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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@710 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2007-07-02 20:04:44 +00:00
parent d3f7f3e86c
commit 03c056ccca
53 changed files with 121 additions and 99 deletions
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1
doc/Eqs/Script.create
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@ -26,6 +26,7 @@ latex fix_wall_lj93
latex improper_class2
latex improper_cvff
latex improper_harmonic
latex pair_airebo
latex pair_buck
latex pair_charmm
latex pair_class2

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doc/Eqs/stress_tensor.jpg
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3
doc/Eqs/stress_tensor.tex
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@ -4,7 +4,8 @@
$$
S_{ab} = - \left[ m v_a v_b +
\frac{1}{2} \sum_{j = 1}^N (a_i - a_j) F_{b_{ij}} \right]
\frac{1}{2} \sum_{j = 1}^{N_p} (a_i - a_j) F_{p_{ij}} +
\frac{1}{2} \sum_{j = 1}^{N_b} (a_i - a_j) F_{b_{ij}} \right]
$$
\end{document}

2
doc/compute_temp_ramp.html
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@ -21,7 +21,7 @@
<LI>vlo,vhi = subtract velocities between vlo and vhi (velocity units)
<LI>dim = <I>x</I> or <I>y</I> or <I>z</I>
<LI>clo,chi = lower and upper bound of domain to subtract from (distance units)
<LI>zero or more keyword/value pairs may be appended to the args
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>units</I>
</UL>
<PRE> <I>units</I> value = <I>lattice</I> or <I>box</I>

2
doc/compute_temp_ramp.txt
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@ -18,7 +18,7 @@ vdim = {vx} or {vy} or {vz}
vlo,vhi = subtract velocities between vlo and vhi (velocity units)
dim = {x} or {y} or {z}
clo,chi = lower and upper bound of domain to subtract from (distance units)
zero or more keyword/value pairs may be appended to the args
zero or more keyword/value pairs may be appended
keyword = {units} :ul
{units} value = {lattice} or {box} :pre

2
doc/create_atoms.html
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@ -25,7 +25,7 @@
<I>single</I> args = x y z
x,y,z = coordinates of a single atom (distance units)
</PRE>
<LI>zero or more keyword/value pairs may be appended to the args
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>basis</I> or <I>units</I>

2
doc/create_atoms.txt
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@ -19,7 +19,7 @@ style = {box} or {region} or {single} :l
region-ID = atoms will only be created if contained in the region
{single} args = x y z
x,y,z = coordinates of a single atom (distance units) :pre
zero or more keyword/value pairs may be appended to the args :l
zero or more keyword/value pairs may be appended :l
keyword = {basis} or {units} :l
{basis} values = M itype
M = which basis atom

2
doc/delete_bonds.html
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@ -28,7 +28,7 @@
<I>improper</I> args = an improper type
<I>stats</I> args = none
</PRE>
<LI>zero or more keywords may be appended to the args
<LI>zero or more keywords may be appended
<LI>keyword = <I>undo</I> or <I>remove</I> or <I>special</I>

2
doc/delete_bonds.txt
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@ -22,7 +22,7 @@ style = {multi} or {atom} or {bond} or {angle} or {dihedral} or
{dihedral} args = a dihedral type
{improper} args = an improper type
{stats} args = none :pre
zero or more keywords may be appended to the args :l
zero or more keywords may be appended :l
keyword = {undo} or {remove} or {special} :l
:ule

2
doc/displace_atoms.html
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@ -30,7 +30,7 @@
dx,dy,dz = random displacement magnitude in each dimension (distance units)
seed = random # seed (8 digits or less)
</PRE>
<LI>zero or more keyword/value pairs may be appended to the args
<LI>zero or more keyword/value pairs may be appended
<PRE> keyword = <I>units</I>
value = <I>box</I> or <I>lattice</I>

2
doc/displace_atoms.txt
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@ -24,7 +24,7 @@ style = {move} or {ramp} or {random} :l
{random} args = dx dy dz seed
dx,dy,dz = random displacement magnitude in each dimension (distance units)
seed = random # seed (8 digits or less) :pre
zero or more keyword/value pairs may be appended to the args :l
zero or more keyword/value pairs may be appended :l
keyword = {units}
value = {box} or {lattice} :pre
:ule

2
doc/displace_box.html
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@ -36,7 +36,7 @@
<I>delta</I> value = dtilt
dtilt = change in tilt factor at end of run (distance units)
</PRE>
<LI>zero or more keyword/value pairs may be appended to the args
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>remap</I> or <I>units</I>

2
doc/displace_box.txt
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@ -31,7 +31,7 @@ parameter = {x} or {y} or {z} or {xy} or {xz} or {yz}
{delta} value = dtilt
dtilt = change in tilt factor at end of run (distance units) :pre
zero or more keyword/value pairs may be appended to the args :l
zero or more keyword/value pairs may be appended :l
keyword = {remap} or {units} :l
{remap} value = {x} or {none}
x = remap coords of atoms in group into deforming box

39
doc/dump.html
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@ -39,7 +39,7 @@
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz,
quatw, quati, quatj, quatk, tqx, tqy, tqz,
epair, ke, etotal, centro,
epair, ebond, ke, etotal, centro,
sxx, syy, szz, sxy, sxz, syz,
c_ID, c_ID[N]
tag = atom ID
@ -56,8 +56,9 @@
quatw,quati,quatj,quatk = quaternion components for aspherical particles
tqx,tqy,tqz = torque on aspherical particles
epair = per-atom pairwise energy
epair = per-atom bond energy
ke = per-atom kinetic energy
etotal = per-atom total energy (ke + epair)
etotal = per-atom total energy (ke + epair, not ebond)
centro = per-atom centro-symmetry parameter
sxx, syy, szz, sxy, sxz, syz = per-atom stress tensor components
c_ID = scalar per-atom quantity calculated by a compute identified by its ID
@ -240,15 +241,17 @@ are specific to aspherical particles defined with an atom style of
define the orientiation of the particle. The final 3 give the
rotational torque on the particle.
</P>
<P>The <I>epair</I>, <I>ke</I>, <I>etotal</I>, <I>centro</I>, and <I>sxx</I>, etc keywords print
the pairwise energy, kinetic energy, total energy (pairwise +
kinetic), centro-symmetry parameter, and components of the per-atom
stress tensor for each atom. These quantities are calculated by
computes that the dump defines, as if these commands had been issued:
<P>The <I>epair</I>, <I>ebond</I>, <I>ke</I>, <I>etotal</I>, <I>centro</I>, and <I>sxx</I>, etc
keywords print the pairwise energy, bond energy, kinetic energy, total
energy (pairwise + kinetic), centro-symmetry parameter, and components
of the per-atom stress tensor for each atom. These quantities are
calculated by computes that the dump defines, as if these commands had
been issued:
</P>
<PRE>compute dump-ID_epair/atom group-ID <A HREF = "compute_epair_atom.html">epair/atom</A>
compute dump-ID_ebond/atom group-ID <A HREF = "compute_ebond_atom.html">ebond/atom</A>
compute dump-ID_ke/atom group-ID <A HREF = "compute_ke_atom.html">ke/atom</A>
compute dump-ID_etotal/atom group-ID <A HREF = "compute_etotal_atom.html">etotal/atom</A>
compute dump-ID_etotal/atom group-ID <A HREF = "compute_etotal_atom.html">etotal/atom</A> dump-ID_epair/atom
compute dump-ID_centro/atom group-ID <A HREF = "compute_centro_atom.html">centro/atom</A>
compute dump-ID_stress/atom group-ID <A HREF = "compute_stress_atom.html">stress/atom</A>
</PRE>
@ -256,10 +259,16 @@ compute dump-ID_stress/atom group-ID <A HREF = "compute_stress_atom.html">stress
details on what is computed for each atom. Note that the ID of each
new compute is the dump-ID with the compute style appended (with an
underscore). The group for each new compute is the same as the dump
group.
group. Note that for <I>etotal</I>, an auxiliary compute for calculating
the pairwise energy is created, since the <A HREF = "compute_etotal_atom.html">compute
etotal/atom</A> command requires it as an extra
argument.
</P>
<P>Note that the <I>etotal</I> keyword does not include energy contributions
due to bonds, angles, etc that the atom is part of.
<P>IMPORTANT NOTE: The <I>etotal</I> keyword does NOT include contributions
due to bonds, angles, etc that the atom is part of. The bond
contribution can be computed separately via the <I>ebond</I> keyword.
Currently, there is no way in LAMMPS to dump per-atom energy for
angles, dihedrals, improper, or long-range interactions.
</P>
<P>The <I>sxx</I>, <I>syy</I>, <I>szz</I>, <I>sxy</I>, <I>sxz</I>, <I>syz</I> keywords access the 6
components of the stress tensor calculated for each atom by the
@ -311,9 +320,11 @@ files are written with, which will result in a compile-time error when
a lo-level include file is not found. Putting this style in a package
makes it easy to exclude from a LAMMPS build for those machines.
</P>
<P>Granular systems and granular pair potentials cannot be used to
compute per-atom energy and stress. The <A HREF = "fix_gran_diag.html">fix
gran/diag</A> command should be used instead.
<P>Some pair potentials do not allow the calculation of per-atom energy
and stress via the <I>epair</I>, <I>etotal</I>, <I>sxx</I>, etc keywords. One of
these are the granular pair potentials. However, for those
potentials, the <A HREF = "fix_gran_diag.html">fix gran/diag</A> command can be used
instead.
</P>
<P><B>Related commands:</B>
</P>

39
doc/dump.txt
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@ -30,7 +30,7 @@ args = list of arguments for a particular style :l
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz,
quatw, quati, quatj, quatk, tqx, tqy, tqz,
epair, ke, etotal, centro,
epair, ebond, ke, etotal, centro,
sxx, syy, szz, sxy, sxz, syz,
c_ID, c_ID\[N\]
tag = atom ID
@ -47,8 +47,9 @@ args = list of arguments for a particular style :l
quatw,quati,quatj,quatk = quaternion components for aspherical particles
tqx,tqy,tqz = torque on aspherical particles
epair = per-atom pairwise energy
epair = per-atom bond energy
ke = per-atom kinetic energy
etotal = per-atom total energy (ke + epair)
etotal = per-atom total energy (ke + epair, not ebond)
centro = per-atom centro-symmetry parameter
sxx, syy, szz, sxy, sxz, syz = per-atom stress tensor components
c_ID = scalar per-atom quantity calculated by a compute identified by its ID
@ -230,15 +231,17 @@ are specific to aspherical particles defined with an atom style of
define the orientiation of the particle. The final 3 give the
rotational torque on the particle.
The {epair}, {ke}, {etotal}, {centro}, and {sxx}, etc keywords print
the pairwise energy, kinetic energy, total energy (pairwise +
kinetic), centro-symmetry parameter, and components of the per-atom
stress tensor for each atom. These quantities are calculated by
computes that the dump defines, as if these commands had been issued:
The {epair}, {ebond}, {ke}, {etotal}, {centro}, and {sxx}, etc
keywords print the pairwise energy, bond energy, kinetic energy, total
energy (pairwise + kinetic), centro-symmetry parameter, and components
of the per-atom stress tensor for each atom. These quantities are
calculated by computes that the dump defines, as if these commands had
been issued:
compute dump-ID_epair/atom group-ID "epair/atom"_compute_epair_atom.html
compute dump-ID_ebond/atom group-ID "ebond/atom"_compute_ebond_atom.html
compute dump-ID_ke/atom group-ID "ke/atom"_compute_ke_atom.html
compute dump-ID_etotal/atom group-ID "etotal/atom"_compute_etotal_atom.html
compute dump-ID_etotal/atom group-ID "etotal/atom"_compute_etotal_atom.html dump-ID_epair/atom
compute dump-ID_centro/atom group-ID "centro/atom"_compute_centro_atom.html
compute dump-ID_stress/atom group-ID "stress/atom"_compute_stress_atom.html :pre
@ -246,10 +249,16 @@ See the corresponding "compute"_compute.html style commands for
details on what is computed for each atom. Note that the ID of each
new compute is the dump-ID with the compute style appended (with an
underscore). The group for each new compute is the same as the dump
group.
group. Note that for {etotal}, an auxiliary compute for calculating
the pairwise energy is created, since the "compute
etotal/atom"_compute_etotal_atom.html command requires it as an extra
argument.
Note that the {etotal} keyword does not include energy contributions
due to bonds, angles, etc that the atom is part of.
IMPORTANT NOTE: The {etotal} keyword does NOT include contributions
due to bonds, angles, etc that the atom is part of. The bond
contribution can be computed separately via the {ebond} keyword.
Currently, there is no way in LAMMPS to dump per-atom energy for
angles, dihedrals, improper, or long-range interactions.
The {sxx}, {syy}, {szz}, {sxy}, {sxz}, {syz} keywords access the 6
components of the stress tensor calculated for each atom by the
@ -301,9 +310,11 @@ files are written with, which will result in a compile-time error when
a lo-level include file is not found. Putting this style in a package
makes it easy to exclude from a LAMMPS build for those machines.
Granular systems and granular pair potentials cannot be used to
compute per-atom energy and stress. The "fix
gran/diag"_fix_gran_diag.html command should be used instead.
Some pair potentials do not allow the calculation of per-atom energy
and stress via the {epair}, {etotal}, {sxx}, etc keywords. One of
these are the granular pair potentials. However, for those
potentials, the "fix gran/diag"_fix_gran_diag.html command can be used
instead.
[Related commands:]

2
doc/fix_ave_spatial.html
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@ -39,7 +39,7 @@
<I>atom</I> arg = <I>vx</I> or <I>vy</I> or <I>vz</I> or <I>fx</I> or <I>fy</I> or <I>fz</I>
<I>compute</I> arg = compute-ID that calculates per-atom quantities
</PRE>
<LI>zero or more keyword/value pairs may be appended to the args
<LI>zero or more keyword/value pairs may be appended
<PRE>keyword = <I>norm</I> or <I>units</I>
<I>norm</I> value = <I>all</I> or <I>sample</I>

2
doc/fix_ave_spatial.txt
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@ -27,7 +27,7 @@ style = {density} or {atom} or {compute} :l
{atom} arg = {vx} or {vy} or {vz} or {fx} or {fy} or {fz}
{compute} arg = compute-ID that calculates per-atom quantities :pre
zero or more keyword/value pairs may be appended to the args :l
zero or more keyword/value pairs may be appended :l
keyword = {norm} or {units}
{norm} value = {all} or {sample}
{units} value = {box} or {lattice} or {reduced} :pre

2
doc/fix_deform.html
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@ -55,7 +55,7 @@
<PRE> <I>trate</I> value = R
R = true shear strain rate (1/time units)
</PRE>
<LI>zero or more keyword/value pairs may be appended to the args
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>remap</I> or <I>units</I>

2
doc/fix_deform.txt
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@ -47,7 +47,7 @@ parameter = {x} or {y} or {z} or {xy} or {xz} or {yz}
{trate} value = R
R = true shear strain rate (1/time units) :pre
zero or more keyword/value pairs may be appended to the args :l
zero or more keyword/value pairs may be appended :l
keyword = {remap} or {units} :l
{remap} value = {x} or {v} or {none}
x = remap coords of atoms in group into deforming box

4
doc/fix_indent.html
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@ -13,7 +13,7 @@
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID indent k keyword args ...
<PRE>fix ID group-ID indent k keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
@ -21,7 +21,7 @@
<LI>k = force constant for indenter surface (force/distance^2 units)
<LI>one or more keyword/value pairs may be appended to the args
<LI>one or more keyword/value pairs may be appended
<LI>keyword = <I>sphere</I> or <I>cylinder</I> or <I>vel</I> or <I>rstart</I> or <I>units</I>

4
doc/fix_indent.txt
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@ -10,12 +10,12 @@ fix indent command :h3
[Syntax:]
fix ID group-ID indent k keyword args ... :pre
fix ID group-ID indent k keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
indent = style name of this fix command :l
k = force constant for indenter surface (force/distance^2 units) :l
one or more keyword/value pairs may be appended to the args :l
one or more keyword/value pairs may be appended :l
keyword = {sphere} or {cylinder} or {vel} or {rstart} or {units} :l
{sphere} args = x y z R
x,y,z = initial position of center of indenter

2
doc/fix_langevin.html
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@ -25,7 +25,7 @@
<LI>seed = random # seed to use for white noise (8 digits or less)
<LI>zero or more keyword/value pairs may be appended to the args
<LI>zero or more keyword/value pairs may be appended
<PRE>keyword = <I>axes</I> or <I>scale</I> or <I>region</I>
<I>axes</I> values = xflag yflag zflag

2
doc/fix_langevin.txt
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@ -17,7 +17,7 @@ langevin = style name of this fix command :l
Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
damp = damping parameter (time units) :l
seed = random # seed to use for white noise (8 digits or less) :l
zero or more keyword/value pairs may be appended to the args :l
zero or more keyword/value pairs may be appended :l
keyword = {axes} or {scale} or {region}
{axes} values = xflag yflag zflag
xflag,yflag,zflag = 0/1 to exclude/include a dimension in the thermostat

2
doc/fix_momentum.html
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@ -20,7 +20,7 @@
<LI>momentum = style name of this fix command
<LI>N = adjust the momentum every this many timesteps
one or more keyword/value pairs may be appended to the args
one or more keyword/value pairs may be appended
<LI>keyword = <I>linear</I> or <I>angular</I>

2
doc/fix_momentum.txt
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@ -15,7 +15,7 @@ fix ID group-ID momentum N keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
momentum = style name of this fix command :l
N = adjust the momentum every this many timesteps
one or more keyword/value pairs may be appended to the args :l
one or more keyword/value pairs may be appended :l
keyword = {linear} or {angular} :l
{linear} values = xflag yflag zflag
xflag,yflag,zflag = 0/1 to exclude/include each dimension

2
doc/fix_nph.html
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@ -33,7 +33,7 @@
start/end (0/1) of run (pressure units)
Pdamp = pressure damping parameter (time units)
</PRE>
<LI>zero or more keyword/value pairs may be appended to the args
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>drag</I> or <I>dilate</I>

2
doc/fix_nph.txt
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@ -27,7 +27,7 @@ p-style = {xyz} or {xy} or {yz} or {xz} or {aniso} :l
start/end (0/1) of run (pressure units)
Pdamp = pressure damping parameter (time units) :pre
zero or more keyword/value pairs may be appended to the args :l
zero or more keyword/value pairs may be appended :l
keyword = {drag} or {dilate} :l
{drag} value = drag factor added to barostat (0.0 = no drag)
{dilate} value = {all} or {partial} :pre

2
doc/fix_npt.html
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@ -32,7 +32,7 @@
Px_start,Px_stop,... = desired pressure in x,y,z at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
</PRE>
<LI>zero or more keyword/value pairs may be appended to the args
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>drag</I> or <I>dilate</I>

2
doc/fix_npt.txt
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@ -24,7 +24,7 @@ p-style = {xyz} or {xy} or {yz} or {xz} or {aniso} :l
Px_start,Px_stop,... = desired pressure in x,y,z at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units) :pre
zero or more keyword/value pairs may be appended to the args :l
zero or more keyword/value pairs may be appended :l
keyword = {drag} or {dilate} :l
{drag} value = drag factor added to barostat/thermostat (0.0 = no drag)
{dilate} value = {all} or {partial} :pre

2
doc/fix_npt_asphere.html
View File

@ -32,7 +32,7 @@
Px_start,Px_stop,... = desired pressure in x,y,z at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
</PRE>
<LI>zero or more keyword/value pairs may be appended to the args
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>drag</I> or <I>dilate</I>

2
doc/fix_npt_asphere.txt
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@ -24,7 +24,7 @@ p-style = {xyz} or {xy} or {yz} or {xz} or {aniso} :l
Px_start,Px_stop,... = desired pressure in x,y,z at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units) :pre
zero or more keyword/value pairs may be appended to the args :l
zero or more keyword/value pairs may be appended :l
keyword = {drag} or {dilate} :l
{drag} value = drag factor added to barostat/thermostat (0.0 = no drag)
{dilate} value = {all} or {partial} :pre

2
doc/fix_nvt.html
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@ -23,7 +23,7 @@
<LI>Tdamp = temperature damping parameter (time units)
<LI>zero or more keyword/value pairs may be appended to the args
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>drag</I>

2
doc/fix_nvt.txt
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@ -17,7 +17,7 @@ nvt = style name of this fix command :l
Tstart,Tstop = desired temperature at start/end of run :l
Tdamp = temperature damping parameter (time units) :l
zero or more keyword/value pairs may be appended to the args :l
zero or more keyword/value pairs may be appended :l
keyword = {drag} :l
{drag} value = drag factor added to thermostat (0.0 = no drag) :pre
:ule

2
doc/fix_nvt_asphere.html
View File

@ -23,7 +23,7 @@
<LI>Tdamp = temperature damping parameter (time units)
<LI>zero or more keyword/value pairs may be appended to the args
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>drag</I>

2
doc/fix_nvt_asphere.txt
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@ -17,7 +17,7 @@ nvt/asphere = style name of this fix command :l
Tstart,Tstop = desired temperature at start/end of run :l
Tdamp = temperature damping parameter (time units) :l
zero or more keyword/value pairs may be appended to the args :l
zero or more keyword/value pairs may be appended :l
keyword = {drag} :l
{drag} value = drag factor added to thermostat (0.0 = no drag) :pre
:ule

2
doc/fix_nvt_sllod.html
View File

@ -23,7 +23,7 @@
<LI>Tdamp = temperature damping parameter (time units)
<LI>zero or more keyword/value pairs may be appended to the args
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>drag</I>

2
doc/fix_nvt_sllod.txt
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@ -17,7 +17,7 @@ nvt/sllod = style name of this fix command :l
Tstart,Tstop = desired temperature at start/end of run :l
Tdamp = temperature damping parameter (time units) :l
zero or more keyword/value pairs may be appended to the args :l
zero or more keyword/value pairs may be appended :l
keyword = {drag} :l
{drag} value = drag factor added to thermostat (0.0 = no drag) :pre
:ule

2
doc/fix_recenter.html
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@ -21,7 +21,7 @@
<LI>x,y,z = constrain center-of-mass to these coords (distance units), any coord can also be NULL or INIT (see below)
<LI>zero or more keyword/value pairs may be appended to the args
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>shift</I> or <I>units</I>

2
doc/fix_recenter.txt
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@ -16,7 +16,7 @@ ID, group-ID are documented in "fix"_fix.html command :ulb,l
recenter = style name of this fix command :l
x,y,z = constrain center-of-mass to these coords (distance units), \
any coord can also be NULL or INIT (see below) :l
zero or more keyword/value pairs may be appended to the args :l
zero or more keyword/value pairs may be appended :l
keyword = {shift} or {units} :l
{shift} value = group-ID
group-ID = group of atoms whose coords are shifted

2
doc/fix_temp_rescale.html
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@ -21,7 +21,7 @@
<LI>Tstart,Tstop = desired temperature at start/end of run (temperature units)
<LI>window = only rescale if temperature is outside this window (temperature units)
<LI>fraction = rescale to target temperature by this fraction
<LI>zero or more keyword/value pairs may be appended to the args
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>region</I>
</UL>
<PRE> <I>region</I> values = region-ID of region to apply rescaling to

2
doc/fix_temp_rescale.txt
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@ -18,7 +18,7 @@ N = perform rescaling every N steps
Tstart,Tstop = desired temperature at start/end of run (temperature units)
window = only rescale if temperature is outside this window (temperature units)
fraction = rescale to target temperature by this fraction
zero or more keyword/value pairs may be appended to the args
zero or more keyword/value pairs may be appended
keyword = {region} :ul
{region} values = region-ID of region to apply rescaling to :pre

2
doc/fix_viscous.html
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@ -25,7 +25,7 @@
<LI>keyword = <I>b</I> or <I>a</I> or <I>t</I> or <I>m</I>
<LI>zero or more keyword/value pairs may be appended to the args
<LI>zero or more keyword/value pairs may be appended
<PRE>keyword = <I>scale</I>
<I>scale</I> values = type ratio

2
doc/fix_viscous.txt
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@ -17,7 +17,7 @@ viscous = style name of this fix command :l
gamma = damping coefficient (force/velocity units) :l
zero or more keyword/value pairs can be appended :l
keyword = {b} or {a} or {t} or {m} :l
zero or more keyword/value pairs may be appended to the args :l
zero or more keyword/value pairs may be appended :l
keyword = {scale}
{scale} values = type ratio
type = atom type (1-N)

2
doc/fix_wall_reflect.html
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@ -17,7 +17,7 @@
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>wall/reflect = style name of this fix command
<LI>one or more keyword/value pairs may be appended to the args
<LI>one or more keyword/value pairs may be appended
<LI>keyword = <I>xlo</I> or <I>xhi</I> or <I>ylo</I> or <I>yhi</I> or <I>zlo</I> or <I>zhi</I>
</UL>
<P><B>Examples:</B>

2
doc/fix_wall_reflect.txt
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@ -14,7 +14,7 @@ fix ID group-ID wall/reflect keyword ... :pre
ID, group-ID are documented in "fix"_fix.html command
wall/reflect = style name of this fix command
one or more keyword/value pairs may be appended to the args
one or more keyword/value pairs may be appended
keyword = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} :ul
[Examples:]

21
doc/pair_sw.html
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@ -98,17 +98,16 @@ entries would be required, etc.
<P>As annotated above, the first element in the entry is the center atom
in a three-body interaction. Thus an entry for SiCC means a Si atom
with 2 C atoms as neighbors. By symmetry, three-body parameters for
SiCSi and SiSiC entries should be the same. The parameters used for
the two-body interaction come
from the entry where the 2nd element is repeated. Thus the two-body
parameters for Si interacting with C, comes from the SiCC entry.
Again by symmetry, the two-body parameters in the SiCC
and CSiSi entries should thus be the same.
The parameters used for a particular three-body
interaction come from the entry with the corresponding three elements.
The parameters used only for two-body interactions (A, B, p, and q)
in entries whose 2nd and 3rd element are different (e.g. SiCSi)
are not used for anything and can be set to 0.0 if desired.
SiCSi and SiSiC entries should be the same. The parameters used for
the two-body interaction come from the entry where the 2nd element is
repeated. Thus the two-body parameters for Si interacting with C,
comes from the SiCC entry. Again by symmetry, the two-body parameters
in the SiCC and CSiSi entries should thus be the same. The parameters
used for a particular three-body interaction come from the entry with
the corresponding three elements. The parameters used only for
two-body interactions (A, B, p, and q) in entries whose 2nd and 3rd
element are different (e.g. SiCSi) are not used for anything and can
be set to 0.0 if desired.
</P>
<HR>

21
doc/pair_sw.txt
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@ -95,17 +95,16 @@ entries would be required, etc.
As annotated above, the first element in the entry is the center atom
in a three-body interaction. Thus an entry for SiCC means a Si atom
with 2 C atoms as neighbors. By symmetry, three-body parameters for
SiCSi and SiSiC entries should be the same. The parameters used for
the two-body interaction come
from the entry where the 2nd element is repeated. Thus the two-body
parameters for Si interacting with C, comes from the SiCC entry.
Again by symmetry, the two-body parameters in the SiCC
and CSiSi entries should thus be the same.
The parameters used for a particular three-body
interaction come from the entry with the corresponding three elements.
The parameters used only for two-body interactions (A, B, p, and q)
in entries whose 2nd and 3rd element are different (e.g. SiCSi)
are not used for anything and can be set to 0.0 if desired.
SiCSi and SiSiC entries should be the same. The parameters used for
the two-body interaction come from the entry where the 2nd element is
repeated. Thus the two-body parameters for Si interacting with C,
comes from the SiCC entry. Again by symmetry, the two-body parameters
in the SiCC and CSiSi entries should thus be the same. The parameters
used for a particular three-body interaction come from the entry with
the corresponding three elements. The parameters used only for
two-body interactions (A, B, p, and q) in entries whose 2nd and 3rd
element are different (e.g. SiCSi) are not used for anything and can
be set to 0.0 if desired.
:line

2
doc/region.html
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@ -42,7 +42,7 @@
N = # of regions to follow, must be 2 or greater
reg-ID1,reg-ID2, ... = IDs of regions to intersect
</PRE>
<LI>zero or more keyword/value pairs may be appended to the args
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>side</I> or <I>units</I>

2
doc/region.txt
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@ -36,7 +36,7 @@ style = {block} or {cylinder} or {prism} or {sphere} or {union} or {intersect} :
{intersect} args = N reg-ID1 reg-ID2 ...
N = # of regions to follow, must be 2 or greater
reg-ID1,reg-ID2, ... = IDs of regions to intersect :pre
zero or more keyword/value pairs may be appended to the args :l
zero or more keyword/value pairs may be appended :l
keyword = {side} or {units} :l
{side} value = {in} or {out}
{in} = the region is inside the specified geometry

2
doc/set.html
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@ -19,7 +19,7 @@
<LI>ID = atom ID or group ID or region ID
<LI>one or more keyword/value pairs may be appended to the args
<LI>one or more keyword/value pairs may be appended
<LI>keyword = <I>type</I> or <I>type/fraction</I> or <I>mol</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>vx</I> or <I>vy</I> or <I>vz</I> or <I>charge</I> or <I>dipole</I> or <I>dipole/random</I> or <I>quat/random</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I>

2
doc/set.txt
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@ -14,7 +14,7 @@ set style ID keyword value ... :pre
style = {atom} or {group} or {region} :ulb,l
ID = atom ID or group ID or region ID :l
one or more keyword/value pairs may be appended to the args :l
one or more keyword/value pairs may be appended :l
keyword = {type} or {type/fraction} or {mol} or \
{x} or {y} or {z} or {vx} or {vy} or {vz} or \
{charge} or {dipole} or {dipole/random} or {quat/random} or \

2
doc/velocity.html
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@ -35,7 +35,7 @@
<I>linear</I> = zero the linear momentum
<I>angular</I> = zero the angular momentum
</PRE>
<LI>zero or more keyword/value pairs may be appended to the args
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>dist</I> or <I>sum</I> or <I>mom</I> or <I>rot</I> or <I>temp</I> or <I>loop</I> or <I>units</I>

2
doc/velocity.txt
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@ -30,7 +30,7 @@ style = {create} or {set} or {scale} or {ramp} or {zero} :l
{linear} = zero the linear momentum
{angular} = zero the angular momentum :pre
zero or more keyword/value pairs may be appended to the args :l
zero or more keyword/value pairs may be appended :l
keyword = {dist} or {sum} or {mom} or {rot} or {temp} or {loop} or {units} :l
{dist} value = {uniform} or {gaussian}
{sum} value = {no} or {yes}