diff --git a/doc/src/Howto_spc.rst b/doc/src/Howto_spc.rst index 5431376924..f7c2cf6142 100644 --- a/doc/src/Howto_spc.rst +++ b/doc/src/Howto_spc.rst @@ -15,18 +15,18 @@ atoms and the water molecule to run a rigid SPC model. | H mass = 1.008 | O charge = -0.820 | H charge = 0.410 -| LJ epsilon of OO = 0.1553 -| LJ sigma of OO = 3.166 -| LJ epsilon, sigma of OH, HH = 0.0 -| r0 of OH bond = 1.0 -| theta of HOH angle = 109.47 +| LJ :math:`\epsilon` of OO = 0.1553 +| LJ :math:`\sigma` of OO = 3.166 +| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0 +| :math:`r_0` of OH bond = 1.0 +| :math:`\theta` of HOH angle = 109.47\ :math:`^{\circ}` | Note that as originally proposed, the SPC model was run with a 9 -Angstrom cutoff for both LJ and Coulombic terms. It can also be used -with long-range Coulombics (Ewald or PPPM in LAMMPS), without changing -any of the parameters above, though it becomes a different model in -that mode of usage. +Angstrom cutoff for both LJ and Coulomb terms. It can also be used +with long-range electrostatic solvers (e.g. Ewald or PPPM in LAMMPS) +without changing any of the parameters above, although it becomes +a different model in that mode of usage. The SPC/E (extended) water model is the same, except the partial charge assignments change: diff --git a/doc/src/Howto_tip3p.rst b/doc/src/Howto_tip3p.rst index 1178aa8b67..7f7ddbdf2a 100644 --- a/doc/src/Howto_tip3p.rst +++ b/doc/src/Howto_tip3p.rst @@ -20,19 +20,19 @@ set to 0.0, it corresponds to the original 1983 TIP3P model | H mass = 1.008 | O charge = -0.834 | H charge = 0.417 -| LJ epsilon of OO = 0.1521 -| LJ sigma of OO = 3.1507 -| LJ epsilon of HH = 0.0460 -| LJ sigma of HH = 0.4000 -| LJ epsilon of OH = 0.0836 -| LJ sigma of OH = 1.7753 +| LJ :math:`\epsilon` of OO = 0.1521 +| LJ :math:`\sigma` of OO = 3.1507 +| LJ :math:`\epsilon` of HH = 0.0460 +| LJ :math:`\sigma` of HH = 0.4000 +| LJ :math:`\epsilon` of OH = 0.0836 +| LJ :math:`\sigma` of OH = 1.7753 | K of OH bond = 450 -| r0 of OH bond = 0.9572 +| :math:`r_0` of OH bond = 0.9572 | K of HOH angle = 55 -| theta of HOH angle = 104.52 +| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}` | -These are the parameters to use for TIP3P with a long-range Coulombic +These are the parameters to use for TIP3P with a long-range Coulomb solver (e.g. Ewald or PPPM in LAMMPS), see :ref:`(Price) ` for details: @@ -40,13 +40,13 @@ details: | H mass = 1.008 | O charge = -0.830 | H charge = 0.415 -| LJ epsilon of OO = 0.102 -| LJ sigma of OO = 3.188 -| LJ epsilon, sigma of OH, HH = 0.0 +| LJ :math:`\epsilon` of OO = 0.102 +| LJ :math:`\sigma` of OO = 3.188 +| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0 | K of OH bond = 450 -| r0 of OH bond = 0.9572 +| :math:`r_0` of OH bond = 0.9572 | K of HOH angle = 55 -| theta of HOH angle = 104.52 +| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}` | Wikipedia also has a nice article on `water models `_. diff --git a/doc/src/Howto_tip4p.rst b/doc/src/Howto_tip4p.rst index f96fd15a17..e3129ae06a 100644 --- a/doc/src/Howto_tip4p.rst +++ b/doc/src/Howto_tip4p.rst @@ -11,7 +11,7 @@ angle style of *harmonic* or *charmm* should also be used. A TIP4P model is run with LAMMPS using either this command for a cutoff model: -:doc:`pair_style lj/cut/tip4p/cut ` +* :doc:`pair_style lj/cut/tip4p/cut ` or these two commands for a long-range model: @@ -31,13 +31,13 @@ coefficients. | H mass = 1.008 | O charge = -1.040 | H charge = 0.520 -| r0 of OH bond = 0.9572 -| theta of HOH angle = 104.52 +| :math:`r_0` of OH bond = 0.9572 +| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}` | OM distance = 0.15 -| LJ epsilon of O-O = 0.1550 -| LJ sigma of O-O = 3.1536 -| LJ epsilon, sigma of OH, HH = 0.0 -| Coulombic cutoff = 8.5 +| LJ :math:`\epsilon` of O-O = 0.1550 +| LJ :math:`\sigma` of O-O = 3.1536 +| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0 +| Coulomb cutoff = 8.5 | For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005); @@ -47,13 +47,13 @@ http://dx.doi.org/10.1063/1.1931662) these values can be used: | H mass = 1.008 | O charge = -1.1794 | H charge = 0.5897 -| r0 of OH bond = 0.9572 -| theta of HOH angle = 104.52 +| :math:`r_0` of OH bond = 0.9572 +| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}` | OM distance = 0.1577 -| LJ epsilon of O-O = 0.21084 -| LJ sigma of O-O = 3.1668 -| LJ epsilon, sigma of OH, HH = 0.0 -| Coulombic cutoff = 8.5 +| LJ :math:`\epsilon` of O-O = 0.21084 +| LJ :math:`\sigma` of O-O = 3.1668 +| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0 +| Coulomb cutoff = 8.5 | For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005); @@ -63,13 +63,13 @@ http://dx.doi.org/10.1063/1.2121687), these values can be used: | H mass = 1.008 | O charge = -1.1128 | H charge = 0.5564 -| r0 of OH bond = 0.9572 -| theta of HOH angle = 104.52 +| :math:`r_0` of OH bond = 0.9572 +| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}` | OM distance = 0.1546 -| LJ epsilon of O-O = 0.1852 -| LJ sigma of O-O = 3.1589 -| LJ epsilon, sigma of OH, HH = 0.0 -| Coulombic cutoff = 8.5 +| LJ :math:`\epsilon` of O-O = 0.1852 +| LJ :math:`\sigma` of O-O = 3.1589 +| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0 +| Coulomb cutoff = 8.5 | These are the parameters to use for TIP4P with a long-range Coulombic @@ -79,12 +79,12 @@ solver (e.g. Ewald or PPPM in LAMMPS): | H mass = 1.008 | O charge = -1.0484 | H charge = 0.5242 -| r0 of OH bond = 0.9572 -| theta of HOH angle = 104.52 +| :math:`r_0` of OH bond = 0.9572 +| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}` | OM distance = 0.1250 -| LJ epsilon of O-O = 0.16275 -| LJ sigma of O-O = 3.16435 -| LJ epsilon, sigma of OH, HH = 0.0 +| LJ :math:`\epsilon` of O-O = 0.16275 +| LJ :math:`\sigma` of O-O = 3.16435 +| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0 | Note that the when using the TIP4P pair style, the neighbor list