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changed rstfile names, style names, and description about FF for SPICA

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yskmiyazaki
2022-07-08 16:54:01 +09:00
parent 7d06ee9aa7
commit 796bc28f94
11 changed files with 118 additions and 90 deletions
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2
doc/src/Commands_bond.rst
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@ -92,7 +92,7 @@ OPT.
* :doc:`harmonic (iko) <angle_harmonic>`
* :doc:`mm3 <angle_mm3>`
* :doc:`quartic (o) <angle_quartic>`
* :doc:`sdk (o) <angle_sdk>`
* :doc:`spica (o) <angle_spica>`
* :doc:`table (o) <angle_table>`
.. _dihedral:

6
doc/src/Commands_pair.rst
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@ -179,9 +179,9 @@ OPT.
* :doc:`lj/long/tip4p/long (o) <pair_lj_long>`
* :doc:`lj/mdf <pair_mdf>`
* :doc:`lj/relres (o) <pair_lj_relres>`
* :doc:`lj/sdk (gko) <pair_sdk>`
* :doc:`lj/sdk/coul/long (go) <pair_sdk>`
* :doc:`lj/sdk/coul/msm (o) <pair_sdk>`
* :doc:`lj/spica (gko) <pair_spica>`
* :doc:`lj/spica/coul/long (go) <pair_spica>`
* :doc:`lj/spica/coul/msm (o) <pair_spica>`
* :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
* :doc:`lj/smooth (go) <pair_lj_smooth>`
* :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`

8
doc/src/Errors_messages.rst
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@ -1291,7 +1291,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Cannot use chosen neighbor list style with lj/gromacs/kk*
Self-explanatory.
*Cannot use chosen neighbor list style with lj/sdk/kk*
*Cannot use chosen neighbor list style with lj/spica/kk*
That style is not supported by Kokkos.
*Cannot use chosen neighbor list style with pair eam/kk*
@ -1659,10 +1659,10 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Cannot use newton pair with lj/gromacs/gpu pair style*
Self-explanatory.
*Cannot use newton pair with lj/sdk/coul/long/gpu pair style*
*Cannot use newton pair with lj/spica/coul/long/gpu pair style*
Self-explanatory.
*Cannot use newton pair with lj/sdk/gpu pair style*
*Cannot use newton pair with lj/spica/gpu pair style*
Self-explanatory.
*Cannot use newton pair with lj96/cut/gpu pair style*
@ -6782,7 +6782,7 @@ keyword to allow for additional bonds to be formed
This is because the computation of constraint forces within a water
molecule adds forces to atoms owned by other processors.
*Pair style lj/sdk/coul/long/gpu requires atom attribute q*
*Pair style lj/spica/coul/long/gpu requires atom attribute q*
The atom style defined does not have this attribute.
*Pair style nb3b/harmonic requires atom IDs*

21
doc/src/Packages_details.rst
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@ -35,7 +35,7 @@ page gives those details.
* :ref:`BPM <PKG-BPM>`
* :ref:`BROWNIAN <PKG-BROWNIAN>`
* :ref:`CG-DNA <PKG-CG-DNA>`
* :ref:`CG-SDK <PKG-CG-SDK>`
* :ref:`CG-SPICA <PKG-CG-SPICA>`
* :ref:`CLASS2 <PKG-CLASS2>`
* :ref:`COLLOID <PKG-COLLOID>`
* :ref:`COLVARS <PKG-COLVARS>`
@ -365,27 +365,26 @@ The CG-DNA package requires that also the `MOLECULE <PKG-MOLECULE>`_ and
----------
.. _PKG-CG-SDK:
.. _PKG-CG-SPICA:
CG-SDK package
CG-SPICA package
------------------
**Contents:**
Several pair styles and an angle style which implement the
coarse-grained SDK model of Shinoda, DeVane, and Klein which enables
simulation of ionic liquids, electrolytes, lipids and charged amino
acids.
coarse-grained SPICA (formerly called SDK) model which enables
simulation of biological or soft material systems.
**Author:** Axel Kohlmeyer (Temple U).
**Supporting info:**
* src/CG-SDK: filenames -> commands
* src/CG-SDK/README
* :doc:`pair_style lj/sdk/\* <pair_sdk>`
* :doc:`angle_style sdk <angle_sdk>`
* examples/PACKAGES/cgsdk
* src/CG-SPICA: filenames -> commands
* src/CG-SPICA/README
* :doc:`pair_style lj/spica/\* <pair_spica>`
* :doc:`angle_style spica <angle_spica>`
* examples/PACKAGES/cgspica
* https://www.lammps.org/pictures.html#cg
----------

8
doc/src/Packages_list.rst
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@ -73,10 +73,10 @@ whether an extra library is needed to build and use the package:
- src/CG-DNA/README
- PACKAGES/cgdna
- no
* - :ref:`CG-SDK <PKG-CG-SDK>`
- SDK coarse-graining model
- :doc:`pair_style lj/sdk <pair_sdk>`
- PACKAGES/cgsdk
* - :ref:`CG-SPICA <PKG-CG-SPICA>`
- SPICA (SDK) coarse-graining model
- :doc:`pair_style lj/spica <pair_spica>`
- PACKAGES/cgspica
- no
* - :ref:`CLASS2 <PKG-CLASS2>`
- class 2 force fields

37
doc/src/angle_sdk.rst → doc/src/angle_spica.rst
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@ -1,32 +1,32 @@
.. index:: angle_style sdk
.. index:: angle_style sdk/omp
.. index:: angle_style spica
.. index:: angle_style spica/omp
angle_style sdk command
=======================
angle_style spica command
=========================
Accelerator Variants: *sdk/omp*
Accelerator Variants: *spica/omp*
Syntax
""""""
.. code-block:: LAMMPS
angle_style sdk
angle_style spica
angle_style sdk/omp
angle_style spica/omp
Examples
""""""""
.. code-block:: LAMMPS
angle_style sdk
angle_style spica
angle_coeff 1 300.0 107.0
Description
"""""""""""
The *sdk* angle style is a combination of the harmonic angle potential,
The *spica* angle style is a combination of the harmonic angle potential,
.. math::
@ -34,10 +34,10 @@ The *sdk* angle style is a combination of the harmonic angle potential,
where :math:`\theta_0` is the equilibrium value of the angle and
:math:`K` a prefactor, with the *repulsive* part of the non-bonded
*lj/sdk* pair style between the atoms 1 and 3. This angle potential is
intended for coarse grained MD simulations with the CMM parameterization
using the :doc:`pair_style lj/sdk <pair_sdk>`. Relative to the
pair_style *lj/sdk*, however, the energy is shifted by
*lj/spica* pair style between the atoms 1 and 3. This angle potential is
intended for coarse grained MD simulations with the SPICA (formerly called SDK) parameterization
using the :doc:`pair_style lj/spica <pair_spica>`. Relative to the
pair_style *lj/spica*, however, the energy is shifted by
:math:`\epsilon`, to avoid sudden jumps. Note that the usual 1/2 factor
is included in :math:`K`.
@ -51,9 +51,12 @@ The following coefficients must be defined for each angle type via the
radians internally; hence :math:`K` is effectively energy per
radian\^2.
The required *lj/sdk* parameters are extracted automatically from the
The required *lj/spica* parameters are extracted automatically from the
pair_style.
Style *sdk*, the original implementation of style *spica*, is available
for backward compatibility.
----------
.. include:: accel_styles.rst
@ -64,14 +67,14 @@ Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
CG-SDK package. See the :doc:`Build package <Build_package>` doc
CG-SPICA package. See the :doc:`Build package <Build_package>` doc
page for more info.
Related commands
""""""""""""""""
:doc:`angle_coeff <angle_coeff>`, :doc:`angle_style harmonic <angle_harmonic>`, :doc:`pair_style lj/sdk <pair_sdk>`,
:doc:`pair_style lj/sdk/coul/long <pair_sdk>`
:doc:`angle_coeff <angle_coeff>`, :doc:`angle_style harmonic <angle_harmonic>`, :doc:`pair_style lj/spica <pair_spica>`,
:doc:`pair_style lj/spica/coul/long <pair_spica>`
Default
"""""""

2
doc/src/angle_style.rst
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@ -91,7 +91,7 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
* :doc:`harmonic <angle_harmonic>` - harmonic angle
* :doc:`mm3 <angle_mm3>` - anharmonic angle
* :doc:`quartic <angle_quartic>` - angle with cubic and quartic terms
* :doc:`sdk <angle_sdk>` - harmonic angle with repulsive SDK pair style between 1-3 atoms
* :doc:`spica <angle_spica>` - harmonic angle with repulsive SPICA pair style between 1-3 atoms
* :doc:`table <angle_table>` - tabulated by angle
----------

99
doc/src/pair_sdk.rst → doc/src/pair_spica.rst
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@ -1,27 +1,27 @@
.. index:: pair_style lj/sdk
.. index:: pair_style lj/sdk/gpu
.. index:: pair_style lj/sdk/kk
.. index:: pair_style lj/sdk/omp
.. index:: pair_style lj/sdk/coul/long
.. index:: pair_style lj/sdk/coul/long/gpu
.. index:: pair_style lj/sdk/coul/long/omp
.. index:: pair_style lj/sdk/coul/msm
.. index:: pair_style lj/sdk/coul/msm/omp
.. index:: pair_style lj/spica
.. index:: pair_style lj/spica/gpu
.. index:: pair_style lj/spica/kk
.. index:: pair_style lj/spica/omp
.. index:: pair_style lj/spica/coul/long
.. index:: pair_style lj/spica/coul/long/gpu
.. index:: pair_style lj/spica/coul/long/omp
.. index:: pair_style lj/spica/coul/msm
.. index:: pair_style lj/spica/coul/msm/omp
pair_style lj/sdk command
=========================
pair_style lj/spica command
===========================
Accelerator Variants: *lj/sdk/gpu*, *lj/sdk/kk*, *lj/sdk/omp*
Accelerator Variants: *lj/spica/gpu*, *lj/spica/kk*, *lj/spica/omp*
pair_style lj/sdk/coul/long command
===================================
pair_style lj/spica/coul/long command
=====================================
Accelerator Variants: *lj/sdk/coul/long/gpu*, *lj/sdk/coul/long/omp*
Accelerator Variants: *lj/spica/coul/long/gpu*, *lj/spica/coul/long/omp*
pair_style lj/sdk/coul/msm command
==================================
pair_style lj/spica/coul/msm command
====================================
Accelerator Variants: *lj/sdk/coul/msm/omp*
Accelerator Variants: *lj/spica/coul/msm/omp*
Syntax
""""""
@ -30,14 +30,14 @@ Syntax
pair_style style args
* style = *lj/sdk* or *lj/sdk/coul/long*
* style = *lj/spica* or *lj/spica/coul/long*
* args = list of arguments for a particular style
.. parsed-literal::
*lj/sdk* args = cutoff
*lj/spica* args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
*lj/sdk/coul/long* args = cutoff (cutoff2)
*lj/spica/coul/long* args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
@ -46,21 +46,21 @@ Examples
.. code-block:: LAMMPS
pair_style lj/sdk 2.5
pair_style lj/spica 2.5
pair_coeff 1 1 lj12_6 1 1.1 2.8
pair_style lj/sdk/coul/long 10.0
pair_style lj/sdk/coul/long 10.0 12.0
pair_style lj/spica/coul/long 10.0
pair_style lj/spica/coul/long 10.0 12.0
pair_coeff 1 1 lj9_6 100.0 3.5 12.0
pair_style lj/sdk/coul/msm 10.0
pair_style lj/sdk/coul/msm 10.0 12.0
pair_style lj/spica/coul/msm 10.0
pair_style lj/spica/coul/msm 10.0 12.0
pair_coeff 1 1 lj9_6 100.0 3.5 12.0
Description
"""""""""""
The *lj/sdk* styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential,
The *lj/spica* styles compute a 9/6, 12/4, 12/5, or 12/6 Lennard-Jones potential,
given by
.. math::
@ -71,14 +71,19 @@ given by
E = & \frac{3\sqrt{3}}{2} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^4 \right]
\qquad r < r_c \\
E = & \frac{12}{7}\left(\frac{12}{5}\right)^{\left(\frac{5}{7}\right)} \epsilon
\left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^5 \right]
\qquad r < r_c \\
E = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right]
\qquad r < r_c
as required for the SDK Coarse-grained MD parameterization discussed in
:ref:`(Shinoda) <Shinoda3>` and :ref:`(DeVane) <DeVane>`. Rc is the cutoff.
as required for the SPICA (formerly called SDK) and the pSPICA Coarse-grained MD parameterization discussed in
:ref:`(Shinoda) <Shinoda3>`, :ref:`(DeVane) <DeVane>`, :ref:`(Seo) <Seo>`, and :ref:`(Miyazaki) <Miyazaki>`.
Rc is the cutoff.
Style *lj/sdk/coul/long* computes the adds Coulombic interactions
Style *lj/spica/coul/long* computes the adds Coulombic interactions
with an additional damping factor applied so it can be used in
conjunction with the :doc:`kspace_style <kspace_style>` command and
its *ewald* or *pppm* or *pppm/cg* option. The Coulombic cutoff
@ -92,7 +97,7 @@ above, or in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands, or by mixing as described below:
* cg_type (lj9_6, lj12_4, or lj12_6)
* cg_type (lj9_6, lj12_4, lj12_5, or lj12_6)
* epsilon (energy units)
* sigma (distance units)
* cutoff1 (distance units)
@ -108,11 +113,15 @@ and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair.
For *lj/sdk/coul/long* and *lj/sdk/coul/msm* only the LJ cutoff can be
For *lj/spica/coul/long* and *lj/spica/coul/msm* only the LJ cutoff can be
specified since a Coulombic cutoff cannot be specified for an
individual I,J type pair. All type pairs use the same global
Coulombic cutoff specified in the pair_style command.
The original implementation of the above styles are
style *lj/sdk*, *lj/sdk/coul/long*, and *lj/sdk/coul/msm*,
and available for backward compatibility.
----------
.. include:: accel_styles.rst
@ -123,24 +132,24 @@ Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/sdk pair styles *cannot* be mixed,
and cutoff distance for all of the lj/spica pair styles *cannot* be mixed,
since different pairs may have different exponents. So all parameters
for all pairs have to be specified explicitly through the "pair_coeff"
command. Defining then in a data file is also not supported, due to
limitations of that file format.
All of the lj/sdk pair styles support the
All of the lj/spica pair styles support the
:doc:`pair_modify <pair_modify>` shift option for the energy of the
Lennard-Jones portion of the pair interaction.
The *lj/sdk/coul/long* pair styles support the
The *lj/spica/coul/long* pair styles support the
:doc:`pair_modify <pair_modify>` table option since they can tabulate
the short-range portion of the long-range Coulombic interaction.
All of the lj/sdk pair styles write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do
All of the lj/spica pair styles write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
The lj/sdk and lj/cut/coul/long pair styles do not support
The lj/spica and lj/cut/coul/long pair styles do not support
the use of the *inner*, *middle*, and *outer* keywords of the :doc:`run_style respa <run_style>` command.
----------
@ -148,8 +157,8 @@ the use of the *inner*, *middle*, and *outer* keywords of the :doc:`run_style re
Restrictions
""""""""""""
All of the lj/sdk pair styles are part of the CG-SDK package. The
*lj/sdk/coul/long* style also requires the KSPACE package to be built
All of the lj/spica pair styles are part of the CG-SPICA package. The
*lj/spica/coul/long* style also requires the KSPACE package to be built
(which is enabled by default). They are only enabled if LAMMPS was
built with that package. See the :doc:`Build package <Build_package>`
doc page for more info.
@ -157,7 +166,7 @@ doc page for more info.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`angle_style sdk <angle_sdk>`
:doc:`pair_coeff <pair_coeff>`, :doc:`angle_style spica <angle_spica>`
Default
"""""""
@ -168,8 +177,16 @@ none
.. _Shinoda3:
**(Shinoda)** Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).
**(Shinoda)** Shinoda, DeVane, Klein, Mol Sim, 33, 27-36 (2007).
.. _DeVane:
**(DeVane)** Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).
.. _Seo:
**(Seo)** Seo, Shinoda, J Chem Theory Comput, 15, 762-774 (2019).
.. _Miyazaki:
**(Miyazaki)** Miyazaki, Okazaki, Shinoda, J Chem Theory Comput, 16, 782-793 (2020).

6
doc/src/pair_style.rst
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@ -258,9 +258,9 @@ accelerated styles exist.
* :doc:`lj/long/tip4p/long <pair_lj_long>` - long-range LJ and long-range Coulomb for TIP4P water
* :doc:`lj/mdf <pair_mdf>` - LJ potential with a taper function
* :doc:`lj/relres <pair_lj_relres>` - LJ using multiscale Relative Resolution (RelRes) methodology :ref:`(Chaimovich) <Chaimovich2>`.
* :doc:`lj/sdk <pair_sdk>` - LJ for SDK coarse-graining
* :doc:`lj/sdk/coul/long <pair_sdk>` - LJ for SDK coarse-graining with long-range Coulomb
* :doc:`lj/sdk/coul/msm <pair_sdk>` - LJ for SDK coarse-graining with long-range Coulomb via MSM
* :doc:`lj/spica <pair_spica>` - LJ for SPICA coarse-graining
* :doc:`lj/spica/coul/long <pair_spica>` - LJ for SPICA coarse-graining with long-range Coulomb
* :doc:`lj/spica/coul/msm <pair_spica>` - LJ for SPICA coarse-graining with long-range Coulomb via MSM
* :doc:`lj/sf/dipole/sf <pair_dipole>` - LJ with dipole interaction with shifted forces
* :doc:`lj/smooth <pair_lj_smooth>` - smoothed Lennard-Jones potential
* :doc:`lj/smooth/linear <pair_lj_smooth_linear>` - linear smoothed LJ potential