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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11906 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-05-02 21:47:08 +00:00
parent 5e0c91dc3e
commit 19267785f5
16 changed files with 57 additions and 38 deletions
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10
doc/Section_python.html
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@ -545,12 +545,12 @@ this:
natoms = lmp.get_natoms()
n3 = 3*natoms
x = (n3*c_double)()
x<B>0</B> = x coord of atom with ID 1
x<B>1</B> = y coord of atom with ID 1
x<B>2</B> = z coord of atom with ID 1
x<B>3</B> = x coord of atom with ID 2
x[0] = x coord of atom with ID 1
x[1] = y coord of atom with ID 1
x[2] = z coord of atom with ID 1
x[3] = x coord of atom with ID 2
...
x<B>n3-1</B> = z coord of atom with ID natoms
x[n3-1] = z coord of atom with ID natoms
lmp.scatter_coords("x",1,3,x)
</PRE>
<P>Alternatively, you can just change values in the vector returned by

10
doc/Section_python.txt
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@ -540,12 +540,12 @@ from ctypes import *
natoms = lmp.get_natoms()
n3 = 3*natoms
x = (n3*c_double)()
x[0] = x coord of atom with ID 1
x[1] = y coord of atom with ID 1
x[2] = z coord of atom with ID 1
x[3] = x coord of atom with ID 2
x\[0\] = x coord of atom with ID 1
x\[1\] = y coord of atom with ID 1
x\[2\] = z coord of atom with ID 1
x\[3\] = x coord of atom with ID 2
...
x[n3-1] = z coord of atom with ID natoms
x\[n3-1\] = z coord of atom with ID natoms
lmp.scatter_coords("x",1,3,x) :pre
Alternatively, you can just change values in the vector returned by

7
doc/compute_property_atom.html
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@ -34,6 +34,7 @@
corner1x, corner1y, corner1z,
corner2x, corner2y, corner2z,
corner3x, corner3y, corner3z,
nbonds,
i_name, d_name
</PRE>
<PRE> id = atom ID
@ -60,7 +61,8 @@
ervel = electron radial velocity
erforce = electron radial force
end12x, end12y, end12z = end points of line segment
coner123x, corner123y, corner123z = corner points of triangle
corner123x, corner123y, corner123z = corner points of triangle
nbonds = number of bonds
i_name = custom integer vector with name
d_name = custom integer vector with name
</PRE>
@ -111,6 +113,9 @@ line segment particles and define the end points of each line segment.
<I>corner2z</I>, <I>corner3x</I>, <I>corner3y</I>, <I>corner3z</I>, are defined for
triangular particles and define the corner points of each triangle.
</P>
<P><I>nbonds</I> is available for all molecular atom styles and refers to
the number of explicit bonds attached to an atom.
</P>
<P>The <I>i_name</I> and <I>d_name</I> attributes refer to custom integer and
floating-point properties that have been added to each atom via the
<A HREF = "fix_property_atom.html">fix property/atom</A> command. When that command

7
doc/compute_property_atom.txt
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@ -28,6 +28,7 @@ input = one or more atom attributes :l
corner1x, corner1y, corner1z,
corner2x, corner2y, corner2z,
corner3x, corner3y, corner3z,
nbonds,
i_name, d_name :pre
id = atom ID
mol = molecule ID
@ -53,7 +54,8 @@ input = one or more atom attributes :l
ervel = electron radial velocity
erforce = electron radial force
end12x, end12y, end12z = end points of line segment
coner123x, corner123y, corner123z = corner points of triangle
corner123x, corner123y, corner123z = corner points of triangle
nbonds = number of bonds
i_name = custom integer vector with name
d_name = custom integer vector with name :pre
:ule
@ -103,6 +105,9 @@ line segment particles and define the end points of each line segment.
{corner2z}, {corner3x}, {corner3y}, {corner3z}, are defined for
triangular particles and define the corner points of each triangle.
{nbonds} is available for all molecular atom styles and refers to
the number of explicit bonds attached to an atom.
The {i_name} and {d_name} attributes refer to custom integer and
floating-point properties that have been added to each atom via the
"fix property/atom"_fix_property_atom.html command. When that command

2
doc/compute_vacf.html
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@ -43,7 +43,7 @@ coefficient of the diffusing atoms. This can be computed in the
following manner, using the <A HREF = "variable.html">variable trap()</A> function:
</P>
<PRE>compute 2 all vacf
fix 5 all vector 1 c_2<B>4</B>
fix 5 all vector 1 c_2[4]
variable diff equal dt*trap(f_5)
thermo_style custom step v_diff
</PRE>

2
doc/compute_vacf.txt
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@ -40,7 +40,7 @@ coefficient of the diffusing atoms. This can be computed in the
following manner, using the "variable trap()"_variable.html function:
compute 2 all vacf
fix 5 all vector 1 c_2[4]
fix 5 all vector 1 c_2\[4\]
variable diff equal dt*trap(f_5)
thermo_style custom step v_diff :pre

19
doc/dump.html
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@ -25,7 +25,7 @@
<LI>group-ID = ID of the group of atoms to be dumped
<LI>style = <I>atom</I> or <I>atom/mpiio</I> or <I>cfg</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I> or <I>xyz/mpiio</I> or <I>image</I> or <I>molfile</I> or <I>local</I> or <I>custom</I> or <I>custom/mpiio</I>
<LI>style = <I>atom</I> or <I>atom/mpiio</I> or <I>cfg</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I> or <I>xyz/mpiio</I> or <I>image</I> or <I>movie</I> or <I>molfile</I> or <I>local</I> or <I>custom</I> or <I>custom/mpiio</I>
<LI>N = dump every this many timesteps
@ -44,6 +44,8 @@
</PRE>
<PRE> <I>image</I> args = discussed on <A HREF = "dump_image.html">dump image</A> doc page
</PRE>
<PRE> <I>movie</I> args = discussed on <A HREF = "dump_image.html">dump image</A> doc page
</PRE>
<PRE> <I>molfile</I> args = discussed on <A HREF = "dump_molfile.html">dump molfile</A> doc page
</PRE>
<PRE> <I>local</I> args = list of local attributes
@ -105,19 +107,20 @@ dump 2 subgroup atom 50 dump.run.mpiio.bin
dump 4a all custom 100 dump.myforce.* id type x y vx fx
dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress<B>2</B>
dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2]
dump 1 all xtc 1000 file.xtc
dump e_data all custom 100 dump.eff id type x y z spin eradius fx fy fz eforce
</PRE>
<P><B>Description:</B>
</P>
<P>Dump a snapshot of atom quantities to one or more files every N
timesteps in one of several styles. The <I>image</I> style is the
exception; it creates a JPG or PPM image file of the atom
configuration every N timesteps, as discussed on the <A HREF = "dump_image.html">dump
image</A> doc page. The timesteps on which dump output
is written can also be controlled by a variable; see the <A HREF = "dump_modify.html">dump_modify
every</A> command for details.
timesteps in one of several styles. The <I>image</I> and <I>movie</I> styles are
the exception: the <I>image</I> style renders a JPG, PNG, or PPM image file
of the atom configuration every N timesteps while the <I>movie</I> style
combines and compresses them into a movie file; both are discussed in
detail on the <A HREF = "dump_image.html">dump image</A> doc page. The timesteps on
which dump output is written can also be controlled by a variable.
See the <A HREF = "dump_modify.html">dump_modify every</A> command.
</P>
<P>Only information for atoms in the specified group is dumped. The
<A HREF = "dump_modify.html">dump_modify thresh and region</A> commands can also

19
doc/dump.txt
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@ -17,7 +17,7 @@ dump ID group-ID style N file args :pre
ID = user-assigned name for the dump :ulb,l
group-ID = ID of the group of atoms to be dumped :l
style = {atom} or {atom/mpiio} or {cfg} or {dcd} or {xtc} or {xyz} or {xyz/mpiio} or {image} or {molfile} or {local} or {custom} or {custom/mpiio} :l
style = {atom} or {atom/mpiio} or {cfg} or {dcd} or {xtc} or {xyz} or {xyz/mpiio} or {image} or {movie} or {molfile} or {local} or {custom} or {custom/mpiio} :l
N = dump every this many timesteps :l
file = name of file to write dump info to :l
args = list of arguments for a particular style :l
@ -31,6 +31,8 @@ args = list of arguments for a particular style :l
{image} args = discussed on "dump image"_dump_image.html doc page :pre
{movie} args = discussed on "dump image"_dump_image.html doc page :pre
{molfile} args = discussed on "dump molfile"_dump_molfile.html doc page :pre
{local} args = list of local attributes
@ -91,19 +93,20 @@ dump 2 subgroup atom 50 dump.run.mpiio.bin
dump 4a all custom 100 dump.myforce.* id type x y vx fx
dump 4b flow custom 100 dump.%.myforce id type c_myF\[3\] v_ke
dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2]
dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress\[2\]
dump 1 all xtc 1000 file.xtc
dump e_data all custom 100 dump.eff id type x y z spin eradius fx fy fz eforce :pre
[Description:]
Dump a snapshot of atom quantities to one or more files every N
timesteps in one of several styles. The {image} style is the
exception; it creates a JPG or PPM image file of the atom
configuration every N timesteps, as discussed on the "dump
image"_dump_image.html doc page. The timesteps on which dump output
is written can also be controlled by a variable; see the "dump_modify
every"_dump_modify.html command for details.
timesteps in one of several styles. The {image} and {movie} styles are
the exception: the {image} style renders a JPG, PNG, or PPM image file
of the atom configuration every N timesteps while the {movie} style
combines and compresses them into a movie file; both are discussed in
detail on the "dump image"_dump_image.html doc page. The timesteps on
which dump output is written can also be controlled by a variable.
See the "dump_modify every"_dump_modify.html command.
Only information for atoms in the specified group is dumped. The
"dump_modify thresh and region"_dump_modify.html commands can also

2
doc/dump_modify.html
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@ -282,7 +282,7 @@ dump file as a (large) integer, then you need to use an appropriate
format. For example, these commands:
</P>
<PRE>compute 1 all property/local batom1 batom2
dump 1 all local 100 tmp.bonds index c_1<B>1</B> c_1<B>2</B>
dump 1 all local 100 tmp.bonds index c_1[1] c_1[2]
dump_modify 1 format "%d %0.0f %0.0f"
</PRE>
<P>will output the two atom IDs for atoms in each bond as integers. If

2
doc/dump_modify.txt
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@ -270,7 +270,7 @@ dump file as a (large) integer, then you need to use an appropriate
format. For example, these commands:
compute 1 all property/local batom1 batom2
dump 1 all local 100 tmp.bonds index c_1[1] c_1[2]
dump 1 all local 100 tmp.bonds index c_1\[1\] c_1\[2\]
dump_modify 1 format "%d %0.0f %0.0f" :pre
will output the two atom IDs for atoms in each bond as integers. If

2
doc/fix_restrain.html
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@ -31,7 +31,7 @@
atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
theta0 = equilibrium angle theta (degrees)
<I>bond</I> args = atom1 atom2 atom3 atom4 Kstart Kstop phi0
<I>dihedral</I> args = atom1 atom2 atom3 atom4 Kstart Kstop phi0
atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
phi0 = equilibrium dihedral angle phi (degrees)

2
doc/fix_restrain.txt
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@ -24,7 +24,7 @@ keyword = {bond} or {angle} or {dihedral} :l
atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
theta0 = equilibrium angle theta (degrees)
{bond} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0
{dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0
atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
phi0 = equilibrium dihedral angle phi (degrees) :pre

2
doc/pair_coul_diel.html
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@ -11,6 +11,8 @@
<H3>pair_style coul/diel command
</H3>
<H3>pair_style coul/diel/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style coul/diel cutoff

1
doc/pair_coul_diel.txt
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@ -7,6 +7,7 @@
:line
pair_style coul/diel command :h3
pair_style coul/diel/omp command :h3
[Syntax:]

4
doc/pair_lj_long.html
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@ -34,7 +34,7 @@
<I>off</I> = omit Coulombic term
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<I>lj/cut/tip4p/long</I> args = flag_lj flag_coul otype htype btype atype qdist cutoff (cutoff2)
<I>lj/long/tip4p/long</I> args = flag_lj flag_coul otype htype btype atype qdist cutoff (cutoff2)
flag_lj = <I>long</I> or <I>cut</I>
<I>long</I> = use Kspace long-range summation for dispersion 1/r^6 term
<I>cut</I> = use a cutoff
@ -83,7 +83,7 @@ settings. The <A HREF = "#Veld">In 't Veld</A> paper has more details on when i
appropriate to include long-range 1/r^6 interactions, using this
potential.
</P>
<P>Style <I>lj/cut/tip4p/long</I> implements the TIP4P water model of
<P>Style <I>lj/long/tip4p/long</I> implements the TIP4P water model of
<A HREF = "#Jorgensen">(Jorgensen)</A>, which introduces a massless site located a
short distance away from the oxygen atom along the bisector of the HOH
angle. The atomic types of the oxygen and hydrogen atoms, the bond

4
doc/pair_lj_long.txt
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@ -27,7 +27,7 @@ args = list of arguments for a particular style :ul
{off} = omit Coulombic term
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{lj/cut/tip4p/long} args = flag_lj flag_coul otype htype btype atype qdist cutoff (cutoff2)
{lj/long/tip4p/long} args = flag_lj flag_coul otype htype btype atype qdist cutoff (cutoff2)
flag_lj = {long} or {cut}
{long} = use Kspace long-range summation for dispersion 1/r^6 term
{cut} = use a cutoff
@ -76,7 +76,7 @@ settings. The "In 't Veld"_#Veld paper has more details on when it is
appropriate to include long-range 1/r^6 interactions, using this
potential.
Style {lj/cut/tip4p/long} implements the TIP4P water model of
Style {lj/long/tip4p/long} implements the TIP4P water model of
"(Jorgensen)"_#Jorgensen, which introduces a massless site located a
short distance away from the oxygen atom along the bisector of the HOH
angle. The atomic types of the oxygen and hydrogen atoms, the bond