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 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 diff --git a/doc/atom_modify.txt b/doc/atom_modify.txt index e738ba4275..a7de56ad12 100644 --- a/doc/atom_modify.txt +++ b/doc/atom_modify.txt @@ -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 diff --git a/doc/info.html b/doc/info.html index c91f46345c..0a9dec096e 100644 --- a/doc/info.html +++ b/doc/info.html @@ -15,20 +15,30 @@
info args-
args = one or more of the following keywords: out, all, system, computes, dumps, fixes, groups, regions, variables, time, or configuration + out values = screen, log, append filename, overwrite filename:ul +
Examples:
info system -info groups computes variables +info groups computes variables +info all out log +info all out append info.txt
Description:
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. +
+The out 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 +log argument selects the log file instead. With the append and +overwrite option, followed by a filename, the output is written +to that file, which is either appended to or overwritten, respectively. +
+The all flag activates printing all categories listed below.
The system category prints a general system overview listing. This includes the unit style, atom style, number of atoms, bonds, angles, @@ -68,6 +78,8 @@ reported.
-Default: none +
Default: +
+The out option has the default screen.
diff --git a/doc/read_data.html b/doc/read_data.html index 072c396b30..cf535e3665 100644 --- a/doc/read_data.html +++ b/doc/read_data.html @@ -19,9 +19,28 @@ fix args = fix-ID header-string section-string
+ 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
@@ -33,6 +52,8 @@
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
Description:
@@ -45,6 +66,140 @@ Also see the explanation of the -restart
switch 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 command. Note that atoms
+read from the data file are also always added to the "all" group. The
+group command discusses atom groups, as used in LAMMPS.
+
+The use of the fix keyword is discussed below.
+
+
+
+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
+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 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 command can be used
+to move a subset of atoms after they have been read from a data file.
+Likewise, the delete_atoms 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 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.
+
+
+
+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.
@@ -88,6 +243,8 @@ the 2 words in "Bond Coeffs", is not valid.
+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
@@ -183,7 +340,11 @@ 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)
@@ -222,6 +383,11 @@ in the LAMMPS data structures for storing these neighbors. See the
special_bonds and molecule 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 and specify how many of the atoms are
@@ -243,6 +409,8 @@ the maximum values defined in any of the template molecules.
+Format of the body of a data file
+
These are the section keywords for the body of the file.
read_dump, read_restart, create_atoms, write_data
-Default: none +
Default: +
+The default for all the extra keywords is 0.