Unverified Commit 5d0800be authored by Axel Kohlmeyer's avatar Axel Kohlmeyer Committed by GitHub
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Merge pull request #2204 from rbberger/doc-changes 

Documentation Changes: split pair_lj.rst
parents 558d2eb8 54337137

doc/src/Commands_pair.rst

+8 −8
Original line number Diff line number Diff line
@@ -136,22 +136,22 @@ OPT. 
   * :doc:`lj/class2/soft <pair_fep_soft>`

   * :doc:`lj/cubic (go) <pair_lj_cubic>`

   * :doc:`lj/cut (gikot) <pair_lj>`

   * :doc:`lj/cut/coul/cut (gko) <pair_lj>`

   * :doc:`lj/cut/coul/cut (gko) <pair_lj_cut_coul>`

   * :doc:`lj/cut/coul/cut/soft (o) <pair_fep_soft>`

   * :doc:`lj/cut/coul/debye (gko) <pair_lj>`

   * :doc:`lj/cut/coul/dsf (gko) <pair_lj>`

   * :doc:`lj/cut/coul/long (gikot) <pair_lj>`

   * :doc:`lj/cut/coul/debye (gko) <pair_lj_cut_coul>`

   * :doc:`lj/cut/coul/dsf (gko) <pair_lj_cut_coul>`

   * :doc:`lj/cut/coul/long (gikot) <pair_lj_cut_coul>`

   * :doc:`lj/cut/coul/long/cs <pair_cs>`

   * :doc:`lj/cut/coul/long/soft (o) <pair_fep_soft>`

   * :doc:`lj/cut/coul/msm (go) <pair_lj>`

   * :doc:`lj/cut/coul/wolf (o) <pair_lj>`

   * :doc:`lj/cut/coul/msm (go) <pair_lj_cut_coul>`

   * :doc:`lj/cut/coul/wolf (o) <pair_lj_cut_coul>`

   * :doc:`lj/cut/dipole/cut (go) <pair_dipole>`

   * :doc:`lj/cut/dipole/long (g) <pair_dipole>`

   * :doc:`lj/cut/dipole/sf (go) <pair_dipole>`

   * :doc:`lj/cut/soft (o) <pair_fep_soft>`

   * :doc:`lj/cut/thole/long (o) <pair_thole>`

   * :doc:`lj/cut/tip4p/cut (o) <pair_lj>`

   * :doc:`lj/cut/tip4p/long (got) <pair_lj>`

   * :doc:`lj/cut/tip4p/cut (o) <pair_lj_cut_tip4p>`

   * :doc:`lj/cut/tip4p/long (got) <pair_lj_cut_tip4p>`

   * :doc:`lj/cut/tip4p/long/soft (o) <pair_fep_soft>`

   * :doc:`lj/expand (gko) <pair_lj_expand>`

   * :doc:`lj/expand/coul/long (g) <pair_lj_expand>`

doc/src/Howto_bioFF.rst

+2 −2
Original line number Diff line number Diff line
@@ -102,8 +102,8 @@ documentation for the formula it computes. 
* :doc:`pair_style <pair_buck>` buck/coul/cut

* :doc:`pair_style <pair_buck>` buck/coul/long

* :doc:`pair_style <pair_lj>` lj/cut

* :doc:`pair_style <pair_lj>` lj/cut/coul/cut

* :doc:`pair_style <pair_lj>` lj/cut/coul/long

* :doc:`pair_style <pair_lj_cut_coul>` lj/cut/coul/cut

* :doc:`pair_style <pair_lj_cut_coul>` lj/cut/coul/long



* :doc:`pair_style <pair_hbond_dreiding>` hbond/dreiding/lj

* :doc:`pair_style <pair_hbond_dreiding>` hbond/dreiding/morse

doc/src/Howto_tip4p.rst

+3 −3
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@@ -11,11 +11,11 @@ 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_cut_tip4p>`



or these two commands for a long-range model:



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

* :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>`

* :doc:`kspace_style pppm/tip4p <kspace_style>`



For both models, the bond lengths and bond angles should be held fixed
@@ -95,7 +95,7 @@ typically best in an efficiency sense to use a LJ cutoff >= Coulomb 
cutoff + 2\*(OM distance), to shrink the size of the neighbor list.

This leads to slightly larger cost for the long-range calculation, so

you can test the trade-off for your model.  The OM distance and the LJ

and Coulombic cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long <pair_lj>` command.

and Coulombic cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>` command.



Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.

doc/src/compute_fep.rst

+57 −57
Original line number Diff line number Diff line
@@ -160,63 +160,63 @@ pair styles and parameters that can be used with this compute. See 
the doc pages for individual pair styles and their energy formulas for

the meaning of these parameters:



+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`born <pair_born>`                                                      | a,b,c                   | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`buck <pair_buck>`                                                      | a,c                     | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`buck/mdf <pair_mdf>`                                                   | a,c                     | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`coul/cut <pair_coul>`                                                  | scale                   | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`coul/cut/soft <pair_fep_soft>`                                         | lambda                  | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`coul/long, coul/msm <pair_coul>`                                       | scale                   | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`coul/long/soft <pair_fep_soft>`                                        | scale, lambda           | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`eam <pair_eam>`                                                        | scale                   | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`gauss <pair_gauss>`                                                    | a                       | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`lennard/mdf <pair_mdf>`                                                | a,b                     | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`lj/class2 <pair_class2>`                                               | epsilon,sigma           | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`lj/class2/coul/cut, lj/class2/coul/long <pair_class2>`                 | epsilon,sigma           | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`lj/cut <pair_lj>`                                                      | epsilon,sigma           | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`lj/cut/soft <pair_fep_soft>`                                           | epsilon,sigma,lambda    | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

| :doc:`lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm <pair_lj>` | epsilon,sigma           | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm <pair_lj_cut_coul>` | epsilon,sigma           | type pairs |

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`lj/cut/coul/cut/soft, lj/cut/coul/long/soft <pair_fep_soft>`           | epsilon,sigma,lambda    | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

| :doc:`lj/cut/tip4p/cut, lj/cut/tip4p/long <pair_lj>`                | epsilon,sigma           | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`lj/cut/tip4p/cut, lj/cut/tip4p/long <pair_lj_cut_tip4p>`               | epsilon,sigma           | type pairs |

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`lj/cut/tip4p/long/soft <pair_fep_soft>`                                | epsilon,sigma,lambda    | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`lj/expand <pair_lj_expand>`                                            | epsilon,sigma,delta     | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`lj/mdf <pair_mdf>`                                                     | epsilon,sigma           | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`lj/sf/dipole/sf <pair_dipole>`                                         | epsilon,sigma,scale     | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`mie/cut <pair_mie>`                                                    | epsilon,sigma,gamR,gamA | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`morse, morse/smooth/linear <pair_morse>`                               | d0,r0,alpha             | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`morse/soft <pair_morse>`                                               | d0,r0,alpha,lambda      | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`nm/cut <pair_nm>`                                                      | e0,r0,nn,mm             | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`nm/cut/coul/cut, nm/cut/coul/long <pair_nm>`                           | e0,r0,nn,mm             | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`ufm <pair_ufm>`                                                        | epsilon,sigma,scale     | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+

| :doc:`soft <pair_soft>`                                                      | a                       | type pairs |

+---------------------------------------------------------------------+-------------------------+------------+

+------------------------------------------------------------------------------+-------------------------+------------+



Note that it is easy to add new potentials and their parameters to

this list.  All it typically takes is adding an extract() method to

doc/src/fix_adapt.rst

+79 −81

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