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Merge branch 'develop' into patch-8

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This commit is contained in:
Axel Kohlmeyer
2024-01-25 09:04:29 -05:00
parent 921ddffda2 54794a45de
commit 2a95c09d77
181 changed files with 6059 additions and 3445 deletions
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2
doc/src/Commands_bond.rst
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@ -124,7 +124,7 @@ OPT.
*
*
* :doc:`charmm (iko) <dihedral_charmm>`
* :doc:`charmmfsw <dihedral_charmm>`
* :doc:`charmmfsw (k) <dihedral_charmm>`
* :doc:`class2 (ko) <dihedral_class2>`
* :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>`
* :doc:`fourier (io) <dihedral_fourier>`

2
doc/src/Commands_pair.rst
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@ -146,7 +146,7 @@ OPT.
* :doc:`lj/charmm/coul/long/soft (o) <pair_fep_soft>`
* :doc:`lj/charmm/coul/msm (o) <pair_charmm>`
* :doc:`lj/charmmfsw/coul/charmmfsh <pair_charmm>`
* :doc:`lj/charmmfsw/coul/long <pair_charmm>`
* :doc:`lj/charmmfsw/coul/long (k) <pair_charmm>`
* :doc:`lj/class2 (gko) <pair_class2>`
* :doc:`lj/class2/coul/cut (ko) <pair_class2>`
* :doc:`lj/class2/coul/cut/soft <pair_fep_soft>`

66
doc/src/Developer_updating.rst
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@ -20,6 +20,7 @@ Available topics in mostly chronological order are:
- `Use ev_init() to initialize variables derived from eflag and vflag`_
- `Use utils::numeric() functions instead of force->numeric()`_
- `Use utils::open_potential() function to open potential files`_
- `Use symbolic Atom and AtomVec constants instead of numerical values`_
- `Simplify customized error messages`_
- `Use of "override" instead of "virtual"`_
- `Simplified and more compact neighbor list requests`_
@ -196,6 +197,71 @@ New:
fp = utils::open_potential(filename, lmp);
Use symbolic Atom and AtomVec constants instead of numerical values
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 18Sep2020
Properties in LAMMPS that were represented by integer values (0, 1,
2, 3) to indicate settings in the ``Atom`` and ``AtomVec`` classes (or
classes derived from it) (and its derived classes) have been converted
to use scoped enumerators instead.
.. list-table::
:header-rows: 1
:widths: auto
* - Symbolic Constant
- Value
- Symbolic Constant
- Value
* - Atom::GROW
- 0
- Atom::MAP_NONE
- 0
* - Atom::RESTART
- 1
- Atom::MAP_ARRAY
- 1
* - Atom::BORDER
- 2
- Atom::MAP_HASH
- 2
* - Atom::ATOMIC
- 0
- Atom::MAP_YES
- 3
* - Atom::MOLECULAR
- 1
- AtomVec::PER_ATOM
- 0
* - Atom::TEMPLATE
- 2
- AtomVec::PER_TYPE
- 1
Old:
.. code-block:: c++
molecular = 0;
mass_type = 1;
if (atom->molecular == 2)
if (atom->map_style == 2)
atom->add_callback(0);
atom->delete_callback(id,1);
New:
.. code-block:: c++
molecular = Atom::ATOMIC;
mass_type = AtomVec::PER_TYPE;
if (atom->molecular == Atom::TEMPLATE)
if (atom->map_style == Atom::MAP_HASH)
atom->add_callback(Atom::GROW);
atom->delete_callback(id,Atom::RESTART);
Simplify customized error messages
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

4
doc/src/angle_charmm.rst
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@ -70,7 +70,9 @@ for more info.
Related commands
""""""""""""""""
:doc:`angle_coeff <angle_coeff>`
:doc:`angle_coeff <angle_coeff>`, :doc:`pair_style lj/charmm variants <pair_charmm>`,
:doc:`dihedral_style charmm <dihedral_charmm>`,
:doc:`dihedral_style charmmfsw <dihedral_charmm>`, :doc:`fix cmap <fix_cmap>`
Default
"""""""

19
doc/src/angle_lepton.rst
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@ -11,7 +11,16 @@ Syntax
.. code-block:: LAMMPS
angle_style lepton
angle_style style args
* style = *lepton*
* args = optional arguments
.. parsed-literal::
args = *auto_offset* or *no_offset*
*auto_offset* = offset the potential energy so that the value at theta0 is 0.0 (default)
*no_offset* = do not offset the potential energy
Examples
""""""""
@ -19,6 +28,7 @@ Examples
.. code-block:: LAMMPS
angle_style lepton
angle_style lepton no_offset
angle_coeff 1 120.0 "k*theta^2; k=250.0"
angle_coeff 2 90.0 "k2*theta^2 + k3*theta^3 + k4*theta^4; k2=300.0; k3=-100.0; k4=50.0"
@ -41,6 +51,13 @@ angle coefficient. For example `"200.0*theta^2"` represents a
U_{angle,i} = K (\theta_i - \theta_0)^2 = K \theta^2 \qquad \theta = \theta_i - \theta_0
.. versionchanged:: TBD
By default the potential energy U is shifted so that the value U is 0.0
for $theta = theta_0$. This is equivalent to using the optional keyword
*auto_offset*. When using the keyword *no_offset* instead, the
potential energy is not shifted.
The `Lepton library <https://simtk.org/projects/lepton>`_, that the
*lepton* angle style interfaces with, evaluates this expression string
at run time to compute the pairwise energy. It also creates an

4
doc/src/bond_bpm_rotational.rst
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@ -147,8 +147,8 @@ By default, pair forces are not calculated between bonded particles.
Pair forces can alternatively be overlaid on top of bond forces by setting
the *overlay/pair* keyword to *yes*. These settings require specific
:doc:`special_bonds <special_bonds>` settings described in the
restrictions. Further details can be found in the :doc:`how to
<Howto_bpm>` page on BPMs.
restrictions. Further details can be found in the :doc:`how to <Howto_bpm>`
page on BPMs.
.. versionadded:: 28Mar2023

4
doc/src/bond_bpm_spring.rst
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@ -113,8 +113,8 @@ By default, pair forces are not calculated between bonded particles.
Pair forces can alternatively be overlaid on top of bond forces by setting
the *overlay/pair* keyword to *yes*. These settings require specific
:doc:`special_bonds <special_bonds>` settings described in the
restrictions. Further details can be found in the :doc:`how to
<Howto_bpm>` page on BPMs.
restrictions. Further details can be found in the :doc:`how to <Howto_bpm>`
page on BPMs.
.. versionadded:: 28Mar2023

19
doc/src/bond_lepton.rst
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@ -11,7 +11,16 @@ Syntax
.. code-block:: LAMMPS
bond_style lepton
bond_style style args
* style = *lepton*
* args = optional arguments
.. parsed-literal::
args = *auto_offset* or *no_offset*
*auto_offset* = offset the potential energy so that the value at r0 is 0.0 (default)
*no_offset* = do not offset the potential energy
Examples
""""""""
@ -19,6 +28,7 @@ Examples
.. code-block:: LAMMPS
bond_style lepton
bond_style lepton no_offset
bond_coeff 1 1.5 "k*r^2; k=250.0"
bond_coeff 2 1.1 "k2*r^2 + k3*r^3 + k4*r^4; k2=300.0; k3=-100.0; k4=50.0"
@ -40,6 +50,13 @@ constant *K* of 200.0 energy units:
U_{bond,i} = K (r_i - r_0)^2 = K r^2 \qquad r = r_i - r_0
.. versionchanged:: TBD
By default the potential energy U is shifted so that he value U is 0.0
for $r = r_0$. This is equivalent to using the optional keyword
*auto_offset*. When using the keyword *no_offset* instead, the
potential energy is not shifted.
The `Lepton library <https://simtk.org/projects/lepton>`_, that the
*lepton* bond style interfaces with, evaluates this expression string at
run time to compute the pairwise energy. It also creates an analytical

7
doc/src/dihedral_charmm.rst
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@ -3,6 +3,7 @@
.. index:: dihedral_style charmm/kk
.. index:: dihedral_style charmm/omp
.. index:: dihedral_style charmmfsw
.. index:: dihedral_style charmmfsw/kk
dihedral_style charmm command
=============================
@ -12,6 +13,8 @@ Accelerator Variants: *charmm/intel*, *charmm/kk*, *charmm/omp*
dihedral_style charmmfsw command
================================
Accelerator Variants: *charmmfsw/kk*
Syntax
""""""
@ -144,7 +147,9 @@ for more info.
Related commands
""""""""""""""""
:doc:`dihedral_coeff <dihedral_coeff>`
:doc:`dihedral_coeff <dihedral_coeff>`,
:doc:`pair_style lj/charmm variants <pair_charmm>`,
:doc:`angle_style charmm <angle_charmm>`, :doc:`fix cmap <fix_cmap>`
Default
"""""""

2
doc/src/fix_qeq.rst
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@ -232,8 +232,6 @@ These fixes are part of the QEQ package. They are only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
These qeq fixes are not compatible with the GPU and USER-INTEL packages.
These qeq fixes will ignore electric field contributions from
:doc:`fix efield <fix_efield>`.

138
doc/src/molecule.rst
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@ -126,14 +126,50 @@ molecule (header keyword = inertia).
Format of a molecule file
"""""""""""""""""""""""""
The format of an individual molecule file is similar but
(not identical) to the data file read by the :doc:`read_data <read_data>`
commands, and is as follows.
The format of an individual molecule file looks similar but is
different than that of a data file read by the :doc:`read_data <read_data>`
commands. Here is a simple example for a TIP3P water molecule:
.. code-block::
# Water molecule. TIP3P geometry
# header section:
3 atoms
2 bonds
1 angles
# body section:
Coords
1 0.00000 -0.06556 0.00000
2 0.75695 0.52032 0.00000
3 -0.75695 0.52032 0.00000
Types
1 1 # O
2 2 # H
3 2 # H
Charges
1 -0.834
2 0.417
3 0.417
Bonds
1 1 1 2
2 1 1 3
Angles
1 1 2 1 3
A molecule file has a header and a body. The header appears first. The
first line of the header and thus of the molecule file is *always* skipped;
it typically contains a description of the file or a comment from the software
that created the file.
first line of the header and thus of the molecule file is *always*
skipped; it typically contains a description of the file or a comment
from the software that created the file.
Then lines are read one line at a time. Lines can have a trailing
comment starting with '#' that is ignored. There *must* be at least one
@ -158,25 +194,62 @@ appear if the value(s) are different than the default, except when
defining a *body* particle, which requires setting the number of
*atoms* to 1, and setting the *inertia* in a specific section (see below).
* N *atoms* = # of atoms N in molecule, default = 0
* Nb *bonds* = # of bonds Nb in molecule, default = 0
* Na *angles* = # of angles Na in molecule, default = 0
* Nd *dihedrals* = # of dihedrals Nd in molecule, default = 0
* Ni *impropers* = # of impropers Ni in molecule, default = 0
* Nf *fragments* = # of fragments Nf in molecule, default = 0
* Ninteger Ndouble *body* = # of integer and floating-point values
in body particle, default = 0
* Mtotal *mass* = total mass of molecule
* Xc Yc Zc *com* = coordinates of center-of-mass of molecule
* Ixx Iyy Izz Ixy Ixz Iyz *inertia* = 6 components of inertia tensor of molecule
.. list-table::
:header-rows: 1
:widths: auto
For *mass*, *com*, and *inertia*, the default is for LAMMPS to
calculate this quantity itself if needed, assuming the molecules
consist of a set of point particles or finite-size particles (with a
non-zero diameter) that do not overlap. If finite-size particles in
the molecule do overlap, LAMMPS will not account for the overlap
effects when calculating any of these 3 quantities, so you should
pre-compute them yourself and list the values in the file.
* - Number(s)
- Keyword
- Meaning
- Default Value
* - N
- atoms
- # of atoms N in molecule
- 0
* - Nb
- bonds
- # of bonds Nb in molecule
- 0
* - Na
- angles
- # of angles Na in molecule
- 0
* - Nd
- dihedrals
- # of dihedrals Nd in molecule
- 0
* - Ni
- impropers
- # of impropers Ni in molecule
- 0
* - Nf
- fragments
- # of fragments Nf in molecule
- 0
* - Ninteger Ndouble
- body
- # of integer and floating-point values in body particle
- 0
* - Mtotal
- mass
- total mass of molecule
- computed
* - Xc Yc Zc
- com
- coordinates of center-of-mass of molecule
- computed
* - Ixx Iyy Izz Ixy Ixz Iyz
- inertia
- 6 components of inertia tensor of molecule
- computed
For *mass*, *com*, and *inertia*, the default is for LAMMPS to calculate
this quantity itself if needed, assuming the molecules consist of a set
of point particles or finite-size particles (with a non-zero diameter)
that do **not** overlap. If finite-size particles in the molecule
**do** overlap, LAMMPS will not account for the overlap effects when
calculating any of these 3 quantities, so you should pre-compute them
yourself and list the values in the file.
The mass and center-of-mass coordinates (Xc,Yc,Zc) are
self-explanatory. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz)
@ -188,7 +261,7 @@ internally.
These are the allowed section keywords for the body of the file.
* *Coords, Types, Molecules, Fragments, Charges, Diameters, Masses* = atom-property sections
* *Coords, Types, Molecules, Fragments, Charges, Diameters, Dipoles, Masses* = atom-property sections
* *Bonds, Angles, Dihedrals, Impropers* = molecular topology sections
* *Special Bond Counts, Special Bonds* = special neighbor info
* *Shake Flags, Shake Atoms, Shake Bond Types* = SHAKE info
@ -303,6 +376,21 @@ not listed, the default diameter of each atom in the molecule is 1.0.
----------
.. versionadded:: TBD
*Dipoles* section:
* one line per atom
* line syntax: ID mux muy muz
* mux,muy,muz = x-, y-, and z-component of point dipole vector of atom
This section is only allowed for :doc:`atom styles <atom_style>` that
support particles with point dipoles, e.g. atom_style dipole. If not
listed, the default dipole component of each atom in the molecule is set
to 0.0.
----------
*Masses* section:
* one line per atom

7
doc/src/pair_charmm.rst
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@ -16,6 +16,7 @@
.. index:: pair_style lj/charmm/coul/msm/omp
.. index:: pair_style lj/charmmfsw/coul/charmmfsh
.. index:: pair_style lj/charmmfsw/coul/long
.. index:: pair_style lj/charmmfsw/coul/long/kk
pair_style lj/charmm/coul/charmm command
========================================
@ -43,6 +44,8 @@ pair_style lj/charmmfsw/coul/charmmfsh command
pair_style lj/charmmfsw/coul/long command
=========================================
Accelerator Variants: *lj/charmmfsw/coul/long/kk*
Syntax
""""""
@ -281,7 +284,9 @@ page for more info.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`
:doc:`pair_coeff <pair_coeff>`, :doc:`angle_style charmm <angle_charmm>`,
:doc:`dihedral_style charmm <dihedral_charmm>`,
:doc:`dihedral_style charmmfsw <dihedral_charmm>`, :doc:`fix cmap <fix_cmap>`
Default
"""""""

6
doc/src/pair_lepton.rst
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@ -72,7 +72,7 @@ interactions between particles which depend on the distance and have a
cutoff. The potential function must be provided as an expression string
using "r" as the distance variable. With pair style *lepton/coul* one
may additionally reference the charges of the two atoms of the pair with
"qi" and "qj", respectively. With pair style *lepton/coul* one may
"qi" and "qj", respectively. With pair style *lepton/sphere* one may
instead reference the radii of the two atoms of the pair with "radi" and
"radj", respectively; this is half of the diameter that can be set in
:doc:`data files <read_data>` or the :doc:`set command <set>`.
@ -166,8 +166,8 @@ mixing. Thus, expressions for *all* I,J pairs must be specified
explicitly.
Only pair style *lepton* supports the :doc:`pair_modify shift <pair_modify>`
option for shifting the energy of the pair interaction so that it is
0 at the cutoff, pair styles *lepton/coul* and *lepton/sphere* do *not*.
option for shifting the potential energy of the pair interaction so that
it is 0 at the cutoff, pair styles *lepton/coul* and *lepton/sphere* do *not*.
The :doc:`pair_modify table <pair_modify>` options are not relevant for
the these pair styles.