forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6250 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
458150a9fe
commit
575de169b9
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@ -25,7 +25,7 @@
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x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
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vx, vy, vz, fx, fy, fz,
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q, mux, muy, muz, mu,
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radius, omegax, omegay, omegaz,
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radius, diameter, omegax, omegay, omegaz,
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angmomx, angmomy, angmomz,
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shapex,shapey, shapez,
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quatw, quati, quatj, quatk, tqx, tqy, tqz,
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@ -44,16 +44,16 @@
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q = atom charge
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mux,muy,muz = orientation of dipole moment of atom
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mu = magnitude of dipole moment of atom
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radius = radius of spherical particle
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radius,diameter = radius,diameter of spherical particle
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omegax,omegay,omegaz = angular velocity of extended particle
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angmomx,angmomy,angmomz = angular momentum of extended particle
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shapex,shapey,shapez = 3 diameters of ellipsoidal particle
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quatw,quati,quatj,quatk = quaternion components for aspherical particles
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tqx,tqy,tqz = torque on extended particles
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spin = electron spin
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eradius = electron radius
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ervel = electron radial velocity
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erforce = electron radial force
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shapex,shapey,shapez = 3 diameters of aspherical particle
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quatw,quati,quatj,quatk = quaternion components for aspherical particles
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</PRE>
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</UL>
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@ -74,14 +74,25 @@ inputs. See for example, the <A HREF = "compute_reduce.html">compute reduce</A>
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variable</A> commands.
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</P>
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<P>The list of possible attributes is the same as that used by the <A HREF = "dump.html">dump
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custom</A> command, which describes their meaning. Basically,
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this list gives your input script access to any per-atom quantity
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stored by LAMMPS.
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custom</A> command, which describes their meaning, with some
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additional quantities that are only defined for certain <A HREF = "atom_style.html">atom
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styles</A>. Basically, this list gives your input script
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access to any per-atom quantity stored by LAMMPS.
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</P>
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<P>The values are stored in a per-atom vector or array as
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discussed below. Zeroes are stored for atoms not in the specified
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group.
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</P>
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<P>The additional quantities only accessible via this command (and not
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directly via the <A HREF = "dump.html">dump custom</A> command are as follows.
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</P>
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<P><I>Shapex</I>, <I>shapey</I>, and <I>shapez</I> are defined for ellipsoidal particles
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and define the 3d shape of each particle. <I>Quatw</I>, <I>quati</I>, <I>quatj</I>,
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and <I>quatk</I> are also defined for ellipsoidal particles and store the
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4-vector quaternion representing the orientation of each particle.
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See the <A HREF = "set.html">set</A> command for an explanation of the quaternion
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vector.
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</P>
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<P><B>Output info:</B>
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</P>
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<P>This compute calculates a per-atom vector or per-atom array depending
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@ -19,7 +19,7 @@ input = one or more atom attributes :l
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x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
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vx, vy, vz, fx, fy, fz,
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q, mux, muy, muz, mu,
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radius, omegax, omegay, omegaz,
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radius, diameter, omegax, omegay, omegaz,
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angmomx, angmomy, angmomz,
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shapex,shapey, shapez,
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quatw, quati, quatj, quatk, tqx, tqy, tqz,
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@ -38,16 +38,16 @@ input = one or more atom attributes :l
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q = atom charge
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mux,muy,muz = orientation of dipole moment of atom
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mu = magnitude of dipole moment of atom
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radius = radius of spherical particle
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radius,diameter = radius,diameter of spherical particle
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omegax,omegay,omegaz = angular velocity of extended particle
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angmomx,angmomy,angmomz = angular momentum of extended particle
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shapex,shapey,shapez = 3 diameters of ellipsoidal particle
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quatw,quati,quatj,quatk = quaternion components for aspherical particles
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tqx,tqy,tqz = torque on extended particles
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spin = electron spin
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eradius = electron radius
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ervel = electron radial velocity
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erforce = electron radial force :pre
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erforce = electron radial force
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shapex,shapey,shapez = 3 diameters of aspherical particle
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quatw,quati,quatj,quatk = quaternion components for aspherical particles :pre
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:ule
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[Examples:]
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@ -67,14 +67,25 @@ inputs. See for example, the "compute reduce"_compute_reduce.html,
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variable"_variable.html commands.
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The list of possible attributes is the same as that used by the "dump
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custom"_dump.html command, which describes their meaning. Basically,
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this list gives your input script access to any per-atom quantity
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stored by LAMMPS.
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custom"_dump.html command, which describes their meaning, with some
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additional quantities that are only defined for certain "atom
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styles"_atom_style.html. Basically, this list gives your input script
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access to any per-atom quantity stored by LAMMPS.
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The values are stored in a per-atom vector or array as
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discussed below. Zeroes are stored for atoms not in the specified
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group.
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The additional quantities only accessible via this command (and not
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directly via the "dump custom"_dump.html command are as follows.
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{Shapex}, {shapey}, and {shapez} are defined for ellipsoidal particles
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and define the 3d shape of each particle. {Quatw}, {quati}, {quatj},
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and {quatk} are also defined for ellipsoidal particles and store the
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4-vector quaternion representing the orientation of each particle.
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See the "set"_set.html command for an explanation of the quaternion
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vector.
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[Output info:]
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This compute calculates a per-atom vector or per-atom array depending
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@ -46,12 +46,12 @@
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f_ID[N] = Nth column of local array calculated by a fix with ID
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</PRE>
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<PRE> <I>custom</I> args = list of atom attributes
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possible attributes = id, mol, type, mass,
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possible attributes = id, mol, type, element, mass,
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x, y, z, xs, ys, zs, xu, yu, zu,
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xsu, ysu, zsu, ix, iy, iz,
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vx, vy, vz, fx, fy, fz,
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q, mux, muy, muz, mu,
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radius, omegax, omegay, omegaz,
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radius, diameter, omegax, omegay, omegaz,
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angmomx, angmomy, angmomz, tqx, tqy, tqz,
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spin, eradius, ervel, erforce,
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c_ID, c_ID[N], f_ID, f_ID[N], v_name
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@ -59,6 +59,7 @@
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<PRE> id = atom ID
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mol = molecule ID
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type = atom type
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element = name of atom element, as defined by <A HREF = "dump_modify.html">dump_modify</A> command
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mass = atom mass
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x,y,z = unscaled atom coordinates
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xs,ys,zs = scaled atom coordinates
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@ -70,7 +71,7 @@
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q = atom charge
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mux,muy,muz = orientation of dipole moment of atom
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mu = magnitude of dipole moment of atom
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radius = radius of spherical particle
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radius,diameter = radius,diameter of spherical particle
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omegax,omegay,omegaz = angular velocity of extended particle
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angmomx,angmomy,angmomz = angular momentum of extended particle
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tqx,tqy,tqz = torque on extended particles
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@ -390,13 +391,17 @@ array calculated by the fix.
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<P>This section explains the atom attributes that can be specified as
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part of the <I>custom</I> and <I>cfg</I> styles.
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</P>
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<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>,
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<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>,
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<I>fz</I>, <I>q</I> attributes are self-explanatory.
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</P>
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<P><I>Id</I> is the atom ID. <I>Mol</I> is the molecule ID, included in the data
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file for molecular systems. <I>Type</I> is the atom type. <I>Mass</I> is the
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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
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of atom velocity and force and atomic charge.
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file for molecular systems. <I>Type</I> is the atom type. <I>Element</I> is
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typically the chemical name of an element, which you must assign to
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each type via the <A HREF = "dump_modify.html">dump_modify element</A> command.
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More generally, it can be any string you wish to associated with an
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atom type. <I>Mass</I> is the atom mass. <I>Vx</I>, <I>vy</I>, <I>vz</I>, <I>fx</I>, <I>fy</I>,
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<I>fz</I>, and <I>q</I> are components of atom velocity and force and atomic
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charge.
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</P>
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<P>There are several options for outputting atom coordinates. The <I>x</I>,
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<I>y</I>, <I>z</I> attributes write atom coordinates "unscaled", in the
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@ -425,9 +430,9 @@ defined with an atom style of <I>dipole</I>. They give the orientation of
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the atom's point dipole moment. The <I>mu</I> attribute gives the
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magnitude of the atom's dipole moment.
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</P>
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<P>The <I>radius</I> attribute is specific to extended spherical particles
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that have a finite size, such as those defined with an atom style of
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<I>sphere</I>.
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<P>The <I>radius</I> and <I>diameter</I> attributes are specific to extended
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spherical particles that have a finite size, such as those defined
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with an atom style of <I>sphere</I>.
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</P>
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<P>The <I>omegax</I>, <I>omegay</I>, and <I>omegaz</I> attributes are specific to
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extended spherical or aspherical particles that have an angular
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|
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25
doc/dump.txt
25
doc/dump.txt
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@ -36,12 +36,12 @@ args = list of arguments for a particular style :l
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f_ID\[N\] = Nth column of local array calculated by a fix with ID :pre
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{custom} args = list of atom attributes
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possible attributes = id, mol, type, mass,
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possible attributes = id, mol, type, element, mass,
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x, y, z, xs, ys, zs, xu, yu, zu,
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xsu, ysu, zsu, ix, iy, iz,
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vx, vy, vz, fx, fy, fz,
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q, mux, muy, muz, mu,
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radius, omegax, omegay, omegaz,
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radius, diameter, omegax, omegay, omegaz,
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angmomx, angmomy, angmomz, tqx, tqy, tqz,
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spin, eradius, ervel, erforce,
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c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
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@ -49,6 +49,7 @@ args = list of arguments for a particular style :l
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id = atom ID
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mol = molecule ID
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type = atom type
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element = name of atom element, as defined by "dump_modify"_dump_modify.html command
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mass = atom mass
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x,y,z = unscaled atom coordinates
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xs,ys,zs = scaled atom coordinates
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@ -60,7 +61,7 @@ args = list of arguments for a particular style :l
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q = atom charge
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mux,muy,muz = orientation of dipole moment of atom
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mu = magnitude of dipole moment of atom
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radius = radius of spherical particle
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radius,diameter = radius,diameter of spherical particle
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omegax,omegay,omegaz = angular velocity of extended particle
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angmomx,angmomy,angmomz = angular momentum of extended particle
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tqx,tqy,tqz = torque on extended particles
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@ -379,13 +380,17 @@ array calculated by the fix.
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This section explains the atom attributes that can be specified as
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part of the {custom} and {cfg} styles.
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The {id}, {mol}, {type}, {mass}, {vx}, {vy}, {vz}, {fx}, {fy},
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The {id}, {mol}, {type}, {element}, {mass}, {vx}, {vy}, {vz}, {fx}, {fy},
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{fz}, {q} attributes are self-explanatory.
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{Id} is the atom ID. {Mol} is the molecule ID, included in the data
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file for molecular systems. {Type} is the atom type. {Mass} is the
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atom mass. {Vx}, {vy}, {vz}, {fx}, {fy}, {fz}, and {q} are components
|
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of atom velocity and force and atomic charge.
|
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file for molecular systems. {Type} is the atom type. {Element} is
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typically the chemical name of an element, which you must assign to
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each type via the "dump_modify element"_dump_modify.html command.
|
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More generally, it can be any string you wish to associated with an
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atom type. {Mass} is the atom mass. {Vx}, {vy}, {vz}, {fx}, {fy},
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{fz}, and {q} are components of atom velocity and force and atomic
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charge.
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There are several options for outputting atom coordinates. The {x},
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{y}, {z} attributes write atom coordinates "unscaled", in the
|
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|
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@ -414,9 +419,9 @@ defined with an atom style of {dipole}. They give the orientation of
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the atom's point dipole moment. The {mu} attribute gives the
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magnitude of the atom's dipole moment.
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|
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The {radius} attribute is specific to extended spherical particles
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that have a finite size, such as those defined with an atom style of
|
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{sphere}.
|
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The {radius} and {diameter} attributes are specific to extended
|
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spherical particles that have a finite size, such as those defined
|
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with an atom style of {sphere}.
|
||||
|
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The {omegax}, {omegay}, and {omegaz} attributes are specific to
|
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extended spherical or aspherical particles that have an angular
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|
|
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@ -11,12 +11,9 @@
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<H3>dump image command
|
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</H3>
|
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<P>NOTE: The dump image command has not yet been released as part of
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LAMMPS.
|
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</P>
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<P><B>Syntax:</B>
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</P>
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<PRE>dump ID group-ID image N file keyword value ...
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<PRE>dump ID group-ID image N file x y z type type keyword value ...
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</PRE>
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<UL><LI>ID = user-assigned name for the dump
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@ -30,43 +27,47 @@ LAMMPS.
|
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<LI>zero or more keyword/value pairs may be appended
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<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>
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<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>
|
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|
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<PRE> <I>atom</I> values = color diam
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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
|
||||
D = numeric value for atom diameter (distance units)
|
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<I>bond</I> values = color diam
|
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color = <I>none</I> or <I>atom</I> or <I>type</I>
|
||||
diam = D or <I>type</I>
|
||||
D = numeric value for bond diameter (distance units)
|
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<I>size</I> values = width height
|
||||
width = width of image in # of pixels
|
||||
height = height of image in # of pixels
|
||||
<I>view</I> values = theta phi
|
||||
theta = view angle from +z axis (degrees)
|
||||
phi = azimuthal view angle (degrees)
|
||||
theta or phi can be a variable (see below)
|
||||
<I>center</I> values = flag Cx Cy Cz = center point of image (distance units)
|
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flag = "s" for static, "d" for dynamic
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Cx,Cy,Cz can be variables (see below)
|
||||
<I>up</I> values = Ux Uy Uz = components of up vector
|
||||
Ux,Uy,Uz can be variables (see below)
|
||||
<I>zoom</I> value = factor = scale image size by this factor
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factor can be a variable (see below)
|
||||
<I>persp</I> value = factor = perspective setting
|
||||
factor can be a variable (see below)
|
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<I>box</I> values = yes/no diam
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yes/no = do or do not draw simulation box lines
|
||||
diam = diameter of box lines as fraction of shortest box length
|
||||
<I>axes</I> values = yes/no length diam
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||||
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
|
||||
<I>shiny</I> value = factor
|
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factor = shinyness of spheres and cylinders from 0.0 to 1.0
|
||||
<I>ssao</I> value = yes/no
|
||||
yes/no = turn on/off SSAO depth shading
|
||||
<PRE> <I>atom</I> values = color diam = color and size of atoms
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color = <I>none</I> or <I>type</I> or <I>element</I> or atom-attribute
|
||||
diam = number or <I>type</I> or <I>element</I> or atom-attribute
|
||||
number = numeric value for atom diameter (distance units)
|
||||
<I>bond</I> values = color diam = color and width of bonds
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||||
color = <I>none</I> or <I>atom</I> or <I>type</I>
|
||||
diam = number or <I>type</I>
|
||||
numer = numeric value for bond diameter (distance units)
|
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<I>size</I> values = width height = size of images
|
||||
width = width of image in # of pixels
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height = height of image in # of pixels
|
||||
<I>view</I> values = theta phi = view of simulation box
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theta = view angle from +z axis (degrees)
|
||||
phi = azimuthal view angle (degrees)
|
||||
theta or phi can be a variable (see below)
|
||||
<I>center</I> values = flag Cx Cy Cz = center point of image
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flag = "s" for static, "d" for dynamic
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Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box)
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Cx,Cy,Cz can be variables (see below)
|
||||
<I>up</I> values = Ux Uy Uz = direction that is "up" in image
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||||
Ux,Uy,Uz = components of up vector
|
||||
Ux,Uy,Uz can be variables (see below)
|
||||
<I>zoom</I> 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)
|
||||
<I>persp</I> value = factor = amount of "perspective" in image
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||||
factor = amount of perspective (0 = none, < 1 = some, > 1 = highly skewed)
|
||||
factor can be a variable (see below)
|
||||
<I>box</I> 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
|
||||
<I>axes</I> values = yes/no length diam = draw xyz axes
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||||
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
|
||||
<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>
|
||||
|
||||
</UL>
|
||||
|
|
@ -79,8 +80,9 @@ LAMMPS.
|
|||
<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
|
||||
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 <A HREF = "dump.html">dump</A> doc page.
|
||||
details below. Other dump styles store snapshots of numerical data
|
||||
asociated with atoms in various formats, as discussed on the
|
||||
<A HREF = "dump.html">dump</A> doc page.
|
||||
</P>
|
||||
<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
|
||||
|
|
@ -88,13 +90,14 @@ alter what atoms are included in the image.
|
|||
</P>
|
||||
<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
|
||||
PPM file is created. To write out JPG files, you must build LAMMPS
|
||||
with a JPEG library. See <A HREF = "Section_start.html#2_2_4">this section</A> 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 <A HREF = "Section_start.html#2_2_4">this
|
||||
section</A> of the manual for instructions on
|
||||
how to do this.
|
||||
</P>
|
||||
<P>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.
|
||||
</P>
|
||||
<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
|
||||
can be useful if the dump command is invoked after a minimization
|
||||
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
|
||||
for <I>dcd</I> style).
|
||||
using the <A HREF = "dump_modify.html">dump_modify every</A> command.
|
||||
</P>
|
||||
<P>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
|
||||
<A HREF = "dump_modify.html">dump_modify pad</A> 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.
|
||||
<P>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 <A HREF = "dump_modify.html">dump_modify pad</A> 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.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
|
|
@ -130,14 +131,14 @@ assigning colors to atoms, bonds, and other image features.
|
|||
<HR>
|
||||
|
||||
<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
|
||||
value), then no atoms are drawn.
|
||||
the image. If <I>none</I> is specified for the <I>color</I> value (with any
|
||||
<I>diam</I> value), then no atoms are drawn.
|
||||
</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>If <I>type</I> 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:
|
||||
<P>If <I>type</I> is specified for the <I>color</I> value, then the color of each
|
||||
atom is determined by its atom type. By default the mapping of types
|
||||
to colors is as follows:
|
||||
</P>
|
||||
<UL><LI>type 1 = red
|
||||
<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
|
||||
<A HREF = "dump_modify.html">dump_modify acolor</A> command.
|
||||
</P>
|
||||
<P>If <I>element</I> 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
|
||||
<A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualization package.
|
||||
<P>If <I>element</I> is specified for the <I>color</I> 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 <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualization package.
|
||||
</P>
|
||||
|
||||
|
||||
<P>An atom-attribute can also be used for the color value. Any attribute
|
||||
listed on the <A HREF = "dump.html">dump custom</A> doc page can be used, e.g. vx,
|
||||
fy, q, spin, etc. This includes per-atom quantities calculated by a
|
||||
<A HREF = "compute.html">compute</A>, <A HREF = "fix.html">fix</A>, or <A HREF = "variable.html">variable</A>.
|
||||
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.
|
||||
<P>An atom-attribute can also be used for the <I>color</I> value. Any
|
||||
attribute listed on the <A HREF = "dump.html">dump custom</A> doc page can be used,
|
||||
e.g. vx, fy, q, spin, etc. This includes per-atom quantities
|
||||
calculated by a <A HREF = "compute.html">compute</A>, <A HREF = "fix.html">fix</A>, or
|
||||
<A HREF = "variable.html">variable</A>. 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.
|
||||
</P>
|
||||
<P>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".
|
||||
</P>
|
||||
<P>The diam value can be a numeric value <I>D</I> or <I>type</I> or <I>element</I> or
|
||||
<I>radius</I> or <I>shape</I> or an atom-attribute.
|
||||
<P>The <I>diam</I> value can be a numeric value or <I>type</I> or <I>element</I> or an
|
||||
atom-attribute.
|
||||
</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
|
||||
<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>If <I>type</I> 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 <A HREF = "dump_modify.html">dump_modify
|
||||
<P>If <I>type</I> 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 <A HREF = "dump_modify.html">dump_modify
|
||||
adiam</A> command.
|
||||
</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
|
||||
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 <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualization package.
|
||||
element has a diameter associated with it, which is the same as the
|
||||
diameters used by the <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualization package.
|
||||
</P>
|
||||
<P>If <I>radius</I> or <I>shape</I> 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.
|
||||
</P>
|
||||
<P>An atom-attribute can also be used for the diam value. Any attribute
|
||||
listed on the <A HREF = "dump.html">dump custom</A> doc page can be used, e.g. vx,
|
||||
fy, q, spin, etc. This includes per-atom quantities calculated by a
|
||||
<A HREF = "compute.html">compute</A>, <A HREF = "fix.html">fix</A>, or <A HREF = "variable.html">variable</A>.
|
||||
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>An atom-attribute can also be used for the <I>diam</I> value. Any
|
||||
attribute listed on the <A HREF = "dump.html">dump custom</A> doc page can be used,
|
||||
e.g. vx, fy, q, spin, radius, etc. This includes per-atom quantities
|
||||
calculated by a <A HREF = "compute.html">compute</A>, <A HREF = "fix.html">fix</A>, or
|
||||
<A HREF = "variable.html">variable</A>. 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 <A HREF = "atom_style.html">atom_style sphere</A> define a per-particle radius,
|
||||
which can be used as an atom-attribute.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<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.
|
||||
</P>
|
||||
<P>If <I>atom</I> 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.
|
||||
<P>If <I>atom</I> is specified for the <I>color</I> 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.
|
||||
</P>
|
||||
<P>If <I>type</I> 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:
|
||||
<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 bond
|
||||
types to colors is as follows:
|
||||
</P>
|
||||
<UL><LI>type 1 = red
|
||||
<LI>type 2 = green
|
||||
|
|
@ -228,57 +227,58 @@ to colors is as follows:
|
|||
<LI>type 5 = aqua
|
||||
<LI>type 6 = cyan
|
||||
</UL>
|
||||
<P>and repeats itself for types > 6. This mapping can be changed by the
|
||||
<A HREF = "dump_modify.html">dump_modify bcolor</A> command.
|
||||
<P>and repeats itself for bond types > 6. This mapping can be changed by
|
||||
the <A HREF = "dump_modify.html">dump_modify bcolor</A> command.
|
||||
</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>If a numeric value <I>D</I> is specified, then all bond will be drawn with
|
||||
that diameter, e.g. 1.0, which is in distance units in whatever
|
||||
<A HREF = "units.html">units</A> you are using, e.g. Angstroms.
|
||||
<P>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
|
||||
<A HREF = "units.html">units</A> the input script uses, e.g. Angstroms.
|
||||
</P>
|
||||
<P>If <I>type</I> 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 <A HREF = "dump_modify.html">dump_modify
|
||||
<P>If <I>type</I> is specified for the <I>diam</I> 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 <A HREF = "dump_modify.html">dump_modify
|
||||
bdiam</A> command.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The <I>size</I> keyword determines the width and height of the created
|
||||
image files, in numbers of pixels in each direction.
|
||||
<P>The <I>size</I> keyword sets the width and height of the created images,
|
||||
i.e. the number of pixels in each direction.
|
||||
</P>
|
||||
<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
|
||||
they control how the simulation box appears in the image.
|
||||
</P>
|
||||
<P>All of the <I>view</I>, <I>center</I>, <I>up</I>, <I>zoom</I>, and <I>persp</I> 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.
|
||||
<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 quantities, whose meaning is explained below.
|
||||
Any of them can also be specified as an <A HREF = "variable.html">equal-style
|
||||
variable</A>, 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.
|
||||
</P>
|
||||
<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
|
||||
axis, and must be an angle from 0 to 180 degrees. The <I>phi</I> setting
|
||||
is an azimuthal angle around the z axis and can be positive or
|
||||
negative.
|
||||
box is viewed, looking towards the <I>center</I> point. The <I>theta</I> value
|
||||
is the vertical angle from the +z axis, and must be an angle from 0 to
|
||||
180 degrees. The <I>phi</I> 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 <I>center</I> point.
|
||||
</P>
|
||||
<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
|
||||
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 <I>Cx</I>, <I>Cy</I>, or <I>Cz</I> you may get a blank image. Internally, <I>Cx</I>,
|
||||
<I>Cy</I>, and <I>Cz</I> are converted into a point in simulation space. If
|
||||
<I>flag</I> is set to "s" for static, then this conversion is done once, at
|
||||
the time the dump command is issued. If <I>flag</I> is set to "d" for
|
||||
the center of the image. Note, however, that if you choose strange
|
||||
values for <I>Cx</I>, <I>Cy</I>, or <I>Cz</I> you may get a blank image. Internally,
|
||||
<I>Cx</I>, <I>Cy</I>, and <I>Cz</I> are converted into a point in simulation space.
|
||||
If <I>flag</I> is set to "s" for static, then this conversion is done once,
|
||||
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
|
||||
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.
|
|||
<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
|
||||
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
|
||||
and user-specified up vector. Thus this internal vector is computed
|
||||
from the user-specified <I>up</I> vector as
|
||||
<I>pni</I> 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 <I>up</I> vector as
|
||||
</P>
|
||||
<PRE>up_internal = view cross (up cross view)
|
||||
</PRE>
|
||||
<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
|
||||
<I>phi</I> settings.
|
||||
<I>phi</I> values.
|
||||
</P>
|
||||
<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> >
|
||||
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>The <I>persp</I> 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 <I>factor</I> setting of 0.0
|
||||
means that parallel lines will meet at infininty (1.0/factor), which
|
||||
is an orthographic rendering with no persepctive. A <I>factor</I> setting
|
||||
between 0.0 and 1.0 will introduce more perspective. A <I>factor</I> > 1
|
||||
will create a highly skewed image with a large amount of perspective.
|
||||
</P>
|
||||
<P>The <I>dynamic</I> keyword
|
||||
determines the color and thickness of bonds
|
||||
rendered in the image.
|
||||
<P>The <I>persp</I> 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 <I>factor</I> value
|
||||
of 0.0 means that parallel lines will meet at infininty (1.0/factor),
|
||||
which is an orthographic rendering with no persepctive. A <I>factor</I>
|
||||
value between 0.0 and 1.0 will introduce more perspective. A <I>factor</I>
|
||||
value > 1 will create a highly skewed image with a large amount of
|
||||
perspective.
|
||||
</P>
|
||||
<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
|
||||
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
|
||||
fraction of the shortest box lenght in x, y, or z. The color of the
|
||||
box boundaires can be set with the <A HREF = "dump_modify.html">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 <A HREF = "dump_modify.html">dump_modify
|
||||
boxcolor</A> command.
|
||||
</P>
|
||||
<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
|
||||
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
|
||||
red,green/blue. The origin of these cylinders will be offset
|
||||
from the lower left corner of the box by 10%. The <I>length</I> setting
|
||||
determines how long the cylinders will be. The <I>diam</I> 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 <I>length</I> setting determines
|
||||
how long the cylinders will be as a fraction of the respective box
|
||||
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>
|
||||
<HR>
|
||||
|
||||
<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
|
||||
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.
|
||||
</P>
|
||||
<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
|
||||
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 <I>no</I> 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 <I>no</I> is set, no depth shading is performed.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
|
|
@ -424,7 +422,6 @@ documentation for details.
|
|||
<LI>up = 0 1 0 (for 2d)
|
||||
<LI>zoom = 1.0
|
||||
<LI>persp = 0.0
|
||||
<LI>dynamic = no
|
||||
<LI>box = yes 0.01
|
||||
<LI>axes = no 0.0 0.0
|
||||
<LI>shiny = 1.0
|
||||
|
|
|
|||
|
|
@ -8,12 +8,9 @@
|
|||
|
||||
dump image command :h3
|
||||
|
||||
NOTE: The dump image command has not yet been released as part of
|
||||
LAMMPS.
|
||||
|
||||
[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
|
||||
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
|
||||
file = name of file to write image to :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
|
||||
{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 :pre
|
||||
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 = 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 :pre
|
||||
:ule
|
||||
|
||||
[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
|
||||
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"_dump.html doc page.
|
||||
details below. Other dump styles store snapshots of numerical data
|
||||
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
|
||||
"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.
|
||||
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"_Section_start.html#2_2_4 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"_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
|
||||
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
|
||||
|
||||
|
|
@ -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
|
||||
can be useful if the dump command is invoked after a minimization
|
||||
ended on an arbitrary timestep. N can be changed between runs by
|
||||
using the "dump_modify every"_dump_modify.html command (not allowed
|
||||
for {dcd} style).
|
||||
using the "dump_modify every"_dump_modify.html command.
|
||||
|
||||
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"_dump_modify.html 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"_dump_modify.html 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.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -119,14 +120,14 @@ assigning colors to atoms, bonds, and other image features.
|
|||
:line
|
||||
|
||||
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:
|
||||
|
||||
type 1 = red
|
||||
type 2 = green
|
||||
|
|
@ -138,21 +139,22 @@ type 6 = cyan :ul
|
|||
and repeats itself for types > 6. This mapping can be changed by the
|
||||
"dump_modify acolor"_dump_modify.html 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"_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"_atomeye visualization package.
|
||||
|
||||
:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)
|
||||
|
||||
An atom-attribute can also be used for the color value. Any attribute
|
||||
listed on the "dump custom"_dump.html doc page can be used, e.g. vx,
|
||||
fy, q, spin, etc. This includes per-atom quantities calculated by a
|
||||
"compute"_compute.html, "fix"_fix.html, or "variable"_variable.html.
|
||||
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"_dump.html doc page can be used,
|
||||
e.g. vx, fy, q, spin, etc. This includes per-atom quantities
|
||||
calculated by a "compute"_compute.html, "fix"_fix.html, or
|
||||
"variable"_variable.html. 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
|
||||
|
|
@ -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
|
||||
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"_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
|
||||
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"_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
|
||||
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"_atomeye visualization package.
|
||||
element has a diameter associated with it, which is the same as the
|
||||
diameters used by the "AtomEye"_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"_dump.html doc page can be used, e.g. vx,
|
||||
fy, q, spin, etc. This includes per-atom quantities calculated by a
|
||||
"compute"_compute.html, "fix"_fix.html, or "variable"_variable.html.
|
||||
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"_dump.html doc page can be used,
|
||||
e.g. vx, fy, q, spin, radius, etc. This includes per-atom quantities
|
||||
calculated by a "compute"_compute.html, "fix"_fix.html, or
|
||||
"variable"_variable.html. 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"_atom_style.html define a per-particle radius,
|
||||
which can be used as an atom-attribute.
|
||||
|
||||
:line
|
||||
|
||||
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:
|
||||
|
||||
type 1 = red
|
||||
type 2 = green
|
||||
|
|
@ -217,57 +216,58 @@ type 4 = yellow
|
|||
type 5 = aqua
|
||||
type 6 = cyan :ul
|
||||
|
||||
and repeats itself for types > 6. This mapping can be changed by the
|
||||
"dump_modify bcolor"_dump_modify.html command.
|
||||
and repeats itself for bond types > 6. This mapping can be changed by
|
||||
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
|
||||
that diameter, e.g. 1.0, which is in distance units in whatever
|
||||
"units"_units.html 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"_units.html 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"_dump_modify.html command.
|
||||
|
||||
:line
|
||||
|
||||
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.
|
||||
|
||||
: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
|
||||
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"_variable.html, 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.
|
||||
|
|
@ -275,33 +275,30 @@ 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
|
||||
|
||||
up_internal = view cross (up cross view) :pre
|
||||
|
||||
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.
|
||||
|
||||
: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
|
||||
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"_dump_modify.html command.
|
||||
|
||||
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).
|
||||
|
||||
:line
|
||||
|
||||
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.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -413,7 +411,6 @@ up = 0 0 1 (for 3d)
|
|||
up = 0 1 0 (for 2d)
|
||||
zoom = 1.0
|
||||
persp = 0.0
|
||||
dynamic = no
|
||||
box = yes 0.01
|
||||
axes = no 0.0 0.0
|
||||
shiny = 1.0
|
||||
|
|
|
|||
|
|
@ -11,9 +11,6 @@
|
|||
|
||||
<H3>dump_modify command
|
||||
</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>
|
||||
<PRE>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 <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)
|
||||
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>bcolor</I> 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
|
||||
</PRE>
|
||||
<P>NOTE: add some image examples
|
||||
</P>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<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
|
||||
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 <A HREF = "dump.html">dump custom</A> 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 <A HREF = "dump.html">dump custom</A> command, with the exception
|
||||
of the <I>element</I> 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.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
|
|
@ -509,6 +509,8 @@ box size stored with the snapshot.
|
|||
<LI>adiam = * 1.0
|
||||
<LI>amap = min max cf 2 0.0 blue 1.0 red
|
||||
<LI>append = no
|
||||
<LI>bcolor = * red/green/blue/yellow/aqua/cyan
|
||||
<LI>bdiam = * 0.5
|
||||
<LI>bgcolor = black
|
||||
<LI>boxcolor = yellow
|
||||
<LI>color = 140 color names are pre-defined as listed below
|
||||
|
|
|
|||
|
|
@ -8,9 +8,6 @@
|
|||
|
||||
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:]
|
||||
|
||||
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
|
||||
"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)
|
||||
|
|
@ -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
|
||||
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)
|
||||
|
|
@ -95,6 +92,8 @@ dump_modify xtcdump precision 10000
|
|||
dump_modify 1 every 1000
|
||||
dump_modify 1 every v_myVar :pre
|
||||
|
||||
NOTE: add some image examples
|
||||
|
||||
[Description:]
|
||||
|
||||
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
|
||||
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"_dump.html 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"_dump.html 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.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -502,6 +502,8 @@ acolor = * red/green/blue/yellow/aqua/cyan
|
|||
adiam = * 1.0
|
||||
amap = min max cf 2 0.0 blue 1.0 red
|
||||
append = no
|
||||
bcolor = * red/green/blue/yellow/aqua/cyan
|
||||
bdiam = * 0.5
|
||||
bgcolor = black
|
||||
boxcolor = yellow
|
||||
color = 140 color names are pre-defined as listed below
|
||||
|
|
|
|||
Loading…
Reference in New Issue