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Split pair_lj.rst into three files

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This commit is contained in:
Richard Berger
2020-07-01 14:27:06 -04:00
parent f46ba32627
commit 0a18c52414
16 changed files with 787 additions and 551 deletions
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16
doc/src/Commands_pair.rst
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@ -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>`

4
doc/src/Howto_bioFF.rst
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@ -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

6
doc/src/Howto_tip4p.rst
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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>`_.

114
doc/src/compute_fep.rst
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@ -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/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/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 |
+---------------------------------------------------------------------+-------------------------+------------+
+------------------------------------------------------------------------------+-------------------------+------------+
| :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_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_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

160
doc/src/fix_adapt.rst
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@ -123,87 +123,85 @@ current list of pair styles and parameters that can be varied by this
fix. 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:`born/coul/long, born/coul/msm <pair_born>` | coulombic_cutoff | type global |
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`buck <pair_buck>` | a,c | type pairs |
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`buck/coul/long, buck/coul/msm <pair_buck>` | coulombic_cutoff | type global |
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
| :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/debye <pair_coul>` | scale | type pairs |
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`coul/dsf <pair_coul>` | coulombic_cutoff | type global |
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`coul/long, coul/msm <pair_coul>` | coulombic_cutoff, scale | type pairs |
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`coul/long/soft <pair_fep_soft>` | scale, lambda, coulombic_cutoff | type pairs |
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`eam, eam/alloy, eam/fs <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,coulombic_cutoff | type pairs |
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`lj/cut <pair_lj>` | epsilon,sigma | type pairs |
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm <pair_lj>` | epsilon,sigma,coulombic_cutoff | type pairs |
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`lj/cut/coul/cut/soft, lj/cut/coul/long/soft <pair_fep_soft>` | epsilon,sigma,lambda,coulombic_cutoff | type pairs |
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`lj/cut/coul/dsf <pair_lj>` | cutoff | type global |
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`lj/cut/tip4p/cut <pair_lj>` | epsilon,sigma,coulombic_cutoff | type pairs |
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`lj/cut/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:`lubricate <pair_lubricate>` | mu | global |
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`mie/cut <pair_mie>` | epsilon,sigma,gamma_repulsive,gamma_attractive | 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,m,n | type pairs |
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`nm/cut/coul/cut, nm/cut/coul/long <pair_nm>` | E0,R0,m,n,coulombic_cutoff | type pairs |
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`reax/c <pair_reaxc>` | chi, eta, gamma | type global |
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`spin/dmi <pair_spin_dmi>` | coulombic_cutoff | type global |
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`spin/exchange <pair_spin_exchange>` | coulombic_cutoff | type global |
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`spin/magelec <pair_spin_magelec>` | coulombic_cutoff | type global |
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`spin/neel <pair_spin_neel>` | coulombic_cutoff | type global |
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`table <pair_table>` | table_cutoff | type pairs |
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`ufm <pair_ufm>` | epsilon,sigma | type pairs |
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`soft <pair_soft>` | a | type pairs |
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
| | | |
+---------------------------------------------------------------------+--------------------------------------------------+-------------+
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`born <pair_born>` | a,b,c | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`born/coul/long, born/coul/msm <pair_born>` | coulombic_cutoff | type global |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`buck <pair_buck>` | a,c | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`buck/coul/long, buck/coul/msm <pair_buck>` | coulombic_cutoff | type global |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :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/debye <pair_coul>` | scale | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`coul/dsf <pair_coul>` | coulombic_cutoff | type global |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`coul/long, coul/msm <pair_coul>` | coulombic_cutoff, scale | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`coul/long/soft <pair_fep_soft>` | scale, lambda, coulombic_cutoff | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`eam, eam/alloy, eam/fs <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,coulombic_cutoff | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`lj/cut <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,coulombic_cutoff | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`lj/cut/coul/cut/soft, lj/cut/coul/long/soft <pair_fep_soft>` | epsilon,sigma,lambda,coulombic_cutoff | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`lj/cut/coul/dsf <pair_lj_cut_coul>` | cutoff | type global |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`lj/cut/tip4p/cut <pair_lj_cut_tip4p>` | epsilon,sigma,coulombic_cutoff | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`lj/cut/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:`lubricate <pair_lubricate>` | mu | global |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`mie/cut <pair_mie>` | epsilon,sigma,gamma_repulsive,gamma_attractive | 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,m,n | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`nm/cut/coul/cut, nm/cut/coul/long <pair_nm>` | E0,R0,m,n,coulombic_cutoff | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`reax/c <pair_reaxc>` | chi, eta, gamma | type global |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`spin/dmi <pair_spin_dmi>` | coulombic_cutoff | type global |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`spin/exchange <pair_spin_exchange>` | coulombic_cutoff | type global |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`spin/magelec <pair_spin_magelec>` | coulombic_cutoff | type global |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`spin/neel <pair_spin_neel>` | coulombic_cutoff | type global |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`table <pair_table>` | table_cutoff | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`ufm <pair_ufm>` | epsilon,sigma | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`soft <pair_soft>` | a | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
.. note::

114
doc/src/fix_adapt_fep.rst
View File

@ -117,63 +117,63 @@ change. This is the current list of pair styles and parameters that
can be varied by this fix. 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/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/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 |
+---------------------------------------------------------------------+-------------------------+------------+
+------------------------------------------------------------------------------+-------------------------+------------+
| :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_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_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::

2
doc/src/fix_tune_kspace.rst
View File

@ -93,7 +93,7 @@ Related commands
""""""""""""""""
:doc:`kspace_style <kspace_style>`, :doc:`boundary <boundary>`
:doc:`kspace_modify <kspace_modify>`, :doc:`pair_style lj/cut/coul/long <pair_lj>`, :doc:`pair_style lj/charmm/coul/long <pair_charmm>`, :doc:`pair_style lj/long <pair_lj_long>`, :doc:`pair_style lj/long/coul/long <pair_lj_long>`,
:doc:`kspace_modify <kspace_modify>`, :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`, :doc:`pair_style lj/charmm/coul/long <pair_charmm>`, :doc:`pair_style lj/long <pair_lj_long>`, :doc:`pair_style lj/long/coul/long <pair_lj_long>`,
:doc:`pair_style buck/coul/long <pair_buck>`
Default

2
doc/src/kspace_style.rst
View File

@ -437,7 +437,7 @@ virial, so this contribution is not included.
Related commands
""""""""""""""""
:doc:`kspace_modify <kspace_modify>`, :doc:`pair_style lj/cut/coul/long <pair_lj>`, :doc:`pair_style lj/charmm/coul/long <pair_charmm>`, :doc:`pair_style lj/long/coul/long <pair_lj_long>`, :doc:`pair_style buck/coul/long <pair_buck>`
:doc:`kspace_modify <kspace_modify>`, :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`, :doc:`pair_style lj/charmm/coul/long <pair_charmm>`, :doc:`pair_style lj/long/coul/long <pair_lj_long>`, :doc:`pair_style buck/coul/long <pair_buck>`
Default
"""""""

2
doc/src/minimize.rst
View File

@ -231,7 +231,7 @@ so that its energy is 0.0 at the cutoff via the
:doc:`pair_modify <pair_modify>` command. See the doc pages for
individual :doc:`pair styles <pair_style>` for details. Note that
Coulombic potentials always have a cutoff, unless versions with a
long-range component are used (e.g. :doc:`pair_style lj/cut/coul/long <pair_lj>`). The CHARMM potentials go to 0.0 at
long-range component are used (e.g. :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`). The CHARMM potentials go to 0.0 at
the cutoff (e.g. :doc:`pair_style lj/charmm/coul/charmm <pair_charmm>`),
as do the GROMACS potentials (e.g. :doc:`pair_style lj/gromacs <pair_gromacs>`).

2
doc/src/pair_cs.rst
View File

@ -120,7 +120,7 @@ the "/cs" in the name:
* :doc:`pair_style buck/coul/long <pair_buck>`
* :doc:`pair_style coul/long <pair_coul>`
* :doc:`pair_style coul/wolf <pair_coul>`
* :doc:`pair_style lj/cut/coul/long <pair_lj>`
* :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`
* :doc:`pair_style lj/class2/coul/long <pair_class2>`
except that they correctly treat the special case where the distance

362
doc/src/pair_lj.rst
View File

@ -1,109 +1,15 @@
.. index:: pair_style lj/cut
.. index:: pair_style lj/cut/gpu
.. index:: pair_style lj/cut/intel
.. index:: pair_style lj/cut/kk
.. index:: pair_style lj/cut/opt
.. index:: pair_style lj/cut/omp
pair_style lj/cut command
=========================
pair_style lj/cut/gpu command
=============================
pair_style lj/cut/intel command
===============================
pair_style lj/cut/kk command
============================
pair_style lj/cut/opt command
=============================
pair_style lj/cut/omp command
=============================
pair_style lj/cut/coul/cut command
==================================
pair_style lj/cut/coul/cut/gpu command
======================================
pair_style lj/cut/coul/cut/kk command
=====================================
pair_style lj/cut/coul/cut/omp command
======================================
pair_style lj/cut/coul/debye command
====================================
pair_style lj/cut/coul/debye/gpu command
========================================
pair_style lj/cut/coul/debye/kk command
=======================================
pair_style lj/cut/coul/debye/omp command
========================================
pair_style lj/cut/coul/dsf command
==================================
pair_style lj/cut/coul/dsf/gpu command
======================================
pair_style lj/cut/coul/dsf/kk command
=====================================
pair_style lj/cut/coul/dsf/omp command
======================================
pair_style lj/cut/coul/long command
===================================
pair_style lj/cut/coul/long/gpu command
=======================================
pair_style lj/cut/coul/long/kk command
======================================
pair_style lj/cut/coul/long/intel command
=========================================
pair_style lj/cut/coul/long/opt command
=======================================
pair_style lj/cut/coul/long/omp command
=======================================
pair_style lj/cut/coul/msm command
==================================
pair_style lj/cut/coul/msm/gpu command
======================================
pair_style lj/cut/coul/msm/omp command
======================================
pair_style lj/cut/coul/wolf command
===================================
pair_style lj/cut/coul/wolf/omp command
=======================================
pair_style lj/cut/tip4p/cut command
===================================
pair_style lj/cut/tip4p/cut/omp command
=======================================
pair_style lj/cut/tip4p/long command
====================================
pair_style lj/cut/tip4p/long/gpu command
========================================
pair_style lj/cut/tip4p/long/omp command
========================================
pair_style lj/cut/tip4p/long/opt command
========================================
Accelerator Variants: *lj/cut/gpu*, *lj/cut/intel*, *lj/cut/kk*, *lj/cut/opt*, *lj/cut/omp*
Syntax
""""""
@ -112,46 +18,13 @@ Syntax
pair_style style args
* style = *lj/cut* or *lj/cut/coul/cut* or *lj/cut/coul/debye* or *lj/cut/coul/dsf* or *lj/cut/coul/long* *lj/cut/coul/msm* or *lj/cut/tip4p/long*
* style = *lj/cut*
* args = list of arguments for a particular style
.. parsed-literal::
*lj/cut* args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
*lj/cut/coul/cut* args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
*lj/cut/coul/debye* args = kappa cutoff (cutoff2)
kappa = inverse of the Debye length (inverse distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
*lj/cut/coul/dsf* args = alpha cutoff (cutoff2)
alpha = damping parameter (inverse distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (distance units)
*lj/cut/coul/long* args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
*lj/cut/coul/msm* args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
*lj/cut/coul/wolf* args = alpha cutoff (cutoff2)
alpha = damping parameter (inverse distance units)
cutoff = global cutoff for LJ (and Coulombic if only 2 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
*lj/cut/tip4p/cut* args = otype htype btype atype qdist cutoff (cutoff2)
otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters
qdist = distance from O atom to massless charge (distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
*lj/cut/tip4p/long* args = otype htype btype atype qdist cutoff (cutoff2)
otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters
qdist = distance from O atom to massless charge (distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
Examples
""""""""
@ -162,46 +35,6 @@ Examples
pair_coeff * * 1 1
pair_coeff 1 1 1 1.1 2.8
pair_style lj/cut/coul/cut 10.0
pair_style lj/cut/coul/cut 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
pair_coeff 1 1 100.0 3.5 9.0 9.0
pair_style lj/cut/coul/debye 1.5 3.0
pair_style lj/cut/coul/debye 1.5 2.5 5.0
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.0 1.5 2.5
pair_coeff 1 1 1.0 1.5 2.5 5.0
pair_style lj/cut/coul/dsf 0.05 2.5 10.0
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.0 1.0 2.5
pair_style lj/cut/coul/long 10.0
pair_style lj/cut/coul/long 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
pair_style lj/cut/coul/msm 10.0
pair_style lj/cut/coul/msm 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0
pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 10.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
pair_style lj/cut/coul/wolf 0.2 5. 10.0
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.0 1.0 2.5
pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0
pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
Description
"""""""""""
@ -214,141 +47,29 @@ given by
\left(\frac{\sigma}{r}\right)^6 \right]
\qquad r < r_c
Rc is the cutoff.
:math:`r_c` is the cutoff.
Style *lj/cut/coul/cut* adds a Coulombic pairwise interaction given by
See the :doc:`lj/cut/coul <pair_lj_cut_coul>` styles to add a Coulombic
pairwise interaction and the :doc:`lj/cut/tip4p <pair_lj_cut_tip4p>` styles to
add the TIP4P water model.
.. math::
Coefficients
""""""""""""
E = \frac{C q_i q_j}{\epsilon r} \qquad r < r_c
where C is an energy-conversion constant, :math:`q_i` and :math:`q_j`
are the charges on the 2 atoms, and :math:`\epsilon` is the dielectric
constant which can be set by the :doc:`dielectric <dielectric>` command.
If one cutoff is specified in the pair_style command, it is used for
both the LJ and Coulombic terms. If two cutoffs are specified, they are
used as cutoffs for the LJ and Coulombic terms respectively.
Style *lj/cut/coul/debye* adds an additional exp() damping factor
to the Coulombic term, given by
.. math::
E = \frac{C q_i q_j}{\epsilon r} \exp(- \kappa r) \qquad r < r_c
where :math:`\kappa` is the inverse of the Debye length. This potential
is another way to mimic the screening effect of a polar solvent.
Style *lj/cut/coul/dsf* computes the Coulombic term via the damped
shifted force model described in :ref:`Fennell <Fennell2>`, given by:
.. math::
E =
q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} +
\left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} + \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2 r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c
where :math:`\alpha` is the damping parameter and erfc() is the complementary
error-function. This potential is essentially a short-range,
spherically-truncated, charge-neutralized, shifted, pairwise *1/r*
summation. The potential is based on Wolf summation, proposed as an
alternative to Ewald summation for condensed phase systems where
charge screening causes electrostatic interactions to become
effectively short-ranged. In order for the electrostatic sum to be
absolutely convergent, charge neutralization within the cutoff radius
is enforced by shifting the potential through placement of image
charges on the cutoff sphere. Convergence can often be improved by
setting :math:`\alpha` to a small non-zero value.
Styles *lj/cut/coul/long* and *lj/cut/coul/msm* compute the same
Coulombic interactions as style *lj/cut/coul/cut* except that an
additional damping factor is applied to the Coulombic term so it can
be used in conjunction with the :doc:`kspace_style <kspace_style>`
command and its *ewald* or *pppm* option. The Coulombic cutoff
specified for this style means that pairwise interactions within this
distance are computed directly; interactions outside that distance are
computed in reciprocal space.
Style *coul/wolf* adds a Coulombic pairwise interaction via the Wolf
summation method, described in :ref:`Wolf <Wolf1>`, given by:
.. math::
E_i = \frac{1}{2} \sum_{j \neq i}
\frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} +
\frac{1}{2} \sum_{j \neq i}
\frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
where :math:`\alpha` is the damping parameter, and erfc() is the
complementary error-function terms. This potential is essentially a
short-range, spherically-truncated, charge-neutralized, shifted,
pairwise *1/r* summation. With a manipulation of adding and subtracting
a self term (for i = j) to the first and second term on the
right-hand-side, respectively, and a small enough :math:`\alpha` damping
parameter, the second term shrinks and the potential becomes a
rapidly-converging real-space summation. With a long enough cutoff and
small enough :math:`\alpha` parameter, the energy and forces calculated by the
Wolf summation method approach those of the Ewald sum. So it is a means
of getting effective long-range interactions with a short-range
potential.
Styles *lj/cut/tip4p/cut* and *lj/cut/tip4p/long* implement the TIP4P
water model of :ref:`(Jorgensen) <Jorgensen2>`, which introduces a massless
site located a short distance away from the oxygen atom along the
bisector of the HOH angle. The atomic types of the oxygen and
hydrogen atoms, the bond and angle types for OH and HOH interactions,
and the distance to the massless charge site are specified as
pair_style arguments. Style *lj/cut/tip4p/cut* uses a cutoff for
Coulomb interactions; style *lj/cut/tip4p/long* is for use with a
long-range Coulombic solver (Ewald or PPPM).
.. note::
For each TIP4P water molecule in your system, the atom IDs for
the O and 2 H atoms must be consecutive, with the O atom first. This
is to enable LAMMPS to "find" the 2 H atoms associated with each O
atom. For example, if the atom ID of an O atom in a TIP4P water
molecule is 500, then its 2 H atoms must have IDs 501 and 502.
See the :doc:`Howto tip4p <Howto_tip4p>` doc page for more information
on how to use the TIP4P pair styles and lists of parameters to set.
Note that the neighbor list cutoff for Coulomb interactions is
effectively extended by a distance 2\*qdist when using the TIP4P pair
style, to account for the offset distance of the fictitious charges on
O atoms in water molecules. Thus it is typically best in an
efficiency sense to use a LJ cutoff >= Coulombic cutoff + 2\*qdist, 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.
For all of the *lj/cut* pair styles, the following coefficients must
be defined for each pair of atoms types via the
:doc:`pair_coeff <pair_coeff>` command as in the examples above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands, or by mixing as
described below:
The following coefficients must be defined for each pair of atoms types via the
:doc:`pair_coeff <pair_coeff>` command as in the examples above, or in the data
file or restart files read by the :doc:`read_data <read_data>` or
:doc:`read_restart <read_restart>` commands, or by mixing as described below:
* :math:`\epsilon` (energy units)
* :math:`\sigma` (distance units)
* cutoff1 (distance units)
* cutoff2 (distance units)
* LJ cutoff (distance units)
Note that :math:`\sigma` is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum at :math:`2^{\frac{1}{6}} \sigma`.
The latter 2 coefficients are optional. If not specified, the global
LJ and Coulombic cutoffs specified in the pair_style command are used.
If only one cutoff is specified, it is used as the cutoff for both LJ
and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair. You cannot specify 2 cutoffs for style *lj/cut*\ , since it
has no Coulombic terms.
For *lj/cut/coul/long* and *lj/cut/coul/msm* and *lj/cut/tip4p/cut*
and *lj/cut/tip4p/long* only the LJ cutoff can be specified since a
Coulombic cutoff cannot be specified for an individual I,J type pair.
All type pairs use the same global Coulombic cutoff specified in the
pair_style command.
The last coefficient is optional. If not specified, the global
LJ cutoff specified in the pair_style command are used.
----------
@ -381,21 +102,17 @@ instructions on how to use the accelerated styles effectively.
----------
**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
**Mixing, shift, table, tail correction, restart, rRESPA info:**
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/cut pair styles can be mixed.
The default mix value is *geometric*\ . See the "pair_modify" command
The default mix value is *geometric*. See the "pair_modify" command
for details.
All of the *lj/cut* pair styles support the
:doc:`pair_modify <pair_modify>` shift option for the energy of the
Lennard-Jones portion of the pair interaction.
The *lj/cut/coul/long* and *lj/cut/tip4p/long* pair styles support the
:doc:`pair_modify <pair_modify>` table option since they can tabulate
the short-range portion of the long-range Coulombic interaction.
All of the *lj/cut* pair styles support the
:doc:`pair_modify <pair_modify>` tail option for adding a long-range
tail correction to the energy and pressure for the Lennard-Jones
@ -404,7 +121,7 @@ portion of the pair interaction.
All of the *lj/cut* pair styles write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
The *lj/cut* and *lj/cut/coul/long* pair styles support the use of the
The *lj/cut* pair styles support the use of the
*inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_style respa <run_style>` command, meaning the pairwise forces can be
partitioned by distance at different levels of the rRESPA hierarchy.
The other styles only support the *pair* keyword of run_style respa.
@ -412,30 +129,17 @@ See the :doc:`run_style <run_style>` command for details.
----------
Restrictions
""""""""""""
The *lj/cut/coul/long* and *lj/cut/tip4p/long* styles are part of the
KSPACE package. The *lj/cut/tip4p/cut* style is part of the MOLECULE
package. These styles are only enabled if LAMMPS was built with those
packages. See the :doc:`Build package <Build_package>` doc page for
more info.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`
* :doc:`pair_coeff <pair_coeff>`
* :doc:`pair_style lj/cut/coul/cut <pair_lj_cut_coul>`
* :doc:`pair_style lj/cut/coul/debye <pair_lj_cut_coul>`
* :doc:`pair_style lj/cut/coul/dsf <pair_lj_cut_coul>`
* :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`
* :doc:`pair_style lj/cut/coul/msm <pair_lj_cut_coul>`
* :doc:`pair_style lj/cut/coul/wolf <pair_lj_cut_coul>`
* :doc:`pair_style lj/cut/tip4p/cut <pair_lj_cut_tip4p>`
* :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>`
**Default:** none
----------
.. _Jorgensen2:
**(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).
.. _Fennell2:
**(Fennell)** C. J. Fennell, J. D. Gezelter, J Chem Phys, 124,
234104 (2006).

326
doc/src/pair_lj_cut_coul.rst Normal file
View File

@ -0,0 +1,326 @@
.. index:: pair_style lj/cut/coul/cut
.. index:: pair_style lj/cut/coul/cut/gpu
.. index:: pair_style lj/cut/coul/cut/kk
.. index:: pair_style lj/cut/coul/cut/omp
.. index:: pair_style lj/cut/coul/debye
.. index:: pair_style lj/cut/coul/debye/gpu
.. index:: pair_style lj/cut/coul/debye/kk
.. index:: pair_style lj/cut/coul/debye/omp
.. index:: pair_style lj/cut/coul/dsf
.. index:: pair_style lj/cut/coul/dsf/gpu
.. index:: pair_style lj/cut/coul/dsf/kk
.. index:: pair_style lj/cut/coul/dsf/omp
.. index:: pair_style lj/cut/coul/long
.. index:: pair_style lj/cut/coul/long/gpu
.. index:: pair_style lj/cut/coul/long/kk
.. index:: pair_style lj/cut/coul/long/intel
.. index:: pair_style lj/cut/coul/long/opt
.. index:: pair_style lj/cut/coul/long/omp
.. index:: pair_style lj/cut/coul/msm
.. index:: pair_style lj/cut/coul/msm/gpu
.. index:: pair_style lj/cut/coul/msm/omp
.. index:: pair_style lj/cut/coul/wolf
.. index:: pair_style lj/cut/coul/wolf/omp
pair_style lj/cut/coul/cut command
==================================
Accelerator Variants: *lj/cut/coul/cut/gpu*, *lj/cut/coul/cut/kk*, *lj/cut/coul/cut/omp*
pair_style lj/cut/coul/debye command
====================================
Accelerator Variants: *lj/cut/coul/debye/gpu*, lj/cut/coul/debye/kk, *lj/cut/coul/debye/omp*
pair_style lj/cut/coul/dsf command
==================================
Accelerator Variants: *lj/cut/coul/dsf/gpu*, *lj/cut/coul/dsf/kk*, *lj/cut/coul/dsf/omp*
pair_style lj/cut/coul/long command
===================================
Accelerator Variants: *lj/cut/coul/long/gpu*, *lj/cut/coul/long/kk*, *lj/cut/coul/long/intel*, *lj/cut/coul/long/opt*, *lj/cut/coul/long/omp*
pair_style lj/cut/coul/msm command
==================================
Accelerator Variants: *lj/cut/coul/msm/gpu*, *lj/cut/coul/msm/omp*
pair_style lj/cut/coul/wolf command
===================================
Accelerator Variants: *lj/cut/coul/wolf/omp*
Syntax
""""""
.. code-block:: LAMMPS
pair_style style args
* style = *lj/cut/coul/cut* or *lj/cut/coul/debye* or *lj/cut/coul/dsf* or *lj/cut/coul/long* *lj/cut/coul/msm* or *lj/cut/coul/wolf*
* args = list of arguments for a particular style
.. parsed-literal::
*lj/cut/coul/cut* args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
*lj/cut/coul/debye* args = kappa cutoff (cutoff2)
kappa = inverse of the Debye length (inverse distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
*lj/cut/coul/dsf* args = alpha cutoff (cutoff2)
alpha = damping parameter (inverse distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (distance units)
*lj/cut/coul/long* args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
*lj/cut/coul/msm* args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
*lj/cut/coul/wolf* args = alpha cutoff (cutoff2)
alpha = damping parameter (inverse distance units)
cutoff = global cutoff for LJ (and Coulombic if only 2 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
Examples
""""""""
.. code-block:: LAMMPS
pair_style lj/cut/coul/cut 10.0
pair_style lj/cut/coul/cut 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
pair_coeff 1 1 100.0 3.5 9.0 9.0
pair_style lj/cut/coul/debye 1.5 3.0
pair_style lj/cut/coul/debye 1.5 2.5 5.0
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.0 1.5 2.5
pair_coeff 1 1 1.0 1.5 2.5 5.0
pair_style lj/cut/coul/dsf 0.05 2.5 10.0
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.0 1.0 2.5
pair_style lj/cut/coul/long 10.0
pair_style lj/cut/coul/long 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
pair_style lj/cut/coul/msm 10.0
pair_style lj/cut/coul/msm 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
pair_style lj/cut/coul/wolf 0.2 5. 10.0
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.0 1.0 2.5
Description
"""""""""""
The *lj/cut/coul* styles compute the standard 12/6 Lennard-Jones potential,
given by
.. math::
E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right]
\qquad r < r_c
Rc is the cutoff.
Style *lj/cut/coul/cut* adds a Coulombic pairwise interaction given by
.. math::
E = \frac{C q_i q_j}{\epsilon r} \qquad r < r_c
where C is an energy-conversion constant, :math:`q_i` and :math:`q_j`
are the charges on the 2 atoms, and :math:`\epsilon` is the dielectric
constant which can be set by the :doc:`dielectric <dielectric>` command.
If one cutoff is specified in the pair_style command, it is used for
both the LJ and Coulombic terms. If two cutoffs are specified, they are
used as cutoffs for the LJ and Coulombic terms respectively.
Style *lj/cut/coul/debye* adds an additional exp() damping factor
to the Coulombic term, given by
.. math::
E = \frac{C q_i q_j}{\epsilon r} \exp(- \kappa r) \qquad r < r_c
where :math:`\kappa` is the inverse of the Debye length. This potential
is another way to mimic the screening effect of a polar solvent.
Style *lj/cut/coul/dsf* computes the Coulombic term via the damped
shifted force model described in :ref:`Fennell <Fennell2>`, given by:
.. math::
E =
q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} +
\left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} + \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2 r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c
where :math:`\alpha` is the damping parameter and erfc() is the complementary
error-function. This potential is essentially a short-range,
spherically-truncated, charge-neutralized, shifted, pairwise *1/r*
summation. The potential is based on Wolf summation, proposed as an
alternative to Ewald summation for condensed phase systems where
charge screening causes electrostatic interactions to become
effectively short-ranged. In order for the electrostatic sum to be
absolutely convergent, charge neutralization within the cutoff radius
is enforced by shifting the potential through placement of image
charges on the cutoff sphere. Convergence can often be improved by
setting :math:`\alpha` to a small non-zero value.
Styles *lj/cut/coul/long* and *lj/cut/coul/msm* compute the same
Coulombic interactions as style *lj/cut/coul/cut* except that an
additional damping factor is applied to the Coulombic term so it can
be used in conjunction with the :doc:`kspace_style <kspace_style>`
command and its *ewald* or *pppm* option. The Coulombic cutoff
specified for this style means that pairwise interactions within this
distance are computed directly; interactions outside that distance are
computed in reciprocal space.
Style *coul/wolf* adds a Coulombic pairwise interaction via the Wolf
summation method, described in :ref:`Wolf <Wolf1>`, given by:
.. math::
E_i = \frac{1}{2} \sum_{j \neq i}
\frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} +
\frac{1}{2} \sum_{j \neq i}
\frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
where :math:`\alpha` is the damping parameter, and erfc() is the
complementary error-function terms. This potential is essentially a
short-range, spherically-truncated, charge-neutralized, shifted,
pairwise *1/r* summation. With a manipulation of adding and subtracting
a self term (for i = j) to the first and second term on the
right-hand-side, respectively, and a small enough :math:`\alpha` damping
parameter, the second term shrinks and the potential becomes a
rapidly-converging real-space summation. With a long enough cutoff and
small enough :math:`\alpha` parameter, the energy and forces calculated by the
Wolf summation method approach those of the Ewald sum. So it is a means
of getting effective long-range interactions with a short-range
potential.
Coefficients
""""""""""""
For all of the *lj/cut/coul* pair styles, the following coefficients must
be defined for each pair of atoms types via the
:doc:`pair_coeff <pair_coeff>` command as in the examples above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands, or by mixing as
described below:
* :math:`\epsilon` (energy units)
* :math:`\sigma` (distance units)
* cutoff1 (distance units)
* cutoff2 (distance units)
Note that :math:`\sigma` is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum at :math:`2^{\frac{1}{6}} \sigma`.
The latter 2 coefficients are optional. If not specified, the global
LJ and Coulombic cutoffs specified in the pair_style command are used.
If only one cutoff is specified, it is used as the cutoff for both LJ
and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair.
For *lj/cut/coul/long* and *lj/cut/coul/msm* only the LJ cutoff can be
specified since a Coulombic cutoff cannot be specified for an individual I,J
type pair. All type pairs use the same global Coulombic cutoff specified in
the pair_style command.
----------
A version of these styles with a soft core, *lj/cut/soft*\ , suitable
for use in free energy calculations, is part of the USER-FEP package and
is documented with the :doc:`pair_style */soft <pair_fep_soft>`
styles. The version with soft core is only available if LAMMPS was built
with that package. See the :doc:`Build package <Build_package>` doc page
for more info.
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
----------
**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/cut pair styles can be mixed.
The default mix value is *geometric*\ . See the "pair_modify" command
for details.
All of the *lj/cut* pair styles support the
:doc:`pair_modify <pair_modify>` shift option for the energy of the
Lennard-Jones portion of the pair interaction.
The *lj/cut/coul/long* pair styles support the
:doc:`pair_modify <pair_modify>` table option since they can tabulate
the short-range portion of the long-range Coulombic interaction.
All of the *lj/cut* pair styles support the
:doc:`pair_modify <pair_modify>` tail option for adding a long-range
tail correction to the energy and pressure for the Lennard-Jones
portion of the pair interaction.
All of the *lj/cut* pair styles write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
The *lj/cut/coul/long* pair styles support the use of the
*inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_style respa <run_style>` command, meaning the pairwise forces can be
partitioned by distance at different levels of the rRESPA hierarchy.
The other styles only support the *pair* keyword of run_style respa.
See the :doc:`run_style <run_style>` command for details.
----------
Restrictions
""""""""""""
The *lj/cut/coul/long* styles are part of the KSPACE package.
These styles are only enabled if LAMMPS was built with those
packages. See the :doc:`Build package <Build_package>` doc page for
more info.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`
**Default:** none
----------
.. _Fennell2:
**(Fennell)** C. J. Fennell, J. D. Gezelter, J Chem Phys, 124,
234104 (2006).

208
doc/src/pair_lj_cut_tip4p.rst Normal file
View File

@ -0,0 +1,208 @@
.. index:: pair_style lj/cut/tip4p/cut
.. index:: pair_style lj/cut/tip4p/cut/omp
.. index:: pair_style lj/cut/tip4p/long
.. index:: pair_style lj/cut/tip4p/long/gpu
.. index:: pair_style lj/cut/tip4p/long/omp
.. index:: pair_style lj/cut/tip4p/long/opt
pair_style lj/cut/tip4p/cut command
===================================
Accelerator Variants: *lj/cut/tip4p/cut/omp*
pair_style lj/cut/tip4p/long command
====================================
Accelerator Variants: *lj/cut/tip4p/long/gpu*, *lj/cut/tip4p/long/omp*, *lj/cut/tip4p/long/opt*
Syntax
""""""
.. code-block:: LAMMPS
pair_style style args
* style = *lj/cut/tip4p/cut* or *lj/cut/tip4p/long*
* args = list of arguments for a particular style
.. parsed-literal::
*lj/cut/tip4p/cut* args = otype htype btype atype qdist cutoff (cutoff2)
otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters
qdist = distance from O atom to massless charge (distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
*lj/cut/tip4p/long* args = otype htype btype atype qdist cutoff (cutoff2)
otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters
qdist = distance from O atom to massless charge (distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
Examples
""""""""
.. code-block:: LAMMPS
pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0
pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 10.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0
pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
Description
"""""""""""
The *lj/cut/tip4p* styles compute the standard 12/6 Lennard-Jones potential,
given by
.. math::
E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right]
\qquad r < r_c
and implement the TIP4P
water model of :ref:`(Jorgensen) <Jorgensen2>`, which introduces a massless
site located a short distance away from the oxygen atom along the
bisector of the HOH angle. The atomic types of the oxygen and
hydrogen atoms, the bond and angle types for OH and HOH interactions,
and the distance to the massless charge site are specified as
pair_style arguments. Style *lj/cut/tip4p/cut* uses a cutoff for
Coulomb interactions; style *lj/cut/tip4p/long* is for use with a
long-range Coulombic solver (Ewald or PPPM).
.. note::
For each TIP4P water molecule in your system, the atom IDs for
the O and 2 H atoms must be consecutive, with the O atom first. This
is to enable LAMMPS to "find" the 2 H atoms associated with each O
atom. For example, if the atom ID of an O atom in a TIP4P water
molecule is 500, then its 2 H atoms must have IDs 501 and 502.
See the :doc:`Howto tip4p <Howto_tip4p>` doc page for more information
on how to use the TIP4P pair styles and lists of parameters to set.
Note that the neighbor list cutoff for Coulomb interactions is
effectively extended by a distance 2\*qdist when using the TIP4P pair
style, to account for the offset distance of the fictitious charges on
O atoms in water molecules. Thus it is typically best in an
efficiency sense to use a LJ cutoff >= Coulombic cutoff + 2\*qdist, 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.
Coefficients
""""""""""""
For all of the *lj/cut* pair styles, the following coefficients must
be defined for each pair of atoms types via the
:doc:`pair_coeff <pair_coeff>` command as in the examples above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands, or by mixing as
described below:
* :math:`\epsilon` (energy units)
* :math:`\sigma` (distance units)
* LJ cutoff (distance units)
Note that :math:`\sigma` is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum at :math:`2^{\frac{1}{6}} \sigma`.
The last coefficient is optional. If not specified, the global
LJ cutoff specified in the pair_style command is used.
For *lj/cut/tip4p/cut* and *lj/cut/tip4p/long* only the LJ cutoff can be
specified since a Coulombic cutoff cannot be specified for an individual I,J
type pair. All type pairs use the same global Coulombic cutoff specified in
the pair_style command.
----------
A version of these styles with a soft core, *lj/cut/soft*\ , suitable
for use in free energy calculations, is part of the USER-FEP package and
is documented with the :doc:`pair_style */soft <pair_fep_soft>`
styles. The version with soft core is only available if LAMMPS was built
with that package. See the :doc:`Build package <Build_package>` doc page
for more info.
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
----------
**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/cut pair styles can be mixed.
The default mix value is *geometric*\ . See the "pair_modify" command
for details.
All of the *lj/cut* pair styles support the
:doc:`pair_modify <pair_modify>` shift option for the energy of the
Lennard-Jones portion of the pair interaction.
The *lj/cut/coul/long* and *lj/cut/tip4p/long* pair styles support the
:doc:`pair_modify <pair_modify>` table option since they can tabulate
the short-range portion of the long-range Coulombic interaction.
All of the *lj/cut* pair styles support the
:doc:`pair_modify <pair_modify>` tail option for adding a long-range
tail correction to the energy and pressure for the Lennard-Jones
portion of the pair interaction.
All of the *lj/cut* pair styles write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
The *lj/cut* and *lj/cut/coul/long* pair styles support the use of the
*inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_style respa <run_style>` command, meaning the pairwise forces can be
partitioned by distance at different levels of the rRESPA hierarchy.
The other styles only support the *pair* keyword of run_style respa.
See the :doc:`run_style <run_style>` command for details.
----------
Restrictions
""""""""""""
The *lj/cut/tip4p/long* styles are part of the
KSPACE package. The *lj/cut/tip4p/cut* style is part of the MOLECULE
package. These styles are only enabled if LAMMPS was built with those
packages. See the :doc:`Build package <Build_package>` doc page for
more info.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`
**Default:** none
----------
.. _Jorgensen2:
**(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).

16
doc/src/pair_style.rst
View File

@ -201,21 +201,21 @@ accelerated styles exist.
* :doc:`lj/class2/soft <pair_fep_soft>` - COMPASS (class 2) force field with no Coulomb with a soft core
* :doc:`lj/cubic <pair_lj_cubic>` - LJ with cubic after inflection point
* :doc:`lj/cut <pair_lj>` - cutoff Lennard-Jones potential without Coulomb
* :doc:`lj/cut/coul/cut <pair_lj>` - LJ with cutoff Coulomb
* :doc:`lj/cut/coul/cut <pair_lj_cut_coul>` - LJ with cutoff Coulomb
* :doc:`lj/cut/coul/cut/soft <pair_fep_soft>` - LJ with cutoff Coulomb with a soft core
* :doc:`lj/cut/coul/debye <pair_lj>` - LJ with Debye screening added to Coulomb
* :doc:`lj/cut/coul/dsf <pair_lj>` - LJ with Coulomb via damped shifted forces
* :doc:`lj/cut/coul/long <pair_lj>` - LJ with long-range Coulomb
* :doc:`lj/cut/coul/debye <pair_lj_cut_coul>` - LJ with Debye screening added to Coulomb
* :doc:`lj/cut/coul/dsf <pair_lj_cut_coul>` - LJ with Coulomb via damped shifted forces
* :doc:`lj/cut/coul/long <pair_lj_cut_coul>` - LJ with long-range Coulomb
* :doc:`lj/cut/coul/long/cs <pair_cs>` - LJ with long-range Coulomb with core/shell adjustments
* :doc:`lj/cut/coul/long/soft <pair_fep_soft>` - LJ with long-range Coulomb with a soft core
* :doc:`lj/cut/coul/msm <pair_lj>` - LJ with long-range MSM Coulomb
* :doc:`lj/cut/coul/wolf <pair_lj>` - LJ with Coulomb via Wolf potential
* :doc:`lj/cut/coul/msm <pair_lj_cut_coul>` - LJ with long-range MSM Coulomb
* :doc:`lj/cut/coul/wolf <pair_lj_cut_coul>` - LJ with Coulomb via Wolf potential
* :doc:`lj/cut/dipole/cut <pair_dipole>` - point dipoles with cutoff
* :doc:`lj/cut/dipole/long <pair_dipole>` - point dipoles with long-range Ewald
* :doc:`lj/cut/soft <pair_fep_soft>` - LJ with a soft core
* :doc:`lj/cut/thole/long <pair_thole>` - LJ with Coulomb with thole damping
* :doc:`lj/cut/tip4p/cut <pair_lj>` - LJ with cutoff Coulomb for TIP4P water
* :doc:`lj/cut/tip4p/long <pair_lj>` - LJ with long-range Coulomb for TIP4P water
* :doc:`lj/cut/tip4p/cut <pair_lj_cut_tip4p>` - LJ with cutoff Coulomb for TIP4P water
* :doc:`lj/cut/tip4p/long <pair_lj_cut_tip4p>` - LJ with long-range Coulomb for TIP4P water
* :doc:`lj/cut/tip4p/long/soft <pair_fep_soft>` - LJ with cutoff Coulomb for TIP4P water with a soft core
* :doc:`lj/expand <pair_lj_expand>` - Lennard-Jones for variable size particles
* :doc:`lj/expand/coul/long <pair_lj_expand>` - Lennard-Jones for variable size particles with long-range Coulomb

2
doc/src/pair_table.rst
View File

@ -98,7 +98,7 @@ more of the optional keywords listed above for the pair_style command.
These are *ewald* or *pppm* or *msm* or *dispersion* or *tip4p*\ . This
is so LAMMPS can insure the short-range potential and long-range
solver are compatible with each other, as it does for other
short-range pair styles, such as :doc:`pair_style lj/cut/coul/long <pair_lj>`. Note that it is up to you to insure
short-range pair styles, such as :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`. Note that it is up to you to insure
the tabulated values for each pair of atom types has the correct
functional form to be compatible with the matching long-range solver.

2
doc/src/pair_thole.rst
View File

@ -182,7 +182,7 @@ Related commands
""""""""""""""""
:doc:`fix drude <fix_drude>`, :doc:`fix langevin/drude <fix_langevin_drude>`, :doc:`fix drude/transform <fix_drude_transform>`, :doc:`compute temp/drude <compute_temp_drude>`
:doc:`pair_style lj/cut/coul/long <pair_lj>`
:doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`
**Default:** none