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typeset symbols in water model howtos

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Axel Kohlmeyer 2020-03-10 16:20:52 -04:00
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18
doc/src/Howto_spc.rst
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@ -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:

28
doc/src/Howto_tip3p.rst
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@ -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) <Price1>` 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 <http://en.wikipedia.org/wiki/Water_model>`_.

48
doc/src/Howto_tip4p.rst
View File

@ -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 <pair_lj>`
* :doc:`pair_style lj/cut/tip4p/cut <pair_lj>`
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