forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13628 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
3341c4de6b
commit
936e136b9d
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@ -24,12 +24,13 @@
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<LI>keyword = <I>offset</I> or <I>auto</I>
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<PRE> <I>offset</I> values = toff boff aoff doff ioff
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toff = offset to add to atom type
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boff = offset to add to bond type
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aoff = offset to add to angle type
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doff = offset to add to dihedral type
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ioff = offset to add to improper type
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<I>auto</I> value = none = generate special bond lists automatically
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toff = offset to add to atom types
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boff = offset to add to bond types
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aoff = offset to add to angle types
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doff = offset to add to dihedral types
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ioff = offset to add to improper types
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<I>auto</I> value = none
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generate special bond lists automatically if <I>auto</I> is specified
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</PRE>
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</UL>
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@ -65,15 +66,15 @@ contains multiple molecules. The <A HREF = "atom_style.html">atom_style
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template</A> command allows multiple-molecule templates
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to define a system with more than one templated molecule.
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</P>
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<P>The optional <I>offset</I> keyword will add the specified offset values to
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the atom types, bond types, angle types, dihedral types, and improper
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<P>The optional <I>offset</I> keyword adds the specified offset values to the
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atom types, bond types, angle types, dihedral types, and improper
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types as they are read from the molecule file. E.g. if <I>toff</I> = 2,
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and the file uses atom types 1,2,3, then each created molecule will
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have atom types 3,4,5. This makes it easy to use the same molecule
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template file in different simulations. Note that the same offsets
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are applied to the molecules in all specified files. All five offset
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values are required, but individual values will be ignored if the
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molecule template does not define that attribute.
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values must be speicified, but individual values will be ignored if
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the molecule template does not use that attribute (e.g. no bonds).
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</P>
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<P>The optional <I>auto</I> keyword can be used for molecules with bonds
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instead of listing neighbors within the molecular topology explicitly.
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@ -450,6 +451,10 @@ of SHAKE clusters.
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<P><A HREF = "fix_deposit.html">fix deposit</A>, <A HREF = "fix_pour.html">fix pour</A>,
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<A HREF = "fix_gcmc.html">fix_gcmc</A>
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</P>
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<P><B>Default:</B> none
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<P><B>Default:</B>
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</P>
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<P>The default keyword values are offset 0 0 0 0 0, and no
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auto-generation of special bond lists. The latter is overridden in
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the <I>auto</I> keyword is used.
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</P>
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</HTML>
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@ -17,12 +17,13 @@ file1,file2,... = names of files containing molecule descriptions :l
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zero or more keyword/value pairs may be appended :l
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keyword = {offset} or {auto} :l
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{offset} values = toff boff aoff doff ioff
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toff = offset to add to atom type
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boff = offset to add to bond type
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aoff = offset to add to angle type
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doff = offset to add to dihedral type
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ioff = offset to add to improper type
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{auto} value = none = generate special bond lists automatically :pre
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toff = offset to add to atom types
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boff = offset to add to bond types
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aoff = offset to add to angle types
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doff = offset to add to dihedral types
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ioff = offset to add to improper types
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{auto} value = none
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generate special bond lists automatically if {auto} is specified :pre
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:ule
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[Examples:]
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@ -57,15 +58,15 @@ contains multiple molecules. The "atom_style
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template"_atom_style.html command allows multiple-molecule templates
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to define a system with more than one templated molecule.
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The optional {offset} keyword will add the specified offset values to
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the atom types, bond types, angle types, dihedral types, and improper
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The optional {offset} keyword adds the specified offset values to the
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atom types, bond types, angle types, dihedral types, and improper
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types as they are read from the molecule file. E.g. if {toff} = 2,
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and the file uses atom types 1,2,3, then each created molecule will
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have atom types 3,4,5. This makes it easy to use the same molecule
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template file in different simulations. Note that the same offsets
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are applied to the molecules in all specified files. All five offset
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values are required, but individual values will be ignored if the
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molecule template does not define that attribute.
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values must be speicified, but individual values will be ignored if
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the molecule template does not use that attribute (e.g. no bonds).
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The optional {auto} keyword can be used for molecules with bonds
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instead of listing neighbors within the molecular topology explicitly.
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@ -442,4 +443,8 @@ of SHAKE clusters.
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"fix deposit"_fix_deposit.html, "fix pour"_fix_pour.html,
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"fix_gcmc"_fix_gcmc.html
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[Default:] none
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[Default:]
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The default keyword values are offset 0 0 0 0 0, and no
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auto-generation of special bond lists. The latter is overridden in
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the {auto} keyword is used.
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@ -19,9 +19,23 @@
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<LI>zero or more keyword/arg pairs may be appended
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<LI>keyword = <I>fix</I>
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<LI>keyword = <I>add</I> or <I>offset</I> or <I>shift</I> or <I>group</I> or <I>fix</I>
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<PRE> <I>fix</I> args = fix-ID header-string section-string
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<PRE> <I>add</I> arg = <I>append</I> or <I>Nstart</I> or <I>merge</I>
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append = add new atoms with IDs appended to current IDs
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Nstart = add new atoms with IDs starting with Nstart
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merge = add new atoms with their IDs, assumed to not conflict with atoms that already exist
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<I>offset</I> args = toff boff aoff doff ioff
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toff = offset to add to atom types
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boff = offset to add to bond types
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aoff = offset to add to angle types
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doff = offset to add to dihedral types
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ioff = offset to add to improper types
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<I>shift</I> args = Sx Sy Sz
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Sx,Sy,Sz = distance to shift atoms when adding to system (distance units)
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<I>group</I> args = groupID
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groupID = add atoms in data file to this group
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<I>fix</I> args = fix-ID header-string section-string
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fix-ID = ID of fix to process header lines and sections of data file
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header-string = header lines containing this string will be passed to fix
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section-string = section names with this string will be passed to fix
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@ -33,6 +47,8 @@
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<PRE>read_data data.lj
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read_data ../run7/data.polymer.gz
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read_data data.protein fix mycmap crossterm CMAP
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read_data data.water add append offset 3 1 1 1 1 shift 0.0 0.0 50.0
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read_data data.water add merge 1 group solvent
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</PRE>
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<P><B>Description:</B>
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</P>
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@ -45,6 +61,77 @@ Also see the explanation of the <A HREF = "Section_start.html#start_7">-restart
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switch</A> which can convert a restart file to
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a data file.
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</P>
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<P>This command can also be used to add new atoms and their properties to
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an existing system by using the <I>add</I> keyword. If a simulation box
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does not yet exist, the <I>add</I> keyword cannot be used; the box size is
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defined in the data file. If a simulation box does exist, due to
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using the <A HREF = "create_box.html">create_box</A> command, or a previous
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read_data command, then the <I>add</I> keyword must be used. The box
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information in the new data file will be ignored.
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</P>
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<P>The three choices for the <I>add</I> argument affect how the IDs of atoms
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in the data file are treated. If <I>append</I> is specified, atoms in the
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data file are added to the current system, with their atom IDs reset
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so that an atomID = M in the data file becomes atomID = N+M, where N
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is the largest atom ID in the current system. This rule is applied to
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all occurrences of atom IDs in the data file, e.g. in the Velocity or
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Bonds section. If <I>Nstart</I> is specified, then a numeric value is
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given, e.g. 1000, so that atomID in the data file becomes atomID =
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1000+M. If <I>merge</I> is specified, the data file atoms are added to the
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current system without changing their IDs. They are assumed to merge
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(without conflict) with the currently defined atoms. It is up to you
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to insure there are no multiply defined atom IDs, as LAMMPS cannot
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easily check that this is the case.
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</P>
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<P>The <I>offset</I> and <I>shift</I> keywords can only be used if
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the <I>add</I> keyword is also used.
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</P>
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<P>The <I>offset</I> keyword adds the specified offset values to the atom
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types, bond types, angle types, dihedral types, and improper types as
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they are read from the data file. E.g. if <I>toff</I> = 2, and the file
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uses atom types 1,2,3, then the added atoms will have atom types
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3,4,5. These offsets apply to all occurrences of types in the data
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file, e.g. for the Atoms or Masses or Pair Coeffs or Bond Coeffs
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sections. This makes it easy to use atoms and molecules and their
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attributes from a data file in different simulations. All five offset
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values must be specified, but individual values will be ignored if the
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data file does not use that attribute (e.g. no bonds).
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</P>
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<P>The <I>shift</I> keyword can be used to specify a displacement applied to
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the coordinates of each atom. This is a mechanism for adding
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structured collections of atoms at different locations within the
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simulation box, to build up a complex geometry. It is up to you to
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insure atoms do not overlap unphysically which would lead to bad
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dynamics. The <A HREF = "delete_atoms.html">delete_atoms</A> command can be used to
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remove overlapping atoms.
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</P>
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<P>The <I>group</I> keyword adds all the atoms in the data file to the
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specified group-ID. The group will be created if it does not already
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exist. This is useful if you wish to change the coordinates of a
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particular set of atoms in a more complex way than can be done via the
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<I>shift</I> keyword, after using the read_data command multiple times.
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E.g. a group of atoms can be diplaced via the
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<A HREF = "displace_atoms.html">displate_atoms</A> command, which includes options
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for rotation or rescaling.
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</P>
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<P>The use of the <I>fix</I> keyword is discussed below.
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</P>
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<P>IMPORTANT NOTE: You cannot use the <I>append</I> keyword if a previously
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read-in data file defined any per-type quantities, e.g. via Masses or
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Pair Coeffs or Bond Coeffs sections. This is because those
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definitions trigger the allocation of arrays with length = # of
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currently defined types, and they cannot be reallocated. There are
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two solutions to this issue. The first is to define the per-type
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quantities in the input script, after all data files are read,
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e.g. via the <A HREF = "mass.html">mass</A> or <A HREF = "pair_coeff.html">pair_coeff</A> command.
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The second is to use the <A HREF = "create_box">create_box</A> command to create the
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simulation box and use its various options to define the total number
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of types of all kinds (atom, bond, etc). Then use the <I>merge</I> keyword
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to read as many data files as needed, with Masses, Pair Coeffs, etc
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sections that are indexed with appropriate types.
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</P>
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<HR>
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<P>The structure of the data file is important, though many settings and
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sections are optional or can come in any order. See the examples
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directory for sample data files for different problems.
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|
|
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@ -14,19 +14,34 @@ read_data file keyword args ... :pre
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file = name of data file to read in :ulb,l
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zero or more keyword/arg pairs may be appended :l
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keyword = {fix} :l
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keyword = {add} or {offset} or {shift} or {group} or {fix} :l
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{add} arg = {append} or {Nstart} or {merge}
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append = add new atoms with IDs appended to current IDs
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Nstart = add new atoms with IDs starting with Nstart
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merge = add new atoms with their IDs, assumed to not conflict with atoms that already exist
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{offset} args = toff boff aoff doff ioff
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toff = offset to add to atom types
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boff = offset to add to bond types
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aoff = offset to add to angle types
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doff = offset to add to dihedral types
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ioff = offset to add to improper types
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{shift} args = Sx Sy Sz
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Sx,Sy,Sz = distance to shift atoms when adding to system (distance units)
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{group} args = groupID
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groupID = add atoms in data file to this group
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{fix} args = fix-ID header-string section-string
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fix-ID = ID of fix to process header lines and sections of data file
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header-string = header lines containing this string will be passed to fix
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section-string = section names with this string will be passed to fix :pre
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:ule
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[Examples:]
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read_data data.lj
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read_data ../run7/data.polymer.gz
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read_data data.protein fix mycmap crossterm CMAP :pre
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read_data data.protein fix mycmap crossterm CMAP
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read_data data.water add append offset 3 1 1 1 1 shift 0.0 0.0 50.0
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read_data data.water add merge 1 group solvent :pre
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[Description:]
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@ -39,6 +54,77 @@ Also see the explanation of the "-restart command-line
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switch"_Section_start.html#start_7 which can convert a restart file to
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a data file.
|
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|
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This command can also be used to add new atoms and their properties to
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an existing system by using the {add} keyword. If a simulation box
|
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does not yet exist, the {add} keyword cannot be used; the box size is
|
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defined in the data file. If a simulation box does exist, due to
|
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using the "create_box"_create_box.html command, or a previous
|
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read_data command, then the {add} keyword must be used. The box
|
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information in the new data file will be ignored.
|
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|
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The three choices for the {add} argument affect how the IDs of atoms
|
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in the data file are treated. If {append} is specified, atoms in the
|
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data file are added to the current system, with their atom IDs reset
|
||||
so that an atomID = M in the data file becomes atomID = N+M, where N
|
||||
is the largest atom ID in the current system. This rule is applied to
|
||||
all occurrences of atom IDs in the data file, e.g. in the Velocity or
|
||||
Bonds section. If {Nstart} is specified, then a numeric value is
|
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given, e.g. 1000, so that atomID in the data file becomes atomID =
|
||||
1000+M. If {merge} is specified, the data file atoms are added to the
|
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current system without changing their IDs. They are assumed to merge
|
||||
(without conflict) with the currently defined atoms. It is up to you
|
||||
to insure there are no multiply defined atom IDs, as LAMMPS cannot
|
||||
easily check that this is the case.
|
||||
|
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The {offset} and {shift} keywords can only be used if
|
||||
the {add} keyword is also used.
|
||||
|
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The {offset} keyword adds the specified offset values to the atom
|
||||
types, bond types, angle types, dihedral types, and improper types as
|
||||
they are read from the data file. E.g. if {toff} = 2, and the file
|
||||
uses atom types 1,2,3, then the added atoms will have atom types
|
||||
3,4,5. These offsets apply to all occurrences of types in the data
|
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file, e.g. for the Atoms or Masses or Pair Coeffs or Bond Coeffs
|
||||
sections. This makes it easy to use atoms and molecules and their
|
||||
attributes from a data file in different simulations. All five offset
|
||||
values must be specified, but individual values will be ignored if the
|
||||
data file does not use that attribute (e.g. no bonds).
|
||||
|
||||
The {shift} keyword can be used to specify a displacement applied to
|
||||
the coordinates of each atom. This is a mechanism for adding
|
||||
structured collections of atoms at different locations within the
|
||||
simulation box, to build up a complex geometry. It is up to you to
|
||||
insure atoms do not overlap unphysically which would lead to bad
|
||||
dynamics. The "delete_atoms"_delete_atoms.html command can be used to
|
||||
remove overlapping atoms.
|
||||
|
||||
The {group} keyword adds all the atoms in the data file to the
|
||||
specified group-ID. The group will be created if it does not already
|
||||
exist. This is useful if you wish to change the coordinates of a
|
||||
particular set of atoms in a more complex way than can be done via the
|
||||
{shift} keyword, after using the read_data command multiple times.
|
||||
E.g. a group of atoms can be diplaced via the
|
||||
"displate_atoms"_displace_atoms.html command, which includes options
|
||||
for rotation or rescaling.
|
||||
|
||||
The use of the {fix} keyword is discussed below.
|
||||
|
||||
IMPORTANT NOTE: You cannot use the {append} keyword if a previously
|
||||
read-in data file defined any per-type quantities, e.g. via Masses or
|
||||
Pair Coeffs or Bond Coeffs sections. This is because those
|
||||
definitions trigger the allocation of arrays with length = # of
|
||||
currently defined types, and they cannot be reallocated. There are
|
||||
two solutions to this issue. The first is to define the per-type
|
||||
quantities in the input script, after all data files are read,
|
||||
e.g. via the "mass"_mass.html or "pair_coeff"_pair_coeff.html command.
|
||||
The second is to use the "create_box"_create_box command to create the
|
||||
simulation box and use its various options to define the total number
|
||||
of types of all kinds (atom, bond, etc). Then use the {merge} keyword
|
||||
to read as many data files as needed, with Masses, Pair Coeffs, etc
|
||||
sections that are indexed with appropriate types.
|
||||
|
||||
:line
|
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|
||||
The structure of the data file is important, though many settings and
|
||||
sections are optional or can come in any order. See the examples
|
||||
directory for sample data files for different problems.
|
||||
|
|
|
|||
Loading…
Reference in New Issue