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update docs for hybrid style updates

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This commit is contained in:
Axel Kohlmeyer
2021-08-02 21:53:31 -04:00
parent c1c31c6b04
commit 0938bc8999
2 changed files with 33 additions and 8 deletions
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2
doc/src/dihedral_hybrid.rst
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@ -57,7 +57,7 @@ If *class2* is one of the dihedral hybrid styles, the same rule holds
for specifying additional AngleTorsion (and EndBondTorsion, etc) for specifying additional AngleTorsion (and EndBondTorsion, etc)
coefficients either via the input script or in the data file. coefficients either via the input script or in the data file.
I.e. *class2* must be added to each line after the dihedral type. For I.e. *class2* must be added to each line after the dihedral type. For
lines in the AngleTorsion (or EndBondTorsion, etc) section of the data lines in the AngleTorsion (or EndBondTorsion, etc) Coeffs section of the data
file for dihedral types that are not *class2*, you must use an file for dihedral types that are not *class2*, you must use an
dihedral style of *skip* as a placeholder, e.g. dihedral style of *skip* as a placeholder, e.g.

39
doc/src/improper_hybrid.rst
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@ -40,13 +40,38 @@ potential with coefficients 120.0, 30 for :math:`K`, :math:`\chi_0`.
Improper type 2 would be computed with a *cvff* potential with coefficients Improper type 2 would be computed with a *cvff* potential with coefficients
20.0, -1, 2 for K, d, and n, respectively. 20.0, -1, 2 for K, d, and n, respectively.
If the improper *class2* potential is one of the hybrid styles, it If improper coefficients are specified in the data file read via the
requires additional AngleAngle coefficients be specified in the data :doc:`read_data <read_data>` command, then the same rule applies.
file. These lines must also have an additional "class2" argument E.g. "harmonic" or "cvff", must be added after the improper type, for
added after the improper type. For improper types which are assigned each line in the "Improper Coeffs" section, e.g.
to other hybrid styles, use the style name (e.g. "harmonic")
appropriate to that style. The AngleAngle coeffs for that improper .. parsed-literal::
type will then be ignored.
Improper Coeffs
1 harmonic 120.0 30
2 cvff 20.0 -1 2
...
If *class2* is one of the improper hybrid styles, the same rule holds
for specifying additional AngleAngle coefficients either via the input
script or in the data file. I.e. *class2* must be added to each line
after the improper type. For
lines in the AngleAngle Coeffs section of the data
file for dihedral types that are not *class2*, you must use an
improper style of *skip* as a placeholder, e.g.
.. parsed-literal::
AngleAngle Coeffs
1 skip
2 class2 0.0 0.0 0.0 115.06 130.01 115.06
...
Note that it is not necessary to use the improper style *skip* in the
input script, since AngleAngle coefficients
need not be specified at all for improper types that are not *class2*.
An improper style of *none* can be specified as the second argument to An improper style of *none* can be specified as the second argument to
the improper_coeff command, if you desire to turn off certain improper the improper_coeff command, if you desire to turn off certain improper