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27
doc/compute_property_atom.html
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@ -25,7 +25,7 @@
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz, x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz, vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, mu, q, mux, muy, muz, mu,
radius, omegax, omegay, omegaz, radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz, angmomx, angmomy, angmomz,
shapex,shapey, shapez, shapex,shapey, shapez,
quatw, quati, quatj, quatk, tqx, tqy, tqz, quatw, quati, quatj, quatk, tqx, tqy, tqz,
@ -44,16 +44,16 @@
q = atom charge q = atom charge
mux,muy,muz = orientation of dipole moment of atom mux,muy,muz = orientation of dipole moment of atom
mu = magnitude of dipole moment of atom mu = magnitude of dipole moment of atom
radius = radius of spherical particle radius,diameter = radius,diameter of spherical particle
omegax,omegay,omegaz = angular velocity of extended particle omegax,omegay,omegaz = angular velocity of extended particle
angmomx,angmomy,angmomz = angular momentum of extended particle angmomx,angmomy,angmomz = angular momentum of extended particle
shapex,shapey,shapez = 3 diameters of ellipsoidal particle
quatw,quati,quatj,quatk = quaternion components for aspherical particles
tqx,tqy,tqz = torque on extended particles tqx,tqy,tqz = torque on extended particles
spin = electron spin spin = electron spin
eradius = electron radius eradius = electron radius
ervel = electron radial velocity ervel = electron radial velocity
erforce = electron radial force erforce = electron radial force
shapex,shapey,shapez = 3 diameters of aspherical particle
quatw,quati,quatj,quatk = quaternion components for aspherical particles
</PRE> </PRE>
</UL> </UL>
@ -74,14 +74,25 @@ inputs. See for example, the <A HREF = "compute_reduce.html">compute reduce</A>
variable</A> commands. variable</A> commands.
</P> </P>
<P>The list of possible attributes is the same as that used by the <A HREF = "dump.html">dump <P>The list of possible attributes is the same as that used by the <A HREF = "dump.html">dump
custom</A> command, which describes their meaning. Basically, custom</A> command, which describes their meaning, with some
this list gives your input script access to any per-atom quantity additional quantities that are only defined for certain <A HREF = "atom_style.html">atom
stored by LAMMPS. styles</A>. Basically, this list gives your input script
access to any per-atom quantity stored by LAMMPS.
</P> </P>
<P>The values are stored in a per-atom vector or array as <P>The values are stored in a per-atom vector or array as
discussed below. Zeroes are stored for atoms not in the specified discussed below. Zeroes are stored for atoms not in the specified
group. group.
</P> </P>
<P>The additional quantities only accessible via this command (and not
directly via the <A HREF = "dump.html">dump custom</A> command are as follows.
</P>
<P><I>Shapex</I>, <I>shapey</I>, and <I>shapez</I> are defined for ellipsoidal particles
and define the 3d shape of each particle. <I>Quatw</I>, <I>quati</I>, <I>quatj</I>,
and <I>quatk</I> are also defined for ellipsoidal particles and store the
4-vector quaternion representing the orientation of each particle.
See the <A HREF = "set.html">set</A> command for an explanation of the quaternion
vector.
</P>
<P><B>Output info:</B> <P><B>Output info:</B>
</P> </P>
<P>This compute calculates a per-atom vector or per-atom array depending <P>This compute calculates a per-atom vector or per-atom array depending

27
doc/compute_property_atom.txt
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@ -19,7 +19,7 @@ input = one or more atom attributes :l
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz, x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz, vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, mu, q, mux, muy, muz, mu,
radius, omegax, omegay, omegaz, radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz, angmomx, angmomy, angmomz,
shapex,shapey, shapez, shapex,shapey, shapez,
quatw, quati, quatj, quatk, tqx, tqy, tqz, quatw, quati, quatj, quatk, tqx, tqy, tqz,
@ -38,16 +38,16 @@ input = one or more atom attributes :l
q = atom charge q = atom charge
mux,muy,muz = orientation of dipole moment of atom mux,muy,muz = orientation of dipole moment of atom
mu = magnitude of dipole moment of atom mu = magnitude of dipole moment of atom
radius = radius of spherical particle radius,diameter = radius,diameter of spherical particle
omegax,omegay,omegaz = angular velocity of extended particle omegax,omegay,omegaz = angular velocity of extended particle
angmomx,angmomy,angmomz = angular momentum of extended particle angmomx,angmomy,angmomz = angular momentum of extended particle
shapex,shapey,shapez = 3 diameters of ellipsoidal particle
quatw,quati,quatj,quatk = quaternion components for aspherical particles
tqx,tqy,tqz = torque on extended particles tqx,tqy,tqz = torque on extended particles
spin = electron spin spin = electron spin
eradius = electron radius eradius = electron radius
ervel = electron radial velocity ervel = electron radial velocity
erforce = electron radial force :pre erforce = electron radial force
shapex,shapey,shapez = 3 diameters of aspherical particle
quatw,quati,quatj,quatk = quaternion components for aspherical particles :pre
:ule :ule
[Examples:] [Examples:]
@ -67,14 +67,25 @@ inputs. See for example, the "compute reduce"_compute_reduce.html,
variable"_variable.html commands. variable"_variable.html commands.
The list of possible attributes is the same as that used by the "dump The list of possible attributes is the same as that used by the "dump
custom"_dump.html command, which describes their meaning. Basically, custom"_dump.html command, which describes their meaning, with some
this list gives your input script access to any per-atom quantity additional quantities that are only defined for certain "atom
stored by LAMMPS. styles"_atom_style.html. Basically, this list gives your input script
access to any per-atom quantity stored by LAMMPS.
The values are stored in a per-atom vector or array as The values are stored in a per-atom vector or array as
discussed below. Zeroes are stored for atoms not in the specified discussed below. Zeroes are stored for atoms not in the specified
group. group.
The additional quantities only accessible via this command (and not
directly via the "dump custom"_dump.html command are as follows.
{Shapex}, {shapey}, and {shapez} are defined for ellipsoidal particles
and define the 3d shape of each particle. {Quatw}, {quati}, {quatj},
and {quatk} are also defined for ellipsoidal particles and store the
4-vector quaternion representing the orientation of each particle.
See the "set"_set.html command for an explanation of the quaternion
vector.
[Output info:] [Output info:]
This compute calculates a per-atom vector or per-atom array depending This compute calculates a per-atom vector or per-atom array depending

25
doc/dump.html
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@ -46,12 +46,12 @@
f_ID[N] = Nth column of local array calculated by a fix with ID f_ID[N] = Nth column of local array calculated by a fix with ID
</PRE> </PRE>
<PRE> <I>custom</I> args = list of atom attributes <PRE> <I>custom</I> args = list of atom attributes
possible attributes = id, mol, type, mass, possible attributes = id, mol, type, element, mass,
x, y, z, xs, ys, zs, xu, yu, zu, x, y, z, xs, ys, zs, xu, yu, zu,
xsu, ysu, zsu, ix, iy, iz, xsu, ysu, zsu, ix, iy, iz,
vx, vy, vz, fx, fy, fz, vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, mu, q, mux, muy, muz, mu,
radius, omegax, omegay, omegaz, radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz, tqx, tqy, tqz, angmomx, angmomy, angmomz, tqx, tqy, tqz,
spin, eradius, ervel, erforce, spin, eradius, ervel, erforce,
c_ID, c_ID[N], f_ID, f_ID[N], v_name c_ID, c_ID[N], f_ID, f_ID[N], v_name
@ -59,6 +59,7 @@
<PRE> id = atom ID <PRE> id = atom ID
mol = molecule ID mol = molecule ID
type = atom type type = atom type
element = name of atom element, as defined by <A HREF = "dump_modify.html">dump_modify</A> command
mass = atom mass mass = atom mass
x,y,z = unscaled atom coordinates x,y,z = unscaled atom coordinates
xs,ys,zs = scaled atom coordinates xs,ys,zs = scaled atom coordinates
@ -70,7 +71,7 @@
q = atom charge q = atom charge
mux,muy,muz = orientation of dipole moment of atom mux,muy,muz = orientation of dipole moment of atom
mu = magnitude of dipole moment of atom mu = magnitude of dipole moment of atom
radius = radius of spherical particle radius,diameter = radius,diameter of spherical particle
omegax,omegay,omegaz = angular velocity of extended particle omegax,omegay,omegaz = angular velocity of extended particle
angmomx,angmomy,angmomz = angular momentum of extended particle angmomx,angmomy,angmomz = angular momentum of extended particle
tqx,tqy,tqz = torque on extended particles tqx,tqy,tqz = torque on extended particles
@ -390,13 +391,17 @@ array calculated by the fix.
<P>This section explains the atom attributes that can be specified as <P>This section explains the atom attributes that can be specified as
part of the <I>custom</I> and <I>cfg</I> styles. part of the <I>custom</I> and <I>cfg</I> styles.
</P> </P>
<P>The <I>id</I>, <I>mol</I>, <I>type</I>, <I>mass</I>, <I>vx</I>, <I>vy</I>, <I>vz</I>, <I>fx</I>, <I>fy</I>, <P>The <I>id</I>, <I>mol</I>, <I>type</I>, <I>element</I>, <I>mass</I>, <I>vx</I>, <I>vy</I>, <I>vz</I>, <I>fx</I>, <I>fy</I>,
<I>fz</I>, <I>q</I> attributes are self-explanatory. <I>fz</I>, <I>q</I> attributes are self-explanatory.
</P> </P>
<P><I>Id</I> is the atom ID. <I>Mol</I> is the molecule ID, included in the data <P><I>Id</I> is the atom ID. <I>Mol</I> is the molecule ID, included in the data
file for molecular systems. <I>Type</I> is the atom type. <I>Mass</I> is the file for molecular systems. <I>Type</I> is the atom type. <I>Element</I> is
atom mass. <I>Vx</I>, <I>vy</I>, <I>vz</I>, <I>fx</I>, <I>fy</I>, <I>fz</I>, and <I>q</I> are components typically the chemical name of an element, which you must assign to
of atom velocity and force and atomic charge. each type via the <A HREF = "dump_modify.html">dump_modify element</A> command.
More generally, it can be any string you wish to associated with an
atom type. <I>Mass</I> is the atom mass. <I>Vx</I>, <I>vy</I>, <I>vz</I>, <I>fx</I>, <I>fy</I>,
<I>fz</I>, and <I>q</I> are components of atom velocity and force and atomic
charge.
</P> </P>
<P>There are several options for outputting atom coordinates. The <I>x</I>, <P>There are several options for outputting atom coordinates. The <I>x</I>,
<I>y</I>, <I>z</I> attributes write atom coordinates "unscaled", in the <I>y</I>, <I>z</I> attributes write atom coordinates "unscaled", in the
@ -425,9 +430,9 @@ defined with an atom style of <I>dipole</I>. They give the orientation of
the atom's point dipole moment. The <I>mu</I> attribute gives the the atom's point dipole moment. The <I>mu</I> attribute gives the
magnitude of the atom's dipole moment. magnitude of the atom's dipole moment.
</P> </P>
<P>The <I>radius</I> attribute is specific to extended spherical particles <P>The <I>radius</I> and <I>diameter</I> attributes are specific to extended
that have a finite size, such as those defined with an atom style of spherical particles that have a finite size, such as those defined
<I>sphere</I>. with an atom style of <I>sphere</I>.
</P> </P>
<P>The <I>omegax</I>, <I>omegay</I>, and <I>omegaz</I> attributes are specific to <P>The <I>omegax</I>, <I>omegay</I>, and <I>omegaz</I> attributes are specific to
extended spherical or aspherical particles that have an angular extended spherical or aspherical particles that have an angular

25
doc/dump.txt
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@ -36,12 +36,12 @@ args = list of arguments for a particular style :l
f_ID\[N\] = Nth column of local array calculated by a fix with ID :pre f_ID\[N\] = Nth column of local array calculated by a fix with ID :pre
{custom} args = list of atom attributes {custom} args = list of atom attributes
possible attributes = id, mol, type, mass, possible attributes = id, mol, type, element, mass,
x, y, z, xs, ys, zs, xu, yu, zu, x, y, z, xs, ys, zs, xu, yu, zu,
xsu, ysu, zsu, ix, iy, iz, xsu, ysu, zsu, ix, iy, iz,
vx, vy, vz, fx, fy, fz, vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, mu, q, mux, muy, muz, mu,
radius, omegax, omegay, omegaz, radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz, tqx, tqy, tqz, angmomx, angmomy, angmomz, tqx, tqy, tqz,
spin, eradius, ervel, erforce, spin, eradius, ervel, erforce,
c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
@ -49,6 +49,7 @@ args = list of arguments for a particular style :l
id = atom ID id = atom ID
mol = molecule ID mol = molecule ID
type = atom type type = atom type
element = name of atom element, as defined by "dump_modify"_dump_modify.html command
mass = atom mass mass = atom mass
x,y,z = unscaled atom coordinates x,y,z = unscaled atom coordinates
xs,ys,zs = scaled atom coordinates xs,ys,zs = scaled atom coordinates
@ -60,7 +61,7 @@ args = list of arguments for a particular style :l
q = atom charge q = atom charge
mux,muy,muz = orientation of dipole moment of atom mux,muy,muz = orientation of dipole moment of atom
mu = magnitude of dipole moment of atom mu = magnitude of dipole moment of atom
radius = radius of spherical particle radius,diameter = radius,diameter of spherical particle
omegax,omegay,omegaz = angular velocity of extended particle omegax,omegay,omegaz = angular velocity of extended particle
angmomx,angmomy,angmomz = angular momentum of extended particle angmomx,angmomy,angmomz = angular momentum of extended particle
tqx,tqy,tqz = torque on extended particles tqx,tqy,tqz = torque on extended particles
@ -379,13 +380,17 @@ array calculated by the fix.
This section explains the atom attributes that can be specified as This section explains the atom attributes that can be specified as
part of the {custom} and {cfg} styles. part of the {custom} and {cfg} styles.
The {id}, {mol}, {type}, {mass}, {vx}, {vy}, {vz}, {fx}, {fy}, The {id}, {mol}, {type}, {element}, {mass}, {vx}, {vy}, {vz}, {fx}, {fy},
{fz}, {q} attributes are self-explanatory. {fz}, {q} attributes are self-explanatory.
{Id} is the atom ID. {Mol} is the molecule ID, included in the data {Id} is the atom ID. {Mol} is the molecule ID, included in the data
file for molecular systems. {Type} is the atom type. {Mass} is the file for molecular systems. {Type} is the atom type. {Element} is
atom mass. {Vx}, {vy}, {vz}, {fx}, {fy}, {fz}, and {q} are components typically the chemical name of an element, which you must assign to
of atom velocity and force and atomic charge. each type via the "dump_modify element"_dump_modify.html command.
More generally, it can be any string you wish to associated with an
atom type. {Mass} is the atom mass. {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}, There are several options for outputting atom coordinates. The {x},
{y}, {z} attributes write atom coordinates "unscaled", in the {y}, {z} attributes write atom coordinates "unscaled", in the
@ -414,9 +419,9 @@ defined with an atom style of {dipole}. They give the orientation of
the atom's point dipole moment. The {mu} attribute gives the the atom's point dipole moment. The {mu} attribute gives the
magnitude of the atom's dipole moment. magnitude of the atom's dipole moment.
The {radius} attribute is specific to extended spherical particles The {radius} and {diameter} attributes are specific to extended
that have a finite size, such as those defined with an atom style of spherical particles that have a finite size, such as those defined
{sphere}. with an atom style of {sphere}.
The {omegax}, {omegay}, and {omegaz} attributes are specific to The {omegax}, {omegay}, and {omegaz} attributes are specific to
extended spherical or aspherical particles that have an angular extended spherical or aspherical particles that have an angular

327
doc/dump_image.html
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@ -11,12 +11,9 @@
<H3>dump image command <H3>dump image command
</H3> </H3>
<P>NOTE: The dump image command has not yet been released as part of
LAMMPS.
</P>
<P><B>Syntax:</B> <P><B>Syntax:</B>
</P> </P>
<PRE>dump ID group-ID image N file keyword value ... <PRE>dump ID group-ID image N file x y z type type keyword value ...
</PRE> </PRE>
<UL><LI>ID = user-assigned name for the dump <UL><LI>ID = user-assigned name for the dump
@ -30,43 +27,47 @@ LAMMPS.
<LI>zero or more keyword/value pairs may be appended <LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>atom</I> or <I>bond</I> or <I>size</I> or <I>view</I> or <I>center</I> or <I>up</I> or <I>zoom</I> or <I>persp</I> or <I>box</I> or <I>dynamic</I> or <I>box</I> or <I>axes</I> or <I>shiny</I> or <I>ssao</I> <LI>keyword = <I>atom</I> or <I>bond</I> or <I>size</I> or <I>view</I> or <I>center</I> or <I>up</I> or <I>zoom</I> or <I>persp</I> or <I>box</I> or <I>axes</I> or <I>shiny</I> or <I>ssao</I>
<PRE> <I>atom</I> values = color diam <PRE> <I>atom</I> values = color diam = color and size of atoms
color = <I>none</I> or <I>type</I> or <I>element</I> or atom-attribute color = <I>none</I> or <I>type</I> or <I>element</I> or atom-attribute
diam = D or <I>type</I> or <I>element</I> or <I>radius</I> or <I>shape</I> or atom-attribute diam = number or <I>type</I> or <I>element</I> or atom-attribute
D = numeric value for atom diameter (distance units) number = numeric value for atom diameter (distance units)
<I>bond</I> values = color diam <I>bond</I> values = color diam = color and width of bonds
color = <I>none</I> or <I>atom</I> or <I>type</I> color = <I>none</I> or <I>atom</I> or <I>type</I>
diam = D or <I>type</I> diam = number or <I>type</I>
D = numeric value for bond diameter (distance units) numer = numeric value for bond diameter (distance units)
<I>size</I> values = width height <I>size</I> values = width height = size of images
width = width of image in # of pixels width = width of image in # of pixels
height = height of image in # of pixels height = height of image in # of pixels
<I>view</I> values = theta phi <I>view</I> values = theta phi = view of simulation box
theta = view angle from +z axis (degrees) theta = view angle from +z axis (degrees)
phi = azimuthal view angle (degrees) phi = azimuthal view angle (degrees)
theta or phi can be a variable (see below) theta or phi can be a variable (see below)
<I>center</I> values = flag Cx Cy Cz = center point of image (distance units) <I>center</I> values = flag Cx Cy Cz = center point of image
flag = "s" for static, "d" for dynamic flag = "s" for static, "d" for dynamic
Cx,Cy,Cz can be variables (see below) Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box)
<I>up</I> values = Ux Uy Uz = components of up vector Cx,Cy,Cz can be variables (see below)
Ux,Uy,Uz can be variables (see below) <I>up</I> values = Ux Uy Uz = direction that is "up" in image
<I>zoom</I> value = factor = scale image size by this factor Ux,Uy,Uz = components of up vector
factor can be a variable (see below) Ux,Uy,Uz can be variables (see below)
<I>persp</I> value = factor = perspective setting <I>zoom</I> value = factor = size that simulation box appears in image
factor can be a variable (see below) factor = scale image size by factor > 1 to enlarge, factor < 1 to shrink
<I>box</I> values = yes/no diam factor can be a variable (see below)
yes/no = do or do not draw simulation box lines <I>persp</I> value = factor = amount of "perspective" in image
diam = diameter of box lines as fraction of shortest box length factor = amount of perspective (0 = none, < 1 = some, > 1 = highly skewed)
<I>axes</I> values = yes/no length diam factor can be a variable (see below)
yes/no = do or do not draw xyz axes lines next to simulation box <I>box</I> values = yes/no diam = draw outline of simulation box
length = length of axes lines as fraction of respective box lengths yes/no = do or do not draw simulation box lines
diam = diameter of axes lines as fraction of shortest box length diam = diameter of box lines as fraction of shortest box length
<I>shiny</I> value = factor <I>axes</I> values = yes/no length diam = draw xyz axes
factor = shinyness of spheres and cylinders from 0.0 to 1.0 yes/no = do or do not draw xyz axes lines next to simulation box
<I>ssao</I> value = yes/no length = length of axes lines as fraction of respective box lengths
yes/no = turn on/off SSAO depth shading diam = diameter of axes lines as fraction of shortest box length
<I>shiny</I> value = factor = shinyness of spheres and cylinders
factor = shinyness of spheres and cylinders from 0.0 to 1.0
<I>ssao</I> value = yes/no = SSAO depth shading
yes/no = turn depth shading on/off
</PRE> </PRE>
</UL> </UL>
@ -79,8 +80,9 @@ LAMMPS.
<P>Dump an image (picture) of the atom configuration every N timesteps as <P>Dump an image (picture) of the atom configuration every N timesteps as
either a JPG or PPM file. A series of such images can easily be either a JPG or PPM file. A series of such images can easily be
converted into an animated movie of your simulation; see further converted into an animated movie of your simulation; see further
details below. Other dump styles store snapshots of atom quantities details below. Other dump styles store snapshots of numerical data
in various formats, as discussed on the <A HREF = "dump.html">dump</A> doc page. asociated with atoms in various formats, as discussed on the
<A HREF = "dump.html">dump</A> doc page.
</P> </P>
<P>Only atoms in the specified group are rendered in the image. The <P>Only atoms in the specified group are rendered in the image. The
<A HREF = "dump_modify.html">dump_modify region and thresh</A> commands can also <A HREF = "dump_modify.html">dump_modify region and thresh</A> commands can also
@ -88,13 +90,14 @@ alter what atoms are included in the image.
</P> </P>
<P>The filename suffix determines whether a JPG or PPM file is created. <P>The filename suffix determines whether a JPG or PPM file is created.
If the suffix is ".jpg" or ".jpeg", then a JPG file is created, else a If the suffix is ".jpg" or ".jpeg", then a JPG file is created, else a
PPM file is created. To write out JPG files, you must build LAMMPS PPM file is created, which is a text-based format. To write out JPG
with a JPEG library. See <A HREF = "Section_start.html#2_2_4">this section</A> of files, you must build LAMMPS with a JPEG library. See <A HREF = "Section_start.html#2_2_4">this
the manual for instructions on how to do this. section</A> of the manual for instructions on
how to do this.
</P> </P>
<P>IMPORTANT NOTE: Because periodic boundary conditions are enforced only <P>IMPORTANT NOTE: Because periodic boundary conditions are enforced only
on timesteps when neighbor lists are rebuilt, the coordinates of an on timesteps when neighbor lists are rebuilt, the coordinates of an
atom image may be slightly outside the simulation box. atom in the image may be slightly outside the simulation box.
</P> </P>
<HR> <HR>
@ -106,18 +109,16 @@ if the current timestep is not a multiple of N. This behavior can be
changed via the <A HREF = "dump_modify.html">dump_modify first</A> command, which changed via the <A HREF = "dump_modify.html">dump_modify first</A> command, which
can be useful if the dump command is invoked after a minimization can be useful if the dump command is invoked after a minimization
ended on an arbitrary timestep. N can be changed between runs by ended on an arbitrary timestep. N can be changed between runs by
using the <A HREF = "dump_modify.html">dump_modify every</A> command (not allowed using the <A HREF = "dump_modify.html">dump_modify every</A> command.
for <I>dcd</I> style).
</P> </P>
<P>Dump image filenames must contain a wildcard character "*". If a "*" <P>Dump image filenames must contain a wildcard character "*", so that
character appears in the filename, then one file per snapshot is one image file per snapshot is written. The "*" character is replaced
written and the "*" character is replaced with the timestep value. with the timestep value. For example, tmp.dump.*.jpg becomes
For example, tmp.dump.*.jpg becomes tmp.dump.0.jpg, tmp.dump.0.jpg, tmp.dump.10000.jpg, tmp.dump.20000.jpg, etc. Note
tmp.dump.10000.jpg, tmp.dump.20000.jpg, etc. Note that the that the <A HREF = "dump_modify.html">dump_modify pad</A> command can be used to
<A HREF = "dump_modify.html">dump_modify pad</A> command can be used to insure all insure all timestep numbers are the same length (e.g. 00010), which
timestep numbers are the same length (e.g. 00010), which can make it can make it easier to convert a series of images into a movie in the
easier to convert a series of images into a movie in the correct correct ordering.
ordering.
</P> </P>
<HR> <HR>
@ -130,14 +131,14 @@ assigning colors to atoms, bonds, and other image features.
<HR> <HR>
<P>The <I>atom</I> keyword determines the color and size of atoms rendered in <P>The <I>atom</I> keyword determines the color and size of atoms rendered in
the image. If <I>none</I> is specified for the color value (with any diam the image. If <I>none</I> is specified for the <I>color</I> value (with any
value), then no atoms are drawn. <I>diam</I> value), then no atoms are drawn.
</P> </P>
<P>The color value can be <I>type</I> or <I>element</I> or an atom-attribute. <P>The <I>color</I> value can be <I>type</I> or <I>element</I> or an atom-attribute.
</P> </P>
<P>If <I>type</I> is specified for the color <P>If <I>type</I> is specified for the <I>color</I> value, then the color of each
value, then the color of each atom is determined by its atom type. atom is determined by its atom type. By default the mapping of types
By default the mapping of types to colors is as follows: to colors is as follows:
</P> </P>
<UL><LI>type 1 = red <UL><LI>type 1 = red
<LI>type 2 = green <LI>type 2 = green
@ -149,21 +150,22 @@ By default the mapping of types to colors is as follows:
<P>and repeats itself for types > 6. This mapping can be changed by the <P>and repeats itself for types > 6. This mapping can be changed by the
<A HREF = "dump_modify.html">dump_modify acolor</A> command. <A HREF = "dump_modify.html">dump_modify acolor</A> command.
</P> </P>
<P>If <I>element</I> is specified for the color value, then the color of each <P>If <I>element</I> is specified for the <I>color</I> value, then the color of
atom is determined by which element it is, which in turn is specified each atom is determined by which element it is, which in turn is
by the element-to-type mapping specified by the "dump_modify element" specified by the element-to-type mapping specified by the "dump_modify
command. By default every atom type is C (carbon). Every element has element" command. By default every atom type is C (carbon). Every
a color associated with it, which is the same as used by the element has a color associated with it, which is the same as the
<A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualization package. colors used by the <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualization package.
</P> </P>
<P>An atom-attribute can also be used for the color value. Any attribute <P>An atom-attribute can also be used for the <I>color</I> value. Any
listed on the <A HREF = "dump.html">dump custom</A> doc page can be used, e.g. vx, attribute listed on the <A HREF = "dump.html">dump custom</A> doc page can be used,
fy, q, spin, etc. This includes per-atom quantities calculated by a e.g. vx, fy, q, spin, etc. This includes per-atom quantities
<A HREF = "compute.html">compute</A>, <A HREF = "fix.html">fix</A>, or <A HREF = "variable.html">variable</A>. calculated by a <A HREF = "compute.html">compute</A>, <A HREF = "fix.html">fix</A>, or
For example, if "vx" is used as the per-atom attribute, then the color <A HREF = "variable.html">variable</A>. For example, if "vx" is used as the
of the atom will depend on the x-component of its velocity. per-atom attribute, then the color of the atom will depend on the
x-component of its velocity.
</P> </P>
<P>The association of a per-atom value with a specific color is <P>The association of a per-atom value with a specific color is
determined by a "color map", which can be specified via the determined by a "color map", which can be specified via the
@ -174,52 +176,49 @@ color map is defined, that mapping can take place via interpolation so
that a value of -3.2 is halfway between "red" and "blue", or that a value of -3.2 is halfway between "red" and "blue", or
discretely so that the value of -3.2 is "orange". discretely so that the value of -3.2 is "orange".
</P> </P>
<P>The diam value can be a numeric value <I>D</I> or <I>type</I> or <I>element</I> or <P>The <I>diam</I> value can be a numeric value or <I>type</I> or <I>element</I> or an
<I>radius</I> or <I>shape</I> or an atom-attribute. atom-attribute.
</P> </P>
<P>If a numeric value <I>D</I> is specified, then all atoms will be drawn with <P>If a numeric value is specified, then all atoms will be drawn with
that diameter, e.g. 1.5, which is in distance units in whatever that diameter, e.g. 1.5, which is in distance units in whatever
<A HREF = "units.html">units</A> you are using, e.g. Angstroms. <A HREF = "units.html">units</A> the input scripts uses, e.g. Angstroms.
</P> </P>
<P>If <I>type</I> is specified for the diam value then the color of each atom <P>If <I>type</I> is specified for the diam value then the diamter of each
is determined by its atom type. By default all types have diameter atom is determined by its atom type. By default all types have
1.0. This mapping can be changed by the <A HREF = "dump_modify.html">dump_modify diameter 1.0. This mapping can be changed by the <A HREF = "dump_modify.html">dump_modify
adiam</A> command. adiam</A> command.
</P> </P>
<P>If <I>element</I> is specified for the diam value, then the diamater of <P>If <I>element</I> is specified for the <I>diam</I> value, then the diamater of
each atom is determined by which element it is, which in turn is each atom is determined by which element it is, which in turn is
specified by the element-to-type mapping specified by the "dump_modify specified by the element-to-type mapping specified by the "dump_modify
element" command. By default every atom type is C (carbon). Every element" command. By default every atom type is C (carbon). Every
element has a diamtere associated with it, which is the same as used element has a diameter associated with it, which is the same as the
by the <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualization package. diameters used by the <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualization package.
</P> </P>
<P>If <I>radius</I> or <I>shape</I> is specified for the diam value then those the <P>An atom-attribute can also be used for the <I>diam</I> value. Any
atom style you are using must define those attributes. The radius or attribute listed on the <A HREF = "dump.html">dump custom</A> doc page can be used,
shape of the individual atom is then used to draw it. Currently, only e.g. vx, fy, q, spin, radius, etc. This includes per-atom quantities
spherical shapes are allowed. Support for ellipsoids will be added calculated by a <A HREF = "compute.html">compute</A>, <A HREF = "fix.html">fix</A>, or
later. <A HREF = "variable.html">variable</A>. For example, if "vx" is used as the
</P> per-atom attribute, then the diameter of the atom will depend on the
<P>An atom-attribute can also be used for the diam value. Any attribute x-component of its velocity, which must be >= 0.0, else the atom will
listed on the <A HREF = "dump.html">dump custom</A> doc page can be used, e.g. vx, not be drawn. Note that finite-size spherical particles, as defined
fy, q, spin, etc. This includes per-atom quantities calculated by a by <A HREF = "atom_style.html">atom_style sphere</A> define a per-particle radius,
<A HREF = "compute.html">compute</A>, <A HREF = "fix.html">fix</A>, or <A HREF = "variable.html">variable</A>. which can be used as an atom-attribute.
For example, if "vx" is used as the per-atom attribute, then the
diameter of the atom will depend on the x-component of its velocity,
which will assumed to be >= 0.0, else the atom will not be drawn.
</P> </P>
<HR> <HR>
<P>The <I>bond</I> keyword determines the color and thickness or diameter of <P>The <I>bond</I> keyword determines the color and thickness or diameter of
bonds rendered in the image. If <I>none</I> is specified for the color bonds rendered in the image. If <I>none</I> is specified for the <I>color</I>
value (with any diam value), then no bonds are drawn. value (with any diam value), then no bonds are drawn.
</P> </P>
<P>If <I>atom</I> is specified for the color value, then the each bond is <P>If <I>atom</I> is specified for the <I>color</I> value, then each bond is drawn
drawn in 2 halves, with the color of each half being the color of the in 2 halves, with the color of each half being the color of the atom
atom at that end of the bond. at that end of the bond.
</P> </P>
<P>If <I>type</I> is specified for the color value, then the color of each <P>If <I>type</I> is specified for the <I>color</I> value, then the color of each
bond is determined by its bond type. By default the mapping of types bond is determined by its bond type. By default the mapping of bond
to colors is as follows: types to colors is as follows:
</P> </P>
<UL><LI>type 1 = red <UL><LI>type 1 = red
<LI>type 2 = green <LI>type 2 = green
@ -228,57 +227,58 @@ to colors is as follows:
<LI>type 5 = aqua <LI>type 5 = aqua
<LI>type 6 = cyan <LI>type 6 = cyan
</UL> </UL>
<P>and repeats itself for types > 6. This mapping can be changed by the <P>and repeats itself for bond types > 6. This mapping can be changed by
<A HREF = "dump_modify.html">dump_modify bcolor</A> command. the <A HREF = "dump_modify.html">dump_modify bcolor</A> command.
</P> </P>
<P>The diam value can be a numeric value <I>D</I> or <I>type</I>. <P>The <I>diam</I> value can be a numeric value or <I>type</I>.
</P> </P>
<P>If a numeric value <I>D</I> is specified, then all bond will be drawn with <P>If a numeric value is specified, then all bond will be drawn with that
that diameter, e.g. 1.0, which is in distance units in whatever diameter, e.g. 1.0, which is in distance units in whatever
<A HREF = "units.html">units</A> you are using, e.g. Angstroms. <A HREF = "units.html">units</A> the input script uses, e.g. Angstroms.
</P> </P>
<P>If <I>type</I> is specified for the diam value then the color of each bond <P>If <I>type</I> is specified for the <I>diam</I> value then the color of each
is determined by its bond type. By default all types have diameter bond is determined by its bond type. By default all types have
0.5. This mapping can be changed by the <A HREF = "dump_modify.html">dump_modify diameter 0.5. This mapping can be changed by the <A HREF = "dump_modify.html">dump_modify
bdiam</A> command. bdiam</A> command.
</P> </P>
<HR> <HR>
<P>The <I>size</I> keyword determines the width and height of the created <P>The <I>size</I> keyword sets the width and height of the created images,
image files, in numbers of pixels in each direction. i.e. the number of pixels in each direction.
</P> </P>
<HR> <HR>
<P>The <I>view</I>, <I>center</I>, <I>up</I>, <I>zoom</I>, and <I>persp</I> settings determine how <P>The <I>view</I>, <I>center</I>, <I>up</I>, <I>zoom</I>, and <I>persp</I> values determine how
3d simulation space is mapped to the 2d plane of the image. Basically 3d simulation space is mapped to the 2d plane of the image. Basically
they control how the simulation box appears in the image. they control how the simulation box appears in the image.
</P> </P>
<P>All of the <I>view</I>, <I>center</I>, <I>up</I>, <I>zoom</I>, and <I>persp</I> settings can be <P>All of the <I>view</I>, <I>center</I>, <I>up</I>, <I>zoom</I>, and <I>persp</I> values can be
specified as numeric values, whose meaning is explained below. But specified as numeric quantities, whose meaning is explained below.
any of them can also be specified as an equal-style variable, by using Any of them can also be specified as an <A HREF = "variable.html">equal-style
v_name as the setting, where "name" is the variable name. In this variable</A>, by using v_name as the value, where "name" is
case the variable will be evaluated on the timestep each image is the variable name. In this case the variable will be evaluated on the
created to create a new setting. If the equal-style variable is timestep each image is created to create a new value. If the
time-dependent, this is a means of changing the way the simulation box equal-style variable is time-dependent, this is a means of changing
appears from image to image, effectively doing a pan or fly-by view of the way the simulation box appears from image to image, effectively
your simulation. doing a pan or fly-by view of your simulation.
</P> </P>
<P>The <I>view</I> keyword determines the viewpoint from which the simulation <P>The <I>view</I> keyword determines the viewpoint from which the simulation
box is viewed. The <I>theta</I> setting is the vertical angle from the +z box is viewed, looking towards the <I>center</I> point. The <I>theta</I> value
axis, and must be an angle from 0 to 180 degrees. The <I>phi</I> setting is the vertical angle from the +z axis, and must be an angle from 0 to
is an azimuthal angle around the z axis and can be positive or 180 degrees. The <I>phi</I> value is an azimuthal angle around the z axis
negative. and can be positive or negative. A value of 0.0 is a view along the
+x axis, towards the <I>center</I> point.
</P> </P>
<P>The <I>center</I> keyword determines the point in simulation space that <P>The <I>center</I> keyword determines the point in simulation space that
will be at the center of the image. <I>Cx</I>, <I>Cy</I>, and <I>Cz</I> are will be at the center of the image. <I>Cx</I>, <I>Cy</I>, and <I>Cz</I> are
speficied as fractions of the box dimensions, so that (0.5,0.5,0.5) is speficied as fractions of the box dimensions, so that (0.5,0.5,0.5) is
the center of the simulation box. These values do not have to be the center of the simulation box. These values do not have to be
between 0.0 and 1.0, if you want the simulation box to be offset from between 0.0 and 1.0, if you want the simulation box to be offset from
the center of the image. Note, however, that if you choose odd values the center of the image. Note, however, that if you choose strange
for <I>Cx</I>, <I>Cy</I>, or <I>Cz</I> you may get a blank image. Internally, <I>Cx</I>, values for <I>Cx</I>, <I>Cy</I>, or <I>Cz</I> you may get a blank image. Internally,
<I>Cy</I>, and <I>Cz</I> are converted into a point in simulation space. If <I>Cx</I>, <I>Cy</I>, and <I>Cz</I> are converted into a point in simulation space.
<I>flag</I> is set to "s" for static, then this conversion is done once, at If <I>flag</I> is set to "s" for static, then this conversion is done once,
the time the dump command is issued. If <I>flag</I> is set to "d" for at the time the dump command is issued. If <I>flag</I> is set to "d" for
dynamic then the conversion is performed every time a new image is dynamic then the conversion is performed every time a new image is
created. If the box size or shape is changing, this will adjust the created. If the box size or shape is changing, this will adjust the
center point in simulation space. center point in simulation space.
@ -286,33 +286,30 @@ center point in simulation space.
<P>The <I>up</I> keyword determines what direction in simulation space will be <P>The <I>up</I> keyword determines what direction in simulation space will be
"up" in the image. Internally it is stored as a vector that is in the "up" in the image. Internally it is stored as a vector that is in the
plane perpendicular to the view vector implied by the <I>theta</I> and plane perpendicular to the view vector implied by the <I>theta</I> and
<I>pni</I> settings, and which is in the plane defined by the view vector <I>pni</I> values, and which is also in the plane defined by the view
and user-specified up vector. Thus this internal vector is computed vector and user-specified up vector. Thus this internal vector is
from the user-specified <I>up</I> vector as computed from the user-specified <I>up</I> vector as
</P> </P>
<PRE>up_internal = view cross (up cross view) <PRE>up_internal = view cross (up cross view)
</PRE> </PRE>
<P>This means the only restriction on the specified <I>up</I> vector is that <P>This means the only restriction on the specified <I>up</I> vector is that
it cannot be parallel to the <I>view</I> vector, implied by the <I>theta</I> and it cannot be parallel to the <I>view</I> vector, implied by the <I>theta</I> and
<I>phi</I> settings. <I>phi</I> values.
</P> </P>
<P>The <I>zoom</I> keyword scales the size of the simulation box as it appears <P>The <I>zoom</I> keyword scales the size of the simulation box as it appears
in the image. The default <I>factor</I> setting of 1 should display an in the image. The default <I>factor</I> value of 1 should display an
image mostly filled by the atoms in the simulation box. A <I>factor</I> > image mostly filled by the atoms in the simulation box. A <I>factor</I> >
1 will make the simulation box larger; a <I>factor</I> < 1 will make it 1 will make the simulation box larger; a <I>factor</I> < 1 will make it
smaller. smaller. <I>Factor</I> must be a value > 0.0.
</P> </P>
<P>The <I>persp</I> keyword how much depth perspective is present in the <P>The <I>persp</I> keyword determines how much depth perspective is present
image. Depth persepctive makes lines that are parallel in simulation in the image. Depth perspective makes lines that are parallel in
space appear non-parallel in the image. A <I>factor</I> setting of 0.0 simulation space appear non-parallel in the image. A <I>factor</I> value
means that parallel lines will meet at infininty (1.0/factor), which of 0.0 means that parallel lines will meet at infininty (1.0/factor),
is an orthographic rendering with no persepctive. A <I>factor</I> setting which is an orthographic rendering with no persepctive. A <I>factor</I>
between 0.0 and 1.0 will introduce more perspective. A <I>factor</I> > 1 value between 0.0 and 1.0 will introduce more perspective. A <I>factor</I>
will create a highly skewed image with a large amount of perspective. value > 1 will create a highly skewed image with a large amount of
</P> perspective.
<P>The <I>dynamic</I> keyword
determines the color and thickness of bonds
rendered in the image.
</P> </P>
<HR> <HR>
@ -320,31 +317,32 @@ rendered in the image.
rendered as thin cylinders in the image. If <I>no</I> is set, then the box rendered as thin cylinders in the image. If <I>no</I> is set, then the box
boundaries are not drawn and the <I>diam</I> setting is ignored. If <I>yes</I> boundaries are not drawn and the <I>diam</I> setting is ignored. If <I>yes</I>
is set, the 12 edges of the box are drawn, with a diameter that is a is set, the 12 edges of the box are drawn, with a diameter that is a
fraction of the shortest box lenght in x, y, or z. The color of the fraction of the shortest box length in x,y,z (for 3d) or x,y (for 2d).
box boundaires can be set with the <A HREF = "dump_modify.html">dump_modify The color of the box boundaries can be set with the <A HREF = "dump_modify.html">dump_modify
boxcolor</A> command. boxcolor</A> command.
</P> </P>
<P>The <I>axes</I> keyword determines how the coordinate axes are rendered as <P>The <I>axes</I> keyword determines how the coordinate axes are rendered as
thin cylinders in the image. If <I>no</I> is set, then the axes are not thin cylinders in the image. If <I>no</I> is set, then the axes are not
drawn and the <I>length</I> and <I>diam</I> settings are ignored. If <I>yes</I> is drawn and the <I>length</I> and <I>diam</I> settings are ignored. If <I>yes</I> is
set, 3 thin cylinders are drawn to represent the x,y,z axes in colors set, 3 thin cylinders are drawn to represent the x,y,z axes in colors
red,green/blue. The origin of these cylinders will be offset red,green,blue. The origin of these cylinders will be offset from the
from the lower left corner of the box by 10%. The <I>length</I> setting lower left corner of the box by 10%. The <I>length</I> setting determines
determines how long the cylinders will be. The <I>diam</I> setting how long the cylinders will be as a fraction of the respective box
determines their thickness. lengths. The <I>diam</I> setting determines their thickness as a fraction
of the shortest box length in x,y,z (for 3d) or x,y (for 2d).
</P> </P>
<HR> <HR>
<P>The <I>shiny</I> keyword determines how shiny the objects rendered in the <P>The <I>shiny</I> keyword determines how shiny the objects rendered in the
image will appear. This must be a value 0.0 <= S <= 1.0, where S = 1 image will appear. The factor value must be a value 0.0 <= factor <=
is a highly-reflective surface and S = 0 is a rough non-shiny surface. 1.0, where factor = 1 is a highly reflective surface and factor = 0 is
a rough non-shiny surface.
</P> </P>
<P>The <I>ssao</I> keyword turns on/off a screen space ambient occlusion <P>The <I>ssao</I> keyword turns on/off a screen space ambient occlusion
(SSAO) model for depth shading. If <I>yes</I> is set, then atoms further (SSAO) model for depth shading. If <I>yes</I> is set, then atoms further
away from the viewer are darkened, which is perceived as depth by the away from the viewer are darkened, which is perceived as depth. The
viewer. The calculation of this effect can increase the cost of calculation of this effect can increase the cost of computing the
computing the image by roughly 2x. If <I>no</I> is set, the depth shading image by roughly 2x. If <I>no</I> is set, no depth shading is performed.
is not performed.
</P> </P>
<HR> <HR>
@ -424,7 +422,6 @@ documentation for details.
<LI>up = 0 1 0 (for 2d) <LI>up = 0 1 0 (for 2d)
<LI>zoom = 1.0 <LI>zoom = 1.0
<LI>persp = 0.0 <LI>persp = 0.0
<LI>dynamic = no
<LI>box = yes 0.01 <LI>box = yes 0.01
<LI>axes = no 0.0 0.0 <LI>axes = no 0.0 0.0
<LI>shiny = 1.0 <LI>shiny = 1.0

327
doc/dump_image.txt
View File

@ -8,12 +8,9 @@
dump image command :h3 dump image command :h3
NOTE: The dump image command has not yet been released as part of
LAMMPS.
[Syntax:] [Syntax:]
dump ID group-ID image N file keyword value ... :pre dump ID group-ID image N file x y z type type keyword value ... :pre
ID = user-assigned name for the dump :ulb,l ID = user-assigned name for the dump :ulb,l
group-ID = ID of the group of atoms to be imaged :l group-ID = ID of the group of atoms to be imaged :l
@ -21,42 +18,46 @@ image = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or
N = dump every this many timesteps :l N = dump every this many timesteps :l
file = name of file to write image to :l file = name of file to write image to :l
zero or more keyword/value pairs may be appended :l zero or more keyword/value pairs may be appended :l
keyword = {atom} or {bond} or {size} or {view} or {center} or {up} or {zoom} or {persp} or {box} or {dynamic} or {box} or {axes} or {shiny} or {ssao} :l keyword = {atom} or {bond} or {size} or {view} or {center} or {up} or {zoom} or {persp} or {box} or {axes} or {shiny} or {ssao} :l
{atom} values = color diam {atom} values = color diam = color and size of atoms
color = {none} or {type} or {element} or atom-attribute color = {none} or {type} or {element} or atom-attribute
diam = D or {type} or {element} or {radius} or {shape} or atom-attribute diam = number or {type} or {element} or atom-attribute
D = numeric value for atom diameter (distance units) number = numeric value for atom diameter (distance units)
{bond} values = color diam {bond} values = color diam = color and width of bonds
color = {none} or {atom} or {type} color = {none} or {atom} or {type}
diam = D or {type} diam = number or {type}
D = numeric value for bond diameter (distance units) numer = numeric value for bond diameter (distance units)
{size} values = width height {size} values = width height = size of images
width = width of image in # of pixels width = width of image in # of pixels
height = height of image in # of pixels height = height of image in # of pixels
{view} values = theta phi {view} values = theta phi = view of simulation box
theta = view angle from +z axis (degrees) theta = view angle from +z axis (degrees)
phi = azimuthal view angle (degrees) phi = azimuthal view angle (degrees)
theta or phi can be a variable (see below) theta or phi can be a variable (see below)
{center} values = flag Cx Cy Cz = center point of image (distance units) {center} values = flag Cx Cy Cz = center point of image
flag = "s" for static, "d" for dynamic flag = "s" for static, "d" for dynamic
Cx,Cy,Cz can be variables (see below) Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box)
{up} values = Ux Uy Uz = components of up vector Cx,Cy,Cz can be variables (see below)
Ux,Uy,Uz can be variables (see below) {up} values = Ux Uy Uz = direction that is "up" in image
{zoom} value = factor = scale image size by this factor Ux,Uy,Uz = components of up vector
factor can be a variable (see below) Ux,Uy,Uz can be variables (see below)
{persp} value = factor = perspective setting {zoom} value = factor = size that simulation box appears in image
factor can be a variable (see below) factor = scale image size by factor > 1 to enlarge, factor < 1 to shrink
{box} values = yes/no diam factor can be a variable (see below)
yes/no = do or do not draw simulation box lines {persp} value = factor = amount of "perspective" in image
diam = diameter of box lines as fraction of shortest box length factor = amount of perspective (0 = none, < 1 = some, > 1 = highly skewed)
{axes} values = yes/no length diam factor can be a variable (see below)
yes/no = do or do not draw xyz axes lines next to simulation box {box} values = yes/no diam = draw outline of simulation box
length = length of axes lines as fraction of respective box lengths yes/no = do or do not draw simulation box lines
diam = diameter of axes lines as fraction of shortest box length diam = diameter of box lines as fraction of shortest box length
{shiny} value = factor {axes} values = yes/no length diam = draw xyz axes
factor = shinyness of spheres and cylinders from 0.0 to 1.0 yes/no = do or do not draw xyz axes lines next to simulation box
{ssao} value = yes/no length = length of axes lines as fraction of respective box lengths
yes/no = turn on/off SSAO depth shading :pre diam = diameter of axes lines as fraction of shortest box length
{shiny} value = factor = shinyness of spheres and cylinders
factor = shinyness of spheres and cylinders from 0.0 to 1.0
{ssao} value = yes/no = SSAO depth shading
yes/no = turn depth shading on/off :pre
:ule :ule
[Examples:] [Examples:]
@ -68,8 +69,9 @@ dump myDump all image 100 dump.*.jpg :pre
Dump an image (picture) of the atom configuration every N timesteps as Dump an image (picture) of the atom configuration every N timesteps as
either a JPG or PPM file. A series of such images can easily be either a JPG or PPM file. A series of such images can easily be
converted into an animated movie of your simulation; see further converted into an animated movie of your simulation; see further
details below. Other dump styles store snapshots of atom quantities details below. Other dump styles store snapshots of numerical data
in various formats, as discussed on the "dump"_dump.html doc page. asociated with atoms in various formats, as discussed on the
"dump"_dump.html doc page.
Only atoms in the specified group are rendered in the image. The Only atoms in the specified group are rendered in the image. The
"dump_modify region and thresh"_dump_modify.html commands can also "dump_modify region and thresh"_dump_modify.html commands can also
@ -77,13 +79,14 @@ alter what atoms are included in the image.
The filename suffix determines whether a JPG or PPM file is created. The filename suffix determines whether a JPG or PPM file is created.
If the suffix is ".jpg" or ".jpeg", then a JPG file is created, else a If the suffix is ".jpg" or ".jpeg", then a JPG file is created, else a
PPM file is created. To write out JPG files, you must build LAMMPS PPM file is created, which is a text-based format. To write out JPG
with a JPEG library. See "this section"_Section_start.html#2_2_4 of files, you must build LAMMPS with a JPEG library. See "this
the manual for instructions on how to do this. section"_Section_start.html#2_2_4 of the manual for instructions on
how to do this.
IMPORTANT NOTE: Because periodic boundary conditions are enforced only IMPORTANT NOTE: Because periodic boundary conditions are enforced only
on timesteps when neighbor lists are rebuilt, the coordinates of an on timesteps when neighbor lists are rebuilt, the coordinates of an
atom image may be slightly outside the simulation box. atom in the image may be slightly outside the simulation box.
:line :line
@ -95,18 +98,16 @@ if the current timestep is not a multiple of N. This behavior can be
changed via the "dump_modify first"_dump_modify.html command, which changed via the "dump_modify first"_dump_modify.html command, which
can be useful if the dump command is invoked after a minimization can be useful if the dump command is invoked after a minimization
ended on an arbitrary timestep. N can be changed between runs by ended on an arbitrary timestep. N can be changed between runs by
using the "dump_modify every"_dump_modify.html command (not allowed using the "dump_modify every"_dump_modify.html command.
for {dcd} style).
Dump image filenames must contain a wildcard character "*". If a "*" Dump image filenames must contain a wildcard character "*", so that
character appears in the filename, then one file per snapshot is one image file per snapshot is written. The "*" character is replaced
written and the "*" character is replaced with the timestep value. with the timestep value. For example, tmp.dump.*.jpg becomes
For example, tmp.dump.*.jpg becomes tmp.dump.0.jpg, tmp.dump.0.jpg, tmp.dump.10000.jpg, tmp.dump.20000.jpg, etc. Note
tmp.dump.10000.jpg, tmp.dump.20000.jpg, etc. Note that the that the "dump_modify pad"_dump_modify.html command can be used to
"dump_modify pad"_dump_modify.html command can be used to insure all insure all timestep numbers are the same length (e.g. 00010), which
timestep numbers are the same length (e.g. 00010), which can make it can make it easier to convert a series of images into a movie in the
easier to convert a series of images into a movie in the correct correct ordering.
ordering.
:line :line
@ -119,14 +120,14 @@ assigning colors to atoms, bonds, and other image features.
:line :line
The {atom} keyword determines the color and size of atoms rendered in The {atom} keyword determines the color and size of atoms rendered in
the image. If {none} is specified for the color value (with any diam the image. If {none} is specified for the {color} value (with any
value), then no atoms are drawn. {diam} value), then no atoms are drawn.
The color value can be {type} or {element} or an atom-attribute. The {color} value can be {type} or {element} or an atom-attribute.
If {type} is specified for the color If {type} is specified for the {color} value, then the color of each
value, then the color of each atom is determined by its atom type. atom is determined by its atom type. By default the mapping of types
By default the mapping of types to colors is as follows: to colors is as follows:
type 1 = red type 1 = red
type 2 = green type 2 = green
@ -138,21 +139,22 @@ type 6 = cyan :ul
and repeats itself for types > 6. This mapping can be changed by the and repeats itself for types > 6. This mapping can be changed by the
"dump_modify acolor"_dump_modify.html command. "dump_modify acolor"_dump_modify.html command.
If {element} is specified for the color value, then the color of each If {element} is specified for the {color} value, then the color of
atom is determined by which element it is, which in turn is specified each atom is determined by which element it is, which in turn is
by the element-to-type mapping specified by the "dump_modify element" specified by the element-to-type mapping specified by the "dump_modify
command. By default every atom type is C (carbon). Every element has element" command. By default every atom type is C (carbon). Every
a color associated with it, which is the same as used by the element has a color associated with it, which is the same as the
"AtomEye"_atomeye visualization package. colors used by the "AtomEye"_atomeye visualization package.
:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A) :link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)
An atom-attribute can also be used for the color value. Any attribute An atom-attribute can also be used for the {color} value. Any
listed on the "dump custom"_dump.html doc page can be used, e.g. vx, attribute listed on the "dump custom"_dump.html doc page can be used,
fy, q, spin, etc. This includes per-atom quantities calculated by a e.g. vx, fy, q, spin, etc. This includes per-atom quantities
"compute"_compute.html, "fix"_fix.html, or "variable"_variable.html. calculated by a "compute"_compute.html, "fix"_fix.html, or
For example, if "vx" is used as the per-atom attribute, then the color "variable"_variable.html. For example, if "vx" is used as the
of the atom will depend on the x-component of its velocity. per-atom attribute, then the color of the atom will depend on the
x-component of its velocity.
The association of a per-atom value with a specific color is The association of a per-atom value with a specific color is
determined by a "color map", which can be specified via the determined by a "color map", which can be specified via the
@ -163,52 +165,49 @@ color map is defined, that mapping can take place via interpolation so
that a value of -3.2 is halfway between "red" and "blue", or that a value of -3.2 is halfway between "red" and "blue", or
discretely so that the value of -3.2 is "orange". discretely so that the value of -3.2 is "orange".
The diam value can be a numeric value {D} or {type} or {element} or The {diam} value can be a numeric value or {type} or {element} or an
{radius} or {shape} or an atom-attribute. atom-attribute.
If a numeric value {D} is specified, then all atoms will be drawn with If a numeric value is specified, then all atoms will be drawn with
that diameter, e.g. 1.5, which is in distance units in whatever that diameter, e.g. 1.5, which is in distance units in whatever
"units"_units.html you are using, e.g. Angstroms. "units"_units.html the input scripts uses, e.g. Angstroms.
If {type} is specified for the diam value then the color of each atom If {type} is specified for the diam value then the diamter of each
is determined by its atom type. By default all types have diameter atom is determined by its atom type. By default all types have
1.0. This mapping can be changed by the "dump_modify diameter 1.0. This mapping can be changed by the "dump_modify
adiam"_dump_modify.html command. adiam"_dump_modify.html command.
If {element} is specified for the diam value, then the diamater of If {element} is specified for the {diam} value, then the diamater of
each atom is determined by which element it is, which in turn is each atom is determined by which element it is, which in turn is
specified by the element-to-type mapping specified by the "dump_modify specified by the element-to-type mapping specified by the "dump_modify
element" command. By default every atom type is C (carbon). Every element" command. By default every atom type is C (carbon). Every
element has a diamtere associated with it, which is the same as used element has a diameter associated with it, which is the same as the
by the "AtomEye"_atomeye visualization package. diameters used by the "AtomEye"_atomeye visualization package.
If {radius} or {shape} is specified for the diam value then those the An atom-attribute can also be used for the {diam} value. Any
atom style you are using must define those attributes. The radius or attribute listed on the "dump custom"_dump.html doc page can be used,
shape of the individual atom is then used to draw it. Currently, only e.g. vx, fy, q, spin, radius, etc. This includes per-atom quantities
spherical shapes are allowed. Support for ellipsoids will be added calculated by a "compute"_compute.html, "fix"_fix.html, or
later. "variable"_variable.html. For example, if "vx" is used as the
per-atom attribute, then the diameter of the atom will depend on the
An atom-attribute can also be used for the diam value. Any attribute x-component of its velocity, which must be >= 0.0, else the atom will
listed on the "dump custom"_dump.html doc page can be used, e.g. vx, not be drawn. Note that finite-size spherical particles, as defined
fy, q, spin, etc. This includes per-atom quantities calculated by a by "atom_style sphere"_atom_style.html define a per-particle radius,
"compute"_compute.html, "fix"_fix.html, or "variable"_variable.html. which can be used as an atom-attribute.
For example, if "vx" is used as the per-atom attribute, then the
diameter of the atom will depend on the x-component of its velocity,
which will assumed to be >= 0.0, else the atom will not be drawn.
:line :line
The {bond} keyword determines the color and thickness or diameter of The {bond} keyword determines the color and thickness or diameter of
bonds rendered in the image. If {none} is specified for the color bonds rendered in the image. If {none} is specified for the {color}
value (with any diam value), then no bonds are drawn. value (with any diam value), then no bonds are drawn.
If {atom} is specified for the color value, then the each bond is If {atom} is specified for the {color} value, then each bond is drawn
drawn in 2 halves, with the color of each half being the color of the in 2 halves, with the color of each half being the color of the atom
atom at that end of the bond. at that end of the bond.
If {type} is specified for the color value, then the color of each If {type} is specified for the {color} value, then the color of each
bond is determined by its bond type. By default the mapping of types bond is determined by its bond type. By default the mapping of bond
to colors is as follows: types to colors is as follows:
type 1 = red type 1 = red
type 2 = green type 2 = green
@ -217,57 +216,58 @@ type 4 = yellow
type 5 = aqua type 5 = aqua
type 6 = cyan :ul type 6 = cyan :ul
and repeats itself for types > 6. This mapping can be changed by the and repeats itself for bond types > 6. This mapping can be changed by
"dump_modify bcolor"_dump_modify.html command. the "dump_modify bcolor"_dump_modify.html command.
The diam value can be a numeric value {D} or {type}. The {diam} value can be a numeric value or {type}.
If a numeric value {D} is specified, then all bond will be drawn with If a numeric value is specified, then all bond will be drawn with that
that diameter, e.g. 1.0, which is in distance units in whatever diameter, e.g. 1.0, which is in distance units in whatever
"units"_units.html you are using, e.g. Angstroms. "units"_units.html the input script uses, e.g. Angstroms.
If {type} is specified for the diam value then the color of each bond If {type} is specified for the {diam} value then the color of each
is determined by its bond type. By default all types have diameter bond is determined by its bond type. By default all types have
0.5. This mapping can be changed by the "dump_modify diameter 0.5. This mapping can be changed by the "dump_modify
bdiam"_dump_modify.html command. bdiam"_dump_modify.html command.
:line :line
The {size} keyword determines the width and height of the created The {size} keyword sets the width and height of the created images,
image files, in numbers of pixels in each direction. i.e. the number of pixels in each direction.
:line :line
The {view}, {center}, {up}, {zoom}, and {persp} settings determine how The {view}, {center}, {up}, {zoom}, and {persp} values determine how
3d simulation space is mapped to the 2d plane of the image. Basically 3d simulation space is mapped to the 2d plane of the image. Basically
they control how the simulation box appears in the image. they control how the simulation box appears in the image.
All of the {view}, {center}, {up}, {zoom}, and {persp} settings can be All of the {view}, {center}, {up}, {zoom}, and {persp} values can be
specified as numeric values, whose meaning is explained below. But specified as numeric quantities, whose meaning is explained below.
any of them can also be specified as an equal-style variable, by using Any of them can also be specified as an "equal-style
v_name as the setting, where "name" is the variable name. In this variable"_variable.html, by using v_name as the value, where "name" is
case the variable will be evaluated on the timestep each image is the variable name. In this case the variable will be evaluated on the
created to create a new setting. If the equal-style variable is timestep each image is created to create a new value. If the
time-dependent, this is a means of changing the way the simulation box equal-style variable is time-dependent, this is a means of changing
appears from image to image, effectively doing a pan or fly-by view of the way the simulation box appears from image to image, effectively
your simulation. doing a pan or fly-by view of your simulation.
The {view} keyword determines the viewpoint from which the simulation The {view} keyword determines the viewpoint from which the simulation
box is viewed. The {theta} setting is the vertical angle from the +z box is viewed, looking towards the {center} point. The {theta} value
axis, and must be an angle from 0 to 180 degrees. The {phi} setting is the vertical angle from the +z axis, and must be an angle from 0 to
is an azimuthal angle around the z axis and can be positive or 180 degrees. The {phi} value is an azimuthal angle around the z axis
negative. and can be positive or negative. A value of 0.0 is a view along the
+x axis, towards the {center} point.
The {center} keyword determines the point in simulation space that The {center} keyword determines the point in simulation space that
will be at the center of the image. {Cx}, {Cy}, and {Cz} are will be at the center of the image. {Cx}, {Cy}, and {Cz} are
speficied as fractions of the box dimensions, so that (0.5,0.5,0.5) is speficied as fractions of the box dimensions, so that (0.5,0.5,0.5) is
the center of the simulation box. These values do not have to be the center of the simulation box. These values do not have to be
between 0.0 and 1.0, if you want the simulation box to be offset from between 0.0 and 1.0, if you want the simulation box to be offset from
the center of the image. Note, however, that if you choose odd values the center of the image. Note, however, that if you choose strange
for {Cx}, {Cy}, or {Cz} you may get a blank image. Internally, {Cx}, values for {Cx}, {Cy}, or {Cz} you may get a blank image. Internally,
{Cy}, and {Cz} are converted into a point in simulation space. If {Cx}, {Cy}, and {Cz} are converted into a point in simulation space.
{flag} is set to "s" for static, then this conversion is done once, at If {flag} is set to "s" for static, then this conversion is done once,
the time the dump command is issued. If {flag} is set to "d" for at the time the dump command is issued. If {flag} is set to "d" for
dynamic then the conversion is performed every time a new image is dynamic then the conversion is performed every time a new image is
created. If the box size or shape is changing, this will adjust the created. If the box size or shape is changing, this will adjust the
center point in simulation space. center point in simulation space.
@ -275,33 +275,30 @@ center point in simulation space.
The {up} keyword determines what direction in simulation space will be The {up} keyword determines what direction in simulation space will be
"up" in the image. Internally it is stored as a vector that is in the "up" in the image. Internally it is stored as a vector that is in the
plane perpendicular to the view vector implied by the {theta} and plane perpendicular to the view vector implied by the {theta} and
{pni} settings, and which is in the plane defined by the view vector {pni} values, and which is also in the plane defined by the view
and user-specified up vector. Thus this internal vector is computed vector and user-specified up vector. Thus this internal vector is
from the user-specified {up} vector as computed from the user-specified {up} vector as
up_internal = view cross (up cross view) :pre up_internal = view cross (up cross view) :pre
This means the only restriction on the specified {up} vector is that This means the only restriction on the specified {up} vector is that
it cannot be parallel to the {view} vector, implied by the {theta} and it cannot be parallel to the {view} vector, implied by the {theta} and
{phi} settings. {phi} values.
The {zoom} keyword scales the size of the simulation box as it appears The {zoom} keyword scales the size of the simulation box as it appears
in the image. The default {factor} setting of 1 should display an in the image. The default {factor} value of 1 should display an
image mostly filled by the atoms in the simulation box. A {factor} > image mostly filled by the atoms in the simulation box. A {factor} >
1 will make the simulation box larger; a {factor} < 1 will make it 1 will make the simulation box larger; a {factor} < 1 will make it
smaller. smaller. {Factor} must be a value > 0.0.
The {persp} keyword how much depth perspective is present in the The {persp} keyword determines how much depth perspective is present
image. Depth persepctive makes lines that are parallel in simulation in the image. Depth perspective makes lines that are parallel in
space appear non-parallel in the image. A {factor} setting of 0.0 simulation space appear non-parallel in the image. A {factor} value
means that parallel lines will meet at infininty (1.0/factor), which of 0.0 means that parallel lines will meet at infininty (1.0/factor),
is an orthographic rendering with no persepctive. A {factor} setting which is an orthographic rendering with no persepctive. A {factor}
between 0.0 and 1.0 will introduce more perspective. A {factor} > 1 value between 0.0 and 1.0 will introduce more perspective. A {factor}
will create a highly skewed image with a large amount of perspective. value > 1 will create a highly skewed image with a large amount of
perspective.
The {dynamic} keyword
determines the color and thickness of bonds
rendered in the image.
:line :line
@ -309,31 +306,32 @@ The {box} keyword determines how the simulation box boundaries are
rendered as thin cylinders in the image. If {no} is set, then the box rendered as thin cylinders in the image. If {no} is set, then the box
boundaries are not drawn and the {diam} setting is ignored. If {yes} boundaries are not drawn and the {diam} setting is ignored. If {yes}
is set, the 12 edges of the box are drawn, with a diameter that is a is set, the 12 edges of the box are drawn, with a diameter that is a
fraction of the shortest box lenght in x, y, or z. The color of the fraction of the shortest box length in x,y,z (for 3d) or x,y (for 2d).
box boundaires can be set with the "dump_modify The color of the box boundaries can be set with the "dump_modify
boxcolor"_dump_modify.html command. boxcolor"_dump_modify.html command.
The {axes} keyword determines how the coordinate axes are rendered as The {axes} keyword determines how the coordinate axes are rendered as
thin cylinders in the image. If {no} is set, then the axes are not thin cylinders in the image. If {no} is set, then the axes are not
drawn and the {length} and {diam} settings are ignored. If {yes} is drawn and the {length} and {diam} settings are ignored. If {yes} is
set, 3 thin cylinders are drawn to represent the x,y,z axes in colors set, 3 thin cylinders are drawn to represent the x,y,z axes in colors
red,green/blue. The origin of these cylinders will be offset red,green,blue. The origin of these cylinders will be offset from the
from the lower left corner of the box by 10%. The {length} setting lower left corner of the box by 10%. The {length} setting determines
determines how long the cylinders will be. The {diam} setting how long the cylinders will be as a fraction of the respective box
determines their thickness. lengths. The {diam} setting determines their thickness as a fraction
of the shortest box length in x,y,z (for 3d) or x,y (for 2d).
:line :line
The {shiny} keyword determines how shiny the objects rendered in the The {shiny} keyword determines how shiny the objects rendered in the
image will appear. This must be a value 0.0 <= S <= 1.0, where S = 1 image will appear. The factor value must be a value 0.0 <= factor <=
is a highly-reflective surface and S = 0 is a rough non-shiny surface. 1.0, where factor = 1 is a highly reflective surface and factor = 0 is
a rough non-shiny surface.
The {ssao} keyword turns on/off a screen space ambient occlusion The {ssao} keyword turns on/off a screen space ambient occlusion
(SSAO) model for depth shading. If {yes} is set, then atoms further (SSAO) model for depth shading. If {yes} is set, then atoms further
away from the viewer are darkened, which is perceived as depth by the away from the viewer are darkened, which is perceived as depth. The
viewer. The calculation of this effect can increase the cost of calculation of this effect can increase the cost of computing the
computing the image by roughly 2x. If {no} is set, the depth shading image by roughly 2x. If {no} is set, no depth shading is performed.
is not performed.
:line :line
@ -413,7 +411,6 @@ up = 0 0 1 (for 3d)
up = 0 1 0 (for 2d) up = 0 1 0 (for 2d)
zoom = 1.0 zoom = 1.0
persp = 0.0 persp = 0.0
dynamic = no
box = yes 0.01 box = yes 0.01
axes = no 0.0 0.0 axes = no 0.0 0.0
shiny = 1.0 shiny = 1.0

24
doc/dump_modify.html
View File

@ -11,9 +11,6 @@
<H3>dump_modify command <H3>dump_modify command
</H3> </H3>
<P>NOTE: This keywords below which are only relevant for the dump image
command have not yet been released as part of LAMMPS.
</P>
<P><B>Syntax:</B> <P><B>Syntax:</B>
</P> </P>
<PRE>dump_modify dump-ID keyword values ... <PRE>dump_modify dump-ID keyword values ...
@ -39,7 +36,7 @@ command have not yet been released as part of LAMMPS.
"s" for sequential "s" for sequential
"a" for absolute "a" for absolute
"f" for fractional "f" for fractional
delta = binsize (only used for style "s" = sequential) delta = binsize (only used for style "s", otherwise ignored)
binsize = range is divided into bins of this width binsize = range is divided into bins of this width
N = # of subsequent entries N = # of subsequent entries
entry = value color (for continuous style) entry = value color (for continuous style)
@ -47,9 +44,9 @@ command have not yet been released as part of LAMMPS.
color = name of color used for that value color = name of color used for that value
entry = lo hi color (for discrete style) entry = lo hi color (for discrete style)
lo/hi = number or <I>min</I> or <I>max</I> = lower/upper bound of subset of range lo/hi = number or <I>min</I> or <I>max</I> = lower/upper bound of subset of range
color = name of color used for that value color = name of color used for that subset of values
entry = color (for sequential style) entry = color (for sequential style)
color = name of color used for a bin within range color = name of color used for a bin of values
<I>append</I> arg = <I>yes</I> or <I>no</I> <I>append</I> arg = <I>yes</I> or <I>no</I>
<I>bcolor</I> args = type color <I>bcolor</I> args = type color
type = bond type or range of types (see below) type = bond type or range of types (see below)
@ -102,6 +99,8 @@ dump_modify xtcdump precision 10000
dump_modify 1 every 1000 dump_modify 1 every 1000
dump_modify 1 every v_myVar dump_modify 1 every v_myVar
</PRE> </PRE>
<P>NOTE: add some image examples
</P>
<P><B>Description:</B> <P><B>Description:</B>
</P> </P>
<P>Modify the parameters of a previously defined dump command. Not all <P>Modify the parameters of a previously defined dump command. Not all
@ -477,11 +476,12 @@ cost, as well as memory, versus unsorted output.
only atoms whose attributes meet all the threshold criteria are only atoms whose attributes meet all the threshold criteria are
written to the dump file or included in the image. The possible written to the dump file or included in the image. The possible
attributes that can be tested for are the same as those that can be attributes that can be tested for are the same as those that can be
specified in the <A HREF = "dump.html">dump custom</A> command. Note that different specified in the <A HREF = "dump.html">dump custom</A> command, with the exception
attributes can be output by the dump custom command than are used as of the <I>element</I> attribute, since it is not a numeric value. Note
threshold criteria by the dump_modify command. E.g. you can output that different attributes can be output by the dump custom command
the coordinates and stress of atoms whose energy is above some than are used as threshold criteria by the dump_modify command.
threshold. E.g. you can output the coordinates and stress of atoms whose energy
is above some threshold.
</P> </P>
<HR> <HR>
@ -509,6 +509,8 @@ box size stored with the snapshot.
<LI>adiam = * 1.0 <LI>adiam = * 1.0
<LI>amap = min max cf 2 0.0 blue 1.0 red <LI>amap = min max cf 2 0.0 blue 1.0 red
<LI>append = no <LI>append = no
<LI>bcolor = * red/green/blue/yellow/aqua/cyan
<LI>bdiam = * 0.5
<LI>bgcolor = black <LI>bgcolor = black
<LI>boxcolor = yellow <LI>boxcolor = yellow
<LI>color = 140 color names are pre-defined as listed below <LI>color = 140 color names are pre-defined as listed below

24
doc/dump_modify.txt
View File

@ -8,9 +8,6 @@
dump_modify command :h3 dump_modify command :h3
NOTE: This keywords below which are only relevant for the dump image
command have not yet been released as part of LAMMPS.
[Syntax:] [Syntax:]
dump_modify dump-ID keyword values ... :pre dump_modify dump-ID keyword values ... :pre
@ -33,7 +30,7 @@ keyword = {acolor} or {adiam} or {amap} or {append} or {bcolor} or {bdiam} or {b
"s" for sequential "s" for sequential
"a" for absolute "a" for absolute
"f" for fractional "f" for fractional
delta = binsize (only used for style "s" = sequential) delta = binsize (only used for style "s", otherwise ignored)
binsize = range is divided into bins of this width binsize = range is divided into bins of this width
N = # of subsequent entries N = # of subsequent entries
entry = value color (for continuous style) entry = value color (for continuous style)
@ -41,9 +38,9 @@ keyword = {acolor} or {adiam} or {amap} or {append} or {bcolor} or {bdiam} or {b
color = name of color used for that value color = name of color used for that value
entry = lo hi color (for discrete style) entry = lo hi color (for discrete style)
lo/hi = number or {min} or {max} = lower/upper bound of subset of range lo/hi = number or {min} or {max} = lower/upper bound of subset of range
color = name of color used for that value color = name of color used for that subset of values
entry = color (for sequential style) entry = color (for sequential style)
color = name of color used for a bin within range color = name of color used for a bin of values
{append} arg = {yes} or {no} {append} arg = {yes} or {no}
{bcolor} args = type color {bcolor} args = type color
type = bond type or range of types (see below) type = bond type or range of types (see below)
@ -95,6 +92,8 @@ dump_modify xtcdump precision 10000
dump_modify 1 every 1000 dump_modify 1 every 1000
dump_modify 1 every v_myVar :pre dump_modify 1 every v_myVar :pre
NOTE: add some image examples
[Description:] [Description:]
Modify the parameters of a previously defined dump command. Not all Modify the parameters of a previously defined dump command. Not all
@ -470,11 +469,12 @@ The {thresh} keyword only applies to the dump {custom} and {cfg} and
only atoms whose attributes meet all the threshold criteria are only atoms whose attributes meet all the threshold criteria are
written to the dump file or included in the image. The possible written to the dump file or included in the image. The possible
attributes that can be tested for are the same as those that can be attributes that can be tested for are the same as those that can be
specified in the "dump custom"_dump.html command. Note that different specified in the "dump custom"_dump.html command, with the exception
attributes can be output by the dump custom command than are used as of the {element} attribute, since it is not a numeric value. Note
threshold criteria by the dump_modify command. E.g. you can output that different attributes can be output by the dump custom command
the coordinates and stress of atoms whose energy is above some than are used as threshold criteria by the dump_modify command.
threshold. E.g. you can output the coordinates and stress of atoms whose energy
is above some threshold.
:line :line
@ -502,6 +502,8 @@ acolor = * red/green/blue/yellow/aqua/cyan
adiam = * 1.0 adiam = * 1.0
amap = min max cf 2 0.0 blue 1.0 red amap = min max cf 2 0.0 blue 1.0 red
append = no append = no
bcolor = * red/green/blue/yellow/aqua/cyan
bdiam = * 0.5
bgcolor = black bgcolor = black
boxcolor = yellow boxcolor = yellow
color = 140 color names are pre-defined as listed below color = 140 color names are pre-defined as listed below