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Axel Kohlmeyer
2024-09-29 21:41:54 -04:00
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doc/src/Run_formats.rst
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@ -24,18 +24,18 @@ standard. This is compatible with ASCII, since the first 128 values are
identical with the ASCIII encoding. It is important to note, however,
that there are Unicode characters that look similar or even identical to
ASCII characters, but have a different representation. As a general
rule, these characters are not be correctly recognized by LAMMPS. For
some parts of LAMMPS' text processing, there are translation tables with
known "lookalike" characters that will transparently substitute them
with their ASCII equivalents. Non-ASCII lookalike characters are often
used by web browsers or PDF viewers to improve the readability of
text. Thus, when using copy-n-paste to transfer text from such an
rule, these characters are not correctly recognized by LAMMPS. For some
parts of LAMMPS' text processing, translation tables with known
"lookalike" characters are used that transparently substitute non-ASCII
characters with their ASCII equivalents. Non-ASCII lookalike characters
are often used by web browsers or PDF viewers to improve the readability
of text. Thus, when using copy-n-paste to transfer text from such an
application to your input file, you may unintentionally create text that
is not fully in ASCII encoding and may cause errors when LAMMPS is
trying to read it.
is not exclusively using ASCII encoding and may cause errors when LAMMPS
is trying to read it.
Lines with non-printable and non-ASCII characters in text files can be
detected for example with:
detected for example with a (Linux) command like the following:
.. code-block:: bash
@ -71,9 +71,55 @@ Input file
A LAMMPS input file is a text file with commands. It is read
line-by-line and each line is processed *immediately*. Before looking
for commands and executing them, there is a pre-processing step where
`${variable}` and `$(expression)` constructs are expanded or evaluated
comments (text starting with a pound sign '#') are removed,
`${variable}` and `$(expression)` constructs are expanded or evaluated,
and lines that end in the ampersand character '&' are combined with the
next line (similar to Fortran 90 free format source code).
next line (similar to Fortran 90 free format source code). After the
pre-processing, lines are split into "words" and the first word must be a
:doc:`command <Commands_all>` and everything . Below are some example lines:
.. code-block:: LAMMPS
# full line comment
# some global settings
units lj
atom_style atomic
# ^^ command ^^ argument(s)
variable x index 1 # may be overridden from command line with -var x <value>
variable xx equal 20*$x # variable "xx" is always 20 time "x"
lattice fcc 0.8442
# multi-line command, uses spacing from "lattice" command
region box block 0.0 ${xx} &
0.0 40.0 &
0.0 30.0
# create simulation box and fillwith atoms according to lattice setting
create_box 1 box
create_atoms 1 box
# set force field and parameters
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
# run simulation
fix 1 all nve
run 1000
The pivotal command in this example input is the :doc:`create_box
command <create_box>`. It defines the simulation system and many
parameters that go with it: units, atom style, number of atom types (and
other types) and more. Those settings are *locked in* after the box is
created. Commands that change these kind of settings are only allowed
**before** a simulation box is created and many other commands are only
allowed **after** the simulation box is defined (e.g. :doc:`pair_coeff
<pair_coeff>`). Very few commands (e.g. :doc:`pair_style <pair_style>`)
may be used in either part of the input. The :doc:`read_data
<read_data>` and :doc:`read_restart <read_restart>` commands also create
the system box and thus have a similar pivotal function.
The LAMMPS input syntax has minimal support for conditionals and loops,
but if more complex operations are required, it is recommended to use
@ -86,14 +132,16 @@ minimization. To trigger actions on specific conditions **during**
a run is a non-trivial operation that usually requires adopting one
of the available fix commands or creating a new one.
LAMMPS commands can change the internal state and thus the order of
commands matters and reordering them can produce different results.
LAMMPS commands change the internal state and thus the order of commands
matters and reordering them can produce different results. For example,
the region defined by the :doc:`region command <region>` in the example
above depends on the :doc:`lattice setting <lattice>` and thus its
dimensions will be different depending on the order of the two commands.
Each line must have an "end-of-line" character (line feed or carriage
return plus line feed). Some text editors do not automatically insert
one which may have the result that LAMMPS ignores the last command.
It is thus recommended, to always have an empty line at the end of an
input file.
one which may cause LAMMPS to ignore the last command. It is thus
recommended, to always have an empty line at the end of an input file.
The specific details describing how LAMMPS input is processed and parsed
are explained in :doc:`Commands_parse`.
@ -101,6 +149,70 @@ are explained in :doc:`Commands_parse`.
Data file
^^^^^^^^^
A LAMMPS data file contains a description of a system suitable for
reading with the :doc:`read_data command <read_data>`. This is commonly
used for setting up more complex and particularly molecular systems
which can be difficult to achieve with the commands :doc:`create_box
<create_box>` and :doc:`create_atoms <create_atoms>` alone. Also, data
files can be used as a portable alternatives to a :doc:`binary restart
file <restart>`. A restart file can be converted into a data file
from the :doc:`command line <Run_options>`.
The file is generally structured into a header section at the very
beginning of the file and multiple titled sections like "Atoms",
Masses", "Pair Coeffs", and so on. The data file **always** starts
with a "title" line, which will be **ignored** by LAMMPS. Omitting
the title line can lead to unexpected behavior as then a line of
the header with an actual setting may be ignored. This is often a
line with the "atoms" keyword, which results in LAMMPS assuming that
there are no atoms in the data file and thus throwing an error on the
contents of the "Atoms" section. The title line may contain some
keywords that can be used by external programs to convey information
about the system, that is not required and not read by LAMMPS.
Data files may contain comments, which start with the pound sign '#'.
There must be at least one blank between a valid keyword and the pound
sign.
.. code-block:: bash
LAMMPS Title line (ignored)
# full line comment
10 atoms # comment
4 atom types
-36.840194 64.211560 xlo xhi
-41.013691 68.385058 ylo yhi
-29.768095 57.139462 zlo zhi
Masses
1 12.0110
2 12.0110
3 15.9990
4 1.0080
Pair Coeffs
1 0.110000 3.563595 0.110000 3.563595
2 0.080000 3.670503 0.010000 3.385415
3 0.120000 3.029056 0.120000 2.494516
4 0.022000 2.351973 0.022000 2.351973
Atoms # full
1 1 1 0.560 43.99993 58.52678 36.78550 0 0 0
2 1 2 -0.270 45.10395 58.23499 35.86693 0 0 0
3 1 3 -0.510 43.81519 59.54928 37.43995 0 0 0
4 1 4 0.090 45.71714 57.34797 36.13434 0 0 0
5 1 4 0.090 45.72261 59.13657 35.67007 0 0 0
6 1 4 0.090 44.66624 58.09539 34.85538 0 0 0
7 1 3 -0.470 43.28193 57.47427 36.91953 0 0 0
8 1 4 0.070 42.07157 57.45486 37.62418 0 0 0
9 1 1 0.510 42.19985 57.57789 39.12163 0 0 0
10 1 1 0.510 41.88641 58.62251 39.70398 0 0 0
# ^^atomID ^^molID ^^type ^^charge ^^xcoord ^^ycoord ^^ycoord ^^image^^flags
Molecule file
^^^^^^^^^^^^^