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Oliver Henrich
2024-05-28 11:19:32 +01:00
parent 09a57c01da
commit 017d69f0e1
12 changed files with 24 additions and 33 deletions
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8
doc/src/bond_oxdna.rst
View File

@ -58,8 +58,7 @@ Examples
be changed without reparameterizing the entire model. They are provided in forms
compatible with both *units lj* and *units real* (see documentation of :doc:`units <units>`).
These can also be read from a potential file with correct unit style by specifying the name
of the file. Several potential files for each unit style are included in the
/potentials/ directory of the LAMMPS distribution.
of the file. Several potential files for each unit style are included in the /potentials/ directory of the LAMMPS distribution.
Description
"""""""""""
@ -146,7 +145,7 @@ For each style oxdna, oxdna2 and oxrna2, the first parameter argument can be a f
bond_style oxdna/fene
bond_coeff * oxdna.lj
will be interpreted as a request to read the (FENE) potential :ref:`(Ouldridge) <Ouldridge0>` parameters from the file with the given name.
will be interpreted as a request to read the (FENE) potential :ref:`(Ouldridge) <Ouldridge0>` parameters from the file with the given name.
The file can define multiple potential parameters for both bonded and pair interactions, but for the above bonded interactions there must exist in the file a line of the form:
.. code-block:: LAMMPS
@ -154,8 +153,7 @@ The file can define multiple potential parameters for both bonded and pair inter
* fene epsilon delta r0
There are sample potential files for each unit style in the /potentials/ directory of the LAMMPS distribution. The potential file unit system must align with
the units defined via the :doc:`units <units>` command. For conversion between different *LJ* and *real* unit systems for oxDNA, the python tool *lj2real.py* located in the examples/PACKAGES/cgdna/util/
directory can be used. This tool assumes similar file structure to the examples found in examples/PACKAGES/cgdna/examples/.
the units defined via the :doc:`units <units>` command. For conversion between different *LJ* and *real* unit systems for oxDNA, the python tool *lj2real.py* located in the examples/PACKAGES/cgdna/util/ directory can be used. This tool assumes similar file structure to the examples found in examples/PACKAGES/cgdna/examples/.
----------

9
doc/src/pair_oxdna.rst
View File

@ -90,8 +90,7 @@ Examples
.. note::
The coefficients in the above examples are provided in forms compatible with both *units lj* and *units real* (see documentation of :doc:`units <units>`).
These can also be read from a potential file with correct unit style by specifying the name of the file. Several potential files for each unit style are included in the
/potentials/ directory of the LAMMPS distribution.
These can also be read from a potential file with correct unit style by specifying the name of the file. Several potential files for each unit style are included in the /potentials/ directory of the LAMMPS distribution.
Description
"""""""""""
@ -159,8 +158,7 @@ For each pair style above the first non-modifiable argument can be a filename, a
pair_coeff 1 4 oxdna/hbond seqav oxdna.lj
will be interpreted as a request to read the corresponding hydrogen bonding potential parameters from the file with the given name.
The file can define multiple potential parameters for both bonded and pair interactions, but for the example pair interaction above there must exist in the file a line of the form:
will be interpreted as a request to read the corresponding hydrogen bonding potential parameters from the file with the given name. The file can define multiple potential parameters for both bonded and pair interactions, but for the example pair interaction above there must exist in the file a line of the form:
.. code-block:: LAMMPS
@ -182,8 +180,7 @@ If potential customization is required, the potential file reading can be mixed
will read the stacking and coaxial stacking potential parameters from the manual specification and all others from the potential file *oxdna.lj*.
There are sample potential files for each unit style in the /potentials/ directory of the LAMMPS distribution. The potential file unit system must align with
the units defined via the :doc:`units <units>` command. For conversion between different *LJ* and *real* unit systems for oxDNA, the python tool *lj2real.py* located in the examples/PACKAGES/cgdna/util/
directory can be used. This tool assumes similar file structure to the examples found in examples/PACKAGES/cgdna/examples/.
the units defined via the :doc:`units <units>` command. For conversion between different *LJ* and *real* unit systems for oxDNA, the python tool *lj2real.py* located in the examples/PACKAGES/cgdna/util/ directory can be used. This tool assumes similar file structure to the examples found in examples/PACKAGES/cgdna/examples/.
----------

8
doc/src/pair_oxdna2.rst
View File

@ -102,8 +102,7 @@ Examples
.. note::
The coefficients in the above examples are provided in forms compatible with both *units lj* and *units real* (see documentation of :doc:`units <units>`).
These can also be read from a potential file with correct unit style by specifying the name of the file. Several potential files for each unit style are included in the
/potentials/ directory of the LAMMPS distribution.
These can also be read from a potential file with correct unit style by specifying the name of the file. Several potential files for each unit style are included in the /potentials/ directory of the LAMMPS distribution.
Description
"""""""""""
@ -170,7 +169,7 @@ Therefore the following command:
pair_coeff 1 4 oxdna2/hbond seqdep oxdna.real
will be interpreted as a request to read the corresponding hydrogen bonding potential parameters from the file with the given name.
will be interpreted as a request to read the corresponding hydrogen bonding potential parameters from the file with the given name.
The file can define multiple potential parameters for both bonded and pair interactions, but for the example pair interaction above there must exist in the file a line of the form:
.. code-block:: LAMMPS
@ -194,8 +193,7 @@ If potential customization is required, the potential file reading can be mixed
will read the excluded volume and Debye-Hueckel effective charge *qeff* parameters from the manual specification and all others from the potential file *oxdna2.lj*.
There are sample potential files for each unit style in the /potentials/ directory of the LAMMPS distribution. The potential file unit system must align with
the units defined via the :doc:`units <units>` command. For conversion between different *LJ* and *real* unit systems for oxDNA, the python tool *lj2real.py* located in the examples/PACKAGES/cgdna/util/
directory can be used. This tool assumes similar file structure to the examples found in examples/PACKAGES/cgdna/examples/.
the units defined via the :doc:`units <units>` command. For conversion between different *LJ* and *real* unit systems for oxDNA, the python tool *lj2real.py* located in the examples/PACKAGES/cgdna/util/ directory can be used. This tool assumes similar file structure to the examples found in examples/PACKAGES/cgdna/examples/.
----------

10
doc/src/pair_oxrna2.rst
View File

@ -41,7 +41,7 @@ Syntax
*oxrna2/stk* args = seq T xi kappa 6.0 0.43 0.93 0.35 0.78 0.9 0 0.95 0.9 0 0.95 1.3 0 0.8 1.3 0 0.8 2.0 0.65 2.0 0.65
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
T = temperature (LJ units: 0.1 = 300 K, real units: 300 = 300 K)
T = temperature (LJ units: 0.1 = 300 K, real units: 300 = 300 K)
xi = 1.40206 (LJ units) or 8.35864576375849 (real units), temperature-independent coefficient in stacking strength
kappa = 2.77 (LJ units) or 0.005504556 (real units), coefficient of linear temperature dependence in stacking strength
*oxrna2/hbond* args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
@ -106,8 +106,7 @@ Examples
.. note::
The coefficients in the above examples are provided in forms compatible with both *units lj* and *units real* (see documentation of :doc:`units <units>`).
These can also be read from a potential file with correct unit style by specifying the name of the file. Several potential files for each unit style are included in the
/potentials/ directory of the LAMMPS distribution.
These can also be read from a potential file with correct unit style by specifying the name of the file. Several potential files for each unit style are included in the /potentials/ directory of the LAMMPS distribution.
Description
"""""""""""
@ -174,7 +173,7 @@ Therefore the following command:
pair_coeff 3 4 oxrna2/hbond seqdep oxrna2.lj
will be interpreted as a request to read the corresponding hydrogen bonding potential parameters from the file with the given name.
will be interpreted as a request to read the corresponding hydrogen bonding potential parameters from the file with the given name.
The file can define multiple potential parameters for both bonded and pair interactions, but for the example pair interaction above there must exist in the file a line of the form:
.. code-block:: LAMMPS
@ -199,8 +198,7 @@ If potential customization is required, the potential file reading can be mixed
will read the excluded volume and Debye-Hueckel effective charge *qeff* parameters from the manual specification and all others from the potential file *oxrna2.lj*.
There are sample potential files for each unit style in the /potentials/ directory of the LAMMPS distribution. The potential file unit system must align with
the units defined via the :doc:`units <units>` command. For conversion between different *LJ* and *real* unit systems for oxDNA, the python tool *lj2real.py* located in the examples/PACKAGES/cgdna/util/
directory can be used. This tool assumes similar file structure to the examples found in examples/PACKAGES/cgdna/examples/.
the units defined via the :doc:`units <units>` command. For conversion between different *LJ* and *real* unit systems for oxDNA, the python tool *lj2real.py* located in the examples/PACKAGES/cgdna/util/ directory can be used. This tool assumes similar file structure to the examples found in examples/PACKAGES/cgdna/examples/.
----------