forked from lijiext/lammps
improve layout and logical structure. add references
This commit is contained in:
Axel Kohlmeyer
parent
44a54324c1
commit
57711f0dcb
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@ -7,6 +7,7 @@ alphabetically. Style options for entries like fix, compute, pair etc.
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have their own pages where they are listed alphabetically.
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Initialization:
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------------------------------
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* :doc:`newton <newton>`,
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* :doc:`package <package>`,
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@ -15,6 +16,7 @@ Initialization:
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* :doc:`units <units>`
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Setup simulation box:
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------------------------------
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* :doc:`boundary <boundary>`,
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* :doc:`box <box>`,
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@ -25,6 +27,7 @@ Setup simulation box:
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* :doc:`region <region>`
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Setup atoms:
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------------------------------
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* :doc:`atom_modify <atom_modify>`,
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* :doc:`atom_style <atom_style>`,
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@ -45,6 +48,7 @@ Setup atoms:
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* :doc:`velocity <velocity>`
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Force fields:
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------------------------------
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* :doc:`angle_coeff <angle_coeff>`,
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* :doc:`angle_style <angle_style>`,
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@ -65,6 +69,7 @@ Force fields:
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* :doc:`special_bonds <special_bonds>`
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Settings:
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------------------------------
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* :doc:`comm_modify <comm_modify>`,
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* :doc:`comm_style <comm_style>`,
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@ -80,6 +85,7 @@ Settings:
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* :doc:`timestep <timestep>`
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Operations within timestepping (fixes) and diagnostics (computes):
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------------------------------------------------------------------------------------------
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* :doc:`compute <compute>`,
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* :doc:`compute_modify <compute_modify>`,
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@ -89,6 +95,7 @@ Operations within timestepping (fixes) and diagnostics (computes):
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* :doc:`unfix <unfix>`
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Output:
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------------------------------
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* :doc:`dump image <dump_image>`,
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* :doc:`dump movie <dump_image>`,
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@ -105,6 +112,7 @@ Output:
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* :doc:`write_restart <write_restart>`
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Actions:
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------------------------------
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* :doc:`minimize <minimize>`,
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* :doc:`neb <neb>`,
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@ -116,6 +124,7 @@ Actions:
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* :doc:`temper <temper>`
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Input script control:
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------------------------------
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* :doc:`clear <clear>`,
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* :doc:`echo <echo>`,
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@ -9,134 +9,151 @@ file names or user-chosen ID strings.
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Here are 6 rules for how each line in the input script is parsed by
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LAMMPS:
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(1) If the last printable character on the line is a "&" character,
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the command is assumed to continue on the next line. The next line is
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concatenated to the previous line by removing the "&" character and
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line break. This allows long commands to be continued across two or
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more lines. See the discussion of triple quotes in (6) for how to
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continue a command across multiple line without using "&" characters.
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.. _one:
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(2) All characters from the first "#" character onward are treated as
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comment and discarded. See an exception in (6). Note that a
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comment after a trailing "&" character will prevent the command from
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continuing on the next line. Also note that for multi-line commands a
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single leading "#" will comment out the entire command.
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1. If the last printable character on the line is a "&" character, the
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command is assumed to continue on the next line. The next line is
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concatenated to the previous line by removing the "&" character and
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line break. This allows long commands to be continued across two or
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more lines. See the discussion of triple quotes in :ref:`6 <six>`
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for how to continue a command across multiple line without using "&"
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characters.
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.. code-block:: LAMMPS
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.. _two:
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# this is a comment
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2. All characters from the first "#" character onward are treated as
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comment and discarded. The exception to this rule is described in
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:ref:`6 <six>`. Note that a comment after a trailing "&" character
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will prevent the command from continuing on the next line. Also note
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that for multi-line commands a single leading "#" will comment out
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the entire command.
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(3) The line is searched repeatedly for $ characters, which indicate
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variables that are replaced with a text string. See an exception in
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(6).
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.. code-block:: LAMMPS
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If the $ is followed by curly brackets, then the variable name is the
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text inside the curly brackets. If no curly brackets follow the $,
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then the variable name is the single character immediately following
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the $. Thus ${myTemp} and $x refer to variable names "myTemp" and
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"x".
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# this is a comment
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timestep 1.0 # this is also a comment
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How the variable is converted to a text string depends on what style
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of variable it is; see the :doc:`variable <variable>` doc page for details.
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It can be a variable that stores multiple text strings, and return one
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of them. The returned text string can be multiple "words" (space
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separated) which will then be interpreted as multiple arguments in the
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input command. The variable can also store a numeric formula which
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will be evaluated and its numeric result returned as a string.
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.. _three:
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As a special case, if the $ is followed by parenthesis, then the text
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inside the parenthesis is treated as an "immediate" variable and
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evaluated as an :doc:`equal-style variable <variable>`. This is a way
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to use numeric formulas in an input script without having to assign
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them to variable names. For example, these 3 input script lines:
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3. The line is searched repeatedly for $ characters, which indicate
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variables that are replaced with a text string. The exception to
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this rule is described in :ref:`6 <six>`.
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If the $ is followed by text in curly brackets '{}', then the
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variable name is the text inside the curly brackets. If no curly
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brackets follow the $, then the variable name is the single character
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immediately following the $. Thus ${myTemp} and $x refer to variables
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named "myTemp" and "x", while "$xx" will be interpreted as a variable
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named "x" followed by an "x" character.
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How the variable is converted to a text string depends on what style
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of variable it is; see the :doc:`variable <variable>` doc page for
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details. It can be a variable that stores multiple text strings, and
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return one of them. The returned text string can be multiple "words"
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(space separated) which will then be interpreted as multiple
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arguments in the input command. The variable can also store a
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numeric formula which will be evaluated and its numeric result
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returned as a string.
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As a special case, if the $ is followed by parenthesis "()", then the
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text inside the parenthesis is treated as an "immediate" variable and
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evaluated as an :doc:`equal-style variable <variable>`. This is a
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way to use numeric formulas in an input script without having to
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assign them to variable names. For example, these 3 input script
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lines:
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.. code-block:: LAMMPS
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variable X equal (xlo+xhi)/2+sqrt(v_area)
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region 1 block $X 2 INF INF EDGE EDGE
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variable X delete
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can be replaced by:
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.. code-block:: LAMMPS
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region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
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so that you do not have to define (or discard) a temporary variable,
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"X" in this case.
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Additionally, the "immediate" variable expression may be followed by
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a colon, followed by a C-style format string, e.g. ":%f" or ":%.10g".
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The format string must be appropriate for a double-precision
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floating-point value. The format string is used to output the result
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of the variable expression evaluation. If a format string is not
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specified a high-precision "%.20g" is used as the default.
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This can be useful for formatting print output to a desired precision:
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.. code-block:: LAMMPS
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.. code-block:: LAMMPS
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variable X equal (xlo+xhi)/2+sqrt(v_area)
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region 1 block $X 2 INF INF EDGE EDGE
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variable X delete
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print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom"
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can be replaced by
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Note that neither the curly-bracket or immediate form of variables
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can contain nested $ characters for other variables to substitute
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for. Thus you may **NOT** do this:
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.. code-block:: LAMMPS
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.. code-block:: LAMMPS
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variable a equal 2
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variable b2 equal 4
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print "B2 = ${b$a}"
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region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
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Nor can you specify an expression like "$($x-1.0)" for an immediate
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variable, but you could use $(v\_x-1.0), since the latter is valid
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syntax for an :doc:`equal-style variable <variable>`.
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so that you do not have to define (or discard) a temporary variable X.
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See the :doc:`variable <variable>` command for more details of how
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strings are assigned to variables and evaluated, and how they can
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be used in input script commands.
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Additionally, the "immediate" variable expression may be followed by a
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colon, followed by a C-style format string, e.g. ":%f" or ":%.10g".
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The format string must be appropriate for a double-precision
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floating-point value. The format string is used to output the result
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of the variable expression evaluation. If a format string is not
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specified a high-precision "%.20g" is used as the default.
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.. _four:
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This can be useful for formatting print output to a desired precision:
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4. The line is broken into "words" separated by white-space (tabs,
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spaces). Note that words can thus contain letters, digits,
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underscores, or punctuation characters.
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.. _five:
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5. The first word is the command name. All successive words in the line
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are arguments.
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.. code-block:: LAMMPS
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.. _six:
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print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom"
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6. If you want text with spaces to be treated as a single argument, it
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can be enclosed in either single or double or triple quotes. A long
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single argument enclosed in single or double quotes can span multiple
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lines if the "&" character is used, as described above. When the
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lines are concatenated together (and the "&" characters and line
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breaks removed), the text will become a single line. If you want
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multiple lines of an argument to retain their line breaks, the text
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can be enclosed in triple quotes, in which case "&" characters are
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not needed. For example:
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Note that neither the curly-bracket or immediate form of variables can
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contain nested $ characters for other variables to substitute for.
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Thus you cannot do this:
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.. code-block:: LAMMPS
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.. code-block:: LAMMPS
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variable a equal 2
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variable b2 equal 4
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print "B2 = ${b$a}"
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Nor can you specify this $($x-1.0) for an immediate variable, but
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you could use $(v\_x-1.0), since the latter is valid syntax for an
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:doc:`equal-style variable <variable>`.
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See the :doc:`variable <variable>` command for more details of how
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strings are assigned to variables and evaluated, and how they can be
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used in input script commands.
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(4) The line is broken into "words" separated by white-space (tabs,
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spaces). Note that words can thus contain letters, digits,
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underscores, or punctuation characters.
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(5) The first word is the command name. All successive words in the
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line are arguments.
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(6) If you want text with spaces to be treated as a single argument,
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it can be enclosed in either single or double or triple quotes. A
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long single argument enclosed in single or double quotes can span
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multiple lines if the "&" character is used, as described above. When
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the lines are concatenated together (and the "&" characters and line
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breaks removed), the text will become a single line. If you want
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multiple lines of an argument to retain their line breaks, the text
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can be enclosed in triple quotes, in which case "&" characters are not
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needed. For example:
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.. code-block:: LAMMPS
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print "Volume = $v"
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print 'Volume = $v'
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if "${steps} > 1000" then quit
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variable a string "red green blue &
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print "Volume = $v"
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print 'Volume = $v'
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if "${steps} > 1000" then quit
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variable a string "red green blue &
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purple orange cyan"
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print """
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System volume = $v
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System temperature = $t
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"""
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print """
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System volume = $v
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System temperature = $t
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"""
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In each case, the single, double, or triple quotes are removed when
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the single argument they enclose is stored internally.
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In each case, the single, double, or triple quotes are removed when
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the single argument they enclose is stored internally.
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See the :doc:`dump modify format <dump_modify>`, :doc:`print <print>`,
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:doc:`if <if>`, and :doc:`python <python>` commands for examples.
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See the :doc:`dump modify format <dump_modify>`, :doc:`print
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<print>`, :doc:`if <if>`, and :doc:`python <python>` commands for
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examples.
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A "#" or "$" character that is between quotes will not be treated as a
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comment indicator in (2) or substituted for as a variable in (3).
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A "#" or "$" character that is between quotes will not be treated as
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a comment indicator in :ref:`2 <two>` or substituted for as a
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variable in :ref:`3 <three>`.
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.. note::
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@ -8,17 +8,20 @@ page.
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A LAMMPS input script typically has 4 parts:
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1. Initialization
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2. Atom definition
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3. Settings
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4. Run a simulation
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1. :ref:`Initialization <init>`
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2. :ref:`System definition <system>`
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3. :ref:`Settings <settings>`
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4. :ref:`Run a simulation <run>`
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The last 2 parts can be repeated as many times as desired. I.e. run a
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simulation, change some settings, run some more, etc. Each of the 4
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parts is now described in more detail. Remember that almost all
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commands need only be used if a non-default value is desired.
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(1) Initialization
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.. _init:
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Initialization
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------------------------------
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Set parameters that need to be defined before atoms are created or
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read-in from a file.
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@ -34,23 +37,33 @@ commands tell LAMMPS what kinds of force fields are being used:
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:doc:`angle_style <angle_style>`, :doc:`dihedral_style <dihedral_style>`,
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:doc:`improper_style <improper_style>`.
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(2) Atom definition
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.. _system:
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There are 3 ways to define atoms in LAMMPS. Read them in from a data
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or restart file via the :doc:`read_data <read_data>` or
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:doc:`read_restart <read_restart>` commands. These files can contain
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molecular topology information. Or create atoms on a lattice (with no
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molecular topology), using these commands: :doc:`lattice <lattice>`,
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:doc:`region <region>`, :doc:`create_box <create_box>`,
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:doc:`create_atoms <create_atoms>`. The entire set of atoms can be
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duplicated to make a larger simulation using the
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:doc:`replicate <replicate>` command.
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System definition
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------------------------------
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(3) Settings
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There are 3 ways to define the simulation cell and reserve space for
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force field info and fill it with atoms in LAMMPS. Read them in from
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(1) a data file or (2) a restart file via the :doc:`read_data
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<read_data>` or :doc:`read_restart <read_restart>` commands,
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respectively. These files can also contain molecular topology
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information. Or (3) create a simulation cell and fill it with atoms on
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a lattice (with no molecular topology), using these commands:
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:doc:`lattice <lattice>`, :doc:`region <region>`, :doc:`create_box
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<create_box>`, :doc:`create_atoms <create_atoms>` or
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:doc:`read_dump <read_dump>`.
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The entire set of atoms can be duplicated to make a larger simulation
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using the :doc:`replicate <replicate>` command.
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.. _settings:
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Settings
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------------------------------
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Once atoms and molecular topology are defined, a variety of settings
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can be specified: force field coefficients, simulation parameters,
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output options, etc.
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output options, and more.
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Force field coefficients are set by these commands (they can also be
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set in the read-in files): :doc:`pair_coeff <pair_coeff>`,
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@ -77,7 +90,10 @@ commands.
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Output options are set by the :doc:`thermo <thermo>`, :doc:`dump <dump>`,
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and :doc:`restart <restart>` commands.
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(4) Run a simulation
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.. _run:
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Run a simulation
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------------------------------
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A molecular dynamics simulation is run using the :doc:`run <run>`
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command. Energy minimization (molecular statics) is performed using
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@ -4,17 +4,17 @@ LAMMPS features
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LAMMPS is a classical molecular dynamics (MD) code with these general
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classes of functionality:
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* :ref:`General features <general>`
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* :ref:`Particle and model types <particle>`
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* :ref:`Interatomic potentials (force fields) <ff>`
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* :ref:`Atom creation <create>`
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* :ref:`Ensembles, constraints, and boundary conditions <ensemble>`
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* :ref:`Integrators <integrate>`
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* :ref:`Diagnostics <diag>`
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* :ref:`Output <output>`
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* :ref:`Multi-replica models <replica1>`
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* :ref:`Pre- and post-processing <prepost>`
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* :ref:`Specialized features (beyond MD itself) <special>`
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1. :ref:`General features <general>`
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2. :ref:`Particle and model types <particle>`
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3. :ref:`Interatomic potentials (force fields) <ff>`
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4. :ref:`Atom creation <create>`
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5. :ref:`Ensembles, constraints, and boundary conditions <ensemble>`
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6. :ref:`Integrators <integrate>`
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7. :ref:`Diagnostics <diag>`
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8. :ref:`Output <output>`
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9. :ref:`Multi-replica models <replica1>`
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10. :ref:`Pre- and post-processing <prepost>`
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11. :ref:`Specialized features (beyond MD itself) <special>`
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----------
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