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@ -50,6 +50,12 @@ Examples
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pair_style hybrid/overlay e3b 1 lj/cut/tip4p/long 1 2 1 1 0.15 8.5
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pair_coeff * * e3b preset 2011
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Used in example input script:
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.. parsed-literal::
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examples/PACKAGES/e3b/in.e3b-tip4p2005
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Description
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"""""""""""
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@ -68,21 +74,27 @@ The *e3b* style computes an \"explicit three-body\" (E3B) potential for water :r
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0 & r>R_f\\
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\end{cases}
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This potential was developed as a water model that includes the three-body cooperativity of hydrogen bonding explicitly.
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To use it in this way, it must be applied in conjunction with a conventional two-body water model, through *pair_style hybrid/overlay*.
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The three body interactions are split into three types: A, B, and C.
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Type A corresponds to anti-cooperative double hydrogen bond donor interactions.
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Type B corresponds to the cooperative interaction of molecules that both donate and accept a hydrogen bond.
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Type C corresponds to anti-cooperative double hydrogen bond acceptor interactions.
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The three-body interactions are smoothly cutoff by the switching function s(r) between Rs and Rc3.
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The two-body interactions are designed to correct for the effective many-body interactions implicitly included in the conventional two-body potential.
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The two-body interactions are cut off sharply at Rc2, because K3 is typically significantly smaller than K2.
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See :ref:`(Kumar 2008) <Kumar>` for more details.
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This potential was developed as a water model that includes the
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three-body cooperativity of hydrogen bonding explicitly. To use it in
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this way, it must be applied in conjunction with a conventional two-body
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water model, through pair style :doc:`hybrid/overlay <pair_hybrid>`. The
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three body interactions are split into three types: A, B, and C. Type A
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corresponds to anti-cooperative double hydrogen bond donor interactions.
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Type B corresponds to the cooperative interaction of molecules that both
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donate and accept a hydrogen bond. Type C corresponds to
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anti-cooperative double hydrogen bond acceptor interactions. The
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three-body interactions are smoothly cutoff by the switching function
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s(r) between Rs and Rc3. The two-body interactions are designed to
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correct for the effective many-body interactions implicitly included in
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the conventional two-body potential. The two-body interactions are cut
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off sharply at Rc2, because K3 is typically significantly smaller than
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K2. See :ref:`(Kumar 2008) <Kumar>` for more details.
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Only a single *pair_coeff* command is used with the *e3b* style.
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The first two arguments must be \* \*.
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The oxygen atom type for the pair style is passed as the only argument to the *pair_style* command, not in the *pair_coeff* command.
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The hydrogen atom type is inferred by the ordering of the atoms.
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Only a single :doc:`pair_coeff <pair_coeff>` command is used with the
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*e3b* style and the first two arguments must be \* \*. The oxygen atom
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type for the pair style is passed as the only argument to the
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*pair_style* command, not in the *pair_coeff* command. The hydrogen
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atom type is inferred from the ordering of the atoms.
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.. note::
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@ -90,26 +102,41 @@ The hydrogen atom type is inferred by the ordering of the atoms.
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Each water molecule must have consecutive IDs with the oxygen first.
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This pair style does not test that this criteria is met.
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The *pair_coeff* command must have at least one keyword/value pair, as described above.
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The *preset* keyword sets the potential parameters to the values used in :ref:`(Tainter 2011) <Tainter2011>` or :ref:`(Tainter 2015) <Tainter2015>`.
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To use the water models defined in those references, the *e3b* style should always be used in conjunction with an *lj/cut/tip4p/long* style through *pair_style hybrid/overlay*, as demonstrated in the second example above.
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The *preset 2011* option should be used with the :doc:`TIP4P water model <Howto_tip4p>`.
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The *preset 2015* option should be used with the :doc:`TIP4P/2005 water model <Howto_tip4p>`.
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If the *preset* keyword is used, no other keyword is needed.
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Changes to the preset parameters can be made by specifying the *preset* keyword followed by the specific parameter to change, like *Ea*\ .
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Note that the other keywords must come after *preset* in the pair_style command.
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The *e3b* style can also be used to implement any three-body potential of the same form by specifying all the keywords except *neigh*\ : *Ea*, *Eb*, *Ec*, *E2*, *K3*, *K2*, *Rc3*, *Rc2*, *Rs*, and *bondL*\ .
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The keyword *bondL* specifies the intramolecular OH bond length of the water model being used.
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This is needed to include H atoms that are within the cutoff even when the attached oxygen atom is not.
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The *pair_coeff* command must have at least one keyword/value pair, as
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described above. The *preset* keyword sets the potential parameters to
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the values used in :ref:`(Tainter 2011) <Tainter2011>` or
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:ref:`(Tainter 2015) <Tainter2015>`. To use the water models defined in
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those references, the *e3b* style should always be used in conjunction
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with an *lj/cut/tip4p/long* style through *pair_style hybrid/overlay*,
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as demonstrated in the second example above. The *preset 2011* option
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should be used with the :doc:`TIP4P water model <Howto_tip4p>`. The
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*preset 2015* option should be used with the :doc:`TIP4P/2005 water
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model <Howto_tip4p>`. If the *preset* keyword is used, no other keyword
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is needed. Changes to the preset parameters can be made by specifying
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the *preset* keyword followed by the specific parameter to change, like
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*Ea*\ . Note that the other keywords must come after *preset* in the
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pair_style command. The *e3b* style can also be used to implement any
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three-body potential of the same form by specifying all the keywords
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except *neigh*\ : *Ea*, *Eb*, *Ec*, *E2*, *K3*, *K2*, *Rc3*, *Rc2*,
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*Rs*, and *bondL*\ . The keyword *bondL* specifies the intramolecular
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OH bond length of the water model being used. This is needed to include
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H atoms that are within the cutoff even when the attached oxygen atom is
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not.
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This pair style allocates arrays sized according to the number of pairwise interactions within Rc3.
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To do this it needs an estimate for the number of water molecules within Rc3 of an oxygen atom.
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This estimate defaults to 10 and can be changed using the *neigh* keyword, which takes an integer as an argument.
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If the neigh setting is too small, the simulation will fail with the error "neigh is too small".
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If the neigh setting is too large, the pair style will use more memory than necessary.
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This pair style allocates arrays sized according to the number of
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pairwise interactions within Rc3. To do this it needs an estimate for
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the number of water molecules within Rc3 of an oxygen atom. This
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estimate defaults to 10 and can be changed using the *neigh* keyword,
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which takes an integer as an argument. If the neigh setting is too
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small, the simulation will fail with the error "neigh is too small". If
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the neigh setting is too large, the pair style will use more memory than
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necessary.
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This pair style tallies a breakdown of the total E3B potential energy into sub-categories, which can be accessed via the :doc:`compute pair <compute_pair>` command as a vector of values of length 4.
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The 4 values correspond to the terms in the first equation above: the E2 term, the Ea term, the Eb term, and the Ec term.
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This pair style tallies a breakdown of the total E3B potential energy
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into sub-categories, which can be accessed via the :doc:`compute pair
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<compute_pair>` command as a vector of values of length 4. The 4 values
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correspond to the terms in the first equation above: the E2 term, the Ea
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term, the Eb term, and the Ec term.
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See the examples/PACKAGES/e3b directory for a complete example script.
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Axel Kohlmeyer