diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index fc5a49bf8a..888a445daa 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -136,22 +136,22 @@ OPT. * :doc:`lj/class2/soft ` * :doc:`lj/cubic (go) ` * :doc:`lj/cut (gikot) ` - * :doc:`lj/cut/coul/cut (gko) ` + * :doc:`lj/cut/coul/cut (gko) ` * :doc:`lj/cut/coul/cut/soft (o) ` - * :doc:`lj/cut/coul/debye (gko) ` - * :doc:`lj/cut/coul/dsf (gko) ` - * :doc:`lj/cut/coul/long (gikot) ` + * :doc:`lj/cut/coul/debye (gko) ` + * :doc:`lj/cut/coul/dsf (gko) ` + * :doc:`lj/cut/coul/long (gikot) ` * :doc:`lj/cut/coul/long/cs ` * :doc:`lj/cut/coul/long/soft (o) ` - * :doc:`lj/cut/coul/msm (go) ` - * :doc:`lj/cut/coul/wolf (o) ` + * :doc:`lj/cut/coul/msm (go) ` + * :doc:`lj/cut/coul/wolf (o) ` * :doc:`lj/cut/dipole/cut (go) ` * :doc:`lj/cut/dipole/long (g) ` * :doc:`lj/cut/dipole/sf (go) ` * :doc:`lj/cut/soft (o) ` * :doc:`lj/cut/thole/long (o) ` - * :doc:`lj/cut/tip4p/cut (o) ` - * :doc:`lj/cut/tip4p/long (got) ` + * :doc:`lj/cut/tip4p/cut (o) ` + * :doc:`lj/cut/tip4p/long (got) ` * :doc:`lj/cut/tip4p/long/soft (o) ` * :doc:`lj/expand (gko) ` * :doc:`lj/expand/coul/long (g) ` diff --git a/doc/src/Howto_bioFF.rst b/doc/src/Howto_bioFF.rst index e7bfcdfdb2..bac1b566e1 100644 --- a/doc/src/Howto_bioFF.rst +++ b/doc/src/Howto_bioFF.rst @@ -102,8 +102,8 @@ documentation for the formula it computes. * :doc:`pair_style ` buck/coul/cut * :doc:`pair_style ` buck/coul/long * :doc:`pair_style ` lj/cut -* :doc:`pair_style ` lj/cut/coul/cut -* :doc:`pair_style ` lj/cut/coul/long +* :doc:`pair_style ` lj/cut/coul/cut +* :doc:`pair_style ` lj/cut/coul/long * :doc:`pair_style ` hbond/dreiding/lj * :doc:`pair_style ` hbond/dreiding/morse diff --git a/doc/src/Howto_tip4p.rst b/doc/src/Howto_tip4p.rst index 1aa5712b19..9856b8fbe7 100644 --- a/doc/src/Howto_tip4p.rst +++ b/doc/src/Howto_tip4p.rst @@ -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 ` +* :doc:`pair_style lj/cut/tip4p/cut ` or these two commands for a long-range model: -* :doc:`pair_style lj/cut/tip4p/long ` +* :doc:`pair_style lj/cut/tip4p/long ` * :doc:`kspace_style pppm/tip4p ` 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 ` command. +and Coulombic cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long ` command. Wikipedia also has a nice article on `water models `_. diff --git a/doc/src/compute_fep.rst b/doc/src/compute_fep.rst index c2e0271ee8..50ad50561b 100644 --- a/doc/src/compute_fep.rst +++ b/doc/src/compute_fep.rst @@ -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 ` | a,b,c | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`buck ` | a,c | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`buck/mdf ` | a,c | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`coul/cut ` | scale | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`coul/cut/soft ` | lambda | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`coul/long, coul/msm ` | scale | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`coul/long/soft ` | scale, lambda | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`eam ` | scale | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`gauss ` | a | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`lennard/mdf ` | a,b | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`lj/class2 ` | epsilon,sigma | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`lj/class2/coul/cut, lj/class2/coul/long ` | epsilon,sigma | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`lj/cut ` | epsilon,sigma | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`lj/cut/soft ` | epsilon,sigma,lambda | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm ` | epsilon,sigma | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`lj/cut/coul/cut/soft, lj/cut/coul/long/soft ` | epsilon,sigma,lambda | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`lj/cut/tip4p/cut, lj/cut/tip4p/long ` | epsilon,sigma | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`lj/cut/tip4p/long/soft ` | epsilon,sigma,lambda | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`lj/expand ` | epsilon,sigma,delta | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`lj/mdf ` | epsilon,sigma | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`lj/sf/dipole/sf ` | epsilon,sigma,scale | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`mie/cut ` | epsilon,sigma,gamR,gamA | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`morse, morse/smooth/linear ` | d0,r0,alpha | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`morse/soft ` | d0,r0,alpha,lambda | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`nm/cut ` | e0,r0,nn,mm | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`nm/cut/coul/cut, nm/cut/coul/long ` | e0,r0,nn,mm | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`ufm ` | epsilon,sigma,scale | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`soft ` | a | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`born ` | a,b,c | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`buck ` | a,c | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`buck/mdf ` | a,c | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`coul/cut ` | scale | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`coul/cut/soft ` | lambda | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`coul/long, coul/msm ` | scale | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`coul/long/soft ` | scale, lambda | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`eam ` | scale | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`gauss ` | a | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`lennard/mdf ` | a,b | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`lj/class2 ` | epsilon,sigma | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`lj/class2/coul/cut, lj/class2/coul/long ` | epsilon,sigma | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`lj/cut ` | epsilon,sigma | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`lj/cut/soft ` | epsilon,sigma,lambda | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm ` | epsilon,sigma | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`lj/cut/coul/cut/soft, lj/cut/coul/long/soft ` | epsilon,sigma,lambda | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`lj/cut/tip4p/cut, lj/cut/tip4p/long ` | epsilon,sigma | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`lj/cut/tip4p/long/soft ` | epsilon,sigma,lambda | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`lj/expand ` | epsilon,sigma,delta | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`lj/mdf ` | epsilon,sigma | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`lj/sf/dipole/sf ` | epsilon,sigma,scale | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`mie/cut ` | epsilon,sigma,gamR,gamA | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`morse, morse/smooth/linear ` | d0,r0,alpha | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`morse/soft ` | d0,r0,alpha,lambda | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`nm/cut ` | e0,r0,nn,mm | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`nm/cut/coul/cut, nm/cut/coul/long ` | e0,r0,nn,mm | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`ufm ` | epsilon,sigma,scale | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`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 diff --git a/doc/src/fix_adapt.rst b/doc/src/fix_adapt.rst index 5745c0f69e..4a9bc99e9b 100644 --- a/doc/src/fix_adapt.rst +++ b/doc/src/fix_adapt.rst @@ -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 ` | a,b,c | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`born/coul/long, born/coul/msm ` | coulombic_cutoff | type global | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`buck ` | a,c | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`buck/coul/long, buck/coul/msm ` | coulombic_cutoff | type global | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`buck/mdf ` | a,c | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`coul/cut ` | scale | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`coul/cut/soft ` | lambda | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`coul/debye ` | scale | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`coul/dsf ` | coulombic_cutoff | type global | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`coul/long, coul/msm ` | coulombic_cutoff, scale | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`coul/long/soft ` | scale, lambda, coulombic_cutoff | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`eam, eam/alloy, eam/fs ` | scale | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`gauss ` | a | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`lennard/mdf ` | A,B | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`lj/class2 ` | epsilon,sigma | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`lj/class2/coul/cut, lj/class2/coul/long ` | epsilon,sigma,coulombic_cutoff | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`lj/cut ` | epsilon,sigma | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm ` | epsilon,sigma,coulombic_cutoff | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`lj/cut/coul/cut/soft, lj/cut/coul/long/soft ` | epsilon,sigma,lambda,coulombic_cutoff | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`lj/cut/coul/dsf ` | cutoff | type global | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`lj/cut/tip4p/cut ` | epsilon,sigma,coulombic_cutoff | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`lj/cut/soft ` | epsilon,sigma,lambda | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`lj/expand ` | epsilon,sigma,delta | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`lj/mdf ` | epsilon,sigma | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`lj/sf/dipole/sf ` | epsilon,sigma,scale | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`lubricate ` | mu | global | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`mie/cut ` | epsilon,sigma,gamma_repulsive,gamma_attractive | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`morse, morse/smooth/linear ` | D0,R0,alpha | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`morse/soft ` | D0,R0,alpha,lambda | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`nm/cut ` | E0,R0,m,n | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`nm/cut/coul/cut, nm/cut/coul/long ` | E0,R0,m,n,coulombic_cutoff | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`reax/c ` | chi, eta, gamma | type global | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`spin/dmi ` | coulombic_cutoff | type global | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`spin/exchange ` | coulombic_cutoff | type global | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`spin/magelec ` | coulombic_cutoff | type global | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`spin/neel ` | coulombic_cutoff | type global | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`table ` | table_cutoff | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`ufm ` | epsilon,sigma | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`soft ` | a | type pairs | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ -| | | | -+---------------------------------------------------------------------+--------------------------------------------------+-------------+ ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`born ` | a,b,c | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`born/coul/long, born/coul/msm ` | coulombic_cutoff | type global | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`buck ` | a,c | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`buck/coul/long, buck/coul/msm ` | coulombic_cutoff | type global | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`buck/mdf ` | a,c | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`coul/cut ` | scale | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`coul/cut/soft ` | lambda | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`coul/debye ` | scale | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`coul/dsf ` | coulombic_cutoff | type global | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`coul/long, coul/msm ` | coulombic_cutoff, scale | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`coul/long/soft ` | scale, lambda, coulombic_cutoff | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`eam, eam/alloy, eam/fs ` | scale | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`gauss ` | a | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`lennard/mdf ` | A,B | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`lj/class2 ` | epsilon,sigma | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`lj/class2/coul/cut, lj/class2/coul/long ` | epsilon,sigma,coulombic_cutoff | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`lj/cut ` | epsilon,sigma | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm ` | epsilon,sigma,coulombic_cutoff | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`lj/cut/coul/cut/soft, lj/cut/coul/long/soft ` | epsilon,sigma,lambda,coulombic_cutoff | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`lj/cut/coul/dsf ` | cutoff | type global | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`lj/cut/tip4p/cut ` | epsilon,sigma,coulombic_cutoff | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`lj/cut/soft ` | epsilon,sigma,lambda | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`lj/expand ` | epsilon,sigma,delta | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`lj/mdf ` | epsilon,sigma | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`lj/sf/dipole/sf ` | epsilon,sigma,scale | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`lubricate ` | mu | global | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`mie/cut ` | epsilon,sigma,gamma_repulsive,gamma_attractive | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`morse, morse/smooth/linear ` | D0,R0,alpha | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`morse/soft ` | D0,R0,alpha,lambda | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`nm/cut ` | E0,R0,m,n | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`nm/cut/coul/cut, nm/cut/coul/long ` | E0,R0,m,n,coulombic_cutoff | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`reax/c ` | chi, eta, gamma | type global | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`spin/dmi ` | coulombic_cutoff | type global | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`spin/exchange ` | coulombic_cutoff | type global | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`spin/magelec ` | coulombic_cutoff | type global | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`spin/neel ` | coulombic_cutoff | type global | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`table ` | table_cutoff | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`ufm ` | epsilon,sigma | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`soft ` | a | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ .. note:: diff --git a/doc/src/fix_adapt_fep.rst b/doc/src/fix_adapt_fep.rst index 3e5d419353..d587690473 100644 --- a/doc/src/fix_adapt_fep.rst +++ b/doc/src/fix_adapt_fep.rst @@ -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 ` | a,b,c | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`buck ` | a,c | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`buck/mdf ` | a,c | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`coul/cut ` | scale | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`coul/cut/soft ` | lambda | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`coul/long, coul/msm ` | scale | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`coul/long/soft ` | scale, lambda | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`eam ` | scale | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`gauss ` | a | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`lennard/mdf ` | a,b | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`lj/class2 ` | epsilon,sigma | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`lj/class2/coul/cut, lj/class2/coul/long ` | epsilon,sigma | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`lj/cut ` | epsilon,sigma | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`lj/cut/soft ` | epsilon,sigma,lambda | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm ` | epsilon,sigma | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`lj/cut/coul/cut/soft, lj/cut/coul/long/soft ` | epsilon,sigma,lambda | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`lj/cut/tip4p/cut, lj/cut/tip4p/long ` | epsilon,sigma | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`lj/cut/tip4p/long/soft ` | epsilon,sigma,lambda | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`lj/expand ` | epsilon,sigma,delta | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`lj/mdf ` | epsilon,sigma | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`lj/sf/dipole/sf ` | epsilon,sigma,scale | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`mie/cut ` | epsilon,sigma,gamR,gamA | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`morse, morse/smooth/linear ` | d0,r0,alpha | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`morse/soft ` | d0,r0,alpha,lambda | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`nm/cut ` | e0,r0,nn,mm | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`nm/cut/coul/cut, nm/cut/coul/long ` | e0,r0,nn,mm | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`ufm ` | epsilon,sigma,scale | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ -| :doc:`soft ` | a | type pairs | -+---------------------------------------------------------------------+-------------------------+------------+ ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`born ` | a,b,c | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`buck ` | a,c | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`buck/mdf ` | a,c | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`coul/cut ` | scale | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`coul/cut/soft ` | lambda | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`coul/long, coul/msm ` | scale | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`coul/long/soft ` | scale, lambda | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`eam ` | scale | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`gauss ` | a | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`lennard/mdf ` | a,b | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`lj/class2 ` | epsilon,sigma | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`lj/class2/coul/cut, lj/class2/coul/long ` | epsilon,sigma | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`lj/cut ` | epsilon,sigma | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`lj/cut/soft ` | epsilon,sigma,lambda | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm ` | epsilon,sigma | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`lj/cut/coul/cut/soft, lj/cut/coul/long/soft ` | epsilon,sigma,lambda | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`lj/cut/tip4p/cut, lj/cut/tip4p/long ` | epsilon,sigma | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`lj/cut/tip4p/long/soft ` | epsilon,sigma,lambda | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`lj/expand ` | epsilon,sigma,delta | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`lj/mdf ` | epsilon,sigma | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`lj/sf/dipole/sf ` | epsilon,sigma,scale | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`mie/cut ` | epsilon,sigma,gamR,gamA | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`morse, morse/smooth/linear ` | d0,r0,alpha | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`morse/soft ` | d0,r0,alpha,lambda | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`nm/cut ` | e0,r0,nn,mm | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`nm/cut/coul/cut, nm/cut/coul/long ` | e0,r0,nn,mm | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`ufm ` | epsilon,sigma,scale | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ +| :doc:`soft ` | a | type pairs | ++------------------------------------------------------------------------------+-------------------------+------------+ .. note:: diff --git a/doc/src/fix_qbmsst.rst b/doc/src/fix_qbmsst.rst index b7a4f49300..112c5f1842 100644 --- a/doc/src/fix_qbmsst.rst +++ b/doc/src/fix_qbmsst.rst @@ -15,7 +15,7 @@ Syntax * dir = *x* or *y* or *z* * shockvel = shock velocity (strictly positive, velocity units) * zero or more keyword/value pairs may be appended -* keyword = *q* or *mu* or *p0* or *v0* or *e0* or *tscale* or *damp* or *seed*\ or *f_max* or *N_f* or *eta* or *beta* or *T_init* +* keyword = *q* or *mu* or *p0* or *v0* or *e0* or *tscale* or *damp* or *seed* or *f_max* or *N_f* or *eta* or *beta* or *T_init* .. parsed-literal:: diff --git a/doc/src/fix_tune_kspace.rst b/doc/src/fix_tune_kspace.rst index 66a3fef024..744db9dcf3 100644 --- a/doc/src/fix_tune_kspace.rst +++ b/doc/src/fix_tune_kspace.rst @@ -93,7 +93,7 @@ Related commands """""""""""""""" :doc:`kspace_style `, :doc:`boundary ` -:doc:`kspace_modify `, :doc:`pair_style lj/cut/coul/long `, :doc:`pair_style lj/charmm/coul/long `, :doc:`pair_style lj/long `, :doc:`pair_style lj/long/coul/long `, +:doc:`kspace_modify `, :doc:`pair_style lj/cut/coul/long `, :doc:`pair_style lj/charmm/coul/long `, :doc:`pair_style lj/long `, :doc:`pair_style lj/long/coul/long `, :doc:`pair_style buck/coul/long ` Default diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst index 4b28c0a3c3..5b45b00353 100644 --- a/doc/src/kspace_style.rst +++ b/doc/src/kspace_style.rst @@ -437,7 +437,7 @@ virial, so this contribution is not included. Related commands """""""""""""""" -:doc:`kspace_modify `, :doc:`pair_style lj/cut/coul/long `, :doc:`pair_style lj/charmm/coul/long `, :doc:`pair_style lj/long/coul/long `, :doc:`pair_style buck/coul/long ` +:doc:`kspace_modify `, :doc:`pair_style lj/cut/coul/long `, :doc:`pair_style lj/charmm/coul/long `, :doc:`pair_style lj/long/coul/long `, :doc:`pair_style buck/coul/long ` Default """"""" diff --git a/doc/src/minimize.rst b/doc/src/minimize.rst index d14d988555..d300672ebb 100644 --- a/doc/src/minimize.rst +++ b/doc/src/minimize.rst @@ -231,7 +231,7 @@ so that its energy is 0.0 at the cutoff via the :doc:`pair_modify ` command. See the doc pages for individual :doc:`pair styles ` 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 `). The CHARMM potentials go to 0.0 at +long-range component are used (e.g. :doc:`pair_style lj/cut/coul/long `). The CHARMM potentials go to 0.0 at the cutoff (e.g. :doc:`pair_style lj/charmm/coul/charmm `), as do the GROMACS potentials (e.g. :doc:`pair_style lj/gromacs `). diff --git a/doc/src/pair_cs.rst b/doc/src/pair_cs.rst index 9790c2defd..438d982d73 100644 --- a/doc/src/pair_cs.rst +++ b/doc/src/pair_cs.rst @@ -120,7 +120,7 @@ the "/cs" in the name: * :doc:`pair_style buck/coul/long ` * :doc:`pair_style coul/long ` * :doc:`pair_style coul/wolf ` -* :doc:`pair_style lj/cut/coul/long ` +* :doc:`pair_style lj/cut/coul/long ` * :doc:`pair_style lj/class2/coul/long ` except that they correctly treat the special case where the distance diff --git a/doc/src/pair_lj.rst b/doc/src/pair_lj.rst index 21357ab45f..31b73d2c3a 100644 --- a/doc/src/pair_lj.rst +++ b/doc/src/pair_lj.rst @@ -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 """"""""""" @@ -214,150 +47,36 @@ 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 ` styles to add a Coulombic +pairwise interaction and the :doc:`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 ` 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 `, 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 ` -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 `, 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) `, 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 ` 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 ` command as in the examples above, or in -the data file or restart files read by the :doc:`read_data ` -or :doc:`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 ` command as in the examples above, or in the data +file or restart files read by the :doc:`read_data ` or +:doc:`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. ---------- 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 ` -styles. The version with soft core is only available if LAMMPS was built -with that package. See the :doc:`Build package ` doc page -for more info. +styles. ---------- @@ -381,21 +100,17 @@ 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 ` 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 ` 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 ` tail option for adding a long-range tail correction to the energy and pressure for the Lennard-Jones @@ -404,7 +119,7 @@ portion of the pair interaction. All of the *lj/cut* pair styles write their information to :doc:`binary restart files `, 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 ` 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 +127,17 @@ See the :doc:`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 ` doc page for -more info. - Related commands """""""""""""""" -:doc:`pair_coeff ` +* :doc:`pair_coeff ` +* :doc:`pair_style lj/cut/coul/cut ` +* :doc:`pair_style lj/cut/coul/debye ` +* :doc:`pair_style lj/cut/coul/dsf ` +* :doc:`pair_style lj/cut/coul/long ` +* :doc:`pair_style lj/cut/coul/msm ` +* :doc:`pair_style lj/cut/coul/wolf ` +* :doc:`pair_style lj/cut/tip4p/cut ` +* :doc:`pair_style lj/cut/tip4p/long ` **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). diff --git a/doc/src/pair_lj_cut_coul.rst b/doc/src/pair_lj_cut_coul.rst new file mode 100644 index 0000000000..fda3fd29c5 --- /dev/null +++ b/doc/src/pair_lj_cut_coul.rst @@ -0,0 +1,328 @@ +.. 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 + +:math:`r_c` 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 :math:`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 ` 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 `, 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 ` +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 `, 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 ` command as in the examples above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`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/coul/soft*\ and +*lj/cut/coul/long/soft*\ , suitable for use in free energy calculations, is +part of the USER-FEP package and is documented with the :doc:`pair_style */soft ` styles. + +---------- + +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 ` 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 ` 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 ` when you invoke LAMMPS, or you can use the +:doc:`suffix ` command in your input script. + +See the :doc:`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 ` 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 ` 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 ` 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 `, 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 ` 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 ` 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 ` doc page for +more info. + +Related commands +"""""""""""""""" + +:doc:`pair_coeff ` + +**Default:** none + +---------- + +.. _Wolf3: + +**(Wolf)** D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem +Phys, 110, 8254 (1999). + +.. _Fennell2: + +**(Fennell)** C. J. Fennell, J. D. Gezelter, J Chem Phys, 124, +234104 (2006). diff --git a/doc/src/pair_lj_cut_tip4p.rst b/doc/src/pair_lj_cut_tip4p.rst new file mode 100644 index 0000000000..cbfd6b9a17 --- /dev/null +++ b/doc/src/pair_lj_cut_tip4p.rst @@ -0,0 +1,230 @@ +.. 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 + +:math:`r_c` is the cutoff. + +They add Coulombic pairwise interactions given by + +.. math:: + + E = \frac{C q_i q_j}{\epsilon r} \qquad r < r_c + +where :math:`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 ` 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/tip4p/long* compute the same +Coulombic interactions as style *lj/cut/tip4p/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 ` +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. + +The *lj/cut/tip4p* styles implement the TIP4P +water model of :ref:`(Jorgensen) `, 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 ` 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 ` command as in the examples above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`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/tip4p/long/soft*\ , suitable +for use in free energy calculations, is part of the USER-FEP package and +is documented with the :doc:`pair_style */soft ` +styles. + +---------- + +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 ` 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 ` 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 ` when you invoke LAMMPS, or you can use the +:doc:`suffix ` command in your input script. + +See the :doc:`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 ` 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 ` 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 ` 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 `, 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 ` 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 ` 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 ` doc page for +more info. + +Related commands +"""""""""""""""" + +:doc:`pair_coeff ` + +**Default:** none + +---------- + +.. _Jorgensen2: + +**(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem +Phys, 79, 926 (1983). diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 443573743d..4feaeacad0 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -201,21 +201,21 @@ accelerated styles exist. * :doc:`lj/class2/soft ` - COMPASS (class 2) force field with no Coulomb with a soft core * :doc:`lj/cubic ` - LJ with cubic after inflection point * :doc:`lj/cut ` - cutoff Lennard-Jones potential without Coulomb -* :doc:`lj/cut/coul/cut ` - LJ with cutoff Coulomb +* :doc:`lj/cut/coul/cut ` - LJ with cutoff Coulomb * :doc:`lj/cut/coul/cut/soft ` - LJ with cutoff Coulomb with a soft core -* :doc:`lj/cut/coul/debye ` - LJ with Debye screening added to Coulomb -* :doc:`lj/cut/coul/dsf ` - LJ with Coulomb via damped shifted forces -* :doc:`lj/cut/coul/long ` - LJ with long-range Coulomb +* :doc:`lj/cut/coul/debye ` - LJ with Debye screening added to Coulomb +* :doc:`lj/cut/coul/dsf ` - LJ with Coulomb via damped shifted forces +* :doc:`lj/cut/coul/long ` - LJ with long-range Coulomb * :doc:`lj/cut/coul/long/cs ` - LJ with long-range Coulomb with core/shell adjustments * :doc:`lj/cut/coul/long/soft ` - LJ with long-range Coulomb with a soft core -* :doc:`lj/cut/coul/msm ` - LJ with long-range MSM Coulomb -* :doc:`lj/cut/coul/wolf ` - LJ with Coulomb via Wolf potential +* :doc:`lj/cut/coul/msm ` - LJ with long-range MSM Coulomb +* :doc:`lj/cut/coul/wolf ` - LJ with Coulomb via Wolf potential * :doc:`lj/cut/dipole/cut ` - point dipoles with cutoff * :doc:`lj/cut/dipole/long ` - point dipoles with long-range Ewald * :doc:`lj/cut/soft ` - LJ with a soft core * :doc:`lj/cut/thole/long ` - LJ with Coulomb with thole damping -* :doc:`lj/cut/tip4p/cut ` - LJ with cutoff Coulomb for TIP4P water -* :doc:`lj/cut/tip4p/long ` - LJ with long-range Coulomb for TIP4P water +* :doc:`lj/cut/tip4p/cut ` - LJ with cutoff Coulomb for TIP4P water +* :doc:`lj/cut/tip4p/long ` - LJ with long-range Coulomb for TIP4P water * :doc:`lj/cut/tip4p/long/soft ` - LJ with cutoff Coulomb for TIP4P water with a soft core * :doc:`lj/expand ` - Lennard-Jones for variable size particles * :doc:`lj/expand/coul/long ` - Lennard-Jones for variable size particles with long-range Coulomb diff --git a/doc/src/pair_table.rst b/doc/src/pair_table.rst index 19b95fd5d3..cb01e56e85 100644 --- a/doc/src/pair_table.rst +++ b/doc/src/pair_table.rst @@ -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 `. Note that it is up to you to insure +short-range pair styles, such as :doc:`pair_style lj/cut/coul/long `. 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. diff --git a/doc/src/pair_thole.rst b/doc/src/pair_thole.rst index 7adf267469..9850ed4f44 100644 --- a/doc/src/pair_thole.rst +++ b/doc/src/pair_thole.rst @@ -182,7 +182,7 @@ Related commands """""""""""""""" :doc:`fix drude `, :doc:`fix langevin/drude `, :doc:`fix drude/transform `, :doc:`compute temp/drude ` -:doc:`pair_style lj/cut/coul/long ` +:doc:`pair_style lj/cut/coul/long ` **Default:** none