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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13695 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2015-07-23 15:47:33 +00:00
parent a683f516ba
commit 6c84ca5377
2 changed files with 42 additions and 74 deletions
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58
doc/molecule.html
View File

@ -21,16 +21,14 @@
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>offset</I> or <I>auto</I>
<LI>keyword = <I>offset</I>
<PRE> <I>offset</I> values = toff boff aoff doff ioff
toff = offset to add to atom types
boff = offset to add to bond types
aoff = offset to add to angle types
doff = offset to add to dihedral types
ioff = offset to add to improper types
<I>auto</I> value = none
generate special bond lists automatically if <I>auto</I> is specified
ioff = offset to add to improper types
</PRE>
</UL>
@ -39,7 +37,7 @@
<PRE>molecule 1 mymol
molecule 1 co2.txt h2o.txt
molecule CO2 co2.txt
molecule 1 mymol offset 6 9 18 23 14 auto
molecule 1 mymol offset 6 9 18 23 14
</PRE>
<P><B>Description:</B>
</P>
@ -70,29 +68,12 @@ to define a system with more than one templated molecule.
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 must be speicified, but individual values will be ignored if
the molecule template does not use that attribute (e.g. no bonds).
</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
molecules are consistent. E.g. if one molecule represents H2O and
another CO2, then you probably do not want each molecule file to
define 2 atom types and a single bond type, because they will conflict
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. You can also
use the <I>offset</I> keyword to shift all of these type values to new
values for a particular simulation.
have atom types 3,4,5. This is to make 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 must be speicified, but individual values will be
ignored if the molecule template does not use that attribute (e.g. no
bonds).
</P>
<P>IMPORTANT NOTE: This command can be used to define molecules with
bonds, angles, dihedrals, imporopers, or special bond lists of
@ -166,12 +147,17 @@ 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 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.
Special Bonds sections can also be used, if desired, to explicitly
list the 1-2, 1-3, 1-4 neighbors within the molecule topology (see
details below). This is optional since if these sections are not
included, LAMMPS will auto-generate this information. Note that
LAMMPS uses this info 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. One
reason to list the special bond info explicitly is for the
<A HREF = "tutorial_drude.html">thermalized Drude oscillator model</A> which treats
the bonds between nuclear cores and Drude electrons in a different
manner.
</P>
<P>IMPORTANT NOTE: Whether a section is required depends on how the
molecule template is used by other LAMMPS commands. For example, to
@ -453,8 +439,6 @@ of SHAKE clusters.
</P>
<P><B>Default:</B>
</P>
<P>The default keyword values are offset 0 0 0 0 0, and no
auto-generation of special bond lists. The latter is overridden in
the <I>auto</I> keyword is used.
<P>The default keyword value is offset 0 0 0 0 0.
</P>
</HTML>

58
doc/molecule.txt
View File

@ -15,15 +15,13 @@ molecule ID file1 file2 ... keyword values ... :pre
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
keyword = {offset} :l
{offset} values = toff boff aoff doff ioff
toff = offset to add to atom types
boff = offset to add to bond types
aoff = offset to add to angle types
doff = offset to add to dihedral types
ioff = offset to add to improper types
{auto} value = none
generate special bond lists automatically if {auto} is specified :pre
ioff = offset to add to improper types :pre
:ule
[Examples:]
@ -31,7 +29,7 @@ keyword = {offset} or {auto} :l
molecule 1 mymol
molecule 1 co2.txt h2o.txt
molecule CO2 co2.txt
molecule 1 mymol offset 6 9 18 23 14 auto :pre
molecule 1 mymol offset 6 9 18 23 14 :pre
[Description:]
@ -62,29 +60,12 @@ The optional {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 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 must be speicified, but individual values will be ignored if
the molecule template does not use that attribute (e.g. no bonds).
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
molecules are consistent. E.g. if one molecule represents H2O and
another CO2, then you probably do not want each molecule file to
define 2 atom types and a single bond type, because they will conflict
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. You can also
use the {offset} keyword to shift all of these type values to new
values for a particular simulation.
have atom types 3,4,5. This is to make 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 must be speicified, but individual values will be
ignored if the molecule template does not use that attribute (e.g. no
bonds).
IMPORTANT NOTE: This command can be used to define molecules with
bonds, angles, dihedrals, imporopers, or special bond lists of
@ -158,12 +139,17 @@ 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 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.
Special Bonds sections can also be used, if desired, to explicitly
list the 1-2, 1-3, 1-4 neighbors within the molecule topology (see
details below). This is optional since if these sections are not
included, LAMMPS will auto-generate this information. Note that
LAMMPS uses this info to properly exclude or weight bonded pairwise
interactions between bonded atoms. See the
"special_bonds"_special_bonds.html command for more details. One
reason to list the special bond info explicitly is for the
"thermalized Drude oscillator model"_tutorial_drude.html which treats
the bonds between nuclear cores and Drude electrons in a different
manner.
IMPORTANT NOTE: Whether a section is required depends on how the
molecule template is used by other LAMMPS commands. For example, to
@ -445,6 +431,4 @@ of SHAKE clusters.
[Default:]
The default keyword values are offset 0 0 0 0 0, and no
auto-generation of special bond lists. The latter is overridden in
the {auto} keyword is used.
The default keyword value is offset 0 0 0 0 0.