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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14376 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2015-12-15 23:32:24 +00:00
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12
doc/Section_howto.html
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@ -363,8 +363,8 @@ commands like <a class="reference internal" href="pair_coeff.html"><em>pair_coef
<a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>. See <a class="reference internal" href="Section_tools.html"><em>Section_tools</em></a>
for additional tools that can use CHARMM or AMBER to assign force
field coefficients and convert their output into LAMMPS input.</p>
<p>See <a class="reference internal" href="special_bonds.html#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force
field. See <a class="reference internal" href="special_bonds.html#cornell"><span>(Cornell)</span></a> for a description of the AMBER force
<p>See <a class="reference internal" href="pair_charmm.html#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force
field. See <a class="reference internal" href="dihedral_charmm.html#cornell"><span>(Cornell)</span></a> for a description of the AMBER force
field.</p>
<p>These style choices compute force field formulas that are consistent
with common options in CHARMM or AMBER. See each command&#8217;s
@ -389,7 +389,7 @@ atoms involved in the bond, angle, or torsion terms. DREIDING has an
<a class="reference internal" href="pair_hbond_dreiding.html"><em>explicit hydrogen bond term</em></a> to describe
interactions involving a hydrogen atom on very electronegative atoms
(N, O, F).</p>
<p>See <a class="reference internal" href="special_bonds.html#mayo"><span>(Mayo)</span></a> for a description of the DREIDING force field</p>
<p>See <a class="reference internal" href="pair_hbond_dreiding.html#mayo"><span>(Mayo)</span></a> for a description of the DREIDING force field</p>
<p>These style choices compute force field formulas that are consistent
with the DREIDING force field. See each command&#8217;s
documentation for the formula it computes.</p>
@ -587,7 +587,7 @@ computations between frozen atoms by using this command:</p>
<div class="section" id="tip3p-water-model">
<span id="howto-7"></span><h2>6.7. TIP3P water model<a class="headerlink" href="#tip3p-water-model" title="Permalink to this headline"></a></h2>
<p>The TIP3P water model as implemented in CHARMM
<a class="reference internal" href="special_bonds.html#mackerell"><span>(MacKerell)</span></a> specifies a 3-site rigid water molecule with
<a class="reference internal" href="pair_charmm.html#mackerell"><span>(MacKerell)</span></a> specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
In LAMMPS the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command can be used to hold
the two O-H bonds and the H-O-H angle rigid. A bond style of
@ -766,7 +766,7 @@ the partial charge assignemnts change:</p>
<div class="line">H charge = 0.4238</div>
<div class="line"><br /></div>
</div>
<p>See the <a class="reference internal" href="fix_temp_berendsen.html#berendsen"><span>(Berendsen)</span></a> reference for more details on both
<p>See the <a class="reference internal" href="#berendsen"><span>(Berendsen)</span></a> reference for more details on both
the SPC and SPC/E models.</p>
<p>Wikipedia also has a nice article on <a class="reference external" href="http://en.wikipedia.org/wiki/Water_model">water models</a>.</p>
<hr class="docutils" />
@ -2749,7 +2749,7 @@ fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector
model, representes induced dipoles by a pair of charges (the core atom
and the Drude particle) connected by a harmonic spring. The Drude
model has a number of features aimed at its use in molecular systems
(<a class="reference internal" href="tutorial_drude.html#lamoureux"><span>Lamoureux and Roux</span></a>):</p>
(<a class="reference internal" href="#lamoureux"><span>Lamoureux and Roux</span></a>):</p>
<ul class="simple">
<li>Thermostating of the additional degrees of freedom associated with the
induced dipoles at very low temperature, in terms of the reduced

2
doc/angle_charmm.html
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@ -152,7 +152,7 @@ angle_coeff 1 300.0 107.0 50.0 3.0
<p>with an additional Urey_Bradley term based on the distance <em>r</em> between
the 1st and 3rd atoms in the angle. K, theta0, Kub, and Rub are
coefficients defined for each angle type.</p>
<p>See <a class="reference internal" href="special_bonds.html#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force
<p>See <a class="reference internal" href="pair_charmm.html#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force
field.</p>
<p>The following coefficients must be defined for each angle type via the
<a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command as in the example above, or in

2
doc/angle_class2.html
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@ -151,7 +151,7 @@ angle_coeff * ba 3.6551 24.895 1.0119 1.5228
<p>where Ea is the angle term, Ebb is a bond-bond term, and Eba is a
bond-angle term. Theta0 is the equilibrium angle and r1 and r2 are
the equilibrium bond lengths.</p>
<p>See <a class="reference internal" href="pair_modify.html#sun"><span>(Sun)</span></a> for a description of the COMPASS class2 force field.</p>
<p>See <a class="reference internal" href="pair_class2.html#sun"><span>(Sun)</span></a> for a description of the COMPASS class2 force field.</p>
<p>Coefficients for the Ea, Ebb, and Eba formulas must be defined for
each angle type via the <a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command as in
the example above, or in the data file or restart files read by the

2
doc/angle_cosine_periodic.html
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@ -151,7 +151,7 @@ used for an octahedral complex and <em>n</em> = 3 might be used for a
trigonal center:</p>
<img alt="_images/angle_cosine_periodic.jpg" class="align-center" src="_images/angle_cosine_periodic.jpg" />
<p>where C, B and n are coefficients defined for each angle type.</p>
<p>See <a class="reference internal" href="special_bonds.html#mayo"><span>(Mayo)</span></a> for a description of the DREIDING force field</p>
<p>See <a class="reference internal" href="pair_hbond_dreiding.html#mayo"><span>(Mayo)</span></a> for a description of the DREIDING force field</p>
<p>The following coefficients must be defined for each angle type via the
<a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command as in the example above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>

2
doc/bond_class2.html
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@ -147,7 +147,7 @@ bond_coeff 1 1.0 100.0 80.0 80.0
<p>The <em>class2</em> bond style uses the potential</p>
<img alt="_images/bond_class2.jpg" class="align-center" src="_images/bond_class2.jpg" />
<p>where r0 is the equilibrium bond distance.</p>
<p>See <a class="reference internal" href="pair_modify.html#sun"><span>(Sun)</span></a> for a description of the COMPASS class2 force field.</p>
<p>See <a class="reference internal" href="pair_class2.html#sun"><span>(Sun)</span></a> for a description of the COMPASS class2 force field.</p>
<p>The following coefficients must be defined for each bond type via the
<a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a> command as in the example above, or in
the data file or restart files read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>

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doc/bond_fene.html
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@ -150,7 +150,7 @@ bond_coeff 1 30.0 1.5 1.0 1.0
<p>The <em>fene</em> bond style uses the potential</p>
<img alt="_images/bond_fene.jpg" class="align-center" src="_images/bond_fene.jpg" />
<p>to define a finite extensible nonlinear elastic (FENE) potential
<a class="reference internal" href="special_bonds.html#kremer"><span>(Kremer)</span></a>, used for bead-spring polymer models. The first
<a class="reference internal" href="bond_fene_expand.html#kremer"><span>(Kremer)</span></a>, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive. The
first term extends to R0, the maximum extent of the bond. The 2nd
term is cutoff at 2^(1/6) sigma, the minimum of the LJ potential.</p>

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doc/bond_fene_expand.html
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@ -147,7 +147,7 @@ bond_coeff 1 30.0 1.5 1.0 1.0 0.5
<p>The <em>fene/expand</em> bond style uses the potential</p>
<img alt="_images/bond_fene_expand.jpg" class="align-center" src="_images/bond_fene_expand.jpg" />
<p>to define a finite extensible nonlinear elastic (FENE) potential
<a class="reference internal" href="special_bonds.html#kremer"><span>(Kremer)</span></a>, used for bead-spring polymer models. The first
<a class="reference internal" href="#kremer"><span>(Kremer)</span></a>, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive.</p>
<p>The <em>fene/expand</em> bond style is similar to <em>fene</em> except that an extra
shift factor of delta (positive or negative) is added to <em>r</em> to

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doc/compute_saed.html
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@ -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

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doc/compute_xrd.html
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@ -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,

4
doc/dihedral_charmm.html
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@ -149,9 +149,9 @@ dihedral_coeff 1 120.0 1 60 0.5
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>charmm</em> dihedral style uses the potential</p>
<img alt="_images/dihedral_charmm.jpg" class="align-center" src="_images/dihedral_charmm.jpg" />
<p>See <a class="reference internal" href="special_bonds.html#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force
<p>See <a class="reference internal" href="pair_charmm.html#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force
field. This dihedral style can also be used for the AMBER force field
(see comment on weighting factors below). See <a class="reference internal" href="special_bonds.html#cornell"><span>(Cornell)</span></a>
(see comment on weighting factors below). See <a class="reference internal" href="#cornell"><span>(Cornell)</span></a>
for a description of the AMBER force field.</p>
<p>The following coefficients must be defined for each dihedral type via the
<a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a> command as in the example above, or in

2
doc/dihedral_class2.html
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@ -156,7 +156,7 @@ Eebt is an end-bond-torsion term, Eat is an angle-torsion term, Eaat
is an angle-angle-torsion term, and Ebb13 is a bond-bond-13 term.</p>
<p>Theta1 and theta2 are equilibrium angles and r1 r2 r3 are equilibrium
bond lengths.</p>
<p>See <a class="reference internal" href="pair_modify.html#sun"><span>(Sun)</span></a> for a description of the COMPASS class2 force field.</p>
<p>See <a class="reference internal" href="pair_class2.html#sun"><span>(Sun)</span></a> for a description of the COMPASS class2 force field.</p>
<p>Coefficients for the Ed, Embt, Eebt, Eat, Eaat, and Ebb13 formulas
must be defined for each dihedral type via the
<a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a> command as in the example above,

10
doc/fix_lb_fluid.html
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@ -210,7 +210,7 @@ finite difference LB integrator is used. If <em>LBtype</em> is set equal to
functions,</p>
<img alt="_images/fix_lb_fluid_properties.jpg" class="align-center" src="_images/fix_lb_fluid_properties.jpg" />
<p>Full details of the lattice-Boltzmann algorithm used can be found in
<a class="reference internal" href="fix_lb_viscous.html#mackay"><span>Mackay et al.</span></a>.</p>
<a class="reference internal" href="#mackay"><span>Mackay et al.</span></a>.</p>
<p>The fluid is coupled to the MD particles described by <em>group-ID</em>
through a velocity dependent force. The contribution to the fluid
force on a given lattice mesh site j due to MD particle alpha is
@ -242,7 +242,7 @@ using the <em>setArea</em> keyword.</p>
<p>The user also has the option of specifying their own value for the
force coupling constant, for all the MD particles associated with the
fix, through the use of the <em>setGamma</em> keyword. This may be useful
when modelling porous particles. See <a class="reference internal" href="fix_lb_viscous.html#mackay"><span>Mackay et al.</span></a> for a
when modelling porous particles. See <a class="reference internal" href="#mackay"><span>Mackay et al.</span></a> for a
detailed description of the method by which the user can choose an
appropriate gamma value.</p>
<div class="admonition note">
@ -256,7 +256,7 @@ This fix adds the hydrodynamic force to the total force acting on the
particles, after which any of the built-in LAMMPS integrators can be
used to integrate the particle motion. However, if the user specifies
their own value for the force coupling constant, as mentioned in
<a class="reference internal" href="fix_lb_viscous.html#mackay"><span>Mackay et al.</span></a>, the built-in LAMMPS integrators may prove to
<a class="reference internal" href="#mackay"><span>Mackay et al.</span></a>, the built-in LAMMPS integrators may prove to
be unstable. Therefore, we have included our own integrators <a class="reference internal" href="fix_lb_rigid_pc_sphere.html"><em>fix lb/rigid/pc/sphere</em></a>, and <a class="reference internal" href="fix_lb_pc.html"><em>fix lb/pc</em></a>, to solve for the particle motion in these
cases. These integrators should not be used with the
<a class="reference internal" href="fix_lb_viscous.html"><em>lb/viscous</em></a> fix, as they add hydrodynamic forces
@ -341,7 +341,7 @@ N timesteps.</p>
<p>If the keyword <em>trilinear</em> is used, the trilinear stencil is used to
interpolate the particle nodes onto the fluid mesh. By default, the
immersed boundary method, Peskin stencil is used. Both of these
interpolation methods are described in <a class="reference internal" href="fix_lb_viscous.html#mackay"><span>Mackay et al.</span></a>.</p>
interpolation methods are described in <a class="reference internal" href="#mackay"><span>Mackay et al.</span></a>.</p>
<p>If the keyword <em>D3Q19</em> is used, the 19 velocity (D3Q19) lattice is
used by the lattice-Boltzmann algorithm. By default, the 15 velocity
(D3Q15) lattice is used.</p>
@ -371,7 +371,7 @@ the fluid densities and velocities at each lattice site are printed to the
screen every N timesteps.</p>
<hr class="docutils" />
<p>For further details, as well as descriptions and results of several
test runs, see <a class="reference internal" href="fix_lb_viscous.html#mackay"><span>Mackay et al.</span></a>. Please include a citation to
test runs, see <a class="reference internal" href="#mackay"><span>Mackay et al.</span></a>. Please include a citation to
this paper if the lb_fluid fix is used in work contributing to
published research.</p>
</div>

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doc/fix_nh.html
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@ -233,11 +233,11 @@ particles will match the target values specified by Tstart/Tstop and
Pstart/Pstop.</p>
<p>The equations of motion used are those of Shinoda et al in
<a class="reference internal" href="pair_sdk.html#shinoda"><span>(Shinoda)</span></a>, which combine the hydrostatic equations of
Martyna, Tobias and Klein in <a class="reference internal" href="fix_rigid.html#martyna"><span>(Martyna)</span></a> with the strain
Martyna, Tobias and Klein in <a class="reference internal" href="#martyna"><span>(Martyna)</span></a> with the strain
energy proposed by Parrinello and Rahman in
<a class="reference internal" href="fix_nh_eff.html#parrinello"><span>(Parrinello)</span></a>. The time integration schemes closely
<a class="reference internal" href="#parrinello"><span>(Parrinello)</span></a>. The time integration schemes closely
follow the time-reversible measure-preserving Verlet and rRESPA
integrators derived by Tuckerman et al in <a class="reference internal" href="run_style.html#tuckerman"><span>(Tuckerman)</span></a>.</p>
integrators derived by Tuckerman et al in <a class="reference internal" href="fix_pimd.html#tuckerman"><span>(Tuckerman)</span></a>.</p>
<hr class="docutils" />
<p>The thermostat parameters for fix styles <em>nvt</em> and <em>npt</em> is specified
using the <em>temp</em> keyword. Other thermostat-related keywords are
@ -394,7 +394,7 @@ freedom. A value of 0 corresponds to no thermostatting of the
barostat variables.</p>
<p>The <em>mtk</em> keyword controls whether or not the correction terms due to
Martyna, Tuckerman, and Klein are included in the equations of motion
<a class="reference internal" href="fix_rigid.html#martyna"><span>(Martyna)</span></a>. Specifying <em>no</em> reproduces the original
<a class="reference internal" href="#martyna"><span>(Martyna)</span></a>. Specifying <em>no</em> reproduces the original
Hoover barostat, whose volume probability distribution function
differs from the true NPT and NPH ensembles by a factor of 1/V. Hence
using <em>yes</em> is more correct, but in many cases the difference is
@ -403,7 +403,7 @@ negligible.</p>
scheme at little extra cost. The initial and final updates of the
thermostat variables are broken up into <em>tloop</em> substeps, each of
length <em>dt</em>/<em>tloop</em>. This corresponds to using a first-order
Suzuki-Yoshida scheme <a class="reference internal" href="run_style.html#tuckerman"><span>(Tuckerman)</span></a>. The keyword <em>ploop</em>
Suzuki-Yoshida scheme <a class="reference internal" href="fix_pimd.html#tuckerman"><span>(Tuckerman)</span></a>. The keyword <em>ploop</em>
does the same thing for the barostat thermostat.</p>
<p>The keyword <em>nreset</em> controls how often the reference dimensions used
to define the strain energy are reset. If this keyword is not used,

2
doc/fix_pimd.html
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@ -171,7 +171,7 @@ index (the second term in the effective potential above). The
quasi-beads also interact with the two neighboring quasi-beads through
the spring potential in imaginary-time space (first term in effective
potential). To sample the canonical ensemble, a Nose-Hoover massive
chain thermostat is applied <a class="reference internal" href="run_style.html#tuckerman"><span>(Tuckerman)</span></a>. With the
chain thermostat is applied <a class="reference internal" href="#tuckerman"><span>(Tuckerman)</span></a>. With the
massive chain algorithm, a chain of NH thermostats is coupled to each
degree of freedom for each quasi-bead. The keyword <em>temp</em> sets the
target temperature for the system and the keyword <em>nhc</em> sets the

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@ -165,7 +165,7 @@ theta angles, since it is always the center atom.</p>
<p>Since atom J is the atom of symmetry, normally the bonds J-I, J-K, J-L
would exist for an improper to be defined between the 4 atoms, but
this is not required.</p>
<p>See <a class="reference internal" href="pair_modify.html#sun"><span>(Sun)</span></a> for a description of the COMPASS class2 force field.</p>
<p>See <a class="reference internal" href="pair_class2.html#sun"><span>(Sun)</span></a> for a description of the COMPASS class2 force field.</p>
<p>Coefficients for the Ei and Eaa formulas must be defined for each
improper type via the <a class="reference internal" href="improper_coeff.html"><em>improper_coeff</em></a> command as
in the example above, or in the data file or restart files read by the

2
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@ -154,7 +154,7 @@ axis and the IJK plane:</p>
<p>If omega0 = 0 the potential term has a minimum for the planar
structure. Otherwise it has two minima at +/- omega0, with a barrier
in between.</p>
<p>See <a class="reference internal" href="special_bonds.html#mayo"><span>(Mayo)</span></a> for a description of the DREIDING force field.</p>
<p>See <a class="reference internal" href="pair_hbond_dreiding.html#mayo"><span>(Mayo)</span></a> for a description of the DREIDING force field.</p>
<p>The following coefficients must be defined for each improper type via
the <a class="reference internal" href="improper_coeff.html"><em>improper_coeff</em></a> command as in the example
above, or in the data file or restart files read by the

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@ -222,7 +222,7 @@ pair_coeff 1 1 100.0 2.0 150.0 3.5
additional switching function S(r) that ramps the energy and force
smoothly to zero between an inner and outer cutoff. It is a widely
used potential in the <a class="reference external" href="http://www.scripps.edu/brooks">CHARMM</a> MD code.
See <a class="reference internal" href="special_bonds.html#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force
See <a class="reference internal" href="#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force
field.</p>
<img alt="_images/pair_charmm.jpg" class="align-center" src="_images/pair_charmm.jpg" />
<p>Both the LJ and Coulombic terms require an inner and outer cutoff.

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@ -213,7 +213,7 @@ pair_coeff 1 1 100.0 3.5 9.0
<p>Rc is the cutoff.</p>
<p>The <em>lj/class2/coul/cut</em> and <em>lj/class2/coul/long</em> styles add a
Coulombic term as described for the <a class="reference internal" href="pair_lj.html"><em>lj/cut</em></a> pair styles.</p>
<p>See <a class="reference internal" href="pair_modify.html#sun"><span>(Sun)</span></a> for a description of the COMPASS class2 force field.</p>
<p>See <a class="reference internal" href="#sun"><span>(Sun)</span></a> for a description of the COMPASS class2 force field.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the

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@ -181,7 +181,7 @@ the donor atom, e.g. in a bond list read in from a data file via the
hydrogen atoms for each donor/acceptor type pair are specified by the
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command (see below).</p>
<p>Style <em>hbond/dreiding/lj</em> is the original DREIDING potential of
<a class="reference internal" href="special_bonds.html#mayo"><span>(Mayo)</span></a>. It uses a LJ 12/10 functional for the Donor-Acceptor
<a class="reference internal" href="#mayo"><span>(Mayo)</span></a>. It uses a LJ 12/10 functional for the Donor-Acceptor
interactions. To match the results in the original paper, use n = 4.</p>
<p>Style <em>hbond/dreiding/morse</em> is an improved version using a Morse
potential for the Donor-Acceptor interactions. <a class="reference internal" href="#liu"><span>(Liu)</span></a> showed

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