From 810d64aba2fb48d382b365d9cd1e2d8c1d9b3d22 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 13 Jan 2009 15:40:11 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2456 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/dump.html | 43 ++++++++++++++++++++++--------------------- doc/dump.txt | 43 ++++++++++++++++++++++--------------------- doc/dump_modify.html | 16 ++++++++++------ doc/dump_modify.txt | 12 ++++++++---- 4 files changed, 62 insertions(+), 52 deletions(-) diff --git a/doc/dump.html b/doc/dump.html index b6791dd3ce..858d5244ba 100644 --- a/doc/dump.html +++ b/doc/dump.html @@ -229,22 +229,30 @@ styles.

This section explains the atom quantities that can be specified as part of the custom style.

-

The id, mol, type, x, y, z, vx, vy, vz, fx, fy, -fz, q keywords are self-explanatory. Id is the atom ID. Mol -is the molecule ID, included in the data file for molecular systems. -The x, y, z keywords write atom coordinates "unscaled", in the +

The id, mol, type, vx, vy, vz, fx, fy, +fz, q keywords are self-explanatory. +

+

Id is the atom ID. Mol is the molecule ID, included in the data +file for molecular systems. Type is the atom type. Vx, vy, +vz, fx, fy, fz, and q are components of atom velocity and +force and atomic charge. +

+

There are several options for outputting atom coordinates. The x, +y, z keywords write atom coordinates "unscaled", in the appropriate distance units (Angstroms, sigma, etc). Use xs, ys, zs if you want the coordinates "scaled" to the box size, -so that each value is 0.0 to 1.0. Use xu, yu, zu if you want -the coordinates "unwrapped" by the image flags for each atom. -Unwrapped means that if the atom has passed thru a periodic boundary -one or more times, the value is printed for what the coordinate would -be if it had not been wrapped back into the periodic box. Note that -using xu, yu, zu means that the coordinate values may be far -outside the box size printed with the snapshot. The image flags can -be printed directly using the ix, iy, iz keywords. The -dump_modify command describes in more detail what -is meant by scaled vs unscaled coordinates and the image flags. +so that each value is 0.0 to 1.0. If the simluation box is triclinic +(tilted), then all atom coords will still be between 0.0 and 1.0. Use +xu, yu, zu if you want the coordinates "unwrapped" by the image +flags for each atom. Unwrapped means that if the atom has passed thru +a periodic boundary one or more times, the value is printed for what +the coordinate would be if it had not been wrapped back into the +periodic box. Note that using xu, yu, zu means that the +coordinate values may be far outside the box size printed with the +snapshot. The image flags can be printed directly using the ix, +iy, iz keywords. The dump_modify command +describes in more detail what is meant by scaled vs unscaled +coordinates and the image flags.

The mux, muy, muz keywords are specific to dipolar systems defined with an atom style of dipole. They give the orientation of @@ -323,13 +331,6 @@ per-atom quantities which could then be output into dump files.

Restrictions:

-

Scaled coordinates cannot be writted to dump files when the simulation -box is triclinic (non-orthogonal). Note that this is the default for -dump style atom; the dump_modify command must be -used to change it. The exception is DCD files which store the tilt -factors for subsequent visualization by programs like -VMD. -

To write gzipped dump files, you must compile LAMMPS with the -DLAMMPS_GZIP option - see the Making LAMMPS section of the documentation. diff --git a/doc/dump.txt b/doc/dump.txt index 96a44766bd..d861e4e5eb 100644 --- a/doc/dump.txt +++ b/doc/dump.txt @@ -219,22 +219,30 @@ styles. This section explains the atom quantities that can be specified as part of the {custom} style. -The {id}, {mol}, {type}, {x}, {y}, {z}, {vx}, {vy}, {vz}, {fx}, {fy}, -{fz}, {q} keywords are self-explanatory. {Id} is the atom ID. {Mol} -is the molecule ID, included in the data file for molecular systems. -The {x}, {y}, {z} keywords write atom coordinates "unscaled", in the +The {id}, {mol}, {type}, {vx}, {vy}, {vz}, {fx}, {fy}, +{fz}, {q} keywords are self-explanatory. + +{Id} is the atom ID. {Mol} is the molecule ID, included in the data +file for molecular systems. {Type} is the atom type. {Vx}, {vy}, +{vz}, {fx}, {fy}, {fz}, and {q} are components of atom velocity and +force and atomic charge. + +There are several options for outputting atom coordinates. The {x}, +{y}, {z} keywords write atom coordinates "unscaled", in the appropriate distance "units"_units.html (Angstroms, sigma, etc). Use {xs}, {ys}, {zs} if you want the coordinates "scaled" to the box size, -so that each value is 0.0 to 1.0. Use {xu}, {yu}, {zu} if you want -the coordinates "unwrapped" by the image flags for each atom. -Unwrapped means that if the atom has passed thru a periodic boundary -one or more times, the value is printed for what the coordinate would -be if it had not been wrapped back into the periodic box. Note that -using {xu}, {yu}, {zu} means that the coordinate values may be far -outside the box size printed with the snapshot. The image flags can -be printed directly using the {ix}, {iy}, {iz} keywords. The -"dump_modify"_dump_modify.html command describes in more detail what -is meant by scaled vs unscaled coordinates and the image flags. +so that each value is 0.0 to 1.0. If the simluation box is triclinic +(tilted), then all atom coords will still be between 0.0 and 1.0. Use +{xu}, {yu}, {zu} if you want the coordinates "unwrapped" by the image +flags for each atom. Unwrapped means that if the atom has passed thru +a periodic boundary one or more times, the value is printed for what +the coordinate would be if it had not been wrapped back into the +periodic box. Note that using {xu}, {yu}, {zu} means that the +coordinate values may be far outside the box size printed with the +snapshot. The image flags can be printed directly using the {ix}, +{iy}, {iz} keywords. The "dump_modify"_dump_modify.html command +describes in more detail what is meant by scaled vs unscaled +coordinates and the image flags. The {mux}, {muy}, {muz} keywords are specific to dipolar systems defined with an atom style of {dipole}. They give the orientation of @@ -313,13 +321,6 @@ per-atom quantities which could then be output into dump files. [Restrictions:] -Scaled coordinates cannot be writted to dump files when the simulation -box is triclinic (non-orthogonal). Note that this is the default for -dump style {atom}; the "dump_modify command"_dump_modify.html must be -used to change it. The exception is DCD files which store the tilt -factors for subsequent visualization by programs like -"VMD"_http://www.ks.uiuc.edu/Research/vmd. - To write gzipped dump files, you must compile LAMMPS with the -DLAMMPS_GZIP option - see the "Making LAMMPS"_Section_start.html#2_2 section of the documentation. diff --git a/doc/dump_modify.html b/doc/dump_modify.html index 6f5fcd7d6f..a442d07627 100644 --- a/doc/dump_modify.html +++ b/doc/dump_modify.html @@ -59,16 +59,20 @@ format string. This option has no effect on the dcd and xtc dump styles since they write binary files.

The scale and image keywords apply only to the dump atom style. -A scale value of yes means atom coords are written in normalized -units from 0.0 to 1.0 in each box dimension. A value of no means -they are written in absolute distance units (e.g. Angstroms or sigma). -If the image value is yes, 3 flags are appended to each atom's +

+

A scale value of yes means atom coords are written in normalized +units from 0.0 to 1.0 in each box dimension. If the simluation box is +triclinic (tilted), then all atom coords will still be between 0.0 and +1.0. A value of no means they are written in absolute distance +units (e.g. Angstroms or sigma). +

+

If the image value is yes, 3 flags are appended to each atom's coords which are the absolute box image of the atom in each dimension. For example, an x image flag of -2 with a normalized coord of 0.5 means the atom is in the center of the box, but has passed thru the box boundary 2 times and is really 2 box lengths to the left of its -current coordinate. Note that for dump style custom these values -can be printed in the dump file by using the appropriate atom +current coordinate. Note that for dump style custom these various +values can be printed in the dump file by using the appropriate atom attributes in the dump command itself.

diff --git a/doc/dump_modify.txt b/doc/dump_modify.txt index 4dcf1ad76f..dc02383c46 100644 --- a/doc/dump_modify.txt +++ b/doc/dump_modify.txt @@ -52,16 +52,20 @@ format string. This option has no effect on the {dcd} and {xtc} dump styles since they write binary files. The {scale} and {image} keywords apply only to the dump {atom} style. + A scale value of {yes} means atom coords are written in normalized -units from 0.0 to 1.0 in each box dimension. A value of {no} means -they are written in absolute distance units (e.g. Angstroms or sigma). +units from 0.0 to 1.0 in each box dimension. If the simluation box is +triclinic (tilted), then all atom coords will still be between 0.0 and +1.0. A value of {no} means they are written in absolute distance +units (e.g. Angstroms or sigma). + If the image value is {yes}, 3 flags are appended to each atom's coords which are the absolute box image of the atom in each dimension. For example, an x image flag of -2 with a normalized coord of 0.5 means the atom is in the center of the box, but has passed thru the box boundary 2 times and is really 2 box lengths to the left of its -current coordinate. Note that for dump style {custom} these values -can be printed in the dump file by using the appropriate atom +current coordinate. Note that for dump style {custom} these various +values can be printed in the dump file by using the appropriate atom attributes in the dump command itself. :link(pizza,http://www.cs.sandia.gov/~sjplimp/pizza.html)