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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13610 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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64
doc/molecule.html
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@ -13,16 +13,32 @@
</H3>
<P><B>Syntax:</B>
</P>
<PRE>molecule ID file1 file2 ...
<PRE>molecule ID file1 file2 ... keyword values ...
</PRE>
<UL><LI>ID = user-assigned name for the molecule template
<UL><LI>ID = user-assigned name for the molecule template
<LI>file1,file2,... = names of files containing molecule descriptions
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>offset</I> or <I>auto</I>
<PRE> <I>offset</I> values = toff boff aoff doff ioff
toff = offset to add to atom type
boff = offset to add to bond type
aoff = offset to add to angle type
doff = offset to add to dihedral type
ioff = offset to add to improper type
<I>auto</I> value = none = generate special bond lists automatically
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>molecule 1 mymol
molecule 1 co2.txt h2o.txt
molecule CO2 co2.txt
molecule CO2 co2.txt
molecule 1 mymol offset 6 9 18 23 14 auto
</PRE>
<P><B>Description:</B>
</P>
@ -49,6 +65,20 @@ contains multiple molecules. The <A HREF = "atom_style.html">atom_style
template</A> command allows multiple-molecule templates
to define a system with more than one templated molecule.
</P>
<P>The optional <I>offset</I> keyword will add the specified offset values to
the atom types, bond types, angle types, dihedral types, and improper
types as they are read from the molecule file. E.g. if <I>toff</I> = 2,
and the file uses atom types 1,2,3, then each created molecule will
have atom types 3,4,5. This makes it easy to use the same molecule
template file in different simulations. Note that the same offsets
are applied to the molecules in all specified files. All five offset
values are required, but individual values will be ignored if the
molecule template does not define that attribute.
</P>
<P>The optional <I>auto</I> keyword can be used for molecules with bonds
instead of listing neighbors within the molecular topology explicitly.
More details are given below.
</P>
<P>IMPORTANT NOTE: When using the <A HREF = "atom_style.html">atom_style template</A>
command with a molecule template that contains multiple molecules, you
should insure the atom types, bond types, angle_types, etc in all the
@ -59,7 +89,23 @@ with each other when a mixture system of H2O and CO2 molecules is
defined, e.g. by the <A HREF = "read_data.html">read_data</A> command. Rather the
H2O molecule should define atom types 1 and 2, and bond type 1. And
the CO2 molecule should define atom types 3 and 4 (or atom types 3 and
2 if a single oxygen type is desired), and bond type 2.
2 if a single oxygen type is desired), and bond type 2. You can also
use the <I>offset</I> keyword to shift all of these type values to new
values for a particular simulation.
</P>
<P>IMPORTANT NOTE: This command can be used to define molecules with
bonds, angles, dihedrals, imporopers, or special bond lists of
neighbors within a molecular topology, so that you can later add the
molecules to your simulation, via one or more of the commands listed
above. If such molecules do not already exist when LAMMPS creates the
simulation box, via the <A HREF = "create_box.html">create_box</A> or
<A HREF = "read_data.html">read_data</A> command, when you later add them you may
overflow the pre-allocated data structures which store molecular
topology information with each atom, and an error will be generated.
Both the <A HREF = "create_box.html">create_box</A> command and the data files read
by the <A HREF = "read_data.html">read_data</A> command have "extra" options which
insure space is allocated for storing topology info for molecules that
are added later.
</P>
<P>The format of an individual molecule file is similar to the data file
read by the <A HREF = "read_data.html">read_data</A> commands, and is as follows.
@ -119,10 +165,12 @@ internally.
<LI><I>Shake Flags, Shake Atoms, Shake Bond Types</I> = SHAKE info
</UL>
<P>If a Bonds section is specified then the Special Bond Counts and
Special Bonds sections must be also, since the latter is needed for
LAMMPS to properly exclude or weight bonded pairwise interactions
between bonded atoms. See the <A HREF = "special_bonds.html">special_bonds</A>
command for more details.
Special Bonds sections must be also unless the optional <I>auto</I> keyword
is defined. This info is needed for LAMMPS to properly exclude or
weight bonded pairwise interactions between bonded atoms. See the
<A HREF = "special_bonds.html">special_bonds</A> command for more details. If the
<I>auto</I> keyword is used, then LAMMPS will generate this information
automatically for the molecule.
</P>
<P>IMPORTANT NOTE: Whether a section is required depends on how the
molecule template is used by other LAMMPS commands. For example, to

61
doc/molecule.txt
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@ -10,16 +10,27 @@ molecule command :h3
[Syntax:]
molecule ID file1 file2 ... :pre
molecule ID file1 file2 ... keyword values ... :pre
ID = user-assigned name for the molecule template
file1,file2,... = names of files containing molecule descriptions :ul
ID = user-assigned name for the molecule template :ulb,l
file1,file2,... = names of files containing molecule descriptions :l
zero or more keyword/value pairs may be appended :l
keyword = {offset} or {auto} :l
{offset} values = toff boff aoff doff ioff
toff = offset to add to atom type
boff = offset to add to bond type
aoff = offset to add to angle type
doff = offset to add to dihedral type
ioff = offset to add to improper type
{auto} value = none = generate special bond lists automatically :pre
:ule
[Examples:]
molecule 1 mymol
molecule 1 co2.txt h2o.txt
molecule CO2 co2.txt :pre
molecule CO2 co2.txt
molecule 1 mymol offset 6 9 18 23 14 auto :pre
[Description:]
@ -46,6 +57,20 @@ contains multiple molecules. The "atom_style
template"_atom_style.html command allows multiple-molecule templates
to define a system with more than one templated molecule.
The optional {offset} keyword will add the specified offset values to
the atom types, bond types, angle types, dihedral types, and improper
types as they are read from the molecule file. E.g. if {toff} = 2,
and the file uses atom types 1,2,3, then each created molecule will
have atom types 3,4,5. This makes it easy to use the same molecule
template file in different simulations. Note that the same offsets
are applied to the molecules in all specified files. All five offset
values are required, but individual values will be ignored if the
molecule template does not define that attribute.
The optional {auto} keyword can be used for molecules with bonds
instead of listing neighbors within the molecular topology explicitly.
More details are given below.
IMPORTANT NOTE: When using the "atom_style template"_atom_style.html
command with a molecule template that contains multiple molecules, you
should insure the atom types, bond types, angle_types, etc in all the
@ -56,7 +81,23 @@ with each other when a mixture system of H2O and CO2 molecules is
defined, e.g. by the "read_data"_read_data.html command. Rather the
H2O molecule should define atom types 1 and 2, and bond type 1. And
the CO2 molecule should define atom types 3 and 4 (or atom types 3 and
2 if a single oxygen type is desired), and bond type 2.
2 if a single oxygen type is desired), and bond type 2. You can also
use the {offset} keyword to shift all of these type values to new
values for a particular simulation.
IMPORTANT NOTE: This command can be used to define molecules with
bonds, angles, dihedrals, imporopers, or special bond lists of
neighbors within a molecular topology, so that you can later add the
molecules to your simulation, via one or more of the commands listed
above. If such molecules do not already exist when LAMMPS creates the
simulation box, via the "create_box"_create_box.html or
"read_data"_read_data.html command, when you later add them you may
overflow the pre-allocated data structures which store molecular
topology information with each atom, and an error will be generated.
Both the "create_box"_create_box.html command and the data files read
by the "read_data"_read_data.html command have "extra" options which
insure space is allocated for storing topology info for molecules that
are added later.
The format of an individual molecule file is similar to the data file
read by the "read_data"_read_data.html commands, and is as follows.
@ -116,10 +157,12 @@ These are the allowed section keywords for the body of the file.
{Shake Flags, Shake Atoms, Shake Bond Types} = SHAKE info :ul
If a Bonds section is specified then the Special Bond Counts and
Special Bonds sections must be also, since the latter is needed for
LAMMPS to properly exclude or weight bonded pairwise interactions
between bonded atoms. See the "special_bonds"_special_bonds.html
command for more details.
Special Bonds sections must be also unless the optional {auto} keyword
is defined. This info is needed for LAMMPS to properly exclude or
weight bonded pairwise interactions between bonded atoms. See the
"special_bonds"_special_bonds.html command for more details. If the
{auto} keyword is used, then LAMMPS will generate this information
automatically for the molecule.
IMPORTANT NOTE: Whether a section is required depends on how the
molecule template is used by other LAMMPS commands. For example, to