forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11151 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
c4bc0ca8f2
commit
5ca5395c16
|
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@ -131,18 +131,20 @@ many timesteps until the desired # of particles has been inserted.
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<P>All other keywords are optional with defaults as shown below.
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</P>
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<P>The <I>diam</I> option is only used when inserting atoms and specifes the
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diameters of inserted particles. For molecule insertion, the
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diameters of individual atoms in the molecule can be specified in the
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file read by the <A HREF = "molecule.html">molecule</A> command. There are 3
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styles: <I>one</I>, <I>range</I>, or <I>poly</I>. For <I>one</I>, all particles will have
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diameter <I>D</I>. For <I>range</I>, the diameter of each particle will be
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chosen randomly and uniformly between the specified <I>Dlo</I> and <I>Dhi</I>
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bounds. For <I>poly</I>, a series of <I>Npoly</I> diameters is specified. For
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each diameter a percentage value from 0.0 to 1.0 is also specified.
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The <I>Npoly</I> percentages must sum to 1.0. For the example shown above
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with "diam 2 0.7 0.4 1.5 0.6", all inserted particles will have a
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diameter of 0.7 or 1.5. 40% of the particles will be small; 60% will
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be large.
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diameters of inserted particles. There are 3 styles: <I>one</I>, <I>range</I>,
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or <I>poly</I>. For <I>one</I>, all particles will have diameter <I>D</I>. For
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<I>range</I>, the diameter of each particle will be chosen randomly and
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uniformly between the specified <I>Dlo</I> and <I>Dhi</I> bounds. For <I>poly</I>, a
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series of <I>Npoly</I> diameters is specified. For each diameter a
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percentage value from 0.0 to 1.0 is also specified. The <I>Npoly</I>
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percentages must sum to 1.0. For the example shown above with "diam 2
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0.7 0.4 1.5 0.6", all inserted particles will have a diameter of 0.7
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or 1.5. 40% of the particles will be small; 60% will be large.
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</P>
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<P>Note that for molecule insertion, the diameters of individual atoms in
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the molecule can be specified in the file read by the
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<A HREF = "molecule.html">molecule</A> command. If not specified, the diameter of
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each atom in the molecule has a default diameter of 1.0.
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</P>
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<P>The <I>dens</I> and <I>vel</I> options enable inserted particles to have a range
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of densities or xy velocities. The specific values for a particular
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|
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@ -120,18 +120,20 @@ many timesteps until the desired # of particles has been inserted.
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All other keywords are optional with defaults as shown below.
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The {diam} option is only used when inserting atoms and specifes the
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diameters of inserted particles. For molecule insertion, the
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diameters of individual atoms in the molecule can be specified in the
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file read by the "molecule"_molecule.html command. There are 3
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styles: {one}, {range}, or {poly}. For {one}, all particles will have
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diameter {D}. For {range}, the diameter of each particle will be
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chosen randomly and uniformly between the specified {Dlo} and {Dhi}
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bounds. For {poly}, a series of {Npoly} diameters is specified. For
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each diameter a percentage value from 0.0 to 1.0 is also specified.
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The {Npoly} percentages must sum to 1.0. For the example shown above
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with "diam 2 0.7 0.4 1.5 0.6", all inserted particles will have a
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diameter of 0.7 or 1.5. 40% of the particles will be small; 60% will
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be large.
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diameters of inserted particles. There are 3 styles: {one}, {range},
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or {poly}. For {one}, all particles will have diameter {D}. For
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{range}, the diameter of each particle will be chosen randomly and
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uniformly between the specified {Dlo} and {Dhi} bounds. For {poly}, a
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series of {Npoly} diameters is specified. For each diameter a
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percentage value from 0.0 to 1.0 is also specified. The {Npoly}
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percentages must sum to 1.0. For the example shown above with "diam 2
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0.7 0.4 1.5 0.6", all inserted particles will have a diameter of 0.7
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or 1.5. 40% of the particles will be small; 60% will be large.
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Note that for molecule insertion, the diameters of individual atoms in
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the molecule can be specified in the file read by the
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"molecule"_molecule.html command. If not specified, the diameter of
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each atom in the molecule has a default diameter of 1.0.
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The {dens} and {vel} options enable inserted particles to have a range
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of densities or xy velocities. The specific values for a particular
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|
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@ -27,10 +27,16 @@ molecule CO2 co2.txt
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</P>
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<P>Define a molecule template that can be used as part of other LAMMPS
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commands, typically to define a collection of particles as a bonded
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molecule or a rigid body. Commands that use molecule templates
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include (or will include) <A HREF = "fix_deposit.html">fix deposit</A>, <A HREF = "fix_pour.html">fix
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pour</A>, and <A HREF = "fix_gcmc.html">fix gcmc</A>.
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molecule or a rigid body. Commands that currently use molecule
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templates (or will in the future) include:
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</P>
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<UL><LI><A HREF = "fix_deposit.html">fix deposit</A>
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<LI><A HREF = "fix_pour.html">fix pour</A>
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<LI><A HREF = "fix_rigid.html">fix rigid/small</A>
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<LI><A HREF = "fix_shake.html">fix shake</A>
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<LI><A HREF = "fix_gcmc.html">fix gcmc</A> (not yet)
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<LI><A HREF = "create_atoms.html">create_atoms</A> (not yet)
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</UL>
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<P>The ID of a molecule template can only contain alphanumeric characters
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and underscores.
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</P>
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@ -86,7 +92,8 @@ internally.
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</P>
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<UL><LI><I>Coords, Types, Charges, Diameters, Masses</I> = atom-property sections
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<LI><I>Bonds, Angles, Dihedrals, Impropers</I> = molecular topology sections
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<LI><I>Special Bond Counts, Special Bonds</I> = special neighbor info
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<LI><I>Special Bond Counts, Special Bonds</I> = special neighbor info
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<LI><I>Shake Flags, Shake Atoms, Shake Bond Types</I> = SHAKE info
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</UL>
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<P>IMPORTANT NOTE: Whether a section is required depends on how the
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molecule template is used by other LAMMPS commands. For example, to
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@ -104,10 +111,10 @@ templates for more details.
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<P>Each section is listed below in alphabetic order. The format of each
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section is described including the number of lines it must contain and
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rules (if any) for whether it can appear in the data file. In each
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case the ID is ignored; it is simply included for readability as a
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number from 1 to Nlines for the section, indicating which atom (or
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bond, etc) the entry applies to. The lines are assumed to be listed
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in order from 1 to Nlines.
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case the ID is ignored; it is simply included for readability, and
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should be a number from 1 to Nlines for the section, indicating which
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atom (or bond, etc) the entry applies to. The lines are assumed to be
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listed in order from 1 to Nlines, but LAMMPS does not check for this.
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</P>
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<HR>
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@ -134,8 +141,8 @@ in order from 1 to Nlines.
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<LI>q = charge on atom
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</UL>
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<P>This section is only allowed for <A HREF = "atom_style.html">atom styles</A> that
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support charge. If not listed, the default charge on each atom in the
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molecule is 0.0.
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support charge. If this section is not included, the default charge
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on each atom in the molecule is 0.0.
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</P>
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<HR>
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@ -159,9 +166,10 @@ not listed, the default diameter of each atom in the molecule is 1.0.
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</UL>
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<P>This section is only allowed for <A HREF = "atom_style.html">atom styles</A> that
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support per-atom mass, as opposed to per-type mass. See the
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<A HREF = "mass.html">mass</A> command for details. If not listed, the default mass
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for each atom is derived from its volume (see Diameters section) and a
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default density of 1.0, in <A HREF = "units.html">units</A> of mass/volume.
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<A HREF = "mass.html">mass</A> command for details. If this section is not
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included, the default mass for each atom is derived from its volume
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(see Diameters section) and a default density of 1.0, in
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<A HREF = "units.html">units</A> of mass/volume.
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</P>
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<HR>
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@ -253,6 +261,103 @@ appears, the Special Bond Counts section must also appear. If this
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section is not specied, the atoms in the molecule will have no special
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bonds.
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</P>
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<P><I>Shake Flags</I> section:
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</P>
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<UL><LI>one line per atom
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<LI>line syntax: ID flag
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<LI>flag = 0,1,2,3,4
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</UL>
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<P>This section is only needed when molecules created using the template
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will be constrained by SHAKE via the "fix shake" command. The other
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two Shake sections must also appear in the file, following this one.
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</P>
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<P>The meaning of the flag for each atom is as follows. See the <A HREF = "fix_shake.html">fix
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shake</A> doc page for a further description of SHAKE
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clusters.
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</P>
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<UL><LI>0 = not part of a SHAKE cluster
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<LI>1 = part of a SHAKE angle cluster (two bonds and the angle they form)
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<LI>2 = part of a 2-atom SHAKE cluster with a single bond
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<LI>3 = part of a 3-atom SHAKE cluster with two bonds
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<LI>4 = part of a 4-atom SHAKE cluster with three bonds
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</UL>
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<P><I>Shake Atoms</I> section:
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</P>
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<UL><LI>one line per atom
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<LI>line syntax: ID a b c d
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<LI>a,b,c,d = IDs of atoms in cluster
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</UL>
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<P>This section is only needed when molecules created using the template
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will be constrained by SHAKE via the "fix shake" command. The other
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two Shake sections must also appear in the file.
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</P>
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<P>The a,b,c,d values are atom IDs (from 1 to Natoms) for all the atoms
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in the SHAKE cluster that this atom belongs to. The number of values
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that must appear is determined by the shake flag for the atom (see the
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Shake Flags section above). All atoms in a particular cluster should
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list their a,b,c,d values identically.
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</P>
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<P>If flag = 0, no a,b,c,d values are listed on the line, just the
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(ignored) ID.
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</P>
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<P>If flag = 1, a,b,c are listed, where a = ID of central atom in the
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angle, and b,c the other two atoms in the angle.
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</P>
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<P>If flag = 2, a,b are listed, where a = ID of atom in bond with the the
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lowest ID, and b = ID of atom in bond with the highest ID.
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</P>
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<P>If flag = 3, a,b,c are listed, where a = ID of central atom,
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and b,c = IDs of other two atoms bonded to the central atom.
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||||
</P>
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||||
<P>If flag = 4, a,b,c,d are listed, where a = ID of central atom,
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and b,c,d = IDs of other three atoms bonded to the central atom.
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</P>
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<P>See the <A HREF = "fix_shake.html">fix shake</A> doc page for a further description
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of SHAKE clusters.
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</P>
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<P><I>Shake Bond Types</I> section:
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</P>
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<UL><LI>one line per atom
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<LI>line syntax: ID a b c
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<LI>a,b,c = bond types of bonds in cluster
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||||
</UL>
|
||||
<P>This section is only needed when molecules created using the template
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||||
will be constrained by SHAKE via the "fix shake" command. The other
|
||||
two Shake sections must also appear in the file.
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||||
</P>
|
||||
<P>The a,b,c values are bond types (from 1 to Nbondtypes) for all bonds
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||||
in the SHAKE cluster that this atom belongs to. The number of values
|
||||
that must appear is determined by the shake flag for the atom (see the
|
||||
Shake Flags section above). All atoms in a particular cluster should
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||||
list their a,b,c values identically.
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||||
</P>
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||||
<P>If flag = 0, no a,b,c values are listed on the line, just the
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||||
(ignored) ID.
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||||
</P>
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<P>If flag = 1, a,b,c are listed, where a = bondtype of the bond between
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||||
the central atom and the first non-central atom (value b in the Shake
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Atoms section), b = bondtype of the bond between the central atom and
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the 2nd non-central atom (value c in the Shake Atoms section), and c =
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the angle type (1 to Nangletypes) of the angle between the 3 atoms.
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||||
</P>
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||||
<P>If flag = 2, only a is listed, where a = bondtype of the bond between
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||||
the 2 atoms in the cluster.
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||||
</P>
|
||||
<P>If flag = 3, a,b are listed, where a = bondtype of the bond between
|
||||
the central atom and the first non-central atom (value b in the Shake
|
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Atoms section), and b = bondtype of the bond between the central atom
|
||||
and the 2nd non-central atom (value c in the Shake Atoms section).
|
||||
</P>
|
||||
<P>If flag = 4, a,b,c are listed, where a = bondtype of the bond between
|
||||
the central atom and the first non-central atom (value b in the Shake
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||||
Atoms section), b = bondtype of the bond between the central atom and
|
||||
the 2nd non-central atom (value c in the Shake Atoms section), and c =
|
||||
bondtype of the bond between the central atom and the 3rd non-central
|
||||
atom (value d in the Shake Atoms section).
|
||||
</P>
|
||||
<P>See the <A HREF = "fix_shake.html">fix shake</A> doc page for a further description
|
||||
of SHAKE clusters.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><B>Restrictions:</B> none
|
||||
|
|
|
|||
131
doc/molecule.txt
131
doc/molecule.txt
|
|
@ -24,9 +24,15 @@ molecule CO2 co2.txt :pre
|
|||
|
||||
Define a molecule template that can be used as part of other LAMMPS
|
||||
commands, typically to define a collection of particles as a bonded
|
||||
molecule or a rigid body. Commands that use molecule templates
|
||||
include (or will include) "fix deposit"_fix_deposit.html, "fix
|
||||
pour"_fix_pour.html, and "fix gcmc"_fix_gcmc.html.
|
||||
molecule or a rigid body. Commands that currently use molecule
|
||||
templates (or will in the future) include:
|
||||
|
||||
"fix deposit"_fix_deposit.html
|
||||
"fix pour"_fix_pour.html
|
||||
"fix rigid/small"_fix_rigid.html
|
||||
"fix shake"_fix_shake.html
|
||||
"fix gcmc"_fix_gcmc.html (not yet)
|
||||
"create_atoms"_create_atoms.html (not yet) :ul
|
||||
|
||||
The ID of a molecule template can only contain alphanumeric characters
|
||||
and underscores.
|
||||
|
|
@ -83,7 +89,8 @@ These are the allowed section keywords for the body of the file.
|
|||
|
||||
{Coords, Types, Charges, Diameters, Masses} = atom-property sections
|
||||
{Bonds, Angles, Dihedrals, Impropers} = molecular topology sections
|
||||
{Special Bond Counts, Special Bonds} = special neighbor info :ul
|
||||
{Special Bond Counts, Special Bonds} = special neighbor info
|
||||
{Shake Flags, Shake Atoms, Shake Bond Types} = SHAKE info :ul
|
||||
|
||||
IMPORTANT NOTE: Whether a section is required depends on how the
|
||||
molecule template is used by other LAMMPS commands. For example, to
|
||||
|
|
@ -101,10 +108,10 @@ templates for more details.
|
|||
Each section is listed below in alphabetic order. The format of each
|
||||
section is described including the number of lines it must contain and
|
||||
rules (if any) for whether it can appear in the data file. In each
|
||||
case the ID is ignored; it is simply included for readability as a
|
||||
number from 1 to Nlines for the section, indicating which atom (or
|
||||
bond, etc) the entry applies to. The lines are assumed to be listed
|
||||
in order from 1 to Nlines.
|
||||
case the ID is ignored; it is simply included for readability, and
|
||||
should be a number from 1 to Nlines for the section, indicating which
|
||||
atom (or bond, etc) the entry applies to. The lines are assumed to be
|
||||
listed in order from 1 to Nlines, but LAMMPS does not check for this.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -131,8 +138,8 @@ line syntax: ID q
|
|||
q = charge on atom :ul
|
||||
|
||||
This section is only allowed for "atom styles"_atom_style.html that
|
||||
support charge. If not listed, the default charge on each atom in the
|
||||
molecule is 0.0.
|
||||
support charge. If this section is not included, the default charge
|
||||
on each atom in the molecule is 0.0.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -156,9 +163,10 @@ mass = mass of atom :ul
|
|||
|
||||
This section is only allowed for "atom styles"_atom_style.html that
|
||||
support per-atom mass, as opposed to per-type mass. See the
|
||||
"mass"_mass.html command for details. If not listed, the default mass
|
||||
for each atom is derived from its volume (see Diameters section) and a
|
||||
default density of 1.0, in "units"_units.html of mass/volume.
|
||||
"mass"_mass.html command for details. If this section is not
|
||||
included, the default mass for each atom is derived from its volume
|
||||
(see Diameters section) and a default density of 1.0, in
|
||||
"units"_units.html of mass/volume.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -250,6 +258,103 @@ appears, the Special Bond Counts section must also appear. If this
|
|||
section is not specied, the atoms in the molecule will have no special
|
||||
bonds.
|
||||
|
||||
{Shake Flags} section:
|
||||
|
||||
one line per atom
|
||||
line syntax: ID flag
|
||||
flag = 0,1,2,3,4 :ul
|
||||
|
||||
This section is only needed when molecules created using the template
|
||||
will be constrained by SHAKE via the "fix shake" command. The other
|
||||
two Shake sections must also appear in the file, following this one.
|
||||
|
||||
The meaning of the flag for each atom is as follows. See the "fix
|
||||
shake"_fix_shake.html doc page for a further description of SHAKE
|
||||
clusters.
|
||||
|
||||
0 = not part of a SHAKE cluster
|
||||
1 = part of a SHAKE angle cluster (two bonds and the angle they form)
|
||||
2 = part of a 2-atom SHAKE cluster with a single bond
|
||||
3 = part of a 3-atom SHAKE cluster with two bonds
|
||||
4 = part of a 4-atom SHAKE cluster with three bonds :ul
|
||||
|
||||
{Shake Atoms} section:
|
||||
|
||||
one line per atom
|
||||
line syntax: ID a b c d
|
||||
a,b,c,d = IDs of atoms in cluster :ul
|
||||
|
||||
This section is only needed when molecules created using the template
|
||||
will be constrained by SHAKE via the "fix shake" command. The other
|
||||
two Shake sections must also appear in the file.
|
||||
|
||||
The a,b,c,d values are atom IDs (from 1 to Natoms) for all the atoms
|
||||
in the SHAKE cluster that this atom belongs to. The number of values
|
||||
that must appear is determined by the shake flag for the atom (see the
|
||||
Shake Flags section above). All atoms in a particular cluster should
|
||||
list their a,b,c,d values identically.
|
||||
|
||||
If flag = 0, no a,b,c,d values are listed on the line, just the
|
||||
(ignored) ID.
|
||||
|
||||
If flag = 1, a,b,c are listed, where a = ID of central atom in the
|
||||
angle, and b,c the other two atoms in the angle.
|
||||
|
||||
If flag = 2, a,b are listed, where a = ID of atom in bond with the the
|
||||
lowest ID, and b = ID of atom in bond with the highest ID.
|
||||
|
||||
If flag = 3, a,b,c are listed, where a = ID of central atom,
|
||||
and b,c = IDs of other two atoms bonded to the central atom.
|
||||
|
||||
If flag = 4, a,b,c,d are listed, where a = ID of central atom,
|
||||
and b,c,d = IDs of other three atoms bonded to the central atom.
|
||||
|
||||
See the "fix shake"_fix_shake.html doc page for a further description
|
||||
of SHAKE clusters.
|
||||
|
||||
{Shake Bond Types} section:
|
||||
|
||||
one line per atom
|
||||
line syntax: ID a b c
|
||||
a,b,c = bond types of bonds in cluster :ul
|
||||
|
||||
This section is only needed when molecules created using the template
|
||||
will be constrained by SHAKE via the "fix shake" command. The other
|
||||
two Shake sections must also appear in the file.
|
||||
|
||||
The a,b,c values are bond types (from 1 to Nbondtypes) for all bonds
|
||||
in the SHAKE cluster that this atom belongs to. The number of values
|
||||
that must appear is determined by the shake flag for the atom (see the
|
||||
Shake Flags section above). All atoms in a particular cluster should
|
||||
list their a,b,c values identically.
|
||||
|
||||
If flag = 0, no a,b,c values are listed on the line, just the
|
||||
(ignored) ID.
|
||||
|
||||
If flag = 1, a,b,c are listed, where a = bondtype of the bond between
|
||||
the central atom and the first non-central atom (value b in the Shake
|
||||
Atoms section), b = bondtype of the bond between the central atom and
|
||||
the 2nd non-central atom (value c in the Shake Atoms section), and c =
|
||||
the angle type (1 to Nangletypes) of the angle between the 3 atoms.
|
||||
|
||||
If flag = 2, only a is listed, where a = bondtype of the bond between
|
||||
the 2 atoms in the cluster.
|
||||
|
||||
If flag = 3, a,b are listed, where a = bondtype of the bond between
|
||||
the central atom and the first non-central atom (value b in the Shake
|
||||
Atoms section), and b = bondtype of the bond between the central atom
|
||||
and the 2nd non-central atom (value c in the Shake Atoms section).
|
||||
|
||||
If flag = 4, a,b,c are listed, where a = bondtype of the bond between
|
||||
the central atom and the first non-central atom (value b in the Shake
|
||||
Atoms section), b = bondtype of the bond between the central atom and
|
||||
the 2nd non-central atom (value c in the Shake Atoms section), and c =
|
||||
bondtype of the bond between the central atom and the 3rd non-central
|
||||
atom (value d in the Shake Atoms section).
|
||||
|
||||
See the "fix shake"_fix_shake.html doc page for a further description
|
||||
of SHAKE clusters.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:] none
|
||||
|
|
|
|||
Loading…
Reference in New Issue