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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11153 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2014-01-07 18:31:26 +00:00
parent ed5011e588
commit 7d07af25b5
2 changed files with 24 additions and 10 deletions
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17
doc/fix_deposit.html
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@ -29,14 +29,10 @@
<LI>one or more keyword/value pairs may be appended to args <LI>one or more keyword/value pairs may be appended to args
<LI>keyword = <I>region</I> or <I>mol</I> or <I>id</I> or <I>global</I> or <I>local</I> or <I>near</I> or <I>attempt</I> or <I>rate</I> or <I>vx</I> or <I>vy</I> or <I>vz</I> or <I>units</I> <LI>keyword = <I>region</I> or <I>id</I> or <I>global</I> or <I>local</I> or <I>near</I> or <I>attempt</I> or <I>rate</I> or <I>vx</I> or <I>vy</I> or <I>vz</I> or <I>mol</I> or <I>rigid</I> or <I>shake</I> or <I>units</I>
<PRE> <I>region</I> value = region-ID <PRE> <I>region</I> value = region-ID
region-ID = ID of region to use as insertion volume region-ID = ID of region to use as insertion volume
<I>mol</I> value = template-ID
template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command
<I>rigid</I> value = fix-ID
fix-ID = ID of <A HREF = "fix_rigid.html">fix rigid/small</A> command
<I>id</I> value = <I>max</I> or <I>next</I> <I>id</I> value = <I>max</I> or <I>next</I>
max = atom ID for new atom(s) is max ID of all current atoms plus one max = atom ID for new atom(s) is max ID of all current atoms plus one
next = atom ID for new atom(s) increments by one for every deposition next = atom ID for new atom(s) increments by one for every deposition
@ -59,6 +55,12 @@
vzlo,vzhi = range of z velocities for inserted atom/molecule (velocity units) vzlo,vzhi = range of z velocities for inserted atom/molecule (velocity units)
<I>target</I> values = tx ty tz <I>target</I> values = tx ty tz
tx,ty,tz = location of target point (distance units) tx,ty,tz = location of target point (distance units)
<I>mol</I> value = template-ID
template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command
<I>rigid</I> value = fix-ID
fix-ID = ID of <A HREF = "fix_rigid.html">fix rigid/small</A> command
<I>shake</I> value = fix-ID
fix-ID = ID of <A HREF = "fix_shake.html">fix shake</A> command
<I>units</I> value = <I>lattice</I> or <I>box</I> <I>units</I> value = <I>lattice</I> or <I>box</I>
lattice = the geometry is defined in lattice units lattice = the geometry is defined in lattice units
box = the geometry is defined in simulation box units box = the geometry is defined in simulation box units
@ -130,6 +132,11 @@ treated as rigid bodies, use the <I>rigid</I> keyword, specifying as its
value the ID of a separate <A HREF = "fix_rigid_small.html">fix rigid/small</A> value the ID of a separate <A HREF = "fix_rigid_small.html">fix rigid/small</A>
command which also appears in your input script. command which also appears in your input script.
</P> </P>
<P>If you wish to insert molecules via the <I>mol</I> keyword, that will have
their bonds or angles constrained via SHAKE, use the <I>shake</I> keyword,
specifying as its value the ID of a separate <A HREF = "fix_shake.html">fix
shake</A> command which also appears in your input script.
</P>
<P>Each timestep a particle is inserted, the coordinates for its atoms <P>Each timestep a particle is inserted, the coordinates for its atoms
are chosen as follows. For insertion of individual atoms, the are chosen as follows. For insertion of individual atoms, the
"position" referred to in the following description is the coordinate "position" referred to in the following description is the coordinate

17
doc/fix_deposit.txt
View File

@ -19,13 +19,9 @@ type = atom type to assign to inserted atoms (offset for moleclue insertion) :l
M = insert a single atom or molecule every M steps :l M = insert a single atom or molecule every M steps :l
seed = random # seed (positive integer) :l seed = random # seed (positive integer) :l
one or more keyword/value pairs may be appended to args :l one or more keyword/value pairs may be appended to args :l
keyword = {region} or {mol} or {id} or {global} or {local} or {near} or {attempt} or {rate} or {vx} or {vy} or {vz} or {units} :l keyword = {region} or {id} or {global} or {local} or {near} or {attempt} or {rate} or {vx} or {vy} or {vz} or {mol} or {rigid} or {shake} or {units} :l
{region} value = region-ID {region} value = region-ID
region-ID = ID of region to use as insertion volume region-ID = ID of region to use as insertion volume
{mol} value = template-ID
template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
{rigid} value = fix-ID
fix-ID = ID of "fix rigid/small"_fix_rigid.html command
{id} value = {max} or {next} {id} value = {max} or {next}
max = atom ID for new atom(s) is max ID of all current atoms plus one max = atom ID for new atom(s) is max ID of all current atoms plus one
next = atom ID for new atom(s) increments by one for every deposition next = atom ID for new atom(s) increments by one for every deposition
@ -48,6 +44,12 @@ keyword = {region} or {mol} or {id} or {global} or {local} or {near} or {attempt
vzlo,vzhi = range of z velocities for inserted atom/molecule (velocity units) vzlo,vzhi = range of z velocities for inserted atom/molecule (velocity units)
{target} values = tx ty tz {target} values = tx ty tz
tx,ty,tz = location of target point (distance units) tx,ty,tz = location of target point (distance units)
{mol} value = template-ID
template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
{rigid} value = fix-ID
fix-ID = ID of "fix rigid/small"_fix_rigid.html command
{shake} value = fix-ID
fix-ID = ID of "fix shake"_fix_shake.html command
{units} value = {lattice} or {box} {units} value = {lattice} or {box}
lattice = the geometry is defined in lattice units lattice = the geometry is defined in lattice units
box = the geometry is defined in simulation box units :pre box = the geometry is defined in simulation box units :pre
@ -118,6 +120,11 @@ treated as rigid bodies, use the {rigid} keyword, specifying as its
value the ID of a separate "fix rigid/small"_fix_rigid_small.html value the ID of a separate "fix rigid/small"_fix_rigid_small.html
command which also appears in your input script. command which also appears in your input script.
If you wish to insert molecules via the {mol} keyword, that will have
their bonds or angles constrained via SHAKE, use the {shake} keyword,
specifying as its value the ID of a separate "fix
shake"_fix_shake.html command which also appears in your input script.
Each timestep a particle is inserted, the coordinates for its atoms Each timestep a particle is inserted, the coordinates for its atoms
are chosen as follows. For insertion of individual atoms, the are chosen as follows. For insertion of individual atoms, the
"position" referred to in the following description is the coordinate "position" referred to in the following description is the coordinate