diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst index 6e52573b3e..82c9d0bd78 100644 --- a/doc/src/Errors_messages.rst +++ b/doc/src/Errors_messages.rst @@ -301,7 +301,7 @@ Doc page with :doc:`WARNING messages ` 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 diff --git a/doc/src/Examples.rst b/doc/src/Examples.rst index 36b486d31f..21ab13e2d4 100644 --- a/doc/src/Examples.rst +++ b/doc/src/Examples.rst @@ -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 | +------------+--------------------------------------------------------------------------------------------------+ diff --git a/doc/src/Howto_manifold.rst b/doc/src/Howto_manifold.rst index 239c32b342..41e1fb6a4c 100644 --- a/doc/src/Howto_manifold.rst +++ b/doc/src/Howto_manifold.rst @@ -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) ` | A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB | +----------------+----------------+----------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+ diff --git a/doc/src/Python_examples.rst b/doc/src/Python_examples.rst index c3b0381e64..976358801e 100644 --- a/doc/src/Python_examples.rst +++ b/doc/src/Python_examples.rst @@ -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 | | +----------------------------------------------------------------+--------------------------------------------------+ ---------- diff --git a/doc/src/compute_chunk_atom.rst b/doc/src/compute_chunk_atom.rst index aa404fd4da..ead17e3f7c 100644 --- a/doc/src/compute_chunk_atom.rst +++ b/doc/src/compute_chunk_atom.rst @@ -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 `. -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 `. -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 ` 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 diff --git a/doc/src/compute_global_atom.rst b/doc/src/compute_global_atom.rst index 1b301f700e..e9adb0317b 100644 --- a/doc/src/compute_global_atom.rst +++ b/doc/src/compute_global_atom.rst @@ -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 ` doc page for details. If no bracketed integer is appended, the per-atom @@ -144,7 +144,7 @@ styles and :doc:`add them to LAMMPS `. 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 ` 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 `. 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 `. 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 ` 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 ` 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 `. 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 `. Vector-style variables can reference thermodynamic keywords and various other attributes of diff --git a/doc/src/compute_reduce.rst b/doc/src/compute_reduce.rst index 3391f3c3cb..7599343d2e 100644 --- a/doc/src/compute_reduce.rst +++ b/doc/src/compute_reduce.rst @@ -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 ` 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 ` doc page for details. If no bracketed integer @@ -133,7 +133,7 @@ compute styles and :doc:`add them to LAMMPS `. 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 ` 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 `. Atom-style variables can reference thermodynamic keywords and various per-atom attributes, or diff --git a/doc/src/compute_slice.rst b/doc/src/compute_slice.rst index 7262f2c368..c8211269bc 100644 --- a/doc/src/compute_slice.rst +++ b/doc/src/compute_slice.rst @@ -55,7 +55,7 @@ vector. Each listed input must be a global vector or column of a global array calculated by another :doc:`compute ` or :doc:`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 ` 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 `. -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 ` 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 `. -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 ` command for details. Note that variables of style *vector* define a formula diff --git a/doc/src/dump_image.rst b/doc/src/dump_image.rst index fabe2643b1..0477e5d718 100644 --- a/doc/src/dump_image.rst +++ b/doc/src/dump_image.rst @@ -193,7 +193,7 @@ atoms rendered in the image. They can be any atom attribute defined for the :doc:`dump custom ` command, including *type* and *element*\ . This includes per-atom quantities calculated by a :doc:`compute `, :doc:`fix `, or :doc:`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. diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index 465f92ecfb..5f7f42b4be 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -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. diff --git a/doc/src/fix.rst b/doc/src/fix.rst index 263ce9991c..2182ce7460 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -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 diff --git a/doc/src/fix_ave_atom.rst b/doc/src/fix_ave_atom.rst index 40c61239cb..93ff48ce0f 100644 --- a/doc/src/fix_ave_atom.rst +++ b/doc/src/fix_ave_atom.rst @@ -121,7 +121,7 @@ an input value from that compute. which can be provided by the :doc:`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 `. 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 `. 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 ` 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 diff --git a/doc/src/fix_ave_chunk.rst b/doc/src/fix_ave_chunk.rst index 34116a56a2..b19cce417c 100644 --- a/doc/src/fix_ave_chunk.rst +++ b/doc/src/fix_ave_chunk.rst @@ -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 `. 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 `. 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 diff --git a/doc/src/fix_ave_correlate.rst b/doc/src/fix_ave_correlate.rst index c921e8e55b..c42159e89b 100644 --- a/doc/src/fix_ave_correlate.rst +++ b/doc/src/fix_ave_correlate.rst @@ -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 `. 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 `. -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 `. -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 diff --git a/doc/src/fix_ave_histo.rst b/doc/src/fix_ave_histo.rst index b9437834f0..158f259695 100644 --- a/doc/src/fix_ave_histo.rst +++ b/doc/src/fix_ave_histo.rst @@ -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 ` 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 `. 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 `. -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 `. -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 diff --git a/doc/src/fix_ave_time.rst b/doc/src/fix_ave_time.rst index 9d121488cc..efa8095d69 100644 --- a/doc/src/fix_ave_time.rst +++ b/doc/src/fix_ave_time.rst @@ -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 ` 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 `. -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 `. -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 diff --git a/doc/src/fix_controller.rst b/doc/src/fix_controller.rst index 45ff47f868..2fd5f17c95 100644 --- a/doc/src/fix_controller.rst +++ b/doc/src/fix_controller.rst @@ -152,7 +152,7 @@ The process variable *pvar* can be specified as the output of a :doc:`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 ` 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 `. -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 ` 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 `. -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 ` 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 ` 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. diff --git a/doc/src/fix_rx.rst b/doc/src/fix_rx.rst index c79fd2178b..0d8af574c1 100644 --- a/doc/src/fix_rx.rst +++ b/doc/src/fix_rx.rst @@ -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 ` 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 ` command using the "d_" prefix or by +either with the :doc:`set ` command using the "d\_" prefix or by reading directly the concentrations from a data file. For the latter case, the :doc:`read_data ` command with the fix keyword should be specified, where the fix-ID will be the "fix rx`ID with a `_ suffix, e.g. diff --git a/doc/src/fix_vector.rst b/doc/src/fix_vector.rst index 8cf6d900f4..81922dea8a 100644 --- a/doc/src/fix_vector.rst +++ b/doc/src/fix_vector.rst @@ -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 `. 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 `. -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 `. -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 diff --git a/doc/src/pair_resquared.rst b/doc/src/pair_resquared.rst index 34a441b608..5bb4de7cb2 100644 --- a/doc/src/pair_resquared.rst +++ b/doc/src/pair_resquared.rst @@ -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) `: diff --git a/doc/src/variable.rst b/doc/src/variable.rst index b1d86cd873..0e30efc0ab 100644 --- a/doc/src/variable.rst +++ b/doc/src/variable.rst @@ -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 ` 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 ` or :doc:`dump custom ` or :doc:`thermo_style ` commands) if you wish it to evaluate a variable periodically during a run. It can also be used in a