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This commit is contained in:
Oliver Henrich
2020-07-03 17:48:49 +01:00
parent f9dc2b7ca8
commit 59aa8a5e12
3 changed files with 25 additions and 22 deletions
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1
doc/src/Commands_fix.rst
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@ -148,6 +148,7 @@ OPT.
* :doc:`oneway <fix_oneway>`
* :doc:`orient/bcc <fix_orient>`
* :doc:`orient/fcc <fix_orient>`
* :doc:`orient/eco <fix_orient_eco>`
* :doc:`phonon <fix_phonon>`
* :doc:`pimd <fix_pimd>`
* :doc:`planeforce <fix_planeforce>`

34
doc/src/fix_bond_create.rst
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@ -20,7 +20,7 @@ Syntax
* bondtype = type of created bonds
* zero or more keyword/value pairs may be appended to args
* keyword = *iparam* or *jparam* or *prob* or *atype* or *dtype* or *itype* or *aconstrain*
.. parsed-literal::
*iparam* values = maxbond, newtype
@ -117,15 +117,15 @@ and 1.0. A uniform random number between 0.0 and 1.0 is generated and
the eligible bond is only created if the random number < fraction.
The *aconstrain* keyword allows to specify a minimal and maximal angle
*amin* and *amax* between the two prospective bonding partners and a
third particle that is already bonded to one of the two partners.
Such a criterion can be important, for instance when new angle
potentials are simultaneously introduced after the formation of the
new bond. Without a restriction on the permissible angle, and for
stiffer angle potentials very large energies can arise and lead to
*amin* and *amax* between the two prospective bonding partners and a
third particle that is already bonded to one of the two partners.
Such a criterion can be important, for instance when new angle
potentials are simultaneously introduced after the formation of the
new bond. Without a restriction on the permissible angle, and for
stiffer angle potentials very large energies can arise and lead to
uncontrolled behavior.
Any bond that is created is assigned a bond type of *bondtype*.
Any bond that is created is assigned a bond type of *bondtype*
When a bond is created, data structures within LAMMPS that store bond
topology are updated to reflect the creation. If the bond is part of
@ -169,13 +169,13 @@ of type *angletype*\ , with parameters assigned by the corresponding
.. note::
LAMMPS stores and maintains a data structure with a list of the
1st, 2nd, and 3rd neighbors of each atom (within the bond topology of
first, second, and third neighbors of each atom (within the bond topology of
the system) for use in weighting pairwise interactions for bonded
atoms. Note that adding a single bond always adds a new 1st neighbor
but may also induce \*many\* new 2nd and 3rd neighbors, depending on the
atoms. Note that adding a single bond always adds a new first neighbor
but may also induce \*many\* new second and third neighbors, depending on the
molecular topology of your system. The "extra special per atom"
parameter must typically be set to allow for the new maximum total
size (1st + 2nd + 3rd neighbors) of this per-atom list. There are 2
size (first + second + third neighbors) of this per-atom list. There are 2
ways to do this. See the :doc:`read_data <read_data>` or
:doc:`create_box <create_box>` commands for details.
@ -187,12 +187,12 @@ of type *angletype*\ , with parameters assigned by the corresponding
considered for pairwise interactions, using the weighting rules set by
the :doc:`special_bonds <special_bonds>` command. Consider a new bond
created between atoms I,J. If J has a bonded neighbor K, then K
becomes a 2nd neighbor of I. Even if the *atype* keyword is not used
becomes a second neighbor of I. Even if the *atype* keyword is not used
to create angle I-J-K, the pairwise interaction between I and K will
be potentially turned off or weighted by the 1-3 weighting specified
by the :doc:`special_bonds <special_bonds>` command. This is the case
even if the "angle yes" option was used with that command. The same
is true for 3rd neighbors (1-4 interactions), the *dtype* keyword, and
is true for third neighbors (1-4 interactions), the *dtype* keyword, and
the "dihedral yes" option used with the
:doc:`special_bonds <special_bonds>` command.
@ -252,12 +252,12 @@ Restrictions
""""""""""""
This fix is part of the MC package. It is only enabled if LAMMPS was
built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
built with that package. See the :doc:`Build package <Build_package>`
doc page for more info.
The *aconstrain* keyword is only available
The *aconstrain* keyword is only available
when LAMMPS was built with the FixBondCreateAngle class.
Related commands
""""""""""""""""