Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
# Resolved Conflicts: # doc/Manual.html # doc/Manual.txt # src/USER-SMTBQ/pair_smtbq.cpp
This commit is contained in:
Axel Kohlmeyer
@ -134,8 +134,8 @@
|
||||
|
||||
<H1></H1><div class="section" id="lammps-documentation">
|
||||
<h1>LAMMPS-ICMS Documentation<a class="headerlink" href="#lammps-documentation" title="Permalink to this headline">¶</a></h1>
|
||||
<div class="section" id="dec-2015-version">
|
||||
<h2>24 Dec 2015 version<a class="headerlink" href="#dec-2015-version" title="Permalink to this headline">¶</a></h2>
|
||||
<div class="section" id="jan-2016-version">
|
||||
<h2>11 Jan 2016 version<a class="headerlink" href="#jan-2016-version" title="Permalink to this headline">¶</a></h2>
|
||||
</div>
|
||||
<div class="section" id="version-info">
|
||||
<h2>Version info:<a class="headerlink" href="#version-info" title="Permalink to this headline">¶</a></h2>
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
<!-- HTML_ONLY -->
|
||||
<HEAD>
|
||||
<TITLE>LAMMPS-ICMS Users Manual</TITLE>
|
||||
<META NAME="docnumber" CONTENT="24 Dec 2015 version">
|
||||
<META NAME="docnumber" CONTENT="11 Jan 2016 version">
|
||||
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
|
||||
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
|
||||
</HEAD>
|
||||
@ -21,7 +21,7 @@
|
||||
<H1></H1>
|
||||
|
||||
LAMMPS-ICMS Documentation :c,h3
|
||||
24 Dec 2015 version :c,h4
|
||||
11 Jan 2016 version :c,h4
|
||||
|
||||
Version info: :h4
|
||||
|
||||
|
||||
@ -171,7 +171,7 @@ style = <em>bin/1d</em> or <em>bin/2d</em> or <em>bin/3d</em> or <em>bin/sphere<
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>zero or more keyword/values pairs may be appended</li>
|
||||
<li>keyword = <em>region</em> or <em>nchunk</em> or <em>static</em> or <em>compress</em> or <em>bound</em> or <em>discard</em> or <em>units</em></li>
|
||||
<li>keyword = <em>region</em> or <em>nchunk</em> or <em>static</em> or <em>compress</em> or <em>bound</em> or <em>discard</em> or <em>pbc</em> or <em>units</em></li>
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>region</em> value = region-ID
|
||||
@ -198,6 +198,8 @@ style = <em>bin/1d</em> or <em>bin/2d</em> or <em>bin/3d</em> or <em>bin/sphere<
|
||||
x/y/z = <em>x</em> or <em>y</em> or <em>z</em> to bound sptial bins in this dimension
|
||||
lo = <em>lower</em> or coordinate value (distance units)
|
||||
hi = <em>upper</em> or coordinate value (distance units)
|
||||
<em>pbc</em> value = <em>no</em> or <em>yes</em>
|
||||
yes = use periodic distance for bin/sphere and bin/cylinder styles
|
||||
<em>units</em> value = <em>box</em> or <em>lattice</em> or <em>reduced</em>
|
||||
</pre>
|
||||
</div>
|
||||
@ -616,6 +618,19 @@ value, which is assumed to be inside (or at least near) the simulation
|
||||
box boundaries, though LAMMPS does not check for this. Note that
|
||||
using the <em>bound</em> keyword typically reduces the total number of bins
|
||||
and thus the number of chunks <em>Nchunk</em>.</p>
|
||||
<p>The <em>pbc</em> keyword only applies to the <em>bin/sphere</em> and <em>bin/cylinder</em>
|
||||
styles. If set to <em>yes</em>, the distance an atom is from the sphere
|
||||
origin or cylinder axis is calculated in a minimum image sense with
|
||||
respect to periodic dimensions, when determining which bin the atom is
|
||||
in. I.e. if x is a periodic dimension and the distance between the
|
||||
atom and the sphere center in the x dimension is greater than 0.5 *
|
||||
simulation box length in x, then a box length is subtracted to give a
|
||||
distance < 0.5 * simulation box length. This allosws the sphere or
|
||||
cylinder center to be near a box edge, and atoms on the other side of
|
||||
the periodic box will still be close to the center point/axis. Note
|
||||
that with a setting of <em>yes</em>, the outer sphere or cylinder radius must
|
||||
also be <= 0.5 * simulation box length in any periodic dimension
|
||||
except for the cylinder axis dimension, or an error is generated.</p>
|
||||
<p>The <em>units</em> keyword only applies to the <em>binning</em> styles; otherwise it
|
||||
is ignored. For the <em>bin/1d</em>, <em>bin/2d</em>, <em>bin/3d</em> styles, it
|
||||
determines the meaning of the distance units used for the bin sizes
|
||||
@ -683,6 +698,7 @@ the restarted simulation begins.</p>
|
||||
<li>discard = yes, for all styles except binning</li>
|
||||
<li>discard = mixed, for binning styles</li>
|
||||
<li>bound = lower and upper in all dimensions</li>
|
||||
<li>pbc = no</li>
|
||||
<li>units = lattice</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
@ -48,7 +48,7 @@ style = {bin/1d} or {bin/2d} or {bin/3d} or {bin/sphere} or {type} or {molecule}
|
||||
v_name = per-atom vector calculated by an atom-style variable with name :pre
|
||||
|
||||
zero or more keyword/values pairs may be appended :l
|
||||
keyword = {region} or {nchunk} or {static} or {compress} or {bound} or {discard} or {units} :l
|
||||
keyword = {region} or {nchunk} or {static} or {compress} or {bound} or {discard} or {pbc} or {units} :l
|
||||
{region} value = region-ID
|
||||
region-ID = ID of region atoms must be in to be part of a chunk
|
||||
{nchunk} value = {once} or {every}
|
||||
@ -73,6 +73,8 @@ keyword = {region} or {nchunk} or {static} or {compress} or {bound} or {discard}
|
||||
x/y/z = {x} or {y} or {z} to bound sptial bins in this dimension
|
||||
lo = {lower} or coordinate value (distance units)
|
||||
hi = {upper} or coordinate value (distance units)
|
||||
{pbc} value = {no} or {yes}
|
||||
yes = use periodic distance for bin/sphere and bin/cylinder styles
|
||||
{units} value = {box} or {lattice} or {reduced} :pre
|
||||
:ule
|
||||
|
||||
@ -570,6 +572,20 @@ box boundaries, though LAMMPS does not check for this. Note that
|
||||
using the {bound} keyword typically reduces the total number of bins
|
||||
and thus the number of chunks {Nchunk}.
|
||||
|
||||
The {pbc} keyword only applies to the {bin/sphere} and {bin/cylinder}
|
||||
styles. If set to {yes}, the distance an atom is from the sphere
|
||||
origin or cylinder axis is calculated in a minimum image sense with
|
||||
respect to periodic dimensions, when determining which bin the atom is
|
||||
in. I.e. if x is a periodic dimension and the distance between the
|
||||
atom and the sphere center in the x dimension is greater than 0.5 *
|
||||
simulation box length in x, then a box length is subtracted to give a
|
||||
distance < 0.5 * simulation box length. This allosws the sphere or
|
||||
cylinder center to be near a box edge, and atoms on the other side of
|
||||
the periodic box will still be close to the center point/axis. Note
|
||||
that with a setting of {yes}, the outer sphere or cylinder radius must
|
||||
also be <= 0.5 * simulation box length in any periodic dimension
|
||||
except for the cylinder axis dimension, or an error is generated.
|
||||
|
||||
The {units} keyword only applies to the {binning} styles; otherwise it
|
||||
is ignored. For the {bin/1d}, {bin/2d}, {bin/3d} styles, it
|
||||
determines the meaning of the distance units used for the bin sizes
|
||||
@ -645,4 +661,5 @@ compress = no
|
||||
discard = yes, for all styles except binning
|
||||
discard = mixed, for binning styles
|
||||
bound = lower and upper in all dimensions
|
||||
pbc = no
|
||||
units = lattice :ul
|
||||
|
||||
@ -169,7 +169,7 @@ fix saed/vtk 1 1 1 c_2 file Ni_000.saed
|
||||
<div class="section" id="description">
|
||||
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Define a computation that calculates electron diffraction intensity as
|
||||
described in <a class="reference internal" href="fix_saed_vtk.html#coleman"><span>(Coleman)</span></a> on a mesh of reciprocal lattice nodes
|
||||
described in <a class="reference internal" href="compute_xrd.html#coleman"><span>(Coleman)</span></a> on a mesh of reciprocal lattice nodes
|
||||
defined by the entire simulation domain (or manually) using simulated
|
||||
radiation of wavelength lambda.</p>
|
||||
<p>The electron diffraction intensity I at each reciprocal lattice point
|
||||
@ -212,13 +212,14 @@ the <em>Kmax</em>, <em>Zone</em>, and <em>dR_Ewald</em> parameters. The rectili
|
||||
created about the origin of reciprocal space is terminated at the
|
||||
boundary of a sphere of radius <em>Kmax</em> centered at the origin. If
|
||||
<em>Zone</em> parameters z1=z2=z3=0 are used, diffraction intensities are
|
||||
computed throughout the entire spherical volume - note this can greatly
|
||||
increase the cost of computation. Otherwise, <em>Zone</em> parameters will
|
||||
denote the z1=h, z2=k, and z3=l (in a global since) zone axis of an
|
||||
intersecting Ewald sphere. Diffraction intensities will only be
|
||||
computed at the intersection of the reciprocal lattice mesh and a
|
||||
<em>dR_Ewald</em> thick surface of the Ewald sphere. See the example 3D
|
||||
intestiety data and the intersection of a [010] zone axis in the below image.</p>
|
||||
computed throughout the entire spherical volume - note this can
|
||||
greatly increase the cost of computation. Otherwise, <em>Zone</em>
|
||||
parameters will denote the z1=h, z2=k, and z3=l (in a global since)
|
||||
zone axis of an intersecting Ewald sphere. Diffraction intensities
|
||||
will only be computed at the intersection of the reciprocal lattice
|
||||
mesh and a <em>dR_Ewald</em> thick surface of the Ewald sphere. See the
|
||||
example 3D intestiety data and the intersection of a [010] zone axis
|
||||
in the below image.</p>
|
||||
<a data-lightbox="group-default"
|
||||
href="_images/saed_ewald_intersect.jpg"
|
||||
class=""
|
||||
@ -279,6 +280,8 @@ options.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
||||
<p>This compute is part of the USER-DIFFRACTION package. It is only
|
||||
enabled if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
|
||||
<p>The compute_saed command does not work for triclinic cells.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
|
||||
@ -87,13 +87,14 @@ the {Kmax}, {Zone}, and {dR_Ewald} parameters. The rectilinear mesh
|
||||
created about the origin of reciprocal space is terminated at the
|
||||
boundary of a sphere of radius {Kmax} centered at the origin. If
|
||||
{Zone} parameters z1=z2=z3=0 are used, diffraction intensities are
|
||||
computed throughout the entire spherical volume - note this can greatly
|
||||
increase the cost of computation. Otherwise, {Zone} parameters will
|
||||
denote the z1=h, z2=k, and z3=l (in a global since) zone axis of an
|
||||
intersecting Ewald sphere. Diffraction intensities will only be
|
||||
computed at the intersection of the reciprocal lattice mesh and a
|
||||
{dR_Ewald} thick surface of the Ewald sphere. See the example 3D
|
||||
intestiety data and the intersection of a \[010\] zone axis in the below image.
|
||||
computed throughout the entire spherical volume - note this can
|
||||
greatly increase the cost of computation. Otherwise, {Zone}
|
||||
parameters will denote the z1=h, z2=k, and z3=l (in a global since)
|
||||
zone axis of an intersecting Ewald sphere. Diffraction intensities
|
||||
will only be computed at the intersection of the reciprocal lattice
|
||||
mesh and a {dR_Ewald} thick surface of the Ewald sphere. See the
|
||||
example 3D intestiety data and the intersection of a \[010\] zone axis
|
||||
in the below image.
|
||||
|
||||
:c,image(JPG/saed_ewald_intersect_small.jpg,JPG/saed_ewald_intersect.jpg)
|
||||
|
||||
@ -151,6 +152,10 @@ All array values calculated by this compute are "intensive".
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This compute is part of the USER-DIFFRACTION package. It is only
|
||||
enabled if LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
The compute_saed command does not work for triclinic cells.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
@ -167,7 +167,7 @@ fix 2 all ave/histo/weight 1 1 1 10 100 250 c_2[1] c_2[2] mode vector file Deg2T
|
||||
<div class="section" id="description">
|
||||
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Define a computation that calculates x-ray diffraction intensity as described
|
||||
in <a class="reference internal" href="fix_saed_vtk.html#coleman"><span>(Coleman)</span></a> on a mesh of reciprocal lattice nodes defined
|
||||
in <a class="reference internal" href="#coleman"><span>(Coleman)</span></a> on a mesh of reciprocal lattice nodes defined
|
||||
by the entire simulation domain (or manually) using a simulated radiation
|
||||
of wavelength lambda.</p>
|
||||
<p>The x-ray diffraction intensity, I, at each reciprocal lattice point, k,
|
||||
@ -297,13 +297,15 @@ which by the mesh. The global array has 2 columns.</p>
|
||||
<p>The first column contains the diffraction angle in the units (radians
|
||||
or degrees) provided with the <em>2Theta</em> values. The second column contains
|
||||
the computed diffraction intensities as described above.</p>
|
||||
<p>The array can be accessed by any command that uses global values
|
||||
from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>this section</span></a> for an overview of LAMMPS output
|
||||
options.</p>
|
||||
<p>The array can be accessed by any command that uses global values from
|
||||
a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>this section</span></a>
|
||||
for an overview of LAMMPS output options.</p>
|
||||
<p>All array values calculated by this compute are “intensive”.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
||||
<p>This compute is part of the USER-DIFFRACTION package. It is only
|
||||
enabled if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
|
||||
<p>The compute_xrd command does not work for triclinic cells.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
|
||||
@ -163,14 +163,18 @@ The first column contains the diffraction angle in the units (radians
|
||||
or degrees) provided with the {2Theta} values. The second column contains
|
||||
the computed diffraction intensities as described above.
|
||||
|
||||
The array can be accessed by any command that uses global values
|
||||
from a compute as input. See "this section"_Section_howto.html#howto_15 for an overview of LAMMPS output
|
||||
options.
|
||||
The array can be accessed by any command that uses global values from
|
||||
a compute as input. See "this section"_Section_howto.html#howto_15
|
||||
for an overview of LAMMPS output options.
|
||||
|
||||
All array values calculated by this compute are "intensive".
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This compute is part of the USER-DIFFRACTION package. It is only
|
||||
enabled if LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
The compute_xrd command does not work for triclinic cells.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
@ -138,10 +138,10 @@
|
||||
<li>input = one or more atom attributes</li>
|
||||
</ul>
|
||||
<div class="highlight-python"><div class="highlight"><pre>possible attributes = id, mol, type, mass,
|
||||
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
|
||||
x, y, z, xs, ys, zs, xu, yu, zu, xsu, ysu, zsu, ix, iy, iz,
|
||||
vx, vy, vz, fx, fy, fz,
|
||||
q, mux, muy, muz,
|
||||
radius, omegax, omegay, omegaz,
|
||||
q, mux, muy, muz, mu,
|
||||
radius, diameter, omegax, omegay, omegaz,
|
||||
angmomx, angmomy, angmomz, tqx, tqy, tqz,
|
||||
c_ID, c_ID[N], f_ID, f_ID[N], v_name,
|
||||
d_name, i_name
|
||||
@ -154,12 +154,14 @@ mass = atom mass
|
||||
x,y,z = unscaled atom coordinates
|
||||
xs,ys,zs = scaled atom coordinates
|
||||
xu,yu,zu = unwrapped atom coordinates
|
||||
xsu,ysu,zsu = scaled unwrapped atom coordinates
|
||||
ix,iy,iz = box image that the atom is in
|
||||
vx,vy,vz = atom velocities
|
||||
fx,fy,fz = forces on atoms
|
||||
q = atom charge
|
||||
mux,muy,muz = orientation of dipolar atom
|
||||
radius = radius of spherical particle
|
||||
mu = magnitued of dipole moment of atom
|
||||
radius,diameter = radius.diameter of spherical particle
|
||||
omegax,omegay,omegaz = angular velocity of spherical particle
|
||||
angmomx,angmomy,angmomz = angular momentum of aspherical particle
|
||||
tqx,tqy,tqz = torque on finite-size particles
|
||||
@ -195,25 +197,23 @@ time the fix is defined. If <em>N</em> is 0, then the values are never
|
||||
updated, so this is a way of archiving an atom attribute at a given
|
||||
time for future use in a calculation or output. See the discussion of
|
||||
<a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a> that take fixes as
|
||||
inputs. And see for example, the <a class="reference internal" href="compute_reduce.html"><em>compute reduce</em></a>, <a class="reference internal" href="fix_ave_atom.html"><em>fix ave/atom</em></a>, <a class="reference internal" href="fix_ave_histo.html"><em>fix ave/histo</em></a>, <a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a>,
|
||||
and <a class="reference internal" href="variable.html"><em>atom-style variable</em></a> commands.</p>
|
||||
inputs.</p>
|
||||
<p>If <em>N</em> is not zero, then the attributes will be updated every <em>N</em>
|
||||
steps.</p>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">Actually, only atom attributes specified by keywords like <em>xu</em>
|
||||
or <em>vy</em> are initially stored immediately at the point in your input
|
||||
script when the fix is defined. Attributes specified by a compute,
|
||||
fix, or variable are not initially stored until the first run
|
||||
following the fix definition begins. This is because calculating
|
||||
those attributes may require quantities that are not defined in
|
||||
between runs.</p>
|
||||
<div class="admonition warning">
|
||||
<p class="first admonition-title">Warning</p>
|
||||
<p class="last">Actually, only atom attributes specified by keywords
|
||||
like <em>xu</em> or <em>vy</em> or <em>radius</em> are initially stored immediately at the
|
||||
point in your input script when the fix is defined. Attributes
|
||||
specified by a compute, fix, or variable are not initially stored
|
||||
until the first run following the fix definition begins. This is
|
||||
because calculating those attributes may require quantities that are
|
||||
not defined in between runs.</p>
|
||||
</div>
|
||||
<p>The list of possible attributes is the same as that used by the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command, which describes their meaning.</p>
|
||||
<p>If the <em>com</em> keyword is set to <em>yes</em> then the <em>xu</em>, <em>yu</em>, and <em>zu</em>
|
||||
inputs store the position of each atom relative to the center-of-mass
|
||||
of the group of atoms, instead of storing the absolute position. This
|
||||
option is used by the <a class="reference internal" href="compute_msd.html"><em>compute msd</em></a> command.</p>
|
||||
of the group of atoms, instead of storing the absolute position.</p>
|
||||
<p>The requested values are stored in a per-atom vector or array as
|
||||
discussed below. Zeroes are stored for atoms not in the specified
|
||||
group.</p>
|
||||
|
||||
@ -17,10 +17,10 @@ store/state = style name of this fix command :l
|
||||
N = store atom attributes every N steps, N = 0 for initial store only :l
|
||||
input = one or more atom attributes :l
|
||||
possible attributes = id, mol, type, mass,
|
||||
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
|
||||
x, y, z, xs, ys, zs, xu, yu, zu, xsu, ysu, zsu, ix, iy, iz,
|
||||
vx, vy, vz, fx, fy, fz,
|
||||
q, mux, muy, muz,
|
||||
radius, omegax, omegay, omegaz,
|
||||
q, mux, muy, muz, mu,
|
||||
radius, diameter, omegax, omegay, omegaz,
|
||||
angmomx, angmomy, angmomz, tqx, tqy, tqz,
|
||||
c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name,
|
||||
d_name, i_name :pre
|
||||
@ -32,12 +32,14 @@ input = one or more atom attributes :l
|
||||
x,y,z = unscaled atom coordinates
|
||||
xs,ys,zs = scaled atom coordinates
|
||||
xu,yu,zu = unwrapped atom coordinates
|
||||
xsu,ysu,zsu = scaled unwrapped atom coordinates
|
||||
ix,iy,iz = box image that the atom is in
|
||||
vx,vy,vz = atom velocities
|
||||
fx,fy,fz = forces on atoms
|
||||
q = atom charge
|
||||
mux,muy,muz = orientation of dipolar atom
|
||||
radius = radius of spherical particle
|
||||
mu = magnitued of dipole moment of atom
|
||||
radius,diameter = radius.diameter of spherical particle
|
||||
omegax,omegay,omegaz = angular velocity of spherical particle
|
||||
angmomx,angmomy,angmomz = angular momentum of aspherical particle
|
||||
tqx,tqy,tqz = torque on finite-size particles
|
||||
@ -67,29 +69,25 @@ time the fix is defined. If {N} is 0, then the values are never
|
||||
updated, so this is a way of archiving an atom attribute at a given
|
||||
time for future use in a calculation or output. See the discussion of
|
||||
"output commands"_Section_howto.html#howto_15 that take fixes as
|
||||
inputs. And see for example, the "compute
|
||||
reduce"_compute_reduce.html, "fix ave/atom"_fix_ave_atom.html, "fix
|
||||
ave/histo"_fix_ave_histo.html, "fix ave/spatial"_fix_ave_spatial.html,
|
||||
and "atom-style variable"_variable.html commands.
|
||||
inputs.
|
||||
|
||||
If {N} is not zero, then the attributes will be updated every {N}
|
||||
steps.
|
||||
|
||||
NOTE: Actually, only atom attributes specified by keywords like {xu}
|
||||
or {vy} are initially stored immediately at the point in your input
|
||||
script when the fix is defined. Attributes specified by a compute,
|
||||
fix, or variable are not initially stored until the first run
|
||||
following the fix definition begins. This is because calculating
|
||||
those attributes may require quantities that are not defined in
|
||||
between runs.
|
||||
IMPORTANT NOTE: Actually, only atom attributes specified by keywords
|
||||
like {xu} or {vy} or {radius} are initially stored immediately at the
|
||||
point in your input script when the fix is defined. Attributes
|
||||
specified by a compute, fix, or variable are not initially stored
|
||||
until the first run following the fix definition begins. This is
|
||||
because calculating those attributes may require quantities that are
|
||||
not defined in between runs.
|
||||
|
||||
The list of possible attributes is the same as that used by the "dump
|
||||
custom"_dump.html command, which describes their meaning.
|
||||
|
||||
If the {com} keyword is set to {yes} then the {xu}, {yu}, and {zu}
|
||||
inputs store the position of each atom relative to the center-of-mass
|
||||
of the group of atoms, instead of storing the absolute position. This
|
||||
option is used by the "compute msd"_compute_msd.html command.
|
||||
of the group of atoms, instead of storing the absolute position.
|
||||
|
||||
The requested values are stored in a per-atom vector or array as
|
||||
discussed below. Zeroes are stored for atoms not in the specified
|
||||
|
||||
File diff suppressed because one or more lines are too long
45
doc/set.html
45
doc/set.html
@ -139,7 +139,7 @@
|
||||
<li><p class="first">one or more keyword/value pairs may be appended</p>
|
||||
</li>
|
||||
<li><dl class="first docutils">
|
||||
<dt>keyword = <em>type</em> or <em>type/fraction</em> or <em>mol</em> or <em>x</em> or <em>y</em> or <em>z</em> or <em>charge</em> or <em>dipole</em> or <em>dipole/random</em> or <em>quat</em> or <em>quat/random</em> or <em>diameter</em> or <em>shape</em> or <em>length</em> or <em>tri</em> or <em>theta</em> or <em>angmom</em> or <em>omega</em> or <em>mass</em> or <em>density</em> or <em>volume</em> or <em>image</em> or</dt>
|
||||
<dt>keyword = <em>type</em> or <em>type/fraction</em> or <em>mol</em> or <em>x</em> or <em>y</em> or <em>z</em> or <em>charge</em> or <em>dipole</em> or <em>dipole/random</em> or <em>quat</em> or <em>quat/random</em> or <em>diameter</em> or <em>shape</em> or <em>length</em> or <em>tri</em> or <em>theta</em> or <em>theta/random</em> or <em>angmom</em> or <em>omega</em> or <em>mass</em> or <em>density</em> or <em>volume</em> or <em>image</em> or</dt>
|
||||
<dd><p class="first last"><em>bond</em> or <em>angle</em> or <em>dihedral</em> or <em>improper</em> or
|
||||
<em>meso_e</em> or <em>meso_cv</em> or <em>meso_rho</em> or <em>smd_contact_radius</em> or <em>smd_mass_density</em> or <em>i_name</em> or <em>d_name</em></p>
|
||||
</dd>
|
||||
@ -184,6 +184,8 @@
|
||||
<em>theta</em> value = angle (degrees)
|
||||
angle = orientation of line segment with respect to x-axis
|
||||
angle can be an atom-style variable (see below)
|
||||
<em>theta/random</em> value = seed
|
||||
seed = random # seed (positive integer) for line segment orienations
|
||||
<em>angmom</em> values = Lx Ly Lz
|
||||
Lx,Ly,Lz = components of angular momentum vector (distance-mass-velocity units)
|
||||
any of Lx,Ly,Lz can be an atom-style variable (see below)
|
||||
@ -318,19 +320,20 @@ vector to set as the orientation of the dipole moment vectors of the
|
||||
selected atoms. The magnitude of the dipole moment is set
|
||||
by the length of this orientation vector.</p>
|
||||
<p>Keyword <em>dipole/random</em> randomizes the orientation of the dipole
|
||||
moment vectors of the selected atoms and sets the magnitude of each to
|
||||
the specified <em>Dlen</em> value. For 2d systems, the z component of the
|
||||
moment vectors for the selected atoms and sets the magnitude of each
|
||||
to the specified <em>Dlen</em> value. For 2d systems, the z component of the
|
||||
orientation is set to 0.0. Random numbers are used in such a way that
|
||||
the orientation of a particular atom is the same, regardless of how
|
||||
many processors are being used. This keyword does not allow use of an
|
||||
atom-style variable.</p>
|
||||
<p>Keyword <em>quat</em> uses the specified values to create a quaternion
|
||||
(4-vector) that represents the orientation of the selected atoms. The
|
||||
particles must be ellipsoids as defined by the <a class="reference internal" href="atom_style.html"><em>atom_style ellipsoid</em></a> command or triangles as defined by the
|
||||
<a class="reference internal" href="atom_style.html"><em>atom_style tri</em></a> command. Note that particles defined
|
||||
by <a class="reference internal" href="atom_style.html"><em>atom_style ellipsoid</em></a> have 3 shape parameters.
|
||||
The 3 values must be non-zero for each particle set by this command.
|
||||
They are used to specify the aspect ratios of an ellipsoidal particle,
|
||||
particles must define a quaternion for their orientation
|
||||
(e.g. ellipsoids, triangles, body particles) as defined by the
|
||||
<a class="reference internal" href="atom_style.html"><em>atom_style</em></a> command. Note that particles defined by
|
||||
<a class="reference internal" href="atom_style.html"><em>atom_style ellipsoid</em></a> have 3 shape parameters. The 3
|
||||
values must be non-zero for each particle set by this command. They
|
||||
are used to specify the aspect ratios of an ellipsoidal particle,
|
||||
which is oriented by default with its x-axis along the simulation
|
||||
box’s x-axis, and similarly for y and z. If this body is rotated (via
|
||||
the right-hand rule) by an angle theta around a unit rotation vector
|
||||
@ -340,16 +343,16 @@ c*sin(theta/2)). The theta and a,b,c values are the arguments to the
|
||||
<em>quat</em> keyword. LAMMPS normalizes the quaternion in case (a,b,c) was
|
||||
not specified as a unit vector. For 2d systems, the a,b,c values are
|
||||
ignored, since a rotation vector of (0,0,1) is the only valid choice.</p>
|
||||
<p>Keyword <em>quat/random</em> randomizes the orientation of the quaternion of
|
||||
the selected atoms. The particles must be ellipsoids as defined by
|
||||
the <a class="reference internal" href="atom_style.html"><em>atom_style ellipsoid</em></a> command or triangles as
|
||||
defined by the <a class="reference internal" href="atom_style.html"><em>atom_style tri</em></a> command. Random
|
||||
numbers are used in such a way that the orientation of a particular
|
||||
atom is the same, regardless of how many processors are being used.
|
||||
For 2d systems, only orientations in the xy plane are generated. As
|
||||
with keyword <em>quat</em>, for ellipsoidal particles, the 3 shape values
|
||||
must be non-zero for each particle set by this command. This keyword
|
||||
does not allow use of an atom-style variable.</p>
|
||||
<p>Keyword <em>quat/random</em> randomizes the orientation of the quaternion for
|
||||
the selected atoms. The particles must define a quaternion for their
|
||||
orientation (e.g. ellipsoids, triangles, body particles) as defined by
|
||||
the <a class="reference internal" href="atom_style.html"><em>atom_style</em></a> command. Random numbers are used in
|
||||
such a way that the orientation of a particular atom is the same,
|
||||
regardless of how many processors are being used. For 2d systems,
|
||||
only orientations in the xy plane are generated. As with keyword
|
||||
<em>quat</em>, for ellipsoidal particles, the 3 shape values must be non-zero
|
||||
for each particle set by this command. This keyword does not allow
|
||||
use of an atom-style variable.</p>
|
||||
<p>Keyword <em>diameter</em> sets the size of the selected atoms. The particles
|
||||
must be finite-size spheres as defined by the <a class="reference internal" href="atom_style.html"><em>atom_style sphere</em></a> command. The diameter of a particle can be
|
||||
set to 0.0, which means they will be treated as point particles. Note
|
||||
@ -385,6 +388,12 @@ density, e.g. via the <a class="reference internal" href="read_data.html"><em>re
|
||||
<p>Keyword <em>theta</em> sets the orientation of selected atoms. The particles
|
||||
must be line segments as defined by the <a class="reference internal" href="atom_style.html"><em>atom_style line</em></a> command. The specified value is used to set the
|
||||
orientation angle of the line segments with respect to the x axis.</p>
|
||||
<p>Keyword <em>theta/random</em> randomizes the orientation of theta for the
|
||||
selected atoms. The particles must be line segments as defined by the
|
||||
<a class="reference internal" href="atom_style.html"><em>atom_style line</em></a> command. Random numbers are used in
|
||||
such a way that the orientation of a particular atom is the same,
|
||||
regardless of how many processors are being used. This keyword does
|
||||
not allow use of an atom-style variable.</p>
|
||||
<p>Keyword <em>angmom</em> sets the angular momentum of selected atoms. The
|
||||
particles must be ellipsoids as defined by the <a class="reference internal" href="atom_style.html"><em>atom_style ellipsoid</em></a> command or triangles as defined by the
|
||||
<a class="reference internal" href="atom_style.html"><em>atom_style tri</em></a> command. The angular momentum vector
|
||||
|
||||
47
doc/set.txt
47
doc/set.txt
@ -18,7 +18,7 @@ one or more keyword/value pairs may be appended :l
|
||||
keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
|
||||
{charge} or {dipole} or {dipole/random} or {quat} or \
|
||||
{quat/random} or {diameter} or {shape} or \
|
||||
{length} or {tri} or {theta} or {angmom} or {omega} or \
|
||||
{length} or {tri} or {theta} or {theta/random} or {angmom} or {omega} or \
|
||||
{mass} or {density} or {volume} or {image} or
|
||||
{bond} or {angle} or {dihedral} or {improper} or
|
||||
{meso_e} or {meso_cv} or {meso_rho} or \
|
||||
@ -61,6 +61,8 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
|
||||
{theta} value = angle (degrees)
|
||||
angle = orientation of line segment with respect to x-axis
|
||||
angle can be an atom-style variable (see below)
|
||||
{theta/random} value = seed
|
||||
seed = random # seed (positive integer) for line segment orienations
|
||||
{angmom} values = Lx Ly Lz
|
||||
Lx,Ly,Lz = components of angular momentum vector (distance-mass-velocity units)
|
||||
any of Lx,Ly,Lz can be an atom-style variable (see below)
|
||||
@ -209,8 +211,8 @@ selected atoms. The magnitude of the dipole moment is set
|
||||
by the length of this orientation vector.
|
||||
|
||||
Keyword {dipole/random} randomizes the orientation of the dipole
|
||||
moment vectors of the selected atoms and sets the magnitude of each to
|
||||
the specified {Dlen} value. For 2d systems, the z component of the
|
||||
moment vectors for the selected atoms and sets the magnitude of each
|
||||
to the specified {Dlen} value. For 2d systems, the z component of the
|
||||
orientation is set to 0.0. Random numbers are used in such a way that
|
||||
the orientation of a particular atom is the same, regardless of how
|
||||
many processors are being used. This keyword does not allow use of an
|
||||
@ -218,12 +220,12 @@ atom-style variable.
|
||||
|
||||
Keyword {quat} uses the specified values to create a quaternion
|
||||
(4-vector) that represents the orientation of the selected atoms. The
|
||||
particles must be ellipsoids as defined by the "atom_style
|
||||
ellipsoid"_atom_style.html command or triangles as defined by the
|
||||
"atom_style tri"_atom_style.html command. Note that particles defined
|
||||
by "atom_style ellipsoid"_atom_style.html have 3 shape parameters.
|
||||
The 3 values must be non-zero for each particle set by this command.
|
||||
They are used to specify the aspect ratios of an ellipsoidal particle,
|
||||
particles must define a quaternion for their orientation
|
||||
(e.g. ellipsoids, triangles, body particles) as defined by the
|
||||
"atom_style"_atom_style.html command. Note that particles defined by
|
||||
"atom_style ellipsoid"_atom_style.html have 3 shape parameters. The 3
|
||||
values must be non-zero for each particle set by this command. They
|
||||
are used to specify the aspect ratios of an ellipsoidal particle,
|
||||
which is oriented by default with its x-axis along the simulation
|
||||
box's x-axis, and similarly for y and z. If this body is rotated (via
|
||||
the right-hand rule) by an angle theta around a unit rotation vector
|
||||
@ -234,16 +236,16 @@ c*sin(theta/2)). The theta and a,b,c values are the arguments to the
|
||||
not specified as a unit vector. For 2d systems, the a,b,c values are
|
||||
ignored, since a rotation vector of (0,0,1) is the only valid choice.
|
||||
|
||||
Keyword {quat/random} randomizes the orientation of the quaternion of
|
||||
the selected atoms. The particles must be ellipsoids as defined by
|
||||
the "atom_style ellipsoid"_atom_style.html command or triangles as
|
||||
defined by the "atom_style tri"_atom_style.html command. Random
|
||||
numbers are used in such a way that the orientation of a particular
|
||||
atom is the same, regardless of how many processors are being used.
|
||||
For 2d systems, only orientations in the xy plane are generated. As
|
||||
with keyword {quat}, for ellipsoidal particles, the 3 shape values
|
||||
must be non-zero for each particle set by this command. This keyword
|
||||
does not allow use of an atom-style variable.
|
||||
Keyword {quat/random} randomizes the orientation of the quaternion for
|
||||
the selected atoms. The particles must define a quaternion for their
|
||||
orientation (e.g. ellipsoids, triangles, body particles) as defined by
|
||||
the "atom_style"_atom_style.html command. Random numbers are used in
|
||||
such a way that the orientation of a particular atom is the same,
|
||||
regardless of how many processors are being used. For 2d systems,
|
||||
only orientations in the xy plane are generated. As with keyword
|
||||
{quat}, for ellipsoidal particles, the 3 shape values must be non-zero
|
||||
for each particle set by this command. This keyword does not allow
|
||||
use of an atom-style variable.
|
||||
|
||||
Keyword {diameter} sets the size of the selected atoms. The particles
|
||||
must be finite-size spheres as defined by the "atom_style
|
||||
@ -289,6 +291,13 @@ must be line segments as defined by the "atom_style
|
||||
line"_atom_style.html command. The specified value is used to set the
|
||||
orientation angle of the line segments with respect to the x axis.
|
||||
|
||||
Keyword {theta/random} randomizes the orientation of theta for the
|
||||
selected atoms. The particles must be line segments as defined by the
|
||||
"atom_style line"_atom_style.html command. Random numbers are used in
|
||||
such a way that the orientation of a particular atom is the same,
|
||||
regardless of how many processors are being used. This keyword does
|
||||
not allow use of an atom-style variable.
|
||||
|
||||
Keyword {angmom} sets the angular momentum of selected atoms. The
|
||||
particles must be ellipsoids as defined by the "atom_style
|
||||
ellipsoid"_atom_style.html command or triangles as defined by the
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (23 Oct 2015)
|
||||
LAMMPS (24 Dec 2015)
|
||||
# Al2O3 crystal, qeq on, minimizes, then calculates elastic constants
|
||||
|
||||
variable T_depart equal 300
|
||||
@ -64,6 +64,7 @@ velocity all create 300 277387
|
||||
|
||||
pair_style smtbq
|
||||
pair_coeff * * ffield.smtbq.Al Al
|
||||
Reading potential file ffield.smtbq.Al with DATE: 2015-10-22
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 20 delay 0 check yes
|
||||
@ -100,20 +101,20 @@ Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
|
||||
8 298.92698 770.098 -5600.6212 64.875459 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
9 298.64244 780.92261 -5600.5595 64.813707 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
10 298.32468 793.00943 -5600.4905 64.744743 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
Loop time of 5.10336 on 1 procs for 10 steps with 1680 atoms
|
||||
Loop time of 5.10475 on 1 procs for 10 steps with 1680 atoms
|
||||
|
||||
Performance: 0.034 ns/day, 708.800 hours/ns, 1.959 timesteps/s
|
||||
Performance: 0.034 ns/day, 708.993 hours/ns, 1.959 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.1023 | 5.1023 | 5.1023 | 0.0 | 99.98
|
||||
Pair | 5.1037 | 5.1037 | 5.1037 | 0.0 | 99.98
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00045538 | 0.00045538 | 0.00045538 | 0.0 | 0.01
|
||||
Output | 0.00024509 | 0.00024509 | 0.00024509 | 0.0 | 0.00
|
||||
Modify | 0.00026131 | 0.00026131 | 0.00026131 | 0.0 | 0.01
|
||||
Other | | 0.0001056 | | | 0.00
|
||||
Comm | 0.00044179 | 0.00044179 | 0.00044179 | 0.0 | 0.01
|
||||
Output | 0.00024772 | 0.00024772 | 0.00024772 | 0.0 | 0.00
|
||||
Modify | 0.00026011 | 0.00026011 | 0.00026011 | 0.0 | 0.01
|
||||
Other | | 0.0001063 | | | 0.00
|
||||
|
||||
Nlocal: 1680 ave 1680 max 1680 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -186,7 +187,7 @@ Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
|
||||
50 298.32468 2486.1481 -5600.8719 64.744743 -5536.1271 28.615167 34.699435 28.038181 27839.955
|
||||
51 298.32468 2498.3384 -5600.8721 64.744743 -5536.1274 28.616069 34.696071 28.039596 27839.537
|
||||
52 298.32468 2443.1247 -5600.8722 64.744743 -5536.1274 28.617616 34.696737 28.039439 27841.421
|
||||
Loop time of 36.9389 on 1 procs for 42 steps with 1680 atoms
|
||||
Loop time of 36.8807 on 1 procs for 42 steps with 1680 atoms
|
||||
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
@ -202,12 +203,12 @@ Minimization stats:
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 36.918 | 36.918 | 36.918 | 0.0 | 99.94
|
||||
Pair | 36.86 | 36.86 | 36.86 | 0.0 | 99.95
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0033035 | 0.0033035 | 0.0033035 | 0.0 | 0.01
|
||||
Output | 0.0011785 | 0.0011785 | 0.0011785 | 0.0 | 0.00
|
||||
Comm | 0.0032628 | 0.0032628 | 0.0032628 | 0.0 | 0.01
|
||||
Output | 0.001102 | 0.001102 | 0.001102 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.01603 | | | 0.04
|
||||
Other | | 0.0159 | | | 0.04
|
||||
|
||||
Nlocal: 1680 ave 1680 max 1680 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -247,20 +248,20 @@ Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
|
||||
60 297.05416 2489.245 -5600.5964 64.469006 -5536.1274 28.617616 34.696737 28.039439 27841.421
|
||||
61 296.74469 2500.7159 -5600.5293 64.401842 -5536.1274 28.617616 34.696737 28.039439 27841.421
|
||||
62 296.40194 2513.4457 -5600.4549 64.327455 -5536.1274 28.617616 34.696737 28.039439 27841.421
|
||||
Loop time of 5.13028 on 1 procs for 10 steps with 1680 atoms
|
||||
Loop time of 5.13584 on 1 procs for 10 steps with 1680 atoms
|
||||
|
||||
Performance: 0.034 ns/day, 712.539 hours/ns, 1.949 timesteps/s
|
||||
Performance: 0.034 ns/day, 713.311 hours/ns, 1.947 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.1292 | 5.1292 | 5.1292 | 0.0 | 99.98
|
||||
Pair | 5.1346 | 5.1346 | 5.1346 | 0.0 | 99.98
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00045729 | 0.00045729 | 0.00045729 | 0.0 | 0.01
|
||||
Output | 0.00024509 | 0.00024509 | 0.00024509 | 0.0 | 0.00
|
||||
Modify | 0.00026488 | 0.00026488 | 0.00026488 | 0.0 | 0.01
|
||||
Other | | 0.0001016 | | | 0.00
|
||||
Comm | 0.00047112 | 0.00047112 | 0.00047112 | 0.0 | 0.01
|
||||
Output | 0.00036144 | 0.00036144 | 0.00036144 | 0.0 | 0.01
|
||||
Modify | 0.00029016 | 0.00029016 | 0.00029016 | 0.0 | 0.01
|
||||
Other | | 0.0001101 | | | 0.00
|
||||
|
||||
Nlocal: 1680 ave 1680 max 1680 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
278
examples/USER/smtbq/log.smtbq.Al.g++.4
Normal file
278
examples/USER/smtbq/log.smtbq.Al.g++.4
Normal file
@ -0,0 +1,278 @@
|
||||
LAMMPS (24 Dec 2015)
|
||||
# Al2O3 crystal, qeq on, minimizes, then calculates elastic constants
|
||||
|
||||
variable T_depart equal 300
|
||||
variable dt equal 0.0002
|
||||
|
||||
#Constante
|
||||
variable rac3 equal sqrt(3.0)
|
||||
variable rac1_2 equal sqrt(0.5)
|
||||
variable rac3_2 equal sqrt(1.5)
|
||||
|
||||
#Structure
|
||||
variable a equal 4.05
|
||||
|
||||
variable nx equal 10
|
||||
variable ny equal 7
|
||||
variable nz equal 4
|
||||
|
||||
variable bx equal ${a}*${nx}*${rac1_2}
|
||||
variable bx equal 4.05*${nx}*${rac1_2}
|
||||
variable bx equal 4.05*10*${rac1_2}
|
||||
variable bx equal 4.05*10*0.707106781186548
|
||||
variable by equal ${a}*${ny}*${rac3_2}
|
||||
variable by equal 4.05*${ny}*${rac3_2}
|
||||
variable by equal 4.05*7*${rac3_2}
|
||||
variable by equal 4.05*7*1.22474487139159
|
||||
variable bz equal ${a}*${nz}*${rac3}
|
||||
variable bz equal 4.05*${nz}*${rac3}
|
||||
variable bz equal 4.05*4*${rac3}
|
||||
variable bz equal 4.05*4*1.73205080756888
|
||||
# =======================================================================
|
||||
|
||||
units metal
|
||||
atom_style charge
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
|
||||
lattice sc 1.0
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
region box_vide prism 0 ${bx} 0 ${by} 0 ${bz} 0.0 0.0 0.0
|
||||
region box_vide prism 0 28.6378246380552 0 ${by} 0 ${bz} 0.0 0.0 0.0
|
||||
region box_vide prism 0 28.6378246380552 0 34.7215171039516 0 ${bz} 0.0 0.0 0.0
|
||||
region box_vide prism 0 28.6378246380552 0 34.7215171039516 0 28.0592230826159 0.0 0.0 0.0
|
||||
create_box 1 box_vide
|
||||
Created triclinic box = (0 0 0) to (28.6378 34.7215 28.0592) with tilt (0 0 0)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
|
||||
# Aluminium atoms z = [111]
|
||||
lattice custom ${a} a1 ${rac1_2} 0.0 0.0 a2 0.0 ${rac3_2} 0.0 a3 0.0 0.0 ${rac3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.166666667 0.33333 basis 0.0 0.666666667 0.33333 basis 0.0 0.333333333 0.66667 basis 0.5 0.833333333 0.66667
|
||||
lattice custom 4.05 a1 ${rac1_2} 0.0 0.0 a2 0.0 ${rac3_2} 0.0 a3 0.0 0.0 ${rac3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.166666667 0.33333 basis 0.0 0.666666667 0.33333 basis 0.0 0.333333333 0.66667 basis 0.5 0.833333333 0.66667
|
||||
lattice custom 4.05 a1 0.707106781186548 0.0 0.0 a2 0.0 ${rac3_2} 0.0 a3 0.0 0.0 ${rac3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.166666667 0.33333 basis 0.0 0.666666667 0.33333 basis 0.0 0.333333333 0.66667 basis 0.5 0.833333333 0.66667
|
||||
lattice custom 4.05 a1 0.707106781186548 0.0 0.0 a2 0.0 1.22474487139159 0.0 a3 0.0 0.0 ${rac3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.166666667 0.33333 basis 0.0 0.666666667 0.33333 basis 0.0 0.333333333 0.66667 basis 0.5 0.833333333 0.66667
|
||||
lattice custom 4.05 a1 0.707106781186548 0.0 0.0 a2 0.0 1.22474487139159 0.0 a3 0.0 0.0 1.73205080756888 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.166666667 0.33333 basis 0.0 0.666666667 0.33333 basis 0.0 0.333333333 0.66667 basis 0.5 0.833333333 0.66667
|
||||
Lattice spacing in x,y,z = 2.86378 4.96022 7.01481
|
||||
|
||||
create_atoms 1 region box_vide
|
||||
Created 1680 atoms
|
||||
|
||||
mass 1 26.98
|
||||
|
||||
velocity all create ${T_depart} 277387
|
||||
velocity all create 300 277387
|
||||
|
||||
pair_style smtbq
|
||||
pair_coeff * * ffield.smtbq.Al Al
|
||||
Reading potential file ffield.smtbq.Al with DATE: 2015-10-22
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 20 delay 0 check yes
|
||||
|
||||
timestep ${dt}
|
||||
timestep 0.0002
|
||||
|
||||
thermo_style custom step temp press pe ke etotal lx ly lz vol
|
||||
thermo_modify flush yes
|
||||
thermo 1
|
||||
|
||||
|
||||
#dump 5 all custom 1 box_Al.lammpstrj id type q x y z
|
||||
|
||||
fix 3 all nve
|
||||
run 10
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 20 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11.6714
|
||||
ghost atom cutoff = 11.6714
|
||||
binsize = 5.8357 -> bins = 5 6 5
|
||||
Memory usage per processor = 4.2858 Mbytes
|
||||
Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
|
||||
0 300 729.26605 -5600.8541 65.108335 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
1 299.98339 729.897 -5600.8505 65.104731 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
2 299.93356 731.7909 -5600.8397 65.093915 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
3 299.8505 734.94708 -5600.8217 65.07589 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
4 299.73426 739.36449 -5600.7964 65.050662 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
5 299.58486 745.04171 -5600.764 65.018238 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
6 299.40234 751.97694 -5600.7244 64.978627 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
7 299.18677 760.16798 -5600.6776 64.931841 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
8 298.9382 769.6122 -5600.6237 64.877894 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
9 298.65669 780.3065 -5600.5626 64.8168 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
10 298.34234 792.24735 -5600.4943 64.748578 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
Loop time of 1.49703 on 4 procs for 10 steps with 1680 atoms
|
||||
|
||||
Performance: 0.115 ns/day, 207.920 hours/ns, 6.680 timesteps/s
|
||||
98.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.4956 | 1.4957 | 1.4957 | 0.0 | 99.91
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00078988 | 0.00090927 | 0.0010064 | 0.3 | 0.06
|
||||
Output | 0.00022459 | 0.00027347 | 0.00034189 | 0.3 | 0.02
|
||||
Modify | 6.4373e-05 | 7.8619e-05 | 9.3222e-05 | 0.1 | 0.01
|
||||
Other | | 8.106e-05 | | | 0.01
|
||||
|
||||
Nlocal: 420 ave 484 max 360 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Nghost: 4305 ave 4365 max 4241 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 159600 ave 183920 max 136800 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 638400
|
||||
Ave neighs/atom = 380
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 3
|
||||
#thermo 15
|
||||
fix 1 all box/relax tri 0.0 vmax 0.001
|
||||
minimize 1.0e-8 1.0e-10 1000 10000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11.6714
|
||||
ghost atom cutoff = 11.6714
|
||||
binsize = 5.8357 -> bins = 5 6 5
|
||||
Memory usage per processor = 5.4127 Mbytes
|
||||
Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
|
||||
10 298.34234 792.24735 -5600.4943 64.748578 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
11 298.34234 2483.41 -5600.5251 64.748578 -5535.7765 28.617939 34.697415 28.039749 27842.588
|
||||
12 298.34234 3212.2068 -5600.6294 64.748578 -5535.8809 28.605195 34.685635 28.035928 27816.95
|
||||
13 298.34234 1756.312 -5600.6529 64.748578 -5535.9044 28.62806 34.701751 28.05036 27866.456
|
||||
14 298.34234 845.30512 -5600.6668 64.748578 -5535.9182 28.652683 34.704776 28.055059 27897.528
|
||||
15 298.34234 1950.7901 -5600.7433 64.748578 -5535.9948 28.66644 34.670055 28.031028 27859.115
|
||||
16 298.34234 2860.9521 -5600.7579 64.748578 -5536.0093 28.637802 34.669634 28.028024 27827.963
|
||||
17 298.34234 2406.0293 -5600.7642 64.748578 -5536.0156 28.624953 34.689277 28.040313 27843.439
|
||||
18 298.34234 2531.6658 -5600.7645 64.748578 -5536.0159 28.619984 34.690929 28.039526 27839.151
|
||||
19 298.34234 2410.8263 -5600.7651 64.748578 -5536.0166 28.615355 34.70117 28.039934 27843.27
|
||||
20 298.34234 2538.4705 -5600.7654 64.748578 -5536.0169 28.613142 34.700755 28.038049 27838.913
|
||||
21 298.34234 2455.2909 -5600.7657 64.748578 -5536.0171 28.615273 34.700334 28.039158 27841.749
|
||||
22 298.34234 2578.5637 -5600.766 64.748578 -5536.0174 28.614997 34.695849 28.038814 27837.541
|
||||
23 298.34234 2413.5858 -5600.7667 64.748578 -5536.0181 28.617591 34.695982 28.041829 27843.164
|
||||
24 298.34234 2575.34 -5600.7677 64.748578 -5536.0191 28.614711 34.696953 28.038299 27837.636
|
||||
25 298.34234 2313.5501 -5600.7689 64.748578 -5536.0203 28.618801 34.702208 28.039031 27846.559
|
||||
26 298.34234 2589.6554 -5600.7724 64.748578 -5536.0239 28.622807 34.692685 28.033282 27837.106
|
||||
27 298.34234 2258.4841 -5600.7755 64.748578 -5536.0269 28.633037 34.683012 28.042438 27848.382
|
||||
28 298.34234 2668.7002 -5600.7789 64.748578 -5536.0303 28.632179 34.665065 28.043666 27834.358
|
||||
29 298.34234 2339.309 -5600.8141 64.748578 -5536.0655 28.626885 34.675842 28.051214 27845.356
|
||||
30 298.34234 2846.4227 -5600.8223 64.748578 -5536.0737 28.612492 34.69364 28.033449 27828.006
|
||||
31 298.34234 2534.6985 -5600.8246 64.748578 -5536.076 28.611965 34.709562 28.031793 27838.619
|
||||
32 298.34234 2278.6053 -5600.8262 64.748578 -5536.0776 28.617042 34.703828 28.040241 27847.349
|
||||
33 298.34234 2477.381 -5600.8269 64.748578 -5536.0783 28.616395 34.695005 28.041167 27840.56
|
||||
34 298.34234 2561.8128 -5600.8271 64.748578 -5536.0785 28.615917 34.69647 28.037549 27837.678
|
||||
35 298.34234 2470.4145 -5600.8273 64.748578 -5536.0787 28.617208 34.699332 28.037111 27840.795
|
||||
36 298.34234 2415.0452 -5600.8276 64.748578 -5536.079 28.617651 34.69562 28.041578 27842.683
|
||||
37 298.34234 2514.0703 -5600.8277 64.748578 -5536.0791 28.616929 34.693138 28.040886 27839.303
|
||||
38 298.34234 2515.7338 -5600.828 64.748578 -5536.0794 28.619947 34.694884 28.03646 27839.244
|
||||
39 298.34234 2402.2948 -5600.8281 64.748578 -5536.0796 28.620623 34.69709 28.037911 27843.113
|
||||
40 298.34234 2457.1081 -5600.8289 64.748578 -5536.0804 28.612617 34.697892 28.043218 27841.237
|
||||
41 298.34234 2729.4589 -5600.8299 64.748578 -5536.0814 28.610746 34.694899 28.038106 27831.941
|
||||
42 298.34234 2487.8313 -5600.8331 64.748578 -5536.0845 28.620239 34.701333 28.031882 27840.157
|
||||
43 298.34234 1959.1329 -5600.8393 64.748578 -5536.0908 28.609631 34.719775 28.045509 27858.164
|
||||
44 298.34234 2535.5621 -5600.8461 64.748578 -5536.0975 28.587496 34.720535 28.046731 27838.433
|
||||
45 298.34234 2978.3628 -5600.858 64.748578 -5536.1095 28.609197 34.699148 28.027451 27823.264
|
||||
46 298.34234 2351.5532 -5600.8632 64.748578 -5536.1146 28.624986 34.701661 28.031447 27844.605
|
||||
47 298.34234 2294.1629 -5600.8704 64.748578 -5536.1218 28.614261 34.700247 28.045027 27846.522
|
||||
48 298.34234 2528.0548 -5600.871 64.748578 -5536.1225 28.612265 34.696612 28.041878 27838.536
|
||||
49 298.34234 2516.2649 -5600.8715 64.748578 -5536.1229 28.618047 34.695729 28.037328 27838.936
|
||||
50 298.34234 2461.5711 -5600.8715 64.748578 -5536.1229 28.61865 34.696255 28.038191 27840.802
|
||||
Loop time of 10.0107 on 4 procs for 40 steps with 1680 atoms
|
||||
|
||||
98.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-5600.49433365 -5600.87146764 -5600.87150075
|
||||
Force two-norm initial, final = 50.9055 1.01476
|
||||
Force max component initial, final = 29.378 0.811083
|
||||
Final line search alpha, max atom move = 0.00128157 0.00103946
|
||||
Iterations, force evaluations = 40 75
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 9.9932 | 9.9933 | 9.9933 | 0.0 | 99.83
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0059471 | 0.0059789 | 0.0059991 | 0.0 | 0.06
|
||||
Output | 0.00088 | 0.0010666 | 0.0015972 | 0.9 | 0.01
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.01039 | | | 0.10
|
||||
|
||||
Nlocal: 420 ave 426 max 416 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Nghost: 4305 ave 4309 max 4299 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 159600 ave 161880 max 158080 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 638400
|
||||
Ave neighs/atom = 380
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
thermo 1
|
||||
fix 3 all nve
|
||||
run 10
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 20 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11.6714
|
||||
ghost atom cutoff = 11.6714
|
||||
binsize = 5.8357 -> bins = 5 6 5
|
||||
Memory usage per processor = 4.2877 Mbytes
|
||||
Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
|
||||
50 298.34234 2461.5711 -5600.8715 64.748578 -5536.1229 28.61865 34.696255 28.038191 27840.802
|
||||
51 298.30489 2462.7206 -5600.8634 64.740449 -5536.1229 28.61865 34.696255 28.038191 27840.802
|
||||
52 298.23415 2465.1307 -5600.848 64.725096 -5536.1229 28.61865 34.696255 28.038191 27840.802
|
||||
53 298.13012 2468.8007 -5600.8254 64.702519 -5536.1229 28.61865 34.696255 28.038191 27840.802
|
||||
54 297.99284 2473.7295 -5600.7956 64.672726 -5536.1229 28.61865 34.696255 28.038191 27840.802
|
||||
55 297.82234 2479.9155 -5600.7586 64.635722 -5536.1229 28.61865 34.696255 28.038191 27840.802
|
||||
56 297.61866 2487.3567 -5600.7144 64.591518 -5536.1229 28.61865 34.696255 28.038191 27840.802
|
||||
57 297.38185 2496.0508 -5600.663 64.540124 -5536.1229 28.61865 34.696255 28.038191 27840.802
|
||||
58 297.11198 2505.9952 -5600.6045 64.481554 -5536.1229 28.61865 34.696255 28.038191 27840.802
|
||||
59 296.80911 2517.1867 -5600.5387 64.415823 -5536.1229 28.61865 34.696255 28.038191 27840.802
|
||||
60 296.47332 2529.6221 -5600.4659 64.342947 -5536.1229 28.61865 34.696255 28.038191 27840.802
|
||||
Loop time of 1.2969 on 4 procs for 10 steps with 1680 atoms
|
||||
|
||||
Performance: 0.133 ns/day, 180.125 hours/ns, 7.711 timesteps/s
|
||||
98.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.2955 | 1.2955 | 1.2955 | 0.0 | 99.89
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00080395 | 0.00095397 | 0.0010161 | 0.3 | 0.07
|
||||
Output | 0.00023341 | 0.00028217 | 0.00041556 | 0.5 | 0.02
|
||||
Modify | 7.2241e-05 | 7.993e-05 | 8.8692e-05 | 0.1 | 0.01
|
||||
Other | | 8.166e-05 | | | 0.01
|
||||
|
||||
Nlocal: 420 ave 424 max 416 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 4305 ave 4309 max 4301 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 159600 ave 161120 max 158080 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
|
||||
Total # of neighbors = 638400
|
||||
Ave neighs/atom = 380
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:13
|
||||
210
examples/USER/smtbq/log.smtbq.Al2O3.g++.4
Normal file
210
examples/USER/smtbq/log.smtbq.Al2O3.g++.4
Normal file
@ -0,0 +1,210 @@
|
||||
LAMMPS (24 Dec 2015)
|
||||
# Al2O3 crystal, qeq on, minimizes, then calculates elastic constants
|
||||
|
||||
variable T_depart equal 300
|
||||
|
||||
variable dt equal 0.0002
|
||||
|
||||
# =======================================================================
|
||||
|
||||
units metal
|
||||
atom_style charge
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
read_data data.Alpha
|
||||
triclinic box = (0 0 0) to (23.769 24.7015 25.9564) with tilt (0 0 0)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
1800 atoms
|
||||
# ^ Orthorombic box of corundum strcture
|
||||
|
||||
mass 1 16.00
|
||||
group Oxy type 1
|
||||
1080 atoms in group Oxy
|
||||
compute chargeOxy Oxy property/atom q
|
||||
compute q_Oxy Oxy reduce ave c_chargeOxy
|
||||
|
||||
mass 2 26.98
|
||||
group Al type 2
|
||||
720 atoms in group Al
|
||||
compute chargeAl Al property/atom q
|
||||
compute q_Al Al reduce ave c_chargeAl
|
||||
|
||||
velocity all create ${T_depart} 277387
|
||||
velocity all create 300 277387
|
||||
|
||||
pair_style smtbq
|
||||
pair_coeff * * ffield.smtbq.Al2O3 O Al
|
||||
Reading potential file ffield.smtbq.Al2O3 with DATE: 2015-10-22
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 20 delay 0 check yes
|
||||
|
||||
timestep ${dt}
|
||||
timestep 0.0002
|
||||
|
||||
thermo_style custom step temp press pe ke etotal c_q_Al c_q_Oxy lx ly lz vol
|
||||
thermo_modify flush yes
|
||||
thermo 1
|
||||
|
||||
#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z
|
||||
|
||||
fix 3 all nve
|
||||
run 10
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 20 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11.6714
|
||||
ghost atom cutoff = 11.6714
|
||||
binsize = 5.8357 -> bins = 5 5 5
|
||||
Memory usage per processor = 3.94008 Mbytes
|
||||
Step Temp Press PotEng KinEng TotEng q_Al q_Oxy Lx Ly Lz Volume
|
||||
0 300 91921.482 -11494.543 69.7617 -11424.781 2.6095997 -1.7397331 23.769 24.7015 25.9564 15239.78
|
||||
1 299.96467 91922.303 -11494.535 69.753485 -11424.781 2.6095996 -1.739733 23.769 24.7015 25.9564 15239.78
|
||||
2 299.75126 91933.246 -11494.485 69.703859 -11424.781 2.6095978 -1.7397318 23.769 24.7015 25.9564 15239.78
|
||||
3 299.36045 91954.835 -11494.394 69.61298 -11424.781 2.6095941 -1.7397294 23.769 24.7015 25.9564 15239.78
|
||||
4 298.79335 91986.343 -11494.262 69.481107 -11424.781 2.6095886 -1.7397257 23.769 24.7015 25.9564 15239.78
|
||||
5 298.05151 92027.62 -11494.09 69.3086 -11424.781 2.6095812 -1.7397208 23.769 24.7015 25.9564 15239.78
|
||||
6 297.13689 92078.615 -11493.877 69.095915 -11424.781 2.6095721 -1.7397147 23.769 24.7015 25.9564 15239.78
|
||||
7 296.05187 92139.141 -11493.625 68.843606 -11424.781 2.6095613 -1.7397075 23.769 24.7015 25.9564 15239.78
|
||||
8 294.79923 92209.15 -11493.334 68.552319 -11424.781 2.6095488 -1.7396992 23.769 24.7015 25.9564 15239.78
|
||||
9 293.38215 92288.12 -11493.004 68.222793 -11424.781 2.6095347 -1.7396898 23.769 24.7015 25.9564 15239.78
|
||||
10 291.80421 92376.81 -11492.637 67.855859 -11424.781 2.6095191 -1.7396794 23.769 24.7015 25.9564 15239.78
|
||||
Loop time of 43.8203 on 4 procs for 10 steps with 1800 atoms
|
||||
|
||||
Performance: 0.004 ns/day, 6086.154 hours/ns, 0.228 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 43.817 | 43.817 | 43.817 | 0.0 | 99.99
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0020506 | 0.0024325 | 0.0026755 | 0.5 | 0.01
|
||||
Output | 0.00047874 | 0.00057358 | 0.00084901 | 0.7 | 0.00
|
||||
Modify | 9.8944e-05 | 0.00010616 | 0.00011468 | 0.1 | 0.00
|
||||
Other | | 0.0001459 | | | 0.00
|
||||
|
||||
Nlocal: 450 ave 450 max 450 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 6820 ave 6820 max 6820 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 361800 ave 361800 max 361800 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1447200
|
||||
Ave neighs/atom = 804
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 3
|
||||
thermo 1
|
||||
fix 1 all box/relax tri 0.0 vmax 0.001
|
||||
minimize 1.0e-3 1.0e-5 1000 10000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11.6714
|
||||
ghost atom cutoff = 11.6714
|
||||
binsize = 5.8357 -> bins = 5 5 5
|
||||
Memory usage per processor = 5.31508 Mbytes
|
||||
Step Temp Press PotEng KinEng TotEng q_Al q_Oxy Lx Ly Lz Volume
|
||||
10 291.80421 92376.81 -11492.637 67.855859 -11424.781 2.6095191 -1.7396794 23.769 24.7015 25.9564 15239.78
|
||||
11 291.80421 84416.246 -11494.722 67.855859 -11426.866 2.6087748 -1.7391832 23.787835 24.721015 25.982356 15279.17
|
||||
Loop time of 6.48552 on 4 procs for 1 steps with 1800 atoms
|
||||
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-11492.6369832 -11492.6369832 -11494.7221261
|
||||
Force two-norm initial, final = 1453.27 1325.26
|
||||
Force max component initial, final = 968.201 892.249
|
||||
Final line search alpha, max atom move = 1.03284e-06 0.000921553
|
||||
Iterations, force evaluations = 1 1
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 6.4848 | 6.4848 | 6.4848 | 0.0 | 99.99
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00037098 | 0.00037396 | 0.00037694 | 0.0 | 0.01
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.0003674 | | | 0.01
|
||||
|
||||
Nlocal: 450 ave 450 max 450 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 6759 ave 6772 max 6750 min
|
||||
Histogram: 1 1 0 0 1 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 361140 ave 361150 max 361130 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 1444562
|
||||
Ave neighs/atom = 802.534
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
thermo 1
|
||||
fix 3 all nve
|
||||
run 10
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 20 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11.6714
|
||||
ghost atom cutoff = 11.6714
|
||||
binsize = 5.8357 -> bins = 5 5 5
|
||||
Memory usage per processor = 4.19008 Mbytes
|
||||
Step Temp Press PotEng KinEng TotEng q_Al q_Oxy Lx Ly Lz Volume
|
||||
11 291.80421 84416.246 -11494.722 67.855859 -11426.866 2.6087748 -1.7391832 23.787835 24.721015 25.982356 15279.17
|
||||
12 290.08293 84514.767 -11494.322 67.455594 -11426.866 2.6087578 -1.7391718 23.787835 24.721015 25.982356 15279.17
|
||||
13 288.21041 84622.406 -11493.886 67.020161 -11426.866 2.6087394 -1.7391596 23.787835 24.721015 25.982356 15279.17
|
||||
14 286.19128 84738.689 -11493.417 66.550634 -11426.866 2.6087199 -1.7391466 23.787835 24.721015 25.982356 15279.17
|
||||
15 284.03049 84864.242 -11492.914 66.048166 -11426.866 2.6086993 -1.7391329 23.787835 24.721015 25.982356 15279.17
|
||||
16 281.73331 84998.125 -11492.38 65.513983 -11426.866 2.6086776 -1.7391184 23.787835 24.721015 25.982356 15279.17
|
||||
17 279.30534 85140.233 -11491.815 64.949384 -11426.866 2.6086551 -1.7391034 23.787835 24.721015 25.982356 15279.17
|
||||
18 276.75244 85290.405 -11491.221 64.355737 -11426.866 2.6086319 -1.7390879 23.787835 24.721015 25.982356 15279.17
|
||||
19 274.08079 85448.449 -11490.6 63.734472 -11426.866 2.608608 -1.739072 23.787835 24.721015 25.982356 15279.17
|
||||
20 271.29678 85614.064 -11489.953 63.087082 -11426.866 2.6085837 -1.7390558 23.787835 24.721015 25.982356 15279.17
|
||||
21 268.40708 85786.72 -11489.281 62.415114 -11426.865 2.608559 -1.7390393 23.787835 24.721015 25.982356 15279.17
|
||||
Loop time of 47.1154 on 4 procs for 10 steps with 1800 atoms
|
||||
|
||||
Performance: 0.004 ns/day, 6543.802 hours/ns, 0.212 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 47.112 | 47.112 | 47.112 | 0.0 | 99.99
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0019891 | 0.0023952 | 0.0026395 | 0.5 | 0.01
|
||||
Output | 0.0004952 | 0.00062233 | 0.00096345 | 0.8 | 0.00
|
||||
Modify | 0.00010109 | 0.00010723 | 0.00012183 | 0.1 | 0.00
|
||||
Other | | 0.0001532 | | | 0.00
|
||||
|
||||
Nlocal: 450 ave 450 max 450 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 6611 ave 6620 max 6600 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 360316 ave 360333 max 360300 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 1441262
|
||||
Ave neighs/atom = 800.701
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:01:48
|
||||
256
examples/USER/smtbq/log.smtbq.TiO2.g++.4
Normal file
256
examples/USER/smtbq/log.smtbq.TiO2.g++.4
Normal file
@ -0,0 +1,256 @@
|
||||
LAMMPS (24 Dec 2015)
|
||||
# Al2O3 crystal, qeq on, minimizes, then calculates elastic constants
|
||||
|
||||
variable T_depart equal 300
|
||||
|
||||
variable dt equal 0.0002
|
||||
|
||||
variable a equal 4.5937
|
||||
variable c equal 2.9587
|
||||
variable ca equal ${c}/${a}
|
||||
variable ca equal 2.9587/${a}
|
||||
variable ca equal 2.9587/4.5937
|
||||
|
||||
variable nx equal 6
|
||||
variable ny equal 6
|
||||
variable nz equal 11
|
||||
|
||||
variable bx equal ${a}*${nx}
|
||||
variable bx equal 4.5937*${nx}
|
||||
variable bx equal 4.5937*6
|
||||
variable by equal ${a}*${ny}
|
||||
variable by equal 4.5937*${ny}
|
||||
variable by equal 4.5937*6
|
||||
variable bz equal ${c}*${nz}
|
||||
variable bz equal 2.9587*${nz}
|
||||
variable bz equal 2.9587*11
|
||||
# =======================================================================
|
||||
|
||||
units metal
|
||||
atom_style charge
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
|
||||
lattice sc 1.0
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
region box_vide prism 0 ${bx} 0 ${by} 0 ${bz} 0.0 0.0 0.0
|
||||
region box_vide prism 0 27.5622 0 ${by} 0 ${bz} 0.0 0.0 0.0
|
||||
region box_vide prism 0 27.5622 0 27.5622 0 ${bz} 0.0 0.0 0.0
|
||||
region box_vide prism 0 27.5622 0 27.5622 0 32.5457 0.0 0.0 0.0
|
||||
create_box 2 box_vide
|
||||
Created triclinic box = (0 0 0) to (27.5622 27.5622 32.5457) with tilt (0 0 0)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
|
||||
#lattice sc 1.0
|
||||
#region box_TiO2 block 0 ${bx} 0 ${by} 0 ${bz}
|
||||
|
||||
# titanium atoms
|
||||
lattice custom ${a} origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
|
||||
lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
|
||||
lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 0.644077758669482 basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
|
||||
Lattice spacing in x,y,z = 4.5937 4.5937 2.9587
|
||||
|
||||
create_atoms 2 region box_vide
|
||||
Created 792 atoms
|
||||
|
||||
# Oxygen atoms
|
||||
lattice custom ${a} origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5
|
||||
lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5
|
||||
lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 0.644077758669482 basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5
|
||||
Lattice spacing in x,y,z = 4.5937 4.5937 2.9587
|
||||
|
||||
create_atoms 1 region box_vide
|
||||
Created 1584 atoms
|
||||
|
||||
|
||||
mass 1 16.00
|
||||
group Oxy type 1
|
||||
1584 atoms in group Oxy
|
||||
compute chargeOxy Oxy property/atom q
|
||||
compute q_Oxy Oxy reduce ave c_chargeOxy
|
||||
|
||||
mass 2 47.867
|
||||
group Ti type 2
|
||||
792 atoms in group Ti
|
||||
compute chargeTi Ti property/atom q
|
||||
compute q_Ti Ti reduce ave c_chargeTi
|
||||
|
||||
velocity all create ${T_depart} 277387
|
||||
velocity all create 300 277387
|
||||
|
||||
pair_style smtbq
|
||||
pair_coeff * * ffield.smtbq.TiO2 O Ti
|
||||
Reading potential file ffield.smtbq.TiO2 with DATE: 2015-10-22
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 20 delay 0 check yes
|
||||
|
||||
timestep ${dt}
|
||||
timestep 0.0002
|
||||
|
||||
thermo_style custom step temp press pe ke etotal c_q_Ti c_q_Oxy lx ly lz vol
|
||||
thermo_modify flush yes
|
||||
thermo 1
|
||||
|
||||
|
||||
#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z
|
||||
|
||||
fix 3 all nve
|
||||
run 10
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 20 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.6744
|
||||
ghost atom cutoff = 12.6744
|
||||
binsize = 6.3372 -> bins = 5 5 6
|
||||
Memory usage per processor = 4.60415 Mbytes
|
||||
Step Temp Press PotEng KinEng TotEng q_Ti q_Oxy Lx Ly Lz Volume
|
||||
0 300 44365.066 -15815.239 92.097853 -15723.142 2.5521775 -1.2760888 27.5622 27.5622 32.5457 24724.15
|
||||
1 299.90799 44372.657 -15815.211 92.069608 -15723.142 2.5521771 -1.2760885 27.5622 27.5622 32.5457 24724.15
|
||||
2 299.64406 44386.645 -15815.13 91.988581 -15723.142 2.5521705 -1.2760852 27.5622 27.5622 32.5457 24724.15
|
||||
3 299.20863 44406.97 -15814.997 91.854908 -15723.142 2.5521584 -1.2760792 27.5622 27.5622 32.5457 24724.15
|
||||
4 298.60246 44433.509 -15814.812 91.668818 -15723.143 2.552141 -1.2760705 27.5622 27.5622 32.5457 24724.15
|
||||
5 297.82659 44466.206 -15814.574 91.430631 -15723.144 2.5521181 -1.276059 27.5622 27.5622 32.5457 24724.15
|
||||
6 296.88235 44505.016 -15814.285 91.140758 -15723.144 2.5520898 -1.2760449 27.5622 27.5622 32.5457 24724.15
|
||||
7 295.77139 44549.856 -15813.945 90.7997 -15723.145 2.5520562 -1.2760281 27.5622 27.5622 32.5457 24724.15
|
||||
8 294.49562 44600.663 -15813.555 90.408048 -15723.147 2.5520173 -1.2760087 27.5622 27.5622 32.5457 24724.15
|
||||
9 293.05725 44657.353 -15813.114 89.966478 -15723.148 2.5519732 -1.2759866 27.5622 27.5622 32.5457 24724.15
|
||||
10 291.45876 44719.821 -15812.625 89.475755 -15723.149 2.551924 -1.275962 27.5622 27.5622 32.5457 24724.15
|
||||
Loop time of 161.071 on 4 procs for 10 steps with 2376 atoms
|
||||
|
||||
Performance: 0.001 ns/day, 22370.960 hours/ns, 0.062 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 161.07 | 161.07 | 161.07 | 0.0 |100.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0021119 | 0.0024694 | 0.0026705 | 0.4 | 0.00
|
||||
Output | 0.00060225 | 0.00070065 | 0.00098777 | 0.6 | 0.00
|
||||
Modify | 0.00012326 | 0.00013238 | 0.00014782 | 0.1 | 0.00
|
||||
Other | | 0.0001593 | | | 0.00
|
||||
|
||||
Nlocal: 594 ave 630 max 558 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 7638 ave 7674 max 7602 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 492624 ave 522720 max 462528 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 1970496
|
||||
Ave neighs/atom = 829.333
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 3
|
||||
#thermo 15
|
||||
fix 1 all box/relax tri 0.0 vmax 0.001
|
||||
minimize 1.0e-3 1.0e-5 1000 10000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.6744
|
||||
ghost atom cutoff = 12.6744
|
||||
binsize = 6.3372 -> bins = 5 5 6
|
||||
Memory usage per processor = 5.97915 Mbytes
|
||||
Step Temp Press PotEng KinEng TotEng q_Ti q_Oxy Lx Ly Lz Volume
|
||||
10 291.45876 44719.821 -15812.625 89.475755 -15723.149 2.551924 -1.275962 27.5622 27.5622 32.5457 24724.15
|
||||
11 291.45876 38966.735 -15814.114 89.475755 -15724.638 2.5514114 -1.2757057 27.582769 27.582778 32.578246 24785.835
|
||||
Loop time of 22.3212 on 4 procs for 1 steps with 2376 atoms
|
||||
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-15812.6250198 -15812.6250198 -15814.1138993
|
||||
Force two-norm initial, final = 1103.27 950.466
|
||||
Force max component initial, final = 758.704 657.184
|
||||
Final line search alpha, max atom move = 1.31804e-06 0.000866193
|
||||
Iterations, force evaluations = 1 1
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 22.32 | 22.32 | 22.32 | 0.0 |100.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00042605 | 0.00043178 | 0.00043893 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.0004204 | | | 0.00
|
||||
|
||||
Nlocal: 594 ave 600 max 587 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Nghost: 7638 ave 7645 max 7632 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 492126 ave 497133 max 486366 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 1968506
|
||||
Ave neighs/atom = 828.496
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
thermo 1
|
||||
fix 3 all nve
|
||||
run 10
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 20 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.6744
|
||||
ghost atom cutoff = 12.6744
|
||||
binsize = 6.3372 -> bins = 5 5 6
|
||||
Memory usage per processor = 4.85415 Mbytes
|
||||
Step Temp Press PotEng KinEng TotEng q_Ti q_Oxy Lx Ly Lz Volume
|
||||
11 291.45876 38966.735 -15814.114 89.475755 -15724.638 2.5514114 -1.2757057 27.582769 27.582778 32.578246 24785.835
|
||||
12 289.71602 39034.428 -15813.58 88.940745 -15724.639 2.5513568 -1.2756784 27.582769 27.582778 32.578246 24785.835
|
||||
13 287.81994 39107.705 -15813 88.358662 -15724.641 2.5512976 -1.2756488 27.582769 27.582778 32.578246 24785.835
|
||||
14 285.77378 39186.429 -15812.373 87.730505 -15724.642 2.5512335 -1.2756168 27.582769 27.582778 32.578246 24785.835
|
||||
15 283.58105 39270.434 -15811.702 87.057353 -15724.644 2.5511647 -1.2755824 27.582769 27.582778 32.578246 24785.835
|
||||
16 281.24552 39359.544 -15810.986 86.340362 -15724.646 2.5510913 -1.2755457 27.582769 27.582778 32.578246 24785.835
|
||||
17 278.77119 39453.574 -15810.229 85.580761 -15724.648 2.5510134 -1.2755067 27.582769 27.582778 32.578246 24785.835
|
||||
18 276.16232 39552.323 -15809.43 84.779855 -15724.65 2.5509311 -1.2754655 27.582769 27.582778 32.578246 24785.835
|
||||
19 273.42337 39655.586 -15808.592 83.939017 -15724.652 2.5508445 -1.2754223 27.582769 27.582778 32.578246 24785.835
|
||||
20 270.55904 39763.139 -15807.715 83.05969 -15724.655 2.5507538 -1.2753769 27.582769 27.582778 32.578246 24785.835
|
||||
21 267.57425 39874.754 -15806.801 82.14338 -15724.658 2.5506591 -1.2753296 27.582769 27.582778 32.578246 24785.835
|
||||
Loop time of 170.172 on 4 procs for 10 steps with 2376 atoms
|
||||
|
||||
Performance: 0.001 ns/day, 23634.979 hours/ns, 0.059 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 170.17 | 170.17 | 170.17 | 0.0 |100.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0025029 | 0.0028628 | 0.0030224 | 0.4 | 0.00
|
||||
Output | 0.00063372 | 0.00081372 | 0.0011685 | 0.7 | 0.00
|
||||
Modify | 0.00012541 | 0.0001539 | 0.00021005 | 0.3 | 0.00
|
||||
Other | | 0.0001655 | | | 0.00
|
||||
|
||||
Nlocal: 594 ave 600 max 587 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Nghost: 7638 ave 7645 max 7632 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 490100 ave 495079 max 484284 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 1960398
|
||||
Ave neighs/atom = 825.083
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:06:39
|
||||
@ -98,25 +98,16 @@ int BodyNparticle::unpack_border_body(AtomVecBody::Bonus *bonus, double *buf)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BodyNparticle::data_body(int ibonus, int ninteger, int ndouble,
|
||||
char **ifile, char **dfile)
|
||||
int *ifile, double *dfile)
|
||||
{
|
||||
AtomVecBody::Bonus *bonus = &avec->bonus[ibonus];
|
||||
|
||||
// error in data file if any values are NULL
|
||||
|
||||
for (int i = 0; i < ninteger; i++)
|
||||
if (ifile[i] == NULL)
|
||||
error->one(FLERR,"Invalid format in Bodies section of data file");
|
||||
for (int i = 0; i < ndouble; i++)
|
||||
if (dfile[i] == NULL)
|
||||
error->one(FLERR,"Invalid format in Bodies section of data file");
|
||||
|
||||
// set ninteger, ndouble in bonus and allocate 2 vectors of ints, doubles
|
||||
|
||||
if (ninteger != 1)
|
||||
error->one(FLERR,"Incorrect # of integer values in "
|
||||
"Bodies section of data file");
|
||||
int nsub = atoi(ifile[0]);
|
||||
int nsub = ifile[0];
|
||||
if (nsub < 1)
|
||||
error->one(FLERR,"Incorrect integer value in "
|
||||
"Bodies section of data file");
|
||||
@ -133,12 +124,12 @@ void BodyNparticle::data_body(int ibonus, int ninteger, int ndouble,
|
||||
// diagonalize inertia tensor
|
||||
|
||||
double tensor[3][3];
|
||||
tensor[0][0] = atof(dfile[0]);
|
||||
tensor[1][1] = atof(dfile[1]);
|
||||
tensor[2][2] = atof(dfile[2]);
|
||||
tensor[0][1] = tensor[1][0] = atof(dfile[3]);
|
||||
tensor[0][2] = tensor[2][0] = atof(dfile[4]);
|
||||
tensor[1][2] = tensor[2][1] = atof(dfile[5]);
|
||||
tensor[0][0] = dfile[0];
|
||||
tensor[1][1] = dfile[1];
|
||||
tensor[2][2] = dfile[2];
|
||||
tensor[0][1] = tensor[1][0] = dfile[3];
|
||||
tensor[0][2] = tensor[2][0] = dfile[4];
|
||||
tensor[1][2] = tensor[2][1] = dfile[5];
|
||||
|
||||
double *inertia = bonus->inertia;
|
||||
double evectors[3][3];
|
||||
@ -188,9 +179,9 @@ void BodyNparticle::data_body(int ibonus, int ninteger, int ndouble,
|
||||
int j = 6;
|
||||
int k = 0;
|
||||
for (int i = 0; i < nsub; i++) {
|
||||
delta[0] = atof(dfile[j]);
|
||||
delta[1] = atof(dfile[j+1]);
|
||||
delta[2] = atof(dfile[j+2]);
|
||||
delta[0] = dfile[j];
|
||||
delta[1] = dfile[j+1];
|
||||
delta[2] = dfile[j+2];
|
||||
MathExtra::transpose_matvec(ex_space,ey_space,ez_space,
|
||||
delta,&bonus->dvalue[k]);
|
||||
j += 3;
|
||||
@ -198,6 +189,43 @@ void BodyNparticle::data_body(int ibonus, int ninteger, int ndouble,
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
return radius of body particle defined by ifile/dfile params
|
||||
params are ordered as in data file
|
||||
called by Molecule class which needs single body size
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double BodyNparticle::radius_body(int ninteger, int ndouble,
|
||||
int *ifile, double *dfile)
|
||||
{
|
||||
int nsub = ifile[0];
|
||||
if (nsub < 1)
|
||||
error->one(FLERR,"Incorrect integer value in "
|
||||
"Bodies section of data file");
|
||||
if (ndouble != 6 + 3*nsub)
|
||||
error->one(FLERR,"Incorrect # of floating-point values in "
|
||||
"Bodies section of data file");
|
||||
|
||||
// sub-particle coords are relative to body center at (0,0,0)
|
||||
// offset = 6 for sub-particle coords
|
||||
|
||||
double onerad;
|
||||
double maxrad = 0.0;
|
||||
double delta[3];
|
||||
|
||||
int offset = 6;
|
||||
for (int i = 0; i < nsub; i++) {
|
||||
delta[0] = dfile[offset];
|
||||
delta[1] = dfile[offset+1];
|
||||
delta[2] = dfile[offset+2];
|
||||
offset += 3;
|
||||
onerad = MathExtra::len3(delta);
|
||||
maxrad = MAX(maxrad,onerad);
|
||||
}
|
||||
|
||||
return maxrad;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int BodyNparticle::noutcol()
|
||||
|
||||
@ -34,7 +34,8 @@ class BodyNparticle : public Body {
|
||||
|
||||
int pack_border_body(struct AtomVecBody::Bonus *, double *);
|
||||
int unpack_border_body(struct AtomVecBody::Bonus *, double *);
|
||||
void data_body(int, int, int, char **, char **);
|
||||
void data_body(int, int, int, int *, double *);
|
||||
double radius_body(int, int, int *, double *);
|
||||
|
||||
int noutrow(int);
|
||||
int noutcol();
|
||||
|
||||
@ -74,13 +74,14 @@ ComputeTempCS::ComputeTempCS(LAMMPS *lmp, int narg, char **arg) :
|
||||
strcpy(id_fix,id);
|
||||
strcat(id_fix,"_COMPUTE_STORE");
|
||||
|
||||
char **newarg = new char*[5];
|
||||
char **newarg = new char*[6];
|
||||
newarg[0] = id_fix;
|
||||
newarg[1] = group->names[igroup];
|
||||
newarg[2] = (char *) "STORE";
|
||||
newarg[3] = (char *) "0";
|
||||
newarg[4] = (char *) "1";
|
||||
modify->add_fix(5,newarg);
|
||||
newarg[3] = (char *) "peratom";
|
||||
newarg[4] = (char *) "0";
|
||||
newarg[5] = (char *) "1";
|
||||
modify->add_fix(6,newarg);
|
||||
fix = (FixStore *) modify->fix[modify->nfix-1];
|
||||
delete [] newarg;
|
||||
|
||||
|
||||
@ -378,6 +378,13 @@ void FixPour::pre_exchange()
|
||||
|
||||
if (next_reneighbor != update->ntimestep) return;
|
||||
|
||||
// clear ghost count and any ghost bonus data internal to AtomVec
|
||||
// same logic as beginning of Comm::exchange()
|
||||
// do it now b/c inserting atoms will overwrite ghost atoms
|
||||
|
||||
atom->nghost = 0;
|
||||
atom->avec->clear_bonus();
|
||||
|
||||
// find current max atom and molecule IDs if necessary
|
||||
|
||||
if (!idnext) find_maxid();
|
||||
@ -638,7 +645,11 @@ void FixPour::pre_exchange()
|
||||
radtmp = newcoord[3];
|
||||
atom->radius[n] = radtmp;
|
||||
atom->rmass[n] = 4.0*MY_PI/3.0 * radtmp*radtmp*radtmp * denstmp;
|
||||
} else atom->add_molecule_atom(onemols[imol],m,n,maxtag_all);
|
||||
} else {
|
||||
onemols[imol]->quat_external = quat;
|
||||
atom->add_molecule_atom(onemols[imol],m,n,maxtag_all);
|
||||
}
|
||||
|
||||
modify->create_attribute(n);
|
||||
}
|
||||
}
|
||||
@ -667,7 +678,8 @@ void FixPour::pre_exchange()
|
||||
// reset global natoms,nbonds,etc
|
||||
// increment maxtag_all and maxmol_all if necessary
|
||||
// if global map exists, reset it now instead of waiting for comm
|
||||
// since adding atoms messes up ghosts
|
||||
// since other pre-exchange fixes may use it
|
||||
// invoke map_init() b/c atom count has grown
|
||||
|
||||
if (ninserted_atoms) {
|
||||
atom->natoms += ninserted_atoms;
|
||||
@ -682,7 +694,6 @@ void FixPour::pre_exchange()
|
||||
if (maxtag_all >= MAXTAGINT)
|
||||
error->all(FLERR,"New atom IDs exceed maximum allowed ID");
|
||||
if (atom->map_style) {
|
||||
atom->nghost = 0;
|
||||
atom->map_init();
|
||||
atom->map_set();
|
||||
}
|
||||
@ -1008,23 +1019,24 @@ void *FixPour::extract(const char *str, int &itype)
|
||||
|
||||
} else {
|
||||
|
||||
// find a molecule in template with matching type
|
||||
// loop over onemols molecules
|
||||
// skip a molecule with no atoms as large as itype
|
||||
|
||||
oneradius = 0.0;
|
||||
for (int i = 0; i < nmol; i++) {
|
||||
if (itype-ntype > onemols[i]->ntypes) continue;
|
||||
if (itype > ntype+onemols[i]->ntypes) continue;
|
||||
double *radius = onemols[i]->radius;
|
||||
int *type = onemols[i]->type;
|
||||
int natoms = onemols[i]->natoms;
|
||||
|
||||
// check radii of matching types in Molecule
|
||||
// check radii of atoms in Molecule with matching types
|
||||
// default to 0.5, if radii not defined in Molecule
|
||||
// same as atom->avec->create_atom(), invoked in pre_exchange()
|
||||
|
||||
oneradius = 0.0;
|
||||
for (int i = 0; i < natoms; i++)
|
||||
if (type[i] == itype-ntype) {
|
||||
if (type[i]+ntype == itype) {
|
||||
if (radius) oneradius = MAX(oneradius,radius[i]);
|
||||
else oneradius = 0.5;
|
||||
else oneradius = MAX(oneradius,0.5);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@ -301,6 +301,13 @@ void FixDeposit::pre_exchange()
|
||||
|
||||
if (next_reneighbor != update->ntimestep) return;
|
||||
|
||||
// clear ghost count and any ghost bonus data internal to AtomVec
|
||||
// same logic as beginning of Comm::exchange()
|
||||
// do it now b/c inserting atoms will overwrite ghost atoms
|
||||
|
||||
atom->nghost = 0;
|
||||
atom->avec->clear_bonus();
|
||||
|
||||
// compute current offset = bottom of insertion volume
|
||||
|
||||
double offset = 0.0;
|
||||
@ -524,8 +531,10 @@ void FixDeposit::pre_exchange()
|
||||
atom->v[n][0] = vnew[0];
|
||||
atom->v[n][1] = vnew[1];
|
||||
atom->v[n][2] = vnew[2];
|
||||
if (mode == MOLECULE)
|
||||
if (mode == MOLECULE) {
|
||||
onemols[imol]->quat_external = quat;
|
||||
atom->add_molecule_atom(onemols[imol],m,n,maxtag_all);
|
||||
}
|
||||
modify->create_attribute(n);
|
||||
}
|
||||
}
|
||||
@ -559,7 +568,8 @@ void FixDeposit::pre_exchange()
|
||||
// reset global natoms,nbonds,etc
|
||||
// increment maxtag_all and maxmol_all if necessary
|
||||
// if global map exists, reset it now instead of waiting for comm
|
||||
// since adding atoms messes up ghosts
|
||||
// since other pre-exchange fixes may use it
|
||||
// invoke map_init() b/c atom count has grown
|
||||
|
||||
if (success) {
|
||||
atom->natoms += natom;
|
||||
@ -576,7 +586,6 @@ void FixDeposit::pre_exchange()
|
||||
error->all(FLERR,"New atom IDs exceed maximum allowed ID");
|
||||
if (mode == MOLECULE && atom->molecule_flag) maxmol_all++;
|
||||
if (atom->map_style) {
|
||||
atom->nghost = 0;
|
||||
atom->map_init();
|
||||
atom->map_set();
|
||||
}
|
||||
@ -811,23 +820,24 @@ void *FixDeposit::extract(const char *str, int &itype)
|
||||
|
||||
} else {
|
||||
|
||||
// find a molecule in template with matching type
|
||||
// loop over onemols molecules
|
||||
// skip a molecule with no atoms as large as itype
|
||||
|
||||
oneradius = 0.0;
|
||||
for (int i = 0; i < nmol; i++) {
|
||||
if (itype-ntype > onemols[i]->ntypes) continue;
|
||||
if (itype > ntype+onemols[i]->ntypes) continue;
|
||||
double *radius = onemols[i]->radius;
|
||||
int *type = onemols[i]->type;
|
||||
int natoms = onemols[i]->natoms;
|
||||
|
||||
// check radii of matching types in Molecule
|
||||
// check radii of atoms in Molecule with matching types
|
||||
// default to 0.5, if radii not defined in Molecule
|
||||
// same as atom->avec->create_atom(), invoked in pre_exchange()
|
||||
|
||||
oneradius = 0.0;
|
||||
for (int i = 0; i < natoms; i++)
|
||||
if (type[i] == itype-ntype) {
|
||||
if (type[i]+ntype == itype) {
|
||||
if (radius) oneradius = MAX(oneradius,radius[i]);
|
||||
else oneradius = 0.5;
|
||||
else oneradius = MAX(oneradius,0.5);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@ -154,13 +154,14 @@ void TAD::command(int narg, char **arg)
|
||||
|
||||
// create FixStore object to store revert state
|
||||
|
||||
narg2 = 5;
|
||||
narg2 = 6;
|
||||
args = new char*[narg2];
|
||||
args[0] = (char *) "tad_revert";
|
||||
args[1] = (char *) "all";
|
||||
args[2] = (char *) "STORE";
|
||||
args[3] = (char *) "0";
|
||||
args[4] = (char *) "7";
|
||||
args[3] = (char *) "peratom";
|
||||
args[4] = (char *) "0";
|
||||
args[5] = (char *) "7";
|
||||
modify->add_fix(narg2,args);
|
||||
fix_revert = (FixStore *) modify->fix[modify->nfix-1];
|
||||
delete [] args;
|
||||
|
||||
@ -224,11 +224,12 @@ void FixAdaptFEP::post_constructor()
|
||||
id_fix_diam = NULL;
|
||||
id_fix_chg = NULL;
|
||||
|
||||
char **newarg = new char*[5];
|
||||
char **newarg = new char*[6];
|
||||
newarg[1] = group->names[igroup];
|
||||
newarg[2] = (char *) "STORE";
|
||||
newarg[3] = (char *) "1";
|
||||
newarg[3] = (char *) "peratom";
|
||||
newarg[4] = (char *) "1";
|
||||
newarg[5] = (char *) "1";
|
||||
|
||||
if (diamflag) {
|
||||
int n = strlen(id) + strlen("_FIX_STORE_DIAM") + 1;
|
||||
@ -236,7 +237,7 @@ void FixAdaptFEP::post_constructor()
|
||||
strcpy(id_fix_diam,id);
|
||||
strcat(id_fix_diam,"_FIX_STORE_DIAM");
|
||||
newarg[0] = id_fix_diam;
|
||||
modify->add_fix(5,newarg);
|
||||
modify->add_fix(6,newarg);
|
||||
fix_diam = (FixStore *) modify->fix[modify->nfix-1];
|
||||
|
||||
if (fix_diam->restart_reset) fix_diam->restart_reset = 0;
|
||||
@ -259,7 +260,7 @@ void FixAdaptFEP::post_constructor()
|
||||
strcpy(id_fix_chg,id);
|
||||
strcat(id_fix_chg,"_FIX_STORE_CHG");
|
||||
newarg[0] = id_fix_chg;
|
||||
modify->add_fix(5,newarg);
|
||||
modify->add_fix(6,newarg);
|
||||
fix_chg = (FixStore *) modify->fix[modify->nfix-1];
|
||||
|
||||
if (fix_chg->restart_reset) fix_chg->restart_reset = 0;
|
||||
|
||||
@ -828,9 +828,7 @@ void PairSMTBQ::read_file(char *file)
|
||||
}
|
||||
|
||||
//A adapter au STO
|
||||
ncov = params[0].sto * params[0].n0;
|
||||
for (i=1; i<num_atom_types; i++)
|
||||
ncov = min(ncov,params[i].sto * params[i].n0);
|
||||
ncov = min((params[0].sto)*(params[0].n0),(params[1].sto)*(params[1].n0));
|
||||
|
||||
if (verbose) printf (" Parametre ncov = %f\n",ncov);
|
||||
if (verbose) printf (" ********************************************* \n");
|
||||
@ -914,7 +912,7 @@ void PairSMTBQ::compute(int eflag, int vflag)
|
||||
|
||||
// Charges Communication
|
||||
// ----------------------
|
||||
forward(q) ; reverse(q);
|
||||
forward(q) ; // reverse(q);
|
||||
|
||||
memory->create(nmol,nteam+1,"pair:nmol");
|
||||
memory->create(tmp,nteam+1,7,"pair:tmp");
|
||||
@ -1271,7 +1269,9 @@ void PairSMTBQ::tabqeq()
|
||||
double aCoeff,bCoeff,rcoupe,nang;
|
||||
|
||||
int n = atom->ntypes;
|
||||
int nmax = atom->nmax;
|
||||
int nlocal = atom->nlocal;
|
||||
int nghost = atom->nghost;
|
||||
nmax = atom->nmax;
|
||||
|
||||
verbose = 1;
|
||||
verbose = 0;
|
||||
@ -1284,6 +1284,7 @@ void PairSMTBQ::tabqeq()
|
||||
|
||||
|
||||
if (verbose) printf ("kmax %d, ds %f, nmax %d\n",kmax,ds,nmax);
|
||||
if (verbose) printf ("nlocal = %d, nghost = %d\n",nlocal,nghost);
|
||||
if (verbose) printf ("nntypes %d, kmax %d, rc %f, n %d\n",nntype,kmax,rc,n);
|
||||
|
||||
// allocate arrays
|
||||
@ -2396,9 +2397,9 @@ void PairSMTBQ::QForce_charge(int loop)
|
||||
// to calculate the N-body forces
|
||||
// ================================================
|
||||
|
||||
forward (sbcov) ; reverse (sbcov);
|
||||
forward (coord) ; reverse (coord);
|
||||
forward (sbmet) ; reverse (sbmet);
|
||||
forward (sbcov) ; // reverse (sbcov);
|
||||
forward (coord) ; // reverse (coord);
|
||||
forward (sbmet) ; // reverse (sbmet);
|
||||
|
||||
|
||||
if (nteam == 0) return; //no oxide
|
||||
@ -2655,7 +2656,7 @@ void PairSMTBQ::Charge()
|
||||
|
||||
// Communication des charges
|
||||
// ---------------------------
|
||||
forward(q) ; reverse(q);
|
||||
forward(q) ; // reverse(q);
|
||||
|
||||
|
||||
// Calcul des potentiel
|
||||
@ -2735,7 +2736,7 @@ void PairSMTBQ::Charge()
|
||||
// =======================================
|
||||
// Charge Communication.
|
||||
// =======================================
|
||||
forward(q); reverse(q);
|
||||
forward(q); // reverse(q);
|
||||
|
||||
//:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
|
||||
// ==========================================
|
||||
@ -3124,7 +3125,7 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
|
||||
// Groups communication
|
||||
// OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
|
||||
for (i = 0; i < nproc; i++) {
|
||||
forward_int(flag_gp[i]); reverse_int(flag_gp[i]);
|
||||
forward_int(flag_gp[i]); //reverse_int(flag_gp[i]);
|
||||
}
|
||||
// ---
|
||||
|
||||
@ -3214,7 +3215,7 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
|
||||
Group Communication between proc for unification
|
||||
================================================== */
|
||||
for (i = 0; i < nproc; i++) {
|
||||
forward_int(flag_gp[i]); reverse_int(flag_gp[i]);
|
||||
forward_int(flag_gp[i]);// reverse_int(flag_gp[i]);
|
||||
}
|
||||
|
||||
// =============== End of COMM =================
|
||||
@ -3404,7 +3405,7 @@ int PairSMTBQ::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, in
|
||||
buf[m++] = tab_comm[j];
|
||||
// if (j < 3) printf ("[%d] %d pfc %d %d buf_send = %f \n",me,n,i,m-1,buf[m-1]);
|
||||
}
|
||||
return 1;
|
||||
return m;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -3433,7 +3434,7 @@ int PairSMTBQ::pack_reverse_comm(int n, int first, double *buf)
|
||||
buf[m++] = tab_comm[i];
|
||||
// if (i<first+3) printf ("[%d] prc %d %d buf_send = %f \n",me,i,m-1,buf[m-1]);
|
||||
}
|
||||
return 1;
|
||||
return m;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
42
src/atom.cpp
42
src/atom.cpp
@ -1318,45 +1318,51 @@ void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus, tagint id_offset)
|
||||
void Atom::data_bodies(int n, char *buf, AtomVecBody *avec_body,
|
||||
tagint id_offset)
|
||||
{
|
||||
int j,m,tagdata,ninteger,ndouble;
|
||||
int j,m,nvalues,tagdata,ninteger,ndouble;
|
||||
|
||||
int maxint = 0;
|
||||
int maxdouble = 0;
|
||||
char **ivalues = NULL;
|
||||
char **dvalues = NULL;
|
||||
int *ivalues = NULL;
|
||||
double *dvalues = NULL;
|
||||
|
||||
// loop over lines of body data
|
||||
// tokenize the lines into ivalues and dvalues
|
||||
// if I own atom tag, unpack its values
|
||||
// if I own atom tag, tokenize lines into ivalues/dvalues, call data_body()
|
||||
// else skip values
|
||||
|
||||
for (int i = 0; i < n; i++) {
|
||||
if (i == 0) tagdata = ATOTAGINT(strtok(buf," \t\n\r\f")) + id_offset;
|
||||
else tagdata = ATOTAGINT(strtok(NULL," \t\n\r\f")) + id_offset;
|
||||
|
||||
ninteger = atoi(strtok(NULL," \t\n\r\f"));
|
||||
ndouble = atoi(strtok(NULL," \t\n\r\f"));
|
||||
if (tagdata <= 0 || tagdata > map_tag_max)
|
||||
error->one(FLERR,"Invalid atom ID in Bodies section of data file");
|
||||
|
||||
ninteger = force->inumeric(FLERR,strtok(NULL," \t\n\r\f"));
|
||||
ndouble = force->inumeric(FLERR,strtok(NULL," \t\n\r\f"));
|
||||
|
||||
if ((m = map(tagdata)) >= 0) {
|
||||
if (ninteger > maxint) {
|
||||
delete [] ivalues;
|
||||
maxint = ninteger;
|
||||
ivalues = new char*[maxint];
|
||||
ivalues = new int[maxint];
|
||||
}
|
||||
if (ndouble > maxdouble) {
|
||||
delete [] dvalues;
|
||||
maxdouble = ndouble;
|
||||
dvalues = new char*[maxdouble];
|
||||
dvalues = new double[maxdouble];
|
||||
}
|
||||
|
||||
for (j = 0; j < ninteger; j++)
|
||||
ivalues[j] = strtok(NULL," \t\n\r\f");
|
||||
ivalues[j] = force->inumeric(FLERR,strtok(NULL," \t\n\r\f"));
|
||||
for (j = 0; j < ndouble; j++)
|
||||
dvalues[j] = strtok(NULL," \t\n\r\f");
|
||||
dvalues[j] = force->numeric(FLERR,strtok(NULL," \t\n\r\f"));
|
||||
|
||||
if (tagdata <= 0 || tagdata > map_tag_max)
|
||||
error->one(FLERR,"Invalid atom ID in Bodies section of data file");
|
||||
|
||||
if ((m = map(tagdata)) >= 0)
|
||||
avec_body->data_body(m,ninteger,ndouble,ivalues,dvalues);
|
||||
|
||||
} else {
|
||||
nvalues = ninteger + ndouble; // number of values to skip
|
||||
for (j = 0; j < nvalues; j++)
|
||||
strtok(NULL," \t\n\r\f");
|
||||
}
|
||||
}
|
||||
|
||||
delete [] ivalues;
|
||||
@ -1588,6 +1594,12 @@ void Atom::add_molecule_atom(Molecule *onemol, int iatom,
|
||||
else if (rmass_flag)
|
||||
rmass[ilocal] = 4.0*MY_PI/3.0 *
|
||||
radius[ilocal]*radius[ilocal]*radius[ilocal];
|
||||
if (onemol->bodyflag) {
|
||||
body[ilocal] = 0; // as if a body read from data file
|
||||
onemol->avec_body->data_body(ilocal,onemol->nibody,onemol->ndbody,
|
||||
onemol->ibodyparams,onemol->dbodyparams);
|
||||
onemol->avec_body->set_quat(ilocal,onemol->quat_external);
|
||||
}
|
||||
|
||||
if (molecular != 1) return;
|
||||
|
||||
|
||||
@ -26,6 +26,10 @@
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
// debug
|
||||
#include "update.h"
|
||||
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -48,6 +52,7 @@ AtomVecBody::AtomVecBody(LAMMPS *lmp) : AtomVec(lmp)
|
||||
atom->body_flag = 1;
|
||||
atom->rmass_flag = 1;
|
||||
atom->angmom_flag = atom->torque_flag = 1;
|
||||
atom->radius_flag = 1;
|
||||
|
||||
nlocal_bonus = nghost_bonus = nmax_bonus = 0;
|
||||
bonus = NULL;
|
||||
@ -103,7 +108,7 @@ void AtomVecBody::process_args(int narg, char **arg)
|
||||
// bptr values = max number of additional ivalues/dvalues from Body class
|
||||
|
||||
size_forward = 7 + bptr->size_forward;
|
||||
size_border = 16 + bptr->size_border;
|
||||
size_border = 18 + bptr->size_border;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -128,6 +133,7 @@ void AtomVecBody::grow(int n)
|
||||
v = memory->grow(atom->v,nmax,3,"atom:v");
|
||||
f = memory->grow(atom->f,nmax*comm->nthreads,3,"atom:f");
|
||||
|
||||
radius = memory->grow(atom->radius,nmax,"atom:radius");
|
||||
rmass = memory->grow(atom->rmass,nmax,"atom:rmass");
|
||||
angmom = memory->grow(atom->angmom,nmax,3,"atom:angmom");
|
||||
torque = memory->grow(atom->torque,nmax*comm->nthreads,3,"atom:torque");
|
||||
@ -147,7 +153,8 @@ void AtomVecBody::grow_reset()
|
||||
tag = atom->tag; type = atom->type;
|
||||
mask = atom->mask; image = atom->image;
|
||||
x = atom->x; v = atom->v; f = atom->f;
|
||||
rmass = atom->rmass; angmom = atom->angmom; torque = atom->torque;
|
||||
radius = atom->radius; rmass = atom->rmass;
|
||||
angmom = atom->angmom; torque = atom->torque;
|
||||
body = atom->body;
|
||||
}
|
||||
|
||||
@ -183,6 +190,7 @@ void AtomVecBody::copy(int i, int j, int delflag)
|
||||
v[j][1] = v[i][1];
|
||||
v[j][2] = v[i][2];
|
||||
|
||||
radius[j] = radius[i];
|
||||
rmass[j] = rmass[i];
|
||||
angmom[j][0] = angmom[i][0];
|
||||
angmom[j][1] = angmom[i][1];
|
||||
@ -571,6 +579,8 @@ int AtomVecBody::pack_border(int n, int *list, double *buf,
|
||||
buf[m++] = ubuf(tag[j]).d;
|
||||
buf[m++] = ubuf(type[j]).d;
|
||||
buf[m++] = ubuf(mask[j]).d;
|
||||
buf[m++] = radius[j];
|
||||
buf[m++] = rmass[j];
|
||||
if (body[j] < 0) buf[m++] = ubuf(0).d;
|
||||
else {
|
||||
buf[m++] = ubuf(1).d;
|
||||
@ -606,6 +616,8 @@ int AtomVecBody::pack_border(int n, int *list, double *buf,
|
||||
buf[m++] = ubuf(tag[j]).d;
|
||||
buf[m++] = ubuf(type[j]).d;
|
||||
buf[m++] = ubuf(mask[j]).d;
|
||||
buf[m++] = radius[j];
|
||||
buf[m++] = rmass[j];
|
||||
if (body[j] < 0) buf[m++] = ubuf(0).d;
|
||||
else {
|
||||
buf[m++] = ubuf(1).d;
|
||||
@ -651,6 +663,8 @@ int AtomVecBody::pack_border_vel(int n, int *list, double *buf,
|
||||
buf[m++] = ubuf(tag[j]).d;
|
||||
buf[m++] = ubuf(type[j]).d;
|
||||
buf[m++] = ubuf(mask[j]).d;
|
||||
buf[m++] = radius[j];
|
||||
buf[m++] = rmass[j];
|
||||
if (body[j] < 0) buf[m++] = ubuf(0).d;
|
||||
else {
|
||||
buf[m++] = ubuf(1).d;
|
||||
@ -693,6 +707,8 @@ int AtomVecBody::pack_border_vel(int n, int *list, double *buf,
|
||||
buf[m++] = ubuf(tag[j]).d;
|
||||
buf[m++] = ubuf(type[j]).d;
|
||||
buf[m++] = ubuf(mask[j]).d;
|
||||
buf[m++] = radius[j];
|
||||
buf[m++] = rmass[j];
|
||||
if (body[j] < 0) buf[m++] = ubuf(0).d;
|
||||
else {
|
||||
buf[m++] = ubuf(1).d;
|
||||
@ -777,6 +793,8 @@ int AtomVecBody::pack_border_hybrid(int n, int *list, double *buf)
|
||||
m = 0;
|
||||
for (i = 0; i < n; i++) {
|
||||
j = list[i];
|
||||
buf[m++] = radius[j];
|
||||
buf[m++] = rmass[j];
|
||||
if (body[j] < 0) buf[m++] = ubuf(0).d;
|
||||
else {
|
||||
buf[m++] = ubuf(1).d;
|
||||
@ -814,6 +832,8 @@ void AtomVecBody::unpack_border(int n, int first, double *buf)
|
||||
tag[i] = (tagint) ubuf(buf[m++]).i;
|
||||
type[i] = (int) ubuf(buf[m++]).i;
|
||||
mask[i] = (int) ubuf(buf[m++]).i;
|
||||
radius[i] = buf[m++];
|
||||
rmass[i] = buf[m++];
|
||||
body[i] = (int) ubuf(buf[m++]).i;
|
||||
if (body[i] == 0) body[i] = -1;
|
||||
else {
|
||||
@ -862,6 +882,8 @@ void AtomVecBody::unpack_border_vel(int n, int first, double *buf)
|
||||
tag[i] = (tagint) ubuf(buf[m++]).i;
|
||||
type[i] = (int) ubuf(buf[m++]).i;
|
||||
mask[i] = (int) ubuf(buf[m++]).i;
|
||||
radius[i] = buf[m++];
|
||||
rmass[i] = buf[m++];
|
||||
body[i] = (int) ubuf(buf[m++]).i;
|
||||
if (body[i] == 0) body[i] = -1;
|
||||
else {
|
||||
@ -909,6 +931,8 @@ int AtomVecBody::unpack_border_hybrid(int n, int first, double *buf)
|
||||
m = 0;
|
||||
last = first + n;
|
||||
for (i = first; i < last; i++) {
|
||||
radius[i] = buf[m++];
|
||||
rmass[i] = buf[m++];
|
||||
body[i] = (int) ubuf(buf[m++]).i;
|
||||
if (body[i] == 0) body[i] = -1;
|
||||
else {
|
||||
@ -954,7 +978,7 @@ int AtomVecBody::pack_exchange(int i, double *buf)
|
||||
buf[m++] = ubuf(type[i]).d;
|
||||
buf[m++] = ubuf(mask[i]).d;
|
||||
buf[m++] = ubuf(image[i]).d;
|
||||
|
||||
buf[m++] = radius[i];
|
||||
buf[m++] = rmass[i];
|
||||
buf[m++] = angmom[i][0];
|
||||
buf[m++] = angmom[i][1];
|
||||
@ -1008,7 +1032,7 @@ int AtomVecBody::unpack_exchange(double *buf)
|
||||
type[nlocal] = (int) ubuf(buf[m++]).i;
|
||||
mask[nlocal] = (int) ubuf(buf[m++]).i;
|
||||
image[nlocal] = (imageint) ubuf(buf[m++]).i;
|
||||
|
||||
radius[nlocal] = buf[m++];
|
||||
rmass[nlocal] = buf[m++];
|
||||
angmom[nlocal][0] = buf[m++];
|
||||
angmom[nlocal][1] = buf[m++];
|
||||
@ -1067,11 +1091,11 @@ int AtomVecBody::size_restart()
|
||||
int nlocal = atom->nlocal;
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (body[i] >= 0) {
|
||||
n += 25;
|
||||
n += 26;
|
||||
if (intdoubleratio == 1) n += bonus[body[i]].ninteger;
|
||||
else n += (bonus[body[i]].ninteger+1)/2;
|
||||
n += bonus[body[i]].ndouble;
|
||||
} else n += 16;
|
||||
} else n += 17;
|
||||
|
||||
if (atom->nextra_restart)
|
||||
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
|
||||
@ -1101,6 +1125,7 @@ int AtomVecBody::pack_restart(int i, double *buf)
|
||||
buf[m++] = v[i][1];
|
||||
buf[m++] = v[i][2];
|
||||
|
||||
buf[m++] = radius[i];
|
||||
buf[m++] = rmass[i];
|
||||
buf[m++] = angmom[i][0];
|
||||
buf[m++] = angmom[i][1];
|
||||
@ -1161,6 +1186,7 @@ int AtomVecBody::unpack_restart(double *buf)
|
||||
v[nlocal][1] = buf[m++];
|
||||
v[nlocal][2] = buf[m++];
|
||||
|
||||
radius[nlocal] = buf[m++];
|
||||
rmass[nlocal] = buf[m++];
|
||||
angmom[nlocal][0] = buf[m++];
|
||||
angmom[nlocal][1] = buf[m++];
|
||||
@ -1228,6 +1254,7 @@ void AtomVecBody::create_atom(int itype, double *coord)
|
||||
v[nlocal][1] = 0.0;
|
||||
v[nlocal][2] = 0.0;
|
||||
|
||||
radius[nlocal] = 0.5;
|
||||
rmass[nlocal] = 1.0;
|
||||
angmom[nlocal][0] = 0.0;
|
||||
angmom[nlocal][1] = 0.0;
|
||||
@ -1274,6 +1301,7 @@ void AtomVecBody::data_atom(double *coord, imageint imagetmp, char **values)
|
||||
angmom[nlocal][0] = 0.0;
|
||||
angmom[nlocal][1] = 0.0;
|
||||
angmom[nlocal][2] = 0.0;
|
||||
radius[nlocal] = 0.5;
|
||||
|
||||
atom->nlocal++;
|
||||
}
|
||||
@ -1302,12 +1330,12 @@ int AtomVecBody::data_atom_hybrid(int nlocal, char **values)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AtomVecBody::data_body(int m, int ninteger, int ndouble,
|
||||
char **ivalues, char **dvalues)
|
||||
int *ivalues, double *dvalues)
|
||||
{
|
||||
if (body[m]) error->one(FLERR,"Assigning body parameters to non-body atom");
|
||||
if (nlocal_bonus == nmax_bonus) grow_bonus();
|
||||
bptr->data_body(nlocal_bonus,ninteger,ndouble,ivalues,dvalues);
|
||||
bonus[nlocal_bonus].ilocal = m;
|
||||
bptr->data_body(nlocal_bonus,ninteger,ndouble,ivalues,dvalues);
|
||||
body[m] = nlocal_bonus++;
|
||||
}
|
||||
|
||||
@ -1448,6 +1476,29 @@ int AtomVecBody::write_vel_hybrid(FILE *fp, double *buf)
|
||||
return 3;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
body computes its size based on ivalues/dvalues and returns it
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double AtomVecBody::radius_body(int ninteger, int ndouble,
|
||||
int *ivalues, double *dvalues)
|
||||
{
|
||||
return bptr->radius_body(ninteger,ndouble,ivalues,dvalues);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
reset quat orientation for atom M to quat_external
|
||||
called by Atom:add_molecule_atom()
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AtomVecBody::set_quat(int m, double *quat_external)
|
||||
{
|
||||
if (body[m] < 0) error->one(FLERR,"Assigning quat to non-body atom");
|
||||
double *quat = bonus[body[m]].quat;
|
||||
quat[0] = quat_external[0]; quat[1] = quat_external[1];
|
||||
quat[2] = quat_external[2]; quat[3] = quat_external[3];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
return # of bytes of allocated memory
|
||||
------------------------------------------------------------------------- */
|
||||
@ -1464,6 +1515,7 @@ bigint AtomVecBody::memory_usage()
|
||||
if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3);
|
||||
if (atom->memcheck("f")) bytes += memory->usage(f,nmax*comm->nthreads,3);
|
||||
|
||||
if (atom->memcheck("radius")) bytes += memory->usage(radius,nmax);
|
||||
if (atom->memcheck("rmass")) bytes += memory->usage(rmass,nmax);
|
||||
if (atom->memcheck("angmom")) bytes += memory->usage(angmom,nmax,3);
|
||||
if (atom->memcheck("torque")) bytes +=
|
||||
|
||||
@ -85,13 +85,19 @@ class AtomVecBody : public AtomVec {
|
||||
// manipulate Bonus data structure for extra atom info
|
||||
|
||||
void clear_bonus();
|
||||
void data_body(int, int, int, char **, char **);
|
||||
void data_body(int, int, int, int *, double *);
|
||||
|
||||
// methods used by other classes to query/set body info
|
||||
|
||||
double radius_body(int, int, int *, double *);
|
||||
void set_quat(int, double *);
|
||||
|
||||
private:
|
||||
tagint *tag;
|
||||
int *type,*mask;
|
||||
imageint *image;
|
||||
double **x,**v,**f;
|
||||
double *radius;
|
||||
double *rmass;
|
||||
double **angmom,**torque;
|
||||
int *body;
|
||||
|
||||
@ -41,11 +41,13 @@ class Body : protected Pointers {
|
||||
virtual int unpack_border_body(struct AtomVecBody::Bonus *,
|
||||
double *) {return 0;}
|
||||
|
||||
virtual void data_body(int, int, int, char **, char **) = 0;
|
||||
virtual void data_body(int, int, int, int*, double *) = 0;
|
||||
virtual int noutrow(int) = 0;
|
||||
virtual int noutcol() = 0;
|
||||
virtual void output(int, int, double *) = 0;
|
||||
virtual int image(int, double, double, int *&, double **&) = 0;
|
||||
|
||||
virtual double radius_body(int, int, int *, double *) {return 0.0;}
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
@ -191,6 +191,7 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
maxflag[1] = UPPER;
|
||||
maxflag[2] = UPPER;
|
||||
scaleflag = LATTICE;
|
||||
pbcflag = 0;
|
||||
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg],"region") == 0) {
|
||||
@ -269,6 +270,12 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
else if (strcmp(arg[iarg+1],"reduced") == 0) scaleflag = REDUCED;
|
||||
else error->all(FLERR,"Illegal compute chunk/atom command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"pbc") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal compute chunk/atom command");
|
||||
if (strcmp(arg[iarg+1],"no") == 0) pbcflag = 0;
|
||||
else if (strcmp(arg[iarg+1],"yes") == 0) pbcflag = 1;
|
||||
else error->all(FLERR,"Illegal compute chunk/atom command");
|
||||
iarg += 2;
|
||||
} else error->all(FLERR,"Illegal compute chunk/atom command");
|
||||
}
|
||||
|
||||
@ -572,13 +579,14 @@ void ComputeChunkAtom::init()
|
||||
strcpy(id_fix,id);
|
||||
strcat(id_fix,"_COMPUTE_STORE");
|
||||
|
||||
char **newarg = new char*[5];
|
||||
char **newarg = new char*[6];
|
||||
newarg[0] = id_fix;
|
||||
newarg[1] = group->names[igroup];
|
||||
newarg[2] = (char *) "STORE";
|
||||
newarg[3] = (char *) "1";
|
||||
newarg[3] = (char *) "peratom";
|
||||
newarg[4] = (char *) "1";
|
||||
modify->add_fix(5,newarg);
|
||||
newarg[5] = (char *) "1";
|
||||
modify->add_fix(6,newarg);
|
||||
fixstore = (FixStore *) modify->fix[modify->nfix-1];
|
||||
delete [] newarg;
|
||||
}
|
||||
@ -1265,7 +1273,7 @@ int ComputeChunkAtom::setup_xyz_bins()
|
||||
int ComputeChunkAtom::setup_sphere_bins()
|
||||
{
|
||||
// convert sorigin_user to sorigin
|
||||
// sorigin is always in box units, for orthogonal or triclinic domains
|
||||
// sorigin,srad are always in box units, for orthogonal or triclinic domains
|
||||
// lamda2x works for either orthogonal or triclinic
|
||||
|
||||
if (scaleflag == REDUCED) {
|
||||
@ -1280,6 +1288,23 @@ int ComputeChunkAtom::setup_sphere_bins()
|
||||
sradmax = sradmax_user;
|
||||
}
|
||||
|
||||
// if pbcflag set, sradmax must be < 1/2 box in any periodic dim
|
||||
// treat orthongonal and triclinic the same
|
||||
// check every time bins are created
|
||||
|
||||
if (pbcflag) {
|
||||
double *prd_half = domain->prd_half;
|
||||
int *periodicity = domain->periodicity;
|
||||
int flag = 0;
|
||||
if (periodicity[0] && sradmax > prd_half[0]) flag = 1;
|
||||
if (periodicity[1] && sradmax > prd_half[1]) flag = 1;
|
||||
if (domain->dimension == 3 &&
|
||||
periodicity[2] && sradmax > prd_half[2]) flag = 1;
|
||||
if (flag)
|
||||
error->all(FLERR,"Compute chunk/atom bin/sphere radius "
|
||||
"is too large for periodic box");
|
||||
}
|
||||
|
||||
sinvrad = nsbin / (sradmax-sradmin);
|
||||
|
||||
// allocate and set bin coordinates
|
||||
@ -1328,6 +1353,21 @@ int ComputeChunkAtom::setup_cylinder_bins()
|
||||
cradmax = cradmax_user;
|
||||
}
|
||||
|
||||
// if pbcflag set, sradmax must be < 1/2 box in any periodic non-axis dim
|
||||
// treat orthongonal and triclinic the same
|
||||
// check every time bins are created
|
||||
|
||||
if (pbcflag) {
|
||||
double *prd_half = domain->prd_half;
|
||||
int *periodicity = domain->periodicity;
|
||||
int flag = 0;
|
||||
if (periodicity[cdim1] && sradmax > prd_half[cdim1]) flag = 1;
|
||||
if (periodicity[cdim2] && sradmax > prd_half[cdim2]) flag = 1;
|
||||
if (flag)
|
||||
error->all(FLERR,"Compute chunk/atom bin/cylinder radius "
|
||||
"is too large for periodic box");
|
||||
}
|
||||
|
||||
cinvrad = ncbin / (cradmax-cradmin);
|
||||
|
||||
// allocate and set radial bin coordinates
|
||||
@ -1743,6 +1783,7 @@ void ComputeChunkAtom::atom2binsphere()
|
||||
double *boxlo = domain->boxlo;
|
||||
double *boxhi = domain->boxhi;
|
||||
double *prd = domain->prd;
|
||||
double *prd_half = domain->prd_half;
|
||||
int *periodicity = domain->periodicity;
|
||||
|
||||
// remap each atom's relevant coords back into box via PBC if necessary
|
||||
@ -1773,6 +1814,33 @@ void ComputeChunkAtom::atom2binsphere()
|
||||
dx = xremap - sorigin[0];
|
||||
dy = yremap - sorigin[1];
|
||||
dz = zremap - sorigin[2];
|
||||
|
||||
// if requested, apply PBC to distance from sphere center
|
||||
// treat orthogonal and triclinic the same
|
||||
// with dx,dy,dz = lengths independent of each other
|
||||
// so do not use domain->minimum_image() which couples for triclinic
|
||||
|
||||
if (pbcflag) {
|
||||
if (periodicity[0]) {
|
||||
if (fabs(dx) > prd_half[0]) {
|
||||
if (dx < 0.0) dx += prd[0];
|
||||
else dx -= prd[0];
|
||||
}
|
||||
}
|
||||
if (periodicity[1]) {
|
||||
if (fabs(dy) > prd_half[1]) {
|
||||
if (dy < 0.0) dy += prd[1];
|
||||
else dy -= prd[1];
|
||||
}
|
||||
}
|
||||
if (periodicity[2]) {
|
||||
if (fabs(dz) > prd_half[2]) {
|
||||
if (dz < 0.0) dz += prd[2];
|
||||
else dz -= prd[2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
r = sqrt(dx*dx + dy*dy + dz*dz);
|
||||
|
||||
ibin = static_cast<int> ((r - sradmin) * sinvrad);
|
||||
@ -1792,7 +1860,6 @@ void ComputeChunkAtom::atom2binsphere()
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
assign each atom to a cylindrical bin
|
||||
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ComputeChunkAtom::atom2bincylinder()
|
||||
@ -1812,6 +1879,7 @@ void ComputeChunkAtom::atom2bincylinder()
|
||||
double *boxlo = domain->boxlo;
|
||||
double *boxhi = domain->boxhi;
|
||||
double *prd = domain->prd;
|
||||
double *prd_half = domain->prd_half;
|
||||
int *periodicity = domain->periodicity;
|
||||
|
||||
// remap each atom's relevant coords back into box via PBC if necessary
|
||||
@ -1837,6 +1905,26 @@ void ComputeChunkAtom::atom2bincylinder()
|
||||
|
||||
d1 = remap1 - corigin[cdim1];
|
||||
d2 = remap2 - corigin[cdim2];
|
||||
|
||||
// if requested, apply PBC to distance from cylinder axis
|
||||
// treat orthogonal and triclinic the same
|
||||
// with d1,d2 = lengths independent of each other
|
||||
|
||||
if (pbcflag) {
|
||||
if (periodicity[cdim1]) {
|
||||
if (fabs(d1) > prd_half[cdim1]) {
|
||||
if (d1 < 0.0) d1 += prd[cdim1];
|
||||
else d1 -= prd[cdim1];
|
||||
}
|
||||
}
|
||||
if (periodicity[cdim2]) {
|
||||
if (fabs(d2) > prd_half[cdim2]) {
|
||||
if (d2 < 0.0) d2 += prd[cdim2];
|
||||
else d2 -= prd[cdim2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
r = sqrt(d1*d1 + d2*d2);
|
||||
|
||||
rbin = static_cast<int> ((r - cradmin) * cinvrad);
|
||||
|
||||
@ -51,7 +51,7 @@ class ComputeChunkAtom : public Compute {
|
||||
int which,binflag;
|
||||
int regionflag,nchunksetflag,nchunkflag,discard;
|
||||
int limit,limitstyle,limitfirst;
|
||||
int scaleflag;
|
||||
int scaleflag,pbcflag;
|
||||
double xscale,yscale,zscale;
|
||||
int argindex;
|
||||
char *cfvid;
|
||||
|
||||
@ -45,13 +45,14 @@ ComputeDisplaceAtom::ComputeDisplaceAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
strcpy(id_fix,id);
|
||||
strcat(id_fix,"_COMPUTE_STORE");
|
||||
|
||||
char **newarg = new char*[5];
|
||||
char **newarg = new char*[6];
|
||||
newarg[0] = id_fix;
|
||||
newarg[1] = group->names[igroup];
|
||||
newarg[2] = (char *) "STORE";
|
||||
newarg[3] = (char *) "1";
|
||||
newarg[4] = (char *) "3";
|
||||
modify->add_fix(5,newarg);
|
||||
newarg[3] = (char *) "peratom";
|
||||
newarg[4] = (char *) "1";
|
||||
newarg[5] = (char *) "3";
|
||||
modify->add_fix(6,newarg);
|
||||
fix = (FixStore *) modify->fix[modify->nfix-1];
|
||||
delete [] newarg;
|
||||
|
||||
|
||||
@ -65,13 +65,14 @@ ComputeMSD::ComputeMSD(LAMMPS *lmp, int narg, char **arg) :
|
||||
strcpy(id_fix,id);
|
||||
strcat(id_fix,"_COMPUTE_STORE");
|
||||
|
||||
char **newarg = new char*[5];
|
||||
char **newarg = new char*[6];
|
||||
newarg[0] = id_fix;
|
||||
newarg[1] = group->names[igroup];
|
||||
newarg[2] = (char *) "STORE";
|
||||
newarg[3] = (char *) "1";
|
||||
newarg[4] = (char *) "3";
|
||||
modify->add_fix(5,newarg);
|
||||
newarg[3] = (char *) "peratom";
|
||||
newarg[4] = (char *) "1";
|
||||
newarg[5] = (char *) "3";
|
||||
modify->add_fix(6,newarg);
|
||||
fix = (FixStore *) modify->fix[modify->nfix-1];
|
||||
delete [] newarg;
|
||||
|
||||
|
||||
@ -42,13 +42,14 @@ ComputeVACF::ComputeVACF(LAMMPS *lmp, int narg, char **arg) :
|
||||
strcpy(id_fix,id);
|
||||
strcat(id_fix,"_COMPUTE_STORE");
|
||||
|
||||
char **newarg = new char*[5];
|
||||
char **newarg = new char*[6];
|
||||
newarg[0] = id_fix;
|
||||
newarg[1] = group->names[igroup];
|
||||
newarg[2] = (char *) "STORE";
|
||||
newarg[3] = (char *) "1";
|
||||
newarg[4] = (char *) "3";
|
||||
modify->add_fix(5,newarg);
|
||||
newarg[3] = (char *) "peratom";
|
||||
newarg[4] = (char *) "1";
|
||||
newarg[5] = (char *) "3";
|
||||
modify->add_fix(6,newarg);
|
||||
fix = (FixStore *) modify->fix[modify->nfix-1];
|
||||
delete [] newarg;
|
||||
|
||||
|
||||
@ -347,6 +347,13 @@ void CreateAtoms::command(int narg, char **arg)
|
||||
}
|
||||
}
|
||||
|
||||
// clear ghost count and any ghost bonus data internal to AtomVec
|
||||
// same logic as beginning of Comm::exchange()
|
||||
// do it now b/c creating atoms will overwrite ghost atoms
|
||||
|
||||
atom->nghost = 0;
|
||||
atom->avec->clear_bonus();
|
||||
|
||||
// add atoms/molecules in one of 3 ways
|
||||
|
||||
bigint natoms_previous = atom->natoms;
|
||||
@ -400,11 +407,10 @@ void CreateAtoms::command(int narg, char **arg)
|
||||
if (atom->tag_enable) atom->tag_extend();
|
||||
atom->tag_check();
|
||||
|
||||
// create global mapping of atoms
|
||||
// zero nghost in case are adding new atoms to existing atoms
|
||||
// if global map exists, reset it
|
||||
// invoke map_init() b/c atom count has grown
|
||||
|
||||
if (atom->map_style) {
|
||||
atom->nghost = 0;
|
||||
atom->map_init();
|
||||
atom->map_set();
|
||||
}
|
||||
@ -595,7 +601,7 @@ void CreateAtoms::add_single()
|
||||
if (mode == ATOM) atom->avec->create_atom(ntype,xone);
|
||||
else if (quatone[0] == 0.0 && quatone[1] == 0.0 && quatone[2] == 0.0)
|
||||
add_molecule(xone);
|
||||
else add_molecule(xone,&quatone[0]);
|
||||
else add_molecule(xone,quatone);
|
||||
}
|
||||
}
|
||||
|
||||
@ -807,6 +813,10 @@ void CreateAtoms::add_molecule(double *center, double *quat_user)
|
||||
int n;
|
||||
double r[3],rotmat[3][3],quat[4],xnew[3];
|
||||
|
||||
if (quat_user) {
|
||||
quat[0] = quat_user[0]; quat[1] = quat_user[1];
|
||||
quat[2] = quat_user[2]; quat[3] = quat_user[3];
|
||||
} else {
|
||||
if (domain->dimension == 3) {
|
||||
r[0] = ranmol->uniform() - 0.5;
|
||||
r[1] = ranmol->uniform() - 0.5;
|
||||
@ -815,16 +825,13 @@ void CreateAtoms::add_molecule(double *center, double *quat_user)
|
||||
r[0] = r[1] = 0.0;
|
||||
r[2] = 1.0;
|
||||
}
|
||||
|
||||
if (quat_user) {
|
||||
quat[0] = quat_user[0]; quat[1] = quat_user[1];
|
||||
quat[2] = quat_user[2]; quat[3] = quat_user[3];
|
||||
} else {
|
||||
double theta = ranmol->uniform() * MY_2PI;
|
||||
MathExtra::norm3(r);
|
||||
double theta = ranmol->uniform() * MY_2PI;
|
||||
MathExtra::axisangle_to_quat(r,theta,quat);
|
||||
}
|
||||
|
||||
MathExtra::quat_to_mat(quat,rotmat);
|
||||
onemol->quat_external = quat;
|
||||
|
||||
// create atoms in molecule with atom ID = 0 and mol ID = 0
|
||||
// reset in caller after all moleclues created by all procs
|
||||
|
||||
@ -210,11 +210,12 @@ void FixAdapt::post_constructor()
|
||||
id_fix_diam = NULL;
|
||||
id_fix_chg = NULL;
|
||||
|
||||
char **newarg = new char*[5];
|
||||
char **newarg = new char*[6];
|
||||
newarg[1] = group->names[igroup];
|
||||
newarg[2] = (char *) "STORE";
|
||||
newarg[3] = (char *) "1";
|
||||
newarg[3] = (char *) "peratom";
|
||||
newarg[4] = (char *) "1";
|
||||
newarg[5] = (char *) "1";
|
||||
|
||||
if (diamflag) {
|
||||
int n = strlen(id) + strlen("_FIX_STORE_DIAM") + 1;
|
||||
@ -222,7 +223,7 @@ void FixAdapt::post_constructor()
|
||||
strcpy(id_fix_diam,id);
|
||||
strcat(id_fix_diam,"_FIX_STORE_DIAM");
|
||||
newarg[0] = id_fix_diam;
|
||||
modify->add_fix(5,newarg);
|
||||
modify->add_fix(6,newarg);
|
||||
fix_diam = (FixStore *) modify->fix[modify->nfix-1];
|
||||
|
||||
if (fix_diam->restart_reset) fix_diam->restart_reset = 0;
|
||||
@ -245,7 +246,7 @@ void FixAdapt::post_constructor()
|
||||
strcpy(id_fix_chg,id);
|
||||
strcat(id_fix_chg,"_FIX_STORE_CHG");
|
||||
newarg[0] = id_fix_chg;
|
||||
modify->add_fix(5,newarg);
|
||||
modify->add_fix(6,newarg);
|
||||
fix_chg = (FixStore *) modify->fix[modify->nfix-1];
|
||||
|
||||
if (fix_chg->restart_reset) fix_chg->restart_reset = 0;
|
||||
|
||||
@ -15,49 +15,91 @@
|
||||
#include <string.h>
|
||||
#include "fix_store.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
enum{GLOBAL,PERATOM};
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixStore::FixStore(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
|
||||
{
|
||||
if (narg != 5) error->all(FLERR,"Illegal fix store command");
|
||||
if (narg != 6) error->all(FLERR,"Illegal fix store command");
|
||||
|
||||
// syntax: id group style 0/1 nvalue
|
||||
// 0/1 flag = not-store or store values in restart file
|
||||
// 4th arg determines GLOBAL vs PERATOM values
|
||||
// syntax: id group style peratom 0/1 nvalue
|
||||
// 0/1 flag = not-store or store peratom values in restart file
|
||||
// nvalue = # of peratom values, N=1 is vector, N>1 is array
|
||||
// syntax: id group style global nrow ncol
|
||||
// Nrow by Ncol array of global values
|
||||
// Ncol=1 is vector, Nrow>1 is array
|
||||
|
||||
restart_peratom = force->inumeric(FLERR,arg[3]);
|
||||
nvalues = force->inumeric(FLERR,arg[4]);
|
||||
if (strcmp(arg[3],"peratom") == 0) flavor = PERATOM;
|
||||
else if (strcmp(arg[3],"global") == 0) flavor = GLOBAL;
|
||||
else error->all(FLERR,"Invalid fix store command");
|
||||
|
||||
// GLOBAL values are always written to restart file
|
||||
// PERATOM restart_peratom is set by caller
|
||||
|
||||
if (flavor == GLOBAL) {
|
||||
restart_global = 1;
|
||||
nrow = force->inumeric(FLERR,arg[4]);
|
||||
ncol = force->inumeric(FLERR,arg[5]);
|
||||
if (nrow <= 0 || ncol <= 0)
|
||||
error->all(FLERR,"Invalid fix store command");
|
||||
vecflag = 0;
|
||||
if (ncol == 1) vecflag = 1;
|
||||
} else {
|
||||
restart_peratom = force->inumeric(FLERR,arg[4]);
|
||||
nvalues = force->inumeric(FLERR,arg[5]);
|
||||
if (restart_peratom < 0 or restart_peratom > 1 || nvalues <= 0)
|
||||
error->all(FLERR,"Invalid fix store command");
|
||||
vecflag = 0;
|
||||
if (nvalues == 1) vecflag = 1;
|
||||
|
||||
// perform initial allocation of atom-based array
|
||||
// register with Atom class
|
||||
}
|
||||
|
||||
vstore = NULL;
|
||||
astore = NULL;
|
||||
|
||||
// allocate vector or array
|
||||
// for PERATOM, register with Atom class
|
||||
|
||||
if (flavor == GLOBAL) {
|
||||
if (vecflag) memory->create(vstore,nrow,"fix/store:vstore");
|
||||
else memory->create(astore,nrow,ncol,"fix/store:astore");
|
||||
}
|
||||
if (flavor == PERATOM) {
|
||||
grow_arrays(atom->nmax);
|
||||
atom->add_callback(0);
|
||||
if (restart_peratom) atom->add_callback(1);
|
||||
}
|
||||
|
||||
// zero the storage
|
||||
// since may be exchanged before filled by caller
|
||||
// PERATOM may be exchanged before filled by caller
|
||||
|
||||
if (flavor == GLOBAL) {
|
||||
if (vecflag)
|
||||
for (int i = 0; i < nrow; i++) vstore[i] = 0.0;
|
||||
else
|
||||
for (int i = 0; i < nrow; i++)
|
||||
for (int j = 0; j < ncol; j++)
|
||||
astore[i][j] = 0.0;
|
||||
}
|
||||
if (flavor == PERATOM) {
|
||||
int nlocal = atom->nlocal;
|
||||
if (vecflag)
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
vstore[i] = 0.0;
|
||||
for (int i = 0; i < nlocal; i++) vstore[i] = 0.0;
|
||||
else
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
for (int j = 0; j < nvalues; j++)
|
||||
astore[i][j] = 0.0;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -65,8 +107,10 @@ FixStore::~FixStore()
|
||||
{
|
||||
// unregister callbacks to this fix from Atom class
|
||||
|
||||
if (flavor == PERATOM) {
|
||||
atom->delete_callback(id,0);
|
||||
if (restart_peratom) atom->delete_callback(id,1);
|
||||
}
|
||||
|
||||
memory->destroy(vstore);
|
||||
memory->destroy(astore);
|
||||
@ -81,13 +125,32 @@ int FixStore::setmask()
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
memory usage of local atom-based array
|
||||
write global array to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixStore::memory_usage()
|
||||
void FixStore::write_restart(FILE *fp)
|
||||
{
|
||||
double bytes = atom->nmax*nvalues * sizeof(double);
|
||||
return bytes;
|
||||
int n = nrow*ncol;
|
||||
if (comm->me == 0) {
|
||||
int size = n * sizeof(double);
|
||||
fwrite(&size,sizeof(int),1,fp);
|
||||
if (vecflag) fwrite(vstore,sizeof(double),n,fp);
|
||||
else fwrite(&astore[0][0],sizeof(double),n,fp);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
use global array from restart file to restart the Fix
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixStore::restart(char *buf)
|
||||
{
|
||||
// HOWTO insure size of buf is the same
|
||||
|
||||
int n = nrow*ncol;
|
||||
double *dbuf = (double *) buf;
|
||||
if (vecflag) memcpy(vstore,dbuf,n*sizeof(double));
|
||||
else memcpy(&astore[0][0],dbuf,n*sizeof(double));
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -189,3 +252,15 @@ int FixStore::size_restart(int nlocal)
|
||||
{
|
||||
return nvalues+1;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
memory usage of local atom-based array
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixStore::memory_usage()
|
||||
{
|
||||
double bytes;
|
||||
if (flavor == GLOBAL) bytes += nrow*ncol * sizeof(double);
|
||||
if (flavor == PERATOM) bytes += atom->nmax*nvalues * sizeof(double);
|
||||
return bytes;
|
||||
}
|
||||
|
||||
@ -20,20 +20,25 @@ FixStyle(STORE,FixStore)
|
||||
#ifndef LMP_FIX_STORE_H
|
||||
#define LMP_FIX_STORE_H
|
||||
|
||||
#include <stdio.h>
|
||||
#include "fix.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixStore : public Fix {
|
||||
public:
|
||||
double *vstore; // vector storage if nvalues = 1
|
||||
double **astore; // array storage if nvalues > 1
|
||||
int nrow,ncol; // size of global data array
|
||||
int nvalues; // number of per-atom values
|
||||
double *vstore; // vector storage for GLOBAL or PERATOM
|
||||
double **astore; // array storage for GLOBAL or PERATOM
|
||||
|
||||
FixStore(class LAMMPS *, int, char **);
|
||||
~FixStore();
|
||||
int setmask();
|
||||
|
||||
double memory_usage();
|
||||
void write_restart(FILE *);
|
||||
void restart(char *);
|
||||
|
||||
void grow_arrays(int);
|
||||
void copy_arrays(int, int, int);
|
||||
int pack_exchange(int, double *);
|
||||
@ -43,9 +48,11 @@ class FixStore : public Fix {
|
||||
int size_restart(int);
|
||||
int maxsize_restart();
|
||||
|
||||
double memory_usage();
|
||||
|
||||
private:
|
||||
int nvalues; // total # of values per atom
|
||||
int vecflag; // 1 if nvalues = 1
|
||||
int flavor; // GLOBAL or PERATOM
|
||||
int vecflag; // 1 if ncol=1 or nvalues=1
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
@ -105,6 +105,19 @@ FixStoreState::FixStoreState(LAMMPS *lmp, int narg, char **arg) :
|
||||
if (domain->triclinic)
|
||||
pack_choice[nvalues++] = &FixStoreState::pack_zu_triclinic;
|
||||
else pack_choice[nvalues++] = &FixStoreState::pack_zu;
|
||||
} else if (strcmp(arg[iarg],"xsu") == 0) {
|
||||
if (domain->triclinic)
|
||||
pack_choice[nvalues++] = &FixStoreState::pack_xsu_triclinic;
|
||||
else pack_choice[nvalues++] = &FixStoreState::pack_xsu;
|
||||
} else if (strcmp(arg[iarg],"ysu") == 0) {
|
||||
if (domain->triclinic)
|
||||
pack_choice[nvalues++] = &FixStoreState::pack_ysu_triclinic;
|
||||
else pack_choice[nvalues++] = &FixStoreState::pack_ysu;
|
||||
} else if (strcmp(arg[iarg],"zsu") == 0) {
|
||||
if (domain->triclinic)
|
||||
pack_choice[nvalues++] = &FixStoreState::pack_zsu_triclinic;
|
||||
else pack_choice[nvalues++] = &FixStoreState::pack_zsu;
|
||||
|
||||
} else if (strcmp(arg[iarg],"ix") == 0) {
|
||||
pack_choice[nvalues++] = &FixStoreState::pack_ix;
|
||||
} else if (strcmp(arg[iarg],"iy") == 0) {
|
||||
@ -145,12 +158,22 @@ FixStoreState::FixStoreState(LAMMPS *lmp, int narg, char **arg) :
|
||||
error->all(FLERR,
|
||||
"Fix store/state for atom property that isn't allocated");
|
||||
pack_choice[nvalues++] = &FixStoreState::pack_muz;
|
||||
} else if (strcmp(arg[iarg],"mu") == 0) {
|
||||
if (!atom->mu_flag)
|
||||
error->all(FLERR,
|
||||
"Fix store/state for atom property that isn't allocated");
|
||||
pack_choice[nvalues++] = &FixStoreState::pack_mu;
|
||||
|
||||
} else if (strcmp(arg[iarg],"radius") == 0) {
|
||||
if (!atom->radius_flag)
|
||||
error->all(FLERR,
|
||||
"Fix store/state for atom property that isn't allocated");
|
||||
pack_choice[nvalues++] = &FixStoreState::pack_radius;
|
||||
} else if (strcmp(arg[iarg],"diameter") == 0) {
|
||||
if (!atom->radius_flag)
|
||||
error->all(FLERR,
|
||||
"Fix store/state for atom property that isn't allocated");
|
||||
pack_choice[nvalues++] = &FixStoreState::pack_diameter;
|
||||
} else if (strcmp(arg[iarg],"omegax") == 0) {
|
||||
if (!atom->omega_flag)
|
||||
error->all(FLERR,
|
||||
@ -989,6 +1012,128 @@ void FixStoreState::pack_zu_triclinic(int n)
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixStoreState::pack_xsu(int n)
|
||||
{
|
||||
double **x = atom->x;
|
||||
imageint *image = atom->image;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double boxxlo = domain->boxlo[0];
|
||||
double invxprd = 1.0/domain->xprd;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit)
|
||||
vbuf[n] = (x[i][0]-boxxlo)*invxprd + ((image[i] & IMGMASK) - IMGMAX);
|
||||
else vbuf[n] = 0.0;
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixStoreState::pack_ysu(int n)
|
||||
{
|
||||
double **x = atom->x;
|
||||
imageint *image = atom->image;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double boxylo = domain->boxlo[1];
|
||||
double invyprd = 1.0/domain->yprd;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit)
|
||||
vbuf[n] = (x[i][1]-boxylo)*invyprd + (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
else vbuf[n] = 0.0;
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixStoreState::pack_zsu(int n)
|
||||
{
|
||||
double **x = atom->x;
|
||||
imageint *image = atom->image;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double boxzlo = domain->boxlo[2];
|
||||
double invzprd = 1.0/domain->zprd;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit)
|
||||
vbuf[n] = (x[i][2]-boxzlo)*invzprd + (image[i] >> IMG2BITS) - IMGMAX;
|
||||
else vbuf[n] = 0.0;
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpCustom::pack_xsu_triclinic(int n)
|
||||
{
|
||||
double **x = atom->x;
|
||||
imageint *image = atom->image;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double *boxlo = domain->boxlo;
|
||||
double *h_inv = domain->h_inv;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit)
|
||||
vbuf[n] = h_inv[0]*(x[i][0]-boxlo[0]) + h_inv[5]*(x[i][1]-boxlo[1]) +
|
||||
h_inv[4]*(x[i][2]-boxlo[2]) + (image[i] & IMGMASK) - IMGMAX;
|
||||
else vbuf[n] = 0.0;
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpCustom::pack_ysu_triclinic(int n)
|
||||
{
|
||||
double **x = atom->x;
|
||||
imageint *image = atom->image;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double *boxlo = domain->boxlo;
|
||||
double *h_inv = domain->h_inv;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit)
|
||||
vbuf[n] = h_inv[1]*(x[i][1]-boxlo[1]) + h_inv[3]*(x[i][2]-boxlo[2]) +
|
||||
(image[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
else vbuf[n] = 0.0;
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpCustom::pack_zsu_triclinic(int n)
|
||||
{
|
||||
double **x = atom->x;
|
||||
imageint *image = atom->image;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double *boxlo = domain->boxlo;
|
||||
double *h_inv = domain->h_inv;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit)
|
||||
buf[n] = h_inv[2]*(x[i][2]-boxlo[2]) + (image[i] >> IMG2BITS) - IMGMAX;
|
||||
else vbuf[n] = 0.0;
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixStoreState::pack_ix(int n)
|
||||
{
|
||||
imageint *image = atom->image;
|
||||
@ -1184,6 +1329,21 @@ void FixStoreState::pack_muz(int n)
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixStoreState::pack_mu(int n)
|
||||
{
|
||||
double **mu = atom->mu;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) vbuf[n] = mu[i][3];
|
||||
else vbuf[n] = 0.0;
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixStoreState::pack_radius(int n)
|
||||
{
|
||||
double *radius = atom->radius;
|
||||
@ -1199,6 +1359,21 @@ void FixStoreState::pack_radius(int n)
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixStoreState::pack_diameter(int n)
|
||||
{
|
||||
double *radius = atom->radius;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) vbuf[n] = 2.0*radius[i];
|
||||
else vbuf[n] = 0.0;
|
||||
n += nvalues;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixStoreState::pack_omegax(int n)
|
||||
{
|
||||
double **omega = atom->omega;
|
||||
|
||||
@ -79,6 +79,13 @@ class FixStoreState : public Fix {
|
||||
void pack_xu_triclinic(int);
|
||||
void pack_yu_triclinic(int);
|
||||
void pack_zu_triclinic(int);
|
||||
void pack_xsu(int);
|
||||
void pack_ysu(int);
|
||||
void pack_zsu(int);
|
||||
void pack_xsu_triclinic(int);
|
||||
void pack_ysu_triclinic(int);
|
||||
void pack_zsu_triclinic(int);
|
||||
|
||||
void pack_ix(int);
|
||||
void pack_iy(int);
|
||||
void pack_iz(int);
|
||||
@ -93,7 +100,9 @@ class FixStoreState : public Fix {
|
||||
void pack_mux(int);
|
||||
void pack_muy(int);
|
||||
void pack_muz(int);
|
||||
void pack_mu(int);
|
||||
void pack_radius(int);
|
||||
void pack_diameter(int);
|
||||
void pack_omegax(int);
|
||||
void pack_omegay(int);
|
||||
void pack_omegaz(int);
|
||||
|
||||
@ -16,6 +16,7 @@
|
||||
#include "molecule.h"
|
||||
#include "atom.h"
|
||||
#include "atom_vec.h"
|
||||
#include "atom_vec_body.h"
|
||||
#include "force.h"
|
||||
#include "comm.h"
|
||||
#include "domain.h"
|
||||
@ -163,7 +164,8 @@ Molecule::~Molecule()
|
||||
compute center = geometric center of molecule
|
||||
also compute:
|
||||
dx = displacement of each atom from center
|
||||
molradius = radius of molecule from center including finite-size particles
|
||||
molradius = radius of molecule from center
|
||||
including finite-size particles or body particles
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Molecule::compute_center()
|
||||
@ -446,6 +448,13 @@ void Molecule::read(int flag)
|
||||
itensor[4] *= sizescale*sizescale*sizescale*sizescale*sizescale;
|
||||
itensor[5] *= sizescale*sizescale*sizescale*sizescale*sizescale;
|
||||
}
|
||||
else if (strstr(line,"body")) {
|
||||
bodyflag = 1;
|
||||
avec_body = (AtomVecBody *) atom->style_match("body");
|
||||
if (!avec_body)
|
||||
error->all(FLERR,"Molecule file requires atom style body");
|
||||
sscanf(line,"%d %d",&nibody,&ndbody);
|
||||
}
|
||||
|
||||
else break;
|
||||
}
|
||||
@ -542,6 +551,19 @@ void Molecule::read(int flag)
|
||||
if (flag) shaketype_read(line);
|
||||
else skip_lines(natoms,line);
|
||||
|
||||
} else if (strcmp(keyword,"Body Integers") == 0) {
|
||||
if (bodyflag == 0 || nibody == 0)
|
||||
error->all(FLERR,"Molecule file has body params "
|
||||
"but no setting for them");
|
||||
ibodyflag = 1;
|
||||
body(flag,0,line);
|
||||
} else if (strcmp(keyword,"Body Doubles") == 0) {
|
||||
if (bodyflag == 0 || ndbody == 0)
|
||||
error->all(FLERR,"Molecule file has body params "
|
||||
"but no setting for them");
|
||||
dbodyflag = 1;
|
||||
body(flag,1,line);
|
||||
|
||||
} else error->one(FLERR,"Unknown section in molecule file");
|
||||
|
||||
parse_keyword(1,line,keyword);
|
||||
@ -560,6 +582,10 @@ void Molecule::read(int flag)
|
||||
error->all(FLERR,"Molecule file has special flags but no bonds");
|
||||
if ((shakeflagflag || shakeatomflag || shaketypeflag) && !shakeflag)
|
||||
error->all(FLERR,"Molecule file shake info is incomplete");
|
||||
if (bodyflag && nibody && ibodyflag == 0)
|
||||
error->all(FLERR,"Molecule file has no Body Integers section");
|
||||
if (bodyflag && ndbody && dbodyflag == 0)
|
||||
error->all(FLERR,"Molecule file has no Body Doubles section");
|
||||
}
|
||||
|
||||
// auto-generate special bonds
|
||||
@ -570,6 +596,21 @@ void Molecule::read(int flag)
|
||||
maxspecial = atom->maxspecial;
|
||||
if (flag) special_generate();
|
||||
}
|
||||
|
||||
// body particle must have natom = 1
|
||||
// set radius by having body class compute its own radius
|
||||
|
||||
if (bodyflag) {
|
||||
radiusflag = 1;
|
||||
if (natoms != 1)
|
||||
error->all(FLERR,"Molecule natoms must be 1 for body particle");
|
||||
if (sizescale != 1.0)
|
||||
error->all(FLERR,"Molecule sizescale must be 1.0 for body particle");
|
||||
if (flag) {
|
||||
radius[0] = avec_body->radius_body(nibody,ndbody,ibodyparams,dbodyparams);
|
||||
maxradius = radius[0];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -1244,6 +1285,44 @@ void Molecule::shaketype_read(char *line)
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
read body params from file
|
||||
pflag = 0/1 for integer/double params
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Molecule::body(int flag, int pflag, char *line)
|
||||
{
|
||||
int i,ncount;
|
||||
|
||||
int nparam = nibody;
|
||||
if (pflag) nparam = ndbody;
|
||||
|
||||
int nword = 0;
|
||||
while (nword < nparam) {
|
||||
readline(line);
|
||||
|
||||
ncount = atom->count_words(line);
|
||||
if (ncount == 0)
|
||||
error->one(FLERR,"Too few values in body section of molecule file");
|
||||
if (nword+ncount > nparam)
|
||||
error->all(FLERR,"Too many values in body section of molecule file");
|
||||
|
||||
if (flag) {
|
||||
if (pflag == 0) {
|
||||
ibodyparams[nword++] = force->inumeric(FLERR,strtok(line," \t\n\r\f"));
|
||||
for (i = 1; i < ncount; i++)
|
||||
ibodyparams[nword++] =
|
||||
force->inumeric(FLERR,strtok(NULL," \t\n\r\f"));
|
||||
} else {
|
||||
dbodyparams[nword++] = force->numeric(FLERR,strtok(line," \t\n\r\f"));
|
||||
for (i = 1; i < ncount; i++)
|
||||
dbodyparams[nword++] =
|
||||
force->numeric(FLERR,strtok(NULL," \t\n\r\f"));
|
||||
}
|
||||
} else nword += ncount;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
error check molecule attributes and topology against system settings
|
||||
flag = 0, just check this molecule
|
||||
@ -1318,6 +1397,7 @@ void Molecule::initialize()
|
||||
nbonds = nangles = ndihedrals = nimpropers = 0;
|
||||
ntypes = 0;
|
||||
nbondtypes = nangletypes = ndihedraltypes = nimpropertypes = 0;
|
||||
nibody = ndbody = 0;
|
||||
|
||||
bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
|
||||
maxspecial = 0;
|
||||
@ -1326,6 +1406,7 @@ void Molecule::initialize()
|
||||
bondflag = angleflag = dihedralflag = improperflag = 0;
|
||||
nspecialflag = specialflag = 0;
|
||||
shakeflag = shakeflagflag = shakeatomflag = shaketypeflag = 0;
|
||||
bodyflag = ibodyflag = dbodyflag = 0;
|
||||
|
||||
centerflag = massflag = comflag = inertiaflag = 0;
|
||||
tag_require = 0;
|
||||
@ -1359,6 +1440,9 @@ void Molecule::initialize()
|
||||
shake_atom = NULL;
|
||||
shake_type = NULL;
|
||||
|
||||
ibodyparams = NULL;
|
||||
dbodyparams = NULL;
|
||||
|
||||
dx = NULL;
|
||||
dxcom = NULL;
|
||||
dxbody = NULL;
|
||||
@ -1445,6 +1529,11 @@ void Molecule::allocate()
|
||||
memory->create(shake_atom,natoms,4,"molecule:shake_flag");
|
||||
memory->create(shake_type,natoms,3,"molecule:shake_flag");
|
||||
}
|
||||
|
||||
if (bodyflag) {
|
||||
if (nibody) memory->create(ibodyparams,nibody,"molecule:ibodyparams");
|
||||
if (ndbody) memory->create(dbodyparams,ndbody,"molecule:dbodyparams");
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -1493,6 +1582,9 @@ void Molecule::deallocate()
|
||||
memory->destroy(dx);
|
||||
memory->destroy(dxcom);
|
||||
memory->destroy(dxbody);
|
||||
|
||||
memory->destroy(ibodyparams);
|
||||
memory->destroy(dbodyparams);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
||||
@ -26,11 +26,13 @@ class Molecule : protected Pointers {
|
||||
int last; // 1 if last molecule in set, else 0
|
||||
|
||||
// number of atoms,bonds,etc in molecule
|
||||
// nibody,ndbody = # of integer/double fields in body
|
||||
|
||||
int natoms;
|
||||
int nbonds,nangles,ndihedrals,nimpropers;
|
||||
int ntypes;
|
||||
int nbondtypes,nangletypes,ndihedraltypes,nimpropertypes;
|
||||
int nibody,ndbody;
|
||||
|
||||
// max bond,angle,etc per atom
|
||||
|
||||
@ -43,6 +45,7 @@ class Molecule : protected Pointers {
|
||||
int bondflag,angleflag,dihedralflag,improperflag;
|
||||
int nspecialflag,specialflag;
|
||||
int shakeflag,shakeflagflag,shakeatomflag,shaketypeflag;
|
||||
int bodyflag,ibodyflag,dbodyflag;
|
||||
|
||||
// 1 if attribute defined or computed, 0 if not
|
||||
|
||||
@ -83,6 +86,10 @@ class Molecule : protected Pointers {
|
||||
tagint **shake_atom;
|
||||
int **shake_type;
|
||||
|
||||
class AtomVecBody *avec_body;
|
||||
int *ibodyparams; // integer and double body params
|
||||
double *dbodyparams;
|
||||
|
||||
double center[3]; // geometric center of molecule
|
||||
double masstotal; // total mass of molecule
|
||||
double com[3]; // center of mass of molecule
|
||||
@ -102,6 +109,9 @@ class Molecule : protected Pointers {
|
||||
double **dxbody; // displacement of each atom relative to COM
|
||||
// in body frame (diagonalized interia tensor)
|
||||
|
||||
double *quat_external; // orientation imposed by external class
|
||||
// e.g. FixPour or CreateAtoms
|
||||
|
||||
Molecule(class LAMMPS *, int, char **, int &);
|
||||
~Molecule();
|
||||
void compute_center();
|
||||
@ -134,6 +144,7 @@ class Molecule : protected Pointers {
|
||||
void shakeflag_read(char *);
|
||||
void shakeatom_read(char *);
|
||||
void shaketype_read(char *);
|
||||
void body(int, int, char *);
|
||||
|
||||
void initialize();
|
||||
void allocate();
|
||||
|
||||
@ -1469,7 +1469,7 @@ void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
|
||||
|
||||
void ReadData::bodies(int firstpass)
|
||||
{
|
||||
int i,m,nchunk,nline,nmax,ninteger,ndouble,nword,onebody,tmp;
|
||||
int i,m,nchunk,nline,nmax,ninteger,ndouble,nword,ncount,onebody,tmp;
|
||||
char *eof;
|
||||
|
||||
int mapflag = 0;
|
||||
@ -1500,8 +1500,7 @@ void ReadData::bodies(int firstpass)
|
||||
sscanf(&buffer[m],"%d %d %d",&tmp,&ninteger,&ndouble);
|
||||
m += strlen(&buffer[m]);
|
||||
|
||||
// read lines one at a time into buffer
|
||||
// make copy of line and count words
|
||||
// read lines one at a time into buffer and count words
|
||||
// count to ninteger and ndouble until have enough lines
|
||||
|
||||
onebody = 0;
|
||||
@ -1510,23 +1509,29 @@ void ReadData::bodies(int firstpass)
|
||||
while (nword < ninteger) {
|
||||
eof = fgets(&buffer[m],MAXLINE,fp);
|
||||
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
|
||||
nword += atom->count_words(&buffer[m],copy);
|
||||
ncount = atom->count_words(&buffer[m],copy);
|
||||
if (ncount == 0)
|
||||
error->one(FLERR,"Too few values in body lines in data file");
|
||||
nword += ncount;
|
||||
m += strlen(&buffer[m]);
|
||||
onebody++;
|
||||
}
|
||||
if (nword > ninteger)
|
||||
error->one(FLERR,"Too many value in body lines in data file");
|
||||
error->one(FLERR,"Too many values in body lines in data file");
|
||||
|
||||
nword = 0;
|
||||
while (nword < ndouble) {
|
||||
eof = fgets(&buffer[m],MAXLINE,fp);
|
||||
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
|
||||
nword += atom->count_words(&buffer[m],copy);
|
||||
ncount = atom->count_words(&buffer[m],copy);
|
||||
if (ncount == 0)
|
||||
error->one(FLERR,"Too few values in body lines in data file");
|
||||
nword += ncount;
|
||||
m += strlen(&buffer[m]);
|
||||
onebody++;
|
||||
}
|
||||
if (nword > ndouble)
|
||||
error->one(FLERR,"Too many value in body lines in data file");
|
||||
error->one(FLERR,"Too many values in body lines in data file");
|
||||
|
||||
if (onebody+1 > MAXBODY)
|
||||
error->one(FLERR,
|
||||
|
||||
59
src/set.cpp
59
src/set.cpp
@ -21,6 +21,7 @@
|
||||
#include "atom_vec_ellipsoid.h"
|
||||
#include "atom_vec_line.h"
|
||||
#include "atom_vec_tri.h"
|
||||
#include "atom_vec_body.h"
|
||||
#include "domain.h"
|
||||
#include "region.h"
|
||||
#include "group.h"
|
||||
@ -41,7 +42,7 @@ using namespace MathConst;
|
||||
|
||||
enum{ATOM_SELECT,MOL_SELECT,TYPE_SELECT,GROUP_SELECT,REGION_SELECT};
|
||||
enum{TYPE,TYPE_FRACTION,MOLECULE,X,Y,Z,CHARGE,MASS,SHAPE,LENGTH,TRI,
|
||||
DIPOLE,DIPOLE_RANDOM,QUAT,QUAT_RANDOM,THETA,ANGMOM,OMEGA,
|
||||
DIPOLE,DIPOLE_RANDOM,QUAT,QUAT_RANDOM,THETA,THETA_RANDOM,ANGMOM,OMEGA,
|
||||
DIAMETER,DENSITY,VOLUME,IMAGE,BOND,ANGLE,DIHEDRAL,IMPROPER,
|
||||
MESO_E,MESO_CV,MESO_RHO,SMD_MASS_DENSITY,SMD_CONTACT_RADIUS,INAME,DNAME};
|
||||
|
||||
@ -221,7 +222,7 @@ void Set::command(int narg, char **arg)
|
||||
else zvalue = force->numeric(FLERR,arg[iarg+3]);
|
||||
if (strstr(arg[iarg+4],"v_") == arg[iarg+4]) varparse(arg[iarg+4],4);
|
||||
else wvalue = force->numeric(FLERR,arg[iarg+4]);
|
||||
if (!atom->ellipsoid_flag && !atom->tri_flag)
|
||||
if (!atom->ellipsoid_flag && !atom->tri_flag && !atom->body_flag)
|
||||
error->all(FLERR,"Cannot set this attribute for this atom style");
|
||||
set(QUAT);
|
||||
iarg += 5;
|
||||
@ -229,7 +230,7 @@ void Set::command(int narg, char **arg)
|
||||
} else if (strcmp(arg[iarg],"quat/random") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
|
||||
ivalue = force->inumeric(FLERR,arg[iarg+1]);
|
||||
if (!atom->ellipsoid_flag && !atom->tri_flag)
|
||||
if (!atom->ellipsoid_flag && !atom->tri_flag && !atom->body_flag)
|
||||
error->all(FLERR,"Cannot set this attribute for this atom style");
|
||||
if (ivalue <= 0)
|
||||
error->all(FLERR,"Invalid random number seed in set command");
|
||||
@ -248,6 +249,16 @@ void Set::command(int narg, char **arg)
|
||||
set(THETA);
|
||||
iarg += 2;
|
||||
|
||||
} else if (strcmp(arg[iarg],"theta/random") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
|
||||
ivalue = force->inumeric(FLERR,arg[iarg+1]);
|
||||
if (!atom->line_flag)
|
||||
error->all(FLERR,"Cannot set this attribute for this atom style");
|
||||
if (ivalue <= 0)
|
||||
error->all(FLERR,"Invalid random number seed in set command");
|
||||
set(THETA_RANDOM);
|
||||
iarg += 2;
|
||||
|
||||
} else if (strcmp(arg[iarg],"angmom") == 0) {
|
||||
if (iarg+4 > narg) error->all(FLERR,"Illegal set command");
|
||||
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
|
||||
@ -256,7 +267,7 @@ void Set::command(int narg, char **arg)
|
||||
else yvalue = force->numeric(FLERR,arg[iarg+2]);
|
||||
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) varparse(arg[iarg+3],3);
|
||||
else zvalue = force->numeric(FLERR,arg[iarg+3]);
|
||||
if (!atom->ellipsoid_flag && !atom->tri_flag)
|
||||
if (!atom->angmom_flag)
|
||||
error->all(FLERR,"Cannot set this attribute for this atom style");
|
||||
set(ANGMOM);
|
||||
iarg += 4;
|
||||
@ -269,7 +280,7 @@ void Set::command(int narg, char **arg)
|
||||
else yvalue = force->numeric(FLERR,arg[iarg+2]);
|
||||
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) varparse(arg[iarg+3],3);
|
||||
else zvalue = force->numeric(FLERR,arg[iarg+3]);
|
||||
if (!atom->sphere_flag)
|
||||
if (!atom->omega_flag)
|
||||
error->all(FLERR,"Cannot set this attribute for this atom style");
|
||||
set(OMEGA);
|
||||
iarg += 4;
|
||||
@ -558,6 +569,7 @@ void Set::set(int keyword)
|
||||
(AtomVecEllipsoid *) atom->style_match("ellipsoid");
|
||||
AtomVecLine *avec_line = (AtomVecLine *) atom->style_match("line");
|
||||
AtomVecTri *avec_tri = (AtomVecTri *) atom->style_match("tri");
|
||||
AtomVecBody *avec_body = (AtomVecBody *) atom->style_match("body");
|
||||
|
||||
int nlocal = atom->nlocal;
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
@ -604,7 +616,8 @@ void Set::set(int keyword)
|
||||
else if (keyword == MESO_E) atom->e[i] = dvalue;
|
||||
else if (keyword == MESO_CV) atom->cv[i] = dvalue;
|
||||
else if (keyword == MESO_RHO) atom->rho[i] = dvalue;
|
||||
else if (keyword == SMD_MASS_DENSITY) { // set mass from volume and supplied mass density
|
||||
else if (keyword == SMD_MASS_DENSITY) {
|
||||
// set mass from volume and supplied mass density
|
||||
atom->rmass[i] = atom->vfrac[i] * dvalue;
|
||||
}
|
||||
else if (keyword == SMD_CONTACT_RADIUS) atom->contact_radius[i] = dvalue;
|
||||
@ -678,7 +691,8 @@ void Set::set(int keyword)
|
||||
mu[i][2]*mu[i][2]);
|
||||
}
|
||||
|
||||
// set quaternion orientation of ellipsoid or tri particle
|
||||
// set quaternion orientation of ellipsoid or tri or body particle
|
||||
// enforce quat rotation vector in z dir for 2d systems
|
||||
|
||||
else if (keyword == QUAT) {
|
||||
double *quat;
|
||||
@ -686,8 +700,13 @@ void Set::set(int keyword)
|
||||
quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
|
||||
else if (avec_tri && atom->tri[i] >= 0)
|
||||
quat = avec_tri->bonus[atom->tri[i]].quat;
|
||||
else if (avec_body && atom->body[i] >= 0)
|
||||
quat = avec_body->bonus[atom->body[i]].quat;
|
||||
else
|
||||
error->one(FLERR,"Cannot set quaternion for atom that has none");
|
||||
if (domain->dimension == 2 && (xvalue != 0.0 || yvalue != 0.0))
|
||||
error->one(FLERR,"Cannot set quaternion with xy components "
|
||||
"for 2d system");
|
||||
|
||||
double theta2 = MY_PI2 * wvalue/180.0;
|
||||
double sintheta2 = sin(theta2);
|
||||
@ -706,7 +725,7 @@ void Set::set(int keyword)
|
||||
avec_line->bonus[atom->line[i]].theta = dvalue;
|
||||
}
|
||||
|
||||
// set angmom of ellipsoidal or tri particle
|
||||
// set angmom or omega of particle
|
||||
|
||||
else if (keyword == ANGMOM) {
|
||||
atom->angmom[i][0] = xvalue;
|
||||
@ -720,7 +739,6 @@ void Set::set(int keyword)
|
||||
atom->omega[i][2] = zvalue;
|
||||
}
|
||||
|
||||
|
||||
// reset any or all of 3 image flags
|
||||
|
||||
else if (keyword == IMAGE) {
|
||||
@ -768,7 +786,9 @@ void Set::setrandom(int keyword)
|
||||
|
||||
AtomVecEllipsoid *avec_ellipsoid =
|
||||
(AtomVecEllipsoid *) atom->style_match("ellipsoid");
|
||||
AtomVecLine *avec_line = (AtomVecLine *) atom->style_match("line");
|
||||
AtomVecTri *avec_tri = (AtomVecTri *) atom->style_match("tri");
|
||||
AtomVecBody *avec_body = (AtomVecBody *) atom->style_match("body");
|
||||
|
||||
RanPark *random = new RanPark(lmp,1);
|
||||
double **x = atom->x;
|
||||
@ -828,7 +848,7 @@ void Set::setrandom(int keyword)
|
||||
}
|
||||
}
|
||||
|
||||
// set quaternions to random orientations in 3d or 2d
|
||||
// set quaternions to random orientations in 3d and 2d
|
||||
|
||||
} else if (keyword == QUAT_RANDOM) {
|
||||
int nlocal = atom->nlocal;
|
||||
@ -842,6 +862,8 @@ void Set::setrandom(int keyword)
|
||||
quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
|
||||
else if (avec_tri && atom->tri[i] >= 0)
|
||||
quat = avec_tri->bonus[atom->tri[i]].quat;
|
||||
else if (avec_body && atom->body[i] >= 0)
|
||||
quat = avec_body->bonus[atom->body[i]].quat;
|
||||
else
|
||||
error->one(FLERR,"Cannot set quaternion for atom that has none");
|
||||
|
||||
@ -864,6 +886,8 @@ void Set::setrandom(int keyword)
|
||||
if (select[i]) {
|
||||
if (avec_ellipsoid && atom->ellipsoid[i] >= 0)
|
||||
quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
|
||||
else if (avec_body && atom->body[i] >= 0)
|
||||
quat = avec_body->bonus[atom->body[i]].quat;
|
||||
else
|
||||
error->one(FLERR,"Cannot set quaternion for atom that has none");
|
||||
|
||||
@ -876,6 +900,21 @@ void Set::setrandom(int keyword)
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
// set theta to random orientation in 2d
|
||||
|
||||
} else if (keyword == QUAT_RANDOM) {
|
||||
int nlocal = atom->nlocal;
|
||||
double theta;
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
if (select[i]) {
|
||||
if (atom->line[i] < 0)
|
||||
error->one(FLERR,"Cannot set theta for atom that is not a line");
|
||||
random->reset(seed,x[i]);
|
||||
avec_line->bonus[atom->line[i]].theta = MY_2PI*random->uniform();
|
||||
count++;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
delete random;
|
||||
|
||||
@ -4480,13 +4480,14 @@ VarReader::VarReader(LAMMPS *lmp, char *name, char *file, int flag) :
|
||||
strcpy(id_fix,name);
|
||||
strcat(id_fix,"_VARIABLE_STORE");
|
||||
|
||||
char **newarg = new char*[5];
|
||||
char **newarg = new char*[6];
|
||||
newarg[0] = id_fix;
|
||||
newarg[1] = (char *) "all";
|
||||
newarg[2] = (char *) "STORE";
|
||||
newarg[3] = (char *) "0";
|
||||
newarg[4] = (char *) "1";
|
||||
modify->add_fix(5,newarg);
|
||||
newarg[3] = (char *) "peratom";
|
||||
newarg[4] = (char *) "0";
|
||||
newarg[5] = (char *) "1";
|
||||
modify->add_fix(6,newarg);
|
||||
fixstore = (FixStore *) modify->fix[modify->nfix-1];
|
||||
delete [] newarg;
|
||||
|
||||
|
||||
@ -1 +1 @@
|
||||
#define LAMMPS_VERSION "24 Dec 2015"
|
||||
#define LAMMPS_VERSION "11 Jan 2016"
|
||||
|
||||
Reference in New Issue
Block a user