);
int style_match(const char *, const char *);
void atoms();

2
src/version.h
View File

@ -1 +1 @@
#define LAMMPS_VERSION "17 Jul 2015"
#define LAMMPS_VERSION "18 Jul 2015"