Created new feature branch for PR as per request
This commit is contained in:
Oliver Henrich
Binary file not shown.
@ -10,7 +10,7 @@ Syntax
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atom_style style args
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* style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *molecular* or *peri* or *smd* or *sph* or *sphere* or *spin* or *tdpd* or *tri* or *template* or *hybrid*
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* style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *molecular* or *oxdna* or *peri* or *smd* or *sph* or *sphere* or *spin* or *tdpd* or *tri* or *template* or *hybrid*
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.. parsed-literal::
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@ -110,6 +110,8 @@ quantities.
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *molecular* | bonds, angles, dihedrals, impropers | uncharged molecules |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *oxdna* | nucleotide polarity | coarse-grained DNA and RNA models |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *peri* | mass, volume | mesoscopic Peridynamic models |
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+--------------+-----------------------------------------------------+--------------------------------------+
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| *smd* | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles |
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@ -193,8 +195,14 @@ position, which is represented by the eradius = electron size.
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For the *peri* style, the particles are spherical and each stores a
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per-particle mass and volume.
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The *oxdna* style is for coarse-grained nucleotides and stores the
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3'-to-5' polarity of the nucleotide strand, which is set through
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the bond topology in the data file. The first (second) atom in a
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bond definition is understood to point towards the 3'-end (5'-end)
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of the strand. Note that this style is part of the USER-CGDNA package.
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The *dpd* style is for dissipative particle dynamics (DPD) particles.
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Note that it is part of the DPD-REACT package, and is not for use with
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Note that it is part of the USER-DPD package, and is not for use with
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the :doc:`pair_style dpd or dpd/stat <pair_dpd>` commands, which can
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simply use atom_style atomic. Atom_style dpd extends DPD particle
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properties with internal temperature (dpdTheta), internal conductive
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@ -319,7 +327,7 @@ styles take the same arguments and should produce the same results,
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except for round-off and precision issues.
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Note that other acceleration packages in LAMMPS, specifically the GPU,
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INTEL, OPENMP, and OPT packages do not use accelerated atom
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USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom
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styles.
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The accelerated styles are part of the KOKKOS package. They are only
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@ -352,24 +360,26 @@ The *dipole* style is part of the DIPOLE package.
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The *peri* style is part of the PERI package for Peridynamics.
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The *electron* style is part of the EFF package for :doc:`electronic force fields <pair_eff>`.
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The *oxdna* style is part of the USER-CGDNA package for coarse-grained simulation of DNA and RNA.
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The *dpd* style is part of the DPD-REACT package for dissipative
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The *electron* style is part of the USER-EFF package for :doc:`electronic force fields <pair_eff>`.
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The *dpd* style is part of the USER-DPD package for dissipative
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particle dynamics (DPD).
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The *edpd*\ , *mdpd*\ , and *tdpd* styles are part of the DPD-MESO package
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The *edpd*\ , *mdpd*\ , and *tdpd* styles are part of the USER-MESODPD package
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for energy-conserving dissipative particle dynamics (eDPD), many-body
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dissipative particle dynamics (mDPD), and transport dissipative particle
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dynamics (tDPD), respectively.
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The *sph* style is part of the SPH package for smoothed particle
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The *sph* style is part of the USER-SPH package for smoothed particle
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hydrodynamics (SPH). See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
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The *mesont* style is part of the MESONT package.
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The *mesont* style is part of the USER-MESONT package.
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The *spin* style is part of the SPIN package.
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The *wavepacket* style is part of the AWPMD package for the
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The *wavepacket* style is part of the USER-AWPMD package for the
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:doc:`antisymmetrized wave packet MD method <pair_awpmd>`.
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Related commands
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||||
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@ -76,17 +76,26 @@ commands:
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The coefficients in the above example have to be kept fixed and cannot
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be changed without reparameterizing the entire model.
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.. note::
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This bond style has to be used with the *atom_style hybrid bond ellipsoid oxdna*
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(see documentation of :doc:`atom_style <atom_style>`). The *atom_style oxdna*
|
||||
stores the 3'-to-5' polarity of the nucleotide strand, which is set through
|
||||
the bond topology in the data file. The first (second) atom in a bond definition
|
||||
is understood to point towards the 3'-end (5'-end) of the strand.
|
||||
|
||||
|
||||
Example input and data files for DNA and RNA duplexes can be found in
|
||||
examples/PACKAGES/cgdna/examples/oxDNA/ , /oxDNA2/ and /oxRNA2/. A simple python
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examples/USER/cgdna/examples/oxDNA/ , /oxDNA2/ and /oxRNA2/. A simple python
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setup tool which creates single straight or helical DNA strands, DNA/RNA
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duplexes or arrays of DNA/RNA duplexes can be found in
|
||||
examples/PACKAGES/cgdna/util/.
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examples/USER/cgdna/util/.
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||||
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Please cite :ref:`(Henrich) <Henrich0>` in any publication that uses
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||||
this implementation. The article contains general information
|
||||
on the model, its implementation and performance as well as the structure of
|
||||
the data and input file. The preprint version of the article can be found
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`here <PDF/CG-DNA.pdf>`_.
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`here <PDF/USER-CGDNA.pdf>`_.
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Please cite also the relevant oxDNA/oxRNA publications. These are
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:ref:`(Ouldridge) <Ouldridge0>` and
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:ref:`(Ouldridge-DPhil) <Ouldridge-DPhil0>` for oxDNA,
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@ -101,14 +110,14 @@ Restrictions
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""""""""""""
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|
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This bond style can only be used if LAMMPS was built with the
|
||||
CG-DNA package and the MOLECULE and ASPHERE package. See the
|
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USER-CGDNA package and the MOLECULE and ASPHERE package. See the
|
||||
:doc:`Build package <Build_package>` doc page for more info.
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||||
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Related commands
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""""""""""""""""
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:doc:`pair_style oxdna/excv <pair_oxdna>`, :doc:`pair_style oxdna2/excv <pair_oxdna2>`, :doc:`pair_style oxrna2/excv <pair_oxrna2>`,
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:doc:`bond_coeff <bond_coeff>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
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:doc:`bond_coeff <bond_coeff>`, :doc:`atom_style oxdna <atom_style>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
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Default
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"""""""
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@ -91,15 +91,23 @@ for a detailed description of the oxDNA force field.
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||||
or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
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||||
the temperature coefficients have to be matched to the one used in the fix.
|
||||
|
||||
Example input and data files for DNA duplexes can be found in examples/PACKAGES/cgdna/examples/oxDNA/ and /oxDNA2/.
|
||||
.. note::
|
||||
|
||||
These pair styles have to be used with the *atom_style hybrid bond ellipsoid oxdna*
|
||||
(see documentation of :doc:`atom_style <atom_style>`). The *atom_style oxdna*
|
||||
stores the 3'-to-5' polarity of the nucleotide strand, which is set through
|
||||
the bond topology in the data file. The first (second) atom in a bond definition
|
||||
is understood to point towards the 3'-end (5'-end) of the strand.
|
||||
|
||||
Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
|
||||
A simple python setup tool which creates single straight or helical DNA strands,
|
||||
DNA duplexes or arrays of DNA duplexes can be found in examples/PACKAGES/cgdna/util/.
|
||||
DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
|
||||
|
||||
Please cite :ref:`(Henrich) <Henrich1>` in any publication that uses
|
||||
this implementation. The article contains general information
|
||||
on the model, its implementation and performance as well as the structure of
|
||||
the data and input file. The preprint version of the article can be found
|
||||
`here <PDF/CG-DNA.pdf>`_.
|
||||
`here <PDF/USER-CGDNA.pdf>`_.
|
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Please cite also the relevant oxDNA publications
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:ref:`(Ouldridge) <Ouldridge1>`,
|
||||
:ref:`(Ouldridge-DPhil) <Ouldridge-DPhil1>`
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||||
@ -111,7 +119,7 @@ Restrictions
|
||||
""""""""""""
|
||||
|
||||
These pair styles can only be used if LAMMPS was built with the
|
||||
CG-DNA package and the MOLECULE and ASPHERE package. See the
|
||||
USER-CGDNA package and the MOLECULE and ASPHERE package. See the
|
||||
:doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
Related commands
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||||
@ -120,7 +128,7 @@ Related commands
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:doc:`bond_style oxdna/fene <bond_oxdna>`, :doc:`pair_coeff <pair_coeff>`,
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:doc:`bond_style oxdna2/fene <bond_oxdna>`, :doc:`pair_style oxdna2/excv <pair_oxdna2>`,
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:doc:`bond_style oxrna2/fene <bond_oxdna>`, :doc:`pair_style oxrna2/excv <pair_oxrna2>`,
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:doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
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:doc:`atom_style oxdna <atom_style>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
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Default
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"""""""
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@ -100,15 +100,23 @@ and :ref:`(Ouldridge) <Ouldridge2>` for a detailed description of the oxDNA2 fo
|
||||
e.g. through :doc:`fix langevin <fix_langevin>` or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
|
||||
the temperature coefficients have to be matched to the one used in the fix.
|
||||
|
||||
Example input and data files for DNA duplexes can be found in examples/PACKAGES/cgdna/examples/oxDNA/ and /oxDNA2/.
|
||||
.. note::
|
||||
|
||||
These pair styles have to be used with the *atom_style hybrid bond ellipsoid oxdna*
|
||||
(see documentation of :doc:`atom_style <atom_style>`). The *atom_style oxdna*
|
||||
stores the 3'-to-5' polarity of the nucleotide strand, which is set through
|
||||
the bond topology in the data file. The first (second) atom in a bond definition
|
||||
is understood to point towards the 3'-end (5'-end) of the strand.
|
||||
|
||||
Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
|
||||
A simple python setup tool which creates single straight or helical DNA strands,
|
||||
DNA duplexes or arrays of DNA duplexes can be found in examples/PACKAGES/cgdna/util/.
|
||||
DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
|
||||
|
||||
Please cite :ref:`(Henrich) <Henrich2>` in any publication that uses
|
||||
this implementation. The article contains general information
|
||||
on the model, its implementation and performance as well as the structure of
|
||||
the data and input file. The preprint version of the article can be found
|
||||
`here <PDF/CG-DNA.pdf>`_.
|
||||
`here <PDF/USER-CGDNA.pdf>`_.
|
||||
Please cite also the relevant oxDNA2 publications
|
||||
:ref:`(Snodin) <Snodin2>` and :ref:`(Sulc) <Sulc2>`.
|
||||
|
||||
@ -118,7 +126,7 @@ Restrictions
|
||||
""""""""""""
|
||||
|
||||
These pair styles can only be used if LAMMPS was built with the
|
||||
CG-DNA package and the MOLECULE and ASPHERE package. See the
|
||||
USER-CGDNA package and the MOLECULE and ASPHERE package. See the
|
||||
:doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
Related commands
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||||
@ -127,7 +135,7 @@ Related commands
|
||||
:doc:`bond_style oxdna2/fene <bond_oxdna>`, :doc:`pair_coeff <pair_coeff>`,
|
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:doc:`bond_style oxdna/fene <bond_oxdna>`, :doc:`pair_style oxdna/excv <pair_oxdna>`,
|
||||
:doc:`bond_style oxrna2/fene <bond_oxdna>`, :doc:`pair_style oxrna2/excv <pair_oxrna2>`,
|
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:doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
|
||||
:doc:`atom_style oxdna <atom_style>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
@ -101,15 +101,23 @@ and :ref:`(Ouldridge) <Ouldridge3>` for a detailed description of the oxRNA2 fo
|
||||
e.g. through :doc:`fix langevin <fix_langevin>` or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
|
||||
the temperature coefficients have to be matched to the one used in the fix.
|
||||
|
||||
Example input and data files for DNA duplexes can be found in examples/PACKAGES/cgdna/examples/oxDNA/ and /oxDNA2/.
|
||||
.. note::
|
||||
|
||||
These pair styles have to be used with the *atom_style hybrid bond ellipsoid oxdna*
|
||||
(see documentation of :doc:`atom_style <atom_style>`). The *atom_style oxdna*
|
||||
stores the 3'-to-5' polarity of the nucleotide strand, which is set through
|
||||
the bond topology in the data file. The first (second) atom in a bond definition
|
||||
is understood to point towards the 3'-end (5'-end) of the strand.
|
||||
|
||||
Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
|
||||
A simple python setup tool which creates single straight or helical DNA strands,
|
||||
DNA duplexes or arrays of DNA duplexes can be found in examples/PACKAGES/cgdna/util/.
|
||||
DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
|
||||
|
||||
Please cite :ref:`(Henrich) <Henrich3>` in any publication that uses
|
||||
this implementation. The article contains general information
|
||||
on the model, its implementation and performance as well as the structure of
|
||||
the data and input file. The preprint version of the article can be found
|
||||
`here <PDF/CG-DNA.pdf>`_.
|
||||
`here <PDF/USER-CGDNA.pdf>`_.
|
||||
Please cite also the relevant oxRNA2 publications
|
||||
:ref:`(Sulc1) <Sulc31>` and :ref:`(Sulc2) <Sulc32>`.
|
||||
|
||||
@ -119,7 +127,7 @@ Restrictions
|
||||
""""""""""""
|
||||
|
||||
These pair styles can only be used if LAMMPS was built with the
|
||||
CG-DNA package and the MOLECULE and ASPHERE package. See the
|
||||
USER-CGDNA package and the MOLECULE and ASPHERE package. See the
|
||||
:doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
Related commands
|
||||
@ -128,7 +136,7 @@ Related commands
|
||||
:doc:`bond_style oxrna2/fene <bond_oxdna>`, :doc:`pair_coeff <pair_coeff>`,
|
||||
:doc:`bond_style oxdna/fene <bond_oxdna>`, :doc:`pair_style oxdna/excv <pair_oxdna>`,
|
||||
:doc:`bond_style oxdna2/fene <bond_oxdna>`, :doc:`pair_style oxdna2/excv <pair_oxdna2>`,
|
||||
:doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
|
||||
:doc:`atom_style oxdna <atom_style>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
@ -1325,7 +1325,6 @@ hyperradius
|
||||
hyperspherical
|
||||
hysteretic
|
||||
hz
|
||||
IAP
|
||||
Ibanez
|
||||
iatom
|
||||
ibar
|
||||
@ -1648,8 +1647,6 @@ larentzos
|
||||
Larentzos
|
||||
Laroche
|
||||
lars
|
||||
LATBOLTZ
|
||||
latboltz
|
||||
latencies
|
||||
Latour
|
||||
latourr
|
||||
@ -1800,8 +1797,6 @@ Lysogorskiy
|
||||
Lyulin
|
||||
lz
|
||||
Maaravi
|
||||
MACHDYN
|
||||
machdyn
|
||||
Mackay
|
||||
Mackrodt
|
||||
Macromolecules
|
||||
@ -1896,7 +1891,8 @@ mdi
|
||||
mdpd
|
||||
mDPD
|
||||
meam
|
||||
MEAM
|
||||
meamc
|
||||
MEAMC
|
||||
meamf
|
||||
meanDist
|
||||
mech
|
||||
@ -2323,6 +2319,7 @@ Ntriples
|
||||
Ntype
|
||||
ntypes
|
||||
Ntypes
|
||||
nucleotide
|
||||
nucleotides
|
||||
nullptr
|
||||
num
|
||||
@ -2680,7 +2677,6 @@ qoverride
|
||||
qqr
|
||||
qqrd
|
||||
qtb
|
||||
Quadfel
|
||||
quadratically
|
||||
quadrupolar
|
||||
Quant
|
||||
@ -2740,7 +2736,7 @@ README
|
||||
realtime
|
||||
reamin
|
||||
reax
|
||||
REAXFF
|
||||
REAXC
|
||||
ReaxFF
|
||||
rebo
|
||||
recursing
|
||||
@ -2862,7 +2858,6 @@ Rossky
|
||||
rosybrown
|
||||
rotationally
|
||||
Rotenberg
|
||||
Rothenburg
|
||||
Rovigatti
|
||||
royalblue
|
||||
rozero
|
||||
|
||||
@ -72,7 +72,7 @@ between two individual nucleotides can be established.
|
||||
|
||||
/******************************************************************************/
|
||||
|
||||
/examples/oxRNA2/duplex4
|
||||
/examples/oxRNA2/duplex2
|
||||
|
||||
This example uses the duplex2 with the oxRNA2 force field instead of oxDNA or
|
||||
oxDNA2 force field. Sequence-dependent stacking and hydrogen-bonding
|
||||
|
||||
@ -1,15 +1,14 @@
|
||||
# LAMMPS data file
|
||||
LAMMPS data file via write_data, version 27 May 2021
|
||||
|
||||
10 atoms
|
||||
10 ellipsoids
|
||||
8 bonds
|
||||
|
||||
4 atom types
|
||||
8 bonds
|
||||
1 bond types
|
||||
10 ellipsoids
|
||||
|
||||
# System size
|
||||
-20.000000 20.000000 xlo xhi
|
||||
-20.000000 20.000000 ylo yhi
|
||||
-20.000000 20.000000 zlo zhi
|
||||
-20 20 xlo xhi
|
||||
-20 20 ylo yhi
|
||||
-20 20 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
@ -18,56 +17,52 @@ Masses
|
||||
3 3.1575
|
||||
4 3.1575
|
||||
|
||||
# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
|
||||
Atoms
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1
|
||||
2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1
|
||||
3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1
|
||||
4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1
|
||||
5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1
|
||||
6 4 -4.829362784135484e-01 3.560513319622209e-01 1.559051420521249e+00 2 1 1
|
||||
7 1 -1.824198365552941e-01 5.715968887521516e-01 1.169288565390937e+00 2 1 1
|
||||
8 2 1.874009511073395e-01 5.699832309147913e-01 7.795257102606243e-01 2 1 1
|
||||
9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1
|
||||
10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1
|
||||
1 1 -0.33741452300167507 -0.43708835412476305 0.6450685042019271 1 1 3.7269849963023267 0 0 0
|
||||
2 2 -0.32142606102826937 -0.7137743037592722 1.1817366147004618 1 1 3.7269849963023267 0 0 0
|
||||
3 3 -0.130363628207774 -0.9147144801536078 1.62581312195109 1 1 3.7269849963023267 0 0 0
|
||||
4 4 0.16795127962282844 -0.9808507459807022 2.0894908590909003 1 1 3.7269849963023267 0 0 0
|
||||
5 1 0.46370423490634166 -0.7803347954883079 2.4251986815515827 1 1 3.7269849963023267 0 0 0
|
||||
6 4 -0.4462950185476711 0.09062163051035639 2.4668941268777607 2 1 3.7269849963023267 0 0 0
|
||||
7 1 -0.03377054097560965 0.20979847489755046 2.078208732038921 2 1 3.7269849963023267 0 0 0
|
||||
8 2 0.3297325391466579 0.17657587120899895 1.7206328374934152 2 1 3.7269849963023267 0 0 0
|
||||
9 3 0.6063699309305985 0.04682595158675571 1.2335049647817748 2 1 3.7269849963023267 0 0 0
|
||||
10 4 0.8003979559814726 -0.364393011459011 0.9884025318908612 2 1 3.7269849963023267 0 0 0
|
||||
|
||||
# Atom-ID, translational velocity, angular momentum
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
1 0.320321385294804 -0.13632815939410442 -0.029398292452023418 0.3064009492028237 -0.15808560233691588 0.35878007201886397
|
||||
2 0.16868594667473025 -0.04950805613064363 0.15811007290373785 -0.07666583909321756 -0.0008074676325318194 -0.21475821019816385
|
||||
3 -0.22924557018300165 0.08381876748892438 -0.0919832851533896 0.4039387481683193 0.6123610642545824 -0.11063432848545783
|
||||
4 -0.22186204313310393 0.04952817499985707 -0.0693642101605732 -0.1358248430264938 0.4118493572385653 -0.056529305922687775
|
||||
5 0.08156431270087049 -0.2564594759800144 0.1724544416027875 0.05439894663158808 0.09338481510384318 0.3205408219238883
|
||||
6 0.03598698404367743 -0.04868642973674152 0.02860105256592922 0.04007709957283992 -0.317943400069374 0.36438025397586354
|
||||
7 -0.00822868972307372 0.047514932936351305 -0.027726409420297023 0.18356392696891796 -0.49877294396308003 0.06993313839189567
|
||||
8 -0.07177147672242379 0.1718272727853115 0.39056151182616994 -0.16728362538690794 -0.47839708820957955 -0.17897249005947627
|
||||
9 -0.1748638855727651 -0.0781638161351808 0.0560181565271157 -0.28062568580131014 0.2405396522734162 -0.4311598357169048
|
||||
10 0.18870318272756448 -0.1066780134639517 0.12610657946741227 -0.05740397100183697 0.36748833227892685 0.1498775724372025
|
||||
|
||||
# Atom-ID, shape, quaternion
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01
|
||||
3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01
|
||||
4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01
|
||||
5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01
|
||||
6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.499720515246527e-01 -3.123349185122326e-01 -0.000000000000000e+00
|
||||
7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.074754054847401e-01 -5.899012371043604e-01 0.000000000000000e+00
|
||||
8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.863723567357896e-01 -8.100416404457959e-01 0.000000000000000e+00
|
||||
9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252947e-01 0.000000000000000e+00
|
||||
10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 1.110223024625157e-16 1.000000000000000e+00 -0.000000000000000e+00
|
||||
|
||||
# Bond topology
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 6 7
|
||||
6 1 7 8
|
||||
7 1 8 9
|
||||
8 1 9 10
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 6 7
|
||||
6 1 7 8
|
||||
7 1 8 9
|
||||
8 1 9 10
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341 1.173984503142341 1.173984503142341 0.9890278201757743 0.01779228232037064 -0.14337734159225404 0.030827642240801516
|
||||
2 1.173984503142341 1.173984503142341 1.173984503142341 0.939687458852748 0.04174166924055095 -0.023337773785056866 0.338674565089608
|
||||
3 1.173984503142341 1.173984503142341 1.173984503142341 0.8210113150655425 0.03012140921736572 0.017666019956944813 0.5698429897612057
|
||||
4 1.173984503142341 1.173984503142341 1.173984503142341 0.6623662858285051 -0.028186343967346823 0.022942552517501488 0.7482981175276918
|
||||
5 1.173984503142341 1.173984503142341 1.173984503142341 0.3601488726765216 0.0513614985821682 0.0724224158335286 0.9286602067807472
|
||||
6 1.173984503142341 1.173984503142341 1.173984503142341 0.11941234710084649 0.9244660117493703 -0.35317942248051865 -0.07979711784524246
|
||||
7 1.173984503142341 1.173984503142341 1.173984503142341 -0.17949125421205164 0.7412884899431119 -0.6379094464220707 0.1065166771202199
|
||||
8 1.173984503142341 1.173984503142341 1.173984503142341 -0.10483691088405202 0.5508895999584645 -0.8250090480220789 0.06992811634525403
|
||||
9 1.173984503142341 1.173984503142341 1.173984503142341 0.07777239911646 -0.3724087549185288 0.9103052384821374 -0.1631181963720798
|
||||
10 1.173984503142341 1.173984503142341 1.173984503142341 0.16279109707978262 0.027148630125149613 0.9849325709665359 -0.0516705065113425
|
||||
|
||||
@ -11,11 +11,11 @@ newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex1
|
||||
@ -40,27 +40,16 @@ pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793
|
||||
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
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 3.8
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
@ -71,10 +60,10 @@ variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
write_data last_config.${number}.* nocoeff
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -1,15 +1,14 @@
|
||||
# LAMMPS data file
|
||||
LAMMPS data file via write_data, version 27 May 2021
|
||||
|
||||
16 atoms
|
||||
16 ellipsoids
|
||||
13 bonds
|
||||
|
||||
4 atom types
|
||||
13 bonds
|
||||
1 bond types
|
||||
16 ellipsoids
|
||||
|
||||
# System size
|
||||
-20.000000 20.000000 xlo xhi
|
||||
-20.000000 20.000000 ylo yhi
|
||||
-20.000000 20.000000 zlo zhi
|
||||
-20 20 xlo xhi
|
||||
-20 20 ylo yhi
|
||||
-20 20 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
@ -18,79 +17,75 @@ Masses
|
||||
3 3.1575
|
||||
4 3.1575
|
||||
|
||||
# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
|
||||
Atoms
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1
|
||||
2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1
|
||||
3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1
|
||||
4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1
|
||||
5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1
|
||||
6 2 5.999771538385027e-01 -5.235921299024461e-03 1.948814275651561e+00 1 1 1
|
||||
7 3 4.890766774371325e-01 3.475687034056071e-01 2.338577130781873e+00 1 1 1
|
||||
8 4 1.923677943514057e-01 5.683261666476170e-01 2.728339985912185e+00 1 1 1
|
||||
9 1 -1.923677943514057e-01 -5.683261666476170e-01 2.728339985912185e+00 2 1 1
|
||||
10 2 -4.890766774371324e-01 -3.475687034056071e-01 2.338577130781873e+00 2 1 1
|
||||
11 3 -5.999771538385025e-01 5.235921299024461e-03 1.948814275651561e+00 2 1 1
|
||||
12 4 -4.829362784135481e-01 3.560513319622207e-01 1.559051420521249e+00 2 1 1
|
||||
13 1 -1.824198365552940e-01 5.715968887521514e-01 1.169288565390936e+00 2 1 1
|
||||
14 2 1.874009511073395e-01 5.699832309147912e-01 7.795257102606241e-01 2 1 1
|
||||
15 3 4.860249842674773e-01 3.518234140414733e-01 3.897628551303119e-01 2 1 1
|
||||
16 4 5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1
|
||||
1 1 -0.6133472972454725 -0.657478171669766 0.36065226351201896 1 1 3.7269849963023267 0 0 0
|
||||
2 2 -0.45262764247356363 -1.0030650534345913 0.7258693379233347 1 1 3.7269849963023267 0 0 0
|
||||
3 3 -0.0988342108522641 -1.239775807128057 1.069462285786363 1 1 3.7269849963023267 0 0 0
|
||||
4 4 0.2937771854299732 -1.2579750924899842 1.4258916086606965 1 1 3.7269849963023267 0 0 0
|
||||
5 1 0.6286896795685137 -1.0183343395119744 1.7689346339672825 1 1 3.7269849963023267 0 0 0
|
||||
6 2 0.7901522619067926 -0.6766341805565266 2.1540160705495754 1 1 3.7269849963023267 0 0 0
|
||||
7 3 0.7115777184886863 -0.40195579325143455 2.569568683291525 1 1 3.7269849963023267 0 0 0
|
||||
8 4 0.46973310377005234 -0.30251697967107033 3.0668007117519216 1 1 3.7269849963023267 0 0 0
|
||||
9 1 0.4056113349449848 -1.443775499211898 3.0590726503341124 2 1 3.7269849963023267 0 0 0
|
||||
10 2 -0.032028429059287516 -1.2947520971164723 2.7201071151392187 2 1 3.7269849963023267 0 0 0
|
||||
11 3 -0.31613855112314065 -0.908414175906161 2.4125207871782006 2 1 3.7269849963023267 0 0 0
|
||||
12 4 -0.38939391251821 -0.4866605488242819 2.006177777000426 2 1 3.7269849963023267 0 0 0
|
||||
13 1 -0.06232643040853296 -0.07155965522127403 1.5593206052730733 3 1 3.7269849963023267 0 0 0
|
||||
14 2 0.17884090390913376 -0.05516721349427172 1.021273149730912 3 1 3.7269849963023267 0 0 0
|
||||
15 3 0.4513439961906 -0.23795607383274572 0.5957328539615993 3 1 3.7269849963023267 0 0 0
|
||||
16 4 0.5077649359807965 -0.5565625134533538 0.1655875784458841 3 1 3.7269849963023267 0 0 0
|
||||
|
||||
# Atom-ID, translational velocity, angular momentum
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
11 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
12 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
13 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
14 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
15 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
16 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
1 0.05386890022865587 0.02262922525602673 0.24882291144736746 0.1772010258006941 -0.29588531700001014 -0.2624137503614725
|
||||
2 -0.03995003075629463 0.26969511063701984 -0.18986454548195664 -0.030614539375968176 -0.11769518931480599 0.040074702426473215
|
||||
3 -0.20784535295201376 -0.13628722357673043 -0.06062477950201746 -0.03676034584820381 -0.06308707793373186 -0.14798601576087625
|
||||
4 -0.23969824181316998 -0.5624721730878831 0.032474422905036715 -0.16523645965016515 0.2860623077030974 0.33543519753105877
|
||||
5 -0.16114897356828353 -0.22889697470760145 -0.13553324962649563 0.07151030852881342 -0.09415592891043179 0.13422881539312292
|
||||
6 -0.04701706588477693 0.19216715585110036 0.14588242791297215 0.09218622989776322 -0.5640128930702024 0.09287105657777776
|
||||
7 0.05098438305112513 -0.038459555522009595 -0.14244196285749675 0.3479046835475834 0.4244922695910593 -0.13582882604358357
|
||||
8 0.37827971348411926 -0.04953992506010833 0.1626392045834847 0.0442887659636129 0.07868414126013584 -0.12713600444325032
|
||||
9 0.04912038408665491 0.041260647318716696 0.012223856334495234 0.03282916621721876 -0.00012670547095256 0.155978785417696
|
||||
10 0.1939216183073483 0.11075235485381942 -0.0405050516019971 -0.17008135001813812 -0.4563093565840761 -0.30318513627039506
|
||||
11 -0.351360733920646 -0.18822419067535692 0.36147938199051305 -0.3708221604627426 -0.49108381825941216 0.09435948331955418
|
||||
12 -0.1188642917357977 0.22355282456551884 0.009265586122144348 -0.28230100188858365 0.10276485660828892 0.10175233476780697
|
||||
13 -0.1446616296238799 -0.11552059909787235 0.1331477187595642 -0.25498721890374343 0.2754663721641154 0.05806416868630132
|
||||
14 0.051547120035862544 -0.36611026510775635 -0.06630782880801242 -0.11999847173316518 0.0684476892288605 0.2161595932308759
|
||||
15 -0.20214244962091388 0.23341226933559608 0.008133374252278069 -0.17013911124135248 0.01870292260510287 -0.2682954134361106
|
||||
16 -0.19202131162868008 -0.08105295741355378 -0.0469350810885074 0.017332107652647588 -0.32876588862807693 0.1085334141225924
|
||||
|
||||
# Atom-ID, shape, quaternion
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01
|
||||
3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01
|
||||
4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01
|
||||
5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01
|
||||
6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 4.363309284746654e-03 0.000000000000000e+00 0.000000000000000e+00 9.999904807207346e-01
|
||||
7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -3.040330609254902e-01 0.000000000000000e+00 0.000000000000000e+00 9.526614812535865e-01
|
||||
8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.828323126827837e-01 0.000000000000000e+00 0.000000000000000e+00 -8.125924533816677e-01
|
||||
9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.125924533816681e-01 5.828323126827832e-01 -0.000000000000000e+00
|
||||
10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.526614812535864e-01 3.040330609254902e-01 0.000000000000000e+00
|
||||
11 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.999904807207346e-01 -4.363309284746654e-03 0.000000000000000e+00
|
||||
12 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.499720515246526e-01 -3.123349185122325e-01 0.000000000000000e+00
|
||||
13 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.074754054847402e-01 -5.899012371043603e-01 0.000000000000000e+00
|
||||
14 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.863723567357898e-01 -8.100416404457959e-01 0.000000000000000e+00
|
||||
15 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252948e-01 0.000000000000000e+00
|
||||
16 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 2.775557561562893e-17 1.000000000000000e+00 -0.000000000000000e+00
|
||||
|
||||
# Bond topology
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 9 10
|
||||
9 1 10 11
|
||||
10 1 11 12
|
||||
11 1 13 14
|
||||
12 1 14 15
|
||||
13 1 15 16
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 9 10
|
||||
9 1 10 11
|
||||
10 1 11 12
|
||||
11 1 13 14
|
||||
12 1 14 15
|
||||
13 1 15 16
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341 1.173984503142341 1.173984503142341 0.9964752158482045 -0.053253555733239796 0.011391163807102514 -0.06380787090289707
|
||||
2 1.173984503142341 1.173984503142341 1.173984503142341 0.9369923833143513 0.11220716044648564 0.06732538499716349 0.3239168400846305
|
||||
3 1.173984503142341 1.173984503142341 1.173984503142341 0.797964932091827 0.14473096354527873 0.18374142699366386 0.5554673737937029
|
||||
4 1.173984503142341 1.173984503142341 1.173984503142341 0.5660864821344559 0.14688275499481052 0.09873742533340191 0.8051226439917721
|
||||
5 1.173984503142341 1.173984503142341 1.173984503142341 0.2533023785125306 0.12062313161679827 0.08583012223905846 0.9559922359911086
|
||||
6 1.173984503142341 1.173984503142341 1.173984503142341 -0.03855807343534716 0.08405913137017908 0.02236505169306371 0.9954632800204194
|
||||
7 1.173984503142341 1.173984503142341 1.173984503142341 -0.45592844330248017 0.1004550065061007 -0.052524745294758785 0.8827679181910482
|
||||
8 1.173984503142341 1.173984503142341 1.173984503142341 0.768021221540491 -0.009582139884533599 0.03658677589040892 -0.63930665074644
|
||||
9 1.173984503142341 1.173984503142341 1.173984503142341 -0.23299975754512345 0.688686395231341 0.6747873944883376 -0.12682324016841584
|
||||
10 1.173984503142341 1.173984503142341 1.173984503142341 -0.24662061871907232 0.8744456399178389 0.39370836087823996 -0.13970261209395163
|
||||
11 1.173984503142341 1.173984503142341 1.173984503142341 -0.087475900850909 0.977367602388229 0.14493549113095577 -0.12686307572668784
|
||||
12 1.173984503142341 1.173984503142341 1.173984503142341 -0.03181169300779214 0.9634374984140112 -0.2442360692534371 -0.10547485630879185
|
||||
13 1.173984503142341 1.173984503142341 1.173984503142341 -0.032786070696572266 0.7922941528811777 -0.6084214170523915 -0.03191282109962717
|
||||
14 1.173984503142341 1.173984503142341 1.173984503142341 0.047188686288341455 0.6316396208287698 -0.7737349519945348 0.011783095844627799
|
||||
15 1.173984503142341 1.173984503142341 1.173984503142341 -0.05869980642620335 -0.34229358203414423 0.9376740835056508 0.012519965878508689
|
||||
16 1.173984503142341 1.173984503142341 1.173984503142341 -0.08582818143150042 0.0008707732197394232 0.9939540921464659 -0.0684691735853161
|
||||
|
||||
@ -11,11 +11,11 @@ newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex2
|
||||
@ -40,27 +40,16 @@ pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793
|
||||
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
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
fix 1 all nve/asphere
|
||||
fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 3.8
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
@ -71,10 +60,10 @@ variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
write_data last_config.${number}.* nocoeff
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -1,15 +1,14 @@
|
||||
# LAMMPS data file
|
||||
LAMMPS data file via write_data, version 27 May 2021
|
||||
|
||||
10 atoms
|
||||
10 ellipsoids
|
||||
8 bonds
|
||||
|
||||
4 atom types
|
||||
8 bonds
|
||||
1 bond types
|
||||
10 ellipsoids
|
||||
|
||||
# System size
|
||||
-20.000000 20.000000 xlo xhi
|
||||
-20.000000 20.000000 ylo yhi
|
||||
-20.000000 20.000000 zlo zhi
|
||||
-20 20 xlo xhi
|
||||
-20 20 ylo yhi
|
||||
-20 20 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
@ -18,56 +17,52 @@ Masses
|
||||
3 3.1575
|
||||
4 3.1575
|
||||
|
||||
# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
|
||||
Atoms
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1
|
||||
2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1
|
||||
3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1
|
||||
4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1
|
||||
5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1
|
||||
6 4 -4.829362784135484e-01 3.560513319622209e-01 1.559051420521249e+00 2 1 1
|
||||
7 1 -1.824198365552941e-01 5.715968887521516e-01 1.169288565390937e+00 2 1 1
|
||||
8 2 1.874009511073395e-01 5.699832309147913e-01 7.795257102606243e-01 2 1 1
|
||||
9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1
|
||||
10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1
|
||||
1 1 -0.33741452300167507 -0.43708835412476305 0.6450685042019271 1 1 3.7269849963023267 0 0 0
|
||||
2 2 -0.32142606102826937 -0.7137743037592722 1.1817366147004618 1 1 3.7269849963023267 0 0 0
|
||||
3 3 -0.130363628207774 -0.9147144801536078 1.62581312195109 1 1 3.7269849963023267 0 0 0
|
||||
4 4 0.16795127962282844 -0.9808507459807022 2.0894908590909003 1 1 3.7269849963023267 0 0 0
|
||||
5 1 0.46370423490634166 -0.7803347954883079 2.4251986815515827 1 1 3.7269849963023267 0 0 0
|
||||
6 4 -0.4462950185476711 0.09062163051035639 2.4668941268777607 2 1 3.7269849963023267 0 0 0
|
||||
7 1 -0.03377054097560965 0.20979847489755046 2.078208732038921 2 1 3.7269849963023267 0 0 0
|
||||
8 2 0.3297325391466579 0.17657587120899895 1.7206328374934152 2 1 3.7269849963023267 0 0 0
|
||||
9 3 0.6063699309305985 0.04682595158675571 1.2335049647817748 2 1 3.7269849963023267 0 0 0
|
||||
10 4 0.8003979559814726 -0.364393011459011 0.9884025318908612 2 1 3.7269849963023267 0 0 0
|
||||
|
||||
# Atom-ID, translational velocity, angular momentum
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
1 0.320321385294804 -0.13632815939410442 -0.029398292452023418 0.3064009492028237 -0.15808560233691588 0.35878007201886397
|
||||
2 0.16868594667473025 -0.04950805613064363 0.15811007290373785 -0.07666583909321756 -0.0008074676325318194 -0.21475821019816385
|
||||
3 -0.22924557018300165 0.08381876748892438 -0.0919832851533896 0.4039387481683193 0.6123610642545824 -0.11063432848545783
|
||||
4 -0.22186204313310393 0.04952817499985707 -0.0693642101605732 -0.1358248430264938 0.4118493572385653 -0.056529305922687775
|
||||
5 0.08156431270087049 -0.2564594759800144 0.1724544416027875 0.05439894663158808 0.09338481510384318 0.3205408219238883
|
||||
6 0.03598698404367743 -0.04868642973674152 0.02860105256592922 0.04007709957283992 -0.317943400069374 0.36438025397586354
|
||||
7 -0.00822868972307372 0.047514932936351305 -0.027726409420297023 0.18356392696891796 -0.49877294396308003 0.06993313839189567
|
||||
8 -0.07177147672242379 0.1718272727853115 0.39056151182616994 -0.16728362538690794 -0.47839708820957955 -0.17897249005947627
|
||||
9 -0.1748638855727651 -0.0781638161351808 0.0560181565271157 -0.28062568580131014 0.2405396522734162 -0.4311598357169048
|
||||
10 0.18870318272756448 -0.1066780134639517 0.12610657946741227 -0.05740397100183697 0.36748833227892685 0.1498775724372025
|
||||
|
||||
# Atom-ID, shape, quaternion
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01
|
||||
3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01
|
||||
4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01
|
||||
5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01
|
||||
6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.499720515246527e-01 -3.123349185122326e-01 -0.000000000000000e+00
|
||||
7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.074754054847401e-01 -5.899012371043604e-01 0.000000000000000e+00
|
||||
8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.863723567357896e-01 -8.100416404457959e-01 0.000000000000000e+00
|
||||
9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252947e-01 0.000000000000000e+00
|
||||
10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 1.110223024625157e-16 1.000000000000000e+00 -0.000000000000000e+00
|
||||
|
||||
# Bond topology
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 6 7
|
||||
6 1 7 8
|
||||
7 1 8 9
|
||||
8 1 9 10
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 6 7
|
||||
6 1 7 8
|
||||
7 1 8 9
|
||||
8 1 9 10
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341 1.173984503142341 1.173984503142341 0.9890278201757743 0.01779228232037064 -0.14337734159225404 0.030827642240801516
|
||||
2 1.173984503142341 1.173984503142341 1.173984503142341 0.939687458852748 0.04174166924055095 -0.023337773785056866 0.338674565089608
|
||||
3 1.173984503142341 1.173984503142341 1.173984503142341 0.8210113150655425 0.03012140921736572 0.017666019956944813 0.5698429897612057
|
||||
4 1.173984503142341 1.173984503142341 1.173984503142341 0.6623662858285051 -0.028186343967346823 0.022942552517501488 0.7482981175276918
|
||||
5 1.173984503142341 1.173984503142341 1.173984503142341 0.3601488726765216 0.0513614985821682 0.0724224158335286 0.9286602067807472
|
||||
6 1.173984503142341 1.173984503142341 1.173984503142341 0.11941234710084649 0.9244660117493703 -0.35317942248051865 -0.07979711784524246
|
||||
7 1.173984503142341 1.173984503142341 1.173984503142341 -0.17949125421205164 0.7412884899431119 -0.6379094464220707 0.1065166771202199
|
||||
8 1.173984503142341 1.173984503142341 1.173984503142341 -0.10483691088405202 0.5508895999584645 -0.8250090480220789 0.06992811634525403
|
||||
9 1.173984503142341 1.173984503142341 1.173984503142341 0.07777239911646 -0.3724087549185288 0.9103052384821374 -0.1631181963720798
|
||||
10 1.173984503142341 1.173984503142341 1.173984503142341 0.16279109707978262 0.027148630125149613 0.9849325709665359 -0.0516705065113425
|
||||
|
||||
@ -2,6 +2,7 @@ variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
variable rhos equal 0.2
|
||||
|
||||
units lj
|
||||
|
||||
@ -11,11 +12,11 @@ newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex1
|
||||
@ -38,30 +39,19 @@ pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 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
|
||||
pair_coeff * * oxdna2/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 * * 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 ${T} 1.0 0.815
|
||||
pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 3.8
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
@ -72,10 +62,10 @@ variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
write_data last_config.${number}.* nocoeff
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -1,15 +1,14 @@
|
||||
# LAMMPS data file
|
||||
LAMMPS data file via write_data, version 27 May 2021
|
||||
|
||||
16 atoms
|
||||
16 ellipsoids
|
||||
13 bonds
|
||||
|
||||
4 atom types
|
||||
13 bonds
|
||||
1 bond types
|
||||
16 ellipsoids
|
||||
|
||||
# System size
|
||||
-20.000000 20.000000 xlo xhi
|
||||
-20.000000 20.000000 ylo yhi
|
||||
-20.000000 20.000000 zlo zhi
|
||||
-20 20 xlo xhi
|
||||
-20 20 ylo yhi
|
||||
-20 20 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
@ -18,79 +17,75 @@ Masses
|
||||
3 3.1575
|
||||
4 3.1575
|
||||
|
||||
# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
|
||||
Atoms
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1
|
||||
2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1
|
||||
3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1
|
||||
4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1
|
||||
5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1
|
||||
6 2 5.999771538385027e-01 -5.235921299024461e-03 1.948814275651561e+00 1 1 1
|
||||
7 3 4.890766774371325e-01 3.475687034056071e-01 2.338577130781873e+00 1 1 1
|
||||
8 4 1.923677943514057e-01 5.683261666476170e-01 2.728339985912185e+00 1 1 1
|
||||
9 1 -1.923677943514057e-01 -5.683261666476170e-01 2.728339985912185e+00 2 1 1
|
||||
10 2 -4.890766774371324e-01 -3.475687034056071e-01 2.338577130781873e+00 2 1 1
|
||||
11 3 -5.999771538385025e-01 5.235921299024461e-03 1.948814275651561e+00 2 1 1
|
||||
12 4 -4.829362784135481e-01 3.560513319622207e-01 1.559051420521249e+00 2 1 1
|
||||
13 1 -1.824198365552940e-01 5.715968887521514e-01 1.169288565390936e+00 2 1 1
|
||||
14 2 1.874009511073395e-01 5.699832309147912e-01 7.795257102606241e-01 2 1 1
|
||||
15 3 4.860249842674773e-01 3.518234140414733e-01 3.897628551303119e-01 2 1 1
|
||||
16 4 5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1
|
||||
1 1 -0.6133472972454725 -0.657478171669766 0.36065226351201896 1 1 3.7269849963023267 0 0 0
|
||||
2 2 -0.45262764247356363 -1.0030650534345913 0.7258693379233347 1 1 3.7269849963023267 0 0 0
|
||||
3 3 -0.0988342108522641 -1.239775807128057 1.069462285786363 1 1 3.7269849963023267 0 0 0
|
||||
4 4 0.2937771854299732 -1.2579750924899842 1.4258916086606965 1 1 3.7269849963023267 0 0 0
|
||||
5 1 0.6286896795685137 -1.0183343395119744 1.7689346339672825 1 1 3.7269849963023267 0 0 0
|
||||
6 2 0.7901522619067926 -0.6766341805565266 2.1540160705495754 1 1 3.7269849963023267 0 0 0
|
||||
7 3 0.7115777184886863 -0.40195579325143455 2.569568683291525 1 1 3.7269849963023267 0 0 0
|
||||
8 4 0.46973310377005234 -0.30251697967107033 3.0668007117519216 1 1 3.7269849963023267 0 0 0
|
||||
9 1 0.4056113349449848 -1.443775499211898 3.0590726503341124 2 1 3.7269849963023267 0 0 0
|
||||
10 2 -0.032028429059287516 -1.2947520971164723 2.7201071151392187 2 1 3.7269849963023267 0 0 0
|
||||
11 3 -0.31613855112314065 -0.908414175906161 2.4125207871782006 2 1 3.7269849963023267 0 0 0
|
||||
12 4 -0.38939391251821 -0.4866605488242819 2.006177777000426 2 1 3.7269849963023267 0 0 0
|
||||
13 1 -0.06232643040853296 -0.07155965522127403 1.5593206052730733 3 1 3.7269849963023267 0 0 0
|
||||
14 2 0.17884090390913376 -0.05516721349427172 1.021273149730912 3 1 3.7269849963023267 0 0 0
|
||||
15 3 0.4513439961906 -0.23795607383274572 0.5957328539615993 3 1 3.7269849963023267 0 0 0
|
||||
16 4 0.5077649359807965 -0.5565625134533538 0.1655875784458841 3 1 3.7269849963023267 0 0 0
|
||||
|
||||
# Atom-ID, translational velocity, angular momentum
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
11 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
12 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
13 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
14 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
15 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
16 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
1 0.05386890022865587 0.02262922525602673 0.24882291144736746 0.1772010258006941 -0.29588531700001014 -0.2624137503614725
|
||||
2 -0.03995003075629463 0.26969511063701984 -0.18986454548195664 -0.030614539375968176 -0.11769518931480599 0.040074702426473215
|
||||
3 -0.20784535295201376 -0.13628722357673043 -0.06062477950201746 -0.03676034584820381 -0.06308707793373186 -0.14798601576087625
|
||||
4 -0.23969824181316998 -0.5624721730878831 0.032474422905036715 -0.16523645965016515 0.2860623077030974 0.33543519753105877
|
||||
5 -0.16114897356828353 -0.22889697470760145 -0.13553324962649563 0.07151030852881342 -0.09415592891043179 0.13422881539312292
|
||||
6 -0.04701706588477693 0.19216715585110036 0.14588242791297215 0.09218622989776322 -0.5640128930702024 0.09287105657777776
|
||||
7 0.05098438305112513 -0.038459555522009595 -0.14244196285749675 0.3479046835475834 0.4244922695910593 -0.13582882604358357
|
||||
8 0.37827971348411926 -0.04953992506010833 0.1626392045834847 0.0442887659636129 0.07868414126013584 -0.12713600444325032
|
||||
9 0.04912038408665491 0.041260647318716696 0.012223856334495234 0.03282916621721876 -0.00012670547095256 0.155978785417696
|
||||
10 0.1939216183073483 0.11075235485381942 -0.0405050516019971 -0.17008135001813812 -0.4563093565840761 -0.30318513627039506
|
||||
11 -0.351360733920646 -0.18822419067535692 0.36147938199051305 -0.3708221604627426 -0.49108381825941216 0.09435948331955418
|
||||
12 -0.1188642917357977 0.22355282456551884 0.009265586122144348 -0.28230100188858365 0.10276485660828892 0.10175233476780697
|
||||
13 -0.1446616296238799 -0.11552059909787235 0.1331477187595642 -0.25498721890374343 0.2754663721641154 0.05806416868630132
|
||||
14 0.051547120035862544 -0.36611026510775635 -0.06630782880801242 -0.11999847173316518 0.0684476892288605 0.2161595932308759
|
||||
15 -0.20214244962091388 0.23341226933559608 0.008133374252278069 -0.17013911124135248 0.01870292260510287 -0.2682954134361106
|
||||
16 -0.19202131162868008 -0.08105295741355378 -0.0469350810885074 0.017332107652647588 -0.32876588862807693 0.1085334141225924
|
||||
|
||||
# Atom-ID, shape, quaternion
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01
|
||||
3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01
|
||||
4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01
|
||||
5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01
|
||||
6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 4.363309284746654e-03 0.000000000000000e+00 0.000000000000000e+00 9.999904807207346e-01
|
||||
7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -3.040330609254902e-01 0.000000000000000e+00 0.000000000000000e+00 9.526614812535865e-01
|
||||
8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.828323126827837e-01 0.000000000000000e+00 0.000000000000000e+00 -8.125924533816677e-01
|
||||
9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.125924533816681e-01 5.828323126827832e-01 -0.000000000000000e+00
|
||||
10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.526614812535864e-01 3.040330609254902e-01 0.000000000000000e+00
|
||||
11 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.999904807207346e-01 -4.363309284746654e-03 0.000000000000000e+00
|
||||
12 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.499720515246526e-01 -3.123349185122325e-01 0.000000000000000e+00
|
||||
13 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.074754054847402e-01 -5.899012371043603e-01 0.000000000000000e+00
|
||||
14 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.863723567357898e-01 -8.100416404457959e-01 0.000000000000000e+00
|
||||
15 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252948e-01 0.000000000000000e+00
|
||||
16 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 2.775557561562893e-17 1.000000000000000e+00 -0.000000000000000e+00
|
||||
|
||||
# Bond topology
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 9 10
|
||||
9 1 10 11
|
||||
10 1 11 12
|
||||
11 1 13 14
|
||||
12 1 14 15
|
||||
13 1 15 16
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 9 10
|
||||
9 1 10 11
|
||||
10 1 11 12
|
||||
11 1 13 14
|
||||
12 1 14 15
|
||||
13 1 15 16
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341 1.173984503142341 1.173984503142341 0.9964752158482045 -0.053253555733239796 0.011391163807102514 -0.06380787090289707
|
||||
2 1.173984503142341 1.173984503142341 1.173984503142341 0.9369923833143513 0.11220716044648564 0.06732538499716349 0.3239168400846305
|
||||
3 1.173984503142341 1.173984503142341 1.173984503142341 0.797964932091827 0.14473096354527873 0.18374142699366386 0.5554673737937029
|
||||
4 1.173984503142341 1.173984503142341 1.173984503142341 0.5660864821344559 0.14688275499481052 0.09873742533340191 0.8051226439917721
|
||||
5 1.173984503142341 1.173984503142341 1.173984503142341 0.2533023785125306 0.12062313161679827 0.08583012223905846 0.9559922359911086
|
||||
6 1.173984503142341 1.173984503142341 1.173984503142341 -0.03855807343534716 0.08405913137017908 0.02236505169306371 0.9954632800204194
|
||||
7 1.173984503142341 1.173984503142341 1.173984503142341 -0.45592844330248017 0.1004550065061007 -0.052524745294758785 0.8827679181910482
|
||||
8 1.173984503142341 1.173984503142341 1.173984503142341 0.768021221540491 -0.009582139884533599 0.03658677589040892 -0.63930665074644
|
||||
9 1.173984503142341 1.173984503142341 1.173984503142341 -0.23299975754512345 0.688686395231341 0.6747873944883376 -0.12682324016841584
|
||||
10 1.173984503142341 1.173984503142341 1.173984503142341 -0.24662061871907232 0.8744456399178389 0.39370836087823996 -0.13970261209395163
|
||||
11 1.173984503142341 1.173984503142341 1.173984503142341 -0.087475900850909 0.977367602388229 0.14493549113095577 -0.12686307572668784
|
||||
12 1.173984503142341 1.173984503142341 1.173984503142341 -0.03181169300779214 0.9634374984140112 -0.2442360692534371 -0.10547485630879185
|
||||
13 1.173984503142341 1.173984503142341 1.173984503142341 -0.032786070696572266 0.7922941528811777 -0.6084214170523915 -0.03191282109962717
|
||||
14 1.173984503142341 1.173984503142341 1.173984503142341 0.047188686288341455 0.6316396208287698 -0.7737349519945348 0.011783095844627799
|
||||
15 1.173984503142341 1.173984503142341 1.173984503142341 -0.05869980642620335 -0.34229358203414423 0.9376740835056508 0.012519965878508689
|
||||
16 1.173984503142341 1.173984503142341 1.173984503142341 -0.08582818143150042 0.0008707732197394232 0.9939540921464659 -0.0684691735853161
|
||||
|
||||
@ -2,6 +2,7 @@ variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
variable rhos equal 0.2
|
||||
|
||||
units lj
|
||||
|
||||
@ -11,11 +12,11 @@ newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex2
|
||||
@ -38,30 +39,19 @@ pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 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
|
||||
pair_coeff * * oxdna2/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 * * 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 ${T} 1.0 0.815
|
||||
pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
fix 1 all nve/asphere
|
||||
fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 3.8
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
@ -72,10 +62,10 @@ variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
write_data last_config.${number}.* nocoeff
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -1,73 +1,68 @@
|
||||
# LAMMPS data file
|
||||
LAMMPS data file via write_data, version 27 May 2021
|
||||
|
||||
10 atoms
|
||||
10 ellipsoids
|
||||
8 bonds
|
||||
|
||||
4 atom types
|
||||
8 bonds
|
||||
1 bond types
|
||||
10 ellipsoids
|
||||
|
||||
# System size
|
||||
-20.000000 20.000000 xlo xhi
|
||||
-20.000000 20.000000 ylo yhi
|
||||
-20.000000 20.000000 zlo zhi
|
||||
-20 20 xlo xhi
|
||||
-20 20 ylo yhi
|
||||
-20 20 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 1.0
|
||||
2 1.0
|
||||
3 1.0
|
||||
4 1.0
|
||||
1 1
|
||||
2 1
|
||||
3 1
|
||||
4 1
|
||||
|
||||
# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
|
||||
Atoms
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1
|
||||
2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1
|
||||
3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1
|
||||
4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1
|
||||
5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1
|
||||
6 4 -4.829362784135484e-01 3.560513319622209e-01 1.559051420521249e+00 2 1 1
|
||||
7 1 -1.824198365552941e-01 5.715968887521516e-01 1.169288565390937e+00 2 1 1
|
||||
8 2 1.874009511073395e-01 5.699832309147913e-01 7.795257102606243e-01 2 1 1
|
||||
9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1
|
||||
10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1
|
||||
1 1 -0.11270997503399371 -0.7862611620723637 1.3165400870544903 1 1 0.060395054525384434 0 0 0
|
||||
2 2 -0.16100240482903602 -1.0148422652606093 1.7725173088171975 1 1 0.060395054525384434 0 0 0
|
||||
3 3 -0.07298109176865208 -1.2058352049378398 2.2155374630046025 1 1 0.060395054525384434 0 0 0
|
||||
4 4 0.20885923193243378 -1.2688318677749852 2.7293157091426354 1 1 0.060395054525384434 0 0 0
|
||||
5 1 0.4977080746488808 -1.1877183116613397 3.1217952838980874 1 1 0.060395054525384434 0 0 0
|
||||
6 4 -0.2268968274787041 -0.189603020612256 3.1084583050105072 2 1 0.060395054525384434 0 0 0
|
||||
7 1 -0.0350302960648884 -0.11245734514413211 2.7014501755341493 2 1 0.060395054525384434 0 0 0
|
||||
8 2 0.25244681036675387 -0.03694235704351071 2.3220950502861553 2 1 0.060395054525384434 0 0 0
|
||||
9 3 0.6676541258850296 -0.19471246409842435 2.0340464261767104 2 1 0.060395054525384434 0 0 0
|
||||
10 4 0.934602266948905 -0.5194117909409754 1.8612193115349325 2 1 0.060395054525384434 0 0 0
|
||||
|
||||
# Atom-ID, translational velocity, angular momentum
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
1 0.7350861197179651 -0.21340767305489933 0.039697389523131524 0.514970941606362 -0.5778402699166201 0.41643574848945447
|
||||
2 0.45886825731636693 0.15479323180826426 0.45998155912439004 -0.09532046111956156 -0.028811462065931184 0.1672428695820793
|
||||
3 -0.10009582230026307 -0.1356043155573722 -0.1357102030132947 0.512435093836635 0.8794667047362844 -0.4062045597142004
|
||||
4 -0.030407148345627223 -0.009119685021467273 0.2894674569635424 -0.22197357320787495 0.46474035192627294 -0.07166539037437039
|
||||
5 0.021807141873185235 -0.3544326055489752 0.4440408124043861 -0.019877710182688496 0.008454084203717545 -0.16574323908949498
|
||||
6 0.058814594979770644 -0.23964725458291067 0.09430081861001074 -0.16841516333125345 -0.27499692207835863 0.49231682345951117
|
||||
7 -0.004278840261670186 0.011171100752661912 -0.10686407869958243 0.3533956051874728 -0.5781793964284943 0.171273466705473
|
||||
8 -0.5678723978567293 -0.05635280062816237 -0.12337612014269532 -0.06293014166900977 -0.5548255617488771 -0.3948679676680598
|
||||
9 0.07493146865794496 0.37868089841113717 0.11143666048372917 -0.35561925325917687 -0.3453461570214745 -0.5277976799082732
|
||||
10 -0.48819053761319386 -0.11027061946453155 0.19465531836187655 0.10340969323917759 0.3809806548307742 0.25623918588602335
|
||||
|
||||
# Atom-ID, shape, quaternion
|
||||
Ellipsoids
|
||||
|
||||
1 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01
|
||||
3 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01
|
||||
4 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01
|
||||
5 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01
|
||||
6 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 0.000000000000000e+00 9.499720515246527e-01 -3.123349185122326e-01 -0.000000000000000e+00
|
||||
7 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 0.000000000000000e+00 8.074754054847401e-01 -5.899012371043604e-01 0.000000000000000e+00
|
||||
8 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 0.000000000000000e+00 5.863723567357896e-01 -8.100416404457959e-01 0.000000000000000e+00
|
||||
9 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252947e-01 0.000000000000000e+00
|
||||
10 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 -0.000000000000000e+00 1.110223024625157e-16 1.000000000000000e+00 -0.000000000000000e+00
|
||||
|
||||
# Bond topology
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 6 7
|
||||
6 1 7 8
|
||||
7 1 8 9
|
||||
8 1 9 10
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 6 7
|
||||
6 1 7 8
|
||||
7 1 8 9
|
||||
8 1 9 10
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 3.1622776601683795 3.1622776601683795 3.1622776601683795 0.9824438652148015 -0.023183015026523597 -0.18238525095550406 0.031657854475291056
|
||||
2 3.1622776601683795 3.1622776601683795 3.1622776601683795 0.9303156820429525 0.02962373336578937 -0.07607439157272995 0.3575581814380256
|
||||
3 3.1622776601683795 3.1622776601683795 3.1622776601683795 0.7912072782182723 -0.043679545103099016 -0.05996218100443608 0.6070318583758278
|
||||
4 3.1622776601683795 3.1622776601683795 3.1622776601683795 0.6531869542452552 -0.03659000162837596 0.004181596561545229 0.7563005281201641
|
||||
5 3.1622776601683795 3.1622776601683795 3.1622776601683795 0.3249781771672557 0.06207197535108856 0.03689277251937633 0.9429608568635791
|
||||
6 3.1622776601683795 3.1622776601683795 3.1622776601683795 0.08029535222204207 0.8726095530830543 -0.46831094470633033 -0.11309325067392484
|
||||
7 3.1622776601683795 3.1622776601683795 3.1622776601683795 -0.1303991484205687 0.7764383491760718 -0.6081660772848121 0.10135864274905797
|
||||
8 3.1622776601683795 3.1622776601683795 3.1622776601683795 -0.14971034142173664 0.5769499085020084 -0.7973230447846137 0.09482393688465168
|
||||
9 3.1622776601683795 3.1622776601683795 3.1622776601683795 0.21130729744233523 -0.37917864508185584 0.8946270178621702 -0.10590221939385809
|
||||
10 3.1622776601683795 3.1622776601683795 3.1622776601683795 0.34278400171414436 0.15185237372800306 0.9252984668160771 0.05712032974191834
|
||||
|
||||
@ -2,6 +2,7 @@ variable number equal 3
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
variable rhos equal 0.2
|
||||
|
||||
units lj
|
||||
|
||||
@ -11,11 +12,11 @@ newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex3
|
||||
@ -38,30 +39,19 @@ pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 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
|
||||
pair_coeff * * oxdna2/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 * * 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 ${T} 1.0 0.815
|
||||
pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 3.8
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
@ -72,10 +62,10 @@ variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
write_data last_config.${number}.* nocoeff
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -1,130 +1,132 @@
|
||||
# LAMMPS data file
|
||||
LAMMPS data file via write_data, version 27 May 2021
|
||||
|
||||
26 atoms
|
||||
26 ellipsoids
|
||||
24 bonds
|
||||
|
||||
4 atom types
|
||||
24 bonds
|
||||
1 bond types
|
||||
26 ellipsoids
|
||||
|
||||
# System size
|
||||
-20.000000 20.000000 xlo xhi
|
||||
-20.000000 20.000000 ylo yhi
|
||||
-20.000000 20.000000 zlo zhi
|
||||
-20 20 xlo xhi
|
||||
-20 20 ylo yhi
|
||||
-20 20 zlo zhi
|
||||
|
||||
# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
|
||||
Atoms
|
||||
Masses
|
||||
|
||||
1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1
|
||||
2 2 -4.957432645895970e-01 -3.379920348381733e-01 3.897628551303122e-01 1 1 1
|
||||
3 3 -2.192046146198370e-01 -5.585242491865227e-01 7.795257102606244e-01 1 1 1
|
||||
4 4 1.335125603737887e-01 -5.849567473090943e-01 1.169288565390937e+00 1 1 1
|
||||
5 1 4.398311230978960e-01 -4.081036426625517e-01 1.559051420521249e+00 1 1 1
|
||||
6 2 5.932984957350773e-01 -8.942535970570469e-02 1.948814275651561e+00 1 1 1
|
||||
7 3 5.405813207414517e-01 2.603302434705350e-01 2.338577130781873e+00 1 1 1
|
||||
8 4 3.000000000000002e-01 5.196152422706634e-01 2.728339985912185e+00 1 1 1
|
||||
9 1 -4.483805615185452e-02 5.983222783087083e-01 3.118102841042497e+00 1 1 1
|
||||
10 2 -3.740938811152403e-01 4.690988894808181e-01 3.507865696172809e+00 1 1 1
|
||||
11 3 -5.733436834716847e-01 1.768531046465427e-01 3.897628551303121e+00 1 1 1
|
||||
12 4 -5.733436834716849e-01 -1.768531046465427e-01 4.287391406433434e+00 1 1 1
|
||||
13 1 -3.740938811152403e-01 -4.690988894808182e-01 4.677154261563746e+00 1 1 1
|
||||
14 4 3.740938811152403e-01 4.690988894808182e-01 4.677154261563746e+00 2 1 1
|
||||
15 1 5.733436834716849e-01 1.768531046465427e-01 4.287391406433434e+00 2 1 1
|
||||
16 2 5.733436834716849e-01 -1.768531046465426e-01 3.897628551303122e+00 2 1 1
|
||||
17 3 3.740938811152403e-01 -4.690988894808181e-01 3.507865696172810e+00 2 1 1
|
||||
18 4 4.483805615185462e-02 -5.983222783087085e-01 3.118102841042498e+00 2 1 1
|
||||
19 1 -3.000000000000003e-01 -5.196152422706636e-01 2.728339985912186e+00 2 1 1
|
||||
20 2 -5.405813207414519e-01 -2.603302434705351e-01 2.338577130781874e+00 2 1 1
|
||||
21 3 -5.932984957350776e-01 8.942535970570474e-02 1.948814275651561e+00 2 1 1
|
||||
22 4 -4.398311230978962e-01 4.081036426625520e-01 1.559051420521249e+00 2 1 1
|
||||
23 1 -1.335125603737888e-01 5.849567473090947e-01 1.169288565390937e+00 2 1 1
|
||||
24 2 2.192046146198373e-01 5.585242491865231e-01 7.795257102606246e-01 2 1 1
|
||||
25 3 4.957432645895974e-01 3.379920348381736e-01 3.897628551303123e-01 2 1 1
|
||||
26 4 6.000000000000006e-01 0.000000000000000e+00 1.110223024625157e-16 2 1 1
|
||||
1 3.1575
|
||||
2 3.1575
|
||||
3 3.1575
|
||||
4 3.1575
|
||||
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -0.5974293795290144 -0.47217734566783476 0.1149860099192362 1 1 3.7269849963023267 0 0 0
|
||||
2 2 -0.3607975285447209 -0.8084200276362509 0.5005631273908187 1 1 3.7269849963023267 0 0 0
|
||||
3 3 -0.1880165420620915 -0.9339012982528754 0.9372222930006777 1 1 3.7269849963023267 0 0 0
|
||||
4 4 0.18789028377909187 -0.8807473585891459 1.3080750447260532 1 1 3.7269849963023267 0 0 0
|
||||
5 1 0.46680288593900887 -0.6314504249974493 1.6544618495816525 1 1 3.7269849963023267 0 0 0
|
||||
6 2 0.6156490001978658 -0.24344915610488765 1.9998398114466447 1 1 3.7269849963023267 0 0 0
|
||||
7 3 0.5475869309223161 0.10633006738807783 2.395688109397028 1 1 3.7269849963023267 0 0 0
|
||||
8 4 0.3964561058464781 0.33864915662119616 2.855380256681012 1 1 3.7269849963023267 0 0 0
|
||||
9 1 0.09151778690925949 0.33572177117709545 3.2793107140407853 1 1 3.7269849963023267 0 0 0
|
||||
10 2 -0.260700239272384 0.23452584272483473 3.622064753017485 1 1 3.7269849963023267 0 0 0
|
||||
11 3 -0.44049173083867876 -0.04240311520575983 4.057361772274168 1 1 3.7269849963023267 0 0 0
|
||||
12 4 -0.48111471327910416 -0.3913669550617015 4.465217350523367 1 1 3.7269849963023267 0 0 0
|
||||
13 1 -0.3029890593292223 -0.6218232516387349 4.889919411438907 1 1 3.7269849963023267 0 0 0
|
||||
14 4 0.36538593166250877 0.467104033114044 4.885957202043727 2 1 3.7269849963023267 0 0 0
|
||||
15 1 0.5837256243756591 0.1432569770282543 4.587937684834979 2 1 3.7269849963023267 0 0 0
|
||||
16 2 0.7270895848434721 -0.21648156960230241 4.19127441749994 2 1 3.7269849963023267 0 0 0
|
||||
17 3 0.5694364623788377 -0.5971020505771416 3.7905394408535833 2 1 3.7269849963023267 0 0 0
|
||||
18 4 0.32183479629572403 -0.7826674384502239 3.3981789941001397 2 1 3.7269849963023267 0 0 0
|
||||
19 1 0.027943077828669855 -0.8173952163019756 2.892497591992246 2 1 3.7269849963023267 0 0 0
|
||||
20 2 -0.34389471043742403 -0.6801076538339801 2.6010059142333977 2 1 3.7269849963023267 0 0 0
|
||||
21 3 -0.5722337592890715 -0.31543771192866543 2.2496367888009035 2 1 3.7269849963023267 0 0 0
|
||||
22 4 -0.5243059431454682 -0.018794840926191582 1.6669602274961965 2 1 3.7269849963023267 0 0 0
|
||||
23 1 -0.4467049661654279 0.15318137385858244 1.1669311078565738 2 1 3.7269849963023267 0 0 0
|
||||
24 2 -0.04279541944801792 0.24071675674438053 0.7924196804793574 2 1 3.7269849963023267 0 0 0
|
||||
25 3 0.33688934798342335 0.1390449738629785 0.42004977704361546 2 1 3.7269849963023267 0 0 0
|
||||
26 4 0.5381606093378432 -0.28366941895261566 0.04905784853961178 2 1 3.7269849963023267 0 0 0
|
||||
|
||||
# Atom-ID, translational, rotational velocity
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
11 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
12 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
13 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
14 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
15 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
16 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
17 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
18 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
19 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
20 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
21 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
22 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
23 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
24 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
25 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
26 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
1 -0.1420563695014878 -0.2339928257547227 0.1871716305399088 -0.046333854442252194 0.08160574816172744 0.2791824603833533
|
||||
2 0.03390382747481304 0.2912921705525512 -0.1828986721885175 0.09422531767061365 -0.044398236946770545 0.011069519340877812
|
||||
3 0.05351747745964457 -0.3700026678535097 -0.01469442373794632 0.10875858697088675 0.2373869034785703 0.15028498953263314
|
||||
4 0.1107696836820372 0.012571134739153464 0.23554381030898286 0.11411649786729211 -0.23899527406990237 0.11196343804383825
|
||||
5 0.21949033826324368 -0.4153000294565104 0.18426481814713022 0.2497206165366295 0.2505624077277829 -0.35347918243093
|
||||
6 -0.24019769428878804 -0.16423570219236758 -0.003762466815720382 0.062008045889015595 0.22340307597010978 -0.38223196779931135
|
||||
7 0.12372477399377596 0.10393016373901434 0.08008946447311854 -0.15063203100274558 0.08544129561789665 -0.3233996805084572
|
||||
8 0.03216353270652909 -0.1291938805451393 0.1736283537356162 -0.17577447248216746 0.11132849782859955 -0.13659117762014125
|
||||
9 0.016485625003622013 0.01204732455105311 0.012268845318149781 -0.10829791072979295 0.1325154323216732 0.061321711941405295
|
||||
10 -0.10017034720683878 -0.09274368063499111 0.0712704971413183 -0.08539556363371427 -0.10194584018083674 0.12395163271335013
|
||||
11 0.1553620769751766 -0.017877616757193807 -0.1679552227127468 -0.11302061465460307 0.10833285249943261 -0.29004856929349787
|
||||
12 -0.25308607960176693 0.05651778438229357 -0.28293751231512154 0.08875447438401544 -0.0424858854741496 0.4807657704475166
|
||||
13 -0.006525152792083277 0.05278468067247092 0.0923614993309851 -0.17068957621149589 -0.21396827821680875 -0.22336174340467796
|
||||
14 -0.09024428084565417 0.19407821508904713 -0.27279958154128003 0.16579397498898726 0.05605196163049078 0.18139063086724955
|
||||
15 0.2329539015603435 0.08926675461196792 0.01755751945261716 0.14895763843533014 0.05566424996653055 0.038429304115211504
|
||||
16 -0.012766107314323394 -0.05870276075293287 0.22459362070331024 -0.051898555487544795 0.11349183901118838 -0.35625338947479507
|
||||
17 -0.20400754456760709 -0.43178141581578006 -0.05213026263746946 -0.16561150375144387 -0.08257869123336893 -0.31368221607714253
|
||||
18 0.26408469209202234 0.004101215813165573 -0.11409222616552296 -0.37751548716793587 0.021230702354981583 0.23218952685038605
|
||||
19 -0.2811352347889802 0.25474603468997514 0.0038005485218010606 0.2164466860189806 -0.3924452117278991 0.22754829879548555
|
||||
20 -0.34129793271588454 0.05074672818229578 -0.03388446943745919 -0.1368254010552013 -0.1547809974693013 -0.03266259795645136
|
||||
21 -0.25700758391191114 0.04693154859703793 0.08362546455733241 -0.08661574368141227 -0.030723569920460755 -0.18740437515161282
|
||||
22 0.08529314327765061 0.10662056255177826 -0.0742729015142829 -0.4671828719407557 -0.19246067344838313 0.20137866804242557
|
||||
23 -0.09337250162399305 -0.1907111010034805 0.19278254253312255 0.017795209772695803 -0.36506106427644847 0.24972052729172167
|
||||
24 -0.16063305395742022 0.12278800901705311 0.0513923554335936 -0.09716260028970423 -0.26401680055506943 0.08202659665577536
|
||||
25 -0.14736287972598905 0.09699085150412592 -0.20751532907712478 0.05612191742480806 -0.13929212905625324 0.034890079586931765
|
||||
26 -0.060417626533246734 0.35551862988152244 -0.19673503245092067 0.014766691426271806 0.02762183997756995 -0.20597323908506235
|
||||
|
||||
# Atom-ID, shape, quaternion
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.555728057861408e-01 0.000000000000000e+00 0.000000000000000e+00 2.947551744109042e-01
|
||||
3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.262387743159949e-01 0.000000000000000e+00 0.000000000000000e+00 5.633200580636221e-01
|
||||
4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 6.234898018587335e-01 0.000000000000000e+00 0.000000000000000e+00 7.818314824680299e-01
|
||||
5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.653410243663950e-01 0.000000000000000e+00 0.000000000000000e+00 9.308737486442042e-01
|
||||
6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 7.473009358642424e-02 0.000000000000000e+00 0.000000000000000e+00 9.972037971811802e-01
|
||||
7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -2.225209339563144e-01 0.000000000000000e+00 0.000000000000000e+00 9.749279121818237e-01
|
||||
8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -5.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 8.660254037844387e-01
|
||||
9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 7.330518718298263e-01 -0.000000000000000e+00 0.000000000000000e+00 -6.801727377709196e-01
|
||||
10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.009688679024190e-01 -0.000000000000000e+00 0.000000000000000e+00 -4.338837391175581e-01
|
||||
11 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.888308262251286e-01 -0.000000000000000e+00 0.000000000000000e+00 -1.490422661761745e-01
|
||||
12 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.888308262251286e-01 0.000000000000000e+00 0.000000000000000e+00 1.490422661761745e-01
|
||||
13 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.009688679024190e-01 0.000000000000000e+00 0.000000000000000e+00 4.338837391175582e-01
|
||||
14 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 -4.338837391175582e-01 9.009688679024190e-01 0.000000000000000e+00
|
||||
15 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -1.490422661761746e-01 9.888308262251286e-01 0.000000000000000e+00
|
||||
16 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 1.490422661761745e-01 9.888308262251286e-01 -0.000000000000000e+00
|
||||
17 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 4.338837391175581e-01 9.009688679024190e-01 -0.000000000000000e+00
|
||||
18 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 6.801727377709192e-01 7.330518718298267e-01 0.000000000000000e+00
|
||||
19 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.660254037844386e-01 5.000000000000001e-01 0.000000000000000e+00
|
||||
20 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.749279121818235e-01 2.225209339563145e-01 0.000000000000000e+00
|
||||
21 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.972037971811801e-01 -7.473009358642428e-02 0.000000000000000e+00
|
||||
22 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.308737486442041e-01 -3.653410243663952e-01 0.000000000000000e+00
|
||||
23 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 7.818314824680296e-01 -6.234898018587339e-01 0.000000000000000e+00
|
||||
24 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.633200580636215e-01 -8.262387743159952e-01 0.000000000000000e+00
|
||||
25 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -2.947551744109044e-01 9.555728057861407e-01 0.000000000000000e+00
|
||||
26 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 -0.000000000000000e+00
|
||||
|
||||
# Bond topology
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 8 9
|
||||
9 1 9 10
|
||||
10 1 10 11
|
||||
11 1 11 12
|
||||
12 1 12 13
|
||||
13 1 14 15
|
||||
14 1 15 16
|
||||
15 1 16 17
|
||||
16 1 17 18
|
||||
17 1 18 19
|
||||
18 1 19 20
|
||||
19 1 20 21
|
||||
20 1 21 22
|
||||
21 1 22 23
|
||||
22 1 23 24
|
||||
23 1 24 25
|
||||
24 1 25 26
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 8 9
|
||||
9 1 9 10
|
||||
10 1 10 11
|
||||
11 1 11 12
|
||||
12 1 12 13
|
||||
13 1 14 15
|
||||
14 1 15 16
|
||||
15 1 16 17
|
||||
16 1 17 18
|
||||
17 1 18 19
|
||||
18 1 19 20
|
||||
19 1 20 21
|
||||
20 1 21 22
|
||||
21 1 22 23
|
||||
22 1 23 24
|
||||
23 1 24 25
|
||||
24 1 25 26
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341 1.173984503142341 1.173984503142341 0.9970278940278272 0.0014876174054512252 0.0750547523448584 0.017319055267040844
|
||||
2 1.173984503142341 1.173984503142341 1.173984503142341 0.9059171712388804 0.007913225291438054 0.04634256838354512 0.42083705406683053
|
||||
3 1.173984503142341 1.173984503142341 1.173984503142341 0.7657426991864452 0.028071560533125216 0.13224385975981257 0.6287779160305484
|
||||
4 1.173984503142341 1.173984503142341 1.173984503142341 0.5238981696613685 0.0516703526741727 0.1609645534282743 0.8348360887142046
|
||||
5 1.173984503142341 1.173984503142341 1.173984503142341 0.30973290897949424 0.0750672191209306 0.23962885621884192 0.9170651279902646
|
||||
6 1.173984503142341 1.173984503142341 1.173984503142341 -0.050269263744563454 0.08142241031464711 0.09584085715741358 0.9907865170259763
|
||||
7 1.173984503142341 1.173984503142341 1.173984503142341 -0.3805122714271814 0.08965734720629535 0.057827749665601925 0.9186010683391725
|
||||
8 1.173984503142341 1.173984503142341 1.173984503142341 -0.6066322463100545 0.015286960797006149 0.035984536832974555 0.7940206166563465
|
||||
9 1.173984503142341 1.173984503142341 1.173984503142341 0.771660293819677 0.02607541526374929 -0.08047223278265907 -0.6303845520092687
|
||||
10 1.173984503142341 1.173984503142341 1.173984503142341 0.9119628434851113 0.03686258000931541 -0.11017000132786052 -0.3934812487336936
|
||||
11 1.173984503142341 1.173984503142341 1.173984503142341 0.9917294290821066 0.05835078551401739 -0.08073737536574405 -0.08092837290732445
|
||||
12 1.173984503142341 1.173984503142341 1.173984503142341 0.9763527785523285 0.06753089597617556 0.004847281702108697 0.205307899901351
|
||||
13 1.173984503142341 1.173984503142341 1.173984503142341 0.8553397145502984 0.1399133966151149 0.07233200118835512 0.49354462388392356
|
||||
14 1.173984503142341 1.173984503142341 1.173984503142341 0.014416326682630282 -0.533642571147991 0.8442695396252617 0.04718813669228716
|
||||
15 1.173984503142341 1.173984503142341 1.173984503142341 0.14095892784917538 -0.2201285495070387 0.9406003462562982 -0.21666792788520955
|
||||
16 1.173984503142341 1.173984503142341 1.173984503142341 0.07323967796304806 0.05035907488974361 0.963136526452943 -0.2539053850556888
|
||||
17 1.173984503142341 1.173984503142341 1.173984503142341 0.030254986187638885 0.39195467212588947 0.9164794947567249 -0.07430684019611289
|
||||
18 1.173984503142341 1.173984503142341 1.173984503142341 -0.03080283760241768 0.6526511470205414 0.7481495879677094 -0.11562810865943304
|
||||
19 1.173984503142341 1.173984503142341 1.173984503142341 -0.09450197979153381 0.7469150592813072 0.6556128255138505 -0.0579576833217777
|
||||
20 1.173984503142341 1.173984503142341 1.173984503142341 -0.12903334341475137 0.9222523214328698 0.3501336268694509 -0.10103214950765672
|
||||
21 1.173984503142341 1.173984503142341 1.173984503142341 -0.0069954457806870336 0.9888131084284681 -0.09413955816471489 -0.11548785185859346
|
||||
22 1.173984503142341 1.173984503142341 1.173984503142341 0.029336230851923526 0.9805894852440379 -0.19236800606724952 -0.02404573205262194
|
||||
23 1.173984503142341 1.173984503142341 1.173984503142341 0.03080980270092377 0.872234086776475 -0.4869211139732921 0.03415088124407873
|
||||
24 1.173984503142341 1.173984503142341 1.173984503142341 0.007237815450514786 0.690265186998662 -0.7210993183911308 0.05913847022922672
|
||||
25 1.173984503142341 1.173984503142341 1.173984503142341 0.06694683426684143 -0.46894411325316443 0.8712038661029582 -0.12889283810247346
|
||||
26 1.173984503142341 1.173984503142341 1.173984503142341 0.07581973147109407 -0.10215114654759445 0.9759556607577902 -0.17699451916228467
|
||||
|
||||
@ -1,130 +1,136 @@
|
||||
# LAMMPS data file
|
||||
LAMMPS data file via write_data, version 27 May 2021
|
||||
|
||||
26 atoms
|
||||
26 ellipsoids
|
||||
24 bonds
|
||||
|
||||
8 atom types
|
||||
24 bonds
|
||||
1 bond types
|
||||
26 ellipsoids
|
||||
|
||||
# System size
|
||||
-20.000000 20.000000 xlo xhi
|
||||
-20.000000 20.000000 ylo yhi
|
||||
-20.000000 20.000000 zlo zhi
|
||||
-20 20 xlo xhi
|
||||
-20 20 ylo yhi
|
||||
-20 20 zlo zhi
|
||||
|
||||
# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
|
||||
Atoms
|
||||
Masses
|
||||
|
||||
1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1
|
||||
2 2 -4.957432645895970e-01 -3.379920348381733e-01 3.897628551303122e-01 1 1 1
|
||||
3 3 -2.192046146198370e-01 -5.585242491865227e-01 7.795257102606244e-01 1 1 1
|
||||
4 4 1.335125603737887e-01 -5.849567473090943e-01 1.169288565390937e+00 1 1 1
|
||||
5 5 4.398311230978960e-01 -4.081036426625517e-01 1.559051420521249e+00 1 1 1
|
||||
6 6 5.932984957350773e-01 -8.942535970570469e-02 1.948814275651561e+00 1 1 1
|
||||
7 7 5.405813207414517e-01 2.603302434705350e-01 2.338577130781873e+00 1 1 1
|
||||
8 8 3.000000000000002e-01 5.196152422706634e-01 2.728339985912185e+00 1 1 1
|
||||
9 1 -4.483805615185452e-02 5.983222783087083e-01 3.118102841042497e+00 1 1 1
|
||||
10 2 -3.740938811152403e-01 4.690988894808181e-01 3.507865696172809e+00 1 1 1
|
||||
11 7 -5.733436834716847e-01 1.768531046465427e-01 3.897628551303121e+00 1 1 1
|
||||
12 8 -5.733436834716849e-01 -1.768531046465427e-01 4.287391406433434e+00 1 1 1
|
||||
13 1 -3.740938811152403e-01 -4.690988894808182e-01 4.677154261563746e+00 1 1 1
|
||||
14 4 3.740938811152403e-01 4.690988894808182e-01 4.677154261563746e+00 2 1 1
|
||||
15 5 5.733436834716849e-01 1.768531046465427e-01 4.287391406433434e+00 2 1 1
|
||||
16 6 5.733436834716849e-01 -1.768531046465426e-01 3.897628551303122e+00 2 1 1
|
||||
17 3 3.740938811152403e-01 -4.690988894808181e-01 3.507865696172810e+00 2 1 1
|
||||
18 4 4.483805615185462e-02 -5.983222783087085e-01 3.118102841042498e+00 2 1 1
|
||||
19 5 -3.000000000000003e-01 -5.196152422706636e-01 2.728339985912186e+00 2 1 1
|
||||
20 6 -5.405813207414519e-01 -2.603302434705351e-01 2.338577130781874e+00 2 1 1
|
||||
21 7 -5.932984957350776e-01 8.942535970570474e-02 1.948814275651561e+00 2 1 1
|
||||
22 8 -4.398311230978962e-01 4.081036426625520e-01 1.559051420521249e+00 2 1 1
|
||||
23 1 -1.335125603737888e-01 5.849567473090947e-01 1.169288565390937e+00 2 1 1
|
||||
24 2 2.192046146198373e-01 5.585242491865231e-01 7.795257102606246e-01 2 1 1
|
||||
25 3 4.957432645895974e-01 3.379920348381736e-01 3.897628551303123e-01 2 1 1
|
||||
26 4 6.000000000000006e-01 0.000000000000000e+00 1.110223024625157e-16 2 1 1
|
||||
1 3.1575
|
||||
2 3.1575
|
||||
3 3.1575
|
||||
4 3.1575
|
||||
5 3.1575
|
||||
6 3.1575
|
||||
7 3.1575
|
||||
8 3.1575
|
||||
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -0.5974293795290144 -0.47217734566783476 0.1149860099192362 1 1 3.7269849963023267 0 0 0
|
||||
2 2 -0.3607975285447209 -0.8084200276362509 0.5005631273908187 1 1 3.7269849963023267 0 0 0
|
||||
3 3 -0.1880165420620915 -0.9339012982528754 0.9372222930006777 1 1 3.7269849963023267 0 0 0
|
||||
4 4 0.18789028377909187 -0.8807473585891459 1.3080750447260532 1 1 3.7269849963023267 0 0 0
|
||||
5 5 0.46680288593900887 -0.6314504249974493 1.6544618495816525 1 1 3.7269849963023267 0 0 0
|
||||
6 6 0.6156490001978658 -0.24344915610488765 1.9998398114466447 1 1 3.7269849963023267 0 0 0
|
||||
7 7 0.5475869309223161 0.10633006738807783 2.395688109397028 1 1 3.7269849963023267 0 0 0
|
||||
8 8 0.3964561058464781 0.33864915662119616 2.855380256681012 1 1 3.7269849963023267 0 0 0
|
||||
9 1 0.09151778690925949 0.33572177117709545 3.2793107140407853 1 1 3.7269849963023267 0 0 0
|
||||
10 2 -0.260700239272384 0.23452584272483473 3.622064753017485 1 1 3.7269849963023267 0 0 0
|
||||
11 7 -0.44049173083867876 -0.04240311520575983 4.057361772274168 1 1 3.7269849963023267 0 0 0
|
||||
12 8 -0.48111471327910416 -0.3913669550617015 4.465217350523367 1 1 3.7269849963023267 0 0 0
|
||||
13 1 -0.3029890593292223 -0.6218232516387349 4.889919411438907 1 1 3.7269849963023267 0 0 0
|
||||
14 4 0.36538593166250877 0.467104033114044 4.885957202043727 2 1 3.7269849963023267 0 0 0
|
||||
15 5 0.5837256243756591 0.1432569770282543 4.587937684834979 2 1 3.7269849963023267 0 0 0
|
||||
16 6 0.7270895848434721 -0.21648156960230241 4.19127441749994 2 1 3.7269849963023267 0 0 0
|
||||
17 3 0.5694364623788377 -0.5971020505771416 3.7905394408535833 2 1 3.7269849963023267 0 0 0
|
||||
18 4 0.32183479629572403 -0.7826674384502239 3.3981789941001397 2 1 3.7269849963023267 0 0 0
|
||||
19 5 0.027943077828669855 -0.8173952163019756 2.892497591992246 2 1 3.7269849963023267 0 0 0
|
||||
20 6 -0.34389471043742403 -0.6801076538339801 2.6010059142333977 2 1 3.7269849963023267 0 0 0
|
||||
21 7 -0.5722337592890715 -0.31543771192866543 2.2496367888009035 2 1 3.7269849963023267 0 0 0
|
||||
22 8 -0.5243059431454682 -0.018794840926191582 1.6669602274961965 2 1 3.7269849963023267 0 0 0
|
||||
23 1 -0.4467049661654279 0.15318137385858244 1.1669311078565738 2 1 3.7269849963023267 0 0 0
|
||||
24 2 -0.04279541944801792 0.24071675674438053 0.7924196804793574 2 1 3.7269849963023267 0 0 0
|
||||
25 3 0.33688934798342335 0.1390449738629785 0.42004977704361546 2 1 3.7269849963023267 0 0 0
|
||||
26 4 0.5381606093378432 -0.28366941895261566 0.04905784853961178 2 1 3.7269849963023267 0 0 0
|
||||
|
||||
# Atom-ID, translational, rotational velocity
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
11 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
12 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
13 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
14 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
15 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
16 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
17 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
18 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
19 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
20 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
21 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
22 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
23 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
24 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
25 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
26 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
1 -0.1420563695014878 -0.2339928257547227 0.1871716305399088 -0.046333854442252194 0.08160574816172744 0.2791824603833533
|
||||
2 0.03390382747481304 0.2912921705525512 -0.1828986721885175 0.09422531767061365 -0.044398236946770545 0.011069519340877812
|
||||
3 0.05351747745964457 -0.3700026678535097 -0.01469442373794632 0.10875858697088675 0.2373869034785703 0.15028498953263314
|
||||
4 0.1107696836820372 0.012571134739153464 0.23554381030898286 0.11411649786729211 -0.23899527406990237 0.11196343804383825
|
||||
5 0.21949033826324368 -0.4153000294565104 0.18426481814713022 0.2497206165366295 0.2505624077277829 -0.35347918243093
|
||||
6 -0.24019769428878804 -0.16423570219236758 -0.003762466815720382 0.062008045889015595 0.22340307597010978 -0.38223196779931135
|
||||
7 0.12372477399377596 0.10393016373901434 0.08008946447311854 -0.15063203100274558 0.08544129561789665 -0.3233996805084572
|
||||
8 0.03216353270652909 -0.1291938805451393 0.1736283537356162 -0.17577447248216746 0.11132849782859955 -0.13659117762014125
|
||||
9 0.016485625003622013 0.01204732455105311 0.012268845318149781 -0.10829791072979295 0.1325154323216732 0.061321711941405295
|
||||
10 -0.10017034720683878 -0.09274368063499111 0.0712704971413183 -0.08539556363371427 -0.10194584018083674 0.12395163271335013
|
||||
11 0.1553620769751766 -0.017877616757193807 -0.1679552227127468 -0.11302061465460307 0.10833285249943261 -0.29004856929349787
|
||||
12 -0.25308607960176693 0.05651778438229357 -0.28293751231512154 0.08875447438401544 -0.0424858854741496 0.4807657704475166
|
||||
13 -0.006525152792083277 0.05278468067247092 0.0923614993309851 -0.17068957621149589 -0.21396827821680875 -0.22336174340467796
|
||||
14 -0.09024428084565417 0.19407821508904713 -0.27279958154128003 0.16579397498898726 0.05605196163049078 0.18139063086724955
|
||||
15 0.2329539015603435 0.08926675461196792 0.01755751945261716 0.14895763843533014 0.05566424996653055 0.038429304115211504
|
||||
16 -0.012766107314323394 -0.05870276075293287 0.22459362070331024 -0.051898555487544795 0.11349183901118838 -0.35625338947479507
|
||||
17 -0.20400754456760709 -0.43178141581578006 -0.05213026263746946 -0.16561150375144387 -0.08257869123336893 -0.31368221607714253
|
||||
18 0.26408469209202234 0.004101215813165573 -0.11409222616552296 -0.37751548716793587 0.021230702354981583 0.23218952685038605
|
||||
19 -0.2811352347889802 0.25474603468997514 0.0038005485218010606 0.2164466860189806 -0.3924452117278991 0.22754829879548555
|
||||
20 -0.34129793271588454 0.05074672818229578 -0.03388446943745919 -0.1368254010552013 -0.1547809974693013 -0.03266259795645136
|
||||
21 -0.25700758391191114 0.04693154859703793 0.08362546455733241 -0.08661574368141227 -0.030723569920460755 -0.18740437515161282
|
||||
22 0.08529314327765061 0.10662056255177826 -0.0742729015142829 -0.4671828719407557 -0.19246067344838313 0.20137866804242557
|
||||
23 -0.09337250162399305 -0.1907111010034805 0.19278254253312255 0.017795209772695803 -0.36506106427644847 0.24972052729172167
|
||||
24 -0.16063305395742022 0.12278800901705311 0.0513923554335936 -0.09716260028970423 -0.26401680055506943 0.08202659665577536
|
||||
25 -0.14736287972598905 0.09699085150412592 -0.20751532907712478 0.05612191742480806 -0.13929212905625324 0.034890079586931765
|
||||
26 -0.060417626533246734 0.35551862988152244 -0.19673503245092067 0.014766691426271806 0.02762183997756995 -0.20597323908506235
|
||||
|
||||
# Atom-ID, shape, quaternion
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.555728057861408e-01 0.000000000000000e+00 0.000000000000000e+00 2.947551744109042e-01
|
||||
3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.262387743159949e-01 0.000000000000000e+00 0.000000000000000e+00 5.633200580636221e-01
|
||||
4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 6.234898018587335e-01 0.000000000000000e+00 0.000000000000000e+00 7.818314824680299e-01
|
||||
5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.653410243663950e-01 0.000000000000000e+00 0.000000000000000e+00 9.308737486442042e-01
|
||||
6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 7.473009358642424e-02 0.000000000000000e+00 0.000000000000000e+00 9.972037971811802e-01
|
||||
7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -2.225209339563144e-01 0.000000000000000e+00 0.000000000000000e+00 9.749279121818237e-01
|
||||
8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -5.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 8.660254037844387e-01
|
||||
9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 7.330518718298263e-01 -0.000000000000000e+00 0.000000000000000e+00 -6.801727377709196e-01
|
||||
10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.009688679024190e-01 -0.000000000000000e+00 0.000000000000000e+00 -4.338837391175581e-01
|
||||
11 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.888308262251286e-01 -0.000000000000000e+00 0.000000000000000e+00 -1.490422661761745e-01
|
||||
12 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.888308262251286e-01 0.000000000000000e+00 0.000000000000000e+00 1.490422661761745e-01
|
||||
13 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.009688679024190e-01 0.000000000000000e+00 0.000000000000000e+00 4.338837391175582e-01
|
||||
14 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 -4.338837391175582e-01 9.009688679024190e-01 0.000000000000000e+00
|
||||
15 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -1.490422661761746e-01 9.888308262251286e-01 0.000000000000000e+00
|
||||
16 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 1.490422661761745e-01 9.888308262251286e-01 -0.000000000000000e+00
|
||||
17 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 4.338837391175581e-01 9.009688679024190e-01 -0.000000000000000e+00
|
||||
18 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 6.801727377709192e-01 7.330518718298267e-01 0.000000000000000e+00
|
||||
19 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.660254037844386e-01 5.000000000000001e-01 0.000000000000000e+00
|
||||
20 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.749279121818235e-01 2.225209339563145e-01 0.000000000000000e+00
|
||||
21 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.972037971811801e-01 -7.473009358642428e-02 0.000000000000000e+00
|
||||
22 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.308737486442041e-01 -3.653410243663952e-01 0.000000000000000e+00
|
||||
23 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 7.818314824680296e-01 -6.234898018587339e-01 0.000000000000000e+00
|
||||
24 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.633200580636215e-01 -8.262387743159952e-01 0.000000000000000e+00
|
||||
25 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -2.947551744109044e-01 9.555728057861407e-01 0.000000000000000e+00
|
||||
26 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 -0.000000000000000e+00
|
||||
|
||||
# Bond topology
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 8 9
|
||||
9 1 9 10
|
||||
10 1 10 11
|
||||
11 1 11 12
|
||||
12 1 12 13
|
||||
13 1 14 15
|
||||
14 1 15 16
|
||||
15 1 16 17
|
||||
16 1 17 18
|
||||
17 1 18 19
|
||||
18 1 19 20
|
||||
19 1 20 21
|
||||
20 1 21 22
|
||||
21 1 22 23
|
||||
22 1 23 24
|
||||
23 1 24 25
|
||||
24 1 25 26
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 8 9
|
||||
9 1 9 10
|
||||
10 1 10 11
|
||||
11 1 11 12
|
||||
12 1 12 13
|
||||
13 1 14 15
|
||||
14 1 15 16
|
||||
15 1 16 17
|
||||
16 1 17 18
|
||||
17 1 18 19
|
||||
18 1 19 20
|
||||
19 1 20 21
|
||||
20 1 21 22
|
||||
21 1 22 23
|
||||
22 1 23 24
|
||||
23 1 24 25
|
||||
24 1 25 26
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341 1.173984503142341 1.173984503142341 0.9970278940278272 0.0014876174054512252 0.0750547523448584 0.017319055267040844
|
||||
2 1.173984503142341 1.173984503142341 1.173984503142341 0.9059171712388804 0.007913225291438054 0.04634256838354512 0.42083705406683053
|
||||
3 1.173984503142341 1.173984503142341 1.173984503142341 0.7657426991864452 0.028071560533125216 0.13224385975981257 0.6287779160305484
|
||||
4 1.173984503142341 1.173984503142341 1.173984503142341 0.5238981696613685 0.0516703526741727 0.1609645534282743 0.8348360887142046
|
||||
5 1.173984503142341 1.173984503142341 1.173984503142341 0.30973290897949424 0.0750672191209306 0.23962885621884192 0.9170651279902646
|
||||
6 1.173984503142341 1.173984503142341 1.173984503142341 -0.050269263744563454 0.08142241031464711 0.09584085715741358 0.9907865170259763
|
||||
7 1.173984503142341 1.173984503142341 1.173984503142341 -0.3805122714271814 0.08965734720629535 0.057827749665601925 0.9186010683391725
|
||||
8 1.173984503142341 1.173984503142341 1.173984503142341 -0.6066322463100545 0.015286960797006149 0.035984536832974555 0.7940206166563465
|
||||
9 1.173984503142341 1.173984503142341 1.173984503142341 0.771660293819677 0.02607541526374929 -0.08047223278265907 -0.6303845520092687
|
||||
10 1.173984503142341 1.173984503142341 1.173984503142341 0.9119628434851113 0.03686258000931541 -0.11017000132786052 -0.3934812487336936
|
||||
11 1.173984503142341 1.173984503142341 1.173984503142341 0.9917294290821066 0.05835078551401739 -0.08073737536574405 -0.08092837290732445
|
||||
12 1.173984503142341 1.173984503142341 1.173984503142341 0.9763527785523285 0.06753089597617556 0.004847281702108697 0.205307899901351
|
||||
13 1.173984503142341 1.173984503142341 1.173984503142341 0.8553397145502984 0.1399133966151149 0.07233200118835512 0.49354462388392356
|
||||
14 1.173984503142341 1.173984503142341 1.173984503142341 0.014416326682630282 -0.533642571147991 0.8442695396252617 0.04718813669228716
|
||||
15 1.173984503142341 1.173984503142341 1.173984503142341 0.14095892784917538 -0.2201285495070387 0.9406003462562982 -0.21666792788520955
|
||||
16 1.173984503142341 1.173984503142341 1.173984503142341 0.07323967796304806 0.05035907488974361 0.963136526452943 -0.2539053850556888
|
||||
17 1.173984503142341 1.173984503142341 1.173984503142341 0.030254986187638885 0.39195467212588947 0.9164794947567249 -0.07430684019611289
|
||||
18 1.173984503142341 1.173984503142341 1.173984503142341 -0.03080283760241768 0.6526511470205414 0.7481495879677094 -0.11562810865943304
|
||||
19 1.173984503142341 1.173984503142341 1.173984503142341 -0.09450197979153381 0.7469150592813072 0.6556128255138505 -0.0579576833217777
|
||||
20 1.173984503142341 1.173984503142341 1.173984503142341 -0.12903334341475137 0.9222523214328698 0.3501336268694509 -0.10103214950765672
|
||||
21 1.173984503142341 1.173984503142341 1.173984503142341 -0.0069954457806870336 0.9888131084284681 -0.09413955816471489 -0.11548785185859346
|
||||
22 1.173984503142341 1.173984503142341 1.173984503142341 0.029336230851923526 0.9805894852440379 -0.19236800606724952 -0.02404573205262194
|
||||
23 1.173984503142341 1.173984503142341 1.173984503142341 0.03080980270092377 0.872234086776475 -0.4869211139732921 0.03415088124407873
|
||||
24 1.173984503142341 1.173984503142341 1.173984503142341 0.007237815450514786 0.690265186998662 -0.7210993183911308 0.05913847022922672
|
||||
25 1.173984503142341 1.173984503142341 1.173984503142341 0.06694683426684143 -0.46894411325316443 0.8712038661029582 -0.12889283810247346
|
||||
26 1.173984503142341 1.173984503142341 1.173984503142341 0.07581973147109407 -0.10215114654759445 0.9759556607577902 -0.17699451916228467
|
||||
|
||||
@ -1,10 +1,11 @@
|
||||
variable number equal 1
|
||||
variable ofreq equal 10000
|
||||
variable efreq equal 10000
|
||||
variable number equal 4
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
variable ntype equal 4
|
||||
|
||||
variable T equal 0.1
|
||||
variable rhos equal 0.2
|
||||
|
||||
units lj
|
||||
|
||||
@ -14,20 +15,21 @@ newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 10 delay 0 check yes
|
||||
|
||||
read_data data.duplex4.4type
|
||||
|
||||
mass * 3.1575 # sets per-type mass if not in data file
|
||||
set atom * mass 3.1575 # sets per-atom mass
|
||||
|
||||
group all type 1 4
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
# oxDNA2 bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
special_bonds lj 0 1 1
|
||||
@ -52,28 +54,19 @@ jump in.duplex4.4type loop
|
||||
|
||||
pair_coeff * * oxdna2/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 * * 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 ${T} 0.2 0.815
|
||||
pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815
|
||||
|
||||
# Langevin dynamics
|
||||
fix 1 all nve/asphere
|
||||
fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10
|
||||
|
||||
timestep 1e-4
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 3.8
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
@ -84,14 +77,10 @@ variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le "
|
||||
|
||||
#restart 10000 config0_restart config1_restart
|
||||
|
||||
run 100000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
|
||||
@ -1,10 +1,11 @@
|
||||
variable number equal 1
|
||||
variable ofreq equal 10000
|
||||
variable efreq equal 10000
|
||||
variable number equal 8
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
variable ntype equal 8
|
||||
|
||||
variable T equal 0.1
|
||||
variable rhos equal 0.2
|
||||
|
||||
units lj
|
||||
|
||||
@ -14,20 +15,21 @@ newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 10 delay 0 check yes
|
||||
|
||||
read_data data.duplex4.8type
|
||||
|
||||
mass * 3.1575 # sets per-type mass if not in data file
|
||||
set atom * mass 3.1575 # sets per-atom mass
|
||||
|
||||
group all type 1 8
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
# oxDNA2 bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
special_bonds lj 0 1 1
|
||||
@ -52,28 +54,19 @@ jump in.duplex4.8type loop
|
||||
|
||||
pair_coeff * * oxdna2/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 * * 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 ${T} 0.2 0.815
|
||||
pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815
|
||||
|
||||
# Langevin dynamics
|
||||
fix 1 all nve/asphere
|
||||
fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10
|
||||
|
||||
timestep 1e-4
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 3.8
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
@ -84,14 +77,10 @@ variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le "
|
||||
|
||||
#restart 10000 config0_restart config1_restart
|
||||
|
||||
run 100000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -1,244 +0,0 @@
|
||||
LAMMPS (30 Jun 2020)
|
||||
variable number equal 1
|
||||
variable ofreq equal 10000
|
||||
variable efreq equal 10000
|
||||
|
||||
variable ntype equal 4
|
||||
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156)
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 10 delay 0 check yes
|
||||
|
||||
read_data data.duplex4.4type
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
26 atoms
|
||||
reading velocities ...
|
||||
26 velocities
|
||||
26 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
24 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.003 seconds
|
||||
mass * 3.1575 # sets per-type mass if not in data file
|
||||
set atom * mass 3.1575 # sets per-atom mass
|
||||
26 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
26 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
special_bonds lj 0 1 1
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
|
||||
# oxDNA pair interactions
|
||||
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 ${T} 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
|
||||
pair_coeff * * oxdna2/hbond seqdep 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
|
||||
|
||||
label loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 4
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 1%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
variable comp equal ${base}+3
|
||||
variable comp equal 1+3
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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
|
||||
pair_coeff 1 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
next base
|
||||
jump in.duplex4.4type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 4
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 2%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
variable comp equal ${base}+1
|
||||
variable comp equal 2+1
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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
|
||||
pair_coeff 2 ${comp} oxdna2/hbond seqdep 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
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 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
|
||||
next base
|
||||
jump in.duplex4.4type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 4
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 3%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
next base
|
||||
jump in.duplex4.4type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 4
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 4%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
next base
|
||||
jump in.duplex4.4type loop
|
||||
|
||||
pair_coeff * * oxdna2/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 * * 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 ${T} 0.2 0.815
|
||||
pair_coeff * * oxdna2/dh 0.1 0.2 0.815
|
||||
|
||||
# Langevin dynamics
|
||||
fix 1 all nve/asphere
|
||||
fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10
|
||||
|
||||
timestep 1e-4
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 10000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le "
|
||||
|
||||
#restart 10000 config0_restart config1_restart
|
||||
|
||||
run 100000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.6389877
|
||||
ghost atom cutoff = 4.6389877
|
||||
binsize = 2.3194939, bins = 18 18 18
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
WARNING: Communication cutoff adjusted to 4.638987723814632 (../comm.cpp:690)
|
||||
0 ekin = 0 | erot = 0 | epot = -41.6285382417448 | etot = -41.6285382417448
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.771 | 9.771 | 9.771 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.6384018 0.037304147 -1.6010976 6.7769766e-05
|
||||
10000 ekin = 0.876675896491307 | erot = 3.01631310953192 | epot = -43.6949424313443 | etot = -39.8019534253211
|
||||
20000 ekin = 1.02178060459022 | erot = 1.54107635735041 | epot = -40.2257383206528 | etot = -37.6628813587121
|
||||
30000 ekin = 1.77819697871127 | erot = 2.67180081099997 | epot = -40.9840548186678 | etot = -36.5340570289565
|
||||
40000 ekin = 2.55095642638533 | erot = 2.97955929579275 | epot = -40.0756048400153 | etot = -34.5450891178372
|
||||
50000 ekin = 2.43321388920862 | erot = 3.63137266285959 | epot = -39.3718897377946 | etot = -33.3073031857264
|
||||
60000 ekin = 2.51123200110303 | erot = 3.95693243683571 | epot = -38.8877878920178 | etot = -32.4196234540791
|
||||
70000 ekin = 3.33444097207872 | erot = 4.12593683683079 | epot = -38.7679893452499 | etot = -31.3076115363404
|
||||
80000 ekin = 3.41969296989344 | erot = 3.46589964095079 | epot = -37.5712487729465 | etot = -30.6856561621023
|
||||
90000 ekin = 3.53106755106414 | erot = 3.40955821292295 | epot = -35.9319384430368 | etot = -28.9913126790497
|
||||
100000 ekin = 3.47860763041501 | erot = 3.95117534418391 | epot = -37.6128506757402 | etot = -30.1830677011413
|
||||
100000 0.09276287 -1.4972391 0.050590991 -1.3128555 0.00017815014
|
||||
Loop time of 7.33046 on 1 procs for 100000 steps with 26 atoms
|
||||
|
||||
Performance: 117864.395 tau/day, 13641.712 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 6.4814 | 6.4814 | 6.4814 | 0.0 | 88.42
|
||||
Bond | 0.16262 | 0.16262 | 0.16262 | 0.0 | 2.22
|
||||
Neigh | 4.2e-05 | 4.2e-05 | 4.2e-05 | 0.0 | 0.00
|
||||
Comm | 0.019555 | 0.019555 | 0.019555 | 0.0 | 0.27
|
||||
Output | 0.00131 | 0.00131 | 0.00131 | 0.0 | 0.02
|
||||
Modify | 0.64596 | 0.64596 | 0.64596 | 0.0 | 8.81
|
||||
Other | | 0.01961 | | | 0.27
|
||||
|
||||
Nlocal: 26.0 ave 26.0 max 26.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0.0 ave 0.0 max 0.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 299.0 ave 299.0 max 299.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 299
|
||||
Ave neighs/atom = 11.5
|
||||
Ave special neighs/atom = 5.076923076923077
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
|
||||
|
||||
Total wall time: 0:00:07
|
||||
@ -1,244 +0,0 @@
|
||||
LAMMPS (30 Jun 2020)
|
||||
variable number equal 1
|
||||
variable ofreq equal 10000
|
||||
variable efreq equal 10000
|
||||
|
||||
variable ntype equal 4
|
||||
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156)
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 10 delay 0 check yes
|
||||
|
||||
read_data data.duplex4.4type
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
26 atoms
|
||||
reading velocities ...
|
||||
26 velocities
|
||||
26 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
24 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.004 seconds
|
||||
mass * 3.1575 # sets per-type mass if not in data file
|
||||
set atom * mass 3.1575 # sets per-atom mass
|
||||
26 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
26 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
special_bonds lj 0 1 1
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
|
||||
# oxDNA pair interactions
|
||||
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 ${T} 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
|
||||
pair_coeff * * oxdna2/hbond seqdep 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
|
||||
|
||||
label loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 4
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 1%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
variable comp equal ${base}+3
|
||||
variable comp equal 1+3
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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
|
||||
pair_coeff 1 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
next base
|
||||
jump in.duplex4.4type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 4
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 2%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
variable comp equal ${base}+1
|
||||
variable comp equal 2+1
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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
|
||||
pair_coeff 2 ${comp} oxdna2/hbond seqdep 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
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 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
|
||||
next base
|
||||
jump in.duplex4.4type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 4
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 3%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
next base
|
||||
jump in.duplex4.4type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 4
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 4%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
next base
|
||||
jump in.duplex4.4type loop
|
||||
|
||||
pair_coeff * * oxdna2/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 * * 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 ${T} 0.2 0.815
|
||||
pair_coeff * * oxdna2/dh 0.1 0.2 0.815
|
||||
|
||||
# Langevin dynamics
|
||||
fix 1 all nve/asphere
|
||||
fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10
|
||||
|
||||
timestep 1e-4
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 10000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le "
|
||||
|
||||
#restart 10000 config0_restart config1_restart
|
||||
|
||||
run 100000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.6389877
|
||||
ghost atom cutoff = 4.6389877
|
||||
binsize = 2.3194939, bins = 18 18 18
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
WARNING: Communication cutoff adjusted to 4.638987723814632 (../comm.cpp:690)
|
||||
0 ekin = 0 | erot = 0 | epot = -41.6285382417448 | etot = -41.6285382417448
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.756 | 9.813 | 9.871 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.6384018 0.037304147 -1.6010976 6.7769766e-05
|
||||
10000 ekin = 0.705506935391957 | erot = 3.21864563172922 | epot = -44.0640899615318 | etot = -40.1399373944106
|
||||
20000 ekin = 1.16547426389222 | erot = 1.69259899672632 | epot = -41.827511978894 | etot = -38.9694387182755
|
||||
30000 ekin = 2.07592540045025 | erot = 2.81661265099434 | epot = -41.8258727293348 | etot = -36.9333346778902
|
||||
40000 ekin = 3.0352692177735 | erot = 2.43995587980307 | epot = -41.3155342467788 | etot = -35.8403091492022
|
||||
50000 ekin = 2.69044710203348 | erot = 2.86176633025683 | epot = -40.5544750556414 | etot = -35.0022616233511
|
||||
60000 ekin = 2.90956639769978 | erot = 2.84679944563592 | epot = -39.7474408128141 | etot = -33.9910749694784
|
||||
70000 ekin = 1.89941118514544 | erot = 3.71508585194422 | epot = -38.9575890625426 | etot = -33.3430920254529
|
||||
80000 ekin = 2.43472912058895 | erot = 3.11589280920166 | epot = -39.844809532279 | etot = -34.2941876024883
|
||||
90000 ekin = 2.3759389593227 | erot = 3.25835921096947 | epot = -38.913072246407 | etot = -33.2787740761149
|
||||
100000 ekin = 3.23901515322217 | erot = 3.3464944524431 | epot = -38.6302041314432 | etot = -32.044694525778
|
||||
100000 0.086373737 -1.5432369 0.057459797 -1.3611996 7.7958353e-05
|
||||
Loop time of 6.09292 on 4 procs for 100000 steps with 26 atoms
|
||||
|
||||
Performance: 141803.976 tau/day, 16412.497 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.047712 | 2.5625 | 5.2874 | 157.3 | 42.06
|
||||
Bond | 0.007398 | 0.053166 | 0.10097 | 19.8 | 0.87
|
||||
Neigh | 1.8e-05 | 1.8e-05 | 1.8e-05 | 0.0 | 0.00
|
||||
Comm | 0.29205 | 2.9624 | 5.4188 | 143.0 | 48.62
|
||||
Output | 0.000866 | 0.00099325 | 0.001303 | 0.0 | 0.02
|
||||
Modify | 0.016247 | 0.18354 | 0.37524 | 39.2 | 3.01
|
||||
Other | | 0.3303 | | | 5.42
|
||||
|
||||
Nlocal: 6.5 ave 14.0 max 0.0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 18.5 ave 24.0 max 12.0 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Neighs: 113.75 ave 239.0 max 0.0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 455
|
||||
Ave neighs/atom = 17.5
|
||||
Ave special neighs/atom = 5.076923076923077
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
|
||||
|
||||
Total wall time: 0:00:06
|
||||
@ -1,286 +0,0 @@
|
||||
LAMMPS (30 Jun 2020)
|
||||
variable number equal 1
|
||||
variable ofreq equal 10000
|
||||
variable efreq equal 10000
|
||||
|
||||
variable ntype equal 8
|
||||
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156)
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 10 delay 0 check yes
|
||||
|
||||
read_data data.duplex4.8type
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
26 atoms
|
||||
reading velocities ...
|
||||
26 velocities
|
||||
26 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
24 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.002 seconds
|
||||
mass * 3.1575 # sets per-type mass if not in data file
|
||||
set atom * mass 3.1575 # sets per-atom mass
|
||||
26 settings made for mass
|
||||
|
||||
group all type 1 8
|
||||
26 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
special_bonds lj 0 1 1
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
|
||||
# oxDNA pair interactions
|
||||
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 ${T} 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
|
||||
pair_coeff * * oxdna2/hbond seqdep 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
|
||||
|
||||
label loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 1%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
variable comp equal ${base}+3
|
||||
variable comp equal 1+3
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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
|
||||
pair_coeff 1 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 2%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
variable comp equal ${base}+1
|
||||
variable comp equal 2+1
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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
|
||||
pair_coeff 2 ${comp} oxdna2/hbond seqdep 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
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 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
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 3%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 4%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 5%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
variable comp equal ${base}+3
|
||||
variable comp equal 5+3
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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
|
||||
pair_coeff 5 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 5 8 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 6%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
variable comp equal ${base}+1
|
||||
variable comp equal 6+1
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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
|
||||
pair_coeff 6 ${comp} oxdna2/hbond seqdep 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
|
||||
pair_coeff 6 7 oxdna2/hbond seqdep 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
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 7%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 8%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
|
||||
pair_coeff * * oxdna2/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 * * 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 ${T} 0.2 0.815
|
||||
pair_coeff * * oxdna2/dh 0.1 0.2 0.815
|
||||
|
||||
# Langevin dynamics
|
||||
fix 1 all nve/asphere
|
||||
fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10
|
||||
|
||||
timestep 1e-4
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 10000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le "
|
||||
|
||||
#restart 10000 config0_restart config1_restart
|
||||
|
||||
run 100000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.6389877
|
||||
ghost atom cutoff = 4.6389877
|
||||
binsize = 2.3194939, bins = 18 18 18
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
WARNING: Communication cutoff adjusted to 4.638987723814632 (../comm.cpp:690)
|
||||
0 ekin = 0 | erot = 0 | epot = -41.6285382417448 | etot = -41.6285382417448
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.771 | 9.771 | 9.771 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.6384018 0.037304147 -1.6010976 6.7769766e-05
|
||||
10000 ekin = 0.876675896491307 | erot = 3.01631310953192 | epot = -43.6949424313443 | etot = -39.8019534253211
|
||||
20000 ekin = 1.02178060459022 | erot = 1.54107635735041 | epot = -40.2257383206528 | etot = -37.6628813587121
|
||||
30000 ekin = 1.77819697871127 | erot = 2.67180081099997 | epot = -40.9840548186678 | etot = -36.5340570289565
|
||||
40000 ekin = 2.55095642638533 | erot = 2.97955929579275 | epot = -40.0756048400153 | etot = -34.5450891178372
|
||||
50000 ekin = 2.43321388920862 | erot = 3.63137266285959 | epot = -39.3718897377946 | etot = -33.3073031857264
|
||||
60000 ekin = 2.51123200110303 | erot = 3.95693243683571 | epot = -38.8877878920178 | etot = -32.4196234540791
|
||||
70000 ekin = 3.33444097207872 | erot = 4.12593683683079 | epot = -38.7679893452499 | etot = -31.3076115363404
|
||||
80000 ekin = 3.41969296989344 | erot = 3.46589964095079 | epot = -37.5712487729465 | etot = -30.6856561621023
|
||||
90000 ekin = 3.53106755106414 | erot = 3.40955821292295 | epot = -35.9319384430368 | etot = -28.9913126790497
|
||||
100000 ekin = 3.47860763041501 | erot = 3.95117534418391 | epot = -37.6128506757402 | etot = -30.1830677011413
|
||||
100000 0.09276287 -1.4972391 0.050590991 -1.3128555 0.00017815014
|
||||
Loop time of 7.44606 on 1 procs for 100000 steps with 26 atoms
|
||||
|
||||
Performance: 116034.458 tau/day, 13429.914 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 6.5843 | 6.5843 | 6.5843 | 0.0 | 88.43
|
||||
Bond | 0.16149 | 0.16149 | 0.16149 | 0.0 | 2.17
|
||||
Neigh | 4.3e-05 | 4.3e-05 | 4.3e-05 | 0.0 | 0.00
|
||||
Comm | 0.022595 | 0.022595 | 0.022595 | 0.0 | 0.30
|
||||
Output | 0.001492 | 0.001492 | 0.001492 | 0.0 | 0.02
|
||||
Modify | 0.65313 | 0.65313 | 0.65313 | 0.0 | 8.77
|
||||
Other | | 0.02299 | | | 0.31
|
||||
|
||||
Nlocal: 26.0 ave 26.0 max 26.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0.0 ave 0.0 max 0.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 299.0 ave 299.0 max 299.0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 299
|
||||
Ave neighs/atom = 11.5
|
||||
Ave special neighs/atom = 5.076923076923077
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
|
||||
|
||||
Total wall time: 0:00:07
|
||||
@ -1,286 +0,0 @@
|
||||
LAMMPS (30 Jun 2020)
|
||||
variable number equal 1
|
||||
variable ofreq equal 10000
|
||||
variable efreq equal 10000
|
||||
|
||||
variable ntype equal 8
|
||||
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156)
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 10 delay 0 check yes
|
||||
|
||||
read_data data.duplex4.8type
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
26 atoms
|
||||
reading velocities ...
|
||||
26 velocities
|
||||
26 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
24 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.004 seconds
|
||||
mass * 3.1575 # sets per-type mass if not in data file
|
||||
set atom * mass 3.1575 # sets per-atom mass
|
||||
26 settings made for mass
|
||||
|
||||
group all type 1 8
|
||||
26 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
special_bonds lj 0 1 1
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
|
||||
# oxDNA pair interactions
|
||||
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 ${T} 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
|
||||
pair_coeff * * oxdna2/hbond seqdep 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
|
||||
|
||||
label loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 1%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
variable comp equal ${base}+3
|
||||
variable comp equal 1+3
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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
|
||||
pair_coeff 1 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 2%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
variable comp equal ${base}+1
|
||||
variable comp equal 2+1
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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
|
||||
pair_coeff 2 ${comp} oxdna2/hbond seqdep 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
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 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
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 3%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 4%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 5%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
variable comp equal ${base}+3
|
||||
variable comp equal 5+3
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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
|
||||
pair_coeff 5 ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 5 8 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 6%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
variable comp equal ${base}+1
|
||||
variable comp equal 6+1
|
||||
pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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
|
||||
pair_coeff 6 ${comp} oxdna2/hbond seqdep 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
|
||||
pair_coeff 6 7 oxdna2/hbond seqdep 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
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 7%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
variable base loop ${ntype}
|
||||
variable base loop 8
|
||||
variable basemod equal ${base}%4
|
||||
variable basemod equal 8%4
|
||||
if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45"
|
||||
if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 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"
|
||||
next base
|
||||
jump in.duplex4.8type loop
|
||||
|
||||
pair_coeff * * oxdna2/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 * * 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 ${T} 0.2 0.815
|
||||
pair_coeff * * oxdna2/dh 0.1 0.2 0.815
|
||||
|
||||
# Langevin dynamics
|
||||
fix 1 all nve/asphere
|
||||
fix 2 all langevin ${T} ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin 0.1 ${T} 25.0 457145 angmom 10
|
||||
fix 2 all langevin 0.1 0.1 25.0 457145 angmom 10
|
||||
|
||||
timestep 1e-4
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 10000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
dump out all custom ${ofreq} out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom 10000 out.${number}.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump out all custom 10000 out.1.txt id mol type x y z ix iy iz c_quat[1] c_quat[2] c_quat[3] c_quat[4] vx vy vz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %13.6le %13.6le %13.6le %d %d %d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le "
|
||||
|
||||
#restart 10000 config0_restart config1_restart
|
||||
|
||||
run 100000
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.6389877
|
||||
ghost atom cutoff = 4.6389877
|
||||
binsize = 2.3194939, bins = 18 18 18
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
WARNING: Communication cutoff adjusted to 4.638987723814632 (../comm.cpp:690)
|
||||
0 ekin = 0 | erot = 0 | epot = -41.6285382417448 | etot = -41.6285382417448
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.756 | 9.813 | 9.871 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.6384018 0.037304147 -1.6010976 6.7769766e-05
|
||||
10000 ekin = 0.705506935391957 | erot = 3.21864563172922 | epot = -44.0640899615318 | etot = -40.1399373944106
|
||||
20000 ekin = 1.16547426389222 | erot = 1.69259899672632 | epot = -41.827511978894 | etot = -38.9694387182755
|
||||
30000 ekin = 2.07592540045025 | erot = 2.81661265099434 | epot = -41.8258727293348 | etot = -36.9333346778902
|
||||
40000 ekin = 3.0352692177735 | erot = 2.43995587980307 | epot = -41.3155342467788 | etot = -35.8403091492022
|
||||
50000 ekin = 2.69044710203348 | erot = 2.86176633025683 | epot = -40.5544750556414 | etot = -35.0022616233511
|
||||
60000 ekin = 2.90956639769978 | erot = 2.84679944563592 | epot = -39.7474408128141 | etot = -33.9910749694784
|
||||
70000 ekin = 1.89941118514544 | erot = 3.71508585194422 | epot = -38.9575890625426 | etot = -33.3430920254529
|
||||
80000 ekin = 2.43472912058895 | erot = 3.11589280920166 | epot = -39.844809532279 | etot = -34.2941876024883
|
||||
90000 ekin = 2.3759389593227 | erot = 3.25835921096947 | epot = -38.913072246407 | etot = -33.2787740761149
|
||||
100000 ekin = 3.23901515322217 | erot = 3.3464944524431 | epot = -38.6302041314432 | etot = -32.044694525778
|
||||
100000 0.086373737 -1.5432369 0.057459797 -1.3611996 7.7958353e-05
|
||||
Loop time of 6.15993 on 4 procs for 100000 steps with 26 atoms
|
||||
|
||||
Performance: 140261.437 tau/day, 16233.963 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.049533 | 2.573 | 5.3124 | 157.6 | 41.77
|
||||
Bond | 0.007709 | 0.055244 | 0.10383 | 20.2 | 0.90
|
||||
Neigh | 1.8e-05 | 1.875e-05 | 1.9e-05 | 0.0 | 0.00
|
||||
Comm | 0.32774 | 3.0114 | 5.4815 | 142.5 | 48.89
|
||||
Output | 0.000925 | 0.0010595 | 0.00137 | 0.6 | 0.02
|
||||
Modify | 0.016369 | 0.18492 | 0.37491 | 39.3 | 3.00
|
||||
Other | | 0.3343 | | | 5.43
|
||||
|
||||
Nlocal: 6.5 ave 14.0 max 0.0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 18.5 ave 24.0 max 12.0 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Neighs: 113.75 ave 239.0 max 0.0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 455
|
||||
Ave neighs/atom = 17.5
|
||||
Ave special neighs/atom = 5.076923076923077
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
|
||||
|
||||
Total wall time: 0:00:06
|
||||
91
examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/data.duplex2
Normal file
91
examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/data.duplex2
Normal file
@ -0,0 +1,91 @@
|
||||
LAMMPS data file via write_data, version 27 May 2021
|
||||
|
||||
16 atoms
|
||||
4 atom types
|
||||
13 bonds
|
||||
1 bond types
|
||||
16 ellipsoids
|
||||
|
||||
-20 20 xlo xhi
|
||||
-20 20 ylo yhi
|
||||
-20 20 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 3.1575
|
||||
2 3.1575
|
||||
3 3.1575
|
||||
4 3.1575
|
||||
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 -0.6133472972454725 -0.657478171669766 0.36065226351201896 1 1 3.7269849963023267 0 0 0
|
||||
2 2 -0.45262764247356363 -1.0030650534345913 0.7258693379233347 1 1 3.7269849963023267 0 0 0
|
||||
3 3 -0.0988342108522641 -1.239775807128057 1.069462285786363 1 1 3.7269849963023267 0 0 0
|
||||
4 4 0.2937771854299732 -1.2579750924899842 1.4258916086606965 1 1 3.7269849963023267 0 0 0
|
||||
5 1 0.6286896795685137 -1.0183343395119744 1.7689346339672825 1 1 3.7269849963023267 0 0 0
|
||||
6 2 0.7901522619067926 -0.6766341805565266 2.1540160705495754 1 1 3.7269849963023267 0 0 0
|
||||
7 3 0.7115777184886863 -0.40195579325143455 2.569568683291525 1 1 3.7269849963023267 0 0 0
|
||||
8 4 0.46973310377005234 -0.30251697967107033 3.0668007117519216 1 1 3.7269849963023267 0 0 0
|
||||
9 1 0.4056113349449848 -1.443775499211898 3.0590726503341124 2 1 3.7269849963023267 0 0 0
|
||||
10 2 -0.032028429059287516 -1.2947520971164723 2.7201071151392187 2 1 3.7269849963023267 0 0 0
|
||||
11 3 -0.31613855112314065 -0.908414175906161 2.4125207871782006 2 1 3.7269849963023267 0 0 0
|
||||
12 4 -0.38939391251821 -0.4866605488242819 2.006177777000426 2 1 3.7269849963023267 0 0 0
|
||||
13 1 -0.06232643040853296 -0.07155965522127403 1.5593206052730733 3 1 3.7269849963023267 0 0 0
|
||||
14 2 0.17884090390913376 -0.05516721349427172 1.021273149730912 3 1 3.7269849963023267 0 0 0
|
||||
15 3 0.4513439961906 -0.23795607383274572 0.5957328539615993 3 1 3.7269849963023267 0 0 0
|
||||
16 4 0.5077649359807965 -0.5565625134533538 0.1655875784458841 3 1 3.7269849963023267 0 0 0
|
||||
|
||||
Velocities
|
||||
|
||||
1 0.05386890022865587 0.02262922525602673 0.24882291144736746 0.1772010258006941 -0.29588531700001014 -0.2624137503614725
|
||||
2 -0.03995003075629463 0.26969511063701984 -0.18986454548195664 -0.030614539375968176 -0.11769518931480599 0.040074702426473215
|
||||
3 -0.20784535295201376 -0.13628722357673043 -0.06062477950201746 -0.03676034584820381 -0.06308707793373186 -0.14798601576087625
|
||||
4 -0.23969824181316998 -0.5624721730878831 0.032474422905036715 -0.16523645965016515 0.2860623077030974 0.33543519753105877
|
||||
5 -0.16114897356828353 -0.22889697470760145 -0.13553324962649563 0.07151030852881342 -0.09415592891043179 0.13422881539312292
|
||||
6 -0.04701706588477693 0.19216715585110036 0.14588242791297215 0.09218622989776322 -0.5640128930702024 0.09287105657777776
|
||||
7 0.05098438305112513 -0.038459555522009595 -0.14244196285749675 0.3479046835475834 0.4244922695910593 -0.13582882604358357
|
||||
8 0.37827971348411926 -0.04953992506010833 0.1626392045834847 0.0442887659636129 0.07868414126013584 -0.12713600444325032
|
||||
9 0.04912038408665491 0.041260647318716696 0.012223856334495234 0.03282916621721876 -0.00012670547095256 0.155978785417696
|
||||
10 0.1939216183073483 0.11075235485381942 -0.0405050516019971 -0.17008135001813812 -0.4563093565840761 -0.30318513627039506
|
||||
11 -0.351360733920646 -0.18822419067535692 0.36147938199051305 -0.3708221604627426 -0.49108381825941216 0.09435948331955418
|
||||
12 -0.1188642917357977 0.22355282456551884 0.009265586122144348 -0.28230100188858365 0.10276485660828892 0.10175233476780697
|
||||
13 -0.1446616296238799 -0.11552059909787235 0.1331477187595642 -0.25498721890374343 0.2754663721641154 0.05806416868630132
|
||||
14 0.051547120035862544 -0.36611026510775635 -0.06630782880801242 -0.11999847173316518 0.0684476892288605 0.2161595932308759
|
||||
15 -0.20214244962091388 0.23341226933559608 0.008133374252278069 -0.17013911124135248 0.01870292260510287 -0.2682954134361106
|
||||
16 -0.19202131162868008 -0.08105295741355378 -0.0469350810885074 0.017332107652647588 -0.32876588862807693 0.1085334141225924
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 9 10
|
||||
9 1 10 11
|
||||
10 1 11 12
|
||||
11 1 13 14
|
||||
12 1 14 15
|
||||
13 1 15 16
|
||||
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341 1.173984503142341 1.173984503142341 0.9964752158482045 -0.053253555733239796 0.011391163807102514 -0.06380787090289707
|
||||
2 1.173984503142341 1.173984503142341 1.173984503142341 0.9369923833143513 0.11220716044648564 0.06732538499716349 0.3239168400846305
|
||||
3 1.173984503142341 1.173984503142341 1.173984503142341 0.797964932091827 0.14473096354527873 0.18374142699366386 0.5554673737937029
|
||||
4 1.173984503142341 1.173984503142341 1.173984503142341 0.5660864821344559 0.14688275499481052 0.09873742533340191 0.8051226439917721
|
||||
5 1.173984503142341 1.173984503142341 1.173984503142341 0.2533023785125306 0.12062313161679827 0.08583012223905846 0.9559922359911086
|
||||
6 1.173984503142341 1.173984503142341 1.173984503142341 -0.03855807343534716 0.08405913137017908 0.02236505169306371 0.9954632800204194
|
||||
7 1.173984503142341 1.173984503142341 1.173984503142341 -0.45592844330248017 0.1004550065061007 -0.052524745294758785 0.8827679181910482
|
||||
8 1.173984503142341 1.173984503142341 1.173984503142341 0.768021221540491 -0.009582139884533599 0.03658677589040892 -0.63930665074644
|
||||
9 1.173984503142341 1.173984503142341 1.173984503142341 -0.23299975754512345 0.688686395231341 0.6747873944883376 -0.12682324016841584
|
||||
10 1.173984503142341 1.173984503142341 1.173984503142341 -0.24662061871907232 0.8744456399178389 0.39370836087823996 -0.13970261209395163
|
||||
11 1.173984503142341 1.173984503142341 1.173984503142341 -0.087475900850909 0.977367602388229 0.14493549113095577 -0.12686307572668784
|
||||
12 1.173984503142341 1.173984503142341 1.173984503142341 -0.03181169300779214 0.9634374984140112 -0.2442360692534371 -0.10547485630879185
|
||||
13 1.173984503142341 1.173984503142341 1.173984503142341 -0.032786070696572266 0.7922941528811777 -0.6084214170523915 -0.03191282109962717
|
||||
14 1.173984503142341 1.173984503142341 1.173984503142341 0.047188686288341455 0.6316396208287698 -0.7737349519945348 0.011783095844627799
|
||||
15 1.173984503142341 1.173984503142341 1.173984503142341 -0.05869980642620335 -0.34229358203414423 0.9376740835056508 0.012519965878508689
|
||||
16 1.173984503142341 1.173984503142341 1.173984503142341 -0.08582818143150042 0.0008707732197394232 0.9939540921464659 -0.0684691735853161
|
||||
@ -1,7 +1,8 @@
|
||||
variable number equal 4
|
||||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
variable rhos equal 0.5
|
||||
|
||||
units lj
|
||||
|
||||
@ -11,14 +12,14 @@ newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_style hybrid bond ellipsoid oxdna
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex4
|
||||
read_data data.duplex2
|
||||
|
||||
set atom * mass 3.1575
|
||||
|
||||
@ -31,38 +32,27 @@ special_bonds lj 0 1 1
|
||||
|
||||
# oxRNA2 pair interactions
|
||||
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 ${T} 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/hbond seqdep 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
|
||||
pair_coeff 1 4 oxrna2/hbond seqdep 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
|
||||
pair_coeff 2 3 oxrna2/hbond seqdep 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
|
||||
pair_coeff 3 4 oxrna2/hbond seqdep 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
|
||||
pair_coeff * * oxrna2/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
|
||||
pair_coeff * * oxrna2/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
|
||||
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 ${T} 0.5 1.02455
|
||||
pair_coeff * * oxrna2/dh ${T} ${rhos} 1.02455
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
comm_modify cutoff 2.5
|
||||
fix 3 all balance 1000 1.03 shift xyz 10 1.03
|
||||
comm_modify cutoff 3.8
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
compute quat all property/atom quatw quati quatj quatk
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
@ -73,10 +63,10 @@ variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f %13.9f"
|
||||
dump out all custom ${ofreq} out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz
|
||||
dump_modify out sort id
|
||||
dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le"
|
||||
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
write_data last_config.${number}.* nocoeff
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -1,96 +0,0 @@
|
||||
# LAMMPS data file
|
||||
16 atoms
|
||||
16 ellipsoids
|
||||
13 bonds
|
||||
|
||||
4 atom types
|
||||
1 bond types
|
||||
|
||||
# System size
|
||||
-20.000000 20.000000 xlo xhi
|
||||
-20.000000 20.000000 ylo yhi
|
||||
-20.000000 20.000000 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 3.1575
|
||||
2 3.1575
|
||||
3 3.1575
|
||||
4 3.1575
|
||||
|
||||
# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
|
||||
Atoms
|
||||
|
||||
1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1
|
||||
2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1
|
||||
3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1
|
||||
4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1
|
||||
5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1
|
||||
6 2 5.999771538385027e-01 -5.235921299024461e-03 1.948814275651561e+00 1 1 1
|
||||
7 3 4.890766774371325e-01 3.475687034056071e-01 2.338577130781873e+00 1 1 1
|
||||
8 4 1.923677943514057e-01 5.683261666476170e-01 2.728339985912185e+00 1 1 1
|
||||
9 1 -1.923677943514057e-01 -5.683261666476170e-01 2.728339985912185e+00 2 1 1
|
||||
10 2 -4.890766774371324e-01 -3.475687034056071e-01 2.338577130781873e+00 2 1 1
|
||||
11 3 -5.999771538385025e-01 5.235921299024461e-03 1.948814275651561e+00 2 1 1
|
||||
12 4 -4.829362784135481e-01 3.560513319622207e-01 1.559051420521249e+00 2 1 1
|
||||
13 1 -1.824198365552940e-01 5.715968887521514e-01 1.169288565390936e+00 2 1 1
|
||||
14 2 1.874009511073395e-01 5.699832309147912e-01 7.795257102606241e-01 2 1 1
|
||||
15 3 4.860249842674773e-01 3.518234140414733e-01 3.897628551303119e-01 2 1 1
|
||||
16 4 5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1
|
||||
|
||||
# Atom-ID, translational velocity, angular momentum
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
11 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
12 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
13 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
14 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
15 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
16 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
|
||||
# Atom-ID, shape, quaternion
|
||||
Ellipsoids
|
||||
|
||||
1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01
|
||||
3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01
|
||||
4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01
|
||||
5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01
|
||||
6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 4.363309284746654e-03 0.000000000000000e+00 0.000000000000000e+00 9.999904807207346e-01
|
||||
7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -3.040330609254902e-01 0.000000000000000e+00 0.000000000000000e+00 9.526614812535865e-01
|
||||
8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 5.828323126827837e-01 0.000000000000000e+00 0.000000000000000e+00 -8.125924533816677e-01
|
||||
9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.125924533816681e-01 5.828323126827832e-01 -0.000000000000000e+00
|
||||
10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.526614812535864e-01 3.040330609254902e-01 0.000000000000000e+00
|
||||
11 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.999904807207346e-01 -4.363309284746654e-03 0.000000000000000e+00
|
||||
12 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.499720515246526e-01 -3.123349185122325e-01 0.000000000000000e+00
|
||||
13 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.074754054847402e-01 -5.899012371043603e-01 0.000000000000000e+00
|
||||
14 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.863723567357898e-01 -8.100416404457959e-01 0.000000000000000e+00
|
||||
15 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252948e-01 0.000000000000000e+00
|
||||
16 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 2.775557561562893e-17 1.000000000000000e+00 -0.000000000000000e+00
|
||||
|
||||
# Bond topology
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 9 10
|
||||
9 1 10 11
|
||||
10 1 11 12
|
||||
11 1 13 14
|
||||
12 1 14 15
|
||||
13 1 15 16
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
12
src/.gitignore
vendored
12
src/.gitignore
vendored
@ -70,8 +70,8 @@
|
||||
|
||||
/meam*.h
|
||||
/meam*.cpp
|
||||
/pair_meam.cpp
|
||||
/pair_meam.h
|
||||
/pair_meamc.cpp
|
||||
/pair_meamc.h
|
||||
|
||||
/compute_mliap.cpp
|
||||
/compute_mliap.h
|
||||
@ -314,6 +314,8 @@
|
||||
/atom_vec_granular.h
|
||||
/atom_vec_molecular.cpp
|
||||
/atom_vec_molecular.h
|
||||
/atom_vec_oxdna.cpp
|
||||
/atom_vec_oxdna.h
|
||||
/atom_vec_peri.cpp
|
||||
/atom_vec_peri.h
|
||||
/atom_vec_template.cpp
|
||||
@ -386,8 +388,6 @@
|
||||
/compute_erotate_rigid.h
|
||||
/compute_event_displace.cpp
|
||||
/compute_event_displace.h
|
||||
/compute_fabric.cpp
|
||||
/compute_fabric.h
|
||||
/compute_fep.cpp
|
||||
/compute_fep.h
|
||||
/compute_force_tally.cpp
|
||||
@ -1431,10 +1431,6 @@
|
||||
/pair_thole.h
|
||||
/pair_buck_mdf.cpp
|
||||
/pair_buck_mdf.h
|
||||
/pair_dpd.cpp
|
||||
/pair_dpd.h
|
||||
/pair_dpd_tstat.cpp
|
||||
/pair_dpd_tstat.h
|
||||
/pair_dpd_ext.cpp
|
||||
/pair_dpd_ext.h
|
||||
/pair_dpd_ext_tstat.cpp
|
||||
|
||||
@ -28,6 +28,8 @@ action () {
|
||||
|
||||
# list of files with dependcies
|
||||
|
||||
action atom_vec_oxdna.cpp atom_vec.h
|
||||
action atom_vec_oxdna.h atom_vec.h
|
||||
action bond_oxdna_fene.cpp bond_fene.h
|
||||
action bond_oxdna2_fene.cpp bond_fene.h
|
||||
action bond_oxrna2_fene.cpp bond_fene.h
|
||||
|
||||
103
src/CG-DNA/atom_vec_oxdna.cpp
Normal file
103
src/CG-DNA/atom_vec_oxdna.cpp
Normal file
@ -0,0 +1,103 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "atom_vec_oxdna.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
AtomVecOxdna::AtomVecOxdna(LAMMPS *lmp) : AtomVec(lmp)
|
||||
{
|
||||
molecular = Atom::MOLECULAR;
|
||||
bonds_allow = 1;
|
||||
mass_type = PER_TYPE;
|
||||
|
||||
atom->molecule_flag = 1;
|
||||
|
||||
// strings with peratom variables to include in each AtomVec method
|
||||
// strings cannot contain fields in corresponding AtomVec default strings
|
||||
// order of fields in a string does not matter
|
||||
// except: fields_data_atom & fields_data_vel must match data file
|
||||
|
||||
fields_grow = (char *) "id5p";
|
||||
fields_copy = (char *) "id5p";
|
||||
fields_comm = (char *) "";
|
||||
fields_comm_vel = (char *) "";
|
||||
fields_reverse = (char *) "";
|
||||
fields_border = (char *) "id5p";
|
||||
fields_border_vel = (char *) "";
|
||||
fields_exchange = (char *) "id5p";
|
||||
fields_restart = (char *) "id5p";
|
||||
fields_create = (char *) "";
|
||||
fields_data_atom = (char *) "id type x";
|
||||
fields_data_vel = (char *) "id v";
|
||||
|
||||
setup_fields();
|
||||
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
AtomVecOxdna::~AtomVecOxdna()
|
||||
{
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set local copies of all grow ptrs used by this class, except defaults
|
||||
needed in replicate when 2 atom classes exist and it calls pack_restart()
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AtomVecOxdna::grow_pointers()
|
||||
{
|
||||
id5p = atom->id5p;
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
process bond information as per data file
|
||||
store 5' partner to inform 3'->5' bond directionality
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AtomVecOxdna::data_bonds_post(int n, char *buf, tagint id_offset)
|
||||
{
|
||||
|
||||
int m,tmp,itype,rv;
|
||||
tagint atom1,atom2;
|
||||
char *next;
|
||||
|
||||
tagint *id5p = atom->id5p;
|
||||
|
||||
if (comm->me == 0) utils::logmesg(lmp,"Setting oxDNA 3'->5' bond directionality ...\n");
|
||||
|
||||
for (int i = 0; i < n; i++) {
|
||||
|
||||
next = strchr(buf,'\n');
|
||||
*next = '\0';
|
||||
rv = sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT,
|
||||
&tmp,&itype,&atom1,&atom2);
|
||||
|
||||
if (id_offset) {
|
||||
atom1 += id_offset;
|
||||
atom2 += id_offset;
|
||||
}
|
||||
|
||||
if ((m = atom->map(atom1)) >= 0) {
|
||||
id5p[m] = atom2;
|
||||
}
|
||||
|
||||
buf = next + 1;
|
||||
}
|
||||
}
|
||||
48
src/CG-DNA/atom_vec_oxdna.h
Normal file
48
src/CG-DNA/atom_vec_oxdna.h
Normal file
@ -0,0 +1,48 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef ATOM_CLASS
|
||||
// clang-format off
|
||||
AtomStyle(oxdna,AtomVecOxdna);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_ATOM_VEC_OXDNA_H
|
||||
#define LMP_ATOM_VEC_OXDNA_H
|
||||
|
||||
#include "atom.h"
|
||||
#include "atom_vec.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class AtomVecOxdna : public AtomVec {
|
||||
public:
|
||||
AtomVecOxdna(class LAMMPS *);
|
||||
~AtomVecOxdna();
|
||||
|
||||
void grow_pointers();
|
||||
virtual void data_bonds_post(int, char *, tagint);
|
||||
|
||||
private:
|
||||
tagint *id5p;
|
||||
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
*/
|
||||
@ -29,6 +29,7 @@
|
||||
#include "error.h"
|
||||
|
||||
#include "atom_vec_ellipsoid.h"
|
||||
#include "atom_vec_oxdna.h"
|
||||
#include "math_extra.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
@ -42,26 +43,26 @@ PairOxdnaStk::PairOxdnaStk(LAMMPS *lmp) : Pair(lmp)
|
||||
writedata = 1;
|
||||
|
||||
// sequence-specific stacking strength
|
||||
// A:0 C:1 G:2 T:3, 5'- [i][j] -3'
|
||||
// A:0 C:1 G:2 T:3, 3'- [i][j] -5'
|
||||
|
||||
eta_st[0][0] = 1.11960;
|
||||
eta_st[0][1] = 1.00852;
|
||||
eta_st[0][2] = 0.96950;
|
||||
eta_st[0][3] = 0.99632;
|
||||
eta_st[1][0] = 1.00852;
|
||||
eta_st[2][0] = 0.96950;
|
||||
eta_st[3][0] = 0.99632;
|
||||
|
||||
eta_st[1][0] = 1.01889;
|
||||
eta_st[0][1] = 1.01889;
|
||||
eta_st[1][1] = 0.97804;
|
||||
eta_st[1][2] = 1.02681;
|
||||
eta_st[1][3] = 0.96950;
|
||||
eta_st[2][1] = 1.02681;
|
||||
eta_st[3][1] = 0.96950;
|
||||
|
||||
eta_st[2][0] = 0.98169;
|
||||
eta_st[2][1] = 1.05913;
|
||||
eta_st[0][2] = 0.98169;
|
||||
eta_st[1][2] = 1.05913;
|
||||
eta_st[2][2] = 0.97804;
|
||||
eta_st[2][3] = 1.00852;
|
||||
eta_st[3][2] = 1.00852;
|
||||
|
||||
eta_st[3][0] = 0.94694;
|
||||
eta_st[3][1] = 0.98169;
|
||||
eta_st[3][2] = 1.01889;
|
||||
eta_st[0][3] = 0.94694;
|
||||
eta_st[1][3] = 0.98169;
|
||||
eta_st[2][3] = 1.01889;
|
||||
eta_st[3][3] = 0.96383;
|
||||
|
||||
}
|
||||
@ -244,11 +245,13 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
int **bondlist = neighbor->bondlist;
|
||||
int nbondlist = neighbor->nbondlist;
|
||||
|
||||
tagint *id5p = atom->id5p;
|
||||
|
||||
AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
|
||||
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
|
||||
int *ellipsoid = atom->ellipsoid;
|
||||
|
||||
int a,b,in,atype,btype;
|
||||
int a,b,btemp,in,atype,btype;
|
||||
|
||||
double f1,f4t4,f4t5,f4t6,f5c1,f5c2;
|
||||
double df1,df4t4,df4t5,df4t6,df5c1,df5c2;
|
||||
@ -261,8 +264,19 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
|
||||
for (in = 0; in < nbondlist; in++) {
|
||||
|
||||
a = bondlist[in][1];
|
||||
b = bondlist[in][0];
|
||||
a = bondlist[in][0];
|
||||
b = bondlist[in][1];
|
||||
|
||||
// directionality test: a -> b is 3' -> 5'
|
||||
if(atom->tag[b] != id5p[a]) {
|
||||
|
||||
btemp = b;
|
||||
b = a;
|
||||
a = btemp;
|
||||
|
||||
}
|
||||
|
||||
// a now in 3' direction, b in 5' direction
|
||||
|
||||
qa=bonus[ellipsoid[a]].quat;
|
||||
MathExtra::q_to_exyz(qa,ax,ay,az);
|
||||
@ -279,30 +293,11 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
rb_cst[1] = d_cst*bx[1];
|
||||
rb_cst[2] = d_cst*bx[2];
|
||||
|
||||
// vector stacking site b to a
|
||||
delr_st[0] = x[a][0] + ra_cst[0] - x[b][0] - rb_cst[0];
|
||||
delr_st[1] = x[a][1] + ra_cst[1] - x[b][1] - rb_cst[1];
|
||||
delr_st[2] = x[a][2] + ra_cst[2] - x[b][2] - rb_cst[2];
|
||||
// vector stacking site a to b
|
||||
delr_st[0] = x[b][0] + rb_cst[0] - x[a][0] - ra_cst[0];
|
||||
delr_st[1] = x[b][1] + rb_cst[1] - x[a][1] - ra_cst[1];
|
||||
delr_st[2] = x[b][2] + rb_cst[2] - x[a][2] - ra_cst[2];
|
||||
|
||||
// test for directionality of vector b to a
|
||||
tptofp = MFOxdna::is_3pto5p(delr_st,bz);
|
||||
|
||||
// if b to a is 5' to 3' we need to swap roles of a and b
|
||||
if (tptofp == -1) {
|
||||
|
||||
std::swap(a,b);
|
||||
std::swap(ax,bx);
|
||||
std::swap(ay,by);
|
||||
std::swap(az,bz);
|
||||
std::swap(ra_cst,rb_cst);
|
||||
|
||||
delr_st[0] *= -1;
|
||||
delr_st[1] *= -1;
|
||||
delr_st[2] *= -1;
|
||||
|
||||
}
|
||||
|
||||
// a now in 5' direction, b in 3' direction
|
||||
atype = type[a];
|
||||
btype = type[b];
|
||||
|
||||
@ -325,9 +320,9 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
rb_cs[2] = d_cs*bx[2];
|
||||
|
||||
// vector backbone site b to a
|
||||
delr_ss[0] = (x[a][0] + ra_cs[0] - x[b][0] - rb_cs[0]);
|
||||
delr_ss[1] = (x[a][1] + ra_cs[1] - x[b][1] - rb_cs[1]);
|
||||
delr_ss[2] = (x[a][2] + ra_cs[2] - x[b][2] - rb_cs[2]);
|
||||
delr_ss[0] = (x[b][0] + rb_cs[0] - x[a][0] - ra_cs[0]);
|
||||
delr_ss[1] = (x[b][1] + rb_cs[1] - x[a][1] - ra_cs[1]);
|
||||
delr_ss[2] = (x[b][2] + rb_cs[2] - x[a][2] - ra_cs[2]);
|
||||
|
||||
rsq_ss = delr_ss[0]*delr_ss[0] + delr_ss[1]*delr_ss[1] + delr_ss[2]*delr_ss[2];
|
||||
r_ss = sqrt(rsq_ss);
|
||||
@ -345,7 +340,7 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
if (f1) {
|
||||
|
||||
// theta4 angle and correction
|
||||
cost4 = MathExtra::dot3(az,bz);
|
||||
cost4 = MathExtra::dot3(bz,az);
|
||||
if (cost4 > 1.0) cost4 = 1.0;
|
||||
if (cost4 < -1.0) cost4 = -1.0;
|
||||
theta4 = acos(cost4);
|
||||
@ -357,7 +352,7 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
if (f4t4) {
|
||||
|
||||
// theta5 angle and correction
|
||||
cost5p = MathExtra::dot3(delr_st_norm,az);
|
||||
cost5p = MathExtra::dot3(delr_st_norm,bz);
|
||||
if (cost5p > 1.0) cost5p = 1.0;
|
||||
if (cost5p < -1.0) cost5p = -1.0;
|
||||
theta5p = acos(cost5p);
|
||||
@ -368,16 +363,16 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
// early rejection criterium
|
||||
if (f4t5) {
|
||||
|
||||
cost6p = MathExtra::dot3(delr_st_norm,bz);
|
||||
cost6p = MathExtra::dot3(delr_st_norm,az);
|
||||
if (cost6p > 1.0) cost6p = 1.0;
|
||||
if (cost6p < -1.0) cost6p = -1.0;
|
||||
theta6p = acos(cost6p);
|
||||
|
||||
cosphi1 = MathExtra::dot3(delr_ss_norm,ay);
|
||||
cosphi1 = MathExtra::dot3(delr_ss_norm,by);
|
||||
if (cosphi1 > 1.0) cosphi1 = 1.0;
|
||||
if (cosphi1 < -1.0) cosphi1 = -1.0;
|
||||
|
||||
cosphi2 = MathExtra::dot3(delr_ss_norm,by);
|
||||
cosphi2 = MathExtra::dot3(delr_ss_norm,ay);
|
||||
if (cosphi2 > 1.0) cosphi2 = 1.0;
|
||||
if (cosphi2 < -1.0) cosphi2 = -1.0;
|
||||
|
||||
@ -385,11 +380,10 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
b_st6[atype][btype], dtheta_st6_c[atype][btype]);
|
||||
|
||||
f5c1 = F5(-cosphi1, a_st1[atype][btype], -cosphi_st1_ast[atype][btype], b_st1[atype][btype],
|
||||
cosphi_st1_c[atype][btype]);
|
||||
-cosphi_st1_c[atype][btype]);
|
||||
|
||||
f5c2 = F5(-cosphi2, a_st2[atype][btype], -cosphi_st2_ast[atype][btype], b_st2[atype][btype],
|
||||
cosphi_st2_c[atype][btype]);
|
||||
|
||||
-cosphi_st2_c[atype][btype]);
|
||||
|
||||
evdwl = f1 * f4t4 * f4t5 * f4t6 * f5c1 * f5c2;
|
||||
|
||||
@ -410,10 +404,10 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
b_st6[atype][btype], dtheta_st6_c[atype][btype])/sin(theta6p);
|
||||
|
||||
df5c1 = DF5(-cosphi1, a_st1[atype][btype], -cosphi_st1_ast[atype][btype], b_st1[atype][btype],
|
||||
cosphi_st1_c[atype][btype]);
|
||||
-cosphi_st1_c[atype][btype]);
|
||||
|
||||
df5c2 = DF5(-cosphi2, a_st2[atype][btype], -cosphi_st2_ast[atype][btype], b_st2[atype][btype],
|
||||
cosphi_st2_c[atype][btype]);
|
||||
-cosphi_st2_c[atype][btype]);
|
||||
|
||||
|
||||
// force, torque and virial contribution for forces between stacking sites
|
||||
@ -446,9 +440,9 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
finc = -f1 * f4t4 * df4t5 * f4t6 * f5c1 * f5c2 * rinv_st;
|
||||
fpair += finc;
|
||||
|
||||
delf[0] += (delr_st_norm[0]*cost5p - az[0]) * finc;
|
||||
delf[1] += (delr_st_norm[1]*cost5p - az[1]) * finc;
|
||||
delf[2] += (delr_st_norm[2]*cost5p - az[2]) * finc;
|
||||
delf[0] += (delr_st_norm[0]*cost5p - bz[0]) * finc;
|
||||
delf[1] += (delr_st_norm[1]*cost5p - bz[1]) * finc;
|
||||
delf[2] += (delr_st_norm[2]*cost5p - bz[2]) * finc;
|
||||
|
||||
}
|
||||
|
||||
@ -458,28 +452,27 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
finc = -f1 * f4t4 * f4t5 * df4t6 * f5c1 * f5c2 * rinv_st;
|
||||
fpair += finc;
|
||||
|
||||
delf[0] += (delr_st_norm[0]*cost6p - bz[0]) * finc;
|
||||
delf[1] += (delr_st_norm[1]*cost6p - bz[1]) * finc;
|
||||
delf[2] += (delr_st_norm[2]*cost6p - bz[2]) * finc;
|
||||
delf[0] += (delr_st_norm[0]*cost6p - az[0]) * finc;
|
||||
delf[1] += (delr_st_norm[1]*cost6p - az[1]) * finc;
|
||||
delf[2] += (delr_st_norm[2]*cost6p - az[2]) * finc;
|
||||
|
||||
}
|
||||
|
||||
// increment forces and torques
|
||||
|
||||
if (newton_bond || a < nlocal) {
|
||||
|
||||
f[a][0] += delf[0];
|
||||
f[a][1] += delf[1];
|
||||
f[a][2] += delf[2];
|
||||
f[a][0] -= delf[0];
|
||||
f[a][1] -= delf[1];
|
||||
f[a][2] -= delf[2];
|
||||
|
||||
MathExtra::cross3(ra_cst,delf,delta);
|
||||
|
||||
}
|
||||
if (newton_bond || b < nlocal) {
|
||||
|
||||
f[b][0] -= delf[0];
|
||||
f[b][1] -= delf[1];
|
||||
f[b][2] -= delf[2];
|
||||
f[b][0] += delf[0];
|
||||
f[b][1] += delf[1];
|
||||
f[b][2] += delf[2];
|
||||
|
||||
MathExtra::cross3(rb_cst,delf,deltb);
|
||||
|
||||
@ -487,16 +480,16 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
|
||||
if (newton_bond || a < nlocal) {
|
||||
|
||||
torque[a][0] += delta[0];
|
||||
torque[a][1] += delta[1];
|
||||
torque[a][2] += delta[2];
|
||||
torque[a][0] -= delta[0];
|
||||
torque[a][1] -= delta[1];
|
||||
torque[a][2] -= delta[2];
|
||||
|
||||
}
|
||||
if (newton_bond || b < nlocal) {
|
||||
|
||||
torque[b][0] -= deltb[0];
|
||||
torque[b][1] -= deltb[1];
|
||||
torque[b][2] -= deltb[2];
|
||||
torque[b][0] += deltb[0];
|
||||
torque[b][1] += deltb[1];
|
||||
torque[b][2] += deltb[2];
|
||||
|
||||
}
|
||||
|
||||
@ -505,7 +498,7 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
// (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986))
|
||||
|
||||
if (evflag) ev_tally_xyz(a,b,nlocal,newton_bond,evdwl,
|
||||
delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
|
||||
delf[0],delf[1],delf[2],x[b][0]-x[a][0],x[b][1]-x[a][1],x[b][2]-x[a][2]);
|
||||
|
||||
// force, torque and virial contribution for forces between backbone sites
|
||||
|
||||
@ -529,9 +522,9 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
finc = -f1 * f4t4 * f4t5 * f4t6 * df5c1 * f5c2 * rinv_ss;
|
||||
fpair += finc;
|
||||
|
||||
delf[0] += (delr_ss_norm[0]*cosphi1 - ay[0]) * finc;
|
||||
delf[1] += (delr_ss_norm[1]*cosphi1 - ay[1]) * finc;
|
||||
delf[2] += (delr_ss_norm[2]*cosphi1 - ay[2]) * finc;
|
||||
delf[0] += (delr_ss_norm[0]*cosphi1 - by[0]) * finc;
|
||||
delf[1] += (delr_ss_norm[1]*cosphi1 - by[1]) * finc;
|
||||
delf[2] += (delr_ss_norm[2]*cosphi1 - by[2]) * finc;
|
||||
|
||||
}
|
||||
|
||||
@ -541,28 +534,27 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
finc = -f1 * f4t4 * f4t5 * f4t6 * f5c1 * df5c2 * rinv_ss;
|
||||
fpair += finc;
|
||||
|
||||
delf[0] += (delr_ss_norm[0]*cosphi2 - by[0]) * finc;
|
||||
delf[1] += (delr_ss_norm[1]*cosphi2 - by[1]) * finc;
|
||||
delf[2] += (delr_ss_norm[2]*cosphi2 - by[2]) * finc;
|
||||
delf[0] += (delr_ss_norm[0]*cosphi2 - ay[0]) * finc;
|
||||
delf[1] += (delr_ss_norm[1]*cosphi2 - ay[1]) * finc;
|
||||
delf[2] += (delr_ss_norm[2]*cosphi2 - ay[2]) * finc;
|
||||
|
||||
}
|
||||
|
||||
// increment forces and torques
|
||||
|
||||
if (newton_bond || a < nlocal) {
|
||||
|
||||
f[a][0] += delf[0];
|
||||
f[a][1] += delf[1];
|
||||
f[a][2] += delf[2];
|
||||
f[a][0] -= delf[0];
|
||||
f[a][1] -= delf[1];
|
||||
f[a][2] -= delf[2];
|
||||
|
||||
MathExtra::cross3(ra_cs,delf,delta);
|
||||
|
||||
}
|
||||
if (newton_bond || b < nlocal) {
|
||||
|
||||
f[b][0] -= delf[0];
|
||||
f[b][1] -= delf[1];
|
||||
f[b][2] -= delf[2];
|
||||
f[b][0] += delf[0];
|
||||
f[b][1] += delf[1];
|
||||
f[b][2] += delf[2];
|
||||
|
||||
MathExtra::cross3(rb_cs,delf,deltb);
|
||||
|
||||
@ -570,22 +562,22 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
|
||||
if (newton_bond || a < nlocal) {
|
||||
|
||||
torque[a][0] += delta[0];
|
||||
torque[a][1] += delta[1];
|
||||
torque[a][2] += delta[2];
|
||||
torque[a][0] -= delta[0];
|
||||
torque[a][1] -= delta[1];
|
||||
torque[a][2] -= delta[2];
|
||||
|
||||
}
|
||||
if (newton_bond || b < nlocal) {
|
||||
|
||||
torque[b][0] -= deltb[0];
|
||||
torque[b][1] -= deltb[1];
|
||||
torque[b][2] -= deltb[2];
|
||||
torque[b][0] += deltb[0];
|
||||
torque[b][1] += deltb[1];
|
||||
torque[b][2] += deltb[2];
|
||||
|
||||
}
|
||||
|
||||
// increment virial only
|
||||
if (evflag) ev_tally_xyz(a,b,nlocal,newton_bond,0.0,
|
||||
delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
|
||||
delf[0],delf[1],delf[2],x[b][0]-x[a][0],x[b][1]-x[a][1],x[b][2]-x[a][2]);
|
||||
|
||||
// pure torques not expressible as r x f
|
||||
|
||||
@ -600,7 +592,7 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
if (theta4) {
|
||||
|
||||
tpair = -f1 * df4t4 * f4t5 * f4t6 * f5c1 * f5c2;
|
||||
MathExtra::cross3(bz,az,t4dir);
|
||||
MathExtra::cross3(az,bz,t4dir);
|
||||
|
||||
delta[0] += t4dir[0]*tpair;
|
||||
delta[1] += t4dir[1]*tpair;
|
||||
@ -616,11 +608,11 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
if (theta5p) {
|
||||
|
||||
tpair = -f1 * f4t4 * df4t5 * f4t6 * f5c1 * f5c2;
|
||||
MathExtra::cross3(delr_st_norm,az,t5pdir);
|
||||
MathExtra::cross3(delr_st_norm,bz,t5pdir);
|
||||
|
||||
delta[0] += t5pdir[0] * tpair;
|
||||
delta[1] += t5pdir[1] * tpair;
|
||||
delta[2] += t5pdir[2] * tpair;
|
||||
deltb[0] += t5pdir[0] * tpair;
|
||||
deltb[1] += t5pdir[1] * tpair;
|
||||
deltb[2] += t5pdir[2] * tpair;
|
||||
|
||||
}
|
||||
|
||||
@ -628,11 +620,11 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
if (theta6p) {
|
||||
|
||||
tpair = -f1 * f4t4 * f4t5 * df4t6 * f5c1 * f5c2;
|
||||
MathExtra::cross3(delr_st_norm,bz,t6pdir);
|
||||
MathExtra::cross3(delr_st_norm,az,t6pdir);
|
||||
|
||||
deltb[0] -= t6pdir[0] * tpair;
|
||||
deltb[1] -= t6pdir[1] * tpair;
|
||||
deltb[2] -= t6pdir[2] * tpair;
|
||||
delta[0] -= t6pdir[0] * tpair;
|
||||
delta[1] -= t6pdir[1] * tpair;
|
||||
delta[2] -= t6pdir[2] * tpair;
|
||||
|
||||
}
|
||||
|
||||
@ -640,11 +632,11 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
if (cosphi1) {
|
||||
|
||||
tpair = -f1 * f4t4 * f4t5 * f4t6 * df5c1 * f5c2;
|
||||
MathExtra::cross3(delr_ss_norm,ay,cosphi1dir);
|
||||
MathExtra::cross3(delr_ss_norm,by,cosphi1dir);
|
||||
|
||||
delta[0] += cosphi1dir[0] * tpair;
|
||||
delta[1] += cosphi1dir[1] * tpair;
|
||||
delta[2] += cosphi1dir[2] * tpair;
|
||||
deltb[0] += cosphi1dir[0] * tpair;
|
||||
deltb[1] += cosphi1dir[1] * tpair;
|
||||
deltb[2] += cosphi1dir[2] * tpair;
|
||||
|
||||
}
|
||||
|
||||
@ -652,27 +644,27 @@ void PairOxdnaStk::compute(int eflag, int vflag)
|
||||
if (cosphi2) {
|
||||
|
||||
tpair = -f1 * f4t4 * f4t5 * f4t6 * f5c1 * df5c2;
|
||||
MathExtra::cross3(delr_ss_norm,by,cosphi2dir);
|
||||
MathExtra::cross3(delr_ss_norm,ay,cosphi2dir);
|
||||
|
||||
deltb[0] -= cosphi2dir[0] * tpair;
|
||||
deltb[1] -= cosphi2dir[1] * tpair;
|
||||
deltb[2] -= cosphi2dir[2] * tpair;
|
||||
delta[0] -= cosphi2dir[0] * tpair;
|
||||
delta[1] -= cosphi2dir[1] * tpair;
|
||||
delta[2] -= cosphi2dir[2] * tpair;
|
||||
|
||||
}
|
||||
|
||||
// increment torques
|
||||
if (newton_bond || a < nlocal) {
|
||||
|
||||
torque[a][0] += delta[0];
|
||||
torque[a][1] += delta[1];
|
||||
torque[a][2] += delta[2];
|
||||
torque[a][0] -= delta[0];
|
||||
torque[a][1] -= delta[1];
|
||||
torque[a][2] -= delta[2];
|
||||
|
||||
}
|
||||
if (newton_bond || b < nlocal) {
|
||||
|
||||
torque[b][0] -= deltb[0];
|
||||
torque[b][1] -= deltb[1];
|
||||
torque[b][2] -= deltb[2];
|
||||
torque[b][0] += deltb[0];
|
||||
torque[b][1] += deltb[1];
|
||||
torque[b][2] += deltb[2];
|
||||
|
||||
}
|
||||
|
||||
@ -935,6 +927,17 @@ void PairOxdnaStk::coeff(int narg, char **arg)
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
atom_style hybrid bond ellipsoid oxdna required
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairOxdnaStk::init_style()
|
||||
{
|
||||
if (!atom->style_match("oxdna")) {
|
||||
error->all(FLERR,"Must use 'atom_style hybrid bond ellipsoid oxdna' with pair style oxdna/stk, oxdna2/stk or oxrna2/stk");
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
neighbor callback to inform pair style of neighbor list to use regular
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
@ -32,6 +32,7 @@ class PairOxdnaStk : public Pair {
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
void init_list(int, class NeighList *);
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
|
||||
@ -19,6 +19,7 @@
|
||||
|
||||
#include "atom.h"
|
||||
#include "atom_vec_ellipsoid.h"
|
||||
#include "atom_vec_oxdna.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
@ -44,26 +45,26 @@ PairOxrna2Stk::PairOxrna2Stk(LAMMPS *lmp) : Pair(lmp)
|
||||
writedata = 1;
|
||||
|
||||
// sequence-specific stacking strength
|
||||
// A:0 C:1 G:2 U:3, 5'- [i][j] -3'
|
||||
// A:0 C:1 G:2 U:3, 3'- [i][j] -5'
|
||||
|
||||
eta_st[0][0] = 0.93851;
|
||||
eta_st[0][1] = 1.12901;
|
||||
eta_st[0][2] = 1.15626;
|
||||
eta_st[0][3] = 0.88850;
|
||||
eta_st[1][0] = 1.12901;
|
||||
eta_st[2][0] = 1.15626;
|
||||
eta_st[3][0] = 0.88850;
|
||||
|
||||
eta_st[1][0] = 0.86331;
|
||||
eta_st[0][1] = 0.86331;
|
||||
eta_st[1][1] = 1.05060;
|
||||
eta_st[1][2] = 0.90982;
|
||||
eta_st[1][3] = 0.83252;
|
||||
eta_st[2][1] = 0.90982;
|
||||
eta_st[3][1] = 0.83252;
|
||||
|
||||
eta_st[2][0] = 0.99407;
|
||||
eta_st[2][1] = 1.14333;
|
||||
eta_st[0][2] = 0.99407;
|
||||
eta_st[1][2] = 1.14333;
|
||||
eta_st[2][2] = 1.06573;
|
||||
eta_st[2][3] = 0.91705;
|
||||
eta_st[3][2] = 0.91705;
|
||||
|
||||
eta_st[3][0] = 0.98804;
|
||||
eta_st[3][1] = 1.04949;
|
||||
eta_st[3][2] = 1.12063;
|
||||
eta_st[0][3] = 0.98804;
|
||||
eta_st[1][3] = 1.04949;
|
||||
eta_st[2][3] = 1.12063;
|
||||
eta_st[3][3] = 0.83818;
|
||||
|
||||
}
|
||||
@ -261,11 +262,13 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
int **bondlist = neighbor->bondlist;
|
||||
int nbondlist = neighbor->nbondlist;
|
||||
|
||||
tagint *id5p = atom->id5p;
|
||||
|
||||
AtomVecEllipsoid *avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
|
||||
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
|
||||
int *ellipsoid = atom->ellipsoid;
|
||||
|
||||
int a,b,in,atype,btype;
|
||||
int a,b,btemp,in,atype,btype;
|
||||
|
||||
double f1,f4t5,f4t6,f4t9,f4t10,f5c1,f5c2;
|
||||
double df1,df4t5,df4t6,df4t9,df4t10,df5c1,df5c2;
|
||||
@ -278,62 +281,43 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
|
||||
for (in = 0; in < nbondlist; in++) {
|
||||
|
||||
a = bondlist[in][1];
|
||||
b = bondlist[in][0];
|
||||
a = bondlist[in][0];
|
||||
b = bondlist[in][1];
|
||||
|
||||
// directionality test: a -> b is 3' -> 5'
|
||||
if(atom->tag[b] != id5p[a]) {
|
||||
|
||||
btemp = b;
|
||||
b = a;
|
||||
a = btemp;
|
||||
|
||||
}
|
||||
|
||||
// a now in 3' direction, b in 5' direction
|
||||
|
||||
qa=bonus[ellipsoid[a]].quat;
|
||||
MathExtra::q_to_exyz(qa,ax,ay,az);
|
||||
qb=bonus[ellipsoid[b]].quat;
|
||||
MathExtra::q_to_exyz(qb,bx,by,bz);
|
||||
|
||||
// vector COM a - 3'-stacking site a
|
||||
ra_cst[0] = d_cst_x_3p*ax[0] + d_cst_y_3p*ay[0];
|
||||
ra_cst[1] = d_cst_x_3p*ax[1] + d_cst_y_3p*ay[1];
|
||||
ra_cst[2] = d_cst_x_3p*ax[2] + d_cst_y_3p*ay[2];
|
||||
// vector COM a - 5'-stacking site a
|
||||
ra_cst[0] = d_cst_x_5p*ax[0] + d_cst_y_5p*ay[0];
|
||||
ra_cst[1] = d_cst_x_5p*ax[1] + d_cst_y_5p*ay[1];
|
||||
ra_cst[2] = d_cst_x_5p*ax[2] + d_cst_y_5p*ay[2];
|
||||
|
||||
// vector COM b - 5'-stacking site b
|
||||
rb_cst[0] = d_cst_x_5p*bx[0] + d_cst_y_5p*by[0];
|
||||
rb_cst[1] = d_cst_x_5p*bx[1] + d_cst_y_5p*by[1];
|
||||
rb_cst[2] = d_cst_x_5p*bx[2] + d_cst_y_5p*by[2];
|
||||
// vector COM b - 3'-stacking site b
|
||||
rb_cst[0] = d_cst_x_3p*bx[0] + d_cst_y_3p*by[0];
|
||||
rb_cst[1] = d_cst_x_3p*bx[1] + d_cst_y_3p*by[1];
|
||||
rb_cst[2] = d_cst_x_3p*bx[2] + d_cst_y_3p*by[2];
|
||||
|
||||
// vector 5'-stacking site b to 3'-stacking site a
|
||||
delr_st[0] = x[a][0] + ra_cst[0] - x[b][0] - rb_cst[0];
|
||||
delr_st[1] = x[a][1] + ra_cst[1] - x[b][1] - rb_cst[1];
|
||||
delr_st[2] = x[a][2] + ra_cst[2] - x[b][2] - rb_cst[2];
|
||||
// vector 5'-stacking site a to 3'-stacking site b
|
||||
delr_st[0] = x[b][0] + rb_cst[0] - x[a][0] - ra_cst[0];
|
||||
delr_st[1] = x[b][1] + rb_cst[1] - x[a][1] - ra_cst[1];
|
||||
delr_st[2] = x[b][2] + rb_cst[2] - x[a][2] - ra_cst[2];
|
||||
|
||||
// test for directionality of vector b to a
|
||||
tptofp = MFOxdna::is_3pto5p(delr_st,bz);
|
||||
|
||||
// if b to a is 5' to 3' we need to swap roles of a and b
|
||||
if (tptofp == -1) {
|
||||
|
||||
std::swap(a,b);
|
||||
std::swap(ax,bx);
|
||||
std::swap(ay,by);
|
||||
std::swap(az,bz);
|
||||
|
||||
}
|
||||
|
||||
// a now in 5' direction, b in 3' direction
|
||||
atype = type[a];
|
||||
btype = type[b];
|
||||
|
||||
// calculate again
|
||||
// vector COM a - 3'-stacking site a
|
||||
ra_cst[0] = d_cst_x_3p*ax[0] + d_cst_y_3p*ay[0];
|
||||
ra_cst[1] = d_cst_x_3p*ax[1] + d_cst_y_3p*ay[1];
|
||||
ra_cst[2] = d_cst_x_3p*ax[2] + d_cst_y_3p*ay[2];
|
||||
|
||||
// vector COM b - 5'-stacking site b
|
||||
rb_cst[0] = d_cst_x_5p*bx[0] + d_cst_y_5p*by[0];
|
||||
rb_cst[1] = d_cst_x_5p*bx[1] + d_cst_y_5p*by[1];
|
||||
rb_cst[2] = d_cst_x_5p*bx[2] + d_cst_y_5p*by[2];
|
||||
|
||||
// vector 5'-stacking site b to 3'-stacking site a
|
||||
delr_st[0] = x[a][0] + ra_cst[0] - x[b][0] - rb_cst[0];
|
||||
delr_st[1] = x[a][1] + ra_cst[1] - x[b][1] - rb_cst[1];
|
||||
delr_st[2] = x[a][2] + ra_cst[2] - x[b][2] - rb_cst[2];
|
||||
|
||||
rsq_st = delr_st[0]*delr_st[0] + delr_st[1]*delr_st[1] + delr_st[2]*delr_st[2];
|
||||
r_st = sqrt(rsq_st);
|
||||
rinv_st = 1.0/r_st;
|
||||
@ -352,10 +336,10 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
rb_cs[1] = d_cs_x*bx[1] + d_cs_z*bz[1];
|
||||
rb_cs[2] = d_cs_x*bx[2] + d_cs_z*bz[2];
|
||||
|
||||
// vector backbone site b to a
|
||||
delr_ss[0] = (x[a][0] + ra_cs[0] - x[b][0] - rb_cs[0]);
|
||||
delr_ss[1] = (x[a][1] + ra_cs[1] - x[b][1] - rb_cs[1]);
|
||||
delr_ss[2] = (x[a][2] + ra_cs[2] - x[b][2] - rb_cs[2]);
|
||||
// vector backbone site a to b
|
||||
delr_ss[0] = (x[b][0] + rb_cs[0] - x[a][0] - ra_cs[0]);
|
||||
delr_ss[1] = (x[b][1] + rb_cs[1] - x[a][1] - ra_cs[1]);
|
||||
delr_ss[2] = (x[b][2] + rb_cs[2] - x[a][2] - ra_cs[2]);
|
||||
|
||||
rsq_ss = delr_ss[0]*delr_ss[0] + delr_ss[1]*delr_ss[1] + delr_ss[2]*delr_ss[2];
|
||||
r_ss = sqrt(rsq_ss);
|
||||
@ -373,7 +357,7 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
if (f1) {
|
||||
|
||||
// theta5 angle and correction
|
||||
cost5p = MathExtra::dot3(delr_st_norm,az);
|
||||
cost5p = MathExtra::dot3(delr_st_norm,bz);
|
||||
if (cost5p > 1.0) cost5p = 1.0;
|
||||
if (cost5p < -1.0) cost5p = -1.0;
|
||||
theta5p = acos(cost5p);
|
||||
@ -384,18 +368,18 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
// early rejection criterium
|
||||
if (f4t5) {
|
||||
|
||||
cost6p = MathExtra::dot3(delr_st_norm,bz);
|
||||
cost6p = MathExtra::dot3(delr_st_norm,az);
|
||||
if (cost6p > 1.0) cost6p = 1.0;
|
||||
if (cost6p < -1.0) cost6p = -1.0;
|
||||
theta6p = acos(cost6p);
|
||||
|
||||
aux3p[0] = d3p_x * ax[0] + d3p_y * ay[0] + d3p_z * az[0];
|
||||
aux3p[1] = d3p_x * ax[1] + d3p_y * ay[1] + d3p_z * az[1];
|
||||
aux3p[2] = d3p_x * ax[2] + d3p_y * ay[2] + d3p_z * az[2];
|
||||
aux5p[0] = d5p_x * ax[0] + d5p_y * ay[0] + d5p_z * az[0];
|
||||
aux5p[1] = d5p_x * ax[1] + d5p_y * ay[1] + d5p_z * az[1];
|
||||
aux5p[2] = d5p_x * ax[2] + d5p_y * ay[2] + d5p_z * az[2];
|
||||
|
||||
aux5p[0] = d5p_x * bx[0] + d5p_y * by[0] + d5p_z * bz[0];
|
||||
aux5p[1] = d5p_x * bx[1] + d5p_y * by[1] + d5p_z * bz[1];
|
||||
aux5p[2] = d5p_x * bx[2] + d5p_y * by[2] + d5p_z * bz[2];
|
||||
aux3p[0] = d3p_x * bx[0] + d3p_y * by[0] + d3p_z * bz[0];
|
||||
aux3p[1] = d3p_x * bx[1] + d3p_y * by[1] + d3p_z * bz[1];
|
||||
aux3p[2] = d3p_x * bx[2] + d3p_y * by[2] + d3p_z * bz[2];
|
||||
|
||||
cost9 = MathExtra::dot3(delr_ss_norm,aux3p);
|
||||
if (cost9 > 1.0) cost9 = 1.0;
|
||||
@ -407,11 +391,11 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
if (cost10 < -1.0) cost10 = -1.0;
|
||||
theta10 = acos(cost10);
|
||||
|
||||
cosphi1 = MathExtra::dot3(delr_ss_norm,ay);
|
||||
cosphi1 = MathExtra::dot3(delr_ss_norm,by);
|
||||
if (cosphi1 > 1.0) cosphi1 = 1.0;
|
||||
if (cosphi1 < -1.0) cosphi1 = -1.0;
|
||||
|
||||
cosphi2 = MathExtra::dot3(delr_ss_norm,by);
|
||||
cosphi2 = MathExtra::dot3(delr_ss_norm,ay);
|
||||
if (cosphi2 > 1.0) cosphi2 = 1.0;
|
||||
if (cosphi2 < -1.0) cosphi2 = -1.0;
|
||||
|
||||
@ -425,10 +409,10 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
b_st10[atype][btype], dtheta_st10_c[atype][btype]);
|
||||
|
||||
f5c1 = F5(-cosphi1, a_st1[atype][btype], -cosphi_st1_ast[atype][btype], b_st1[atype][btype],
|
||||
cosphi_st1_c[atype][btype]);
|
||||
-cosphi_st1_c[atype][btype]);
|
||||
|
||||
f5c2 = F5(-cosphi2, a_st2[atype][btype], -cosphi_st2_ast[atype][btype], b_st2[atype][btype],
|
||||
cosphi_st2_c[atype][btype]);
|
||||
-cosphi_st2_c[atype][btype]);
|
||||
|
||||
|
||||
evdwl = f1 * f4t5 * f4t6 * f4t9 * f4t10 * f5c1 * f5c2;
|
||||
@ -453,10 +437,10 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
b_st10[atype][btype], dtheta_st10_c[atype][btype])/sin(theta10);
|
||||
|
||||
df5c1 = DF5(-cosphi1, a_st1[atype][btype], -cosphi_st1_ast[atype][btype], b_st1[atype][btype],
|
||||
cosphi_st1_c[atype][btype]);
|
||||
-cosphi_st1_c[atype][btype]);
|
||||
|
||||
df5c2 = DF5(-cosphi2, a_st2[atype][btype], -cosphi_st2_ast[atype][btype], b_st2[atype][btype],
|
||||
cosphi_st2_c[atype][btype]);
|
||||
-cosphi_st2_c[atype][btype]);
|
||||
|
||||
|
||||
// force, torque and virial contribution for forces between stacking sites
|
||||
@ -489,9 +473,9 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
finc = -f1 * df4t5 * f4t6 * f4t9 * f4t10 * f5c1 * f5c2 * rinv_st;
|
||||
fpair += finc;
|
||||
|
||||
delf[0] += (delr_st_norm[0]*cost5p - az[0]) * finc;
|
||||
delf[1] += (delr_st_norm[1]*cost5p - az[1]) * finc;
|
||||
delf[2] += (delr_st_norm[2]*cost5p - az[2]) * finc;
|
||||
delf[0] += (delr_st_norm[0]*cost5p - bz[0]) * finc;
|
||||
delf[1] += (delr_st_norm[1]*cost5p - bz[1]) * finc;
|
||||
delf[2] += (delr_st_norm[2]*cost5p - bz[2]) * finc;
|
||||
|
||||
}
|
||||
|
||||
@ -501,28 +485,27 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
finc = -f1 * f4t5 * df4t6 * f4t9 * f4t10 * f5c1 * f5c2 * rinv_st;
|
||||
fpair += finc;
|
||||
|
||||
delf[0] += (delr_st_norm[0]*cost6p - bz[0]) * finc;
|
||||
delf[1] += (delr_st_norm[1]*cost6p - bz[1]) * finc;
|
||||
delf[2] += (delr_st_norm[2]*cost6p - bz[2]) * finc;
|
||||
delf[0] += (delr_st_norm[0]*cost6p - az[0]) * finc;
|
||||
delf[1] += (delr_st_norm[1]*cost6p - az[1]) * finc;
|
||||
delf[2] += (delr_st_norm[2]*cost6p - az[2]) * finc;
|
||||
|
||||
}
|
||||
|
||||
// increment forces and torques
|
||||
|
||||
if (newton_bond || a < nlocal) {
|
||||
|
||||
f[a][0] += delf[0];
|
||||
f[a][1] += delf[1];
|
||||
f[a][2] += delf[2];
|
||||
f[a][0] -= delf[0];
|
||||
f[a][1] -= delf[1];
|
||||
f[a][2] -= delf[2];
|
||||
|
||||
MathExtra::cross3(ra_cst,delf,delta);
|
||||
|
||||
}
|
||||
if (newton_bond || b < nlocal) {
|
||||
|
||||
f[b][0] -= delf[0];
|
||||
f[b][1] -= delf[1];
|
||||
f[b][2] -= delf[2];
|
||||
f[b][0] += delf[0];
|
||||
f[b][1] += delf[1];
|
||||
f[b][2] += delf[2];
|
||||
|
||||
MathExtra::cross3(rb_cst,delf,deltb);
|
||||
|
||||
@ -530,16 +513,16 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
|
||||
if (newton_bond || a < nlocal) {
|
||||
|
||||
torque[a][0] += delta[0];
|
||||
torque[a][1] += delta[1];
|
||||
torque[a][2] += delta[2];
|
||||
torque[a][0] -= delta[0];
|
||||
torque[a][1] -= delta[1];
|
||||
torque[a][2] -= delta[2];
|
||||
|
||||
}
|
||||
if (newton_bond || b < nlocal) {
|
||||
|
||||
torque[b][0] -= deltb[0];
|
||||
torque[b][1] -= deltb[1];
|
||||
torque[b][2] -= deltb[2];
|
||||
torque[b][0] += deltb[0];
|
||||
torque[b][1] += deltb[1];
|
||||
torque[b][2] += deltb[2];
|
||||
|
||||
}
|
||||
|
||||
@ -547,8 +530,8 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
// NOTE: The virial is calculated on the 'molecular' basis.
|
||||
// (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986))
|
||||
|
||||
if (evflag) ev_tally_xyz(a,b,nlocal,newton_bond,evdwl,
|
||||
delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
|
||||
if (evflag) ev_tally_xyz(b,a,nlocal,newton_bond,evdwl,
|
||||
delf[0],delf[1],delf[2],x[b][0]-x[a][0],x[b][1]-x[a][1],x[b][2]-x[a][2]);
|
||||
|
||||
// force, torque and virial contribution for forces between backbone sites
|
||||
|
||||
@ -596,9 +579,9 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
finc = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * df5c1 * f5c2 * rinv_ss;
|
||||
fpair += finc;
|
||||
|
||||
delf[0] += (delr_ss_norm[0]*cosphi1 - ay[0]) * finc;
|
||||
delf[1] += (delr_ss_norm[1]*cosphi1 - ay[1]) * finc;
|
||||
delf[2] += (delr_ss_norm[2]*cosphi1 - ay[2]) * finc;
|
||||
delf[0] += (delr_ss_norm[0]*cosphi1 - by[0]) * finc;
|
||||
delf[1] += (delr_ss_norm[1]*cosphi1 - by[1]) * finc;
|
||||
delf[2] += (delr_ss_norm[2]*cosphi1 - by[2]) * finc;
|
||||
|
||||
}
|
||||
|
||||
@ -608,28 +591,27 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
finc = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * f5c1 * df5c2 * rinv_ss;
|
||||
fpair += finc;
|
||||
|
||||
delf[0] += (delr_ss_norm[0]*cosphi2 - by[0]) * finc;
|
||||
delf[1] += (delr_ss_norm[1]*cosphi2 - by[1]) * finc;
|
||||
delf[2] += (delr_ss_norm[2]*cosphi2 - by[2]) * finc;
|
||||
delf[0] += (delr_ss_norm[0]*cosphi2 - ay[0]) * finc;
|
||||
delf[1] += (delr_ss_norm[1]*cosphi2 - ay[1]) * finc;
|
||||
delf[2] += (delr_ss_norm[2]*cosphi2 - ay[2]) * finc;
|
||||
|
||||
}
|
||||
|
||||
// increment forces and torques
|
||||
|
||||
if (newton_bond || a < nlocal) {
|
||||
|
||||
f[a][0] += delf[0];
|
||||
f[a][1] += delf[1];
|
||||
f[a][2] += delf[2];
|
||||
f[a][0] -= delf[0];
|
||||
f[a][1] -= delf[1];
|
||||
f[a][2] -= delf[2];
|
||||
|
||||
MathExtra::cross3(ra_cs,delf,delta);
|
||||
|
||||
}
|
||||
if (newton_bond || b < nlocal) {
|
||||
|
||||
f[b][0] -= delf[0];
|
||||
f[b][1] -= delf[1];
|
||||
f[b][2] -= delf[2];
|
||||
f[b][0] += delf[0];
|
||||
f[b][1] += delf[1];
|
||||
f[b][2] += delf[2];
|
||||
|
||||
MathExtra::cross3(rb_cs,delf,deltb);
|
||||
|
||||
@ -637,22 +619,22 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
|
||||
if (newton_bond || a < nlocal) {
|
||||
|
||||
torque[a][0] += delta[0];
|
||||
torque[a][1] += delta[1];
|
||||
torque[a][2] += delta[2];
|
||||
torque[a][0] -= delta[0];
|
||||
torque[a][1] -= delta[1];
|
||||
torque[a][2] -= delta[2];
|
||||
|
||||
}
|
||||
if (newton_bond || b < nlocal) {
|
||||
|
||||
torque[b][0] -= deltb[0];
|
||||
torque[b][1] -= deltb[1];
|
||||
torque[b][2] -= deltb[2];
|
||||
torque[b][0] += deltb[0];
|
||||
torque[b][1] += deltb[1];
|
||||
torque[b][2] += deltb[2];
|
||||
|
||||
}
|
||||
|
||||
// increment virial only
|
||||
if (evflag) ev_tally_xyz(a,b,nlocal,newton_bond,0.0,
|
||||
delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
|
||||
if (evflag) ev_tally_xyz(b,a,nlocal,newton_bond,0.0,
|
||||
delf[0],delf[1],delf[2],x[b][0]-x[a][0],x[b][1]-x[a][1],x[b][2]-x[a][2]);
|
||||
|
||||
// pure torques not expressible as r x f
|
||||
|
||||
@ -667,11 +649,11 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
if (theta5p) {
|
||||
|
||||
tpair = -f1 * df4t5 * f4t6 * f4t9 * f4t10 * f5c1 * f5c2;
|
||||
MathExtra::cross3(delr_st_norm,az,t5pdir);
|
||||
MathExtra::cross3(delr_st_norm,bz,t5pdir);
|
||||
|
||||
delta[0] += t5pdir[0] * tpair;
|
||||
delta[1] += t5pdir[1] * tpair;
|
||||
delta[2] += t5pdir[2] * tpair;
|
||||
deltb[0] += t5pdir[0] * tpair;
|
||||
deltb[1] += t5pdir[1] * tpair;
|
||||
deltb[2] += t5pdir[2] * tpair;
|
||||
|
||||
}
|
||||
|
||||
@ -679,11 +661,11 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
if (theta6p) {
|
||||
|
||||
tpair = -f1 * f4t5 * df4t6 * f4t9 * f4t10 * f5c1 * f5c2;
|
||||
MathExtra::cross3(delr_st_norm,bz,t6pdir);
|
||||
MathExtra::cross3(delr_st_norm,az,t6pdir);
|
||||
|
||||
deltb[0] -= t6pdir[0] * tpair;
|
||||
deltb[1] -= t6pdir[1] * tpair;
|
||||
deltb[2] -= t6pdir[2] * tpair;
|
||||
delta[0] -= t6pdir[0] * tpair;
|
||||
delta[1] -= t6pdir[1] * tpair;
|
||||
delta[2] -= t6pdir[2] * tpair;
|
||||
|
||||
}
|
||||
|
||||
@ -693,9 +675,9 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
tpair = -f1 * f4t5 * f4t6 * df4t9 * f4t10 * f5c1 * f5c2;
|
||||
MathExtra::cross3(delr_ss_norm,aux3p,t9dir);
|
||||
|
||||
delta[0] += t9dir[0] * tpair;
|
||||
delta[1] += t9dir[1] * tpair;
|
||||
delta[2] += t9dir[2] * tpair;
|
||||
deltb[0] += t9dir[0] * tpair;
|
||||
deltb[1] += t9dir[1] * tpair;
|
||||
deltb[2] += t9dir[2] * tpair;
|
||||
|
||||
}
|
||||
|
||||
@ -705,9 +687,9 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
tpair = -f1 * f4t5 * f4t6 * f4t9 * df4t10 * f5c1 * f5c2;
|
||||
MathExtra::cross3(delr_ss_norm,aux5p,t10dir);
|
||||
|
||||
deltb[0] -= t10dir[0] * tpair;
|
||||
deltb[1] -= t10dir[1] * tpair;
|
||||
deltb[2] -= t10dir[2] * tpair;
|
||||
delta[0] -= t10dir[0] * tpair;
|
||||
delta[1] -= t10dir[1] * tpair;
|
||||
delta[2] -= t10dir[2] * tpair;
|
||||
|
||||
}
|
||||
|
||||
@ -715,11 +697,11 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
if (cosphi1) {
|
||||
|
||||
tpair = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * df5c1 * f5c2;
|
||||
MathExtra::cross3(delr_ss_norm,ay,cosphi1dir);
|
||||
MathExtra::cross3(delr_ss_norm,by,cosphi1dir);
|
||||
|
||||
delta[0] += cosphi1dir[0] * tpair;
|
||||
delta[1] += cosphi1dir[1] * tpair;
|
||||
delta[2] += cosphi1dir[2] * tpair;
|
||||
deltb[0] += cosphi1dir[0] * tpair;
|
||||
deltb[1] += cosphi1dir[1] * tpair;
|
||||
deltb[2] += cosphi1dir[2] * tpair;
|
||||
|
||||
}
|
||||
|
||||
@ -727,27 +709,27 @@ void PairOxrna2Stk::compute(int eflag, int vflag)
|
||||
if (cosphi2) {
|
||||
|
||||
tpair = -f1 * f4t5 * f4t6 * f4t9 * f4t10 * f5c1 * df5c2;
|
||||
MathExtra::cross3(delr_ss_norm,by,cosphi2dir);
|
||||
MathExtra::cross3(delr_ss_norm,ay,cosphi2dir);
|
||||
|
||||
deltb[0] -= cosphi2dir[0] * tpair;
|
||||
deltb[1] -= cosphi2dir[1] * tpair;
|
||||
deltb[2] -= cosphi2dir[2] * tpair;
|
||||
delta[0] -= cosphi2dir[0] * tpair;
|
||||
delta[1] -= cosphi2dir[1] * tpair;
|
||||
delta[2] -= cosphi2dir[2] * tpair;
|
||||
|
||||
}
|
||||
|
||||
// increment torques
|
||||
if (newton_bond || a < nlocal) {
|
||||
|
||||
torque[a][0] += delta[0];
|
||||
torque[a][1] += delta[1];
|
||||
torque[a][2] += delta[2];
|
||||
torque[a][0] -= delta[0];
|
||||
torque[a][1] -= delta[1];
|
||||
torque[a][2] -= delta[2];
|
||||
|
||||
}
|
||||
if (newton_bond || b < nlocal) {
|
||||
|
||||
torque[b][0] -= deltb[0];
|
||||
torque[b][1] -= deltb[1];
|
||||
torque[b][2] -= deltb[2];
|
||||
torque[b][0] += deltb[0];
|
||||
torque[b][1] += deltb[1];
|
||||
torque[b][2] += deltb[2];
|
||||
|
||||
}
|
||||
|
||||
@ -1027,6 +1009,17 @@ void PairOxrna2Stk::coeff(int narg, char **arg)
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
atom_style hybrid bond ellipsoid oxdna required
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairOxrna2Stk::init_style()
|
||||
{
|
||||
if (!atom->style_match("oxdna")) {
|
||||
error->all(FLERR,"Must use 'atom_style hybrid bond ellipsoid oxdna' with pair style oxdna/stk, oxdna2/stk or oxrna2/stk");
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
neighbor callback to inform pair style of neighbor list to use regular
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
@ -31,6 +31,7 @@ class PairOxrna2Stk : public Pair {
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
void init_list(int, class NeighList *);
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
|
||||
47
src/atom.cpp
47
src/atom.cpp
@ -161,7 +161,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
|
||||
|
||||
sp = fm = fm_long = nullptr;
|
||||
|
||||
// EFF and AWPMD packages
|
||||
// USER-EFF and USER-AWPMD packages
|
||||
|
||||
spin = nullptr;
|
||||
eradius = ervel = erforce = nullptr;
|
||||
@ -169,23 +169,27 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
|
||||
cs = csforce = vforce = nullptr;
|
||||
etag = nullptr;
|
||||
|
||||
// DPD-REACT package
|
||||
// USER-CGDNA package
|
||||
|
||||
id5p = nullptr;
|
||||
|
||||
// USER-DPD package
|
||||
|
||||
uCond = uMech = uChem = uCG = uCGnew = nullptr;
|
||||
duChem = dpdTheta = nullptr;
|
||||
|
||||
// MESO package
|
||||
// USER-MESO package
|
||||
|
||||
cc = cc_flux = nullptr;
|
||||
edpd_temp = edpd_flux = edpd_cv = nullptr;
|
||||
|
||||
// MESONT package
|
||||
// USER-MESONT package
|
||||
|
||||
length = nullptr;
|
||||
buckling = nullptr;
|
||||
bond_nt = nullptr;
|
||||
|
||||
// MACHDYN package
|
||||
// USER-SMD package
|
||||
|
||||
contact_radius = nullptr;
|
||||
smd_data_9 = nullptr;
|
||||
@ -194,12 +198,12 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
|
||||
eff_plastic_strain_rate = nullptr;
|
||||
damage = nullptr;
|
||||
|
||||
// SPH package
|
||||
// USER-SPH package
|
||||
|
||||
rho = drho = esph = desph = cv = nullptr;
|
||||
vest = nullptr;
|
||||
|
||||
// DIELECTRIC package
|
||||
// USER-DIELECTRIC package
|
||||
|
||||
area = ed = em = epsilon = curvature = q_unscaled = nullptr;
|
||||
|
||||
@ -457,14 +461,14 @@ void Atom::peratom_create()
|
||||
add_peratom("fm",&fm,DOUBLE,3,1);
|
||||
add_peratom("fm_long",&fm_long,DOUBLE,3,1);
|
||||
|
||||
// EFF package
|
||||
// USER-EFF package
|
||||
|
||||
add_peratom("spin",&spin,INT,0);
|
||||
add_peratom("eradius",&eradius,DOUBLE,0);
|
||||
add_peratom("ervel",&ervel,DOUBLE,0);
|
||||
add_peratom("erforce",&erforce,DOUBLE,0,1); // set per-thread flag
|
||||
|
||||
// AWPMD package
|
||||
// USER-AWPMD package
|
||||
|
||||
add_peratom("cs",&cs,DOUBLE,2);
|
||||
add_peratom("csforce",&csforce,DOUBLE,2);
|
||||
@ -472,7 +476,11 @@ void Atom::peratom_create()
|
||||
add_peratom("ervelforce",&ervelforce,DOUBLE,0);
|
||||
add_peratom("etag",&etag,INT,0);
|
||||
|
||||
// DPD-REACT package
|
||||
// USER-CGDNA package
|
||||
|
||||
add_peratom("id5p",&id5p,tagintsize,0);
|
||||
|
||||
// USER-DPD package
|
||||
|
||||
add_peratom("dpdTheta",&dpdTheta,DOUBLE,0);
|
||||
add_peratom("uCond",&uCond,DOUBLE,0);
|
||||
@ -482,7 +490,7 @@ void Atom::peratom_create()
|
||||
add_peratom("uCGnew",&uCGnew,DOUBLE,0);
|
||||
add_peratom("duChem",&duChem,DOUBLE,0);
|
||||
|
||||
// MESO package
|
||||
// USER-MESO package
|
||||
|
||||
add_peratom("edpd_cv",&edpd_cv,DOUBLE,0);
|
||||
add_peratom("edpd_temp",&edpd_temp,DOUBLE,0);
|
||||
@ -491,13 +499,13 @@ void Atom::peratom_create()
|
||||
add_peratom("cc",&cc,DOUBLE,1);
|
||||
add_peratom("cc_flux",&cc_flux,DOUBLE,1,1); // set per-thread flag
|
||||
|
||||
// MESONT package
|
||||
// USER-MESONT package
|
||||
|
||||
add_peratom("length",&length,DOUBLE,0);
|
||||
add_peratom("buckling",&buckling,INT,0);
|
||||
add_peratom("bond_nt",&bond_nt,tagintsize,2);
|
||||
|
||||
// SPH package
|
||||
// USER-SPH package
|
||||
|
||||
add_peratom("rho",&rho,DOUBLE,0);
|
||||
add_peratom("drho",&drho,DOUBLE,0,1); // set per-thread flag
|
||||
@ -506,7 +514,7 @@ void Atom::peratom_create()
|
||||
add_peratom("vest",&vest,DOUBLE,3);
|
||||
add_peratom("cv",&cv,DOUBLE,0);
|
||||
|
||||
// MACHDYN package
|
||||
// USER-SMD package
|
||||
|
||||
add_peratom("contact_radius",&contact_radius,DOUBLE,0);
|
||||
add_peratom("smd_data_9",&smd_data_9,DOUBLE,1);
|
||||
@ -515,7 +523,7 @@ void Atom::peratom_create()
|
||||
add_peratom("eff_plastic_strain_rate",&eff_plastic_strain_rate,DOUBLE,0);
|
||||
add_peratom("damage",&damage,DOUBLE,0);
|
||||
|
||||
// DIELECTRIC package
|
||||
// USER-DIELECTRIC package
|
||||
|
||||
add_peratom("area",&area,DOUBLE,0);
|
||||
add_peratom("ed",&ed,DOUBLE,0);
|
||||
@ -1292,6 +1300,7 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
buf = next + 1;
|
||||
}
|
||||
}
|
||||
@ -2646,7 +2655,7 @@ void *Atom::extract(const char *name)
|
||||
if (strcmp(name,"cv") == 0) return (void *) cv;
|
||||
if (strcmp(name,"vest") == 0) return (void *) vest;
|
||||
|
||||
// MESONT package
|
||||
// USER-MESONT package
|
||||
if (strcmp(name,"length") == 0) return (void *) length;
|
||||
if (strcmp(name,"buckling") == 0) return (void *) buckling;
|
||||
if (strcmp(name,"bond_nt") == 0) return (void *) bond_nt;
|
||||
@ -2663,7 +2672,7 @@ void *Atom::extract(const char *name)
|
||||
if (strcmp(name,"dpdTheta") == 0) return (void *) dpdTheta;
|
||||
if (strcmp(name,"edpd_temp") == 0) return (void *) edpd_temp;
|
||||
|
||||
// DIELECTRIC
|
||||
// USER-DIELECTRIC
|
||||
if (strcmp(name,"area") == 0) return (void *) area;
|
||||
if (strcmp(name,"ed") == 0) return (void *) ed;
|
||||
if (strcmp(name,"em") == 0) return (void *) em;
|
||||
@ -2739,7 +2748,7 @@ int Atom::extract_datatype(const char *name)
|
||||
if (strcmp(name,"cv") == 0) return LAMMPS_DOUBLE;
|
||||
if (strcmp(name,"vest") == 0) return LAMMPS_DOUBLE_2D;
|
||||
|
||||
// MESONT package
|
||||
// USER-MESONT package
|
||||
if (strcmp(name,"length") == 0) return LAMMPS_DOUBLE;
|
||||
if (strcmp(name,"buckling") == 0) return LAMMPS_INT;
|
||||
if (strcmp(name,"bond_nt") == 0) return LAMMPS_TAGINT_2D;
|
||||
@ -2754,7 +2763,7 @@ int Atom::extract_datatype(const char *name)
|
||||
if (strcmp(name,"dpdTheta") == 0) return LAMMPS_DOUBLE;
|
||||
if (strcmp(name,"edpd_temp") == 0) return LAMMPS_DOUBLE;
|
||||
|
||||
// DIELECTRIC
|
||||
// USER-DIELECTRIC
|
||||
if (strcmp(name,"area") == 0) return LAMMPS_DOUBLE;
|
||||
if (strcmp(name,"ed") == 0) return LAMMPS_DOUBLE;
|
||||
if (strcmp(name,"em") == 0) return LAMMPS_DOUBLE;
|
||||
|
||||
20
src/atom.h
20
src/atom.h
@ -114,7 +114,7 @@ class Atom : protected Pointers {
|
||||
|
||||
double **sp, **fm, **fm_long;
|
||||
|
||||
// EFF and AWPMD packages
|
||||
// USER_EFF and USER-AWPMD packages
|
||||
|
||||
int *spin;
|
||||
double *eradius, *ervel, *erforce;
|
||||
@ -122,14 +122,18 @@ class Atom : protected Pointers {
|
||||
double **cs, **csforce, **vforce;
|
||||
int *etag;
|
||||
|
||||
// DPD-REACT package
|
||||
// USER-CGDNA package
|
||||
|
||||
tagint *id5p;
|
||||
|
||||
// USER-DPD package
|
||||
|
||||
double *uCond, *uMech, *uChem, *uCGnew, *uCG;
|
||||
double *duChem;
|
||||
double *dpdTheta;
|
||||
int nspecies_dpd;
|
||||
|
||||
// MESO package
|
||||
// USER-MESO package
|
||||
|
||||
double **cc, **cc_flux; // cc = chemical concentration
|
||||
double *edpd_temp, *edpd_flux; // temperature and heat flux
|
||||
@ -137,13 +141,13 @@ class Atom : protected Pointers {
|
||||
double *edpd_cv; // heat capacity
|
||||
int cc_species;
|
||||
|
||||
// MESONT package
|
||||
// USER-MESONT package
|
||||
|
||||
double *length;
|
||||
int *buckling;
|
||||
tagint **bond_nt;
|
||||
|
||||
// MACHDYN package
|
||||
// USER-SMD package
|
||||
|
||||
double *contact_radius;
|
||||
double **smd_data_9;
|
||||
@ -152,12 +156,12 @@ class Atom : protected Pointers {
|
||||
double *eff_plastic_strain_rate;
|
||||
double *damage;
|
||||
|
||||
// SPH package
|
||||
// USER-SPH package
|
||||
|
||||
double *rho, *drho, *esph, *desph, *cv;
|
||||
double **vest;
|
||||
|
||||
// DIELECTRIC package
|
||||
// USER-DIELECTRIC package
|
||||
|
||||
double *area,*ed,*em,*epsilon,*curvature,*q_unscaled;
|
||||
|
||||
@ -187,7 +191,7 @@ class Atom : protected Pointers {
|
||||
|
||||
int sp_flag;
|
||||
|
||||
// MACHDYN package
|
||||
// USER-SMD package
|
||||
|
||||
int x0_flag;
|
||||
int smd_flag, damage_flag;
|
||||
|
||||
@ -129,6 +129,8 @@ class AtomVec : protected Pointers {
|
||||
virtual void data_atom_bonus(int, char **) {}
|
||||
virtual void data_body(int, int, int, int *, double *) {}
|
||||
|
||||
virtual void data_bonds_post(int, char *, tagint) {}
|
||||
|
||||
virtual void pack_data(double **);
|
||||
virtual void write_data(FILE *, int, double **);
|
||||
virtual void pack_data_pre(int) {}
|
||||
|
||||
@ -71,6 +71,7 @@ ReadData::ReadData(LAMMPS *lmp) : Command(lmp)
|
||||
keyword = new char[MAXLINE];
|
||||
style = new char[MAXLINE];
|
||||
buffer = new char[CHUNK*MAXLINE];
|
||||
buffer_post = new char[CHUNK*MAXLINE];
|
||||
ncoeffarg = maxcoeffarg = 0;
|
||||
coeffarg = nullptr;
|
||||
fp = nullptr;
|
||||
@ -86,6 +87,11 @@ ReadData::ReadData(LAMMPS *lmp) : Command(lmp)
|
||||
avec_tri = (AtomVecTri *) atom->style_match("tri");
|
||||
nbodies = 0;
|
||||
avec_body = (AtomVecBody *) atom->style_match("body");
|
||||
|
||||
if (atom->style_match("oxdna"))
|
||||
avec = (AtomVec *) atom->style_match("oxdna");
|
||||
else
|
||||
avec = atom->avec;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -96,6 +102,7 @@ ReadData::~ReadData()
|
||||
delete [] keyword;
|
||||
delete [] style;
|
||||
delete [] buffer;
|
||||
delete [] buffer_post;
|
||||
memory->sfree(coeffarg);
|
||||
|
||||
for (int i = 0; i < nfix; i++) {
|
||||
@ -1333,7 +1340,9 @@ void ReadData::bonds(int firstpass)
|
||||
nchunk = MIN(nbonds-nread,CHUNK);
|
||||
eof = utils::read_lines_from_file(fp,nchunk,MAXLINE,buffer,me,world);
|
||||
if (eof) error->all(FLERR,"Unexpected end of data file");
|
||||
strcpy(buffer_post,buffer);
|
||||
atom->data_bonds(nchunk,buffer,count,id_offset,boffset);
|
||||
if (!firstpass) avec->data_bonds_post(nchunk,buffer_post,id_offset);
|
||||
nread += nchunk;
|
||||
}
|
||||
|
||||
|
||||
@ -32,7 +32,7 @@ class ReadData : public Command {
|
||||
|
||||
private:
|
||||
int me, compressed;
|
||||
char *line, *keyword, *buffer, *style;
|
||||
char *line, *keyword, *buffer, *buffer_post, *style;
|
||||
FILE *fp;
|
||||
char **coeffarg;
|
||||
int ncoeffarg, maxcoeffarg;
|
||||
@ -54,6 +54,7 @@ class ReadData : public Command {
|
||||
class AtomVecTri *avec_tri;
|
||||
bigint nbodies;
|
||||
class AtomVecBody *avec_body;
|
||||
class AtomVec *avec;
|
||||
|
||||
// box info
|
||||
|
||||
|
||||
Reference in New Issue
Block a user