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some more fixups

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This commit is contained in:
Axel Kohlmeyer
2020-03-13 16:59:24 -04:00
parent a990f1dc89
commit 0c0308db3e
21 changed files with 72 additions and 72 deletions
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2
doc/src/Errors_messages.rst
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@ -301,7 +301,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
Specified bond type is not valid.
*Bad fix ID in fix append/atoms command*
The value of the fix_id for keyword spatial must start with 'f_'.
The value of the fix_id for keyword spatial must start with "f\_".
*Bad grid of processors*
The 3d grid of processors defined by the processors command does not

4
doc/src/Examples.rst
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@ -132,7 +132,7 @@ Lowercase directories
+-------------+------------------------------------------------------------------+
| reax | RDX and TATB models using the ReaxFF |
+-------------+------------------------------------------------------------------+
| rerun | use of rerun and read_dump commands |
| rerun | use of rerun and read_dump commands |
+-------------+------------------------------------------------------------------+
| rigid | rigid bodies modeled as independent or coupled |
+-------------+------------------------------------------------------------------+
@ -195,7 +195,7 @@ Uppercase directories
+------------+--------------------------------------------------------------------------------------------------+
| ELASTIC | compute elastic constants at zero temperature |
+------------+--------------------------------------------------------------------------------------------------+
| ELASTIC_T | compute elastic constants at finite temperature |
| ELASTIC_T | compute elastic constants at finite temperature |
+------------+--------------------------------------------------------------------------------------------------+
| HEAT | compute thermal conductivity for LJ and water via fix ehex |
+------------+--------------------------------------------------------------------------------------------------+

8
doc/src/Howto_manifold.rst
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@ -19,17 +19,17 @@ to the relevant fixes.
+----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
| cylinder | R | x\^2 + y\^2 - R\^2 = 0 | Cylinder along z-axis, axis going through (0,0,0) |
+----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
| cylinder_dent | R l a | x\^2 + y\^2 - r(z)\^2 = 0, r(x) = R if \| z \| > l, r(z) = R - a\*(1 + cos(z/l))/2 otherwise | A cylinder with a dent around z = 0 |
| cylinder_dent | R l a | x\^2 + y\^2 - r(z)\^2 = 0, r(x) = R if \| z \| > l, r(z) = R - a\*(1 + cos(z/l))/2 otherwise | A cylinder with a dent around z = 0 |
+----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
| dumbbell | a A B c | -( x\^2 + y\^2 ) + (a\^2 - z\^2/c\^2) \* ( 1 + (A\*sin(B\*z\^2))\^4) = 0 | A dumbbell |
+----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
| ellipsoid | a b c | (x/a)\^2 + (y/b)\^2 + (z/c)\^2 = 0 | An ellipsoid |
+----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
| gaussian_bump | A l rc1 rc2 | if( x < rc1) -z + A \* exp( -x\^2 / (2 l\^2) ); else if( x < rc2 ) -z + a + b\*x + c\*x\^2 + d\*x\^3; else z | A Gaussian bump at x = y = 0, smoothly tapered to a flat plane z = 0. |
| gaussian_bump | A l rc1 rc2 | if( x < rc1) -z + A \* exp( -x\^2 / (2 l\^2) ); else if( x < rc2 ) -z + a + b\*x + c\*x\^2 + d\*x\^3; else z | A Gaussian bump at x = y = 0, smoothly tapered to a flat plane z = 0. |
+----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
| plane | a b c x0 y0 z0 | a\*(x-x0) + b\*(y-y0) + c\*(z-z0) = 0 | A plane with normal (a,b,c) going through point (x0,y0,z0) |
+----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
| plane_wiggle | a w | z - a\*sin(w\*x) = 0 | A plane with a sinusoidal modulation on z along x. |
| plane_wiggle | a w | z - a\*sin(w\*x) = 0 | A plane with a sinusoidal modulation on z along x. |
+----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
| sphere | R | x\^2 + y\^2 + z\^2 - R\^2 = 0 | A sphere of radius R |
+----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
@ -37,7 +37,7 @@ to the relevant fixes.
+----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
| spine | a, A, B, B2, c | -(x\^2 + y\^2) + (a\^2 - z\^2/f(z)\^2)\*(1 + (A\*sin(g(z)\*z\^2))\^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise | An approximation to a dendritic spine |
+----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
| spine_two | a, A, B, B2, c | -(x\^2 + y\^2) + (a\^2 - z\^2/f(z)\^2)\*(1 + (A\*sin(g(z)\*z\^2))\^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise | Another approximation to a dendritic spine |
| spine_two | a, A, B, B2, c | -(x\^2 + y\^2) + (a\^2 - z\^2/f(z)\^2)\*(1 + (A\*sin(g(z)\*z\^2))\^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise | Another approximation to a dendritic spine |
+----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+
| thylakoid | wB LB lB | Various, see :ref:`(Paquay) <Paquay1>` | A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB |
+----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+

6
doc/src/Python_examples.rst
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@ -20,11 +20,11 @@ distribution.
+----------------------------------------------------------------+--------------------------------------------------+
| GUI go/stop/temperature-slider to control LAMMPS | plot.py |
+----------------------------------------------------------------+--------------------------------------------------+
| real-time temperature plot with GnuPlot via Pizza.py | viz_tool.py |
| real-time temperature plot with GnuPlot via Pizza.py | viz_tool.py |
+----------------------------------------------------------------+--------------------------------------------------+
| real-time viz via some viz package | vizplotgui_tool.py |
| real-time viz via some viz package | vizplotgui_tool.py |
+----------------------------------------------------------------+--------------------------------------------------+
| combination of viz_tool.py and plot.py and gui.py | |
| combination of viz_tool.py and plot.py and gui.py | |
+----------------------------------------------------------------+--------------------------------------------------+
----------

6
doc/src/compute_chunk_atom.rst
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@ -270,14 +270,14 @@ chunk ID to the atom. *Nchunk* is set to the largest chunk ID. Note
that this excludes atoms which are not in the specified group or
optional region.
If the style begins with "c_", a compute ID must follow which has been
If the style begins with "c\_", a compute ID must follow which has been
previously defined in the input script. If no bracketed integer is
appended, the per-atom vector calculated by the compute is used. If a
bracketed integer is appended, the Ith column of the per-atom array
calculated by the compute is used. Users can also write code for
their own compute styles and :doc:`add them to LAMMPS <Modify>`.
If the style begins with "f_", a fix ID must follow which has been
If the style begins with "f\_", a fix ID must follow which has been
previously defined in the input script. If no bracketed integer is
appended, the per-atom vector calculated by the fix is used. If a
bracketed integer is appended, the Ith column of the per-atom array
@ -286,7 +286,7 @@ their values on certain timesteps, which must be compatible with the
timestep on which this compute accesses the fix, else an error
results. Users can also write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`.
If a value begins with "v_", a variable name for an *atom* or
If a value begins with "v\_", a variable name for an *atom* or
*atomfile* style :doc:`variable <variable>` must follow which has been
previously defined in the input script. Variables of style *atom* can
reference thermodynamic keywords and various per-atom attributes, or

12
doc/src/compute_global_atom.rst
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@ -133,7 +133,7 @@ simple rounded down to convert the value to integer indices. The
final values should range from 1 to N (inclusive), since they are used
to access values from N-length vectors.
If *index* begins with "c_", a compute ID must follow which has been
If *index* begins with "c\_", a compute ID must follow which has been
previously defined in the input script. The compute must generate
per-atom quantities. See the individual :doc:`compute <compute>` doc
page for details. If no bracketed integer is appended, the per-atom
@ -144,7 +144,7 @@ styles and :doc:`add them to LAMMPS <Modify>`. See the
discussion above for how I can be specified with a wildcard asterisk
to effectively specify multiple values.
If *index* begins with "f_", a fix ID must follow which has been
If *index* begins with "f\_", a fix ID must follow which has been
previously defined in the input script. The Fix must generate
per-atom quantities. See the individual :doc:`fix <fix>` doc page for
details. Note that some fixes only produce their values on certain
@ -157,7 +157,7 @@ own fix style and :doc:`add them to LAMMPS <Modify>`. See the
discussion above for how I can be specified with a wildcard asterisk
to effectively specify multiple values.
If *index* begins with "v_", a variable name must follow which has
If *index* begins with "v\_", a variable name must follow which has
been previously defined in the input script. It must be an
:doc:`atom-style variable <variable>`. Atom-style variables can
reference thermodynamic keywords and various per-atom attributes, or
@ -171,7 +171,7 @@ This section explains the kinds of *input* values that can be used.
Note that inputs reference global values, as contrasted with the
*index* parameter which must reference per-atom values.
If a value begins with "c_", a compute ID must follow which has been
If a value begins with "c\_", a compute ID must follow which has been
previously defined in the input script. The compute must generate a
global vector or array. See the individual :doc:`compute <compute>` doc
page for details. If no bracketed integer is appended, the vector
@ -181,7 +181,7 @@ used. Users can also write code for their own compute styles and :doc:`add them
I can be specified with a wildcard asterisk to effectively specify
multiple values.
If a value begins with "f_", a fix ID must follow which has been
If a value begins with "f\_", a fix ID must follow which has been
previously defined in the input script. The fix must generate a
global vector or array. See the individual :doc:`fix <fix>` doc page
for details. Note that some fixes only produce their values on
@ -194,7 +194,7 @@ own fix style and :doc:`add them to LAMMPS <Modify>`. See the
discussion above for how I can be specified with a wildcard asterisk
to effectively specify multiple values.
If a value begins with "v_", a variable name must follow which has
If a value begins with "v\_", a variable name must follow which has
been previously defined in the input script. It must be a
:doc:`vector-style variable <variable>`. Vector-style variables can
reference thermodynamic keywords and various other attributes of

6
doc/src/compute_reduce.rst
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@ -122,7 +122,7 @@ self-explanatory. Note that other atom attributes can be used as
inputs to this fix by using the :doc:`compute property/atom <compute_property_atom>` command and then specifying
an input value from that compute.
If a value begins with "c_", a compute ID must follow which has been
If a value begins with "c\_", a compute ID must follow which has been
previously defined in the input script. Computes can generate
per-atom or local quantities. See the individual
:doc:`compute <compute>` doc page for details. If no bracketed integer
@ -133,7 +133,7 @@ compute styles and :doc:`add them to LAMMPS <Modify>`. See the
discussion above for how I can be specified with a wildcard asterisk
to effectively specify multiple values.
If a value begins with "f_", a fix ID must follow which has been
If a value begins with "f\_", a fix ID must follow which has been
previously defined in the input script. Fixes can generate per-atom
or local quantities. See the individual :doc:`fix <fix>` doc page for
details. Note that some fixes only produce their values on certain
@ -145,7 +145,7 @@ is used. Users can also write code for their own fix style and :doc:`add them t
be specified with a wildcard asterisk to effectively specify multiple
values.
If a value begins with "v_", a variable name must follow which has
If a value begins with "v\_", a variable name must follow which has
been previously defined in the input script. It must be an
:doc:`atom-style variable <variable>`. Atom-style variables can
reference thermodynamic keywords and various per-atom attributes, or

6
doc/src/compute_slice.rst
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@ -55,7 +55,7 @@ vector. Each listed input must be a global vector or column of a
global array calculated by another :doc:`compute <compute>` or
:doc:`fix <fix>`.
If an input value begins with "c_", a compute ID must follow which has
If an input value begins with "c\_", a compute ID must follow which has
been previously defined in the input script and which generates a
global vector or array. See the individual :doc:`compute <compute>` doc
page for details. If no bracketed integer is appended, the vector
@ -63,7 +63,7 @@ calculated by the compute is used. If a bracketed integer is
appended, the Ith column of the array calculated by the compute is
used. Users can also write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
If a value begins with "f_", a fix ID must follow which has been
If a value begins with "f\_", a fix ID must follow which has been
previously defined in the input script and which generates a global
vector or array. See the individual :doc:`fix <fix>` doc page for
details. Note that some fixes only produce their values on certain
@ -73,7 +73,7 @@ appended, the vector calculated by the fix is used. If a bracketed
integer is appended, the Ith column of the array calculated by the fix
is used. Users can also write code for their own fix style and :doc:`add them to LAMMPS <Modify>`.
If an input value begins with "v_", a variable name must follow which
If an input value begins with "v\_", a variable name must follow which
has been previously defined in the input script. Only vector-style
variables can be referenced. See the :doc:`variable <variable>` command
for details. Note that variables of style *vector* define a formula

2
doc/src/dump_image.rst
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@ -193,7 +193,7 @@ atoms rendered in the image. They can be any atom attribute defined
for the :doc:`dump custom <dump>` command, including *type* and
*element*\ . This includes per-atom quantities calculated by a
:doc:`compute <compute>`, :doc:`fix <fix>`, or :doc:`variable <variable>`,
which are prefixed by "c_", "f_", or "v_" respectively. Note that the
which are prefixed by "c\_", "f\_", or "v\_" respectively. Note that the
*diameter* setting can be overridden with a numeric value applied to
all atoms by the optional *adiam* keyword.

2
doc/src/dump_modify.rst
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@ -461,7 +461,7 @@ The *refresh* keyword only applies to the dump *custom*\ , *cfg*\ ,
*image*\ , and *movie* styles. It allows an "incremental" dump file to
be written, by refreshing a compute that is used as a threshold for
determining which atoms are included in a dump snapshot. The
specified *c_ID* gives the ID of the compute. It is prefixed by "c_"
specified *c_ID* gives the ID of the compute. It is prefixed by "c\_"
to indicate a compute, which is the only current option. At some
point, other options may be added, e.g. fixes or variables.

6
doc/src/fix.rst
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@ -103,11 +103,11 @@ discussed below, it can be referenced via the following bracket
notation, where ID is the ID of the fix:
+-------------+--------------------------------------------+
| f_ID | entire scalar, vector, or array |
| f_ID | entire scalar, vector, or array |
+-------------+--------------------------------------------+
| f_ID[I] | one element of vector, one column of array |
| f_ID[I] | one element of vector, one column of array |
+-------------+--------------------------------------------+
| f_ID[I][J] | one element of array |
| f_ID[I][J] | one element of array |
+-------------+--------------------------------------------+
In other words, using one bracket reduces the dimension of the

6
doc/src/fix_ave_atom.rst
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@ -121,7 +121,7 @@ an input value from that compute.
which can be provided by the :doc:`compute property/atom <compute_property_atom>` command via its xu,yu,zu
attributes.
If a value begins with "c_", a compute ID must follow which has been
If a value begins with "c\_", a compute ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the per-atom vector calculated by the compute is used. If a
bracketed term containing an index I is appended, the Ith column of
@ -130,7 +130,7 @@ write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
be specified with a wildcard asterisk to effectively specify multiple
values.
If a value begins with "f_", a fix ID must follow which has been
If a value begins with "f\_", a fix ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the per-atom vector calculated by the fix is used. If a
bracketed term containing an index I is appended, the Ith column of
@ -141,7 +141,7 @@ write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`. See
specified with a wildcard asterisk to effectively specify multiple
values.
If a value begins with "v_", a variable name must follow which has
If a value begins with "v\_", a variable name must follow which has
been previously defined in the input script as an :doc:`atom-style variable <variable>` Variables of style *atom* can reference
thermodynamic keywords, or invoke other computes, fixes, or variables
when they are evaluated, so this is a very general means of generating

6
doc/src/fix_ave_chunk.rst
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@ -265,7 +265,7 @@ of atoms to calculate their temperature. The compute allows the
center-of-mass velocity of each chunk to be subtracted before
calculating the temperature; this fix does not.
If a value begins with "c_", a compute ID must follow which has been
If a value begins with "c\_", a compute ID must follow which has been
previously defined in the input script. If no bracketed integer is
appended, the per-atom vector calculated by the compute is used. If a
bracketed integer is appended, the Ith column of the per-atom array
@ -274,7 +274,7 @@ their own compute styles and :doc:`add them to LAMMPS <Modify>`.
See the discussion above for how I can be specified with a wildcard
asterisk to effectively specify multiple values.
If a value begins with "f_", a fix ID must follow which has been
If a value begins with "f\_", a fix ID must follow which has been
previously defined in the input script. If no bracketed integer is
appended, the per-atom vector calculated by the fix is used. If a
bracketed integer is appended, the Ith column of the per-atom array
@ -285,7 +285,7 @@ own fix styles and :doc:`add them to LAMMPS <Modify>`. See the
discussion above for how I can be specified with a wildcard asterisk
to effectively specify multiple values.
If a value begins with "v_", a variable name must follow which has
If a value begins with "v\_", a variable name must follow which has
been previously defined in the input script. Variables of style
*atom* can reference thermodynamic keywords and various per-atom
attributes, or invoke other computes, fixes, or variables when they

6
doc/src/fix_ave_correlate.rst
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@ -169,7 +169,7 @@ default, then *Nfreq* >= (\ *Nrepeat*\ -1)\*\ *Nevery* is required.
----------
If a value begins with "c_", a compute ID must follow which has been
If a value begins with "c\_", a compute ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the compute is used. If a
bracketed term is appended, the Ith element of the global vector
@ -185,7 +185,7 @@ or :doc:`fix temp/rescale <fix_temp_rescale>`. See the doc pages for
these commands which give the IDs of these computes. Users can also
write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
If a value begins with "f_", a fix ID must follow which has been
If a value begins with "f\_", a fix ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the fix is used. If a
bracketed term is appended, the Ith element of the global vector
@ -197,7 +197,7 @@ Note that some fixes only produce their values on certain timesteps,
which must be compatible with *Nevery*\ , else an error will result.
Users can also write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`.
If a value begins with "v_", a variable name must follow which has
If a value begins with "v\_", a variable name must follow which has
been previously defined in the input script. Only equal-style or
vector-style variables can be referenced; the latter requires a
bracketed term to specify the Ith element of the vector calculated by

6
doc/src/fix_ave_histo.rst
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@ -176,7 +176,7 @@ self-explanatory. Note that other atom attributes can be used as
inputs to this fix by using the :doc:`compute property/atom <compute_property_atom>` command and then specifying
an input value from that compute.
If a value begins with "c_", a compute ID must follow which has been
If a value begins with "c\_", a compute ID must follow which has been
previously defined in the input script. If *mode* = scalar, then if
no bracketed term is appended, the global scalar calculated by the
compute is used. If a bracketed term is appended, the Ith element of
@ -196,7 +196,7 @@ or :doc:`fix temp/rescale <fix_temp_rescale>`. See the doc pages for
these commands which give the IDs of these computes. Users can also
write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
If a value begins with "f_", a fix ID must follow which has been
If a value begins with "f\_", a fix ID must follow which has been
previously defined in the input script. If *mode* = scalar, then if
no bracketed term is appended, the global scalar calculated by the fix
is used. If a bracketed term is appended, the Ith element of the
@ -212,7 +212,7 @@ Note that some fixes only produce their values on certain timesteps,
which must be compatible with *Nevery*\ , else an error will result.
Users can also write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`.
If a value begins with "v_", a variable name must follow which has
If a value begins with "v\_", a variable name must follow which has
been previously defined in the input script. If *mode* = scalar, then
only equal-style or vector-style variables can be used, which both
produce global values. In this mode, a vector-style variable requires

6
doc/src/fix_ave_time.rst
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@ -155,7 +155,7 @@ averaging is done; values are simply generated on timesteps
----------
If a value begins with "c_", a compute ID must follow which has been
If a value begins with "c\_", a compute ID must follow which has been
previously defined in the input script. If *mode* = scalar, then if
no bracketed term is appended, the global scalar calculated by the
compute is used. If a bracketed term is appended, the Ith element of
@ -173,7 +173,7 @@ not in your input script, but by :doc:`thermodynamic output <thermo_style>` or o
the doc pages for these commands which give the IDs of these computes.
Users can also write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
If a value begins with "f_", a fix ID must follow which has been
If a value begins with "f\_", a fix ID must follow which has been
previously defined in the input script. If *mode* = scalar, then if
no bracketed term is appended, the global scalar calculated by the fix
is used. If a bracketed term is appended, the Ith element of the
@ -188,7 +188,7 @@ Note that some fixes only produce their values on certain timesteps,
which must be compatible with *Nevery*\ , else an error will result.
Users can also write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`.
If a value begins with "v_", a variable name must follow which has
If a value begins with "v\_", a variable name must follow which has
been previously defined in the input script. If *mode* = scalar, then
only equal-style or vector-style variables can be used, which both
produce global values. In this mode, a vector-style variable requires

8
doc/src/fix_controller.rst
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@ -152,7 +152,7 @@ The process variable *pvar* can be specified as the output of a
:doc:`variable <variable>`. In each case, the compute, fix, or variable
must produce a global quantity, not a per-atom or local quantity.
If *pvar* begins with "c_", a compute ID must follow which has been
If *pvar* begins with "c\_", a compute ID must follow which has been
previously defined in the input script and which generates a global
scalar or vector. See the individual :doc:`compute <compute>` doc page
for details. If no bracketed integer is appended, the scalar
@ -160,7 +160,7 @@ calculated by the compute is used. If a bracketed integer is
appended, the Ith value of the vector calculated by the compute is
used. Users can also write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
If *pvar* begins with "f_", a fix ID must follow which has been
If *pvar* begins with "f\_", a fix ID must follow which has been
previously defined in the input script and which generates a global
scalar or vector. See the individual :doc:`fix <fix>` doc page for
details. Note that some fixes only produce their values on certain
@ -170,7 +170,7 @@ is appended, the scalar calculated by the fix is used. If a bracketed
integer is appended, the Ith value of the vector calculated by the fix
is used. Users can also write code for their own fix style and :doc:`add them to LAMMPS <Modify>`.
If *pvar* begins with "v_", a variable name must follow which has been
If *pvar* begins with "v\_", a variable name must follow which has been
previously defined in the input script. Only equal-style variables
can be referenced. See the :doc:`variable <variable>` command for
details. Note that variables of style *equal* define a formula which
@ -183,7 +183,7 @@ The target value *setpoint* for the process variable must be a numeric
value, in whatever units *pvar* is defined for.
The control variable *cvar* must be the name of an :doc:`internal-style variable <variable>` previously defined in the input script. Note
that it is not specified with a "v_" prefix, just the name of the
that it is not specified with a "v\_" prefix, just the name of the
variable. It must be an internal-style variable, because this fix
updates its value directly. Note that other commands can use an
equal-style versus internal-style variable interchangeably.

2
doc/src/fix_rx.rst
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@ -189,7 +189,7 @@ Note that the species tags that are defined in the reaction equations
are used by the :doc:`fix eos/table/rx <fix_eos_table_rx>` command to
define the thermodynamic properties of each species. Furthermore, the
number of species molecules (i.e., concentration) can be specified
either with the :doc:`set <set>` command using the "d_" prefix or by
either with the :doc:`set <set>` command using the "d\_" prefix or by
reading directly the concentrations from a data file. For the latter
case, the :doc:`read_data <read_data>` command with the fix keyword
should be specified, where the fix-ID will be the "fix rx`ID with a <SPECIES">`_ suffix, e.g.

6
doc/src/fix_vector.rst
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@ -86,7 +86,7 @@ sufficient size.
----------
If a value begins with "c_", a compute ID must follow which has been
If a value begins with "c\_", a compute ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the compute is used. If a
bracketed term is appended, the Ith element of the global vector
@ -100,7 +100,7 @@ or :doc:`fix temp/rescale <fix_temp_rescale>`. See the doc pages for
these commands which give the IDs of these computes. Users can also
write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
If a value begins with "f_", a fix ID must follow which has been
If a value begins with "f\_", a fix ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the fix is used. If a
bracketed term is appended, the Ith element of the global vector
@ -110,7 +110,7 @@ Note that some fixes only produce their values on certain timesteps,
which must be compatible with *Nevery*\ , else an error will result.
Users can also write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`.
If a value begins with "v_", a variable name must follow which has
If a value begins with "v\_", a variable name must follow which has
been previously defined in the input script. An equal-style or
vector-style variable can be referenced; the latter requires a
bracketed term to specify the Ith element of the vector calculated by

2
doc/src/pair_resquared.rst
View File

@ -141,7 +141,7 @@ interactions are computed by another hybrid pair potential), then you
still need to insure the epsilon a,b,c coefficients are assigned to
that type in a "pair_coeff I J" command.
For large uniform molecules it has been shown that the epsilon_\*_\*
For large uniform molecules it has been shown that the :math:`\epsilon_{*,*}`
energy parameters are approximately representable in terms of local
contact curvatures :ref:`(Everaers) <Everaers3>`:

36
doc/src/variable.rst
View File

@ -485,11 +485,11 @@ references, and references to other variables.
+--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Atom vectors | id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q |
+--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Compute references | c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i] |
| Compute references | c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i] |
+--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Fix references | f_ID, f_ID[i], f_ID[i][j], F_ID, F_ID[i] |
| Fix references | f_ID, f_ID[i], f_ID[i][j], F_ID, F_ID[i] |
+--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Other variables | v_name, v_name[i] |
| Other variables | v_name, v_name[i] |
+--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
Most of the formula elements produce a scalar value. Some produce a
@ -1038,11 +1038,11 @@ reference means, since computes only produce either global or per-atom
quantities, never both.
+-------------+-------------------------------------------------------------------------------------------------------+
| c_ID | global scalar, or per-atom vector |
| c_ID | global scalar, or per-atom vector |
+-------------+-------------------------------------------------------------------------------------------------------+
| c_ID[I] | Ith element of global vector, or atom I's value in per-atom vector, or Ith column from per-atom array |
| c_ID[I] | Ith element of global vector, or atom I's value in per-atom vector, or Ith column from per-atom array |
+-------------+-------------------------------------------------------------------------------------------------------+
| c_ID[I][J] | I,J element of global array, or atom I's Jth value in per-atom array |
| c_ID[I][J] | I,J element of global array, or atom I's Jth value in per-atom array |
+-------------+-------------------------------------------------------------------------------------------------------+
For I and J indices, integers can be specified or a variable name,
@ -1092,17 +1092,17 @@ column of an per-atom array. See the doc pages for individual fixes
to see what kind of values they produce.
The different kinds of fix references are exactly the same as the
compute references listed in the above table, where "c_" is replaced
by "f_". Again, there is typically no ambiguity (see exception below)
compute references listed in the above table, where "c\_" is replaced
by "f\_". Again, there is typically no ambiguity (see exception below)
as to what a reference means, since fixes only produce either global
or per-atom quantities, never both.
+-------------+-------------------------------------------------------------------------------------------------------+
| f_ID | global scalar, or per-atom vector |
| f_ID | global scalar, or per-atom vector |
+-------------+-------------------------------------------------------------------------------------------------------+
| f_ID[I] | Ith element of global vector, or atom I's value in per-atom vector, or Ith column from per-atom array |
| f_ID[I] | Ith element of global vector, or atom I's value in per-atom vector, or Ith column from per-atom array |
+-------------+-------------------------------------------------------------------------------------------------------+
| f_ID[I][J] | I,J element of global array, or atom I's Jth value in per-atom array |
| f_ID[I][J] | I,J element of global array, or atom I's Jth value in per-atom array |
+-------------+-------------------------------------------------------------------------------------------------------+
For I and J indices, integers can be specified or a variable name,
@ -1169,15 +1169,15 @@ There is no ambiguity as to what a reference means, since variables
produce only a global scalar or global vector or per-atom vector.
+------------+----------------------------------------------------------------------+
| v_name | global scalar from equal-style variable |
| v_name | global scalar from equal-style variable |
+------------+----------------------------------------------------------------------+
| v_name | global vector from vector-style variable |
| v_name | global vector from vector-style variable |
+------------+----------------------------------------------------------------------+
| v_name | per-atom vector from atom-style or atomfile-style variable |
| v_name | per-atom vector from atom-style or atomfile-style variable |
+------------+----------------------------------------------------------------------+
| v_name[I] | Ith element of a global vector from vector-style variable |
| v_name[I] | Ith element of a global vector from vector-style variable |
+------------+----------------------------------------------------------------------+
| v_name[I] | value of atom with ID = I from atom-style or atomfile-style variable |
| v_name[I] | value of atom with ID = I from atom-style or atomfile-style variable |
+------------+----------------------------------------------------------------------+
For the I index, an integer can be specified or a variable name,
@ -1199,7 +1199,7 @@ formula immediately without using the variable command to define a
named variable.
More generally, there is a difference between referencing a variable
with a leading $ sign (e.g. $x or ${abc}) versus with a leading "v_"
with a leading $ sign (e.g. $x or ${abc}) versus with a leading "v\_"
(e.g. v_x or v_abc). The former can be used in any input script
command, including a variable command. The input script parser
evaluates the reference variable immediately and substitutes its value
@ -1208,7 +1208,7 @@ into the command. As explained on the :doc:`Commands parse <Commands_parse>` do
this $((xlo+xhi)/2+sqrt(v_area)) in an input script command evaluates
the string between the parenthesis as an equal-style variable formula.
Referencing a variable with a leading "v_" is an optional or required
Referencing a variable with a leading "v\_" is an optional or required
kind of argument for some commands (e.g. the :doc:`fix ave/chunk <fix_ave_chunk>` or :doc:`dump custom <dump>` or
:doc:`thermo_style <thermo_style>` commands) if you wish it to evaluate
a variable periodically during a run. It can also be used in a