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

doc/Section_howto.html

@@ -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
+<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="special_bonds.html#cornell"><span>(Cornell)</span></a> for a description of the AMBER 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

doc/angle_charmm.html

@@ -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

doc/angle_class2.html

@@ -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

doc/angle_cosine_periodic.html

@@ -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>

doc/bond_class2.html

@@ -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>

doc/bond_fene.html

@@ -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>

doc/bond_fene_expand.html

@@ -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

doc/compute_saed.html

@@ -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

doc/compute_xrd.html

@@ -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,

doc/dihedral_charmm.html

@@ -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

doc/dihedral_class2.html

@@ -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,

doc/fix_lb_fluid.html

@@ -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>

doc/fix_nh.html

@@ -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,

doc/fix_pimd.html

@@ -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

doc/improper_class2.html

@@ -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

doc/improper_umbrella.html

@@ -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

doc/pair_charmm.html

@@ -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.

doc/pair_class2.html

@@ -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

doc/pair_hbond_dreiding.html

@@ -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