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cgDNA 'real' units and potential file reading for non-modifiable potential parameters (#15)

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* oxDNA potential file reading and real units

This allows for pair and bond coefficients to be read from an appropriately formatted potential file, and also allows for the use of 'real' units within oxDNA1. The correct backend coefficients for pair and bonded interactions are set when the atom vector is initialised through the "ConstantsOxdna" class, based on the units specified within the input file.

* Extract seqav/seqdep and temp from potential files

Also includes miscellaneous string consistency changes and removes unnecessary parameter from reader.next_line instances.

* oxDNA2 potential file reading and real units

This extends previous changes to oxDNA2 specific potentials, being FENE, excluded volume, coaxial stacking and Debye-Hückel. Units now default to LJ values rather than 0.

* oxDNA potential files

* LJ <-> real units conversion tool

Converts standard oxDNA data and input file to real units, with inverse flag available for real -> LJ.

* oxRNA2 potential file reading and real units

For RNA, d_cs_x is treated as d_cs within ConstantsOxdna in order to reduce code duplication and complexity.

* Reparameterise real units

* Generalise PotentialFileReader logs

* Extract stk xi and kappa from potential files

This allows users to edit these values from the input script, as is documented, rather than them being within the potential files.

* Real unit and potential file documentation

This adds examples for real unit parameters and specific potential file documentation for each bond and pair style.
This commit is contained in:
Kierran Falloon
2024-05-03 15:00:29 +01:00
committed by GitHub
parent ca675b557f
commit 775a73b67c
29 changed files with 1970 additions and 203 deletions
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50
doc/src/bond_oxdna.rst
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@ -27,6 +27,7 @@ Examples
.. code-block:: LAMMPS .. code-block:: LAMMPS
# LJ units
bond_style oxdna/fene bond_style oxdna/fene
bond_coeff * 2.0 0.25 0.7525 bond_coeff * 2.0 0.25 0.7525
@ -36,6 +37,30 @@ Examples
bond_style oxrna2/fene bond_style oxrna2/fene
bond_coeff * 2.0 0.25 0.76107 bond_coeff * 2.0 0.25 0.76107
bond_style oxdna/fene
bond_coeff * oxdna.lj
# Real units
bond_style oxdna/fene
bond_coeff * 11.92337812042065 2.1295 6.409795
bond_style oxdna2/fene
bond_coeff * 11.92337812042065 2.1295 6.4430152
bond_style oxrna2/fene
bond_coeff * 11.92337812042065 2.1295 6.482800913
bond_style oxrna2/fene
bond_coeff * oxrna2.real
.. note::
The coefficients in the above examples have to be kept fixed and cannot
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.
Description Description
""""""""""" """""""""""
@ -73,8 +98,6 @@ commands:
*oxdna2/hbond* and an additional Debye-Hueckel pair style *oxdna2/hbond* and an additional Debye-Hueckel pair style
*oxdna2/dh* have to be defined. The same applies to the oxRNA2 *oxdna2/dh* have to be defined. The same applies to the oxRNA2
:ref:`(Sulc1) <Sulc01>` styles. :ref:`(Sulc1) <Sulc01>` styles.
The coefficients in the above example have to be kept fixed and cannot
be changed without reparameterizing the entire model.
.. note:: .. note::
@ -113,6 +136,29 @@ and for sequence-specific hydrogen-bonding and stacking interactions
---------- ----------
Potential file reading
""""""""""""""""""""""
For each style oxdna, oxdna2 and oxrna2, the first parameter argument can be a filename, and if it is, no further arguments should be supplied. Therefore the following command:
.. code-block:: LAMMPS
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.
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
* 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/.
----------
Restrictions Restrictions
"""""""""""" """"""""""""

74
doc/src/pair_oxdna.rst
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@ -49,6 +49,7 @@ Examples
.. code-block:: LAMMPS .. code-block:: LAMMPS
# LJ units
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna/stk seqdep 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 pair_coeff * * oxdna/stk seqdep 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
@ -58,6 +59,40 @@ Examples
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv oxdna.lj
pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 oxdna.lj
pair_coeff * * oxdna/hbond seqav oxdna.lj
pair_coeff 1 4 oxdna/hbond seqav oxdna.lj
pair_coeff 2 3 oxdna/hbond seqav oxdna.lj
pair_coeff * * oxdna/xstk oxdna.lj
pair_coeff * * oxdna/coaxstk oxdna.lj
# Real units
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
pair_coeff * * oxdna/stk seqdep 300.0 8.01727944817084 0.005279604 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
pair_coeff 1 4 oxdna/hbond seqdep 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
pair_coeff 2 3 oxdna/hbond seqdep 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
pair_coeff * * oxdna/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0.0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna/coaxstk 3.77965257404268 3.4072 5.1108 1.87396 4.94044 2.0 2.541592654 0.65 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 -0.65 2.0 -0.65
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv oxdna.real
pair_coeff * * oxdna/stk seqav 300.0 8.01727944817084 0.005279604 oxdna.real
pair_coeff * * oxdna/hbond seqav oxdna.real
pair_coeff 1 4 oxdna/hbond seqav oxdna.real
pair_coeff 2 3 oxdna/hbond seqav oxdna.real
pair_coeff * * oxdna/xstk oxdna.real
pair_coeff * * oxdna/coaxstk oxdna.real
.. 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.
Description Description
""""""""""" """""""""""
@ -85,7 +120,7 @@ for a detailed description of the oxDNA force field.
*oxdna/fene* for the connectivity of the phosphate backbone (see also documentation of *oxdna/fene* for the connectivity of the phosphate backbone (see also documentation of
:doc:`bond_style oxdna/fene <bond_oxdna>`). Most of the coefficients :doc:`bond_style oxdna/fene <bond_oxdna>`). Most of the coefficients
in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
Exceptions are the first four coefficients after *oxdna/stk* (seq=seqdep, T=0.1, xi=1.3448 and kappa=2.6568 in the above example) Exceptions are the first four coefficients after *oxdna/stk* (seq=seqdep, T=0.1, xi=1.3448 and kappa=2.6568 and corresponding *real unit* equivalents in the above examples)
and the first coefficient after *oxdna/hbond* (seq=seqdep in the above example). and the first coefficient after *oxdna/hbond* (seq=seqdep in the above example).
When using a Langevin thermostat, e.g. through :doc:`fix langevin <fix_langevin>` When using a Langevin thermostat, e.g. through :doc:`fix langevin <fix_langevin>`
or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>` or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
@ -115,6 +150,43 @@ and :ref:`(Sulc) <Sulc1>`.
---------- ----------
Potential file reading
""""""""""""""""""""""
For each pair style above the first non-modifiable argument can be a filename, and if it is, no further arguments should be supplied. Therefore the following command:
.. code-block:: LAMMPS
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:
.. code-block:: LAMMPS
1 4 hbond <coefficients>
If potential customization is required, the potential file reading can be mixed with the manual specification of the potential parameters. For example, the following command:
.. code-block:: LAMMPS
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv oxdna.lj
pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/hbond seqav oxdna.lj
pair_coeff 1 4 oxdna/hbond seqav oxdna.lj
pair_coeff 2 3 oxdna/hbond seqav oxdna.lj
pair_coeff * * oxdna/xstk oxdna.lj
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
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/.
----------
Restrictions Restrictions
"""""""""""" """"""""""""

79
doc/src/pair_oxdna2.rst
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@ -57,6 +57,7 @@ Examples
.. code-block:: LAMMPS .. code-block:: LAMMPS
# LJ units
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
@ -67,6 +68,43 @@ Examples
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
pair_coeff * * oxdna2/dh 0.1 0.5 0.815 pair_coeff * * oxdna2/dh 0.1 0.5 0.815
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv oxdna2.lj
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 oxdna2.lj
pair_coeff * * oxdna2/hbond seqdep oxdna2.lj
pair_coeff 1 4 oxdna2/hbond seqdep oxdna2.lj
pair_coeff 2 3 oxdna2/hbond seqdep oxdna2.lj
pair_coeff * * oxdna2/xstk oxdna2.lj
pair_coeff * * oxdna2/coaxstk oxdna2.lj
pair_coeff * * oxdna2/dh 0.1 0.5 oxdna2.lj
# Real units
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
pair_coeff * * oxdna2/stk seqdep 300.0 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0.0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna2/coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 40.0 3.116592653589793
pair_coeff * * oxdna2/dh 300.0 0.5 0.815
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv oxdna2.real
pair_coeff * * oxdna2/stk seqdep 300.0 8.06199211612242 0.005309213 oxdna2.real
pair_coeff * * oxdna2/hbond seqdep oxdna2.real
pair_coeff 1 4 oxdna2/hbond seqdep oxdna2.real
pair_coeff 2 3 oxdna2/hbond seqdep oxdna2.real
pair_coeff * * oxdna2/xstk oxdna2.real
pair_coeff * * oxdna2/coaxstk oxdna2.real
pair_coeff * * oxdna2/dh 300.0 0.5 oxdna2.real
.. 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.
Description Description
""""""""""" """""""""""
@ -94,7 +132,7 @@ and :ref:`(Ouldridge) <Ouldridge2>` for a detailed description of the oxDNA2 fo
*oxdna2/fene* for the connectivity of the phosphate backbone (see also documentation of *oxdna2/fene* for the connectivity of the phosphate backbone (see also documentation of
:doc:`bond_style oxdna2/fene <bond_oxdna>`). Most of the coefficients :doc:`bond_style oxdna2/fene <bond_oxdna>`). Most of the coefficients
in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
Exceptions are the first four coefficients after *oxdna2/stk* (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 in the above example), Exceptions are the first four coefficients after *oxdna2/stk* (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 and corresponding *real unit* equivalents in the above examples).
the first coefficient after *oxdna2/hbond* (seq=seqdep in the above example) and the three coefficients the first coefficient after *oxdna2/hbond* (seq=seqdep in the above example) and the three coefficients
after *oxdna2/dh* (T=0.1, rhos=0.5, qeff=0.815 in the above example). When using a Langevin thermostat after *oxdna2/dh* (T=0.1, rhos=0.5, qeff=0.815 in the above example). When using a Langevin thermostat
e.g. through :doc:`fix langevin <fix_langevin>` or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>` e.g. through :doc:`fix langevin <fix_langevin>` or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
@ -122,6 +160,45 @@ Please cite also the relevant oxDNA2 publications
---------- ----------
Potential file reading
""""""""""""""""""""""
For each pair style above the first non-modifiable argument can be a filename (with exception of Debye-Hueckel, for which the effective charge argument can be a filename), and if it is, no further arguments should be supplied.
Therefore the following command:
.. code-block:: LAMMPS
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.
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
1 4 hbond <coefficients>
If potential customization is required, the potential file reading can be mixed with the manual specification of the potential parameters. For example, the following command:
.. code-block:: LAMMPS
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 oxdna2.lj
pair_coeff * * oxdna2/hbond seqdep oxdna2.lj
pair_coeff 1 4 oxdna2/hbond seqdep oxdna2.lj
pair_coeff 2 3 oxdna2/hbond seqdep oxdna2.lj
pair_coeff * * oxdna2/xstk oxdna2.lj
pair_coeff * * oxdna2/coaxstk oxdna2.lj
pair_coeff * * oxdna2/dh 0.1 0.5 0.815
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/.
----------
Restrictions Restrictions
"""""""""""" """"""""""""

85
doc/src/pair_oxrna2.rst
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@ -57,6 +57,7 @@ Examples
.. code-block:: LAMMPS .. code-block:: LAMMPS
# LJ units
pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
pair_coeff * * oxrna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 pair_coeff * * oxrna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 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 pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 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
@ -68,11 +69,51 @@ Examples
pair_coeff * * oxrna2/coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65 pair_coeff * * oxrna2/coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65
pair_coeff * * oxrna2/dh 0.1 0.5 1.02455 pair_coeff * * oxrna2/dh 0.1 0.5 1.02455
pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
pair_coeff * * oxrna2/excv oxrna2.lj
pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 oxrna2.lj
pair_coeff * * oxrna2/hbond seqdep oxrna2.lj
pair_coeff 1 4 oxrna2/hbond seqdep oxrna2.lj
pair_coeff 2 3 oxrna2/hbond seqdep oxrna2.lj
pair_coeff 3 4 oxrna2/hbond seqdep oxrna2.lj
pair_coeff * * oxrna2/xstk oxrna2.lj
pair_coeff * * oxrna2/coaxstk oxrna2.lj
pair_coeff * * oxrna2/dh 0.1 0.5 oxrna2.lj
# Real units
pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
pair_coeff * * oxrna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
pair_coeff * * oxrna2/stk seqdep 300.0 8.35864576375849 0.005504556 0.70439070204273 3.66274 7.92174 2.9813 6.64404 0.9 0.0 0.95 0.9 0.0 0.95 1.3 0.0 0.8 1.3 0.0 0.8 2.0 0.65 2.0 0.65
pair_coeff * * oxrna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 3 4 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxrna2/xstk 4.92690859644113 4.259 5.1108 3.57756 4.94044 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68
pair_coeff * * oxrna2/coaxstk 6.57330882442206 4.259 5.1108 3.57756 4.94044 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65
pair_coeff * * oxrna2/dh 300.0 0.5 1.02455
pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
pair_coeff * * oxrna2/excv oxrna2.real
pair_coeff * * oxrna2/stk seqdep 300.0 8.35864576375849 0.005504556 oxrna2.real
pair_coeff * * oxrna2/hbond seqdep oxrna2.real
pair_coeff 1 4 oxrna2/hbond seqdep oxrna2.real
pair_coeff 2 3 oxrna2/hbond seqdep oxrna2.real
pair_coeff 3 4 oxrna2/hbond seqdep oxrna2.real
pair_coeff * * oxrna2/xstk oxrna2.real
pair_coeff * * oxrna2/coaxstk oxrna2.real
pair_coeff * * oxrna2/dh 300.0 0.5 oxrna2.real
.. 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.
Description Description
""""""""""" """""""""""
The *oxrna2* pair styles compute the pairwise-additive parts of the oxDNA force field The *oxrna2* pair styles compute the pairwise-additive parts of the oxDNA force field
for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the for coarse-grained modelling of RNA. The effective interaction between the nucleotides consists of potentials for the
excluded volume interaction *oxrna2/excv*, the stacking *oxrna2/stk*, cross-stacking *oxrna2/xstk* excluded volume interaction *oxrna2/excv*, the stacking *oxrna2/stk*, cross-stacking *oxrna2/xstk*
and coaxial stacking interaction *oxrna2/coaxstk*, electrostatic Debye-Hueckel interaction *oxrna2/dh* and coaxial stacking interaction *oxrna2/coaxstk*, electrostatic Debye-Hueckel interaction *oxrna2/dh*
as well as the hydrogen-bonding interaction *oxrna2/hbond* between complementary pairs of nucleotides on as well as the hydrogen-bonding interaction *oxrna2/hbond* between complementary pairs of nucleotides on
@ -95,7 +136,7 @@ and :ref:`(Ouldridge) <Ouldridge3>` for a detailed description of the oxRNA2 fo
*oxrna2/fene* for the connectivity of the phosphate backbone (see also documentation of *oxrna2/fene* for the connectivity of the phosphate backbone (see also documentation of
:doc:`bond_style oxrna2/fene <bond_oxdna>`). Most of the coefficients :doc:`bond_style oxrna2/fene <bond_oxdna>`). Most of the coefficients
in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
Exceptions are the first four coefficients after *oxrna2/stk* (seq=seqdep, T=0.1, xi=1.40206 and kappa=2.77 in the above example), Exceptions are the first four coefficients after *oxrna2/stk* (seq=seqdep, T=0.1, xi=1.40206 and kappa=2.77 and corresponding *real unit* equivalents in the above examples),
the first coefficient after *oxrna2/hbond* (seq=seqdep in the above example) and the three coefficients the first coefficient after *oxrna2/hbond* (seq=seqdep in the above example) and the three coefficients
after *oxrna2/dh* (T=0.1, rhos=0.5, qeff=1.02455 in the above example). When using a Langevin thermostat after *oxrna2/dh* (T=0.1, rhos=0.5, qeff=1.02455 in the above example). When using a Langevin thermostat
e.g. through :doc:`fix langevin <fix_langevin>` or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>` e.g. through :doc:`fix langevin <fix_langevin>` or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
@ -123,6 +164,46 @@ Please cite also the relevant oxRNA2 publications
---------- ----------
Potential file reading
""""""""""""""""""""""
For each pair style above the first non-modifiable argument can be a filename (with exception of Debye-Hueckel, for which the effective charge argument can be a filename), and if it is, no further arguments should be supplied.
Therefore the following command:
.. code-block:: LAMMPS
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.
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
3 4 hbond <coefficients>
If potential customization is required, the potential file reading can be mixed with the manual specification of the potential parameters. For example, the following command:
.. code-block:: LAMMPS
pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
pair_coeff * * oxrna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxrna2/stk seqdep 0.1 1.40206 2.77 oxrna2.lj
pair_coeff * * oxrna2/hbond seqdep oxrna2.lj
pair_coeff 1 4 oxrna2/hbond seqdep oxrna2.lj
pair_coeff 2 3 oxrna2/hbond seqdep oxrna2.lj
pair_coeff 3 4 oxrna2/hbond seqdep oxrna2.lj
pair_coeff * * oxrna2/xstk oxrna2.lj
pair_coeff * * oxrna2/coaxstk oxrna2.lj
pair_coeff * * oxrna2/dh 0.1 0.5 1.02455
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/.
----------
Restrictions Restrictions
"""""""""""" """"""""""""

604
examples/PACKAGES/cgdna/util/lj2real.py Normal file
View File

@ -0,0 +1,604 @@
"""
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Kierran Falloon (University of Strathclyde, Glasgow)
Oliver Henrich (University of Strathclyde, Glasgow)
------------------------------------------------------------------------- */
Program:
Usage:
$$ python lj2real.py <datafile> <inputfile> [-i]
$$ [-i] flag is optional and is used to convert real -> LJ units.
Requirements:
LAMMPS data file and input file.
This script assumes a input and data file structure similar to those found in examples/PACKAGES/cgdna/examples/.
"""
import datetime
import os
import sys
class Sections:
"""Sections of the data file"""
def __init__(
self,
bounds: bool,
masses: bool,
atoms: bool,
velocities: bool,
ellipsoids: bool,
):
self.bounds = bounds # xlo, xhi, ylo, yhi, zlo, zhi
self.masses = masses # Masses
self.atoms = atoms # Atoms
self.velocities = velocities # Velocities
self.ellipsoids = ellipsoids # Ellipsoids
# Conversion factors
class ConversionFactors:
"""Conversion factors for LJ to real units"""
def __init__(self, invert: bool = False):
self.inverted = False
self.temp_conv_factor = 3000.038822
self.energy_conv_factor = 5.961689060210325
self.kT_conv_factor = 0.001987204155
self.mass_conv_factor = 100.0277580236
self.length_conv_factor = 8.518
self.time_conv_factor = 1706.0
self.vel_conv_factor = 0.004992966002344666
self.angular_mom_conv_factor = 4.254188991883894
self.density_conv_factor = 0.2687551067436886
self.oxdna_fene_string = "11.92337812042065 2.1295 6.409795"
self.oxdna_excv_string = "11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576"
self.oxdna_stk_string = "0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65"
self.oxdna_hbond_string = "0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45"
self.oxdna_hbond_1_4_2_3_string = "6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45"
self.oxdna_xstk_string = "3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68"
self.oxdna_coaxstk_string = "3.77965257404268 3.4072 5.1108 1.87396 4.94044 2.0 2.541592654 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2 -0.65 2 -0.65"
self.oxdna2_fene_string = "11.92337812042065 2.1295 6.4430152"
self.oxdna2_excv_string = "11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576"
self.oxdna2_stk_string = "0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65"
self.oxdna2_hbond_string = "0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45"
self.oxdna2_hbond_1_4_2_3_string = "6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45"
self.oxdna2_xstk_string = "3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68"
self.oxdna2_coaxstk_string = "4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793"
self.oxrna2_fene_string = "11.92337812042065 2.1295 6.482800913"
self.oxrna2_excv_string = "11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576"
self.oxrna2_stk_string = "0.70439070204273 3.66274 7.92174 2.9813 6.64404 0.9 0.0 0.95 0.9 0.0 0.95 1.3 0.0 0.8 1.3 0.0 0.8 2.0 0.65 2.0 0.65"
self.oxrna2_hbond_string = "0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
self.oxrna2_hbond_1_4_2_3_3_4_string = "5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
self.oxrna2_xstk_string = "4.92690859644113 4.259 5.1108 3.57756 4.94044 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68"
self.oxrna2_coaxstk_string = "6.57330882442206 4.259 5.1108 3.57756 4.94044 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65"
if invert:
self.invert()
def invert(self):
"""Inverts the conversion factors for real -> LJ"""
self.inverted = True
self.temp_conv_factor = 1.0 / self.temp_conv_factor
self.energy_conv_factor = 1.0 / self.energy_conv_factor
self.kT_conv_factor = 1.0 / self.kT_conv_factor
self.mass_conv_factor = 1.0 / self.mass_conv_factor
self.length_conv_factor = 1.0 / self.length_conv_factor
self.time_conv_factor = 1.0 / self.time_conv_factor
self.vel_conv_factor = 1.0 / self.vel_conv_factor
self.angular_mom_conv_factor = 1.0 / self.angular_mom_conv_factor
self.density_conv_factor = 1.0 / self.density_conv_factor
self.oxdna_fene_string = "2.0 0.25 0.7525"
self.oxdna_excv_string = "2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32"
self.oxdna_stk_string = (
"6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65"
)
self.oxdna_hbond_string = "0.0 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"
self.oxdna_hbond_1_4_2_3_string = "1.077 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"
self.oxdna_xstk_string = "47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68"
self.oxdna_coaxstk_string = "46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65"
self.oxdna2_fene_string = "2.0 0.25 0.7564"
self.oxdna2_excv_string = "2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32"
self.oxdna2_stk_string = (
"6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65"
)
self.oxdna2_hbond_string = "0.0 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"
self.oxdna2_hbond_1_4_2_3_string = "1.0678 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"
self.oxdna2_xstk_string = "47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68"
self.oxdna2_coaxstk_string = "58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793"
self.oxrna2_fene_string = "2.0 0.25 0.761070781051"
self.oxrna2_excv_string = "2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32"
self.oxrna2_stk_string = "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"
self.oxrna2_hbond_string = "0.0 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"
self.oxrna2_hbond_1_4_2_3_3_4_string = "0.870439 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"
self.oxrna2_xstk_string = "59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68"
self.oxrna2_coaxstk_string = "80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65"
def check_datafile_header(line: str, sections: Sections):
"""Checks for headers to modify corresponding data, since datafile is split into headers.
Modifies the Sections object to keep track of the current section.
Args:
line (str): The line to check
masses_section (bool): If the current section is the masses section
atoms_section (bool): If the current section is the atoms section
velocities_section (bool): If the current section is the velocities section
ellipsoids_section (bool): If the current section is the ellipsoids section
"""
if any(header in line for header in ["xlo", "xhi", "ylo", "yhi", "zlo", "zhi"]):
sections.bounds = True
sections.masses = False
sections.atoms = False
sections.velocities = False
sections.ellipsoids = False
elif "Masses" in line:
sections.bounds = False
sections.masses = True
sections.atoms = False
sections.velocities = False
sections.ellipsoids = False
elif "Atoms" in line:
sections.bounds = False
sections.masses = False
sections.atoms = True
sections.velocities = False
sections.ellipsoids = False
elif "Velocities" in line:
sections.bounds = False
sections.masses = False
sections.atoms = False
sections.velocities = True
sections.ellipsoids = False
elif "Ellipsoids" in line:
sections.bounds = False
sections.masses = False
sections.atoms = False
sections.velocities = False
sections.ellipsoids = True
elif "Bonds" in line:
sections.bounds = False
sections.masses = False
sections.atoms = False
sections.velocities = False
sections.ellipsoids = False
def modify_datafile(datafile_path: str, conversion_factors: ConversionFactors):
"""Modifies the file by header to use real units.
Args:
datafile_path (str): The path to the file to modify
"""
lines_changed = 0
current_section = Sections(False, False, False, False, False)
with open(datafile_path, "r", encoding="UTF-8") as file:
lines = file.readlines()
if conversion_factors.inverted:
lines[0] = (
"LAMMPS data file in LJ units via oxdna lj2real.py, date "
+ str(datetime.date.today())
+ "\n"
)
else:
lines[0] = (
"LAMMPS data file in real units via oxdna lj2real.py, date "
+ str(datetime.date.today())
+ "\n"
)
for i, line in enumerate(lines):
check_datafile_header(line, current_section) # check for headers
elements = line.split()
if (
not elements
or elements[0] == "#"
or any(
header in line
for header in ["Masses", "Atoms", "Velocities", "Ellipsoids", "Bonds"]
)
):
continue
# modify the line based on the current section it is in
if current_section.bounds:
elements[0:2] = [
str(int(float(x) * conversion_factors.length_conv_factor))
for x in elements[0:2]
]
lines[i] = " ".join(elements) + "\n"
lines_changed += 1
if current_section.masses:
elements[1] = str(
round(float(elements[1]) * conversion_factors.mass_conv_factor, 4)
)
lines[i] = " ".join(elements) + "\n"
lines_changed += 1
elif current_section.atoms:
elements[2:5] = [
str(float(x) * conversion_factors.length_conv_factor)
for x in elements[2:5]
]
elements[7] = str(
float(elements[7]) * conversion_factors.density_conv_factor
)
lines[i] = " ".join(elements) + "\n"
lines_changed += 1
elif current_section.velocities:
elements[1:4] = [
str(float(x) * conversion_factors.vel_conv_factor)
for x in elements[1:4]
]
elements[4:7] = [
str(float(x) * conversion_factors.angular_mom_conv_factor)
for x in elements[4:7]
]
lines[i] = " ".join(elements) + "\n"
lines_changed += 1
elif current_section.ellipsoids:
elements[1:4] = [
str(float(x) * conversion_factors.length_conv_factor)
for x in elements[1:4]
]
lines[i] = " ".join(elements) + "\n"
lines_changed += 1
if conversion_factors.inverted:
new_datafile_path = datafile_path + "_lj"
else:
new_datafile_path = datafile_path + "_real"
with open(new_datafile_path, "w", encoding="UTF-8") as file:
file.writelines(lines)
if lines_changed == 0:
print(
"Warning: No lines changed in data file. Ensure correct usage: python lj2real.py <datafile> <inputfile> [-i]"
)
else:
print(f"Data file lines changed: {lines_changed}")
return new_datafile_path
def modify_inputfile(inputfile_path: str, conversion_factors: ConversionFactors):
"""Modifies the input file line by line to use real units.
Args:
inputfile_path (str): The path to the input file to modify
"""
lines_changed = 0
oxdna2_flag, oxrna2_flag = False, False
with open(inputfile_path, "r", encoding="UTF-8") as file:
lines = file.readlines()
for i, line in enumerate(lines):
if "oxdna2" in line and not oxdna2_flag:
oxdna2_flag = True
print("Note: oxdna2 found in input file. Using oxdna2 conversion factors.")
if "oxrna2" in line and not oxrna2_flag:
oxrna2_flag = True
print("Note: oxrna2 found in input file. Using oxrna2 conversion factors.")
if oxdna2_flag and oxrna2_flag:
print(
"Warning: Both oxdna2 and oxrna2 found in input file. Output will likely be incorrect."
)
if "variable T" in line:
old_value = line.split()[3]
new_value = str(
round(float(old_value) * conversion_factors.temp_conv_factor, 1)
)
lines[i] = line.replace(old_value, new_value)
lines_changed += 1
elif "units" in line:
if conversion_factors.inverted:
lines[i] = "units lj\n"
else:
lines[i] = "units real\n"
lines_changed += 1
elif "atom_modify" in line:
elements = line.split()
elements[3] = str(
round(float(elements[3]) * conversion_factors.length_conv_factor, 3)
)
lines[i] = " ".join(elements) + "\n"
lines_changed += 1
elif "neighbor" in line:
elements = line.split()
elements[1] = str(
round(float(elements[1]) * conversion_factors.length_conv_factor, 3)
)
lines[i] = " ".join(elements) + "\n"
lines_changed += 1
elif "read_data" in line:
elements = line.split()
if conversion_factors.inverted:
elements[1] = elements[1] + "_lj"
else:
elements[1] = (
elements[1] + "_real"
) # naming convention of datafile after conversion
lines[i] = " ".join(elements) + "\n"
lines_changed += 1
elif "mass" in line:
elements = line.split()
elements[4] = str(
round(float(elements[4]) * conversion_factors.mass_conv_factor, 4)
)
lines[i] = " ".join(elements) + "\n"
lines_changed += 1
elif "bond_coeff" in line or "pair_coeff" in line:
if ".lj" in line or ".real" in line:
if conversion_factors.inverted:
line = line.replace(".real", ".lj")
else:
line = line.replace(".lj", ".real")
lines[i] = line
lines_changed += 1
if "stk" in line and "xstk" not in line and "coaxstk" not in line:
elements = line.split()
elements[6] = str( # convert xi
round(
float(elements[6]) * conversion_factors.energy_conv_factor,
14,
)
)
elements[7] = str( # convert kappa
round(float(elements[7]) * conversion_factors.kT_conv_factor, 9)
)
lines[i] = " ".join(elements) + "\n"
else:
elements = line.split()
if "bond_coeff" in line:
if oxdna2_flag:
elements[2:] = conversion_factors.oxdna2_fene_string.split()
elif oxrna2_flag:
elements[2:] = conversion_factors.oxrna2_fene_string.split()
else:
elements[2:] = conversion_factors.oxdna_fene_string.split()
elif "excv" in line:
if oxdna2_flag:
elements[4:] = conversion_factors.oxdna2_excv_string.split()
elif oxrna2_flag:
elements[4:] = conversion_factors.oxrna2_excv_string.split()
else:
elements[4:] = conversion_factors.oxdna_excv_string.split()
elif "stk" in line:
if "coaxstk" in line:
if oxdna2_flag:
elements[4:] = (
conversion_factors.oxdna2_coaxstk_string.split()
)
elif oxrna2_flag:
elements[4:] = (
conversion_factors.oxrna2_coaxstk_string.split()
)
else:
elements[4:] = (
conversion_factors.oxdna_coaxstk_string.split()
)
elif "xstk" in line:
if oxdna2_flag:
elements[4:] = conversion_factors.oxdna2_xstk_string.split()
elif oxrna2_flag:
elements[4:] = conversion_factors.oxrna2_xstk_string.split()
else:
elements[4:] = conversion_factors.oxdna_xstk_string.split()
else: # stk
elements[6] = str( # convert xi
round(
float(elements[6])
* conversion_factors.energy_conv_factor,
14,
)
)
elements[7] = str( # convert kappa
round(
float(elements[7]) * conversion_factors.kT_conv_factor,
9,
)
)
if oxdna2_flag:
elements[8:] = conversion_factors.oxdna2_stk_string.split()
elif oxrna2_flag:
elements[8:] = conversion_factors.oxrna2_stk_string.split()
else:
elements[8:] = conversion_factors.oxdna_stk_string.split()
elif "hbond" in line:
if elements[1] == "*" and elements[2] == "*":
if oxdna2_flag:
elements[5:] = (
conversion_factors.oxdna2_hbond_string.split()
)
elif oxrna2_flag:
elements[5:] = (
conversion_factors.oxrna2_hbond_string.split()
)
else:
elements[5:] = conversion_factors.oxdna_hbond_string.split()
else:
if oxdna2_flag:
elements[5:] = (
conversion_factors.oxdna2_hbond_1_4_2_3_string.split()
)
elif oxrna2_flag:
elements[5:] = (
conversion_factors.oxrna2_hbond_1_4_2_3_3_4_string.split()
)
else:
elements[5:] = (
conversion_factors.oxdna_hbond_1_4_2_3_string.split()
)
lines[i] = " ".join(elements) + "\n"
lines_changed += 1
elif "langevin" in line:
elements = line.split()
elements[6] = str(
round(float(elements[6]) * conversion_factors.time_conv_factor, 2)
)
lines[i] = " ".join(elements) + "\n"
lines_changed += 1
elif "timestep" in line:
elements = line.split()
elements[1] = str(
round(float(elements[1]) * conversion_factors.time_conv_factor, 5)
)
lines[i] = " ".join(elements) + "\n"
lines_changed += 1
elif "comm_modify" in line:
elements = line.split()
elements[2] = str(
round(float(elements[2]) * conversion_factors.length_conv_factor, 1)
)
lines[i] = " ".join(elements) + "\n"
lines_changed += 1
else:
continue
if conversion_factors.inverted:
new_inputfile_path = inputfile_path + "_lj"
else:
new_inputfile_path = inputfile_path + "_real"
with open(new_inputfile_path, "w", encoding="UTF-8") as file:
if conversion_factors.inverted:
file.write(
"# LAMMPS input file in LJ units via oxdna lj2real.py, date "
+ str(datetime.date.today())
+ "\n"
)
else:
file.write(
"# LAMMPS input file in real units via oxdna lj2real.py, date "
+ str(datetime.date.today())
+ "\n"
)
file.writelines(lines)
if lines_changed == 0:
print(
"Warning: No lines changed in input file. Ensure correct usage: python lj2real.py <datafile> <inputfile> [-i]"
)
else:
print(f"Input file lines changed: {lines_changed}")
return new_inputfile_path
def main():
"""Main function"""
print(
"\nLAMMPS data and input file conversion to real units via oxdna convert_data.py\n"
"Note: This script assumes a input and data file structure similar to those found in examples/PACKAGES/cgdna/examples/.\n"
"Ensure output is checked for correctness."
)
if len(sys.argv) > 2:
datafile_path = sys.argv[1]
inputfile_path = sys.argv[2]
invert = False
if len(sys.argv) > 3:
if sys.argv[3] == "-i":
invert = True
print("Performing real -> LJ conversion.")
else:
print(
"Invalid flag. Usage: python lj2real.py <datafile> <inputfile> [-i]"
)
sys.exit(1)
if invert:
conversion_factors = ConversionFactors(invert=True)
print(
"\nUsing conversion factors (real T, m, l, t, v, ρ -> LJ T*, m*, l*, t*, v*, ρ*):"
)
else:
conversion_factors = ConversionFactors(invert=False)
print(
"\nUsing conversion factors (LJ T*, m*, l*, t*, v*, ρ* -> real T, m, l, t, v, ρ):"
)
else:
print("\nUsage: python lj2real.py <datafile> <inputfile> [-i]")
print("\t[-i] flag is optional and is used to convert real -> LJ units.\n")
sys.exit(1)
conversion_factors_string = (
f"Temperature T\t≈ {round(conversion_factors.temp_conv_factor, 6)} T* (K)\n"
f"Energy ε\t≈ {round(conversion_factors.energy_conv_factor, 6)} ε* (kcal/mol)\n"
f"Mass m\t\t≈ {round(conversion_factors.mass_conv_factor, 6)} m* (g/mol)\n"
f"Length l\t≈ {round(conversion_factors.length_conv_factor, 6)} l* (Å)\n"
f"Time t\t\t≈ {round(conversion_factors.time_conv_factor, 6)} t* (fs)\n"
f"Velocity v\t≈ {round(conversion_factors.vel_conv_factor, 6)} v* (Å/fs)\n"
f"AngMom l\t≈ {round(conversion_factors.angular_mom_conv_factor, 6)} (g/mol Å^2/fs)\n"
f"Density ρ\t≈ {round(conversion_factors.density_conv_factor, 6)} ρ* (g/cm^3)\n"
f"Calculated using Sengar, Ouldridge, Henrich, Rovigatti, & Šulc. Front Mol Biosci 8 (2021). & https://docs.lammps.org/units.html.\n"
f"See examples/PACKAGES/cgdna/util/lj2real.py for exact conversion factors.\n"
)
print(conversion_factors_string)
print("Current directory: ", os.getcwd())
try:
new_datafile_path = modify_datafile(datafile_path, conversion_factors)
print(f"New data file: {new_datafile_path}")
except Exception as e:
print(f"Error modifying data file: {e}")
try:
new_inputfile_path = modify_inputfile(inputfile_path, conversion_factors)
print(f"New input file: {new_inputfile_path}\n")
except Exception as e:
print(f"Error modifying input file: {e}")
if __name__ == "__main__":
main()

10
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# DATE: 2024-04-21 UNITS: lj CONTRIBUTOR: Oliver Henrich, oliver.henrich@strath.ac.uk CITATION: Ouldridge, Louis, and Doye, J Chem Phys, 134, 8 (2011)
#
* fene 2.0 0.25 0.7525
* * excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
* * stk 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
* * hbond 0.0 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
1 4 hbond 1.077 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
2 3 hbond 1.077 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
* * xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
* * coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65

10
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# DATE: 2024-04-26 UNITS: real CONTRIBUTOR: Oliver Henrich, oliver.henrich@strath.ac.uk
#
* fene 11.92337812042065 2.1295 6.409795
* * excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
* * stk 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
* * hbond 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
1 4 hbond 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
2 3 hbond 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
* * xstk 3.902852174 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0.0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
* * coaxstk 3.77965257404268 3.4072 5.1108 1.87396 4.94044 2.0 2.541592654 0.65 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 -0.65 2.0 -0.65

11
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# DATE: 2024-04-21 UNITS: lj CONTRIBUTOR: Oliver Henrich, oliver.henrich@strath.ac.uk CITATION: Snodin, Randisi, Mosayebi, Šulc et. al., J Chem Phys, 142, 23 (2015)
#
* fene 2.0 0.25 0.7564
* * excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
* * stk 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
* * hbond 0.0 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
1 4 hbond 1.0678 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
2 3 hbond 1.0678 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
* * xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
* * coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
* * dh 0.815

11
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# DATE: 2024-04-26 UNITS: real CONTRIBUTOR: Oliver Henrich, oliver.henrich@strath.ac.uk
#
* fene 11.92337812042065 2.1295 6.4430152
* * excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
* * stk 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65
* * hbond 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
1 4 hbond 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
2 3 hbond 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45
* * xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0.0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
* * coaxstk 4.80673207785863 3.4072 5.1108 1.87396 4.94044 2.0 2.891592653589793 0.65 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 40.0 3.116592653589793
* * dh 0.815

12
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# DATE: 2024-04-19 UNITS: lj CONTRIBUTOR: Oliver Henrich, oliver.henrich@strath.ac.uk CITATION: Šulc, Romano, Ouldridge, Rovigatti, Doye, Louis, J Chem Phys, 140, 23 (2014)
#
* fene 2.0 0.25 0.761070781051
* * excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
* * stk 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
* * hbond 0.0 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
1 4 hbond 0.870439 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
2 3 hbond 0.870439 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
3 4 hbond 0.870439 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
* * xstk 59.9626 0.5 0.6 0.42 0.58 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68
* * coaxstk 80 0.5 0.6 0.42 0.58 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65
* * dh 1.02455

12
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# DATE: 2024-04-26 UNITS: real CONTRIBUTOR: Oliver Henrich, oliver.henrich@strath.ac.uk
#
* fene 11.92337812042065 2.1295 6.482800913
* * excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
* * stk 0.70439070204273 3.66274 7.92174 2.9813 6.64404 0.9 0.0 0.95 0.9 0.0 0.95 1.3 0.0 0.8 1.3 0.0 0.8 2.0 0.65 2.0 0.65
* * hbond 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
1 4 hbond 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
2 3 hbond 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
3 4 hbond 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
* * xstk 4.92690859644113 4.259 5.1108 3.57756 4.94044 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68
* * coaxstk 6.57330882442206 4.259 5.1108 3.57756 4.94044 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65
* * dh 1.02455

4
src/CG-DNA/atom_vec_oxdna.cpp
View File

@ -12,6 +12,7 @@
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "atom_vec_oxdna.h" #include "atom_vec_oxdna.h"
#include "constants_oxdna.h"
#include "atom.h" #include "atom.h"
#include "error.h" #include "error.h"
@ -45,6 +46,9 @@ AtomVecOxdna::AtomVecOxdna(LAMMPS *lmp) : AtomVec(lmp)
if (!force->newton_bond) if (!force->newton_bond)
error->warning(FLERR, "Write_data command requires newton on to preserve 3'->5' bond polarity"); error->warning(FLERR, "Write_data command requires newton on to preserve 3'->5' bond polarity");
// initialize oxDNA units
ConstantsOxdna constants(lmp);
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------

5
src/CG-DNA/bond_oxdna2_fene.cpp
View File

@ -15,6 +15,7 @@
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "bond_oxdna2_fene.h" #include "bond_oxdna2_fene.h"
#include "constants_oxdna.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -24,8 +25,8 @@ using namespace LAMMPS_NS;
void BondOxdna2Fene::compute_interaction_sites(double e1[3], double e2[3], double /*e3*/[3], void BondOxdna2Fene::compute_interaction_sites(double e1[3], double e2[3], double /*e3*/[3],
double r[3]) const double r[3]) const
{ {
constexpr double d_cs_x = -0.34; double d_cs_x = ConstantsOxdna::get_d_cs_x();
constexpr double d_cs_y = +0.3408; double d_cs_y = ConstantsOxdna::get_d_cs_y();
r[0] = d_cs_x * e1[0] + d_cs_y * e2[0]; r[0] = d_cs_x * e1[0] + d_cs_y * e2[0];
r[1] = d_cs_x * e1[1] + d_cs_y * e2[1]; r[1] = d_cs_x * e1[1] + d_cs_y * e2[1];

46
src/CG-DNA/bond_oxdna_fene.cpp
View File

@ -18,10 +18,12 @@
#include "atom.h" #include "atom.h"
#include "comm.h" #include "comm.h"
#include "constants_oxdna.h"
#include "error.h" #include "error.h"
#include "force.h" #include "force.h"
#include "memory.h" #include "memory.h"
#include "neighbor.h" #include "neighbor.h"
#include "potential_file_reader.h"
#include "update.h" #include "update.h"
#include "math_extra.h" #include "math_extra.h"
@ -49,7 +51,7 @@ BondOxdnaFene::~BondOxdnaFene()
void BondOxdnaFene::compute_interaction_sites(double e1[3], double /*e2*/[3], double /*e3*/[3], void BondOxdnaFene::compute_interaction_sites(double e1[3], double /*e2*/[3], double /*e3*/[3],
double r[3]) const double r[3]) const
{ {
constexpr double d_cs = -0.4; double d_cs = ConstantsOxdna::get_d_cs();
r[0] = d_cs * e1[0]; r[0] = d_cs * e1[0];
r[1] = d_cs * e1[1]; r[1] = d_cs * e1[1];
@ -295,15 +297,49 @@ void BondOxdnaFene::allocate()
void BondOxdnaFene::coeff(int narg, char **arg) void BondOxdnaFene::coeff(int narg, char **arg)
{ {
if (narg != 4) error->all(FLERR, "Incorrect args for bond coefficients in oxdna/fene"); if (narg != 2 && narg != 4) error->all(FLERR, "Incorrect args for bond coefficients in oxdna/fene");
if (!allocated) allocate(); if (!allocated) allocate();
int ilo, ihi; int ilo, ihi;
utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error); utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error);
double k_one = utils::numeric(FLERR, arg[1], false, lmp); double k_one;
double Delta_one = utils::numeric(FLERR, arg[2], false, lmp); double Delta_one;
double r0_one = utils::numeric(FLERR, arg[3], false, lmp); double r0_one;
if (narg == 4) {
k_one = utils::numeric(FLERR, arg[1], false, lmp);
Delta_one = utils::numeric(FLERR, arg[2], false, lmp);
r0_one = utils::numeric(FLERR, arg[3], false, lmp);
} else {
if (comm->me == 0) { // read values from potential file
PotentialFileReader reader(lmp, arg[1], "oxdna potential", " (fene)");
char * line;
std::string iloc, potential_name;
while(line = reader.next_line()) {
try {
ValueTokenizer values(line);
iloc = values.next_string();
potential_name = values.next_string();
if (iloc == arg[0] && potential_name == "fene") {
k_one = values.next_double();
Delta_one = values.next_double();
r0_one = values.next_double();
break;
} else continue;
} catch (std::exception &e) {
error->one(FLERR, "Problem parsing oxDNA potential file: {}", e.what());
}
}
if (iloc != arg[0] || potential_name != "fene") error->one(FLERR, "No corresponding fene potential found in file {} for bond type {}", arg[1], arg[0]);
}
MPI_Bcast(&k_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&Delta_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&r0_one, 1, MPI_DOUBLE, 0, world);
}
int count = 0; int count = 0;

6
src/CG-DNA/bond_oxrna2_fene.cpp
View File

@ -16,6 +16,8 @@
#include "bond_oxrna2_fene.h" #include "bond_oxrna2_fene.h"
#include "constants_oxdna.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -25,8 +27,8 @@ using namespace LAMMPS_NS;
void BondOxrna2Fene::compute_interaction_sites(double e1[3], double /*e2*/[3], double e3[3], void BondOxrna2Fene::compute_interaction_sites(double e1[3], double /*e2*/[3], double e3[3],
double r[3]) const double r[3]) const
{ {
constexpr double d_cs_x = -0.4; double d_cs_x = ConstantsOxdna::get_d_cs();
constexpr double d_cs_z = +0.2; double d_cs_z = ConstantsOxdna::get_d_cs_z();
r[0] = d_cs_x * e1[0] + d_cs_z * e3[0]; r[0] = d_cs_x * e1[0] + d_cs_z * e3[0];
r[1] = d_cs_x * e1[1] + d_cs_z * e3[1]; r[1] = d_cs_x * e1[1] + d_cs_z * e3[1];

69
src/CG-DNA/constants_oxdna.cpp Normal file
View File

@ -0,0 +1,69 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Oliver Henrich (University of Strathclyde, Glasgow)
Kierran Falloon (University of Strathclyde, Glasgow)
------------------------------------------------------------------------- */
#include "constants_oxdna.h"
namespace LAMMPS_NS {
ConstantsOxdna::ConstantsOxdna(class LAMMPS *lmp) : Pointers(lmp)
{
// set oxDNA units
units = update->unit_style;
real_flag = utils::strmatch(units.c_str(), "^real");
if (real_flag) set_real_units();
}
// default to lj units
// oxDNA 1 parameters
double ConstantsOxdna::d_cs = -0.4;
double ConstantsOxdna::d_cst = +0.34;
double ConstantsOxdna::d_chb = +0.4;
double ConstantsOxdna::d_cb = +0.4;
// oxDNA 2 parameters
double ConstantsOxdna::d_cs_x = -0.34;
double ConstantsOxdna::d_cs_y = +0.3408;
double ConstantsOxdna::lambda_dh_one_prefactor = +0.3616455075438555; // = C1
double ConstantsOxdna::qeff_dh_pf_one_prefactor = +0.08173808693529228; // = C2
// oxRNA 2 parameters
double ConstantsOxdna::d_cs_z = +0.2;
double ConstantsOxdna::d_cst_x_3p = +0.4;
double ConstantsOxdna::d_cst_y_3p = +0.1;
double ConstantsOxdna::d_cst_x_5p = +0.124906078525;
double ConstantsOxdna::d_cst_y_5p = -0.00866274917473;
void ConstantsOxdna::set_real_units()
{
// oxDNA 1 parameters in real units
d_cs = -3.4072;
d_cst = +2.89612;
d_chb = +3.4072;
d_cb = +3.4072;
// oxDNA 2 parameters in real units
d_cs_x = -2.89612;
d_cs_y = +2.9029344;
lambda_dh_one_prefactor = +0.05624154892; // = C1 * 8.518 * sqrt(k_B/4.142e-20)
qeff_dh_pf_one_prefactor = +4.15079634587587; // = C2 * 5.961689060210325 * 8.518
// oxRNA 2 parameters in real units
// d_cs_x = -3.4072 = d_cs for RNA
d_cs_z = +1.7036;
d_cst_x_3p = +3.4072,
d_cst_y_3p = +0.8518;
d_cst_x_5p = +1.063949977,
d_cst_y_5p = -0.07378929747;
};
} // namespace LAMMPS_NS

65
src/CG-DNA/constants_oxdna.h Normal file
View File

@ -0,0 +1,65 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef CONSTANTS_OXDNA_H
#define CONSTANTS_OXDNA_H
#include "update.h"
namespace LAMMPS_NS {
class ConstantsOxdna : protected Pointers {
public:
ConstantsOxdna(class LAMMPS *lmp);
virtual ~ConstantsOxdna(){};
// oxDNA 1 getters
static double get_d_cs() { return d_cs; }
static double get_d_cst() { return d_cst; }
static double get_d_chb() { return d_chb; }
static double get_d_cb() { return d_cb; }
// oxDNA 2 getters
static double get_d_cs_x() { return d_cs_x; }
static double get_d_cs_y() { return d_cs_y; }
static double get_lambda_dh_one_prefactor() { return lambda_dh_one_prefactor; }
static double get_qeff_dh_pf_one_prefactor() { return qeff_dh_pf_one_prefactor; }
// oxRNA 2 getters
static double get_d_cs_z() { return d_cs_z; }
static double get_d_cst_x_3p() { return d_cst_x_3p; }
static double get_d_cst_y_3p() { return d_cst_y_3p; }
static double get_d_cst_x_5p() { return d_cst_x_5p; }
static double get_d_cst_y_5p() { return d_cst_y_5p; }
private:
std::string units;
bool real_flag;
void set_real_units();
// oxDNA 1 parameters
static double d_cs, d_cst, d_chb, d_cb;
// oxDNA 2 parameters
static double d_cs_x, d_cs_y;
static double lambda_dh_one_prefactor, qeff_dh_pf_one_prefactor;
// oxRNA 2 parameters
static double d_cs_z;
static double d_cst_x_3p, d_cst_y_3p;
static double d_cst_x_5p, d_cst_y_5p;
};
} // namespace LAMMPS_NS
#endif

80
src/CG-DNA/pair_oxdna2_coaxstk.cpp
View File

@ -19,6 +19,7 @@
#include "atom.h" #include "atom.h"
#include "comm.h" #include "comm.h"
#include "constants_oxdna.h"
#include "error.h" #include "error.h"
#include "force.h" #include "force.h"
#include "math_const.h" #include "math_const.h"
@ -26,6 +27,7 @@
#include "memory.h" #include "memory.h"
#include "mf_oxdna.h" #include "mf_oxdna.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "potential_file_reader.h"
#include <cmath> #include <cmath>
#include <cstring> #include <cstring>
@ -113,7 +115,8 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)
double cosphi3; double cosphi3;
// distances COM-backbone site, COM-stacking site // distances COM-backbone site, COM-stacking site
double d_cs=-0.4, d_cst=+0.34; double d_cs = ConstantsOxdna::get_d_cs();
double d_cst = ConstantsOxdna::get_d_cst();
// vectors COM-backbone site, COM-stacking site in lab frame // vectors COM-backbone site, COM-stacking site in lab frame
double ra_cs[3],ra_cst[3]; double ra_cs[3],ra_cst[3];
double rb_cs[3],rb_cst[3]; double rb_cs[3],rb_cst[3];
@ -557,7 +560,7 @@ void PairOxdna2Coaxstk::coeff(int narg, char **arg)
{ {
int count; int count;
if (narg != 21) error->all(FLERR,"Incorrect args for pair coefficients in oxdna2/coaxstk"); if (narg != 3 && narg != 21) error->all(FLERR,"Incorrect args for pair coefficients in oxdna2/coaxstk");
if (!allocated) allocate(); if (!allocated) allocate();
int ilo,ihi,jlo,jhi; int ilo,ihi,jlo,jhi;
@ -584,6 +587,7 @@ void PairOxdna2Coaxstk::coeff(int narg, char **arg)
double AA_cxst1_one, BB_cxst1_one; double AA_cxst1_one, BB_cxst1_one;
if (narg == 21) {
k_cxst_one = utils::numeric(FLERR,arg[2],false,lmp); k_cxst_one = utils::numeric(FLERR,arg[2],false,lmp);
cut_cxst_0_one = utils::numeric(FLERR,arg[3],false,lmp); cut_cxst_0_one = utils::numeric(FLERR,arg[3],false,lmp);
cut_cxst_c_one = utils::numeric(FLERR,arg[4],false,lmp); cut_cxst_c_one = utils::numeric(FLERR,arg[4],false,lmp);
@ -608,6 +612,78 @@ void PairOxdna2Coaxstk::coeff(int narg, char **arg)
AA_cxst1_one = utils::numeric(FLERR,arg[19],false,lmp); AA_cxst1_one = utils::numeric(FLERR,arg[19],false,lmp);
BB_cxst1_one = utils::numeric(FLERR,arg[20],false,lmp); BB_cxst1_one = utils::numeric(FLERR,arg[20],false,lmp);
} else {
if (comm->me == 0) { // read values from potential file
PotentialFileReader reader(lmp, arg[2], "oxdna potential", " (coaxstk)");
char * line;
std::string iloc, jloc, potential_name;
while(line = reader.next_line()) {
try {
ValueTokenizer values(line);
iloc = values.next_string();
jloc = values.next_string();
potential_name = values.next_string();
if (iloc == arg[0] && jloc == arg[1] && potential_name == "coaxstk") {
k_cxst_one = values.next_double();
cut_cxst_0_one = values.next_double();
cut_cxst_c_one = values.next_double();
cut_cxst_lo_one = values.next_double();
cut_cxst_hi_one = values.next_double();
a_cxst1_one = values.next_double();
theta_cxst1_0_one = values.next_double();
dtheta_cxst1_ast_one = values.next_double();
a_cxst4_one = values.next_double();
theta_cxst4_0_one = values.next_double();
dtheta_cxst4_ast_one = values.next_double();
a_cxst5_one = values.next_double();
theta_cxst5_0_one = values.next_double();
dtheta_cxst5_ast_one = values.next_double();
a_cxst6_one = values.next_double();
theta_cxst6_0_one = values.next_double();
dtheta_cxst6_ast_one = values.next_double();
AA_cxst1_one = values.next_double();
BB_cxst1_one = values.next_double();
break;
} else continue;
} catch (std::exception &e) {
error->one(FLERR, "Problem parsing oxDNA2 potential file: {}", e.what());
}
}
if (iloc != arg[0] || jloc != arg[1] || potential_name != "coaxstk") error->one(FLERR, "No corresponding coaxstk potential found in file {} for pair type {} {}", arg[2], arg[0], arg[1]);
}
MPI_Bcast(&k_cxst_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_cxst_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_cxst_c_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_cxst_lo_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_cxst_hi_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_cxst1_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_cxst1_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_cxst1_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_cxst4_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_cxst4_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_cxst4_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_cxst5_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_cxst5_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_cxst5_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_cxst6_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_cxst6_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_cxst6_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&AA_cxst1_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&BB_cxst1_one, 1, MPI_DOUBLE, 0, world);
}
b_cxst_lo_one = 0.25 * (cut_cxst_lo_one - cut_cxst_0_one) * (cut_cxst_lo_one - cut_cxst_0_one)/ b_cxst_lo_one = 0.25 * (cut_cxst_lo_one - cut_cxst_0_one) * (cut_cxst_lo_one - cut_cxst_0_one)/
(0.5 * (cut_cxst_lo_one - cut_cxst_0_one) * (cut_cxst_lo_one - cut_cxst_0_one) - (0.5 * (cut_cxst_lo_one - cut_cxst_0_one) * (cut_cxst_lo_one - cut_cxst_0_one) -

40
src/CG-DNA/pair_oxdna2_dh.cpp
View File

@ -19,11 +19,13 @@
#include "atom.h" #include "atom.h"
#include "comm.h" #include "comm.h"
#include "constants_oxdna.h"
#include "error.h" #include "error.h"
#include "force.h" #include "force.h"
#include "math_extra.h" #include "math_extra.h"
#include "memory.h" #include "memory.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "potential_file_reader.h"
#include <cmath> #include <cmath>
#include <cstring> #include <cstring>
@ -66,7 +68,8 @@ PairOxdna2Dh::~PairOxdna2Dh()
void PairOxdna2Dh::compute_interaction_sites(double e1[3], void PairOxdna2Dh::compute_interaction_sites(double e1[3],
double e2[3], double /*e3*/[3], double r[3]) double e2[3], double /*e3*/[3], double r[3])
{ {
double d_cs_x=-0.34, d_cs_y=+0.3408; double d_cs_x = ConstantsOxdna::get_d_cs_x();
double d_cs_y = ConstantsOxdna::get_d_cs_y();
r[0] = d_cs_x*e1[0] + d_cs_y*e2[0]; r[0] = d_cs_x*e1[0] + d_cs_y*e2[0];
r[1] = d_cs_x*e1[1] + d_cs_y*e2[1]; r[1] = d_cs_x*e1[1] + d_cs_y*e2[1];
@ -303,7 +306,30 @@ void PairOxdna2Dh::coeff(int narg, char **arg)
T = utils::numeric(FLERR,arg[2],false,lmp); T = utils::numeric(FLERR,arg[2],false,lmp);
rhos_dh_one = utils::numeric(FLERR,arg[3],false,lmp); rhos_dh_one = utils::numeric(FLERR,arg[3],false,lmp);
qeff_dh_one = utils::numeric(FLERR,arg[4],false,lmp);
if (utils::strmatch(arg[4], "^[a-zA-Z0-9]*\\.[a-zA-Z]+$") == true) { // if last arg is a potential file
if (comm->me == 0) { // read value from potential file
PotentialFileReader reader(lmp, arg[4], "oxdna potential", " (dh)");
char * line;
std::string iloc, jloc, potential_name;
while(line = reader.next_line()) {
try {
ValueTokenizer values(line);
iloc = values.next_string();
jloc = values.next_string();
potential_name = values.next_string();
if (iloc == arg[0] && jloc == arg[1] && potential_name == "dh") {
qeff_dh_one = values.next_double();
break;
} else continue;
} catch (std::exception &e) {
error->one(FLERR, "Problem parsing oxDNA2 potential file: {}", e.what());
}
}
if (iloc != arg[0] || jloc != arg[1] || potential_name != "dh") error->one(FLERR, "No corresponding dh potential found in file {} for pair type {} {}", arg[4], arg[0], arg[1]);
}
MPI_Bcast(&qeff_dh_one, 1, MPI_DOUBLE, 0, world);
} else qeff_dh_one = utils::numeric(FLERR,arg[4],false,lmp); // else, it is effective charge
double lambda_dh_one, kappa_dh_one, qeff_dh_pf_one; double lambda_dh_one, kappa_dh_one, qeff_dh_pf_one;
double b_dh_one, cut_dh_ast_one, cut_dh_c_one; double b_dh_one, cut_dh_ast_one, cut_dh_c_one;
@ -315,7 +341,8 @@ void PairOxdna2Dh::coeff(int narg, char **arg)
The numerical factor is the Debye length in s.u. The numerical factor is the Debye length in s.u.
lambda(T = 300 K = 0.1) = lambda(T = 300 K = 0.1) =
sqrt(eps_0 * eps_r * k_B * T/(2 * N_A * e^2 * 1000 mol/m^3)) sqrt(eps_0 * eps_r * k_B * T/(2 * N_A * e^2 * 1000 mol/m^3))
* 1/oxDNA_energy_unit * 1/oxDNA_length_unit for LJ units, or;
* [(8.518 * sqrt(k_B / 4.142e-20))/oxDNA_length_unit] for real units
(see B. Snodin et al., J. Chem. Phys. 142, 234901 (2015).) (see B. Snodin et al., J. Chem. Phys. 142, 234901 (2015).)
We use We use
@ -328,7 +355,7 @@ void PairOxdna2Dh::coeff(int narg, char **arg)
oxDNA_length_unit = 8.518e-10 m oxDNA_length_unit = 8.518e-10 m
*/ */
lambda_dh_one = 0.3616455075438555*sqrt(T/0.1/rhos_dh_one); lambda_dh_one = ConstantsOxdna::get_lambda_dh_one_prefactor()*sqrt(T/0.1/rhos_dh_one);
kappa_dh_one = 1.0/lambda_dh_one; kappa_dh_one = 1.0/lambda_dh_one;
// prefactor in DH interaction containing qeff^2 // prefactor in DH interaction containing qeff^2
@ -337,14 +364,15 @@ void PairOxdna2Dh::coeff(int narg, char **arg)
NOTE: NOTE:
The numerical factor is The numerical factor is
qeff_dh_pf = e^2/(4 * pi * eps_0 * eps_r) qeff_dh_pf = e^2/(4 * pi * eps_0 * eps_r)
* 1/(oxDNA_energy_unit * oxDNA_length_unit) * 1/(oxDNA_energy_unit * oxDNA_length_unit) for LJ units, or;
* [(~5.96169* 8.518)/(oxDNA_energy_unit * oxDNA_length_unit)] for real units
(see B. Snodin et al., J. Chem. Phys. 142, 234901 (2015).) (see B. Snodin et al., J. Chem. Phys. 142, 234901 (2015).)
In addition to the above units we use In addition to the above units we use
oxDNA_energy_unit = 4.142e-20 J oxDNA_energy_unit = 4.142e-20 J
*/ */
qeff_dh_pf_one = 0.08173808693529228*qeff_dh_one*qeff_dh_one; qeff_dh_pf_one = ConstantsOxdna::get_qeff_dh_pf_one_prefactor()*qeff_dh_one*qeff_dh_one;
// smoothing parameters - determined through continuity and differentiability // smoothing parameters - determined through continuity and differentiability

5
src/CG-DNA/pair_oxdna2_excv.cpp
View File

@ -14,6 +14,7 @@
Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "constants_oxdna.h"
#include "pair_oxdna2_excv.h" #include "pair_oxdna2_excv.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -24,7 +25,9 @@ using namespace LAMMPS_NS;
void PairOxdna2Excv::compute_interaction_sites(double e1[3], double e2[3], double /*e3*/[3], void PairOxdna2Excv::compute_interaction_sites(double e1[3], double e2[3], double /*e3*/[3],
double rs[3], double rb[3]) double rs[3], double rb[3])
{ {
double d_cs_x = -0.34, d_cs_y = +0.3408, d_cb = +0.4; double d_cs_x = ConstantsOxdna::get_d_cs_x();
double d_cs_y = ConstantsOxdna::get_d_cs_y();
double d_cb = ConstantsOxdna::get_d_cb();
rs[0] = d_cs_x * e1[0] + d_cs_y * e2[0]; rs[0] = d_cs_x * e1[0] + d_cs_y * e2[0];
rs[1] = d_cs_x * e1[1] + d_cs_y * e2[1]; rs[1] = d_cs_x * e1[1] + d_cs_y * e2[1];

84
src/CG-DNA/pair_oxdna_coaxstk.cpp
View File

@ -19,6 +19,7 @@
#include "atom.h" #include "atom.h"
#include "comm.h" #include "comm.h"
#include "constants_oxdna.h"
#include "error.h" #include "error.h"
#include "force.h" #include "force.h"
#include "math_const.h" #include "math_const.h"
@ -26,6 +27,7 @@
#include "memory.h" #include "memory.h"
#include "mf_oxdna.h" #include "mf_oxdna.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "potential_file_reader.h"
#include <cmath> #include <cmath>
#include <cstring> #include <cstring>
@ -124,7 +126,8 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
double dcdrax,dcdray,dcdraz; double dcdrax,dcdray,dcdraz;
// distances COM-backbone site, COM-stacking site // distances COM-backbone site, COM-stacking site
double d_cs=-0.4, d_cst=+0.34; double d_cs = ConstantsOxdna::get_d_cs();
double d_cst = ConstantsOxdna::get_d_cst();
// vectors COM-backbone site, COM-stacking site in lab frame // vectors COM-backbone site, COM-stacking site in lab frame
double ra_cs[3],ra_cst[3]; double ra_cs[3],ra_cst[3];
double rb_cs[3],rb_cst[3]; double rb_cs[3],rb_cst[3];
@ -691,7 +694,7 @@ void PairOxdnaCoaxstk::coeff(int narg, char **arg)
{ {
int count; int count;
if (narg != 23) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/coaxstk"); if (narg != 3 && narg != 23) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/coaxstk");
if (!allocated) allocate(); if (!allocated) allocate();
int ilo,ihi,jlo,jhi; int ilo,ihi,jlo,jhi;
@ -719,6 +722,7 @@ void PairOxdnaCoaxstk::coeff(int narg, char **arg)
double a_cxst3p_one, cosphi_cxst3p_ast_one, b_cxst3p_one, cosphi_cxst3p_c_one; double a_cxst3p_one, cosphi_cxst3p_ast_one, b_cxst3p_one, cosphi_cxst3p_c_one;
double a_cxst4p_one, cosphi_cxst4p_ast_one, b_cxst4p_one, cosphi_cxst4p_c_one; double a_cxst4p_one, cosphi_cxst4p_ast_one, b_cxst4p_one, cosphi_cxst4p_c_one;
if (narg == 23) {
k_cxst_one = utils::numeric(FLERR,arg[2],false,lmp); k_cxst_one = utils::numeric(FLERR,arg[2],false,lmp);
cut_cxst_0_one = utils::numeric(FLERR,arg[3],false,lmp); cut_cxst_0_one = utils::numeric(FLERR,arg[3],false,lmp);
cut_cxst_c_one = utils::numeric(FLERR,arg[4],false,lmp); cut_cxst_c_one = utils::numeric(FLERR,arg[4],false,lmp);
@ -745,6 +749,82 @@ void PairOxdnaCoaxstk::coeff(int narg, char **arg)
cosphi_cxst3p_ast_one = utils::numeric(FLERR,arg[20],false,lmp); cosphi_cxst3p_ast_one = utils::numeric(FLERR,arg[20],false,lmp);
a_cxst4p_one = utils::numeric(FLERR,arg[21],false,lmp); a_cxst4p_one = utils::numeric(FLERR,arg[21],false,lmp);
cosphi_cxst4p_ast_one = utils::numeric(FLERR,arg[22],false,lmp); cosphi_cxst4p_ast_one = utils::numeric(FLERR,arg[22],false,lmp);
} else {
if (comm->me == 0) { // read values from potential file
PotentialFileReader reader(lmp, arg[2], "oxdna potential", " (coaxstk)");
char * line;
std::string iloc, jloc, potential_name;
while(line = reader.next_line()) {
try {
ValueTokenizer values(line);
iloc = values.next_string();
jloc = values.next_string();
potential_name = values.next_string();
if (iloc == arg[0] && jloc == arg[1] && potential_name == "coaxstk") {
k_cxst_one = values.next_double();
cut_cxst_0_one = values.next_double();
cut_cxst_c_one = values.next_double();
cut_cxst_lo_one = values.next_double();
cut_cxst_hi_one = values.next_double();
a_cxst1_one = values.next_double();
theta_cxst1_0_one = values.next_double();
dtheta_cxst1_ast_one = values.next_double();
a_cxst4_one = values.next_double();
theta_cxst4_0_one = values.next_double();
dtheta_cxst4_ast_one = values.next_double();
a_cxst5_one = values.next_double();
theta_cxst5_0_one = values.next_double();
dtheta_cxst5_ast_one = values.next_double();
a_cxst6_one = values.next_double();
theta_cxst6_0_one = values.next_double();
dtheta_cxst6_ast_one = values.next_double();
a_cxst3p_one = values.next_double();
cosphi_cxst3p_ast_one = values.next_double();
a_cxst4p_one = values.next_double();
cosphi_cxst4p_ast_one = values.next_double();
break;
} else continue;
} catch (std::exception &e) {
error->one(FLERR, "Problem parsing oxDNA potential file: {}", e.what());
}
}
if (iloc != arg[0] || jloc != arg[1] || potential_name != "coaxstk") error->one(FLERR, "No corresponding coaxstk potential found in file {} for pair type {} {}", arg[2], arg[0], arg[1]);
}
MPI_Bcast(&k_cxst_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_cxst_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_cxst_c_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_cxst_lo_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_cxst_hi_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_cxst1_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_cxst1_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_cxst1_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_cxst4_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_cxst4_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_cxst4_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_cxst5_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_cxst5_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_cxst5_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_cxst6_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_cxst6_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_cxst6_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_cxst3p_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cosphi_cxst3p_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_cxst4p_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cosphi_cxst4p_ast_one, 1, MPI_DOUBLE, 0, world);
}
b_cxst_lo_one = 0.25 * (cut_cxst_lo_one - cut_cxst_0_one) * (cut_cxst_lo_one - cut_cxst_0_one)/ b_cxst_lo_one = 0.25 * (cut_cxst_lo_one - cut_cxst_0_one) * (cut_cxst_lo_one - cut_cxst_0_one)/
(0.5 * (cut_cxst_lo_one - cut_cxst_0_one) * (cut_cxst_lo_one - cut_cxst_0_one) - (0.5 * (cut_cxst_lo_one - cut_cxst_0_one) * (cut_cxst_lo_one - cut_cxst_0_one) -

78
src/CG-DNA/pair_oxdna_excv.cpp
View File

@ -20,12 +20,14 @@
#include "atom.h" #include "atom.h"
#include "atom_vec_ellipsoid.h" #include "atom_vec_ellipsoid.h"
#include "comm.h" #include "comm.h"
#include "constants_oxdna.h"
#include "error.h" #include "error.h"
#include "force.h" #include "force.h"
#include "math_extra.h" #include "math_extra.h"
#include "memory.h" #include "memory.h"
#include "mf_oxdna.h" #include "mf_oxdna.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "potential_file_reader.h"
#include <cmath> #include <cmath>
#include <cstring> #include <cstring>
@ -97,7 +99,8 @@ PairOxdnaExcv::~PairOxdnaExcv()
void PairOxdnaExcv::compute_interaction_sites(double e1[3], double /*e2*/[3], void PairOxdnaExcv::compute_interaction_sites(double e1[3], double /*e2*/[3],
double /*e3*/[3], double rs[3], double rb[3]) double /*e3*/[3], double rs[3], double rb[3])
{ {
double d_cs=-0.4, d_cb=+0.4; double d_cs = ConstantsOxdna::get_d_cs();
double d_cb = ConstantsOxdna::get_d_cb();
rs[0] = d_cs*e1[0]; rs[0] = d_cs*e1[0];
rs[1] = d_cs*e1[1]; rs[1] = d_cs*e1[1];
@ -500,7 +503,7 @@ void PairOxdnaExcv::coeff(int narg, char **arg)
{ {
int count; int count;
if (narg != 11) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/excv"); if (narg != 3 && narg != 11) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/excv");
if (!allocated) allocate(); if (!allocated) allocate();
int ilo,ihi,jlo,jhi; int ilo,ihi,jlo,jhi;
@ -518,12 +521,73 @@ void PairOxdnaExcv::coeff(int narg, char **arg)
double epsilon_bb_one, sigma_bb_one; double epsilon_bb_one, sigma_bb_one;
double cut_bb_ast_one, cut_bb_c_one, b_bb_one; double cut_bb_ast_one, cut_bb_c_one, b_bb_one;
if (narg == 11) {
// Excluded volume interaction // Excluded volume interaction
// LJ parameters // LJ parameters
epsilon_ss_one = utils::numeric(FLERR,arg[2],false,lmp); epsilon_ss_one = utils::numeric(FLERR,arg[2],false,lmp);
sigma_ss_one = utils::numeric(FLERR,arg[3],false,lmp); sigma_ss_one = utils::numeric(FLERR,arg[3],false,lmp);
cut_ss_ast_one = utils::numeric(FLERR,arg[4],false,lmp); cut_ss_ast_one = utils::numeric(FLERR,arg[4],false,lmp);
// LJ parameters
epsilon_sb_one = utils::numeric(FLERR,arg[5],false,lmp);
sigma_sb_one = utils::numeric(FLERR,arg[6],false,lmp);
cut_sb_ast_one = utils::numeric(FLERR,arg[7],false,lmp);
// LJ parameters
epsilon_bb_one = utils::numeric(FLERR,arg[8],false,lmp);
sigma_bb_one = utils::numeric(FLERR,arg[9],false,lmp);
cut_bb_ast_one = utils::numeric(FLERR,arg[10],false,lmp);
} else {
if (comm->me == 0) {
PotentialFileReader reader(lmp, arg[2], "oxdna potential", " (excv)");
char * line;
std::string iloc, jloc, potential_name;
while(line = reader.next_line()) {
try {
ValueTokenizer values(line);
iloc = values.next_string();
jloc = values.next_string();
potential_name = values.next_string();
if (iloc == arg[0] && jloc == arg[1] && potential_name == "excv") {
// Excluded volume interaction
// LJ parameters
epsilon_ss_one = values.next_double();
sigma_ss_one = values.next_double();
cut_ss_ast_one = values.next_double();
// LJ parameters
epsilon_sb_one = values.next_double();
sigma_sb_one = values.next_double();
cut_sb_ast_one = values.next_double();
// LJ parameters
epsilon_bb_one = values.next_double();
sigma_bb_one = values.next_double();
cut_bb_ast_one = values.next_double();
break;
} else continue;
} catch (std::exception &e) {
error->one(FLERR, "Problem parsing oxDNA potential file: {}", e.what());
}
}
if (iloc != arg[0] || jloc != arg[1] || potential_name != "excv") error->one(FLERR, "No corresponding excv potential found in file {} for pair type {} {}", arg[2], arg[0], arg[1]);
}
MPI_Bcast(&epsilon_ss_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&sigma_ss_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_ss_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&epsilon_sb_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&sigma_sb_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_sb_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&epsilon_bb_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&sigma_bb_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_bb_ast_one, 1, MPI_DOUBLE, 0, world);
}
// smoothing - determined through continuity and differentiability // smoothing - determined through continuity and differentiability
b_ss_one = 4.0/sigma_ss_one b_ss_one = 4.0/sigma_ss_one
*(6.0*pow(sigma_ss_one/cut_ss_ast_one,7)-12.0*pow(sigma_ss_one/cut_ss_ast_one,13)) *(6.0*pow(sigma_ss_one/cut_ss_ast_one,7)-12.0*pow(sigma_ss_one/cut_ss_ast_one,13))
@ -550,11 +614,6 @@ void PairOxdnaExcv::coeff(int narg, char **arg)
count = 0; count = 0;
// LJ parameters
epsilon_sb_one = utils::numeric(FLERR,arg[5],false,lmp);
sigma_sb_one = utils::numeric(FLERR,arg[6],false,lmp);
cut_sb_ast_one = utils::numeric(FLERR,arg[7],false,lmp);
// smoothing - determined through continuity and differentiability // smoothing - determined through continuity and differentiability
b_sb_one = 4.0/sigma_sb_one b_sb_one = 4.0/sigma_sb_one
*(6.0*pow(sigma_sb_one/cut_sb_ast_one,7)-12.0*pow(sigma_sb_one/cut_sb_ast_one,13)) *(6.0*pow(sigma_sb_one/cut_sb_ast_one,7)-12.0*pow(sigma_sb_one/cut_sb_ast_one,13))
@ -581,11 +640,6 @@ void PairOxdnaExcv::coeff(int narg, char **arg)
count = 0; count = 0;
// LJ parameters
epsilon_bb_one = utils::numeric(FLERR,arg[8],false,lmp);
sigma_bb_one = utils::numeric(FLERR,arg[9],false,lmp);
cut_bb_ast_one = utils::numeric(FLERR,arg[10],false,lmp);
// smoothing - determined through continuity and differentiability // smoothing - determined through continuity and differentiability
b_bb_one = 4.0/sigma_bb_one b_bb_one = 4.0/sigma_bb_one
*(6.0*pow(sigma_bb_one/cut_bb_ast_one,7)-12.0*pow(sigma_bb_one/cut_bb_ast_one,13)) *(6.0*pow(sigma_bb_one/cut_bb_ast_one,7)-12.0*pow(sigma_bb_one/cut_bb_ast_one,13))

93
src/CG-DNA/pair_oxdna_hbond.cpp
View File

@ -19,12 +19,14 @@
#include "atom.h" #include "atom.h"
#include "comm.h" #include "comm.h"
#include "constants_oxdna.h"
#include "error.h" #include "error.h"
#include "force.h" #include "force.h"
#include "math_extra.h" #include "math_extra.h"
#include "memory.h" #include "memory.h"
#include "mf_oxdna.h" #include "mf_oxdna.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "potential_file_reader.h"
#include <cmath> #include <cmath>
#include <cstring> #include <cstring>
@ -145,7 +147,7 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
double theta8,t8dir[3],cost8; double theta8,t8dir[3],cost8;
// distance COM-hbonding site // distance COM-hbonding site
double d_chb=+0.4; double d_chb = ConstantsOxdna::get_d_chb();
// vectors COM-h-bonding site in lab frame // vectors COM-h-bonding site in lab frame
double ra_chb[3],rb_chb[3]; double ra_chb[3],rb_chb[3];
// Cartesian unit vectors in lab frame // Cartesian unit vectors in lab frame
@ -634,7 +636,7 @@ void PairOxdnaHbond::coeff(int narg, char **arg)
{ {
int count; int count;
if (narg != 27) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/hbond"); if (narg != 4 && narg != 27) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/hbond");
if (!allocated) allocate(); if (!allocated) allocate();
int ilo,ihi,jlo,jhi,imod4,jmod4; int ilo,ihi,jlo,jhi,imod4,jmod4;
@ -671,6 +673,7 @@ void PairOxdnaHbond::coeff(int narg, char **arg)
if (strcmp(arg[2],"seqav") == 0) seqdepflag = 0; if (strcmp(arg[2],"seqav") == 0) seqdepflag = 0;
if (strcmp(arg[2],"seqdep") == 0) seqdepflag = 1; if (strcmp(arg[2],"seqdep") == 0) seqdepflag = 1;
if (narg == 27) {
epsilon_hb_one = utils::numeric(FLERR,arg[3],false,lmp); epsilon_hb_one = utils::numeric(FLERR,arg[3],false,lmp);
a_hb_one = utils::numeric(FLERR,arg[4],false,lmp); a_hb_one = utils::numeric(FLERR,arg[4],false,lmp);
cut_hb_0_one = utils::numeric(FLERR,arg[5],false,lmp); cut_hb_0_one = utils::numeric(FLERR,arg[5],false,lmp);
@ -701,6 +704,92 @@ void PairOxdnaHbond::coeff(int narg, char **arg)
a_hb8_one = utils::numeric(FLERR,arg[24],false,lmp); a_hb8_one = utils::numeric(FLERR,arg[24],false,lmp);
theta_hb8_0_one = utils::numeric(FLERR,arg[25],false,lmp); theta_hb8_0_one = utils::numeric(FLERR,arg[25],false,lmp);
dtheta_hb8_ast_one = utils::numeric(FLERR,arg[26],false,lmp); dtheta_hb8_ast_one = utils::numeric(FLERR,arg[26],false,lmp);
} else { // read values from potential file
if (comm->me == 0) {
PotentialFileReader reader(lmp, arg[3], "oxdna potential", " (hbond)");
char * line;
std::string iloc, jloc, potential_name;
while(line = reader.next_line()) {
try {
ValueTokenizer values(line);
iloc = values.next_string();
jloc = values.next_string();
potential_name = values.next_string();
if (iloc == arg[0] && jloc == arg[1] && potential_name == "hbond") {
epsilon_hb_one = values.next_double();
a_hb_one = values.next_double();
cut_hb_0_one = values.next_double();
cut_hb_c_one = values.next_double();
cut_hb_lo_one = values.next_double();
cut_hb_hi_one = values.next_double();
a_hb1_one = values.next_double();
theta_hb1_0_one = values.next_double();
dtheta_hb1_ast_one = values.next_double();
a_hb2_one = values.next_double();
theta_hb2_0_one = values.next_double();
dtheta_hb2_ast_one = values.next_double();
a_hb3_one = values.next_double();
theta_hb3_0_one = values.next_double();
dtheta_hb3_ast_one = values.next_double();
a_hb4_one = values.next_double();
theta_hb4_0_one = values.next_double();
dtheta_hb4_ast_one = values.next_double();
a_hb7_one = values.next_double();
theta_hb7_0_one = values.next_double();
dtheta_hb7_ast_one = values.next_double();
a_hb8_one = values.next_double();
theta_hb8_0_one = values.next_double();
dtheta_hb8_ast_one = values.next_double();
break;
} else continue;
} catch (std::exception &e) {
error->one(FLERR, "Problem parsing oxDNA potential file: {}", e.what());
}
}
if (iloc != arg[0] || jloc != arg[1] || potential_name != "hbond") error->one(FLERR, "No corresponding hbond potential found in file {} for pair type {} {}", arg[3], arg[0], arg[1]);
}
MPI_Bcast(&epsilon_hb_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_hb_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_hb_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_hb_c_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_hb_lo_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_hb_hi_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_hb1_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_hb1_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_hb1_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_hb2_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_hb2_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_hb2_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_hb3_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_hb3_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_hb3_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_hb4_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_hb4_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_hb4_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_hb7_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_hb7_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_hb7_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_hb8_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_hb8_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_hb8_ast_one, 1, MPI_DOUBLE, 0, world);
}
b_hb_lo_one = 2*a_hb_one*exp(-a_hb_one*(cut_hb_lo_one-cut_hb_0_one))* b_hb_lo_one = 2*a_hb_one*exp(-a_hb_one*(cut_hb_lo_one-cut_hb_0_one))*
2*a_hb_one*exp(-a_hb_one*(cut_hb_lo_one-cut_hb_0_one))* 2*a_hb_one*exp(-a_hb_one*(cut_hb_lo_one-cut_hb_0_one))*

71
src/CG-DNA/pair_oxdna_stk.cpp
View File

@ -19,6 +19,7 @@
#include "atom.h" #include "atom.h"
#include "comm.h" #include "comm.h"
#include "constants_oxdna.h"
#include "error.h" #include "error.h"
#include "force.h" #include "force.h"
#include "math_extra.h" #include "math_extra.h"
@ -26,6 +27,7 @@
#include "mf_oxdna.h" #include "mf_oxdna.h"
#include "neighbor.h" #include "neighbor.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "potential_file_reader.h"
#include <cmath> #include <cmath>
#include <cstring> #include <cstring>
@ -223,7 +225,8 @@ void PairOxdnaStk::compute(int eflag, int vflag)
double cosphi1,cosphi2,cosphi1dir[3],cosphi2dir[3]; double cosphi1,cosphi2,cosphi1dir[3],cosphi2dir[3];
// distances COM-backbone site, COM-stacking site // distances COM-backbone site, COM-stacking site
double d_cs=-0.4, d_cst=+0.34; double d_cs = ConstantsOxdna::get_d_cs();
double d_cst = ConstantsOxdna::get_d_cst();
// vectors COM-backbone site, COM-stacking site in lab frame // vectors COM-backbone site, COM-stacking site in lab frame
double ra_cs[3],ra_cst[3]; double ra_cs[3],ra_cst[3];
double rb_cs[3],rb_cst[3]; double rb_cs[3],rb_cst[3];
@ -775,7 +778,7 @@ void PairOxdnaStk::coeff(int narg, char **arg)
{ {
int count; int count;
if (narg != 24) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/stk"); if (narg != 7 && narg != 24) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/stk");
if (!allocated) allocate(); if (!allocated) allocate();
int ilo,ihi,jlo,jhi,imod4,jmod4; int ilo,ihi,jlo,jhi,imod4,jmod4;
@ -812,6 +815,7 @@ void PairOxdnaStk::coeff(int narg, char **arg)
kappa_st_one = utils::numeric(FLERR,arg[5],false,lmp); kappa_st_one = utils::numeric(FLERR,arg[5],false,lmp);
epsilon_st_one = stacking_strength(xi_st_one, kappa_st_one, T); epsilon_st_one = stacking_strength(xi_st_one, kappa_st_one, T);
if (narg == 24) { // values are listed in input
a_st_one = utils::numeric(FLERR,arg[6],false,lmp); a_st_one = utils::numeric(FLERR,arg[6],false,lmp);
cut_st_0_one = utils::numeric(FLERR,arg[7],false,lmp); cut_st_0_one = utils::numeric(FLERR,arg[7],false,lmp);
cut_st_c_one = utils::numeric(FLERR,arg[8],false,lmp); cut_st_c_one = utils::numeric(FLERR,arg[8],false,lmp);
@ -831,6 +835,69 @@ void PairOxdnaStk::coeff(int narg, char **arg)
cosphi_st1_ast_one = utils::numeric(FLERR,arg[21],false,lmp); cosphi_st1_ast_one = utils::numeric(FLERR,arg[21],false,lmp);
a_st2_one = utils::numeric(FLERR,arg[22],false,lmp); a_st2_one = utils::numeric(FLERR,arg[22],false,lmp);
cosphi_st2_ast_one = utils::numeric(FLERR,arg[23],false,lmp); cosphi_st2_ast_one = utils::numeric(FLERR,arg[23],false,lmp);
} else { // read values from potential file
if (comm->me == 0) {
PotentialFileReader reader(lmp, arg[6], "oxdna potential", " (stk)");
char * line;
std::string iloc, jloc, potential_name;
while(line = reader.next_line()) {
try {
ValueTokenizer values(line);
iloc = values.next_string();
jloc = values.next_string();
potential_name = values.next_string();
if (iloc == arg[0] && jloc == arg[1] && potential_name == "stk") {
a_st_one = values.next_double();
cut_st_0_one = values.next_double();
cut_st_c_one = values.next_double();
cut_st_lo_one = values.next_double();
cut_st_hi_one = values.next_double();
a_st4_one = values.next_double();
theta_st4_0_one = values.next_double();
dtheta_st4_ast_one = values.next_double();
a_st5_one = values.next_double();
theta_st5_0_one = values.next_double();
dtheta_st5_ast_one = values.next_double();
a_st6_one = values.next_double();
theta_st6_0_one = values.next_double();
dtheta_st6_ast_one = values.next_double();
a_st1_one = values.next_double();
cosphi_st1_ast_one = values.next_double();
a_st2_one = values.next_double();
cosphi_st2_ast_one = values.next_double();
break;
} else continue;
} catch (std::exception &e) {
error->one(FLERR, "Problem parsing oxDNA potential file: {}", e.what());
}
}
if (iloc != arg[0] || jloc != arg[1] || potential_name != "stk") error->one(FLERR, "No corresponding stk potential found in file {} for pair type {} {}", arg[4], arg[0], arg[1]);
}
MPI_Bcast(&a_st_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_st_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_st_c_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_st_lo_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_st_hi_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_st4_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_st4_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_st4_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_st5_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_st5_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_st5_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_st6_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_st6_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_st6_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_st1_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cosphi_st1_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_st2_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cosphi_st2_ast_one, 1, MPI_DOUBLE, 0, world);
}
b_st_lo_one = 2*a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))* b_st_lo_one = 2*a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))*
2*a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))* 2*a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))*

89
src/CG-DNA/pair_oxdna_xstk.cpp
View File

@ -19,6 +19,7 @@
#include "atom.h" #include "atom.h"
#include "comm.h" #include "comm.h"
#include "constants_oxdna.h"
#include "error.h" #include "error.h"
#include "force.h" #include "force.h"
#include "math_const.h" #include "math_const.h"
@ -26,6 +27,7 @@
#include "memory.h" #include "memory.h"
#include "mf_oxdna.h" #include "mf_oxdna.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "potential_file_reader.h"
#include <cmath> #include <cmath>
#include <cstring> #include <cstring>
@ -122,7 +124,7 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
double theta8,theta8p,t8dir[3],cost8; double theta8,theta8p,t8dir[3],cost8;
// distance COM-h-bonding site // distance COM-h-bonding site
double d_chb=+0.4; double d_chb = ConstantsOxdna::get_d_chb();
// vectors COM-h-bonding site in lab frame // vectors COM-h-bonding site in lab frame
double ra_chb[3],rb_chb[3]; double ra_chb[3],rb_chb[3];
// Cartesian unit vectors in lab frame // Cartesian unit vectors in lab frame
@ -631,7 +633,7 @@ void PairOxdnaXstk::coeff(int narg, char **arg)
{ {
int count; int count;
if (narg != 25) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/xstk"); if (narg != 3 && narg != 25) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/xstk");
if (!allocated) allocate(); if (!allocated) allocate();
int ilo,ihi,jlo,jhi; int ilo,ihi,jlo,jhi;
@ -662,6 +664,7 @@ void PairOxdnaXstk::coeff(int narg, char **arg)
double a_xst8_one, theta_xst8_0_one, dtheta_xst8_ast_one; double a_xst8_one, theta_xst8_0_one, dtheta_xst8_ast_one;
double b_xst8_one, dtheta_xst8_c_one; double b_xst8_one, dtheta_xst8_c_one;
if (narg == 25) {
k_xst_one = utils::numeric(FLERR,arg[2],false,lmp); k_xst_one = utils::numeric(FLERR,arg[2],false,lmp);
cut_xst_0_one = utils::numeric(FLERR,arg[3],false,lmp); cut_xst_0_one = utils::numeric(FLERR,arg[3],false,lmp);
cut_xst_c_one = utils::numeric(FLERR,arg[4],false,lmp); cut_xst_c_one = utils::numeric(FLERR,arg[4],false,lmp);
@ -691,6 +694,88 @@ void PairOxdnaXstk::coeff(int narg, char **arg)
a_xst8_one = utils::numeric(FLERR,arg[22],false,lmp); a_xst8_one = utils::numeric(FLERR,arg[22],false,lmp);
theta_xst8_0_one = utils::numeric(FLERR,arg[23],false,lmp); theta_xst8_0_one = utils::numeric(FLERR,arg[23],false,lmp);
dtheta_xst8_ast_one = utils::numeric(FLERR,arg[24],false,lmp); dtheta_xst8_ast_one = utils::numeric(FLERR,arg[24],false,lmp);
} else {
if (comm->me == 0) {
PotentialFileReader reader(lmp, arg[2], "oxdna potential", " (xstk)");
char * line;
std::string iloc, jloc, potential_name;
while(line = reader.next_line()) {
try {
ValueTokenizer values(line);
iloc = values.next_string();
jloc = values.next_string();
potential_name = values.next_string();
if (iloc == arg[0] && jloc == arg[1] && potential_name == "xstk") {
k_xst_one = values.next_double();
cut_xst_0_one = values.next_double();
cut_xst_c_one = values.next_double();
cut_xst_lo_one = values.next_double();
cut_xst_hi_one = values.next_double();
a_xst1_one = values.next_double();
theta_xst1_0_one = values.next_double();
dtheta_xst1_ast_one = values.next_double();
a_xst2_one = values.next_double();
theta_xst2_0_one = values.next_double();
dtheta_xst2_ast_one = values.next_double();
a_xst3_one = values.next_double();
theta_xst3_0_one = values.next_double();
dtheta_xst3_ast_one = values.next_double();
a_xst4_one = values.next_double();
theta_xst4_0_one = values.next_double();
dtheta_xst4_ast_one = values.next_double();
a_xst7_one = values.next_double();
theta_xst7_0_one = values.next_double();
dtheta_xst7_ast_one = values.next_double();
a_xst8_one = values.next_double();
theta_xst8_0_one = values.next_double();
dtheta_xst8_ast_one = values.next_double();
break;
} else continue;
} catch (std::exception &e) {
error->one(FLERR, "Problem parsing oxDNA potential file: {}", e.what());
}
}
if (iloc != arg[0] || jloc != arg[1] || potential_name != "xstk") error->one(FLERR, "No corresponding xstk potential found in file {} for pair type {} {}", arg[2], arg[0], arg[1]);
}
MPI_Bcast(&k_xst_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_xst_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_xst_c_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_xst_lo_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_xst_hi_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_xst1_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_xst1_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_xst1_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_xst2_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_xst2_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_xst2_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_xst3_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_xst3_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_xst3_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_xst4_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_xst4_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_xst4_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_xst7_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_xst7_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_xst7_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_xst8_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_xst8_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_xst8_ast_one, 1, MPI_DOUBLE, 0, world);
}
b_xst_lo_one = 0.25 * (cut_xst_lo_one - cut_xst_0_one) * (cut_xst_lo_one - cut_xst_0_one)/ b_xst_lo_one = 0.25 * (cut_xst_lo_one - cut_xst_0_one) * (cut_xst_lo_one - cut_xst_0_one)/

5
src/CG-DNA/pair_oxrna2_dh.cpp
View File

@ -16,6 +16,8 @@
#include "pair_oxrna2_dh.h" #include "pair_oxrna2_dh.h"
#include "constants_oxdna.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -24,7 +26,8 @@ using namespace LAMMPS_NS;
void PairOxrna2Dh::compute_interaction_sites(double e1[3], double /*e2*/[3], double e3[3], void PairOxrna2Dh::compute_interaction_sites(double e1[3], double /*e2*/[3], double e3[3],
double r[3]) double r[3])
{ {
double d_cs_x = -0.4, d_cs_z = +0.2; double d_cs_x = ConstantsOxdna::get_d_cs();
double d_cs_z = ConstantsOxdna::get_d_cs_z();
r[0] = d_cs_x * e1[0] + d_cs_z * e3[0]; r[0] = d_cs_x * e1[0] + d_cs_z * e3[0];
r[1] = d_cs_x * e1[1] + d_cs_z * e3[1]; r[1] = d_cs_x * e1[1] + d_cs_z * e3[1];

6
src/CG-DNA/pair_oxrna2_excv.cpp
View File

@ -17,6 +17,8 @@
#include "pair_oxrna2_excv.h" #include "pair_oxrna2_excv.h"
#include "constants_oxdna.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -25,7 +27,9 @@ using namespace LAMMPS_NS;
void PairOxrna2Excv::compute_interaction_sites(double e1[3], double /*e2*/[3], void PairOxrna2Excv::compute_interaction_sites(double e1[3], double /*e2*/[3],
double e3[3], double rs[3], double rb[3]) double e3[3], double rs[3], double rb[3])
{ {
double d_cs_x=-0.4, d_cs_z=+0.2, d_cb=+0.4; double d_cs_x = ConstantsOxdna::get_d_cs();
double d_cs_z = ConstantsOxdna::get_d_cs_z();
double d_cb = ConstantsOxdna::get_d_cb();
rs[0] = d_cs_x*e1[0] + d_cs_z*e3[0]; rs[0] = d_cs_x*e1[0] + d_cs_z*e3[0];
rs[1] = d_cs_x*e1[1] + d_cs_z*e3[1]; rs[1] = d_cs_x*e1[1] + d_cs_z*e3[1];

87
src/CG-DNA/pair_oxrna2_stk.cpp
View File

@ -19,6 +19,7 @@
#include "atom.h" #include "atom.h"
#include "comm.h" #include "comm.h"
#include "constants_oxdna.h"
#include "error.h" #include "error.h"
#include "force.h" #include "force.h"
#include "math_const.h" #include "math_const.h"
@ -27,6 +28,7 @@
#include "mf_oxdna.h" #include "mf_oxdna.h"
#include "neighbor.h" #include "neighbor.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "potential_file_reader.h"
#include <cmath> #include <cmath>
#include <cstring> #include <cstring>
@ -233,9 +235,12 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
double cosphi1,cosphi2,cosphi1dir[3],cosphi2dir[3]; double cosphi1,cosphi2,cosphi1dir[3],cosphi2dir[3];
// distances COM-backbone site, COM-3' and COM-5' stacking site // distances COM-backbone site, COM-3' and COM-5' stacking site
double d_cs_x=-0.4, d_cs_z=+0.2; double d_cs_x = ConstantsOxdna::get_d_cs();
double d_cst_x_3p=+0.4, d_cst_y_3p=+0.1; double d_cs_z = ConstantsOxdna::get_d_cs_z();
double d_cst_x_5p=+0.124906078525, d_cst_y_5p=-0.00866274917473; double d_cst_x_3p = ConstantsOxdna::get_d_cst_x_3p();
double d_cst_y_3p = ConstantsOxdna::get_d_cst_y_3p();
double d_cst_x_5p = ConstantsOxdna::get_d_cst_x_5p();
double d_cst_y_5p = ConstantsOxdna::get_d_cst_y_5p();
// 3' and p5' auxiliary vectors // 3' and p5' auxiliary vectors
double d3p_x=-0.462510,d3p_y=-0.528218,d3p_z=+0.712089; double d3p_x=-0.462510,d3p_y=-0.528218,d3p_z=+0.712089;
@ -842,7 +847,7 @@ void PairOxrna2Stk::coeff(int narg, char **arg)
{ {
int count; int count;
if (narg != 27) error->all(FLERR,"Incorrect args for pair coefficients in oxrna2/stk"); if (narg != 7 && narg != 27) error->all(FLERR,"Incorrect args for pair coefficients in oxrna2/stk");
if (!allocated) allocate(); if (!allocated) allocate();
int ilo,ihi,jlo,jhi; int ilo,ihi,jlo,jhi;
@ -882,6 +887,7 @@ void PairOxrna2Stk::coeff(int narg, char **arg)
kappa_st_one = utils::numeric(FLERR,arg[5],false,lmp); kappa_st_one = utils::numeric(FLERR,arg[5],false,lmp);
epsilon_st_one = stacking_strength(xi_st_one, kappa_st_one, T); epsilon_st_one = stacking_strength(xi_st_one, kappa_st_one, T);
if (narg == 27) {
a_st_one = utils::numeric(FLERR,arg[6],false,lmp); a_st_one = utils::numeric(FLERR,arg[6],false,lmp);
cut_st_0_one = utils::numeric(FLERR,arg[7],false,lmp); cut_st_0_one = utils::numeric(FLERR,arg[7],false,lmp);
cut_st_c_one = utils::numeric(FLERR,arg[8],false,lmp); cut_st_c_one = utils::numeric(FLERR,arg[8],false,lmp);
@ -906,6 +912,79 @@ void PairOxrna2Stk::coeff(int narg, char **arg)
cosphi_st1_ast_one = utils::numeric(FLERR,arg[24],false,lmp); cosphi_st1_ast_one = utils::numeric(FLERR,arg[24],false,lmp);
a_st2_one = utils::numeric(FLERR,arg[25],false,lmp); a_st2_one = utils::numeric(FLERR,arg[25],false,lmp);
cosphi_st2_ast_one = utils::numeric(FLERR,arg[26],false,lmp); cosphi_st2_ast_one = utils::numeric(FLERR,arg[26],false,lmp);
} else { // read values from potential file
if (comm->me == 0) {
PotentialFileReader reader(lmp, arg[6], "oxdna potential", " (stk)");
char * line;
std::string iloc, jloc, potential_name;
while(line = reader.next_line()) {
try {
ValueTokenizer values(line);
iloc = values.next_string();
jloc = values.next_string();
potential_name = values.next_string();
if (iloc == arg[0] && jloc == arg[1] && potential_name == "stk") {
a_st_one = values.next_double();
cut_st_0_one = values.next_double();
cut_st_c_one = values.next_double();
cut_st_lo_one = values.next_double();
cut_st_hi_one = values.next_double();
a_st5_one = values.next_double();
theta_st5_0_one = values.next_double();
dtheta_st5_ast_one = values.next_double();
a_st6_one = values.next_double();
theta_st6_0_one = values.next_double();
dtheta_st6_ast_one = values.next_double();
a_st9_one = values.next_double();
theta_st9_0_one = values.next_double();
dtheta_st9_ast_one = values.next_double();
a_st10_one = values.next_double();
theta_st10_0_one = values.next_double();
dtheta_st10_ast_one = values.next_double();
a_st1_one = values.next_double();
cosphi_st1_ast_one = values.next_double();
a_st2_one = values.next_double();
cosphi_st2_ast_one = values.next_double();
break;
} else continue;
} catch (std::exception &e) {
error->one(FLERR, "Problem parsing oxDNA potential file: {}", e.what());
}
}
if (iloc != arg[0] || jloc != arg[1] || potential_name != "stk") error->one(FLERR, "No corresponding stk potential found in file {} for pair type {} {}", arg[4], arg[0], arg[1]);
}
MPI_Bcast(&a_st_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_st_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_st_c_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_st_lo_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_st_hi_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_st5_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_st5_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_st5_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_st6_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_st6_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_st6_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_st9_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_st9_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_st9_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_st10_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_st10_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_st10_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_st1_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cosphi_st1_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_st2_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cosphi_st2_ast_one, 1, MPI_DOUBLE, 0, world);
}
b_st_lo_one = 2*a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))* b_st_lo_one = 2*a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))*
2*a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))* 2*a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))*

80
src/CG-DNA/pair_oxrna2_xstk.cpp
View File

@ -19,6 +19,7 @@
#include "atom.h" #include "atom.h"
#include "comm.h" #include "comm.h"
#include "constants_oxdna.h"
#include "error.h" #include "error.h"
#include "force.h" #include "force.h"
#include "math_const.h" #include "math_const.h"
@ -26,6 +27,7 @@
#include "memory.h" #include "memory.h"
#include "mf_oxdna.h" #include "mf_oxdna.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "potential_file_reader.h"
#include <cmath> #include <cmath>
#include <cstring> #include <cstring>
@ -116,7 +118,7 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)
double theta8,theta8p,t8dir[3],cost8; double theta8,theta8p,t8dir[3],cost8;
// distance COM-h-bonding site // distance COM-h-bonding site
double d_chb=+0.4; double d_chb = ConstantsOxdna::get_d_chb();
// vectors COM-h-bonding site in lab frame // vectors COM-h-bonding site in lab frame
double ra_chb[3],rb_chb[3]; double ra_chb[3],rb_chb[3];
@ -581,7 +583,7 @@ void PairOxrna2Xstk::coeff(int narg, char **arg)
{ {
int count; int count;
if (narg != 22) error->all(FLERR,"Incorrect args for pair coefficients in oxrna2/xstk"); if (narg != 3 && narg != 22) error->all(FLERR,"Incorrect args for pair coefficients in oxrna2/xstk");
if (!allocated) allocate(); if (!allocated) allocate();
int ilo,ihi,jlo,jhi; int ilo,ihi,jlo,jhi;
@ -609,6 +611,7 @@ void PairOxrna2Xstk::coeff(int narg, char **arg)
double a_xst8_one, theta_xst8_0_one, dtheta_xst8_ast_one; double a_xst8_one, theta_xst8_0_one, dtheta_xst8_ast_one;
double b_xst8_one, dtheta_xst8_c_one; double b_xst8_one, dtheta_xst8_c_one;
if (narg == 22) {
k_xst_one = utils::numeric(FLERR,arg[2],false,lmp); k_xst_one = utils::numeric(FLERR,arg[2],false,lmp);
cut_xst_0_one = utils::numeric(FLERR,arg[3],false,lmp); cut_xst_0_one = utils::numeric(FLERR,arg[3],false,lmp);
cut_xst_c_one = utils::numeric(FLERR,arg[4],false,lmp); cut_xst_c_one = utils::numeric(FLERR,arg[4],false,lmp);
@ -634,7 +637,80 @@ void PairOxrna2Xstk::coeff(int narg, char **arg)
a_xst8_one = utils::numeric(FLERR,arg[19],false,lmp); a_xst8_one = utils::numeric(FLERR,arg[19],false,lmp);
theta_xst8_0_one = utils::numeric(FLERR,arg[20],false,lmp); theta_xst8_0_one = utils::numeric(FLERR,arg[20],false,lmp);
dtheta_xst8_ast_one = utils::numeric(FLERR,arg[21],false,lmp); dtheta_xst8_ast_one = utils::numeric(FLERR,arg[21],false,lmp);
} else {
if (comm->me == 0) {
PotentialFileReader reader(lmp, arg[2], "oxdna potential", " (xstk)");
char * line;
std::string iloc, jloc, potential_name;
while(line = reader.next_line()) {
try {
ValueTokenizer values(line);
iloc = values.next_string();
jloc = values.next_string();
potential_name = values.next_string();
if (iloc == arg[0] && jloc == arg[1] && potential_name == "xstk") {
k_xst_one = values.next_double();
cut_xst_0_one = values.next_double();
cut_xst_c_one = values.next_double();
cut_xst_lo_one = values.next_double();
cut_xst_hi_one = values.next_double();
a_xst1_one = values.next_double();
theta_xst1_0_one = values.next_double();
dtheta_xst1_ast_one = values.next_double();
a_xst2_one = values.next_double();
theta_xst2_0_one = values.next_double();
dtheta_xst2_ast_one = values.next_double();
a_xst3_one = values.next_double();
theta_xst3_0_one = values.next_double();
dtheta_xst3_ast_one = values.next_double();
a_xst7_one = values.next_double();
theta_xst7_0_one = values.next_double();
dtheta_xst7_ast_one = values.next_double();
a_xst8_one = values.next_double();
theta_xst8_0_one = values.next_double();
dtheta_xst8_ast_one = values.next_double();
break;
} else continue;
} catch (std::exception &e) {
error->one(FLERR, "Problem parsing oxDNA potential file: {}", e.what());
}
}
if (iloc != arg[0] || jloc != arg[1] || potential_name != "xstk") error->one(FLERR, "No corresponding xstk potential found in file {} for pair type {} {}", arg[2], arg[0], arg[1]);
}
MPI_Bcast(&k_xst_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_xst_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_xst_c_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_xst_lo_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_xst_hi_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_xst1_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_xst1_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_xst1_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_xst2_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_xst2_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_xst2_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_xst3_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_xst3_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_xst3_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_xst7_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_xst7_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_xst7_ast_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&a_xst8_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&theta_xst8_0_one, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&dtheta_xst8_ast_one, 1, MPI_DOUBLE, 0, world);
}
b_xst_lo_one = 0.25 * (cut_xst_lo_one - cut_xst_0_one) * (cut_xst_lo_one - cut_xst_0_one)/ b_xst_lo_one = 0.25 * (cut_xst_lo_one - cut_xst_0_one) * (cut_xst_lo_one - cut_xst_0_one)/
(0.5 * (cut_xst_lo_one - cut_xst_0_one) * (cut_xst_lo_one - cut_xst_0_one) - (0.5 * (cut_xst_lo_one - cut_xst_0_one) * (cut_xst_lo_one - cut_xst_0_one) -