forked from lijiext/lammps
Added triclinic cell keywords and tilt factor scaling options
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6429 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
athomps
parent
a78c881832
commit
0511b7caa1
|
|
@ -755,8 +755,8 @@ See the <A HREF = "dump.html">dump</A> command for more information on XTC files
|
|||
particles. The <A HREF = "boundary.html">boundary</A> command sets the boundary
|
||||
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
|
||||
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
|
||||
(xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simluation box
|
||||
is created, e.g. by the <A HREF = "create_box.html">create_box</A> or
|
||||
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
|
||||
|
|
@ -768,14 +768,14 @@ custom</A> command.
|
|||
<P>LAMMPS also allows simulations to be perfored in non-orthogonal
|
||||
simulation boxes shaped as a parallelepiped with triclinic symmetry.
|
||||
The parallelepiped 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
|
||||
= (xy,yhi-ylo,0); C = (xz,yz,zhi-zlo). <I>Xy,xz,yz</I> can be 0.0 or
|
||||
3 edge vectors starting from the origin given by <B>a</B> = (xhi-xlo,0,0); <B>b</B>
|
||||
= (xy,yhi-ylo,0); <B>c</B> = (xz,yz,zhi-zlo). <I>Xy,xz,yz</I> can be 0.0 or
|
||||
positive or negative values and are called "tilt factors" because they
|
||||
are the amount of displacement applied to faces of an originally
|
||||
orthogonal box to transform it into the parallelepiped. Note that in
|
||||
LAMMPS the triclinic simulation box edge vectors A,B,C cannot be
|
||||
arbitrary vectors. As indicated, A must be aligned with the x axis, B
|
||||
must be in the xy plane, and C is arbitrary. However, this is not a
|
||||
LAMMPS the triclinic simulation box edge vectors <B>a</B>, <B>b</B>, and <B>c</B> cannot be
|
||||
arbitrary vectors. As indicated, <B>a</B> must be aligned with the x axis, <B>b</B>
|
||||
must be in the xy plane, and <B>c</B> is arbitrary. However, this is not a
|
||||
restriction since it is possible to rotate any set of 3 crystal basis
|
||||
vectors so that they meet this restriction.
|
||||
</P>
|
||||
|
|
@ -817,14 +817,25 @@ equivalent.
|
|||
</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,c lattice constants
|
||||
are the scalar lengths of the 3 A,B,C edge vectors defined above. The
|
||||
<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>
|
||||
<P>The inverse relationship can be written as follows:
|
||||
</P>
|
||||
<CENTER><IMG SRC = "Eqs/box_inverse.jpg">
|
||||
</CENTER>
|
||||
<P>The values of <I>a</I>, <I>b</I>, <I>c</I> , <I>alpha</I>, <I>beta</I> , and <I>gamma</I> can be printed
|
||||
out or accessed by computes using the
|
||||
<A HREF = "thermo_style.html">thermo_style custom</A> keywords
|
||||
<I>cella</I>, <I>cellb</I>, <I>cellc</I>, <I>cellalpha</I>, <I>cellbeta</I>, <I>cellgamma</I>,
|
||||
respectively.
|
||||
</P>
|
||||
<P>As discussed on the <A HREF = "dump.html">dump</A> command doc page, when the BOX
|
||||
BOUNDS for a snapshot is written to a dump file for a triclinic box,
|
||||
an orthogonal bounding box which encloses the triclinic simulation box
|
||||
|
|
@ -1158,7 +1169,7 @@ discussed below, it can be referenced via the following bracket
|
|||
notation, where ID in this case is the ID of a compute. The leading
|
||||
"c_" would be replaced by "f_" for a fix, or "v_" for a variable:
|
||||
</P>
|
||||
<DIV ALIGN=center><TABLE BORDER=1 >
|
||||
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
|
||||
<TR><TD >c_ID </TD><TD > entire scalar, vector, or array</TD></TR>
|
||||
<TR><TD >c_ID[I] </TD><TD > one element of vector, one column of array</TD></TR>
|
||||
<TR><TD >c_ID[I][J] </TD><TD > one element of array
|
||||
|
|
@ -1357,7 +1368,7 @@ data and scalar/vector/array data.
|
|||
input, that could be an element of a vector or array. Likewise a
|
||||
vector input could be a column of an array.
|
||||
</P>
|
||||
<DIV ALIGN=center><TABLE BORDER=1 >
|
||||
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
|
||||
<TR><TD >Command</TD><TD > Input</TD><TD > Output</TD><TD ></TD></TR>
|
||||
<TR><TD ><A HREF = "thermo_style.html">thermo_style custom</A></TD><TD > global scalars</TD><TD > screen, log file</TD><TD ></TD></TR>
|
||||
<TR><TD ><A HREF = "dump.html">dump custom</A></TD><TD > per-atom vectors</TD><TD > dump file</TD><TD ></TD></TR>
|
||||
|
|
|
|||
|
|
@ -747,8 +747,8 @@ 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
|
||||
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
|
||||
starting from the origin given by [a] = (xhi-xlo,0,0); [b] =
|
||||
(0,yhi-ylo,0); [c] = (0,0,zhi-zlo). The 6 parameters
|
||||
(xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simluation box
|
||||
is created, e.g. by the "create_box"_create_box.html or
|
||||
"read_data"_read_data.html or "read_restart"_read_restart.html
|
||||
|
|
@ -760,14 +760,14 @@ custom"_thermo_style.html command.
|
|||
LAMMPS also allows simulations to be perfored in non-orthogonal
|
||||
simulation boxes shaped as a parallelepiped with triclinic symmetry.
|
||||
The parallelepiped 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
|
||||
= (xy,yhi-ylo,0); C = (xz,yz,zhi-zlo). {Xy,xz,yz} can be 0.0 or
|
||||
3 edge vectors starting from the origin given by [a] = (xhi-xlo,0,0); [b]
|
||||
= (xy,yhi-ylo,0); [c] = (xz,yz,zhi-zlo). {Xy,xz,yz} can be 0.0 or
|
||||
positive or negative values and are called "tilt factors" because they
|
||||
are the amount of displacement applied to faces of an originally
|
||||
orthogonal box to transform it into the parallelepiped. Note that in
|
||||
LAMMPS the triclinic simulation box edge vectors A,B,C cannot be
|
||||
arbitrary vectors. As indicated, A must be aligned with the x axis, B
|
||||
must be in the xy plane, and C is arbitrary. However, this is not a
|
||||
LAMMPS the triclinic simulation box edge vectors [a], [b], and [c] cannot be
|
||||
arbitrary vectors. As indicated, [a] must be aligned with the x axis, [b]
|
||||
must be in the xy plane, and [c] is arbitrary. However, this is not a
|
||||
restriction since it is possible to rotate any set of 3 crystal basis
|
||||
vectors so that they meet this restriction.
|
||||
|
||||
|
|
@ -809,14 +809,25 @@ equivalent.
|
|||
|
||||
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,c lattice constants
|
||||
are the scalar lengths of the 3 A,B,C edge vectors defined above. The
|
||||
{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)
|
||||
|
||||
The inverse relationship can be written as follows:
|
||||
|
||||
:c,image(Eqs/box_inverse.jpg)
|
||||
|
||||
The values of {a}, {b}, {c} , {alpha}, {beta} , and {gamma} can be printed
|
||||
out or accessed by computes using the
|
||||
"thermo_style custom"_thermo_style.html keywords
|
||||
{cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta}, {cellgamma},
|
||||
respectively.
|
||||
|
||||
As discussed on the "dump"_dump.html command doc page, when the BOX
|
||||
BOUNDS for a snapshot is written to a dump file for a triclinic box,
|
||||
an orthogonal bounding box which encloses the triclinic simulation box
|
||||
|
|
|
|||
|
|
@ -46,7 +46,10 @@ keyword = <I>temp</I> or <I>iso</I> or <I>aniso</I> or <I>tri</I> or <I>x</I> or
|
|||
<I>ploop</I> value = number of sub-cycles to perform on barostat thermostat
|
||||
<I>nreset</I> value = reset reference cell every this many timesteps
|
||||
<I>drag</I> value = drag factor added to barostat/thermostat (0.0 = no drag)
|
||||
<I>dilate</I> value = <I>all</I> or <I>partial</I>
|
||||
<I>dilate</I> value = <I>all</I> or <I>partial</I>
|
||||
<I>scaleyz</I> value = <I>yes</I> or <I>no</I> = scale yz with lz
|
||||
<I>scalexz</I> value = <I>yes</I> or <I>no</I> = scale xz with lz
|
||||
<I>scalexy</I> value = <I>yes</I> or <I>no</I> = scale xy with ly
|
||||
</PRE>
|
||||
|
||||
</UL>
|
||||
|
|
@ -272,6 +275,16 @@ specified values of the external stress tensor. A value of <I>nstep</I>
|
|||
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.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>IMPORTANT NOTE: Using a barostat coupled to tilt dimensions <I>xy</I>,
|
||||
|
|
@ -483,6 +496,12 @@ the meaning of the xy,xz,yz tilt factors.
|
|||
make the external T = 0.0 at some timestep during the simulation which
|
||||
is not allowed in the Nose/Hoover formulation.
|
||||
</P>
|
||||
<P>The <I>scaleyz yes</I> and <I>scalexz yes</I> keyword/value pairs can not be used
|
||||
for 2D simulations. <I>scaleyz yes</I>, <I>scalexz yes</I>, and <I>scalexy yes</I> options
|
||||
can only be used if the 2nd dimension in the keyword is periodic,
|
||||
and if the tilt factor is not coupled to the barostat via keywords
|
||||
<I>tri</I>, <I>yz</I>, <I>xz</I>, and <I>xy</I>.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "run_style.html">run_style</A>
|
||||
|
|
@ -490,7 +509,9 @@ is not allowed in the Nose/Hoover formulation.
|
|||
<P><B>Default:</B>
|
||||
</P>
|
||||
<P>The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
|
||||
ploop = 1, nreset = 0, drag = 0.0, dilate = all, and couple = none.
|
||||
ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none,
|
||||
scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and
|
||||
not coupled to barostat, otherwise no.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
|
|
|
|||
|
|
@ -37,7 +37,10 @@ keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {y
|
|||
{ploop} value = number of sub-cycles to perform on barostat thermostat
|
||||
{nreset} value = reset reference cell every this many timesteps
|
||||
{drag} value = drag factor added to barostat/thermostat (0.0 = no drag)
|
||||
{dilate} value = {all} or {partial} :pre
|
||||
{dilate} value = {all} or {partial}
|
||||
{scaleyz} value = {yes} or {no} = scale yz with lz
|
||||
{scalexz} value = {yes} or {no} = scale xz with lz
|
||||
{scalexy} value = {yes} or {no} = scale xy with ly :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
|
@ -262,6 +265,16 @@ specified values of the external stress tensor. A value of {nstep}
|
|||
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.
|
||||
|
||||
:line
|
||||
|
||||
IMPORTANT NOTE: Using a barostat coupled to tilt dimensions {xy},
|
||||
|
|
@ -473,6 +486,12 @@ 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
|
||||
is not allowed in the Nose/Hoover formulation.
|
||||
|
||||
The {scaleyz yes} and {scalexz yes} keyword/value pairs can not be used
|
||||
for 2D simulations. {scaleyz yes}, {scalexz yes}, and {scalexy yes} options
|
||||
can only be used if the 2nd dimension in the keyword is periodic,
|
||||
and if the tilt factor is not coupled to the barostat via keywords
|
||||
{tri}, {yz}, {xz}, and {xy}.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix nve"_fix_nve.html, "fix_modify"_fix_modify.html, "run_style"_run_style.html
|
||||
|
|
@ -480,7 +499,9 @@ is not allowed in the Nose/Hoover formulation.
|
|||
[Default:]
|
||||
|
||||
The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
|
||||
ploop = 1, nreset = 0, drag = 0.0, dilate = all, and couple = none.
|
||||
ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none,
|
||||
scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and
|
||||
not coupled to barostat, otherwise no.
|
||||
|
||||
:line
|
||||
|
||||
|
|
|
|||
|
|
@ -30,6 +30,7 @@
|
|||
xy, xz, yz, xlat, ylat, zlat,
|
||||
pxx, pyy, pzz, pxy, pxz, pyz,
|
||||
fmax, fnorm,
|
||||
cella, cellb, cellc, cellalpha, cellbeta, cellgamma,
|
||||
c_ID, c_ID[I], c_ID[I][J],
|
||||
f_ID, f_ID[I], f_ID[I][J],
|
||||
v_name
|
||||
|
|
@ -65,6 +66,8 @@
|
|||
pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
|
||||
fmax = max component of force on any atom in any dimension
|
||||
fnorm = length of force vector for all atoms
|
||||
cella,cellb,cellc = periodic cell lattice constants a,b,c
|
||||
cellalpha, cellbeta, cellgamma = periodic cell angles alpha,beta,gamma
|
||||
c_ID = global scalar value calculated by a compute with ID
|
||||
c_ID[I] = Ith component of global vector calculated by a compute with ID
|
||||
c_ID[I][J] = I,J component of global array calculated by a compute with ID
|
||||
|
|
@ -230,6 +233,14 @@ calculates the maximum force in any dimension on any atom in the
|
|||
system, or the infinity-norm of the force vector for the system. The
|
||||
<I>fnorm</I> keyword calculates the 2-norm or length of the force vector.
|
||||
</P>
|
||||
<P>The keywords <I>cella</I>, <I>cellb</I>, <I>cellc</I>, <I>cellalpha</I>, <I>cellbeta</I>, <I>cellgamma</I>,
|
||||
correspond to the usual crystallographic quantities that define
|
||||
the periodic unit cell of a crystal.
|
||||
See <A HREF = "Section_howto.html#4_12">this section</A> of the doc pages for a
|
||||
geometric description of triclinic periodic cells, including
|
||||
a precise defintion of these quantities in terms of the internal
|
||||
LAMMPS cell dimensions <I>lx</I>, <I>ly</I>, <I>lz</I>, <I>yz</I>, <I>xz</I>, <I>xy</I>,
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The <I>c_ID</I> and <I>c_ID[I]</I> and <I>c_ID[I][J]</I> keywords allow global
|
||||
|
|
|
|||
|
|
@ -25,6 +25,7 @@ args = list of arguments for a particular style :l
|
|||
xy, xz, yz, xlat, ylat, zlat,
|
||||
pxx, pyy, pzz, pxy, pxz, pyz,
|
||||
fmax, fnorm,
|
||||
cella, cellb, cellc, cellalpha, cellbeta, cellgamma,
|
||||
c_ID, c_ID\[I\], c_ID\[I\]\[J\],
|
||||
f_ID, f_ID\[I\], f_ID\[I\]\[J\],
|
||||
v_name
|
||||
|
|
@ -60,6 +61,8 @@ args = list of arguments for a particular style :l
|
|||
pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
|
||||
fmax = max component of force on any atom in any dimension
|
||||
fnorm = length of force vector for all atoms
|
||||
cella,cellb,cellc = periodic cell lattice constants a,b,c
|
||||
cellalpha, cellbeta, cellgamma = periodic cell angles alpha,beta,gamma
|
||||
c_ID = global scalar value calculated by a compute with ID
|
||||
c_ID\[I\] = Ith component of global vector calculated by a compute with ID
|
||||
c_ID\[I\]\[J\] = I,J component of global array calculated by a compute with ID
|
||||
|
|
@ -224,6 +227,14 @@ calculates the maximum force in any dimension on any atom in the
|
|||
system, or the infinity-norm of the force vector for the system. The
|
||||
{fnorm} keyword calculates the 2-norm or length of the force vector.
|
||||
|
||||
The keywords {cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta}, {cellgamma},
|
||||
correspond to the usual crystallographic quantities that define
|
||||
the periodic unit cell of a crystal.
|
||||
See "this section"_Section_howto.html#4_12 of the doc pages for a
|
||||
geometric description of triclinic periodic cells, including
|
||||
a precise defintion of these quantities in terms of the internal
|
||||
LAMMPS cell dimensions {lx}, {ly}, {lz}, {yz}, {xz}, {xy},
|
||||
|
||||
:line
|
||||
|
||||
The {c_ID} and {c_ID\[I\]} and {c_ID\[I\]\[J\]} keywords allow global
|
||||
|
|
|
|||
Loading…
Reference in New Issue