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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13352 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2015-04-01 00:21:56 +00:00
parent bb28465783
commit dddce90b0c
8 changed files with 123 additions and 95 deletions
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28
doc/fix_deposit.html
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@ -162,8 +162,8 @@ shake</A> command which also appears in your input script.
<P>Each timestep a particle is inserted, the coordinates for its atoms
are chosen as follows. For insertion of individual atoms, the
"position" referred to in the following description is the coordinate
of the atom. For insertion of molecule, the "position<A HREF = "molecule.html"> is the
geometric center of the molecule; see the (molecule</A> doc
of the atom. For insertion of molecule, the "position" is the
geometric center of the molecule; see the <A HREF = "molecule.html">molecule</A> doc
page for details. A random rotation of the molecule around its center
point is performed, which determines the coordinates all the
individual atoms.
@ -183,14 +183,22 @@ particles is less than the <I>delta</I> setting.
<P>Once a trial x,y,z position has been selected, the insertion is only
performed if no current atom in the simulation is within a distance R
of any atom in the new particle, including the effect of periodic
boundary conditions if applicable. Note that the default value for R
is 0.0, which will allow atoms to strongly overlap if you are
inserting where other atoms are present. This distance test is
performed independently for each atom in an inserted molecule, based
on the randomly rotated configuration of the molecule. If this test
fails, a new random position within the insertion volume is chosen and
another trial is made. Up to Q attempts are made. If the particle is
not successfully inserted, LAMMPS prints a warning message.
boundary conditions if applicable. R is defined by the <I>near</I>
keyword. Note that the default value for R is 0.0, which will allow
atoms to strongly overlap if you are inserting where other atoms are
present. This distance test is performed independently for each atom
in an inserted molecule, based on the randomly rotated configuration
of the molecule. If this test fails, a new random position within the
insertion volume is chosen and another trial is made. Up to Q
attempts are made. If the particle is not successfully inserted,
LAMMPS prints a warning message.
</P>
<P>IMPORTANT NOTE: If you are inserting finite size particles or a
molecule or rigid body consisting of finite-size particles, then you
should typically set R larger than the distance at which any inserted
particle may overlap with either a previouly inserted particle or an
existing particle. LAMMPS will issue a warning if R is smaller than
this value, based on the radii of existing and inserted particles.
</P>
<P>The <I>rate</I> option moves the insertion volume in the z direction (3d)
or y direction (2d). This enables particles to be inserted from a

26
doc/fix_deposit.txt
View File

@ -151,7 +151,7 @@ Each timestep a particle is inserted, the coordinates for its atoms
are chosen as follows. For insertion of individual atoms, the
"position" referred to in the following description is the coordinate
of the atom. For insertion of molecule, the "position" is the
geometric center of the molecule; see the (molecule"_molecule.html doc
geometric center of the molecule; see the "molecule"_molecule.html doc
page for details. A random rotation of the molecule around its center
point is performed, which determines the coordinates all the
individual atoms.
@ -171,14 +171,22 @@ particles is less than the {delta} setting.
Once a trial x,y,z position has been selected, the insertion is only
performed if no current atom in the simulation is within a distance R
of any atom in the new particle, including the effect of periodic
boundary conditions if applicable. Note that the default value for R
is 0.0, which will allow atoms to strongly overlap if you are
inserting where other atoms are present. This distance test is
performed independently for each atom in an inserted molecule, based
on the randomly rotated configuration of the molecule. If this test
fails, a new random position within the insertion volume is chosen and
another trial is made. Up to Q attempts are made. If the particle is
not successfully inserted, LAMMPS prints a warning message.
boundary conditions if applicable. R is defined by the {near}
keyword. Note that the default value for R is 0.0, which will allow
atoms to strongly overlap if you are inserting where other atoms are
present. This distance test is performed independently for each atom
in an inserted molecule, based on the randomly rotated configuration
of the molecule. If this test fails, a new random position within the
insertion volume is chosen and another trial is made. Up to Q
attempts are made. If the particle is not successfully inserted,
LAMMPS prints a warning message.
IMPORTANT NOTE: If you are inserting finite size particles or a
molecule or rigid body consisting of finite-size particles, then you
should typically set R larger than the distance at which any inserted
particle may overlap with either a previouly inserted particle or an
existing particle. LAMMPS will issue a warning if R is smaller than
this value, based on the radii of existing and inserted particles.
The {rate} option moves the insertion volume in the z direction (3d)
or y direction (2d). This enables particles to be inserted from a

69
doc/fix_rigid.html
View File

@ -129,7 +129,7 @@ ensemble, as described below.
rigid/small. The NVE/NVT/NPT/NHT versions belong to one of the two
variants, as their style names indicate.
</P>
<P>IMPORTANT NOTE: Not all of the bodystyle options and keyword/value
<P>IMPORTANT NOTE: Not all of the <I>bodystyle</I> options and keyword/value
options are available for both the <I>rigid</I> and <I>rigid/small</I> variants.
See details below.
</P>
@ -183,6 +183,8 @@ command), setting the force on them to 0.0 (via the <A HREF = "fix_setforce.html
setforce</A> command), and integrating them as usual
(e.g. via the <A HREF = "fix_nve.html">fix nve</A> command).
</P>
<P>NOTE: edit this
</P>
<P>IMPORTANT NOTE: The aggregate properties of each rigid body are
calculated at the start of each simulation run. These include its
center of mass, moments of inertia, and net velocity and angular
@ -201,9 +203,9 @@ via several options.
</P>
<P>IMPORTANT NOTE: With fix rigid/small, which requires bodystyle
<I>molecule</I>, you can define a system that has no rigid bodies
initially. This is useful when you are adding rigid bodies on-the-fly
via commands such as <A HREF = "fix_deposit.html">fix deposit</A> or <A HREF = "fix_pour.html">fix
pour</A>.
initially. This is useful when you are using the <I>mol</I> keyword in
conjunction with another fix that is adding rigid bodies on-the-fly,
such as <A HREF = "fix_deposit.html">fix deposit</A> or <A HREF = "fix_pour.html">fix pour</A>.
</P>
<P>For bodystyle <I>single</I> the entire fix group of atoms is treated as one
rigid body. This option is only allowed for fix rigid and its
@ -471,17 +473,25 @@ associated with the fix rigid commands.
</P>
<HR>
<P>The <I>mol</I> keyword can only be used with fix rigid/small. It should be
<P>The <I>mol</I> keyword can only be used with fix rigid/small. It must be
used when other commands, such as <A HREF = "fix_deposit.html">fix deposit</A> or
<A HREF = "fix_pour.html">fix pour</A>, add rigid bodies on-the-fly during a
simulation. You specify a <I>template-ID</I> previously defined using the
<A HREF = "molecule.html">molecule</A> command, which reads a file that defines the
molecule. You must use the same <I>template-ID</I> that the command adding
rigid bodies uses. The coordinates, atom types, atom diameters,
center-of-mass, and moments of inertia can be specified in the
molecule file. See the <A HREF = "molecule.html">molecule</A> command for details.
The only settings required to be in this file are the coordinates and
types of atoms in the molecule.
molecule. You must use the same <I>template-ID</I> that the other fix
which is adding rigid bodies uses. The coordinates, atom types, atom
diameters, center-of-mass, and moments of inertia can be specified in
the molecule file. See the <A HREF = "molecule.html">molecule</A> command for
details. The only settings required to be in this file are the
coordinates and types of atoms in the molecule, in which case the
molecule command calculates the other quantities itself.
</P>
<P>Note that these other fixes create new rigid bodies, in addition to
those defined initially by this fix via the <I>bodystyle</I> setting.
</P>
<P>Also note that when using the <I>mol</I> keyword, extra restart information
about all rigid bodies is written out whenever a restart file is
written out. See the IMPORTANT NOTE in the next section for details.
</P>
<HR>
@ -505,6 +515,8 @@ comment lines starting with "#" which are ignored. The first
non-blank, non-comment line should list N = the number of lines to
follow. The N successive lines contain the following information:
</P>
<P>NOTE: edit this
</P>
<PRE>ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
...
@ -528,26 +540,16 @@ the simulation box XYZ axes, not with respect to the prinicpal axes of
the rigid body itself. LAMMPS performs the latter calculation
internally.
</P>
<P>IMPORTANT NOTE: If you use the <I>infile</I> keyword and write restart
files during a simulation, then each time a restart file is written,
the fix also write an auxiliary restart file with the name
<P>IMPORTANT NOTE: If you use the <I>infile</I> or <I>mol</I> keywords and write
restart files during a simulation, then each time a restart file is
written, the fix also write an auxiliary restart file with the name
rfile.rigid, where "rfile" is the name of the restart file,
e.g. tmp.restart.10000 and tmp.restart.10000.rigid. This auxiliary
file is in the same format described above and contains info on the
current center-of-mass and 6 moments of inertia. Thus it can be used
in a new input script that restarts the run and re-specifies a rigid
fix using an <I>infile</I> keyword and the appropriate filename. Note that
the auxiliary file will contain one line for every rigid body, even if
the original file only listed a subset of the rigid bodies.
</P>
<P>IMPORTANT NOTE: If you are using fix rigid/small and defining a system
that has no rigid bodies initially, because they will be added
on-the-fly by commands such as <A HREF = "fix_deposit.html">fix deposit</A> or <A HREF = "fix_pour.html">fix
pour</A>, you may still wish to use the <I>infile</I> keyword.
This is so that restart files written during the simulation will
output an auxiliary restart file as described above with information
on the new rigid bodies. In this case the initial <I>infile</I> file
should use N = 0.
file is in the same format described above. Thus it can be used in a
new input script that restarts the run and re-specifies a rigid fix
using an <I>infile</I> keyword and the appropriate filename. Note that the
auxiliary file will contain one line for every rigid body, even if the
original file only listed a subset of the rigid bodies.
</P>
<HR>
@ -656,9 +658,12 @@ more instructions on how to use the accelerated styles effectively.
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about the <I>rigid</I> and <I>rigid/small</I> and <I>rigid/nve</I>
fixes are written to <A HREF = "restart.html">binary restart files</A>. For style
<I>rigid/nvt</I> the state of the Nose/Hoover thermostat is written to
<A HREF = "restart.html">binary restart files</A>. See the
fixes are written to <A HREF = "restart.html">binary restart files</A>. The
exception is if the <I>infile</I> or <I>mol</I> keyword is used, in which case
an auxiliary file is written out with rigid body information each time
a restart file is written, as explained above for the <I>infile</I>
keyword. For style <I>rigid/nvt</I> the state of the Nose/Hoover
thermostat is written to <A HREF = "restart.html">binary restart files</A>. See the
<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
a fix in an input script that reads a restart file, so that the
operation of the fix continues in an uninterrupted fashion.

71
doc/fix_rigid.txt
View File

@ -111,7 +111,7 @@ There are two main variants of this fix, fix rigid and fix
rigid/small. The NVE/NVT/NPT/NHT versions belong to one of the two
variants, as their style names indicate.
IMPORTANT NOTE: Not all of the bodystyle options and keyword/value
IMPORTANT NOTE: Not all of the {bodystyle} options and keyword/value
options are available for both the {rigid} and {rigid/small} variants.
See details below.
@ -165,6 +165,10 @@ command), setting the force on them to 0.0 (via the "fix
setforce"_fix_setforce.html command), and integrating them as usual
(e.g. via the "fix nve"_fix_nve.html command).
NOTE: edit this
IMPORTANT NOTE: The aggregate properties of each rigid body are
calculated at the start of each simulation run. These include its
center of mass, moments of inertia, and net velocity and angular
@ -183,9 +187,9 @@ via several options.
IMPORTANT NOTE: With fix rigid/small, which requires bodystyle
{molecule}, you can define a system that has no rigid bodies
initially. This is useful when you are adding rigid bodies on-the-fly
via commands such as "fix deposit"_fix_deposit.html or "fix
pour"_fix_pour.html.
initially. This is useful when you are using the {mol} keyword in
conjunction with another fix that is adding rigid bodies on-the-fly,
such as "fix deposit"_fix_deposit.html or "fix pour"_fix_pour.html.
For bodystyle {single} the entire fix group of atoms is treated as one
rigid body. This option is only allowed for fix rigid and its
@ -453,17 +457,25 @@ associated with the fix rigid commands.
:line
The {mol} keyword can only be used with fix rigid/small. It should be
The {mol} keyword can only be used with fix rigid/small. It must be
used when other commands, such as "fix deposit"_fix_deposit.html or
"fix pour"_fix_pour.html, add rigid bodies on-the-fly during a
simulation. You specify a {template-ID} previously defined using the
"molecule"_molecule.html command, which reads a file that defines the
molecule. You must use the same {template-ID} that the command adding
rigid bodies uses. The coordinates, atom types, atom diameters,
center-of-mass, and moments of inertia can be specified in the
molecule file. See the "molecule"_molecule.html command for details.
The only settings required to be in this file are the coordinates and
types of atoms in the molecule.
molecule. You must use the same {template-ID} that the other fix
which is adding rigid bodies uses. The coordinates, atom types, atom
diameters, center-of-mass, and moments of inertia can be specified in
the molecule file. See the "molecule"_molecule.html command for
details. The only settings required to be in this file are the
coordinates and types of atoms in the molecule, in which case the
molecule command calculates the other quantities itself.
Note that these other fixes create new rigid bodies, in addition to
those defined initially by this fix via the {bodystyle} setting.
Also note that when using the {mol} keyword, extra restart information
about all rigid bodies is written out whenever a restart file is
written out. See the IMPORTANT NOTE in the next section for details.
:line
@ -487,6 +499,8 @@ comment lines starting with "#" which are ignored. The first
non-blank, non-comment line should list N = the number of lines to
follow. The N successive lines contain the following information:
NOTE: edit this
ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
...
@ -510,26 +524,16 @@ the simulation box XYZ axes, not with respect to the prinicpal axes of
the rigid body itself. LAMMPS performs the latter calculation
internally.
IMPORTANT NOTE: If you use the {infile} keyword and write restart
files during a simulation, then each time a restart file is written,
the fix also write an auxiliary restart file with the name
IMPORTANT NOTE: If you use the {infile} or {mol} keywords and write
restart files during a simulation, then each time a restart file is
written, the fix also write an auxiliary restart file with the name
rfile.rigid, where "rfile" is the name of the restart file,
e.g. tmp.restart.10000 and tmp.restart.10000.rigid. This auxiliary
file is in the same format described above and contains info on the
current center-of-mass and 6 moments of inertia. Thus it can be used
in a new input script that restarts the run and re-specifies a rigid
fix using an {infile} keyword and the appropriate filename. Note that
the auxiliary file will contain one line for every rigid body, even if
the original file only listed a subset of the rigid bodies.
IMPORTANT NOTE: If you are using fix rigid/small and defining a system
that has no rigid bodies initially, because they will be added
on-the-fly by commands such as "fix deposit"_fix_deposit.html or "fix
pour"_fix_pour.html, you may still wish to use the {infile} keyword.
This is so that restart files written during the simulation will
output an auxiliary restart file as described above with information
on the new rigid bodies. In this case the initial {infile} file
should use N = 0.
file is in the same format described above. Thus it can be used in a
new input script that restarts the run and re-specifies a rigid fix
using an {infile} keyword and the appropriate filename. Note that the
auxiliary file will contain one line for every rigid body, even if the
original file only listed a subset of the rigid bodies.
:line
@ -638,9 +642,12 @@ more instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about the {rigid} and {rigid/small} and {rigid/nve}
fixes are written to "binary restart files"_restart.html. For style
{rigid/nvt} the state of the Nose/Hoover thermostat is written to
"binary restart files"_restart.html. See the
fixes are written to "binary restart files"_restart.html. The
exception is if the {infile} or {mol} keyword is used, in which case
an auxiliary file is written out with rigid body information each time
a restart file is written, as explained above for the {infile}
keyword. For style {rigid/nvt} the state of the Nose/Hoover
thermostat is written to "binary restart files"_restart.html. See the
"read_restart"_read_restart.html command for info on how to re-specify
a fix in an input script that reads a restart file, so that the
operation of the fix continues in an uninterrupted fashion.

4
doc/group.html
View File

@ -254,9 +254,9 @@ variable rad equal 18-(step/v_nsteps)*(18-5)
region ss sphere 20 20 0 v_rad
group mobile dynamic all region ss
fix 1 mobile nve
run $<I>nsteps</I>
run ${nsteps}
group mobile static
run $<I>nsteps</I>
run ${nsteps}
</PRE>
<P>IMPORTANT NOTE: All fixes and computes take a group ID as an argument,
but they do not all allow for use of a dynamic group. If you get an

4
doc/group.txt
View File

@ -250,9 +250,9 @@ variable rad equal 18-(step/v_nsteps)*(18-5)
region ss sphere 20 20 0 v_rad
group mobile dynamic all region ss
fix 1 mobile nve
run ${nsteps}
run $\{nsteps\}
group mobile static
run ${nsteps} :pre
run $\{nsteps\} :pre
IMPORTANT NOTE: All fixes and computes take a group ID as an argument,
but they do not all allow for use of a dynamic group. If you get an

8
doc/molecule.html
View File

@ -1,5 +1,5 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
<CENTER><<A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
@ -97,9 +97,9 @@ appear if the value(s) are different than the default.
</UL>
<P>For <I>mass</I>, <I>com</I>, and <I>inertia</I>, the default is for LAMMPS to
calculate this quantity itself if needed, assuming the molecules
consists of a set of point particles. You typically only need to
specify these values for a rigid body consisting of overlapping
finite-size particles.
consists of a set of point particles. You only need to specify these
values for a rigid body consisting of finite-size particles,
especially if they are overlapping.
</P>
<P>The mass and center-of-mass coordinates (Xc,Yc,Zc) are
self-explanatory. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz)

8
doc/molecule.txt
View File

@ -1,4 +1,4 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
<"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
@ -94,9 +94,9 @@ Ixx Iyy Izz Ixy Ixz Iyz {inertia} = 6 components of inertia tensor of molecule :
For {mass}, {com}, and {inertia}, the default is for LAMMPS to
calculate this quantity itself if needed, assuming the molecules
consists of a set of point particles. You typically only need to
specify these values for a rigid body consisting of overlapping
finite-size particles.
consists of a set of point particles. You only need to specify these
values for a rigid body consisting of finite-size particles,
especially if they are overlapping.
The mass and center-of-mass coordinates (Xc,Yc,Zc) are
self-explanatory. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz)