From 5b52b17784d990873c2b4a473e952a753e55fa37 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 4 Dec 2009 00:04:34 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3499 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_howto.html | 18 +++++++++--------- doc/Section_howto.txt | 18 +++++++++--------- doc/compute_displace_atom.html | 23 ++++++++++++----------- doc/compute_displace_atom.txt | 23 ++++++++++++----------- 4 files changed, 42 insertions(+), 40 deletions(-) diff --git a/doc/Section_howto.html b/doc/Section_howto.html index f29e739c90..4cd1fe78ef 100644 --- a/doc/Section_howto.html +++ b/doc/Section_howto.html @@ -986,15 +986,15 @@ be specified (c_ID, f_ID, v_name), where a compute output. Each of these are described in turn.

In LAMMPS, a compute comes in two flavors: ones that -compute global values (e.g. temperature, pressure tensor) and ones -that compute per-atom values. Only global quantities from a compute -can be used for thermodynamic output. The user-defined ID of the -compute is used along with an optional subscript as part of the -thermo_style command. E.g. c_myTemp outputs the -single scalar value generated by the compute; c_myTemp[2] outputs -the 2nd vector value. Note that there is a compute -reduce command which can sum per-atom quantities -into a global scalar or vector. +compute global values (a scalar or a vector, e.g. temperature, +6-element pressure tensor) and ones that compute per-atom values. +Only global quantities from a compute can be used for thermodynamic +output. The user-defined ID of the compute is used along with an +optional subscript as part of the thermo_style +command. E.g. c_myTemp outputs the single scalar value generated by +the compute; c_myTemp[2] outputs the 2nd vector value. Note that +there is a compute reduce command which can sum +per-atom quantities into a global scalar or vector.

Fixes can generate global scalar or vector values which can be output with thermodynamic output, e.g. the energy of an indenter's diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index 7caebe1630..4c57cdddac 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -979,15 +979,15 @@ be specified (c_ID, f_ID, v_name), where a "compute"_compute.html or output. Each of these are described in turn. In LAMMPS, a "compute"_compute.html comes in two flavors: ones that -compute global values (e.g. temperature, pressure tensor) and ones -that compute per-atom values. Only global quantities from a compute -can be used for thermodynamic output. The user-defined ID of the -compute is used along with an optional subscript as part of the -"thermo_style"_thermo_style.html command. E.g. c_myTemp outputs the -single scalar value generated by the compute; c_myTemp\[2\] outputs -the 2nd vector value. Note that there is a "compute -reduce"_compute_reduce.html command which can sum per-atom quantities -into a global scalar or vector. +compute global values (a scalar or a vector, e.g. temperature, +6-element pressure tensor) and ones that compute per-atom values. +Only global quantities from a compute can be used for thermodynamic +output. The user-defined ID of the compute is used along with an +optional subscript as part of the "thermo_style"_thermo_style.html +command. E.g. c_myTemp outputs the single scalar value generated by +the compute; c_myTemp\[2\] outputs the 2nd vector value. Note that +there is a "compute reduce"_compute_reduce.html command which can sum +per-atom quantities into a global scalar or vector. "Fixes"_fix.html can generate global scalar or vector values which can be output with thermodynamic output, e.g. the energy of an indenter's diff --git a/doc/compute_displace_atom.html b/doc/compute_displace_atom.html index 949c0a6ec1..0b76b05331 100644 --- a/doc/compute_displace_atom.html +++ b/doc/compute_displace_atom.html @@ -28,12 +28,13 @@ atom in the group from its original coordinates, including all effects 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. +

A vector of four quantites per atom is calculated by this compute. +The first 3 elements of the vector 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 displacement of an atom is from its original position at the time +the compute command was issued. To store the original coordinates, the compute creates its own fix of style "coord/original", as if this command had been issued:

@@ -58,11 +59,11 @@ image command.

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. +and the computed displacement will not reflect its true displacement. +See the fix rigid command for details. Thus, to +compute the displacement 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, @@ -74,9 +75,9 @@ file.

Output info:

This compute calculates a vector of length 4 for each atom, which can -be accessed by indices 1-4 by any command that uses per-atom computes -as input. See this section for an overview -of LAMMPS output options. +be accessed by indices 1-4 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_displace_atom.txt b/doc/compute_displace_atom.txt index 85e2c45c50..acf9dcd73b 100644 --- a/doc/compute_displace_atom.txt +++ b/doc/compute_displace_atom.txt @@ -25,12 +25,13 @@ 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. -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. +A vector of four quantites per atom is calculated by this compute. +The first 3 elements of the vector 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 displacement of an atom is from its original position at the time +the compute command was issued. To store the original coordinates, the compute creates its own fix of style "coord/original", as if this command had been issued: @@ -55,11 +56,11 @@ image"_set.html command. 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. +and the computed displacement will not reflect its true displacement. +See the "fix rigid"_fix_rigid.html command for details. Thus, to +compute the displacement 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, @@ -71,9 +72,9 @@ file. [Output info:] This compute calculates a vector of length 4 for each atom, which can -be accessed by indices 1-4 by any command that uses per-atom computes -as input. See "this section"_Section_howto.html#4_15 for an overview -of LAMMPS output options. +be accessed by indices 1-4 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