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Merge pull request #2679 from akohlmey/more-unittests

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Expand unit tests
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Axel Kohlmeyer
2021-04-02 17:51:29 -04:00
committed by GitHub
parent 7995fd8923 c4f59764d4
commit b976c2d13c
67 changed files with 7451 additions and 2485 deletions
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2
doc/src/Commands_pair.rst
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@ -187,7 +187,7 @@ OPT.
* :doc:`mgpt <pair_mgpt>`
* :doc:`mie/cut (g) <pair_mie>`
* :doc:`mliap <pair_mliap>`
* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
* :doc:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
* :doc:`momb <pair_momb>`
* :doc:`morse (gkot) <pair_morse>`
* :doc:`morse/smooth/linear (o) <pair_morse>`

2
doc/src/Packages_details.rst
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@ -2479,6 +2479,6 @@ which discuss the `QuickFF <quickff_>`_ methodology.
* :doc:`bond_style mm3 <bond_mm3>`
* :doc:`improper_style distharm <improper_distharm>`
* :doc:`improper_style sqdistharm <improper_sqdistharm>`
* :doc:`pair_style mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
* :doc:`pair_style mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
* :doc:`pair_style lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
* examples/USER/yaff

12
doc/src/fix_halt.rst
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@ -115,6 +115,18 @@ The version with "bondmax" will just run somewhat faster, due to less
overhead in computing bond lengths and not storing them in a separate
compute.
A variable can be used to implement a large variety of conditions,
including to stop when a specific file exists. Example:
.. code-block:: LAMMPS
variable exit equal is_file(EXIT)
fix 10 all halt 100 v_exit != 0 error soft
Will stop the current run command when a file ``EXIT`` is created
in the current working directory. The condition can be cleared
by removing the file through the :doc:`shell <shell>` command.
The choice of operators listed above are the usual comparison
operators. The XOR operation (exclusive or) is also included as "\|\^".
In this context, XOR means that if either the attribute or avalue is

55
doc/src/pair_lj_switch3_coulgauss_long.rst
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@ -1,8 +1,12 @@
.. index:: pair_style lj/switch3/coulgauss/long
.. index:: pair_style mm3/switch3/coulgauss/long
pair_style lj/switch3/coulgauss/long command
============================================
pair_style mm3/switch3/coulgauss/long command
=============================================
Syntax
""""""
@ -10,7 +14,7 @@ Syntax
pair_style style args
* style = *lj/switch3/coulgauss/long*
* style = *lj/switch3/coulgauss/long* or *mm3/switch3/coulgauss/long*
* args = list of arguments for a particular style
.. parsed-literal::
@ -20,6 +24,11 @@ Syntax
cutoff2 = global cutoff for Coulombic (optional) (distance units)
width = width parameter of the smoothing function (distance units)
*mm3/switch3/coulgauss/long* args = cutoff (cutoff2) width
cutoff = global cutoff for MM3 (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
width = width parameter of the smoothing function (distance units)
Examples
""""""""
@ -31,6 +40,12 @@ Examples
pair_style lj/switch3/coulgauss/long 12.0 10.0 3.0
pair_coeff 1 0.2 2.5 1.2
pair_style mm3/switch3/coulgauss/long 12.0 3.0
pair_coeff 1 0.2 2.5 1.2
pair_style mm3/switch3/coulgauss/long 12.0 10.0 3.0
pair_coeff 1 0.2 2.5 1.2
Description
"""""""""""
@ -41,8 +56,17 @@ vdW potential
E = 4\epsilon \left[ \left(\frac{\sigma}{r}\right)^{12}-\left(\frac{\sigma}{r}\right)^{6} \right]
, which goes smoothly to zero at the cutoff r_c as defined
by the switching function
The *mm3/switch3/coulgauss/long* style evaluates the MM3
vdW potential :ref:`(Allinger) <mm3-allinger1989>`
.. math::
E & = \epsilon_{ij} \left[ -2.25 \left(\frac{r_{v,ij}}{r_{ij}}\right)^6 + 1.84(10)^5 \exp\left[-12.0 r_{ij}/r_{v,ij}\right] \right] S_3(r_{ij}) \\
r_{v,ij} & = r_{v,i} + r_{v,j} \\
\epsilon_{ij} & = \sqrt{\epsilon_i \epsilon_j}
Both potentials go smoothly to zero at the cutoff r_c as defined by the
switching function
.. math::
@ -85,14 +109,35 @@ commands:
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/long pair styles can be mixed.
The default mix value is *geometric*\ . See the "pair_modify" command
for details.
Shifting the potential energy is not necessary because the switching
function ensures that the potential is zero at the cut-off.
These pair styles support the :doc:`pair_modify <pair_modify>` table and
options since they can tabulate the short-range portion of the
long-range Coulombic interactions.
Thes pair styles do not support the :doc:`pair_modify <pair_modify>`
tail option for adding a long-range tail correction to the
Lennard-Jones portion of the energy and pressure.
These 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.
These pair styles can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. They do not support the
*inner*\ , *middle*\ , *outer* keywords.
Restrictions
""""""""""""
These styles are part of the USER-YAFF package. They are only
enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
These styles are part of the USER-YAFF package. They are only enabled
if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.
Related commands
""""""""""""""""

109
doc/src/pair_mm3_switch3_coulgauss_long.rst
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@ -1,109 +0,0 @@
.. index:: pair_style mm3/switch3/coulgauss/long
pair_style mm3/switch3/coulgauss/long command
=============================================
Syntax
""""""
.. code-block:: LAMMPS
pair_style style args
* style = *mm3/switch3/coulgauss/long*
* args = list of arguments for a particular style
.. parsed-literal::
*mm3/switch3/coulgauss/long* args = cutoff (cutoff2) width
cutoff = global cutoff for MM3 (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
width = width parameter of the smoothing function (distance units)
Examples
""""""""
.. code-block:: LAMMPS
pair_style mm3/switch3/coulgauss/long 12.0 3.0
pair_coeff 1 0.2 2.5 1.2
pair_style mm3/switch3/coulgauss/long 12.0 10.0 3.0
pair_coeff 1 0.2 2.5 1.2
Description
"""""""""""
The *mm3/switch3/coulgauss/long* style evaluates the MM3
vdW potential :ref:`(Allinger) <mm3-allinger1989>`
.. math::
E & = \epsilon_{ij} \left[ -2.25 \left(\frac{r_{v,ij}}{r_{ij}}\right)^6 + 1.84(10)^5 \exp\left[-12.0 r_{ij}/r_{v,ij}\right] \right] S_3(r_{ij}) \\
r_{v,ij} & = r_{v,i} + r_{v,j} \\
\epsilon_{ij} & = \sqrt{\epsilon_i \epsilon_j}
, which goes smoothly to zero at the cutoff r_c as defined
by the switching function
.. math::
S_3(r) = \left\lbrace \begin{array}{ll}
1 & \quad\mathrm{if}\quad r < r_\mathrm{c} - w \\
3x^2 - 2x^3 & \quad\mathrm{if}\quad r < r_\mathrm{c} \quad\mathrm{with\quad} x=\frac{r_\mathrm{c} - r}{w} \\
0 & \quad\mathrm{if}\quad r >= r_\mathrm{c}
\end{array} \right.
where w is the width defined in the arguments. This potential
is combined with Coulomb interaction between Gaussian charge densities:
.. math::
E = \frac{q_i q_j \mathrm{erf}\left( r/\sqrt{\gamma_1^2+\gamma_2^2} \right) }{\epsilon r_{ij}}
where :math:`q_i` and :math:`q_j` are the charges on the 2 atoms,
epsilon is the dielectric constant which can be set by the
:doc:`dielectric <dielectric>` command, ::math:`\gamma_i` and
:math:`\gamma_j` are the widths of the Gaussian charge distribution and
erf() is the error-function. This style has to be used in conjunction
with the :doc:`kspace_style <kspace_style>` command
If one cutoff is specified it is used for both the vdW and Coulomb
terms. If two cutoffs are specified, the first is used as the cutoff
for the vdW terms, and the second is the cutoff for the Coulombic term.
The following coefficients must be defined for each pair of atoms
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
above, or in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands:
* :math:`\epsilon` (energy)
* :math:`r_v` (distance)
* :math:`\gamma` (distance)
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
Mixing rules are fixed for this style as defined above.
Shifting the potential energy is not necessary because the switching
function ensures that the potential is zero at the cut-off.
Restrictions
""""""""""""
These styles are part of the USER-YAFF package. They are only
enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`
Default
"""""""
none

2
doc/src/pair_style.rst
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@ -250,7 +250,7 @@ accelerated styles exist.
* :doc:`mgpt <pair_mgpt>` - simplified model generalized pseudopotential theory (MGPT) potential
* :doc:`mesont/tpm <pair_mesont_tpm>` - nanotubes mesoscopic force field
* :doc:`mie/cut <pair_mie>` - Mie potential
* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>` - smoothed MM3 vdW potential with Gaussian electrostatics
* :doc:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>` - smoothed MM3 vdW potential with Gaussian electrostatics
* :doc:`momb <pair_momb>` - Many-Body Metal-Organic (MOMB) force field
* :doc:`morse <pair_morse>` - Morse potential
* :doc:`morse/smooth/linear <pair_morse>` - linear smoothed Morse potential

10
doc/src/variable.rst
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@ -65,8 +65,8 @@ Syntax
bound(group,dir,region), gyration(group,region), ke(group,reigon),
angmom(group,dim,region), torque(group,dim,region),
inertia(group,dimdim,region), omega(group,dim,region)
special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x)
feature functions = is_active(category,feature,exact), is_defined(category,id,exact)
special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name)
feature functions = is_available(category,feature), is_active(category,feature), is_defined(category,id)
atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
atom vector = id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q
compute references = c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i]
@ -429,7 +429,7 @@ argument. For *equal*\ -style variables the formula computes a scalar
quantity, which becomes the value of the variable whenever it is
evaluated. For *vector*\ -style variables the formula must compute a
vector of quantities, which becomes the value of the variable whenever
it is evaluated. The calculated vector can be on length one, but it
it is evaluated. The calculated vector can be of length one, but it
cannot be a simple scalar value like that produced by an equal-style
compute. I.e. the formula for a vector-style variable must have at
least one quantity in it that refers to a global vector produced by a
@ -821,6 +821,10 @@ Special Functions
Special functions take specific kinds of arguments, meaning their
arguments cannot be formulas themselves.
The is_file(x) function is a test whether 'x' is a (readable) file
and returns 1 in this case, otherwise it returns 0. For that 'x'
is taken as a literal string and must not have any blanks in it.
The sum(x), min(x), max(x), ave(x), trap(x), and slope(x) functions
each take 1 argument which is of the form "c_ID" or "c_ID[N]" or
"f_ID" or "f_ID[N]" or "v_name". The first two are computes and the