Description:
Defines a computation that calculates the local lattice structure -according to (Ackland). +according to the formulation given in (Ackland).
In contrast to the centro-symmetry parameter this method is stable against temperature boost, because it is based not on the distance between particles but the angles. Therefore statistical fluctuations are averaged out a little more. A comparison with the Common Neighbor -Analysis metric is made in the paper.. +Analysis metric is made in the paper.
The result is a number which is mapped to the following different lattice structures: @@ -49,6 +49,13 @@ is dumped). Thus it can be inefficient to compute/dump this quantity too frequently or to have multiple compute/dump commands, each of which computes this quantity.-
+Output info: +
+This compute calculates a scalar quantity for each atom, which can be +accessed by any command that uses per-atom computes as input. See +this section for an overview of LAMMPS +output options. +
Restrictions: none
Related commands: diff --git a/doc/compute_ackland_atom.txt b/doc/compute_ackland_atom.txt index aa9455681c..3f86b63c1d 100644 --- a/doc/compute_ackland_atom.txt +++ b/doc/compute_ackland_atom.txt @@ -22,14 +22,14 @@ compute 1 all ackland/atom :pre [Description:] Defines a computation that calculates the local lattice structure -according to "(Ackland)"_#Ackland. +according to the formulation given in "(Ackland)"_#Ackland. In contrast to the "centro-symmetry parameter"_compute_centro_atom.html this method is stable against temperature boost, because it is based not on the distance between particles but the angles. Therefore statistical fluctuations are averaged out a little more. A comparison with the Common Neighbor -Analysis metric is made in the paper.. +Analysis metric is made in the paper. The result is a number which is mapped to the following different lattice structures: @@ -46,6 +46,13 @@ is dumped). Thus it can be inefficient to compute/dump this quantity too frequently or to have multiple compute/dump commands, each of which computes this quantity.- +[Output info:] + +This compute calculates a scalar quantity for each atom, which can be +accessed by any command that uses per-atom computes as input. See +"this section"_Section_howto.html#4_15 for an overview of LAMMPS +output options. + [Restrictions:] none [Related commands:] diff --git a/doc/compute_centro_atom.html b/doc/compute_centro_atom.html index 0ab284bb27..597c924e02 100644 --- a/doc/compute_centro_atom.html +++ b/doc/compute_centro_atom.html @@ -50,6 +50,13 @@ is dumped). Thus it can be inefficient to compute/dump this quantity too frequently or to have multiple compute/dump commands, each of a centro/atom style.
+Output info: +
+This compute calculates a scalar quantity for each atom, which can be +accessed by any command that uses per-atom computes as input. See +this section for an overview of LAMMPS +output options. +
Restrictions: none
Related commands: none diff --git a/doc/compute_centro_atom.txt b/doc/compute_centro_atom.txt index 3b29970c4c..a892f8c44b 100644 --- a/doc/compute_centro_atom.txt +++ b/doc/compute_centro_atom.txt @@ -47,6 +47,13 @@ is dumped). Thus it can be inefficient to compute/dump this quantity too frequently or to have multiple compute/dump commands, each of a {centro/atom} style. +[Output info:] + +This compute calculates a scalar quantity for each atom, which can be +accessed by any command that uses per-atom computes as input. See +"this section"_Section_howto.html#4_15 for an overview of LAMMPS +output options. + [Restrictions:] none [Related commands:] none diff --git a/doc/compute_coord_atom.html b/doc/compute_coord_atom.html index 0ca8c899e9..dad25393e3 100644 --- a/doc/compute_coord_atom.html +++ b/doc/compute_coord_atom.html @@ -42,6 +42,13 @@ is dumped). Thus it can be inefficient to compute/dump this quantity too frequently or to have multiple compute/dump commands, each of a coord/atom style.
+Output info: +
+This compute calculates a scalar quantity for each atom, which can be +accessed by any command that uses per-atom computes as input. See +this section for an overview of LAMMPS +output options. +
Restrictions: none
Related commands: none diff --git a/doc/compute_coord_atom.txt b/doc/compute_coord_atom.txt index 74d69872da..f6f869a0a0 100644 --- a/doc/compute_coord_atom.txt +++ b/doc/compute_coord_atom.txt @@ -39,6 +39,13 @@ is dumped). Thus it can be inefficient to compute/dump this quantity too frequently or to have multiple compute/dump commands, each of a {coord/atom} style. +[Output info:] + +This compute calculates a scalar quantity for each atom, which can be +accessed by any command that uses per-atom computes as input. See +"this section"_Section_howto.html#4_15 for an overview of LAMMPS +output options. + [Restrictions:] none [Related commands:] none diff --git a/doc/compute_displace_atom.html b/doc/compute_displace_atom.html new file mode 100644 index 0000000000..f638748711 --- /dev/null +++ b/doc/compute_displace_atom.html @@ -0,0 +1,61 @@ + +
Syntax: +
+compute ID group-ID displace/atom fix-ID ++
Examples: +
+compute 1 all displace/atom myCoords ++
Description: +
+Define a computation that calculates the current displacement of each +atom in the group from its original coordinates, including all effects +due to atoms passing thru periodic boundaries. The original +coordinates are stored by a fix +coord/original command, whose ID must be +specified with this compute. They are the coordinates at the time the +fix command was issued. The displacement can be output directly via +the dump custom command. It could also be used to +calculate a diffusion coefficient for a group of atoms, as is done by +the fix msd command. +
+The value of the displacement will be 0.0 for atoms not in the +specified compute group. Note that the fix defines its own group and +stores (0.0,0.0,0.0) for the original coordinates of any atom not in +the fix group. +
+Output info: +
+This compute calculates a vector of length 4 for each atom, which can +be accessed by indices 1-4 by any command that uses per-atom computes +as input. See this section for an overview +of LAMMPS output options. The first 3 components of the vector are +the x,y,z displacements. The 4th component is the total displacement, +i.e. sqrt(dx*dx + dy*dy + dz*dz). +
+Restrictions: none +
+Related commands: +
+ +Default: none +
+ diff --git a/doc/compute_displace_atom.txt b/doc/compute_displace_atom.txt new file mode 100644 index 0000000000..2ea1a81429 --- /dev/null +++ b/doc/compute_displace_atom.txt @@ -0,0 +1,56 @@ +"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 + +compute displace/atom command :h3 + +[Syntax:] + +compute ID group-ID displace/atom fix-ID :pre + +ID, group-ID are documented in "compute"_compute.html command +displace/atom = style name of this compute command +fix-ID = ID of a fix of style "coord/original"_fix_coord_original.html :ul + +[Examples:] + +compute 1 all displace/atom myCoords :pre + +[Description:] + +Define a computation that calculates the current displacement of each +atom in the group from its original coordinates, including all effects +due to atoms passing thru periodic boundaries. The original +coordinates are stored by a "fix +coord/original"_fix_coord_original.html command, whose ID must be +specified with this compute. They are the coordinates at the time the +fix command was issued. The displacement can be output directly via +the "dump custom"_dump.html command. It could also be used to +calculate a diffusion coefficient for a group of atoms, as is done by +the "fix msd"_fix_msd.html command. + +The value of the displacement will be 0.0 for atoms not in the +specified compute group. Note that the fix defines its own group and +stores (0.0,0.0,0.0) for the original coordinates of any atom not in +the fix group. + +[Output info:] + +This compute calculates a vector of length 4 for each atom, which can +be accessed by indices 1-4 by any command that uses per-atom computes +as input. See "this section"_Section_howto.html#4_15 for an overview +of LAMMPS output options. The first 3 components of the vector are +the x,y,z displacements. The 4th component is the total displacement, +i.e. sqrt(dx*dx + dy*dy + dz*dz). + +[Restrictions:] none + +[Related commands:] + +"dump custom"_dump.html, "fix msd"_fix_msd.html + +[Default:] none diff --git a/doc/compute_ke_atom.html b/doc/compute_ke_atom.html index 4dadfe7f53..6abe1abb4a 100644 --- a/doc/compute_ke_atom.html +++ b/doc/compute_ke_atom.html @@ -33,6 +33,13 @@ specified compute group.The kinetic energy is simply 1/2 m v^2, where m is the mass and v is the velocity of each atom.
+Output info: +
+This compute calculates a scalar quantity for each atom, which can be +accessed by any command that uses per-atom computes as input. See +this section for an overview of LAMMPS +output options. +
Restrictions: none
Related commands: diff --git a/doc/compute_ke_atom.txt b/doc/compute_ke_atom.txt index d3701bbce4..5d8344678d 100644 --- a/doc/compute_ke_atom.txt +++ b/doc/compute_ke_atom.txt @@ -30,6 +30,13 @@ specified compute group. The kinetic energy is simply 1/2 m v^2, where m is the mass and v is the velocity of each atom. +[Output info:] + +This compute calculates a scalar quantity for each atom, which can be +accessed by any command that uses per-atom computes as input. See +"this section"_Section_howto.html#4_15 for an overview of LAMMPS +output options. + [Restrictions:] none [Related commands:] diff --git a/doc/compute_pe_atom.html b/doc/compute_pe_atom.html index 630fe9675a..89d4f3ea1d 100644 --- a/doc/compute_pe_atom.html +++ b/doc/compute_pe_atom.html @@ -55,6 +55,13 @@ E.g. 1/4 of the dihedral energy to each of the 4 atoms. pairwise interactions between 1-4 atoms. The energy contribution of these terms is included in the pair energy, not the dihedral energy.
+Output info: +
+This compute calculates a scalar quantity for each atom, which can be +accessed by any command that uses per-atom computes as input. See +this section for an overview of LAMMPS +output options. +
Restrictions: none
Related commands: diff --git a/doc/compute_pe_atom.txt b/doc/compute_pe_atom.txt index ace2cd1ec8..2b4a6c83a2 100644 --- a/doc/compute_pe_atom.txt +++ b/doc/compute_pe_atom.txt @@ -52,6 +52,13 @@ The "dihedral_style charmm"_dihedral_charmm.html style calculates pairwise interactions between 1-4 atoms. The energy contribution of these terms is included in the pair energy, not the dihedral energy. +[Output info:] + +This compute calculates a scalar quantity for each atom, which can be +accessed by any command that uses per-atom computes as input. See +"this section"_Section_howto.html#4_15 for an overview of LAMMPS +output options. + [Restrictions:] none [Related commands:] diff --git a/doc/compute_stress_atom.html b/doc/compute_stress_atom.html index 485dd22651..383e91ab83 100644 --- a/doc/compute_stress_atom.html +++ b/doc/compute_stress_atom.html @@ -33,9 +33,10 @@ tensor for each atom in a group. The tensor for each atom has 6 components: xx, yy, zz, xy, xz, yz. See the compute pressure command if you want the stress tensor (pressure) of the entire system. The 6 components can be accessed by -indices 1-6 by any command that uses per-atom computes, e.g. the dump -custom command or fix ave/spatial -command or fix ave/atom command. See this +indices 1-6 by any command that uses per-atom computes as input, +e.g. the dump custom command or fix +ave/spatial command or fix +ave/atom command. See this section for an overview.
The stress tensor for atom I is given by the following formula, @@ -97,6 +98,14 @@ possible to compute. There are also a few pair styles for manybody potentials that are not yet instrumented to yield per-atom stress. See the Restrictions below.
+Output info: +
+This compute calculates a vector of length 6 for each atom, which can +be accessed by indices 1-6 by any command that uses per-atom computes +as input. See this section for an overview +of LAMMPS output options. The 6 components of the vector are ordered +xx, yy, zz, xy, xz, yz. +
Restrictions:
These pair styles do not yet tabulate per-atom virial information to diff --git a/doc/compute_stress_atom.txt b/doc/compute_stress_atom.txt index 927634aa67..e0d0b676d4 100644 --- a/doc/compute_stress_atom.txt +++ b/doc/compute_stress_atom.txt @@ -29,9 +29,10 @@ tensor for each atom in a group. The tensor for each atom has 6 components: xx, yy, zz, xy, xz, yz. See the "compute pressure"_compute_pressure.html command if you want the stress tensor (pressure) of the entire system. The 6 components can be accessed by -indices 1-6 by any command that uses per-atom computes, e.g. the "dump -custom"_dump.html command or "fix ave/spatial"_fix_ave_spatial.html -command or "fix ave/atom"_fix_ave_atom.html command. See "this +indices 1-6 by any command that uses per-atom computes as input, +e.g. the "dump custom"_dump.html command or "fix +ave/spatial"_fix_ave_spatial.html command or "fix +ave/atom"_fix_ave_atom.html command. See "this section"_Section_howto.html#4_15 for an overview. The stress tensor for atom {I} is given by the following formula, @@ -93,6 +94,14 @@ possible to compute. There are also a few pair styles for manybody potentials that are not yet instrumented to yield per-atom stress. See the Restrictions below. +[Output info:] + +This compute calculates a vector of length 6 for each atom, which can +be accessed by indices 1-6 by any command that uses per-atom computes +as input. See "this section"_Section_howto.html#4_15 for an overview +of LAMMPS output options. The 6 components of the vector are ordered +xx, yy, zz, xy, xz, yz. + [Restrictions:] These pair styles do not yet tabulate per-atom virial information to diff --git a/doc/fix_ave_atom.html b/doc/fix_ave_atom.html index b687a956da..53eb8a967b 100644 --- a/doc/fix_ave_atom.html +++ b/doc/fix_ave_atom.html @@ -53,7 +53,7 @@ ave/spatial or dump custom commands.
Each listed value is averaged independently. The group specified with the command means only atoms within the group have their averages -computed. Atoms not in the group have their result set to 0.0. +computed. Atoms not in the group have their result(s) set to 0.0.
Each listed value can be an atom attribute (position, velocity, force component) or can be the result of a compute or diff --git a/doc/fix_ave_atom.txt b/doc/fix_ave_atom.txt index d0d111625c..d52fecd722 100644 --- a/doc/fix_ave_atom.txt +++ b/doc/fix_ave_atom.txt @@ -42,7 +42,7 @@ ave/spatial"_fix_ave_spatial.html or "dump custom"_dump.html commands. Each listed value is averaged independently. The group specified with the command means only atoms within the group have their averages -computed. Atoms not in the group have their result set to 0.0. +computed. Atoms not in the group have their result(s) set to 0.0. Each listed value can be an atom attribute (position, velocity, force component) or can be the result of a "compute"_compute.html or