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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7687 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2012-02-03 20:21:28 +00:00
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32
doc/Section_howto.html
View File

@ -758,7 +758,7 @@ See the <A HREF = "dump.html">dump</A> command for more information on XTC files
</H4>
<P>By default, LAMMPS uses an orthogonal simulation box to encompass the
particles. The <A HREF = "boundary.html">boundary</A> command sets the boundary
conditions of the box (periodic, non-periodic, etc). The orthogonal
conditions of the box (periodic, non-,periodic, etc). The orthogonal
box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors
starting from the origin given by <B>a</B> = (xhi-xlo,0,0); <B>b</B> =
(0,yhi-ylo,0); <B>c</B> = (0,0,zhi-zlo). The 6 parameters
@ -818,16 +818,26 @@ the x box length is 10 and the xy tilt factor must be between -5 and
+(yhi-ylo)/2. Note that this is not a limitation, since if the
maximum tilt factor is 5 (as in this example), then configurations
with tilt = ..., -15, -5, 5, 15, 25, ... are geometrically all
equivalent.
equivalent. If the box tilt exceeds this limit during a dynamics run
(e.g. via the <A HREF = "fix_deform.html">fix deform</A> command), then the box is
"flipped" to an equivalent shape with a tilt factor within the bounds,
so the run can continue. See the <A HREF = "fix_deform.html">fix deform</A> doc
page for further details.
</P>
<P>The one exception to this rule is if the 1st dimension in the tilt
factor (x for xy) is non-periodic. In that case, the limits on the
tilt factor are not enforced, since flipping the box in that dimension
does not change the atom positions due to non-periodicity. In this
mode, if you tilt the system to extreme angles, the simulation will
simply become inefficient, due to the highly skewed simulation box.
</P>
<P>Triclinic crystal structures are often defined using three lattice
constants <I>a</I>, <I>b</I>, and <I>c</I>, and three angles <I>alpha</I>, <I>beta</I> and
<I>gamma</I>. Note that in this nomenclature, the a, b, and c lattice constants
are the scalar lengths of the edge vectors <B>a</B>, <B>b</B>, and <B>c</B> defined
above. The
relationship between these 6 quantities (a,b,c,alpha,beta,gamma) and
the LAMMPS box sizes (lx,ly,lz) = (xhi-xlo,yhi-ylo,zhi-zlo) and tilt
factors (xy,xz,yz) is as follows:
<I>gamma</I>. Note that in this nomenclature, the a, b, and c lattice
constants are the scalar lengths of the edge vectors <B>a</B>, <B>b</B>, and <B>c</B>
defined above. The relationship between these 6 quantities
(a,b,c,alpha,beta,gamma) and the LAMMPS box sizes (lx,ly,lz) =
(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows:
</P>
<CENTER><IMG SRC = "Eqs/box.jpg">
</CENTER>
@ -910,9 +920,9 @@ LAMMPS for computational efficiency to be 1/2 of the parallel box
length. However, <A HREF = "fix_deform.html">fix deform</A> can continuously strain
a box by an arbitrary amount. As discussed in the <A HREF = "fix_deform.html">fix
deform</A> command, when the tilt value reaches a limit,
the box is re-shaped to the opposite limit which is an equivalent
tiling of periodic space. The strain rate can then continue to change
as before. In a long NEMD simulation these box re-shaping events may
the box is flipped to the opposite limit which is an equivalent tiling
of periodic space. The strain rate can then continue to change as
before. In a long NEMD simulation these box re-shaping events may
occur many times.
</P>
<P>In a NEMD simulation, the "remap" option of <A HREF = "fix_deform.html">fix

32
doc/Section_howto.txt
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@ -749,7 +749,7 @@ See the "dump"_dump.html command for more information on XTC files.
By default, LAMMPS uses an orthogonal simulation box to encompass the
particles. The "boundary"_boundary.html command sets the boundary
conditions of the box (periodic, non-periodic, etc). The orthogonal
conditions of the box (periodic, non-,periodic, etc). The orthogonal
box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors
starting from the origin given by [a] = (xhi-xlo,0,0); [b] =
(0,yhi-ylo,0); [c] = (0,0,zhi-zlo). The 6 parameters
@ -809,16 +809,26 @@ the x box length is 10 and the xy tilt factor must be between -5 and
+(yhi-ylo)/2. Note that this is not a limitation, since if the
maximum tilt factor is 5 (as in this example), then configurations
with tilt = ..., -15, -5, 5, 15, 25, ... are geometrically all
equivalent.
equivalent. If the box tilt exceeds this limit during a dynamics run
(e.g. via the "fix deform"_fix_deform.html command), then the box is
"flipped" to an equivalent shape with a tilt factor within the bounds,
so the run can continue. See the "fix deform"_fix_deform.html doc
page for further details.
The one exception to this rule is if the 1st dimension in the tilt
factor (x for xy) is non-periodic. In that case, the limits on the
tilt factor are not enforced, since flipping the box in that dimension
does not change the atom positions due to non-periodicity. In this
mode, if you tilt the system to extreme angles, the simulation will
simply become inefficient, due to the highly skewed simulation box.
Triclinic crystal structures are often defined using three lattice
constants {a}, {b}, and {c}, and three angles {alpha}, {beta} and
{gamma}. Note that in this nomenclature, the a, b, and c lattice constants
are the scalar lengths of the edge vectors [a], [b], and [c] defined
above. The
relationship between these 6 quantities (a,b,c,alpha,beta,gamma) and
the LAMMPS box sizes (lx,ly,lz) = (xhi-xlo,yhi-ylo,zhi-zlo) and tilt
factors (xy,xz,yz) is as follows:
{gamma}. Note that in this nomenclature, the a, b, and c lattice
constants are the scalar lengths of the edge vectors [a], [b], and [c]
defined above. The relationship between these 6 quantities
(a,b,c,alpha,beta,gamma) and the LAMMPS box sizes (lx,ly,lz) =
(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows:
:c,image(Eqs/box.jpg)
@ -901,9 +911,9 @@ LAMMPS for computational efficiency to be 1/2 of the parallel box
length. However, "fix deform"_fix_deform.html can continuously strain
a box by an arbitrary amount. As discussed in the "fix
deform"_fix_deform.html command, when the tilt value reaches a limit,
the box is re-shaped to the opposite limit which is an equivalent
tiling of periodic space. The strain rate can then continue to change
as before. In a long NEMD simulation these box re-shaping events may
the box is flipped to the opposite limit which is an equivalent tiling
of periodic space. The strain rate can then continue to change as
before. In a long NEMD simulation these box re-shaping events may
occur many times.
In a NEMD simulation, the "remap" option of "fix

14
doc/boundary.html
View File

@ -60,6 +60,20 @@ face has a value of 50.0 in the data file, the face will always be
positioned at 50.0 or above, even if the maximum z-extent of all the
atoms becomes less than 50.0.
</P>
<P>For triclinic (non-orthogonal) simulation boxes, if the 2nd dimension
of a tilt factor (e.g. y for xy) is periodic, then the periodicity is
enforced with the tilt factor offset. If the 1st dimension is
shrink-wrapped, then the shrink wrapping is applied to the tilted box
face, to encompass the atoms. E.g. for a positive xy tilt, the xlo
and xhi faces of the box are planes tilting in the +y direction as y
increases. These tilted planes are shrink-wrapped around the atoms to
determine the x extent of the box.
</P>
<P>See <A HREF = "Section_howto.html#howto_12">Section_howto 12</A> of the doc pages
for a geometric description of triclinic boxes, as defined by LAMMPS,
and how to transform these parameters to and from other commonly used
triclinic representations.
</P>
<P><B>Restrictions:</B>
</P>
<P>This command cannot be used after the simulation box is defined by a

14
doc/boundary.txt
View File

@ -55,6 +55,20 @@ face has a value of 50.0 in the data file, the face will always be
positioned at 50.0 or above, even if the maximum z-extent of all the
atoms becomes less than 50.0.
For triclinic (non-orthogonal) simulation boxes, if the 2nd dimension
of a tilt factor (e.g. y for xy) is periodic, then the periodicity is
enforced with the tilt factor offset. If the 1st dimension is
shrink-wrapped, then the shrink wrapping is applied to the tilted box
face, to encompass the atoms. E.g. for a positive xy tilt, the xlo
and xhi faces of the box are planes tilting in the +y direction as y
increases. These tilted planes are shrink-wrapped around the atoms to
determine the x extent of the box.
See "Section_howto 12"_Section_howto.html#howto_12 of the doc pages
for a geometric description of triclinic boxes, as defined by LAMMPS,
and how to transform these parameters to and from other commonly used
triclinic representations.
[Restrictions:]
This command cannot be used after the simulation box is defined by a

46
doc/fix_deform.html
View File

@ -99,13 +99,12 @@ continuously strained system. See the <A HREF = "fix_nvt_sllod.html">fix
nvt/sllod</A> and <A HREF = "compute_temp_deform.html">compute
temp/deform</A> commands for more details.
</P>
<P>Any parameter varied by this command must refer to a periodic
dimension - see the <A HREF = "boundary.html">boundary</A> command. For parameters
<I>xy</I>, <I>xz</I>, and <I>yz</I>, the 2nd dimension must be periodic, e.g. <I>y</I> for
<I>xy</I>. Dimensions not varied by this command can be periodic or
non-periodic. Dimensions corresponding to unspecified parameters can
also be controlled by a <A HREF = "fix_nh.html">fix npt</A> or <A HREF = "fix_nh.html">fix nph</A>
command.
<P>For the <I>x</I>, <I>y</I>, <I>z</I> parameters, the associated dimension cannot be
shrink-wrapped. For the <I>xy</I>, <I>yz</I>, <I>xz</I> parameters, the associated
2nd dimension cannot be shrink-wrapped. Dimensions not varied by this
command can be periodic or non-periodic. Dimensions corresponding to
unspecified parameters can also be controlled by a <A HREF = "fix_nh.html">fix
npt</A> or <A HREF = "fix_nh.html">fix nph</A> command.
</P>
<P>The size and shape of the simulation box at the beginning of the
simulation run were either specified by the
@ -433,16 +432,23 @@ example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
applied via the <I>xy</I>, <I>xz</I>, or <I>yz</I> parameters, the following
algorithm is used. If <I>prd</I> is the associated parallel box length (10
in the example above), then if the tilt factor exceeds the accepted
range of -5 to 5 during the simulation, then the box is re-shaped to
the other limit (an equivalent box) and the simulation continues.
Thus for this example, if the initial xy tilt factor was 0.0 and "xy
final 100.0" was specified, then during the simulation the xy tilt
factor would increase from 0.0 to 5.0, the box would be re-shaped so
that the tilt factor becomes -5.0, the tilt factor would increase from
-5.0 to 5.0, the box would be re-shaped again, etc. The re-shaping
would occur 10 times and the final tilt factor at the end of the
simulation would be 0.0. During each re-shaping event, atoms are
remapped into the new box in the appropriate manner.
range of -5 to 5 during the simulation, then the box is flipped to the
other limit (an equivalent box) and the simulation continues. Thus
for this example, if the initial xy tilt factor was 0.0 and "xy final
100.0" was specified, then during the simulation the xy tilt factor
would increase from 0.0 to 5.0, the box would be flipped so that the
tilt factor becomes -5.0, the tilt factor would increase from -5.0 to
5.0, the box would be flipped again, etc. The flip occurs 10 times
and the final tilt factor at the end of the simulation would be 0.0.
During each flip event, atoms are remapped into the new box in the
appropriate manner.
</P>
<P>The one exception to this rule is if the 1st dimension in the tilt
factor (x for xy) is non-periodic. In that case, the limits on the
tilt factor are not enforced, since flipping the box in that dimension
does not change the atom positions due to non-periodicity. In this
mode, if you tilt the system to extreme angles, the simulation will
simply become inefficient due to the highly skewed simulation box.
</P>
<HR>
@ -519,7 +525,11 @@ and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
</P>
<P><B>Restrictions:</B>
</P>
<P>Any box dimension varied by this fix must be periodic.
<P>You cannot apply x, y, or z deformations to a dimension that is
shrink-wrapped via the <A HREF = "boundary.html">boundary</A> comamnd.
</P>
<P>You cannot apply xy, yz, or xz deformations to a 2nd dimension (y in
xy) that is shrink-wrapped via the <A HREF = "boundary.html">boundary</A> comamnd.
</P>
<P><B>Related commands:</B>
</P>

46
doc/fix_deform.txt
View File

@ -89,13 +89,12 @@ continuously strained system. See the "fix
nvt/sllod"_fix_nvt_sllod.html and "compute
temp/deform"_compute_temp_deform.html commands for more details.
Any parameter varied by this command must refer to a periodic
dimension - see the "boundary"_boundary.html command. For parameters
{xy}, {xz}, and {yz}, the 2nd dimension must be periodic, e.g. {y} for
{xy}. Dimensions not varied by this command can be periodic or
non-periodic. Dimensions corresponding to unspecified parameters can
also be controlled by a "fix npt"_fix_nh.html or "fix nph"_fix_nh.html
command.
For the {x}, {y}, {z} parameters, the associated dimension cannot be
shrink-wrapped. For the {xy}, {yz}, {xz} parameters, the associated
2nd dimension cannot be shrink-wrapped. Dimensions not varied by this
command can be periodic or non-periodic. Dimensions corresponding to
unspecified parameters can also be controlled by a "fix
npt"_fix_nh.html or "fix nph"_fix_nh.html command.
The size and shape of the simulation box at the beginning of the
simulation run were either specified by the
@ -423,16 +422,23 @@ To obey this constraint and allow for large shear deformations to be
applied via the {xy}, {xz}, or {yz} parameters, the following
algorithm is used. If {prd} is the associated parallel box length (10
in the example above), then if the tilt factor exceeds the accepted
range of -5 to 5 during the simulation, then the box is re-shaped to
the other limit (an equivalent box) and the simulation continues.
Thus for this example, if the initial xy tilt factor was 0.0 and "xy
final 100.0" was specified, then during the simulation the xy tilt
factor would increase from 0.0 to 5.0, the box would be re-shaped so
that the tilt factor becomes -5.0, the tilt factor would increase from
-5.0 to 5.0, the box would be re-shaped again, etc. The re-shaping
would occur 10 times and the final tilt factor at the end of the
simulation would be 0.0. During each re-shaping event, atoms are
remapped into the new box in the appropriate manner.
range of -5 to 5 during the simulation, then the box is flipped to the
other limit (an equivalent box) and the simulation continues. Thus
for this example, if the initial xy tilt factor was 0.0 and "xy final
100.0" was specified, then during the simulation the xy tilt factor
would increase from 0.0 to 5.0, the box would be flipped so that the
tilt factor becomes -5.0, the tilt factor would increase from -5.0 to
5.0, the box would be flipped again, etc. The flip occurs 10 times
and the final tilt factor at the end of the simulation would be 0.0.
During each flip event, atoms are remapped into the new box in the
appropriate manner.
The one exception to this rule is if the 1st dimension in the tilt
factor (x for xy) is non-periodic. In that case, the limits on the
tilt factor are not enforced, since flipping the box in that dimension
does not change the atom positions due to non-periodicity. In this
mode, if you tilt the system to extreme angles, the simulation will
simply become inefficient due to the highly skewed simulation box.
:line
@ -509,7 +515,11 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
Any box dimension varied by this fix must be periodic.
You cannot apply x, y, or z deformations to a dimension that is
shrink-wrapped via the "boundary"_boundary.html comamnd.
You cannot apply xy, yz, or xz deformations to a 2nd dimension (y in
xy) that is shrink-wrapped via the "boundary"_boundary.html comamnd.
[Related commands:]

68
doc/fix_nh.html
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@ -276,15 +276,14 @@ means that every <I>nstep</I> timesteps, the reference dimensions are set
to those of the current simulation domain.
</P>
<P>The <I>scaleyz</I>, <I>scalexz</I>, and <I>scalexy</I> keywords control whether or
not the corresponding tilt factors are scaled with the
associated box dimensions
when barostatting triclinic periodic cells.
The default values <I>yes</I> will turn on scaling, which corresponds to
adjusting the linear dimensions of the cell while preserving its shape.
Choosing <I>no</I> ensures that the tilt factors are not scaled with the
box dimensions. See below for restrictions and default values in different
situations. In older versions of LAMMPS, scaling of tilt factors was not
performed. The old behavior can be recovered by setting all three
not the corresponding tilt factors are scaled with the associated box
dimensions when barostatting triclinic periodic cells. The default
values <I>yes</I> will turn on scaling, which corresponds to adjusting the
linear dimensions of the cell while preserving its shape. Choosing
<I>no</I> ensures that the tilt factors are not scaled with the box
dimensions. See below for restrictions and default values in different
situations. In older versions of LAMMPS, scaling of tilt factors was
not performed. The old behavior can be recovered by setting all three
scale keywords to <I>no</I>.
</P>
<HR>
@ -292,24 +291,24 @@ scale keywords to <I>no</I>.
<P>IMPORTANT NOTE: Using a barostat coupled to tilt dimensions <I>xy</I>,
<I>xz</I>, <I>yz</I> can sometimes result in arbitrarily large values of the
tilt dimensions, i.e. a dramatically deformed simulation box. LAMMPS
allows the tilt factors to grow a little beyond the normal limit
of half the box length (0.6 times the box length), and then performs
allows the tilt factors to grow a little beyond the normal limit of
half the box length (0.6 times the box length), and then performs
flipping or re-shaping to an equivalent periodic cell. The re-shaping
operation is described in more detail in the doc page for
<A HREF = "fix_deform.html">fix deform</A>. Both the barostat dynamics and
the atom trajectories are unaffected by this operation. However,
if a tilt factor is incremented by a large amount (1.5 times the
box length) on a single timestep, LAMMPS can not accomodate
this event and will terminate the simulation
with an error. This error typically
indicates that there is something badly wrong with how the simulation
was constructed, such as specifying values of <I>Pstart</I> that are
too far from the current stress value, or specifying a timestep that
is too large. Triclinic barostatting should be used with
care. This also is true for other barostat styles, although they tend
to be more forgiving of insults. In particular, it is important to
recognize that equilibrium liquids can not support a shear stress and
that equilibrium solids can not support shear stresses that exceed the yield stress.
operation is described in more detail in the doc page for <A HREF = "fix_deform.html">fix
deform</A>. Both the barostat dynamics and the atom
trajectories are unaffected by this operation. However, if a tilt
factor is incremented by a large amount (1.5 times the box length) on
a single timestep, LAMMPS can not accomodate this event and will
terminate the simulation with an error. This error typically indicates
that there is something badly wrong with how the simulation was
constructed, such as specifying values of <I>Pstart</I> that are too far
from the current stress value, or specifying a timestep that is too
large. Triclinic barostatting should be used with care. This also is
true for other barostat styles, although they tend to be more
forgiving of insults. In particular, it is important to recognize that
equilibrium liquids can not support a shear stress and that
equilibrium solids can not support shear stresses that exceed the
yield stress.
</P>
<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_temp_berendsen.html">fix
temp/berendsen</A> command which performs
@ -493,14 +492,15 @@ space measure of the underlying non-Hamiltonian equations of motion.
</P>
<P><B>Restrictions:</B>
</P>
<P>Non-periodic dimensions cannot be barostatted. <I>Z</I>, <I>xz</I>, and <I>yz</I>,
cannot be barostatted 2D simulations. <I>Xy</I>, <I>xz</I>, and <I>yz</I> can only
be barostatted if the simulation domain is triclinic and the 2nd
dimension in the keyword (<I>y</I> dimension in <I>xy</I>) is periodic. The
<A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read data</A>, and
<A HREF = "read_restart.html">read_restart</A> commands specify whether the
simulation box is orthogonal or non-orthogonal (triclinic) and explain
the meaning of the xy,xz,yz tilt factors.
<P><I>X</I>, <I>y</I>, <I>z</I> cannot be barostatted if the associated dimension is not
periodic. <I>Xy</I>, <I>xz</I>, and <I>yz</I> can only be barostatted if the
simulation domain is triclinic and the 2nd dimension in the keyword
(<I>y</I> dimension in <I>xy</I>) is periodic. <I>Z</I>, <I>xz</I>, and <I>yz</I>, cannot be
barostatted for 2D simulations. The <A HREF = "create_box.html">create_box</A>,
<A HREF = "read_data.html">read data</A>, and <A HREF = "read_restart.html">read_restart</A>
commands specify whether the simulation box is orthogonal or
non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz
tilt factors.
</P>
<P>For the <I>temp</I> keyword, the final Tstop cannot be 0.0 since it would
make the external T = 0.0 at some timestep during the simulation which

68
doc/fix_nh.txt
View File

@ -266,15 +266,14 @@ means that every {nstep} timesteps, the reference dimensions are set
to those of the current simulation domain.
The {scaleyz}, {scalexz}, and {scalexy} keywords control whether or
not the corresponding tilt factors are scaled with the
associated box dimensions
when barostatting triclinic periodic cells.
The default values {yes} will turn on scaling, which corresponds to
adjusting the linear dimensions of the cell while preserving its shape.
Choosing {no} ensures that the tilt factors are not scaled with the
box dimensions. See below for restrictions and default values in different
situations. In older versions of LAMMPS, scaling of tilt factors was not
performed. The old behavior can be recovered by setting all three
not the corresponding tilt factors are scaled with the associated box
dimensions when barostatting triclinic periodic cells. The default
values {yes} will turn on scaling, which corresponds to adjusting the
linear dimensions of the cell while preserving its shape. Choosing
{no} ensures that the tilt factors are not scaled with the box
dimensions. See below for restrictions and default values in different
situations. In older versions of LAMMPS, scaling of tilt factors was
not performed. The old behavior can be recovered by setting all three
scale keywords to {no}.
:line
@ -282,24 +281,24 @@ scale keywords to {no}.
IMPORTANT NOTE: Using a barostat coupled to tilt dimensions {xy},
{xz}, {yz} can sometimes result in arbitrarily large values of the
tilt dimensions, i.e. a dramatically deformed simulation box. LAMMPS
allows the tilt factors to grow a little beyond the normal limit
of half the box length (0.6 times the box length), and then performs
allows the tilt factors to grow a little beyond the normal limit of
half the box length (0.6 times the box length), and then performs
flipping or re-shaping to an equivalent periodic cell. The re-shaping
operation is described in more detail in the doc page for
"fix deform"_fix_deform.html. Both the barostat dynamics and
the atom trajectories are unaffected by this operation. However,
if a tilt factor is incremented by a large amount (1.5 times the
box length) on a single timestep, LAMMPS can not accomodate
this event and will terminate the simulation
with an error. This error typically
indicates that there is something badly wrong with how the simulation
was constructed, such as specifying values of {Pstart} that are
too far from the current stress value, or specifying a timestep that
is too large. Triclinic barostatting should be used with
care. This also is true for other barostat styles, although they tend
to be more forgiving of insults. In particular, it is important to
recognize that equilibrium liquids can not support a shear stress and
that equilibrium solids can not support shear stresses that exceed the yield stress.
operation is described in more detail in the doc page for "fix
deform"_fix_deform.html. Both the barostat dynamics and the atom
trajectories are unaffected by this operation. However, if a tilt
factor is incremented by a large amount (1.5 times the box length) on
a single timestep, LAMMPS can not accomodate this event and will
terminate the simulation with an error. This error typically indicates
that there is something badly wrong with how the simulation was
constructed, such as specifying values of {Pstart} that are too far
from the current stress value, or specifying a timestep that is too
large. Triclinic barostatting should be used with care. This also is
true for other barostat styles, although they tend to be more
forgiving of insults. In particular, it is important to recognize that
equilibrium liquids can not support a shear stress and that
equilibrium solids can not support shear stresses that exceed the
yield stress.
IMPORTANT NOTE: Unlike the "fix
temp/berendsen"_fix_temp_berendsen.html command which performs
@ -483,14 +482,15 @@ space measure of the underlying non-Hamiltonian equations of motion.
[Restrictions:]
Non-periodic dimensions cannot be barostatted. {Z}, {xz}, and {yz},
cannot be barostatted 2D simulations. {Xy}, {xz}, and {yz} can only
be barostatted if the simulation domain is triclinic and the 2nd
dimension in the keyword ({y} dimension in {xy}) is periodic. The
"create_box"_create_box.html, "read data"_read_data.html, and
"read_restart"_read_restart.html commands specify whether the
simulation box is orthogonal or non-orthogonal (triclinic) and explain
the meaning of the xy,xz,yz tilt factors.
{X}, {y}, {z} cannot be barostatted if the associated dimension is not
periodic. {Xy}, {xz}, and {yz} can only be barostatted if the
simulation domain is triclinic and the 2nd dimension in the keyword
({y} dimension in {xy}) is periodic. {Z}, {xz}, and {yz}, cannot be
barostatted for 2D simulations. The "create_box"_create_box.html,
"read data"_read_data.html, and "read_restart"_read_restart.html
commands specify whether the simulation box is orthogonal or
non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz
tilt factors.
For the {temp} keyword, the final Tstop cannot be 0.0 since it would
make the external T = 0.0 at some timestep during the simulation which