The list of possible attributes is the same as that used by the dump -custom command, which describes their meaning. Basically, -this list gives your input script access to any per-atom quantity -stored by LAMMPS. +custom command, which describes their meaning, with some +additional quantities that are only defined for certain atom +styles. 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 discussed below. Zeroes are stored for atoms not in the specified group.
+The additional quantities only accessible via this command (and not +directly via the dump custom 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 command for an explanation of the quaternion +vector. +
Output info:
This compute calculates a per-atom vector or per-atom array depending diff --git a/doc/compute_property_atom.txt b/doc/compute_property_atom.txt index 3b3047f6fb..60972bce46 100644 --- a/doc/compute_property_atom.txt +++ b/doc/compute_property_atom.txt @@ -19,7 +19,7 @@ input = one or more atom attributes :l x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz, vx, vy, vz, fx, fy, fz, q, mux, muy, muz, mu, - radius, omegax, omegay, omegaz, + radius, diameter, omegax, omegay, omegaz, angmomx, angmomy, angmomz, shapex,shapey, shapez, quatw, quati, quatj, quatk, tqx, tqy, tqz, @@ -38,16 +38,16 @@ input = one or more atom attributes :l q = atom charge mux,muy,muz = orientation 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 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 spin = electron spin eradius = electron radius 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 [Examples:] @@ -67,14 +67,25 @@ inputs. See for example, the "compute reduce"_compute_reduce.html, variable"_variable.html commands. The list of possible attributes is the same as that used by the "dump -custom"_dump.html command, which describes their meaning. Basically, -this list gives your input script access to any per-atom quantity -stored by LAMMPS. +custom"_dump.html command, which describes their meaning, with some +additional quantities that are only defined for certain "atom +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 discussed below. Zeroes are stored for atoms not in the specified 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:] This compute calculates a per-atom vector or per-atom array depending diff --git a/doc/dump.html b/doc/dump.html index f95117f5bc..6f9c2c462f 100644 --- a/doc/dump.html +++ b/doc/dump.html @@ -46,12 +46,12 @@ f_ID[N] = Nth column of local array calculated by a fix with ID
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,
xsu, ysu, zsu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, mu,
- radius, omegax, omegay, omegaz,
+ radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz, tqx, tqy, tqz,
spin, eradius, ervel, erforce,
c_ID, c_ID[N], f_ID, f_ID[N], v_name
@@ -59,6 +59,7 @@
id = atom ID
mol = molecule ID
type = atom type
+ element = name of atom element, as defined by dump_modify command
mass = atom mass
x,y,z = unscaled atom coordinates
xs,ys,zs = scaled atom coordinates
@@ -70,7 +71,7 @@
q = atom charge
mux,muy,muz = orientation 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
angmomx,angmomy,angmomz = angular momentum of extended particle
tqx,tqy,tqz = torque on extended particles
@@ -390,13 +391,17 @@ array calculated by the fix.
This section explains the atom attributes that can be specified as
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.
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
-atom mass. Vx, vy, vz, fx, fy, fz, and q are components
-of atom velocity and force and atomic charge.
+file for molecular systems. Type is the atom type. Element is
+typically the chemical name of an element, which you must assign to
+each type via the dump_modify element 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,
y, z attributes write atom coordinates "unscaled", in the
@@ -425,9 +430,9 @@ defined with an atom style of dipole. They give the orientation of
the atom's point dipole moment. The mu attribute gives the
magnitude of the atom's dipole moment.
-The radius attribute is specific to extended spherical particles
-that have a finite size, such as those defined with an atom style of
-sphere.
+
The radius and diameter attributes are specific to extended
+spherical particles that have a finite size, such as those defined
+with an atom style of sphere.
The omegax, omegay, and omegaz attributes are specific to
extended spherical or aspherical particles that have an angular
diff --git a/doc/dump.txt b/doc/dump.txt
index 11d0a9d730..02f10b1d12 100644
--- a/doc/dump.txt
+++ b/doc/dump.txt
@@ -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
{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,
xsu, ysu, zsu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, mu,
- radius, omegax, omegay, omegaz,
+ radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz, tqx, tqy, tqz,
spin, eradius, ervel, erforce,
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
mol = molecule ID
type = atom type
+ element = name of atom element, as defined by "dump_modify"_dump_modify.html command
mass = atom mass
x,y,z = unscaled atom coordinates
xs,ys,zs = scaled atom coordinates
@@ -60,7 +61,7 @@ args = list of arguments for a particular style :l
q = atom charge
mux,muy,muz = orientation 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
angmomx,angmomy,angmomz = angular momentum of extended particle
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
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.
{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
-atom mass. {Vx}, {vy}, {vz}, {fx}, {fy}, {fz}, and {q} are components
-of atom velocity and force and atomic charge.
+file for molecular systems. {Type} is the atom type. {Element} is
+typically the chemical name of an element, which you must assign to
+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},
{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
magnitude of the atom's dipole moment.
-The {radius} attribute is specific to extended spherical particles
-that have a finite size, such as those defined with an atom style of
-{sphere}.
+The {radius} and {diameter} attributes are specific to extended
+spherical particles that have a finite size, such as those defined
+with an atom style of {sphere}.
The {omegax}, {omegay}, and {omegaz} attributes are specific to
extended spherical or aspherical particles that have an angular
diff --git a/doc/dump_image.html b/doc/dump_image.html
index a700b3e8e0..4a628847fe 100644
--- a/doc/dump_image.html
+++ b/doc/dump_image.html
@@ -11,12 +11,9 @@
dump image command
-NOTE: The dump image command has not yet been released as part of
-LAMMPS.
-
Syntax:
-dump ID group-ID image N file keyword value ...
+dump ID group-ID image N file x y z type type keyword value ...
atom values = color diam - color = none or type or element or atom-attribute - diam = D or type or element or radius or shape or atom-attribute - D = numeric value for atom diameter (distance units) - bond values = color diam - color = none or atom or type - diam = D or type - D = numeric value for bond diameter (distance units) - size values = width height - width = width of image in # of pixels - height = height of image in # of pixels - view values = theta phi - theta = view angle from +z axis (degrees) - phi = azimuthal view angle (degrees) - theta or phi can be a variable (see below) - center values = flag Cx Cy Cz = center point of image (distance units) - flag = "s" for static, "d" for dynamic - Cx,Cy,Cz can be variables (see below) - up values = Ux Uy Uz = components of up vector - Ux,Uy,Uz can be variables (see below) - zoom value = factor = scale image size by this factor - factor can be a variable (see below) - persp value = factor = perspective setting - factor can be a variable (see below) - box values = yes/no diam - yes/no = do or do not draw simulation box lines - diam = diameter of box lines as fraction of shortest box length - axes values = yes/no length diam - yes/no = do or do not draw xyz axes lines next to simulation box - length = length of axes lines as fraction of respective box lengths - diam = diameter of axes lines as fraction of shortest box length - shiny value = factor - factor = shinyness of spheres and cylinders from 0.0 to 1.0 - ssao value = yes/no - yes/no = turn on/off SSAO depth shading +atom values = color diam = color and size of atoms + color = none or type or element or atom-attribute + diam = number or type or element or atom-attribute + number = numeric value for atom diameter (distance units) + bond values = color diam = color and width of bonds + color = none or atom or type + diam = number or type + numer = numeric value for bond diameter (distance units) + size values = width height = size of images + width = width of image in # of pixels + height = height of image in # of pixels + view values = theta phi = view of simulation box + theta = view angle from +z axis (degrees) + phi = azimuthal view angle (degrees) + theta or phi can be a variable (see below) + center values = flag Cx Cy Cz = center point of image + flag = "s" for static, "d" for dynamic + Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box) + Cx,Cy,Cz can be variables (see below) + up values = Ux Uy Uz = direction that is "up" in image + Ux,Uy,Uz = components of up vector + Ux,Uy,Uz can be variables (see below) + zoom value = factor = size that simulation box appears in image + factor = scale image size by factor > 1 to enlarge, factor < 1 to shrink + factor can be a variable (see below) + persp value = factor = amount of "perspective" in image + factor = amount of perspective (0 = none, < 1 = some, > 1 = highly skewed) + factor can be a variable (see below) + box values = yes/no diam = draw outline of simulation box + yes/no = do or do not draw simulation box lines + diam = diameter of box lines as fraction of shortest box length + axes values = yes/no length diam = draw xyz axes + yes/no = do or do not draw xyz axes lines next to simulation box + length = length of axes lines as fraction of respective box lengths + 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
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 converted into an animated movie of your simulation; see further -details below. Other dump styles store snapshots of atom quantities -in various formats, as discussed on the dump doc page. +details below. Other dump styles store snapshots of numerical data +asociated with atoms in various formats, as discussed on the +dump doc page.
Only atoms in the specified group are rendered in the image. The dump_modify region and thresh commands can also @@ -88,13 +90,14 @@ alter what atoms are included in the image.
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 -PPM file is created. To write out JPG files, you must build LAMMPS -with a JPEG library. See this section of -the manual for instructions on how to do this. +PPM file is created, which is a text-based format. To write out JPG +files, you must build LAMMPS with a JPEG library. See this +section of the manual for instructions on +how to do this.
IMPORTANT NOTE: Because periodic boundary conditions are enforced only 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.
Dump image filenames must contain a wildcard character "*". If a "*" -character appears in the filename, then one file per snapshot is -written and the "*" character is replaced with the timestep value. -For example, tmp.dump.*.jpg becomes tmp.dump.0.jpg, -tmp.dump.10000.jpg, tmp.dump.20000.jpg, etc. Note that the -dump_modify pad command can be used to insure all -timestep numbers are the same length (e.g. 00010), which can make it -easier to convert a series of images into a movie in the correct -ordering. +
Dump image filenames must contain a wildcard character "*", so that +one image file per snapshot is written. The "*" character is replaced +with the timestep value. For example, tmp.dump.*.jpg becomes +tmp.dump.0.jpg, tmp.dump.10000.jpg, tmp.dump.20000.jpg, etc. Note +that the dump_modify pad command can be used to +insure all timestep numbers are the same length (e.g. 00010), which +can make it easier to convert a series of images into a movie in the +correct ordering.
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 -value), then no atoms are drawn. +the image. If none is specified for the color value (with any +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 -value, then the color of each atom is determined by its atom type. -By default the mapping of types to colors is as follows: +
If type is specified for the color value, then the color of each +atom is determined by its atom type. By default the mapping of types +to colors is as follows:
and repeats itself for types > 6. This mapping can be changed by the dump_modify acolor command.
-If element is specified for the color value, then the color of 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 element" -command. By default every atom type is C (carbon). Every element has -a color associated with it, which is the same as used by the -AtomEye visualization package. +
If element is specified for the color value, then the color of +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 +element" command. By default every atom type is C (carbon). Every +element has a color associated with it, which is the same as the +colors used by the AtomEye visualization package.
-An atom-attribute can also be used for the color value. Any attribute -listed on the dump custom doc page can be used, e.g. vx, -fy, q, spin, etc. This includes per-atom quantities calculated by a -compute, fix, or variable. -For example, if "vx" is used as the per-atom attribute, then the color -of the atom will depend on the x-component of its velocity. +
An atom-attribute can also be used for the color value. Any +attribute listed on the dump custom doc page can be used, +e.g. vx, fy, q, spin, etc. This includes per-atom quantities +calculated by a compute, fix, or +variable. For example, if "vx" is used as the +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 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 discretely so that the value of -3.2 is "orange".
-The diam value can be a numeric value D or type or element or -radius or shape or an atom-attribute. +
The diam value can be a numeric value or type or element or an +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 -units you are using, e.g. Angstroms. +units the input scripts uses, e.g. Angstroms.
-If type is specified for the diam value then the color of each atom
-is determined by its atom type. By default all types have diameter
-1.0. This mapping can be changed by the dump_modify
+ If type is specified for the diam value then the diamter of each
+atom is determined by its atom type. By default all types have
+diameter 1.0. This mapping can be changed by the dump_modify
adiam 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
specified by the element-to-type mapping specified by the "dump_modify
element" command. By default every atom type is C (carbon). Every
-element has a diamtere associated with it, which is the same as used
-by the AtomEye visualization package.
+element has a diameter associated with it, which is the same as the
+diameters used by the AtomEye visualization package.
If radius or shape is specified for the diam value then those the
-atom style you are using must define those attributes. The radius or
-shape of the individual atom is then used to draw it. Currently, only
-spherical shapes are allowed. Support for ellipsoids will be added
-later.
- An atom-attribute can also be used for the diam value. Any attribute
-listed on the dump custom doc page can be used, e.g. vx,
-fy, q, spin, etc. This includes per-atom quantities calculated by a
-compute, fix, or variable.
-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.
+ An atom-attribute can also be used for the diam value. Any
+attribute listed on the dump custom doc page can be used,
+e.g. vx, fy, q, spin, radius, etc. This includes per-atom quantities
+calculated by a compute, fix, or
+variable. 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 must be >= 0.0, else the atom will
+not be drawn. Note that finite-size spherical particles, as defined
+by atom_style sphere define a per-particle radius,
+which can be used as an atom-attribute.
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.
If atom is specified for the color value, then the each bond is
-drawn in 2 halves, with the color of each half being the color of the
-atom at that end of the bond.
+ If atom is specified for the color value, then each bond is drawn
+in 2 halves, with the color of each half being the color of the atom
+at that end of the bond.
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
-to colors is as follows:
+ 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 bond
+types to colors is as follows:
and repeats itself for types > 6. This mapping can be changed by the
-dump_modify bcolor command.
+ and repeats itself for bond types > 6. This mapping can be changed by
+the dump_modify bcolor 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
-that diameter, e.g. 1.0, which is in distance units in whatever
-units you are using, e.g. Angstroms.
+ If a numeric value is specified, then all bond will be drawn with that
+diameter, e.g. 1.0, which is in distance units in whatever
+units the input script uses, e.g. Angstroms.
If type is specified for the diam value then the color of each bond
-is determined by its bond type. By default all types have diameter
-0.5. This mapping can be changed by the dump_modify
+ If type is specified for the diam value then the color of each
+bond is determined by its bond type. By default all types have
+diameter 0.5. This mapping can be changed by the dump_modify
bdiam command.
The size keyword determines the width and height of the created
-image files, in numbers of pixels in each direction.
+ The size keyword sets the width and height of the created images,
+i.e. the number of pixels in each direction.
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
they control how the simulation box appears in the image.
All of the view, center, up, zoom, and persp settings can be
-specified as numeric values, whose meaning is explained below. But
-any of them can also be specified as an equal-style variable, by using
-v_name as the setting, where "name" is the variable name. In this
-case the variable will be evaluated on the timestep each image is
-created to create a new setting. If the equal-style variable is
-time-dependent, this is a means of changing the way the simulation box
-appears from image to image, effectively doing a pan or fly-by view of
-your simulation.
+ All of the view, center, up, zoom, and persp values can be
+specified as numeric quantities, whose meaning is explained below.
+Any of them can also be specified as an equal-style
+variable, by using v_name as the value, where "name" is
+the variable name. In this case the variable will be evaluated on the
+timestep each image is created to create a new value. If the
+equal-style variable is time-dependent, this is a means of changing
+the way the simulation box appears from image to image, effectively
+doing a pan or fly-by view of your simulation.
The view keyword determines the viewpoint from which the simulation
-box is viewed. The theta setting is the vertical angle from the +z
-axis, and must be an angle from 0 to 180 degrees. The phi setting
-is an azimuthal angle around the z axis and can be positive or
-negative.
+box is viewed, looking towards the center point. The theta value
+is the vertical angle from the +z axis, and must be an angle from 0 to
+180 degrees. The phi value is an azimuthal angle around the z axis
+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
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
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
-the center of the image. Note, however, that if you choose odd values
-for Cx, Cy, or Cz you may get a blank image. Internally, Cx,
-Cy, and Cz are converted into a point in simulation space. If
-flag is set to "s" for static, then this conversion is done once, at
-the time the dump command is issued. If flag is set to "d" for
+the center of the image. Note, however, that if you choose strange
+values for Cx, Cy, or Cz you may get a blank image. Internally,
+Cx, Cy, and Cz are converted into a point in simulation space.
+If flag is set to "s" for static, then this conversion is done once,
+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
created. If the box size or shape is changing, this will adjust the
center point in simulation space.
@@ -286,33 +286,30 @@ center point in simulation space.
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
plane perpendicular to the view vector implied by the theta and
-pni settings, and which is in the plane defined by the view vector
-and user-specified up vector. Thus this internal vector is computed
-from the user-specified up vector as
+pni values, and which is also in the plane defined by the view
+vector and user-specified up vector. Thus this internal vector is
+computed from the user-specified up vector as
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
-phi settings.
+phi values.
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 >
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
-image. Depth persepctive makes lines that are parallel in simulation
-space appear non-parallel in the image. A factor setting of 0.0
-means that parallel lines will meet at infininty (1.0/factor), which
-is an orthographic rendering with no persepctive. A factor setting
-between 0.0 and 1.0 will introduce more perspective. A factor > 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.
+ The persp keyword determines how much depth perspective is present
+in the image. Depth perspective makes lines that are parallel in
+simulation space appear non-parallel in the image. A factor value
+of 0.0 means that parallel lines will meet at infininty (1.0/factor),
+which is an orthographic rendering with no persepctive. A factor
+value between 0.0 and 1.0 will introduce more perspective. A factor
+value > 1 will create a highly skewed image with a large amount of
+perspective.
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
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
-red,green/blue. The origin of these cylinders will be offset
-from the lower left corner of the box by 10%. The length setting
-determines how long the cylinders will be. The diam setting
-determines their thickness.
+red,green,blue. The origin of these cylinders will be offset from the
+lower left corner of the box by 10%. The length setting determines
+how long the cylinders will be as a fraction of the respective box
+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).
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
-is a highly-reflective surface and S = 0 is a rough non-shiny surface.
+image will appear. The factor value must be a value 0.0 <= factor <=
+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
(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
-viewer. The calculation of this effect can increase the cost of
-computing the image by roughly 2x. If no is set, the depth shading
-is not performed.
+away from the viewer are darkened, which is perceived as depth. The
+calculation of this effect can increase the cost of computing the
+image by roughly 2x. If no is set, no depth shading is performed.
NOTE: This keywords below which are only relevant for the dump image
-command have not yet been released as part of LAMMPS.
- Syntax:
NOTE: add some image examples
+ Description:
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
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
-specified in the dump custom command. Note that different
-attributes can be output by the dump custom command than are used as
-threshold criteria by the dump_modify command. E.g. you can output
-the coordinates and stress of atoms whose energy is above some
-threshold.
+specified in the dump custom command, with the exception
+of the element attribute, since it is not a numeric value. Note
+that different attributes can be output by the dump custom command
+than are used as threshold criteria by the dump_modify command.
+E.g. you can output the coordinates and stress of atoms whose energy
+is above some threshold.
-
-
-up_internal = view cross (up cross view)
@@ -320,31 +317,32 @@ rendered in the image.
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
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
-box boundaires can be set with the dump_modify
+fraction of the shortest box length in x,y,z (for 3d) or x,y (for 2d).
+The color of the box boundaries can be set with the dump_modify
boxcolor command.
@@ -424,7 +422,6 @@ documentation for details.
dump_modify command
-dump_modify dump-ID keyword values ...
@@ -39,7 +36,7 @@ command have not yet been released as part of LAMMPS.
"s" for sequential
"a" for absolute
"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
N = # of subsequent entries
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
entry = lo hi color (for discrete style)
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)
- 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
bcolor args = type color
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 v_myVar
+
@@ -509,6 +509,8 @@ box size stored with the snapshot.