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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11838 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2014-04-29 22:23:31 +00:00
parent 9c889c3f34
commit 3f09726907
5 changed files with 69 additions and 55 deletions
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8
doc/Section_commands.html
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@ -402,10 +402,10 @@ of each style or click on the style itself for a full description:
<TR ALIGN="center"><TD ><A HREF = "fix_nve_sphere.html">nve/sphere</A></TD><TD ><A HREF = "fix_nve_tri.html">nve/tri</A></TD><TD ><A HREF = "fix_nh.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere</A></TD><TD ><A HREF = "fix_oneway.html">oneway</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_property_atom.html">property/atom</A></TD><TD ><A HREF = "fix_qeq_comb.html">qeq/comb</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_restrain.html">restrain</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nph</A></TD><TD ><A HREF = "fix_rigid.html">rigid/npt</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nve</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nvt</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_srd.html">srd</A></TD><TD ><A HREF = "fix_store_force.html">store/force</A></TD><TD ><A HREF = "fix_store_state.html">store/state</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_csvr.html">temp/csvr</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_tune_kspace.html">tune/kspace</A></TD><TD ><A HREF = "fix_vector.html">vector</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall.html">wall/harmonic</A></TD><TD ><A HREF = "fix_wall.html">wall/lj1043</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall_piston.html">wall/piston</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wall_region.html">wall/region</A></TD><TD ><A HREF = "fix_wall_srd.html">wall/srd</A>
<TR ALIGN="center"><TD ><A HREF = "fix_rigid.html">rigid/small/nph</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/npt</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/nve</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/nvt</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_srd.html">srd</A></TD><TD ><A HREF = "fix_store_force.html">store/force</A></TD><TD ><A HREF = "fix_store_state.html">store/state</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_csvr.html">temp/csvr</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_tune_kspace.html">tune/kspace</A></TD><TD ><A HREF = "fix_vector.html">vector</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall.html">wall/harmonic</A></TD><TD ><A HREF = "fix_wall.html">wall/lj1043</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_piston.html">wall/piston</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wall_region.html">wall/region</A></TD><TD ><A HREF = "fix_wall_srd.html">wall/srd</A>
</TD></TR></TABLE></DIV>
<P>These are fix styles contributed by users, which can be used if

4
doc/Section_commands.txt
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@ -531,6 +531,10 @@ of each style or click on the style itself for a full description:
"rigid/nve"_fix_rigid.html,
"rigid/nvt"_fix_rigid.html,
"rigid/small"_fix_rigid.html,
"rigid/small/nph"_fix_rigid.html,
"rigid/small/npt"_fix_rigid.html,
"rigid/small/nve"_fix_rigid.html,
"rigid/small/nvt"_fix_rigid.html,
"setforce"_fix_setforce.html,
"shake"_fix_shake.html,
"spring"_fix_spring.html,

12
doc/compute_voronoi_atom.html
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@ -117,12 +117,12 @@ is the number of atoms currently in the Voronoi volume defined by this
atom at the time of the first invocation of the compute (note that the
atom may have moved significantly). The second column contains the
total number of atoms sharing the Voronoi cell of the stored
tessellation at the location of the current atom. Numbers in column one
can be any positive integer including zero, while column two values will
always be greater than zero. Column one data can be used to locate
vacancies (the coordinates are given by the atom coordinates at the
time step when the compute was first invoked), while column two data
can be used to identify interstitial atoms.
tessellation at the location of the current atom. Numbers in column
one can be any positive integer including zero, while column two
values will always be greater than zero. Column one data can be used
to locate vacancies (the coordinates are given by the atom coordinates
at the time step when the compute was first invoked), while column two
data can be used to identify interstitial atoms.
</P>
<HR>

45
doc/fix_rigid.html
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@ -21,13 +21,21 @@
</H3>
<H3>fix rigid/small command
</H3>
<H3>fix rigid/nve/small command
</H3>
<H3>fix rigid/nvt/small command
</H3>
<H3>fix rigid/npt/small command
</H3>
<H3>fix rigid/nph/small command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID style bodystyle args keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>style = <I>rigid</I> or <I>rigid/nve</I> or <I>rigid/nvt</I> or <I>rigid/npt</I> or <I>rigid/nph</I> or <I>rigid/small</I>
<LI>style = <I>rigid</I> or <I>rigid/nve</I> or <I>rigid/nvt</I> or <I>rigid/npt</I> or <I>rigid/nph</I> or <I>rigid/small</I> or <I>rigid/nve/small</I> or <I>rigid/nvt/small</I> or <I>rigid/npt/small</I> or <I>rigid/nph/small</I>
<LI>bodystyle = <I>single</I> or <I>molecule</I> or <I>group</I>
@ -39,7 +47,7 @@
</PRE>
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>langevin</I> or <I>temp</I> or <I>iso</I> or <I>aniso</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>couple</I> or <I>tparam</I> or <I>pchain</I> or <I>dilate</I> or <I>force</I> or <I>torque</I> or <I>infile</I> or <I>mol</I>
<LI>keyword = <I>langevin</I> or <I>temp</I> or <I>iso</I> or <I>aniso</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>couple</I> or <I>tparam</I> or <I>pchain</I> or <I>dilate</I> or <I>force</I> or <I>torque</I> or <I>infile</I>
<PRE> <I>langevin</I> values = Tstart Tstop Tperiod seed
Tstart,Tstop = desired temperature at start/stop of run (temperature units)
@ -88,6 +96,7 @@ fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off
fix 1 rods rigid/npt molecule temp 300.0 300.0 100.0 iso 0.5 0.5 10.0
fix 1 particles rigid/npt molecule temp 1.0 1.0 5.0 x 0.5 0.5 1.0 z 0.5 0.5 1.0 couple xz
fix 1 water rigid/nph molecule iso 0.5 0.5 1.0
fix 1 particles rigid/npt/small molecule temp 1.0 1.0 1.0 iso 0.5 0.5 1.0
</PRE>
<P><B>Description:</B>
</P>
@ -292,17 +301,17 @@ iterations. The <I>rigid/nve</I> style uses the methods described in the
paper by <A HREF = "#Miller">Miller</A>, which are thought to provide better energy
conservation than an iterative approach.
</P>
<P>The <I>rigid/nvt</I> style performs constant NVT integration using a
Nose/Hoover thermostat with chains as described originally in
<A HREF = "#Hoover">(Hoover)</A> and <A HREF = "#Martyna">(Martyna)</A>, which thermostats both
the translational and rotational degrees of freedom of the rigid
bodies. The rigid-body algorithm used by <I>rigid/nvt</I> is described in
the paper by <A HREF = "#Kamberaj">Kamberaj</A>.
<P>The <I>rigid/nvt</I> and <I>rigid/nvt/small</I> styles performs constant NVT
integration using a Nose/Hoover thermostat with chains as described
originally in <A HREF = "#Hoover">(Hoover)</A> and <A HREF = "#Martyna">(Martyna)</A>, which
thermostats both the translational and rotational degrees of freedom
of the rigid bodies. The rigid-body algorithm used by <I>rigid/nvt</I>
is described in the paper by <A HREF = "#Kamberaj">Kamberaj</A>.
</P>
<P>The <I>rigid/npt</I> and <I>rigid/nph</I> styles perform constant NPT or NPH
integration using a Nose/Hoover barostat with chains. For the NPT
case, the same Nose/Hoover thermostat is also used as with
<I>rigid/nvt</I>.
<P>The <I>rigid/npt</I> and <I>rigid/nph</I> (and their /small counterparts) styles
perform constant NPT or NPH integration using a Nose/Hoover barostat
with chains. For the NPT case, the same Nose/Hoover thermostat is also
used as with <I>rigid/nvt</I>.
</P>
<P>The barostat parameters are specified using one or more of the <I>iso</I>,
<I>aniso</I>, <I>x</I>, <I>y</I>, <I>z</I> and <I>couple</I> keywords. These keywords give you
@ -312,8 +321,8 @@ they represent are varied together during a constant-pressure
simulation. The effects of these keywords are similar to those
defined in <A HREF = "fix_nh.html">fix npt/nph</A>
</P>
<P>NOTE: Currently the <I>rigid/npt</I> and <I>rigid/nph</I> styles do not support
triclinic (non-orthongonal) boxes.
<P>NOTE: Currently the <I>rigid/npt</I> and <I>rigid/nph</I> (and their /small
counterparts) styles do not support triclinic (non-orthongonal) boxes.
</P>
<P>The target pressures for each of the 6 components of the stress tensor
can be specified independently via the <I>x</I>, <I>y</I>, <I>z</I> keywords, which
@ -483,12 +492,10 @@ have to list attributes for every rigid body integrated by fix rigid.
Only bodies which the file specifies will have their computed
attributes overridden. The file can contain initial blank lines or
comment lines starting with "#" which are ignored. The first
non-blank, non-comment line should list N, which is the number of
lines to follow. The N successive lines contain the following
information:
non-blank, non-comment line should list N = the number of lines to
follow. The N successive lines contain the following information:
</P>
<PRE>N
ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
<PRE>ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
...
IDN masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz

41
doc/fix_rigid.txt
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@ -12,13 +12,17 @@ fix rigid/nvt command :h3
fix rigid/npt command :h3
fix rigid/nph command :h3
fix rigid/small command :h3
fix rigid/nve/small command :h3
fix rigid/nvt/small command :h3
fix rigid/npt/small command :h3
fix rigid/nph/small command :h3
[Syntax:]
fix ID group-ID style bodystyle args keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
style = {rigid} or {rigid/nve} or {rigid/nvt} or {rigid/npt} or {rigid/nph} or {rigid/small} :l
style = {rigid} or {rigid/nve} or {rigid/nvt} or {rigid/npt} or {rigid/nph} or {rigid/small} or {rigid/nve/small} or {rigid/nvt/small} or {rigid/npt/small} or {rigid/nph/small} :l
bodystyle = {single} or {molecule} or {group} :l
{single} args = none
{molecule} args = none
@ -27,7 +31,7 @@ bodystyle = {single} or {molecule} or {group} :l
groupID1, groupID2, ... = list of N group IDs :pre
zero or more keyword/value pairs may be appended :l
keyword = {langevin} or {temp} or {iso} or {aniso} or {x} or {y} or {z} or {couple} or {tparam} or {pchain} or {dilate} or {force} or {torque} or {infile} or {mol} :l
keyword = {langevin} or {temp} or {iso} or {aniso} or {x} or {y} or {z} or {couple} or {tparam} or {pchain} or {dilate} or {force} or {torque} or {infile} :l
{langevin} values = Tstart Tstop Tperiod seed
Tstart,Tstop = desired temperature at start/stop of run (temperature units)
Tdamp = temperature damping parameter (time units)
@ -73,7 +77,8 @@ fix 1 polychains rigid/small molecule langevin 1.0 1.0 1.0 428984
fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off
fix 1 rods rigid/npt molecule temp 300.0 300.0 100.0 iso 0.5 0.5 10.0
fix 1 particles rigid/npt molecule temp 1.0 1.0 5.0 x 0.5 0.5 1.0 z 0.5 0.5 1.0 couple xz
fix 1 water rigid/nph molecule iso 0.5 0.5 1.0 :pre
fix 1 water rigid/nph molecule iso 0.5 0.5 1.0
fix 1 particles rigid/npt/small molecule temp 1.0 1.0 1.0 iso 0.5 0.5 1.0 :pre
[Description:]
@ -278,17 +283,17 @@ iterations. The {rigid/nve} style uses the methods described in the
paper by "Miller"_#Miller, which are thought to provide better energy
conservation than an iterative approach.
The {rigid/nvt} style performs constant NVT integration using a
Nose/Hoover thermostat with chains as described originally in
"(Hoover)"_#Hoover and "(Martyna)"_#Martyna, which thermostats both
the translational and rotational degrees of freedom of the rigid
bodies. The rigid-body algorithm used by {rigid/nvt} is described in
the paper by "Kamberaj"_#Kamberaj.
The {rigid/nvt} and {rigid/nvt/small} styles performs constant NVT
integration using a Nose/Hoover thermostat with chains as described
originally in "(Hoover)"_#Hoover and "(Martyna)"_#Martyna, which
thermostats both the translational and rotational degrees of freedom
of the rigid bodies. The rigid-body algorithm used by {rigid/nvt}
is described in the paper by "Kamberaj"_#Kamberaj.
The {rigid/npt} and {rigid/nph} styles perform constant NPT or NPH
integration using a Nose/Hoover barostat with chains. For the NPT
case, the same Nose/Hoover thermostat is also used as with
{rigid/nvt}.
The {rigid/npt} and {rigid/nph} (and their /small counterparts) styles
perform constant NPT or NPH integration using a Nose/Hoover barostat
with chains. For the NPT case, the same Nose/Hoover thermostat is also
used as with {rigid/nvt}.
The barostat parameters are specified using one or more of the {iso},
{aniso}, {x}, {y}, {z} and {couple} keywords. These keywords give you
@ -298,8 +303,8 @@ they represent are varied together during a constant-pressure
simulation. The effects of these keywords are similar to those
defined in "fix npt/nph"_fix_nh.html
NOTE: Currently the {rigid/npt} and {rigid/nph} styles do not support
triclinic (non-orthongonal) boxes.
NOTE: Currently the {rigid/npt} and {rigid/nph} (and their /small
counterparts) styles do not support triclinic (non-orthongonal) boxes.
The target pressures for each of the 6 components of the stress tensor
can be specified independently via the {x}, {y}, {z} keywords, which
@ -469,11 +474,9 @@ have to list attributes for every rigid body integrated by fix rigid.
Only bodies which the file specifies will have their computed
attributes overridden. The file can contain initial blank lines or
comment lines starting with "#" which are ignored. The first
non-blank, non-comment line should list N, which is the number of
lines to follow. The N successive lines contain the following
information:
non-blank, non-comment line should list N = the number of lines to
follow. The N successive lines contain the following information:
N
ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
...