Syntax: +
+fix ID group-ID vector Nevery value1 value2 ... ++
c_ID = global scalar calculated by a compute with ID + c_ID[I] = Ith component of global vector calculated by a compute with ID + f_ID = global scalar calculated by a fix with ID + f_ID[I] = Ith component of global vector calculated by a fix with ID + v_name = global value calculated by an equal-style variable with name ++ +
Examples: +
+fix 1 all vector 100 c_myTemp +fix 1 all vector 5 c_myTemp v_integral ++
Description: +
+Use one or more global values as inputs every few timesteps, and +simply store them. For a single specified value, the values are +stored as a global vector of growing length For multiple specified +values, they are stored as rows in a global array, whose number of +rows is growing. The resulting vector or array can be used by other +output commands. +
+One way to to use this command is to accumulate a vector that is +time-integrated using the variable trap() function. +For example the velocity auto-correlation function (VACF) can be +time-integrated, to yield a diffusion coefficient, as follows: +
+compute 2 all vacf +fix 5 all vector 1 c_24 +variable diff equal dt*trap(f_5) +thermo_style custom step v_diff ++
The group specified with this command is ignored. However, note that +specified values may represent calculations performed by computes and +fixes which store their own "group" definitions. +
+Each listed value can be the result of a compute or +fix or the evaluation of an equal-style +variable. In each case, the compute, fix, or variable +must produce a global quantity, not a per-atom or local quantity. +And the global quantity must be a scalar, not a vector or array. +
+Computes that produce global quantities are those which +do not have the word atom in their style name. Only a few +fixes produce global quantities. See the doc pages for +individual fixes for info on which ones produce such values. +Variables of style equal are the only ones that can +be used with this fix. Variables of style atom cannot be used, +since they produce per-atom values. +
+The Nevery argument specifies on what timesteps the input values +will be used in order to be stored. Only timesteps that a multiple +of Nevery, including timestep 0, will contribute values. +
+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 +calculated by the compute is used. +
+Note that there is a compute reduce command +which can sum per-atom quantities into a global scalar or vector which +can thus be accessed by fix vector. Or it can be a compute defined +not in your input script, but by thermodynamic +output or other fixes such as fix nvt +or 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 add them to +LAMMPS. +
+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 +calculated by the fix is used. +
+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 add them to +LAMMPS. +
+If a value 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 variable command +for details. Note that variables of style equal define a formula +which can reference individual atom properties or thermodynamic +keywords, or they can invoke other computes, fixes, or variables when +they are evaluated, so this is a very general means of specifying +quantities to be stored by fix vector. +
+Restart, fix_modify, output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. +
+This fix produces a global vector or global array which can be +accessed by various output commands. +The values can only be accessed on timesteps that are multiples of +Nevery. +
+A vector is produced if only a single input value is specified. +An array is produced if multiple input values are specified. +The length of the vector or the number of rows in the array grows +by 1 every Nevery timesteps. +
+If the fix prouduces a vector, then the entire vector will be either +"intensive" or "extensive", depending on whether the values stored in +the vector are "intensive" or "extensive". If the fix produces an +array, then all elements in the array must be the same, either +"intensive" or "extensive". If a compute or fix provides the value +stored, then the compute or fix determines whether the value is +intensive or extensive; see the doc page for that compute or fix for +further info. Values produced by a variable are treated as intensive. +
+No parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
+Restrictions: none +
+Related commands: +
+ +Default: none +
+ diff --git a/doc/fix_vector.txt b/doc/fix_vector.txt new file mode 100644 index 0000000000..5dd73c4fba --- /dev/null +++ b/doc/fix_vector.txt @@ -0,0 +1,148 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix vector command :h3 + +[Syntax:] + +fix ID group-ID vector Nevery value1 value2 ... :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +ave/time = style name of this fix command :l +Nevery = use input values every this many timesteps :l +one or more input values can be listed :l +value = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l + c_ID = global scalar calculated by a compute with ID + c_ID\[I\] = Ith component of global vector calculated by a compute with ID + f_ID = global scalar calculated by a fix with ID + f_ID\[I\] = Ith component of global vector calculated by a fix with ID + v_name = global value calculated by an equal-style variable with name :pre +:ule + +[Examples:] + +fix 1 all vector 100 c_myTemp +fix 1 all vector 5 c_myTemp v_integral :pre + +[Description:] + +Use one or more global values as inputs every few timesteps, and +simply store them. For a single specified value, the values are +stored as a global vector of growing length For multiple specified +values, they are stored as rows in a global array, whose number of +rows is growing. The resulting vector or array can be used by other +"output commands"_Section_howto.html#howto_15. + +One way to to use this command is to accumulate a vector that is +time-integrated using the "variable trap()"_variable.html function. +For example the velocity auto-correlation function (VACF) can be +time-integrated, to yield a diffusion coefficient, as follows: + +compute 2 all vacf +fix 5 all vector 1 c_2[4] +variable diff equal dt*trap(f_5) +thermo_style custom step v_diff :pre + +The group specified with this command is ignored. However, note that +specified values may represent calculations performed by computes and +fixes which store their own "group" definitions. + +Each listed value can be the result of a "compute"_compute.html or +"fix"_fix.html or the evaluation of an equal-style +"variable"_variable.html. In each case, the compute, fix, or variable +must produce a global quantity, not a per-atom or local quantity. +And the global quantity must be a scalar, not a vector or array. + +"Computes"_compute.html that produce global quantities are those which +do not have the word {atom} in their style name. Only a few +"fixes"_fix.html produce global quantities. See the doc pages for +individual fixes for info on which ones produce such values. +"Variables"_variable.html of style {equal} are the only ones that can +be used with this fix. Variables of style {atom} cannot be used, +since they produce per-atom values. + +The {Nevery} argument specifies on what timesteps the input values +will be used in order to be stored. Only timesteps that a multiple +of {Nevery}, including timestep 0, will contribute values. + +:line + +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 +calculated by the compute is used. + +Note that there is a "compute reduce"_compute_reduce.html command +which can sum per-atom quantities into a global scalar or vector which +can thus be accessed by fix vector. Or it can be a compute defined +not in your input script, but by "thermodynamic +output"_thermo_style.html or other fixes such as "fix nvt"_fix_nh.html +or "fix temp/rescale"_fix_temp_rescale.html. 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 "add them to +LAMMPS"_Section_modify.html. + +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 +calculated by the fix is used. + +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 "add them to +LAMMPS"_Section_modify.html. + +If a value 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 "variable"_variable.html command +for details. Note that variables of style {equal} define a formula +which can reference individual atom properties or thermodynamic +keywords, or they can invoke other computes, fixes, or variables when +they are evaluated, so this is a very general means of specifying +quantities to be stored by fix vector. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. + +This fix produces a global vector or global array which can be +accessed by various "output commands"_Section_howto.html#howto_15. +The values can only be accessed on timesteps that are multiples of +{Nevery}. + +A vector is produced if only a single input value is specified. +An array is produced if multiple input values are specified. +The length of the vector or the number of rows in the array grows +by 1 every {Nevery} timesteps. + +If the fix prouduces a vector, then the entire vector will be either +"intensive" or "extensive", depending on whether the values stored in +the vector are "intensive" or "extensive". If the fix produces an +array, then all elements in the array must be the same, either +"intensive" or "extensive". If a compute or fix provides the value +stored, then the compute or fix determines whether the value is +intensive or extensive; see the doc page for that compute or fix for +further info. Values produced by a variable are treated as intensive. + +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + +[Restrictions:] none + +[Related commands:] + +"compute"_compute.html, "variable"_variable.html + +[Default:] none