diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 82527f4a03..d4f922530a 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -348,9 +348,9 @@ each style or click on the style itself for a full description:
- - - + +
centro/atomcna/atomcoord/atomdamage/atomdisplace/atomerotate/asphere
erotate/sphereevent/displacegroup/groupheat/fluxkeke/atom
pepe/atompressurereducereduce/regionstress/atom
temptemp/aspheretemp/comtemp/deformtemp/partialtemp/profile
temp/ramptemp/regiontemp/sphere +
msdpepe/atompressurereducereduce/region
stress/atomtemptemp/aspheretemp/comtemp/deformtemp/partial
temp/profiletemp/ramptemp/regiontemp/sphere

These are compute styles contributed by users, which can be used if diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 24cf75f6ce..c1a3ca0de9 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -474,6 +474,7 @@ each style or click on the style itself for a full description: "heat/flux"_compute_heat_flux.html, "ke"_compute_ke.html, "ke/atom"_compute_ke_atom.html, +"msd"_compute_msd.html, "pe"_compute_pe.html, "pe/atom"_compute_pe_atom.html, "pressure"_compute_pressure.html, diff --git a/doc/compute.html b/doc/compute.html index 3526433f39..d332d67077 100644 --- a/doc/compute.html +++ b/doc/compute.html @@ -121,6 +121,7 @@ available in LAMMPS:

  • heat/flux - heat flux through a group of atoms
  • ke - translational kinetic energy
  • ke/atom - kinetic energy for each atom +
  • msd - mean-squared displacement of group of atoms
  • pe - potential energy
  • pe/atom - potential energy for each atom
  • pressure - total pressure and pressure tensor diff --git a/doc/compute.txt b/doc/compute.txt index f20d08b9bb..511e461841 100644 --- a/doc/compute.txt +++ b/doc/compute.txt @@ -118,6 +118,7 @@ available in LAMMPS: "heat/flux"_compute_heat_flux.html - heat flux through a group of atoms "ke"_compute_ke.html - translational kinetic energy "ke/atom"_compute_ke_atom.html - kinetic energy for each atom +"msd"_compute_msd.html - mean-squared displacement of group of atoms "pe"_compute_pe.html - potential energy "pe/atom"_compute_pe_atom.html - potential energy for each atom "pressure"_compute_pressure.html - total pressure and pressure tensor diff --git a/doc/compute_ackland_atom.html b/doc/compute_ackland_atom.html index 526a4549af..f9f0340169 100644 --- a/doc/compute_ackland_atom.html +++ b/doc/compute_ackland_atom.html @@ -52,9 +52,9 @@ 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. +accessed by any command that uses per-atom values from a compute as +input. See this section for an overview of +LAMMPS output options.

    Restrictions:

    diff --git a/doc/compute_ackland_atom.txt b/doc/compute_ackland_atom.txt index 8b01568e78..c2fd054da1 100644 --- a/doc/compute_ackland_atom.txt +++ b/doc/compute_ackland_atom.txt @@ -49,9 +49,9 @@ 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. +accessed by any command that uses per-atom values from a compute as +input. See "this section"_Section_howto.html#4_15 for an overview of +LAMMPS output options. [Restrictions:] diff --git a/doc/compute_centro_atom.html b/doc/compute_centro_atom.html index aa257f5559..de92e1a273 100644 --- a/doc/compute_centro_atom.html +++ b/doc/compute_centro_atom.html @@ -53,9 +53,9 @@ too frequently or to have multiple compute/dump commands, each with a

    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. +accessed by any command that uses per-atom values from a compute as +input. See this section for an overview of +LAMMPS output options.

    Restrictions: none

    diff --git a/doc/compute_centro_atom.txt b/doc/compute_centro_atom.txt index 235e1e50b3..6d935246d7 100644 --- a/doc/compute_centro_atom.txt +++ b/doc/compute_centro_atom.txt @@ -50,9 +50,9 @@ too frequently or to have multiple compute/dump commands, each with a [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. +accessed by any command that uses per-atom values from a compute as +input. See "this section"_Section_howto.html#4_15 for an overview of +LAMMPS output options. [Restrictions:] none diff --git a/doc/compute_cna_atom.html b/doc/compute_cna_atom.html index da6bbcf0b5..f581e28b28 100644 --- a/doc/compute_cna_atom.html +++ b/doc/compute_cna_atom.html @@ -76,9 +76,9 @@ too frequently or to have multiple compute/dump commands, each with a

    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. +accessed by any command that uses per-atom values from a compute as +input. See this section for an overview of +LAMMPS output options.

    Restrictions: none

    diff --git a/doc/compute_cna_atom.txt b/doc/compute_cna_atom.txt index 8314d460f3..d67778dbe4 100644 --- a/doc/compute_cna_atom.txt +++ b/doc/compute_cna_atom.txt @@ -73,9 +73,9 @@ too frequently or to have multiple compute/dump commands, each with a [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. +accessed by any command that uses per-atom values from a compute as +input. See "this section"_Section_howto.html#4_15 for an overview of +LAMMPS output options. [Restrictions:] none diff --git a/doc/compute_coord_atom.html b/doc/compute_coord_atom.html index dad25393e3..beabf3d1f8 100644 --- a/doc/compute_coord_atom.html +++ b/doc/compute_coord_atom.html @@ -45,9 +45,9 @@ too frequently or to have multiple compute/dump commands, each of a

    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. +accessed by any command that uses per-atom values from a compute as +input. See this section for an overview of +LAMMPS output options.

    Restrictions: none

    diff --git a/doc/compute_coord_atom.txt b/doc/compute_coord_atom.txt index f6f869a0a0..f8c888b2bc 100644 --- a/doc/compute_coord_atom.txt +++ b/doc/compute_coord_atom.txt @@ -42,9 +42,9 @@ too frequently or to have multiple compute/dump commands, each of a [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. +accessed by any command that uses per-atom values from a compute as +input. See "this section"_Section_howto.html#4_15 for an overview of +LAMMPS output options. [Restrictions:] none diff --git a/doc/compute_damage_atom.html b/doc/compute_damage_atom.html index 0477fdef1d..d060006f33 100644 --- a/doc/compute_damage_atom.html +++ b/doc/compute_damage_atom.html @@ -36,9 +36,9 @@ compute group.

    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. +accessed by any command that uses per-atom values from a compute as +input. See this section for an overview of +LAMMPS output options.

    Restrictions:

    diff --git a/doc/compute_damage_atom.txt b/doc/compute_damage_atom.txt index 15753b137a..57421804c1 100644 --- a/doc/compute_damage_atom.txt +++ b/doc/compute_damage_atom.txt @@ -33,9 +33,9 @@ compute group. [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. +accessed by any command that uses per-atom values from a compute as +input. See "this section"_Section_howto.html#4_15 for an overview of +LAMMPS output options. [Restrictions:] diff --git a/doc/compute_displace_atom.html b/doc/compute_displace_atom.html index a0c8240753..949c0a6ec1 100644 --- a/doc/compute_displace_atom.html +++ b/doc/compute_displace_atom.html @@ -26,9 +26,12 @@

    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. Four quantites per -atom are computed: the x,y,z displacements and the total displacement. -See below for details. +due to atoms passing thru periodic boundaries. +

    +

    A vector of four quantites per atom are calculated by this compute. +The first 3 elements of the cector are the dx,dy,dz displacements. +The 4th component is the total displacement, i.e. sqrt(dx*dx + dy*dy + +dz*dz).

    To store the original coordinates at the time this compute is issued, the compute creates its own fix of style "coord/original", as if this @@ -41,6 +44,9 @@ details. Note that the ID of the new fix is the compute-ID + underscore + "coord_original", and the group for the new fix is the same as the compute group.

    +

    The value of the displacement will be 0.0 for atoms not in the +specified compute group. +

    IMPORTANT NOTE: Fix coord/original stores the initial coordinates in "unwrapped" form, by using the image flags associated with each atom. See the dump custom command for a discussion of @@ -50,11 +56,13 @@ how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the set image command.

    -

    The displacements can be output directly via the dump -custom command. -

    -

    The value of the displacement will be 0.0 for atoms not in the -specified compute group. +

    IMPORTANT NOTE: If an atom is part of a rigid body (see the fix +rigid command), it's periodic image flags are altered, +and the computed MSD will not reflect its true displacement. See the +fix rigid command for details. Thus, to compute the +MSD of rigid bodies as they cross periodic boundaries, you will need +to post-process a dump file containing coordinates of the +atoms in the bodies.

    IMPORTANT NOTE: If you want the quantities calculated by this compute to be continuous when running from a restart file, @@ -68,15 +76,14 @@ file.

    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). +of LAMMPS output options.

    Restrictions: none

    Related commands:

    -

    dump custom, fix msd +

    compute msd, dump custom, fix +coord/original

    Default: none

    diff --git a/doc/compute_displace_atom.txt b/doc/compute_displace_atom.txt index f21343b121..85e2c45c50 100644 --- a/doc/compute_displace_atom.txt +++ b/doc/compute_displace_atom.txt @@ -23,9 +23,12 @@ compute 1 all displace/atom :pre 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. Four quantites per -atom are computed: the x,y,z displacements and the total displacement. -See below for details. +due to atoms passing thru periodic boundaries. + +A vector of four quantites per atom are calculated by this compute. +The first 3 elements of the cector are the dx,dy,dz displacements. +The 4th component is the total displacement, i.e. sqrt(dx*dx + dy*dy + +dz*dz). To store the original coordinates at the time this compute is issued, the compute creates its own fix of style "coord/original", as if this @@ -38,6 +41,9 @@ details. Note that the ID of the new fix is the compute-ID + underscore + "coord_original", and the group for the new fix is the same as the compute group. +The value of the displacement will be 0.0 for atoms not in the +specified compute group. + IMPORTANT NOTE: Fix coord/original stores the initial coordinates in "unwrapped" form, by using the image flags associated with each atom. See the "dump custom"_dump.html command for a discussion of @@ -47,11 +53,13 @@ how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the "set image"_set.html command. -The displacements can be output directly via the "dump -custom"_dump.html command. - -The value of the displacement will be 0.0 for atoms not in the -specified compute group. +IMPORTANT NOTE: If an atom is part of a rigid body (see the "fix +rigid"_fix_rigid.html command), it's periodic image flags are altered, +and the computed MSD will not reflect its true displacement. See the +"fix rigid"_fix_rigid.html command for details. Thus, to compute the +MSD of rigid bodies as they cross periodic boundaries, you will need +to post-process a "dump file"_dump.html containing coordinates of the +atoms in the bodies. IMPORTANT NOTE: If you want the quantities calculated by this compute to be continuous when running from a "restart file"_read_restart.html, @@ -65,14 +73,13 @@ file. 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). +of LAMMPS output options. [Restrictions:] none [Related commands:] -"dump custom"_dump.html, "fix msd"_fix_msd.html +"compute msd"_compute_msd.html, "dump custom"_dump.html, "fix +coord/original"_fix_coord_original.html [Default:] none diff --git a/doc/compute_erotate_asphere.html b/doc/compute_erotate_asphere.html index 0dd269b639..38174f8344 100644 --- a/doc/compute_erotate_asphere.html +++ b/doc/compute_erotate_asphere.html @@ -37,6 +37,11 @@ the same as in 3d.

    Output info:

    +

    This compute calculates a global scalar (the KE). This value can be +used by any command that uses a global scalar value from a compute as +input. See this section for an overview of +LAMMPS output options. +

    The scalar value calculated by this compute is "extensive", meaning it it scales with the number of atoms in the simulation.

    diff --git a/doc/compute_erotate_asphere.txt b/doc/compute_erotate_asphere.txt index 2eaf9b079f..f0eee1bf0e 100644 --- a/doc/compute_erotate_asphere.txt +++ b/doc/compute_erotate_asphere.txt @@ -34,6 +34,11 @@ the same as in 3d. [Output info:] +This compute calculates a global scalar (the KE). This value can be +used by any command that uses a global scalar value from a compute as +input. See "this section"_Section_howto.html#4_15 for an overview of +LAMMPS output options. + The scalar value calculated by this compute is "extensive", meaning it it scales with the number of atoms in the simulation. diff --git a/doc/compute_erotate_sphere.html b/doc/compute_erotate_sphere.html index 6eb3828a32..df846b2ac5 100644 --- a/doc/compute_erotate_sphere.html +++ b/doc/compute_erotate_sphere.html @@ -36,6 +36,11 @@ same as in 3d.

    Output info:

    +

    This compute calculates a global scalar (the KE). This value can be +used by any command that uses a global scalar value from a compute as +input. See this section for an overview of +LAMMPS output options. +

    The scalar value calculated by this compute is "extensive", meaning it it scales with the number of atoms in the simulation.

    diff --git a/doc/compute_erotate_sphere.txt b/doc/compute_erotate_sphere.txt index 82f7c9507b..cb072c01de 100644 --- a/doc/compute_erotate_sphere.txt +++ b/doc/compute_erotate_sphere.txt @@ -33,6 +33,11 @@ same as in 3d. [Output info:] +This compute calculates a global scalar (the KE). This value can be +used by any command that uses a global scalar value from a compute as +input. See "this section"_Section_howto.html#4_15 for an overview of +LAMMPS output options. + The scalar value calculated by this compute is "extensive", meaning it it scales with the number of atoms in the simulation. diff --git a/doc/compute_event_displace.html b/doc/compute_event_displace.html index 6cf9159164..fc94e3cb1c 100644 --- a/doc/compute_event_displace.html +++ b/doc/compute_event_displace.html @@ -38,6 +38,11 @@ further than the threshold distance.

    Output info:

    +

    This compute calculates a global scalar (the flag). This value can be +used by any command that uses a global scalar value from a compute as +input. See this section for an overview of +LAMMPS output options. +

    The scalar value calculated by this compute is "intensive", meaning it is independent of the number of atoms in the simulation.

    diff --git a/doc/compute_event_displace.txt b/doc/compute_event_displace.txt index 4fe020a82a..9ee80549c4 100644 --- a/doc/compute_event_displace.txt +++ b/doc/compute_event_displace.txt @@ -35,6 +35,11 @@ further than the threshold distance. [Output info:] +This compute calculates a global scalar (the flag). This value can be +used by any command that uses a global scalar value from a compute as +input. See "this section"_Section_howto.html#4_15 for an overview of +LAMMPS output options. + The scalar value calculated by this compute is "intensive", meaning it is independent of the number of atoms in the simulation. diff --git a/doc/compute_group_group.html b/doc/compute_group_group.html index c4a6d8d071..0b3e779c5e 100644 --- a/doc/compute_group_group.html +++ b/doc/compute_group_group.html @@ -41,10 +41,16 @@ quantity too frequently.

    Output info:

    -

    The interaction energy calculated by this compute is a scalar -quantity. The interaction force is a vector of length 3. Both the -scalar and vector values calculated by this compute are "extensive", -meaning they scale with the number of atoms in the simulation. +

    This compute calculates a global scalar (the energy) and a global +vector of length 3 (force), which can be accessed by indices 1-3. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See this +section for an overview of LAMMPS output +options. +

    +

    Both the scalar and vector values calculated by this compute are +"extensive", meaning they scale with the number of atoms in the +simulation.

    Restrictions:

    diff --git a/doc/compute_group_group.txt b/doc/compute_group_group.txt index d4650df39a..d1f42357f2 100644 --- a/doc/compute_group_group.txt +++ b/doc/compute_group_group.txt @@ -38,10 +38,16 @@ quantity too frequently. [Output info:] -The interaction energy calculated by this compute is a scalar -quantity. The interaction force is a vector of length 3. Both the -scalar and vector values calculated by this compute are "extensive", -meaning they scale with the number of atoms in the simulation. +This compute calculates a global scalar (the energy) and a global +vector of length 3 (force), which can be accessed by indices 1-3. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See "this +section"_Section_howto.html#4_15 for an overview of LAMMPS output +options. + +Both the scalar and vector values calculated by this compute are +"extensive", meaning they scale with the number of atoms in the +simulation. [Restrictions:] diff --git a/doc/compute_heat_flux.html b/doc/compute_heat_flux.html index 93b9388998..6e95cdb72a 100644 --- a/doc/compute_heat_flux.html +++ b/doc/compute_heat_flux.html @@ -84,12 +84,19 @@ interval and the appropriate unit conversion factors. For real units in LAMMPS, this is 2917703220.0 in this case. The final thermal conductivity value obtained is 0.25 W/mK.

    +

    The 6 components of the vector calculated by this compute are as +follows. The first 3 components are the x, y, z components of the +full heat flux. The next 3 components are the x, y, z components of +just the convective portion of the flux, which is the energy per atom +times the velocity of the atom. +

    Output info:

    -

    This compute calculates a vector of length 6. The 6 components are -the x, y, z components of the full heat flux, followed by the x, y, z -components of just the convective portion of the flux, which is the -energy per atom times the velocity of the atom. +

    This compute calculates a global vector of length 6 (heat flux +vector), which can be accessed by indices 1-6. These values can be +used by any command that uses global vector values from a compute as +input. See this section for an overview of +LAMMPS output options.

    The vector values calculated by this compute are "extensive", meaning they scale with the number of atoms in the simulation. They should be diff --git a/doc/compute_heat_flux.txt b/doc/compute_heat_flux.txt index 2fc8cc064e..f394fcd4c9 100644 --- a/doc/compute_heat_flux.txt +++ b/doc/compute_heat_flux.txt @@ -81,12 +81,19 @@ interval and the appropriate unit conversion factors. For real "units"_units.html in LAMMPS, this is 2917703220.0 in this case. The final thermal conductivity value obtained is 0.25 W/mK. +The 6 components of the vector calculated by this compute are as +follows. The first 3 components are the x, y, z components of the +full heat flux. The next 3 components are the x, y, z components of +just the convective portion of the flux, which is the energy per atom +times the velocity of the atom. + [Output info:] -This compute calculates a vector of length 6. The 6 components are -the x, y, z components of the full heat flux, followed by the x, y, z -components of just the convective portion of the flux, which is the -energy per atom times the velocity of the atom. +This compute calculates a global vector of length 6 (heat flux +vector), which can be accessed by indices 1-6. These values can be +used by any command that uses global vector values from a compute as +input. See "this section"_Section_howto.html#4_15 for an overview of +LAMMPS output options. The vector values calculated by this compute are "extensive", meaning they scale with the number of atoms in the simulation. They should be diff --git a/doc/compute_ke.html b/doc/compute_ke.html index 15c2528b65..b828236e74 100644 --- a/doc/compute_ke.html +++ b/doc/compute_ke.html @@ -45,6 +45,11 @@ include different degrees of freedom (translational, rotational, etc).

    Output info:

    +

    This compute calculates a global scalar (the KE). This value can be +used by any command that uses a global scalar value from a compute as +input. See this section for an overview of +LAMMPS output options. +

    The scalar value calculated by this compute is "extensive", meaning it it scales with the number of atoms in the simulation.

    diff --git a/doc/compute_ke.txt b/doc/compute_ke.txt index 53d8527d2a..8894a616a7 100644 --- a/doc/compute_ke.txt +++ b/doc/compute_ke.txt @@ -42,6 +42,11 @@ include different degrees of freedom (translational, rotational, etc). [Output info:] +This compute calculates a global scalar (the KE). This value can be +used by any command that uses a global scalar value from a compute as +input. See "this section"_Section_howto.html#4_15 for an overview of +LAMMPS output options. + The scalar value calculated by this compute is "extensive", meaning it it scales with the number of atoms in the simulation. diff --git a/doc/compute_ke_atom.html b/doc/compute_ke_atom.html index 8d09870276..f636c1e138 100644 --- a/doc/compute_ke_atom.html +++ b/doc/compute_ke_atom.html @@ -36,9 +36,9 @@ specified compute group.

    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. +accessed by any command that uses per-atom values from a compute as +input. See this section for an overview of +LAMMPS output options.

    Restrictions: none

    diff --git a/doc/compute_ke_atom.txt b/doc/compute_ke_atom.txt index f8225dc060..4cb0036c4c 100644 --- a/doc/compute_ke_atom.txt +++ b/doc/compute_ke_atom.txt @@ -33,9 +33,9 @@ specified compute group. [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. +accessed by any command that uses per-atom values from a compute as +input. See "this section"_Section_howto.html#4_15 for an overview of +LAMMPS output options. [Restrictions:] none diff --git a/doc/compute_pe.html b/doc/compute_pe.html index a48aa247ae..191bf19fca 100644 --- a/doc/compute_pe.html +++ b/doc/compute_pe.html @@ -56,6 +56,11 @@ LAMMPS starts up, as if this command were in the input script:

    Output info:

    +

    This compute calculates a global scalar (the potential energy). This +value can be used by any command that uses a global scalar value from +a compute as input. See this section for an +overview of LAMMPS output options. +

    The scalar value calculated by this compute is "extensive", meaning it it scales with the number of atoms in the simulation.

    diff --git a/doc/compute_pe.txt b/doc/compute_pe.txt index fcb9c146e3..3d9479d39f 100644 --- a/doc/compute_pe.txt +++ b/doc/compute_pe.txt @@ -53,6 +53,11 @@ See the "thermo_style" command for more details. [Output info:] +This compute calculates a global scalar (the potential energy). This +value can be used by any command that uses a global scalar value from +a compute as input. See "this section"_Section_howto.html#4_15 for an +overview of LAMMPS output options. + The scalar value calculated by this compute is "extensive", meaning it it scales with the number of atoms in the simulation. diff --git a/doc/compute_pe_atom.html b/doc/compute_pe_atom.html index a9d8d26ac6..ce2dffc64e 100644 --- a/doc/compute_pe_atom.html +++ b/doc/compute_pe_atom.html @@ -30,12 +30,7 @@ compute 1 all pe/atom pair bond

    Define a computation that computes the per-atom potential energy for each atom in a group. See the compute pe command if -you want the potential energy of the entire system. The per-atom -energies can be accessed as scalar values 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 -section for an overview. +you want the potential energy of the entire system.

    The per-atom energy is calculated by the various pair, bond, etc potentials defined for the simulation. If no extra keywords are @@ -71,9 +66,9 @@ contribution can easily be computed.

    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. +accessed by any command that uses per-atom values from a compute as +input. See this section for an overview of +LAMMPS output options.

    Restrictions:

    diff --git a/doc/compute_pe_atom.txt b/doc/compute_pe_atom.txt index 3d48c6d016..3decb01487 100644 --- a/doc/compute_pe_atom.txt +++ b/doc/compute_pe_atom.txt @@ -27,12 +27,7 @@ compute 1 all pe/atom pair bond :pre Define a computation that computes the per-atom potential energy for each atom in a group. See the "compute pe"_compute_pe.html command if -you want the potential energy of the entire system. The per-atom -energies can be accessed as scalar values 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 -section"_Section_howto.html#4_15 for an overview. +you want the potential energy of the entire system. The per-atom energy is calculated by the various pair, bond, etc potentials defined for the simulation. If no extra keywords are @@ -68,9 +63,9 @@ contribution can easily be computed. [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. +accessed by any command that uses per-atom values from a compute as +input. See "this section"_Section_howto.html#4_15 for an overview of +LAMMPS output options. [Restrictions:] diff --git a/doc/compute_pressure.html b/doc/compute_pressure.html index df260aed1c..3386fe3004 100644 --- a/doc/compute_pressure.html +++ b/doc/compute_pressure.html @@ -47,14 +47,12 @@ and long-range interactions. Fixes that impose constra (e.g. the fix shake command) also contribute to the virial term.

    -

    A 6-component symmetric pressure tensor is also calculated by this -compute whose components can be output by the thermo_style -custom command or accessed by other -compute and fix commands. The equation for -the I,J components (where I and J = x,y,z) is similar to the above -formula, except that the first term uses components of the kinetic -energy tensor and the second term uses components of the virial -tensor: +

    A symmetric pressure tensor, stored as a 6-element vector, is also +calculated by this compute. The 6 components of the vector are +ordered xx, yy, zz, xy, xz, yz. The equation for the I,J components +(where I and J = x,y,z) is similar to the above formula, except that +the first term uses components of the kinetic energy tensor and the +second term uses components of the virial tensor:

    @@ -88,10 +86,16 @@ LAMMPS starts up, as if this command were in the input script:

    Output info:

    +

    This compute calculates a global scalar (the pressure) and a global +vector of length 6 (pressure tensor), which can be accessed by indices +1-6. These values can be used by any command that uses global scalar +or vector values from a compute as input. See this +section for an overview of LAMMPS output +options. +

    The scalar and vector values calculated by this compute are "intensive", meaning they are independent of the number of atoms in -the simulation. The 6 components of the vector are ordered xx, yy, -zz, xy, xz, yz. +the simulation.

    Restrictions: none

    diff --git a/doc/compute_pressure.txt b/doc/compute_pressure.txt index 139fecf4f9..9f40ce8ea4 100644 --- a/doc/compute_pressure.txt +++ b/doc/compute_pressure.txt @@ -44,14 +44,12 @@ and long-range interactions. "Fixes"_fix.html that impose constraints (e.g. the "fix shake"_fix_shake.html command) also contribute to the virial term. -A 6-component symmetric pressure tensor is also calculated by this -compute whose components can be output by the "thermo_style -custom"_thermo_style.html command or accessed by other -"compute"_compute.html and "fix"_fix.html commands. The equation for -the I,J components (where I and J = x,y,z) is similar to the above -formula, except that the first term uses components of the kinetic -energy tensor and the second term uses components of the virial -tensor: +A symmetric pressure tensor, stored as a 6-element vector, is also +calculated by this compute. The 6 components of the vector are +ordered xx, yy, zz, xy, xz, yz. The equation for the I,J components +(where I and J = x,y,z) is similar to the above formula, except that +the first term uses components of the kinetic energy tensor and the +second term uses components of the virial tensor: :c,image(Eqs/pressure_tensor.jpg) @@ -85,10 +83,16 @@ where "thermo_temp" is the ID of a similarly defined compute of style [Output info:] +This compute calculates a global scalar (the pressure) and a global +vector of length 6 (pressure tensor), which can be accessed by indices +1-6. These values can be used by any command that uses global scalar +or vector values from a compute as input. See "this +section"_Section_howto.html#4_15 for an overview of LAMMPS output +options. + The scalar and vector values calculated by this compute are "intensive", meaning they are independent of the number of atoms in -the simulation. The 6 components of the vector are ordered xx, yy, -zz, xy, xz, yz. +the simulation. [Restrictions:] none diff --git a/doc/compute_reduce.html b/doc/compute_reduce.html index c6d54e1d13..f00f209499 100644 --- a/doc/compute_reduce.html +++ b/doc/compute_reduce.html @@ -51,12 +51,7 @@ compute 2 all reduce min c_press2 f_ave v_myKE

    Define a calculation that "reduces" one or more per-atom inputs across all atoms in the group to yield a single global scalar for each listed input. If the compute reduce/region command is used, the selection of -atoms is limited to atoms in the region as well as in the group. The -resulting value(s) can be accessed by any command that uses global -computes, e.g. the thermo custom command or fix -ave/time command or by a variable -command. See this section of the -documentation for an overview of output options. +atoms is limited to atoms in the region as well as in the group.

    The reduction operation is specified by the mode setting. The sum option adds the per-atom quantities into a global total. The min or @@ -100,6 +95,13 @@ divides by the appropriate atom count.

    Output info:

    +

    This compute calculates a global scalar or global vector of length N +where N is the number of inputs, and which can be accessed by indices +1-6. These values can be used by any command that uses global scalar +or vector values from a compute as input. See this +section for an overview of LAMMPS output +options. +

    For sum mode, the scalar and vector values calculated by this compute are "extensive", meaning they scale with the number of atoms in the simulation. For min and max modes, the value(s) are diff --git a/doc/compute_reduce.txt b/doc/compute_reduce.txt index f166d32a7e..4e2a7090ef 100644 --- a/doc/compute_reduce.txt +++ b/doc/compute_reduce.txt @@ -40,12 +40,7 @@ compute 2 all reduce min c_press[2] f_ave v_myKE :pre Define a calculation that "reduces" one or more per-atom inputs across all atoms in the group to yield a single global scalar for each listed input. If the compute reduce/region command is used, the selection of -atoms is limited to atoms in the region as well as in the group. The -resulting value(s) can be accessed by any command that uses global -computes, e.g. the "thermo custom"_therml_style.html command or "fix -ave/time"_fix_ave_time.html command or by a "variable"_variable.html -command. See "this section"_Section_howto.html#4_15 of the -documentation for an overview of output options. +atoms is limited to atoms in the region as well as in the group. The reduction operation is specified by the {mode} setting. The {sum} option adds the per-atom quantities into a global total. The {min} or @@ -89,6 +84,13 @@ divides by the appropriate atom count. [Output info:] +This compute calculates a global scalar or global vector of length N +where N is the number of inputs, and which can be accessed by indices +1-6. These values can be used by any command that uses global scalar +or vector values from a compute as input. See "this +section"_Section_howto.html#4_15 for an overview of LAMMPS output +options. + For {sum} mode, the scalar and vector values calculated by this compute are "extensive", meaning they scale with the number of atoms in the simulation. For {min} and {max} modes, the value(s) are diff --git a/doc/compute_stress_atom.html b/doc/compute_stress_atom.html index 2d362c79d4..92d04fa2fd 100644 --- a/doc/compute_stress_atom.html +++ b/doc/compute_stress_atom.html @@ -29,14 +29,10 @@ compute 1 all stress/atom pair bond

    Define a computation that computes the symmetric per-atom stress tensor for each atom in a group. The tensor for each atom has 6 -components: xx, yy, zz, xy, xz, yz. See the compute +components and is stored as a 6-element vector in the following order: +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 as input, -e.g. the dump custom command or fix -ave/spatial command or fix -ave/atom command. See this -section for an overview. +(pressure) of the entire system.

    The stress tensor for atom I is given by the following formula, where a and b take on values x,y,z to generate the 6 components of @@ -105,10 +101,9 @@ contribution can easily be computed.

    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. +be accessed by indices 1-6 by any command that uses per-atom values +from a compute as input. See this section +for an overview of LAMMPS output options.

    Restrictions: none

    diff --git a/doc/compute_stress_atom.txt b/doc/compute_stress_atom.txt index 7966766ec8..7e6dfbe2a4 100644 --- a/doc/compute_stress_atom.txt +++ b/doc/compute_stress_atom.txt @@ -26,14 +26,10 @@ compute 1 all stress/atom pair bond :pre Define a computation that computes the symmetric per-atom stress tensor for each atom in a group. The tensor for each atom has 6 -components: xx, yy, zz, xy, xz, yz. See the "compute +components and is stored as a 6-element vector in the following order: +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 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. +(pressure) of the entire system. The stress tensor for atom {I} is given by the following formula, where {a} and {b} take on values x,y,z to generate the 6 components of @@ -102,10 +98,9 @@ contribution can easily be computed. [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. +be accessed by indices 1-6 by any command that uses per-atom values +from a compute as input. See "this section"_Section_howto.html#4_15 +for an overview of LAMMPS output options. [Restrictions:] none diff --git a/doc/compute_temp.html b/doc/compute_temp.html index 9275822752..4ff898c4cb 100644 --- a/doc/compute_temp.html +++ b/doc/compute_temp.html @@ -35,10 +35,12 @@ KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the simulation, N = number of atoms in the group, k = Boltzmann constant, and T = temperature.

    -

    A 6-component kinetic energy tensor is also calculated by this compute -for use in the computation of a pressure tensor. The formula for the -components of the tensor is the same as the above formula, except that -v^2 is replaced by vx * vy for the xy component, etc. +

    A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute for use in the computation of a pressure +tensor. The formula for the components of the tensor is the same as +the above formula, except that v^2 is replaced by vx*vy for the xy +component, etc. The 6 components of the vector are ordered xx, yy, +zz, xy, xz, yz.

    The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the dynamic option of the @@ -64,6 +66,13 @@ thermostatting.

    Output info:

    +

    This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See this +section for an overview of LAMMPS output +options. +

    The scalar value calculated by this compute is "intensive", meaning it is independent of the number of atoms in the simulation. The vector values are "extensive", meaning they scale with the number of atoms in diff --git a/doc/compute_temp.txt b/doc/compute_temp.txt index b18e93dba1..a2a9b28226 100644 --- a/doc/compute_temp.txt +++ b/doc/compute_temp.txt @@ -32,10 +32,12 @@ KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the simulation, N = number of atoms in the group, k = Boltzmann constant, and T = temperature. -A 6-component kinetic energy tensor is also calculated by this compute -for use in the computation of a pressure tensor. The formula for the -components of the tensor is the same as the above formula, except that -v^2 is replaced by vx * vy for the xy component, etc. +A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute for use in the computation of a pressure +tensor. The formula for the components of the tensor is the same as +the above formula, except that v^2 is replaced by vx*vy for the xy +component, etc. The 6 components of the vector are ordered xx, yy, +zz, xy, xz, yz. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the {dynamic} option of the @@ -61,6 +63,13 @@ thermostatting. [Output info:] +This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See "this +section"_Section_howto.html#4_15 for an overview of LAMMPS output +options. + The scalar value calculated by this compute is "intensive", meaning it is independent of the number of atoms in the simulation. The vector values are "extensive", meaning they scale with the number of atoms in diff --git a/doc/compute_temp_asphere.html b/doc/compute_temp_asphere.html index 51d98433e7..2d52a0abbf 100644 --- a/doc/compute_temp_asphere.html +++ b/doc/compute_temp_asphere.html @@ -65,11 +65,12 @@ computed from its angular momentum. as ellipsoids, not ellipses, meaning their moments of inertia will be the same as in 3d.

    -

    A 6-component kinetic energy tensor is also calculated by this -compute. The formula for the components of the tensor is the same as -the above formula, except that v^2 and w^2 are replaced by vx*vy and -wx*wy for the xy component, and the appropriate elements of the -inertia tensor are used. +

    A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute. The formula for the components of the +tensor is the same as the above formula, except that v^2 and w^2 are +replaced by vx*vy and wx*wy for the xy component, and the appropriate +elements of the inertia tensor are used. The 6 components of the +vector are ordered xx, yy, zz, xy, xz, yz.

    The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the dynamic option of the @@ -98,6 +99,13 @@ thermostatting.

    Output info:

    +

    This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See this +section for an overview of LAMMPS output +options. +

    The scalar value calculated by this compute is "intensive", meaning it is independent of the number of atoms in the simulation. The vector values are "extensive", meaning they scale with the number of atoms in diff --git a/doc/compute_temp_asphere.txt b/doc/compute_temp_asphere.txt index 02a036bdfe..da9f04d0ec 100755 --- a/doc/compute_temp_asphere.txt +++ b/doc/compute_temp_asphere.txt @@ -62,11 +62,12 @@ IMPORTANT NOTE: For "2d models"_dimension.html, particles are treated as ellipsoids, not ellipses, meaning their moments of inertia will be the same as in 3d. -A 6-component kinetic energy tensor is also calculated by this -compute. The formula for the components of the tensor is the same as -the above formula, except that v^2 and w^2 are replaced by vx*vy and -wx*wy for the xy component, and the appropriate elements of the -inertia tensor are used. +A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute. The formula for the components of the +tensor is the same as the above formula, except that v^2 and w^2 are +replaced by vx*vy and wx*wy for the xy component, and the appropriate +elements of the inertia tensor are used. The 6 components of the +vector are ordered xx, yy, zz, xy, xz, yz. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the {dynamic} option of the @@ -95,6 +96,13 @@ thermostatting. [Output info:] +This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See "this +section"_Section_howto.html#4_15 for an overview of LAMMPS output +options. + The scalar value calculated by this compute is "intensive", meaning it is independent of the number of atoms in the simulation. The vector values are "extensive", meaning they scale with the number of atoms in diff --git a/doc/compute_temp_com.html b/doc/compute_temp_com.html index 4dc7bf0bc1..e2ae904bd1 100644 --- a/doc/compute_temp_com.html +++ b/doc/compute_temp_com.html @@ -39,10 +39,12 @@ KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the simulation, N = number of atoms in the group, k = Boltzmann constant, and T = temperature.

    -

    A 6-component kinetic energy tensor is also calculated by this compute -for use in the computation of a pressure tensor. The formula for the -components of the tensor is the same as the above formula, except that -v^2 is replaced by vx * vy for the xy component, etc. +

    A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute for use in the computation of a pressure +tensor. The formula for the components of the tensor is the same as +the above formula, except that v^2 is replaced by vx*vy for the xy +component, etc. The 6 components of the vector are ordered xx, yy, +zz, xy, xz, yz.

    The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the dynamic option of the @@ -72,6 +74,13 @@ thermostatting.

    Output info:

    +

    This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See this +section for an overview of LAMMPS output +options. +

    The scalar value calculated by this compute is "intensive", meaning it is independent of the number of atoms in the simulation. The vector values are "extensive", meaning they scale with the number of atoms in diff --git a/doc/compute_temp_com.txt b/doc/compute_temp_com.txt index ae21ccfb26..6d7ada434f 100644 --- a/doc/compute_temp_com.txt +++ b/doc/compute_temp_com.txt @@ -36,10 +36,12 @@ KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the simulation, N = number of atoms in the group, k = Boltzmann constant, and T = temperature. -A 6-component kinetic energy tensor is also calculated by this compute -for use in the computation of a pressure tensor. The formula for the -components of the tensor is the same as the above formula, except that -v^2 is replaced by vx * vy for the xy component, etc. +A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute for use in the computation of a pressure +tensor. The formula for the components of the tensor is the same as +the above formula, except that v^2 is replaced by vx*vy for the xy +component, etc. The 6 components of the vector are ordered xx, yy, +zz, xy, xz, yz. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the {dynamic} option of the @@ -69,6 +71,13 @@ thermostatting. [Output info:] +This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See "this +section"_Section_howto.html#4_15 for an overview of LAMMPS output +options. + The scalar value calculated by this compute is "intensive", meaning it is independent of the number of atoms in the simulation. The vector values are "extensive", meaning they scale with the number of atoms in diff --git a/doc/compute_temp_deform.html b/doc/compute_temp_deform.html index f0572b83b9..283776fcdb 100644 --- a/doc/compute_temp_deform.html +++ b/doc/compute_temp_deform.html @@ -63,10 +63,12 @@ or 3 = dimensionality of the simulation, N = number of atoms in the group, k = Boltzmann constant, and T = temperature. Note that v in the kinetic energy formula is the atom's thermal velocity.

    -

    A 6-component kinetic energy tensor is also calculated by this compute -for use in the computation of a pressure tensor. The formula for the -components of the tensor is the same as the above formula, except that -v^2 is replaced by vx * vy for the xy component, etc. +

    A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute for use in the computation of a pressure +tensor. The formula for the components of the tensor is the same as +the above formula, except that v^2 is replaced by vx*vy for the xy +component, etc. The 6 components of the vector are ordered xx, yy, +zz, xy, xz, yz.

    The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the dynamic option of the @@ -96,6 +98,13 @@ thermostatting.

    Output info:

    +

    This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See this +section for an overview of LAMMPS output +options. +

    The scalar value calculated by this compute is "intensive", meaning it is independent of the number of atoms in the simulation. The vector values are "extensive", meaning they scale with the number of atoms in diff --git a/doc/compute_temp_deform.txt b/doc/compute_temp_deform.txt index 7c8bcfaaf8..6aeca74d18 100644 --- a/doc/compute_temp_deform.txt +++ b/doc/compute_temp_deform.txt @@ -60,10 +60,12 @@ or 3 = dimensionality of the simulation, N = number of atoms in the group, k = Boltzmann constant, and T = temperature. Note that v in the kinetic energy formula is the atom's thermal velocity. -A 6-component kinetic energy tensor is also calculated by this compute -for use in the computation of a pressure tensor. The formula for the -components of the tensor is the same as the above formula, except that -v^2 is replaced by vx * vy for the xy component, etc. +A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute for use in the computation of a pressure +tensor. The formula for the components of the tensor is the same as +the above formula, except that v^2 is replaced by vx*vy for the xy +component, etc. The 6 components of the vector are ordered xx, yy, +zz, xy, xz, yz. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the {dynamic} option of the @@ -93,6 +95,13 @@ thermostatting. [Output info:] +This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See "this +section"_Section_howto.html#4_15 for an overview of LAMMPS output +options. + The scalar value calculated by this compute is "intensive", meaning it is independent of the number of atoms in the simulation. The vector values are "extensive", meaning they scale with the number of atoms in diff --git a/doc/compute_temp_partial.html b/doc/compute_temp_partial.html index 0157cc88c2..717e6e5e4c 100644 --- a/doc/compute_temp_partial.html +++ b/doc/compute_temp_partial.html @@ -25,9 +25,9 @@

    Description:

    -

    Define a compute to calculate the temperature of a group of atoms, -after excluding one or more velocity components. A compute of this -style can be used by any command that computes a temperature, +

    Define a computation that calculates the temperature of a group of +atoms, after excluding one or more velocity components. A compute of +this style can be used by any command that computes a temperature, e.g. thermo_modify, fix temp/rescale, fix npt, etc.

    @@ -39,10 +39,12 @@ of KE excludes the x, y, or z dimensions if xflag, yflag, or zflag = 0. The dim parameter is adjusted to give the correct number of degrees of freedom.

    -

    A 6-component kinetic energy tensor is also calculated by this compute -for use in the calculation of a pressure tensor. The formula for the -components of the tensor is the same as the above formula, except that -v^2 is replaced by vx * vy for the xy component, etc. +

    A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute for use in the calculation of a pressure +tensor. The formula for the components of the tensor is the same as +the above formula, except that v^2 is replaced by vx*vy for the xy +component, etc. The 6 components of the vector are ordered xx, yy, +zz, xy, xz, yz.

    The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the dynamic option of the @@ -72,6 +74,13 @@ thermostatting.

    Output info:

    +

    This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See this +section for an overview of LAMMPS output +options. +

    The scalar value calculated by this compute is "intensive", meaning it is independent of the number of atoms in the simulation. The vector values are "extensive", meaning they scale with the number of atoms in diff --git a/doc/compute_temp_partial.txt b/doc/compute_temp_partial.txt index d38a34b07e..e47e702b4e 100644 --- a/doc/compute_temp_partial.txt +++ b/doc/compute_temp_partial.txt @@ -22,9 +22,9 @@ compute newT flow temp/partial 1 1 0 :pre [Description:] -Define a compute to calculate the temperature of a group of atoms, -after excluding one or more velocity components. A compute of this -style can be used by any command that computes a temperature, +Define a computation that calculates the temperature of a group of +atoms, after excluding one or more velocity components. A compute of +this style can be used by any command that computes a temperature, e.g. "thermo_modify"_thermo_modify.html, "fix temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_npt.html, etc. @@ -36,10 +36,12 @@ of KE excludes the x, y, or z dimensions if xflag, yflag, or zflag = 0. The dim parameter is adjusted to give the correct number of degrees of freedom. -A 6-component kinetic energy tensor is also calculated by this compute -for use in the calculation of a pressure tensor. The formula for the -components of the tensor is the same as the above formula, except that -v^2 is replaced by vx * vy for the xy component, etc. +A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute for use in the calculation of a pressure +tensor. The formula for the components of the tensor is the same as +the above formula, except that v^2 is replaced by vx*vy for the xy +component, etc. The 6 components of the vector are ordered xx, yy, +zz, xy, xz, yz. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the {dynamic} option of the @@ -69,6 +71,13 @@ thermostatting. [Output info:] +This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See "this +section"_Section_howto.html#4_15 for an overview of LAMMPS output +options. + The scalar value calculated by this compute is "intensive", meaning it is independent of the number of atoms in the simulation. The vector values are "extensive", meaning they scale with the number of atoms in diff --git a/doc/compute_temp_profile.html b/doc/compute_temp_profile.html index a8b956c003..09d311e6af 100644 --- a/doc/compute_temp_profile.html +++ b/doc/compute_temp_profile.html @@ -77,10 +77,12 @@ T, where KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the simulation, N = number of atoms in the group, k = Boltzmann constant, and T = temperature.

    -

    A 6-component kinetic energy tensor is also calculated by this compute -for use in the calculation of a pressure tensor. The formula for the -components of the tensor is the same as the above formula, except that -v^2 is replaced by vx * vy for the xy component, etc. +

    A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute for use in the computation of a pressure +tensor. The formula for the components of the tensor is the same as +the above formula, except that v^2 is replaced by vx*vy for the xy +component, etc. The 6 components of the vector are ordered xx, yy, +zz, xy, xz, yz.

    The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the dynamic option of the @@ -112,6 +114,13 @@ profile-unbiased thermostat (PUT), as described in (Evans)

    Output info:

    +

    This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See this +section for an overview of LAMMPS output +options. +

    The scalar value calculated by this compute is "intensive", meaning it is independent of the number of atoms in the simulation. The vector values are "extensive", meaning they scale with the number of atoms in diff --git a/doc/compute_temp_profile.txt b/doc/compute_temp_profile.txt index e1dd975198..00c798e8c6 100644 --- a/doc/compute_temp_profile.txt +++ b/doc/compute_temp_profile.txt @@ -69,10 +69,12 @@ T, where KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the simulation, N = number of atoms in the group, k = Boltzmann constant, and T = temperature. -A 6-component kinetic energy tensor is also calculated by this compute -for use in the calculation of a pressure tensor. The formula for the -components of the tensor is the same as the above formula, except that -v^2 is replaced by vx * vy for the xy component, etc. +A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute for use in the computation of a pressure +tensor. The formula for the components of the tensor is the same as +the above formula, except that v^2 is replaced by vx*vy for the xy +component, etc. The 6 components of the vector are ordered xx, yy, +zz, xy, xz, yz. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the {dynamic} option of the @@ -104,6 +106,13 @@ profile-unbiased thermostat (PUT), as described in "(Evans)"_#Evans. [Output info:] +This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See "this +section"_Section_howto.html#4_15 for an overview of LAMMPS output +options. + The scalar value calculated by this compute is "intensive", meaning it is independent of the number of atoms in the simulation. The vector values are "extensive", meaning they scale with the number of atoms in diff --git a/doc/compute_temp_ramp.html b/doc/compute_temp_ramp.html index 642d4db8c1..92cdd30f6a 100644 --- a/doc/compute_temp_ramp.html +++ b/doc/compute_temp_ramp.html @@ -58,10 +58,12 @@ means the distance units are in lattice spacings; e.g. velocity = lattice spacings / tau. The lattice command must have been previously used to define the lattice spacing.

    -

    A 6-component kinetic energy tensor is also calculated by this compute -for use in the calculation of a pressure tensor. The formula for the -components of the tensor is the same as the above formula, except that -v^2 is replaced by vx * vy for the xy component, etc. +

    A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute for use in the computation of a pressure +tensor. The formula for the components of the tensor is the same as +the above formula, except that v^2 is replaced by vx*vy for the xy +component, etc. The 6 components of the vector are ordered xx, yy, +zz, xy, xz, yz.

    The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the dynamic option of the @@ -91,6 +93,13 @@ thermostatting.

    Output info:

    +

    This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See this +section for an overview of LAMMPS output +options. +

    The scalar value calculated by this compute is "intensive", meaning it is independent of the number of atoms in the simulation. The vector values are "extensive", meaning they scale with the number of atoms in diff --git a/doc/compute_temp_ramp.txt b/doc/compute_temp_ramp.txt index 260d0fe70b..4bcc2d73b5 100644 --- a/doc/compute_temp_ramp.txt +++ b/doc/compute_temp_ramp.txt @@ -54,10 +54,12 @@ means the distance units are in lattice spacings; e.g. velocity = lattice spacings / tau. The "lattice"_lattice.html command must have been previously used to define the lattice spacing. -A 6-component kinetic energy tensor is also calculated by this compute -for use in the calculation of a pressure tensor. The formula for the -components of the tensor is the same as the above formula, except that -v^2 is replaced by vx * vy for the xy component, etc. +A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute for use in the computation of a pressure +tensor. The formula for the components of the tensor is the same as +the above formula, except that v^2 is replaced by vx*vy for the xy +component, etc. The 6 components of the vector are ordered xx, yy, +zz, xy, xz, yz. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the {dynamic} option of the @@ -87,6 +89,13 @@ thermostatting. [Output info:] +This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See "this +section"_Section_howto.html#4_15 for an overview of LAMMPS output +options. + The scalar value calculated by this compute is "intensive", meaning it is independent of the number of atoms in the simulation. The vector values are "extensive", meaning they scale with the number of atoms in diff --git a/doc/compute_temp_region.html b/doc/compute_temp_region.html index daf8f0c0a2..f5604f3bed 100644 --- a/doc/compute_temp_region.html +++ b/doc/compute_temp_region.html @@ -46,10 +46,12 @@ dim = 2 or 3 = dimensionality of the simulation, N = number of atoms in both the group and region, k = Boltzmann constant, and T = temperature.

    -

    A 6-component kinetic energy tensor is also calculated by this compute -for use in the computation of a pressure tensor. The formula for the -components of the tensor is the same as the above formula, except that -v^2 is replaced by vx * vy for the xy component, etc. +

    A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute for use in the computation of a pressure +tensor. The formula for the components of the tensor is the same as +the above formula, except that v^2 is replaced by vx*vy for the xy +component, etc. The 6 components of the vector are ordered xx, yy, +zz, xy, xz, yz.

    The number of atoms contributing to the temperature is compute each time the temperature is evaluated since it is assumed atoms can @@ -83,6 +85,13 @@ thermostatting.

    Output info:

    +

    This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See this +section for an overview of LAMMPS output +options. +

    The scalar value calculated by this compute is "intensive", meaning it is independent of the number of atoms in the simulation. The vector values are "extensive", meaning they scale with the number of atoms in diff --git a/doc/compute_temp_region.txt b/doc/compute_temp_region.txt index a74ec40af4..3f744ad3fe 100644 --- a/doc/compute_temp_region.txt +++ b/doc/compute_temp_region.txt @@ -43,10 +43,12 @@ dim = 2 or 3 = dimensionality of the simulation, N = number of atoms in both the group and region, k = Boltzmann constant, and T = temperature. -A 6-component kinetic energy tensor is also calculated by this compute -for use in the computation of a pressure tensor. The formula for the -components of the tensor is the same as the above formula, except that -v^2 is replaced by vx * vy for the xy component, etc. +A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute for use in the computation of a pressure +tensor. The formula for the components of the tensor is the same as +the above formula, except that v^2 is replaced by vx*vy for the xy +component, etc. The 6 components of the vector are ordered xx, yy, +zz, xy, xz, yz. The number of atoms contributing to the temperature is compute each time the temperature is evaluated since it is assumed atoms can @@ -80,6 +82,13 @@ thermostatting. [Output info:] +This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See "this +section"_Section_howto.html#4_15 for an overview of LAMMPS output +options. + The scalar value calculated by this compute is "intensive", meaning it is independent of the number of atoms in the simulation. The vector values are "extensive", meaning they scale with the number of atoms in diff --git a/doc/compute_temp_sphere.html b/doc/compute_temp_sphere.html index 01a2d00d07..fa3050ab7e 100644 --- a/doc/compute_temp_sphere.html +++ b/doc/compute_temp_sphere.html @@ -56,10 +56,11 @@ inertia for a sphere and w is the particle's angular velocity. as spheres, not disks, meaning their moment of inertia will be the same as in 3d.

    -

    A 6-component kinetic energy tensor is also calculated by this -compute. The formula for the components of the tensor is the same as -the above formulas, except that v^2 and w^2 are replaced by vx*vy and -wx*wy for the xy component. +

    A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute. The formula for the components of the +tensor is the same as the above formulas, except that v^2 and w^2 are +replaced by vx*vy and wx*wy for the xy component. The 6 components of +the vector are ordered xx, yy, zz, xy, xz, yz.

    The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the dynamic option of the @@ -88,6 +89,13 @@ thermostatting.

    Output info:

    +

    This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See this +section for an overview of LAMMPS output +options. +

    The scalar value calculated by this compute is "intensive", meaning it is independent of the number of atoms in the simulation. The vector values are "extensive", meaning they scale with the number of atoms in diff --git a/doc/compute_temp_sphere.txt b/doc/compute_temp_sphere.txt index 36b9f02380..8f97e70baf 100755 --- a/doc/compute_temp_sphere.txt +++ b/doc/compute_temp_sphere.txt @@ -53,10 +53,11 @@ IMPORTANT NOTE: For "2d models"_dimension.html, particles are treated as spheres, not disks, meaning their moment of inertia will be the same as in 3d. -A 6-component kinetic energy tensor is also calculated by this -compute. The formula for the components of the tensor is the same as -the above formulas, except that v^2 and w^2 are replaced by vx*vy and -wx*wy for the xy component. +A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute. The formula for the components of the +tensor is the same as the above formulas, except that v^2 and w^2 are +replaced by vx*vy and wx*wy for the xy component. The 6 components of +the vector are ordered xx, yy, zz, xy, xz, yz. The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the {dynamic} option of the @@ -85,6 +86,13 @@ thermostatting. [Output info:] +This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See "this +section"_Section_howto.html#4_15 for an overview of LAMMPS output +options. + The scalar value calculated by this compute is "intensive", meaning it is independent of the number of atoms in the simulation. The vector values are "extensive", meaning they scale with the number of atoms in diff --git a/doc/fix_coord_original.html b/doc/fix_coord_original.html index c4690b5b48..e3328f5ece 100644 --- a/doc/fix_coord_original.html +++ b/doc/fix_coord_original.html @@ -13,14 +13,24 @@

    Syntax:

    -
    fix ID group-ID coord/original 
+
    fix ID group-ID coord/original keyword values ... 
 
    
-