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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3495 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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6
doc/Section_commands.html
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@ -348,9 +348,9 @@ each style or click on the style itself for a full description:
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A>
<TR ALIGN="center"><TD ><A HREF = "compute_msd.html">msd</A></TD><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A>
</TD></TR></TABLE></DIV>
<P>These are compute styles contributed by users, which can be used if

1
doc/Section_commands.txt
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@ -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,

1
doc/compute.html
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@ -121,6 +121,7 @@ available in LAMMPS:
<LI><A HREF = "compute_heat_flux.html">heat/flux</A> - heat flux through a group of atoms
<LI><A HREF = "compute_ke.html">ke</A> - translational kinetic energy
<LI><A HREF = "compute_ke_atom.html">ke/atom</A> - kinetic energy for each atom
<LI><A HREF = "compute_msd.html">msd</A> - mean-squared displacement of group of atoms
<LI><A HREF = "compute_pe.html">pe</A> - potential energy
<LI><A HREF = "compute_pe_atom.html">pe/atom</A> - potential energy for each atom
<LI><A HREF = "compute_pressure.html">pressure</A> - total pressure and pressure tensor

1
doc/compute.txt
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@ -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

6
doc/compute_ackland_atom.html
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@ -52,9 +52,9 @@ which computes this quantity.-
<P><B>Output info:</B>
</P>
<P>This compute calculates a scalar quantity for each atom, which can be
accessed by any command that uses per-atom computes as input. See
<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
output options.
accessed by any command that uses per-atom values from a compute as
input. See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
LAMMPS output options.
</P>
<P><B>Restrictions:</B>
</P>

6
doc/compute_ackland_atom.txt
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@ -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:]

6
doc/compute_centro_atom.html
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@ -53,9 +53,9 @@ too frequently or to have multiple compute/dump commands, each with a
<P><B>Output info:</B>
</P>
<P>This compute calculates a scalar quantity for each atom, which can be
accessed by any command that uses per-atom computes as input. See
<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
output options.
accessed by any command that uses per-atom values from a compute as
input. See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
LAMMPS output options.
</P>
<P><B>Restrictions:</B> none
</P>

6
doc/compute_centro_atom.txt
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@ -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

6
doc/compute_cna_atom.html
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@ -76,9 +76,9 @@ too frequently or to have multiple compute/dump commands, each with a
<P><B>Output info:</B>
</P>
<P>This compute calculates a scalar quantity for each atom, which can be
accessed by any command that uses per-atom computes as input. See
<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
output options.
accessed by any command that uses per-atom values from a compute as
input. See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
LAMMPS output options.
</P>
<P><B>Restrictions:</B> none
</P>

6
doc/compute_cna_atom.txt
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@ -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

6
doc/compute_coord_atom.html
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@ -45,9 +45,9 @@ too frequently or to have multiple compute/dump commands, each of a
<P><B>Output info:</B>
</P>
<P>This compute calculates a scalar quantity for each atom, which can be
accessed by any command that uses per-atom computes as input. See
<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
output options.
accessed by any command that uses per-atom values from a compute as
input. See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
LAMMPS output options.
</P>
<P><B>Restrictions:</B> none
</P>

6
doc/compute_coord_atom.txt
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@ -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

6
doc/compute_damage_atom.html
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@ -36,9 +36,9 @@ compute group.
<P><B>Output info:</B>
</P>
<P>This compute calculates a scalar quantity for each atom, which can be
accessed by any command that uses per-atom computes as input. See
<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
output options.
accessed by any command that uses per-atom values from a compute as
input. See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
LAMMPS output options.
</P>
<P><B>Restrictions:</B>
</P>

6
doc/compute_damage_atom.txt
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@ -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:]

31
doc/compute_displace_atom.html
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@ -26,9 +26,12 @@
</P>
<P>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.
</P>
<P>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).
</P>
<P>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.
</P>
<P>The value of the displacement will be 0.0 for atoms not in the
specified compute group.
</P>
<P>IMPORTANT NOTE: Fix coord/original stores the initial coordinates in
"unwrapped" form, by using the image flags associated with each atom.
See the <A HREF = "dump.html">dump custom</A> 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 <A HREF = "set.html">set
image</A> command.
</P>
<P>The displacements can be output directly via the <A HREF = "dump.html">dump
custom</A> command.
</P>
<P>The value of the displacement will be 0.0 for atoms not in the
specified compute group.
<P>IMPORTANT NOTE: If an atom is part of a rigid body (see the <A HREF = "fix_rigid.html">fix
rigid</A> command), it's periodic image flags are altered,
and the computed MSD will not reflect its true displacement. See the
<A HREF = "fix_rigid.html">fix rigid</A> command for details. Thus, to compute the
MSD of rigid bodies as they cross periodic boundaries, you will need
to post-process a <A HREF = "dump.html">dump file</A> containing coordinates of the
atoms in the bodies.
</P>
<P>IMPORTANT NOTE: If you want the quantities calculated by this compute
to be continuous when running from a <A HREF = "read_restart.html">restart file</A>,
@ -68,15 +76,14 @@ file.
<P>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 <A HREF = "Section_howto.html#4_15">this section</A> 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.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dump.html">dump custom</A>, <A HREF = "fix_msd.html">fix msd</A>
<P><A HREF = "compute_msd.html">compute msd</A>, <A HREF = "dump.html">dump custom</A>, <A HREF = "fix_coord_original.html">fix
coord/original</A>
</P>
<P><B>Default:</B> none
</P>

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doc/compute_displace_atom.txt
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@ -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

5
doc/compute_erotate_asphere.html
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@ -37,6 +37,11 @@ the same as in 3d.
</P>
<P><B>Output info:</B>
</P>
<P>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 <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "extensive", meaning it
it scales with the number of atoms in the simulation.
</P>

5
doc/compute_erotate_asphere.txt
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@ -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.

5
doc/compute_erotate_sphere.html
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@ -36,6 +36,11 @@ same as in 3d.
</P>
<P><B>Output info:</B>
</P>
<P>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 <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "extensive", meaning it
it scales with the number of atoms in the simulation.
</P>

5
doc/compute_erotate_sphere.txt
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@ -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.

5
doc/compute_event_displace.html
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@ -38,6 +38,11 @@ further than the threshold distance.
</P>
<P><B>Output info:</B>
</P>
<P>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 <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "intensive", meaning it
is independent of the number of atoms in the simulation.
</P>

5
doc/compute_event_displace.txt
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@ -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.

14
doc/compute_group_group.html
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@ -41,10 +41,16 @@ quantity too frequently.
</P>
<P><B>Output info:</B>
</P>
<P>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.
<P>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 <A HREF = "Section_howto.html#4_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>Both the scalar and vector values calculated by this compute are
"extensive", meaning they scale with the number of atoms in the
simulation.
</P>
<P><B>Restrictions:</B>
</P>

14
doc/compute_group_group.txt
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@ -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:]

15
doc/compute_heat_flux.html
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@ -84,12 +84,19 @@ interval and the appropriate unit conversion factors. For real
<A HREF = "units.html">units</A> in LAMMPS, this is 2917703220.0 in this case. The
final thermal conductivity value obtained is 0.25 W/mK.
</P>
<P>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.
</P>
<P><B>Output info:</B>
</P>
<P>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.
<P>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 <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
LAMMPS output options.
</P>
<P>The vector values calculated by this compute are "extensive", meaning
they scale with the number of atoms in the simulation. They should be

15
doc/compute_heat_flux.txt
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@ -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

5
doc/compute_ke.html
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@ -45,6 +45,11 @@ include different degrees of freedom (translational, rotational, etc).
</P>
<P><B>Output info:</B>
</P>
<P>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 <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "extensive", meaning it
it scales with the number of atoms in the simulation.
</P>

5
doc/compute_ke.txt
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@ -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.

6
doc/compute_ke_atom.html
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@ -36,9 +36,9 @@ specified compute group.
<P><B>Output info:</B>
</P>
<P>This compute calculates a scalar quantity for each atom, which can be
accessed by any command that uses per-atom computes as input. See
<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
output options.
accessed by any command that uses per-atom values from a compute as
input. See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
LAMMPS output options.
</P>
<P><B>Restrictions:</B> none
</P>

6
doc/compute_ke_atom.txt
View File

@ -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

5
doc/compute_pe.html
View File

@ -56,6 +56,11 @@ LAMMPS starts up, as if this command were in the input script:
</P>
<P><B>Output info:</B>
</P>
<P>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 <A HREF = "Section_howto.html#4_15">this section</A> for an
overview of LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "extensive", meaning it
it scales with the number of atoms in the simulation.
</P>

5
doc/compute_pe.txt
View File

@ -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.

13
doc/compute_pe_atom.html
View File

@ -30,12 +30,7 @@ compute 1 all pe/atom pair bond
</P>
<P>Define a computation that computes the per-atom potential energy for
each atom in a group. See the <A HREF = "compute_pe.html">compute pe</A> 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 <A HREF = "dump.html">dump custom</A> command or <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> command or <A HREF = "fix_ave_atom.html">fix
ave/atom</A> command. See <A HREF = "Section_howto.html#4_15">this
section</A> for an overview.
you want the potential energy of the entire system.
</P>
<P>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.
<P><B>Output info:</B>
</P>
<P>This compute calculates a scalar quantity for each atom, which can be
accessed by any command that uses per-atom computes as input. See
<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
output options.
accessed by any command that uses per-atom values from a compute as
input. See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
LAMMPS output options.
</P>
<P><B>Restrictions:</B>
</P>

13
doc/compute_pe_atom.txt
View File

@ -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:]

24
doc/compute_pressure.html
View File

@ -47,14 +47,12 @@ and long-range interactions. <A HREF = "fix.html">Fixes</A> that impose constra
(e.g. the <A HREF = "fix_shake.html">fix shake</A> command) also contribute to the
virial term.
</P>
<P>A 6-component symmetric pressure tensor is also calculated by this
compute whose components can be output by the <A HREF = "thermo_style.html">thermo_style
custom</A> command or accessed by other
<A HREF = "compute.html">compute</A> and <A HREF = "fix.html">fix</A> 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:
<P>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:
</P>
<CENTER><IMG SRC = "Eqs/pressure_tensor.jpg">
</CENTER>
@ -88,10 +86,16 @@ LAMMPS starts up, as if this command were in the input script:
</P>
<P><B>Output info:</B>
</P>
<P>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 <A HREF = "Section_howto.html#4_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>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.
</P>
<P><B>Restrictions:</B> none
</P>

24
doc/compute_pressure.txt
View File

@ -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

14
doc/compute_reduce.html
View File

@ -51,12 +51,7 @@ compute 2 all reduce min c_press<B>2</B> f_ave v_myKE
<P>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 <A HREF = "therml_style.html">thermo custom</A> command or <A HREF = "fix_ave_time.html">fix
ave/time</A> command or by a <A HREF = "variable.html">variable</A>
command. See <A HREF = "Section_howto.html#4_15">this section</A> of the
documentation for an overview of output options.
atoms is limited to atoms in the region as well as in the group.
</P>
<P>The reduction operation is specified by the <I>mode</I> setting. The <I>sum</I>
option adds the per-atom quantities into a global total. The <I>min</I> or
@ -100,6 +95,13 @@ divides by the appropriate atom count.
</P>
<P><B>Output info:</B>
</P>
<P>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 <A HREF = "Section_howto.html#4_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>For <I>sum</I> mode, the scalar and vector values calculated by this
compute are "extensive", meaning they scale with the number of atoms
in the simulation. For <I>min</I> and <I>max</I> modes, the value(s) are

14
doc/compute_reduce.txt
View File

@ -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

17
doc/compute_stress_atom.html
View File

@ -29,14 +29,10 @@ compute 1 all stress/atom pair bond
</P>
<P>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 <A HREF = "compute_pressure.html">compute
components and is stored as a 6-element vector in the following order:
xx, yy, zz, xy, xz, yz. See the <A HREF = "compute_pressure.html">compute
pressure</A> 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 <A HREF = "dump.html">dump custom</A> command or <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> command or <A HREF = "fix_ave_atom.html">fix
ave/atom</A> command. See <A HREF = "Section_howto.html#4_15">this
section</A> for an overview.
(pressure) of the entire system.
</P>
<P>The stress tensor for atom <I>I</I> is given by the following formula,
where <I>a</I> and <I>b</I> take on values x,y,z to generate the 6 components of
@ -105,10 +101,9 @@ contribution can easily be computed.
<P><B>Output info:</B>
</P>
<P>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 <A HREF = "Section_howto.html#4_15">this section</A> 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 <A HREF = "Section_howto.html#4_15">this section</A>
for an overview of LAMMPS output options.
</P>
<P><B>Restrictions:</B> none
</P>

17
doc/compute_stress_atom.txt
View File

@ -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

17
doc/compute_temp.html
View File

@ -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.
</P>
<P>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.
<P>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.
</P>
<P>The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the <I>dynamic</I> option of the
@ -64,6 +66,13 @@ thermostatting.
</P>
<P><B>Output info:</B>
</P>
<P>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 <A HREF = "Section_howto.html#4_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>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

17
doc/compute_temp.txt
View File

@ -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

18
doc/compute_temp_asphere.html
View File

@ -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.
</P>
<P>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.
<P>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.
</P>
<P>The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the <I>dynamic</I> option of the
@ -98,6 +99,13 @@ thermostatting.
</P>
<P><B>Output info:</B>
</P>
<P>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 <A HREF = "Section_howto.html#4_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>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

18
doc/compute_temp_asphere.txt
View File

@ -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

17
doc/compute_temp_com.html
View File

@ -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.
</P>
<P>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.
<P>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.
</P>
<P>The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the <I>dynamic</I> option of the
@ -72,6 +74,13 @@ thermostatting.
</P>
<P><B>Output info:</B>
</P>
<P>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 <A HREF = "Section_howto.html#4_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>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

17
doc/compute_temp_com.txt
View File

@ -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

17
doc/compute_temp_deform.html
View File

@ -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.
</P>
<P>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.
<P>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.
</P>
<P>The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the <I>dynamic</I> option of the
@ -96,6 +98,13 @@ thermostatting.
</P>
<P><B>Output info:</B>
</P>
<P>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 <A HREF = "Section_howto.html#4_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>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

17
doc/compute_temp_deform.txt
View File

@ -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

23
doc/compute_temp_partial.html
View File

@ -25,9 +25,9 @@
</PRE>
<P><B>Description:</B>
</P>
<P>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,
<P>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. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A>, <A HREF = "fix_npt.html">fix npt</A>, etc.
</P>
@ -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.
</P>
<P>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.
<P>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.
</P>
<P>The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the <I>dynamic</I> option of the
@ -72,6 +74,13 @@ thermostatting.
</P>
<P><B>Output info:</B>
</P>
<P>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 <A HREF = "Section_howto.html#4_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>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

23
doc/compute_temp_partial.txt
View File

@ -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

17
doc/compute_temp_profile.html
View File

@ -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.
</P>
<P>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.
<P>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.
</P>
<P>The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the <I>dynamic</I> option of the
@ -112,6 +114,13 @@ profile-unbiased thermostat (PUT), as described in <A HREF = "#Evans">(Evans)</A
</P>
<P><B>Output info:</B>
</P>
<P>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 <A HREF = "Section_howto.html#4_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>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

17
doc/compute_temp_profile.txt
View File

@ -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

17
doc/compute_temp_ramp.html
View File

@ -58,10 +58,12 @@ means the distance units are in lattice spacings; e.g. velocity =
lattice spacings / tau. The <A HREF = "lattice.html">lattice</A> command must have
been previously used to define the lattice spacing.
</P>
<P>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.
<P>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.
</P>
<P>The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the <I>dynamic</I> option of the
@ -91,6 +93,13 @@ thermostatting.
</P>
<P><B>Output info:</B>
</P>
<P>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 <A HREF = "Section_howto.html#4_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>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

17
doc/compute_temp_ramp.txt
View File

@ -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

17
doc/compute_temp_region.html
View File

@ -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.
</P>
<P>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.
<P>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.
</P>
<P>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.
</P>
<P><B>Output info:</B>
</P>
<P>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 <A HREF = "Section_howto.html#4_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>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

17
doc/compute_temp_region.txt
View File

@ -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

16
doc/compute_temp_sphere.html
View File

@ -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.
</P>
<P>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.
<P>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.
</P>
<P>The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the <I>dynamic</I> option of the
@ -88,6 +89,13 @@ thermostatting.
</P>
<P><B>Output info:</B>
</P>
<P>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 <A HREF = "Section_howto.html#4_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>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

16
doc/compute_temp_sphere.txt
View File

@ -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

23
doc/fix_coord_original.html
View File

@ -13,14 +13,24 @@
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID coord/original
<PRE>fix ID group-ID coord/original keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>coord/original = style name of this fix command
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>com</I>
<PRE> <I>com</I> value = <I>yes</I> or <I>no</I>
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all coord/original
fix 1 upper coord/original com yes
</PRE>
<P><B>Description:</B>
</P>
@ -45,6 +55,11 @@ rigid</A> command), it's periodic image flags are altered,
and its original coordinates may not be what you expect. See the
<A HREF = "fix_rigid.html">fix rigid</A> command for details.
</P>
<P>If the <I>com</I> keyword is set to <I>yes</I> then the position
of each atom relative to the center-of-mass of the group of
atoms is stored, instead of the absolute position. This option
is used by the <A HREF = "compute_msd.html">compute msd</A> command.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the original coordinates of the atoms to <A HREF = "restart.html">binary
@ -71,9 +86,11 @@ minimization</A>.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_msd.html">fix msd</A>, <A HREF = "compute_displace_atom.html">compute
<P><A HREF = "compute_msd.html">compute msd</A>, <A HREF = "compute_displace_atom.html">compute
displace/atom</A>
</P>
<P><B>Default:</B> none
<P><B>Default:</B>
</P>
<P>The option default is com = no.
</P>
</HTML>

24
doc/fix_coord_original.txt
View File

@ -10,14 +10,19 @@ fix coord/original command :h3
[Syntax:]
fix ID group-ID coord/original :pre
fix ID group-ID coord/original keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command
coord/original = style name of this fix command :ul
ID, group-ID are documented in "fix"_fix.html command :ulb,l
coord/original = style name of this fix command :l
zero or more keyword/value pairs may be appended :l
keyword = {com} :l
{com} value = {yes} or {no} :pre
:ule
[Examples:]
fix 1 all coord/original :pre
fix 1 all coord/original
fix 1 upper coord/original com yes :pre
[Description:]
@ -42,6 +47,11 @@ rigid"_fix_rigid.html command), it's periodic image flags are altered,
and its original coordinates may not be what you expect. See the
"fix rigid"_fix_rigid.html command for details.
If the {com} keyword is set to {yes} then the position
of each atom relative to the center-of-mass of the group of
atoms is stored, instead of the absolute position. This option
is used by the "compute msd"_compute_msd.html command.
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the original coordinates of the atoms to "binary
@ -68,7 +78,9 @@ minimization"_minimize.html.
[Related commands:]
"fix msd"_fix_msd.html, "compute
"compute msd"_compute_msd.html, "compute
displace/atom"_compute_displace_atom.html
[Default:] none
[Default:]
The option default is com = no.